The design of macromolecular crystallography diffraction experiments

International Nuclear Information System (INIS)

Evans, Gwyndaf; Axford, Danny; Owen, Robin L.

2011-01-01

Thoughts about the decisions made in designing macromolecular X-ray crystallography experiments at synchrotron beamlines are presented. The measurement of X-ray diffraction data from macromolecular crystals for the purpose of structure determination is the convergence of two processes: the preparation of diffraction-quality crystal samples on the one hand and the construction and optimization of an X-ray beamline and end station on the other. Like sample preparation, a macromolecular crystallography beamline is geared to obtaining the best possible diffraction measurements from crystals provided by the synchrotron user. This paper describes the thoughts behind an experiment that fully exploits both the sample and the beamline and how these map into everyday decisions that users can and should make when visiting a beamline with their most precious crystals

Macromolecular crystallography beamline X25 at the NSLS

Energy Technology Data Exchange (ETDEWEB)

Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E., E-mail: berman@bnl.gov [Brookhaven National Laboratory, PO Box 5000, Upton, NY 11973-5000 (United States)

2014-04-08

A description of the upgraded beamline X25 at the NSLS, operated by the PXRR and the Photon Sciences Directorate serving the Macromolecular Crystallography community, is presented. Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community.

Macromolecular crystallography beamline X25 at the NSLS

International Nuclear Information System (INIS)

Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E.

2014-01-01

A description of the upgraded beamline X25 at the NSLS, operated by the PXRR and the Photon Sciences Directorate serving the Macromolecular Crystallography community, is presented. Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20 µm × 20 µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community

Polydisulfide Manganese(II) Complexes as Non-Gadolinium Biodegradable Macromolecular MRI Contrast Agents

Science.gov (United States)

Ye, Zhen; Jeong, Eun-Kee; Wu, Xueming; Tan, Mingqian; Yin, Shouyu; Lu, Zheng-Rong

2011-01-01

Purpose To develop safe and effective manganese(II) based biodegradable macromolecular MRI contrast agents. Materials and Methods In this study, we synthesized and characterized two polydisulfide manganese(II) complexes, Mn-DTPA cystamine copolymers and Mn-EDTA cystamine copolymers, as new biodegradable macromolecular MRI contrast agents. The contrast enhancement of the two manganese based contrast agents were evaluated in mice bearing MDA-MB-231 human breast carcinoma xenografts, in comparison with MnCl2. Results The T1 and T2 relaxivities were 4.74 and 10.38 mM−1s−1 per manganese at 3T for Mn-DTPA cystamine copolymers (Mn=30.50 kDa) and 6.41 and 9.72 mM−1s−1 for Mn-EDTA cystamine copolymers (Mn= 61.80 kDa). Both polydisulfide Mn(II) complexes showed significant liver, myocardium and tumor enhancement. Conclusion The manganese based polydisulfide contrast agents have a potential to be developed as alternative non-gadolinium contrast agents for MR cancer and myocardium imaging. PMID:22031457

Macromolecular crowding directs extracellular matrix organization and mesenchymal stem cell behavior.

Directory of Open Access Journals (Sweden)

Adam S Zeiger

Full Text Available Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding in vitro by using synthetic macromolecular globules of nm-scale radius at physiological levels of fractional volume occupancy. We quantified the impact of induced crowding on the extracellular and intracellular protein organization of human mesenchymal stem cells (MSCs via immunocytochemistry, atomic force microscopy (AFM, and AFM-enabled nanoindentation. Macromolecular crowding in extracellular culture media directly induced supramolecular assembly and alignment of extracellular matrix proteins deposited by cells, which in turn increased alignment of the intracellular actin cytoskeleton. The resulting cell-matrix reciprocity further affected adhesion, proliferation, and migration behavior of MSCs. Macromolecular crowding can thus aid the design of more physiologically relevant in vitro studies and devices for MSCs and other cells, by increasing the fidelity between materials synthesized by cells in vivo and in vitro.

Macromolecular crowding directs extracellular matrix organization and mesenchymal stem cell behavior.

Science.gov (United States)

Zeiger, Adam S; Loe, Felicia C; Li, Ran; Raghunath, Michael; Van Vliet, Krystyn J

2012-01-01

Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding in vitro by using synthetic macromolecular globules of nm-scale radius at physiological levels of fractional volume occupancy. We quantified the impact of induced crowding on the extracellular and intracellular protein organization of human mesenchymal stem cells (MSCs) via immunocytochemistry, atomic force microscopy (AFM), and AFM-enabled nanoindentation. Macromolecular crowding in extracellular culture media directly induced supramolecular assembly and alignment of extracellular matrix proteins deposited by cells, which in turn increased alignment of the intracellular actin cytoskeleton. The resulting cell-matrix reciprocity further affected adhesion, proliferation, and migration behavior of MSCs. Macromolecular crowding can thus aid the design of more physiologically relevant in vitro studies and devices for MSCs and other cells, by increasing the fidelity between materials synthesized by cells in vivo and in vitro.

Analytical model for macromolecular partitioning during yeast cell division

International Nuclear Information System (INIS)

Kinkhabwala, Ali; Khmelinskii, Anton; Knop, Michael

2014-01-01

Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell — which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles — can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning

What Macromolecular Crowding Can Do to a Protein

Science.gov (United States)

Kuznetsova, Irina M.; Turoverov, Konstantin K.; Uversky, Vladimir N.

2014-01-01

The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area. PMID:25514413

Recent advances in macromolecular prodrugs

DEFF Research Database (Denmark)

Riber, Camilla Frich; Zelikin, Alexander N.

2017-01-01

Macromolecular prodrugs (MP) are high molar mass conjugates, typically carrying several copies of a drug or a drug combination, designed to optimize delivery of the drug, that is — its pharmacokinetics. From its advent several decades ago, design of MP has undergone significant development and es...

Status and prospects of macromolecular crystallography

Indian Academy of Sciences (India)

technique that could be completely automated in most cases. ... major challenge in macromolecular crystallography today is ... tial characterization of crystals in the home source and make a ... opportunities for a generation of structural biolo-.

Automated data collection for macromolecular crystallography.

Science.gov (United States)

Winter, Graeme; McAuley, Katherine E

2011-09-01

An overview, together with some practical advice, is presented of the current status of the automation of macromolecular crystallography (MX) data collection, with a focus on MX beamlines at Diamond Light Source, UK. Copyright © 2011 Elsevier Inc. All rights reserved.

Celebrating macromolecular crystallography: A personal perspective

Directory of Open Access Journals (Sweden)

Abad-Zapatero, Celerino

2015-04-01

Full Text Available The twentieth century has seen an enormous advance in the knowledge of the atomic structures that surround us. The discovery of the first crystal structures of simple inorganic salts by the Braggs in 1914, using the diffraction of X-rays by crystals, provided the critical elements to unveil the atomic structure of matter. Subsequent developments in the field leading to macromolecular crystallography are presented with a personal perspective, related to the cultural milieu of Spain in the late 1950’s. The journey of discovery of the author, as he developed professionally, is interwoven with the expansion of macromolecular crystallography from the first proteins (myoglobin, hemoglobin to the ‘coming of age’ of the field in 1971 and the discoveries that followed, culminating in the determination of the structure of the ribosomes at the turn of the century. A perspective is presented exploring the future of the field and also a reflection about the future generations of Spanish scientists.El siglo XX ha sido testigo del increíble avance que ha experimentado el conocimiento de la estructura atómica de la materia que nos rodea. El descubrimiento de las primeras estructuras atómicas de sales inorgánicas por los Bragg en 1914, empleando difracción de rayos X con cristales, proporcionó los elementos clave para alcanzar tal conocimiento. Posteriores desarrollos en este campo, que condujeron a la cristalografía macromolecular, se presentan aquí desde una perspectiva personal, relacionada con el contexto cultural de la España de la década de los 50. La experiencia del descubrimiento científico, durante mi desarrollo profesional, se integra en el desarrollo de la cristalografía macromolecular, desde las primeras proteínas (míoglobina y hemoglobina, hasta su madurez en 1971 que, con los posteriores descubrimientos, culmina con la determinación del la estructura del ribosoma. Asimismo, se explora el futuro de esta disciplina y se

Structure studies of macromolecular systems

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich; Dohnálek, Jan; Skálová, Tereza; Dušková, Jarmila; Kolenko, Petr

2006-01-01

Roč. 13, č. 3 (2006), s. 136 ISSN 1211-5894. [Czech and Slovak Crystallographic Colloquium. 22.06.2006-24.06.2006, Grenoble] R&D Projects: GA AV ČR IAA4050811; GA MŠk 1K05008 Keywords : structure * X-ray diffraction * synchrotron Subject RIV: CD - Macromolecular Chemistry http://www. xray .cz/ms/default.htm

A neutral polydisulfide containing Gd(III) DOTA monoamide as a redox-sensitive biodegradable macromolecular MRI contrast agent.

Science.gov (United States)

Ye, Zhen; Zhou, Zhuxian; Ayat, Nadia; Wu, Xueming; Jin, Erlei; Shi, Xiaoyue; Lu, Zheng-Rong

2016-01-01

This work aims to develop safe and effective gadolinium (III)-based biodegradable macromolecular MRI contrast agents for blood pool and cancer imaging. A neutral polydisulfide containing macrocyclic Gd-DOTA monoamide (GOLS) was synthesized and characterized. In addition to studying the in vitro degradation of GOLS, its kinetic stability was also investigated in an in vivo model. The efficacy of GOLS for contrast-enhanced MRI was examined with female BALB/c mice bearing 4T1 breast cancer xenografts. The pharmacokinetics, biodistribution, and metabolism of GOLS were also determined in mice. GOLS has an apparent molecular weight of 23.0 kDa with T1 relaxivities of 7.20 mM(-1) s(-1) per Gd at 1.5 T, and 6.62 mM(-1) s(-1) at 7.0 T. GOLS had high kinetic inertness against transmetallation with Zn(2+) ions, and its polymer backbone was readily cleaved by L-cysteine. The agent showed improved efficacy for blood pool and tumor MR imaging. The structural effect on biodistribution and in vivo chelation stability was assessed by comparing GOLS with Gd(HP-DO3A), a negatively charged polydisulfide containing Gd-DOTA monoamide GODC, and a polydisulfide containing Gd-DTPA-bisamide (GDCC). GOLS showed high in vivo chelation stability and minimal tissue deposition of gadolinium. The biodegradable macromolecular contrast agent GOLS is a promising polymeric contrast agent for clinical MR cardiovascular imaging and cancer imaging. Copyright © 2015 John Wiley & Sons, Ltd.

Control of Macromolecular Architectures for Renewable Polymers: Case Studies

Science.gov (United States)

Tang, Chuanbing

The development of sustainable polymers from nature biomass is growing, but facing fierce competition from existing petrochemical-based counterparts. Controlling macromolecular architectures to maximize the properties of renewable polymers is a desirable approach to gain advantages. Given the complexity of biomass, there needs special consideration other than traditional design. In the presentation, I will talk about a few case studies on how macromolecular architectures could tune the properties of sustainable bioplastics and elastomers from renewable biomass such as resin acids (natural rosin) and plant oils.

Macromolecular target prediction by self-organizing feature maps.

Science.gov (United States)

Schneider, Gisbert; Schneider, Petra

2017-03-01

Rational drug discovery would greatly benefit from a more nuanced appreciation of the activity of pharmacologically active compounds against a diverse panel of macromolecular targets. Already, computational target-prediction models assist medicinal chemists in library screening, de novo molecular design, optimization of active chemical agents, drug re-purposing, in the spotting of potential undesired off-target activities, and in the 'de-orphaning' of phenotypic screening hits. The self-organizing map (SOM) algorithm has been employed successfully for these and other purposes. Areas covered: The authors recapitulate contemporary artificial neural network methods for macromolecular target prediction, and present the basic SOM algorithm at a conceptual level. Specifically, they highlight consensus target-scoring by the employment of multiple SOMs, and discuss the opportunities and limitations of this technique. Expert opinion: Self-organizing feature maps represent a straightforward approach to ligand clustering and classification. Some of the appeal lies in their conceptual simplicity and broad applicability domain. Despite known algorithmic shortcomings, this computational target prediction concept has been proven to work in prospective settings with high success rates. It represents a prototypic technique for future advances in the in silico identification of the modes of action and macromolecular targets of bioactive molecules.

Stochastic reaction-diffusion algorithms for macromolecular crowding

Science.gov (United States)

Sturrock, Marc

2016-06-01

Compartment-based (lattice-based) reaction-diffusion algorithms are often used for studying complex stochastic spatio-temporal processes inside cells. In this paper the influence of macromolecular crowding on stochastic reaction-diffusion simulations is investigated. Reaction-diffusion processes are considered on two different kinds of compartmental lattice, a cubic lattice and a hexagonal close packed lattice, and solved using two different algorithms, the stochastic simulation algorithm and the spatiocyte algorithm (Arjunan and Tomita 2010 Syst. Synth. Biol. 4, 35-53). Obstacles (modelling macromolecular crowding) are shown to have substantial effects on the mean squared displacement and average number of molecules in the domain but the nature of these effects is dependent on the choice of lattice, with the cubic lattice being more susceptible to the effects of the obstacles. Finally, improvements for both algorithms are presented.

In situ macromolecular crystallography using microbeams.

Science.gov (United States)

Axford, Danny; Owen, Robin L; Aishima, Jun; Foadi, James; Morgan, Ann W; Robinson, James I; Nettleship, Joanne E; Owens, Raymond J; Moraes, Isabel; Fry, Elizabeth E; Grimes, Jonathan M; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S; Stuart, David I; Evans, Gwyndaf

2012-05-01

Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams. © 2012 International Union of Crystallography

Crowding-facilitated macromolecular transport in attractive micropost arrays.

Science.gov (United States)

Chien, Fan-Tso; Lin, Po-Keng; Chien, Wei; Hung, Cheng-Hsiang; Yu, Ming-Hung; Chou, Chia-Fu; Chen, Yeng-Long

2017-05-02

Our study of DNA dynamics in weakly attractive nanofabricated post arrays revealed crowding enhances polymer transport, contrary to hindered transport in repulsive medium. The coupling of DNA diffusion and adsorption to the microposts results in more frequent cross-post hopping and increased long-term diffusivity with increased crowding density. We performed Langevin dynamics simulations and found maximum long-term diffusivity in post arrays with gap sizes comparable to the polymer radius of gyration. We found that macromolecular transport in weakly attractive post arrays is faster than in non-attractive dense medium. Furthermore, we employed hidden Markov analysis to determine the transition of macromolecular adsorption-desorption on posts and hopping between posts. The apparent free energy barriers are comparable to theoretical estimates determined from polymer conformational fluctuations.

Macromolecular Crystallization in Microfluidics for the International Space Station

Science.gov (United States)

Monaco, Lisa A.; Spearing, Scott

2003-01-01

At NASA's Marshall Space Flight Center, the Iterative Biological Crystallization (IBC) project has begun development on scientific hardware for macromolecular crystallization on the International Space Station (ISS). Currently ISS crystallization research is limited to solution recipes that were prepared on the ground prior to launch. The proposed hardware will conduct solution mixing and dispensing on board the ISS, be fully automated, and have imaging functions via remote commanding from the ground. Utilizing microfluidic technology, IBC will allow for on orbit iterations. The microfluidics LabChip(R) devices that have been developed, along with Caliper Technologies, will greatly benefit researchers by allowing for precise fluid handling of nano/pico liter sized volumes. IBC will maximize the amount of science return by utilizing the microfluidic approach and be a valuable tool to structural biologists investigating medically relevant projects.

In situ macromolecular crystallography using microbeams

International Nuclear Information System (INIS)

Axford, Danny; Owen, Robin L.; Aishima, Jun; Foadi, James; Morgan, Ann W.; Robinson, James I.; Nettleship, Joanne E.; Owens, Raymond J.; Moraes, Isabel; Fry, Elizabeth E.; Grimes, Jonathan M.; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S.; Stuart, David I.; Evans, Gwyndaf

2012-01-01

A sample environment for mounting crystallization trays has been developed on the microfocus beamline I24 at Diamond Light Source. The technical developments and several case studies are described. Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams

In situ macromolecular crystallography using microbeams

Energy Technology Data Exchange (ETDEWEB)

Axford, Danny; Owen, Robin L.; Aishima, Jun [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Morgan, Ann W.; Robinson, James I. [University of Leeds, Leeds LS9 7FT (United Kingdom); Nettleship, Joanne E.; Owens, Raymond J. [Research Complex at Harwell, Rutherford Appleton Laboratory R92, Didcot, Oxfordshire OX11 0DE (United Kingdom); Moraes, Isabel [Imperial College, London SW7 2AZ (United Kingdom); Fry, Elizabeth E.; Grimes, Jonathan M.; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S. [University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

2012-04-17

A sample environment for mounting crystallization trays has been developed on the microfocus beamline I24 at Diamond Light Source. The technical developments and several case studies are described. Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams.

An acoustic on-chip goniometer for room temperature macromolecular crystallography.

Science.gov (United States)

Burton, C G; Axford, D; Edwards, A M J; Gildea, R J; Morris, R H; Newton, M I; Orville, A M; Prince, M; Topham, P D; Docker, P T

2017-12-05

This paper describes the design, development and successful use of an on-chip goniometer for room-temperature macromolecular crystallography via acoustically induced rotations. We present for the first time a low cost, rate-tunable, acoustic actuator for gradual in-fluid sample reorientation about varying axes and its utilisation for protein structure determination on a synchrotron beamline. The device enables the efficient collection of diffraction data via a rotation method from a sample within a surface confined droplet. This method facilitates efficient macromolecular structural data acquisition in fluid environments for dynamical studies.

Gaussian-Based Smooth Dielectric Function: A Surface-Free Approach for Modeling Macromolecular Binding in Solvents

Directory of Open Access Journals (Sweden)

Arghya Chakravorty

2018-03-01

Full Text Available Conventional modeling techniques to model macromolecular solvation and its effect on binding in the framework of Poisson-Boltzmann based implicit solvent models make use of a geometrically defined surface to depict the separation of macromolecular interior (low dielectric constant from the solvent phase (high dielectric constant. Though this simplification saves time and computational resources without significantly compromising the accuracy of free energy calculations, it bypasses some of the key physio-chemical properties of the solute-solvent interface, e.g., the altered flexibility of water molecules and that of side chains at the interface, which results in dielectric properties different from both bulk water and macromolecular interior, respectively. Here we present a Gaussian-based smooth dielectric model, an inhomogeneous dielectric distribution model that mimics the effect of macromolecular flexibility and captures the altered properties of surface bound water molecules. Thus, the model delivers a smooth transition of dielectric properties from the macromolecular interior to the solvent phase, eliminating any unphysical surface separating the two phases. Using various examples of macromolecular binding, we demonstrate its utility and illustrate the comparison with the conventional 2-dielectric model. We also showcase some additional abilities of this model, viz. to account for the effect of electrolytes in the solution and to render the distribution profile of water across a lipid membrane.

A public database of macromolecular diffraction experiments.

Science.gov (United States)

Grabowski, Marek; Langner, Karol M; Cymborowski, Marcin; Porebski, Przemyslaw J; Sroka, Piotr; Zheng, Heping; Cooper, David R; Zimmerman, Matthew D; Elsliger, Marc André; Burley, Stephen K; Minor, Wladek

2016-11-01

The low reproducibility of published experimental results in many scientific disciplines has recently garnered negative attention in scientific journals and the general media. Public transparency, including the availability of `raw' experimental data, will help to address growing concerns regarding scientific integrity. Macromolecular X-ray crystallography has led the way in requiring the public dissemination of atomic coordinates and a wealth of experimental data, making the field one of the most reproducible in the biological sciences. However, there remains no mandate for public disclosure of the original diffraction data. The Integrated Resource for Reproducibility in Macromolecular Crystallography (IRRMC) has been developed to archive raw data from diffraction experiments and, equally importantly, to provide related metadata. Currently, the database of our resource contains data from 2920 macromolecular diffraction experiments (5767 data sets), accounting for around 3% of all depositions in the Protein Data Bank (PDB), with their corresponding partially curated metadata. IRRMC utilizes distributed storage implemented using a federated architecture of many independent storage servers, which provides both scalability and sustainability. The resource, which is accessible via the web portal at http://www.proteindiffraction.org, can be searched using various criteria. All data are available for unrestricted access and download. The resource serves as a proof of concept and demonstrates the feasibility of archiving raw diffraction data and associated metadata from X-ray crystallographic studies of biological macromolecules. The goal is to expand this resource and include data sets that failed to yield X-ray structures in order to facilitate collaborative efforts that will improve protein structure-determination methods and to ensure the availability of `orphan' data left behind for various reasons by individual investigators and/or extinct structural genomics

Macromolecular Networks Containing Fluorinated Cyclic Moieties

Science.gov (United States)

2015-12-12

Briefing Charts 3. DATES COVERED (From - To) 17 Nov 2015 – 12 Dec 2015 4. TITLE AND SUBTITLE Macromolecular Networks Containing Fluorinated Cyclic... FLUORINATED CYCLIC MOIETIES 12 December 2015 Andrew J. Guenthner,1 Scott T. Iacono,2 Cynthia A. Corley,2 Christopher M. Sahagun,3 Kevin R. Lamison,4...Reinforcements Good Flame, Smoke, & Toxicity Characteristics Low Water Uptake with Near Zero Coefficient of Hygroscopic Expansion ∆ DISTRIBUTION A

Design and application of a C++ macromolecular class library.

Science.gov (United States)

Chang, W; Shindyalov, I N; Pu, C; Bourne, P E

1994-01-01

PDBlib is an extensible object oriented class library written in C++ for representing the 3-dimensional structure of biological macromolecules. PDBlib forms the kernel of a larger software framework being developed for assiting in knowledge discovery from macromolecular structure data. The software design strategy used by PDBlib, how the library may be used and several prototype applications that use the library are summarized. PDBlib represents the structural features of proteins, DNA, RNA, and complexes thereof, at a level of detail on a par with that which can be parsed from a Protein Data Bank (PDB) entry. However, the memory resident representation of the macromolecule is independent of the PDB entry and can be obtained from other back-end data sources, for example, existing relational databases and our own object oriented database (OOPDB) built on top of the commercial object oriented database, ObjectStore. At the front-end are several prototype applications that use the library: Macromolecular Query Language (MMQL) is based on a separate class library (MMQLlib) for building complex queries pertaining to macromolecular structure; PDBtool is an interactive structure verification tool; and PDBview, is a structure rendering tool used either as a standalone tool or as part of another application. Each of these software components are described. All software is available via anonymous ftp from cuhhca.hhmi.columbia.edu.

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.

Science.gov (United States)

Maximova, Tatiana; Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth; Shehu, Amarda

2016-04-01

Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts.

Outrunning free radicals in room-temperature macromolecular crystallography

International Nuclear Information System (INIS)

Owen, Robin L.; Axford, Danny; Nettleship, Joanne E.; Owens, Raymond J.; Robinson, James I.; Morgan, Ann W.; Doré, Andrew S.; Lebon, Guillaume; Tate, Christopher G.; Fry, Elizabeth E.; Ren, Jingshan; Stuart, David I.; Evans, Gwyndaf

2012-01-01

A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A 2A adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macromolecular crystallography

Outrunning free radicals in room-temperature macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Owen, Robin L., E-mail: robin.owen@diamond.ac.uk; Axford, Danny [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Nettleship, Joanne E.; Owens, Raymond J. [Rutherford Appleton Laboratory, Didcot OX11 0FA (United Kingdom); The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Robinson, James I.; Morgan, Ann W. [University of Leeds, Leeds LS9 7FT (United Kingdom); Doré, Andrew S. [Heptares Therapeutics Ltd, BioPark, Welwyn Garden City AL7 3AX (United Kingdom); Lebon, Guillaume; Tate, Christopher G. [MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH (United Kingdom); Fry, Elizabeth E.; Ren, Jingshan [The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Stuart, David I. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); The Henry Wellcome Building for Genomic Medicine, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Evans, Gwyndaf [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

2012-06-15

A systematic increase in lifetime is observed in room-temperature protein and virus crystals through the use of reduced exposure times and a fast detector. A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A{sub 2A} adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macromolecular crystallography.

Macromolecular diffusion in crowded media beyond the hard-sphere model.

Science.gov (United States)

Blanco, Pablo M; Garcés, Josep Lluís; Madurga, Sergio; Mas, Francesc

2018-04-25

The effect of macromolecular crowding on diffusion beyond the hard-core sphere model is studied. A new coarse-grained model is presented, the Chain Entanglement Softened Potential (CESP) model, which takes into account the macromolecular flexibility and chain entanglement. The CESP model uses a shoulder-shaped interaction potential that is implemented in the Brownian Dynamics (BD) computations. The interaction potential contains only one parameter associated with the chain entanglement energetic cost (Ur). The hydrodynamic interactions are included in the BD computations via Tokuyama mean-field equations. The model is used to analyze the diffusion of a streptavidin protein among different sized dextran obstacles. For this system, Ur is obtained by fitting the streptavidin experimental long-time diffusion coefficient Dlongversus the macromolecular concentration for D50 (indicating their molecular weight in kg mol-1) dextran obstacles. The obtained Dlong values show better quantitative agreement with experiments than those obtained with hard-core spheres. Moreover, once parametrized, the CESP model is also able to quantitatively predict Dlong and the anomalous exponent (α) for streptavidin diffusion among D10, D400 and D700 dextran obstacles. Dlong, the short-time diffusion coefficient (Dshort) and α are obtained from the BD simulations by using a new empirical expression, able to describe the full temporal evolution of the diffusion coefficient.

A smooth and differentiable bulk-solvent model for macromolecular diffraction

Energy Technology Data Exchange (ETDEWEB)

Fenn, T. D. [Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California (United States); Schnieders, M. J. [Department of Chemistry, Stanford, California (United States); Brunger, A. T., E-mail: brunger@stanford.edu [Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford, California (United States); Departments of Neurology and Neurological Sciences, Structural Biology and Photon Science, Stanford, California (United States)

2010-09-01

A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R{sub free} and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography.

A smooth and differentiable bulk-solvent model for macromolecular diffraction

International Nuclear Information System (INIS)

Fenn, T. D.; Schnieders, M. J.; Brunger, A. T.

2010-01-01

A new method for modeling the bulk solvent in macromolecular diffraction data based on Babinet’s principle is presented. The proposed models offer the advantage of differentiability with respect to atomic coordinates. Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute–solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R free and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy.

Science.gov (United States)

Loquet, Antoine; Tolchard, James; Berbon, Melanie; Martinez, Denis; Habenstein, Birgit

2017-09-17

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13 C/ 15 N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

NMR imaging studies of coal

Energy Technology Data Exchange (ETDEWEB)

Ma, Z.R.; Zhang, P.Z.; Ding, G.L.; Li, L.Y.; Ye, C.H. [University of Science and Technology, Beijing (China). Dept. of Chemistry

1996-06-01

The permeation transportation and swelling behavior of solvents into coal are investigated by NMR imaging using pyridine-d{sub 5} and acetone-d{sub 6}. Images of coal swollen with deuterated solvents illuminate proton distributions of mobile phases within the coal macromolecular networks. More information about the chemical and physical structure of coal can be obtained using NMR imaging techniques.

A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)

Science.gov (United States)

Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2013-06-01

A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

The Postgraduate Study of Macromolecular Sciences at the University of Zagreb (1971-1980

Directory of Open Access Journals (Sweden)

Kunst, B.

2008-07-01

Full Text Available The postgraduate study of macromolecular sciences (PSMS was established at the University of Zagreb in 1971 as a university study in the time of expressed interdisciplinary permeation of natural sciences - physics, chemistry and biology, and application of their achievements in technologicaldisciplines. PSMS was established by a group of prominent university professors from the schools of Science, Chemical Technology, Pharmacy and Medicine, as well as from the Institute of Biology. The study comprised basic fields of macromolecular sciences: organic chemistry of synthetic macromolecules, physical chemistry of macromolecules, physics of macromolecules, biological macromolecules and polymer engineering with polymer application and processing, and teaching was performed in 29 lecture courses lead by 30 professors with their collaborators. PSMS ceased to exist with the change of legislation in Croatia in 1980, when the attitude prevailed to render back postgraduate studies to the university schools. During 9 years of existence of PSMS the MSci grade was awarded to 37 macromolecular experts. It was assessed that the PSMS some thirty years ago was an important example of modern postgraduate education as compared with the international postgraduate development. In concordance with the recent introduction of similar interdisciplinary studies in macromolecular sciences elsewhere in the world, the establishment of a modern interdisciplinary study in the field would be of importance for further development of these sciences in Croatia.

Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect.

Directory of Open Access Journals (Sweden)

Anne-Sophie Coquel

2013-04-01

Full Text Available Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian. Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on

MMTF-An efficient file format for the transmission, visualization, and analysis of macromolecular structures.

Directory of Open Access Journals (Sweden)

Anthony R Bradley

2017-06-01

Full Text Available Recent advances in experimental techniques have led to a rapid growth in complexity, size, and number of macromolecular structures that are made available through the Protein Data Bank. This creates a challenge for macromolecular visualization and analysis. Macromolecular structure files, such as PDB or PDBx/mmCIF files can be slow to transfer, parse, and hard to incorporate into third-party software tools. Here, we present a new binary and compressed data representation, the MacroMolecular Transmission Format, MMTF, as well as software implementations in several languages that have been developed around it, which address these issues. We describe the new format and its APIs and demonstrate that it is several times faster to parse, and about a quarter of the file size of the current standard format, PDBx/mmCIF. As a consequence of the new data representation, it is now possible to visualize structures with millions of atoms in a web browser, keep the whole PDB archive in memory or parse it within few minutes on average computers, which opens up a new way of thinking how to design and implement efficient algorithms in structural bioinformatics. The PDB archive is available in MMTF file format through web services and data that are updated on a weekly basis.

Local analysis of strains and rotations for macromolecular electron microscopy maps

Energy Technology Data Exchange (ETDEWEB)

Martin-Ramos, A.; Prieto, F.; Melero, R.; Martin-Benito, J.; Jonic, S.; Navas-Calvente, J.; Vargas, J.; Oton, J.; Abrishami, V.; Rosa-Trevin, J.L. de la; Gomez-Blanco, J.; Vilas, J.L.; Marabini, R.; Carazo, R.; Sorzano, C.O.S.

2016-07-01

Macromolecular complexes can be considered as molecular nano-machines that must have mobile parts in order to perform their physiological functions. The reordering of their parts is essential to execute their task. These rearrangements induce local strains and rotations which, after analyzing them, may provide relevant information about how the proteins perform their function. In this project these deformations of the macromolecular complexes are characterized, translating into a “mathematical language” the conformational changes of the complexes when they perform their function. Electron Microscopy (EM) volumes are analyzed using a method that uses B-splines as its basis functions. It is shown that the results obtained are consistent with the conformational changes described in their corresponding reference publications. (Author)

[Macromolecular aromatic network characteristics of Chinese power coal analyzed by synchronous fluorescence and X-ray diffraction].

Science.gov (United States)

Ye, Cui-Ping; Feng, Jie; Li, Wen-Ying

2012-07-01

Coal structure, especially the macromolecular aromatic skeleton structure, has a strong influence on coke reactivity and coal gasification, so it is the key to grasp the macromolecular aromatic skeleton coal structure for getting the reasonable high efficiency utilization of coal. However, it is difficult to acquire their information due to the complex compositions and structure of coal. It has been found that the macromolecular aromatic network coal structure would be most isolated if small molecular of coal was first extracted. Then the macromolecular aromatic skeleton coal structure would be clearly analyzed by instruments, such as X-ray diffraction (XRD), fluorescence spectroscopy with synchronous mode (Syn-F), Gel permeation chromatography (GPC) etc. Based on the previous results, according to the stepwise fractional liquid extraction, two Chinese typical power coals, PS and HDG, were extracted by silica gel as stationary phase and acetonitrile, tetrahydrofuran (THF), pyridine and 1-methyl-2-pyrollidinone (NMP) as a solvent group for sequential elution. GPC, Syn-F and XRD were applied to investigate molecular mass distribution, condensed aromatic structure and crystal characteristics. The results showed that the size of aromatic layers (La) is small (3-3.95 nm) and the stacking heights (Lc) are 0.8-1.2 nm. The molecular mass distribution of the macromolecular aromatic network structure is between 400 and 1 130 amu, with condensed aromatic numbers of 3-7 in the structure units.

Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)

Science.gov (United States)

Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2014-01-01

A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

Functionalization of Planet-Satellite Nanostructures Revealed by Nanoscopic Localization of Distinct Macromolecular Species

KAUST Repository

Rossner, Christian

2016-09-26

The development of a straightforward method is reported to form hybrid polymer/gold planet-satellite nanostructures (PlSNs) with functional polymer. Polyacrylate type polymer with benzyl chloride in its backbone as a macromolecular tracer is synthesized to study its localization within PlSNs by analyzing the elemental distribution of chlorine. The functionalized nanohybrid structures are analyzed by scanning transmission electron microscopy, electron energy loss spectroscopy, and spectrum imaging. The results show that the RAFT (reversible addition-fragmentation chain transfer) polymers\\' sulfur containing end groups are colocalized at the gold cores, both within nanohybrids of simple core-shell morphology and within higher order PlSNs, providing microscopic evidence for the affinity of the RAFT group toward gold surfaces. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA., Weinheim.

Macromolecular crystallography research at Trombay

International Nuclear Information System (INIS)

Kannan, K.K.; Chidamrabam, R.

1983-01-01

Neutron diffraction studies of hydrogen positions in small molecules of biological interest at Trombay have provided valuable information that has been used in protein and enzyme structure model-building and in developing hydrogen bond potential functions. The new R-5 reactor is expected to provide higher neutron fluxes and also make possible small-angle neutron scattering studies of large biomolecules and bio-aggregates. In the last few years infrastructure facilities have also been established for macromolecular x-ray crystallography research. Meanwhile, the refinement of carbonic hydrases and lyysozyme structures have been carried out and interesting results obtained on protein dynamics and structure-function relationships. Some interesting presynaptic toxin phospholipases have also taken up for study. (author)

Multi-modal magnetic resonance imaging and histology of vascular function in xenografts using macromolecular contrast agent hyperbranched polyglycerol (HPG-GdF).

Science.gov (United States)

Baker, Jennifer H E; McPhee, Kelly C; Moosvi, Firas; Saatchi, Katayoun; Häfeli, Urs O; Minchinton, Andrew I; Reinsberg, Stefan A

2016-01-01

Macromolecular gadolinium (Gd)-based contrast agents are in development as blood pool markers for MRI. HPG-GdF is a 583 kDa hyperbranched polyglycerol doubly tagged with Gd and Alexa 647 nm dye, making it both MR and histologically visible. In this study we examined the location of HPG-GdF in whole-tumor xenograft sections matched to in vivo DCE-MR images of both HPG-GdF and Gadovist. Despite its large size, we have shown that HPG-GdF extravasates from some tumor vessels and accumulates over time, but does not distribute beyond a few cell diameters from vessels. Fractional plasma volume (fPV) and apparent permeability-surface area product (aPS) parameters were derived from the MR concentration-time curves of HPG-GdF. Non-viable necrotic tumor tissue was excluded from the analysis by applying a novel bolus arrival time (BAT) algorithm to all voxels. aPS derived from HPG-GdF was the only MR parameter to identify a difference in vascular function between HCT116 and HT29 colorectal tumors. This study is the first to relate low and high molecular weight contrast agents with matched whole-tumor histological sections. These detailed comparisons identified tumor regions that appear distinct from each other using the HPG-GdF biomarkers related to perfusion and vessel leakiness, while Gadovist-imaged parameter measures in the same regions were unable to detect variation in vascular function. We have established HPG-GdF as a biocompatible multi-modal high molecular weight contrast agent with application for examining vascular function in both MR and histological modalities. Copyright © 2015 John Wiley & Sons, Ltd.

Dexamethasone attenuates grain sorghum dust extract-induced increase in macromolecular efflux in vivo.

Science.gov (United States)

Akhter, S R; Ikezaki, H; Gao, X P; Rubinstein, I

1999-05-01

The purpose of this study was to determine whether dexamethasone attenuates grain sorghum dust extract-induced increase in macromolecular efflux from the in situ hamster cheek pouch and, if so, whether this response is specific. By using intravital microscopy, we found that an aqueous extract of grain sorghum dust elicited significant, concentration-dependent leaky site formation and increase in clearance of FITC-labeled dextran (FITC-dextran; mol mass, 70 kDa) from the in situ hamster cheek pouch (P grain sorghum dust extract- and substance P-induced increases in macromolecular efflux from the in situ hamster cheek pouch in a specific fashion.

The Joint Structural Biology Group beam lines at the ESRF: Modern macromolecular crystallography

CERN Document Server

Mitchell, E P

2001-01-01

Macromolecular crystallography has evolved considerably over the last decade. Data sets in under an hour are now possible on high throughput beam lines leading to electron density and, possibly, initial models calculated on-site. There are five beam lines currently dedicated to macromolecular crystallography: the ID14 complex and BM-14 (soon to be superseded by ID-29). These lines handle over five hundred projects every six months and demand is increasing. Automated sample handling, alignment and data management protocols will be required to work efficiently with this demanding load. Projects developing these themes are underway within the JSBG.

Isotope labeling for NMR studies of macromolecular structure and interactions

International Nuclear Information System (INIS)

Wright, P.E.

1994-01-01

Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform 13 C, 15 N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific 13 C and 15 N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions

Isotope labeling for NMR studies of macromolecular structure and interactions

Energy Technology Data Exchange (ETDEWEB)

Wright, P.E. [Scripps Research Institute, La Jolla, CA (United States)

1994-12-01

Implementation of biosynthetic methods for uniform or specific isotope labeling of proteins, coupled with the recent development of powerful heteronuclear multidimensional NMR methods, has led to a dramatic increase in the size and complexity of macromolecular systems that are now amenable to NMR structural analysis. In recent years, a new technology has emerged that combines uniform {sup 13}C, {sup 15}N labeling with heteronuclear multidimensional NMR methods to allow NMR structural studies of systems approaching 25 to 30 kDa in molecular weight. In addition, with the introduction of specific {sup 13}C and {sup 15}N labels into ligands, meaningful NMR studies of complexes of even higher molecular weight have become feasible. These advances usher in a new era in which the earlier, rather stringent molecular weight limitations have been greatly surpassed and NMR can begin to address many central biological problems that involve macromolecular structure, dynamics, and interactions.

Macromolecular shape and interactions in layer-by-layer assemblies within cylindrical nanopores.

Science.gov (United States)

Lazzara, Thomas D; Lau, K H Aaron; Knoll, Wolfgang; Janshoff, Andreas; Steinem, Claudia

2012-01-01

Layer-by-layer (LbL) deposition of polyelectrolytes and proteins within the cylindrical nanopores of anodic aluminum oxide (AAO) membranes was studied by optical waveguide spectroscopy (OWS). AAO has aligned cylindrical, nonintersecting pores with a defined pore diameter d(0) and functions as a planar optical waveguide so as to monitor, in situ, the LbL process by OWS. The LbL deposition of globular proteins, i.e., avidin and biotinylated bovine serum albumin was compared with that of linear polyelectrolytes (linear-PEs), both species being of similar molecular weight. LbL deposition within the cylindrical AAO geometry for different pore diameters (d(0) = 25-80 nm) for the various macromolecular species, showed that the multilayer film growth was inhibited at different maximum numbers of LbL steps (n(max)). The value of n(max) was greatest for linear-PEs, while proteins had a lower value. The cylindrical pore geometry imposes a physical limit to LbL growth such that n(max) is strongly dependent on the overall internal structure of the LbL film. For all macromolecular species, deposition was inhibited in native AAO, having pores of d(0) = 25-30 nm. Both, OWS and scanning electron microscopy showed that LbL growth in larger AAO pores (d(0) > 25-30 nm) became inhibited when approaching a pore diameter of d(eff,n_max) = 25-35 nm, a similar size to that of native AAO pores, with d(0) = 25-30 nm. For a reasonable estimation of d(eff,n_max), the actual volume occupied by a macromolecular assembly must be taken into consideration. The results clearly show that electrostatic LbL allowed for compact macromolecular layers, whereas proteins formed loosely packed multilayers.

Variationally optimal selection of slow coordinates and reaction coordinates in macromolecular systems

Science.gov (United States)

Noe, Frank

To efficiently simulate and generate understanding from simulations of complex macromolecular systems, the concept of slow collective coordinates or reaction coordinates is of fundamental importance. Here we will introduce variational approaches to approximate the slow coordinates and the reaction coordinates between selected end-states given MD simulations of the macromolecular system and a (possibly large) basis set of candidate coordinates. We will then discuss how to select physically intuitive order paremeters that are good surrogates of this variationally optimal result. These result can be used in order to construct Markov state models or other models of the stationary and kinetics properties, in order to parametrize low-dimensional / coarse-grained model of the dynamics. Deutsche Forschungsgemeinschaft, European Research Council.

Superhydrophobic hybrid membranes by grafting arc-like macromolecular bridges on graphene sheets: Synthesis, characterization and properties

Science.gov (United States)

Mo, Zhao-Hua; Luo, Zheng; Huang, Qiang; Deng, Jian-Ping; Wu, Yi-Xian

2018-05-01

Grafting single end-tethered polymer chains on the surface of graphene is a conventional way to modify the surface properties of graphene oxide. However, grafting arc-like macromolecular bridges on graphene surfaces has been barely reported. Herein, a novel arc-like polydimethylsiloxane (PDMS) macromolecular bridges grafted graphene sheets (GO-g-Arc PDMS) was successfully synthesized via a confined interface reaction at 90 °C. Both the hydrophilic α- and ω-amino groups of linear hydrophobic NH2-PDMS-NH2 macromolecular chains rapidly reacted with epoxy and carboxyl groups on the surfaces of graphene oxide in water suspension to form arc-like PDMS macromolecular bridges on graphene sheets. The grafting density of arc-like PDMS bridges on graphene sheets can reach up to 0.80 mmol g-1 or 1.32 arc-like bridges per nm2 by this confined interface reaction. The water contact angle (WCA) of the hybrid membrane could be increased with increasing both the grafting density and content of covalent arc-like bridges architecture. The superhydrophobic hybrid membrane with a WCA of 153.4° was prepared by grinding of the above arc-like PDMS bridges grafted graphene hybrid, dispersing in ethanol and filtrating by organic filter membrane. This superhydrophobic hybrid membrane shows good self-cleaning and complete oil-water separation properties, which provides potential applications in anticontamination coating and oil-water separation. To the best of our knowledge, this is the first report on the synthesis of functional hybrid membranes by grafting arc-like PDMS macromolecular bridges on graphene sheets via a confined interface reaction.

Tuning the properties of an anthracene-based PPE-PPV copolymer by fine variation of its macromolecular parameters

Czech Academy of Sciences Publication Activity Database

Tinti, F.; Sabir, F. K.; Gazzano, M.; Righi, S.; Ulbricht, C.; Usluer, Ö.; Pokorná, Veronika; Cimrová, Věra; Yohannes, T.; Egbe, D. A. M.; Camaioni, N.

2013-01-01

Roč. 3, č. 19 (2013), s. 6972-6980 ISSN 2046-2069 R&D Projects: GA ČR GAP106/12/0827; GA ČR(CZ) GA13-26542S Institutional support: RVO:61389013 Keywords : anthracene-containing PPE-PPV copolymer * macromolecular parameters * structural and transport properties Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.708, year: 2013

MxCuBE: a synchrotron beamline control environment customized for macromolecular crystallography experiments

International Nuclear Information System (INIS)

Gabadinho, José; Beteva, Antonia; Guijarro, Matias; Rey-Bakaikoa, Vicente; Spruce, Darren

2010-01-01

MxCuBE is a beamline control environment optimized for the needs of macromolecular crystallography. This paper describes the design of the software and the features that MxCuBE currently provides. The design and features of a beamline control software system for macromolecular crystallography (MX) experiments developed at the European Synchrotron Radiation Facility (ESRF) are described. This system, MxCuBE, allows users to easily and simply interact with beamline hardware components and provides automated routines for common tasks in the operation of a synchrotron beamline dedicated to experiments in MX. Additional functionality is provided through intuitive interfaces that enable the assessment of the diffraction characteristics of samples, experiment planning, automatic data collection and the on-line collection and analysis of X-ray emission spectra. The software can be run in a tandem client-server mode that allows for remote control and relevant experimental parameters and results are automatically logged in a relational database, ISPyB. MxCuBE is modular, flexible and extensible and is currently deployed on eight macromolecular crystallography beamlines at the ESRF. Additionally, the software is installed at MAX-lab beamline I911-3 and at BESSY beamline BL14.1

Enzymes as Green Catalysts for Precision Macromolecular Synthesis.

Science.gov (United States)

Shoda, Shin-ichiro; Uyama, Hiroshi; Kadokawa, Jun-ichi; Kimura, Shunsaku; Kobayashi, Shiro

2016-02-24

The present article comprehensively reviews the macromolecular synthesis using enzymes as catalysts. Among the six main classes of enzymes, the three classes, oxidoreductases, transferases, and hydrolases, have been employed as catalysts for the in vitro macromolecular synthesis and modification reactions. Appropriate design of reaction including monomer and enzyme catalyst produces macromolecules with precisely controlled structure, similarly as in vivo enzymatic reactions. The reaction controls the product structure with respect to substrate selectivity, chemo-selectivity, regio-selectivity, stereoselectivity, and choro-selectivity. Oxidoreductases catalyze various oxidation polymerizations of aromatic compounds as well as vinyl polymerizations. Transferases are effective catalysts for producing polysaccharide having a variety of structure and polyesters. Hydrolases catalyzing the bond-cleaving of macromolecules in vivo, catalyze the reverse reaction for bond forming in vitro to give various polysaccharides and functionalized polyesters. The enzymatic polymerizations allowed the first in vitro synthesis of natural polysaccharides having complicated structures like cellulose, amylose, xylan, chitin, hyaluronan, and chondroitin. These polymerizations are "green" with several respects; nontoxicity of enzyme, high catalyst efficiency, selective reactions under mild conditions using green solvents and renewable starting materials, and producing minimal byproducts. Thus, the enzymatic polymerization is desirable for the environment and contributes to "green polymer chemistry" for maintaining sustainable society.

Implementation of fast macromolecular proton fraction mapping on 1.5 and 3 Tesla clinical MRI scanners: preliminary experience

Science.gov (United States)

Yarnykh, V.; Korostyshevskaya, A.

2017-08-01

Macromolecular proton fraction (MPF) is a biophysical parameter describing the amount of macromolecular protons involved into magnetization exchange with water protons in tissues. MPF represents a significant interest as a magnetic resonance imaging (MRI) biomarker of myelin for clinical applications. A recent fast MPF mapping method enabled clinical translation of MPF measurements due to time-efficient acquisition based on the single-point constrained fit algorithm. However, previous MPF mapping applications utilized only 3 Tesla MRI scanners and modified pulse sequences, which are not commonly available. This study aimed to test the feasibility of MPF mapping implementation on a 1.5 Tesla clinical scanner using standard manufacturer’s sequences and compare the performance of this method between 1.5 and 3 Tesla scanners. MPF mapping was implemented on 1.5 and 3 Tesla MRI units of one manufacturer with either optimized custom-written or standard product pulse sequences. Whole-brain three-dimensional MPF maps obtained from a single volunteer were compared between field strengths and implementation options. MPF maps demonstrated similar quality at both field strengths. MPF values in segmented brain tissues and specific anatomic regions appeared in close agreement. This experiment demonstrates the feasibility of fast MPF mapping using standard sequences on 1.5 T and 3 T clinical scanners.

Effect of macromolecular crowding on the rate of diffusion-limited ...

Indian Academy of Sciences (India)

The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some ...

New Paradigm for Macromolecular Crystallography Experiments at SSRL: Automated Crystal Screening And Remote Data Collection

International Nuclear Information System (INIS)

Soltis, S.M.; Cohen, A.E.; Deacon, A.; Eriksson, T.; Gonzalez, A.; McPhillips, S.; Chui, H.; Dunten, P.; Hollenbeck, M.; Mathews, I.; Miller, M.; Moorhead, P.; Phizackerley, R.P.; Smith, C.; Song, J.; Bedem, H. van dem; Ellis, P.; Kuhn, P.; McPhillips, T.; Sauter, N.; Sharp, K.

2009-01-01

Complete automation of the macromolecular crystallography experiment has been achieved at Stanford Synchrotron Radiation Lightsource (SSRL) through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled crystallography experiments to be carried out from the researchers' home institutions and other remote locations while retaining complete control over even the most challenging systems. A breakthrough component of the system, the Stanford Auto-Mounter (SAM), has enabled the efficient mounting of cryocooled samples without human intervention. Taking advantage of this automation, researchers have successfully screened more than 200 000 samples to select the crystals with the best diffraction quality for data collection as well as to determine optimal crystallization and cryocooling conditions. These systems, which have been deployed on all SSRL macromolecular crystallography beamlines and several beamlines worldwide, are used by more than 80 research groups in remote locations, establishing a new paradigm for macromolecular crystallography experimentation.

In Vitro and In Vivo Evaluation of Microparticulate Drug Delivery Systems Composed of Macromolecular Prodrugs

Directory of Open Access Journals (Sweden)

Yoshiharu Machida

2008-08-01

Full Text Available Macromolecular prodrugs are very useful systems for achieving controlled drug release and drug targeting. In particular, various macromolecule-antitumor drug conjugates enhance the effectiveness and improve the toxic side effects. Also, polymeric micro- and nanoparticles have been actively examined and their in vivo behaviors elucidated, and it has been realized that their particle characteristics are very useful to control drug behavior. Recently, researches based on the combination of the concepts of macromolecular prodrugs and micro- or nanoparticles have been reported, although they are limited. Macromolecular prodrugs enable drugs to be released at a certain controlled release rate based on the features of the macromolecule-drug linkage. Micro- and nanoparticles can control in vivo behavior based on their size, surface charge and surface structure. These merits are expected for systems produced by the combination of each concept. In this review, several micro- or nanoparticles composed of macromolecule-drug conjugates are described for their preparation, in vitro properties and/or in vivo behavior.

Iterative Stable Alignment and Clustering of 2D Transmission Electron Microscope Images

Science.gov (United States)

Yang, Zhengfan; Fang, Jia; Chittuluru, Johnathan; Asturias, Francisco J.; Penczek, Pawel A.

2012-01-01

SUMMARY Identification of homogeneous subsets of images in a macromolecular electron microscopy (EM) image data set is a critical step in single-particle analysis. The task is handled by iterative algorithms, whose performance is compromised by the compounded limitations of image alignment and K-means clustering. Here we describe an approach, iterative stable alignment and clustering (ISAC) that, relying on a new clustering method and on the concepts of stability and reproducibility, can extract validated, homogeneous subsets of images. ISAC requires only a small number of simple parameters and, with minimal human intervention, can eliminate bias from two-dimensional image clustering and maximize the quality of group averages that can be used for ab initio three-dimensional structural determination and analysis of macromolecular conformational variability. Repeated testing of the stability and reproducibility of a solution within ISAC eliminates heterogeneous or incorrect classes and introduces critical validation to the process of EM image clustering. PMID:22325773

Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions.

Science.gov (United States)

Donovan, Preston; Chehreghanianzabi, Yasaman; Rathinam, Muruhan; Zustiak, Silviya Petrova

2016-01-01

The study of diffusion in macromolecular solutions is important in many biomedical applications such as separations, drug delivery, and cell encapsulation, and key for many biological processes such as protein assembly and interstitial transport. Not surprisingly, multiple models for the a-priori prediction of diffusion in macromolecular environments have been proposed. However, most models include parameters that are not readily measurable, are specific to the polymer-solute-solvent system, or are fitted and do not have a physical meaning. Here, for the first time, we develop a homogenization theory framework for the prediction of effective solute diffusivity in macromolecular environments based on physical parameters that are easily measurable and not specific to the macromolecule-solute-solvent system. Homogenization theory is useful for situations where knowledge of fine-scale parameters is used to predict bulk system behavior. As a first approximation, we focus on a model where the solute is subjected to obstructed diffusion via stationary spherical obstacles. We find that the homogenization theory results agree well with computationally more expensive Monte Carlo simulations. Moreover, the homogenization theory agrees with effective diffusivities of a solute in dilute and semi-dilute polymer solutions measured using fluorescence correlation spectroscopy. Lastly, we provide a mathematical formula for the effective diffusivity in terms of a non-dimensional and easily measurable geometric system parameter.

Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions.

Directory of Open Access Journals (Sweden)

Preston Donovan

Full Text Available The study of diffusion in macromolecular solutions is important in many biomedical applications such as separations, drug delivery, and cell encapsulation, and key for many biological processes such as protein assembly and interstitial transport. Not surprisingly, multiple models for the a-priori prediction of diffusion in macromolecular environments have been proposed. However, most models include parameters that are not readily measurable, are specific to the polymer-solute-solvent system, or are fitted and do not have a physical meaning. Here, for the first time, we develop a homogenization theory framework for the prediction of effective solute diffusivity in macromolecular environments based on physical parameters that are easily measurable and not specific to the macromolecule-solute-solvent system. Homogenization theory is useful for situations where knowledge of fine-scale parameters is used to predict bulk system behavior. As a first approximation, we focus on a model where the solute is subjected to obstructed diffusion via stationary spherical obstacles. We find that the homogenization theory results agree well with computationally more expensive Monte Carlo simulations. Moreover, the homogenization theory agrees with effective diffusivities of a solute in dilute and semi-dilute polymer solutions measured using fluorescence correlation spectroscopy. Lastly, we provide a mathematical formula for the effective diffusivity in terms of a non-dimensional and easily measurable geometric system parameter.

PRIGo: a new multi-axis goniometer for macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Waltersperger, Sandro; Olieric, Vincent, E-mail: vincent.olieric@psi.ch; Pradervand, Claude [Paul Scherrer Institute, Villigen PSI (Switzerland); Glettig, Wayne [Centre Suisse d’Electronique et Microtechnique SA, Neuchâtel 2002 (Switzerland); Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias [Paul Scherrer Institute, Villigen PSI (Switzerland); Schulze-Briese, Clemens [Dectris Ltd, Baden 5400 (Switzerland); Wang, Meitian, E-mail: vincent.olieric@psi.ch [Paul Scherrer Institute, Villigen PSI (Switzerland)

2015-05-09

The design and performance of the new multi-axis goniometer PRIGo developed at the Swiss Light Source at Paul Scherrer Institute is described. The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0–90°), followed by a ϕ stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

Progress in rational methods of cryoprotection in macromolecular crystallography

International Nuclear Information System (INIS)

Alcorn, Thomas; Juers, Douglas H.

2010-01-01

Measurements of the average thermal contractions (294→72 K) of 26 different cryosolutions are presented and discussed in conjunction with other recent advances in the rational design of protocols for cryogenic cooling in macromolecular crystallography. Cryogenic cooling of macromolecular crystals is commonly used for X-ray data collection both to reduce crystal damage from radiation and to gather functional information by cryogenically trapping intermediates. However, the cooling process can damage the crystals. Limiting cooling-induced crystal damage often requires cryoprotection strategies, which can involve substantial screening of solution conditions and cooling protocols. Here, recent developments directed towards rational methods for cryoprotection are described. Crystal damage is described in the context of the temperature response of the crystal as a thermodynamic system. As such, the internal and external parts of the crystal typically have different cryoprotection requirements. A key physical parameter, the thermal contraction, of 26 different cryoprotective solutions was measured between 294 and 72 K. The range of contractions was 2–13%, with the more polar cryosolutions contracting less. The potential uses of these results in the development of cryocooling conditions, as well as recent developments in determining minimum cryosolution soaking times, are discussed

Collagen macromolecular drug delivery systems

International Nuclear Information System (INIS)

Gilbert, D.L.

1988-01-01

The objective of this study was to examine collagen for use as a macromolecular drug delivery system by determining the mechanism of release through a matrix. Collagen membranes varying in porosity, crosslinking density, structure and crosslinker were fabricated. Collagen characterized by infrared spectroscopy and solution viscosity was determined to be pure and native. The collagen membranes were determined to possess native vs. non-native quaternary structure and porous vs. dense aggregate membranes by electron microscopy. Collagen monolithic devices containing a model macromolecule (inulin) were fabricated. In vitro release rates were found to be linear with respect to t 1/2 and were affected by crosslinking density, crosslinker and structure. The biodegradation of the collagen matrix was also examined. In vivo biocompatibility, degradation and 14 C-inulin release rates were evaluated subcutaneously in rats

Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.

Science.gov (United States)

Ando, Tadashi; Yu, Isseki; Feig, Michael; Sugita, Yuji

2016-11-23

The cytoplasm of a cell is crowded with many different kinds of macromolecules. The macromolecular crowding affects the thermodynamics and kinetics of biological reactions in a living cell, such as protein folding, association, and diffusion. Theoretical and simulation studies using simplified models focus on the essential features of the crowding effects and provide a basis for analyzing experimental data. In most of the previous studies on the crowding effects, a uniform crowder size is assumed, which is in contrast to the inhomogeneous size distribution of macromolecules in a living cell. Here, we evaluate the free energy changes upon macromolecular association in a cell-like inhomogeneous crowding system via a theory of hard-sphere fluids and free energy calculations using Brownian dynamics trajectories. The inhomogeneous crowding model based on 41 different types of macromolecules represented by spheres with different radii mimics the physiological concentrations of macromolecules in the cytoplasm of Mycoplasma genitalium. The free energy changes of macromolecular association evaluated by the theory and simulations were in good agreement with each other. The crowder size distribution affects both specific and nonspecific molecular associations, suggesting that not only the volume fraction but also the size distribution of macromolecules are important factors for evaluating in vivo crowding effects. This study relates in vitro experiments on macromolecular crowding to in vivo crowding effects by using the theory of hard-sphere fluids with crowder-size heterogeneity.

Quantitative Magnetization Transfer Imaging in Human Brain at 3 T via Selective Inversion Recovery

OpenAIRE

Dortch, Richard D.; Li, Ke; Gochberg, Daniel F.; Welch, E. Brian; Dula, Adrienne N.; Tamhane, Ashish A.; Gore, John C.; Smith, Seth A.

2011-01-01

Quantitative magnetization transfer imaging yields indices describing the interactions between free water protons and immobile, macromolecular protons—including the macromolecular to free pool size ratio (PSR) and the rate of magnetization transfer between pools kmf. This study describes the first implementation of the selective inversion recovery quantitative magnetization transfer method on a clinical 3.0-T scanner in human brain in vivo. Selective inversion recovery data were acquired at 1...

Variable effects of soman on macromolecular secretion by ferret trachea

International Nuclear Information System (INIS)

McBride, R.K.; Zwierzynski, D.J.; Stone, K.K.; Culp, D.J.; Marin, M.G.

1991-01-01

The purpose of this study was to examine the effect of the anticholinesterase agent, soman, on macromolecular secretion by ferret trachea, in vitro. We mounted pieces of ferret trachea in Ussing-type chambers. Secreted sulfated macromolecules were radiolabeled by adding 500 microCi of 35 SO 4 to the submucosal medium and incubating for 17 hr. Soman added to the submucosal side produced a concentration-dependent increase in radiolabeled macromolecular release with a maximal secretory response (mean +/- SD) of 202 +/- 125% (n = 8) relative to the basal secretion rate at a concentration of 10 - 7 M. The addition of either 10 -6 M pralidoxime (acetylcholinesterase reactivator) or 10 -6 M atropine blocked the response to 10 -7 M soman. At soman concentrations greater than 10 -7 M, secretion rate decreased and was not significantly different from basal secretion. Additional experiments utilizing acetylcholine and the acetylcholinesterase inhibitor, physostigmine, suggest that inhibition of secretion by high concentrations of soman may be due to a secondary antagonistic effect of soman on muscarinic receptors

Data Management System at the Photon Factory Macromolecular Crystallography Beamline

International Nuclear Information System (INIS)

Yamada, Y; Matsugaki, N; Chavas, L M G; Hiraki, M; Igarashi, N; Wakatsuki, S

2013-01-01

Macromolecular crystallography is a very powerful tool to investigate three-dimensional structures of macromolecules at the atomic level, and is widely spread among structural biology researchers. Due to recent upgrades of the macromolecular crystallography beamlines at the Photon Factory, beamline throughput has improved, allowing more experiments to be conducted during a user's beam time. Although the number of beamlines has increased, so has the number of beam time applications. Consequently, both the experimental data from users' experiments and data derived from beamline operations have dramatically increased, causing difficulties in organizing these diverse and large amounts of data for the beamline operation staff and users. To overcome this problem, we have developed a data management system by introducing commercial middleware, which consists of a controller, database, and web servers. We have prepared several database projects using this system. Each project is dedicated to a certain aspect such as experimental results, beam time applications, beam time schedule, or beamline operation reports. Then we designed a scheme to link all the database projects.

Macromolecular crystallography with a large format CMOS detector

Energy Technology Data Exchange (ETDEWEB)

Nix, Jay C., E-mail: jcnix@lbl.gov [Molecular Biology Consortium 12003 S. Pulaski Rd. #166 Alsip, IL 60803 U.S.A (United States)

2016-07-27

Recent advances in CMOS technology have allowed the production of large surface area detectors suitable for macromolecular crystallography experiments [1]. The Molecular Biology Consortium (MBC) Beamline 4.2.2 at the Advanced Light Source in Berkeley, CA, has installed a 2952 x 2820 mm RDI CMOS-8M detector with funds from NIH grant S10OD012073. The detector has a 20nsec dead pixel time and performs well with shutterless data collection strategies. The sensor obtains sharp point response and minimal optical distortion by use of a thin fiber-optic plate between the phosphor and sensor module. Shutterless data collections produce high-quality redundant datasets that can be obtained in minutes. The fine-sliced data are suitable for processing in standard crystallographic software packages (XDS, HKL2000, D*TREK, MOSFLM). Faster collection times relative to the previous CCD detector have resulted in a record number of datasets collected in a calendar year and de novo phasing experiments have resulted in publications in both Science and Nature [2,3]. The faster collections are due to a combination of the decreased overhead requirements of shutterless collections combined with exposure times that have decreased by over a factor of 2 for images with comparable signal to noise of the NOIR-1 detector. The overall increased productivity has allowed the development of new beamline capabilities and data collection strategies.

Modeling the multi-scale mechanisms of macromolecular resource allocation

DEFF Research Database (Denmark)

Yang, Laurence; Yurkovich, James T; King, Zachary A

2018-01-01

As microbes face changing environments, they dynamically allocate macromolecular resources to produce a particular phenotypic state. Broad 'omics' data sets have revealed several interesting phenomena regarding how the proteome is allocated under differing conditions, but the functional consequen...... and detail how mathematical models have aided in our understanding of these processes. Ultimately, such modeling efforts have helped elucidate the principles of proteome allocation and hold promise for further discovery....

Pi sampling: a methodical and flexible approach to initial macromolecular crystallization screening

International Nuclear Information System (INIS)

Gorrec, Fabrice; Palmer, Colin M.; Lebon, Guillaume; Warne, Tony

2011-01-01

Pi sampling, derived from the incomplete factorial approach, is an effort to maximize the diversity of macromolecular crystallization conditions and to facilitate the preparation of 96-condition initial screens. The Pi sampling method is derived from the incomplete factorial approach to macromolecular crystallization screen design. The resulting ‘Pi screens’ have a modular distribution of a given set of up to 36 stock solutions. Maximally diverse conditions can be produced by taking into account the properties of the chemicals used in the formulation and the concentrations of the corresponding solutions. The Pi sampling method has been implemented in a web-based application that generates screen formulations and recipes. It is particularly adapted to screens consisting of 96 different conditions. The flexibility and efficiency of Pi sampling is demonstrated by the crystallization of soluble proteins and of an integral membrane-protein sample

Functionalization of Planet-Satellite Nanostructures Revealed by Nanoscopic Localization of Distinct Macromolecular Species

KAUST Repository

Rossner, Christian; Roddatis, Vladimir; Lopatin, Sergei; Vana, Philipp

2016-01-01

The development of a straightforward method is reported to form hybrid polymer/gold planet-satellite nanostructures (PlSNs) with functional polymer. Polyacrylate type polymer with benzyl chloride in its backbone as a macromolecular tracer

Thiomers for oral delivery of hydrophilic macromolecular drugs.

Science.gov (United States)

Bernkop-Schnürch, Andreas; Hoffer, Martin H; Kafedjiiski, Krum

2004-11-01

In recent years thiolated polymers (thiomers) have appeared as a promising new tool in oral drug delivery. Thiomers are obtained by the immobilisation of thio-bearing ligands to mucoadhesive polymeric excipients. By the formation of disulfide bonds with mucus glycoproteins, the mucoadhesive properties of thiomers are up to 130-fold improved compared with the corresponding unmodified polymers. Owing to the formation of inter- and intramolecular disulfide bonds within the thiomer itself, matrix tablets and particulate delivery systems show strong cohesive properties, resulting in comparatively higher stability, prolonged disintegration times and a more controlled drug release. The permeation of hydrophilic macromolecular drugs through the gastrointestinal (GI) mucosa can be improved by the use of thiomers. Furthermore, some thiomers exhibit improved inhibitory properties towards GI peptidases. The efficacy of thiomers in oral drug delivery has been demonstrated by various in vivo studies. A pharmacological efficacy of 1%, for example, was achieved in rats by oral administration of calcitonin tablets comprising a thiomer. Furthermore, tablets comprising a thiomer and pegylated insulin resulted in a pharmacological efficacy of 7% after oral application to diabetic mice. Low-molecular-weight heparin embedded in thiolated polycarbophil led to an absolute bioavailability of > or = 20% after oral administration to rats. In these studies, formulations comprising the corresponding unmodified polymer had only a marginal or no effect. These results indicate drug carrier systems based on thiomers appear to be a promising tool for oral delivery of hydrophilic macromolecular drugs.

ISPyB: an information management system for synchrotron macromolecular crystallography.

Science.gov (United States)

Delagenière, Solange; Brenchereau, Patrice; Launer, Ludovic; Ashton, Alun W; Leal, Ricardo; Veyrier, Stéphanie; Gabadinho, José; Gordon, Elspeth J; Jones, Samuel D; Levik, Karl Erik; McSweeney, Seán M; Monaco, Stéphanie; Nanao, Max; Spruce, Darren; Svensson, Olof; Walsh, Martin A; Leonard, Gordon A

2011-11-15

Individual research groups now analyze thousands of samples per year at synchrotron macromolecular crystallography (MX) resources. The efficient management of experimental data is thus essential if the best possible experiments are to be performed and the best possible data used in downstream processes in structure determination pipelines. Information System for Protein crystallography Beamlines (ISPyB), a Laboratory Information Management System (LIMS) with an underlying data model allowing for the integration of analyses down-stream of the data collection experiment was developed to facilitate such data management. ISPyB is now a multisite, generic LIMS for synchrotron-based MX experiments. Its initial functionality has been enhanced to include improved sample tracking and reporting of experimental protocols, the direct ranking of the diffraction characteristics of individual samples and the archiving of raw data and results from ancillary experiments and post-experiment data processing protocols. This latter feature paves the way for ISPyB to play a central role in future macromolecular structure solution pipelines and validates the application of the approach used in ISPyB to other experimental techniques, such as biological solution Small Angle X-ray Scattering and spectroscopy, which have similar sample tracking and data handling requirements.

Macromolecular systems for vaccine delivery.

Science.gov (United States)

MuŽíková, G; Laga, R

2016-10-20

Vaccines have helped considerably in eliminating some life-threatening infectious diseases in past two hundred years. Recently, human medicine has focused on vaccination against some of the world's most common infectious diseases (AIDS, malaria, tuberculosis, etc.), and vaccination is also gaining popularity in the treatment of cancer or autoimmune diseases. The major limitation of current vaccines lies in their poor ability to generate a sufficient level of protective antibodies and T cell responses against diseases such as HIV, malaria, tuberculosis and cancers. Among the promising vaccination systems that could improve the potency of weakly immunogenic vaccines belong macromolecular carriers (water soluble polymers, polymer particels, micelles, gels etc.) conjugated with antigens and immunistumulatory molecules. The size, architecture, and the composition of the high molecular-weight carrier can significantly improve the vaccine efficiency. This review includes the most recently developed (bio)polymer-based vaccines reported in the literature.

The contrasting effect of macromolecular crowding on amyloid fibril formation.

Directory of Open Access Journals (Sweden)

Qian Ma

Full Text Available Amyloid fibrils associated with neurodegenerative diseases can be considered biologically relevant failures of cellular quality control mechanisms. It is known that in vivo human Tau protein, human prion protein, and human copper, zinc superoxide dismutase (SOD1 have the tendency to form fibril deposits in a variety of tissues and they are associated with different neurodegenerative diseases, while rabbit prion protein and hen egg white lysozyme do not readily form fibrils and are unlikely to cause neurodegenerative diseases. In this study, we have investigated the contrasting effect of macromolecular crowding on fibril formation of different proteins.As revealed by assays based on thioflavin T binding and turbidity, human Tau fragments, when phosphorylated by glycogen synthase kinase-3β, do not form filaments in the absence of a crowding agent but do form fibrils in the presence of a crowding agent, and the presence of a strong crowding agent dramatically promotes amyloid fibril formation of human prion protein and its two pathogenic mutants E196K and D178N. Such an enhancing effect of macromolecular crowding on fibril formation is also observed for a pathological human SOD1 mutant A4V. On the other hand, rabbit prion protein and hen lysozyme do not form amyloid fibrils when a crowding agent at 300 g/l is used but do form fibrils in the absence of a crowding agent. Furthermore, aggregation of these two proteins is remarkably inhibited by Ficoll 70 and dextran 70 at 200 g/l.We suggest that proteins associated with neurodegenerative diseases are more likely to form amyloid fibrils under crowded conditions than in dilute solutions. By contrast, some of the proteins that are not neurodegenerative disease-associated are unlikely to misfold in crowded physiological environments. A possible explanation for the contrasting effect of macromolecular crowding on these two sets of proteins (amyloidogenic proteins and non-amyloidogenic proteins has been

Dynamic contrast-enhanced MRI using a macromolecular MR contrast agent (P792): Evaluation of antivascular drug effect in a rabbit VX2 liver tumor model

Energy Technology Data Exchange (ETDEWEB)

Park, Hee Sun [Dept. of Radiology, Konkuk University School of Medicine, Seoul (Korea, Republic of); Han, Joon Koo; Lee, Jeong Min; Woo, Sung Min; Choi, Byung Ihn [Seoul National University Hospital, Seoul (Korea, Republic of); Kim, Young Il [Dept. of Radiology, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah (United Arab Emirates); Choi, Jin Young [Dept. of Radiology, Yonsei University College of Medicine, Seoul (Korea, Republic of)

2015-10-15

To evaluate the utility of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) using macromolecular contrast agent (P792) for assessment of vascular disrupting drug effect in rabbit VX2 liver tumor models. This study was approved by our Institutional Animal Care and Use Committee. DCE-MRI was performed with 3-T scanner in 13 VX2 liver tumor-bearing rabbits, before, 4 hours after, and 24 hours after administration of vascular disrupting agent (VDA), using gadomelitol (P792, n = 7) or low molecular weight contrast agent (gadoterate meglumine [Gd-DOTA], n = 6). P792 was injected at a of dose 0.05 mmol/kg, while that of Gd-DOTA was 0.2 mmol/kg. DCE-MRI parameters including volume transfer coefficient (Ktrans) and initial area under the gadolinium concentration-time curve until 60 seconds (iAUC) of tumors were compared between the 2 groups at each time point. DCE-MRI parameters were correlated with tumor histopathology. Reproducibility in measurement of DCE-MRI parameters and image quality of source MR were compared between groups. P792 group showed a more prominent decrease in Ktrans and iAUC at 4 hours and 24 hours, as compared to the Gd-DOTA group. Changes in DCE-MRI parameters showed a weak correlation with histologic parameters (necrotic fraction and microvessel density) in both groups. Reproducibility of DCE-MRI parameters and overall image quality was not significantly better in the P792 group, as compared to the Gd-DOTA group. Dynamic contrast-enhanced magnetic resonance imaging using a macromolecular contrast agent shows changes of hepatic perfusion more clearly after administration of the VDA. Gadolinium was required at smaller doses than a low molecular contrast agent.

Dynamic contrast-enhanced MRI using a macromolecular MR contrast agent (P792): Evaluation of antivascular drug effect in a rabbit VX2 liver tumor model

International Nuclear Information System (INIS)

Park, Hee Sun; Han, Joon Koo; Lee, Jeong Min; Woo, Sung Min; Choi, Byung Ihn; Kim, Young Il; Choi, Jin Young

2015-01-01

To evaluate the utility of dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) using macromolecular contrast agent (P792) for assessment of vascular disrupting drug effect in rabbit VX2 liver tumor models. This study was approved by our Institutional Animal Care and Use Committee. DCE-MRI was performed with 3-T scanner in 13 VX2 liver tumor-bearing rabbits, before, 4 hours after, and 24 hours after administration of vascular disrupting agent (VDA), using gadomelitol (P792, n = 7) or low molecular weight contrast agent (gadoterate meglumine [Gd-DOTA], n = 6). P792 was injected at a of dose 0.05 mmol/kg, while that of Gd-DOTA was 0.2 mmol/kg. DCE-MRI parameters including volume transfer coefficient (Ktrans) and initial area under the gadolinium concentration-time curve until 60 seconds (iAUC) of tumors were compared between the 2 groups at each time point. DCE-MRI parameters were correlated with tumor histopathology. Reproducibility in measurement of DCE-MRI parameters and image quality of source MR were compared between groups. P792 group showed a more prominent decrease in Ktrans and iAUC at 4 hours and 24 hours, as compared to the Gd-DOTA group. Changes in DCE-MRI parameters showed a weak correlation with histologic parameters (necrotic fraction and microvessel density) in both groups. Reproducibility of DCE-MRI parameters and overall image quality was not significantly better in the P792 group, as compared to the Gd-DOTA group. Dynamic contrast-enhanced magnetic resonance imaging using a macromolecular contrast agent shows changes of hepatic perfusion more clearly after administration of the VDA. Gadolinium was required at smaller doses than a low molecular contrast agent

Modular strategies for PET imaging agents

International Nuclear Information System (INIS)

Hooker, J.M.

2010-01-01

In recent years, modular and simplified chemical and biological strategies have been developed for the synthesis and implementation of positron emission tomography (PET) radiotracers. New developments in bioconjugation and synthetic methodologies, in combination with advances in macromolecular delivery systems and gene-expression imaging, reflect a need to reduce radiosynthesis burden in order to accelerate imaging agent development. These new approaches, which are often mindful of existing infrastructure and available resources, are anticipated to provide a more approachable entry point for researchers interested in using PET to translate in vitro research to in vivo imaging.

In-vacuum long-wavelength macromolecular crystallography.

Science.gov (United States)

Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

2016-03-01

Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline.

Fluorescence optical imaging in anticancer drug delivery

Czech Academy of Sciences Publication Activity Database

Etrych, Tomáš; Lucas, H.; Janoušková, Olga; Chytil, Petr; Mueller, T.; Mäder, K.

2016-01-01

Roč. 226, 28 March (2016), s. 168-181 ISSN 0168-3659 R&D Projects: GA ČR(CZ) GA15-02986S; GA MŠk(CZ) LO1507 Institutional support: RVO:61389013 Keywords : fluorescence imaging * drug delivery * theranostics Subject RIV: CD - Macromolecular Chemistry Impact factor: 7.786, year: 2016

Workshop on algorithms for macromolecular modeling. Final project report, June 1, 1994--May 31, 1995

Energy Technology Data Exchange (ETDEWEB)

Leimkuhler, B.; Hermans, J.; Skeel, R.D.

1995-07-01

A workshop was held on algorithms and parallel implementations for macromolecular dynamics, protein folding, and structural refinement. This document contains abstracts and brief reports from that workshop.

Enhanced conjugation stability and blood circulation time of macromolecular gadolinium-DTPA contrast agent.

Science.gov (United States)

Jenjob, Ratchapol; Kun, Na; Ghee, Jung Yeon; Shen, Zheyu; Wu, Xiaoxia; Cho, Steve K; Lee, Don Haeng; Yang, Su-Geun

2016-04-01

In this study, we prepared macromolecular MR T1 contrast agent: pullulan-conjugated Gd diethylene triamine pentaacetate (Gd-DTPA-Pullulan) and estimated residual free Gd(3+), chelation stability in competition with metal ions, plasma and tissue pharmacokinetics, and abdominal MR contrast on rats. Residual free Gd(3+) in Gd-DTPA-Pullulan was measured using colorimetric spectroscopy. The transmetalation of Gd(3+) incubated with Ca(2+) was performed by using a dialysis membrane (MWCO 100-500 Da) and investigated by ICP-OES. The plasma concentration profiles of Gd-DTPA-Pullulan were estimated after intravenous injection at a dose 0.1 mmol/kg of Gd. The coronal-plane abdominal images of normal rats were observed by MR imaging. The content of free Gd(3+), the toxic residual form, was less than 0.01%. Chelation stability of Gd-DTPA-Pullulan was estimated, and only 0.2% and 0.00045% of Gd(3+) were released from Gd-DTPA-Pullulan after 2h incubation with Ca(2+) and Fe(2+), respectively. Gd-DTPA-Pullulan displayed the extended plasma half-life (t1/2,α=0.43 h, t1/2,β=2.32 h), much longer than 0.11h and 0.79 h of Gd-EOB-DTPA. Abdominal MR imaging showed Gd-DTPA-Pullulan maintained initial MR contrast for 30 min. The extended plasma half-life of Gd-DTPA-Pullulan probably allows the prolonged MR acquisition time in clinic with enhanced MR contrast. Copyright © 2016 Elsevier B.V. All rights reserved.

Aging changes of macromolecular synthesis in the mitochondria of mouse hepatocytes as revealed by microscopic radioautography

Energy Technology Data Exchange (ETDEWEB)

Nagata, Tetsuji [Shinshu University, Matsumoto (Japan). Dept. of Anatomy and Cell Biology

2007-07-01

This mini-review reports aging changes of macromolecular synthesis in the mitochondria of mouse hepatocytes. We have observed the macromolecular synthesis, such as DNA, RNA and proteins, in the mitochondria of various mammalian cells by means of electron microscopic radioautography technique developed in our laboratory. The number of mitochondria per cell, number of labeled mitochondria per cell with 3H-thymidine, 3H-uridine and 3H-leucine, precursors for DNA, RNA and proteins, respectively, were counted and the labeling indices at various ages, from fetal to postnatal early days and several months to 1 and 2 years in senescence, were calculated, which showed variations due to aging. (author)

Detection and cellular localisation of the synthetic soluble macromolecular drug carrier pHPMA

Czech Academy of Sciences Publication Activity Database

Kissel, M.; Peschke, P.; Šubr, Vladimír; Ulbrich, Karel; Strunz, A. M.; Kühnlein, R.; Debus, J.; Friedrich, E.

2002-01-01

Roč. 29, č. 8 (2002), s. 1055-1062 ISSN 1619-7070 R&D Projects: GA ČR GV307/96/K226 Institutional research plan: CEZ:AV0Z4050913 Keywords : EPR effect * Radiolabelled macromolecules * Pharmacokinetic Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.568, year: 2002

UQlust: combining profile hashing with linear-time ranking for efficient clustering and analysis of big macromolecular data.

Science.gov (United States)

Adamczak, Rafal; Meller, Jarek

2016-12-28

Advances in computing have enabled current protein and RNA structure prediction and molecular simulation methods to dramatically increase their sampling of conformational spaces. The quickly growing number of experimentally resolved structures, and databases such as the Protein Data Bank, also implies large scale structural similarity analyses to retrieve and classify macromolecular data. Consequently, the computational cost of structure comparison and clustering for large sets of macromolecular structures has become a bottleneck that necessitates further algorithmic improvements and development of efficient software solutions. uQlust is a versatile and easy-to-use tool for ultrafast ranking and clustering of macromolecular structures. uQlust makes use of structural profiles of proteins and nucleic acids, while combining a linear-time algorithm for implicit comparison of all pairs of models with profile hashing to enable efficient clustering of large data sets with a low memory footprint. In addition to ranking and clustering of large sets of models of the same protein or RNA molecule, uQlust can also be used in conjunction with fragment-based profiles in order to cluster structures of arbitrary length. For example, hierarchical clustering of the entire PDB using profile hashing can be performed on a typical laptop, thus opening an avenue for structural explorations previously limited to dedicated resources. The uQlust package is freely available under the GNU General Public License at https://github.com/uQlust . uQlust represents a drastic reduction in the computational complexity and memory requirements with respect to existing clustering and model quality assessment methods for macromolecular structure analysis, while yielding results on par with traditional approaches for both proteins and RNAs.

Predictive Mechanical Characterization of Macro-Molecular Material Chemistry Structures of Cement Paste at Nano Scale - Two-phase Macro-Molecular Structures of Calcium Silicate Hydrate, Tri-Calcium Silicate, Di-Calcium Silicate and Calcium Hydroxide

Science.gov (United States)

Padilla Espinosa, Ingrid Marcela

Concrete is a hierarchical composite material with a random structure over a wide range of length scales. At submicron length scale the main component of concrete is cement paste, formed by the reaction of Portland cement clinkers and water. Cement paste acts as a binding matrix for the other components and is responsible for the strength of concrete. Cement paste microstructure contains voids, hydrated and unhydrated cement phases. The main crystalline phases of unhydrated cement are tri-calcium silicate (C3S) and di-calcium silicate (C2S), and of hydrated cement are calcium silicate hydrate (CSH) and calcium hydroxide (CH). Although efforts have been made to comprehend the chemical and physical nature of cement paste, studies at molecular level have primarily been focused on individual components. Present research focuses on the development of a method to model, at molecular level, and analysis of the two-phase combination of hydrated and unhydrated phases of cement paste as macromolecular systems. Computational molecular modeling could help in understanding the influence of the phase interactions on the material properties, and mechanical performance of cement paste. Present work also strives to create a framework for molecular level models suitable for potential better comparisons with low length scale experimental methods, in which the sizes of the samples involve the mixture of different hydrated and unhydrated crystalline phases of cement paste. Two approaches based on two-phase cement paste macromolecular structures, one involving admixed molecular phases, and the second involving cluster of two molecular phases are investigated. The mechanical properties of two-phase macromolecular systems of cement paste consisting of key hydrated phase CSH and unhydrated phases C3S or C2S, as well as CSH with the second hydrated phase CH were calculated. It was found that these cement paste two-phase macromolecular systems predicted an isotropic material behavior. Also

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

Science.gov (United States)

Mallik, Saurav; Kundu, Sudip

2017-07-01

Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Radiation damage to nucleoprotein complexes in macromolecular crystallography

International Nuclear Information System (INIS)

Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary; Ravelli, Raimond B. G.; Carmichael, Ian; Kneale, Geoff; McGeehan, John E.

2015-01-01

Quantitative X-ray induced radiation damage studies employing a model protein–DNA complex revealed a striking partition of damage sites. The DNA component was observed to be far more resistant to specific damage compared with the protein. Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein–DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07–44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N 1 —C and sugar-phosphate C—O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses

Interplay between the bacterial nucleoid protein H-NS and macromolecular crowding in compacting DNA

NARCIS (Netherlands)

Wintraecken, C.H.J.M.

2012-01-01

In this dissertation we discuss H-NS and its connection to nucleoid compaction and organization. Nucleoid formation involves a dramatic reduction in coil volume of the genomic DNA. Four factors are thought to influence coil volume: supercoiling, DNA charge neutralization, macromolecular

Bringing macromolecular machinery to life using 3D animation.

Science.gov (United States)

Iwasa, Janet H

2015-04-01

Over the past decade, there has been a rapid rise in the use of three-dimensional (3D) animation to depict molecular and cellular processes. Much of the growth in molecular animation has been in the educational arena, but increasingly, 3D animation software is finding its way into research laboratories. In this review, I will discuss a number of ways in which 3d animation software can play a valuable role in visualizing and communicating macromolecular structures and dynamics. I will also consider the challenges of using animation tools within the research sphere. Copyright © 2015. Published by Elsevier Ltd.

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

International Nuclear Information System (INIS)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So; Evans, Gwyndaf

2013-01-01

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Aller, Pierre [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz; Cameron, Alex [Imperial College, London SW7 2AZ (United Kingdom); Axford, Danny; Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Armour, Wes [Oxford e-Research Centre (OeRC), Keble Road, Oxford OX1 3QG (United Kingdom); Waterman, David G. [Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

2013-08-01

A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

Recent Major Improvements to the ALS Sector 5 Macromolecular Crystallography Beamlines

International Nuclear Information System (INIS)

Morton, Simon A.; Glossinger, James; Smith-Baumann, Alexis; McKean, John P.; Trame, Christine; Dickert, Jeff; Rozales, Anthony; Dauz, Azer; Taylor, John; Zwart, Petrus; Duarte, Robert; Padmore, Howard; McDermott, Gerry; Adams, Paul

2007-01-01

Although the Advanced Light Source (ALS) was initially conceived primarily as a low energy (1.9GeV) 3rd generation source of VUV and soft x-ray radiation it was realized very early in the development of the facility that a multipole wiggler source coupled with high quality, (brightness preserving), optics would result in a beamline whose performance across the optimal energy range (5-15keV) for macromolecular crystallography (MX) would be comparable to, or even exceed, that of many existing crystallography beamlines at higher energy facilities. Hence, starting in 1996, a suite of three beamlines, branching off a single wiggler source, was constructed, which together formed the ALS Macromolecular Crystallography Facility. From the outset this facility was designed to cater equally to the needs of both academic and industrial users with a heavy emphasis placed on the development and introduction of high throughput crystallographic tools, techniques, and facilities--such as large area CCD detectors, robotic sample handling and automounting facilities, a service crystallography program, and a tightly integrated, centralized, and highly automated beamline control environment for users. This facility was immediately successful, with the primary Multiwavelength Anomalous Diffraction beamline (5.0.2) in particular rapidly becoming one of the foremost crystallographic facilities in the US--responsible for structures such as the 70S ribosome. This success in-turn triggered enormous growth of the ALS macromolecular crystallography community and spurred the development of five additional ALS MX beamlines all utilizing the newly developed superconducting bending magnets ('superbends') as sources. However in the years since the original Sector 5.0 beamlines were built the performance demands of macromolecular crystallography users have become ever more exacting; with growing emphasis placed on studying larger complexes, more difficult structures, weakly diffracting or smaller

Macromolecularly crowded in vitro microenvironments accelerate the production of extracellular matrix-rich supramolecular assemblies.

Science.gov (United States)

Kumar, Pramod; Satyam, Abhigyan; Fan, Xingliang; Collin, Estelle; Rochev, Yury; Rodriguez, Brian J; Gorelov, Alexander; Dillon, Simon; Joshi, Lokesh; Raghunath, Michael; Pandit, Abhay; Zeugolis, Dimitrios I

2015-03-04

Therapeutic strategies based on the principles of tissue engineering by self-assembly put forward the notion that functional regeneration can be achieved by utilising the inherent capacity of cells to create highly sophisticated supramolecular assemblies. However, in dilute ex vivo microenvironments, prolonged culture time is required to develop an extracellular matrix-rich implantable device. Herein, we assessed the influence of macromolecular crowding, a biophysical phenomenon that regulates intra- and extra-cellular activities in multicellular organisms, in human corneal fibroblast culture. In the presence of macromolecules, abundant extracellular matrix deposition was evidenced as fast as 48 h in culture, even at low serum concentration. Temperature responsive copolymers allowed the detachment of dense and cohesive supramolecularly assembled living substitutes within 6 days in culture. Morphological, histological, gene and protein analysis assays demonstrated maintenance of tissue-specific function. Macromolecular crowding opens new avenues for a more rational design in engineering of clinically relevant tissue modules in vitro.

Long-wavelength macromolecular crystallography - First successful native SAD experiment close to the sulfur edge

Science.gov (United States)

Aurelius, O.; Duman, R.; El Omari, K.; Mykhaylyk, V.; Wagner, A.

2017-11-01

Phasing of novel macromolecular crystal structures has been challenging since the start of structural biology. Making use of anomalous diffraction of natively present elements, such as sulfur and phosphorus, for phasing has been possible for some systems, but hindered by the necessity to access longer X-ray wavelengths in order to make most use of the anomalous scattering contributions of these elements. Presented here are the results from a first successful experimental phasing study of a macromolecular crystal structure at a wavelength close to the sulfur K edge. This has been made possible by the in-vacuum setup and the long-wavelength optimised experimental setup at the I23 beamline at Diamond Light Source. In these early commissioning experiments only standard data collection and processing procedures have been applied, in particular no dedicated absorption correction has been used. Nevertheless the success of the experiment demonstrates that the capability to extract phase information can be even further improved once data collection protocols and data processing have been optimised.

The In-Situ One-Step Synthesis of a PDC Macromolecular Pro-Drug and the Fabrication of a Novel Core-Shell Micell.

Science.gov (United States)

Yu, Cui-Yun; Yang, Sa; Li, Zhi-Ping; Huang, Can; Ning, Qian; Huang, Wen; Yang, Wen-Tong; He, Dongxiu; Sun, Lichun

2016-01-01

The development of slow release nano-sized carriers for efficient antineoplastic drug delivery with a biocompatible and biodegradable pectin-based macromolecular pro-drug for tumor therapy has been reported in this study. Pectin-doxorubicin conjugates (PDC), a macromolecular pro-drug, were prepared via an amide condensation reaction, and a novel amphiphilic core-shell micell based on a PDC macromolecular pro-drug (PDC-M) was self-assembled in situ, with pectin as the hydrophilic shell and doxorubicin (DOX) as the hydrophobic core. Then the chemical structure of the PDC macromolecular pro-drug was identified by both Fourier transform infrared spectroscopy (FTIR) and nuclear magnetic resonance spectroscopy ((1)H-NMR), and proved that doxorubicin combined well with the pectin and formed macromolecular pro-drug. The PDC-M were observed to have an unregularly spherical shape and were uniform in size by scanning electron microscopy (SEM). The average particle size of PDC-M, further measured by a Zetasizer nanoparticle analyzer (Nano ZS, Malvern Instruments), was about 140 nm. The encapsulation efficiency and drug loading were 57.82% ± 3.7% (n = 3) and 23.852% ±2.3% (n = 3), respectively. The in vitro drug release behaviors of the resulting PDC-M were studied in a simulated tumor environment (pH 5.0), blood (pH 7.4) and a lysosome media (pH 6.8), and showed a prolonged slow release profile. Assays for antiproliferative effects and flow cytometry of the resulting PDC-M in HepG2 cell lines demonstrated greater properties of delayed and slow release as compared to free DOX. A cell viability study against endothelial cells further revealed that the resulting PDC-M possesses excellent cell compatibilities and low cytotoxicities in comparison with that of the free DOX. Hemolysis activity was investigated in rabbits, and the results also demonstrated that the PDC-M has greater compatibility in comparison with free DOX. This shows that the resulting PDC-M can ameliorate the

MX1: a bending-magnet crystallography beamline serving both chemical and macromolecular crystallography communities at the Australian Synchrotron

International Nuclear Information System (INIS)

Cowieson, Nathan Philip; Aragao, David; Clift, Mark; Ericsson, Daniel J.; Gee, Christine; Harrop, Stephen J.; Mudie, Nathan; Panjikar, Santosh; Price, Jason R.; Riboldi-Tunnicliffe, Alan; Williamson, Rachel; Caradoc-Davies, Tom

2015-01-01

The macromolecular crystallography beamline MX1 at the Australian Synchrotron is described. MX1 is a bending-magnet crystallography beamline at the 3 GeV Australian Synchrotron. The beamline delivers hard X-rays in the energy range from 8 to 18 keV to a focal spot at the sample position of 120 µm FWHM. The beamline endstation and ancillary equipment facilitate local and remote access for both chemical and biological macromolecular crystallography. Here, the design of the beamline and endstation are discussed. The beamline has enjoyed a full user program for the last seven years and scientific highlights from the user program are also presented

Synthesis of branched polymers under continuous-flow microprocess: an improvement of the control of macromolecular architectures.

Science.gov (United States)

Bally, Florence; Serra, Christophe A; Brochon, Cyril; Hadziioannou, Georges

2011-11-15

Polymerization reactions can benefit from continuous-flow microprocess in terms of kinetics control, reactants mixing or simply efficiency when high-throughput screening experiments are carried out. In this work, we perform for the first time the synthesis of branched macromolecular architecture through a controlled/'living' polymerization technique, in tubular microreactor. Just by tuning process parameters, such as flow rates of the reactants, we manage to generate a library of polymers with various macromolecular characteristics. Compared to conventional batch process, polymerization kinetics shows a faster initiation step and more interestingly an improved branching efficiency. Due to reduced diffusion pathway, a characteristic of microsystems, it is thus possible to reach branched polymers exhibiting a denser architecture, and potentially a higher functionality for later applications. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Structural analysis of nanoparticulate carriers for encapsulation of macromolecular drugs

Czech Academy of Sciences Publication Activity Database

Angelov, Borislav; Garamus, V.M.; Drechsler, M.; Angelova, A.

2017-01-01

Roč. 235, Jun (2017), s. 83-89 ISSN 0167-7322 R&D Projects: GA MŠk EF15_003/0000447; GA MŠk EF15_008/0000162 Grant - others:OP VVV - ELIBIO(XE) CZ.02.1.01/0.0/0.0/15_003/0000447; ELI Beamlines(XE) CZ.02.1.01/0.0/0.0/15_008/0000162 Institutional support: RVO:68378271 Keywords : self-assembled nanocarriers * liquid crystalline phase transitions * cationic lipids * macromolecular drugs Subject RIV: BO - Biophysics OBOR OECD: Biophysics Impact factor: 3.648, year: 2016

Protein crystal growth studies at the Center for Macromolecular Crystallography

International Nuclear Information System (INIS)

DeLucas, Lawrence J.; Long, Marianna M.; Moore, Karen M.; Harrington, Michael; McDonald, William T.; Smith, Craig D.; Bray, Terry; Lewis, Johanna; Crysel, William B.; Weise, Lance D.

2000-01-01

The Center for Macromolecular Crystallography (CMC) has been involved in fundamental studies of protein crystal growth (PCG) in microgravity and in our earth-based laboratories. A large group of co-investigators from academia and industry participated in these experiments by providing protein samples and by performing the x-ray crystallographic analysis. These studies have clearly demonstrated the usefulness of a microgravity environment for enhancing the quality and size of protein crystals. Review of the vapor diffusion (VDA) PCG results from nineteen space shuttle missions is given in this paper

Extraction of cobalt ion from textile using a complexing macromolecular surfactant in supercritical carbon dioxide

International Nuclear Information System (INIS)

Chirat, Mathieu; Ribaut, Tiphaine; Clerc, Sebastien; Lacroix-Desmazes, Patrick; Charton, Frederic; Fournel, Bruno

2013-01-01

Cobalt ion under the form of cobalt nitrate is removed from a textile lab coat using supercritical carbon dioxide extraction. The process involves a macromolecular additive of well-defined architecture, acting both as a surfactant and a complexing agent. The extraction efficiency of cobalt reaches 66% when using a poly(1,1,2,2-tetrahydroperfluoro-decyl-acrylate-co-vinyl-benzylphosphonic diacid) gradient copolymer in the presence of water at 160 bar and 40 C. The synergy of the two additives, namely the copolymer and water which are useless if used separately, is pointed out. The potential of the supercritical carbon dioxide process using complexing macromolecular surfactant lies in the ability to modulate the complexing unit as a function of the metal as well as the architecture of the surface-active agent for applications ranging for instance from nuclear decontamination to the recovery of strategic metals. (authors)

E-MSD: the European Bioinformatics Institute Macromolecular Structure Database.

Science.gov (United States)

Boutselakis, H; Dimitropoulos, D; Fillon, J; Golovin, A; Henrick, K; Hussain, A; Ionides, J; John, M; Keller, P A; Krissinel, E; McNeil, P; Naim, A; Newman, R; Oldfield, T; Pineda, J; Rachedi, A; Copeland, J; Sitnov, A; Sobhany, S; Suarez-Uruena, A; Swaminathan, J; Tagari, M; Tate, J; Tromm, S; Velankar, S; Vranken, W

2003-01-01

The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool.

Macromolecular Engineering: New Routes Towards the Synthesis of Well-??Defined Polyethers/Polyesters Co/Terpolymers with Different Architectures

KAUST Repository

Alamri, Haleema

2016-01-01

Macromolecular engineering (as discussed in the first chapter) of homo/copolymers refers to the specific tailoring of these materials for achieving an easy and reproducible synthesis that results in precise molecular

The structural biology center at the APS: an integrated user facility for macromolecular crystallography

International Nuclear Information System (INIS)

Rosenbaum, G.; Westbrook, E.M.

1997-01-01

The Structural Biology Center (SBC) has developed and operates a sector (undulator and bending magnet) of the APS as a user facility for macromolecular crystallography. Crystallographically determined structures of proteins, nucleic acids and their complexes with proteins, viruses, and complexes between macromolecules and small ligands have become of central importance in molecular and cellular biology. Major design goals were to make the extremely high brilliance of the APS available for brilliance limited studies, and to achieve a high throughput of less demanding studies, as well as optimization for MAS-phasing. Crystal samples will include extremely small crystals, crystals with large unit cells (viruses, ribosomes, etc.) and ensembles of closely similar crystal structures for drug design, protein engineering, etc. Data are recorded on a 3000x3000 pixel CCD-area detector (optionally on image plates). The x-ray optics of both beamlines has been designed to produce a highly demagnified image of the source in order to match the focal size with the sizes of the sample and the resolution element of the detector. Vertical focusing is achieved by a flat, cylindrically bent mirror. Horizontal focusing is achieved by sagitally bending the second crystal of the double crystal monochromator. Monochromatic fluxes of 1.3 * 10 13 ph/s into focal sizes of 0.08 mm (horizontal)x0.04 mm (vertical) FWHM (flux density 3.5 * 10 15 ph/s/mm 2 ) have been recorded.copyright 1997 American Institute of Physics

Generalized Born Models of Macromolecular Solvation Effects

Science.gov (United States)

Bashford, Donald; Case, David A.

2000-10-01

It would often be useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson equation are attractive because of their computational efficiency. Here we give an overview of one such approximation, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. We discuss its strengths and weaknesses, both for its fidelity to the underlying continuum model and for its ability to replace explicit consideration of solvent molecules in macromolecular simulations. We focus particularly on versions of the generalized Born model that have a pair-wise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations.

Probing the hydration water diffusion of macromolecular surfaces and interfaces

International Nuclear Information System (INIS)

Ortony, Julia H; Cheng, Chi-Yuan; Franck, John M; Pavlova, Anna; Hunt, Jasmine; Han, Songi; Kausik, Ravinath

2011-01-01

We probe the translational dynamics of the hydration water surrounding the macromolecular surfaces of selected polyelectrolytes, lipid vesicles and intrinsically disordered proteins with site specificity in aqueous solutions. These measurements are made possible by the recent development of a new instrumental and methodological approach based on Overhauser dynamic nuclear polarization (DNP)-enhanced nuclear magnetic resonance (NMR) spectroscopy. This technique selectively amplifies 1 H NMR signals of hydration water around a spin label that is attached to a molecular site of interest. The selective 1 H NMR amplification within molecular length scales of a spin label is achieved by utilizing short-distance range (∼r -3 ) magnetic dipolar interactions between the 1 H spin of water and the electron spin of a nitroxide radical-based label. Key features include the fact that only minute quantities (<10 μl) and dilute (≥100 μM) sample concentrations are needed. There is no size limit on the macromolecule or molecular assembly to be analyzed. Hydration water with translational correlation times between 10 and 800 ps is measured within ∼10 A distance of the spin label, encompassing the typical thickness of a hydration layer with three water molecules across. The hydration water moving within this time scale has significant implications, as this is what is modulated whenever macromolecules or molecular assemblies undergo interactions, binding or conformational changes. We demonstrate, with the examples of polymer complexation, protein aggregation and lipid-polymer interaction, that the measurements of interfacial hydration dynamics can sensitively and site specifically probe macromolecular interactions.

Measurement and Interpretation of Diffuse Scattering in X-Ray Diffraction for Macromolecular Crystallography

Energy Technology Data Exchange (ETDEWEB)

Wall, Michael E. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2017-10-16

X-ray diffraction from macromolecular crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering reflects the mean electron density in the unit cells of the crystal. The diffuse scattering arises from correlations in the variations of electron density that may occur from one unit cell to another, and therefore contains information about collective motions in proteins.

Proceedings of a one-week course on exploiting anomalous scattering in macromolecular structure determination (EMBO'07)

International Nuclear Information System (INIS)

Weiss, M.S.; Shepard, W.; Dauter, Z.; Leslie, A.; Diederichs, K.; Evans, G.; Svensson, O.; Schneider, T.; Bricogne, G.; Dauter, Z.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Leslie, A.; Kabsch, W.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Read, R.; Panjikar, S.; Pannu, N.S.; Dauter, Z.; Weiss, M.S.; McSweeney, S.

2007-01-01

This course, which was directed to young scientists, illustrated both theoretical and practical aspects of macromolecular crystal structure solution using synchrotron radiation. Some software dedicated to data collection, processing and analysis were presented. This document gathers only the slides of the presentations

Proceedings of a one-week course on exploiting anomalous scattering in macromolecular structure determination (EMBO'07)

Energy Technology Data Exchange (ETDEWEB)

Weiss, M S; Shepard, W; Dauter, Z; Leslie, A; Diederichs, K; Evans, G; Svensson, O; Schneider, T; Bricogne, G; Dauter, Z; Flensburg, C; Terwilliger, T; Lamzin, V; Leslie, A; Kabsch, W; Flensburg, C; Terwilliger, T; Lamzin, V; Read, R; Panjikar, S; Pannu, N S; Dauter, Z; Weiss, M S; McSweeney, S

2007-07-01

This course, which was directed to young scientists, illustrated both theoretical and practical aspects of macromolecular crystal structure solution using synchrotron radiation. Some software dedicated to data collection, processing and analysis were presented. This document gathers only the slides of the presentations.

Polycapillary x-ray optics for macromolecular crystallography

International Nuclear Information System (INIS)

Owens, S.M.; Gibson, W.M.; Carter, D.C.; Sisk, R.C.; Ho, J.X.

1996-01-01

Polycapillary x-ray optics have found potential application in many different fields, including antiscatter and magnification in mammography, radiography, x-ray fluorescence, x-ray lithography, and x-ray diffraction techniques. In x-ray diffraction, an optic is used to collect divergent x-rays from a point source and redirect them into a quasi-parallel, or slightly focused beam. Monolithic polycapillary optics have been developed recently for macromolecular crystallography and have already shown considerable gains in diffracted beam intensity over pinhole collimation. Development is being pursued through a series of simulations and prototype optics. Many improvements have been made over the stage 1 prototype reported previously, which include better control over the manufacturing process, reducing the diameter of the output beam, and addition of a slight focusing at the output of the optic to further increase x-ray flux at the sample. The authors report the characteristics and performance of the stage 1 and stage 2 optics

The Postgraduate Study of Macromolecular Sciences at the University of Zagreb (1971-1980)

OpenAIRE

Kunst, B.; Dezelic, D.; Veksli, Z.

2008-01-01

The postgraduate study of macromolecular sciences (PSMS) was established at the University of Zagreb in 1971 as a university study in the time of expressed interdisciplinary permeation of natural sciences - physics, chemistry and biology, and application of their achievements in technologicaldisciplines. PSMS was established by a group of prominent university professors from the schools of Science, Chemical Technology, Pharmacy and Medicine, as well as from the Institute of Biology. The study...

A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF

International Nuclear Information System (INIS)

McCarthy, Andrew A.; Brockhauser, Sandor; Nurizzo, Didier; Theveneau, Pascal; Mairs, Trevor; Spruce, Darren; Guijarro, Matias; Lesourd, Marc; Ravelli, Raimond B. G.; McSweeney, Sean

2009-01-01

The improvement of the X-ray beam quality achieved on ID14-4 by the installation of new X-ray optical elements is described. ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade

Distribution and enzymatic activity of heterotrophic bacteria decomposing selected macromolecular compounds in a Baltic Sea sandy beach

Science.gov (United States)

Podgórska, B.; Mudryk, Z. J.

2003-03-01

The potential capability to decompose macromolecular compounds, and the level of extracellular enzyme activities were determined in heterotrophic bacteria isolated from a sandy beach in Sopot on the Southern Baltic Sea coast. Individual isolates were capable of hydrolysing a wide spectrum of organic macromolecular compounds. Lipids, gelatine, and DNA were hydrolyzed most efficiently. Only a very small percentage of strains were able to decompose cellulose, and no pectinolytic bacteria were found. Except for starch-hydrolysis, no significant differences in the intensity of organic compound decomposition were recorded between horizontal and vertical profiles of the studied beach. Of all the studied extracellular enzymes, alkaline phosphatase, esterase lipase, and leucine acrylaminidase were most active; in contrast, the activity α-fucosidase, α-galactosidase and β-glucouronidase was the weakest. The level of extracellular enzyme activity was similar in both sand layers.

Macromolecular contrast agents for MR mammography: current status

International Nuclear Information System (INIS)

Daldrup-Link, Heike E.; Brasch, Robert C.

2003-01-01

Macromolecular contrast media (MMCM) encompass a new class of diagnostic drugs that can be applied with dynamic MRI to extract both physiologic and morphologic information in breast lesions. Kinetic analysis of dynamic MMCM-enhanced MR data in breast tumor patients provides useful estimates of tumor blood volume and microvascular permeability, typically increased in cancer. These tumor characteristics can be applied to differentiate benign from malignant lesions, to define the angiogenesis status of cancers, and to monitor tumor response to therapy. The most immediate challenge to the development of MMCM-enhanced mammography is the identification of those candidate compounds that demonstrate the requisite long intravascular distribution and have the high tolerance necessary for clinical use. Potential mammographic applications and limitations of various MMCM, defined by either experimental animal testing or clinical testing in patients, are reviewed in this article. (orig.)

Enhanced conjugation stability and blood circulation time of macromolecular gadolinium-DTPA contrast agent

Energy Technology Data Exchange (ETDEWEB)

Jenjob, Ratchapol [Department of New Drug Development, School of Medicine, Inha University, 2F A-dong, Jeongseok Bldg., Sinheung-dong 3-ga, Jung-gu, Incheon 400-712 (Korea, Republic of); Kun, Na [Department of Biotechnology, The Catholic University of Korea, 43 Jibong-ro, Wonmi-gu, Bucheon-si, Gyeonggi-do 420-743 (Korea, Republic of); Ghee, Jung Yeon [Utah-Inha DDS and Advanced Therapeutics, B-403 Meet-You-All Tower, SongdoTechnopark, 7–50, Songdo-dong, Yeonsu-gu, Incheon 406-840 (Korea, Republic of); Shen, Zheyu; Wu, Xiaoxia [Division of Functional Materials and Nano-Devices, Ningbo Institute of Materials Technology & Engineering (NIMTE), Chinese Academy of Sciences, 519 Zhuangshi Street, Zhenhai District, Ningbo, Zhejiang 315201 (China); Cho, Steve K., E-mail: scho@gist.ac.kr [Division of Liberal Arts and Science, GIST College, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of); Lee, Don Haeng [Utah-Inha DDS and Advanced Therapeutics, B-403 Meet-You-All Tower, SongdoTechnopark, 7–50, Songdo-dong, Yeonsu-gu, Incheon 406-840 (Korea, Republic of); Department of Internal Medicine, School of Medicine, Inha University Hospital, Incheon 420-751 (Korea, Republic of); Yang, Su-Geun, E-mail: Sugeun.Yang@Inha.ac.kr [Department of New Drug Development, School of Medicine, Inha University, 2F A-dong, Jeongseok Bldg., Sinheung-dong 3-ga, Jung-gu, Incheon 400-712 (Korea, Republic of)

2016-04-01

In this study, we prepared macromolecular MR T1 contrast agent: pullulan-conjugated Gd diethylene triamine pentaacetate (Gd-DTPA-Pullulan) and estimated residual free Gd{sup 3+}, chelation stability in competition with metal ions, plasma and tissue pharmacokinetics, and abdominal MR contrast on rats. Residual free Gd{sup 3+} in Gd-DTPA-Pullulan was measured using colorimetric spectroscopy. The transmetalation of Gd{sup 3+} incubated with Ca{sup 2+} was performed by using a dialysis membrane (MWCO 100–500 Da) and investigated by ICP-OES. The plasma concentration profiles of Gd-DTPA-Pullulan were estimated after intravenous injection at a dose 0.1 mmol/kg of Gd. The coronal-plane abdominal images of normal rats were observed by MR imaging. The content of free Gd{sup 3+}, the toxic residual form, was less than 0.01%. Chelation stability of Gd-DTPA-Pullulan was estimated, and only 0.2% and 0.00045% of Gd{sup 3+} were released from Gd-DTPA-Pullulan after 2 h incubation with Ca{sup 2+} and Fe{sup 2+}, respectively. Gd-DTPA-Pullulan displayed the extended plasma half-life (t{sub 1/2,α} = 0.43 h, t{sub 1/2,β} = 2.32 h), much longer than 0.11 h and 0.79 h of Gd-EOB-DTPA. Abdominal MR imaging showed Gd-DTPA-Pullulan maintained initial MR contrast for 30 min. The extended plasma half-life of Gd-DTPA-Pullulan probably allows the prolonged MR acquisition time in clinic with enhanced MR contrast. - Highlights: • Macromolecule (pullulan) conjugated Gd contrast agent (Gd-DTPA-Pullulan) showed the extended plasma half-life (t{sub 1/2,α} = 0.43 h, t{sub 1/2,β} = 2.32 h) in comparison with Gd-EOB-DTPA • Gd-DTPA-pullulan T1 contrast agent exhibited strong chelation stability against Gd. • The extended blood circulation attributed the enhanced and prolonged MR contrast on abdominal region of rats. • The extended blood circulation may provide prolonged MR acquisition time window in clinics.

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

Directory of Open Access Journals (Sweden)

Shane Ó Conchúir

Full Text Available The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

Macromolecular crowding compacts unfolded apoflavodoxin and causes severe aggregation of the off-pathway intermediate during apoflavodoxin folding

NARCIS (Netherlands)

Engel, R.; Westphal, A.H.; Huberts, D.; Nabuurs, S.M.; Lindhoud, S.; Visser, A.J.W.G.; Mierlo, van C.P.M.

2008-01-01

To understand how proteins fold in vivo, it is important to investigate the effects of macromolecular crowding on protein folding. Here, the influence of crowding on in vitro apoflavodoxin folding, which involves a relatively stable off-pathway intermediate with molten globule characteristics, is

Proceedings of a one-week course on exploiting anomalous scattering in macromolecular structure determination (EMBO'07)

Energy Technology Data Exchange (ETDEWEB)

Weiss, M.S.; Shepard, W.; Dauter, Z.; Leslie, A.; Diederichs, K.; Evans, G.; Svensson, O.; Schneider, T.; Bricogne, G.; Dauter, Z.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Leslie, A.; Kabsch, W.; Flensburg, C.; Terwilliger, T.; Lamzin, V.; Read, R.; Panjikar, S.; Pannu, N.S.; Dauter, Z.; Weiss, M.S.; McSweeney, S

2007-07-01

This course, which was directed to young scientists, illustrated both theoretical and practical aspects of macromolecular crystal structure solution using synchrotron radiation. Some software dedicated to data collection, processing and analysis were presented. This document gathers only the slides of the presentations.

Probing the Interplay of Size, Shape, and Solution Environment in Macromolecular Diffusion Using a Simple Refraction Experiment

Science.gov (United States)

Mankidy, Bijith D.; Coutinho, Cecil A.; Gupta, Vinay K.

2010-01-01

The diffusion coefficient of polymers is a critical parameter in biomedicine, catalysis, chemical separations, nanotechnology, and other industrial applications. Here, measurement of macromolecular diffusion in solutions is described using a visually instructive, undergraduate-level optical refraction experiment based on Weiner's method. To…

C,N-2-[(Dimethylamino)methyl]phenylplatinum Complexes Functionalized with C60 as Macromolecular Building Blocks

NARCIS (Netherlands)

Koten, G. van; Meijer, M.D.; Wolf, E. de; Lutz, M.H.; Spek, A.L.; Klink, G.P.M. van

2001-01-01

The application of platinum(II) complexes based on the N,N-dimethylbenzylamine ligand (abbreviated as H-C,N) in macromolecular synthesis was demonstrated. Two cationic C,N-platinum moieties were linked with a 4,4'-bipyridine bridge, giving [{C6H4(CH2NMe2)-2-Pt(PPh3)}2(4,4'-bpy)](BF4)2 (2), the

Localization-based super-resolution imaging of cellular structures.

Science.gov (United States)

Kanchanawong, Pakorn; Waterman, Clare M

2013-01-01

Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures.

Grain sorghum dust increases macromolecular efflux from the in situ nasal mucosa.

Science.gov (United States)

Gao, X P

1998-04-01

The purpose of this study was to determine whether an aqueous extract of grain sorghum dust increases macromolecular efflux from the nasal mucosa in vivo and, if so, whether this response is mediated, in part, by substance P. Suffusion of grain sorghum dust extract on the in situ nasal mucosa of anesthetized hamsters elicits a significant increase in clearance of fluorescein isothiocyanate-labeled dextran (FITC-dextran; mol mass, 70 kDa; P grain sorghum dust elicits neurogenic plasma exudation from the in situ nasal mucosa.

Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids

NARCIS (Netherlands)

van Zundert, G. C P; Bonvin, A. M J J

Cryo-electron microscopy provides fascinating structural insight into large macromolecular machines at increasing detail. Despite significant advances in the field, the resolution of the resulting three-dimensional images is still typically insufficient for . de novo model building. To bridge the

Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

Energy Technology Data Exchange (ETDEWEB)

A Soares; D Schneider; J Skinner; M Cowan; R Buono; H Robinson; A Heroux; M Carlucci-Dayton; A Saxena; R Sweet

2011-12-31

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

International Nuclear Information System (INIS)

Soares, A.; Schneider, D.; Skinner, J.; Cowan, M.; Buono, R.; Robinson, H.; Heroux, A.; Carlucci-Dayton, M.; Saxena, A.; Sweet, R.

2008-01-01

The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data

International Nuclear Information System (INIS)

Dosset, Patrice; Hus, Jean-Christophe; Blackledge, Martin; Marion, Dominique

2000-01-01

A novel program has been developed for the interpretation of 15 N relaxation rates in terms of macromolecular anisotropic rotational diffusion. The program is based on a highly efficient simulated annealing/minimization algorithm, designed specifically to search the parametric space described by the isotropic, axially symmetric and fully anisotropic rotational diffusion tensor models. The high efficiency of this algorithm allows extensive noise-based Monte Carlo error analysis. Relevant statistical tests are systematically applied to provide confidence limits for the proposed tensorial models. The program is illustrated here using the example of the cytochrome c' from Rhodobacter capsulatus, a four-helix bundle heme protein, for which data at three different field strengths were independently analysed and compared

¹²⁹ Xe NMR Relaxation-Based Macromolecular Sensing

Energy Technology Data Exchange (ETDEWEB)

Gomes, Muller D. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Dao, Phuong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Jeong, Keunhong [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Slack, Clancy C. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Vassiliou, Christophoros C. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Finbloom, Joel A. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Francis, Matthew B. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Wemmer, David E. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Physical Biosciences Division; Pines, Alexander [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Materials Sciences Division; Univ. of California, Berkeley, CA (United States). Dept. of Chemistry

2016-07-29

A ¹²⁹Xe NMR relaxation-based sensing approach is reported on that exploits changes in the bulk xenon relaxation rate induced by slowed tumbling of a cryptophane-based sensor upon target binding. The amplification afforded by detection of the bulk dissolved xenon allows sensitive detection of targets. The sensor comprises a xenon-binding cryptophane cage, a target interaction element, and a metal chelating agent. Xenon associated with the target-bound cryptophane cage is rapidly relaxed and then detected after exchange with the bulk. Here we show that large macromolecular targets increase the rotational correlation time of xenon, increasing its relaxation rate. Upon binding of a biotin-containing sensor to avidin at 1.5 μM concentration, the free xenon T₂ is reduced by a factor of 4.

Macromolecular synthesis in algal cells

International Nuclear Information System (INIS)

Ishida, M.R.; Kikuchi, Tadatoshi

1980-01-01

The present paper is a review of our experimental results obtained previously on the macromolecular biosyntheses in the cells of blue-green alga Anacystis nidulans as a representative species of prokaryote, and also in those of three species of eukaryotic algae, i.e. Euglena gracilis strain Z, Chlamydomonas reinhardi, and Cyanidium caldarium. In these algal cells, the combined methods consisting of pulse-labelling using 32 P, 3 H- and 14 C-labelled precursors for macromolecules, of their chasing and of the use of inhibitors which block specifically the syntheses of macromolecules such as proteins, RNA and DNA in living cells were very effectively applied for the analyses of the regulatory mechanism in biosyntheses of macromolecules and of the mode of their assembly into the cell structure, especially organelle constituents. Rased on the results obtained thus, the following conclusions are reached: (1) the metabolic pool for syntheses of macromolecules in the cells of prokaryotic blue-green alga is limited to the small extent and such activities couple largely with the photosynthetic mechanism; (2) 70 S ribosomes in the blue-green algal cells are assembled on the surface of thylakoid membranes widely distributed in their cytoplasm; and (3) the cells of eukaryotic unicellular algae used here have biochemical characters specific for already differentiated enzyme system involving in transcription and translation machineries as the same as in higher organisms, but the control mechanism concerning with such macromolecule syntheses are different among each species. (author)

Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Berendzen, Joel

1999-01-01

The correlation of local r.m.s. density is shown to be a good measure of the presence of distinct solvent and macromolecule regions in macromolecular electron-density maps. It has recently been shown that the standard deviation of local r.m.s. electron density is a good indicator of the presence of distinct regions of solvent and protein in macromolecular electron-density maps [Terwilliger & Berendzen (1999 ▶). Acta Cryst. D55, 501–505]. Here, it is demonstrated that a complementary measure, the correlation of local r.m.s. density in adjacent regions on the unit cell, is also a good measure of the presence of distinct solvent and protein regions. The correlation of local r.m.s. density is essentially a measure of how contiguous the solvent (and protein) regions are in the electron-density map. This statistic can be calculated in real space or in reciprocal space and has potential uses in evaluation of heavy-atom solutions in the MIR and MAD methods as well as for evaluation of trial phase sets in ab initio phasing procedures

A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits.

Science.gov (United States)

Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

2014-09-01

As a contribution to the celebration of the year 2014, declared by the United Nations to be 'The International Year of Crystallography', the FEBS Journal is dedicating this issue to papers showcasing the intimate union between macromolecular crystallography and structural biology, both in historical perspective and in current research. Instead of a formal editorial piece, by way of introduction, this review discusses the most important, often iconic, achievements of crystallographers that led to major advances in our understanding of the structure and function of biological macromolecules. We identified at least 42 scientists who received Nobel Prizes in Physics, Chemistry or Medicine for their contributions that included the use of X-rays or neutrons and crystallography, including 24 who made seminal discoveries in macromolecular sciences. Our spotlight is mostly, but not only, on the recipients of this most prestigious scientific honor, presented in approximately chronological order. As a summary of the review, we attempt to construct a genealogy tree of the principal lineages of protein crystallography, leading from the founding members to the present generation. Published 2014. This article is a U.S. Government work and is in the public domain in the USA.

Quantitative magnetization transfer imaging of rodent glioma using selective inversion recovery.

Science.gov (United States)

Xu, Junzhong; Li, Ke; Zu, Zhongliang; Li, Xia; Gochberg, Daniel F; Gore, John C

2014-03-01

Magnetization transfer (MT) provides an indirect means to detect noninvasively variations in macromolecular contents in biological tissues, but, so far, there have been only a few quantitative MT (qMT) studies reported in cancer, all of which used off-resonance pulsed saturation methods. This article describes the first implementation of a different qMT approach, selective inversion recovery (SIR), for the characterization of tumor in vivo using a rodent glioma model. The SIR method is an on-resonance method capable of fitting qMT parameters and T1 relaxation time simultaneously without mapping B0 and B1 , which is very suitable for high-field qMT measurements because of the lower saturation absorption rate. The results show that the average pool size ratio (PSR, the macromolecular pool versus the free water pool) in rat 9 L glioma (5.7%) is significantly lower than that in normal rat gray matter (9.2%) and white matter (17.4%), which suggests that PSR is potentially a sensitive imaging biomarker for the assessment of brain tumor. Despite being less robust, the estimated MT exchange rates also show clear differences from normal tissues (19.7 Hz for tumors versus 14.8 and 10.2 Hz for gray and white mater, respectively). In addition, the influence of confounding effects, e.g. B1 inhomogeneity, on qMT parameter estimates is investigated with numerical simulations. These findings not only help to better understand the changes in the macromolecular contents of tumors, but are also important for the interpretation of other imaging contrasts, such as chemical exchange saturation transfer of tumors. Copyright © 2013 John Wiley & Sons, Ltd.

Evaluation of quantum-chemical methods of radiolysis stability for macromolecular structures

International Nuclear Information System (INIS)

Postolache, Cristian; Matei, Lidia

2005-01-01

The behavior of macromolecular structures in ionising fields was analyzed by quantum-chemical methods. In this study the primary radiolytic effect was analyzed using a two-step radiolytic mechanism: a) ionisation of molecule and spatial redistribution of atoms in order to reach a minimum value of energy, characteristic to the quantum state; b) neutralisation of the molecule by electron capture and its rapid dissociation into free radicals. Chemical bonds suspected to break are located in the distribution region of LUMO orbital and have minimal homolytic dissociation energies. Representative polymer structures (polyethylene, polypropylene, polystyrene, poly α and β polystyrene, polyisobutylene, polytetrafluoroethylene, poly methylsiloxanes) were analyzed. (authors)

The Postgraduate Study of Macromolecular Sciences at the University of Zagreb (1971– 1980)

OpenAIRE

Deželić, D.; Kunst, B.; Veksli, Zorica

2008-01-01

The postgraduate study of macromolecular sciences (PSMS) was established at the University of Zagreb in 1971 as a university study in the time of expressed interdisciplinary permeation of natural sciences - physics, chemistry and biology, and application of their achievements in technological disciplines. PSMS was established by a group of prominent university professors from the schools of Science, Chemical Technology, Pharmacy and Medicine, as well as from the Institute of Biology. The s...

The monitoring system for macromolecular crystallography beamlines at BSRF

International Nuclear Information System (INIS)

Guo Xian; Chang Guangcai; Gan Quan; Shi Hong; Liu Peng; Sun Gongxing

2012-01-01

The monitoring system for macromolecular crystallography beamlines at BSRF (Beijing Synchrotron Radiation Facility) based on LabVIEW is introduced. In order to guarantee a safe, stable, and reliable running for the beamline devices, the system monitors the state of vacuum, cooling-water, optical components, beam, Liquid nitrogen in the beamlines in real time, detects faults and gives the alarm timely. System underlying uses the driver developed for the field devices for data acquisition, Data of collection is uploaded to the data-sharing platform makes it accessible via a network share. The upper system divides modules according to the actual function, and establishes the main interface of the monitoring system of beamline. To Facilitate data storage, management and inquiry, the system use LabSQL toolkit to achieve the interconnection with MySQL database which data of collection is sent to. (authors)

The 2D Structure of the T. brucei Preedited RPS12 mRNA Is Not Affected by Macromolecular Crowding

Directory of Open Access Journals (Sweden)

W.-Matthias Leeder

2017-01-01

Full Text Available Mitochondrial transcript maturation in African trypanosomes requires RNA editing to convert sequence-deficient pre-mRNAs into translatable mRNAs. The different pre-mRNAs have been shown to adopt highly stable 2D folds; however, it is not known whether these structures resemble the in vivo folds given the extreme “crowding” conditions within the mitochondrion. Here, we analyze the effects of macromolecular crowding on the structure of the mitochondrial RPS12 pre-mRNA. We use high molecular mass polyethylene glycol as a macromolecular cosolute and monitor the structure of the RNA globally and with nucleotide resolution. We demonstrate that crowding has no impact on the 2D fold and we conclude that the MFE structure in dilute solvent conditions represents a good proxy for the folding of the pre-mRNA in its mitochondrial solvent context.

Macromolecular Engineering: New Routes Towards the Synthesis of Well-??Defined Polyethers/Polyesters Co/Terpolymers with Different Architectures

KAUST Repository

Alamri, Haleema

2016-05-18

The primary objective of this research was to develop a new and efficient pathway for well-defined multicomponent homo/co/terpolymers of cyclic esters/ethers using an organocatalytic approach with an emphasis on the macromolecular engineering aspects of the overall synthesis. Macromolecular engineering (as discussed in the first chapter) of homo/copolymers refers to the specific tailoring of these materials for achieving an easy and reproducible synthesis that results in precise molecular characteristics, i.e. molecular weight and polydispersity, as well as specific structure and end?group choices. Precise control of these molecular characteristics will provide access to new materials that can be used for pre-targeted purposes such as biomedical applications. Among the most commonly used engineering materials are polyesters (biocompatible and biodegradable) and polyethers (biocompatible), either as homopolymers or when or copolymers with linear structures. The ability to create non-linear structures, for example stars, will open new horizons in the applications of these important polymeric materials. The second part of this thesis describes the synthesis of aliphatic polyesters, particularly polycaprolactone and polylactide, using a metal-free initiator/catalyst system. A phosphazene base (t?BuP2) was used as the catalyst for the ring-opening copolymerization of ?-aprolactone (??CL) and L,Lactide (LLA) at room temperature with a variety of protic initiators in different solvents. These studies provided important information for the design of a metal-free route toward the synthesis of polyester?based (bio) materials. The third part of the thesis describes a novel route for the one?pot synthesis of polyether-b polyester block copolymers with either a linear or a specific macromolecular architecture. Poly (styrene oxide)?b?poly(caprolactone)?b?poly(L,lactide) was prepared using this method with the goal of synthesizing poly(styrene oxide)-based materials since this

Scipion web tools: Easy to use cryo-EM image processing over the web.

Science.gov (United States)

Conesa Mingo, Pablo; Gutierrez, José; Quintana, Adrián; de la Rosa Trevín, José Miguel; Zaldívar-Peraza, Airén; Cuenca Alba, Jesús; Kazemi, Mohsen; Vargas, Javier; Del Cano, Laura; Segura, Joan; Sorzano, Carlos Oscar S; Carazo, Jose María

2018-01-01

Macromolecular structural determination by Electron Microscopy under cryogenic conditions is revolutionizing the field of structural biology, interesting a large community of potential users. Still, the path from raw images to density maps is complex, and sophisticated image processing suites are required in this process, often demanding the installation and understanding of different software packages. Here, we present Scipion Web Tools, a web-based set of tools/workflows derived from the Scipion image processing framework, specially tailored to nonexpert users in need of very precise answers at several key stages of the structural elucidation process. © 2017 The Protein Society.

Effects of far-ultraviolet radiation and oxygen on macromolecular synthesis and protein induction in Bacteroides fragilis BF-2

International Nuclear Information System (INIS)

Schumann, J.P.

1983-11-01

The study deals with the effects of far-UV radiation, oxygen and hydrogen peroxide on macromolecular synthesis and viability in the obligate anaerobe, Bacteroides fragilis, as well as the specific proteins induced in this organism by these different DNA damaging agents. Irradiation of Bacteroides fragilis cells with far-UV light (254 nm) under anaerobic conditions resulted in the immediate, rapid and extensive degradation of DNA which continued for 40 to 60 min after irradiation. DNA degradation after irradiation was inhibited by chloramphenicol and caffeine. RNA and protein synthesis were decreased by UV irradiation and the degree of inhibition was proportional to the UV dose. Colony formation was not affected immediately by UV irradiation and continued for a dose-dependent period prior to inhibition. The relationship between the DNA damage-induced proteins, macromolecular synthesis in damaged B. fragilis cells and the observed physiological responses and inducible repair phenomena after the different DNA damaging treatments in this anaerobe are discussed

Can visco-elastic phase separation, macromolecular crowding and colloidal physics explain nuclear organisation?

Directory of Open Access Journals (Sweden)

Iborra Francisco J

2007-04-01

Full Text Available Abstract Background The cell nucleus is highly compartmentalized with well-defined domains, it is not well understood how this nuclear order is maintained. Many scientists are fascinated by the different set of structures observed in the nucleus to attribute functions to them. In order to distinguish functional compartments from non-functional aggregates, I believe is important to investigate the biophysical nature of nuclear organisation. Results The various nuclear compartments can be divided broadly as chromatin or protein and/or RNA based, and they have very different dynamic properties. The chromatin compartment displays a slow, constrained diffusional motion. On the other hand, the protein/RNA compartment is very dynamic. Physical systems with dynamical asymmetry go to viscoelastic phase separation. This phase separation phenomenon leads to the formation of a long-lived interaction network of slow components (chromatin scattered within domains rich in fast components (protein/RNA. Moreover, the nucleus is packed with macromolecules in the order of 300 mg/ml. This high concentration of macromolecules produces volume exclusion effects that enhance attractive interactions between macromolecules, known as macromolecular crowding, which favours the formation of compartments. In this paper I hypothesise that nuclear compartmentalization can be explained by viscoelastic phase separation of the dynamically different nuclear components, in combination with macromolecular crowding and the properties of colloidal particles. Conclusion I demonstrate that nuclear structure can satisfy the predictions of this hypothesis. I discuss the functional implications of this phenomenon.

Glycogen-graft-poly(2-alkyl-2-oxazolines) - the new versatile biopolymer-based thermoresponsive macromolecular toolbox

Czech Academy of Sciences Publication Activity Database

Pospíšilová, Aneta; Filippov, Sergey K.; Bogomolova, Anna; Turner, S.; Sedláček, Ondřej; Matushkin, Nikolai; Černochová, Zulfiya; Štěpánek, Petr; Hrubý, Martin

2014-01-01

Roč. 4, č. 106 (2014), s. 61580-61588 ISSN 2046-2069 R&D Projects: GA ČR GA13-08336S; GA MŠk(CZ) LH14079 Grant - others:AV ČR(CZ) M200501201; AV ČR(CZ) ASCR/CONICET 2012CZ006 Program:M Institutional support: RVO:61389013 Keywords : glycogen * poly(2-alkyl-2-oxazoline) * hybrid copolymer Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.840, year: 2014

AFM imaging and analysis of local mechanical properties for detection of surface pattern of functional groups

Czech Academy of Sciences Publication Activity Database

Knotek, P.; Chánová, Eliška; Rypáček, František

2013-01-01

Roč. 33, č. 4 (2013), s. 1963-1968 ISSN 0928-4931 R&D Projects: GA ČR GAP108/11/1857; GA ČR GPP108/12/P624 Institutional support: RVO:61389013 Keywords : phase shift image * AFAM * force spectroscopy Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.736, year: 2013

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

Science.gov (United States)

Theobald, Douglas L; Wuttke, Deborah S

2006-09-01

THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

Macromolecular organization of xyloglucan and cellulose in pea epicotyls

International Nuclear Information System (INIS)

Hayashi, T.; Maclachlan, G.

1984-01-01

Xyloglucan is known to occur widely in the primary cell walls of higher plants. This polysaccharide in most dicots possesses a cellulose-like main chain with three of every four consecutive residues substituted with xylose and minor addition of other sugars. Xyloglucan and cellulose metabolism is regulated by different processes; since different enzyme systems are probably required for the synthesis of their 1,4-β-linkages. A macromolecular complex composed of xyloglucan and cellulose only was obtained from elongating regions of etiolated pea stems. It was examined by light microscopy using iodine staining, by radioautography after labeling with [ 3 H]fructose, by fluorescence microscopy using a fluorescein-lectin (fructose-binding) as probe, and by electron microscopy after shadowing. The techniques all demonstrated that the macromolecule was present in files of cell shapes, referred to here as cell-wall ghosts, in which xyloglucan was localized both on and between the cellulose microfibrils

AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory

International Nuclear Information System (INIS)

Yamada, Yusuke; Hiraki, Masahiko; Sasajima, Kumiko; Matsugaki, Naohiro; Igarashi, Noriyuki; Kikuchi, Takashi; Mori, Takeharu; Toyoshima, Akio; Kishimoto, Shunji; Wakatsuki, Soichi; Amano, Yasushi; Warizaya, Masaichi; Sakashita, Hitoshi

2010-01-01

Recent advances in high-throughput techniques for macromolecular crystallography have highlighted the importance of structure-based drug design (SBDD), and the demand for synchrotron use by pharmaceutical researchers has increased. Thus, in collaboration with Astellas Pharma Inc., we have constructed a new high-throughput macromolecular crystallography beamline, AR-NE3A, which is dedicated to SBDD. At AR-NE3A, a photon flux up to three times higher than those at existing high-throughput beams at the Photon Factory, AR-NW12A and BL-5A, can be realized at the same sample positions. Installed in the experimental hutch are a high-precision diffractometer, fast-readout, high-gain CCD detector, and sample exchange robot capable of handling more than two hundred cryo-cooled samples stored in a Dewar. To facilitate high-throughput data collection required for pharmaceutical research, fully automated data collection and processing systems have been developed. Thus, sample exchange, centering, data collection, and data processing are automatically carried out based on the user's pre-defined schedule. Although Astellas Pharma Inc. has a priority access to AR-NE3A, the remaining beam time is allocated to general academic and other industrial users.

Organ specific acute toxicity of the carcinogen trans-4-acetylaminostilbene is not correlated with macromolecular binding.

Science.gov (United States)

Pfeifer, A; Neumann, H G

1986-09-01

trans-4-Acetylaminostilbene (trans-AAS) is acutely toxic in rats and lesions are produced specifically in the glandular stomach. Toxicity is slightly increased by pretreating the animals with phenobarbital (PB) and is completely prevented by pretreatment with methylcholanthrene (MC). The prostaglandin inhibitors, indomethacin and acetyl salicylic acid, do not reduce toxicity. The high efficiency of MC suggested that toxicity is caused by reactive metabolites. trans-[3H]-AAS was administered orally to untreated and to PB- or MC-pretreated female Wistar rats and target doses in different tissues were measured by means of covalent binding to proteins, RNA and DNA. Macromolecular binding in the target tissue of poisoned animals was significantly lower than in liver and kidney and comparable to other non-target tissues. Pretreatment with MC lowered macromolecular binding in all extrahepatic tissues but not in liver. These findings are not in line with tissue specific metabolic activation. The only unique property of the target tissue, glandular stomach, that we observed was a particular affinity for the systemically available parent compound. In the early phase of poisoning, tissue concentrations were exceedingly high and the stomach function was impaired.

Fully automated data collection and processing system on macromolecular crystallography beamlines at the PF

International Nuclear Information System (INIS)

Yamada, Yusuke; Hiraki, Masahiko; Matsugaki, Naohiro; Chavas, Leonard M.G.; Igarashi, Noriyuki; Wakatsuki, Soichi

2012-01-01

Fully automated data collection and processing system has been developed on macromolecular crystallography beamlines at the Photon Factory. In this system, the sample exchange, centering and data collection are sequentially performed for all samples stored in the sample exchange system at a beamline without any manual operations. Data processing of collected data sets is also performed automatically. These results are stored into the database system, and users can monitor the progress and results of automated experiment via a Web browser. (author)

Development of an online UV–visible microspectrophotometer for a macromolecular crystallography beamline

Energy Technology Data Exchange (ETDEWEB)

Shimizu, Nobutaka, E-mail: nobutaka.shimizu@kek.jp [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Shimizu, Tetsuya [RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Baba, Seiki; Hasegawa, Kazuya [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Yamamoto, Masaki [RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Kumasaka, Takashi [SPring-8/JASRI, 1-1-1 Koto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

2013-11-01

An online UV–visible microspectrophotometer has been developed for the macromolecular crystallography beamline at SPring-8. Details of this spectrophotometer are reported. Measurement of the UV–visible absorption spectrum is a convenient technique for detecting chemical changes of proteins, and it is therefore useful to combine spectroscopy and diffraction studies. An online microspectrophotometer for the UV–visible region was developed and installed on the macromolecular crystallography beamline, BL38B1, at SPring-8. This spectrophotometer is equipped with a difference dispersive double monochromator, a mercury–xenon lamp as the light source, and a photomultiplier as the detector. The optical path is mostly constructed using mirrors, in order to obtain high brightness in the UV region, and the confocal optics are assembled using a cross-slit diaphragm like an iris to eliminate stray light. This system can measure optical densities up to a maximum of 4.0. To study the effect of radiation damage, preliminary measurements of glucose isomerase and thaumatin crystals were conducted in the UV region. Spectral changes dependent on X-ray dose were observed at around 280 nm, suggesting that structural changes involving Trp or Tyr residues occurred in the protein crystal. In the case of the thaumatin crystal, a broad peak around 400 nm was also generated after X-ray irradiation, suggesting the cleavage of a disulfide bond. Dose-dependent spectral changes were also observed in cryo-solutions alone, and these changes differed with the composition of the cryo-solution. These responses in the UV region are informative regarding the state of the sample; consequently, this device might be useful for X-ray crystallography.

A facile metal-free "grafting-from" route from acrylamide-based substrate toward complex macromolecular combs

KAUST Repository

Zhao, Junpeng

2013-01-01

High-molecular-weight poly(N,N-dimethylacrylamide-co-acrylamide) was used as a model functional substrate to investigate phosphazene base (t-BuP 4)-promoted metal-free anionic graft polymerization utilizing primary amide moieties as initiating sites. The (co)polymerization of epoxides was proven to be effective, leading to macromolecular combs with side chains being single- or double-graft homopolymer, block copolymer and statistical copolymer. © 2013 The Royal Society of Chemistry.

Macromolecular pHPMA-based nanoparticles with cholesterol for solid tumor targeting: behavior in HSA protein environment

Czech Academy of Sciences Publication Activity Database

Zhang, X.; Niebuur, B.-J.; Chytil, Petr; Etrych, Tomáš; Filippov, Sergey K.; Kikhney, A.; Wieland, D. C. F.; Svergun, D. I.; Papadakis, C. M.

2018-01-01

Roč. 19, č. 2 (2018), s. 470-480 ISSN 1525-7797 R&D Projects: GA ČR(CZ) GC15-10527J; GA MZd(CZ) NV16-28594A; GA MŠk(CZ) LO1507 Institutional support: RVO:61389013 Keywords : polymer carriers * N-(2-hydroxypropyl)methacrylamide * tumor targeting Subject RIV: CD - Macromolecular Chemistry OBOR OECD: Polymer science Impact factor: 5.246, year: 2016

Fluid Physics and Macromolecular Crystal Growth in Microgravity

Science.gov (United States)

Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

2000-01-01

The first protein crystallization experiment in microgravity was launched in April, 1981 and used Germany's Technologische Experimente unter Schwerelosigkeit (TEXUS 3) sounding rocket. The protein P-galactosidase (molecular weight 465Kda) was chosen as the sample with a liquid-liquid diffusion growth method. A sliding device brought the protein, buffer and salt solution into contact when microgravity was reached. The sounding rocket gave six minutes of microgravity time with a cine camera and schlieren optics used to monitor the experiment, a single growth cell. In microgravity a strictly laminar diffusion process was observed in contrast to the turbulent convection seen on the ground. Several single crystals, approx 100micron in length, were formed in the flight which were of inferior but of comparable visual quality to those grown on the ground over several days. A second experiment using the same protocol but with solutions cooled to -8C (kept liquid with glycerol antifreeze) again showed laminar diffusion. The science of macromolecular structural crystallography involves crystallization of the macromolecule followed by use of the crystal for X-ray diffraction experiments to determine the three dimensional structure of the macromolecule. Neutron protein crystallography is employed for elucidation of H/D exchange and for improved definition of the bound solvent (D20). The structural information enables an understanding of how the molecule functions with important potential for rational drug design, improved efficiency of industrial enzymes and agricultural chemical development. The removal of turbulent convection and sedimentation in microgravity, and the assumption that higher quality crystals will be produced, has given rise to the growing number of crystallization experiments now flown. Many experiments can be flown in a small volume with simple, largely automated, equipment - an ideal combination for a microgravity experiment. The term "protein crystal growth

Extracting trends from two decades of microgravity macromolecular crystallization history.

Science.gov (United States)

Judge, Russell A; Snell, Edward H; van der Woerd, Mark J

2005-06-01

Since the 1980s hundreds of macromolecular crystal growth experiments have been performed in the reduced acceleration environment of an orbiting spacecraft. Significant enhancements in structural knowledge have resulted from X-ray diffraction of the crystals grown. Similarly, many samples have shown no improvement or degradation in comparison to those grown on the ground. A complex series of interrelated factors affect these experiments and by building a comprehensive archive of the results it was aimed to identify factors that result in success and those that result in failure. Specifically, it was found that dedicated microgravity missions increase the chance of success when compared with those where crystallization took place as a parasitic aspect of the mission. It was also found that the chance of success could not be predicted based on any discernible property of the macromolecule available to us.

A new paradigm for macromolecular crystallography beamlines derived from high-pressure methodology and results

Energy Technology Data Exchange (ETDEWEB)

Fourme, Roger, E-mail: roger.fourme@synchrotron-soleil.fr [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Girard, Eric [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France); Dhaussy, Anne-Claire [CRISMAT, ENSICAEN, 6 Boulevard du Maréchal Juin, 14000 Caen (France); Medjoubi, Kadda [Synchrotron SOLEIL, BP 48, Saint Aubin, 91192 Gif-sur-Yvette (France); Prangé, Thierry [LCRB (UMR 8015 CNRS), Université Paris Descartes, Faculté de Pharmacie, 4 avenue de l’Observatoire, 75270 Paris (France); Ascone, Isabella [ENSCP (UMR CNRS 7223), 11 rue Pierre et Marie Curie, 75231 Paris Cedex 05 (France); Mezouar, Mohamed [ESRF, BP 220, 38043 Grenoble (France); Kahn, Richard [IBS (UMR 5075 CEA-CNRS-UJF-PSB), 41 rue Jules Horowitz, 38027 Grenoble Cedex (France)

2011-01-01

Macromolecular crystallography at high pressure (HPMX) is a mature technique. Shorter X-ray wavelengths increase data collection efficiency on cryocooled crystals. Extending applications and exploiting spin-off of HPMX will require dedicated synchrotron radiation beamlines based on a new paradigm. Biological structures can now be investigated at high resolution by high-pressure X-ray macromolecular crystallography (HPMX). The number of HPMX studies is growing, with applications to polynucleotides, monomeric and multimeric proteins, complex assemblies and even a virus capsid. Investigations of the effects of pressure perturbation have encompassed elastic compression of the native state, study of proteins from extremophiles and trapping of higher-energy conformers that are often of biological interest; measurements of the compressibility of crystals and macromolecules were also performed. HPMX results were an incentive to investigate short and ultra-short wavelengths for standard biocrystallography. On cryocooled lysozyme crystals it was found that the data collection efficiency using 33 keV photons is increased with respect to 18 keV photons. This conclusion was extended from 33 keV down to 6.5 keV by exploiting previously published data. To be fully exploited, the potential of higher-energy photons requires detectors with a good efficiency. Accordingly, a new paradigm for MX beamlines was suggested, using conventional short and ultra-short wavelengths, aiming at the collection of very high accuracy data on crystals under standard conditions or under high pressure. The main elements of such beamlines are outlined.

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography.

Science.gov (United States)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L; Armour, Wes; Waterman, David G; Iwata, So; Evans, Gwyndaf

2013-08-01

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

A tumor-targeted polymer theranostics platform for positron emission tomography and fluorescence imaging

Czech Academy of Sciences Publication Activity Database

Koziolová, Eva; Goel, S.; Chytil, Petr; Janoušková, Olga; Barnhart, T. E.; Cai, W.; Etrych, Tomáš

2017-01-01

Roč. 9, č. 30 (2017), s. 10906-10918 ISSN 2040-3364 R&D Projects: GA ČR(CZ) GA15-02986S; GA MZd(CZ) NV16-28594A; GA MŠk(CZ) LO1507 Institutional support: RVO:61389013 Keywords : N-(2-hydroxypropyl)methacrylamide (HPMA) copolymers * positron emission tomography ( PET ) * fluorescence imaging Subject RIV: CD - Macromolecular Chemistry OBOR OECD: Polymer science Impact factor: 7.367, year: 2016

An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes

Science.gov (United States)

Li, Huilin; Nguyen, Hong Hanh; Ogorzalek Loo, Rachel R.; Campuzano, Iain D. G.; Loo, Joseph A.

2018-02-01

Mass spectrometry (MS) has become a crucial technique for the analysis of protein complexes. Native MS has traditionally examined protein subunit arrangements, while proteomics MS has focused on sequence identification. These two techniques are usually performed separately without taking advantage of the synergies between them. Here we describe the development of an integrated native MS and top-down proteomics method using Fourier-transform ion cyclotron resonance (FTICR) to analyse macromolecular protein complexes in a single experiment. We address previous concerns of employing FTICR MS to measure large macromolecular complexes by demonstrating the detection of complexes up to 1.8 MDa, and we demonstrate the efficacy of this technique for direct acquirement of sequence to higher-order structural information with several large complexes. We then summarize the unique functionalities of different activation/dissociation techniques. The platform expands the ability of MS to integrate proteomics and structural biology to provide insights into protein structure, function and regulation.

NATO Advanced Study Institute on Evolving Methods for Macromolecular Gystallography

CERN Document Server

Read, Randy J

2007-01-01

X-ray crystallography is the pre-eminent technique for visualizing the structures of macromolecules at atomic resolution. These structures are central to understanding the detailed mechanisms of biological processes, and to discovering novel therapeutics using a structure-based approach. As yet, structures are known for only a small fraction of the proteins encoded by human and pathogenic genomes. To counter the myriad modern threats of disease, there is an urgent need to determine the structures of the thousands of proteins whose structure and function remain unknown. This volume draws on the expertise of leaders in the field of macromolecular crystallography to illuminate the dramatic developments that are accelerating progress in structural biology. Their contributions span the range of techniques from crystallization through data collection, structure solution and analysis, and show how modern high-throughput methods are contributing to a deeper understanding of medical problems.

In vitro evaluation of the monoclonal antibody Cu-64-IgG M75 against human carbonic anhydrase IX and its in vivo imaging

Czech Academy of Sciences Publication Activity Database

Čepa, Adam; Ráliš, Jan; Král, Vlastimil; Paurová, M.; Kučka, Jan; Humajová, J.; Lázníček, M.; Lebeda, Ondřej

2018-01-01

Roč. 133, č. March (2018), s. 9-13 ISSN 0969-8043 Institutional support: RVO:61389005 ; RVO:68378050 ; RVO:61389013 Keywords : IgG M75 * immunoaffinity * imaging * monoclonal atibody * Cu-64 Subject RIV: FP - Other Medical Disciplines; CD - Macromolecular Chemistry (UMCH-V); EB - Genetics ; Molecular Biology (UMG-J) OBOR OECD: Radiology, nuclear medicine and medical imaging; Polymer science (UMCH-V); Biochemical research methods (UMG-J) Impact factor: 1.128, year: 2016

Micelles of zinc protoporphyrin conjugated to N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer for imaging and light-induced antitumor effects in vivo

Czech Academy of Sciences Publication Activity Database

Nakamura, H.; Liao, L.; Hitaka, Y.; Tsukigawa, K.; Šubr, Vladimír; Fang, J.; Ulbrich, Karel; Maeda, H.

2013-01-01

Roč. 165, č. 3 (2013), s. 191-198 ISSN 0168-3659 R&D Projects: GA AV ČR IAAX00500803 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : fluorescence imaging * fluorescent nanoprobe * singlet oxygen Subject RIV: CD - Macromolecular Chemistry Impact factor: 7.261, year: 2013

Permeability to macromolecular contrast media quantified by dynamic MRI correlates with tumor tissue assays of vascular endothelial growth factor (VEGF)

International Nuclear Information System (INIS)

Cyran, Clemens C.; Sennino, Barbara; Fu, Yanjun; Rogut, Victor; Shames, David M.; Chaopathomkul, Bundit; Wendland, Michael F.; McDonald, Donald M.; Brasch, Robert C.; Raatschen, Hans-Juergen

2012-01-01

Purpose: To correlate dynamic MRI assays of macromolecular endothelial permeability with microscopic area–density measurements of vascular endothelial growth factor (VEGF) in tumors. Methods and material: This study compared tumor xenografts from two different human cancer cell lines, MDA-MB-231 tumors (n = 5), and MDA-MB-435 (n = 8), reported to express respectively higher and lower levels of VEGF. Dynamic MRI was enhanced by a prototype macromolecular contrast medium (MMCM), albumin-(Gd-DTPA)35. Quantitative estimates of tumor microvascular permeability (K PS ; μl/min × 100 cm 3 ), obtained using a two-compartment kinetic model, were correlated with immunohistochemical measurements of VEGF in each tumor. Results: Mean K PS was 2.4 times greater in MDA-MB-231 tumors (K PS = 58 ± 30.9 μl/min × 100 cm 3 ) than in MDA-MB-435 tumors (K PS = 24 ± 8.4 μl/min × 100 cm 3 ) (p < 0.05). Correspondingly, the area–density of VEGF in MDA-MB-231 tumors was 2.6 times greater (27.3 ± 2.2%, p < 0.05) than in MDA-MB-435 cancers (10.5 ± 0.5%, p < 0.05). Considering all tumors without regard to cell type, a significant positive correlation (r = 0.67, p < 0.05) was observed between MRI-estimated endothelial permeability and VEGF immunoreactivity. Conclusion: Correlation of MRI assays of endothelial permeability to a MMCM and VEGF immunoreactivity of tumors support the hypothesis that VEGF is a major contributor to increased macromolecular permeability in cancers. When applied clinically, the MMCM-enhanced MRI approach could help to optimize the appropriate application of VEGF-inhibiting therapy on an individual patient basis.

Macromolecular crowding-assisted fabrication of liquid-crystalline imprinted polymers.

Science.gov (United States)

Zhang, Chen; Zhang, Jing; Huang, Yan-Ping; Liu, Zhao-Sheng

2015-04-01

A macromolecular crowding-assisted liquid-crystalline molecularly imprinted monolith (LC-MIM) was prepared successfully for the first time. The imprinted stationary phase was synthesized with polymethyl methacrylate (PMMA) or polystyrene (PS) as the crowding agent, 4-cyanophenyl dicyclohexyl propylene (CPCE) as the liquid-crystal monomer, and hydroquinidine as the pseudo-template for the chiral separation of cinchona alkaloids in HPLC. A low level of cross-linker (26%) has been found to be sufficient to achieve molecular recognition on the crowding-assisted LC-MIM due to the physical cross-linking of mesogenic groups in place of chemical cross-linking, and baseline separation of quinidine and quinine could be achieved with good resolution (R(s) = 2.96), selectivity factor (α = 2.16), and column efficiency (N = 2650 plates/m). In contrast, the LC-MIM prepared without crowding agents displayed the smallest diastereoselectivity (α = 1.90), while the crowding-assisted MIM with high level of cross-linker (80%) obtained the greatest selectivity factor (α = 7.65), but the lowest column efficiency (N = 177 plates/m).

On macromolecular refinement at subatomic resolution with interatomic scatterers

Energy Technology Data Exchange (ETDEWEB)

Afonine, Pavel V., E-mail: pafonine@lbl.gov; Grosse-Kunstleve, Ralf W.; Adams, Paul D. [Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 (United States); Lunin, Vladimir Y. [Institute of Mathematical Problems of Biology, Russian Academy of Sciences, Pushchino 142290 (Russian Federation); Urzhumtsev, Alexandre [IGMBC, 1 Rue L. Fries, 67404 Illkirch and IBMC, 15 Rue R. Descartes, 67084 Strasbourg (France); Faculty of Sciences, Nancy University, 54506 Vandoeuvre-lès-Nancy (France); Lawrence Berkeley National Laboratory, One Cyclotron Road, BLDG 64R0121, Berkeley, CA 94720 (United States)

2007-11-01

Modelling deformation electron density using interatomic scatters is simpler than multipolar methods, produces comparable results at subatomic resolution and can easily be applied to macromolecules. A study of the accurate electron-density distribution in molecular crystals at subatomic resolution (better than ∼1.0 Å) requires more detailed models than those based on independent spherical atoms. A tool that is conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8–1.0 Å, the number of experimental data is insufficient for full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented by additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark data sets gave results that were comparable in quality with the results of multipolar refinement and superior to those for conventional models. Applications to several data sets of both small molecules and macromolecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.

Timely deposition of macromolecular structures is necessary for peer review

International Nuclear Information System (INIS)

Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.; Perrakis, Anastassis

2013-01-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature

Timely deposition of macromolecular structures is necessary for peer review

Energy Technology Data Exchange (ETDEWEB)

Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Soueidan, Hayssam; Wessels, Lodewyk F. A. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam (Netherlands); Perrakis, Anastassis, E-mail: a.perrakis@nki.nl [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

2013-12-01

Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.

A beamline for macromolecular crystallography at the Advanced Light Source

International Nuclear Information System (INIS)

Padmore, H.A.; Earnest, T.; Kim, S.H.; Thompson, A.C.; Robinson, A.L.

1994-08-01

A beamline for macromolecular crystallography has been designed for the ALS. The source will be a 37-pole wiggler with a, 2-T on-axis peak field. The wiggler will illuminate three beamlines, each accepting 3 mrad of horizontal aperture. The central beamline will primarily be used for multiple-wavelength anomalous dispersion measurements in the wavelength range from 4 to 0.9 angstrom. The beamline optics will comprise a double-crystal monochromator with a collimating pre-mirror and a double-focusing mirror after the monochromator. The two side stations will be used for fixed-wavelength experiments within the wavelength range from 1.5 to 0.95 angstrom. The optics will consist of a conventional vertically focusing cylindrical mirror followed by an asymmetrically cut curved-crystal monochromator. This paper presents details of the optimization of the wiggler source for crystallography, gives a description of the beamline configuration, and discusses the reasons for the choices made

Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

Science.gov (United States)

Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So; Evans, Gwyndaf

2013-01-01

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein. PMID:23897484

Comparison of two self-assembled macromolecular prodrug micelles with different conjugate positions of SN38 for enhancing antitumor activity

Directory of Open Access Journals (Sweden)

Liu Y

2015-03-01

Full Text Available Yi Liu,1 Hongyu Piao,1 Ying Gao,1 Caihong Xu,2 Ye Tian,1 Lihong Wang,1 Jinwen Liu,1 Bo Tang,1 Meijuan Zou,1 Gang Cheng1 1Department of Pharmaceutics, Shenyang Pharmaceutical University, Shenyang, Liaoning Province, People’s Republic of China; 2Department of Food Science, Shenyang Normal University, Shenyang, Liaoning Province, People’s Republic of China Abstract: 7-Ethyl-10-hydroxycamptothecin (SN38, an active metabolite of irinotecan (CPT-11, is a remarkably potent antitumor agent. The clinical application of SN38 has been extremely restricted by its insolubility in water. In this study, we successfully synthesized two macromolecular prodrugs of SN38 with different conjugate positions (chitosan-(C10-OHSN38 and chitosan-(C20-OHSN38 to improve the water solubility and antitumor activity of SN38. These prodrugs can self-assemble into micelles in aqueous medium. The particle size, morphology, zeta potential, and in vitro drug release of SN38 and its derivatives, as well as their cytotoxicity, pharmacokinetics, and in vivo antitumor activity in a xenograft BALB/c mouse model were studied. In vitro, chitosan-(C10-OHSN38 (CS-(10sSN38 and chitosan-(C20-OHSN38 (CS-(20sSN38 were 13.3- and 25.9-fold more potent than CPT-11 in the murine colon adenocarcinoma cell line CT26, respectively. The area under the curve (AUC0–24 of SN38 after intravenously administering CS-(10sSN38 and CS-(20sSN38 to Sprague Dawley rats was greatly improved when compared with CPT-11 (both P<0.01. A larger AUC0–24 of CS-(20sSN38 was observed when compared to CS-(10sSN38 (P<0.05. Both of the novel self-assembled chitosan-SN38 prodrugs demonstrated superior anticancer activity to CPT-11 in the CT26 xenograft BALB/c mouse model. We have also investigated the differences between these macromolecular prodrug micelles with regards to enhancing the antitumor activity of SN38. CS-(20sSN38 exhibited better in vivo antitumor activity than CS-(10sSN38 at a dose of 2.5 mg/kg (P<0

Errors in macromolecular synthesis after stress. A study of the possible protective role of the small heat shock proteinsBiochemistry

NARCIS (Netherlands)

Marin Vinader, L.

2006-01-01

The general goal of this thesis was to gain insight in what small heat shock proteins (sHsps) do with respect to macromolecular synthesis during a stressful situation in the cell. It is known that after a non-lethal heat shock, cells are better protected against a subsequent more severe heat shock,

Investigation of a potential macromolecular MRI contrast agent prepared from PPI (G = 2, polypropyleneimine, generation 2) dendrimer bifunctional chelates

Science.gov (United States)

Wang, Jianxin Steven

The long-term objective is to develop magnetic resonance (MR) contrast agents that actively and passively target tumors for diagnosis and therapy. Many diagnostic imaging techniques for cancer lack specificity. A dendrimer based magnetic resonance imaging contrast agent has been developed with large proton relaxation enhancements and high molecular relaxivities. A new type of linear dendrimer based MRI contrast agent that is built from the polypropyleneimine and polyamidoamine dendrimers in which free amines have been conjugated to the chelate DTPA, which further formed the complex with Gadolinium (Gd) was studied. The specific research goals were to test the hypothesis that a linear chelate with macromolecular agents can be used in vitro and in vivo. This work successfully examined the adequacy and viability of the application for this agent in vitro and in vivo. A small animal whole body counter was designed and constructed to allow us to monitor biodistribution and kinetic mechanisms using a radioisotope labeled complex. The procedures of metal labeling, separation and purification have been established from this work. A biodistribution study has been performed using radioisotope induced organ/tissue counting and gamma camera imaging. The ratio of percentage of injected dose per gram organ/tissue for kidney and liver is 3.71 from whole body counter and 3.77 from the gamma camera. The results suggested that retention of Gd (III) is too high and a more kinetically stable chelate should be developed. The pharmacokinetic was evaluated in the whole animal model with the whole body clearance, and a kinetics model was developed. The pharmacokinetic results showed a bi-exponential decay in the animal model with two component excretion constants 1.43e(-5) and 0.0038511, which give half-lives of 3 hours and 33.6 days, respectively. Magnetic resonance imaging of this complex resulted in a 52% contrast enhancement in the rat kidney following the agents' administration in

Site-selective electroless nickel plating on patterned thin films of macromolecular metal complexes.

Science.gov (United States)

Kimura, Mutsumi; Yamagiwa, Hiroki; Asakawa, Daisuke; Noguchi, Makoto; Kurashina, Tadashi; Fukawa, Tadashi; Shirai, Hirofusa

2010-12-01

We demonstrate a simple route to depositing nickel layer patterns using photocross-linked polymer thin films containing palladium catalysts, which can be used as adhesive interlayers for fabrication of nickel patterns on glass and plastic substrates. Electroless nickel patterns can be obtained in three steps: (i) the pattern formation of partially quaterized poly(vinyl pyridine) by UV irradiation, (ii) the formation of macromolecular metal complex with palladium, and (iii) the nickel metallization using electroless plating bath. Metallization is site-selective and allows for a high resolution. And the resulting nickel layered structure shows good adhesion with glass and plastic substrates. The direct patterning of metallic layers onto insulating substrates indicates a great potential for fabricating micro/nano devices.

Aliphatic polyesters for medical imaging and theranostic applications.

Science.gov (United States)

Nottelet, Benjamin; Darcos, Vincent; Coudane, Jean

2015-11-01

Medical imaging is a cornerstone of modern medicine. In that context the development of innovative imaging systems combining biomaterials and contrast agents (CAs)/imaging probes (IPs) for improved diagnostic and theranostic applications focuses intense research efforts. In particular, the classical aliphatic (co)polyesters poly(lactide) (PLA), poly(lactide-co-glycolide) (PLGA) and poly(ɛ-caprolactone) (PCL), attract much attention due to their long track record in the medical field. This review aims therefore at providing a state-of-the-art of polyester-based imaging systems. In a first section a rapid description of the various imaging modalities, including magnetic resonance imaging (MRI), optical imaging, computed tomography (CT), ultrasound (US) and radionuclide imaging (SPECT, PET) will be given. Then, the two main strategies used to combine the CAs/IPs and the polyesters will be discussed. In more detail we will first present the strategies relying on CAs/IPs encapsulation in nanoparticles, micelles, dendrimers or capsules. We will then present chemical modifications of polyesters backbones and/or polyester surfaces to yield macromolecular imaging agents. Finally, opportunities offered by these innovative systems will be illustrated with some recent examples in the fields of cell labeling, diagnostic or theranostic applications and medical devices. Copyright © 2015 Elsevier B.V. All rights reserved.

New Programs Utilizing Light Scattering and Flow Imaging Techniques for Macromolecular Crystal Growth and Fluid Dynamics Studies

Science.gov (United States)

2003-01-01

Dr. Phil Segre, a physicist by training, is a recent addition to the Biotech group, SD46, having joined NASA in August of 2000. Over the past two years he has been developing a laboratory for the study of macromolecular and protein crystal growth. The main apparatus for this work is a Dynamic Light Scattering apparatus, DLS, which is capable of making highly precise measurements of size distributions of both protein solutions and protein crystals. With Drs. Chernov and Thomas (USRA), he has begun a collaboration studying the affects of protein impurities on protein crystal growth and subsequent crystal quality. One of the hypotheses behind the differences between Earth and space grown protein crystals is that the absorption of harmful impurities is reduced in space due to the absence of convective flows. Using DLS measurements we are examining crystal growth with varying amounts of impurities and testing whether there is a strong physical basis behind this hypothesis. With Dr. Joe Ng of UAH he has been collaborating on a project to examine the folding/unfolding dynamics of large RNA complexes. A detailed understanding of this process is necessary for the handling of RNA in biotech applications, and the DLS instrument gives details and results beyond that of other instruments. With Prof. Jim McClymer of the University of Maine (summer faculty visitor to NASA in 2001, 2002), we have been studying the crystallization process in model colloidal suspensions whose behavior in some cases can mimic that of much smaller protein solutions. An understanding of the self-assembly of colloids is the first step in the process of engineering novel materials for photonic and light switching applications. Finally, he has begun an investigation into the physics of particle sedimentation. In addition to the DLS instrument he also has an instrument (called PIV) that can measure flow fields of fluids. The applications are to the dynamics of protein crystal motions both on earth and in

A statistically harmonized alignment-classification in image space enables accurate and robust alignment of noisy images in single particle analysis.

Science.gov (United States)

Kawata, Masaaki; Sato, Chikara

2007-06-01

In determining the three-dimensional (3D) structure of macromolecular assemblies in single particle analysis, a large representative dataset of two-dimensional (2D) average images from huge number of raw images is a key for high resolution. Because alignments prior to averaging are computationally intensive, currently available multireference alignment (MRA) software does not survey every possible alignment. This leads to misaligned images, creating blurred averages and reducing the quality of the final 3D reconstruction. We present a new method, in which multireference alignment is harmonized with classification (multireference multiple alignment: MRMA). This method enables a statistical comparison of multiple alignment peaks, reflecting the similarities between each raw image and a set of reference images. Among the selected alignment candidates for each raw image, misaligned images are statistically excluded, based on the principle that aligned raw images of similar projections have a dense distribution around the correctly aligned coordinates in image space. This newly developed method was examined for accuracy and speed using model image sets with various signal-to-noise ratios, and with electron microscope images of the Transient Receptor Potential C3 and the sodium channel. In every data set, the newly developed method outperformed conventional methods in robustness against noise and in speed, creating 2D average images of higher quality. This statistically harmonized alignment-classification combination should greatly improve the quality of single particle analysis.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

International Nuclear Information System (INIS)

Tsai, Yingssu; McPhillips, Scott E.; González, Ana; McPhillips, Timothy M.; Zinn, Daniel; Cohen, Aina E.; Feese, Michael D.; Bushnell, David; Tiefenbrunn, Theresa; Stout, C. David; Ludaescher, Bertram; Hedman, Britt; Hodgson, Keith O.; Soltis, S. Michael

2013-01-01

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data, performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully

Macromolecular Crystal Growth by Means of Microfluidics

Science.gov (United States)

vanderWoerd, Mark; Ferree, Darren; Spearing, Scott; Monaco, Lisa; Molho, Josh; Spaid, Michael; Brasseur, Mike; Curreri, Peter A. (Technical Monitor)

2002-01-01

We have performed a feasibility study in which we show that chip-based, microfluidic (LabChip(TM)) technology is suitable for protein crystal growth. This technology allows for accurate and reliable dispensing and mixing of very small volumes while minimizing bubble formation in the crystallization mixture. The amount of (protein) solution remaining after completion of an experiment is minimal, which makes this technique efficient and attractive for use with proteins, which are difficult or expensive to obtain. The nature of LabChip(TM) technology renders it highly amenable to automation. Protein crystals obtained in our initial feasibility studies were of excellent quality as determined by X-ray diffraction. Subsequent to the feasibility study, we designed and produced the first LabChip(TM) device specifically for protein crystallization in batch mode. It can reliably dispense and mix from a range of solution constituents into two independent growth wells. We are currently testing this design to prove its efficacy for protein crystallization optimization experiments. In the near future we will expand our design to incorporate up to 10 growth wells per LabChip(TM) device. Upon completion, additional crystallization techniques such as vapor diffusion and liquid-liquid diffusion will be accommodated. Macromolecular crystallization using microfluidic technology is envisioned as a fully automated system, which will use the 'tele-science' concept of remote operation and will be developed into a research facility for the International Space Station as well as on the ground.

Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography

Directory of Open Access Journals (Sweden)

Marius Schmidt

2013-01-01

Full Text Available Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive substrate present in the crystal is activated. This has particular disadvantages that are circumvented when active substrate is directly provided by diffusion. However, then it is prohibitive to use macroscopic crystals because diffusion times become too long. With small micro- and nanocrystals diffusion times are adequately short for most enzymes and the reaction can be swiftly initiated. We demonstrate here that a time-resolved crystallographic experiment becomes feasible by mixing substrate with enzyme nanocrystals which are subsequently injected into the X-ray beam of a pulsed X-ray source.

Structure analysis of molecular systems in the Institute of Macromolecular Chemistry of the Czech Academy of Sciences

Czech Academy of Sciences Publication Activity Database

Hašek, Jindřich

2010-01-01

Roč. 17, 2a (2010), k32-k34 ISSN 1211-5894. [Struktura 2010. Soláň, 14.06.2010-17.06.2010] R&D Projects: GA AV ČR IAA500500701; GA ČR GA305/07/1073 Institutional research plan: CEZ:AV0Z40500505 Keywords : Academy of Sciences of the Czech Republic * X-ray structure analysis * crystallography Subject RIV: CD - Macromolecular Chemistry http:// xray .cz/ms/bul2010-2a/hasek.pdf

Stretchable All-Gel-State Fiber-Shaped Supercapacitors Enabled by Macromolecularly Interconnected 3D Graphene/Nanostructured Conductive Polymer Hydrogels.

Science.gov (United States)

Li, Panpan; Jin, Zhaoyu; Peng, Lele; Zhao, Fei; Xiao, Dan; Jin, Yong; Yu, Guihua

2018-05-01

Nanostructured conductive polymer hydrogels (CPHs) have been extensively applied in energy storage owing to their advantageous features, such as excellent electrochemical activity and relatively high electrical conductivity, yet the fabrication of self-standing and flexible electrode-based CPHs is still hampered by their limited mechanical properties. Herein, macromolecularly interconnected 3D graphene/nanostructured CPH is synthesized via self-assembly of CPHs and graphene oxide macrostructures. The 3D hybrid hydrogel shows uniform interconnectivity and enhanced mechanical properties due to the strong macromolecular interaction between the CPHs and graphene, thus greatly reducing aggregation in the fiber-shaping process. A proof-of-concept all-gel-state fibrous supercapacitor based on the 3D polyaniline/graphene hydrogel is fabricated to demonstrate the outstanding flexibility and mouldability, as well as superior electrochemical properties enabled by this 3D hybrid hydrogel design. The proposed device can achieve a large strain (up to ≈40%), and deliver a remarkable volumetric energy density of 8.80 mWh cm -3 (at power density of 30.77 mW cm -3 ), outperforming many fiber-shaped supercapacitors reported previously. The all-hydrogel design opens up opportunities in the fabrication of next-generation wearable and portable electronics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Design, synthesis, and evaluation of VEGFR-targeted macromolecular MRI contrast agent based on biotin–avidin-specific binding

Science.gov (United States)

Liu, Yongjun; Wu, Xiaoyun; Sun, Xiaohe; Wang, Dan; Zhong, Ying; Jiang, Dandan; Wang, Tianqi; Yu, Dexin; Zhang, Na

2017-01-01

Developing magnetic resonance imaging (MRI) contrast agents with high relaxivity and specificity was essential to increase MRI diagnostic sensitivity and accuracy. In this study, the MRI contrast agent, vascular endothelial growth factor receptor (VEGFR)-targeted poly (l-lysine) (PLL)-diethylene triamine pentacetate acid (DTPA)-gadolinium (Gd) (VEGFR-targeted PLL-DTPA-Gd, VPDG), was designed and prepared to enhance the MRI diagnosis capacity of tumor. Biotin-PLL-DTPA-Gd was synthesized first, then, VEGFR antibody was linked to biotin-PLL-DTPA-Gd using biotin–avidin reaction. In vitro cytotoxicity study results showed that VPDG had low toxicity to MCF-7 cells and HepG2 cells at experimental concentrations. In cell uptake experiments, VPDG could significantly increase the internalization rates (61.75%±5.22%) in VEGFR-positive HepG2 cells compared to PLL-DTPA-Gd (PDG) (25.16%±4.71%, P<0.05). In MRI studies in vitro, significantly higher T1 relaxivity (14.184 mM−1 s−1) was observed compared to Magnevist® (4.9 mM−1 s−1; P<0.01). Furthermore, in vivo MRI study results showed that VPDG could significantly enhance the tumor signal intensity and prolong the diagnostic time (from <1 h to 2.5 h). These results indicated that macromolecular VPDG was a promising MRI contrast agent and held great potential for molecular diagnosis of tumor. PMID:28765707

Macromolecular refinement by model morphing using non-atomic parameterizations.

Science.gov (United States)

Cowtan, Kevin; Agirre, Jon

2018-02-01

Refinement is a critical step in the determination of a model which explains the crystallographic observations and thus best accounts for the missing phase components. The scattering density is usually described in terms of atomic parameters; however, in macromolecular crystallography the resolution of the data is generally insufficient to determine the values of these parameters for individual atoms. Stereochemical and geometric restraints are used to provide additional information, but produce interrelationships between parameters which slow convergence, resulting in longer refinement times. An alternative approach is proposed in which parameters are not attached to atoms, but to regions of the electron-density map. These parameters can move the density or change the local temperature factor to better explain the structure factors. Varying the size of the region which determines the parameters at a particular position in the map allows the method to be applied at different resolutions without the use of restraints. Potential applications include initial refinement of molecular-replacement models with domain motions, and potentially the use of electron density from other sources such as electron cryo-microscopy (cryo-EM) as the refinement model.

Structural changes in the ordering processes of macromolecular compounds

International Nuclear Information System (INIS)

Kobayashi, M.; Tashiro, K.

1998-01-01

In order to clarify the microscopically-viewed relationship between the conformational ordering process and the aggregation process of the macromolecular chains in the phase transitions from melt to solid or from solution to gel, the time-resolved Fourier-transform infrared spectra and small-angle X-ray or neutron scattering data have been analyzed in an organized manner. Two concrete examples were presented. (1) In the gelation phenomenon of syndiotactic polystyrene-organic solvent system, the ordered TTGG conformation is formed and develops with time. This conformational ordering is accelerated by the aggregation of these chain segments, resulting in the formation of macroscopic gel network. (2) In the isothermal crystallization process from the melt of polyethylene, the following ordering mechanism was revealed. The conformationally-disordered short trans conformers appear at first in the random coils of the melt. These disordered trans sequences grow to longer and more regular trans sequences of the orthorhombic-type crystal and then the isolated lamellae are formed. Afterwards, the stacked lamellar structure is developed without change of lamellar thickness but with small decrease in the long period, indicating an insertion of new lamellae between the already produced lamellar layers

Electron tomography of cryo-immobilized plant tissue: a novel approach to studying 3D macromolecular architecture of mature plant cell walls in situ.

Directory of Open Access Journals (Sweden)

Purbasha Sarkar

Full Text Available Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼ 2 nm, and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF, cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Bricogne, Gerard

2014-01-01

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

Energy Technology Data Exchange (ETDEWEB)

Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States); Bricogne, Gerard, E-mail: terwilliger@lanl.gov [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States)

2014-10-01

Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be

C1 Polymerization: a unique tool towards polyethylene-based complex macromolecular architectures

KAUST Repository

Wang, De

2017-05-09

The recent developments in organoborane initiated C1 polymerization (chain grows by one atom at a time) of ylides opens unique horizons towards well-defined/perfectly linear polymethylenes (equivalent to polyethylenes, PE) and PE-based complex macromolecular architectures. The general mechanism of C1 polymerization (polyhomologation) involves the formation of a Lewis complex between a methylide (monomer) and a borane (initiator), followed by migration/insertion of a methylene into the initiator and after oxidation/hydrolysis to afford OH-terminated polyethylenes. This review summarizes efforts towards conventional and newly discovered borane-initiators and ylides (monomers), as well as a combination of polyhomologation with other polymerization methods. Initial efforts dealing with C3 polymerization and the synthesis of the first C1/C3 copolymers are also given. Finally, some thoughts for the future of these polymerizations are presented.

C1 Polymerization: a unique tool towards polyethylene-based complex macromolecular architectures

KAUST Repository

Wang, De; Zhang, Zhen; Hadjichristidis, Nikolaos

2017-01-01

The recent developments in organoborane initiated C1 polymerization (chain grows by one atom at a time) of ylides opens unique horizons towards well-defined/perfectly linear polymethylenes (equivalent to polyethylenes, PE) and PE-based complex macromolecular architectures. The general mechanism of C1 polymerization (polyhomologation) involves the formation of a Lewis complex between a methylide (monomer) and a borane (initiator), followed by migration/insertion of a methylene into the initiator and after oxidation/hydrolysis to afford OH-terminated polyethylenes. This review summarizes efforts towards conventional and newly discovered borane-initiators and ylides (monomers), as well as a combination of polyhomologation with other polymerization methods. Initial efforts dealing with C3 polymerization and the synthesis of the first C1/C3 copolymers are also given. Finally, some thoughts for the future of these polymerizations are presented.

Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes

Directory of Open Access Journals (Sweden)

Sadhna Phanse

2016-03-01

Full Text Available Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (http://www.ebi.ac.uk/pride/archive/projects/PXD002319-http://www.ebi.ac.uk/pride/archive/projects/PXD002328, PPIs via BioGRID (185267; and interaction network projections via (http://metazoa.med.utoronto.ca made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1]. Keywords: Proteomics, Metazoa, Protein complexes, Biochemical, Fractionation

PEGylated chitosan grafted with polyamidoaminedendron as tumor-targeted magnetic resonance imaging contrast agent

International Nuclear Information System (INIS)

Guangyue Zu; Xiaoyan Tong; Yi Cao; Ye Kuang; Yajie Zhang; Min Liu; Renjun Pei

2017-01-01

Macromolecular contrast agents labeled with targeting ligands are now receiving growing interest in tumor-targeted magnetic resonance imaging. In this study, a macromolecular contrast agent based on PEGylated chitosan was synthesized and characterized, and its application as an MRI contrast agent was then demonstrated both in vitro and in vivo. First, the chitosan backbone was partially grafted with poly(ethylene glycol), which was used to improve the in vivo stability, followed by modifying with azide groups. Second, alkynyl-terminated PAMAM dendron modified with gadolinium diethylenetriaminepentaacetic acid (Gd-DTPA) was synthesized and conjugated onto the chitosan backbone through click chemistry. Finally, the obtained mCA was further functionalized with folic acid to improve the target specificity. The obtained FA labeled mCA exhibited higher relaxivity (9.53 mM"-"1.s"-"1) relative to Gd-DTPA (4.25 mM"-"1.s"-"1) and showed negligible toxicity as determined by the WST assay. In vivo MRI results suggested that a relatively high signal enhancement was observed in the tumor region, which made it a promising candidate for tumor-targeted MRI CA. (authors)

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography

International Nuclear Information System (INIS)

Brockhauser, Sandor; Svensson, Olof; Bowler, Matthew W.; Nanao, Max; Gordon, Elspeth; Leal, Ricardo M. F.; Popov, Alexander; Gerring, Matthew; McCarthy, Andrew A.; Gotz, Andy

2012-01-01

A powerful and easy-to-use workflow environment has been developed at the ESRF for combining experiment control with online data analysis on synchrotron beamlines. This tool provides the possibility of automating complex experiments without the need for expertise in instrumentation control and programming, but rather by accessing defined beamline services. The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE

Macromolecular crystallographic results obtained using a 2048x2048 CCD detector at CHESS

International Nuclear Information System (INIS)

Thiel, D.J.; Ealick, S.E.; Tate, M.W.; Gruner, S.M.; Eikenberry, E.F.

1996-01-01

We present results of macromolecular crystallographic experiments performed at the Cornell High Energy Synchrotron Source (CHESS) with a new CCD-based detector. This detector, installed in January 1995, complements a 1024x1024 CCD detector that has been in continuous operation at CHESS since December 1993. The new detector is based on a 4-port, 2048x2048 pixel CCD that is directly coupled to a Gd 2 O 2 S:Tb phosphor by a 3:1 tapered fiber optic. The active area of the phosphor is a square 82 mm on an edge. The readout time is 7 seconds. In the standard mode of operation, the pixel size at the active area is 41 μm on the edge leading to the capability of resolving approximately 200 orders of diffraction across the detector face. The detector also operates in a 1024x1024 mode in which the pixel size is electronically increased by a factor of 4 in area resulting in smaller data files and faster detector readout but at the expense of spatial resolution. Most of the data that has been collected by this detector has been collected in this mode. Dozens of data sets have been collected by many experimenters using this detector at CHESS during the four month period from its installation until the start of the six-month down period of the storage ring. The capabilities of the detector will be illustrated with results from various crystallographic measurements including experiments in which the recorded diffraction patterns extend in resolution as far as 1 A. The results demonstrate that this detector is capable of collecting data of quality at least equal to that of imaging plates but, in many circumstances, with much greater beamline efficiency. copyright 1996 American Institute of Physics

Phase-Separated Liposomes Enhance the Efficiency of Macromolecular Delivery to the Cellular Cytoplasm.

Science.gov (United States)

Imam, Zachary I; Kenyon, Laura E; Ashby, Grant; Nagib, Fatema; Mendicino, Morgan; Zhao, Chi; Gadok, Avinash K; Stachowiak, Jeanne C

2017-10-01

From viruses to organelles, fusion of biological membranes is used by diverse biological systems to deliver macromolecules across membrane barriers. Membrane fusion is also a potentially efficient mechanism for the delivery of macromolecular therapeutics to the cellular cytoplasm. However, a key shortcoming of existing fusogenic liposomal systems is that they are inefficient, requiring a high concentration of fusion-promoting lipids in order to cross cellular membrane barriers. Toward addressing this limitation, our experiments explore the extent to which membrane fusion can be amplified by using the process of lipid membrane phase separation to concentrate fusion-promoting lipids within distinct regions of the membrane surface. We used confocal fluorescence microscopy to investigate the integration of fusion-promoting lipids into a ternary lipid membrane system that separated into liquid-ordered and liquid-disordered membrane phases. Additionally, we quantified the impact of membrane phase separation on the efficiency with which liposomes transferred lipids and encapsulated macromolecules to cells, using a combination of confocal fluorescence imaging and flow cytometry. Here we report that concentrating fusion-promoting lipids within phase-separated lipid domains on the surfaces of liposomes significantly increases the efficiency of liposome fusion with model membranes and cells. In particular, membrane phase separation enhanced the delivery of lipids and model macromolecules to the cytoplasm of tumor cells by at least 4-fold in comparison to homogenous liposomes. Our findings demonstrate that phase separation can enhance membrane fusion by locally concentrating fusion-promoting lipids on the surface of liposomes. This work represents the first application of lipid membrane phase separation in the design of biomaterials-based delivery systems. Additionally, these results lay the ground work for developing fusogenic liposomes that are triggered by physical and

Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components

DEFF Research Database (Denmark)

Jensen, Kaj Frank; Pedersen, Steen

1990-01-01

In this paper, the Escherichia coli cell is considered as a system designed for rapid growth, but limited by the medium. We propose that this very design causes the cell to become subsaturated with precursors and catalytic components at all levels of macromolecular biosynthesis and leads to a mol...

OCTOPUS: an innovative multimodal diffractometer for neutron macromolecular crystallography across the length scales

International Nuclear Information System (INIS)

Blakeley, M.P.; Andersen, K.; Kreuz, M.; Giroud, B.; McSweeney, S.; Mitchell, E.; Teixeira, S.C.M.; Forsyth, V.T.

2011-01-01

We propose to construct a novel protein diffractometer at position H112B. The new instrument will deliver major efficiency gains, as well as offering greatly extended flexibility through the option of several easily interchangeable modes of operation. This proposal builds on the demonstrable need to extend ILL's capacity for high resolution structural studies of protein systems, as well as a need to widen the scope of biological crystallography - in particular for monochromatic studies at both high and low resolution. The development will be carried out in close collaboration with structural biologists at the ESRF, and engineered in such a way that the user interface of the instrument (from sample to software) will be transparently identifiable to a large, dynamic, and driven community of European synchrotron X-ray macromolecular crystallographers. (authors)

Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

DEFF Research Database (Denmark)

Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.

2017-01-01

orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME......Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...... models have 70,000 constraints and variables and will grow larger). We have developed a quadrupleprecision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging...

Recent topics in NMR imaging and MRI

International Nuclear Information System (INIS)

Watanabe, Tokuko

2002-01-01

NMR and NMR imaging (MRI) are finding increasing use not only in the clinical and medical fields, but also in material, physicochemical, biological, geological, industrial and environmental applications. This short review is limited to two topics: new techniques and pulse sequences and their application to non-clinical fields that may have clinical application; and new trends in MR contrast agents. The former topic addresses pulse sequence and data analysis; dynamics such as diffusion, flow, velocity and velocimetry; chemometrics; pharmacological agents; and chemotherapy; the latter topic addresses contrast agents (CA) sensitive to biochemical activity; CA based on water exchange; molecular interactions and stability of CA; characteristics of emerging CA; superparamagnetic CA; and macromolecular CA. (author)

Magnetic resonance imaging of dystonic states

International Nuclear Information System (INIS)

Rutledge, J.N.; Hilal, S.K.; Silver, A.J.; Defendini, R.; Fahn, S.

1988-01-01

Interest in movement disorders is heightened by the recent capability of mapping the distribution of macromolecular complexes of Fe(III) in the brain using heavily T2-weighted images. This is accomplished through contrast caused by their T2 effect, a local inhomogeneity in the magnetic field which dephases spin and results in loss of signal. It is a unique characteristic of the extra-pyramidal system that its nuclei contain high concentrations of iron. The areas especially rich are the substantia nigra and globus pallidus. Lesser amounts of iron are found in the red nucleus, dentate nucleus, nigrostriatal tract, putamen, and caudate nucleus. The reasons for increased concentration of iron in nuclei related to movement are incompletely understood and are reviewed in this chapter

JBluIce-EPICS control system for macromolecular crystallography

International Nuclear Information System (INIS)

Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J.L.; Fischetti, R.F.

2011-01-01

The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

Making microenvironments: A look into incorporating macromolecular crowding into in vitro experiments, to generate biomimetic microenvironments which are capable of directing cell function for tissue engineering applications.

Science.gov (United States)

Benny, Paula; Raghunath, Michael

2017-01-01

Biomimetic microenvironments are key components to successful cell culture and tissue engineering in vitro. One of the most accurate biomimetic microenvironments is that made by the cells themselves. Cell-made microenvironments are most similar to the in vivo state as they are cell-specific and produced by the actual cells which reside in that specific microenvironment. However, cell-made microenvironments have been challenging to re-create in vitro due to the lack of extracellular matrix composition, volume and complexity which are required. By applying macromolecular crowding to current cell culture protocols, cell-made microenvironments, or cell-derived matrices, can be generated at significant rates in vitro. In this review, we will examine the causes and effects of macromolecular crowding and how it has been applied in several in vitro systems including tissue engineering.

Macromolecular contrast media. A new approach for characterising breast tumors with MR-mammography

International Nuclear Information System (INIS)

Daldrup, H.E.; Gossmann, A.; Koeln Univ.; Wendland, M.; Brasch, R.C.; Rosenau, W.

1997-01-01

The value of macromolecular contrast agents (MMCM) for the characterization of benign and malignant breast tumors will be demonstrated in this review. Animal studies suggest a high potential of MMCM to increase the specificity of MR-mammography. The concept of tumor differentiation is based on the pathological hyperpermeability of microvessels in malignant tumors. MMCM show a leak into the interstitium of carcinomas, whereas they are confined to the intravascular space in benign tumors. Capabilities and limitations of the MMCM-prototype. Albumin-Gd-DTPA, for breast tumor characterization will be summarized and compared to the standard low molecular weight contrast agent Gd-DTPA. Initial experience with new MMCM, such as Dendrimers, Gd-DTPA-Polylysine and MS-325 will be outlined. The potential of 'blood-pool'-iron oxides, such as AMI-227 for the evaluation of tumor microvascular permeabilities will be discussed. (orig.) [de

A general approach to break the concentration barrier in single-molecule imaging

KAUST Repository

Loveland, Anna B.

2012-09-09

Single-molecule fluorescence imaging is often incompatible with physiological protein concentrations, as fluorescence background overwhelms an individual molecule\\'s signal. We solve this problem with a new imaging approach called PhADE (PhotoActivation, Diffusion and Excitation). A protein of interest is fused to a photoactivatable protein (mKikGR) and introduced to its surface-immobilized substrate. After photoactivation of mKikGR near the surface, rapid diffusion of the unbound mKikGR fusion out of the detection volume eliminates background fluorescence, whereupon the bound molecules are imaged. We labeled the eukaryotic DNA replication protein flap endonuclease 1 with mKikGR and added it to replication-competent Xenopus laevis egg extracts. PhADE imaging of high concentrations of the fusion construct revealed its dynamics and micrometer-scale movements on individual, replicating DNA molecules. Because PhADE imaging is in principle compatible with any photoactivatable fluorophore, it should have broad applicability in revealing single-molecule dynamics and stoichiometry of macromolecular protein complexes at previously inaccessible fluorophore concentrations. © 2012 Nature America, Inc. All rights reserved.

Rapid automated superposition of shapes and macromolecular models using spherical harmonics.

Science.gov (United States)

Konarev, Petr V; Petoukhov, Maxim V; Svergun, Dmitri I

2016-06-01

A rapid algorithm to superimpose macromolecular models in Fourier space is proposed and implemented ( SUPALM ). The method uses a normalized integrated cross-term of the scattering amplitudes as a proximity measure between two three-dimensional objects. The reciprocal-space algorithm allows for direct matching of heterogeneous objects including high- and low-resolution models represented by atomic coordinates, beads or dummy residue chains as well as electron microscopy density maps and inhomogeneous multi-phase models ( e.g. of protein-nucleic acid complexes). Using spherical harmonics for the computation of the amplitudes, the method is up to an order of magnitude faster than the real-space algorithm implemented in SUPCOMB by Kozin & Svergun [ J. Appl. Cryst. (2001 ▸), 34 , 33-41]. The utility of the new method is demonstrated in a number of test cases and compared with the results of SUPCOMB . The spherical harmonics algorithm is best suited for low-resolution shape models, e.g . those provided by solution scattering experiments, but also facilitates a rapid cross-validation against structural models obtained by other methods.

A Test of Macromolecular Crystallization in Microgravity: Large, Well-Ordered Insulin Crystals

Science.gov (United States)

Borgstahl, Gloria E. O.; Vahedi-Faridi, Ardeschir; Lovelace, Jeff; Bellamy, Henry D.; Snell, Edward H.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Crystals of insulin grown in microgravity on space shuttle mission STS-95 were extremely well-ordered and unusually large (many > 2 mm). The physical characteristics of six microgravity and six earth-grown crystals were examined by X-ray analysis employing superfine f slicing and unfocused synchrotron radiation. This experimental setup allowed hundreds of reflections to be precisely examined for each crystal in a short period of time. The microgravity crystals were on average 34 times larger, had 7 times lower mosaicity, had 54 times higher reflection peak heights and diffracted to significantly higher resolution than their earth grown counterparts. A single mosaic domain model could account for reflections in microgravity crystals whereas reflections from earth crystals required a model with multiple mosaic domains. This statistically significant and unbiased characterization indicates that the microgravity environment was useful for the improvement of crystal growth and resultant diffraction quality in insulin crystals and may be similarly useful for macromolecular crystals in general.

A vibrating membrane bioreactor (VMBR): Macromolecular transmission-influence of extracellular polymeric substances

DEFF Research Database (Denmark)

Beier, Søren; Jonsson, Gunnar Eigil

2009-01-01

The vibrating membrane bioreactor (VMBR) system facilitates the possibility of conducting a separation of macromolecules (BSA) from larger biological components (yeast cells) with a relatively high and stable macromolecular transmission at sub-critical flux. This is not possible to achieve...... for a static non-vibrating membrane module. A BSA transmission of 74% has been measured in the separation of 4g/L BSA from 8 g/L dry weight yeast cells in suspension at sub-critical flux (20L/(m(2) h)). However, this transmission is lower than the 85% BSA transmission measured for at pure 4g/L BSA solution....... This can be ascribed to the presence of extracellular polymeric substances (EPS) from the yeast cells. The initial fouling rate for constant sub-critical flux filtration of unwashed yeast cells is 3-4 times larger than for washed yeast cells (18(mbar/h)/5(mbar/h)). At sub-critical flux, an EPS transmission...

Synthesis and Self-Assembly of Amphiphilic Triblock Terpolymers with Complex Macromolecular Architecture

KAUST Repository

Polymeropoulos, George; Zapsas, George; Hadjichristidis, Nikolaos; Avgeropoulos, Apostolos

2015-01-01

Two star triblock terpolymers (PS-b-P2VP-b-PEO)3 and one dendritic-like terpolymer [PS-b-P2VP-b-(PEO)2]3 of PS (polystyrene), P2VP (poly(2-vinylpyridine)), and PEO (poly(ethylene oxide)), never reported before, were synthesized by combining atom transfer radical and anionic polymerizations. The synthesis involves the transformation of the -Br groups of the previously reported Br-terminated 3-arm star diblock copolymers to one or two -OH groups, followed by anionic polymerization of ethylene oxide to afford the star or dendritic structure, respectively. The well-defined structure of the terpolymers was confirmed by static light scattering, size exclusion chromatography, and NMR spectroscopy. The self-assembly in solution and the morphology in bulk of the terpolymers, studied by dynamic light scattering and transmission electron microscopy, respectively, reveal new insights in the phase separation of these materials with complex macromolecular architecture. © 2015 American Chemical Society.

Control and data acquisition system for the macromolecular crystallography beamline of SSRF

International Nuclear Information System (INIS)

Wang Qisheng; Huang Sheng; Sun Bo; Tang Lin; He Jianhua

2012-01-01

The macromolecular crystallography beamline BL17U1 of Shanghai Synchrotron Radiation Facility (SSRF) is an important platform for structure biological science. High performance of the beamline would benefit the users greatly in their experiment and data acquisition. To take full advantage of the state-of-the-art mechanical and physical design of the beamline, we have made a series of efforts to develop a robust control and data acquisition system, with user-friendly GUI. These were done by adopting EPICS and Blu-Ice systems on the BL17U1 beamline, with considerations on easy accommodation of new beeline components. In this paper, we report the integration of EPICS and Blu-Ice systems. By using the EPICS gateway interface and several new DHS, Blu-Ice was successfully established for the BL17U1 beamline. As a result, the experiment control and data acquisition system is reliable and functional for users. (authors)

Synthesis and Self-Assembly of Amphiphilic Triblock Terpolymers with Complex Macromolecular Architecture

KAUST Repository

Polymeropoulos, George

2015-11-25

Two star triblock terpolymers (PS-b-P2VP-b-PEO)3 and one dendritic-like terpolymer [PS-b-P2VP-b-(PEO)2]3 of PS (polystyrene), P2VP (poly(2-vinylpyridine)), and PEO (poly(ethylene oxide)), never reported before, were synthesized by combining atom transfer radical and anionic polymerizations. The synthesis involves the transformation of the -Br groups of the previously reported Br-terminated 3-arm star diblock copolymers to one or two -OH groups, followed by anionic polymerization of ethylene oxide to afford the star or dendritic structure, respectively. The well-defined structure of the terpolymers was confirmed by static light scattering, size exclusion chromatography, and NMR spectroscopy. The self-assembly in solution and the morphology in bulk of the terpolymers, studied by dynamic light scattering and transmission electron microscopy, respectively, reveal new insights in the phase separation of these materials with complex macromolecular architecture. © 2015 American Chemical Society.

Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm.

Science.gov (United States)

Zhang, Qing; Beard, Daniel A; Schlick, Tamar

2003-12-01

Salt-mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye-Hückel (screened Coulombic) approximation to the Poisson-Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson-Boltzmann solution for the electric field, yielding a approximately 5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK

Stably engineered nanobubbles and ultrasound - An effective platform for enhanced macromolecular delivery to representative cells of the retina.

Directory of Open Access Journals (Sweden)

Sachin S Thakur

Full Text Available Herein we showcase the potential of ultrasound-responsive nanobubbles in enhancing macromolecular permeation through layers of the retina, ultimately leading to significant and direct intracellular delivery; this being effectively demonstrated across three relevant and distinct retinal cell lines. Stably engineered nanobubbles of a highly homogenous and echogenic nature were fully characterised using dynamic light scattering, B-scan ultrasound and transmission electron microscopy (TEM. The nanobubbles appeared as spherical liposome-like structures under TEM, accompanied by an opaque luminal core and darkened corona around their periphery, with both features indicative of efficient gas entrapment and adsorption, respectively. A nanobubble +/- ultrasound sweeping study was conducted next, which determined the maximum tolerated dose for each cell line. Detection of underlying cellular stress was verified using the biomarker heat shock protein 70, measured before and after treatment with optimised ultrasound. Next, with safety to nanobubbles and optimised ultrasound demonstrated, each human or mouse-derived cell population was incubated with biotinylated rabbit-IgG in the presence and absence of ultrasound +/- nanobubbles. Intracellular delivery of antibody in each cell type was then quantified using Cy3-streptavidin. Nanobubbles and optimised ultrasound were found to be negligibly toxic across all cell lines tested. Macromolecular internalisation was achieved to significant, yet varying degrees in all three cell lines. The results of this study pave the way towards better understanding mechanisms underlying cellular responsiveness to ultrasound-triggered drug delivery in future ex vivo and in vivo models of the posterior eye.

Macromolecular crystallization in microgravity generated by a superconducting magnet.

Science.gov (United States)

Wakayama, N I; Yin, D C; Harata, K; Kiyoshi, T; Fujiwara, M; Tanimoto, Y

2006-09-01

About 30% of the protein crystals grown in space yield better X-ray diffraction data than the best crystals grown on the earth. The microgravity environments provided by the application of an upward magnetic force constitute excellent candidates for simulating the microgravity conditions in space. Here, we describe a method to control effective gravity and formation of protein crystals in various levels of effective gravity. Since 2002, the stable and long-time durable microgravity generated by a convenient type of superconducting magnet has been available for protein crystal growth. For the first time, protein crystals, orthorhombic lysozyme, were grown at microgravity on the earth, and it was proved that this microgravity improved the crystal quality effectively and reproducibly. The present method always accompanies a strong magnetic field, and the magnetic field itself seems to improve crystal quality. Microgravity is not always effective for improving crystal quality. When we applied this microgravity to the formation of cubic porcine insulin and tetragonal lysozyme crystals, we observed no dependence of effective gravity on crystal quality. Thus, this kind of test will be useful for selecting promising proteins prior to the space experiments. Finally, the microgravity generated by the magnet is compared with that in space, considering the cost, the quality of microgravity, experimental convenience, etc., and the future use of this microgravity for macromolecular crystal growth is discussed.

Acoustic methods for high-throughput protein crystal mounting at next-generation macromolecular crystallographic beamlines.

Science.gov (United States)

Roessler, Christian G; Kuczewski, Anthony; Stearns, Richard; Ellson, Richard; Olechno, Joseph; Orville, Allen M; Allaire, Marc; Soares, Alexei S; Héroux, Annie

2013-09-01

To take full advantage of advanced data collection techniques and high beam flux at next-generation macromolecular crystallography beamlines, rapid and reliable methods will be needed to mount and align many samples per second. One approach is to use an acoustic ejector to eject crystal-containing droplets onto a solid X-ray transparent surface, which can then be positioned and rotated for data collection. Proof-of-concept experiments were conducted at the National Synchrotron Light Source on thermolysin crystals acoustically ejected onto a polyimide `conveyor belt'. Small wedges of data were collected on each crystal, and a complete dataset was assembled from a well diffracting subset of these crystals. Future developments and implementation will focus on achieving ejection and translation of single droplets at a rate of over one hundred per second.

DA+ data acquisition and analysis software at the Swiss Light Source macromolecular crystallography beamlines.

Science.gov (United States)

Wojdyla, Justyna Aleksandra; Kaminski, Jakub W; Panepucci, Ezequiel; Ebner, Simon; Wang, Xiaoqiang; Gabadinho, Jose; Wang, Meitian

2018-01-01

Data acquisition software is an essential component of modern macromolecular crystallography (MX) beamlines, enabling efficient use of beam time at synchrotron facilities. Developed at the Paul Scherrer Institute, the DA+ data acquisition software is implemented at all three Swiss Light Source (SLS) MX beamlines. DA+ consists of distributed services and components written in Python and Java, which communicate via messaging and streaming technologies. The major components of DA+ are the user interface, acquisition engine, online processing and database. Immediate data quality feedback is achieved with distributed automatic data analysis routines. The software architecture enables exploration of the full potential of the latest instrumentation at the SLS MX beamlines, such as the SmarGon goniometer and the EIGER X 16M detector, and development of new data collection methods.

Macromolecular weight specificity in covalent binding of bromobenzene

International Nuclear Information System (INIS)

Sun, J.D.; Dent, J.G.

1984-01-01

Bromobenzene is a hepatotoxicant that causes centrilobular necrosis. Pretreatment of animals with 3-methylcholanthrene decreases and phenobarbital pretreatment enhances the hepatotoxic action of this compound. We have investigated the macromolecular weight specificity of the covalent interactions of bromobenzene with liver macromolecules following incubation of [ 14 C]bromobenzene in isolated hepatocytes. Hepatocytes were prepared from Fischer-344 rats treated for 3 days with 3-methylcholanthrene, phenobarbital, or normal saline. After a 1-hr incubation, total covalent binding, as measured by sodium dodecyl sulfate-equilibrium dialysis, was twofold less in hepatocytes from 3-methylcholanthrene-treated rats and sixfold greater in hepatocytes from phenobarbital-treated rats, as compared to hepatocytes from control animals. Analysis of the arylated macromolecules by electrophoresis on 15% sodium dodecyl sulfate-polyacrylamide disc gels indicated that in the first 1 to 3 min of incubation substantial amounts of covalently bound radiolabel were associated with macromolecules of between 20,000 and 40,000. The amount of radioactivity associated with these macromolecules rapidly diminished in hepatocytes from control and 3-methylcholanthrene-treated animals. In hepatocytes from phenobarbital-treated animals, the amount of radioactivity associated with macromolecules, 20,000, increased throughout the incubation. The amount of radiolabel associated with macromolecules, 20,000, increased in all incubations. When nontoxic doses of phenylmethylsulfonyl fluoride, a specific inhibitor of serine proteases, were added to control hepatocytes incubated with [ 14 C]-bromobenzene, the decrease in radioactivity associated with larger (greater than 20,000) macromolecules was inhibited and a corresponding lack of increase in radioactivity associated with smaller macromolecules was observed

Structure, function and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding.

Science.gov (United States)

Samiotakis, Antonios; Dhar, Apratim; Ebbinghaus, Simon; Nienhaus, Lea; Homouz, Dirar; Gruebele, Martin; Cheung, Margaret

2010-10-01

We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal) and Sph (spherical compact). With an adjustment for viscosity, crowded wild type PGK and fluorescent PGK are about 15 times or more active in 200 mg/ml Ficoll than in aqueous solution. Our results suggest a new solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates.

Depth-Dependent Anisotropies of Amides and Sugar in Perpendicular and Parallel Sections of Articular Cartilage by Fourier Transform Infrared Imaging (FTIRI)

Science.gov (United States)

Xia, Yang; Mittelstaedt, Daniel; Ramakrishnan, Nagarajan; Szarko, Matthew; Bidthanapally, Aruna

2010-01-01

Full thickness blocks of canine humeral cartilage were microtomed into both perpendicular sections and a series of 100 parallel sections, each 6 μm thick. Fourier Transform Infrared Imaging (FTIRI) was used to image each tissue section eleven times under different infrared polarizations (from 0° to 180° polarization states in 20° increments and with an additional 90° polarization), at a spatial resolution of 6.25 μm and a wavenumber step of 8 cm−1. With increasing depth from the articular surface, amide anisotropies increased in the perpendicular sections and decreased in the parallel sections. Both types of tissue sectioning identified a 90° difference between amide I and amide II in the superficial zone of cartilage. The fibrillar distribution in the parallel sections from the superficial zone was shown to not be random. Sugar had the greatest anisotropy in the upper part of the radial zone in the perpendicular sections. The depth-dependent anisotropic data were fitted with a theoretical equation that contained three signature parameters, which illustrate the arcade structure of collagens with the aid of a fibril model. Infrared imaging of both perpendicular and parallel sections provides the possibility of determining the three-dimensional macromolecular structures in articular cartilage. Being sensitive to the orientation of the macromolecular structure in healthy articular cartilage aids the prospect of detecting the early onset of the tissue degradation that may lead to pathological conditions such as osteoarthritis. PMID:21274999

Macromolecular composition of terrestrial and marine organic matter in sediments across the East Siberian Arctic Shelf

Science.gov (United States)

Sparkes, Robert B.; Doğrul Selver, Ayça; Gustafsson, Örjan; Semiletov, Igor P.; Haghipour, Negar; Wacker, Lukas; Eglinton, Timothy I.; Talbot, Helen M.; van Dongen, Bart E.

2016-10-01

Mobilisation of terrestrial organic carbon (terrOC) from permafrost environments in eastern Siberia has the potential to deliver significant amounts of carbon to the Arctic Ocean, via both fluvial and coastal erosion. Eroded terrOC can be degraded during offshore transport or deposited across the wide East Siberian Arctic Shelf (ESAS). Most studies of terrOC on the ESAS have concentrated on solvent-extractable organic matter, but this represents only a small proportion of the total terrOC load. In this study we have used pyrolysis-gas chromatography-mass spectrometry (py-GCMS) to study all major groups of macromolecular components of the terrOC; this is the first time that this technique has been applied to the ESAS. This has shown that there is a strong offshore trend from terrestrial phenols, aromatics and cyclopentenones to marine pyridines. There is good agreement between proportion phenols measured using py-GCMS and independent quantification of lignin phenol concentrations (r2 = 0.67, p radiocarbon data for bulk OC (14COC) which, when coupled with previous measurements, allows us to produce the most comprehensive 14COC map of the ESAS to date. Combining the 14COC and py-GCMS data suggests that the aromatics group of compounds is likely sourced from old, aged terrOC, in contrast to the phenols group, which is likely sourced from modern woody material. We propose that an index of the relative proportions of phenols and pyridines can be used as a novel terrestrial vs. marine proxy measurement for macromolecular organic matter. Principal component analysis found that various terrestrial vs. marine proxies show different patterns across the ESAS, and it shows that multiple river-ocean transects of surface sediments transition from river-dominated to coastal-erosion-dominated to marine-dominated signatures.

Macromolecular HPMA-based nanoparticles with cholesterol for solid-tumor targeting: detailed study of the inner structure of a highly efficient drug delivery system

Czech Academy of Sciences Publication Activity Database

Filippov, Sergey K.; Chytil, Petr; Konarev, P. V.; Dyakonova, M.; Papadakis, C. M.; Zhigunov, Alexander; Pleštil, Josef; Štěpánek, Petr; Etrych, Tomáš; Ulbrich, Karel; Svergun, D. I.

2012-01-01

Roč. 13, č. 8 (2012), s. 2594-2604 ISSN 1525-7797 R&D Projects: GA MŠk ME09059; GA AV ČR IAAX00500803; GA ČR GAP108/12/0640 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : HPMA * cholesterol * SAXS Subject RIV: CD - Macromolecular Chemistry Impact factor: 5.371, year: 2012

Identification of transcriptional macromolecular associations in human bone using browser based in silico analysis in a giant correlation matrix.

Science.gov (United States)

Reppe, Sjur; Sachse, Daniel; Olstad, Ole K; Gautvik, Vigdis T; Sanderson, Paul; Datta, Harish K; Berg, Jens P; Gautvik, Kaare M

2013-03-01

Intracellular signaling is critically dependent on gene regulatory networks comprising physical molecular interactions. Presently, there is a lack of comprehensive databases for most human tissue types to verify such macromolecular interactions. We present a user friendly browser which helps to identify functional macromolecular interactions in human bone as significant correlations at the transcriptional level. The molecular skeletal phenotype has been characterized by transcriptome analysis of iliac crest bone biopsies from 84 postmenopausal women through quantifications of ~23,000 mRNA species. When the signal levels were inter-correlated, an array containing >260 million correlations was generated, thus recognizing the human bone interactome at the RNA level. The matrix correlation and p values were made easily accessible by a freely available online browser. We show that significant correlations within the giant matrix are reproduced in a replica set of 13 male vertebral biopsies. The identified correlations differ somewhat from transcriptional interactions identified in cell culture experiments and transgenic mice, thus demonstrating that care should be taken in extrapolating such results to the in vivo situation in human bone. The current giant matrix and web browser are a valuable tool for easy access to the human bone transcriptome and molecular interactions represented as significant correlations at the RNA-level. The browser and matrix should be a valuable hypothesis generating tool for identification of regulatory mechanisms and serve as a library of transcript relationships in human bone, a relatively inaccessible tissue. Copyright © 2012 Elsevier Inc. All rights reserved.

Nitrogen limitation in natural populations of cyanobacteria (Spirulina and Oscillatoria spp.) and its effect on macromolecular synthesis

International Nuclear Information System (INIS)

van Rijn, J.; Shilo, M.

1986-01-01

Natural populations of the cyanobacteria Spirulina species and Oscillatoria species obtained from Israeli fish ponds were limited in growth by nitrogen availability in summer. Physiological indicators for nitrogen limitation, such as phycocyanin, chlorophyll a, and carbohydrate content, did not show clear evidence for nitrogen limited growth, since these organisms are capable of vertical migration from and to the nitrogen-rich bottom. By means of 14 C labeling of the cells under simulated pond conditions followed by cell fractionation into macromolecular compounds, it was found that carbohydrates synthesized at the lighted surface were partially utilized for dark protein synthesis at the bottom of these ponds

About Small Streams and Shiny Rocks: Macromolecular Crystal Growth in Microfluidics

Science.gov (United States)

vanderWoerd, Mark; Ferree, Darren; Spearing, Scott; Monaco, Lisa; Molho, Josh; Spaid, Michael; Brasseur, Mike; Curreri, Peter A. (Technical Monitor)

2002-01-01

We are developing a novel technique with which we have grown diffraction quality protein crystals in very small volumes, utilizing chip-based, microfluidic ("LabChip") technology. With this technology volumes smaller than achievable with any laboratory pipette can be dispensed with high accuracy. We have performed a feasibility study in which we crystallized several proteins with the aid of a LabChip device. The protein crystals are of excellent quality as shown by X-ray diffraction. The advantages of this new technology include improved accuracy of dispensing for small volumes, complete mixing of solution constituents without bubble formation, highly repeatable recipe and growth condition replication, and easy automation of the method. We have designed a first LabChip device specifically for protein crystallization in batch mode and can reliably dispense and mix from a range of solution constituents. We are currently testing this design. Upon completion additional crystallization techniques, such as vapor diffusion and liquid-liquid diffusion will be accommodated. Macromolecular crystallization using microfluidic technology is envisioned as a fully automated system, which will use the 'tele-science' concept of remote operation and will be developed into a research facility aboard the International Space Station.

A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source

International Nuclear Information System (INIS)

Pompidor, Guillaume; Dworkowski, Florian S. N.; Thominet, Vincent; Schulze-Briese, Clemens; Fuchs, Martin R.

2013-01-01

The new version MS2 of the in situ on-axis micro-spectrophotometer at the macromolecular crystallography beamline X10SA of the Swiss Light Source supports the concurrent acquisition of Raman, resonance Raman, fluorescence and UV/Vis absorption spectra along with diffraction data. The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years

Integration and global analysis of isothermal titration calorimetry data for studying macromolecular interactions.

Science.gov (United States)

Brautigam, Chad A; Zhao, Huaying; Vargas, Carolyn; Keller, Sandro; Schuck, Peter

2016-05-01

Isothermal titration calorimetry (ITC) is a powerful and widely used method to measure the energetics of macromolecular interactions by recording a thermogram of differential heating power during a titration. However, traditional ITC analysis is limited by stochastic thermogram noise and by the limited information content of a single titration experiment. Here we present a protocol for bias-free thermogram integration based on automated shape analysis of the injection peaks, followed by combination of isotherms from different calorimetric titration experiments into a global analysis, statistical analysis of binding parameters and graphical presentation of the results. This is performed using the integrated public-domain software packages NITPIC, SEDPHAT and GUSSI. The recently developed low-noise thermogram integration approach and global analysis allow for more precise parameter estimates and more reliable quantification of multisite and multicomponent cooperative and competitive interactions. Titration experiments typically take 1-2.5 h each, and global analysis usually takes 10-20 min.

Label-free cellular imaging by broadband coherent anti-Stokes Raman scattering microscopy.

Science.gov (United States)

Parekh, Sapun H; Lee, Young Jong; Aamer, Khaled A; Cicerone, Marcus T

2010-10-20

Raman microspectroscopy can provide the chemical contrast needed to characterize the complex intracellular environment and macromolecular organization in cells without exogenous labels. It has shown a remarkable ability to detect chemical changes underlying cell differentiation and pathology-related chemical changes in tissues but has not been widely adopted for imaging, largely due to low signal levels. Broadband coherent anti-Stokes Raman scattering (B-CARS) offers the same inherent chemical contrast as spontaneous Raman but with increased acquisition rates. To date, however, only spectrally resolved signals from the strong CH-related vibrations have been used for CARS imaging. Here, we obtain Raman spectral images of single cells with a spectral range of 600-3200 cm⁻¹, including signatures from weakly scattering modes as well as CH vibrations. We also show that B-CARS imaging can be used to measure spectral signatures of individual cells at least fivefold faster than spontaneous Raman microspectroscopy and can be used to generate maps of biochemical species in cells. This improved spectral range and signal intensity opens the door for more widespread use of vibrational spectroscopic imaging in biology and clinical diagnostics. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Complex Macromolecular Architectures by Living Cationic Polymerization

KAUST Repository

Alghamdi, Reem D.

2015-05-01

Poly (vinyl ether)-based graft polymers have been synthesized by the combination of living cationic polymerization of vinyl ethers with other living or controlled/ living polymerization techniques (anionic and ATRP). The process involves the synthesis of well-defined homopolymers (PnBVE) and co/terpolymers [PnBVE-b-PCEVE-b-PSiDEGVE (ABC type) and PSiDEGVE-b-PnBVE-b-PSiDEGVE (CAC type)] by sequential living cationic polymerization of n-butyl vinyl ether (nBVE), 2-chloroethyl vinyl ether (CEVE) and tert-butyldimethylsilyl ethylene glycol vinyl ether (SiDEGVE), using mono-functional {[n-butoxyethyl acetate (nBEA)], [1-(2-chloroethoxy) ethyl acetate (CEEA)], [1-(2-(2-(t-butyldimethylsilyloxy)ethoxy) ethoxy) ethyl acetate (SiDEGEA)]} or di-functional [1,4-cyclohexanedimethanol di(1-ethyl acetate) (cHMDEA), (VEMOA)] initiators. The living cationic polymerizations of those monomers were conducted in hexane at -20 0C using Et3Al2Cl3 (catalyst) in the presence of 1 M AcOEt base.[1] The PCEVE segments of the synthesized block terpolymers were then used to react with living macroanions (PS-DPE-Li; poly styrene diphenyl ethylene lithium) to afford graft polymers. The quantitative desilylation of PSiDEGVE segments by n-Bu4N+F- in THF at 0 °C led to graft co- and terpolymers in which the polyalcohol is the outer block. These co-/terpolymers were subsequently subjected to “grafting-from” reactions by atom transfer radical polymerization (ATRP) of styrene to afford more complex macromolecular architectures. The base assisted living cationic polymerization of vinyl ethers were also used to synthesize well-defined α-hydroxyl polyvinylether (PnBVE-OH). The resulting polymers were then modified into an ATRP macro-initiator for the synthesis of well-defined block copolymers (PnBVE-b-PS). Bifunctional PnBVE with terminal malonate groups was also synthesized and used as a precursor for more complex architectures such as H-shaped block copolymer by “grafting-from” or �

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

Energy Technology Data Exchange (ETDEWEB)

Borbulevych, Oleg Y.; Plumley, Joshua A.; Martin, Roger I. [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States); Merz, Kenneth M. Jr [University of Florida, Gainesville, Florida (United States); Westerhoff, Lance M., E-mail: lance@quantumbioinc.com [QuantumBio Inc., 2790 West College Avenue, State College, PA 16801 (United States)

2014-05-01

Semiempirical quantum-chemical X-ray macromolecular refinement using the program DivCon integrated with PHENIX is described. Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein–ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

Super-multiplex vibrational imaging

Science.gov (United States)

Wei, Lu; Chen, Zhixing; Shi, Lixue; Long, Rong; Anzalone, Andrew V.; Zhang, Luyuan; Hu, Fanghao; Yuste, Rafael; Cornish, Virginia W.; Min, Wei

2017-04-01

The ability to visualize directly a large number of distinct molecular species inside cells is increasingly essential for understanding complex systems and processes. Even though existing methods have successfully been used to explore structure-function relationships in nervous systems, to profile RNA in situ, to reveal the heterogeneity of tumour microenvironments and to study dynamic macromolecular assembly, it remains challenging to image many species with high selectivity and sensitivity under biological conditions. For instance, fluorescence microscopy faces a ‘colour barrier’, owing to the intrinsically broad (about 1,500 inverse centimetres) and featureless nature of fluorescence spectra that limits the number of resolvable colours to two to five (or seven to nine if using complicated instrumentation and analysis). Spontaneous Raman microscopy probes vibrational transitions with much narrower resonances (peak width of about 10 inverse centimetres) and so does not suffer from this problem, but weak signals make many bio-imaging applications impossible. Although surface-enhanced Raman scattering offers high sensitivity and multiplicity, it cannot be readily used to image specific molecular targets quantitatively inside live cells. Here we use stimulated Raman scattering under electronic pre-resonance conditions to image target molecules inside living cells with very high vibrational selectivity and sensitivity (down to 250 nanomolar with a time constant of 1 millisecond). We create a palette of triple-bond-conjugated near-infrared dyes that each displays a single peak in the cell-silent Raman spectral window; when combined with available fluorescent probes, this palette provides 24 resolvable colours, with the potential for further expansion. Proof-of-principle experiments on neuronal co-cultures and brain tissues reveal cell-type-dependent heterogeneities in DNA and protein metabolism under physiological and pathological conditions, underscoring the

Macromolecular composition of terrestrial and marine organic matter in sediments across the East Siberian Arctic Shelf

Directory of Open Access Journals (Sweden)

R. B. Sparkes

2016-10-01

Full Text Available Mobilisation of terrestrial organic carbon (terrOC from permafrost environments in eastern Siberia has the potential to deliver significant amounts of carbon to the Arctic Ocean, via both fluvial and coastal erosion. Eroded terrOC can be degraded during offshore transport or deposited across the wide East Siberian Arctic Shelf (ESAS. Most studies of terrOC on the ESAS have concentrated on solvent-extractable organic matter, but this represents only a small proportion of the total terrOC load. In this study we have used pyrolysis–gas chromatography–mass spectrometry (py-GCMS to study all major groups of macromolecular components of the terrOC; this is the first time that this technique has been applied to the ESAS. This has shown that there is a strong offshore trend from terrestrial phenols, aromatics and cyclopentenones to marine pyridines. There is good agreement between proportion phenols measured using py-GCMS and independent quantification of lignin phenol concentrations (r2 = 0.67, p < 0.01, n = 24. Furfurals, thought to represent carbohydrates, show no offshore trend and are likely found in both marine and terrestrial organic matter. We have also collected new radiocarbon data for bulk OC (14COC which, when coupled with previous measurements, allows us to produce the most comprehensive 14COC map of the ESAS to date. Combining the 14COC and py-GCMS data suggests that the aromatics group of compounds is likely sourced from old, aged terrOC, in contrast to the phenols group, which is likely sourced from modern woody material. We propose that an index of the relative proportions of phenols and pyridines can be used as a novel terrestrial vs. marine proxy measurement for macromolecular organic matter. Principal component analysis found that various terrestrial vs. marine proxies show different patterns across the ESAS, and it shows that multiple river–ocean transects of surface sediments transition from river-dominated to

Molecular Imaging Probes for Positron Emission Tomography and Optical Imaging of Sentinel Lymph Node and Tumor

Science.gov (United States)

Qin, Zhengtao

Molecular imaging is visualizations and measurements of in vivo biological processes at the molecular or cellular level using specific imaging probes. As an emerging technology, biocompatible macromolecular or nanoparticle based targeted imaging probes have gained increasing popularities. Those complexes consist of a carrier, an imaging reporter, and a targeting ligand. The active targeting ability dramatically increases the specificity. And the multivalency effect may further reduce the dose while providing a decent signal. In this thesis, sentinel lymph node (SLN) mapping and cancer imaging are two research topics. The focus is to develop molecular imaging probes with high specificity and sensitivity, for Positron Emission Tomography (PET) and optical imaging. The objective of this thesis is to explore dextran radiopharmaceuticals and porous silicon nanoparticles based molecular imaging agents. Dextran polymers are excellent carriers to deliver imaging reporters or therapeutic agents due to its well established safety profile and oligosaccharide conjugation chemistry. There is also a wide selection of dextran polymers with different lengths. On the other hand, Silicon nanoparticles represent another class of biodegradable materials for imaging and drug delivery. The success in fluorescence lifetime imaging and enhancements of the immune activation potency was briefly discussed. Chapter 1 begins with an overview on current molecular imaging techniques and imaging probes. Chapter 2 presents a near-IR dye conjugated probe, IRDye 800CW-tilmanocept. Fluorophore density was optimized to generate the maximum brightness. It was labeled with 68Ga and 99mTc and in vivo SLN mapping was successfully performed in different animals, such as mice, rabbits, dogs and pigs. With 99mTc labeled IRDye 800CW-tilmanocept, chapter 3 introduces a two-day imaging protocol with a hand-held imager. Chapter 4 proposed a method to dual radiolabel the IRDye 800CW-tilmanocept with both 68Ga and

Lactoferricin B inhibits bacterial macromolecular synthesis in Escherichia coli and Bacillus subtilis.

Science.gov (United States)

Ulvatne, Hilde; Samuelsen, Ørjan; Haukland, Hanne H; Krämer, Manuela; Vorland, Lars H

2004-08-15

Most antimicrobial peptides have an amphipathic, cationic structure, and an effect on the cytoplasmic membrane of susceptible bacteria has been postulated as the main mode of action. Other mechanisms have been reported, including inhibition of cellular functions by binding to DNA, RNA and proteins, and the inhibition of DNA and/or protein synthesis. Lactoferricin B (Lfcin B), a cationic peptide derived from bovine lactoferrin, exerts slow inhibitory and bactericidal activity and does not lyse susceptible bacteria, indicating a possible intracellular target. In the present study incorporation of radioactive precursors into DNA, RNA and proteins was used to demonstrate effects of Lfcin B on macromolecular synthesis in bacteria. In Escherichia coli UC 6782, Lfcin B induces an initial increase in protein and RNA synthesis and a decrease in DNA synthesis. After 10 min, the DNA-synthesis increases while protein and RNA-synthesis decreases significantly. In Bacillus subtilis, however, all synthesis of macromolecules is inhibited for at least 20 min. After 20 min RNA-synthesis increases. The results presented here show that Lfcin B at concentrations not sufficient to kill bacterial cells inhibits incorporation of radioactive precursors into macromolecules in both Gram-positive and Gram-negative bacteria.

An 'attachment kinetics-based' volume of fraction method for organic crystallization: a fluid-dynamic approach to macromolecular-crystal engineering

International Nuclear Information System (INIS)

Lappa, Marcello

2003-01-01

This analysis exhibits a strong interdisciplinary nature and deals with advances in protein (crystal) engineering models and computational methods as well as with novel results on the relative importance of 'controlling forces' in macromolecular crystal growth. The attention is focused in particular on microgravity fluid-dynamic aspects. From a numerical point of view, the growing crystal gives rise to a moving boundary problem. A 'kinetic-coefficient-based' volume tracking method is specifically and carefully developed according to the complex properties and mechanisms of macromolecular protein crystal growth taking into account the possibility of anisotropic (faceted) surface-orientation-dependent growth. The method is used to shed some light on the interplay of surface attachment kinetics and mass transport (diffusive or convective) in liquid phase and on several mechanisms still poorly understood. It is shown that the size of a growing crystal plays a 'critical role' in the relative importance of surface effects and in determining the intensity of convection. Convective effects, in turn, are found to impact growth rates, macroscopic structures of precipitates, particle size and morphology as well as the mechanisms driving growth. The paper introduces a novel computational method (that simulates the growth due to the slow addition of solute molecules to a lattice and can handle the shape of organic growing crystals under the influence of natural convection) and, at the same time, represents a quite exhaustive attempt to help organic crystal growers to discern the complex interrelations among the various parameters under one's control (that are not independent of one another) and to elaborate rational guidelines relating to physical factors that can influence the probability of success in crystallizing protein substances

MolProbity: all-atom structure validation for macromolecular crystallography

International Nuclear Information System (INIS)

Chen, Vincent B.; Arendall, W. Bryan III; Headd, Jeffrey J.; Keedy, Daniel A.; Immormino, Robert M.; Kapral, Gary J.; Murray, Laura W.; Richardson, Jane S.; Richardson, David C.

2010-01-01

MolProbity structure validation will diagnose most local errors in macromolecular crystal structures and help to guide their correction. MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors’ contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database

Design, synthesis, and evaluation of VEGFR-targeted macromolecular MRI contrast agent based on biotin–avidin-specific binding

Directory of Open Access Journals (Sweden)

Liu YJ

2017-07-01

Full Text Available Yongjun Liu,1 Xiaoyun Wu,1 Xiaohe Sun,1 Dan Wang,1 Ying Zhong,1 Dandan Jiang,1 Tianqi Wang,1 Dexin Yu,2 Na Zhang1 1School of Pharmaceutical Science, Shandong University, 2Department of Radiology Medicine, Qilu Hospital, Jinan, People’s Republic of China Abstract: Developing magnetic resonance imaging (MRI contrast agents with high relaxivity and specificity was essential to increase MRI diagnostic sensitivity and accuracy. In this study, the MRI contrast agent, vascular endothelial growth factor receptor (VEGFR-targeted poly (l-lysine (PLL-diethylene triamine pentacetate acid (DTPA-gadolinium (Gd (VEGFR-targeted PLL-DTPA-Gd, VPDG, was designed and prepared to enhance the MRI diagnosis capacity of tumor. Biotin-PLL-DTPA-Gd was synthesized first, then, VEGFR antibody was linked to biotin-PLL-DTPA-Gd using biotin–avidin reaction. In vitro cytotoxicity study results showed that VPDG had low toxicity to MCF-7 cells and HepG2 cells at experimental concentrations. In cell uptake experiments, VPDG could significantly increase the internalization rates (61.75%±5.22% in VEGFR-positive HepG2 cells compared to PLL-DTPA-Gd (PDG (25.16%±4.71%, P<0.05. In MRI studies in vitro, significantly higher T1 relaxivity (14.184 mM-1 s-1 was observed compared to Magnevist® (4.9 mM-1 s-1; P<0.01. Furthermore, in vivo MRI study results showed that VPDG could significantly enhance the tumor signal intensity and prolong the diagnostic time (from <1 h to 2.5 h. These results indicated that macromolecular VPDG was a promising MRI contrast agent and held great potential for molecular diagnosis of tumor. Keywords: MRI, contrast agent, VEGFR, biotin–avidin reaction, relaxivity

A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source

International Nuclear Information System (INIS)

Owen, Robin L.; Pearson, Arwen R.; Meents, Alke; Boehler, Pirmin; Thominet, Vincent; Schulze-Briese, Clemens

2009-01-01

Complementary techniques greatly aid the interpretation of macromolecule structures to yield functional information, and can also help to track radiation-induced changes. A new on-axis spectrometer being integrated into the macromolecular crystallography beamlines of the Swiss Light Source is presented. X-ray crystallography at third-generation synchrotron sources permits tremendous insight into the three-dimensional structure of macromolecules. Additional information is, however, often required to aid the transition from structure to function. In situ spectroscopic methods such as UV–Vis absorption and (resonance) Raman can provide this, and can also provide a means of detecting X-ray-induced changes. Here, preliminary results are introduced from an on-axis UV–Vis absorption and Raman multimode spectrometer currently being integrated into the beamline environment at X10SA of the Swiss Light Source. The continuing development of the spectrometer is also outlined

A fast band–Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors

Energy Technology Data Exchange (ETDEWEB)

Aliaga, José I., E-mail: aliaga@uji.es [Depto. Ingeniería y Ciencia de Computadores, Universitat Jaume I, Castellón (Spain); Alonso, Pedro [Departamento de Sistemas Informáticos y Computación, Universitat Politècnica de València (Spain); Badía, José M. [Depto. Ingeniería y Ciencia de Computadores, Universitat Jaume I, Castellón (Spain); Chacón, Pablo [Dept. Biological Chemical Physics, Rocasolano Physics and Chemistry Institute, CSIC, Madrid (Spain); Davidović, Davor [Rudjer Bošković Institute, Centar za Informatiku i Računarstvo – CIR, Zagreb (Croatia); López-Blanco, José R. [Dept. Biological Chemical Physics, Rocasolano Physics and Chemistry Institute, CSIC, Madrid (Spain); Quintana-Ortí, Enrique S. [Depto. Ingeniería y Ciencia de Computadores, Universitat Jaume I, Castellón (Spain)

2016-03-15

We introduce a new iterative Krylov subspace-based eigensolver for the simulation of macromolecular motions on desktop multithreaded platforms equipped with multicore processors and, possibly, a graphics accelerator (GPU). The method consists of two stages, with the original problem first reduced into a simpler band-structured form by means of a high-performance compute-intensive procedure. This is followed by a memory-intensive but low-cost Krylov iteration, which is off-loaded to be computed on the GPU by means of an efficient data-parallel kernel. The experimental results reveal the performance of the new eigensolver. Concretely, when applied to the simulation of macromolecules with a few thousands degrees of freedom and the number of eigenpairs to be computed is small to moderate, the new solver outperforms other methods implemented as part of high-performance numerical linear algebra packages for multithreaded architectures.

A fast band–Krylov eigensolver for macromolecular functional motion simulation on multicore architectures and graphics processors

International Nuclear Information System (INIS)

Aliaga, José I.; Alonso, Pedro; Badía, José M.; Chacón, Pablo; Davidović, Davor; López-Blanco, José R.; Quintana-Ortí, Enrique S.

2016-01-01

We introduce a new iterative Krylov subspace-based eigensolver for the simulation of macromolecular motions on desktop multithreaded platforms equipped with multicore processors and, possibly, a graphics accelerator (GPU). The method consists of two stages, with the original problem first reduced into a simpler band-structured form by means of a high-performance compute-intensive procedure. This is followed by a memory-intensive but low-cost Krylov iteration, which is off-loaded to be computed on the GPU by means of an efficient data-parallel kernel. The experimental results reveal the performance of the new eigensolver. Concretely, when applied to the simulation of macromolecules with a few thousands degrees of freedom and the number of eigenpairs to be computed is small to moderate, the new solver outperforms other methods implemented as part of high-performance numerical linear algebra packages for multithreaded architectures.

An ImageJ-based algorithm for a semi-automated method for microscopic image enhancement and DNA repair foci counting

International Nuclear Information System (INIS)

Klokov, D.; Suppiah, R.

2015-01-01

Proper evaluation of the health risks of low-dose ionizing radiation exposure heavily relies on the ability to accurately measure very low levels of DNA damage in cells. One of the most sensitive methods for measuring DNA damage levels is the quantification of DNA repair foci that consist of macromolecular aggregates of DNA repair proteins, such as γH2AX and 53BP1, forming around individual DNA double-strand breaks. They can be quantified using immunofluorescence microscopy and are widely used as markers of DNA double-strand breaks. However this quantification, if performed manually, may be very tedious and prone to inter-individual bias. Low-dose radiation studies are especially sensitive to this potential bias due to a very low magnitude of the effects anticipated. Therefore, we designed and validated an algorithm for the semi-automated processing of microscopic images and quantification of DNA repair foci. The algorithm uses ImageJ, a freely available image analysis software that is customizable to individual cellular properties or experimental conditions. We validated the algorithm using immunolabeled 53BP1 and γH2AX in normal human fibroblast AG01522 cells under both normal and irradiated conditions. This method is easy to learn, can be used by nontrained personnel, and can help avoiding discrepancies in inter-laboratory comparison studies examining the effects of low-dose radiation. (author)

An ImageJ-based algorithm for a semi-automated method for microscopic image enhancement and DNA repair foci counting

Energy Technology Data Exchange (ETDEWEB)

Klokov, D., E-mail: dmitry.klokov@cnl.ca [Canadian Nuclear Laboratories, Chalk River, Ontario (Canada); Suppiah, R. [Queen' s Univ., Dept. of Biomedical and Molecular Sciences, Kingston, Ontario (Canada)

2015-06-15

Proper evaluation of the health risks of low-dose ionizing radiation exposure heavily relies on the ability to accurately measure very low levels of DNA damage in cells. One of the most sensitive methods for measuring DNA damage levels is the quantification of DNA repair foci that consist of macromolecular aggregates of DNA repair proteins, such as γH2AX and 53BP1, forming around individual DNA double-strand breaks. They can be quantified using immunofluorescence microscopy and are widely used as markers of DNA double-strand breaks. However this quantification, if performed manually, may be very tedious and prone to inter-individual bias. Low-dose radiation studies are especially sensitive to this potential bias due to a very low magnitude of the effects anticipated. Therefore, we designed and validated an algorithm for the semi-automated processing of microscopic images and quantification of DNA repair foci. The algorithm uses ImageJ, a freely available image analysis software that is customizable to individual cellular properties or experimental conditions. We validated the algorithm using immunolabeled 53BP1 and γH2AX in normal human fibroblast AG01522 cells under both normal and irradiated conditions. This method is easy to learn, can be used by nontrained personnel, and can help avoiding discrepancies in inter-laboratory comparison studies examining the effects of low-dose radiation. (author)

Effects of macromolecular crowding on protein conformational changes.

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Hao Dong

2010-07-01

Full Text Available Many protein functions can be directly linked to conformational changes. Inside cells, the equilibria and transition rates between different conformations may be affected by macromolecular crowding. We have recently developed a new approach for modeling crowding effects, which enables an atomistic representation of "test" proteins. Here this approach is applied to study how crowding affects the equilibria and transition rates between open and closed conformations of seven proteins: yeast protein disulfide isomerase (yPDI, adenylate kinase (AdK, orotidine phosphate decarboxylase (ODCase, Trp repressor (TrpR, hemoglobin, DNA beta-glucosyltransferase, and Ap(4A hydrolase. For each protein, molecular dynamics simulations of the open and closed states are separately run. Representative open and closed conformations are then used to calculate the crowding-induced changes in chemical potential for the two states. The difference in chemical-potential change between the two states finally predicts the effects of crowding on the population ratio of the two states. Crowding is found to reduce the open population to various extents. In the presence of crowders with a 15 A radius and occupying 35% of volume, the open-to-closed population ratios of yPDI, AdK, ODCase and TrpR are reduced by 79%, 78%, 62% and 55%, respectively. The reductions for the remaining three proteins are 20-44%. As expected, the four proteins experiencing the stronger crowding effects are those with larger conformational changes between open and closed states (e.g., as measured by the change in radius of gyration. Larger proteins also tend to experience stronger crowding effects than smaller ones [e.g., comparing yPDI (480 residues and TrpR (98 residues]. The potentials of mean force along the open-closed reaction coordinate of apo and ligand-bound ODCase are altered by crowding, suggesting that transition rates are also affected. These quantitative results and qualitative trends will

The effect of macromolecular crowding on the electrostatic component of barnase-barstar binding: a computational, implicit solvent-based study.

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Helena W Qi

Full Text Available Macromolecular crowding within the cell can impact both protein folding and binding. Earlier models of cellular crowding focused on the excluded volume, entropic effect of crowding agents, which generally favors compact protein states. Recently, other effects of crowding have been explored, including enthalpically-related crowder-protein interactions and changes in solvation properties. In this work, we explore the effects of macromolecular crowding on the electrostatic desolvation and solvent-screened interaction components of protein-protein binding. Our simple model enables us to focus exclusively on the electrostatic effects of water depletion on protein binding due to crowding, providing us with the ability to systematically analyze and quantify these potentially intuitive effects. We use the barnase-barstar complex as a model system and randomly placed, uncharged spheres within implicit solvent to model crowding in an aqueous environment. On average, we find that the desolvation free energy penalties incurred by partners upon binding are lowered in a crowded environment and solvent-screened interactions are amplified. At a constant crowder density (fraction of total available volume occupied by crowders, this effect generally increases as the radius of model crowders decreases, but the strength and nature of this trend can depend on the water probe radius used to generate the molecular surface in the continuum model. In general, there is huge variation in desolvation penalties as a function of the random crowder positions. Results with explicit model crowders can be qualitatively similar to those using a lowered "effective" solvent dielectric to account for crowding, although the "best" effective dielectric constant will likely depend on multiple system properties. Taken together, this work systematically demonstrates, quantifies, and analyzes qualitative intuition-based insights into the effects of water depletion due to crowding on the

Endocytic Uptake, Transport and Macromolecular Interactions of Anionic PAMAM Dendrimers within Lung Tissue.

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Morris, Christopher J; Aljayyoussi, Ghaith; Mansour, Omar; Griffiths, Peter; Gumbleton, Mark

2017-12-01

Polyamidoamine (PAMAM) dendrimers are a promising class of nanocarrier with applications in both small and large molecule drug delivery. Here we report a comprehensive evaluation of the uptake and transport pathways that contribute to the lung disposition of dendrimers. Anionic PAMAM dendrimers and control dextran probes were applied to an isolated perfused rat lung (IPRL) model and lung epithelial monolayers. Endocytosis pathways were examined in primary alveolar epithelial cultures by confocal microscopy. Molecular interactions of dendrimers with protein and lipid lung fluid components were studied using small angle neutron scattering (SANS). Dendrimers were absorbed across the intact lung via a passive, size-dependent transport pathway at rates slower than dextrans of similar molecular sizes. SANS investigations of concentration-dependent PAMAM transport in the IPRL confirmed no aggregation of PAMAMs with either albumin or dipalmitoylphosphatidylcholine lung lining fluid components. Distinct endocytic compartments were identified within primary alveolar epithelial cells and their functionality in the rapid uptake of fluorescent dendrimers and model macromolecular probes was confirmed by co-localisation studies. PAMAM dendrimers display favourable lung biocompatibility but modest lung to blood absorption kinetics. These data support the investigation of dendrimer-based carriers for controlled-release drug delivery to the deep lung.

Macromolecular query language (MMQL): prototype data model and implementation.

Science.gov (United States)

Shindyalov, I N; Chang, W; Pu, C; Bourne, P E

1994-11-01

Macromolecular query language (MMQL) is an extensible interpretive language in which to pose questions concerning the experimental or derived features of the 3-D structure of biological macromolecules. MMQL portends to be intuitive with a simple syntax, so that from a user's perspective complex queries are easily written. A number of basic queries and a more complex query--determination of structures containing a five-strand Greek key motif--are presented to illustrate the strengths and weaknesses of the language. The predominant features of MMQL are a filter and pattern grammar which are combined to express a wide range of interesting biological queries. Filters permit the selection of object attributes, for example, compound name and resolution, whereas the patterns currently implemented query primary sequence, close contacts, hydrogen bonding, secondary structure, conformation and amino acid properties (volume, polarity, isoelectric point, hydrophobicity and different forms of exposure). MMQL queries are processed by MMQLlib; a C++ class library, to which new query methods and pattern types are easily added. The prototype implementation described uses PDBlib, another C(++)-based class library from representing the features of biological macromolecules at the level of detail parsable from a PDB file. Since PDBlib can represent data stored in relational and object-oriented databases, as well as PDB files, once these data are loaded they too can be queried by MMQL. Performance metrics are given for queries of PDB files for which all derived data are calculated at run time and compared to a preliminary version of OOPDB, a prototype object-oriented database with a schema based on a persistent version of PDBlib which offers more efficient data access and the potential to maintain derived information. MMQLlib, PDBlib and associated software are available via anonymous ftp from cuhhca.hhmi.columbia.edu.

Vertical Distributions of Macromolecular Composition of Particulate Organic Matter in the Water Column of the Amundsen Sea Polynya During the Summer in 2014

Science.gov (United States)

Kim, Bo Kyung; Lee, SangHoon; Ha, Sun-Yong; Jung, Jinyoung; Kim, Tae Wan; Yang, Eun Jin; Jo, Naeun; Lim, Yu Jeong; Park, Jisoo; Lee, Sang Heon

2018-02-01

Macromolecular compositions (carbohydrates, proteins, and lipids) of particulate organic matter (POM) are crucial as a basic marine food quality. To date, however, one investigation has been carried out in the Amundsen Sea. Water samples for macromolecular compositions were obtained at selected seven stations in the Amundsen Sea Polynya (AP) during the austral summer in 2014 to investigate vertical characteristics of POM. We found that a high proportion of carbohydrates (45.9 ± 11.4%) in photic layer which are significantly different from the previous result (27.9 ± 6.9%) in the AP, 2012. The plausible reason could be the carbohydrate content strongly associated with biomass of the dominant species (Phaeocystis antarctica). The calorific content of food material (FM) in the photic layer obtained in this study is similar with that of the Ross Sea as one of the highest primary productivity regions in the Southern Ocean. Total concentrations, calorific values, and calorific contents of FM were higher in the photic layer than the aphotic layer, which implies that a significant fraction of organic matter underwent degradation. A decreasing proteins/carbohydrates (PRT/CHO) ratio with depth could be caused by preferential nitrogen loss during sinking period. Since the biochemical compositions of POM mostly fixed in photic layers could play an important role in transporting organic carbon into the deep sea, further detail studies on the variations in biochemical compositions and main controlling factors are needed to understand sinking mechanisms of POM.

The Effect of Attractive Interactions and Macromolecular Crowding on Crystallins Association.

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Jiachen Wei

Full Text Available In living systems proteins are typically found in crowded environments where their effective interactions strongly depend on the surrounding medium. Yet, their association and dissociation needs to be robustly controlled in order to enable biological function. Uncontrolled protein aggregation often causes disease. For instance, cataract is caused by the clustering of lens proteins, i.e., crystallins, resulting in enhanced light scattering and impaired vision or blindness. To investigate the molecular origins of cataract formation and to design efficient treatments, a better understanding of crystallin association in macromolecular crowded environment is needed. Here we present a theoretical study of simple coarse grained colloidal models to characterize the general features of how the association equilibrium of proteins depends on the magnitude of intermolecular attraction. By comparing the analytic results to the available experimental data on the osmotic pressure in crystallin solutions, we identify the effective parameters regimes applicable to crystallins. Moreover, the combination of two models allows us to predict that the number of binding sites on crystallin is small, i.e. one to three per protein, which is different from previous estimates. We further observe that the crowding factor is sensitive to the size asymmetry between the reactants and crowding agents, the shape of the protein clusters, and to small variations of intermolecular attraction. Our work may provide general guidelines on how to steer the protein interactions in order to control their association.

A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

Science.gov (United States)

Chatake, Toshiyuki; Fujiwara, Satoru

2016-01-01

A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

Interpretation of ensembles created by multiple iterative rebuilding of macromolecular models

International Nuclear Information System (INIS)

Terwilliger, Thomas C.; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.; Adams, Paul D.; Moriarty, Nigel W.; Zwart, Peter; Read, Randy J.; Turk, Dusan; Hung, Li-Wei

2007-01-01

Heterogeneity in ensembles generated by independent model rebuilding principally reflects the limitations of the data and of the model-building process rather than the diversity of structures in the crystal. Automation of iterative model building, density modification and refinement in macromolecular crystallography has made it feasible to carry out this entire process multiple times. By using different random seeds in the process, a number of different models compatible with experimental data can be created. Sets of models were generated in this way using real data for ten protein structures from the Protein Data Bank and using synthetic data generated at various resolutions. Most of the heterogeneity among models produced in this way is in the side chains and loops on the protein surface. Possible interpretations of the variation among models created by repetitive rebuilding were investigated. Synthetic data were created in which a crystal structure was modelled as the average of a set of ‘perfect’ structures and the range of models obtained by rebuilding a single starting model was examined. The standard deviations of coordinates in models obtained by repetitive rebuilding at high resolution are small, while those obtained for the same synthetic crystal structure at low resolution are large, so that the diversity within a group of models cannot generally be a quantitative reflection of the actual structures in a crystal. Instead, the group of structures obtained by repetitive rebuilding reflects the precision of the models, and the standard deviation of coordinates of these structures is a lower bound estimate of the uncertainty in coordinates of the individual models

The macromolecular complex of ICP and falcipain-2 from Plasmodium: preparation, crystallization and preliminary X-ray diffraction analysis

International Nuclear Information System (INIS)

Hansen, Guido; Schwarzloh, Britta; Rennenberg, Annika; Heussler, Volker T.; Hilgenfeld, Rolf

2011-01-01

The macromolecular complex of ICP (inhibitor of cysteine proteases) from P. berghei and falcipain-2 from P. falciparum has been prepared and crystallized, and a diffraction data set has been collected to a resolution of 2.6 Å. The malaria parasite Plasmodium depends on the tight control of cysteine-protease activity throughout its life cycle. Recently, the characterization of a new class of potent inhibitors of cysteine proteases (ICPs) secreted by Plasmodium has been reported. Here, the recombinant production, purification and crystallization of the inhibitory C-terminal domain of ICP from P. berghei in complex with the P. falciparum haemoglobinase falcipain-2 is described. The 1:1 complex was crystallized in space group P4 3 , with unit-cell parameters a = b = 71.15, c = 120.09 Å. A complete diffraction data set was collected to a resolution of 2.6 Å

Recent Advances in the Analysis of Macromolecular Interactions Using the Matrix-Free Method of Sedimentation in the Analytical Ultracentrifuge

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Stephen E. Harding

2015-03-01

Full Text Available Sedimentation in the analytical ultracentrifuge is a matrix free solution technique with no immobilisation, columns, or membranes required and can be used to study self-association and complex or “hetero”-interactions, stoichiometry, reversibility and interaction strength of a wide variety of macromolecular types and across a very large dynamic range (dissociation constants from 10−12 M to 10−1 M. We extend an earlier review specifically highlighting advances in sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge applied to protein interactions and mucoadhesion and to review recent applications in protein self-association (tetanus toxoid, agrin, protein-like carbohydrate association (aminocelluloses, carbohydrate-protein interactions (polysaccharide-gliadin, nucleic-acid protein (G-duplexes, nucleic acid-carbohydrate (DNA-chitosan and finally carbohydrate-carbohydrate (xanthan-chitosan and a ternary polysaccharide complex interactions.

Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline.

Science.gov (United States)

Shimizu, Nobutaka; Shimizu, Tetsuya; Baba, Seiki; Hasegawa, Kazuya; Yamamoto, Masaki; Kumasaka, Takashi

2013-11-01

Measurement of the UV-visible absorption spectrum is a convenient technique for detecting chemical changes of proteins, and it is therefore useful to combine spectroscopy and diffraction studies. An online microspectrophotometer for the UV-visible region was developed and installed on the macromolecular crystallography beamline, BL38B1, at SPring-8. This spectrophotometer is equipped with a difference dispersive double monochromator, a mercury-xenon lamp as the light source, and a photomultiplier as the detector. The optical path is mostly constructed using mirrors, in order to obtain high brightness in the UV region, and the confocal optics are assembled using a cross-slit diaphragm like an iris to eliminate stray light. This system can measure optical densities up to a maximum of 4.0. To study the effect of radiation damage, preliminary measurements of glucose isomerase and thaumatin crystals were conducted in the UV region. Spectral changes dependent on X-ray dose were observed at around 280 nm, suggesting that structural changes involving Trp or Tyr residues occurred in the protein crystal. In the case of the thaumatin crystal, a broad peak around 400 nm was also generated after X-ray irradiation, suggesting the cleavage of a disulfide bond. Dose-dependent spectral changes were also observed in cryo-solutions alone, and these changes differed with the composition of the cryo-solution. These responses in the UV region are informative regarding the state of the sample; consequently, this device might be useful for X-ray crystallography.

Investigation of the biochemical state of paramagnetic ions in vivo using the magnetic field dependence of 1/T1 of tissue protons (NMRD profile): applications to contrast agents for magnetic resonance imaging

International Nuclear Information System (INIS)

Koenig, S.H.; Brown, R.D. III; Spiller, M.; Wolf, G.L.

1988-01-01

Nuclear magnetic relaxation dispersion (NMRD) profiles of protons are obtained in homogenous aqueous solutions of the paramagnetic ions, Mn 2+ and Gd 3+ and their chelate and macromolecular complexes in vitro, giving information regarding the biochemical state of these ions. Similarly NMRD profiles of protons of excised rabbit tissues containing Mn 2+ and Gd 3+ complexes are obtained. These NMRD profiles are shown to be very useful for determining the fate of potentially useful paramagnetic NMR imaging contrast agents in vivo. (U.K.)

Chiral Recognition in Molecular and Macromolecular Pairs of(S)- and (R)- 1-Cyano-2-Methylpropyl 4’((4-(8-Vinyloxyoctyloxy)Benzoyl) Biphenyl-4-Carboxylate Enantiomers

Science.gov (United States)

1994-06-30

above please provide a graphical abstract of the paper ar, return it to the Editorial Office as soon as possible. 4oeg0 o F-99S or TS A& I DTI•’ I J. u1...TCLSICAON 2.LIMITATION OF ABSTRAC •F oFPORT OF THIS PAGE OF ABSTRACT . unclass ified Graphical Abstracts for Perkin Txans. 1 Example TITLE GRAPHICAL ... ABSTRACT AUTHORS’ N AMES Template (S)-II Chiral recognition in molecular and . -- macromolecular pairs of (S)- and -- (R)-i-cyano-2-methyipropyl 4’-{[4

Macromolecular basis for homocystein-induced changes in proteoglycan structure in growth and arteriosclerosis.

Science.gov (United States)

McCully, K S

1972-01-01

Cell culture monolayers deficient in cystathionine synthetase bound more inorganic sulfate than normal cell monolayers during growth to confluence; this was correlated with the production of granular proteoglycan by the abnormal cells and fibrillar proteoglycan by normal cells. Homocysteine was demonstrated to be an active precursor of esterified sulfate, confirming our previous finding of this sulfation pathway in liver. The cell cultures deficient in cystathionine synthetase were found to assume an abnormal cellular distribution on the surface of the culture dish, resembling the distribution assumed by neoplastic cells with loss of contact inhibition; the degree of abnormality of the cellular distribution was correlated with the amount of granular proteoglycan produced by the cells and the amount of inorganic sulfate binding by the cell monolayers. Pyridoxine was found to increase the growth rate of cell cultures from a patient with pyridoxineresponsive homocystinuria and to increase the production of fibrillar proteoglycan by the cells; no effect of pyridoxine was observed in the cell cultures from a patient who failed to respond to pyridoxine therapy. The findings suggest that the change in macromolecular conformation of cellular proteoglycans from fibrillar to granular is due to increased sulfation of the carbohydrate envelope of the molecule. The significance of the findings is related to the pathogenesis of homocystinuria, the phenomenon of contact inhibition, the action of growth hormone and initiation of arteriosclerotic plaques.

Biopolymer-based material used in optical image correlation

Czech Academy of Sciences Publication Activity Database

Mysliwiec, J.; Kochalska, Anna; Miniewicz, A.

2008-01-01

Roč. 47, č. 11 (2008), s. 1902-1906 ISSN 0003-6935 Institutional research plan: CEZ:AV0Z40500505 Keywords : biopolymer * DNA * optical correlation Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.763, year: 2008

Prospects for simulating macromolecular surfactant chemistry at the ocean–atmosphere boundary

International Nuclear Information System (INIS)

Elliott, S; Burrows, S M; Liu, X; Deal, C; Long, M; Ogunro, O; Wingenter, O; Russell, L M

2014-01-01

Biogenic lipids and polymers are surveyed for their ability to adsorb at the water–air interfaces associated with bubbles, marine microlayers and particles in the overlying boundary layer. Representative ocean biogeochemical regimes are defined in order to estimate local concentrations for the major macromolecular classes. Surfactant equilibria and maximum excess are then derived based on a network of model compounds. Relative local coverage and upward mass transport follow directly, and specific chemical structures can be placed into regional rank order. Lipids and denatured protein-like polymers dominate at the selected locations. The assigned monolayer phase states are variable, whether assessed along bubbles or at the atmospheric spray droplet perimeter. Since oceanic film compositions prove to be irregular, effects on gas and organic transfer are expected to exhibit geographic dependence as well. Moreover, the core arguments extend across the sea–air interface into aerosol–cloud systems. Fundamental nascent chemical properties including mass to carbon ratio and density depend strongly on the geochemical state of source waters. High surface pressures may suppress the Kelvin effect, and marine organic hygroscopicities are almost entirely unconstrained. While bubble adsorption provides a well-known means for transporting lipidic or proteinaceous material into sea spray, the same cannot be said of polysaccharides. Carbohydrates tend to be strongly hydrophilic so that their excess carbon mass is low despite stacked polymeric geometries. Since sugars are abundant in the marine aerosol, gel-based mechanisms may be required to achieve uplift. Uncertainties distill to a global scale dearth of information regarding two dimensional kinetics and equilibria. Nonetheless simulations are recommended, to initiate the process of systems level quantification. (papers)

Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting.

Science.gov (United States)

Farley, Christopher; Burks, Geoffry; Siegert, Thomas; Juers, Douglas H

2014-08-01

In macromolecular cryocrystallography unit-cell parameters can have low reproducibility, limiting the effectiveness of combining data sets from multiple crystals and inhibiting the development of defined repeatable cooling protocols. Here, potential sources of unit-cell variation are investigated and crystal dehydration during loop-mounting is found to be an important factor. The amount of water lost by the unit cell depends on the crystal size, the loop size, the ambient relative humidity and the transfer distance to the cooling medium. To limit water loss during crystal mounting, a threefold strategy has been implemented. Firstly, crystal manipulations are performed in a humid environment similar to the humidity of the crystal-growth or soaking solution. Secondly, the looped crystal is transferred to a vial containing a small amount of the crystal soaking solution. Upon loop transfer, the vial is sealed, which allows transport of the crystal at its equilibrated humidity. Thirdly, the crystal loop is directly mounted from the vial into the cold gas stream. This strategy minimizes the exposure of the crystal to relatively low humidity ambient air, improves the reproducibility of low-temperature unit-cell parameters and offers some new approaches to crystal handling and cryoprotection.

Macromolecular scaffolding: the relationship between nanoscale architecture and function in multichromophoric arrays for organic electronics.

Science.gov (United States)

Palermo, Vincenzo; Schwartz, Erik; Finlayson, Chris E; Liscio, Andrea; Otten, Matthijs B J; Trapani, Sara; Müllen, Klaus; Beljonne, David; Friend, Richard H; Nolte, Roeland J M; Rowan, Alan E; Samorì, Paolo

2010-02-23

The optimization of the electronic properties of molecular materials based on optically or electrically active organic building blocks requires a fine-tuning of their self-assembly properties at surfaces. Such a fine-tuning can be obtained on a scale up to 10 nm by mastering principles of supramolecular chemistry, i.e., by using suitably designed molecules interacting via pre-programmed noncovalent forces. The control and fine-tuning on a greater length scale is more difficult and challenging. This Research News highlights recent results we obtained on a new class of macromolecules that possess a very rigid backbone and side chains that point away from this backbone. Each side chain contains an organic semiconducting moiety, whose position and electronic interaction with neighboring moieties are dictated by the central macromolecular scaffold. A combined experimental and theoretical approach has made it possible to unravel the physical and chemical properties of this system across multiple length scales. The (opto)electronic properties of the new functional architectures have been explored by constructing prototypes of field-effect transistors and solar cells, thereby providing direct insight into the relationship between architecture and function.

Noninvasive optical imaging of nanomedicine biodistribution

Czech Academy of Sciences Publication Activity Database

Kunjachan, S.; Gremse, F.; Theek, B.; Koczera, P.; Pola, Robert; Pechar, Michal; Etrych, Tomáš; Ulbrich, Karel; Storm, G.; Kiessling, F.; Lammers, T.

2013-01-01

Roč. 7, č. 1 (2013), s. 252-262 ISSN 1936-0851 R&D Projects: GA ČR GAP301/11/0325 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : nanomedicine * drug targeting * biodistribution Subject RIV: CD - Macromolecular Chemistry Impact factor: 12.033, year: 2013

Assessing Exhaustiveness of Stochastic Sampling for Integrative Modeling of Macromolecular Structures.

Science.gov (United States)

Viswanath, Shruthi; Chemmama, Ilan E; Cimermancic, Peter; Sali, Andrej

2017-12-05

Modeling of macromolecular structures involves structural sampling guided by a scoring function, resulting in an ensemble of good-scoring models. By necessity, the sampling is often stochastic, and must be exhaustive at a precision sufficient for accurate modeling and assessment of model uncertainty. Therefore, the very first step in analyzing the ensemble is an estimation of the highest precision at which the sampling is exhaustive. Here, we present an objective and automated method for this task. As a proxy for sampling exhaustiveness, we evaluate whether two independently and stochastically generated sets of models are sufficiently similar. The protocol includes testing 1) convergence of the model score, 2) whether model scores for the two samples were drawn from the same parent distribution, 3) whether each structural cluster includes models from each sample proportionally to its size, and 4) whether there is sufficient structural similarity between the two model samples in each cluster. The evaluation also provides the sampling precision, defined as the smallest clustering threshold that satisfies the third, most stringent test. We validate the protocol with the aid of enumerated good-scoring models for five illustrative cases of binary protein complexes. Passing the proposed four tests is necessary, but not sufficient for thorough sampling. The protocol is general in nature and can be applied to the stochastic sampling of any set of models, not just structural models. In addition, the tests can be used to stop stochastic sampling as soon as exhaustiveness at desired precision is reached, thereby improving sampling efficiency; they may also help in selecting a model representation that is sufficiently detailed to be informative, yet also sufficiently coarse for sampling to be exhaustive. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Using support vector machines to improve elemental ion identification in macromolecular crystal structures

Energy Technology Data Exchange (ETDEWEB)

Morshed, Nader [University of California, Berkeley, CA 94720 (United States); Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Echols, Nathaniel, E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); Adams, Paul D., E-mail: nechols@lbl.gov [Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States); University of California, Berkeley, CA 94720 (United States)

2015-05-01

A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

Supramolecular Assembly of Comb-like Macromolecules Induced by Chemical Reactions that Modulate the Macromolecular Interactions In Situ.

Science.gov (United States)

Xia, Hongwei; Fu, Hailin; Zhang, Yanfeng; Shih, Kuo-Chih; Ren, Yuan; Anuganti, Murali; Nieh, Mu-Ping; Cheng, Jianjun; Lin, Yao

2017-08-16

Supramolecular polymerization or assembly of proteins or large macromolecular units by a homogeneous nucleation mechanism can be quite slow and require specific solution conditions. In nature, protein assembly is often regulated by molecules that modulate the electrostatic interactions of the protein subunits for various association strengths. The key to this regulation is the coupling of the assembly process with a reversible or irreversible chemical reaction that occurs within the constituent subunits. However, realizing this complex process by the rational design of synthetic molecules or macromolecules remains a challenge. Herein, we use a synthetic polypeptide-grafted comb macromolecule to demonstrate how the in situ modulation of interactions between the charged macromolecules affects their resulting supramolecular structures. The kinetics of structural formation was studied and can be described by a generalized model of nucleated polymerization containing secondary pathways. Basic thermodynamic analysis indicated the delicate role of the electrostatic interactions between the charged subunits in the reaction-induced assembly process. This approach may be applicable for assembling a variety of ionic soft matters that are amenable to chemical reactions in situ.

Accelerated Development of Supramolecular Corneal Stromal-Like Assemblies from Corneal Fibroblasts in the Presence of Macromolecular Crowders.

Science.gov (United States)

Kumar, Pramod; Satyam, Abhigyan; Fan, Xingliang; Rochev, Yury; Rodriguez, Brian J; Gorelov, Alexander; Joshi, Lokesh; Raghunath, Michael; Pandit, Abhay; Zeugolis, Dimitrios I

2015-07-01

Tissue engineering by self-assembly uses the cells' secretome as a regeneration template and biological factory of trophic factors. Despite the several advantages that have been witnessed in preclinical and clinical settings, the major obstacle for wide acceptance of this technology remains the tardy extracellular matrix formation. In this study, we assessed the influence of macromolecular crowding (MMC)/excluding volume effect, a biophysical phenomenon that accelerates thermodynamic activities and biological processes by several orders of magnitude, in human corneal fibroblast (HCF) culture. Our data indicate that the addition of negatively charged galactose derivative (carrageenan) in HCF culture, even at 0.5% serum, increases by 12-fold tissue-specific matrix deposition, while maintaining physiological cell morphology and protein/gene expression. Gene analysis indicates that a glucose derivative (dextran sulfate) may drive corneal fibroblasts toward a myofibroblast lineage. Collectively, these results indicate that MMC may be suitable not only for clinical translation and commercialization of tissue engineering by self-assembly therapies, but also for the development of in vitro pathophysiology models.

Multifunctional gadolinium-based dendritic macromolecules as liver targeting imaging probes.

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Luo, Kui; Liu, Gang; He, Bin; Wu, Yao; Gong, Qingyong; Song, Bin; Ai, Hua; Gu, Zhongwei

2011-04-01

The quest for highly efficient and safe contrast agents has become the key factor for successful application of magnetic resonance imaging (MRI). The gadolinium (Gd) based dendritic macromolecules, with precise and tunable nanoscopic sizes, are excellent candidates as multivalent MRI probes. In this paper, a novel series of Gd-based multifunctional peptide dendritic probes (generation 2, 3, and 4) possessing highly controlled structures and single molecular weight were designed and prepared as liver MRI probes. These macromolecular Gd-ligand agents exhibited up to 3-fold increase in T(1) relaxivity comparing to Gd-DTPA complexes. No obvious in vitro cytotoxicity was observed from the measured concentrations. These dendritic probes were further functionalized with multiple galactosyl moieties and led to much higher cell uptake in vitro as demonstrated in T(1)-weighted scans. During in vivo animal studies, the probes provided better signal intensity (SI) enhancement in mouse liver, especially at 60 min post-injection, with the most efficient enhancement from the galactosyl moiety decorated third generation dendrimer. The imaging results were verified with analysis of Gd content in liver tissues. The design strategy of multifunctional Gd-ligand peptide dendritic macromolecules in this study may be used for developing other sensitive MRI probes with targeting capability. Copyright © 2011 Elsevier Ltd. All rights reserved.

FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.

Directory of Open Access Journals (Sweden)

Ziv Frankenstein

Full Text Available Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top.

Photochemical internalisation of a macromolecular protein toxin using a cell penetrating peptide-photosensitiser conjugate.

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Wang, Julie T-W; Giuntini, Francesca; Eggleston, Ian M; Bown, Stephen G; MacRobert, Alexander J

2012-01-30

Photochemical internalisation (PCI) is a site-specific technique for improving cellular delivery of macromolecular drugs. In this study, a cell penetrating peptide, containing the core HIV-1 Tat 48-57 sequence, conjugated with a porphyrin photosensitiser has been shown to be effective for PCI. Herein we report an investigation of the photophysical and photobiological properties of a water soluble bioconjugate of the cationic Tat peptide with a hydrophobic tetraphenylporphyrin derivative. The cellular uptake and localisation of the amphiphilic bioconjugate was examined in the HN5 human head and neck squamous cell carcinoma cell line. Efficient cellular uptake and localisation in endo/lysosomal vesicles was found using fluorescence detection, and light-induced, rupture of the vesicles resulting in a more diffuse intracellular fluorescence distribution was observed. Conjugation of the Tat sequence with a hydrophobic porphyrin thus enables cellular delivery of an amphiphilic photosensitiser which can then localise in endo/lysosomal membranes, as required for effective PCI treatment. PCI efficacy was tested in combination with a protein toxin, saporin, and a significant reduction in cell viability was measured versus saporin or photosensitiser treatment alone. This study demonstrates that the cell penetrating peptide-photosensitiser bioconjugation strategy is a promising and versatile approach for enhancing the therapeutic potential of bioactive agents through photochemical internalisation. Copyright © 2011 Elsevier B.V. All rights reserved.

Methyl-β-cyclodextrin quaternary ammonium chitosan conjugate: nanoparticles vs macromolecular soluble complex

Science.gov (United States)

Piras, Anna Maria; Fabiano, Angela; Chiellini, Federica; Zambito, Ylenia

2018-01-01

Purpose The present study aimed to compare a novel cyclodextrin–polymer–drug complex in solution with a dispersed supramolecular nanosize system, made of the same complex, for ability to carry dexamethasone (DEX) across excised rat intestine. Results Methyl-β-cyclodextrin-quaternary ammonium chitosan conjugate (QA-Ch-MCD) was obtained by covalent grafting through a 10-atom spacer. The conjugate was characterized by 1H-NMR, resulting in 24.4% w/w of MCD content. Phase solubility profile analysis of the QA-Ch-MCD/DEX complex yielded an association constant of 14037 M−1, vs 4428 M−1 for the plain MCD/DEX complex. Nanoparticle (NP) dispersions resulted from ionotropic gelation of the QA-Ch-MCD/DEX complex by sodium tripolyphosphate, leading to 9.9%±1.4% drug loading efficiency. The mean diameter and zeta potential for NP were 299±32 nm (polydispersity index [PI] 0.049) and 11.5±1.1 mV, respectively. Those for QA-Ch-MCD/DEX were 2.7±0.4 nm (PI 0.048) and 6.7±0.6 mV. QA-Ch-MCD/DEX solutions and corresponding NP dispersions were compared in vitro for water-assisted transport through mucus, DEX permeation through excised rat intestine, and ex vivo mucoadhesivity. The complex showed higher mucoadhesion and lower transport rate through mucus; also, it provided faster drug permeation across excised rat intestine. Conclusion Carrier adhesion to mucus surface has played a most important role in favoring transepithelial permeation. Then, within the concerns of the present study, the use of NP seems not to provide any determinant advantage over using the simpler macromolecular complex. PMID:29731628

Towards a compact and precise sample holder for macromolecular crystallography.

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Papp, Gergely; Rossi, Christopher; Janocha, Robert; Sorez, Clement; Lopez-Marrero, Marcos; Astruc, Anthony; McCarthy, Andrew; Belrhali, Hassan; Bowler, Matthew W; Cipriani, Florent

2017-10-01

Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of mini

Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data.

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Terwilliger, Thomas C; Bricogne, Gerard

2014-10-01

Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM

International Nuclear Information System (INIS)

Battye, T. Geoff G.; Kontogiannis, Luke; Johnson, Owen; Powell, Harold R.; Leslie, Andrew G. W.

2011-01-01

A new graphical user interface to the MOSFLM program has been developed to simplify the processing of macromolecular diffraction data. The interface, iMOSFLM, allows data processing via a series of clearly defined tasks and provides visual feedback on the progress of each stage. iMOSFLM is a graphical user interface to the diffraction data-integration program MOSFLM. It is designed to simplify data processing by dividing the process into a series of steps, which are normally carried out sequentially. Each step has its own display pane, allowing control over parameters that influence that step and providing graphical feedback to the user. Suitable values for integration parameters are set automatically, but additional menus provide a detailed level of control for experienced users. The image display and the interfaces to the different tasks (indexing, strategy calculation, cell refinement, integration and history) are described. The most important parameters for each step and the best way of assessing success or failure are discussed

In Vitro and In Vivo Biocompatibility Evaluation of Polyallylamine and Macromolecular Heparin Conjugates Modified Alginate Microbeads.

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Vaithilingam, Vijayaganapathy; Steinkjer, Bjørg; Ryan, Liv; Larsson, Rolf; Tuch, Bernard Edward; Oberholzer, Jose; Rokstad, Anne Mari

2017-09-15

Host reactivity to biocompatible immunoisolation devices is a major challenge for cellular therapies, and a human screening model would be of great value. We designed new types of surface modified barium alginate microspheres, and evaluated their inflammatory properties using human whole blood, and the intraperitoneal response after three weeks in Wistar rats. Microspheres were modified using proprietary polyallylamine (PAV) and coupled with macromolecular heparin conjugates (Corline Heparin Conjugate, CHC). The PAV-CHC strategy resulted in uniform and stable coatings with increased anti-clot activity and low cytotoxicity. In human whole blood, PAV coating at high dose (100 µg/ml) induced elevated complement, leukocyte CD11b and inflammatory mediators, and in Wistar rats increased fibrotic overgrowth. Coating of high dose PAV with CHC significantly reduced these responses. Low dose PAV (10 µg/ml) ± CHC and unmodified alginate microbeads showed low responses. That the human whole blood inflammatory reactions paralleled the host response shows a link between inflammatory potential and initial fibrotic response. CHC possessed anti-inflammatory activity, but failed to improve overall biocompatibility. We conclude that the human whole blood assay is an efficient first-phase screening model for inflammation, and a guiding tool in development of new generation microspheres for cell encapsulation therapy.

Macromolecular Design Strategies for Preventing Active-Material Crossover in Non-Aqueous All-Organic Redox-Flow Batteries.

Science.gov (United States)

Doris, Sean E; Ward, Ashleigh L; Baskin, Artem; Frischmann, Peter D; Gavvalapalli, Nagarjuna; Chénard, Etienne; Sevov, Christo S; Prendergast, David; Moore, Jeffrey S; Helms, Brett A

2017-02-01

Intermittent energy sources, including solar and wind, require scalable, low-cost, multi-hour energy storage solutions in order to be effectively incorporated into the grid. All-Organic non-aqueous redox-flow batteries offer a solution, but suffer from rapid capacity fade and low Coulombic efficiency due to the high permeability of redox-active species across the battery's membrane. Here we show that active-species crossover is arrested by scaling the membrane's pore size to molecular dimensions and in turn increasing the size of the active material above the membrane's pore-size exclusion limit. When oligomeric redox-active organics (RAOs) were paired with microporous polymer membranes, the rate of active-material crossover was reduced more than 9000-fold compared to traditional separators at minimal cost to ionic conductivity. This corresponds to an absolute rate of RAO crossover of less than 3 μmol cm -2  day -1 (for a 1.0 m concentration gradient), which exceeds performance targets recently set forth by the battery industry. This strategy was generalizable to both high and low-potential RAOs in a variety of non-aqueous electrolytes, highlighting the versatility of macromolecular design in implementing next-generation redox-flow batteries. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nanodiamonds as novel nanomaterials for biomedical applications: drug delivery and imaging systems.

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Kaur, Randeep; Badea, Ildiko

2013-01-01

Detonation nanodiamonds (NDs) are emerging as delivery vehicles for small chemical drugs and macromolecular biotechnology products due to their primary particle size of 4 to 5 nm, stable inert core, reactive surface, and ability to form hydrogels. Nanoprobe technology capitalizes on the intrinsic fluorescence, high refractive index, and unique Raman signal of the NDs, rendering them attractive for in vitro and in vivo imaging applications. This review provides a brief introduction of the various types of NDs and describes the development of procedures that have led to stable single-digit-sized ND dispersions, a crucial feature for drug delivery systems and nanoprobes. Various approaches used for functionalizing the surface of NDs are highlighted, along with a discussion of their biocompatibility status. The utilization of NDs to provide sustained release and improve the dispersion of hydrophobic molecules, of which chemotherapeutic drugs are the most investigated, is described. The prospects of improving the intracellular delivery of nucleic acids by using NDs as a platform are exemplified. The photoluminescent and optical scattering properties of NDs, together with their applications in cellular labeling, are also reviewed. Considering the progress that has been made in understanding the properties of NDs, they can be envisioned as highly efficient drug delivery and imaging biomaterials for use in animals and humans.

Diffusion-tensor MR imaging of gray and white matter development during normal human brain maturation.

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Mukherjee, Pratik; Miller, Jeffrey H; Shimony, Joshua S; Philip, Joseph V; Nehra, Deepika; Snyder, Abraham Z; Conturo, Thomas E; Neil, Jeffrey J; McKinstry, Robert C

2002-10-01

Conventional MR imaging findings of human brain development are thought to result from decreasing water content, increasing macromolecular concentration, and myelination. We use diffusion-tensor MR imaging to test theoretical models that incorporate hypotheses regarding how these maturational processes influence water diffusion in developing gray and white matter. Experimental data were derived from diffusion-tensor imaging of 167 participants, ages 31 gestational weeks to 11 postnatal years. An isotropic diffusion model was applied to the gray matter of the basal ganglia and thalamus. A model that assumes changes in the magnitude of diffusion while maintaining cylindrically symmetric anisotropy was applied to the white matter of the corpus callosum and internal capsule. Deviations of the diffusion tensor from the ideal model predictions, due to measurement noise, were estimated by using Monte Carlo simulations. Developing gray matter of the basal ganglia and developing white matter of the internal capsule and corpus callosum largely conformed to theory, with only small departures from model predictions in older children. However, data from the thalamus substantially diverged from predicted values, with progressively larger deviations from the model with increasing participant age. Changes in water diffusion during maturation of central gray and white matter structures can largely be explained by theoretical models incorporating simple assumptions regarding the influence of brain water content and myelination, although deviations from theory increase as the brain matures. Diffusion-tensor MR imaging is a powerful method for studying the process of brain development, with both scientific and clinical applications.

Conceptual design of novel IP-conveyor-belt Weissenberg-mode data-collection system with multi-readers for macromolecular crystallography. A comparison between Galaxy and Super Galaxy.

Science.gov (United States)

Sakabe, N; Sakabe, K; Sasaki, K

2004-01-01

Galaxy is a Weissenberg-type high-speed high-resolution and highly accurate fully automatic data-collection system using two cylindrical IP-cassettes each with a radius of 400 mm and a width of 450 mm. It was originally developed for static three-dimensional analysis using X-ray diffraction and was installed on bending-magnet beamline BL6C at the Photon Factory. It was found, however, that Galaxy was also very useful for time-resolved protein crystallography on a time scale of minutes. This has prompted us to design a new IP-conveyor-belt Weissenberg-mode data-collection system called Super Galaxy for time-resolved crystallography with improved time and crystallographic resolution over that achievable with Galaxy. Super Galaxy was designed with a half-cylinder-shaped cassette with a radius of 420 mm and a width of 690 mm. Using 1.0 A incident X-rays, these dimensions correspond to a maximum resolutions of 0.71 A in the vertical direction and 1.58 A in the horizontal. Upper and lower screens can be used to set the frame size of the recorded image. This function is useful not only to reduce the frame exchange time but also to save disk space on the data server. The use of an IP-conveyor-belt and many IP-readers make Super Galaxy well suited for time-resolved, monochromatic X-ray crystallography at a very intense third-generation SR beamline. Here, Galaxy and a conceptual design for Super Galaxy are described, and their suitability for use as data-collection systems for macromolecular time-resolved monochromatic X-ray crystallography are compared.

In vivo mapping of vascular inflammation using multimodal imaging.

Directory of Open Access Journals (Sweden)

Benjamin R Jarrett

2010-10-01

Full Text Available Plaque vulnerability to rupture has emerged as a critical correlate to risk of adverse coronary events but there is as yet no clinical method to assess plaque stability in vivo. In the search to identify biomarkers of vulnerable plaques an association has been found between macrophages and plaque stability--the density and pattern of macrophage localization in lesions is indicative of probability to rupture. In very unstable plaques, macrophages are found in high densities and concentrated in the plaque shoulders. Therefore, the ability to map macrophages in plaques could allow noninvasive assessment of plaque stability. We use a multimodality imaging approach to noninvasively map the distribution of macrophages in vivo. The use of multiple modalities allows us to combine the complementary strengths of each modality to better visualize features of interest. Our combined use of Positron Emission Tomography and Magnetic Resonance Imaging (PET/MRI allows high sensitivity PET screening to identify putative lesions in a whole body view, and high resolution MRI for detailed mapping of biomarker expression in the lesions.Macromolecular and nanoparticle contrast agents targeted to macrophages were developed and tested in three different mouse and rat models of atherosclerosis in which inflamed vascular plaques form spontaneously and/or are induced by injury. For multimodal detection, the probes were designed to contain gadolinium (T1 MRI or iron oxide (T2 MRI, and Cu-64 (PET. PET imaging was utilized to identify regions of macrophage accumulation; these regions were further probed by MRI to visualize macrophage distribution at high resolution. In both PET and MR images the probes enhanced contrast at sites of vascular inflammation, but not in normal vessel walls. MRI was able to identify discrete sites of inflammation that were blurred together at the low resolution of PET. Macrophage content in the lesions was confirmed by histology.The multimodal

Synthesis and evaluation of water-soluble poly(vinyl alcohol)-paclitaxel conjugate as a macromolecular prodrug

International Nuclear Information System (INIS)

Kakinoki, Atsufumi; Kaneo, Yoshiharu; Tanaka, Tetsuro; Hosokawa, Yoshitsugu

2008-01-01

Paclitaxel (PTX) is an antitumor agent for the treatment of various human cancers. Cremophor EL and ethanol are used to formulate PTX in commercial injection solutions, because of its poor solubility in water. However, these agents cause severe allergic reaction upon intravenous administration. The aim of this study is to synthesize water-soluble macromolecular prodrugs of PTX for enhancing the therapeutic efficacy. Poly (vinyl alcohol) (PVA, 80 kDa), water-soluble synthetic polymer, was used as a drug carrier which is safe and stable in the body. The 2'-hydroxyl group of PTX was reacted with succinic anhydride and then carboxylic group of the succinyl spacer was coupled to PVA via ethylene diamine spacer, resulting the water-soluble prodrug of poly (vinyl alcohol)-paclitaxel conjugate (PVA-SPTX). The solubility of PTX was greatly enhanced by the conjugation to PVA. The release of PTX from the conjugate was accelerated at the neutral to basic conditions in in vitro release experiment. [ 125 I]-labeled PVA-SPTX was retained in the blood circulation for several days and was gradually distributed into the tumorous tissue after intravenous injection to the tumor-bearing mice. PVA-SPTX inhibited the growth of sarcoma 180 cells subcutaneously inoculated in mice. It was suggested that the water-solubility of PTX was markedly enhanced by the conjugation to PVA, and PVA-SPTX effectively delivered PTX to the tumorous tissue due to the enhanced permeability and retention (EPR) effect. (author)

Olfactory nerve transport of macromolecular drugs to the brain. A problem in olfactory impaired patients

International Nuclear Information System (INIS)

Shiga, Hideaki; Yamamoto, Junpei; Miwa, Takaki

2012-01-01

Nasal administration of macromolecular drugs (including peptides and nanoparticles) has the potential to enable drug delivery system beyond the blood brain barrier (BBB) via olfactory nerve transport. Basic research on drug deliver systems to the brain via nasal administration has been well reported. Insulin-like growth factor-I (IGF-I) is associated with the development and growth of the central nervous system. Clinical application of IGF-I with nasal administration is intended to enable drug delivery to brain through the BBB. Uptake of IGF-I in the olfactory bulb and central nervous system increased according to the dosage of nasally administered IGF-I in normal ICR mice, however IGF-I uptake in the trigeminal nerve remained unchanged. Olfactory nerve transport is important for the delivery of nasally administered IGF-I to the brain in vivo. Because a safe olfactory nerve tracer has not been clinically available, olfactory nerve transport has not been well studied in humans. Nasal thallium-201 ( 201 Tl) administration has been safely used to assess the direct pathway to the brain via the nose in healthy volunteers with a normal olfactory threshold. 201 Tl olfactory nerve transport has recently been shown to decrease in patients with hyposmia. The olfactory nerve transport function in patients with olfactory disorders will be determined using 201 Tl olfacto-scintigraphy for the exclusion of candidates in a clinical trial to assess the usefulness of nasal administration of IGF-I. (author)

Design of cellulose ether-based macromolecular prodrugs of ciprofloxacin for extended release and enhanced bioavailability.

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Amin, Muhammad; Abbas, Nazia Shahana; Hussain, Muhammad Ajaz; Sher, Muhammad; Edgar, Kevin J

2018-07-01

The present study reveals the syntheses of hydroxypropylcellulose‑(HPC) and hydroxyethylcellulose‑(HEC) based macromolecular prodrugs (MPDs) of ciprofloxacin (CIP) using homogeneous reaction methodology. Covalently loaded drug content (DC) of each prodrug was quantified using UV-Vis spectrophotometry to determine degree of substitution (DS). HPC-ciprofloxacin (HPC-CIP) conjugates showed DS of CIP in the range 0.87-1.15 whereas HEC-ciprofloxacin (HEC-CIP) conjugates showed DS range 0.51-0.75. Transmission electron microscopy revealed that HPC-CIP conjugate 2 and HEC-CIP conjugate 6 self-assembled into nanoparticles of 150-300 and 180-250nm, respectively. Size exclusion chromatography revealed HPC-CIP conjugate 2 and HEC-CIP conjugate 6 as monodisperse systems. In vitro drug release studies indicated 15 and 43% CIP release from HPC-CIP conjugate 2 after 6h in simulated gastric and simulated intestinal fluids (SGF and SIF), respectively. HEC-CIP conjugate 6 showed 16% and 46% release after 6h in SGF and SIF, respectively. HPC-CIP conjugate 2 and HEC-CIP conjugate 6 exhibited half-lives of 10.87 and 11.71h, respectively with area under the curve values of 164 and 175hμgmL -1 , respectively, indicating enhanced bioavailability and improved pharmacokinetic profiles in animal model. Equal antibacterial activities to that of unmodified CIP confirmed their competitive efficacies. Cytotoxicity studies supported their non-toxic nature and biocompatibility. Copyright © 2018 Elsevier B.V. All rights reserved.

Making more matrix: enhancing the deposition of dermal-epidermal junction components in vitro and accelerating organotypic skin culture development, using macromolecular crowding.

Science.gov (United States)

Benny, Paula; Badowski, Cedric; Lane, E Birgitte; Raghunath, Michael

2015-01-01

Skin is one of the most accessible tissues for experimental biomedical sciences, and cultured skin cells represent one of the longest-running clinical applications of stem cell therapy. However, culture-generated skin mimetic multicellular structures are still limited in their application by the time taken to develop these constructs in vitro and by their incomplete differentiation. The development of a functional dermal-epidermal junction (DEJ) is one of the most sought after aspects of cultured skin, and one of the hardest to recreate in vitro. At the DEJ, dermal fibroblasts and epidermal keratinocytes interact to form an interlinked basement membrane of extracellular matrix (ECM), which forms as a concerted action of both keratinocytes and fibroblasts. Successful formation of this basement membrane is essential for take and stability of cultured skin autografts. We studied interactive matrix production by monocultures and cocultures of primary human keratinocytes and fibroblasts in an attempt to improve the efficiency of basement membrane production in culture using mixed macromolecular crowding (mMMC); resulting ECM were enriched with the deposition of collagens I, IV, fibronectin, and laminin 332 (laminin 5) and also in collagen VII, the anchoring fibril component. Our in vitro data point to fibroblasts, rather than keratinocytes, as the major cellular contributors of the DEJ. Not only did we find more collagen VII production and deposition by fibroblasts in comparison to keratinocytes, but also observed that decellularized fibroblast ECM stimulated the production and deposition of collagen VII by keratinocytes, over and above that of keratinocyte monocultures. In confrontation cultures, keratinocytes and fibroblasts showed spontaneous segregation and demarcation of cell boundaries by DEJ protein deposition. Finally, mMMC was used in a classical organotypic coculture protocol with keratinocytes seeded over fibroblast-containing collagen gels. Applied during

Quickly Getting the Best Data from Your Macromolecular Crystals with a New Generation of Beamline Instruments

International Nuclear Information System (INIS)

Cipriani, Florent; Felisaz, Franck; Lavault, Bernard; Brockhauser, Sandor; Ravelli, Raimond; Launer, Ludovic; Leonard, Gordon; Renier, Michel

2007-01-01

While routine Macromolecular x-ray (MX) crystallography has relied on well established techniques for some years all the synchrotrons around the world are improving the throughput of their MX beamlines. Third generation synchrotrons provide small intense beams that make data collection of 5-10 microns sized crystals possible. The EMBL/ESRF MX Group in Grenoble has developed a new generation of instruments to easily collect data on 10 μm size crystals in an automated environment. This work is part of the Grenoble automation program that enables FedEx like crystallography using fully automated data collection and web monitored experiments. Seven ESRF beamlines and the MRC BM14 ESRF/CRG beamline are currently equipped with these latest instruments. We describe here the main features of the MD2x diffractometer family and the SC3 sample changer robot. Although the SC3 was primarily designed to increase the throughput of MX beamlines, it has also been shown to be efficient in improving the quality of the data collected. Strategies in screening a large number of crystals, selecting the best, and collecting a full data set from several re-oriented micro-crystals can now be run with minimum time and effort. The MD2x and SC3 instruments are now commercialised by the company ACCEL GmbH

Optimizing Water Exchange Rates and Rotational Mobility for High-Relaxivity of a Novel Gd-DO3A Derivative Complex Conjugated to Inulin as Macromolecular Contrast Agents for MRI.

Science.gov (United States)

Granato, Luigi; Vander Elst, Luce; Henoumont, Celine; Muller, Robert N; Laurent, Sophie

2018-02-01

Thanks to the understanding of the relationships between the residence lifetime τ M of the coordinated water molecules to macrocyclic Gd-complexes and the rotational mobility τ R of these structures, and according to the theory for paramagnetic relaxation, it is now possible to design macromolecular contrast agents with enhanced relaxivities by optimizing these two parameters through ligand structural modification. We succeeded in accelerating the water exchange rate by inducing steric compression around the water binding site, and by removing the amide function from the DOTA-AA ligand [1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid mono(p-aminoanilide)] (L) previously designed. This new ligand 10[2(1-oxo-1-p-propylthioureidophenylpropyl]-1,4,7,10-tetraazacyclodecane-1,4,7-tetraacetic acid (L 1 ) was then covalently conjugated to API [O-(aminopropyl)inulin] to get the complex API-(GdL 1 )x with intent to slow down the rotational correlation time (τ R ) of the macromolecular complex. The evaluation of the longitudinal relaxivity at different magnetic fields and the study of the 17 O-NMR at variable temperature of the low-molecular-weight compound (GdL 1 ) showed a slight decrease of the τ M value (τM310 = 331 ns vs. τM310 = 450 ns for the GdL complex). Consequently to the increase of the size of the API-(GdL 1 )x complex, the rotational correlation time becomes about 360 times longer compared to the monomeric GdL 1 complex (τ R  = 33,700 ps), which results in an enhanced proton relaxivity. © 2018 Wiley-VHCA AG, Zurich, Switzerland.

Discovery of abundant cellulose microfibers encased in 250 Ma Permian halite: a macromolecular target in the search for life on other planets.

Science.gov (United States)

Griffith, Jack D; Willcox, Smaranda; Powers, Dennis W; Nelson, Roger; Baxter, Bonnie K

2008-04-01

In this study, we utilized transmission electron microscopy to examine the contents of fluid inclusions in halite (NaCl) and solid halite crystals collected 650 m below the surface from the Late Permian Salado Formation in southeastern New Mexico (USA). The halite has been isolated from contaminating groundwater since deposition approximately 250 Ma ago. We show that abundant cellulose microfibers are present in the halite and appear remarkably intact. The cellulose is in the form of 5 nm microfibers as well as composite ropes and mats, and was identified by resistance to 0.5 N NaOH treatment and susceptibility to cellulase enzyme treatment. These cellulose microfibers represent the oldest native biological macromolecules to have been directly isolated, examined biochemically, and visualized (without growth or replication) to date. This discovery points to cellulose as an ideal macromolecular target in the search for life on other planets in our Solar System.

a Study of the Concentration Dependence of Macromolecular Diffusion Using Photon Correlation Spectroscopy.

Science.gov (United States)

Marlowe, Robert Lloyd

The dynamic light scattering technique of photon correlation spectroscopy has been used to investigate the dependence of the mutual diffusion coefficient of a macromolecular system upon concentration. The first part of the research was devoted to the design and construction of a single-clipping autocorrelator based on newly-developed integrated circuits. The resulting 128 channel instrument can perform real time autocorrelation for sample time intervals >(, )10 (mu)s, and batch processed autocorrelation for intervals down to 3 (mu)s. An improved design for a newer, all-digital autocorrelator is given. Homodyne light scattering experiments were then undertaken on monodisperse solutions of polystyrene spheres. The single-mode TEM(,oo) beam of an argon-ion laser ((lamda) = 5145 (ANGSTROM)) was used as the light source; all solutions were studied at room temperature. The scattering angle was varied from 30(DEGREES) to 110(DEGREES). Excellent agreement with the manufacturer's specification for the particle size was obtained from the photon correlation studies. Finally, aqueous solutions of the globular protein ovalbumin, ranging in concentration from 18.9 to 244.3 mg/ml, were illuminated under the same conditions of temperature and wavelength as before; the homodyne scattered light was detected at a fixed scattering angle of 30(DEGREES). The single-clipped photocount autocorrelation function was analyzed using the homodyne exponential integral method of Meneely et al. The resulting diffusion coefficients showed a general linear dependence upon concentration, as predicted by the generalized Stokes-Einstein equation. However, a clear peak in the data was evident at c (TURNEQ) 100 mg/ml, which could not be explained on the basis of a non -interacting particle theory. A semi-quantitative approach based on the Debye-Huckel theory of electrostatic interactions is suggested as the probable cause for the peak's rise, and an excluded volume effect for its decline.

Phase behaviour of macromolecular liquid crystalline materials. Computational studies at the molecular level

International Nuclear Information System (INIS)

Stimson, Lorna M.

2003-01-01

Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a single dendrimer molecule in the gas phase at the atomistic level, semi-atomistic molecular dynamics of a single molecule in liquid crystalline solvents and a coarse-grained molecular dynamics study of the dendrimer in the bulk. The coarse-grained model has been developed and parameterized using the results of the atomistic and semi-atomistic work. The single molecule studies showed that the liquid crystalline dendrimer was able to change its structure by conformational changes in the flexible chains that link the mesogenic groups to the core. Structural change was seen under the application of a mean field ordering potential in the gas phase, and in the presence of liquid crystalline solvents. No liquid crystalline phases were observed for the bulk phase studies of the coarse-grained model. However, when the length of the mesogenic units was increased there was some evidence for microphase separation in these systems. (author)

Macromolecular crowding gives rise to microviscosity, anomalous diffusion and accelerated actin polymerization.

Science.gov (United States)

Rashid, Rafi; Chee, Stella Min Ling; Raghunath, Michael; Wohland, Thorsten

2015-04-30

Macromolecular crowding (MMC) has been used in various in vitro experimental systems to mimic in vivo physiology. This is because the crowded cytoplasm of cells contains many different types of solutes dissolved in an aqueous medium. MMC in the extracellular microenvironment is involved in maintaining stem cells in their undifferentiated state (niche) as well as in aiding their differentiation after they have travelled to new locations outside the niche. MMC at physiologically relevant fractional volume occupancies (FVOs) significantly enhances the adipogenic differentiation of human bone marrow-derived mesenchymal stem cells during chemically induced adipogenesis. The mechanism by which MMC produces this enhancement is not entirely known. In the context of extracellular collagen deposition, we have recently reported the importance of optimizing the FVO while minimizing the bulk viscosity. Two opposing properties will determine the net rate of a biochemical reaction: the negative effect of bulk viscosity and the positive effect of the excluded volume, the latter being expressed by the FVO. In this study we have looked more closely at the effect of viscosity on reaction rates. We have used fluorimetry to measure the rate of actin polymerization and fluorescence correlation spectroscopy (FCS) to measure diffusion of various probes in solutions containing the crowder Ficoll at physiological concentrations. Similar to its effect on collagen, Ficoll enhanced the actin polymerization rate despite increasing the bulk viscosity. Our FCS measurements reveal a relatively minor component of anomalous diffusion. In addition, our measurements do suggest that microviscosity becomes relevant in a crowded environment. We ruled out bulk viscosity as a cause of the rate enhancement by performing the actin polymerization assay in glycerol. These opposite effects of Ficoll and glycerol led us to conclude that microviscosity becomes relevant at the length scale of the reacting

Macromolecular crowding gives rise to microviscosity, anomalous diffusion and accelerated actin polymerization

Science.gov (United States)

Rashid, Rafi; Chee, Stella Min Ling; Raghunath, Michael; Wohland, Thorsten

2015-05-01

Macromolecular crowding (MMC) has been used in various in vitro experimental systems to mimic in vivo physiology. This is because the crowded cytoplasm of cells contains many different types of solutes dissolved in an aqueous medium. MMC in the extracellular microenvironment is involved in maintaining stem cells in their undifferentiated state (niche) as well as in aiding their differentiation after they have travelled to new locations outside the niche. MMC at physiologically relevant fractional volume occupancies (FVOs) significantly enhances the adipogenic differentiation of human bone marrow-derived mesenchymal stem cells during chemically induced adipogenesis. The mechanism by which MMC produces this enhancement is not entirely known. In the context of extracellular collagen deposition, we have recently reported the importance of optimizing the FVO while minimizing the bulk viscosity. Two opposing properties will determine the net rate of a biochemical reaction: the negative effect of bulk viscosity and the positive effect of the excluded volume, the latter being expressed by the FVO. In this study we have looked more closely at the effect of viscosity on reaction rates. We have used fluorimetry to measure the rate of actin polymerization and fluorescence correlation spectroscopy (FCS) to measure diffusion of various probes in solutions containing the crowder Ficoll at physiological concentrations. Similar to its effect on collagen, Ficoll enhanced the actin polymerization rate despite increasing the bulk viscosity. Our FCS measurements reveal a relatively minor component of anomalous diffusion. In addition, our measurements do suggest that microviscosity becomes relevant in a crowded environment. We ruled out bulk viscosity as a cause of the rate enhancement by performing the actin polymerization assay in glycerol. These opposite effects of Ficoll and glycerol led us to conclude that microviscosity becomes relevant at the length scale of the reacting

Characterizing EPR-mediated passive drug targeting using contrast-enhanced functional ultrasound imaging

Czech Academy of Sciences Publication Activity Database

Theek, B.; Gremse, F.; Kunjachan, S.; Fokong, S.; Pola, Robert; Pechar, Michal; Deckers, R.; Storm, G.; Ehling, J.; Kiessling, F.; Lammers, T.

2014-01-01

Roč. 182, 28 May (2014), s. 83-89 ISSN 0168-3659 R&D Projects: GA ČR GCP207/12/J030 Institutional support: RVO:61389013 Keywords : drug targeting * nanomedicine * theranostics Subject RIV: CD - Macromolecular Chemistry Impact factor: 7.705, year: 2014

Fourier Transform Infrared Imaging analysis of dental pulp inflammatory diseases.

Science.gov (United States)

Giorgini, E; Sabbatini, S; Conti, C; Rubini, C; Rocchetti, R; Fioroni, M; Memè, L; Orilisi, G

2017-05-01

Fourier Transform Infrared microspectroscopy let characterize the macromolecular composition and distribution of tissues and cells, by studying the interaction between infrared radiation and matter. Therefore, we hypothesize to exploit this analytical tool in the analysis of inflamed pulps, to detect the different biochemical features related to various degrees of inflammation. IR maps of 13 irreversible and 12 hyperplastic pulpitis, together with 10 normal pulps, were acquired, compared with histological findings and submitted to multivariate (HCA, PCA, SIMCA) and statistical (one-way ANOVA) analysis. The fit of convoluted bands let calculate meaningful band area ratios (means ± s.d., P < 0.05). The infrared imaging analysis pin-pointed higher amounts of water and lower quantities of type I collagen in all inflamed pulps. Specific vibrational markers were defined for irreversible pulpitis (Lipids/Total Biomass, PhII/Total Biomass, CH 2 /CH 3 , and Ty/AII) and hyperplastic ones (OH/Total Biomass, Collagen/Total Biomass, and CH 3 Collagen/Total Biomass). The study confirmed that FTIR microspectroscopy let discriminate tissues' biological features. The infrared imaging analysis evidenced, in inflamed pulps, alterations in tissues' structure and composition. Changes in lipid metabolism, increasing amounts of tyrosine, and the occurrence of phosphorylative processes were highlighted in irreversible pulpitis, while high amounts of water and low quantities of type I collagen were detected in hyperplastic samples. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Data publication with the structural biology data grid supports live analysis

NARCIS (Netherlands)

Meyer, Peter A.; Socias, Stephanie; Key, Jason; Ransey, Elizabeth; Tjon, Emily C.; Buschiazzo, Alejandro; Lei, Ming; Botka, Chris; Withrow, James; Neau, David; Rajashankar, Kanagalaghatta; Anderson, Karen S.; Baxter, Richard H.; Blacklow, Stephen C.; Boggon, Titus J.; Bonvin, Alexandre M J J|info:eu-repo/dai/nl/113691238; Borek, Dominika; Brett, Tom J.; Caflisch, Amedeo; Chang, Chung I.; Chazin, Walter J.; Corbett, Kevin D.; Cosgrove, Michael S.; Crosson, Sean; Dhe-Paganon, Sirano; Di Cera, Enrico; Drennan, Catherine L.; Eck, Michael J.; Eichman, Brandt F.; Fan, Qing R.; Ferré-D'Amaré, Adrian R.; Fromme, J. Christopher; Garcia, K. Christopher; Gaudet, Rachelle; Gong, Peng; Harrison, Stephen C.; Heldwein, Ekaterina E.; Jia, Zongchao; Keenan, Robert J.; Kruse, Andrew C.; Kvansakul, Marc; McLellan, Jason S.; Modis, Yorgo; Nam, Yunsun; Otwinowski, Zbyszek; Pai, Emil F.; Pereira, Pedro José Barbosa; Petosa, Carlo; Raman, C. S.; Rapoport, Tom A.; Roll-Mecak, Antonina; Rosen, Michael K.; Rudenko, Gabby; Schlessinger, Joseph; Schwartz, Thomas U.; Shamoo, Yousif; Sondermann, Holger; Tao, Yizhi J.; Tolia, Niraj H.; Tsodikov, Oleg V.; Westover, Kenneth D.; Wu, Hao; Foster, Ian; Fraser, James S.; Maia, Filipe R N C; Gonen, Tamir; Kirchhausen, Tom; Diederichs, Kay; Crosas, Mercé; Sliz, Piotr

2016-01-01

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology

Verification of novel magnetic nanoparticles as a contrast media for MRI-CT/SPECT imaging

Czech Academy of Sciences Publication Activity Database

Kostiv, Uliana; Laudová, B.; Lobaz, Volodymyr; Kučka, Jan; Franová, P.; Hrubý, Martin; Horák, Daniel; Šefc, L.

2017-01-01

Roč. 13, č. 1 (2017), s. 156 ISSN 1336-7242. [Zjazd chemikov /69./. 11.09.2017-15.09.2017, Horný Smokovec] Institutional support: RVO:61389013 Keywords : magnetic nanoparticles * diagnostics Subject RIV: CD - Macromolecular Chemistry

Measurement of pH micro-heterogeneity in natural cheese matrices by fluorescence lifetime imaging

Czech Academy of Sciences Publication Activity Database

Burdikova, Z.; Svindrych, Z.; Pala, J.; Hickey, C. D.; Wilkinson, M. G.; Pánek, Jiří; Auty, M. A. E.; Periasamy, A.; Sheehan, J. J.

2015-01-01

Roč. 6, March (2015), 183_1-183_10 ISSN 1664-302X Institutional support: RVO:61389013 Keywords : cheese matrix * C-SNARF-4 * Oregon Green Subject RIV: CD - Macromolecular Chemistry Impact factor: 4.165, year: 2015

Electron diffraction, elemental and image analysis of nanocrystals

Czech Academy of Sciences Publication Activity Database

Šlouf, Miroslav; Pavlova, Ewa; Hromádková, Jiřina; Králová, Daniela; Tyrpekl, Václav

2009-01-01

Roč. 16, 2a (2009), s. 33-34 ISSN 1211-5894. [Struktura - Colloquium of Czech and Slovak Crystallographic Association. Hluboká nad Vltavou, 22.06.2009-25.06.2009] R&D Projects: GA AV ČR KAN200520704; GA ČR GA203/07/0717 Institutional research plan: CEZ:AV0Z40500505 Keywords : TEM * electron diffraction * nanocrystals Subject RIV: CD - Macromolecular Chemistry

Innovation in PDT based on EPR effect and non-laser based irradiation

Czech Academy of Sciences Publication Activity Database

Maeda, H.; Fang, J.; Nakamura, H.; Šubr, Vladimír; Ulbrich, Karel

2015-01-01

Roč. 8, č. 2 (2015), S-08 ISSN 1882-6490. [Annual Meeting of the Japanese Society for Molecular Imaging /10./. 20.05.2015-21.05.2015, Tokyo] Institutional support: RVO:61389013 Keywords : HPMA * polymer Subject RIV: CD - Macromolecular Chemistry

Macromolecular 3D SEM reconstruction strategies: Signal to noise ratio and resolution

International Nuclear Information System (INIS)

Woodward, J.D.; Wepf, R.A.

2014-01-01

Three-dimensional scanning electron microscopy generates quantitative volumetric structural data from SEM images of macromolecules. This technique provides a quick and easy way to define the quaternary structure and handedness of protein complexes. Here, we apply a variety of preparation and imaging methods to filamentous actin in order to explore the relationship between resolution, signal-to-noise ratio, structural preservation and dataset size. This information can be used to define successful imaging strategies for different applications. - Highlights: • F-actin SEM datasets were collected using 8 different preparation/ imaging techniques. • Datasets were reconstructed by back projection and compared/analyzed • 3DSEM actin reconstructions can be produced with <100 views of the asymmetric unit. • Negatively stained macromolecules can be reconstructed by 3DSEM to ∼3 nm resolution

A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source

Science.gov (United States)

Pompidor, Guillaume; Dworkowski, Florian S. N.; Thominet, Vincent; Schulze-Briese, Clemens; Fuchs, Martin R.

2013-01-01

The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years. PMID:23955041

A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source.

Science.gov (United States)

Pompidor, Guillaume; Dworkowski, Florian S N; Thominet, Vincent; Schulze-Briese, Clemens; Fuchs, Martin R

2013-09-01

The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of the in situ on-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years.

Improving 2D and 3D Skin In Vitro Models Using Macromolecular Crowding.

Science.gov (United States)

Benny, Paula; Badowski, Cedric; Lane, E Birgitte; Raghunath, Michael

2016-08-22

The glycoprotein family of collagens represents the main structural proteins in the human body, and are key components of biomaterials used in modern tissue engineering. A technical bottleneck is the deposition of collagen in vitro, as it is notoriously slow, resulting in sub-optimal formation of connective tissue and subsequent tissue cohesion, particularly in skin models. Here, we describe a method which involves the addition of differentially-sized sucrose co-polymers to skin cultures to generate macromolecular crowding (MMC), which results in a dramatic enhancement of collagen deposition. Particularly, dermal fibroblasts deposited a significant amount of collagen I/IV/VII and fibronectin under MMC in comparison to controls. The protocol also describes a method to decellularize crowded cell layers, exposing significant amounts of extracellular matrix (ECM) which were retained on the culture surface as evidenced by immunocytochemistry. Total matrix mass and distribution pattern was studied using interference reflection microscopy. Interestingly, fibroblasts, keratinocytes and co-cultures produced cell-derived matrices (CDM) of varying composition and morphology. CDM could be used as "bio-scaffolds" for secondary cell seeding, where the current use of coatings or scaffolds, typically from xenogenic animal sources, can be avoided, thus moving towards more clinically relevant applications. In addition, this protocol describes the application of MMC during the submerged phase of a 3D-organotypic skin co-culture model which was sufficient to enhance ECM deposition in the dermo-epidermal junction (DEJ), in particular, collagen VII, the major component of anchoring fibrils. Electron microscopy confirmed the presence of anchoring fibrils in cultures developed with MMC, as compared to controls. This is significant as anchoring fibrils tether the dermis to the epidermis, hence, having a pre-formed mature DEJ may benefit skin graft recipients in terms of graft stability and

Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

Energy Technology Data Exchange (ETDEWEB)

Laurence, Ted Alfred [Univ. of California, Berkeley, CA (United States)

2002-01-01

Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

Photon-counting single-molecule spectroscopy for studying conformational dynamics and macromolecular interactions

International Nuclear Information System (INIS)

Laurence, Ted Alfred

2002-01-01

Single-molecule methods have the potential to provide information about conformational dynamics and molecular interactions that cannot be obtained by other methods. Removal of ensemble averaging provides several benefits, including the ability to detect heterogeneous populations and the ability to observe asynchronous reactions. Single-molecule diffusion methodologies using fluorescence resonance energy transfer (FRET) are developed to monitor conformational dynamics while minimizing perturbations introduced by interactions between molecules and surfaces. These methods are used to perform studies of the folding of Chymotrypsin Inhibitor 2, a small, single-domain protein, and of single-stranded DNA (ssDNA) homopolymers. Confocal microscopy is used in combination with sensitive detectors to detect bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract fluorescence resonance energy transfer (FRET) efficiency. Advances in data acquisition and analysis techniques that are providing a more complete picture of the accessible molecular information are discussed. Photon Arrival-time Interval Distribution (PAID) analysis is a new method for monitoring macromolecular interactions by fluorescence detection with simultaneous determination of coincidence, brightness, diffusion time, and occupancy (proportional to concentration) of fluorescently-labeled molecules undergoing diffusion in a confocal detection volume. This method is based on recording the time of arrival of all detected photons, and then plotting the two-dimensional histogram of photon pairs, where one axis is the time interval between each pair of photons 1 and 2, and the second axis is the number of other photons detected in the time interval between photons 1 and 2. PAID is related to Fluorescence Correlation Spectroscopy (FCS) by a collapse of this histogram onto the time interval axis. PAID extends auto- and cross-correlation FCS

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging.

Science.gov (United States)

Warren, Anna J; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R; Horrell, Sam; McAuley, Katherine E; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-07-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

Adaptive optics improves multiphoton super-resolution imaging

Science.gov (United States)

Zheng, Wei; Wu, Yicong; Winter, Peter; Shroff, Hari

2018-02-01

Three dimensional (3D) fluorescence microscopy has been essential for biological studies. It allows interrogation of structure and function at spatial scales spanning the macromolecular, cellular, and tissue levels. Critical factors to consider in 3D microscopy include spatial resolution, signal-to-noise (SNR), signal-to-background (SBR), and temporal resolution. Maintaining high quality imaging becomes progressively more difficult at increasing depth (where optical aberrations, induced by inhomogeneities of refractive index in the sample, degrade resolution and SNR), and in thick or densely labeled samples (where out-of-focus background can swamp the valuable, in-focus-signal from each plane). In this report, we introduce our new instrumentation to address these problems. A multiphoton structured illumination microscope was simply modified to integrate an adpative optics system for optical aberrations correction. Firstly, the optical aberrations are determined using direct wavefront sensing with a nonlinear guide star and subsequently corrected using a deformable mirror, restoring super-resolution information. We demonstrate the flexibility of our adaptive optics approach on a variety of semi-transparent samples, including bead phantoms, cultured cells in collagen gels and biological tissues. The performance of our super-resolution microscope is improved in all of these samples, as peak intensity is increased (up to 40-fold) and resolution recovered (up to 176+/-10 nm laterally and 729+/-39 nm axially) at depths up to 250 μm from the coverslip surface.

Nanodiamonds as novel nanomaterials for biomedical applications: drug delivery and imaging systems

Directory of Open Access Journals (Sweden)

Kaur R

2013-01-01

Full Text Available Randeep Kaur, Ildiko BadeaDrug Design and Discovery Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, Saskatchewan, CanadaAbstract: Detonation nanodiamonds (NDs are emerging as delivery vehicles for small chemical drugs and macromolecular biotechnology products due to their primary particle size of 4 to 5 nm, stable inert core, reactive surface, and ability to form hydrogels. Nanoprobe technology capitalizes on the intrinsic fluorescence, high refractive index, and unique Raman signal of the NDs, rendering them attractive for in vitro and in vivo imaging applications. This review provides a brief introduction of the various types of NDs and describes the development of procedures that have led to stable single-digit-sized ND dispersions, a crucial feature for drug delivery systems and nanoprobes. Various approaches used for functionalizing the surface of NDs are highlighted, along with a discussion of their biocompatibility status. The utilization of NDs to provide sustained release and improve the dispersion of hydrophobic molecules, of which chemotherapeutic drugs are the most investigated, is described. The prospects of improving the intracellular delivery of nucleic acids by using NDs as a platform are exemplified. The photoluminescent and optical scattering properties of NDs, together with their applications in cellular labeling, are also reviewed. Considering the progress that has been made in understanding the properties of NDs, they can be envisioned as highly efficient drug delivery and imaging biomaterials for use in animals and humans.Keywords: dispersion, surface functionalization, toxicity, carriers, fluorescence, light scattering

iDC: A comprehensive toolkit for the analysis of residual dipolar couplings for macromolecular structure determination

International Nuclear Information System (INIS)

Wei Yufeng; Werner, Milton H.

2006-01-01

Measurement of residual dipolar couplings (RDCs) has become an important method for the determination and validation of protein or nucleic acid structures by NMRf spectroscopy. A number of toolkits have been devised for the handling of RDC data which run in the Linux/Unix operating environment and require specifically formatted input files. The outputs from these programs, while informative, require format modification prior to the incorporation of this data into commonly used personal computer programs for manuscript preparation. To bridge the gap between analysis and publication, an easy-to-use, comprehensive toolkit for RDC analysis has been created, iDC. iDC is written for the WaveMetrics Igor Pro mathematics program, a widely used graphing and data analysis software program that runs on both Windows PC and Mac OS X computers. Experimental RDC values can be loaded into iDC using simple data formats accessible to Igor's tabular data function. The program can perform most useful RDC analyses, including alignment tensor estimation from a histogram of RDC occurrence versus values and order tensor analysis by singular value decomposition (SVD). SVD analysis can be performed on an entire structure family at once, a feature missing in other applications of this kind. iDC can also import from and export to several different commonly used programs for the analysis of RDC data (DC, PALES, REDCAT) and can prepare formatted files for RDC-based refinement of macromolecular structures using XPLOR-NIH, CNS and ARIA. The graphical user interface provides an easy-to-use I/O for data, structures and formatted outputs

Innovative High-Throughput SAXS Methodologies Based on Photonic Lab-on-a-Chip Sensors: Application to Macromolecular Studies.

Science.gov (United States)

Rodríguez-Ruiz, Isaac; Radajewski, Dimitri; Charton, Sophie; Phamvan, Nhat; Brennich, Martha; Pernot, Petra; Bonneté, Françoise; Teychené, Sébastien

2017-06-02

The relevance of coupling droplet-based Photonic Lab-on-a-Chip (PhLoC) platforms and Small-Angle X-Ray Scattering (SAXS) technique is here highlighted for the performance of high throughput investigations, related to the study of protein macromolecular interactions. With this configuration, minute amounts of sample are required to obtain reliable statistical data. The PhLoC platforms presented in this work are designed to allow and control an effective mixing of precise amounts of proteins, crystallization reagents and buffer in nanoliter volumes, and the subsequent generation of nanodroplets by means of a two-phase flow. Spectrophotometric sensing permits a fine control on droplet generation frequency and stability as well as on concentration conditions, and finally the droplet flow is synchronized to perform synchrotron radiation SAXS measurements in individual droplets (each one acting as an isolated microreactor) to probe protein interactions. With this configuration, droplet physic-chemical conditions can be reproducibly and finely tuned, and monitored without cross-contamination, allowing for the screening of a substantial number of saturation conditions with a small amount of biological material. The setup was tested and validated using lysozyme as a model of study. By means of SAXS experiments, the proteins gyration radius and structure envelope were calculated as a function of protein concentration. The obtained values were found to be in good agreement with previously reported data, but with a dramatic reduction of sample volume requirements compared to studies reported in the literature.

Object detection by correlation coefficients using azimuthally averaged reference projections.

Science.gov (United States)

Nicholson, William V

2004-11-01

A method of computing correlation coefficients for object detection that takes advantage of using azimuthally averaged reference projections is described and compared with two alternative methods-computing a cross-correlation function or a local correlation coefficient versus the azimuthally averaged reference projections. Two examples of an application from structural biology involving the detection of projection views of biological macromolecules in electron micrographs are discussed. It is found that a novel approach to computing a local correlation coefficient versus azimuthally averaged reference projections, using a rotational correlation coefficient, outperforms using a cross-correlation function and a local correlation coefficient in object detection from simulated images with a range of levels of simulated additive noise. The three approaches perform similarly in detecting macromolecular views in electron microscope images of a globular macrolecular complex (the ribosome). The rotational correlation coefficient outperforms the other methods in detection of keyhole limpet hemocyanin macromolecular views in electron micrographs.

Effects of nicotine on cellular proliferation, cell cycle phase distribution, and macromolecular synthesis in human promyelocytic HL-60 leukaemia cells

International Nuclear Information System (INIS)

Konno, S.; Wu, J.M.; Chiao, J.W.

1986-01-01

Addition of nicotine causes a dose- and time-dependent inhibition of cell growth in the human promyelocytic HL-60 leukemia cells, with 4 mM nicotine resulting in a 50% inhibition of cellular proliferation after 48-50h. Accompanying the anticellular effect of nicotine is a significant change in the cell cycle distribution of HL-60 cells. For example, treatment with 4 mM nicotine for 20h causes an increase in the proportion of G1-phase cells (from 49% to 57%) and a significant decrease in the proportion of S-phase cells (from 41% to 32%). These results suggest that nicotine causes partial cell arrest in the G-1 phase which may in part account for its effects on cell growth. To determine whether nicotine changes the cellular uptake/transport to macromolecular precursors, HL-60 cells were treated with 216 mM nicotine for 30h, at the end of which time cells were labelled with ( 3 H)thymidine, ( 3 H)uridine, ( 14 C)lysine and( 35 S)methionine, the trichloroacetic acid soluble and insoluble radioactivities from each of the labelling conditions were determined. These studies show that nicotine mainly affects the ''de novo synthesis'' of proteins. (author)

Similar Endothelial Glycocalyx Structures in Microvessels from a Range of Mammalian Tissues

DEFF Research Database (Denmark)

Arkill, K P; Knupp, C; Michel, C C

2011-01-01

, with a center-to-center fiber spacing of 20 nm and a fiber width of 12 nm, which might explain the observed macromolecular filtering properties. In this study, we used electron micrographs of tissues prepared using perfusion fixation and tannic acid treatment. The digitized images were analyzed using...

Statistical Methods for Single-Particle Electron Cryomicroscopy

DEFF Research Database (Denmark)

Jensen, Katrine Hommelhoff

Electron cryomicroscopy (cryo-EM) is a form of transmission electron microscopy, aimed at reconstructing the 3D structure of a macromolecular complex from a large set of 2D projection images, as they exhibit a very low signal-to-noise ratio (SNR). In the single-particle reconstruction (SPR) probl...

Photodynamic therapy and imaging based on tumor-targeted nanoprobe, polymer-conjugated zinc protoporphyrin

Czech Academy of Sciences Publication Activity Database

Fang, J.; Liao, L.; Yin, H.; Nakamura, H.; Šubr, Vladimír; Ulbrich, Karel; Maeda, H.

2015-01-01

Roč. 2015, č. 4 (2015), s. 1-13 ISSN 2056-5623 R&D Projects: GA ČR(CZ) GAP301/12/1254 Grant - others:AV ČR(CZ) AP0802 Program:Akademická prémie - Praemium Academiae Institutional support: RVO:61389013 Keywords : fluorescent nanoprobe * photodynamic therapy * theranostic nanomedicine Subject RIV: CD - Macromolecular Chemistry

Invited Review Article: Methods for imaging weak-phase objects in electron microscopy

International Nuclear Information System (INIS)

Glaeser, Robert M.

2013-01-01

Contrast has traditionally been produced in electron-microscopy of weak phase objects by simply defocusing the objective lens. There now is renewed interest, however, in using devices that apply a uniform quarter-wave phase shift to the scattered electrons relative to the unscattered beam, or that generate in-focus image contrast in some other way. Renewed activity in making an electron-optical equivalent of the familiar “phase-contrast” light microscope is based in part on the improved possibilities that are now available for device microfabrication. There is also a better understanding that it is important to take full advantage of contrast that can be had at low spatial frequency when imaging large, macromolecular objects. In addition, a number of conceptually new phase-plate designs have been proposed, thus increasing the number of options that are available for development. The advantages, disadvantages, and current status of each of these options is now compared and contrasted. Experimental results that are, indeed, superior to what can be accomplished with defocus-based phase contrast have been obtained recently with two different designs of phase-contrast aperture. Nevertheless, extensive work also has shown that fabrication of such devices is inconsistent, and that their working lifetime is short. The main limitation, in fact, appears to be electrostatic charging of any device that is placed into the electron diffraction pattern. The challenge in fabricating phase plates that are practical to use for routine work in electron microscopy thus may be more in the area of materials science than in the area of electron optics

Biological physics and synchrotron radiation

International Nuclear Information System (INIS)

Filhol, J.M.; Chavanne, J.; Weckert, E.

2001-01-01

This conference deals with the applications of synchrotron radiation to current problems in biology and medicine. Seven sessions take stock on the subject: sources and detectors; inelastic scattering and dynamics; muscle diffraction; reaction mechanisms; macromolecular assemblies; medical applications; imaging and spectroscopy. The document presents the papers abstracts. (A.L.B.)

Biological physics and synchrotron radiation

Energy Technology Data Exchange (ETDEWEB)

Filhol, J M; Chavanne, J [European Synchrotron Radiation Facility, 38 - Grenoble (France); Weckert, E [Hasylab at Desy, Hamburg (Germany); and others

2001-07-01

This conference deals with the applications of synchrotron radiation to current problems in biology and medicine. Seven sessions take stock on the subject: sources and detectors; inelastic scattering and dynamics; muscle diffraction; reaction mechanisms; macromolecular assemblies; medical applications; imaging and spectroscopy. The document presents the papers abstracts. (A.L.B.)

Characterization of macromolecular baseline of human brain using metabolite cycled semi-LASER at 9.4T.

Science.gov (United States)

Giapitzakis, Ioannis-Angelos; Avdievich, Nikolai; Henning, Anke

2018-08-01

Macromolecular resonances (MM) arise mainly from cytosolic proteins and overlap with metabolites, influencing metabolite quantification. Macromolecules can serve as valuable biomarkers for diseases and pathologies. The objectives of this study were to characterize MM at 9.4T in the human brain (occipital and left parietal lobe) and to describe the RF coil setup used for MM acquisition in the two regions. An adiabatic inversion pulse was optimised for metabolite nulling at 9.4T using double inversion recovery and was combined for the first time with metabolite cycled (MC) semi-LASER and appropriate coil configuration. MM spectra (seven volunteers) from two brain locations were averaged and smoothed creating MM templates, which were then parametrized using simulated Voigt-shaped lines within LCModel. Quantification was performed on individual data sets, including corrections for different tissue composition and the T 1 and T 2 relaxation of water. Our coil configuration method resulted in efficient B1+ (>30 T/√kW) for both brain regions. The 15 MM components were detected and quantified in MM baselines of the two brain areas. No significant differences in concentration levels of MM between different regions were found. Two new MM peaks were reported (M7 & M8). Double inversion, which was combined with MC semi-LASER, enabled the acquisition of high spectral resolution MM spectra for both brain regions at 9.4T. The 15 MM components were detected and quantified. Two new MM peaks were reported for the first time (M7 & M8) and preliminarily assigned to β-methylene protons of aspartyl-groups. Magn Reson Med 80:462-473, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.

Macromolecular 'size' and 'hardness' drives structure in solvent-swollen blends of linear, cyclic, and star polymers.

Science.gov (United States)

Gartner, Thomas E; Jayaraman, Arthi

2018-01-17

In this paper, we apply molecular simulation and liquid state theory to uncover the structure and thermodynamics of homopolymer blends of the same chemistry and varying chain architecture in the presence of explicit solvent species. We use hybrid Monte Carlo (MC)/molecular dynamics (MD) simulations in the Gibbs ensemble to study the swelling of ∼12 000 g mol -1 linear, cyclic, and 4-arm star polystyrene chains in toluene. Our simulations show that the macroscopic swelling response is indistinguishable between the various architectures and matches published experimental data for the solvent annealing of linear polystyrene by toluene vapor. We then use standard MD simulations in the NPT ensemble along with polymer reference interaction site model (PRISM) theory to calculate effective polymer-solvent and polymer-polymer Flory-Huggins interaction parameters (χ eff ) in these systems. As seen in the macroscopic swelling results, there are no significant differences in the polymer-solvent and polymer-polymer χ eff between the various architectures. Despite similar macroscopic swelling and effective interaction parameters between various architectures, the pair correlation function between chain centers-of-mass indicates stronger correlations between cyclic or star chains in the linear-cyclic blends and linear-star blends, compared to linear chain-linear chain correlations. Furthermore, we note striking similarities in the chain-level correlations and the radius of gyration of cyclic and 4-arm star architectures of identical molecular weight. Our results indicate that the cyclic and star chains are 'smaller' and 'harder' than their linear counterparts, and through comparison with MD simulations of blends of soft spheres with varying hardness and size we suggest that these macromolecular characteristics are the source of the stronger cyclic-cyclic and star-star correlations.

Limiting factors in single particle cryo electron tomography

Directory of Open Access Journals (Sweden)

Mikhail Kudryashev

2012-07-01

Full Text Available Modern methods of cryo electron microscopy and tomography allow visualization of protein nanomachines in their native state at the nanometer scale. Image processing methods including sub-volume averaging applied to repeating macromolecular elements within tomograms allow exploring their structures within the native context of the cell, avoiding the need for protein isolation and purification. Today, many different data acquisition protocols and software solutions are available to researchers to determine average structures of macromolecular complexes and potentially to classify structural intermediates. Here, we list the density maps reported in the literature, and analyze each structure for the chosen instrumental settings, sample conditions, main processing steps, and obtained resolution. We present conclusions that identify factors currently limiting the resolution gained by this approach.

Magnetic resonance imaging for monitoring the effects of thalidomide on experimental human breast cancers

International Nuclear Information System (INIS)

Cyran, Clemens C.; Sennino, Barbara; McDonald, Donald M.; Chaopathomkul, Bundit; Fu, Yanjun; Rogut, Victor S.; Shames, David M.; Wendland, Michael F.; Brasch, Robert C.

2009-01-01

Thalidomide, which inhibits angiogenesis in certain tumor types, reduced extravasation of a macromolecular contrast medium (MMCM) in a human breast cancer model as assayed by MMCM-enhanced dynamic magnetic resonance imaging (MRI) and fluorescence microscopy in the same tumors. After a 1-week, three-dose course of thalidomide, the mean MRI-assayed endothelial transfer coefficient, K PS , decreased significantly (p 3 . Correspondingly, microscopic measurements of extravasated MMCM, expressed as fractional area of streptavidin staining, were significantly (p PS values correlated significantly (r 2 =0.55, p<0.05) with microscopic measures of MMCM extravasation. However, no significant differences were observed between saline- and thalidomide-treated tumors with respect to rate of growth, vascular richness, or amount of VEGF-containing cells. Because of its sensitivity to the detection of changes in vascular leakage in tumors, this MMCM-enhanced MRI assay could prove useful for monitoring the effects of thalidomide on an individual patient basis. The significant correlation between MRI and fluorescence microscopic measures of MMCM extravasation supports the utility of the non-invasive MRI approach for assessing the action of thalidomide on tumor blood vessels. (orig.)

Integrating macromolecular X-ray diffraction data with the graphical user interface iMosflm.

Science.gov (United States)

Powell, Harold R; Battye, T Geoff G; Kontogiannis, Luke; Johnson, Owen; Leslie, Andrew G W

2017-07-01

X-ray crystallography is the predominant source of structural information for biological macromolecules, providing fundamental insights into biological function. The availability of robust and user-friendly software to process the collected X-ray diffraction images makes the technique accessible to a wider range of scientists. iMosflm/MOSFLM (http://www.mrc-lmb.cam.ac.uk/harry/imosflm) is a software package designed to achieve this goal. The graphical user interface (GUI) version of MOSFLM (called iMosflm) is designed to guide inexperienced users through the steps of data integration, while retaining powerful features for more experienced users. Images from almost all commercially available X-ray detectors can be handled using this software. Although the program uses only 2D profile fitting, it can readily integrate data collected in the 'fine phi-slicing' mode (in which the rotation angle per image is less than the crystal mosaic spread by a factor of at least 2), which is commonly used with modern very fast readout detectors. The GUI provides real-time feedback on the success of the indexing step and the progress of data processing. This feedback includes the ability to monitor detector and crystal parameter refinement and to display the average spot shape in different regions of the detector. Data scaling and merging tasks can be initiated directly from the interface. Using this protocol, a data set of 360 images with ∼2,000 reflections per image can be processed in ∼4 min.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Science.gov (United States)

Borbulevych, Oleg Y; Plumley, Joshua A; Martin, Roger I; Merz, Kenneth M; Westerhoff, Lance M

2014-05-01

Macromolecular crystallographic refinement relies on sometimes dubious stereochemical restraints and rudimentary energy functionals to ensure the correct geometry of the model of the macromolecule and any covalently bound ligand(s). The ligand stereochemical restraint file (CIF) requires a priori understanding of the ligand geometry within the active site, and creation of the CIF is often an error-prone process owing to the great variety of potential ligand chemistry and structure. Stereochemical restraints have been replaced with more robust functionals through the integration of the linear-scaling, semiempirical quantum-mechanics (SE-QM) program DivCon with the PHENIX X-ray refinement engine. The PHENIX/DivCon package has been thoroughly validated on a population of 50 protein-ligand Protein Data Bank (PDB) structures with a range of resolutions and chemistry. The PDB structures used for the validation were originally refined utilizing various refinement packages and were published within the past five years. PHENIX/DivCon does not utilize CIF(s), link restraints and other parameters for refinement and hence it does not make as many a priori assumptions about the model. Across the entire population, the method results in reasonable ligand geometries and low ligand strains, even when the original refinement exhibited difficulties, indicating that PHENIX/DivCon is applicable to both single-structure and high-throughput crystallography.

Macromolecular Competition Titration Method: Accessing Thermodynamics of the Unmodified Macromolecule–Ligand Interactions Through Spectroscopic Titrations of Fluorescent Analogs

Science.gov (United States)

Bujalowski, Wlodzimierz; Jezewska, Maria J.

2011-01-01

Analysis of thermodynamically rigorous binding isotherms provides fundamental information about the energetics of the ligand–macromolecule interactions and often an invaluable insight about the structure of the formed complexes. The Macromolecular Competition Titration (MCT) method enables one to quantitatively obtain interaction parameters of protein–nucleic acid interactions, which may not be available by other methods, particularly for the unmodified long polymer lattices and specific nucleic acid substrates, if the binding is not accompanied by adequate spectroscopic signal changes. The method can be applied using different fluorescent nucleic acids or fluorophores, although the etheno-derivatives of nucleic acid are especially suitable as they are relatively easy to prepare, have significant blue fluorescence, their excitation band lies far from the protein absorption spectrum, and the modification eliminates the possibility of base pairing with other nucleic acids. The MCT method is not limited to the specific size of the reference nucleic acid. Particularly, a simple analysis of the competition titration experiments is described in which the fluorescent, short fragment of nucleic acid, spanning the exact site-size of the protein–nucleic acid complex, and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. Although the MCT method is predominantly discussed as applied to studying protein–nucleic acid interactions, it can generally be applied to any ligand–macromolecule system by monitoring the association reaction using the spectroscopic signal originating from the reference macromolecule in the presence of the competing macromolecule, whose interaction parameters with the ligand are to be determined. PMID:21195223

Orphan receptor GPR179 forms macromolecular complexes with components of metabotropic signaling cascade in retina ON-bipolar neurons.

Science.gov (United States)

Orlandi, Cesare; Cao, Yan; Martemyanov, Kirill A

2013-10-29

In the mammalian retina, synaptic transmission between light-excited rod photoreceptors and downstream ON-bipolar neurons is indispensable for dim vision, and disruption of this process leads to congenital stationary night blindness in human patients. The ON-bipolar neurons use the metabotropic signaling cascade, initiated by the mGluR6 receptor, to generate depolarizing responses to light-induced changes in neurotransmitter glutamate release from the photoreceptor axonal terminals. Evidence for the identity of the components involved in transducing these signals is growing rapidly. Recently, the orphan receptor, GPR179, a member of the G protein-coupled receptor (GPCR) superfamily, has been shown to be indispensable for the synaptic responses of ON-bipolar cells. In our study, we investigated the interaction of GPR179 with principle components of the signal transduction cascade. We used immunoprecipitation and proximity ligation assays in transfected cells and native retinas to characterize the protein-protein interactions involving GPR179. The influence of cascade components on GPR179 localization was examined through immunohistochemical staining of the retinas from genetic mouse models. We demonstrated that, in mouse retinas, GPR179 forms physical complexes with the main components of the metabotropic cascade, recruiting mGluR6, TRPM1, and the RGS proteins. Elimination of mGluR6 or RGS proteins, but not TRPM1, detrimentally affects postsynaptic targeting or GPR179 expression. These observations suggest that the mGluR6 signaling cascade is scaffolded as a macromolecular complex in which the interactions between the components ensure the optimal spatiotemporal characteristics of signal transduction.

Macromolecular competition titration method accessing thermodynamics of the unmodified macromolecule-ligand interactions through spectroscopic titrations of fluorescent analogs.

Science.gov (United States)

Bujalowski, Wlodzimierz; Jezewska, Maria J

2011-01-01

Analysis of thermodynamically rigorous binding isotherms provides fundamental information about the energetics of the ligand-macromolecule interactions and often an invaluable insight about the structure of the formed complexes. The Macromolecular Competition Titration (MCT) method enables one to quantitatively obtain interaction parameters of protein-nucleic acid interactions, which may not be available by other methods, particularly for the unmodified long polymer lattices and specific nucleic acid substrates, if the binding is not accompanied by adequate spectroscopic signal changes. The method can be applied using different fluorescent nucleic acids or fluorophores, although the etheno-derivatives of nucleic acid are especially suitable as they are relatively easy to prepare, have significant blue fluorescence, their excitation band lies far from the protein absorption spectrum, and the modification eliminates the possibility of base pairing with other nucleic acids. The MCT method is not limited to the specific size of the reference nucleic acid. Particularly, a simple analysis of the competition titration experiments is described in which the fluorescent, short fragment of nucleic acid, spanning the exact site-size of the protein-nucleic acid complex, and binding with only a 1:1 stoichiometry to the protein, is used as a reference macromolecule. Although the MCT method is predominantly discussed as applied to studying protein-nucleic acid interactions, it can generally be applied to any ligand-macromolecule system by monitoring the association reaction using the spectroscopic signal originating from the reference macromolecule in the presence of the competing macromolecule, whose interaction parameters with the ligand are to be determined. Copyright © 2011 Elsevier Inc. All rights reserved.

New insight on aliphatic linkages in the macromolecular organic fraction of Orgueil and Murchison meteorites through ruthenium tetroxide oxidation

Science.gov (United States)

Remusat, Laurent; Derenne, Sylvie; Robert, François

2005-09-01

Ruthenium tetroxide oxidation was used to examine the macromolecular insoluble organic matter (IOM) from the Orgueil and Murchison meteorites and especially to characterize the aliphatic linkages. Already applied to various terrestrial samples, ruthenium tetroxide is a selective oxidant which destroys aromatic units, converting them into CO 2, and yields aliphatic and aromatic acids. In our experiment on chondritic IOM, it produces mainly short aliphatic diacids and polycarboxylic aromatic acids. Some short hydroxyacids are also detected. Aliphatic diacids are interpreted as aliphatic bridges between aromatic units in the chemical structure, and polycarboxylic aromatic acids are the result of the fusion of polyaromatic units. The product distribution shows that aliphatic links are short with numerous substitutions. No indigenous monocarboxylic acid was detected, showing that free aliphatic chains must be very short (less than three carbon atoms). The hydroxyacids are related to the occurrence of ester and ether functional groups within the aliphatic bridges between the aromatic units. This technique thus allows us to characterize in detail the aliphatic linkages of the IOMs, and the derived conclusions are in agreement with spectroscopic, pyrolytic, and degradative results previously reported. Compared to terrestrial samples, the aliphatic part of chondritic IOM is shorter and highly substituted. Aromatic units are smaller and more cross-linked than in coals, as already proposed from NMR data. Orgueil and Murchison IOM exhibit some tiny differences, especially in the length of aliphatic chains.

Sodium and T1rho MRI for molecular and diagnostic imaging of articular cartilage.

Science.gov (United States)

Borthakur, Arijitt; Mellon, Eric; Niyogi, Sampreet; Witschey, Walter; Kneeland, J Bruce; Reddy, Ravinder

2006-11-01

In this article, both sodium magnetic resonance (MR) and T1rho relaxation mapping aimed at measuring molecular changes in cartilage for the diagnostic imaging of osteoarthritis are reviewed. First, an introduction to structure of cartilage, its degeneration in osteoarthritis (OA) and an outline of diagnostic imaging methods in quantifying molecular changes and early diagnostic aspects of cartilage degeneration are described. The sodium MRI section begins with a brief overview of the theory of sodium NMR of biological tissues and is followed by a section on multiple quantum filters that can be used to quantify both bi-exponential relaxation and residual quadrupolar interaction. Specifically, (i) the rationale behind the use of sodium MRI in quantifying proteoglycan (PG) changes, (ii) validation studies using biochemical assays, (iii) studies on human OA specimens, (iv) results on animal models and (v) clinical imaging protocols are reviewed. Results demonstrating the feasibility of quantifying PG in OA patients and comparison with that in healthy subjects are also presented. The section concludes with the discussion of advantages and potential issues with sodium MRI and the impact of new technological advancements (e.g. ultra-high field scanners and parallel imaging methods). In the theory section on T1rho, a brief description of (i) principles of measuring T1rho relaxation, (ii) pulse sequences for computing T1rho relaxation maps, (iii) issues regarding radio frequency power deposition, (iv) mechanisms that contribute to T1rho in biological tissues and (v) effects of exchange and dipolar interaction on T1rho dispersion are discussed. Correlation of T1rho relaxation rate with macromolecular content and biomechanical properties in cartilage specimens subjected to trypsin and cytokine-induced glycosaminoglycan depletion and validation against biochemical assay and histopathology are presented. Experimental T1rho data from osteoarthritic specimens, animal models

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

International Nuclear Information System (INIS)

Warren, Anna J.; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R.; Horrell, Sam; McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-01-01

A comparison of X-ray diffraction and radiographic techniques for the location and characterization of protein crystals is demonstrated on membrane protein crystals mounted within lipid cubic phase material. The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

Energy Technology Data Exchange (ETDEWEB)

Warren, Anna J. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Armour, Wes [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Oxford e-Research Centre, 7 Keble Road, Oxford OX1 3QG (United Kingdom); Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); Horrell, Sam [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom); University of Liverpool, Liverpool L69 3BX (United Kingdom); McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE (United Kingdom)

2013-07-01

A comparison of X-ray diffraction and radiographic techniques for the location and characterization of protein crystals is demonstrated on membrane protein crystals mounted within lipid cubic phase material. The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolecular crystallography beamlines at the Diamond Light Source. The technique is particularly useful for microcrystals and for crystals mounted in opaque materials such as lipid cubic phase. X-ray diffraction raster scanning can be used in combination with radiography to allow informed decision-making at the beamline prior to diffraction data collection. It is demonstrated that the X-ray dose required for a full tomography measurement is similar to that for a diffraction grid-scan, but for sample location and shape estimation alone just a few radiographic projections may be required.

Novel Hyaluronic Acid Conjugates for Dual Nuclear Imaging and Therapy in CD44-Expressing Tumors in Mice In Vivo

Science.gov (United States)

Dubey, Ravindra Dhar; Klippstein, Rebecca; Wang, Julie Tzu-Wen; Hodgins, Naomi; Mei, Kuo-Ching; Sosabowski, Jane; Hider, Robert C.; Abbate, Vincenzo; Gupta, Prem N.; Al-Jamal, Khuloud T.

2017-01-01

Hyaluronic acid, a natural CD44 receptor ligand, has attracted attention in the past years as a macromolecular delivery of anticancer agents to cancer. At the same time, the clinical applications of Gemcitabine (Gem) have been hindered by its short biological half-life, high dose and development of drug resistance. This work reports the synthesis of a hyaluronic acid (HA) conjugate for nuclear imaging, and in vivo Gem delivery to CD44-expressing solid tumors in mice. HA was individually conjugated, via amide coupling, to Gem (HA-Gem), 4'-(aminomethyl)fluorescein hydrochloride (HA-4'-AMF) or tris(hydroxypyridinone) amine (HA-THP) for cancer therapy, in vitro tracking or single photon emission computed tomography/computed tomography (SPECT/CT) imaging, respectively. Gem conjugation to HA was directly confirmed by nuclear magnetic resonance (1H NMR), gel permeation chromatography (GPC) and UV-visible spectrometry, or indirectly by a nucleoside transporter inhibition study. Gem conjugation to HA improved its plasma stability, reduced blood hemolysis and resulted in delayed cytotoxicity in vitro. Uptake inhibition studies in colon CT26 and pancreatic PANC-1 cells, by flow cytometry, revealed that uptake of fluorescent HA conjugate is CD44 receptor and macropinocytosis-dependent. Gamma scintigraphy and SPECT/CT imaging confirmed the relatively prolonged blood circulation profile and uptake in CT26 (1.5 % ID/gm) and PANC-1 (1 % ID/gm) subcutaneous tumors at 24 h after intravenous injection in mice. Four injections of HA-Gem at ~15 mg/kg, over a 28-day period, resulted in significant delay in CT26 tumor growth and prolonged mice survival compared to the free drug. This study reports for the first time dual nuclear imaging and drug delivery (Gem) of HA conjugates to solid tumors in mice. The conjugates show great potential in targeting, imaging and killing of CD44-over expressing cells in vivo. This work is likely to open new avenues for the application of HA

Mineral Grains, Dimples, and Hot Volcanic Organic Streams: Dynamic Geological Backstage of Macromolecular Evolution.

Science.gov (United States)

Skoblikow, Nikolai E; Zimin, Andrei A

2018-04-01

, polycondensation, and formation of proto-cellular structures) are combined within a common dynamic geological process. We suppose macromolecular evolution had an extremely fast, "flash" start: the period from volcanic eruption to formation of lithocyte "populations" took not million years but just several tens of minutes. The scenario proposed can be verified experimentally with a three-module setup working with principles of dynamic (flow) chemistry in its core element.

77 FR 54921 - Center for Scientific Review; Notice of Closed Meetings

Science.gov (United States)

2012-09-06

... Committee: Oncology 2--Translational Clinical Integrated Review Group; Basic Mechanisms of Cancer...: Biological Chemistry and Macromolecular Biophysics Integrated Review Group; Macromolecular Structure and...: Biological Chemistry and Macromolecular Biophysics Integrated Review Group; Macromolecular Structure and...

Imaging of block copolymer vesicles in solvated state by wet scanning transmission electron microscopy

Czech Academy of Sciences Publication Activity Database

Šlouf, Miroslav; Lapčíková, Monika; Štěpánek, M.

2011-01-01

Roč. 47, č. 6 (2011), s. 1273-1278 ISSN 0014-3057 R&D Projects: GA ČR GAP208/10/0353; GA AV ČR KAN200520704; GA AV ČR IAA400500703 Institutional research plan: CEZ:AV0Z40500505 Keywords : environmental scanning electron microscopy * self-assembly * amphiphilic block copolymers Subject RIV: CD - Macromolecular Chemistry Impact factor: 2.739, year: 2011

Direct imaging electron microscopy (EM) methods in modern structural biology: overview and comparison with X-ray crystallography and single-particle cryo-EM reconstruction in the studies of large macromolecules.

Science.gov (United States)

Miyaguchi, Katsuyuki

2014-10-01

Determining the structure of macromolecules is important for understanding their function. The fine structure of large macromolecules is currently studied primarily by X-ray crystallography and single-particle cryo-electron microscopy (EM) reconstruction. Before the development of these techniques, macromolecular structure was often examined by negative-staining, rotary-shadowing and freeze-etching EM, which are categorised here as 'direct imaging EM methods'. In this review, the results are summarised by each of the above techniques and compared with respect to four macromolecules: the ryanodine receptor, cadherin, rhodopsin and the ribosome-translocon complex (RTC). The results of structural analysis of the ryanodine receptor and cadherin are consistent between each technique. The results obtained for rhodopsin vary to some extent within each technique and between the different techniques. Finally, the results for RTC are inconsistent between direct imaging EM and other analytical techniques, especially with respect to the space within RTC, the reasons for which are discussed. Then, the role of direct imaging EM methods in modern structural biology is discussed. Direct imaging methods should support and verify the results obtained by other analytical methods capable of solving three-dimensional molecular architecture, and they should still be used as a primary tool for studying macromolecule structure in vivo. © 2014 Société Française des Microscopies and Société de Biologie Cellulaire de France. Published by John Wiley & Sons Ltd.

FlexED8: the first member of a fast and flexible sample-changer family for macromolecular crystallography.

Science.gov (United States)

Papp, Gergely; Felisaz, Franck; Sorez, Clement; Lopez-Marrero, Marcos; Janocha, Robert; Manjasetty, Babu; Gobbo, Alexandre; Belrhali, Hassan; Bowler, Matthew W; Cipriani, Florent

2017-10-01

Automated sample changers are now standard equipment for modern macromolecular crystallography synchrotron beamlines. Nevertheless, most are only compatible with a single type of sample holder and puck. Recent work aimed at reducing sample-handling efforts and crystal-alignment times at beamlines has resulted in a new generation of compact and precise sample holders for cryocrystallography: miniSPINE and NewPin [see the companion paper by Papp et al. (2017, Acta Cryst., D73, 829-840)]. With full data collection now possible within seconds at most advanced beamlines, and future fourth-generation synchrotron sources promising to extract data in a few tens of milliseconds, the time taken to mount and centre a sample is rate-limiting. In this context, a versatile and fast sample changer, FlexED8, has been developed that is compatible with the highly successful SPINE sample holder and with the miniSPINE and NewPin sample holders. Based on a six-axis industrial robot, FlexED8 is equipped with a tool changer and includes a novel open sample-storage dewar with a built-in ice-filtering system. With seven versatile puck slots, it can hold up to 112 SPINE sample holders in uni-pucks, or 252 miniSPINE or NewPin sample holders, with 36 samples per puck. Additionally, a double gripper, compatible with the SPINE sample holders and uni-pucks, allows a reduction in the sample-exchange time from 40 s, the typical time with a standard single gripper, to less than 5 s. Computer vision-based sample-transfer monitoring, sophisticated error handling and automatic error-recovery procedures ensure high reliability. The FlexED8 sample changer has been successfully tested under real conditions on a beamline.

Design, Synthesis and Characterization of Polyethylene-Based Macromolecular Architectures by Combining Polyhomologation with Powerful Linking Chemistry

KAUST Repository

Alkayal, Nazeeha

2016-09-05

Polyhomologation is a powerful method to prepare polyethylene-based materials with controlled molecular weight, topology and composition. This dissertation focuses on the discovery of new synthetic routes to prepare polyethylene-based macromolecular architectures by combining polyhomologation with highly orthogonal and efficient linking reactions such as Diels Alder, copper-catalyzed azide-alkyne cycloaddition (CuAAC), and Glaser. Taking advantage of functionalized polyhomologation initiators, as well as of the efficient coupling chemistry, we were able to synthesize various types of polymethylene (polyethylene)-based materials with complex architectures including linear co/terpolymers, graft terpolymers, and tadpole copolymers. In the first project, a facile synthetic route towards well-defined polymethylene-based co/terpolymers, by combining the anthracene/maleimide Diels–Alder reaction with polyhomologation, is presented. For the synthesis of diblock copolymers the following approach was applied: (a) synthesis of α-anthracene-ω-hydroxy-polymethylene by polyhomologation using tri (9 anthracene-methyl propyl ether) borane as the initiator, (b) synthesis of furan-protected-maleimide-terminated poly(ε-caprolactone) or polyethylene glycol and (c) Diels–Alder reaction between anthracene and maleimide-terminated polymers. In the case of triblock terpolymers, the α-anthracene-ω-hydroxy polymethylene was used as a macroinitiator for the ring-opening polymerization of D, L-lactide to afford an anthracene-terminated PM-b-PLA copolymer, followed by the Diels–Alder reaction with furan-protected maleimide-terminated poly (ε-caprolactone) or polyethylene glycol to give the triblock terpolymers. The synthetic methodology is general and potentially applicable to a range of polymers. The coupling reaction applied in the second project of this dissertation was copper-catalyzed “click” cycloaddition of azides and alkynes (CuAAC). Novel well-defined polyethylene

Determination of macromolecular exchange and PO2 in the microcirculation: a simple system for in vivo fluorescence and phosphorescence videomicroscopy

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Torres L.N.

2001-01-01

Full Text Available We have developed a system with two epi-illumination sources, a DC-regulated lamp for transillumination and mechanical switches for rapid shift of illumination and detection of defined areas (250-750 µm² by fluorescence and phosphorescence videomicroscopy. The system permits investigation of standard microvascular parameters, vascular permeability as well as intra- and extravascular PO2 by phosphorescence quenching of Pd-meso-tetra (4-carboxyphenyl porphine (PORPH. A Pechan prism was used to position a defined region over the photomultiplier and TV camera. In order to validate the system for in vivo use, in vitro tests were performed with probes at concentrations that can be found in microvascular studies. Extensive in vitro evaluations were performed by filling glass capillaries with solutions of various concentrations of FITC-dextran (diluted in blood and in saline mixed with different amounts of PORPH. Fluorescence intensity and phosphorescence decay were determined for each mixture. FITC-dextran solutions without PORPH and PORPH solutions without FITC-dextran were used as references. Phosphorescence decay curves were relatively unaffected by the presence of FITC-dextran at all concentrations tested (0.1 µg/ml to 5 mg/ml. Likewise, fluorescence determinations were performed in the presence of PORPH (0.05 to 0.5 mg/ml. The system was successfully used to study macromolecular extravasation and PO2 in the rat mesentery circulation under controlled conditions and during ischemia-reperfusion.

Hyperbranched Polyethylenebased Macromolecular Architectures: Synthesis, Characterization, and Selfassembly

KAUST Repository

Al-Sulami, Ahlam

2018-05-01

"Chain walking” catalytic polymerization CWCP is a powerful tool for the one-pot synthesis of a unique class of hyperbranched polyethylene HBPE-based macromolecules with a controllable molecular weight, topology, and composition. This dissertation focuses on new synthetic routes to prepare HBPE-based macromolecular architectures by combining the CWCP technique with ring opening polymerization ROP, atom–transfer radical polymerization ATRP, and “click” chemistry. Taking advantage of end-functionalized HBPE, and a new ethynyl-soketal star-shape agent, we were able to synthesize different types of the HBPE-based architectures including hyperbranched-on-hyperbranched core-shell nanostructure, and miktoarm-star-HBPE-based block copolymers. The first part of the dissertation provides a general introduction to the synthesis of polyethylene types with controllable structures. Well-defined polyethylene with different macromolecule architectures were synthesized either for academic or industrial purposes. In the second part, the HBPE with different topologies was synthesized by CWCP, using a α-diimine Pd (II) catalyst. The effect of the temperature and pressure on the catalyst activity and polymer properties, including branch content, molecular weight, distribution, and thermal properties were studied. Two series of samples were synthesized: a) serial samples (A) under pressures of 1, 5, and 27 atm at 5˚C, and b) serial samples (B) at temperatures of 5, 15, and 35 ˚C under 5 atm. Proton nuclear magnetic resonance spectroscopy, 1H NMR, and gel permeation chromatography, GPC, analysis were used to calculate the branching content, molecular weight, and distribution, whereas differential scanning calorimetry, DSC, was used to record the melting and glass transition temperatures as well as the degree of the crystallinity. Well-defined HBPE-based core diblock copolymers with predictable amphiphilic properties are studied in the third part of the project. Hyperbranched

Pathological Assessment of Brain White Matter in Relapsing-Remitting MS Patients using Quantitative Magnetization Transfer Imaging

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Khodarahm Pahlevan

2011-09-01

Full Text Available Introduction: Multiple sclerosis (MS is characterized by lesions in the white matter (WM of the central nervous system. Magnetic resonance imaging is the most specific and sensitive method for diagnosis of multiple sclerosis. However, the ability of conventional MRI to show histopathologic heterogeneity of MS lesions is insufficient. Quantitative magnetization transfer imaging (qMTI is a relatively new method to investigate pathologic processes of the brain tissue occurring in MS patients. Material and Methods: Voxel-based analyses allow regional comparisons between groups to be made for the whole brain in a single analysis. This is done by coregistering data from all individual subjects to a reference brain, generally referred to as the "standard space", and then comparing them on a voxel-by-voxel basis. This study aimed to analyze whole-brain quantitative T1 maps, not to find global changes or changes in selected regions, but specifically to investigate the spatial distribution throughout the brain of T1 increases in MS WM with respect to control WM. In this study, 11 healthy controls, 10 relapsing-remitting (RR MS patients and 13 CIS patients were studied using MT-MRI imaging. MT parameters, including magnetization transfer ratio (MTR, magnetization transfer rate between free protons and restricted macromolecular protons, Ksat and longitudinal relaxation times (with and without MT saturation pulse, T1sat and T1free values were evaluated. Results: The results showed that, at a group level, there is widespread involvement of WM throughout the brain in CIS MS and especially in RRMS, where a significant T1 increase was found in 15.58% of WM voxels (normals < RR. Discussion and Conclusion: This study demonstrates that WM in large parts of the brain is susceptible to disease processes in RR and CIS MS

PREFACE: 2nd International Conference and Young Scientist School ''Magnetic resonance imaging in biomedical research''

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Naumova, A. V.; Khodanovich, M. Y.; Yarnykh, V. L.

2016-02-01

The Second International Conference and Young Scientist School ''Magnetic resonance imaging in biomedical research'' was held on the campus of the National Research Tomsk State University (Tomsk, Russia) on September 7-9, 2015. The conference was focused on magnetic resonance imaging (MRI) applications for biomedical research. The main goal was to bring together basic scientists, clinical researchers and developers of new MRI techniques to bridge the gap between clinical/research needs and advanced technological solutions. The conference fostered research and development in basic and clinical MR science and its application to health care. It also had an educational purpose to promote understanding of cutting-edge MR developments. The conference provided an opportunity for researchers and clinicians to present their recent theoretical developments, practical applications, and to discuss unsolved problems. The program of the conference was divided into three main topics. First day of the conference was devoted to educational lectures on the fundamentals of MRI physics and image acquisition/reconstruction techniques, including recent developments in quantitative MRI. The second day was focused on developments and applications of new contrast agents. Multinuclear and spectroscopic acquisitions as well as functional MRI were presented during the third day of the conference. We would like to highlight the main developments presented at the conference and introduce the prominent speakers. The keynote speaker of the conference Dr. Vasily Yarnykh (University of Washington, Seattle, USA) presented a recently developed MRI method, macromolecular proton fraction (MPF) mapping, as a unique tool for modifying image contrast and a unique tool for quantification of the myelin content in neural tissues. Professor Yury Pirogov (Lomonosov Moscow State University) described development of new fluorocarbon compounds and applications for biomedicine. Drs. Julia Velikina and Alexey

Novel use for polyvinylpyrrolidone as a macromolecular crowder for enhanced extracellular matrix deposition and cell proliferation.

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Rashid, Rafi; Lim, Natalie Sheng Jie; Chee, Stella Min Ling; Png, Si Ning; Wohland, Thorsten; Raghunath, Michael

2014-12-01

Macromolecular crowding (MMC) is a biophysical effect that governs biochemical processes inside and outside of cells. Since standard cell culture media lack this effect, the physiological performance of differentiated and progenitor cells, including extracellular matrix (ECM) deposition, is impaired in vitro. To bring back physiological crowdedness to in vitro systems, we have previously introduced carbohydrate-based macromolecules to culture media and have achieved marked improvements with mixed MMC in terms of ECM deposition and differentiation of mesenchymal stem cells (MSCs). We show here that although this system is successful, it is limited, due to viscosity, to only 33% of the fractional volume occupancy (FVO) of full serum, which we calculated to have an FVO of approximately 54% v/v. We show here that full-serum FVO can be achieved using polyvinylpyrrolidone (PVP) 360 kDa. Under these conditions, ECM deposition in human fibroblasts and MSCs is on par, if not stronger than, with original MMC protocols using carbohydrates, but with a viscosity that is not significantly changed. In addition, we have found that the proliferation rate for bone marrow-derived MSCs and fibroblasts increases slightly in the presence of PVP360, similar to that observed with carbohydrate-based crowders. A palette of MMC compounds is now emerging that enables us to tune the crowdedness of culture media seamlessly from interstitial fluid (9% FVO), in which the majority of tissue cells might be based, to serum environments mimicking intravascular conditions. Despite identical FVO's, individual crowder size effects play a role and different cell types appear to have preferences in terms of FVO and the crowder that this is achieved with. However, in the quest of crowders that we have predicted to have a smoother regulatory approval path, PVP is a highly interesting compound, as it has been widely used in the medical and food industries and shows a novel promising use in cell culture and

Effects of Macromolecular Crowding on Human Adipose Stem Cell Culture in Fetal Bovine Serum, Human Serum, and Defined Xeno-Free/Serum-Free Conditions.

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Patrikoski, Mimmi; Lee, Michelle Hui Ching; Mäkinen, Laura; Ang, Xiu Min; Mannerström, Bettina; Raghunath, Michael; Miettinen, Susanna

2017-01-01

Microenvironment plays an important role for stem cell proliferation and differentiation. Macromolecular crowding (MMC) was recently shown to assist stem cells in forming their own matrix microenvironment in vitro. The ability of MMC to support adipose stem cell (ASC) proliferation, metabolism, and multilineage differentiation was studied under different conditions: fetal bovine serum- (FBS-) and human serum- (HS-) based media and xeno- and serum-free (XF/SF) media. Furthermore, the immunophenotype of ASCs under MMC was evaluated. The proliferative capacity of ASCs under MMC was attenuated in each condition. However, osteogenic differentiation was enhanced under MMC, shown by increased deposition of mineralized matrix in FBS and HS cultures. Likewise, significantly greater lipid droplet accumulation and increased collagen IV deposition indicated enhanced adipogenesis under MMC in FBS and HS cultures. In contrast, chondrogenic differentiation was attenuated in ASCs expanded under MMC. The ASC immunophenotype was maintained under MMC with significantly higher expression of CD54. However, MMC impaired metabolic activity and differentiation capacity of ASCs in XF/SF conditions. Both the supportive and inhibitory effects of MMC on ASC are culture condition dependent. In the presence of serum, MMC maintains ASC immunophenotype and enhances adipogenic and osteogenic differentiation at the cost of reduced proliferation.

Visualization of membrane protein crystals in lipid cubic phase using X-ray imaging

OpenAIRE

Warren, Anna J.; Armour, Wes; Axford, Danny; Basham, Mark; Connolley, Thomas; Hall, David R.; Horrell, Sam; McAuley, Katherine E.; Mykhaylyk, Vitaliy; Wagner, Armin; Evans, Gwyndaf

2013-01-01

The focus in macromolecular crystallography is moving towards even more challenging target proteins that often crystallize on much smaller scales and are frequently mounted in opaque or highly refractive materials. It is therefore essential that X-ray beamline technology develops in parallel to accommodate such difficult samples. In this paper, the use of X-ray microradiography and microtomography is reported as a tool for crystal visualization, location and characterization on the macromolec...

Superresolution Imaging of Aquaporin-4 Cluster Size in Antibody-Stained Paraffin Brain Sections.

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Smith, Alex J; Verkman, Alan S

2015-12-15

The water channel aquaporin-4 (AQP4) forms supramolecular clusters whose size is determined by the ratio of M1- and M23-AQP4 isoforms. In cultured astrocytes, differences in the subcellular localization and macromolecular interactions of small and large AQP4 clusters results in distinct physiological roles for M1- and M23-AQP4. Here, we developed quantitative superresolution optical imaging methodology to measure AQP4 cluster size in antibody-stained paraffin sections of mouse cerebral cortex and spinal cord, human postmortem brain, and glioma biopsy specimens. This methodology was used to demonstrate that large AQP4 clusters are formed in AQP4(-/-) astrocytes transfected with only M23-AQP4, but not in those expressing only M1-AQP4, both in vitro and in vivo. Native AQP4 in mouse cortex, where both isoforms are expressed, was enriched in astrocyte foot-processes adjacent to microcapillaries; clusters in perivascular regions of the cortex were larger than in parenchymal regions, demonstrating size-dependent subcellular segregation of AQP4 clusters. Two-color superresolution imaging demonstrated colocalization of Kir4.1 with AQP4 clusters in perivascular areas but not in parenchyma. Surprisingly, the subcellular distribution of AQP4 clusters was different between gray and white matter astrocytes in spinal cord, demonstrating regional specificity in cluster polarization. Changes in AQP4 subcellular distribution are associated with several neurological diseases and we demonstrate that AQP4 clustering was preserved in a postmortem human cortical brain tissue specimen, but that AQP4 was not substantially clustered in a human glioblastoma specimen despite high-level expression. Our results demonstrate the utility of superresolution optical imaging for measuring the size of AQP4 supramolecular clusters in paraffin sections of brain tissue and support AQP4 cluster size as a primary determinant of its subcellular distribution. Copyright © 2015 Biophysical Society

Indicators of Macromolecular Oxidative Damage and Antioxidant Defence Examinees Exposed to the Radar Frequencies 1.5 - 10.9 GHz

International Nuclear Information System (INIS)

Marjanovic, A.M.; Flajs, D.; Pavicic, I.; Domijan, A.

2011-01-01

Radar is an object-detection system which uses microwaves (Mw). As a result of increased use of radar there is a rising concern regarding health effects of Mw radiation on human body. Living organisms are complex electrochemical systems being evolved in a relatively narrow range of well-defined environmental parameters. For life to be maintained these parameters must be kept within their normal range, since deviations can induce biochemical effects causing cell function impairment and disease. Some theories indicate connection between Mw radiation, oxidative damage as well as antioxidant defence of organism. Aim of this study was to evaluate level and damage of macromolecular structures - proteins and lipids in blood of men occupationally exposed to Mw radiation. Concentration of glutathione (GSH), a known indicator of organism antioxidant defence, was also determined. Blood samples were collected from 27 male workers occupationally exposed to radar frequencies 1.5 to 10.9 GHz. Corresponding control group (N = 8) was a part of study. Concentrations of total and oxidised proteins, protein carbonyls, and GSH were measured by spectrophotometric method, while malondialdeyde (MDA), product of lipid peroxidation, was determined by high performance liquid chromatography (HPLC). Gained concentrations of oxidised proteins, GSH and MDA were presented in relation to total proteins. Concentration of oxidised proteins between control and exposed group of examinees did not show any significant statistical difference. However, concentration of GSH in exposed group was found considerably decreased, while concentration of MDA was found to be increased. Results indicate that Mw radiation of radar operating at frequencies 1.5 - 10.9 GHz could cause damage to proteins and lipids in addition to impairment of antioxidant defence of organism. (author)

Media additives to promote spheroid circularity and compactness in hanging drop platform.

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Leung, Brendan M; Lesher-Perez, Sasha Cai; Matsuoka, Toshiki; Moraes, Christopher; Takayama, Shuichi

2015-02-01

Three-dimensional spheroid cultures have become increasingly popular as drug screening platforms, especially with the advent of different high throughput spheroid forming technologies. However, comparing drug efficacy across different cell types in spheroid culture can be difficult due to variations in spheroid morphologies and transport characteristics. Improving the reproducibility of compact, circular spheroids contributes to standardizing and increasing the fidelity of the desired gradient profiles in these drug screening three-dimensional tissue cultures. In this study we discuss the role that circularity and compaction has on spheroids, and demonstrate the impact methylcellulose (MethoCel) and collagen additives in the culture media can contribute to more compact and circular spheroid morphology. We demonstrate that improved spheroid formation is not a simple function of increased viscosity of the different macromolecule additives, suggesting that other macromolecular characteristics contribute to improved spheroid formation. Of the various macromolecular additives tested for hanging drop culture, MethoCel provided the most desirable spheroid formation. Additionally, the higher viscosity of MethoCel-containing media improved the ease of imaging of cellular spheroids within hanging drop cultures by reducing motion-induced image blur.

A convolutional neural network-based screening tool for X-ray serial crystallography.

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Ke, Tsung Wei; Brewster, Aaron S; Yu, Stella X; Ushizima, Daniela; Yang, Chao; Sauter, Nicholas K

2018-05-01

A new tool is introduced for screening macromolecular X-ray crystallography diffraction images produced at an X-ray free-electron laser light source. Based on a data-driven deep learning approach, the proposed tool executes a convolutional neural network to detect Bragg spots. Automatic image processing algorithms described can enable the classification of large data sets, acquired under realistic conditions consisting of noisy data with experimental artifacts. Outcomes are compared for different data regimes, including samples from multiple instruments and differing amounts of training data for neural network optimization. open access.

Leaching of organic acids from macromolecular organic matter by non-supercritical CO2

Science.gov (United States)

Sauer, P.; Glombitza, C.; Kallmeyer, J.

2012-04-01

The storage of CO2 in underground reservoirs is discussed controversly in the scientific literature. The worldwide search for suitable storage formations also considers coal-bearing strata. CO2 is already injected into seams for enhanced recovery of coal bed methane. However, the effects of increased CO2 concentration, especially on organic matter rich formations, are rarely investigated. The injected CO2 will dissolve in the pore water, causing a decrease in pH and resulting in acidic formation waters. Huge amounts of low molecular weight organic acids (LMWOAs) are chemically bound to the macromolecular matrix of sedimentary organic matter and may be liberated by hydrolysis, which is enhanced by the acidic porewater. Recent investigations outlined the importance of LMWOAs as a feedstock for microbial life in the subsurface [1]. Therefore, injection of CO2 into coal formations may result in enhanced nutrient supply for subsurface microbes. To investigate the effect of high concentrations of dissolved CO2 on the release of LMWOAs from coal we developed an inexpensive high-pressure high temperature system that allows manipulating the partial pressure of dissolved gases at pressures and temperatures up to 60 MPa and 120° C, respectively. In a reservoir vessel, gases are added to saturate the extraction medium to the desired level. Inside the extraction vessel hangs a flexible and inert PVDF sleeve (polyvinylidene fluoride, almost impermeable for gases), holding the sample and separating it from the pressure fluid. The flexibility of the sleeve allows for subsampling without loss of pressure. Coal samples from the DEBITS-1 well, Waikato Basin, NZ (R0 = 0.29, TOC = 30%). were extracted at 90° C and 5 MPa, either with pure or CO2-saturated water. Subsamples were taken at different time points during the extraction. The extracted LMWOAs such as formate, acetate and oxalate were analysed by ion chromatography. Yields of LMWOAs were higher with pure water than with CO2

Compact quantum dots for single-molecule imaging.

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Smith, Andrew M; Nie, Shuming

2012-10-09

Single-molecule imaging is an important tool for understanding the mechanisms of biomolecular function and for visualizing the spatial and temporal heterogeneity of molecular behaviors that underlie cellular biology (1-4). To image an individual molecule of interest, it is typically conjugated to a fluorescent tag (dye, protein, bead, or quantum dot) and observed with epifluorescence or total internal reflection fluorescence (TIRF) microscopy. While dyes and fluorescent proteins have been the mainstay of fluorescence imaging for decades, their fluorescence is unstable under high photon fluxes necessary to observe individual molecules, yielding only a few seconds of observation before complete loss of signal. Latex beads and dye-labeled beads provide improved signal stability but at the expense of drastically larger hydrodynamic size, which can deleteriously alter the diffusion and behavior of the molecule under study. Quantum dots (QDs) offer a balance between these two problematic regimes. These nanoparticles are composed of semiconductor materials and can be engineered with a hydrodynamically compact size with exceptional resistance to photodegradation (5). Thus in recent years QDs have been instrumental in enabling long-term observation of complex macromolecular behavior on the single molecule level. However these particles have still been found to exhibit impaired diffusion in crowded molecular environments such as the cellular cytoplasm and the neuronal synaptic cleft, where their sizes are still too large (4,6,7). Recently we have engineered the cores and surface coatings of QDs for minimized hydrodynamic size, while balancing offsets to colloidal stability, photostability, brightness, and nonspecific binding that have hindered the utility of compact QDs in the past (8,9). The goal of this article is to demonstrate the synthesis, modification, and characterization of these optimized nanocrystals, composed of an alloyed HgxCd1-xSe core coated with an

75 FR 25273 - Center for Scientific Review; Notice of Closed Meetings

Science.gov (United States)

2010-05-07

... Committee: Oncology 1-Basic Translational Integrated Review Group, Cancer Molecular Pathobiology Study... 20892, 301-435-1179, [email protected] . Name of Committee: Biological Chemistry and Macromolecular...: Biological Chemistry and Macromolecular Biophysics Integrated Review Group, Macromolecular Structure and...

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

OpenAIRE

Soichiro Tsujino; Takashi Tomizaki

2016-01-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinn...

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012)

Science.gov (United States)

Foffi, G.; Pastore, A.; Piazza, F.; Temussi, P. A.

2013-08-01

More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). Figure 1. Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Science.gov (United States)

Foffi, G; Pastore, A; Piazza, F; Temussi, P A

2013-08-02

More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). [Formula: see text] Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international

Effects of babassu nut oil on ischemia/reperfusion-induced leukocyte adhesion and macromolecular leakage in the microcirculation: Observation in the hamster cheek pouch

Directory of Open Access Journals (Sweden)

Barbosa Maria do

2012-11-01

Full Text Available Abstract Background The babassu palm tree is native to Brazil and is most densely distributed in the Cocais region of the state of Maranhão, in northeastern Brazil. In addition to the industrial use of refined babassu oil, the milk, the unrefined oil and the nuts in natura are used by families from several communities of African descendants as one of the principal sources of food energy. The objective of this study was to evaluate the effects of babassu oil on microvascular permeability and leukocyte-endothelial interactions induced by ischemia/reperfusion using the hamster cheek pouch microcirculation as experimental model. Methods Twice a day for 14 days, male hamsters received unrefined babassu oil (0.02 ml/dose [BO-2 group], 0.06 ml/dose [BO-6 group], 0.18 ml/dose [BO-18 group] or mineral oil (0.18 ml/dose [MO group]. Observations were made in the cheek pouch and macromolecular permeability increase induced by ischemia/reperfusion (I/R or topical application of histamine, as well as leukocyte-endothelial interaction after I/R were evaluated. Results The mean value of I/R-induced microvascular leakage, determined during reperfusion, was significantly lower in the BO-6 and BO-18 groups than in the MO one (P Conclusions Our findings suggest that unrefined babassu oil reduced microvascular leakage and protected against histamine-induced effects in postcapillary venules and highlights that these almost unexploited nut and its oil might be secure sources of food energy.

Passive tumor targeting of polymer therapeutics: in vivo imaging of both the polymer carrier and the enzymatically cleavable drug model

Czech Academy of Sciences Publication Activity Database

Pola, Robert; Heinrich, A. K.; Mueller, T.; Kostka, Libor; Mäder, K.; Pechar, Michal; Etrych, Tomáš

2016-01-01

Roč. 16, č. 11 (2016), s. 1577-1582 ISSN 1616-5187 R&D Projects: GA ČR(CZ) GA15-02986S; GA ČR(CZ) GA16-17207S; GA MŠk(CZ) LO1507 Institutional support: RVO:61389013 Keywords : polymer drug carriers * tumor targeting * enzymatic release Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.238, year: 2016

Simultaneous determination of sample thickness, tilt, and electron mean free path using tomographic tilt images based on Beer-Lambert law.

Science.gov (United States)

Yan, Rui; Edwards, Thomas J; Pankratz, Logan M; Kuhn, Richard J; Lanman, Jason K; Liu, Jun; Jiang, Wen

2015-11-01

Cryo-electron tomography (cryo-ET) is an emerging technique that can elucidate the architecture of macromolecular complexes and cellular ultrastructure in a near-native state. Some important sample parameters, such as thickness and tilt, are needed for 3-D reconstruction. However, these parameters can currently only be determined using trial 3-D reconstructions. Accurate electron mean free path plays a significant role in modeling image formation process essential for simulation of electron microscopy images and model-based iterative 3-D reconstruction methods; however, their values are voltage and sample dependent and have only been experimentally measured for a limited number of sample conditions. Here, we report a computational method, tomoThickness, based on the Beer-Lambert law, to simultaneously determine the sample thickness, tilt and electron inelastic mean free path by solving an overdetermined nonlinear least square optimization problem utilizing the strong constraints of tilt relationships. The method has been extensively tested with both stained and cryo datasets. The fitted electron mean free paths are consistent with reported experimental measurements. The accurate thickness estimation eliminates the need for a generous assignment of Z-dimension size of the tomogram. Interestingly, we have also found that nearly all samples are a few degrees tilted relative to the electron beam. Compensation of the intrinsic sample tilt can result in horizontal structure and reduced Z-dimension of tomograms. Our fast, pre-reconstruction method can thus provide important sample parameters that can help improve performance of tomographic reconstruction of a wide range of samples. Copyright © 2015 Elsevier Inc. All rights reserved.

Effects of pectin-containing diets on the hepatic macromolecular covalent binding of 2,6-dinitro-[3H]toluene in Fischer-344 rats

International Nuclear Information System (INIS)

deBethizy, J.D.; Sherrill, J.M.; Rickert, D.E.; Hamm, T.E. Jr.

1983-01-01

The influence of diets varying in pectin content on intestinal microfloral metabolic capacity of rats has been investigated as a possible mechanism for the alteration of toxicity of 2,6-dinitrotoluene (2,6-DNT) produced by these diets. Male F-344 rats were fed a purified diet (AIN-76A), AIN-76A plus 5% or 10% citrus pectin, or either of two cereal-based diets that vary in pectin content, NIH-07 or Purina Chow 5002. After 28 days, rats were given tritium-labeled 2,6-DNT (10 or 75 mg/kg po) and killed 12 hr later. Total hepatic macromolecular covalent binding (CVB) was determined by exhaustive extraction. The CVB of 2,6-DNT was found to be independent of diet at 10 mg/kg. However, at 75 mg/kg CVB was increased 40% by feeding 5% pectin in the purified diet and 90% by feeding 10% pectin in the purified diet. Animals fed Purina 5002 and NIH-07 had 135 and 150% higher CVB, respectively, than animals fed the purified diet alone and significantly greater CVB than animals fed the pectin supplemented diets. Elevated (two- to threefold) beta-glucuronidase and nitroreductase activities, microfloral enzymes proposed to be involved in the activation of 2,6-DNT to a toxicant, were found in the cecal contents of animals fed the pectin-containing diets which correlated with a two- to threefold increase in total number of cecal anaerobes. These results suggest that pectin-induced changes in microflora may enhance hepatoxicity after high doses of 2,6-DNT

Operation of the Australian Store.Synchrotron for macromolecular crystallography.

Science.gov (United States)

Meyer, Grischa R; Aragão, David; Mudie, Nathan J; Caradoc-Davies, Tom T; McGowan, Sheena; Bertling, Philip J; Groenewegen, David; Quenette, Stevan M; Bond, Charles S; Buckle, Ashley M; Androulakis, Steve

2014-10-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

Glycogen as a biodegradable construction nanomaterial for in vivo use

Czech Academy of Sciences Publication Activity Database

Filippov, Sergey K.; Sedláček, Ondřej; Bogomolova, Anna; Vetrík, Miroslav; Jirák, D.; Kovář, J.; Kučka, Jan; Bals, S.; Turner, S.; Štěpánek, Petr; Hrubý, Martin

2012-01-01

Roč. 12, č. 12 (2012), s. 1731-1738 ISSN 1616-5187 R&D Projects: GA ČR GA202/09/2078; GA ČR GAP108/12/0640; GA ČR GAP208/10/1600; GA ČR GPP207/10/P054 Institutional research plan: CEZ:AV0Z40500505 Institutional support: RVO:61389013 Keywords : nanoparticles * in vivo imaging * glycogen Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.742, year: 2012

Superparamagnetic Fe3O4 nanoparticles: synthesis by thermal decomposition of iron(III) glucuronate and application in magnetic resonance imaging

Czech Academy of Sciences Publication Activity Database

Patsula, Vitalii; Kosinová, L.; Lovrić, M.; Ferhatovic Hamzic, L.; Rabyk, Mariia; Konefal, Rafal; Paruzel, Aleksandra; Šlouf, Miroslav; Herynek, V.; Gajović, S.; Horák, Daniel

2016-01-01

Roč. 8, č. 11 (2016), s. 7238-7247 ISSN 1944-8244 R&D Projects: GA MŠk(CZ) LH14318; GA MŠk(CZ) LO1507; GA MŠk(CZ) ED1.1.00/02.0109 EU Projects: European Commission(XE) 316120 - GLOWBRAIN Institutional support: RVO:61389013 Keywords : superparamagnetic * nanoparticles * iron oxide Subject RIV: CD - Macromolecular Chemistry Impact factor: 7.504, year: 2016

Liberation of microbial substrates from macromolecular organic matter by non-supercritical CO2

Science.gov (United States)

Sauer, P.; Glombitza, C.; Kallmeyer, J.

2012-12-01

The worldwide search for suitable underground storage formations for CO2 also considers coal-bearing strata. CO2 is already injected into coal seams for enhanced recovery of coal bed methane. However, the geochemical and microbiological effects of increased CO2 concentrations on organic matter rich formations are rarely investigated. The injected CO2 will dissolve in the pore water, causing a decrease in pH and resulting in acidic formation waters. Low molecular weight organic acids (LMWOAs) are chemically bound to the macromolecular matrix of sedimentary organic matter and may be liberated by hydrolysis, which is enhanced under acidic conditions. Recent investigations outlined the importance of LMWOAs as a feedstock for subsurface microbial life [1]. Therefore, injection of CO2 into coal formations may result in enhanced nutrient supply for subsurface microbes. To investigate the effects of highly CO2-saturated waters on the release of LMWOAs from coal, we developed an inexpensive high-pressure-high-temperature system that allows manipulating the concentration of dissolved gases up to 60 MPa and 120°C, respectively. The sample is placed in a flexible, gas-tight and inert PVDF sleeve, separating it from the pressure fluid and allowing for subsampling without loss of pressure. Lignite samples from the DEBITS-1 well, Waikato Basin, NZ and the Welzow-Süd open-cast mine, Niederlausitz, Germany, were extracted at 90° C and 5 MPa, with either pure water, CO2-saturated water, CO2/NO2 or CO2/SO2-saturated water. Subsamples were taken at different time points during the 72 hrs. long extraction. Extraction of LMWOAs from coal samples with our pressurised system resulted in yields that were up to four times higher than those reported for Soxhlet extraction [2]. These higher yields may be explained by the fact that during Soxhlet extraction the sample only gets into contact with freshly distilled water, whereas in our system the extraction fluid is circulated, resulting in

Operation of the Australian Store.Synchrotron for macromolecular crystallography

Energy Technology Data Exchange (ETDEWEB)

Meyer, Grischa R. [Monash University, Clayton, Victoria 3800 (Australia); Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T. [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia); McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M. [Monash University, Clayton, Victoria 3800 (Australia); Bond, Charles S. [The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia (Australia); Buckle, Ashley M. [Monash University, Clayton, Victoria 3800 (Australia); Androulakis, Steve, E-mail: steve.androulakis@monash.edu [Monash Bioinformatics Platform, Monash University, Clayton, Victoria 3800 (Australia)

2014-10-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

Operation of the Australian Store.Synchrotron for macromolecular crystallography

International Nuclear Information System (INIS)

Meyer, Grischa R.; Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T.; McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M.; Bond, Charles S.; Buckle, Ashley M.; Androulakis, Steve

2014-01-01

The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community

The Assessment of Structural Changes in MS Plaques and Normal Appearing White Matter Using Quantitative Magnetization Transfer Imaging (MTI

Directory of Open Access Journals (Sweden)

Masoomeh Fooladi

2007-12-01

breakdown in the macromolecular structure of MS lesions. There was also a significant difference in MTR histogram parameters between the patients and control groups, accompanied by a total shift of NAWM-MTR histogram to the left. Discussion and Conclusion: Based on theobtained result itcan be stated that MS has a diffused nature and the white matter abnormalities occurring outside T2-visible lesions affect the whole brain tissue. Quantitative magnetization transfer imaging can be used as a reliable method to assess both the overall disease burden and the intrinsic nature of the individual lesions in MS patients

Long-range correlations, geometrical structure, and transport properties of macromolecular solutions. The equivalence of configurational statistics and geometrodynamics of large molecules.

Science.gov (United States)

Mezzasalma, Stefano A

2007-12-04

A special theory of Brownian relativity was previously proposed to describe the universal picture arising in ideal polymer solutions. In brief, it redefines a Gaussian macromolecule in a 4-dimensional diffusive spacetime, establishing a (weak) Lorentz-Poincaré invariance between liquid and polymer Einstein's laws for Brownian movement. Here, aimed at inquiring into the effect of correlations, we deepen the extension of the special theory to a general formulation. The previous statistical equivalence, for dynamic trajectories of liquid molecules and static configurations of macromolecules, and rather obvious in uncorrelated systems, is enlarged by a more general principle of equivalence, for configurational statistics and geometrodynamics. Accordingly, the three geodesic motion, continuity, and field equations could be rewritten, and a number of scaling behaviors were recovered in a spacetime endowed with general static isotropic metric (i.e., for equilibrium polymer solutions). We also dealt with universality in the volume fraction and, unexpectedly, found that a hyperscaling relation of the form, (average size) x (diffusivity) x (viscosity)1/2 ~f(N0, phi0) is fulfilled in several regimes, both in the chain monomer number (N) and polymer volume fraction (phi). Entangled macromolecular dynamics was treated as a geodesic light deflection, entaglements acting in close analogy to the field generated by a spherically symmetric mass source, where length fluctuations of the chain primitive path behave as azimuth fluctuations of its shape. Finally, the general transformation rule for translational and diffusive frames gives a coordinate gauge invariance, suggesting a widened Lorentz-Poincaré symmetry for Brownian statistics. We expect this approach to find effective applications to solutions of arbitrarily large molecules displaying a variety of structures, where the effect of geometry is more explicit and significant in itself (e.g., surfactants, lipids, proteins).

The effect of magnetic nanoparticles on neuronal differentiation of induced pluripotent stem cell-derived neural precursors

Czech Academy of Sciences Publication Activity Database

Jiráková, Klára; Šeneklová, Monika; Jirák, D.; Turnovcová, Karolína; Vosmanská, M.; Babič, Michal; Horák, Daniel; Veverka, Pavel; Jendelová, Pavla

2016-01-01

Roč. 11, č. 2016 (2016), s. 6267-6281 E-ISSN 1178-2013 R&D Projects: GA MŠk(CZ) LQ1604; GA MŠk(CZ) ED1.1.00/02.0109; GA MŠk(CZ) 7F14057 Institutional support: RVO:68378041 ; RVO:61389013 ; RVO:68378271 Keywords : neural precursors * magnetic resonance imaging * cell differentiation Subject RIV: FH - Neurology; EB - Genetics ; Molecular Biology (FGU-C); CD - Macromolecular Chemistry (UMCH-V) Impact factor: 4.300, year: 2016

Macromolecular Rate Theory (MMRT) Provides a Thermodynamics Rationale to Underpin the Convergent Temperature Response in Plant Leaf Respiration

Science.gov (United States)

Liang, L. L.; Arcus, V. L.; Heskel, M.; O'Sullivan, O. S.; Weerasinghe, L. K.; Creek, D.; Egerton, J. J. G.; Tjoelker, M. G.; Atkin, O. K.; Schipper, L. A.

2017-12-01

Temperature is a crucial factor in determining the rates of ecosystem processes such as leaf respiration (R) - the flux of plant respired carbon dioxide (CO2) from leaves to the atmosphere. Generally, respiration rate increases exponentially with temperature as modelled by the Arrhenius equation, but a recent study (Heskel et al., 2016) showed a universally convergent temperature response of R using an empirical exponential/polynomial model whereby the exponent in the Arrhenius model is replaced by a quadratic function of temperature. The exponential/polynomial model has been used elsewhere to describe shoot respiration and plant respiration. What are the principles that underlie these empirical observations? Here, we demonstrate that macromolecular rate theory (MMRT), based on transition state theory for chemical kinetics, is equivalent to the exponential/polynomial model. We re-analyse the data from Heskel et al. 2016 using MMRT to show this equivalence and thus, provide an explanation based on thermodynamics, for the convergent temperature response of R. Using statistical tools, we also show the equivalent explanatory power of MMRT when compared to the exponential/polynomial model and the superiority of both of these models over the Arrhenius function. Three meaningful parameters emerge from MMRT analysis: the temperature at which the rate of respiration is maximum (the so called optimum temperature, Topt), the temperature at which the respiration rate is most sensitive to changes in temperature (the inflection temperature, Tinf) and the overall curvature of the log(rate) versus temperature plot (the so called change in heat capacity for the system, ). The latter term originates from the change in heat capacity between an enzyme-substrate complex and an enzyme transition state complex in enzyme-catalysed metabolic reactions. From MMRT, we find the average Topt and Tinf of R are 67.0±1.2 °C and 41.4±0.7 °C across global sites. The average curvature (average

A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures.

Science.gov (United States)

Schellman, J A

1990-08-31

The properties of a simple model for solvation in mixed solvents are explored in this paper. The model is based on the supposition that solvent replacement is a simple one-for-one substitution reaction at macromolecular sites which are independent of one another. This leads to a new form for the binding polynomial in which all terms are associated with ligand interchange rather than ligand addition. The principal solvent acts as one of the ligands. Thermodynamic analysis then shows that thermodynamic binding (i.e., selective interaction) depends on the properties of K'-1, whereas stoichiometric binding (site occupation) depends on K'. K' is a 'practical' interchange equilibrium constant given by (f3/f1)K, where K is the true equilibrium constant for the interchange of components 3 and 1 on the site and f3 and f4 denote their respective activity coefficients on the mole fraction scale. Values of K' less than unity lead to negative selective interaction. It is selective interaction and not occupation number which determines the thermodynamic effects of solvation. When K' greater than 100 on the mole fraction scale or K' greater than 2 on the molality scale (in water), the differences between stoichiometric binding and selective interaction become less than 1%. The theory of this paper is therefore necessary only for very weak binding constants. When K'-1 is small, large concentrations of the added solvent component are required to produce a thermodynamic effect. Under these circumstances the isotherms for the selective interaction and for the excess (or transfer) free energy are strongly dependent on the behavior of the activity coefficients of both solvent components. Two classes of behavior are described depending on whether the components display positive or negative deviations from Raoult's law. Examples which are discussed are aqueous solutions of urea and guanidinium chloride for positive deviations and of sucrose and glucose for negative deviations

Drug targeting and the carriers. Application to chemoembolization and medical imaging

International Nuclear Information System (INIS)

Puisieux, F.; Benoit, J.P.; Roblot-Treupel, L.

1987-01-01

The last fifteen years have seen an increased interest in drug targeting which can be considered as a new way to control the body distribution of drugs when associated with an appropriate carrier. The systems currently studied possess different structures (macromolecular, vesicular and particular) and can be classified into carriers of first, second and third generation. After a brief review of the three types of carriers, this paper focuses on their respective interest in the different fields of radiology: carriers of first generation (microcapsules, microspheres) in chemoembolization, carriers of second generation (liposomes, nanocapsules, nanospheres) in conventional radiology, in computerized tomography, in scintigraphy, in RMN; carriers of third generation (monoclonal antibodies...) in immunoscintigraphy of tumors [fr

The influence of oxygen exposure time on the composition of macromolecular organic matter as revealed by surface sediments on the Murray Ridge (Arabian Sea)

Science.gov (United States)

Nierop, Klaas G. J.; Reichart, Gert-Jan; Veld, Harry; Sinninghe Damsté, Jaap S.

2017-06-01

The Arabian Sea represents a prime example of an open ocean extended oxygen minimum zone (OMZ) with low oxygen concentrations (down to less than 2 μM) between 200 and 1000 m water depth. The OMZ impinges on the ocean floor, affecting organic matter (OM) mineralization. We investigated impact of oxygen depletion on the composition of macromolecular OM (MOM) along a transect through the OMZ on the slopes of the Murray Ridge. This sub-marine high in the northern Arabian Sea, with the top at approximately 500 m below sea surface (mbss), intersects the OMZ. We analyzed sediments deposited in the core of OMZ (suboxic conditions), directly below the OMZ (dysoxic conditions) and well below the OMZ (fully oxic conditions). The upper 18 cm of sediments from three stations recovered at different depths were studied. MOM was investigated by Rock Eval and flash pyrolysis techniques. The MOM was of a predominant marine origin and inferred from their pyrolysis products, most biomolecules (tetra-alkylpyrrole pigments, polysaccharides, proteins and their transformation products, and polyphenols including phlorotannins), showed a progressive relative degradation with increasing exposure to oxygen. Alkylbenzenes and, in particular, aliphatic macromolecules increased relatively. The observed differences in MOM composition between sediment deposited under various bottom water oxygen conditions (i.e. in terms of concentration and exposure time) was much larger than within sediment cores, implying that early diagenetic alteration of organic matter depends largely on bottom water oxygenation rather than subsequent anaerobic degradation within the sediments, even at longer time scales.

Three-dimensional electron microscopy of macromolecular assemblies: visualization of biological molecules in their native state

National Research Council Canada - National Science Library

Frank, J

2006-01-01

... Clusters 2.8 Support Grids 33 33 3 Principle of Image Formation in the Transmission Electron Microscope 34 3.1 Introduction 34 3.2 The Weak-Phase Object Approximation 35 3.3 The Contrast Transfer...

Quantifying the Assembly of Multicomponent Molecular Machines by Single-Molecule Total Internal Reflection Fluorescence Microscopy.

Science.gov (United States)

Boehm, E M; Subramanyam, S; Ghoneim, M; Washington, M Todd; Spies, M

2016-01-01

Large, dynamic macromolecular complexes play essential roles in many cellular processes. Knowing how the components of these complexes associate with one another and undergo structural rearrangements is critical to understanding how they function. Single-molecule total internal reflection fluorescence (TIRF) microscopy is a powerful approach for addressing these fundamental issues. In this article, we first discuss single-molecule TIRF microscopes and strategies to immobilize and fluorescently label macromolecules. We then review the use of single-molecule TIRF microscopy to study the formation of binary macromolecular complexes using one-color imaging and inhibitors. We conclude with a discussion of the use of TIRF microscopy to examine the formation of higher-order (i.e., ternary) complexes using multicolor setups. The focus throughout this article is on experimental design, controls, data acquisition, and data analysis. We hope that single-molecule TIRF microscopy, which has largely been the province of specialists, will soon become as common in the tool box of biophysicists and biochemists as structural approaches have become today. © 2016 Elsevier Inc. All rights reserved.

Looking inside the box: using Raman microspectroscopy to deconstruct microbial biomass stoichiometry one cell at a time

Science.gov (United States)

Hall, Edward K.; Singer, Gabriel A.; Pölzl, Marvin; Hämmerle, Ieda; Schwarz, Christian; Daims, Holger; Maixner, Frank; Battin, Tom J.

2011-01-01

Stoichiometry of microbial biomass is a key determinant of nutrient recycling in a wide variety of ecosystems. However, little is known about the underlying causes of variance in microbial biomass stoichiometry. This is primarily because of technological constraints limiting the analysis of macromolecular composition to large quantities of microbial biomass. Here, we use Raman microspectroscopy (MS), to analyze the macromolecular composition of single cells of two species of bacteria grown on minimal media over a wide range of resource stoichiometry. We show that macromolecular composition, determined from a subset of identified peaks within the Raman spectra, was consistent with macromolecular composition determined using traditional analytical methods. In addition, macromolecular composition determined by Raman MS correlated with total biomass stoichiometry, indicating that analysis with Raman MS included a large proportion of a cell's total macromolecular composition. Growth phase (logarithmic or stationary), resource stoichiometry and species identity each influenced each organism's macromolecular composition and thus biomass stoichiometry. Interestingly, the least variable peaks in the Raman spectra were those responsible for differentiation between species, suggesting a phylogenetically specific cellular architecture. As Raman MS has been previously shown to be applicable to cells sampled directly from complex environments, our results suggest Raman MS is an extremely useful application for evaluating the biomass stoichiometry of environmental microorganisms. This includes the ability to partition microbial biomass into its constituent macromolecules and increase our understanding of how microorganisms in the environment respond to resource heterogeneity.

Synthesis and properties of star HPMA copolymer nanocarriers synthesised by RAFT polymerisation designed for selective anticancer drug delivery and imaging

Czech Academy of Sciences Publication Activity Database

Chytil, Petr; Koziolová, Eva; Janoušková, Olga; Kostka, Libor; Ulbrich, Karel; Etrych, Tomáš

2015-01-01

Roč. 15, č. 6 (2015), s. 839-850 ISSN 1616-5187 R&D Projects: GA ČR GPP207/11/P551; GA ČR(CZ) GCP207/12/J030; GA MŠk(CZ) EE2.3.30.0029; GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61389013 Keywords : drug delivery systems * HPMA copolymers * pH-controlled release Subject RIV: CD - Macromolecular Chemistry Impact factor: 3.680, year: 2015

RGDS- and TAT-conjugated upconversion of NaYF4:Yb3+/Er3+&SiO2 nanoparticles: in vitro human epithelioid cervix carcinoma cellular uptake, imaging, and targeting

Czech Academy of Sciences Publication Activity Database

Kostiv, Uliana; Kotelnikov, Ilya; Proks, Vladimír; Šlouf, Miroslav; Kučka, Jan; Engstová, Hana; Ježek, Petr; Horák, Daniel

2016-01-01

Roč. 8, č. 31 (2016), s. 20422-20431 ISSN 1944-8244 R&D Projects: GA ČR(CZ) GA15-01897S; GA ČR(CZ) GA16-02702S Institutional support: RVO:61389013 ; RVO:67985823 Keywords : upconversion, nanoparticles * RGDS peptide * TAT peptide Subject RIV: CD - Macromolecular Chemistry; BO - Biophysics (FGU-C) Impact factor: 7.504, year: 2016

Spinal imaging and image analysis

CERN Document Server

Yao, Jianhua

2015-01-01

This book is instrumental to building a bridge between scientists and clinicians in the field of spine imaging by introducing state-of-the-art computational methods in the context of clinical applications.  Spine imaging via computed tomography, magnetic resonance imaging, and other radiologic imaging modalities, is essential for noninvasively visualizing and assessing spinal pathology. Computational methods support and enhance the physician’s ability to utilize these imaging techniques for diagnosis, non-invasive treatment, and intervention in clinical practice. Chapters cover a broad range of topics encompassing radiological imaging modalities, clinical imaging applications for common spine diseases, image processing, computer-aided diagnosis, quantitative analysis, data reconstruction and visualization, statistical modeling, image-guided spine intervention, and robotic surgery. This volume serves a broad audience as  contributions were written by both clinicians and researchers, which reflects the inte...

Coordinate transformation based cryo-correlative methods for electron tomography and focused ion beam milling

International Nuclear Information System (INIS)

Fukuda, Yoshiyuki; Schrod, Nikolas; Schaffer, Miroslava; Feng, Li Rebekah; Baumeister, Wolfgang; Lucic, Vladan

2014-01-01

Correlative microscopy allows imaging of the same feature over multiple length scales, combining light microscopy with high resolution information provided by electron microscopy. We demonstrate two procedures for coordinate transformation based correlative microscopy of vitrified biological samples applicable to different imaging modes. The first procedure aims at navigating cryo-electron tomography to cellular regions identified by fluorescent labels. The second procedure, allowing navigation of focused ion beam milling to fluorescently labeled molecules, is based on the introduction of an intermediate scanning electron microscopy imaging step to overcome the large difference between cryo-light microscopy and focused ion beam imaging modes. These methods make it possible to image fluorescently labeled macromolecular complexes in their natural environments by cryo-electron tomography, while minimizing exposure to the electron beam during the search for features of interest. - Highlights: • Correlative light microscopy and focused ion beam milling of vitrified samples. • Coordinate transformation based cryo-correlative method. • Improved correlative light microscopy and cryo-electron tomography

Structural Biology in the context of EGEE

CERN Document Server

García, D; Carazo, J M; Valverde, J R; Moscicki, J; Muraru, A

2007-01-01

Electron microscopy (EM) is a crucial technique, which allows Structural Biology researchers to characterize macromolecular assemblies in distinct functional states. Image processing in three dimensional EM (3D-EM) is used by a flourishing community (exemplarized by the EU funded 3D-EM NoE) and is characterized by voluminous data and large computing requirements, making this a problem well suited for Grid computing and the EGEE infrastructure. There are various steps in the 3D-EM refinement process that may benefit from Grid computing. To start with, large numbers of experimental images need to be averaged. Nowadays, typically tens of thousands of images are used, while future studies may routinely employ millions of images. Our group has been developing Xmipp, a package for single-particle 3D-EM image processing. Using Xmipp, the classification of 91,000 ribosome projections into 4 classes took more than 2500 CPU hours using the resources of the MareNostrum supercomputer at the Barcelona Supercomputing Centr...

Image compression of bone images

International Nuclear Information System (INIS)

Hayrapetian, A.; Kangarloo, H.; Chan, K.K.; Ho, B.; Huang, H.K.

1989-01-01

This paper reports a receiver operating characteristic (ROC) experiment conducted to compare the diagnostic performance of a compressed bone image with the original. The compression was done on custom hardware that implements an algorithm based on full-frame cosine transform. The compression ratio in this study is approximately 10:1, which was decided after a pilot experiment. The image set consisted of 45 hand images, including normal images and images containing osteomalacia and osteitis fibrosa. Each image was digitized with a laser film scanner to 2,048 x 2,048 x 8 bits. Six observers, all board-certified radiologists, participated in the experiment. For each ROC session, an independent ROC curve was constructed and the area under that curve calculated. The image set was randomized for each session, as was the order for viewing the original and reconstructed images. Analysis of variance was used to analyze the data and derive statistically significant results. The preliminary results indicate that the diagnostic quality of the reconstructed image is comparable to that of the original image

Quantification of in vivo 1H magnetic resonance spectroscopy signals with baseline and lineshape estimation

International Nuclear Information System (INIS)

Osorio-Garcia, M I; Sima, D M; Van Huffel, S; Nielsen, F U; Dresselaers, T; Himmelreich, U; Van Leuven, F

2011-01-01

The in vivo quantification of magnetic resonance spectroscopy (MRS) signals is a method to estimate metabolite concentrations of living tissue. Obtaining reliable concentrations is still a challenge due to the experimental conditions affecting spectral quality. Additionally, lipids and macromolecules overlap with the metabolites of interest, affecting their reliable estimation. In this study, we propose to combine the self-deconvolution lineshape estimation method, which accounts for spectral shape distortions, with two different approaches for taking into account the macromolecular baseline contribution: (a) based on macromolecules and lipids measured in vivo using an inversion recovery technique, and (b) based on the simulation of macromolecular resonances using prior knowledge from a database of inversion recovery signals. The ultimate goal is to measure macromolecular and lipid data only once as described in (a) to create macromolecular and lipid profiles. These profiles then can be used as described in (b) for data measured under the same conditions. The method is evaluated on in vivo 1 H MRS signals at 9.4 T from mouse hippocampus. Results show that better metabolite fits are obtained when lineshape and baseline estimations are simultaneously performed and that baseline estimation based on prior knowledge from macromolecular measured signals can be reliably used to replace time-consuming individual macromolecular and lipid acquisitions

SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints

Science.gov (United States)

Curtis, Joseph E.; Raghunandan, Sindhu; Nanda, Hirsh; Krueger, Susan

2012-02-01

A program to construct ensembles of biomolecular structures that are consistent with experimental scattering data are described. Specifically, we generate an ensemble of biomolecular structures by varying sets of backbone dihedral angles that are then filtered using experimentally determined restraints to rapidly determine structures that have scattering profiles that are consistent with scattering data. We discuss an application of these tools to predict a set of structures for the HIV-1 Gag protein, an intrinsically disordered protein, that are consistent with small-angle neutron scattering experimental data. We have assembled these algorithms into a program called SASSIE for structure generation, visualization, and analysis of intrinsically disordered proteins and other macromolecular ensembles using neutron and X-ray scattering restraints. Program summaryProgram title: SASSIE Catalogue identifier: AEKL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3 No. of lines in distributed program, including test data, etc.: 3 991 624 No. of bytes in distributed program, including test data, etc.: 826 Distribution format: tar.gz Programming language: Python, C/C++, Fortran Computer: PC/Mac Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.6.6) RAM: 1 GB Classification: 3 External routines: Python 2.6.5, numpy 1.4.0, swig 1.3.40, scipy 0.8.0, Gnuplot-py-1.8, Tcl 8.5, Tk 8.5, Mac installation requires aquaterm 1.0 (or X window system) and Xcode 3 development tools. Nature of problem: Open source software to generate structures of disordered biological molecules that subsequently allow for the comparison of computational and experimental results is limiting the use of scattering resources. Solution method: Starting with an all atom model of a protein, for example, users can input

Phosphazene-promoted anionic polymerization

KAUST Repository

Zhao, Junpeng; Hadjichristidis, Nikolaos; Gnanou, Yves

2014-01-01

.e. in situ activation (of initiating sites) and polymerization, and summarize the applications of such a mechanism on macromolecular engineering toward functionalized polymers, block copolymers and complex macromolecular architectures.

Polymerization Using Phosphazene Bases

KAUST Repository

Zhao, Junpeng; Hadjichristidis, Nikolaos; Schlaad, Helmut

2015-01-01

. In this chapter, the general features of phosphazenepromoted/catalyzed polymerizations and the applications in macromolecular engineering (synthesis of functionalized polymers, block copolymers, and macromolecular architectures) are discussed with challenges

Speckle imaging algorithms for planetary imaging

Energy Technology Data Exchange (ETDEWEB)

Johansson, E. [Lawrence Livermore National Lab., CA (United States)

1994-11-15

I will discuss the speckle imaging algorithms used to process images of the impact sites of the collision of comet Shoemaker-Levy 9 with Jupiter. The algorithms use a phase retrieval process based on the average bispectrum of the speckle image data. High resolution images are produced by estimating the Fourier magnitude and Fourier phase of the image separately, then combining them and inverse transforming to achieve the final result. I will show raw speckle image data and high-resolution image reconstructions from our recent experiment at Lick Observatory.

Aging changes of molecular synthesis in the respiratory organs as revealed by microscopic radioautography

International Nuclear Information System (INIS)

Nagata, T.

2001-01-01

For the purpose of elucidating the aging changes of macromolecular synthesis such as DNA, RNA, proteins, glycoproteins, glycides and lipids in various organ systems of experimental animals and men, we have studied respiratory organs of aging mice as a series of systematic studies using light and electron microscopic radioautography in various organ systems after incorporations with macromolecular precursors. The experimental animals mainly used were dd Y strain mice at various aging groups from embryo to postnatal day 1 and 3, weeks 1 and 2, months 1, 2, 6, 12 up to 2 year senescent stages. The animals were injected with such macromolecular precursors as 3 H - thymidine for DNA, 3 H-uridine for RNA, 3 H-leucine for proteins, 35 SO 4 for glycoproteins. The results demonstrated that these precursors were incorporated into various cell types in the lungs and tracheas at various ages from perinatal to juvenile, mature and senescent stages showing specific patterns of macromolecular synthesis. It is concluded that these specific pattern of macromolecular synthesis in respective cell types demonstrated the organ specificity of aging. (author)

A simple neridronate-based surface coating strategy for upconversion nanoparticles: highly colloidally stable 125I-radiolabeled NaYF4:Yb3+/Er3+@PEG nanoparticles for multimodal in vivo tissue imaging

Czech Academy of Sciences Publication Activity Database

Kostiv, Uliana; Lobaz, Volodymyr; Kučka, Jan; Švec, Pavel; Sedláček, Ondřej; Hrubý, Martin; Janoušková, Olga; Francová, P.; Kolářová, V.; Šefc, L.; Horák, Daniel

2017-01-01

Roč. 9, č. 43 (2017), s. 16680-16688 ISSN 2040-3364 R&D Projects: GA ČR(CZ) GA15-01897S; GA MZd(CZ) NV16-30544A Institutional support: RVO:61389013 Keywords : upconversion nanoparticles * PEG-neridronate * 125I radiolabeling Subject RIV: CD - Macromolecular Chemistry OBOR OECD: Polymer science Impact factor: 7.367, year: 2016

Cellular Activation of the Self-Quenched Fluorescent Reporter Probe in Tumor Microenvironment

Directory of Open Access Journals (Sweden)

Alexei A. Bogdanov, Jr.

2002-01-01

Full Text Available The effect of intralysosomal proteolysis of near-infrared fluorescent (NIRF self-quenched macromolecular probe (PGC-Cy5.5 has been previously reported and used for tumor imaging. Here we demonstrate that proteolysis can be detected noninvasively in vivo at the cellular level. A codetection of GFP fluorescence (using two-photon excitation and NIRF was performed in tumor-bearing animals injected with PGC-Cy5.5. In vivo microscopy of tumor cells in subdermal tissue layers (up to 160 μm showed a strong Cy5.5 dequenching effect in GFP-negative cells. This observation was corroborated by flow cytometry, sorting, and reverse transcription polymerase chain reaction analysis of tumor-isolated cells. Both GFP-positive (81% total and GFP-negative (19% total populations contained Cy5.5-positive cells. The GFP-negative cells were confirmed to be host mouse cells by the absence of rat cathepsin mRNA signal. The subfraction of GFPnegative cells (2.5-3.0% had seven times higher NIRF intensity than the majority of GFP-positive or GFPnegative cells (372 and 55 AU, respectively. Highly NIRF-positive, FP-negative cells were CD45-and MAC3-positive. Our results indicate that: 1 intracellular proteolysis can be imaged in vivo at the cellular level using cathepsin-sensitive probes; 2 tumor-recruited cells of hematopoetic origin participate most actively in uptake and degradation of long-circulating macromolecular probes.

Membrane mechanisms and intracellular signalling in cell volume regulation

DEFF Research Database (Denmark)

Hoffmann, Else Kay; Dunham, Philip B.

1995-01-01

Volume regulation, Signal transduction, Calcium-calmodulin, Stretch-activated channels, Eicosanoids, Macromolecular crowding, Cytoskeleton, Protein phosphorylation, dephosphorylation.......Volume regulation, Signal transduction, Calcium-calmodulin, Stretch-activated channels, Eicosanoids, Macromolecular crowding, Cytoskeleton, Protein phosphorylation, dephosphorylation....

Retinal Imaging and Image Analysis

Science.gov (United States)

Abràmoff, Michael D.; Garvin, Mona K.; Sonka, Milan

2011-01-01

Many important eye diseases as well as systemic diseases manifest themselves in the retina. While a number of other anatomical structures contribute to the process of vision, this review focuses on retinal imaging and image analysis. Following a brief overview of the most prevalent causes of blindness in the industrialized world that includes age-related macular degeneration, diabetic retinopathy, and glaucoma, the review is devoted to retinal imaging and image analysis methods and their clinical implications. Methods for 2-D fundus imaging and techniques for 3-D optical coherence tomography (OCT) imaging are reviewed. Special attention is given to quantitative techniques for analysis of fundus photographs with a focus on clinically relevant assessment of retinal vasculature, identification of retinal lesions, assessment of optic nerve head (ONH) shape, building retinal atlases, and to automated methods for population screening for retinal diseases. A separate section is devoted to 3-D analysis of OCT images, describing methods for segmentation and analysis of retinal layers, retinal vasculature, and 2-D/3-D detection of symptomatic exudate-associated derangements, as well as to OCT-based analysis of ONH morphology and shape. Throughout the paper, aspects of image acquisition, image analysis, and clinical relevance are treated together considering their mutually interlinked relationships. PMID:22275207

ImageX: new and improved image explorer for astronomical images and beyond

Science.gov (United States)

Hayashi, Soichi; Gopu, Arvind; Kotulla, Ralf; Young, Michael D.

2016-08-01

The One Degree Imager - Portal, Pipeline, and Archive (ODI-PPA) has included the Image Explorer interactive image visualization tool since it went operational. Portal users were able to quickly open up several ODI images within any HTML5 capable web browser, adjust the scaling, apply color maps, and perform other basic image visualization steps typically done on a desktop client like DS9. However, the original design of the Image Explorer required lossless PNG tiles to be generated and stored for all raw and reduced ODI images thereby taking up tens of TB of spinning disk space even though a small fraction of those images were being accessed by portal users at any given time. It also caused significant overhead on the portal web application and the Apache webserver used by ODI-PPA. We found it hard to merge in improvements made to a similar deployment in another project's portal. To address these concerns, we re-architected Image Explorer from scratch and came up with ImageX, a set of microservices that are part of the IU Trident project software suite, with rapid interactive visualization capabilities useful for ODI data and beyond. We generate a full resolution JPEG image for each raw and reduced ODI FITS image before producing a JPG tileset, one that can be rendered using the ImageX frontend code at various locations as appropriate within a web portal (for example: on tabular image listings, views allowing quick perusal of a set of thumbnails or other image sifting activities). The new design has decreased spinning disk requirements, uses AngularJS for the client side Model/View code (instead of depending on backend PHP Model/View/Controller code previously used), OpenSeaDragon to render the tile images, and uses nginx and a lightweight NodeJS application to serve tile images thereby significantly decreasing the Time To First Byte latency by a few orders of magnitude. We plan to extend ImageX for non-FITS images including electron microscopy and radiology scan

Cerebrovascular effects of intraarterial CO2 in quantities required for diagnostic imaging

International Nuclear Information System (INIS)

Coffey, R.; Quisling, R.G.; Mickle, J.P.; Hawkins, I.F. Jr.; Ballinger, W.B.

1984-01-01

The recent development of digital subtraction angiography (DSA) has renewed interest in the use of gasses, especially carbon dioxide, as contrast agents. Both early physiologic studies and recent clinical reports suggest that arterial CO 2 -DSA is a safe and useful diagnostic tool in the examination of extremity circulation. The present study examined the neurologic sequelae, pathologic changes, and effects on the blood-brain barrier to intravenous Evans-Blue and horseradish peroxidase of intracarotid CO 2 , in albino rats. As with other forms of cerebral gas embolization, CO 2 produced multifocal ischemic infarctions and disrupted the blood-brain barrier to macromolecular tracers. The site of the barrier lesion is the endothelial cell membrane, although the precise mechanisms of damage remain unknown

Imaging system design and image interpolation based on CMOS image sensor

Science.gov (United States)

Li, Yu-feng; Liang, Fei; Guo, Rui

2009-11-01

An image acquisition system is introduced, which consists of a color CMOS image sensor (OV9620), SRAM (CY62148), CPLD (EPM7128AE) and DSP (TMS320VC5509A). The CPLD implements the logic and timing control to the system. SRAM stores the image data, and DSP controls the image acquisition system through the SCCB (Omni Vision Serial Camera Control Bus). The timing sequence of the CMOS image sensor OV9620 is analyzed. The imaging part and the high speed image data memory unit are designed. The hardware and software design of the image acquisition and processing system is given. CMOS digital cameras use color filter arrays to sample different spectral components, such as red, green, and blue. At the location of each pixel only one color sample is taken, and the other colors must be interpolated from neighboring samples. We use the edge-oriented adaptive interpolation algorithm for the edge pixels and bilinear interpolation algorithm for the non-edge pixels to improve the visual quality of the interpolated images. This method can get high processing speed, decrease the computational complexity, and effectively preserve the image edges.

FUNDAMENTAL KINETICS OF SUPERCRITICAL COAL LIQUEFACTION: EFFECT OF CATALYSTS AND HYDROGEN-DONOR SOLVENTS; FINAL

International Nuclear Information System (INIS)

Benjamin J. McCoy; J.M. Smith

1998-01-01

This report outlines a distribution kinetics approach to macromolecular reactions that has been applied to several processes. The objective was to develop an understanding of high-temperature, dense-phase thermolytic processes for complex macromolecular systems, such as coal. Experiments and theory are described for chemical models that simulate depolymerization of coal. The approach has been exceptionally successful for the model macromolecular systems. Development of a novel chemical reaction engineering analysis, based on distribution kinetics, was a major accomplishment of the current research

Image registration via optimization over disjoint image regions

Science.gov (United States)

Pitts, Todd; Hathaway, Simon; Karelitz, David B.; Sandusky, John; Laine, Mark Richard

2018-02-06

Technologies pertaining to registering a target image with a base image are described. In a general embodiment, the base image is selected from a set of images, and the target image is an image in the set of images that is to be registered to the base image. A set of disjoint regions of the target image is selected, and a transform to be applied to the target image is computed based on the optimization of a metric over the selected set of disjoint regions. The transform is applied to the target image so as to register the target image with the base image.

ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy [version 1; referees: 2 approved, 1 approved with reservations

Directory of Open Access Journals (Sweden)

Elisabeth Brama

2016-12-01

Full Text Available In-resin fluorescence (IRF protocols preserve fluorescent proteins in resin-embedded cells and tissues for correlative light and electron microscopy, aiding interpretation of macromolecular function within the complex cellular landscape. Dual-contrast IRF samples can be imaged in separate fluorescence and electron microscopes, or in dual-modality integrated microscopes for high resolution correlation of fluorophore to organelle. IRF samples also offer a unique opportunity to automate correlative imaging workflows. Here we present two new locator tools for finding and following fluorescent cells in IRF blocks, enabling future automation of correlative imaging. The ultraLM is a fluorescence microscope that integrates with an ultramicrotome, which enables ‘smart collection’ of ultrathin sections containing fluorescent cells or tissues for subsequent transmission electron microscopy or array tomography. The miniLM is a fluorescence microscope that integrates with serial block face scanning electron microscopes, which enables ‘smart tracking’ of fluorescent structures during automated serial electron image acquisition from large cell and tissue volumes.

ultraLM and miniLM: Locator tools for smart tracking of fluorescent cells in correlative light and electron microscopy.

Science.gov (United States)

Brama, Elisabeth; Peddie, Christopher J; Wilkes, Gary; Gu, Yan; Collinson, Lucy M; Jones, Martin L

2016-12-13

In-resin fluorescence (IRF) protocols preserve fluorescent proteins in resin-embedded cells and tissues for correlative light and electron microscopy, aiding interpretation of macromolecular function within the complex cellular landscape. Dual-contrast IRF samples can be imaged in separate fluorescence and electron microscopes, or in dual-modality integrated microscopes for high resolution correlation of fluorophore to organelle. IRF samples also offer a unique opportunity to automate correlative imaging workflows. Here we present two new locator tools for finding and following fluorescent cells in IRF blocks, enabling future automation of correlative imaging. The ultraLM is a fluorescence microscope that integrates with an ultramicrotome, which enables 'smart collection' of ultrathin sections containing fluorescent cells or tissues for subsequent transmission electron microscopy or array tomography. The miniLM is a fluorescence microscope that integrates with serial block face scanning electron microscopes, which enables 'smart tracking' of fluorescent structures during automated serial electron image acquisition from large cell and tissue volumes.

Protein Crystal Growth

Science.gov (United States)

2003-01-01

In order to rapidly and efficiently grow crystals, tools were needed to automatically identify and analyze the growing process of protein crystals. To meet this need, Diversified Scientific, Inc. (DSI), with the support of a Small Business Innovation Research (SBIR) contract from NASA s Marshall Space Flight Center, developed CrystalScore(trademark), the first automated image acquisition, analysis, and archiving system designed specifically for the macromolecular crystal growing community. It offers automated hardware control, image and data archiving, image processing, a searchable database, and surface plotting of experimental data. CrystalScore is currently being used by numerous pharmaceutical companies and academic and nonprofit research centers. DSI, located in Birmingham, Alabama, was awarded the patent Method for acquiring, storing, and analyzing crystal images on March 4, 2003. Another DSI product made possible by Marshall SBIR funding is VaporPro(trademark), a unique, comprehensive system that allows for the automated control of vapor diffusion for crystallization experiments.

Image processing with ImageJ

CERN Document Server

Pascau, Javier

2013-01-01

The book will help readers discover the various facilities of ImageJ through a tutorial-based approach.This book is targeted at scientists, engineers, technicians, and managers, and anyone who wishes to master ImageJ for image viewing, processing, and analysis. If you are a developer, you will be able to code your own routines after you have finished reading this book. No prior knowledge of ImageJ is expected.

Ultrasonic image analysis and image-guided interventions.

Science.gov (United States)

Noble, J Alison; Navab, Nassir; Becher, H

2011-08-06

The fields of medical image analysis and computer-aided interventions deal with reducing the large volume of digital images (X-ray, computed tomography, magnetic resonance imaging (MRI), positron emission tomography and ultrasound (US)) to more meaningful clinical information using software algorithms. US is a core imaging modality employed in these areas, both in its own right and used in conjunction with the other imaging modalities. It is receiving increased interest owing to the recent introduction of three-dimensional US, significant improvements in US image quality, and better understanding of how to design algorithms which exploit the unique strengths and properties of this real-time imaging modality. This article reviews the current state of art in US image analysis and its application in image-guided interventions. The article concludes by giving a perspective from clinical cardiology which is one of the most advanced areas of clinical application of US image analysis and describing some probable future trends in this important area of ultrasonic imaging research.

Imaging windows for long-term intravital imaging

Science.gov (United States)

Alieva, Maria; Ritsma, Laila; Giedt, Randy J; Weissleder, Ralph; van Rheenen, Jacco

2014-01-01

Intravital microscopy is increasingly used to visualize and quantitate dynamic biological processes at the (sub)cellular level in live animals. By visualizing tissues through imaging windows, individual cells (e.g., cancer, host, or stem cells) can be tracked and studied over a time-span of days to months. Several imaging windows have been developed to access tissues including the brain, superficial fascia, mammary glands, liver, kidney, pancreas, and small intestine among others. Here, we review the development of imaging windows and compare the most commonly used long-term imaging windows for cancer biology: the cranial imaging window, the dorsal skin fold chamber, the mammary imaging window, and the abdominal imaging window. Moreover, we provide technical details, considerations, and trouble-shooting tips on the surgical procedures and microscopy setups for each imaging window and explain different strategies to assure imaging of the same area over multiple imaging sessions. This review aims to be a useful resource for establishing the long-term intravital imaging procedure. PMID:28243510

Improved image alignment method in application to X-ray images and biological images.

Science.gov (United States)

Wang, Ching-Wei; Chen, Hsiang-Chou

2013-08-01

Alignment of medical images is a vital component of a large number of applications throughout the clinical track of events; not only within clinical diagnostic settings, but prominently so in the area of planning, consummation and evaluation of surgical and radiotherapeutical procedures. However, image registration of medical images is challenging because of variations on data appearance, imaging artifacts and complex data deformation problems. Hence, the aim of this study is to develop a robust image alignment method for medical images. An improved image registration method is proposed, and the method is evaluated with two types of medical data, including biological microscopic tissue images and dental X-ray images and compared with five state-of-the-art image registration techniques. The experimental results show that the presented method consistently performs well on both types of medical images, achieving 88.44 and 88.93% averaged registration accuracies for biological tissue images and X-ray images, respectively, and outperforms the benchmark methods. Based on the Tukey's honestly significant difference test and Fisher's least square difference test tests, the presented method performs significantly better than all existing methods (P ≤ 0.001) for tissue image alignment, and for the X-ray image registration, the proposed method performs significantly better than the two benchmark b-spline approaches (P < 0.001). The software implementation of the presented method and the data used in this study are made publicly available for scientific communities to use (http://www-o.ntust.edu.tw/∼cweiwang/ImprovedImageRegistration/). cweiwang@mail.ntust.edu.tw.

Kannan, Dr Kazhiur Kothandapani

Indian Academy of Sciences (India)

Date of birth: 30 September 1939. Specialization: X-ray & Macromolecular Crystallography and Macromolecular Computer Graphics Address: F-206, Redwood, Reheja Residency, III Block, Koramangala, Bengaluru 560 034, Karnataka Contact: Residence: (080) 2550 5829. Mobile: 87627 80061

scikit-image: image processing in Python.

Science.gov (United States)

van der Walt, Stéfan; Schönberger, Johannes L; Nunez-Iglesias, Juan; Boulogne, François; Warner, Joshua D; Yager, Neil; Gouillart, Emmanuelle; Yu, Tony

2014-01-01

scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.

scikit-image: image processing in Python

Directory of Open Access Journals (Sweden)

Stéfan van der Walt

2014-06-01

Full Text Available scikit-image is an image processing library that implements algorithms and utilities for use in research, education and industry applications. It is released under the liberal Modified BSD open source license, provides a well-documented API in the Python programming language, and is developed by an active, international team of collaborators. In this paper we highlight the advantages of open source to achieve the goals of the scikit-image library, and we showcase several real-world image processing applications that use scikit-image. More information can be found on the project homepage, http://scikit-image.org.

Micellar and antibody-targeted polymer therapeutics

Czech Academy of Sciences Publication Activity Database

Etrych, Tomáš; Chytil, Petr; Kovář, Lubomír; Říhová, Blanka; Ulbrich, Karel

2010-01-01

Roč. 295, - (2010), s. 1-12 ISSN 1022-1360. [Prague Meetings on Macromolecules /73./ New Frontiers in Macromolecular Science: From Macromolecular Concepts of Living Matter to Polymers for Better Quality of Life. Prague, 05.07.2009-09.07.2009] R&D Projects: GA AV ČR IAA400500806; GA AV ČR IAAX00500803; GA MŠk 1M0505 Institutional research plan: CEZ:AV0Z40500505; CEZ:AV0Z50200510 Keywords : doxorubicin * drug delivery systems * HPMA copolymers Subject RIV: CD - Macromolecular Chemistry

Automatic UAV Image Geo-Registration by Matching UAV Images to Georeferenced Image Data

Directory of Open Access Journals (Sweden)

Xiangyu Zhuo

2017-04-01

Full Text Available Recent years have witnessed the fast development of UAVs (unmanned aerial vehicles. As an alternative to traditional image acquisition methods, UAVs bridge the gap between terrestrial and airborne photogrammetry and enable flexible acquisition of high resolution images. However, the georeferencing accuracy of UAVs is still limited by the low-performance on-board GNSS and INS. This paper investigates automatic geo-registration of an individual UAV image or UAV image blocks by matching the UAV image(s with a previously taken georeferenced image, such as an individual aerial or satellite image with a height map attached or an aerial orthophoto with a DSM (digital surface model attached. As the biggest challenge for matching UAV and aerial images is in the large differences in scale and rotation, we propose a novel feature matching method for nadir or slightly tilted images. The method is comprised of a dense feature detection scheme, a one-to-many matching strategy and a global geometric verification scheme. The proposed method is able to find thousands of valid matches in cases where SIFT and ASIFT fail. Those matches can be used to geo-register the whole UAV image block towards the reference image data. When the reference images offer high georeferencing accuracy, the UAV images can also be geolocalized in a global coordinate system. A series of experiments involving different scenarios was conducted to validate the proposed method. The results demonstrate that our approach achieves not only decimeter-level registration accuracy, but also comparable global accuracy as the reference images.

Structural alterations in rat liver proteins due to streptozotocin-induced diabetes and the recovery effect of selenium: Fourier transform infrared microspectroscopy and neural network study

Science.gov (United States)

Bozkurt, Ozlem; Haman Bayari, Sevgi; Severcan, Mete; Krafft, Christoph; Popp, Jürgen; Severcan, Feride

2012-07-01

The relation between protein structural alterations and tissue dysfunction is a major concern as protein fibrillation and/or aggregation due to structural alterations has been reported in many disease states. In the current study, Fourier transform infrared microspectroscopic imaging has been used to investigate diabetes-induced changes on protein secondary structure and macromolecular content in streptozotocin-induced diabetic rat liver. Protein secondary structural alterations were predicted using neural network approach utilizing the amide I region. Moreover, the role of selenium in the recovery of diabetes-induced alterations on macromolecular content and protein secondary structure was also studied. The results revealed that diabetes induced a decrease in lipid to protein and glycogen to protein ratios in diabetic livers. Significant alterations in protein secondary structure were observed with a decrease in α-helical and an increase in β-sheet content. Both doses of selenium restored diabetes-induced changes in lipid to protein and glycogen to protein ratios. However, low-dose selenium supplementation was not sufficient to recover the effects of diabetes on protein secondary structure, while a higher dose of selenium fully restored diabetes-induced alterations in protein structure.

Markerless registration for image guided surgery. Preoperative image, intraoperative video image, and patient

International Nuclear Information System (INIS)

Kihara, Tomohiko; Tanaka, Yuko

1998-01-01

Real-time and volumetric acquisition of X-ray CT, MR, and SPECT is the latest trend of the medical imaging devices. A clinical challenge is to use these multi-modality volumetric information complementary on patient in the entire diagnostic and surgical processes. The intraoperative image and patient integration intents to establish a common reference frame by image in diagnostic and surgical processes. This provides a quantitative measure during surgery, for which we have been relied mostly on doctors' skills and experiences. The intraoperative image and patient integration involves various technologies, however, we think one of the most important elements is the development of markerless registration, which should be efficient and applicable to the preoperative multi-modality data sets, intraoperative image, and patient. We developed a registration system which integrates preoperative multi-modality images, intraoperative video image, and patient. It consists of a real-time registration of video camera for intraoperative use, a markerless surface sampling matching of patient and image, our previous works of markerless multi-modality image registration of X-ray CT, MR, and SPECT, and an image synthesis on video image. We think these techniques can be used in many applications which involve video camera like devices such as video camera, microscope, and image Intensifier. (author)

Image processing and recognition for biological images.

Science.gov (United States)

Uchida, Seiichi

2013-05-01

This paper reviews image processing and pattern recognition techniques, which will be useful to analyze bioimages. Although this paper does not provide their technical details, it will be possible to grasp their main tasks and typical tools to handle the tasks. Image processing is a large research area to improve the visibility of an input image and acquire some valuable information from it. As the main tasks of image processing, this paper introduces gray-level transformation, binarization, image filtering, image segmentation, visual object tracking, optical flow and image registration. Image pattern recognition is the technique to classify an input image into one of the predefined classes and also has a large research area. This paper overviews its two main modules, that is, feature extraction module and classification module. Throughout the paper, it will be emphasized that bioimage is a very difficult target for even state-of-the-art image processing and pattern recognition techniques due to noises, deformations, etc. This paper is expected to be one tutorial guide to bridge biology and image processing researchers for their further collaboration to tackle such a difficult target. © 2013 The Author Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

Nucleic Acid Quadratic Indices of the “Macromolecular Graph’s Nucleotides Adjacency Matrix”. Modeling of Footprints after the Interaction of Paromomycin with the HIV-1 Ψ-RNA Packaging Region

Directory of Open Access Journals (Sweden)

Eduardo A. Castro

2004-11-01

Full Text Available This report describes a new set of macromolecular descriptors of relevance to nucleic acid QSAR/QSPR studies, nucleic acids’ quadratic indices. These descriptors are calculated from the macromolecular graph’s nucleotide adjacency matrix. A study of the interaction of the antibiotic Paromomycin with the packaging region of the RNA present in type-1 HIV illustrates this approach. A linear discriminant function gave rise to excellent discrimination between 90.10% (91/101 and 81.82% (9/11 of interacting/noninteracting sites of nucleotides in training and test set, respectively. The LOO crossvalidation procedure was used to assess the stability and predictability of the model. Using this approach, the classification model has shown a LOO global good classification of 91.09%. In addition, the model’s overall predictability oscillates from 89.11% until 87.13%, when n varies from 2 to 3 in leave-n-out jackknife method. This value stabilizes around 88.12% when n was > 3. On the other hand, a linear regression model predicted the local binding affinity constants [log K (10-4M-1] between a specific nucleotide and the aforementioned antibiotic. The linear model explains almost 92% of the variance of the experimental log K (R = 0.96 and s = 0.07 and LOO press statistics evidenced its predictive ability (q2 = 0.85 and scv = 0.09. These models also permit the interpretation of the driving forces of the interaction process. In this sense, developed equations involve short-reaching (k < 3, middle-reaching (4 < k < 9 and far-reaching (k = 10 or greater nucleotide’s quadratic indices. This situation points to electronic and topologic nucleotide’s backbone interactions control of the stability profile of Paromomycin-RNA complexes. Consequently, the present approach represents a novel and rather promising way to chem & bioinformatics research.

IMAGE DESCRIPTIONS FOR SKETCH BASED IMAGE RETRIEVAL

OpenAIRE

SAAVEDRA RONDO, JOSE MANUEL; SAAVEDRA RONDO, JOSE MANUEL

2008-01-01

Due to the massive use of Internet together with the proliferation of media devices, content based image retrieval has become an active discipline in computer science. A common content based image retrieval approach requires that the user gives a regular image (e.g, a photo) as a query. However, having a regular image as query may be a serious problem. Indeed, people commonly use an image retrieval system because they do not count on the desired image. An easy alternative way t...

Image formation and image analysis in electron microscopy

International Nuclear Information System (INIS)

Heel, M. van.

1981-01-01

This thesis covers various aspects of image formation and image analysis in electron microscopy. The imaging of relatively strong objects in partially coherent illumination, the coherence properties of thermionic emission sources and the detection of objects in quantum noise limited images are considered. IMAGIC, a fast, flexible and friendly image analysis software package is described. Intelligent averaging of molecular images is discussed. (C.F.)

ImageSURF: An ImageJ Plugin for Batch Pixel-Based Image Segmentation Using Random Forests

Directory of Open Access Journals (Sweden)

Aidan O'Mara

2017-11-01

Full Text Available Image segmentation is a necessary step in automated quantitative imaging. ImageSURF is a macro-compatible ImageJ2/FIJI plugin for pixel-based image segmentation that considers a range of image derivatives to train pixel classifiers which are then applied to image sets of any size to produce segmentations without bias in a consistent, transparent and reproducible manner. The plugin is available from ImageJ update site http://sites.imagej.net/ImageSURF/ and source code from https://github.com/omaraa/ImageSURF. Funding statement: This research was supported by an Australian Government Research Training Program Scholarship.

High Performance Macromolecular Material

National Research Council Canada - National Science Library

Forest, M

2002-01-01

.... In essence, most commercial high-performance polymers are processed through fiber spinning, following Nature and spider silk, which is still pound-for-pound the toughest liquid crystalline polymer...

Spectroscopy and atomic force microscopy of biomass.

Science.gov (United States)

Tetard, L; Passian, A; Farahi, R H; Kalluri, U C; Davison, B H; Thundat, T

2010-05-01

Scanning probe microscopy has emerged as a powerful approach to a broader understanding of the molecular architecture of cell walls, which may shed light on the challenge of efficient cellulosic ethanol production. We have obtained preliminary images of both Populus and switchgrass samples using atomic force microscopy (AFM). The results show distinctive features that are shared by switchgrass and Populus. These features may be attributable to the lignocellulosic cell wall composition, as the collected images exhibit the characteristic macromolecular globule structures attributable to the lignocellulosic systems. Using both AFM and a single case of mode synthesizing atomic force microscopy (MSAFM) to characterize Populus, we obtained images that clearly show the cell wall structure. The results are of importance in providing a better understanding of the characteristic features of both mature cells as well as developing plant cells. In addition, we present spectroscopic investigation of the same samples.

Fast processing of foreign fiber images by image blocking

Directory of Open Access Journals (Sweden)

Yutao Wu

2014-08-01

Full Text Available In the textile industry, it is always the case that cotton products are constitutive of many types of foreign fibers which affect the overall quality of cotton products. As the foundation of the foreign fiber automated inspection, image process exerts a critical impact on the process of foreign fiber identification. This paper presents a new approach for the fast processing of foreign fiber images. This approach includes five main steps, image block, image pre-decision, image background extraction, image enhancement and segmentation, and image connection. At first, the captured color images were transformed into gray-scale images; followed by the inversion of gray-scale of the transformed images ; then the whole image was divided into several blocks. Thereafter, the subsequent step is to judge which image block contains the target foreign fiber image through image pre-decision. Then we segment the image block via OSTU which possibly contains target images after background eradication and image strengthening. Finally, we connect those relevant segmented image blocks to get an intact and clear foreign fiber target image. The experimental result shows that this method of segmentation has the advantage of accuracy and speed over the other segmentation methods. On the other hand, this method also connects the target image that produce fractures therefore getting an intact and clear foreign fiber target image.

A method of image improvement in three-dimensional imaging

International Nuclear Information System (INIS)

Suto, Yasuzo; Huang, Tewen; Furuhata, Kentaro; Uchino, Masafumi.

1988-01-01

In general, image interpolation is required when the surface configurations of such structures as bones and organs are three-dimensionally constructed from the multi-sliced images obtained by CT. Image interpolation is a processing method whereby an artificial image is inserted between two adjacent slices to make spatial resolution equal to slice resolution in appearance. Such image interpolation makes it possible to increase the image quality of the constructed three-dimensional image. In our newly-developed algorithm, we have converted the presently and subsequently sliced images to distance images, and generated the interpolation images from these two distance images. As a result, compared with the previous method, three-dimensional images with better image quality have been constructed. (author)

Image processing with ImageJ

NARCIS (Netherlands)

Abramoff, M.D.; Magalhães, Paulo J.; Ram, Sunanda J.

2004-01-01

Wayne Rasband of NIH has created ImageJ, an open source Java-written program that is now at version 1.31 and is used for many imaging applications, including those that that span the gamut from skin analysis to neuroscience. ImageJ is in the public domain and runs on any operating system (OS).

Compositional images from the Diffraction Enhanced Imaging technique

International Nuclear Information System (INIS)

Hasnah, M.O.; Zhong, Z.; Parham, C.; Zhang, H.; Chapman, D.

2007-01-01

Diffraction Enhanced Imaging (DEI) derives X-ray contrast from absorption, refraction, and extinction. While the refraction angle image of DEI represents the gradient of the projected mass density of the object, the absorption image measures the projected attenuation (μt)-bar of an object. Using a simple integral method it has been shown that a mass density image (ρt)-bar can be obtained from the refraction angle image. It then is a simple matter to develop a combinational image by dividing these two images to create a μ/ρ image. The μ/ρ is a fundamental property of a material and is therefore useful for identifying the composition of an object. In projection X-ray imaging the μ/ρ image identifies the integrated composition of the elements along the beam path. When applied to DEI computed tomography (CT), the image identifies the composition in each voxel. This method presents a new type of spectroscopy based in radiography. We present the method of obtaining the compositional image, the results of experiments in which we verify the method with known standards and an application of the method to breast cancer imaging

Evaluation of pulmonary emphysema by the fused image of CT image and ventilation SPECT image

International Nuclear Information System (INIS)

Okuda, Ituko; Maruno, Hiromasa; Mori, Kazuaki; Kohno, Tadashi; Kokubo, Takashi

2007-01-01

We evaluated pulmonary emphysema using a diagnostic device that could obtain a CT image, a ventilation single photon emission computed tomography (SPECT) image and a lung perfusion SPECT image in one examination. The fused image made from the CT image and SPECT image had very little position gap between images, and the precision was high. From the fused image, we were able to detect the areas in which emphysematous change was the most marked in the CT image, while the accumulation decrease was most remarkable in the ventilation SPECT image. Thus it was possible to obtain an accurate status of pulmonary emphysema, and our method was regarded as a useful technique. (author)

Improving the Image Quality of Synthetic Transmit Aperture Ultrasound Images - Achieving Real-Time In-Vivo Imaging

DEFF Research Database (Denmark)

Gammelmark, Kim

in-vivo experiments, showed, that TMS imaging can increase the SNR by as much as 17 dB compared to the traditional imaging techniques, which improves the in-vivo image quality to a highly competitive level. An in-vivo evaluation of convex array TMS imaging for abdominal imaging applications......-vivo imaging, and that the obtained image quality is highly competitive with the techniques applied in current medical ultrasound scanners. Hereby, the goals of the PhD have been successfully achieved.......Synthetic transmit aperture (STA) imaging has the potential to increase the image quality of medical ultrasound images beyond the levels obtained by conventional imaging techniques (linear, phased, and convex array imaging). Currently, however, in-vivo applications of STA imaging is limited...

The effect of state medicaid case-mix payment on nursing home resident acuity.

Science.gov (United States)

Feng, Zhanlian; Grabowski, David C; Intrator, Orna; Mor, Vincent

2006-08-01

To examine the relationship between Medicaid case-mix payment and nursing home resident acuity. Longitudinal Minimum Data Set (MDS) resident assessments from 1999 to 2002 and Online Survey Certification and Reporting (OSCAR) data from 1996 to 2002, for all freestanding nursing homes in the 48 contiguous U.S. states. We used a facility fixed-effects model to examine the effect of introducing state case-mix payment on changes in nursing home case-mix acuity. Facility acuity was measured by aggregating the nursing case-mix index (NCMI) from the MDS using the Resource Utilization Group (Version III) resident classification system, separately for new admits and long-stay residents, and by an OSCAR-derived index combining a range of activity of daily living dependencies and special treatment measures. We followed facilities over the study period to create a longitudinal data file based on the MDS and OSCAR, respectively, and linked facilities with longitudinal data on state case-mix payment policies for the same period. Across three acuity measures and two data sources, we found that states shifting to case-mix payment increased nursing home acuity levels over the study period. Specifically, we observed a 2.5 percent increase in the average acuity of new admits and a 1.3 to 1.4 percent increase in the acuity of long-stay residents, following the introduction of case-mix payment. The adoption of case-mix payment increased access to care for higher acuity Medicaid residents.

Nuclear medicine imaging instrumentations for molecular imaging

International Nuclear Information System (INIS)

Chung, Yong Hyun; Song, Tae Yong; Choi, Yong

2004-01-01

Small animal models are extensively utilized in the study of biomedical sciences. Current animal experiments and analysis are largely restricted to in vitro measurements and need to sacrifice animals to perform tissue or molecular analysis. This prevents researchers from observing in vivo the natural evolution of the process under study. Imaging techniques can provide repeatedly in vivo anatomic and molecular information noninvasively. Small animal imaging systems have been developed to assess biological process in experimental animals and increasingly employed in the field of molecular imaging studies. This review outlines the current developments in nuclear medicine imaging instrumentations including fused multi-modality imaging systems for small animal imaging

Image registration of naval IR images

Science.gov (United States)

Rodland, Arne J.

1996-06-01

In a real world application an image from a stabilized sensor on a moving platform will not be 100 percent stabilized. There will always be a small unknown error in the stabilization due to factors such as dynamic deformations in the structure between sensor and reference Inertial Navigation Unit, servo inaccuracies, etc. For a high resolution imaging sensor this stabilization error causes the image to move several pixels in unknown direction between frames. TO be able to detect and track small moving objects from such a sensor, this unknown movement of the sensor image must be estimated. An algorithm that searches for land contours in the image has been evaluated. The algorithm searches for high contrast points distributed over the whole image. As long as moving objects in the scene only cover a small area of the scene, most of the points are located on solid ground. By matching the list of points from frame to frame, the movement of the image due to stabilization errors can be estimated and compensated. The point list is searched for points with diverging movement from the estimated stabilization error. These points are then assumed to be located on moving objects. Points assumed to be located on moving objects are gradually exchanged with new points located in the same area. Most of the processing is performed on the list of points and not on the complete image. The algorithm is therefore very fast and well suited for real time implementation. The algorithm has been tested on images from an experimental IR scanner. Stabilization errors were added artificially to the image such that the output from the algorithm could be compared with the artificially added stabilization errors.

The bio-crystallography beamline (BL41XU) at SPring-8

CERN Document Server

Kawamoto, M; Kamiya, N

2001-01-01

The bio-crystallography beamline (BL41XU), one of two pilot beamlines at SPring-8, was constructed using a standard in-vacuum-type undulator and opened for general users from domestic and overseas countries. Many tests and improvements were carried out on beamline elements and equipment for macromolecular crystallography, especially on the so-called 'pin-post' water cooling crystal of rotated-inclined double crystal monochromator. The maximum brilliance at sample position reached to 4x10 sup 1 sup 5 photons/s/mm sup 2 /mrad sup 2 at an X-ray energy of 11 keV. Commercially available X-ray detectors of CCD and imaging plate were installed in the experimental station. A beamline control software system for beam tracking and an on-line reader for large-format imaging plate were newly developed.

Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture

Science.gov (United States)

Lassahn, Gordon D.; Lancaster, Gregory D.; Apel, William A.; Thompson, Vicki S.

2013-01-08

Image portion identification methods, image parsing methods, image parsing systems, and articles of manufacture are described. According to one embodiment, an image portion identification method includes accessing data regarding an image depicting a plurality of biological substrates corresponding to at least one biological sample and indicating presence of at least one biological indicator within the biological sample and, using processing circuitry, automatically identifying a portion of the image depicting one of the biological substrates but not others of the biological substrates.

Tomographic image reconstruction using training images

DEFF Research Database (Denmark)

Soltani, Sara; Andersen, Martin Skovgaard; Hansen, Per Christian

2017-01-01

We describe and examine an algorithm for tomographic image reconstruction where prior knowledge about the solution is available in the form of training images. We first construct a non-negative dictionary based on prototype elements from the training images; this problem is formulated within...

Advanced Prodrug Strategies in Nucleoside and Non-Nucleoside Antiviral Agents: A Review of the Recent Five Years

Directory of Open Access Journals (Sweden)

Hanadi Sinokrot

2017-10-01

Full Text Available Background: Poor pharmacokinetic profiles and resistance are the main two drawbacks from which currently used antiviral agents suffer, thus make them excellent targets for research, especially in the presence of viral pandemics such as HIV and hepatitis C. Methods: The strategies employed in the studies covered in this review were sorted by the type of drug synthesized into ester prodrugs, targeted delivery prodrugs, macromolecular prodrugs, other nucleoside conjugates, and non-nucleoside drugs. Results: Utilizing the ester prodrug approach a novel isopropyl ester prodrug was found to be potent HIV integrase inhibitor. Further, employing the targeted delivery prodrug zanamivir and valine ester prodrug was made and shown a sole delivery of zanamivir. Additionally, VivaGel, a dendrimer macromolecular prodrug, was found to be very efficient and is now undergoing clinical trials. Conclusions: Of all the strategies employed (ester, targeted delivery, macromolecular, protides and nucleoside analogues, and non-nucleoside analogues prodrugs, the most promising are nucleoside analogues and macromolecular prodrugs. The macromolecular prodrug VivaGel works by two mechanisms: envelope mediated and receptor mediated disruption. Nucleotide analogues have witnessed productive era in the recent past few years. The era of non-interferon based treatment of hepatitis (through direct inhibitors of NS5A has dawned.

Image quality of digital mammography images produced using wet and dry laser imaging systems

International Nuclear Information System (INIS)

Al Khalifah, K.; Brindhaban, A.; AlArfaj, R.; Jassim, O.

2006-01-01

Introduction: A study was carried out to compare the quality of digital mammographic images printed or processed by a wet laser imaging system and a dedicated mammographic dry laser imaging system. Material and methods: Digital images of a tissue equivalent breast phantom were obtained using a GE Senographe 2000D digital mammography system and different target/filter combinations of the X-ray tube. These images were printed on films using the Fuji FL-IM D wet laser imaging system and the Kodak DryView 8600 dry laser imaging system. The quality of images was assessed in terms of detectability of microcalcifications and simulated tumour masses by five radiologists. In addition, the contrast index and speed index of the two systems were measured using the step wedge in the phantom. The unpaired, unequal variance t-test was used to test any statistically significant differences. Results: There were no significant (p < 0.05) differences between the images printed using the two systems in terms of microcalcification and tumour mass detectability. The wet system resulted in slightly higher contrast index while the dry system showed significantly higher speed index. Conclusion: Both wet and dry laser imaging systems can produce mammography images of good quality on which 0.2 mm microcalcifications and 2 mm tumour masses can be detected. Dry systems are preferable due to the absence of wet chemical processing and solid or liquid chemical waste. The wet laser imaging systems, however, still represent a useful alternative to dry laser imaging systems for mammography studies

Macromolecular contrast media. A new approach for characterising breast tumors with MR-mammography; Makromolekulare Kontrastmittel fuer die MR-Mammographie. Ein neuer Ansatz fuer die Charakterisierung von Mammatumoren

Energy Technology Data Exchange (ETDEWEB)

Daldrup, H.E. [Contrast Media Lab., Dept. of Radiology, California Univ., San Francisco, CA (United States)]|[Muenster Univ. (Germany). Inst. fuer Klinische Radiologie; Roberts, T.P.L.; Roberts, H.C. [Contrast Media Lab., Dept. of Radiology, California Univ., San Francisco, CA (United States)]|[Mainz Univ. (Germany). Klinik und Poliklinik fuer Radiologie; Muehler, A. [Contrast Media Lab., Dept. of Radiology, California Univ., San Francisco, CA (United States)]|[Berlex Laboratories, Wayne, NJ (United States); Gossmann, A. [Contrast Media Lab., Dept. of Radiology, California Univ., San Francisco, CA (United States)]|[Koeln Univ. (Germany). Inst. und Poliklinik fuer Radiologische Diagnostik; Wendland, M.; Brasch, R.C. [Muenster Univ. (Germany). Inst. fuer Klinische Radiologie; Rosenau, W. [California Univ., San Francisco, CA (United States). Dept. of Pathology

1997-09-01

The value of macromolecular contrast agents (MMCM) for the characterization of benign and malignant breast tumors will be demonstrated in this review. Animal studies suggest a high potential of MMCM to increase the specificity of MR-mammography. The concept of tumor differentiation is based on the pathological hyperpermeability of microvessels in malignant tumors. MMCM show a leak into the interstitium of carcinomas, whereas they are confined to the intravascular space in benign tumors. Capabilities and limitations of the MMCM-prototype. Albumin-Gd-DTPA, for breast tumor characterization will be summarized and compared to the standard low molecular weight contrast agent Gd-DTPA. Initial experience with new MMCM, such as Dendrimers, Gd-DTPA-Polylysine and MS-325 will be outlined. The potential of `blood-pool`-iron oxides, such as AMI-227 for the evaluation of tumor microvascular permeabilities will be discussed. (orig.) [Deutsch] Diese Uebersicht stellt den Stellenwert makromolekularer Kontrastmittel (MMKM) fuer die MR-tomographische Charakterisierung von benignen und malignen Mammatumoren dar. Aufgrund experimenteller Studien lassen MMKM eine signifikante Verbesserung der Spezifitaet der dynamischen kontrastmittelunterstuetzten MR-Mammographie erwarten. Das differentialdiagnostische Konzept beruht auf der pathologischen Hyperpermeabilitaet von Kapillaren in Karzinomen, die einen MMKM-Austritt in das Tumorinterstitium bedingt, waehrend die intakten Kapillaren benigner Tumoren nicht permeabel fuer MMKM sind. Diagnostische Moeglichkeiten und Grenzen des MMKM-Prototyps, Albumin-Gd-DTPA (92 kD), werden dargestellt und mit dem niedermolekularen Standard-Kontrastmittel Gd-DTPA (500 D) verglichen. Erste Erfahrungen mit neuen, fuer die klinische Anwendung optimierten MMKM-Praeparaten, wie das Kaskadenpolymer, Gd-DTPA-Polylysine und das MS-325 werden vorgestellt. Das Potential von Blood-pool-Eisenoxidpraeparaten, z.B. AMI-227, fuer die Bestimmung von

Television Images and Adolescent Girls' Body Image Disturbance.

Science.gov (United States)

Botta, Renee A.

1999-01-01

Contributes to scholarship on the effects of media images on adolescents, using social-comparison theory and critical-viewing theory. Finds that media do have an impact on body-image disturbance. Suggests that body-image processing is the key to understanding how television images affect adolescent girls' body-image attitudes and behaviors. (SR)

To Image...or Not to Image?

Science.gov (United States)

Bruley, Karina

1996-01-01

Provides a checklist of considerations for installing document image processing with an electronic document management system. Other topics include scanning; indexing; the image file life cycle; benefits of imaging; document-driven workflow; and planning for workplace changes like postsorting, creating a scanning room, redeveloping job tasks and…

Edge-based correlation image registration for multispectral imaging

Science.gov (United States)

Nandy, Prabal [Albuquerque, NM

2009-11-17

Registration information for images of a common target obtained from a plurality of different spectral bands can be obtained by combining edge detection and phase correlation. The images are edge-filtered, and pairs of the edge-filtered images are then phase correlated to produce phase correlation images. The registration information can be determined based on these phase correlation images.

ImageSURF MOAB2 Image Example

OpenAIRE

O'Mara, Aidan R; Collins, Jessica M; King, Anna E; Vickers, James C; Kirkcaldie, Matthew T K

2017-01-01

A set of 2000x2000 confocal fluorescence images of MOAB2-labelled cortex from APPswe/PS1dE9 mouse models of Alzheimer's disease, sparsely annotated pixel labels and reference segmentation examples. Pixels are annotated as signal (red 0xFFFF0000) and background (blue 0xFF0000FF). Images were captured as stitched 12-bit greyscale single-plane images and cropped to size. Image acquisition was performed at 561nm excitation and 615nm emission wavelengths using a Perkin Elmer Ultraview VOX ima...

Transformation invariant image indexing and retrieval for image databases

NARCIS (Netherlands)

Gevers, Th.; Smeulders, A.W.M.

1994-01-01

This paper presents a novel design of an image database system which supports storage, indexing and retrieval of images by content. The image retrieval methodology is based on the observation that images can be discriminated by the presence of image objects and their spatial relations. Images in the

Image processing of integrated video image obtained with a charged-particle imaging video monitor system

International Nuclear Information System (INIS)

Iida, Takao; Nakajima, Takehiro

1988-01-01

A new type of charged-particle imaging video monitor system was constructed for video imaging of the distributions of alpha-emitting and low-energy beta-emitting nuclides. The system can display not only the scintillation image due to radiation on the video monitor but also the integrated video image becoming gradually clearer on another video monitor. The distortion of the image is about 5% and the spatial resolution is about 2 line pairs (lp)mm -1 . The integrated image is transferred to a personal computer and image processing is performed qualitatively and quantitatively. (author)

Hyperspectral small animal fluorescence imaging: spectral selection imaging

Science.gov (United States)

Leavesley, Silas; Jiang, Yanan; Patsekin, Valery; Hall, Heidi; Vizard, Douglas; Robinson, J. Paul

2008-02-01

Molecular imaging is a rapidly growing area of research, fueled by needs in pharmaceutical drug-development for methods for high-throughput screening, pre-clinical and clinical screening for visualizing tumor growth and drug targeting, and a growing number of applications in the molecular biology fields. Small animal fluorescence imaging employs fluorescent probes to target molecular events in vivo, with a large number of molecular targeting probes readily available. The ease at which new targeting compounds can be developed, the short acquisition times, and the low cost (compared to microCT, MRI, or PET) makes fluorescence imaging attractive. However, small animal fluorescence imaging suffers from high optical scattering, absorption, and autofluorescence. Much of these problems can be overcome through multispectral imaging techniques, which collect images at different fluorescence emission wavelengths, followed by analysis, classification, and spectral deconvolution methods to isolate signals from fluorescence emission. We present an alternative to the current method, using hyperspectral excitation scanning (spectral selection imaging), a technique that allows excitation at any wavelength in the visible and near-infrared wavelength range. In many cases, excitation imaging may be more effective at identifying specific fluorescence signals because of the higher complexity of the fluorophore excitation spectrum. Because the excitation is filtered and not the emission, the resolution limit and image shift imposed by acousto-optic tunable filters have no effect on imager performance. We will discuss design of the imager, optimizing the imager for use in small animal fluorescence imaging, and application of spectral analysis and classification methods for identifying specific fluorescence signals.

Preparing diagnostic 3D images for image registration with planning CT images

International Nuclear Information System (INIS)

Tracton, Gregg S.; Miller, Elizabeth P.; Rosenman, Julian; Chang, Sha X.; Sailer, Scott; Boxwala, Azaz; Chaney, Edward L.

1997-01-01

Purpose: Pre-radiotherapy (pre-RT) tomographic images acquired for diagnostic purposes often contain important tumor and/or normal tissue information which is poorly defined or absent in planning CT images. Our two years of clinical experience has shown that computer-assisted 3D registration of pre-RT images with planning CT images often plays an indispensable role in accurate treatment volume definition. Often the only available format of the diagnostic images is film from which the original 3D digital data must be reconstructed. In addition, any digital data, whether reconstructed or not, must be put into a form suitable for incorporation into the treatment planning system. The purpose of this investigation was to identify all problems that must be overcome before this data is suitable for clinical use. Materials and Methods: In the past two years we have 3D-reconstructed 300 diagnostic images from film and digital sources. As a problem was discovered we built a software tool to correct it. In time we collected a large set of such tools and found that they must be applied in a specific order to achieve the correct reconstruction. Finally, a toolkit (ediScan) was built that made all these tools available in the proper manner via a pleasant yet efficient mouse-based user interface. Results: Problems we discovered included different magnifications, shifted display centers, non-parallel image planes, image planes not perpendicular to the long axis of the table-top (shearing), irregularly spaced scans, non contiguous scan volumes, multiple slices per film, different orientations for slice axes (e.g. left-right reversal), slices printed at window settings corresponding to tissues of interest for diagnostic purposes, and printing artifacts. We have learned that the specific steps to correct these problems, in order of application, are: Also, we found that fast feedback and large image capacity (at least 2000 x 2000 12-bit pixels) are essential for practical application

Performances of different protocols for exocellular polysaccharides extraction from milk acid gels: Application to yogurt.

Science.gov (United States)

Nguyen, An Thi-Binh; Nigen, Michaël; Jimenez, Luciana; Ait-Abderrahim, Hassina; Marchesseau, Sylvie; Picart-Palmade, Laetitia

2018-01-15

Dextran or xanthan were used as model exocellular polysaccharides (EPS) to compare the extraction efficiency of EPS from skim milk acid gels using three different protocols. Extraction yields, residual protein concentrations and the macromolecular properties of extracted EPS were determined. For both model EPS, the highest extraction yield (∼80%) was obtained when samples were heated in acidic conditions at the first step of extraction (Protocol 1). Protocols that contained steps of acid/ethanol precipitation without heating (Protocols 2 and 3) show lower extraction yields (∼55%) but allow a better preservation of the EPS macromolecular properties. Changing the pH of acid gels up to 7 before extraction (Protocol 3) improved the extraction yield of anionic EPS without effect on the macromolecular properties of EPS. Protocol 1 was then applied for the quantification of EPS produced during the yogurt fermentation, while Protocol 3 was dedicated to their macromolecular characterization. Copyright © 2017 Elsevier Ltd. All rights reserved.

Maxillofacial imaging

Energy Technology Data Exchange (ETDEWEB)

Larheim, T.A. [Oslo Univ. (Norway). Dept. of Maxillofacial Radiology; Westesson, P.L. [Univ. of Rochester School of Medicine and Dentistry, NY (United States). Div. of Diagnostic and Interventional Radiology

2006-07-01

Maxillofacial imaging has evolved dramatically over the past two decades with development of new cross-sectional imaging techniques. Traditional maxillofacial imaging was based on plain films and dental imaging. However, today's advanced imaging techniques with CT and MRI have only been partially implemented for maxillofacial questions. This book bridges the gap between traditional maxillofacial imaging and advanced medical imaging. We have applied CT and MRI to a variety of maxillofacial cases and these are illustrated with high-quality images and multiple planes. A comprehensive chapter on imaging anatomy is also included. This book is useful for oral and maxillofacial radiologists, oral and maxillofacial surgeons, dentists, radiologists, plastic surgeons, head and neck surgeons, and others that work with severe maxillofacial disorders. (orig.)

Separation method of heavy-ion particle image from gamma-ray mixed images using an imaging plate

CERN Document Server

Yamadera, A; Ohuchi, H; Nakamura, T; Fukumura, A

1999-01-01

We have developed a separation method of alpha-ray and gamma-ray images using the imaging plate (IP). The IP from which the first image was read out by an image reader was annealed at 50 deg. C for 2 h in a drying oven and the second image was read out by the image reader. It was found out that an annealing ratio, k, which is defined as a ratio of the photo-stimulated luminescence (PSL) density at the first measurement to that at the second measurement, was different for alpha rays and gamma rays. By subtracting the second image multiplied by a factor of k from the first image, the alpha-ray image was separated from the alpha and gamma-ray mixed images. This method was applied to identify the images of helium, carbon and neon particles of high energies using the heavy-ion medical accelerator, HIMAC. (author)

The Effects of a Macromolecular Charring Agent with Gas Phase and Condense Phase Synergistic Flame Retardant Capability on the Properties of PP/IFR Composites

Science.gov (United States)

Chen, Hongda; Wang, Jihui; Ding, Anxin; Han, Xia; Sun, Ziheng

2018-01-01

In order to improve the efficiency of intumescent flame retardants (IFRs), a novel macromolecular charring agent named poly(ethanediamine-1,3,5-triazine-p-4-amino-2,2,6,6-tetramethylpiperidine) (PETAT) with gas phase and condense phase synergistic flame-retardant capability was synthesized and subsequently dispersed into polypropylene (PP) in combination with ammonium polyphosphate (APP) via a melt blending method. The chemical structure of PETAT was investigated by Fourier transform infrared spectroscopy (FTIR), and 1H nuclear magnetic resonance (NMR) spectroscopy. Thermal properties of the PETAT and IFR systems were tested by thermogravimetric-derivative thermogravimetric analysis (TGA-DTG) and thermogravimetry–Fourier transform infrared spectroscopy (TG-FTIR). The mechanical properties, thermal stability, flame-retardant properties, water resistance, and structures of char residue in flame-retardant composites were characterized using tensile and flexural strength property tests, TGA, limiting oxygen index (LOI) values before and after soaking, underwritten laboratory-94 (UL-94) vertical burning test, cone calorimetric test (CCT), scanning electron microscopy with energy dispersive X-ray spectrometry (SEM-EDXS), and FTIR. The results indicated that PETAT was successfully synthesized, and when the ratio of APP to PETAT was 2:1 with 25 wt % loading, the novel IFR system could reduce the deterioration of tensile strength and enhance the flexural strength of composites. Meanwhile, the flame-retardant composite was able to pass the UL-94 V-0 rating with an LOI value of 30.3%, and the peak of heat release rate (PHRR), total heat release (THR), and material fire hazard values were considerably decreased compared with others. In addition, composites also exhibited excellent water resistance properties compared with traditional IFR composites. SEM-EDXS and FTIR analyses of the char residues, as well as TG-FTIR analyses of IFR were used to investigate the flame

The Effects of a Macromolecular Charring Agent with Gas Phase and Condense Phase Synergistic Flame Retardant Capability on the Properties of PP/IFR Composites

Directory of Open Access Journals (Sweden)

Hongda Chen

2018-01-01

Full Text Available In order to improve the efficiency of intumescent flame retardants (IFRs, a novel macromolecular charring agent named poly(ethanediamine-1,3,5-triazine-p-4-amino-2,2,6,6-tetramethylpiperidine (PETAT with gas phase and condense phase synergistic flame-retardant capability was synthesized and subsequently dispersed into polypropylene (PP in combination with ammonium polyphosphate (APP via a melt blending method. The chemical structure of PETAT was investigated by Fourier transform infrared spectroscopy (FTIR, and 1H nuclear magnetic resonance (NMR spectroscopy. Thermal properties of the PETAT and IFR systems were tested by thermogravimetric-derivative thermogravimetric analysis (TGA-DTG and thermogravimetry–Fourier transform infrared spectroscopy (TG-FTIR. The mechanical properties, thermal stability, flame-retardant properties, water resistance, and structures of char residue in flame-retardant composites were characterized using tensile and flexural strength property tests, TGA, limiting oxygen index (LOI values before and after soaking, underwritten laboratory-94 (UL-94 vertical burning test, cone calorimetric test (CCT, scanning electron microscopy with energy dispersive X-ray spectrometry (SEM-EDXS, and FTIR. The results indicated that PETAT was successfully synthesized, and when the ratio of APP to PETAT was 2:1 with 25 wt % loading, the novel IFR system could reduce the deterioration of tensile strength and enhance the flexural strength of composites. Meanwhile, the flame-retardant composite was able to pass the UL-94 V-0 rating with an LOI value of 30.3%, and the peak of heat release rate (PHRR, total heat release (THR, and material fire hazard values were considerably decreased compared with others. In addition, composites also exhibited excellent water resistance properties compared with traditional IFR composites. SEM-EDXS and FTIR analyses of the char residues, as well as TG-FTIR analyses of IFR were used to investigate the flame

The Effects of a Macromolecular Charring Agent with Gas Phase and Condense Phase Synergistic Flame Retardant Capability on the Properties of PP/IFR Composites.

Science.gov (United States)

Chen, Hongda; Wang, Jihui; Ni, Aiqing; Ding, Anxin; Han, Xia; Sun, Ziheng

2018-01-11

In order to improve the efficiency of intumescent flame retardants (IFRs), a novel macromolecular charring agent named poly(ethanediamine-1,3,5-triazine-p-4-amino-2,2,6,6-tetramethylpiperidine) (PETAT) with gas phase and condense phase synergistic flame-retardant capability was synthesized and subsequently dispersed into polypropylene (PP) in combination with ammonium polyphosphate (APP) via a melt blending method. The chemical structure of PETAT was investigated by Fourier transform infrared spectroscopy (FTIR), and ¹H nuclear magnetic resonance (NMR) spectroscopy. Thermal properties of the PETAT and IFR systems were tested by thermogravimetric-derivative thermogravimetric analysis (TGA-DTG) and thermogravimetry-Fourier transform infrared spectroscopy (TG-FTIR). The mechanical properties, thermal stability, flame-retardant properties, water resistance, and structures of char residue in flame-retardant composites were characterized using tensile and flexural strength property tests, TGA, limiting oxygen index (LOI) values before and after soaking, underwritten laboratory-94 (UL-94) vertical burning test, cone calorimetric test (CCT), scanning electron microscopy with energy dispersive X-ray spectrometry (SEM-EDXS), and FTIR. The results indicated that PETAT was successfully synthesized, and when the ratio of APP to PETAT was 2:1 with 25 wt % loading, the novel IFR system could reduce the deterioration of tensile strength and enhance the flexural strength of composites. Meanwhile, the flame-retardant composite was able to pass the UL-94 V-0 rating with an LOI value of 30.3%, and the peak of heat release rate (PHRR), total heat release (THR), and material fire hazard values were considerably decreased compared with others. In addition, composites also exhibited excellent water resistance properties compared with traditional IFR composites. SEM-EDXS and FTIR analyses of the char residues, as well as TG-FTIR analyses of IFR were used to investigate the flame

Molecular nucleation mechanisms and control strategies for crystal polymorph selection

Science.gov (United States)

van Driessche, Alexander E. S.; van Gerven, Nani; Bomans, Paul H. H.; Joosten, Rick R. M.; Friedrich, Heiner; Gil-Carton, David; Sommerdijk, Nico A. J. M.; Sleutel, Mike

2018-04-01

The formation of condensed (compacted) protein phases is associated with a wide range of human disorders, such as eye cataracts, amyotrophic lateral sclerosis, sickle cell anaemia and Alzheimer’s disease. However, condensed protein phases have their uses: as crystals, they are harnessed by structural biologists to elucidate protein structures, or are used as delivery vehicles for pharmaceutical applications. The physiochemical properties of crystals can vary substantially between different forms or structures (‘polymorphs’) of the same macromolecule, and dictate their usability in a scientific or industrial context. To gain control over an emerging polymorph, one needs a molecular-level understanding of the pathways that lead to the various macroscopic states and of the mechanisms that govern pathway selection. However, it is still not clear how the embryonic seeds of a macromolecular phase are formed, or how these nuclei affect polymorph selection. Here we use time-resolved cryo-transmission electron microscopy to image the nucleation of crystals of the protein glucose isomerase, and to uncover at molecular resolution the nucleation pathways that lead to two crystalline states and one gelled state. We show that polymorph selection takes place at the earliest stages of structure formation and is based on specific building blocks for each space group. Moreover, we demonstrate control over the system by selectively forming desired polymorphs through site-directed mutagenesis, specifically tuning intermolecular bonding or gel seeding. Our results differ from the present picture of protein nucleation, in that we do not identify a metastable dense liquid as the precursor to the crystalline state. Rather, we observe nucleation events that are driven by oriented attachments between subcritical clusters that already exhibit a degree of crystallinity. These insights suggest ways of controlling macromolecular phase transitions, aiding the development of protein

MRI monitoring of tumor response following angiogenesis inhibition in an experimental human breast cancer model

International Nuclear Information System (INIS)

Turetschek, Karl; Preda, Anda; Shames, David M.; Novikov, Viktor; Roberts, Timothy P.L.; Fu, Yanjun; Brasch, Robert C.; Floyd, Eugenia; Carter, Wayne O.; Wood, Jeanette M.

2003-01-01

The aim of this study was to evaluate the potential of dynamic magnetic resonance imaging (MRI) enhanced by macromolecular contrast agents to monitor noninvasively the therapeutic effect of an anti-angiogenesis VEGF receptor kinase inhibitor in an experimental cancer model. MDA-MB-435, a poorly differentiated human breast cancer cell line, was implanted into the mammary fat pad in 20 female homozygous athymic rats. Animals were assigned randomly to a control (n=10) or drug treatment group (n=10). Baseline dynamic MRI was performed on sequential days using albumin-(GdDTPA) 30 (6.0 nm diameter) and ultrasmall superparamagnetic iron oxide (USPIO) particles (30 nm diameter). Subjects were treated either with PTK787/ZK 222584, a VEGF receptor tyrosine kinase inhibitor, or saline given orally twice daily for 1 week followed by repeat MRI examinations serially using each contrast agent. Employing a unidirectional kinetic model comprising the plasma and interstitial water compartments, tumor microvessel characteristics including fractional plasma volume and transendothelial permeability (K PS ) were estimated for each contrast medium. Tumor growth and the microvascular density, a histologic surrogate of angiogenesis, were also measured. Control tumors significantly increased (P PS ) based on MRI assays using both macromolecular contrast media. In contrast, tumor growth was significantly reduced (P PS values declined slightly. Estimated values for the fractional plasma volume did not differ significantly between treatment groups or contrast agents. Microvascular density counts correlated fairly with the tumor growth rate (r=0.64) and were statistically significant higher (P PS ), using either of two macromolecular contrast media, were able to detect effects of treatment with a VEGF receptor tyrosine kinase inhibitor on tumor vascular permeability. In a clinical setting such quantitative MRI measurements could be used to monitor tumor anti-angiogenesis therapy. (orig.)

Registration of angiographic image on real-time fluoroscopic image for image-guided percutaneous coronary intervention.

Science.gov (United States)

Kim, Dongkue; Park, Sangsoo; Jeong, Myung Ho; Ryu, Jeha

2018-02-01

In percutaneous coronary intervention (PCI), cardiologists must study two different X-ray image sources: a fluoroscopic image and an angiogram. Manipulating a guidewire while alternately monitoring the two separate images on separate screens requires a deep understanding of the anatomy of coronary vessels and substantial training. We propose 2D/2D spatiotemporal image registration of the two images in a single image in order to provide cardiologists with enhanced visual guidance in PCI. The proposed 2D/2D spatiotemporal registration method uses a cross-correlation of two ECG series in each image to temporally synchronize two separate images and register an angiographic image onto the fluoroscopic image. A guidewire centerline is then extracted from the fluoroscopic image in real time, and the alignment of the centerline with vessel outlines of the chosen angiographic image is optimized using the iterative closest point algorithm for spatial registration. A proof-of-concept evaluation with a phantom coronary vessel model with engineering students showed an error reduction rate greater than 74% on wrong insertion to nontarget branches compared to the non-registration method and more than 47% reduction in the task completion time in performing guidewire manipulation for very difficult tasks. Evaluation with a small number of experienced doctors shows a potentially significant reduction in both task completion time and error rate for difficult tasks. The total registration time with real procedure X-ray (angiographic and fluoroscopic) images takes [Formula: see text] 60 ms, which is within the fluoroscopic image acquisition rate of 15 Hz. By providing cardiologists with better visual guidance in PCI, the proposed spatiotemporal image registration method is shown to be useful in advancing the guidewire to the coronary vessel branches, especially those difficult to insert into.

Multispectral image enhancement processing for microsat-borne imager

Science.gov (United States)

Sun, Jianying; Tan, Zheng; Lv, Qunbo; Pei, Linlin

2017-10-01

With the rapid development of remote sensing imaging technology, the micro satellite, one kind of tiny spacecraft, appears during the past few years. A good many studies contribute to dwarfing satellites for imaging purpose. Generally speaking, micro satellites weigh less than 100 kilograms, even less than 50 kilograms, which are slightly larger or smaller than the common miniature refrigerators. However, the optical system design is hard to be perfect due to the satellite room and weight limitation. In most cases, the unprocessed data captured by the imager on the microsatellite cannot meet the application need. Spatial resolution is the key problem. As for remote sensing applications, the higher spatial resolution of images we gain, the wider fields we can apply them. Consequently, how to utilize super resolution (SR) and image fusion to enhance the quality of imagery deserves studying. Our team, the Key Laboratory of Computational Optical Imaging Technology, Academy Opto-Electronics, is devoted to designing high-performance microsat-borne imagers and high-efficiency image processing algorithms. This paper addresses a multispectral image enhancement framework for space-borne imagery, jointing the pan-sharpening and super resolution techniques to deal with the spatial resolution shortcoming of microsatellites. We test the remote sensing images acquired by CX6-02 satellite and give the SR performance. The experiments illustrate the proposed approach provides high-quality images.

Enhancement of image contrast in linacgram through image processing

International Nuclear Information System (INIS)

Suh, Hyun Suk; Shin, Hyun Kyo; Lee, Re Na

2000-01-01

Conventional radiation therapy portal images gives low contrast images. The purpose of this study was to enhance image contrast of a linacgram by developing a low--cost image processing method. Chest linacgram was obtained by irradiating humanoid phantom and scanned using Diagnostic-Pro scanner for image processing. Several types of scan method were used in scanning. These include optical density scan, histogram equalized scan, linear histogram based scan, linear histogram independent scan, linear optical density scan, logarithmic scan, and power square root scan. The histogram distribution of the scanned images were plotted and the ranges of the gray scale were compared among various scan types. The scanned images were then transformed to the gray window by pallette fitting method and the contrast of the reprocessed portal images were evaluated for image improvement. Portal images of patients were also taken at various anatomic sites and the images were processed by Gray Scale Expansion (GSE) method. The patient images were analyzed to examine the feasibility of using the GSE technique in clinic. The histogram distribution showed that minimum and maximum gray scale ranges of 3192 and 21940 were obtained when the image was scanned using logarithmic method and square root method, respectively. Out of 256 gray scale, only 7 to 30% of the steps were used. After expanding the gray scale to full range, contrast of the portal images were improved. Experiment performed with patient image showed that improved identification of organs were achieved by GSE in portal images of knee joint, head and neck, lung, and pelvis. Phantom study demonstrated that the GSE technique improved image contrast of a linacgram. This indicates that the decrease in image quality resulting from the dual exposure, could be improved by expanding the gray scale. As a result, the improved technique will make it possible to compare the digitally reconstructed radiographs (DRR) and simulation image for

Mirror-Image Equivalence and Interhemispheric Mirror-Image Reversal.

Science.gov (United States)

Corballis, Michael C

2018-01-01

Mirror-image confusions are common, especially in children and in some cases of neurological impairment. They can be a special impediment in activities such as reading and writing directional scripts, where mirror-image patterns (such as b and d ) must be distinguished. Treating mirror images as equivalent, though, can also be adaptive in the natural world, which carries no systematic left-right bias and where the same object or event can appear in opposite viewpoints. Mirror-image equivalence and confusion are natural consequences of a bilaterally symmetrical brain. In the course of learning, mirror-image equivalence may be established through a process of symmetrization, achieved through homotopic interhemispheric exchange in the formation of memory circuits. Such circuits would not distinguish between mirror images. Learning to discriminate mirror-image discriminations may depend either on existing brain asymmetries, or on extensive learning overriding the symmetrization process. The balance between mirror-image equivalence and mirror-image discrimination may nevertheless be precarious, with spontaneous confusions or reversals, such as mirror writing, sometimes appearing naturally or as a manifestation of conditions like dyslexia.

Mirror-Image Equivalence and Interhemispheric Mirror-Image Reversal

Directory of Open Access Journals (Sweden)

Michael C. Corballis

2018-04-01

Full Text Available Mirror-image confusions are common, especially in children and in some cases of neurological impairment. They can be a special impediment in activities such as reading and writing directional scripts, where mirror-image patterns (such as b and d must be distinguished. Treating mirror images as equivalent, though, can also be adaptive in the natural world, which carries no systematic left-right bias and where the same object or event can appear in opposite viewpoints. Mirror-image equivalence and confusion are natural consequences of a bilaterally symmetrical brain. In the course of learning, mirror-image equivalence may be established through a process of symmetrization, achieved through homotopic interhemispheric exchange in the formation of memory circuits. Such circuits would not distinguish between mirror images. Learning to discriminate mirror-image discriminations may depend either on existing brain asymmetries, or on extensive learning overriding the symmetrization process. The balance between mirror-image equivalence and mirror-image discrimination may nevertheless be precarious, with spontaneous confusions or reversals, such as mirror writing, sometimes appearing naturally or as a manifestation of conditions like dyslexia.

Continuous imaging space in three-dimensional integral imaging

International Nuclear Information System (INIS)

Zhang Lei; Yang Yong; Wang Jin-Gang; Zhao Xing; Fang Zhi-Liang; Yuan Xiao-Cong

2013-01-01

We report an integral imaging method with continuous imaging space. This method simultaneously reconstructs real and virtual images in the virtual mode, with a minimum gap that separates the entire imaging space into real and virtual space. Experimental results show that the gap is reduced to 45% of that in a conventional integral imaging system with the same parameters. (electromagnetism, optics, acoustics, heat transfer, classical mechanics, and fluid dynamics)

Image reconstruction of dynamic infrared single-pixel imaging system

Science.gov (United States)

Tong, Qi; Jiang, Yilin; Wang, Haiyan; Guo, Limin

2018-03-01

Single-pixel imaging technique has recently received much attention. Most of the current single-pixel imaging is aimed at relatively static targets or the imaging system is fixed, which is limited by the number of measurements received through the single detector. In this paper, we proposed a novel dynamic compressive imaging method to solve the imaging problem, where exists imaging system motion behavior, for the infrared (IR) rosette scanning system. The relationship between adjacent target images and scene is analyzed under different system movement scenarios. These relationships are used to build dynamic compressive imaging models. Simulation results demonstrate that the proposed method can improve the reconstruction quality of IR image and enhance the contrast between the target and the background in the presence of system movement.

Stereoscopic Integrated Imaging Goggles for Multimodal Intraoperative Image Guidance.

Directory of Open Access Journals (Sweden)

Christopher A Mela

Full Text Available We have developed novel stereoscopic wearable multimodal intraoperative imaging and display systems entitled Integrated Imaging Goggles for guiding surgeries. The prototype systems offer real time stereoscopic fluorescence imaging and color reflectance imaging capacity, along with in vivo handheld microscopy and ultrasound imaging. With the Integrated Imaging Goggle, both wide-field fluorescence imaging and in vivo microscopy are provided. The real time ultrasound images can also be presented in the goggle display. Furthermore, real time goggle-to-goggle stereoscopic video sharing is demonstrated, which can greatly facilitate telemedicine. In this paper, the prototype systems are described, characterized and tested in surgeries in biological tissues ex vivo. We have found that the system can detect fluorescent targets with as low as 60 nM indocyanine green and can resolve structures down to 0.25 mm with large FOV stereoscopic imaging. The system has successfully guided simulated cancer surgeries in chicken. The Integrated Imaging Goggle is novel in 4 aspects: it is (a the first wearable stereoscopic wide-field intraoperative fluorescence imaging and display system, (b the first wearable system offering both large FOV and microscopic imaging simultaneously,

Imaging systems in nuclear medicine and image evaluation

International Nuclear Information System (INIS)

Beck, R.; Charleston, D.; Metz, C.

1980-01-01

This project deals with imaging systems in nuclear medicine and image evaluation and is presented as four subprojects. The goal of the first subproject is to improve diagnositc image quality by development of a general computer code for optimizing collimator design. The second subproject deals with a secondary emission and fluorescence technique for thyroid scanning while the third subproject emphasizes the need for more sophisticated image processing systems such as coherent optical spatial filtering systems and digital image processing. The fourth subproject presents a new approach for processing image data by taking into account the energy of each detected gamma-ray photon

Imaging sciences workshop

Energy Technology Data Exchange (ETDEWEB)

Candy, J.V.

1994-11-15

This workshop on the Imaging Sciences sponsored by Lawrence Livermore National Laboratory contains short abstracts/articles submitted by speakers. The topic areas covered include the following: Astronomical Imaging; biomedical imaging; vision/image display; imaging hardware; imaging software; Acoustic/oceanic imaging; microwave/acoustic imaging; computed tomography; physical imaging; imaging algorithms. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

PC image processing

International Nuclear Information System (INIS)

Hwa, Mok Jin Il; Am, Ha Jeng Ung

1995-04-01

This book starts summary of digital image processing and personal computer, and classification of personal computer image processing system, digital image processing, development of personal computer and image processing, image processing system, basic method of image processing such as color image processing and video processing, software and interface, computer graphics, video image and video processing application cases on image processing like satellite image processing, color transformation of image processing in high speed and portrait work system.

Lossy image compression for digital medical imaging systems

Science.gov (United States)

Wilhelm, Paul S.; Haynor, David R.; Kim, Yongmin; Nelson, Alan C.; Riskin, Eve A.

1990-07-01

Image compression at rates of 10:1 or greater could make PACS much more responsive and economically attractive. This paper describes a protocol for subjective and objective evaluation of the fidelity of compressed/decompressed images to the originals and presents the results ofits application to four representative and promising compression methods. The methods examined are predictive pruned tree-structured vector quantization, fractal compression, the discrete cosine transform with equal weighting of block bit allocation, and the discrete cosine transform with human visual system weighting of block bit allocation. Vector quantization is theoretically capable of producing the best compressed images, but has proven to be difficult to effectively implement. It has the advantage that it can reconstruct images quickly through a simple lookup table. Disadvantages are that codebook training is required, the method is computationally intensive, and achieving the optimum performance would require prohibitively long vector dimensions. Fractal compression is a relatively new compression technique, but has produced satisfactory results while being computationally simple. It is fast at both image compression and image reconstruction. Discrete cosine iransform techniques reproduce images well, but have traditionally been hampered by the need for intensive computing to compress and decompress images. A protocol was developed for side-by-side observer comparison of reconstructed images with originals. Three 1024 X 1024 CR (Computed Radiography) images and two 512 X 512 X-ray CT images were viewed at six bit rates (0.2, 0.4, 0.6, 0.9, 1.2, and 1.5 bpp for CR, and 1.0, 1.3, 1.6, 1.9, 2.2, 2.5 bpp for X-ray CT) by nine radiologists at the University of Washington Medical Center. The CR images were viewed on a Pixar II Megascan (2560 X 2048) monitor and the CT images on a Sony (1280 X 1024) monitor. The radiologists' subjective evaluations of image fidelity were compared to

Scintigraphic evaluation of the pharmacokinetics of a soluble polymeric drug carrier

International Nuclear Information System (INIS)

Pimm, M.V.; Perkins, A.C.; Hudecz, F.

1992-01-01

There is a growing interest in the use of macromolecular carriers for therapeutic agents. If these carriers can be labelled with an appropriate gamma-emitter, their biodistribution could be followed by scintigraphy. We have imaged the biodistribution of a synthetic branched polypeptide, based on a poly-L-lysine backbone (average molecular mass 45 kDa). The polymer was conjugated to diethylene triamine penta-acetic acid and labelled by chelation with indium-111. Mice were injected i.v. with labelled material and imaged with a gamma-camera with a pin-hole collimator. Images showed the majority of tracer remaining in the blood pool, but about 35% appeared in the urinary bladder within 1.5 h. When the 111 In-polymer was fractionated by gel filtration chromatography on S-300, the imaging showed that the early eluting material was retained, the intermediate showed some renal clearance, and the late was rapidly excreted. These findings show the value of gamma-scintigraphy for biodistribution studies with such polymeric drug carriers and its potential for clinical pharmacokinetic studies. (orig.)

Folic acid derivatives for PET imaging and therapy addressing folate receptor positive tumors

Energy Technology Data Exchange (ETDEWEB)

Schieferstein, Hanno

2013-07-01

conducted. The synthesis of the folate-boron clusters was straightforward. At first, a linker molecule based on maleic acid was synthesized, which was coupled to the boron cluster via Michael Addition of a thiol and alkene and subsequently coupled to the targeting moiety using CuAAC. The new conjugates of folate and boron clusters led to a significant increase of boron concentration in the cell of about 5-times compared to currently used and approved boron pharmaceuticals. Moreover, azido-folate derivatives were coupled to macromolecular carrier systems (pHPMA), which showed an enhanced and specific accumulation at target sites (up to 2.5-times) during in vivo experiments. A specific blockade could be observed up to 30% indicating an efficient targeting effect. A new kind of nanoparticles consisting of a PDLLA core and p((HPMA)-b-(LMA)) as surfactants were developed and successfully radiolabeled via {sup 18}F-click chemistry in good RCYs of 8±3%. The nanoparticles were obtained via the miniemulsion technique in combination with solvent evaporation. The {sup 18}F-labeled nanoparticles were applied to in vivo testing using a mouse model. PET imaging showed a ''mixed'' biodistribution of low molecular weight as well as high molecular weight systems, indicating a partial loss of the {sup 18}F-labeled surfactant. In conclusion, the presented work successfully utilized the FR-targeting concept in both, the diagnostic field (PET imaging) and for therapeutic approaches (BNCT, drug delivery systems). As a result, the high potential of FR-targeting in oncological applications has been shown and was confirmed by small animal PET imaging.

Folic acid derivatives for PET imaging and therapy addressing folate receptor positive tumors

International Nuclear Information System (INIS)

Schieferstein, Hanno

2013-01-01

the folate-boron clusters was straightforward. At first, a linker molecule based on maleic acid was synthesized, which was coupled to the boron cluster via Michael Addition of a thiol and alkene and subsequently coupled to the targeting moiety using CuAAC. The new conjugates of folate and boron clusters led to a significant increase of boron concentration in the cell of about 5-times compared to currently used and approved boron pharmaceuticals. Moreover, azido-folate derivatives were coupled to macromolecular carrier systems (pHPMA), which showed an enhanced and specific accumulation at target sites (up to 2.5-times) during in vivo experiments. A specific blockade could be observed up to 30% indicating an efficient targeting effect. A new kind of nanoparticles consisting of a PDLLA core and p((HPMA)-b-(LMA)) as surfactants were developed and successfully radiolabeled via 18 F-click chemistry in good RCYs of 8±3%. The nanoparticles were obtained via the miniemulsion technique in combination with solvent evaporation. The 18 F-labeled nanoparticles were applied to in vivo testing using a mouse model. PET imaging showed a ''mixed'' biodistribution of low molecular weight as well as high molecular weight systems, indicating a partial loss of the 18 F-labeled surfactant. In conclusion, the presented work successfully utilized the FR-targeting concept in both, the diagnostic field (PET imaging) and for therapeutic approaches (BNCT, drug delivery systems). As a result, the high potential of FR-targeting in oncological applications has been shown and was confirmed by small animal PET imaging.

Image Analysis for X-ray Imaging of Food

DEFF Research Database (Denmark)

Einarsdottir, Hildur

for quality and safety evaluation of food products. In this effort the fields of statistics, image analysis and statistical learning are combined, to provide analytical tools for determining the aforementioned food traits. The work demonstrated includes a quantitative analysis of heat induced changes......X-ray imaging systems are increasingly used for quality and safety evaluation both within food science and production. They offer non-invasive and nondestructive penetration capabilities to image the inside of food. This thesis presents applications of a novel grating-based X-ray imaging technique...... and defect detection in food. Compared to the complex three dimensional analysis of microstructure, here two dimensional images are considered, making the method applicable for an industrial setting. The advantages obtained by grating-based imaging are compared to conventional X-ray imaging, for both foreign...

Image Processing and Features Extraction of Fingerprint Images ...

African Journals Online (AJOL)

To demonstrate the importance of the image processing of fingerprint images prior to image enrolment or comparison, the set of fingerprint images in databases (a) and (b) of the FVC (Fingerprint Verification Competition) 2000 database were analyzed using a features extraction algorithm. This paper presents the results of ...

Image quality at synthetic brain magnetic resonance imaging in children

Energy Technology Data Exchange (ETDEWEB)

Lee, So Mi; Cho, Seung Hyun; Kim, Won Hwa; Kim, Hye Jung [Kyungpook National University Hospital, Department of Radiology, Daegu (Korea, Republic of); Choi, Young Hun; Cheon, Jung-Eun; Kim, In-One [Seoul National University College of Medicine, Department of Radiology and Institute of Radiation Medicine, Seoul (Korea, Republic of); Cho, Hyun-Hae [Ewha Womans University Mokdong Hospital, Department of Radiology, Seoul (Korea, Republic of); You, Sun-Kyoung [Chungnam National University Hospital, Department of Radiology, Daejeon (Korea, Republic of); Park, Sook-Hyun [Kyungpook National University Hospital, Department of Pediatrics, Daegu (Korea, Republic of); Hwang, Moon Jung [GE Healthcare, MR Applications and Workflow, Seoul (Korea, Republic of)

2017-11-15

The clinical application of the multi-echo, multi-delay technique of synthetic magnetic resonance imaging (MRI) generates multiple sequences in a single acquisition but has mainly been used in adults. To evaluate the image quality of synthetic brain MR in children compared with that of conventional images. Twenty-nine children (median age: 6 years, range: 0-16 years) underwent synthetic and conventional imaging. Synthetic (T2-weighted, T1-weighted and fluid-attenuated inversion recovery [FLAIR]) images with settings matching those of the conventional images were generated. The overall image quality, gray/white matter differentiation, lesion conspicuity and image degradations were rated on a 5-point scale. The relative contrasts were assessed quantitatively and acquisition times for the two imaging techniques were compared. Synthetic images were inferior due to more pronounced image degradations; however, there were no significant differences for T1- and T2-weighted images in children <2 years old. The quality of T1- and T2-weighted images were within the diagnostically acceptable range. FLAIR images showed greatly reduced quality. Gray/white matter differentiation was comparable or better in synthetic T1- and T2-weighted images, but poorer in FLAIR images. There was no effect on lesion conspicuity. Synthetic images had equal or greater relative contrast. Acquisition time was approximately two-thirds of that for conventional sequences. Synthetic T1- and T2-weighted images were diagnostically acceptable, but synthetic FLAIR images were not. Lesion conspicuity and gray/white matter differentiation were comparable to conventional MRI. (orig.)

Luminescence imaging using radionuclides: a potential application in molecular imaging

International Nuclear Information System (INIS)

Park, Jeong Chan; Il An, Gwang; Park, Se-Il; Oh, Jungmin; Kim, Hong Joo; Su Ha, Yeong; Wang, Eun Kyung; Min Kim, Kyeong; Kim, Jung Young; Lee, Jaetae; Welch, Michael J.; Yoo, Jeongsoo

2011-01-01

Introduction: Nuclear and optical imaging are complementary in many aspects and there would be many advantages when optical imaging probes are prepared using radionuclides rather than classic fluorophores, and when nuclear and optical dual images are obtained using single imaging probe. Methods: The luminescence intensities of various radionuclides having different decay modes have been assayed using luminescence imaging and in vitro luminometer. Radioiodinated Herceptin was injected into a tumor-bearing mouse, and luminescence and microPET images were obtained. The plant dipped in [ 32 P]phosphate solution was scanned in luminescence mode. Radio-TLC plate was also imaged in the same imaging mode. Results: Radionuclides emitting high energy β + /β - particles showed higher luminescence signals. NIH3T6.7 tumors were detected in both optical and nuclear imaging. The uptake of [ 32 P]phosphate in plant was easily followed by luminescence imaging. Radio-TLC plate was visualized and radiochemical purity was quantified using luminescence imaging. Conclusion: Many radionuclides with high energetic β + or β - particles during decay were found to be imaged in luminescence mode due mainly to Cerenkov radiation. 'Cerenkov imaging' provides a new optical imaging platform and an invaluable bridge between optical and nuclear imaging. New optical imaging probes could be easily prepared using well-established radioiodination methods. Cerenkov imaging will have more applications in the research field of plant science and autoradiography.

Color image guided depth image super resolution using fusion filter

Science.gov (United States)

He, Jin; Liang, Bin; He, Ying; Yang, Jun

2018-04-01

Depth cameras are currently playing an important role in many areas. However, most of them can only obtain lowresolution (LR) depth images. Color cameras can easily provide high-resolution (HR) color images. Using color image as a guide image is an efficient way to get a HR depth image. In this paper, we propose a depth image super resolution (SR) algorithm, which uses a HR color image as a guide image and a LR depth image as input. We use the fusion filter of guided filter and edge based joint bilateral filter to get HR depth image. Our experimental results on Middlebury 2005 datasets show that our method can provide better quality in HR depth images both numerically and visually.

Epidural fat image in lumbar magnetic resonance image

International Nuclear Information System (INIS)

Nishijima, Yuichiro; Yamasaki, Yasuo; Higashida, Norihiko; Okada, Masato

1993-01-01

To examine epidural fat images, lumbar magnetic resonance (MR) images were retrospectively reviewed in a total of 103 patients with surgically proven lumbar disc herniation (DH, n=57) and lumbar canal stenosis (LCS, n=46). Epidural fat images consisted of middorsal epidural fat (MDF), paramedian ventral fat (PVF) and intervertebral foraminal fat (IFF) ones. In the group of DH, the thickness of MDF image did not correlate with that of subcutaneous fat, suggesting that epidural fat was not affected by body fat. From the pathophysiological point of view, decrease and disappearance of MDF images correlated with compression of the epidural canal. Decrease and disappearance of PVF images lead to suspicious compression of the traversing root. In addition, asymmetrical PVF images were useful for the bilateral diagnosis of herniation. Abnormal findings of IFF images were suggestive of compression of the exiting nerve root at the intervertebral foramen. This was also seen frequently at the non-responsible level in patients over the age of 50. Degenerative and sequentrated spondylolistheses in the group of LCS were more frequently associated with a higher incidence of abnormal findings of IFF images, suggesting the presence of existing nerve root compression. (N.K.)

Improving image quality in portal venography with spectral CT imaging

International Nuclear Information System (INIS)

Zhao, Li-qin; He, Wen; Li, Jian-ying; Chen, Jiang-hong; Wang, Ke-yang; Tan, Li

2012-01-01

Objective: To investigate the effect of energy spectral CT on the image quality of CT portal venography in cirrhosis patients. Materials and methods: 30 portal hypertension patients underwent spectral CT examination using a single-tube, fast dual tube voltage switching technique. 101 sets of monochromatic images were generated from 40 keV to 140 keV. Image noise and contrast-to-noise ratio (CNR) for portal veins from the monochromatic images were measured. An optimal monochromatic image set was selected for obtaining the best CNR for portal veins. The image noise and CNR of the intra-hepatic portal vein and extra-hepatic main stem at the selected monochromatic level were compared with those from the conventional polychromatic images. Image quality was also assessed and compared. Results: The monochromatic images at 51 keV were found to provide the best CNR for both the intra-hepatic and extra-hepatic portal veins. At this energy level, the monochromatic images had about 100% higher CNR than the polychromatic images with a moderate 30% noise increase. The qualitative image quality assessment was also statistically higher with monochromatic images at 51 keV. Conclusion: Monochromatic images at 51 keV for CT portal venography could improve CNR for displaying hepatic portal veins and improve the overall image quality.

Improving image quality in portal venography with spectral CT imaging

Energy Technology Data Exchange (ETDEWEB)

Zhao, Li-qin, E-mail: zhaolqzr@sohu.com [Department of Radiology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing,100050 (China); He, Wen, E-mail: hewen1724@sina.com [Department of Radiology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing,100050 (China); Li, Jian-ying, E-mail: jianying.li@med.ge.com [CT Advanced Application and Research, GE Healthcare, 100176 China (China); Chen, Jiang-hong, E-mail: chenjianghong1973@hotmail.com [Department of Radiology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing,100050 (China); Wang, Ke-yang, E-mail: ke7ke@sina.com [Department of Radiology, Beijing Friendship Hospital Affiliated to Capital Medical University, Beijing,100050 (China); Tan, Li, E-mail: Litan@ge.com [CT product, GE Healthcare, 100176 China (China)

2012-08-15

Objective: To investigate the effect of energy spectral CT on the image quality of CT portal venography in cirrhosis patients. Materials and methods: 30 portal hypertension patients underwent spectral CT examination using a single-tube, fast dual tube voltage switching technique. 101 sets of monochromatic images were generated from 40 keV to 140 keV. Image noise and contrast-to-noise ratio (CNR) for portal veins from the monochromatic images were measured. An optimal monochromatic image set was selected for obtaining the best CNR for portal veins. The image noise and CNR of the intra-hepatic portal vein and extra-hepatic main stem at the selected monochromatic level were compared with those from the conventional polychromatic images. Image quality was also assessed and compared. Results: The monochromatic images at 51 keV were found to provide the best CNR for both the intra-hepatic and extra-hepatic portal veins. At this energy level, the monochromatic images had about 100% higher CNR than the polychromatic images with a moderate 30% noise increase. The qualitative image quality assessment was also statistically higher with monochromatic images at 51 keV. Conclusion: Monochromatic images at 51 keV for CT portal venography could improve CNR for displaying hepatic portal veins and improve the overall image quality.

Image fusion between whole body FDG PET images and whole body MRI images using a full-automatic mutual information-based multimodality image registration software

International Nuclear Information System (INIS)

Uchida, Yoshitaka; Nakano, Yoshitada; Fujibuchi, Toshiou; Isobe, Tomoko; Kazama, Toshiki; Ito, Hisao

2006-01-01

We attempted image fusion between whole body PET and whole body MRI of thirty patients using a full-automatic mutual information (MI) -based multimodality image registration software and evaluated accuracy of this method and impact of the coregistrated imaging on diagnostic accuracy. For 25 of 30 fused images in body area, translating gaps were within 6 mm in all axes and rotating gaps were within 2 degrees around all axes. In head and neck area, considerably much gaps caused by difference of head inclination at imaging occurred in 16 patients, however these gaps were able to decrease by fused separately. In 6 patients, diagnostic accuracy using PET/MRI fused images was superior compared by PET image alone. This work shows that whole body FDG PET images and whole body MRI images can be automatically fused using MI-based multimodality image registration software accurately and this technique can add useful information when evaluating FDG PET images. (author)

Fluorescence Image Segmentation by using Digitally Reconstructed Fluorescence Images

OpenAIRE

Blumer, Clemens; Vivien, Cyprien; Oertner, Thomas G; Vetter, Thomas

2011-01-01

In biological experiments fluorescence imaging is used to image living and stimulated neurons. But the analysis of fluorescence images is a difficult task. It is not possible to conclude the shape of an object from fluorescence images alone. Therefore, it is not feasible to get good manual segmented nor ground truth data from fluorescence images. Supervised learning approaches are not possible without training data. To overcome this issues we propose to synthesize fluorescence images and call...

Direct methods in protein crystallography.

Science.gov (United States)

Karle, J

1989-11-01

It is pointed out that the 'direct methods' of phase determination for small-structure crystallography do not have immediate applicability to macromolecular structures. The term 'direct methods in macromolecular crystallography' is suggested to categorize a spectrum of approaches to macromolecular structure determination in which the analyses are characterized by the use of two-phase and higher-order-phase invariants. The evaluation of the invariants is generally obtained by the use of heavy-atom techniques. The results of a number of the more recent algebraic and probabilistic studies involving isomorphous replacement and anomalous dispersion thus become valid subjects for discussion here. These studies are described and suggestions are also presented concerning future applicability. Additional discussion concerns the special techniques of filtering, the use of non-crystallographic symmetry, some features of maximum entropy and attempts to apply phase-determining formulas to the refinement of macromolecular structure. It is noted that, in addition to the continuing remarkable progress in macromolecular crystallography based on the traditional applications of isomorphous replacement and anomalous dispersion, recent valuable advances have been made in the application of non-crystallographic symmetry, in particular, to virus structures and in applications of filtering. Good progress has also been reported in the application of exact linear algebra to multiple-wavelength anomalous-dispersion investigations of structures containing anomalous scatterers of only moderate scattering power.

Medical Image Tamper Detection Based on Passive Image Authentication.

Science.gov (United States)

Ulutas, Guzin; Ustubioglu, Arda; Ustubioglu, Beste; V Nabiyev, Vasif; Ulutas, Mustafa

2017-12-01

Telemedicine has gained popularity in recent years. Medical images can be transferred over the Internet to enable the telediagnosis between medical staffs and to make the patient's history accessible to medical staff from anywhere. Therefore, integrity protection of the medical image is a serious concern due to the broadcast nature of the Internet. Some watermarking techniques are proposed to control the integrity of medical images. However, they require embedding of extra information (watermark) into image before transmission. It decreases visual quality of the medical image and can cause false diagnosis. The proposed method uses passive image authentication mechanism to detect the tampered regions on medical images. Structural texture information is obtained from the medical image by using local binary pattern rotation invariant (LBPROT) to make the keypoint extraction techniques more successful. Keypoints on the texture image are obtained with scale invariant feature transform (SIFT). Tampered regions are detected by the method by matching the keypoints. The method improves the keypoint-based passive image authentication mechanism (they do not detect tampering when the smooth region is used for covering an object) by using LBPROT before keypoint extraction because smooth regions also have texture information. Experimental results show that the method detects tampered regions on the medical images even if the forged image has undergone some attacks (Gaussian blurring/additive white Gaussian noise) or the forged regions are scaled/rotated before pasting.

Image Gallery

Science.gov (United States)

... R S T U V W X Y Z Image Gallery Share: The Image Gallery contains high-quality digital photographs available from ... Select a category below to view additional thumbnail images. Images are available for direct download in 2 ...

Selections from 2017: Image Processing with AstroImageJ

Science.gov (United States)

Kohler, Susanna

2017-12-01

Editors note:In these last two weeks of 2017, well be looking at a few selections that we havent yet discussed on AAS Nova from among the most-downloaded paperspublished in AAS journals this year. The usual posting schedule will resume in January.AstroImageJ: Image Processing and Photometric Extraction for Ultra-Precise Astronomical Light CurvesPublished January2017The AIJ image display. A wide range of astronomy specific image display options and image analysis tools are available from the menus, quick access icons, and interactive histogram. [Collins et al. 2017]Main takeaway:AstroImageJ is a new integrated software package presented in a publication led byKaren Collins(Vanderbilt University,Fisk University, andUniversity of Louisville). Itenables new users even at the level of undergraduate student, high school student, or amateur astronomer to quickly start processing, modeling, and plotting astronomical image data.Why its interesting:Science doesnt just happen the momenta telescope captures a picture of a distantobject. Instead, astronomical images must firstbe carefully processed to clean up thedata, and this data must then be systematically analyzed to learn about the objects within it. AstroImageJ as a GUI-driven, easily installed, public-domain tool is a uniquelyaccessible tool for thisprocessing and analysis, allowing even non-specialist users to explore and visualizeastronomical data.Some features ofAstroImageJ:(as reported by Astrobites)Image calibration:generate master flat, dark, and bias framesImage arithmetic:combineimages viasubtraction, addition, division, multiplication, etc.Stack editing:easily perform operations on a series of imagesImage stabilization and image alignment featuresPrecise coordinate converters:calculate Heliocentric and Barycentric Julian DatesWCS coordinates:determine precisely where atelescope was pointed for an image by PlateSolving using Astronomy.netMacro and plugin support:write your own macrosMulti-aperture photometry

Medical imaging technology

CERN Document Server

Haidekker, Mark A

2013-01-01

Biomedical imaging is a relatively young discipline that started with Conrad Wilhelm Roentgen’s discovery of the x-ray in 1885. X-ray imaging was rapidly adopted in hospitals around the world. However, it was the advent of computerized data and image processing that made revolutionary new imaging modalities possible. Today, cross-sections and three-dimensional reconstructions of the organs inside the human body is possible with unprecedented speed, detail and quality. This book provides an introduction into the principles of image formation of key medical imaging modalities: X-ray projection imaging, x-ray computed tomography, magnetic resonance imaging, ultrasound imaging, and radionuclide imaging. Recent developments in optical imaging are also covered. For each imaging modality, the introduction into the physical principles and sources of contrast is provided, followed by the methods of image formation, engineering aspects of the imaging devices, and a discussion of strengths and limitations of the modal...

Aggregation of superparamagnetic iron oxide nanoparticles in dilute aqueous dispersions: Effect of coating by double-hydrophilic block polyelectrolyte

Czech Academy of Sciences Publication Activity Database

Hajduová, J.; Uchman, M.; Šafařík, Ivo; Šafaříková, Miroslava; Šlouf, Miroslav; Pispas, S.; Štěpánek, M.

2015-01-01

Roč. 483, oct (2015), s. 1-7 ISSN 0927-7757 R&D Projects: GA TA ČR(CZ) TE01020118 Institutional support: RVO:67179843 ; RVO:61389013 Keywords : magnetic nanoparticles * block polyelectrolytes * aggregation * small-angle light scattering Subject RIV: CD - Macromolecular Chemistry; CD - Macromolecular Chemistry (UMCH-V) Impact factor: 2.760, year: 2015

Real-time polymerase chain reaction as a tool for evaluation of magnetic poly(glycidyl methacrylate)-based microspheres in molecular diagnostics

Czech Academy of Sciences Publication Activity Database

Trachtová, S.; Španová, A.; Horák, Daniel; Kozáková, Hana; Rittich, B.

2016-01-01

Roč. 22, č. 5 (2016), s. 639-646 ISSN 1381-6128 R&D Projects: GA ČR GA15-07268S Institutional support: RVO:61389013 ; RVO:61388971 Keywords : magnetic microspheres * inhibitory effect * real-time polymerase chain Subject RIV: CD - Macromolecular Chemistry; CD - Macromolecular Chemistry (MBU-M) Impact factor: 2.611, year: 2016

Annotating images by mining image search results

NARCIS (Netherlands)

Wang, X.J.; Zhang, L.; Li, X.; Ma, W.Y.

2008-01-01

Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search

Automatic detection of blurred images in UAV image sets

Science.gov (United States)

Sieberth, Till; Wackrow, Rene; Chandler, Jim H.

2016-12-01

Unmanned aerial vehicles (UAV) have become an interesting and active research topic for photogrammetry. Current research is based on images acquired by an UAV, which have a high ground resolution and good spectral and radiometrical resolution, due to the low flight altitudes combined with a high resolution camera. UAV image flights are also cost effective and have become attractive for many applications including, change detection in small scale areas. One of the main problems preventing full automation of data processing of UAV imagery is the degradation effect of blur caused by camera movement during image acquisition. This can be caused by the normal flight movement of the UAV as well as strong winds, turbulence or sudden operator inputs. This blur disturbs the visual analysis and interpretation of the data, causes errors and can degrade the accuracy in automatic photogrammetric processing algorithms. The detection and removal of these images is currently achieved manually, which is both time consuming and prone to error, particularly for large image-sets. To increase the quality of data processing an automated process is necessary, which must be both reliable and quick. This paper describes the development of an automatic filtering process, which is based upon the quantification of blur in an image. Images with known blur are processed digitally to determine a quantifiable measure of image blur. The algorithm is required to process UAV images fast and reliably to relieve the operator from detecting blurred images manually. The newly developed method makes it possible to detect blur caused by linear camera displacement and is based on human detection of blur. Humans detect blurred images best by comparing it to other images in order to establish whether an image is blurred or not. The developed algorithm simulates this procedure by creating an image for comparison using image processing. Creating internally a comparable image makes the method independent of

Image quality (IQ) guided multispectral image compression

Science.gov (United States)

Zheng, Yufeng; Chen, Genshe; Wang, Zhonghai; Blasch, Erik

2016-05-01

Image compression is necessary for data transportation, which saves both transferring time and storage space. In this paper, we focus on our discussion on lossy compression. There are many standard image formats and corresponding compression algorithms, for examples, JPEG (DCT -- discrete cosine transform), JPEG 2000 (DWT -- discrete wavelet transform), BPG (better portable graphics) and TIFF (LZW -- Lempel-Ziv-Welch). The image quality (IQ) of decompressed image will be measured by numerical metrics such as root mean square error (RMSE), peak signal-to-noise ratio (PSNR), and structural Similarity (SSIM) Index. Given an image and a specified IQ, we will investigate how to select a compression method and its parameters to achieve an expected compression. Our scenario consists of 3 steps. The first step is to compress a set of interested images by varying parameters and compute their IQs for each compression method. The second step is to create several regression models per compression method after analyzing the IQ-measurement versus compression-parameter from a number of compressed images. The third step is to compress the given image with the specified IQ using the selected compression method (JPEG, JPEG2000, BPG, or TIFF) according to the regressed models. The IQ may be specified by a compression ratio (e.g., 100), then we will select the compression method of the highest IQ (SSIM, or PSNR). Or the IQ may be specified by a IQ metric (e.g., SSIM = 0.8, or PSNR = 50), then we will select the compression method of the highest compression ratio. Our experiments tested on thermal (long-wave infrared) images (in gray scales) showed very promising results.

Vaccine Images on Twitter: Analysis of What Images are Shared

Science.gov (United States)

Dredze, Mark

2018-01-01

Background Visual imagery plays a key role in health communication; however, there is little understanding of what aspects of vaccine-related images make them effective communication aids. Twitter, a popular venue for discussions related to vaccination, provides numerous images that are shared with tweets. Objective The objectives of this study were to understand how images are used in vaccine-related tweets and provide guidance with respect to the characteristics of vaccine-related images that correlate with the higher likelihood of being retweeted. Methods We collected more than one million vaccine image messages from Twitter and characterized various properties of these images using automated image analytics. We fit a logistic regression model to predict whether or not a vaccine image tweet was retweeted, thus identifying characteristics that correlate with a higher likelihood of being shared. For comparison, we built similar models for the sharing of vaccine news on Facebook and for general image tweets. Results Most vaccine-related images are duplicates (125,916/237,478; 53.02%) or taken from other sources, not necessarily created by the author of the tweet. Almost half of the images contain embedded text, and many include images of people and syringes. The visual content is highly correlated with a tweet’s textual topics. Vaccine image tweets are twice as likely to be shared as nonimage tweets. The sentiment of an image and the objects shown in the image were the predictive factors in determining whether an image was retweeted. Conclusions We are the first to study vaccine images on Twitter. Our findings suggest future directions for the study and use of vaccine imagery and may inform communication strategies around vaccination. Furthermore, our study demonstrates an effective study methodology for image analysis. PMID:29615386

Vaccine Images on Twitter: Analysis of What Images are Shared.

Science.gov (United States)

Chen, Tao; Dredze, Mark

2018-04-03

Visual imagery plays a key role in health communication; however, there is little understanding of what aspects of vaccine-related images make them effective communication aids. Twitter, a popular venue for discussions related to vaccination, provides numerous images that are shared with tweets. The objectives of this study were to understand how images are used in vaccine-related tweets and provide guidance with respect to the characteristics of vaccine-related images that correlate with the higher likelihood of being retweeted. We collected more than one million vaccine image messages from Twitter and characterized various properties of these images using automated image analytics. We fit a logistic regression model to predict whether or not a vaccine image tweet was retweeted, thus identifying characteristics that correlate with a higher likelihood of being shared. For comparison, we built similar models for the sharing of vaccine news on Facebook and for general image tweets. Most vaccine-related images are duplicates (125,916/237,478; 53.02%) or taken from other sources, not necessarily created by the author of the tweet. Almost half of the images contain embedded text, and many include images of people and syringes. The visual content is highly correlated with a tweet's textual topics. Vaccine image tweets are twice as likely to be shared as nonimage tweets. The sentiment of an image and the objects shown in the image were the predictive factors in determining whether an image was retweeted. We are the first to study vaccine images on Twitter. Our findings suggest future directions for the study and use of vaccine imagery and may inform communication strategies around vaccination. Furthermore, our study demonstrates an effective study methodology for image analysis. ©Tao Chen, Mark Dredze. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 03.04.2018.

Image fusion in x-ray differential phase-contrast imaging

Science.gov (United States)

Haas, W.; Polyanskaya, M.; Bayer, F.; Gödel, K.; Hofmann, H.; Rieger, J.; Ritter, A.; Weber, T.; Wucherer, L.; Durst, J.; Michel, T.; Anton, G.; Hornegger, J.

2012-02-01

Phase-contrast imaging is a novel modality in the field of medical X-ray imaging. The pioneer method is the grating-based interferometry which has no special requirements to the X-ray source and object size. Furthermore, it provides three different types of information of an investigated object simultaneously - absorption, differential phase-contrast and dark-field images. Differential phase-contrast and dark-field images represent a completely new information which has not yet been investigated and studied in context of medical imaging. In order to introduce phase-contrast imaging as a new modality into medical environment the resulting information about the object has to be correctly interpreted. The three output images reflect different properties of the same object the main challenge is to combine and visualize these data in such a way that it diminish the information explosion and reduce the complexity of its interpretation. This paper presents an intuitive image fusion approach which allows to operate with grating-based phase-contrast images. It combines information of the three different images and provides a single image. The approach is implemented in a fusion framework which is aimed to support physicians in study and analysis. The framework provides the user with an intuitive graphical user interface allowing to control the fusion process. The example given in this work shows the functionality of the proposed method and the great potential of phase-contrast imaging in medical practice.

Readout-Segmented Echo-Planar Imaging in Diffusion-Weighted MR Imaging in Breast Cancer: Comparison with Single-Shot Echo-Planar Imaging in Image Quality

International Nuclear Information System (INIS)

Kim, Yun Ju; Kim, Sung Hun; Kang, Bong Joo; Park, Chang Suk; Kim, Hyeon Sook; Son, Yo Han; Porter, David Andrew; Song, Byung Joo

2014-01-01

The purpose of this study was to compare the image quality of standard single-shot echo-planar imaging (ss-EPI) and that of readout-segmented EPI (rs-EPI) in patients with breast cancer. Seventy-one patients with 74 breast cancers underwent both ss-EPI and rs-EPI. For qualitative comparison of image quality, three readers independently assessed the two sets of diffusion-weighted (DW) images. To evaluate geometric distortion, a comparison was made between lesion lengths derived from contrast enhanced MR (CE-MR) images and those obtained from the corresponding DW images. For assessment of image parameters, signal-to-noise ratio (SNR), lesion contrast, and contrast-to-noise ratio (CNR) were calculated. The rs-EPI was superior to ss-EPI in most criteria regarding the qualitative image quality. Anatomical structure distinction, delineation of the lesion, ghosting artifact, and overall image quality were significantly better in rs-EPI. Regarding the geometric distortion, lesion length on ss-EPI was significantly different from that of CE-MR, whereas there were no significant differences between CE-MR and rs-EPI. The rs-EPI was superior to ss-EPI in SNR and CNR. Readout-segmented EPI is superior to ss-EPI in the aspect of image quality in DW MR imaging of the breast

Video retrieval by still-image analysis with ImageMiner

Science.gov (United States)

Kreyss, Jutta; Roeper, M.; Alshuth, Peter; Hermes, Thorsten; Herzog, Otthein

1997-01-01

The large amount of available multimedia information (e.g. videos, audio, images) requires efficient and effective annotation and retrieval methods. As videos start playing a more important role in the frame of multimedia, we want to make these available for content-based retrieval. The ImageMiner-System, which was developed at the University of Bremen in the AI group, is designed for content-based retrieval of single images by a new combination of techniques and methods from computer vision and artificial intelligence. In our approach to make videos available for retrieval in a large database of videos and images there are two necessary steps: First, the detection and extraction of shots from a video, which is done by a histogram based method and second, the construction of the separate frames in a shot to one still single images. This is performed by a mosaicing-technique. The resulting mosaiced image gives a one image visualization of the shot and can be analyzed by the ImageMiner-System. ImageMiner has been tested on several domains, (e.g. landscape images, technical drawings), which cover a wide range of applications.