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  1. Increased cardiac index due to terbutaline treatment aggravates capillary-alveolar macromolecular leakage in oleic acid lung injury in dogs

    OpenAIRE

    Briot, Raphael; Bayat, Sam; Anglade, Daniel; Martiel, Jean-Louis; Grimbert, Francis

    2009-01-01

    Introduction We assessed the in vivo effects of terbutaline, a beta2-agonist assumed to reduce microvascular permeability in acute lung injury. Methods We used a recently developed broncho-alveolar lavage (BAL) technique to repeatedly measure (every 15 min. for 4 hours) the time-course of capillary-alveolar leakage of a macromolecule (fluorescein-labeled dextran) in 19 oleic acid (OA) lung injured dogs. BAL was performed in a closed lung sampling site, using a bronchoscope fitted with an infl...

  2. Spectroscopic Approach to Capillary-Alveolar Membrane Damage Induced Acute Lung Injury

    Directory of Open Access Journals (Sweden)

    Jing Wang

    1999-01-01

    Full Text Available BACKGROUND: Acute (or adult respiratory distress syndrome (ARDS is often associated with a high mortality rate in the critical care population. The term acute lung injury (ALI, a primitive phase of ARDS, was introduced by the European and American consensus groups to provide early diagnoses of ARDS. The pathophysiological characterization of ALI/ARDS – an increased pulmonary capillary-alveolar membrane barrier permeability – is generally not included in current intensive care unit diagnosis criteria.

  3. Macromolecular crystallization in microgravity

    Energy Technology Data Exchange (ETDEWEB)

    Snell, Edward H [Biophysics Group, NASA Marshall Space Flight Center, Code XD42, Huntsville, AL 35812 (United States); Helliwell, John R [Department of Chemistry, The University of Manchester, Manchester, M13 9PL (United Kingdom)

    2005-04-01

    Density difference fluid flows and sedimentation of growing crystals are greatly reduced when crystallization takes place in a reduced gravity environment. In the case of macromolecular crystallography a crystal of a biological macromolecule is used for diffraction experiments (x-ray or neutron) so as to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal then the greater the molecular structure detail that can be extracted. It is this structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences, with major potential in understanding disease pathologies. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyse the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry and mathematics meet to enable insight to the fundamentals of life. As the reader will see, there is a great deal of physics involved when the microgravity environment is applied to crystallization, some of it known, and undoubtedly much yet to

  4. Teaching macromolecular modeling.

    OpenAIRE

    Harvey, S C; Tan, R K

    1992-01-01

    Training newcomers to the field of macromolecular modeling is as difficult as is training beginners in x-ray crystallography, nuclear magnetic resonance, or other methods in structural biology. In one or two lectures, the most that can be conveyed is a general sense of the relationship between modeling and other structural methods. If a full semester is available, then students can be taught how molecular structures are built, manipulated, refined, and analyzed on a computer. Here we describe...

  5. Microgravity and Macromolecular Crystallography

    Science.gov (United States)

    Kundrot, Craig E.; Judge, Russell A.; Pusey, Marc L.; Snell, Edward H.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Macromolecular crystal growth has been seen as an ideal experiment to make use of the reduced acceleration environment provided by an orbiting spacecraft. The experiments are small, simply operated and have a high potential scientific and economic impact. In this review we examine the theoretical reasons why microgravity should be a beneficial environment for crystal growth and survey the history of experiments on the Space Shuttle Orbiter, on unmanned spacecraft, and on the Mir space station. Finally we outline the direction for optimizing the future use of orbiting platforms.

  6. Genetics Home Reference: potassium-aggravated myotonia

    Science.gov (United States)

    ... myotonia Patient Support and Advocacy Resources (2 links) Muscular Dystrophy Association Resource list from the University of Kansas Medical Center Genetic Testing Registry (1 link) Potassium aggravated myotonia ClinicalTrials. ...

  7. Aggravation of Parkinson's disease by cinnarizine.

    OpenAIRE

    Martí Massó, J F; J. A. Obeso; Carrera, N; Martínez-Lage, J.M. (J.M.)

    1987-01-01

    The effect of cinnarizine on motor function in Parkinson's disease was evaluated in a randomised double-blind parallel study of 20 patients. Both groups were comparable in age, duration of the disease, dose of levodopa and degree of disability. A significant worsening of mobility was observed in patients treated with cinnarizine (75 mg bd), whilst no change was recorded in patients receiving placebo. Cinnarizine should be added to the list of drugs capable of aggravating Parkinson's disease.

  8. Macromolecular architectures for organic photovoltaics.

    Science.gov (United States)

    Popere, Bhooshan C; Della Pelle, Andrea M; Poe, Ambata; Thayumanavan, S

    2012-03-28

    Research in the field of organic photovoltaics has gained considerable momentum in the last two decades owing to the need for developing low-cost and efficient energy harvesting systems. Elegant molecular architectures have been designed, synthesized and employed as active materials for photovoltaic devices thereby leading to a better molecular structure-device property relationship understanding. In this perspective, we outline new macromolecular scaffolds that have been designed within the purview of each of the three fundamental processes involving light harvesting, charge separation and charge transport.

  9. Emergent Property in Macromolecular Motion

    Institute of Scientific and Technical Information of China (English)

    吴嘉麟

    2003-01-01

    In this paper, the model of inverse cascade fractal super-blocks along one direction (in the positive or negative) in the 3-dimensional space is developed to describe the self-similar motion in macromolecular system. Microscopically the cohesive and dispersed states of the motion blocks are co-existent states with vastly different probability of occurrence.Experimental results and theoretical analysis show that the microscopic cohesive state energy and dispersed state energy of each motion block are respectively equal to the macroscopic glassy state energy kT8 and molten state energy kTm of the system. This singularity unveils topologically the nonintegrability, mathematically the anholonomy, and macroscopically the emergent property. This singularity also reveals that the glass, viscoelastic and melt states are three distinct emergent properties of macromolecular motion from a macroscopic viewpoint. The fractal concept of excluded volume is introduced to depict the random motion at various scales in the system. The Hausdorff dimensions of the excluded volune and the motion blocks are both found equal to 3/2.

  10. Data Mining of Macromolecular Structures.

    Science.gov (United States)

    van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

    2016-01-01

    The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining.

  11. Liver-targeting macromolecular MRI contrast agents

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    Macromolecular ligands with liver-targeting group (pyridoxamine, PM) PHEA-DTPA-PM and PAEA-DTPA-PM were prepared by the incorporation of different amount of diethylenetriaminepentaacetic acid monopyridoxamine group (DTPA-PM) into poly-a, b-[N-(2-hydroxyethyl)-L- aspartamide] (PHEA) and poly-a, b-[N-(2-aminoethyl)-L-aspartamide] (PAEA). The macromolecular ligands thus obtained were further complexed with gadolinium chloride to give macromolecular MRI contrast agents with different Gd(Ⅲ) contents. These macromolecular ligands and their gadolinium complexes were characterized by 1H NMR, IR, UV and elementary analysis. Relaxivity studies showed that these polyaspartamide gadolinium complexes possess higher relaxation effectiveness than that of the clinically used Gd-DTPA. Magnetic resonance imaging of the liver in rats and experimental data of biodistribution in mice indicate that these macromolecular MRI contrast agents containing pyridoxamine exhibit liver-targeting property.

  12. Macromolecular crystallography research at Trombay

    International Nuclear Information System (INIS)

    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)

  13. Pregnancy aggravates proteinuria in subclinical glomerulonephritis in the rat

    NARCIS (Netherlands)

    Faas, MM; Bakker, WW; Poelman, RT; Schuiling, GA

    1999-01-01

    Because subclinical renal disease may be aggravated during pregnancy-as reflected in the occurrence of proteinuria, for example-we investigated whether a subclinical glomerulonephritis (SG) in the non-pregnant rat (passive Heymann nephritis), a condition without proteinuria, is aggravated when the a

  14. Energy transfer in macromolecular arrays

    Science.gov (United States)

    Andrews, David L.; Jenkins, Robert D.

    2003-11-01

    Macromolecular systems comprised of many light-sensitive centres (the photosynthetic unit, dendrimers, and other highly symmetric multichromophore arrays) are important structures offering challenges to theoreticians and synthetic chemists alike. Here we outline novel photophysical interactions predicted and observed in such arrays. Using the tools of molecular quantum electrodynamics (QED) we present quantum amplitudes for a variety of higher-order resonance energy transfer (RET) schemes associated with well-known nonlinear optical effects such as two- and three-photon absorption. The initial analysis is extended to account for situations where the participant donor species are identical and exist in a highly symmetric environment, leading to the possible formation of excitons. It emerges from the QED theory that such excitons are closely associated with the higher-order RET processes. General results are interpreted by analyzing particular molecular architectures which offer interesting features such as rate enhancement or limitation and exciton pathway quenching. Applications in the areas of photosynthesis, molecular logic gates and low-intensity fluorescence energy transfer are predicted.

  15. Fractal Dimensions of Macromolecular Structures

    Science.gov (United States)

    Todoroff, Nickolay; Kunze, Jens; Schreuder, Herman; Hessler, Gerhard; Baringhaus, Karl-Heinz; Schneider, Gisbert

    2014-01-01

    Quantifying the properties of macromolecules is a prerequisite for understanding their roles in biochemical processes. One of the less-explored geometric features of macromolecules is molecular surface irregularity, or ‘roughness’, which can be measured in terms of fractal dimension (D). In this study, we demonstrate that surface roughness correlates with ligand binding potential. We quantified the surface roughnesses of biological macromolecules in a large-scale survey that revealed D values between 2.0 and 2.4. The results of our study imply that surface patches involved in molecular interactions, such as ligand-binding pockets and protein-protein interfaces, exhibit greater local fluctuations in their fractal dimensions than ‘inert’ surface areas. We expect approximately 22 % of a protein’s surface outside of the crystallographically known ligand binding sites to be ligandable. These findings provide a fresh perspective on macromolecular structure and have considerable implications for drug design as well as chemical and systems biology. PMID:26213587

  16. New pharmaceutical applications for macromolecular binders.

    Science.gov (United States)

    Bertrand, Nicolas; Gauthier, Marc A; Bouvet, Céline; Moreau, Pierre; Petitjean, Anne; Leroux, Jean-Christophe; Leblond, Jeanne

    2011-10-30

    Macromolecular binders consist of polymers, dendrimers, and oligomers with binding properties for endogenous or exogenous substrates. This field, at the frontier of host/guest chemistry and pharmacology, has met a renewed interest in the past decade due to the clinical success of several sequestrants, like sevelamer hydrochloride (Renagel®) or sugammadex (Bridion®). In many instances, multivalent binding by the macromolecular drugs can modify the properties of the substrate, and may prevent it from reaching its site of action and/or trigger a biological response. From small (e.g., ions) to larger substrates (e.g., bacteria and cells), this review presents the state-of-the-art of macromolecular binders and provides detailed illustrative examples of recent developments bearing much promise for future pharmaceutical applications. PMID:21571017

  17. Macromolecular mimicry of nucleic acid and protein

    DEFF Research Database (Denmark)

    Nautrup Pedersen, Gitte; Nyborg, Jens; Clark, Brian F

    1999-01-01

    of the concept of macromolecular mimicry. Macromolecular mimicry has further been proposed among initiation and release factors, thereby adding a new element to the description of protein synthesis in bacteria. Such mimicry has also been observed in other biological processes such as autoimmunity, DNA repair......Although proteins and nucleic acids consist of different chemical components, proteins can mimic structures and possibly also functions of nucleic acids. Recently, structural mimicry was observed between two elongation factors in bacterial protein biosynthesis leading to the introduction...

  18. Determining the architectures of macromolecular assemblies

    NARCIS (Netherlands)

    Alber, Frank; Dokudovskaya, Svetlana; Veenhoff, Liesbeth M.; Zhang, Wenzhu; Kipper, Julia; Devos, Damien; Suprapto, Adisetyantari; Karni-Schmidt, Orit; Williams, Rosemary; Chait, Brian T.; Rout, Michael P.; Sali, Andrej

    2007-01-01

    To understand the workings of a living cell, we need to know the architectures of its macromolecular assemblies. Here we show how proteomic data can be used to determine such structures. The process involves the collection of sufficient and diverse high-quality data, translation of these data into s

  19. [Aggravation after Diagnosis of Sudden Sensorineural Hearing Loss].

    Science.gov (United States)

    Fukumoto, Ichiro; Nemoto, Toshimitsu; Tsukuda, Tomoko; Koshizuka, Keiichi

    2015-03-01

    Among 95 patients with sudden sensorineural hearing loss who received inpatient treatment at our hospital within the 27-month period between October 2009 and December 2011, those in whom hearing loss was aggravated after diagnosis were compared with a control group. Hearing loss aggravation was defined as a decrease by 10 dB or more in the mean hearing threshold at 5 frequencies from 250 to 4,000 Hz or decrease of 15 dB or more in the hearing threshold at 2 consecutive frequencies. Hearing loss was aggravated after diagnosis in 22 (23.2%) of the 95 patients, showing a similar tendency to that previously reported. Although the grades of hearing loss in these patients were higher than those in 73 control group patients, according to the sudden hearing loss severity classification, their outcomes were favorable. The hearing loss aggravation group consisted of those with steroid-dependent hearing loss (6) and those who had undergone perilymphatic fistula repair (4), in addition to a large number of patients with idiopathic hearing loss, including suspicious perilymphatic fistula (10). When hearing loss becomes aggravated after the diagnosis of sudden sensorineural hearing loss, it may be important to determine the most appropriate approach in each case, such as a careful and gradual decrease in the adenocortical steroid dose and the consideration of perilymphatic fistula repair.

  20. Growth and dissolution of macromolecular Markov chains

    CERN Document Server

    Gaspard, Pierre

    2016-01-01

    The kinetics and thermodynamics of free living copolymerization are studied for processes with rates depending on k monomeric units of the macromolecular chain behind the unit that is attached or detached. In this case, the sequence of monomeric units in the growing copolymer is a kth-order Markov chain. In the regime of steady growth, the statistical properties of the sequence are determined analytically in terms of the attachment and detachment rates. In this way, the mean growth velocity as well as the thermodynamic entropy production and the sequence disorder can be calculated systematically. These different properties are also investigated in the regime of depolymerization where the macromolecular chain is dissolved by the surrounding solution. In this regime, the entropy production is shown to satisfy Landauer's principle.

  1. Dextran: A promising macromolecular drug carrier

    Directory of Open Access Journals (Sweden)

    Dhaneshwar Suneela

    2006-01-01

    Full Text Available Over the past three decades intensive efforts have been made to design novel systems able to deliver the drug more effectively to the target site. The ongoing intense search for novel and innovative drug delivery systems is predominantly a consequence of the well-established fact that the conventional dosage forms are not sufficiently effective in conveying the drug compound to its site of action and once in the target area, in releasing the active agent over a desired period of time. The potential use of macromolecular prodrugs as a means of achieving targeted drug delivery has attracted considerable interest in recent years. Macromolecules such as antibodies, lipoproteins, lectins, proteins, polypeptides, polysaccharides, natural as well as synthetic polymers offer potential applicabilities as high molecular weight carriers for various therapeutically active compounds. Dextrans serve as one of the most promising macromolecular carrier candidates for a wide variety of therapeutic agents due to their excellent physico-chemical properties and physiological acceptance. The present contribution attempts to review various features of the dextran carrier like its source, structural and physico-chemical characteristics, pharmacokinetic fate and its applications as macromolecular carrier with special emphasis on dextran prodrugs.

  2. 38 CFR 3.306 - Aggravation of preservice disability.

    Science.gov (United States)

    2010-07-01

    ... disability. 3.306 Section 3.306 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS... Connection § 3.306 Aggravation of preservice disability. (a) General. A preexisting injury or disease will be... disability during such service, unless there is a specific finding that the increase in disability is due...

  3. Aggravation of symptomatic occipital epilepsy of childhood by carbamazepine

    Directory of Open Access Journals (Sweden)

    Škrijelj Fadil E.

    2014-01-01

    Full Text Available Introduction. Carbamazepine can lead to aggravation of epileptic seizures in generalized epilepsies (primary or secondary with clinical manifestations of absence (typical or atypical and/or myoclonic seizures. However, some focal epilepsies can be also aggravated by the introduction of carbamazepine. Case report. We presented a 10-year-old boy born after a complicated and prolonged delivery completed by vacuum extraction, of early psychomotor development within normal limits. At the age of 8 years he had the first epileptic seizure of simple occipital type with generalization and urination. Brain magnetic resonance imaging (MRI showed focal cortical reductions in the left parietal and occipital regions. Interictal EEG recorded slowed basic activities above the posterior regions of the left hemisphere, with intermittent occurrence of occipital sharp waves and bioccipital sharp and slow-wave complexes. Initially, treatment with valproate was administered; however, the addition of carbamazepine into therapy induced aggravation of seizures and EEG findings, changed behavior and poor performance at school. By withdrawal of carbamazepine the condition improved both clinically and in EEG findings. Conclusion. Childhood occipital epilepsy lesions show deterioration due to carbamazepine, which if administered induces aggravation of seizures, behavior changes, cognition with occurrence of long-term bilateral discharges, and posterior sharp and slow wave high amplitude complexes recorded by EEG.

  4. Smoothing techniques for macromolecular global optimization

    Energy Technology Data Exchange (ETDEWEB)

    More, J.J.; Wu, Zhijun

    1995-09-01

    We study global optimization problems that arise in macromolecular modeling, and the solution of these problems via continuation and smoothing. Our results unify and extend the theory associated with the use of the Gaussian transform for smoothing. We show that the, Gaussian transform can be viewed as a special case of a generalized transform and that these generalized transforms share many of the properties of the Gaussian transform. We also show that the smoothing behavior of the generalized transform can be studied in terms of the Fourier transform and that these results indicate that the Gaussian transform has superior smoothing properties.

  5. Automated macromolecular crystal detection system and method

    Science.gov (United States)

    Christian, Allen T.; Segelke, Brent; Rupp, Bernard; Toppani, Dominique

    2007-06-05

    An automated macromolecular method and system for detecting crystals in two-dimensional images, such as light microscopy images obtained from an array of crystallization screens. Edges are detected from the images by identifying local maxima of a phase congruency-based function associated with each image. The detected edges are segmented into discrete line segments, which are subsequently geometrically evaluated with respect to each other to identify any crystal-like qualities such as, for example, parallel lines, facing each other, similarity in length, and relative proximity. And from the evaluation a determination is made as to whether crystals are present in each image.

  6. 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

  7. Aggravating andmitigating factors associated with cyclist injury severity in Denmark

    DEFF Research Database (Denmark)

    Kaplan, Sigal; Vavatsoulas,, Konstantinos; Prato, Carlo Giacomo

    2014-01-01

    –80 km/h, slippery road surface, and location of the crash on road sections are aggravating infrastructure factors, while the availability of cycling paths and dense urban development are mitigating factors. Heavy vehicle involvement and conflicts between cyclists going straight or turning left and other......Denmark is one of the leading cycling nations, where cycling trips constitute a large share of the total trips, and cycling safety assumes a top priority position in the agenda of policy makers. The current study sheds light on the aggravating and mitigating factors associated with cyclist injury...... severity on Danish roads by examining a comprehensive set of accidents involving a cyclist and a collision partner between 2007 and 2011. Method: This study estimates a generalized ordered logit model of the severity of cyclist injuries because of its ability to accommodate the ordered-response nature...

  8. The subjective meaning of xerostomia—an aggravating misery

    OpenAIRE

    Folke, Solgun; Paulsson, Gun; Fridlund, Bengt; Söderfeldt, Björn

    2010-01-01

    Xerostomia, the subjective sensation of dry mouth, is associated with qualitative and quantitative changes of saliva. Poor health, certain medications and radiation therapy constitute major risk factors. To gain further understanding of this condition the present study explored the main concern of xerostomia expressed by affl icted adults. Qualitative interviews were conducted with 15 participants and analysed according to the grounded theory method. An aggravating misery was identifi ed as t...

  9. Aggravated neuromuscular symptoms of mercury exposure from dental amalgam fillings.

    Science.gov (United States)

    Akbal, Ayla; Yılmaz, Hınç; Tutkun, Engin; Köş, Durdu Mehmet

    2014-01-01

    Dental amalgam fillings are widely used all over the world. However, their mercury content can lead to various side effects and clinical problems. Acute or chronic mercury exposure can cause several side effects on the central nerve system, renal and hepatic functions, immune system, fetal development and it can play a role on exacerbation of neuromuscular diseases. In this case, we will present a patient with vacuolar myopathy whose symptoms were started and aggravated with her dental amalgam fillings.

  10. Pain in Breast Cancer Treatment: Aggravating Factors and Coping Mechanisms

    OpenAIRE

    Maria de Fatima Guerreiro Godoy; Livia Maria Pereira de Godoy; Stelamarys Barufi; José Maria Pereira de Godoy

    2014-01-01

    The objective of this study was to evaluate pain in women with breast cancer-related lymphedema and the characteristics of aggravating factors and coping mechanisms. The study was conducted in the Clinica Godoy, São Jose do Rio Preto, with a group of 46 women who had undergone surgery for the treatment of breast cancer. The following variables were evaluated: type and length of surgery; number of radiotherapy and chemotherapy sessions; continued feeling of the removed breast (phantom limb), i...

  11. The role of macromolecular stability in desiccation tolerance.

    NARCIS (Netherlands)

    Wolkers, W.

    1998-01-01

    The work presented in this thesis concerns a study on the molecular interactions that play a role in the macromolecular stability of desiccation-tolerant higher plant organs. Fourier transform infrared microspectroscopy was used as the main experimental technique to assess macromolecular structures

  12. 42 CFR 93.408 - Mitigating and aggravating factors in HHS administrative actions.

    Science.gov (United States)

    2010-10-01

    ... 42 Public Health 1 2010-10-01 2010-10-01 false Mitigating and aggravating factors in HHS... and Human Services Research Misconduct Issues § 93.408 Mitigating and aggravating factors in HHS... conserve public funds. HHS considers aggravating and mitigating factors in determining appropriate...

  13. Panorama of ancient metazoan macromolecular complexes.

    Science.gov (United States)

    Wan, Cuihong; Borgeson, Blake; Phanse, Sadhna; Tu, Fan; Drew, Kevin; Clark, Greg; Xiong, Xuejian; Kagan, Olga; Kwan, Julian; Bezginov, Alexandr; Chessman, Kyle; Pal, Swati; Cromar, Graham; Papoulas, Ophelia; Ni, Zuyao; Boutz, Daniel R; Stoilova, Snejana; Havugimana, Pierre C; Guo, Xinghua; Malty, Ramy H; Sarov, Mihail; Greenblatt, Jack; Babu, Mohan; Derry, W Brent; Tillier, Elisabeth R; Wallingford, John B; Parkinson, John; Marcotte, Edward M; Emili, Andrew

    2015-09-17

    Macromolecular complexes are essential to conserved biological processes, but their prevalence across animals is unclear. By combining extensive biochemical fractionation with quantitative mass spectrometry, here we directly examined the composition of soluble multiprotein complexes among diverse metazoan models. Using an integrative approach, we generated a draft conservation map consisting of more than one million putative high-confidence co-complex interactions for species with fully sequenced genomes that encompasses functional modules present broadly across all extant animals. Clustering reveals a spectrum of conservation, ranging from ancient eukaryotic assemblies that have probably served cellular housekeeping roles for at least one billion years, ancestral complexes that have accrued contemporary components, and rarer metazoan innovations linked to multicellularity. We validated these projections by independent co-fractionation experiments in evolutionarily distant species, affinity purification and functional analyses. The comprehensiveness, centrality and modularity of these reconstructed interactomes reflect their fundamental mechanistic importance and adaptive value to animal cell systems. PMID:26344197

  14. Macromolecular diffractive imaging using imperfect crystals

    Science.gov (United States)

    Ayyer, Kartik; Yefanov, Oleksandr M.; Oberthür, Dominik; Roy-Chowdhury, Shatabdi; Galli, Lorenzo; Mariani, Valerio; Basu, Shibom; Coe, Jesse; Conrad, Chelsie E.; Fromme, Raimund; Schaffer, Alexander; Dörner, Katerina; James, Daniel; Kupitz, Christopher; Metz, Markus; Nelson, Garrett; Xavier, Paulraj Lourdu; Beyerlein, Kenneth R.; Schmidt, Marius; Sarrou, Iosifina; Spence, John C. H.; Weierstall, Uwe; White, Thomas A.; Yang, Jay-How; Zhao, Yun; Liang, Mengning; Aquila, Andrew; Hunter, Mark S.; Robinson, Joseph S.; Koglin, Jason E.; Boutet, Sébastien; Fromme, Petra; Barty, Anton; Chapman, Henry N.

    2016-02-01

    The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins—they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-ångström limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 ångströms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 ångströms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing.

  15. Phylogenetic Diversity in the Macromolecular Composition of Microalgae

    Science.gov (United States)

    Finkel, Zoe V.; Follows, Mick J.; Liefer, Justin D.; Brown, Chris M.; Benner, Ina; Irwin, Andrew J.

    2016-01-01

    The elemental stoichiometry of microalgae reflects their underlying macromolecular composition and influences competitive interactions among species and their role in the food web and biogeochemistry. Here we provide a new estimate of the macromolecular composition of microalgae using a hierarchical Bayesian analysis of data compiled from the literature. The median macromolecular composition of nutrient-sufficient exponentially growing microalgae is 32.2% protein, 17.3% lipid, 15.0% carbohydrate, 17.3% ash, 5.7% RNA, 1.1% chlorophyll-a and 1.0% DNA as percent dry weight. Our analysis identifies significant phylogenetic differences in macromolecular composition undetected by previous studies due to small sample sizes and the large inherent variability in macromolecular pools. The phylogenetic differences in macromolecular composition lead to variations in carbon-to-nitrogen ratios that are consistent with independent observations. These phylogenetic differences in macromolecular and elemental composition reflect adaptations in cellular architecture and biochemistry; specifically in the cell wall, the light harvesting apparatus, and storage pools. PMID:27228080

  16. PP005. Vitamin D depletion aggravates hypertension in transgenic rats

    DEFF Research Database (Denmark)

    Bjørkholt Andersen, Louise; Herse, Florian; Christesen, Henrik Thybo;

    2013-01-01

    overexpressing the human renin and angiotensinogen genes, group 1 (n=18) received vitamin D depleted chow; group 2 (n=15) standard chow and intraperitoneal paricalcitol at 800ng/kg thrice weekly; and group 3 (n=15) standard chow and vehicle injections. Blood pressure (tail cuff) and 24-h albuminuria were...... found between groups in mortality or proteinuria. CONCLUSION: Short-term vitamin D depletion aggravated hypertension and end-organ damage in a rat model of angiotensin II-induced hypertension. Short-term interventions with high-dose vitamin D analogues had no protective effect....

  17. Functional Sub-states by High-pressure Macromolecular Crystallography.

    Science.gov (United States)

    Dhaussy, Anne-Claire; Girard, Eric

    2015-01-01

    At the molecular level, high-pressure perturbation is of particular interest for biological studies as it allows trapping conformational substates. Moreover, within the context of high-pressure adaptation of deep-sea organisms, it allows to decipher the molecular determinants of piezophily. To provide an accurate description of structural changes produced by pressure in a macromolecular system, developments have been made to adapt macromolecular crystallography to high-pressure studies. The present chapter is an overview of results obtained so far using high-pressure macromolecular techniques, from nucleic acids to virus capsid through monomeric as well as multimeric proteins.

  18. Aggravation of viral hepatitis by platelet-derived serotonin.

    Science.gov (United States)

    Lang, Philipp A; Contaldo, Claudio; Georgiev, Panco; El-Badry, Ashraf Mohammad; Recher, Mike; Kurrer, Michael; Cervantes-Barragan, Luisa; Ludewig, Burkhard; Calzascia, Thomas; Bolinger, Beatrice; Merkler, Doron; Odermatt, Bernhard; Bader, Michael; Graf, Rolf; Clavien, Pierre-Alain; Hegazy, Ahmed N; Löhning, Max; Harris, Nicola L; Ohashi, Pamela S; Hengartner, Hans; Zinkernagel, Rolf M; Lang, Karl S

    2008-07-01

    More than 500 million people worldwide are persistently infected with hepatitis B virus or hepatitis C virus. Although both viruses are poorly cytopathic, persistence of either virus carries a risk of chronic liver inflammation, potentially resulting in liver steatosis, liver cirrhosis, end-stage liver failure or hepatocellular carcinoma. Virus-specific T cells are a major determinant of the outcome of hepatitis, as they contribute to the early control of chronic hepatitis viruses, but they also mediate immunopathology during persistent virus infection. We have analyzed the role of platelet-derived vasoactive serotonin during virus-induced CD8(+) T cell-dependent immunopathological hepatitis in mice infected with the noncytopathic lymphocytic choriomeningitis virus. After virus infection, platelets were recruited to the liver, and their activation correlated with severely reduced sinusoidal microcirculation, delayed virus elimination and increased immunopathological liver cell damage. Lack of platelet-derived serotonin in serotonin-deficient mice normalized hepatic microcirculatory dysfunction, accelerated virus clearance in the liver and reduced CD8(+) T cell-dependent liver cell damage. In keeping with these observations, serotonin treatment of infected mice delayed entry of activated CD8(+) T cells into the liver, delayed virus control and aggravated immunopathological hepatitis. Thus, vasoactive serotonin supports virus persistence in the liver and aggravates virus-induced immunopathology.

  19. Aldosterone aggravates glucose intolerance induced by high fructose.

    Science.gov (United States)

    Sherajee, Shamshad J; Rafiq, Kazi; Nakano, Daisuke; Mori, Hirohito; Kobara, Hideki; Hitomi, Hirofumi; Fujisawa, Yoshihide; Kobori, Hiroyuki; Masaki, Tsutomu; Nishiyama, Akira

    2013-11-15

    We previously reported that aldosterone impaired vascular insulin signaling in vivo and in vitro. Fructose-enriched diet induces metabolic syndrome including hypertension, insulin resistance, hyperlipidemia and diabetes in animal. In the current study, we hypothesized that aldosterone aggravated fructose feeding-induced glucose intolerance in vivo. Rats were divided into five groups for six-week treatment; uninephrectomy (Unx, n=8), Unx+aldosterone (aldo, 0.75 µg/h, s.c., n=8), Unx+fructose (fruc, 10% in drinking water, n=8), Unx+aldo+fruc, (aldo+fruc, n=8), and Unx+aldo+fruc+spironolactone, a mineralocorticoid receptor antagonist (aldo+fruc+spiro, 20mg/kg/day, p.o., n=8). Aldo+fruc rats manifested the hypertension, and induced glucose intolerance compared to fruc intake rats assessed by oral glucose tolerance test, homeostasis model assessment of insulin resistance and hyperinsulinemic-euglycemic clamp study. Spironolactone, significantly improved the aldosterone-accelerated glucose intolerance. Along with improvement in insulin resistance, spironolactone suppressed upregulated mineralocorticoid receptor (MR) target gene, serum and glucocorticoid-regulated kinases-1 mRNA expression in skeletal muscle in aldo+fruc rats. In conclusion, these data suggested that aldosterone aggravates fructose feeding-induced glucose intolerance through MR activation.

  20. Beyond bullying: Aggravating elements of peer victimization episodes.

    Science.gov (United States)

    Turner, Heather A; Finkelhor, David; Shattuck, Anne; Hamby, Sherry; Mitchell, Kimberly

    2015-09-01

    This study sought to identify features of peer victimization that aggravate negative outcomes in children. The features that were assessed include "power imbalance," a commonly used criterion in defining bullying, and 5 other characteristics: injury, weapon involvement, Internet involvement, sexual content, and bias content. Three outcomes were assessed: level of fear, missing school, and trauma symptoms. A nationally representative sample of 3,164 children and youth ages 6-17 (51.8% male; 68.4% white, 12.5% black, 13.5% Hispanic, 5.7% other race) was obtained through Random Digit Dial and supplemented with an address-based sample to capture cell-phone-only households. One child was randomly selected from each household. Interviews were conducted with parents of children age 6-9 and with the youths themselves if they were age 10-17. Peer victimization was assessed with the Juvenile Victimization Questionnaire (JVQ). Almost half (48.4%) of the entire sample of school-age children experienced at least 1 form of peer victimization in the past year. Injury and power imbalance independently increased the impact on children for all 3 outcomes. Additionally, weapon involvement and sexual content were associated with trauma symptoms, with sexual content having the strongest effect (B = .23, p bullying with its exclusionary power imbalance definition as the central focus for prevention and intervention. We recommend a broader focus on peer victimization along with more research to identify the aggravating features that signal the greatest need for intervention. PMID:25330389

  1. Sequential recovery of macromolecular components of the nucleolus.

    Science.gov (United States)

    Bai, Baoyan; Laiho, Marikki

    2015-01-01

    The nucleolus is involved in a number of cellular processes of importance to cell physiology and pathology, including cell stress responses and malignancies. Studies of macromolecular composition of the nucleolus depend critically on the efficient extraction and accurate quantification of all macromolecular components (e.g., DNA, RNA, and protein). We have developed a TRIzol-based method that efficiently and simultaneously isolates these three macromolecular constituents from the same sample of purified nucleoli. The recovered and solubilized protein can be accurately quantified by the bicinchoninic acid assay and assessed by polyacrylamide gel electrophoresis or by mass spectrometry. We have successfully applied this approach to extract and quantify the responses of all three macromolecular components in nucleoli after drug treatments of HeLa cells, and conducted RNA-Seq analysis of the nucleolar RNA.

  2. A Novel Algorithm for Macromolecular Epitope Matching

    Directory of Open Access Journals (Sweden)

    Stanislav Jakuschev

    2009-03-01

    Full Text Available Many macromolecules, namely proteins, show functional substructures or epitopes defined by characteristic spatial arrangements of groups of specific atoms or residues. The identification of such substructures in a set of macromolecular 3D-structures solves an important problem in molecular biology as it allows the assignment of functions to molecular moieties and thus opens the possibility of a mechanistic understanding of molecular function. We have devised an algorithm that models a functional epitope formed by a group of atoms or residues as set of points in cartesian space with associated functional properties. The algorithm searches for similar epitopes in a database of structures by an efficient multistage comparison of distance sets in the epitope and in the structures from the database. The search results in a list of optimal matches and corresponding optimal superpositions of query epitope and matching epitopes from the database. The algorithm is discussed against the background of related approaches, and it is successfully tested in three application scenarios: global match of two homologous proteins, search for an epitope on a homologous protein, and finding matching epitopes in a protein database.

  3. An upper limit for macromolecular crowding effects

    Directory of Open Access Journals (Sweden)

    Miklos Andrew C

    2011-05-01

    Full Text Available Abstract Background Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ~2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid with particle radii of ~300 nm. Results Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (~0.5 kcal/mol at 37°C, pH 5.4 stabilization at a volume occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions. Conclusions Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dilute solution-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.

  4. 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.

  5. The solvent component of macromolecular crystals

    Energy Technology Data Exchange (ETDEWEB)

    Weichenberger, Christian X. [European Academy of Bozen/Bolzano (EURAC), Viale Druso 1, Bozen/Bolzano, I-39100 Südtirol/Alto Adige (Italy); Afonine, Pavel V. [Lawrence Berkeley National Laboratory (LBNL), 1 Cyclotron Road, Mail Stop 64R0121, Berkeley, CA 94720 (United States); Kantardjieff, Katherine [California State University, San Marcos, CA 92078 (United States); Rupp, Bernhard, E-mail: br@hofkristallamt.org [k.-k. Hofkristallamt, 991 Audrey Place, Vista, CA 92084 (United States); Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck (Austria)

    2015-04-30

    On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.

  6. Adaptive rewiring aggravates the effects of species loss in ecosystems.

    Science.gov (United States)

    Gilljam, David; Curtsdotter, Alva; Ebenman, Bo

    2015-01-01

    Loss of one species in an ecosystem can trigger extinctions of other dependent species. For instance, specialist predators will go extinct following the loss of their only prey unless they can change their diet. It has therefore been suggested that an ability of consumers to rewire to novel prey should mitigate the consequences of species loss by reducing the risk of cascading extinction. Using a new modelling approach on natural and computer-generated food webs we find that, on the contrary, rewiring often aggravates the effects of species loss. This is because rewiring can lead to overexploitation of resources, which eventually causes extinction cascades. Such a scenario is particularly likely if prey species cannot escape predation when rare and if predators are efficient in exploiting novel prey. Indeed, rewiring is a two-edged sword; it might be advantageous for individual predators in the short term, yet harmful for long-term system persistence. PMID:26400367

  7. Structural policy in the context of international competition aggravation

    Directory of Open Access Journals (Sweden)

    Volodymyr Bodrov

    2014-09-01

    Full Text Available This article researches the essence and peculiarities of the structural policy, performs classification of its models and determines possibilities of their use in the context of increasing international competition. It discovers the main components of the economic structure and trends of the state policy regarding their modernization. Measures on improvement of state regulation instruments are offered, factors of influence upon improvement of the Ukrainian economy structure are analyzed and priority goals are systematized which require urgent implementation in the terms of competitive struggle aggravation at the global markets. The article also researches the matter of importance of performing a complex of state functional and selective measures in the form of matrix policy for the purpose of protecting national interests of the country in the context of global challenges

  8. Severe Brown Fat Lipoatrophy Aggravates Atherosclerotic Process in Male Mice.

    Science.gov (United States)

    Gómez-Hernández, Almudena; Beneit, Nuria; Escribano, Óscar; Díaz-Castroverde, Sabela; García-Gómez, Gema; Fernández, Silvia; Benito, Manuel

    2016-09-01

    Obesity is one of the major risk factors for the development of cardiovascular diseases and is characterized by abnormal accumulation of adipose tissue, including perivascular adipose tissue (PVAT). However, brown adipose tissue (BAT) activation reduces visceral adiposity. To demonstrate that severe brown fat lipoatrophy might accelerate atherosclerotic process, we generated a new mouse model without insulin receptor (IR) in BAT and without apolipoprotein (Apo)E (BAT-specific IR knockout [BATIRKO];ApoE(-/-) mice) and assessed vascular and metabolic alterations associated to obesity. In addition, we analyzed the contribution of the adipose organ to vascular inflammation. Brown fat lipoatrophy induces visceral adiposity, mainly in gonadal depot (gonadal white adipose tissue [gWAT]), severe glucose intolerance, high postprandial glucose levels, and a severe defect in acute insulin secretion. BATIRKO;ApoE(-/-) mice showed greater hypertriglyceridemia than the obtained in ApoE(-/-) and hypercholesterolemia similar to ApoE(-/-) mice. BATIRKO;ApoE(-/-) mice, in addition to primary insulin resistance in BAT, also showed a significant decrease in insulin signaling in liver, gWAT, heart, aorta artery, and thoracic PVAT. More importantly, our results suggest that severe brown fat lipoatrophy aggravates the atherosclerotic process, characterized by a significant increase of lipid depots, atherosclerotic coverage, lesion size and complexity, increased macrophage infiltration, and proinflammatory markers expression. Finally, an increase of TNF-α and leptin as well as a decrease of adiponectin by BAT, gWAT, and thoracic PVAT might also be responsible of vascular damage. Our results suggest that severe brown lipoatrophy aggravates atherosclerotic process. Thus, BAT activation might protect against obesity and its associated metabolic alterations. PMID:27414981

  9. Aggravated Cardiac Remodeling post Aortocaval Fistula in Unilateral Nephrectomized Rats.

    Directory of Open Access Journals (Sweden)

    Jie Wu

    Full Text Available Aortocaval fistula (AV in rat is a unique model of volume-overload congestive heart failure and cardiac hypertrophy. Living donor kidney transplantation is regarded as beneficial to allograft recipients and not particularly detrimental to the donors. Impact of AV on animals with mild renal dysfunction is not fully understood. In this study, we explored the effects of AV in unilateral nephrectomized (UNX rats.Adult male Sprague-Dawley (SD rats were divided into Sham (n = 10, UNX (right kidney remove, n = 10, AV (AV established between the levels of renal arteries and iliac bifurcation, n = 18 and UNX+AV (AV at one week after UNX, n = 22, respectively. Renal outcome was measured by glomerular filtration rate, effective renal plasma flow, fractional excretion of sodium, albuminuria, plasma creatinine, and cystatin C. Focal glomerulosclerosis (FGS incidence was evaluated by renal histology. Cardiac function was measured by echocardiography and hemodynamic measurements.UNX alone induced compensatory left kidney enlargement, increased plasma creatinine and cystatin C levels, and slightly reduced glomerular filtration rate and increased FGS. AV induced significant cardiac enlargement and hypertrophy and reduced cardiac function and increased FGS, these changes were aggravated in UNX+AV rats.Although UNX only induces minor renal dysfunction, additional chronic volume overload placement during the adaptation phase of the remaining kidney is associated with aggravated cardiac dysfunction and remodeling in UNX rats, suggesting special medical care is required for UNX or congenital monokidney subjects in case of chronic volume overload as in the case of pregnancy and hyperthyroidism to prevent further adverse cardiorenal events in these individuals.

  10. Macromolecular networks and intelligence in microorganisms

    Science.gov (United States)

    Westerhoff, Hans V.; Brooks, Aaron N.; Simeonidis, Evangelos; García-Contreras, Rodolfo; He, Fei; Boogerd, Fred C.; Jackson, Victoria J.; Goncharuk, Valeri; Kolodkin, Alexey

    2014-01-01

    Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call “intelligence.” Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as “human” and “brain” out of the defining features of “intelligence,” all forms of life – from microbes to humans – exhibit some or all characteristics consistent with “intelligence.” We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo. PMID:25101076

  11. Macromolecular Topography Leaps into the Digital Age

    Science.gov (United States)

    Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

    2003-01-01

    A low-cost, real-time digital topography system is under development which will replace x-ray film and nuclear emulsion plates. The imaging system is based on an inexpensive surveillance camera that offers a 1000x1000 array of 8 im square pixels, anti-blooming circuitry, and very quick read out. Currently, the system directly converts x-rays to an image with no phosphor. The system is small and light and can be easily adapted to work with other crystallographic equipment. Preliminary images have been acquired of cubic insulin at the NSLS x26c beam line. NSLS x26c was configured for unfocused monochromatic radiation. Six reflections were collected with stills spaced from 0.002 to 0.001 degrees apart across the entire oscillation range that the reflections were in diffracting condition. All of the reflections were rotated to the vertical to reduce Lorentz and beam related effects. This particular CCD is designed for short exposure applications (much less than 1 sec) and so has a relatively high dark current leading to noisy raw images. The images are processed to remove background and other system noise with a multi-step approach including the use of wavelets, histogram, and mean window filtering. After processing, animations were constructed with the corresponding reflection profile to show the diffraction of the crystal volume vs. the oscillation angle as well as composite images showing the parts of the crystal with the strongest diffraction for each reflection. The final goal is to correlate features seen in reflection profiles captured with fine phi slicing to those seen in the topography images. With this development macromolecular topography finally comes into the digital age.

  12. 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

  13. Pain in Breast Cancer Treatment: Aggravating Factors and Coping Mechanisms

    Directory of Open Access Journals (Sweden)

    Maria de Fatima Guerreiro Godoy

    2014-01-01

    Full Text Available The objective of this study was to evaluate pain in women with breast cancer-related lymphedema and the characteristics of aggravating factors and coping mechanisms. The study was conducted in the Clinica Godoy, São Jose do Rio Preto, with a group of 46 women who had undergone surgery for the treatment of breast cancer. The following variables were evaluated: type and length of surgery; number of radiotherapy and chemotherapy sessions; continued feeling of the removed breast (phantom limb, infection, intensity of pain, and factors that improve and worsen the pain. The percentage of events was used for statistical analysis. About half the participants (52.1% performed modified radical surgery, with 91.3% removing only one breast; 82.6% of the participants did not perform breast reconstruction surgery. Insignificant pain was reported by 32.60% of the women and 67.3% said they suffered pain; it was mild in 28.8% of the cases (scale 1–5, moderate in 34.8% (scale 6–9, and severe in 4.3%. The main mechanisms used to cope with pain were painkillers in 41.30% of participants, rest in 21.73%, religious ceremonies in 17.39%, and chatting with friends in 8.69%. In conclusion, many mastectomized patients with lymphedema complain of pain, but pain is often underrecognized and undertreated.

  14. Macromolecular crystallography beamline X25 at the NSLS.

    Science.gov (United States)

    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

    2014-05-01

    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.

  15. Tolbutamide attenuates diazoxide-induced aggravation of hypoxic cell injury.

    Science.gov (United States)

    Pissarek, M; Reichelt, C; Krauss, G J; Illes, P

    1998-11-23

    ATP-dependent potassium (KATP) channels of neurons are closed in the presence of physiological levels of intracellular ATP and open when ATP is depleted during hypoxia or metabolic damage. The present study investigates hypoxic alterations of purine and pyrimidine nucleotide levels supposed to intracellularly modulate KATP channels. In addition, the effects of the KATP channel activator diazoxide and its antagonist tolbutamide were investigated on ATP, GTP, CTP and UTP levels in slices of the parietal cortex. Hypoxia was evoked by saturation of the medium with 95% N2-5% CO2 instead of 95% O2-5% CO2 for 5 min. Nucleotide contents were measured by anion-exchange HPLC in neutralized perchloric acid extracts obtained from slices frozen immediately at the end of incubation. Hypoxia per se decreased purine and pyrimidine nucleoside triphosphate contents. Thus, ATP and GTP contents were reduced to 69.9 and 77.6% of the respective normoxic levels. UTP and CTP contents were even more decreased (to 60.9 and 41.6%),, probably because the salvage pathway of these pyrimidine nucleotides is less effective than that of the purine nucleotides ATP and GTP. While tolbutamide (30 microM) had no effect on the hypoxia-induced decrease of nucleotides, diazoxide at 300, but not 30 microM aggravated the decline of ATP, UTP and CTP to 51.8, 37.5 and 28.5% of the contents observed at normoxia; GTP levels also showed a tendency to decrease after diazoxide application. Tolbutamide (300 microM) antagonized the effects of diazoxide (300 but not 30 microM aggravated the decline of ATP, UTP and CTP to 51.8, 37.5 and 28.5% of the contents observed at normoxia; GTP levels also showed a tendency to decrease after diazoxide application. Tolbutamide (300 microM) antagonized the effects of diazoxide (300 MicroM). Nucleoside diphosphate (ADP, GDP and UDP) levels were uniformly increased by hypoxia. There was no hypoxia-induced increase of ADP contents in the presence of tolbutamide (300 microM). The ATP

  16. Dietary hypercholesterolemia aggravates contrast media-induced nephropathy

    Institute of Scientific and Technical Information of China (English)

    杨定位; 贾汝汉; 杨定平; 丁国华; 黄从新

    2004-01-01

    Background Contrast media administration can result in severe nephrotoxicity under pathological conditions such as diabetic nephropathy, congestive heart failure, dehydration, et al. The purpose of this study was to evaluate the effects of dietary hypercholesterolemia on contrast media-induced changes in renal function, blood flow, and histopathology.Methods Rats were fed either on a normal rodent diet (group N) or a high-cholesterol supplemented diet (group H; 4% cholesterol and 1% cholic acid) for 8 weeks. Half of the animals (n =6) from each diet group were then given a tail vein injection of 60% diatrizoate (6 ml/kg; group NC and group HC)and the other half were administered saline. Total serum cholesterol, triglyceride, serum creatinine,creatinine clearance rate, fractional excretion of sodium and potassium, and cortical nitric oxide production were determined one day following contrast media administration. Renal blood flow was determined by color Doppler flow imaging and pulsed-mode Doppler. Renal histopathology was observed by light microscopy.Results Total serum cholesterol and resistance indices of renal blood vessels increased significantly,while creatinine clearance rate and production of nitric oxide in the renal cortex decreased markedly in group HC and group H when compared to group N and group NC. The creatinine clearance rate decreased significantly in group HC compared to group H. Serum creatinine levels and fractional excretion of sodium and potassium in group HC were significantly higher than those in the other three groups. Severe tubular degeneration and necrosis, protein cast accumulation, and medullary congestion were found in group HC.Conclusion Hypercholesterolemia is a risk factor for contrast media-induced nephropathy.Hypercholesterolemia aggravates contrast media-induced nephrotoxicity through the reduced production of nitric oxide.

  17. Metallothionein deficiency aggravates depleted uranium-induced nephrotoxicity.

    Science.gov (United States)

    Hao, Yuhui; Huang, Jiawei; Gu, Ying; Liu, Cong; Li, Hong; Liu, Jing; Ren, Jiong; Yang, Zhangyou; Peng, Shuangqing; Wang, Weidong; Li, Rong

    2015-09-15

    Depleted uranium (DU) has been widely used in both civilian and military activities, and the kidney is the main target organ of DU during acute high-dose exposures. In this study, the nephrotoxicity caused by DU in metallothionein-1/2-null mice (MT-/-) and corresponding wild-type (MT+/+) mice was investigated to determine any associations with MT. Each MT-/- or MT+/+ mouse was pretreated with a single dose of DU (10mg/kg, intraperitoneal injection) or an equivalent volume of saline. After 4days of DU administration, kidney changes were assessed. After DU exposure, serum creatinine and serum urea nitrogen in MT-/- mice significantly increased than in MT+/+ mice, with more severe kidney pathological damage. Moreover, catalase and superoxide dismutase (SOD) decreased, and generation of reactive oxygen species and malondialdehyde increased in MT-/- mice. The apoptosis rate in MT-/- mice significantly increased, with a significant increase in both Bax and caspase 3 and a decrease in Bcl-2. Furthermore, sodium-glucose cotransporter (SGLT) and sodium-phosphate cotransporter (NaPi-II) were significantly reduced after DU exposure, and the change of SGLT was more evident in MT-/- mice. Finally, exogenous MT was used to evaluate the correlation between kidney changes induced by DU and MT doses in MT-/- mice. The results showed that, the pathological damage and cell apoptosis decreased, and SOD and SGLT levels increased with increasing dose of MT. In conclusion, MT deficiency aggravated DU-induced nephrotoxicity, and the molecular mechanisms appeared to be related to the increased oxidative stress and apoptosis, and decreased SGLT expression. PMID:26148447

  18. Effects of macromolecular crowding and osmolyte on human Tau fibrillation.

    Science.gov (United States)

    Wu, Yingying; Teng, Ningning; Li, Sen

    2016-09-01

    Tau fibrillation is reported to be involved in neurodegenerative disorders, such as Alzheimer's disease, in which the natural environment is very crowded in the cells. Understanding the role of crowding environments in regulating Tau fibrillation is of great importance for elucidating the etiology of these diseases. In this experiment, the effects of macromolecular crowding and osmolyte reagents in the crowding environment on Tau fibrillation were studied by thioflavin T binding, SDS-PAGE and TEM assays. Ficoll 70 and Dextran 70 of different concentrations were used as macromolecular crowding reagents inside the cells and showed a strong enhancing effect on the fibrillation of normal and hyperphosphorylated Tau. The enhancing effect of Dextran is stronger than that of Ficoll 70 at the same concentration. In addition, the cellular osmolyte sucrose was found to protect Tau against fibrillation, and inhibit the enhancing effect of macromolecular crowding on Tau fibrillation. A possible model for the fibrillation process of Tau and the effect of macromolecular crowding and osmolyte on this process was proposed based on these experimental results. The information obtained from our study can enhance the understanding of how proteins aggregate and avoid aggregation in crowded physiological environments and might lead to a better understanding of the molecular mechanisms of Alzheimer's disease in vivo. PMID:26683879

  19. Macromolecular crystallography radiation damage research: what’s new?

    OpenAIRE

    Garman, Elspeth F.; Weik, Martin

    2011-01-01

    Radiation damage in macromolecular crystallography has become a mainstream concern over the last ten years. The current status of research into this area is briefly assessed, and the ten new papers published in this issue are set into the context of previous work in the field. Some novel and exciting developments emerging over the last two years are also summarized.

  20. Generating triangulated macromolecular surfaces by Euclidean Distance Transform.

    Directory of Open Access Journals (Sweden)

    Dong Xu

    Full Text Available Macromolecular surfaces are fundamental representations of their three-dimensional geometric shape. Accurate calculation of protein surfaces is of critical importance in the protein structural and functional studies including ligand-protein docking and virtual screening. In contrast to analytical or parametric representation of macromolecular surfaces, triangulated mesh surfaces have been proved to be easy to describe, visualize and manipulate by computer programs. Here, we develop a new algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT. The triangulated surfaces are constructed directly from volumetric solids by a Vertex-Connected Marching Cube algorithm that forms triangles from grid points. Compared to the analytical result, the relative error of the surface calculations by EDTSurf is <2-4% depending on the grid resolution, which is 1.5-4 times lower than the methods in the literature; and yet, the algorithm is faster and costs less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang.bioinformatics.ku.edu/EDTSurf.

  1. Two-center-multipole expansion method: application to macromolecular systems

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Yakubovich, Alexander V.; Solov'yov, Andrey V.;

    2007-01-01

    We propose a theoretical method for the calculation of the interaction energy between macromolecular systems at large distances. The method provides a linear scaling of the computing time with the system size and is considered as an alternative to the well-known fast multipole method. Its efficie...

  2. Imprecise methods may both obscure and aggravate a relation between fat and breast cancer

    DEFF Research Database (Denmark)

    Heitmann, B L; Frederiksen, Peder

    2007-01-01

    Bias in diet reporting may be both random and non-random, and may be found with simpler as well as more advanced dietary instruments. A random bias will contribute to obscure relations between diet and disease. A systematic bias may obscure or aggravate such associations. Underreporting of non......-protein energy has been found to be substantial, particularly among those who are obese or have high dietary intakes. Such a non-random bias on the group level would tend to aggravate associations between dietary non-protein and disease. Whether the net result of the random and non-random bias aggravates...

  3. Metallothionein deficiency aggravates depleted uranium-induced nephrotoxicity

    Energy Technology Data Exchange (ETDEWEB)

    Hao, Yuhui; Huang, Jiawei; Gu, Ying; Liu, Cong; Li, Hong; Liu, Jing; Ren, Jiong; Yang, Zhangyou [State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing 400038 (China); Peng, Shuangqing [Evaluation and Research Center for Toxicology, Institute of Disease Control and Prevention, Academy of Military Medical Science, 20 Dongdajie Street, Fengtai District, Beijing 100071 (China); Wang, Weidong, E-mail: wwdwyl@sina.com [Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Sixth People' s Hospital, Shanghai 200233 (China); Li, Rong, E-mail: yuhui_hao@126.com [State Key Laboratory of Trauma, Burns and Combined Injury, Institute of Combined Injury, Chongqing Engineering Research Center for Nanomedicine, College of Preventive Medicine, Third Military Medical University, No. 30 Gaotanyan Street, Shapingba District, Chongqing 400038 (China)

    2015-09-15

    Depleted uranium (DU) has been widely used in both civilian and military activities, and the kidney is the main target organ of DU during acute high-dose exposures. In this study, the nephrotoxicity caused by DU in metallothionein-1/2-null mice (MT −/−) and corresponding wild-type (MT +/+) mice was investigated to determine any associations with MT. Each MT −/− or MT +/+ mouse was pretreated with a single dose of DU (10 mg/kg, intraperitoneal injection) or an equivalent volume of saline. After 4 days of DU administration, kidney changes were assessed. After DU exposure, serum creatinine and serum urea nitrogen in MT −/− mice significantly increased than in MT +/+ mice, with more severe kidney pathological damage. Moreover, catalase and superoxide dismutase (SOD) decreased, and generation of reactive oxygen species and malondialdehyde increased in MT −/− mice. The apoptosis rate in MT −/− mice significantly increased, with a significant increase in both Bax and caspase 3 and a decrease in Bcl-2. Furthermore, sodium-glucose cotransporter (SGLT) and sodium-phosphate cotransporter (NaPi-II) were significantly reduced after DU exposure, and the change of SGLT was more evident in MT −/− mice. Finally, exogenous MT was used to evaluate the correlation between kidney changes induced by DU and MT doses in MT −/− mice. The results showed that, the pathological damage and cell apoptosis decreased, and SOD and SGLT levels increased with increasing dose of MT. In conclusion, MT deficiency aggravated DU-induced nephrotoxicity, and the molecular mechanisms appeared to be related to the increased oxidative stress and apoptosis, and decreased SGLT expression. - Highlights: • MT −/− and MT +/+ mice were used to evaluate nephrotoxicity of DU. • Renal damage was more evident in the MT −/− mice after exposure to DU. • Exogenous MT also protects against DU-induced nephrotoxicity. • MT deficiency induced more ROS and apoptosis after exposure to

  4. Metallothionein deficiency aggravates depleted uranium-induced nephrotoxicity

    International Nuclear Information System (INIS)

    Depleted uranium (DU) has been widely used in both civilian and military activities, and the kidney is the main target organ of DU during acute high-dose exposures. In this study, the nephrotoxicity caused by DU in metallothionein-1/2-null mice (MT −/−) and corresponding wild-type (MT +/+) mice was investigated to determine any associations with MT. Each MT −/− or MT +/+ mouse was pretreated with a single dose of DU (10 mg/kg, intraperitoneal injection) or an equivalent volume of saline. After 4 days of DU administration, kidney changes were assessed. After DU exposure, serum creatinine and serum urea nitrogen in MT −/− mice significantly increased than in MT +/+ mice, with more severe kidney pathological damage. Moreover, catalase and superoxide dismutase (SOD) decreased, and generation of reactive oxygen species and malondialdehyde increased in MT −/− mice. The apoptosis rate in MT −/− mice significantly increased, with a significant increase in both Bax and caspase 3 and a decrease in Bcl-2. Furthermore, sodium-glucose cotransporter (SGLT) and sodium-phosphate cotransporter (NaPi-II) were significantly reduced after DU exposure, and the change of SGLT was more evident in MT −/− mice. Finally, exogenous MT was used to evaluate the correlation between kidney changes induced by DU and MT doses in MT −/− mice. The results showed that, the pathological damage and cell apoptosis decreased, and SOD and SGLT levels increased with increasing dose of MT. In conclusion, MT deficiency aggravated DU-induced nephrotoxicity, and the molecular mechanisms appeared to be related to the increased oxidative stress and apoptosis, and decreased SGLT expression. - Highlights: • MT −/− and MT +/+ mice were used to evaluate nephrotoxicity of DU. • Renal damage was more evident in the MT −/− mice after exposure to DU. • Exogenous MT also protects against DU-induced nephrotoxicity. • MT deficiency induced more ROS and apoptosis after exposure to

  5. Sleep-related hypoxemia aggravates systematic inflammation in emphysematous rats

    Institute of Scientific and Technical Information of China (English)

    FENG Jing; Ambrose An-Po Chiang; WU Qi; CHEN Bao-yuan; CUI Lin-yang; LIANG Dong-chun; ZHANG Ze-li; YAO Wo

    2010-01-01

    mean linear intercept (MLI) and mean alveolar number (MAN) values than SRHCtrl group. MLI values in SRHStand group were the highest (ail P <0.05). O2Sat in SRHStand rats when SRH exposure was (83.45±1.76)%. Histological scores of lung, liver, pancreas and right carotid artery were higher in emphysematous groups than SRHCtrl group, and SRHStand group were the highest (all P <0.05) (SOD and CAT values were lower and MDA values were higher in groups with emphysema than without and in SRHStand group than in ECtrl group (all P <0.05)). MDA values were the highest in SRHStand group (all P <0.05). Total cellular score in BALF and White blood cell (WBC) in whole blood were the highest in SRHStand group (all P <0.05). Lymphocyte ratios were the highest in SRHStand group both in BALF and blood (all P <0.05). Red blood cell (RBC) and hemoglobin in emphysematous groups were higher than that in SRHCtrl group, and SRHStand group were higher than ECtrl group (all P <0.05).Conclusions With a proper novo model of SRHIE with Wistar rats, we have demonstrated SRH may aggravate the degree of emphysematous changes, polycythemia,oxidative stress and systematic inflammation. SRH and emphysema may have a synergistic action in causing systematic damages, and lymphocyte may be playing a central role in this process. Longer duration and more severe extent of SRHIE exposure also seem to result in more serious systematic damages. The mechanisms of all these concerned processes remain to be studied.

  6. 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.

  7. Macromolecular Brushes as Stabilizers of Hydrophobic Solute Nanoparticles.

    Science.gov (United States)

    Luo, Hanying; Raciti, David; Wang, Chao; Herrera-Alonso, Margarita

    2016-06-01

    Macromolecular brushes bearing poly(ethylene glycol) and poly(d,l-lactide) side chains were used to stabilize hydrophobic solute nanoparticles formed by a rapid change in solvent quality. Unlike linear diblock copolymers with the same hydrophilic and hydrophobic block chemistries, the brush copolymer enabled the formation of ellipsoidal β-carotene nanoparticles, which in cosolvent mixtures developed into rod-like structures, resulting from a combination of Ostwald ripening and particle aggregation. The stabilizing ability of the copolymer was highly dependent on the mobility of the hydrophobic component, influenced by its molecular weight. As shown here, asymmetric amphiphilic macromolecular brushes of this type may be used as hydrophobic drug stabilizers and potentially assist the shape control of nonspherical aggregate morphologies. PMID:27035279

  8. The vibron dressing in α-helicoidal macromolecular chains

    Institute of Scientific and Technical Information of China (English)

    D.(C)evizovi(c); S.Galovi(c); A.Reshetnyak; Z.Ivi(c)

    2013-01-01

    We present a study of the physical properties of the vibrational excitation in α-helicoidal macromolecular chains,caused by the interaction with acoustical and optical phonon modes.The influence of the temperature and the basic system parameters on the vibron dressing have been analyzed by employing the simple mean-field approach based on the variational extension of the Lang-Firsov unitary transformation.The applied approach predicts a region in system parameter space where one has an abrupt transition from a partially dressed (light and mobile) to a fully dressed (immobile) vibron state.We found that the boundary of this region depends on system temperature and the type of bond among structural elements in the macromolecular chain.

  9. 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.

  10. Effects of macromolecular chelators on intestinal cadmium absorption in mice

    Energy Technology Data Exchange (ETDEWEB)

    Andersen, O.; Nielsen, J.B.; Bulman, R.A.

    1989-01-01

    Suppression of absorption by macromolecular chelators have been sucessful with several metals. In this paper a series of immobilized chelators ranging from DTPA to S-containing soft bases have been synthetized and investigated for ability to suppress intestinal uptake of /sup 109/Cd/sup 2+/ in mice. Dextran-O-ethyl-mercaptan, xanthates derived from polysaccharides and polyvinyl alcohol, dithiocarbamates of polyethylene imine and aminoethyl cellulose, and DTPA immobilized on aminopropyl silica were all ineffective. DTPA immobilized on aminoethyl cellulose even enhanced the intestinal uptake. The macromolecular chelators were without extensive effect on organ distribution of absorbed cadmium, except for dithiocarbamate immobilized on polyethylene imine, which enhanced the deposition of cadmium in several organs including the brain. Although the results are discouragign, they indicate that desing and synthesis of immobilized vicinal dithio compounds may represent an avenue for development of non-absorbable chelators with high affinity for cadmium.

  11. Integrating Topology and Geometry for Macro-Molecular Simulations

    OpenAIRE

    Moore, Edward L. F.; Peters, Thomas J.; Ferguson, David R.; Neil F Stewart

    2005-01-01

    Emerging macro-molecular simulations, such as supercoiling of DNA and protein unfolding, have an opportunity to profit from two decades of experience with geometric models within computer-aided geometric design (CAGD). For CAGD, static models are often sufficient, while form and function are inextricably related in biochemistry, resulting in greater attention to critical topological characteristics of these dynamic models. The greater emphasis upon dynamic change in macro-...

  12. Single-particle cryo-electron microscopy of macromolecular assemblies

    OpenAIRE

    Cheng, Kimberley

    2009-01-01

    In this thesis, single-particle cryo-electron microscopy (cryo-EM) was used to study the structure of three macromolecular assemblies: the two hemocyanin isoforms from Rapana thomasiana, the Pyrococcus furiosus chaperonin, and the ribosome from Escherichia coli. Hemocyanins are large respiratory proteins in arthropods and molluscs. Most molluscan hemocyanins exist as two distinct isoforms composed of related polypeptides. In most species the two isoforms differ in terms of their oligomeric st...

  13. Macromolecular Assemblage in the Design of a Synthetic AIDS Vaccine

    Science.gov (United States)

    Defoort, Jean-Philippe; Nardelli, Bernardetta; Huang, Wolin; Ho, David D.; Tam, James P.

    1992-05-01

    We describe a peptide vaccine model based on the mimicry of surface coat protein of a pathogen. This model used a macromolecular assemblage approach to amplify peptide antigens in liposomes or micelles. The key components of the model consisted of an oligomeric lysine scaffolding to amplify peptide antigens covalently 4-fold and a lipophilic membrane-anchoring group to further amplify noncovalently the antigens many-fold in liposomal or micellar form. A peptide antigen derived from the third variable domain of glycoprotein gp120 of human immunodeficiency virus type 1 (HIV-1), consisting of neutralizing, T-helper, and T-cytotoxic epitopes, was used in a macromolecular assemblage model (HIV-1 linear peptide amino acid sequence 308-331 in a tetravalent multiple antigen peptide system linked to tripalmitoyl-S-glycerylcysteine). The latter complex, in liposome or micelle, was used to immunize mice and guinea pigs without any adjuvant and found to induce gp120-specific antibodies that neutralize virus infectivity in vitro, elicit cytokine production, and prime CD8^+ cytotoxic T lymphocytes in vivo. Our results show that the macromolecular assemblage approach bears immunological mimicry of the gp120 of HIV virus and may lead to useful vaccines against HIV infection.

  14. 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.

  15. The contrasting effect of macromolecular crowding on amyloid fibril formation.

    Directory of Open Access Journals (Sweden)

    Qian Ma

    Full Text Available BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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

  16. Impact of synchrotron radiation on macromolecular crystallography: a personal view

    International Nuclear Information System (INIS)

    This article, largely based on personal experiences of the authors, reviews the early history of the application of synchrotron radiation to structural biology, and particularly protein crystallography, to show the tremendous impact that this experimental innovation has had on these disciplines. The introduction of synchrotron radiation sources almost four decades ago has led to a revolutionary change in the way that diffraction data from macromolecular crystals are being collected. Here a brief history of the development of methodologies that took advantage of the availability of synchrotron sources are presented, and some personal experiences with the utilization of synchrotrons in the early days are recalled

  17. 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.

  18. Cardiac voltage-gated calcium channel macromolecular complexes.

    Science.gov (United States)

    Rougier, Jean-Sébastien; Abriel, Hugues

    2016-07-01

    Over the past 20years, a new field of research, called channelopathies, investigating diseases caused by ion channel dysfunction has emerged. Cardiac ion channels play an essential role in the generation of the cardiac action potential. Investigators have largely determined the physiological roles of different cardiac ion channels, but little is known about the molecular determinants of their regulation. The voltage-gated calcium channel Cav1.2 shapes the plateau phase of the cardiac action potential and allows the influx of calcium leading to cardiomyocyte contraction. Studies suggest that the regulation of Cav1.2 channels is not uniform in working cardiomyocytes. The notion of micro-domains containing Cav1.2 channels and different calcium channel interacting proteins, called macro-molecular complex, has been proposed to explain these observations. The objective of this review is to summarize the currently known information on the Cav1.2 macromolecular complexes in the cardiac cell and discuss their implication in cardiac function and disorder. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel. PMID:26707467

  19. Protein stabilization by macromolecular crowding through enthalpy rather than entropy.

    Science.gov (United States)

    Senske, Michael; Törk, Lisa; Born, Benjamin; Havenith, Martina; Herrmann, Christian; Ebbinghaus, Simon

    2014-06-25

    The interior of the cell is a densely crowded environment in which protein stability is affected differently than in dilute solution. Macromolecular crowding is commonly understood in terms of an entropic volume exclusion effect based on hardcore repulsions among the macromolecules. We studied the thermal unfolding of ubiquitin in the presence of different cosolutes (glucose, dextran, poly(ethylene glycol), KCl, urea). Our results show that for a correct dissection of the cosolute-induced changes of the free energy into its enthalpic and entropic contributions, the temperature dependence of the heat capacity change needs to be explicitly taken into account. In contrast to the prediction by the excluded volume theory, we observed an enthalpic stabilization and an entropic destabilization for glucose, dextran, and poly(ethylene glycol). The enthalpic stabilization mechanism induced by the macromolecular crowder dextran was similar to the enthalpic stabilization mechanism of its monomeric building block glucose. In the case of poly(ethylene glycol), entropy is dominating over enthalpy leading to an overall destabilization. We propose a new model to classify cosolute effects in terms of their enthalpic contributions to protein stability.

  20. Identifying and Visualizing Macromolecular Flexibility in Structural Biology.

    Science.gov (United States)

    Palamini, Martina; Canciani, Anselmo; Forneris, Federico

    2016-01-01

    Structural biology comprises a variety of tools to obtain atomic resolution data for the investigation of macromolecules. Conventional structural methodologies including crystallography, NMR and electron microscopy often do not provide sufficient details concerning flexibility and dynamics, even though these aspects are critical for the physiological functions of the systems under investigation. However, the increasing complexity of the molecules studied by structural biology (including large macromolecular assemblies, integral membrane proteins, intrinsically disordered systems, and folding intermediates) continuously demands in-depth analyses of the roles of flexibility and conformational specificity involved in interactions with ligands and inhibitors. The intrinsic difficulties in capturing often subtle but critical molecular motions in biological systems have restrained the investigation of flexible molecules into a small niche of structural biology. Introduction of massive technological developments over the recent years, which include time-resolved studies, solution X-ray scattering, and new detectors for cryo-electron microscopy, have pushed the limits of structural investigation of flexible systems far beyond traditional approaches of NMR analysis. By integrating these modern methods with powerful biophysical and computational approaches such as generation of ensembles of molecular models and selective particle picking in electron microscopy, more feasible investigations of dynamic systems are now possible. Using some prominent examples from recent literature, we review how current structural biology methods can contribute useful data to accurately visualize flexibility in macromolecular structures and understand its important roles in regulation of biological processes.

  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.

  2. Macromolecular Crowding Enhances Thermal Stability of Rabbit Muscle Creatine Kinase

    Institute of Scientific and Technical Information of China (English)

    ZHU Jiang; HE Huawei; LI Sen

    2008-01-01

    The effect of dextran on the conformation (or secondary structure) and thermal stability of creatine kinase (CK) was studied using the far-ultraviolet (UV) circular dichroism (CD) spectra.The results showed that lower concentrations of dextran (less than 60 g/L) induced formation of the secondary CK structures.However,the secondary structure content of CK decreased when the dextran concentrations exceeded 60 g/L.Thermally induced transition curves were measured for CK in the presence of different concentrations of dextran by far-UV CD.The thermal transition curves were fitted to a two-state model by a nonlinear,least-squares method to obtain the transition temperature of the unfolding transition.An increase in the tran- sition temperature was observed with the increase of the dextran concentration.These observations qualita-tively accord with predictions of a previously proposed model for the effect of intermolecular excluded volume (macromolecular crowding) on protein stability and conformation.These findings imply that the effects of macromolecular crowding can have an important influence on our understanding of how protein folding oc-curs in vivo.

  3. 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.

  4. Aggravation and Stress in Parenting: Associations with Coparenting and Father Engagement among Resident Fathers

    Science.gov (United States)

    Bronte-Tinkew, Jacinta; Horowitz, Allison; Carrano, Jennifer

    2010-01-01

    This study uses a sample of 2,139 resident biological fathers from the Fragile Families and Child Wellbeing surveys (baseline and 12-month follow-up), to examine whether paternal aggravation and stress in parenting is associated with father engagement and coparenting and whether this association differs by father's socioeconomic status. Results of…

  5. 33 CFR 20.1315 - Submission of prior records and evidence in aggravation or mitigation.

    Science.gov (United States)

    2010-07-01

    ... PROCEEDINGS OF THE COAST GUARD Supplementary Evidentiary Rules for Suspension and Revocation Hearings § 20... aware. The Coast Guard representative may offer evidence and argument in aggravation of any charge proved. The respondent may offer evidence of, and argument on, prior maritime service, including both...

  6. Street Life: Aggravated and Sexual Assaults among Homeless and Runaway Adolescents.

    Science.gov (United States)

    Terrell, Nathanial Eugene

    1997-01-01

    Examines aggravated and sexual assaults among 240 runaway and homeless adolescents (RHAs) in Des Moines (Iowa). Results suggest RHAs are at risk of life-threatening situations on the streets due to aggressive and abusive parents. Additionally, street life situations have significant impacts on the probability that RHAs will be victims of…

  7. 5 CFR 890.1016 - Aggravating and mitigating factors used to determine the length of permissive debarments.

    Science.gov (United States)

    2010-01-01

    ... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Aggravating and mitigating factors used....1016 Aggravating and mitigating factors used to determine the length of permissive debarments. (a..., or impede official inquiries into the wrongful conduct underlying the debarment. (b)...

  8. 77 FR 26703 - Inflation Adjustment of the Aggravated Maximum Civil Monetary Penalty for a Violation of a...

    Science.gov (United States)

    2012-05-07

    ... Aggravated Maximum Civil Monetary Penalty for a Violation of a Federal Railroad Safety Law or Federal..., FRA published a final rule, pursuant to the Federal Civil Penalties Inflation Adjustment Act of 1990, which increased the aggravated maximum civil monetary penalty that the agency will apply when...

  9. Large-volume protein crystal growth for neutron macromolecular crystallography.

    Science.gov (United States)

    Ng, Joseph D; Baird, James K; Coates, Leighton; Garcia-Ruiz, Juan M; Hodge, Teresa A; Huang, Sijay

    2015-04-01

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations.

  10. Identification of macromolecular complexes in cryoelectron tomograms of phantom cells

    Science.gov (United States)

    Frangakis, Achilleas S.; Böhm, Jochen; Förster, Friedrich; Nickell, Stephan; Nicastro, Daniela; Typke, Dieter; Hegerl, Reiner; Baumeister, Wolfgang

    2002-01-01

    Electron tomograms of intact frozen-hydrated cells are essentially three-dimensional images of the entire proteome of the cell, and they depict the whole network of macromolecular interactions. However, this information is not easily accessible because of the poor signal-to-noise ratio of the tomograms and the crowded nature of the cytoplasm. Here, we describe a template matching algorithm that is capable of detecting and identifying macromolecules in tomographic volumes in a fully automated manner. The algorithm is based on nonlinear cross correlation and incorporates elements of multivariate statistical analysis. Phantom cells, i.e., lipid vesicles filled with macromolecules, provide a realistic experimental scenario for an assessment of the fidelity of this approach. At the current resolution of ≈4 nm, macromolecules in the size range of 0.5–1 MDa can be identified with good fidelity. PMID:12391313

  11. A loop of coagulation factor VIIa influencing macromolecular substrate specificity

    DEFF Research Database (Denmark)

    Bjelke, Jais R; Persson, Egon; Rasmussen, Hanne B;

    2006-01-01

    . The resulting variant exhibited increased intrinsic activity, concurrent with maturation of the active site, a less accessible N-terminus, and, interestingly, an altered macromolecular substrate specificity reflected in an increased ability to cleave factor IX (FIX) and a decreased rate of FX activation....../Met(298{156})Lys-FVIIa with almost the same activity and specificity profile. We conclude that a lysine residue in position 298{156} of FVIIa requires a hydrophilic environment to be fully accommodated. This position appears critical for substrate specificity among the proteases of the blood coagulation......Coagulation factor VIIa (FVIIa) belongs to a family of proteases being part of the stepwise, self-amplifying blood coagulation cascade. To investigate the impact of the mutation Met(298{156})Lys in FVIIa, we replaced the Gly(283{140})-Met(298{156}) loop with the corresponding loop of factor Xa...

  12. Macromolecular and dendrimer-based magnetic resonance contrast agents

    Energy Technology Data Exchange (ETDEWEB)

    Bumb, Ambika; Brechbiel, Martin W. (Radiation Oncology Branch, National Cancer Inst., National Inst. of Health, Bethesda, MD (United States)), e-mail: pchoyke@mail.nih.gov; Choyke, Peter (Molecular Imaging Program, National Cancer Inst., National Inst. of Health, Bethesda, MD (United States))

    2010-09-15

    Magnetic resonance imaging (MRI) is a powerful imaging modality that can provide an assessment of function or molecular expression in tandem with anatomic detail. Over the last 20-25 years, a number of gadolinium-based MR contrast agents have been developed to enhance signal by altering proton relaxation properties. This review explores a range of these agents from small molecule chelates, such as Gd-DTPA and Gd-DOTA, to macromolecular structures composed of albumin, polylysine, polysaccharides (dextran, inulin, starch), poly(ethylene glycol), copolymers of cystamine and cystine with GD-DTPA, and various dendritic structures based on polyamidoamine and polylysine (Gadomers). The synthesis, structure, biodistribution, and targeting of dendrimer-based MR contrast agents are also discussed

  13. An analysis of fractal geometry of macromolecular gelation

    Institute of Scientific and Technical Information of China (English)

    左榘; 陈天红; 冉少峰; 何炳林; 董宝中; 生文君; 杨恒林

    1996-01-01

    With fractal geometry theory and based on experiments, an analysis of fractal geometry behavior of gelation of macromolecules was carried out. Using the cross-linking copolymerization of styrene-divinylbenzene (DVB) as an example, through the determinations of the evolution of the molecular weight, size and the dependence of scattering intensity on the angle of macromolecules by employing laser and synchrotron small angle X-ray scattering, respectively, this chemical reaction was described quantitatively, its fractal behavior was analyzed and the fractal dimension was also measured. By avoiding the complex theories on gelation, this approach is based on modern physical techniques and theories to perform the analysis of the behavior of fractal geometry of macromolecular gelation and thus is able to reveal the rules of this kind of complicated gelation more essentially and profoundly.

  14. Macromolecular Crystallization with Microfluidic Free-Interface Diffusion

    Energy Technology Data Exchange (ETDEWEB)

    Segelke, B

    2005-02-24

    Fluidigm released the Topaz 1.96 and 4.96 crystallization chips in the fall of 2004. Topaz 1.96 and 4.96 are the latest evolution of Fluidigm's microfluidics crystallization technologies that enable ultra low volume rapid screening for macromolecular crystallization. Topaz 1.96 and 4.96 are similar to each other but represent a major redesign of the Topaz system and have of substantially improved ease of automation and ease of use, improved efficiency and even further reduced amount of material needed. With the release of the new Topaz system, Fluidigm continues to set the standard in low volume crystallization screening which is having an increasing impact in the field of structural genomics, and structural biology more generally. In to the future we are likely to see further optimization and increased utility of the Topaz crystallization system, but we are also likely to see further innovation and the emergence of competing technologies.

  15. Macromolecular contrast agents for MR mammography: current status

    International Nuclear Information System (INIS)

    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.)

  16. MR lymphography with macromolecular Gd-DTPA compounds

    International Nuclear Information System (INIS)

    This paper investigates the suitability of macromolecular Gd-DTPA compounds as signal-enhancing lymphographic agents in MR imaging. Two Gd-DTPA polylysin compounds and Gd-DTPA albumin, with molecular weights of 48,000,170,000, and 87,000 daltons, respectively, were tested in rabbits at gadolinium doses of 5 and 15 μmol per animal. Three animals were examined at each dose with T1-weighted sequences. The iliac lymph nodes were imaged prior to and during unilateral endolymphatic infusion into a femoral lymph vessel as well as over a period of 2 hours thereafter. All contrast media showed a homogeneous and pronounced signal enhancement in the lymph nodes during infusion at both doses

  17. Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin

    International Nuclear Information System (INIS)

    The three macromolecular crystallography beamlines BL14.1, BL14.2 and BL14.3 at the BESSY II storage ring at the Helmholtz-Zentrum Berlin are described. Three macromolecular crystallography (MX) beamlines at the Helmholtz-Zentrum Berlin (HZB) are available for the regional, national and international structural biology user community. The state-of-the-art synchrotron beamlines for MX BL14.1, BL14.2 and BL14.3 are located within the low-β section of the BESSY II electron storage ring. All beamlines are fed from a superconducting 7 T wavelength-shifter insertion device. BL14.1 and BL14.2 are energy tunable in the range 5–16 keV, while BL14.3 is a fixed-energy side station operated at 13.8 keV. All three beamlines are equipped with CCD detectors. BL14.1 and BL14.2 are in regular user operation providing about 200 beam days per year and about 600 user shifts to approximately 50 research groups across Europe. BL14.3 has initially been used as a test facility and was brought into regular user mode operation during the year 2010. BL14.1 has recently been upgraded with a microdiffractometer including a mini-κ goniometer and an automated sample changer. Additional user facilities include office space adjacent to the beamlines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources. In this article the instrumentation of the beamlines is described, and a summary of the experimental possibilities of the beamlines and the provided ancillary equipment for the user community is given

  18. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary [University of Oxford, South Parks Road, Oxford OX1 3QU (United Kingdom); Ravelli, Raimond B. G. [Maastricht University, PO Box 616, Maastricht 6200 MD (Netherlands); Carmichael, Ian [University of Notre Dame, Notre Dame, IN 46556 (United States); Kneale, Geoff; McGeehan, John E., E-mail: john.mcgeehan@port.ac.uk [University of Portsmouth, King Henry 1st Street, Portsmouth PO1 2DY (United Kingdom)

    2015-01-30

    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{sub 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.

  19. Postoperative neurological aggravation after anesthesia with sevoflurane in a patient with xeroderma pigmentosum: a case report

    OpenAIRE

    Fjouji, Salaheddine; Bensghir, Mustapha; Yafat, Bahija; Bouhabba, Najib; Boutayeb, Elhoucine; Azendour, Hicham; Kamili, Nordine Drissi

    2013-01-01

    Introduction Xeroderma pigmentosum is a rare autosomal recessive disease that causes changes in skin pigmentation, precancerous lesions and neurological abnormalities. It is a defect in the nucleotide excision repair mechanism. It has been reported that volatile anesthetics has a possible genotoxic side effect and deranged nucleotide excision repair in cells obtained from a patient with xeroderma pigmentosum. We report an unusual case of postoperative neurological aggravation in a patient wit...

  20. Residential characteristics aggravating infestation by Culex quinquefasciatus in a region of Northeastern Brazil

    Directory of Open Access Journals (Sweden)

    Juliana Cavalcanti Correia

    2012-12-01

    Full Text Available OBJECTIVE: Analyse how basic sanitation conditions, water supply and housing conditions affect the concentration of Culex quinquefasciatus METHODS: Populations of C. quinquefasciatus in 61 houses in the municipality of Olinda, PE, were monitored between October 2009 and October 2010. Observations were carried out in homes without the presence of preferred breeding sites in order to identify characteristics that may be aggravating factors for the development of the mosquito. Five aggravating factors were analysed: vegetation cover surrounding the home, number of residents/home, water storage, sewage drainage and water drainage. These characteristics were analysed in terms of presence or absence and as indicators of the degree of infestation, which was estimated through monitoring the concentration of eggs (oviposition traps - BR-OVT and adults (CDC light traps. RESULTS: Sewage drainage to a rudimentary septic tank or to the open air was the most frequent aggravating factor in the homes (91.8%, although the presence of vegetation was the only characteristic that significantly influenced the increase in the number of egg rafts (p = 0.02. The BR-OVT achieved positive results in 95.1% of the evaluations, with the presence of at least one egg raft per month. A total of 2,366 adults were caught, with a mosquito/room/night ratio of 32.9. No significant difference was found in the number of mosquitoes caught in the homes. CONCLUSIONS: Although the sanitation and water supply influence the population density of C. quinquefasciatus, residence features that are not usually considered in control measures can be aggravating factors in sustaining the mosquito population.

  1. Subchondral bone microstructural damage by increased remodelling aggravates experimental osteoarthritis preceded by osteoporosis

    OpenAIRE

    Bellido, Miriam; Lugo, Laura; Roman-Blas, Jorge A; Castañeda, Santos; Caeiro, Jose R; Dapia, Sonia; Calvo, Emilio; Largo, Raquel; Herrero-Beaumont, Gabriel

    2010-01-01

    Introduction Osteoporosis (OP) increases cartilage damage in a combined rabbit model of OP and osteoarthritis (OA). Accordingly, we assessed whether microstructure impairment at subchondral bone aggravates cartilage damage in this experimental model. Methods OP was induced in 20 female rabbits, by ovariectomy and intramuscular injections of methylprednisolone hemisuccinate for four weeks. Ten healthy animals were used as controls. At week 7, OA was surgically induced in left knees of all rabb...

  2. Aggravated stuttering following subthalamic deep brain stimulation in Parkinson's disease - two cases

    Directory of Open Access Journals (Sweden)

    Dietrichs Espen

    2011-04-01

    Full Text Available Abstract Stuttering is a speech disorder with disruption of verbal fluency which is occasionally present in patients with Parkinson's disease (PD. Long-term medical management of PD is frequently complicated by fluctuating motor functions and dyskinesias. High-frequency deep brain stimulation (DBS of the subthalamic nucleus (STN is an effective treatment of motor fluctuations and is the most common surgical procedure in PD. Here we report the re-occurrence and aggravation of stuttering following STN-DBS in two male patients treated for advanced PD. In both patients the speech fluency improved considerably when the neurostimulator was turned off, indicating that stuttering aggravation was related to neurostimulation of the STN itself, its afferent or efferent projections and/or to structures localized in the immediate proximity. This report supports previous studies demonstrating that lesions of the basal ganglia-thalamocortical motor circuit, including the STN, is involved in the development of stuttering. In advanced PD STN-DBS is generally an effective and safe treatment. However, patients with PD and stuttering should be informed about the risk of aggravated symptoms following surgical therapy.

  3. Synthesis of a water-soluble macromolecular light stabilizer containing hindered amine structures

    Institute of Scientific and Technical Information of China (English)

    Wei Ma; Mei Meng; Xue Jiang; Bing-Tao Tang; Shu-Fen Zhang

    2013-01-01

    A novel water-soluble macromolecular light stabilizer was synthesized by grafting 2-chloro-4,6-bis-[(2,2,6,6-tetramethylpiperidin-4-yl)amino]-1,3,5-triazine onto polyvinylamine.The intermediate 2-chloro-4,6-bis-[(2,2,6,6-tetramethylpiperidin-4-yl)amino]-1,3,5-triazine and the obtained macromolecular light stabilizer were characterized by 1H NMR,HRMS,IR and UV spectroscopy.Cotton fabrics dyed with C.I.Reactive Yellow 145,C.l.Reactive Red 195 and C.I.Reactive Blue 19 were finished with the macromolecular light stabilizer,and the lightfastness of the dyes was tested.The results showed that the lightfastness of the reactive dyes was improved by 0.5-1.0 grade after being finished and the macromolecular light stabilizer exhibited good wash fastness and thermal stability.

  4. Rapid Metal -free Macromolecular Coupling via in situ Nitrile Oxide-Activated Alkene Cycloaddition

    OpenAIRE

    Isaacman, Michael J.; Cui, Weibin; Theogarajan, Luke S.

    2014-01-01

    Nitrile oxide 1,3 dipolar cycloaddition is a simple and powerful coupling methodology. However, the self-dimerization of nitrile oxides has prevented the widespread use of this strategy for macromolecular coupling. By combining an in situ nitrile oxide generation with a highly reactive activated dipolarophile, we have overcome these obstacles and present a metal-free macromolecular coupling strategy for the modular synthesis of several ABA triblock copolymers. Nitrile oxides were generated in...

  5. NMR RELAXIVITY AND IMAGING OF NEUTRAL MACROMOLECULAR POLYESTER GADOLINIUM (Ⅲ) COMPLEXES

    Institute of Scientific and Technical Information of China (English)

    Kai-chao Yu; Hong-bing Hu; Mai-li Liu; Han-zhen Yuan; Chao-hui Ye; Ren-xi Zhuo

    1999-01-01

    Five neutral macromolecular polyester gadolinium (Ⅲ) complexes with pendant hydrophobic alkyl and aromatic functional groups were prepared. The longitudinal relaxation rates of these complexes were measured. One of these Gd (Ⅲ) complexes was chosen for the acute toxicity test and T1-weighted imaging measurement. Preliminary results showed that. compared with Gd-DTPA, the neutral macromolecular gadolinium (Ⅲ) complexes provide higher T1 relaxivity enhancement and longer function duration.

  6. JBluIce-EPICS control system for macromolecular crystallography

    International Nuclear Information System (INIS)

    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.

  7. Canadian macromolecular crystallography facility: a suite of fully automated beamlines.

    Science.gov (United States)

    Grochulski, Pawel; Fodje, Michel; Labiuk, Shaunivan; Gorin, James; Janzen, Kathryn; Berg, Russ

    2012-06-01

    The Canadian light source is a 2.9 GeV national synchrotron radiation facility located on the University of Saskatchewan campus in Saskatoon. The small-gap in-vacuum undulator illuminated beamline, 08ID-1, together with the bending magnet beamline, 08B1-1, constitute the Canadian Macromolecular Crystallography Facility (CMCF). The CMCF provides service to more than 50 Principal Investigators in Canada and the United States. Up to 25% of the beam time is devoted to commercial users and the general user program is guaranteed up to 55% of the useful beam time through a peer-review process. CMCF staff provides "Mail-In" crystallography service to users with the highest scored proposals. Both beamlines are equipped with very robust end-stations including on-axis visualization systems, Rayonix 300 CCD series detectors and Stanford-type robotic sample auto-mounters. MxDC, an in-house developed beamline control system, is integrated with a data processing module, AutoProcess, allowing full automation of data collection and data processing with minimal human intervention. Sample management and remote monitoring of experiments is enabled through interaction with a Laboratory Information Management System developed at the facility.

  8. Macromolecular Powder Diffraction: Ready for genuine biological problems.

    Science.gov (United States)

    Karavassili, Fotini; Margiolaki, Irene

    2016-01-01

    Knowledge of 3D structures of biological molecules plays a major role in both understanding important processes of life and developing pharmaceuticals. Among several methods available for structure determination, macromolecular X-ray powder diffraction (XRPD) has transformed over the past decade from an impossible dream to a respectable method. XRPD can be employed in biosciences for various purposes such as observing phase transitions, characterizing bulk pharmaceuticals, determining structures via the molecular replacement method, detecting ligands in protein-ligand complexes, as well as combining micro-sized single crystal crystallographic data and powder diffraction data. Studies using synchrotron and laboratory sources in some standard configuration setups are reported in this review, including their respective advantages and disadvantages. Methods presented here provide an alternative, complementary set of tools to resolve structural problems. A variety of already existing software packages for powder diffraction data processing and analysis, some of which have been adapted to large unit cell studies, are briefly described. This review aims to provide necessary elements of theory and current methods, along with practical explanations, available software packages and highlighted case studies. PMID:26786768

  9. Macromolecular metallurgy of binary mesocrystals via designed multiblock terpolymers.

    Science.gov (United States)

    Xie, Nan; Liu, Meijiao; Deng, Hanlin; Li, Weihua; Qiu, Feng; Shi, An-Chang

    2014-02-26

    Self-assembling block copolymers provide access to the fabrication of various ordered phases. In particular, the ordered spherical phases can be used to engineer soft mesocrystals with domain size at the 5-100 nm scales. Simple block copolymers, such as diblock copolymers, form a limited number of mesocrystals. However multiblock copolymers are capable to form more complex mesocrystals. We demonstrate that designed B1AB2CB3 multiblock terpolymers, in which the A- and C-blocks form spherical domains and the packing of these spheres can be controlled by changing the lengths of the middle and terminal B-blocks, self-assemble into various binary mesocrystals with space group symmetries of a large number of binary ionic crystals, including NaCl, CsCl, ZnS, α-BN, AlB2, CaF2, TiO2, ReO3, Li3Bi, Nb3Sn(A15), and α-Al2O3. This approach can be generalized to other terpolymers as well as to tetrapolymers to obtain ternary mesocrystals. Our study provides a new concept of macromolecular metallurgy for producing crystal phases in a mesoscale and thus makes multiblock copolymers a robust platform for the engineering of functional materials.

  10. Patch-clamp detection of macromolecular translocation along nuclear pores

    Directory of Open Access Journals (Sweden)

    Bustamante J.O.

    1998-01-01

    Full Text Available The present paper reviews the application of patch-clamp principles to the detection and measurement of macromolecular translocation along the nuclear pores. We demonstrate that the tight-seal 'gigaseal' between the pipette tip and the nuclear membrane is possible in the presence of fully operational nuclear pores. We show that the ability to form a gigaseal in nucleus-attached configurations does not mean that only the activity of channels from the outer membrane of the nuclear envelope can be detected. Instead, we show that, in the presence of fully operational nuclear pores, it is likely that the large-conductance ion channel activity recorded derives from the nuclear pores. We conclude the technical section with the suggestion that the best way to demonstrate that the nuclear pores are responsible for ion channel activity is by showing with fluorescence microscopy the nuclear translocation of ions and small molecules and the exclusion of the same from the cisterna enclosed by the two membranes of the envelope. Since transcription factors and mRNAs, two major groups of nuclear macromolecules, use nuclear pores to enter and exit the nucleus and play essential roles in the control of gene activity and expression, this review should be useful to cell and molecular biologists interested in understanding how patch-clamp can be used to quantitate the translocation of such macromolecules into and out of the nucleus

  11. Macromolecular coal structure as revealed by novel diffusion tests

    Energy Technology Data Exchange (ETDEWEB)

    Peppas, N.A.; Olivares, J.; Drummond, R.; Lustig, S.

    1990-01-01

    The main goal of the present work was the elucidation of the mechanistic characteristics of dynamic transport of various penetrants (solvents) in thin sections of coals by examining their penetrant uptake, front swelling and stress development. An important objective of this work was the study of coal network structure in different thermodynamically compatible penetrants and the analysis of dynamic swelling in terms of present anomalous transport theories. Interferometry/polariscopy, surface image analysis and related techniques were used to quantify the stresses and solvent concentration profiles in these sections. Dynamic and equilibrium swelling behavior were correlated using the polar interaction contributions of the solvent solubility parameters. The penetrant front position was followed in thin coal sections as a function of time. The initial front velocity was calculated for various coals and penetrants. Our penetrant studies with thin coal section from the same coal sample but with different thickness show that within the range of 150 {mu}m to 1500{mu}m the transport mechanism of dimethyl formamide in the macromolecular coal network is non-Fickian. In fact, for the thickest samples the transport mechanism is predominately Case-II whereas in the thinner samples penetrant uptake may be diffusion-controlled. Studies in various penetrants such as acetone, cyclohexane, methanol, methyl ethyl ketone, toluene and methylene chloride indicated that penetrant transport is a non-Fickian phenomenon. Stresses and cracks were observed for transport of methylene chloride. 73 refs., 88 figs., 15 tabs.

  12. Synchrotron radiation macromolecular crystallography: science and spin-offs

    Directory of Open Access Journals (Sweden)

    John R. Helliwell

    2015-03-01

    Full Text Available A current overview of synchrotron radiation (SR in macromolecular crystallography (MX instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development.

  13. JBluIce-EPICS control system for macromolecular crystallography.

    Energy Technology Data Exchange (ETDEWEB)

    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. (Biosciences Division); (Univ. of Michigan)

    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.

  14. Polycapillary x-ray optics for macromolecular crystallography

    International Nuclear Information System (INIS)

    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

  15. Automated identification of elemental ions in macromolecular crystal structures

    International Nuclear Information System (INIS)

    The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed

  16. Viola Playing May Be a Strong Aggravating Factor for Temporomandibular Disorder

    Directory of Open Access Journals (Sweden)

    Mahmut Alpayci

    2014-12-01

    Full Text Available Temporomandibular disorder (TMD is the general term used to describe the symptoms originated from temporomandibular joint region. The most common symptom of the disorder is pain during mandibular movement. Etiology of TMD is multifactorial. Several factors such as trauma, occlusal discrepancies, stress, parafunctions, hypermobility, and heredity can make one more vulnerable to this disorder. It has been reported that viola playing might be a predisposing factor for TMD. In this article, we present a 24 year old male patient suffering from TMD symptoms exacerbated by viola playing and emphasize that viola playing may be a powerful aggravating factor for TMD.

  17. Environmental air pollution is an aggravating event for sudden unexpected death in epilepsy

    Directory of Open Access Journals (Sweden)

    Carla A. Scorza

    2013-10-01

    Full Text Available It is extremely difficult to estimate the occurrence of sudden unexpected death in epilepsy (SUDEP. On the other hand, discovering and carefully evaluating new risk factors that may contribute to the onset of cardiovascular abnormalities in people with refractory epilepsy may prevent fatal events in these individuals. In this context, we should not ignore that urban air pollution is a leading problem for environmental health and is able to cause serious cardiovascular dysfunctions that culminate in sudden death. In this regard, we aimed to determine whether environmental exposure to air pollution is an aggravating event for SUDEP.

  18. DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.

    Science.gov (United States)

    Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

    2016-01-01

    Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction's mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein-protein interactions or protein-DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1,040,000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43,000 RNA-mediated interactions, and ∼12,000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network

  19. A Compact X-Ray System for Macromolecular Crystallography. 5

    Science.gov (United States)

    Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Joy, Marshall

    2000-01-01

    We describe the design and performance of a high flux x-ray system for macromolecular crystallography that combines a microfocus x-ray generator (40 gm FWHM spot size at a power level of 46.5Watts) and a 5.5 mm focal distance polycapillary optic. The Cu K(sub alpha) X-ray flux produced by this optimized system is 7.0 times above the X-ray flux previously reported. The X-ray flux from the microfocus system is also 3.2 times higher than that produced by the rotating anode generator equipped with a long focal distance graded multilayer monochromator (Green optic; CMF24-48-Cu6) and 30% less than that produced by the rotating anode generator with the newest design of graded multilayer monochromator (Blue optic; CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 Watts, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42,540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym) 5.0% for the data extending to 1.7A, and 4.8% for the complete set of data to 1.85A. The amplitudes of the reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

  20. A Compact X-Ray System for Macromolecular Crystallography

    Science.gov (United States)

    Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Gibson, Walter; Joy, Marshall

    2000-01-01

    We describe the design and performance of a high flux x-ray system for a macromolecular crystallography that combines a microfocus x-ray generator (40 micrometer full width at half maximum spot size at a power level of 46.5 W) and a collimating polycapillary optic. The Cu Ka lpha x-ray flux produced by this optimized system through a 500,um diam orifice is 7.0 times greater than the x-ray flux previously reported by Gubarev et al. [M. Gubarev et al., J. Appl. Crystallogr. 33, 882 (2000)]. The x-ray flux from the microfocus system is also 2.6 times higher than that produced by a rotating anode generator equipped with a graded multilayer monochromator (green optic, Osmic Inc. CMF24-48-Cu6) and 40% less than that produced by a rotating anode generator with the newest design of graded multilayer monochromator (blue optic, Osmic, Inc. CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 W, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42 540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym)=5.0% for data extending to 1.70 A, and 4.8% for the complete set of data to 1.85 A. The amplitudes of the observed reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

  1. Macromolecular compositions of phytoplankton in the Amundsen Sea, Antarctica

    Science.gov (United States)

    Kim, Bo Kyung; Lee, Jang Han; Joo, HuiTae; Song, Ho Jung; Yang, Eun Jin; Lee, Sang Hoon; Lee, Sang H.

    2016-01-01

    The biochemical compositions (proteins, carbohydrates, and lipids) of phytoplankton provide useful information for their environmental growth conditions and nutritional status as a basic food source for upper trophic consumers. Concentrations of these compositions were assessed at 100, 30, and 1% light penetration depths within the euphotic zone in the Amundsen Sea, Antarctica, using colorimetric techniques. The major inorganic nutrients were generally abundant throughout the study area. The average chlorophyll a (chl-a) concentration was 49.2 mg m-2 (S.D.=±27.6 mg m-2) and large phytoplankton (>20 μm) accounted for 64.1% of the total chl-a concentration. The biochemical compositions of the phytoplankton were not significantly different among different light depths or productivity stations. The overall compositions of proteins, carbohydrates, and lipids from all stations averaged 65.9% (S.D.=±12.5%), 22.4% (S.D.=±10.9%), and 11.7% (S.D.=±6.5%), respectively. Regardless of dominant phytoplankton species, nitrogen-abundant conditions sustained high protein compositions of phytoplankton in the Amundsen Sea during the cruise period. Based on the macromolecular compositions, the average food material (FM) concentration was 219.4 μg L-1 (S.D.=±151.1 μg L-1) and correlated positively with the primary productivity in the Amundsen Sea. High protein/carbohydrate ratios (>1) and large proportions of proteins suggest that phytoplankton provide nitrogen-sufficient foods to higher trophic consumers through a higher efficiency of protein carbon incorporated into herbivores.

  2. 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.

  3. FSH aggravates bone loss in ovariectomised rats with experimental periapical periodontitis

    Science.gov (United States)

    Qian, Hua; Guan, Xiaoyue; Bian, Zhuan

    2016-01-01

    Periapical bone loss is one of the prominent pathological and clinical features of periapical periodontitis. Previous studies have demonstrated that follicle-stimulating hormone (FSH) could directly affect skeletal remodelling by stimulating the formation and the function of osteoclasts in vitro and in vivo. However, the effect of FSH on periapical bone loss remained to be fully elucidated. In the current study, a rat model was established in order to verify the effect of FSH in experimental periapical lesions. It was identified that FSH aggravated the bone loss of periapical lesions. In addition, RANKL-, TRAP-, TNF-α- and IL-1β-positive cells were increased significantly in FSH-treated groups, which indicated that the function of FSH in bone loss may be mediated through the increasing activity of osteoclasts and the increased secretion of inflammatory cytokines. The results of the current study suggested that FSH, independent of oestrogen, may aggravate periapical bone loss by FSH receptors, which may serve an important role in the immune and inflammatory response of the host to root canal and periradicular infection during menopause. PMID:27510616

  4. Orally delivered β-glucans aggravate dextran sulfate sodium (DSS)-induced intestinal inflammation.

    Science.gov (United States)

    Heinsbroek, Sigrid E M; Williams, David L; Welting, Olaf; Meijer, Sybren L; Gordon, Siamon; de Jonge, Wouter J

    2015-12-01

    β-Glucans have beneficial health effects due to their immune modulatory properties. Oral administration of β-glucans affects tumour growth, microbial infection, sepsis, and wound healing. We hypothesized that pre-treatment with orally delivered soluble and particulate β-glucans could ameliorate the development of aggravate dextran sulfate sodium (DSS) induced intestinal inflammation. To study this, mice were orally pre-treated with β-glucans for 14 days. We tested curdlan (a particulate β-(1,3)-glucan), glucan phosphate (a soluble β-(1,3)-glucan), and zymosan (a particle made from Saccharomyces cerevisiae, which contains around 55% β-glucans). Weight loss, colon weight, and feces score did not differ between β-glucan and vehicle treated groups. However, histology scores indicated that β-glucan-treated mice had increased inflammation at a microscopic level suggesting that β-glucan treatment worsened intestinal inflammation. Furthermore, curdlan and zymosan treatment led to increased colonic levels of inflammatory cytokines and chemokines, compared to vehicle. Glucan phosphate treatment did not significantly affect cytokine and chemokine levels. These data suggest that particulate and soluble β-glucans differentially affect the intestinal immune responses. However, no significant differences in other clinical colitis scores between soluble and particulate β-glucans were found in this study. In summary, β-glucans aggravate the course of dextran sulfate sodium (DSS)-induced intestinal inflammation at the level of the mucosa.

  5. Proteasome β5i Subunit Deficiency Affects Opsonin Synthesis and Aggravates Pneumococcal Pneumonia.

    Science.gov (United States)

    Kirschner, Felicia; Reppe, Katrin; Andresen, Nadine; Witzenrath, Martin; Ebstein, Frédéric; Kloetzel, Peter-Michael

    2016-01-01

    Immunoproteasomes, harboring the active site subunits β5i/LMP7, β1i/LMP2, and β2i/MECL1 exert protective, regulatory or modulating functions during infection-induced immune responses. Immunoproteasomes are constitutively expressed in hematopoietic derived cells, constituting the first line of defense against invading pathogens. To clarify the impact of immunoproteasomes on the innate immune response against Streptococcus pneumoniae, we characterized the progression of disease and analyzed the systemic immune response in β5i/LMP7-/- mice. Our data show that β5i/LMP7 deficiency, which affected the subunit composition of proteasomes in murine macrophages and liver, was accompanied by reduced transcription of genes encoding immune modulating molecules such as pentraxins, ficolins, and collectins. The diminished opsonin expression suggested an impaired humoral immune response against invading pneumococci resulting in an aggravated systemic dissemination of S. pneumoniae in β5i/LMP7-/- mice. The impaired bacterial elimination in β5i/LMP7-/- mice was accompanied by an aggravated course of pneumonia with early mortality as a consequence of critical illness during the late phase of disease. In summary our results highlight an unsuspected role for immuno-subunits in modulating the innate immune response to extracellular bacterial infections. PMID:27100179

  6. Consumption of Mercury-contaminated Rice Induces Oxidative Stress and Free Radical Aggravation in Rats

    Institute of Scientific and Technical Information of China (English)

    XIU-LING JI; GUI-WEN JIN; JIN-PING CHENG; WEN-HUA WANG; JING LU; LI-YA QU

    2007-01-01

    Objective To study the oxidative stress induced by consumption of mercury-contaminated rice in rats, and to assess the possible public health risk of mercury contamination in Wanshan mining area. Methods Sprague Dawley rats were fed the mercury-contaminated rice produced from Wanshan area for 90 days. The antioxidant status and the free radicals in rat serum were evaluated. Results High mercury accumulation in organs of rats fed the mercury-contaminated rice confirmed the server pollution of mercury in Wanshan mining area. The intensity of electron spin resonance (ESR) signal increased by 87.38% in rats fed the rice from Wanshan compared with that in the control rats fed the rice from Shanghai, suggesting that chronic dietary consumption of rice from mercury mining area could induce an aggravation of free radicals. Feeding the mercury-contaminated rice was associated with significant decreases in the antioxidant enzymatic activities of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px) and concentration of serum nitric oxide (NO), but it had no effect on serum nitric oxide synthase (NOS) activity. Feeding the mercury-contaminated rice raised the level of serum malonyldialdehyde (MDA), indicating the occurrence of oxidative stress. Conclusion The long-term dietary consumption of mercury-contaminated rice induces the aggravation of free radicals and exerts oxidative stress.

  7. Inhibition of caspase-9 aggravates acute liver injury through suppression of cytoprotective autophagy

    Science.gov (United States)

    Guo, Rui; Lin, Bin; Pan, Jing Fei; Liong, Emily C.; Xu, Ai Min; Youdim, Moussa; Fung, Man Lung; So, Kwok Fai; Tipoe, George L.

    2016-01-01

    Acute liver disease is characterized by inflammation, oxidative stress and necrosis, which can greatly influence the long term clinical outcome and lead to liver failure or cancer. Here, we initially demonstrated the beneficial role of caspase-9-dependent autophagy in acute liver injury. Treatment with caspase-9 inhibitor z-LEHD-FMK in HepG2 cells, AML12 cells and C57BL/b6N mice exacerbated CCl4-induced acute hepatocellular damage, and also down-regulated autophagy markers expression levels, indicating that caspase-9 inhibition may aggravate acute liver damage by suppressing cytoprotective autophagy. CCl4 was used as an acute liver injury inducer which caused oxidative stress and apoptosis through up-regulation of HIF-1α, as well as triggered hepatic inflammation and necroptosis via TLR4/NF-κB pathway. Caspase-9 Thr125 site was firstly phosphorylated by ERK1/2 which subsequently activated the cytoprotective autophagy process to attenuate acute CCl4 injury. Caspase-9 inhibition further aggravated hepatic necroptosis through NF-κB expression, leading to increased pro-inflammatory mediators levels, suggesting a protective role of caspase-9-dependent autophagy in the inflammatory process as well as its possibility being a new therapeutic target for the treatment of acute liver injury. PMID:27580936

  8. Ultrafine particles in the airway aggravated experimental lung injury through impairment in Treg function.

    Science.gov (United States)

    Li, Guanggang; Cao, Yinghua; Sun, Yue; Xu, Ruxiang; Zheng, Zhendong; Song, Haihan

    2016-09-01

    Acute lung injury (ALI) is a life-threatening condition characterized by rapid-onset alveolar-capillary damage mediated by pathogenic proinflammatory immune responses. Since exposure to airway particulate matter (PM) could significantly change the inflammatory status of the individual, we investigated whether PM instillation in the airway could alter the course of ALI, using a murine model with experimental lung injury induced by intratracheal LPS challenge. We found that PM-treated mice presented significantly aggravated lung injury, which was characterized by further reductions in body weight, increased protein concentration in the bronchoalveolar lavage (BAL), and higher mortality rate, compared to control saline-treated mice. The PM-treated mice also presented elevated lung and systemic type 1 T helper cell (Th1) frequency as well as reduced lung regulatory T cell (Treg) frequency, which was associated with severity of lung injury. Further examinations revealed that the Treg function was impaired in PM-treated mice, characterized by significantly repressed transforming growth factor beta production. Adoptive transfer of functional Tregs from control mice to PM-treated mice significantly improved their prognosis after intratracheal LPS challenge. Together, these results demonstrated that first, PM in the airway aggravated lung injury; second, severity of lung injury was associated with T cell subset imbalance in PM-treated mice; and third, PM treatment induced quantitative as well as qualitative changes in the Tregs. PMID:27179778

  9. Hyperglycemia Aggravates Hepatic Ischemia Reperfusion Injury by Inducing Chronic Oxidative Stress and Inflammation

    Directory of Open Access Journals (Sweden)

    Yihan Zhang

    2016-01-01

    Full Text Available Aim. To investigate whether hyperglycemia will aggravate hepatic ischemia reperfusion injury (HIRI and the underlying mechanisms. Methods. Control and streptozotocin-induced diabetic Sprague-Dawley rats were subjected to partial hepatic ischemia reperfusion. Liver histology, transferase, inflammatory cytokines, and oxidative stress were assessed accordingly. Similarly, BRL-3A hepatocytes were subjected to hypoxia/reoxygenation (H/R after high (25 mM or low (5.5 mM glucose culture. Cell viability, reactive oxygen species (ROS, and activation of nuclear factor-erythroid 2-related factor 2 (Nrf2 and nuclear factor of kappa light polypeptide gene enhancer in B-cells (NF-κB were determined. Results. Compared with control, diabetic rats presented more severe hepatic injury and increased hepatic inflammatory cytokines and oxidative stress. HIRI in diabetic rats could be ameliorated by pretreatment of N-acetyl-L-cysteine (NAC or apocynin. Excessive ROS generation and consequent Nrf2 and NF-κB translocation were determined after high glucose exposure. NF-κB translocation and its downstream cytokines were further increased in high glucose cultured group after H/R. While proper regulation of Nrf2 to its downstream antioxidases was observed in low glucose cultured group, no further induction of Nrf2 pathway by H/R after high glucose culture was identified. Conclusion. Hyperglycemia aggravates HIRI, which might be attributed to chronic oxidative stress and inflammation and potential malfunction of antioxidative system.

  10. Early atherosclerosis aggravates renal microvascular loss and fibrosis in swine renal artery stenosis.

    Science.gov (United States)

    Sun, Dong; Eirin, Alfonso; Ebrahimi, Behzad; Textor, Stephen C; Lerman, Amir; Lerman, Lilach O

    2016-04-01

    Renal function in patients with atherosclerosis and renal artery stenosis (ARAS) deteriorates more frequently than in nonatherosclerotic RAS. We hypothesized that ARAS aggravates stenotic-kidney micro vascular loss compared to RAS. Domestic pigs were randomized to normal, RAS, and ARAS (RAS fed a high-cholesterol diet) groups (n = 7 each). Ten weeks later stenotic-kidney oxygenation, renal blood flow, and glomerular filtration rate (GFR) were evaluated in vivo, and micro vascular density by micro-computed tomography. Blood pressure in both RAS and ARAS was elevated; and stenotic-kidney renal blood flow and GFR similarly decreased. RAS decreased the density of small-size cortical microvessels (sized microvessels (200-300 μm). Cortical hypoxia and interstitial fibrosis increased in both RAS and ARAS but correlated inversely with micro vascular density only in RAS. Atherosclerosis aggravates loss of stenotic-kidney microvessels, yet additional determinants likely contribute to cortical hypoxia and fibrosis in swine ARAS. PMID:26879682

  11. An Atherogenic Paigen-Diet Aggravates Nephropathy in Type 2 Diabetic OLETF Rats.

    Science.gov (United States)

    Nozako, Masanori; Koyama, Takashi; Nagano, Chifumi; Sato, Makoto; Matsumoto, Satoshi; Mitani, Kiminobu; Yasufuku, Reiko; Kohashi, Masayuki; Yoshikawa, Tomohiro

    2015-01-01

    Diabetic nephropathy develops in association with hyperglycemia, is aggravated by atherogenic factors such as dyslipidemia, and is sometimes initiated before obvious hyperglycemia is seen. However, the precise mechanisms of progression are still unclear. In this study, we investigated the influence of an atherogenic Paigen diet (PD) on the progression of nephropathy in spontaneous type 2 diabetic OLETF rats. Feeding PD to male OLETF rats for 12 weeks caused an extensive increase in excretion of urinary albumin and markers of tubular injury such as KIM-1 and L-FABP, accompanied by mesangial expansion and tubular atrophy. PD significantly increased plasma total cholesterol concentration, which correlates well with increases in urine albumin excretion and mesangial expansion. Conversely, PD did not change plasma glucose and free fatty acid concentrations. PD enhanced renal levels of mRNA for inflammatory molecules such as KIM-1, MCP-1, TLR4 and TNF-α and promoted macrophage infiltration and lipid accumulation in the tubulointerstitium and glomeruli in OLETF rats. Intriguingly, PD had little effect on urine albumin excretion and renal morphology in normal control LETO rats. This model may be useful in studying the complex mechanisms that aggravate diabetic nephropathy in an atherogenic environment. PMID:26606054

  12. An Atherogenic Paigen-Diet Aggravates Nephropathy in Type 2 Diabetic OLETF Rats.

    Directory of Open Access Journals (Sweden)

    Masanori Nozako

    Full Text Available Diabetic nephropathy develops in association with hyperglycemia, is aggravated by atherogenic factors such as dyslipidemia, and is sometimes initiated before obvious hyperglycemia is seen. However, the precise mechanisms of progression are still unclear. In this study, we investigated the influence of an atherogenic Paigen diet (PD on the progression of nephropathy in spontaneous type 2 diabetic OLETF rats. Feeding PD to male OLETF rats for 12 weeks caused an extensive increase in excretion of urinary albumin and markers of tubular injury such as KIM-1 and L-FABP, accompanied by mesangial expansion and tubular atrophy. PD significantly increased plasma total cholesterol concentration, which correlates well with increases in urine albumin excretion and mesangial expansion. Conversely, PD did not change plasma glucose and free fatty acid concentrations. PD enhanced renal levels of mRNA for inflammatory molecules such as KIM-1, MCP-1, TLR4 and TNF-α and promoted macrophage infiltration and lipid accumulation in the tubulointerstitium and glomeruli in OLETF rats. Intriguingly, PD had little effect on urine albumin excretion and renal morphology in normal control LETO rats. This model may be useful in studying the complex mechanisms that aggravate diabetic nephropathy in an atherogenic environment.

  13. An Atherogenic Paigen-Diet Aggravates Nephropathy in Type 2 Diabetic OLETF Rats

    Science.gov (United States)

    Nozako, Masanori; Koyama, Takashi; Nagano, Chifumi; Sato, Makoto; Matsumoto, Satoshi; Mitani, Kiminobu; Yasufuku, Reiko; Kohashi, Masayuki; Yoshikawa, Tomohiro

    2015-01-01

    Diabetic nephropathy develops in association with hyperglycemia, is aggravated by atherogenic factors such as dyslipidemia, and is sometimes initiated before obvious hyperglycemia is seen. However, the precise mechanisms of progression are still unclear. In this study, we investigated the influence of an atherogenic Paigen diet (PD) on the progression of nephropathy in spontaneous type 2 diabetic OLETF rats. Feeding PD to male OLETF rats for 12 weeks caused an extensive increase in excretion of urinary albumin and markers of tubular injury such as KIM-1 and L-FABP, accompanied by mesangial expansion and tubular atrophy. PD significantly increased plasma total cholesterol concentration, which correlates well with increases in urine albumin excretion and mesangial expansion. Conversely, PD did not change plasma glucose and free fatty acid concentrations. PD enhanced renal levels of mRNA for inflammatory molecules such as KIM-1, MCP-1, TLR4 and TNF-α and promoted macrophage infiltration and lipid accumulation in the tubulointerstitium and glomeruli in OLETF rats. Intriguingly, PD had little effect on urine albumin excretion and renal morphology in normal control LETO rats. This model may be useful in studying the complex mechanisms that aggravate diabetic nephropathy in an atherogenic environment. PMID:26606054

  14. Chronic hypertension aggravates heat stress-induced brain damage: possible neuroprotection by cerebrolysin.

    Science.gov (United States)

    Muresanu, Dafin Fior; Zimmermann-Meinzingen, Sibilla; Sharma, Hari Shanker

    2010-01-01

    Whole body hyperthermia (WBH) aggravates brain edema formation and cell damage in chronic hypertensive rats compared with normotensive animals. In this investigation, we examined the influence of cerebrolysin on WBH-induced edema formation and brain pathology in hypertensive and normotensive rats. Rats subjected to 4 h WBH at 38 degrees C in a biological oxygen demand (BOD) incubator showed breakdown of the blood-brain barrier (BBB), reduced cerebral blood flow (CBF), edema formation and cell injuries in several parts of the brain. These effects were further aggravated in chronic hypertensive rats (two-kidney one clip model (2K1C), for 4 weeks) subjected to WBH. Pretreatment with cerebrolysin (5 mL/kg, 24 h and 30 min before heat stress) markedly attenuated the BBB dysfunction and brain pathology in normal animals. However, in hypertensive animals, a high dose of cerebrolysin (10 mL/kg, 24 h and 30 min before heat stress) was needed to attenuate WBH-induced BBB dysfunction and brain pathology. These observations indicate that heat stress could affect differently in normal and hypertensive conditions. Furthermore, our results suggest that patients suffering from various chronic cardiovascular diseases may respond differently to hyperthermia and to neuroprotective drugs, e.g., cerebrolysin not reported earlier.

  15. Oral Candida as an aggravating factor of mucositis Induced by radiotherapy

    International Nuclear Information System (INIS)

    Antineoplastic treatment induces some undesirable consequences in head and neck cancer patients. Often, the emergence of major clinical manifestations, such as oral mucositis, results in temporary interruption of the treatment, decreasing the patients' quality of life, and increasing hospital costs. Radio-induced or chemo-induced oral mucositis is possibly aggravated by opportunist fungal infections, which turn the mucositis more resistant to the conventional treatments. Objective: this study aims to identify the presence of Candida sp. as a possible aggravating factor of oral mucositis in patients with head and neck cancer under antineoplastic treatment. Method: all patients with radio- or chemo-induced oral mucositis from the Cancer Hospital of Pernambuco, treated between October 2008 and April 2009, were selected for the study. The prevalence of Candida sp was measured through the cytological analysis of oral mucosa in patients with oral mucositis. The fungal presence was correlated with the mucositis severity. Results: the results showed a positive association between fungal colonization and more several lesions (degrees III and IV of mucositis). Conclusion: The outcomes shown may contribute to a solution for unconventional mucosites, which do not respond to the usual treatment. (author)

  16. Changing the warm-up transition of macromolecular system at irradiation

    International Nuclear Information System (INIS)

    Full text: The whole complex of characteristics of macromolecular system is defined by its warm-up condition. So for revealing a consequence of irradiating it is necessary study of warm-up turning the molecules of chain construction from the energy of irradiation. As is well known an irradiation is accompanied by suturing or destruction of separate kinetic units. In given work is studied changing a warm-up interval of high-elastic state of macromolecular system depending on energy of irradiating for the reason extrapolation its results to deciding the applied problems of ecological, metabolically processes. Coming from theories free volume and Boltzmann's distribution were determined changing the temperatures of glassing and viscous current. The variable parameter considered models is a mobility factor, which is defined as an attitude radiation energy to energy of Van-der-Waals interactions and hydrogen bonds, where energy of irradiation is taken much less, than energy of chemical bond. Restriction of energy of inter- and intramolecular chemical unbound kinetic units guarantees wholeness of the macromolecular chains that it is required for functional quality conservations. The obtained results show that than more deflection of mobility factor from units, that broader area high-elastic considered model of macromolecular system. Changing a warm-up interval also enough vastly depends on the free member of deciding, which characterizes a condition of polymer before the irradiation. Rendered that the most vulnerable to irradiating is hard chain macromolecular system

  17. Synthesis and characterization of miktoarm star copolymer of styrene and butadiene using multifunctional macromolecular initiator

    Institute of Scientific and Technical Information of China (English)

    Hai Yan Zhang; Xing Ying Zhang

    2009-01-01

    A new kind of multifunctional macromolecular initiator with Sn-C bonds and polydiene arms was synthesized by living anionic polymerization.At first,polydiene-stannum chloride(PD-SnCl3)was prepared by the reaction of n-butyl-Li(n-BuLi),stannic chloride(SnCl4)and diene.Then PD-SnCl3 was used to react with the dilithium initiator to prepare the multifunctional organic macromolecular initiators.The result suggested that the initiators had a remarkable yield by GPC,nearly 90%.By using these multifunctional macromolecular initiators,styrene and butadiene were effectively polymerized via anionic polymerization,which gave birth to novel miktoarm star copolymers.The relative molecular weight and polydispersity index,microstructure contents,copolymerization components,glass transition temperature(Tg)and morphology of the miktoarm star copolymers were investigated by GPC-UV,1H NMR,DSC and TEM,respectively.

  18. Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions

    Directory of Open Access Journals (Sweden)

    Mukherjee Srabani

    2003-01-01

    Full Text Available During a complex macromolecular reaction multiple changes in molecular conformation and interactions with ligands may occur. X-ray crystallography may provide only a limited set of snapshots of these changes. Solution methods can augment such structural information to provide a more complete picture of a macromolecular reaction. We analyzed the changes in protein conformation and protein:nucleic acid interactions which occur during transcription initiation by using a chemical nuclease tethered to cysteines introduced site-specifically into the RNA polymerase of bacteriophage T7 (T7 RNAP. Changes in cleavage patterns as the polymerase steps through transcription reveal a series of structural transitions which mediate transcription initiation. Cleavage by tethered chemical nucleases is seen to be a powerful method for revealing the conformational dynamics of macromolecular reactions, and has certain advantages over cross-linking or energy transfer approaches.

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

    2009-05-26

    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.

  20. Acute patellofemoral pain: aggravating activities, clinical examination, MRI and ultrasound findings

    DEFF Research Database (Denmark)

    Brushoj, C.; Holmich, P.; Nielsen, M.B.;

    2008-01-01

    Objective: To investigate acute anterior knee pain caused by overuse in terms of pain location, aggravating activities, findings on clinical examination and ultrasound/MRI examination. To determine if acute anterior knee pain caused by overuse should be classified as a subgroup of patellofemoral...... pain syndrome (PFPS). Methods: In a observational study design 30 army recruits with anterior knee pain (mean duration of pain 4 weeks) were examined using the PFPS pain severity scale (PSS), knee pain diagrams, standardised clinical examination, ultrasound and MRI examinations. Results: On PSS typical......%)), but other synovial covered structures including the fat pad of Hoffa (12 patients (40%)), the medial plica and the joint line (12 patients (40%)) were also involved. Only eight patients (27%) experienced pain on the patellofemoral compression test. Only discrete changes was detected on MRI...

  1. Formation of structures in nonlinear media and nonequilibrium thermodynamics of aggravation regimes

    International Nuclear Information System (INIS)

    In a medium, the description of which includes quasilinear transport equations (the thermal conductivity, conductivity and viscosity coefficients depend on temperature, density and magnetic field), the effect of nonlinear bulk heat sources, under specific conditions, generates strongly nonequilibrium processes, the so-called regimes with aggravation. They can cause heat localization and magnetic field phenomena on certain space scales or in certain sections of the mass in a compressible medium. This results in different spatial distribution of the quantities indicated, i.e., development of different types of structures in the medium. The work, on the basis of consideration of the quasilinear thermal conductivity equation with nonlinear bulk heat sources, found the characteristics of the strongly nonequilibrium thermodynamics which cause such a complication of organization of the medium. 88 references

  2. Is Behavioral Regulation in Children With ADHD Aggravated by Comorbid Anxiety Disorder?

    DEFF Research Database (Denmark)

    Sørensen, Lin; Plessen, Kerstin J; Nicholas, Jude;

    2010-01-01

    Background: The present study investigated the impact of coexisting anxiety disorder in children with ADHD on their ability to regulate behavior. Method: Parent reports on the Behavior Rating Inventory of Executive Function (BRIEF) in a comorbid group of children with ADHD and anxiety (n = 11) were...... compared to BRIEF reports in a group of children with a "pure" ADHD (n = 23), a "pure" anxiety (n = 24) and a group without any diagnosis (n = 104) in a 2 (ADHD vs. no ADHD) x 2 (anxiety vs. no anxiety) design. Results: The children with ADHD and anxiety disorder scored significantly higher on the Inhibit...... children is aggravated by comorbid anxiety. (J. of Att. Dis. 2010; XX(X) 1-XX)....

  3. Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction

    Indian Academy of Sciences (India)

    Manish Agrawal; S B Santra; Rajat Anand; Rajaram Swaminathan

    2008-08-01

    The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. 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 of the experimental observations.

  4. Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking

    Directory of Open Access Journals (Sweden)

    Chantal Prévost

    2011-02-01

    Full Text Available Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA.We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  5. Accounting for large amplitude protein deformation during in silico macromolecular docking.

    Science.gov (United States)

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-02-22

    Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success.

  6. THE STEADY/PULSATILE FLOW AND MACROMOLECULAR TRANSPORT IN T-BIFURCATION BLOOD VESSELS

    Institute of Scientific and Technical Information of China (English)

    李丁; 温功碧

    2003-01-01

    A numerical analysis of the steady and pulsatile, macromolecular( such as lowdensity lipopotein ( LDL ), Albumin ) transport in T-bifurcation was proposed. Theinfluence of Reynolds number and mass flow ratio etc. parameters on the velocity field andmass transport were calculated. The computational results predict that the blood flow factorsaffect the macromolecular distribution and the transport across the wall, it shows thathemodynamic play an important role in the process of atherosclerosis . The LDL and Albuminconcentration on the wall varies most greatly in flow bifurcation area where the wall shearstress varies greatly at the branching vessel and the atherosclerosis often appears there.

  7. Obesity does not aggravate vitrification injury in mouse embryos: a prospective study

    Directory of Open Access Journals (Sweden)

    Ma Wenhong

    2012-08-01

    Full Text Available Abstract Background Obesity is associated with poor reproductive outcomes, but few reports have examined thawed embryo transfer in obese women. Many studies have shown that increased lipid accumulation aggravates vitrification injury in porcine and bovine embryos, but oocytes of these species have high lipid contents (63 ng and 161 ng, respectively. Almost nothing is known about lipids in human oocytes except that these cells are anecdotally known to be relatively lipid poor. In this regard, human oocytes are considered to be similar to those of the mouse, which contain approximately 4 ng total lipids/oocyte. To date, no available data show the impact of obesity on vitrification in mouse embryos. The aim of this study was to establish a murine model of maternal diet-induced obesity and to characterize the effect of obesity on vitrification by investigating the survival rate and embryo developmental competence after thawing. Methods Prospective comparisons were performed between six–eight-cell embryos from obese and normal-weight mice and between fresh and vitrified embryos. Female C57BL/6 mice were fed standard rodent chow (normal-weight group or a high-fat diet (obese group for 6 weeks. The mice were mated, zygotes were collected from oviducts and cultured for 3 days, and six–eight-cell embryos were then selected to assess lipid content in fresh embryos and to evaluate differences in apoptosis, survival, and development rates in response to vitrification. Results In fresh embryos from obese mice, the lipid content (0.044 vs 0.030, Pvs.9.3%, Pvs. 93.1%, P Conclusions This study demonstrated that differences in survival and developmental rates between embryos from obese and normal-weight mice were eliminated after vitrification. Thus, maternal obesity does not aggravate vitrification injury, but obesity alone greatly impairs pre-implantation embryo survival and development.

  8. Diabetes mellitus aggravates hemorrhagic transformation after ischemic stroke via mitochondrial defects leading to endothelial apoptosis.

    Directory of Open Access Journals (Sweden)

    Keisuke Mishiro

    Full Text Available Diabetes is a crucial risk factor for stroke and is associated with increased frequency and poor prognosis. Although endothelial dysfunction is a known contributor of stroke, the underlying mechanisms have not been elucidated. The aim of this study was to elucidate the mechanism by which chronic hyperglycemia may contribute to the worsened prognosis following stroke, especially focusing on mitochondrial alterations. We examined the effect of hyperglycemia on hemorrhagic transformation at 24 hours after middle cerebral artery occlusion (MCAO in streptozotocin (STZ -induced diabetic mice. We also examined the effects of high-glucose exposure for 6 days on cell death, mitochondrial functions and morphology in human brain microvascular endothelial cells (HBMVECs or human endothelial cells derived from induced pluripotent stem cells (iCell endothelial cells. Hyperglycemia aggravated hemorrhagic transformation, but not infarction following stroke. High-glucose exposure increased apoptosis, capase-3 activity, and release of apoptosis inducing factor (AIF and cytochrome c in HBMVECs as well as affected mitochondrial functions (decreased cell proliferation, ATP contents, mitochondrial membrane potential, and increased matrix metalloproteinase (MMP-9 activity, but not reactive oxygen species production. Furthermore, morphological aberration of mitochondria was observed in diabetic cells (a great deal of fragmentation, vacuolation, and cristae disruption. A similar phenomena were seen also in iCell endothelial cells. In conclusion, chronic hyperglycemia aggravated hemorrhagic transformation after stroke through mitochondrial dysfunction and morphological alteration, partially via MMP-9 activation, leading to caspase-dependent apoptosis of endothelial cells of diabetic mice. Mitochondria-targeting therapy may be a clinically innovative therapeutic strategy for diabetic complications in the future.

  9. Calreticulin Translocation Aggravates Endoplasmic Reticulum Stress-associated Apoptosis during Cardiomyocyte Hypoxia/Reoxygenation

    Institute of Scientific and Technical Information of China (English)

    Fei-Fei Xu; Xiu-Hua Liu

    2015-01-01

    Background:Calreticulin (CRT) is major Ca2+-binding chaperone mainly resident in the endoplasmic reticulum (ER) lumen.Recently,it has been shown that non-ER CRT regulates a wide array of cellular responses.We previously found that CRT was up-regulated during hypoxia/reoxygenation (H/R) and this study was aimed to investigate whether CRT nuclear translocation aggravates ER stress (ERS)-associated apoptosis during H/R injury in neonatal rat cardiomyocytes.Methods:Apoptosis rate and lactate dehydrogenase (LDH) leakage in culture medium were measured as indices of cell injury.Immunofluorescence staining showed the morphological changes of ER and intracellular translocation of CRT.Western blotting or reverse transcription polymerase chain reaction was used to detect the expression of target molecules.Results:Compared with control,H/R increased apoptosis rate and LDH activity.The ER became condensed and bubbled,and CRT translocated to the nucleus.Western blotting showed up-regulation of CRT,Nrf2,activating transcription factor 4 (ATF4),CHOP and caspase-12 expression after H/R.Exogenous CRT overexpression induced by plasmid transfection before H/R increased cell apoptosis,LDH leakage,ER disorder,CRT nuclear translocation and the expression of ERS-associated molecules.However,administration of the ERS inhibitor,taurine,or CRT siRNA alleviated cell injury,ER disorder,and inhibited ERS-associated apoptosis.Conclusions:Our results indicated that during H/R stress,CRT translocation increases cell apoptosis and LDH leakage,aggravates ER disorder,up-regulates expression of nuclear transcription factors,Nrf2 and ATF4,and activates ERS-associated apoptosis.

  10. Intratracheally administered titanium dioxide or carbon black nanoparticles do not aggravate elastase-induced pulmonary emphysema in rats.

    OpenAIRE

    Roulet Agnès; Armand Lucie; Dagouassat Maylis; Rogerieux Françoise; Simon-Deckers Angélique; Belade Esther; Van Nhieu Jeanne; Lanone Sophie; Pairon Jean-Claude; Lacroix Ghislaine; Boczkowski Jorge

    2012-01-01

    Abstract Background Titanium dioxide (TiO2) and carbon black (CB) nanoparticles (NPs) have biological effects that could aggravate pulmonary emphysema. The aim of this study was to evaluate whether pulmonary administration of TiO2 or CB NPs in rats could induce and/or aggravate elastase-induced emphysema, and to investigate the underlying molecular mechanisms. Methods On day 1, Sprague-Dawley rats were intratracheally instilled with 25 U kg−1 pancreatic porcine elastase or saline. On day 7, t...

  11. Pyelolithotomy by the use of a hydrophilous macromolecular binding material ("pyeloform" pyelotomy).

    Science.gov (United States)

    Nagy, Z; Frang, D; Jávor, A; Götz, F; Szatmári, J; Vizi, L; Kovács, G

    1984-01-01

    The use of a synthetic macromolecular hydrophilous binding material for the extraction of multiple renal calculi (" Pyeloform " pyelotomy) is reported. An account of the results of animal studies in vitro is given and the possibilities of the method in are pointed out. PMID:6724825

  12. Closed Mechanoelectrochemical Cycles of Individual Single-Chain Macromolecular Motors by AFM

    NARCIS (Netherlands)

    Shi, Weiqing; Giannotti, Marina I.; Zhang, Xi; Hempenius, Mark A.; Schönherr, Holger; Vancso, G. Julius

    2007-01-01

    Motor cycles: Mechanoelectrochemical loops of single-chain macromolecular motors based on individual end-grafted poly(ferrocenyldimethylsilane) are shown by AFM to have an efficiency of up to 26 %. Upon oxidation of a prestretched chain, the chain length increases and the force decreases significant

  13. 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 crow

  14. Macromolecular Crowding Modulates Folding Mechanism of α/β Protein Apoflavodoxin

    Science.gov (United States)

    Homouz, D.; Stagg, L.; Wittungstafshede, P.; Cheung, M.

    2009-01-01

    Protein dynamics in cells may be different from that in dilute solutions in vitro since the environment in cells is highly concentrated with other macromolecules. This volume exclusion due to macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, here we have investigated the folding energy landscape of an alpha/beta protein, apoflavodoxin, in the presence of inert macromolecular crowding agents using in silico and in vitro approaches. By coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fraction of crowding agents (phi_c) as well as of crowding agent geometry (sphere or spherocylinder) at high phi_c. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we have identified in silico crowding conditions that best enhance protein stability and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. The test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. We propose that macromolecular crowding effects may be a tool for manipulation of protein folding and function in living cells.

  15. Effect of lysozyme chloride on betel quid chewing aggravated gastric oxidative stress and hemorrhagic ulcer in diabetic rats

    Institute of Scientific and Technical Information of China (English)

    Chen-Road Hung

    2005-01-01

    AIM: To evaluate the protective effect of lysozyme chloride on betel quid chewing (BQC) aggravated gastric oxidative stress and hemorrhagic ulcer in rats with diabetes mellitus (DM).METHODS: Male Wistar rats were challenged intravenously with streptozotocin (65 mg/kg) to induce DM. Rats were fed with regular pellet food or BQC-containing diets. After 90 d, rats were deprived of food for 24 h. Rat stomachs were irrigated for 3 h with normal saline or simulated gastric juice. Rats were killed and gastric specimens were harvested.RESULTS: An enhancement of various gastric ulcerogenic parameters, including acid back-diffusion, mucosal lipid peroxide generation, as well as decreased glutathione levels and mucus content, were observed in DM rats. After feeding DM rats with BQC, an exacerbation of these ulcerogenic parameters was achieved. Gastric juice caused a further aggravation of these ulcerogenic parameters. Daily intragastric lysozyme chloride dose-dependently inhibited exacerbation of various ulcerogenic parameters in those BQC-fed DM rats.CONCLUSION: (1) Gastric juice could aggravate both DM and BQC-fed DM rat hemorrhagic ulcer; (2) BQC exacerbated gastric hemorrhagic ulcer in DM rats via enhancing oxidative stress and reducing defensive factors; (3) lysozyme chloride effectively protected BQC aggravated gastric damage in DM rats.

  16. Aggravation of Risk and Precautionary Measures in Non-Life Insurance: A Tricky Scope for the Insurer?

    Directory of Open Access Journals (Sweden)

    Olavi-Jüri Luik

    2015-12-01

    Full Text Available Aggravation of risk and failure to take precautionary measures are focal issues in non-life insurance in terms of potential partial or full release of the insurer from the duty to perform. Not infrequently, it is difficult to draw a line between the aggravation of risk on the one hand, and non-compliance with precautionary measures on the other, since a particular action by a policyholder may present both situations. At the same time, the legal remedies available to the insurer regarding these two situations are different in scope. The aggravation of risk and non-compliance with precautionary measures are precisely the bases on which insurers actually reduce indemnity or refuse to compensate for damages. This article explores the differences between insurance laws in the Baltic states—specifically, the Estonian Law of Obligations Act, the Latvian Insurance Contract Law and Lithuanian rules contained in the Civil Code and Insurance Law. The article explores the differences between the Baltic states’ insurance laws and the Principles of European Insurance Contract Law (PEICL with regard to a policyholder’s duty in relation to aggravation of risk and precautionary measures, as the rights and obligations of policyholders do change where the optional instrument is applied. The article also includes comparisons to German, Finnish and Russian insurance law.

  17. 77 FR 24415 - Inflation Adjustment of the Aggravated Maximum Civil Monetary Penalty for a Violation of a...

    Science.gov (United States)

    2012-04-24

    ... ``older safety statutes'': the Safety Appliance Acts (then codified at 45 U.S.C. 1-16); the Locomotive... $650, the ordinary maximum of $25,000, and the aggravated maximum CMP of $100,000). See 73 FR 79698...-adjusted $550. 69 FR 30591 (May 28, 2004) and 69 FR 62817 (Oct. 28, 2004). (In 2004, FRA had determined,...

  18. Does objectively measured daily duration of forward bending predict development and aggravation of low-back pain?

    DEFF Research Database (Denmark)

    Lagersted-Olsen, Julie; Thomsen, Birthe Lykke; Holtermann, Andreas;

    2016-01-01

    OBJECTIVES: The aim of this paper was to investigate if objectively measured daily duration of forward bending of the trunk increases the risk of the development or aggravation of low-back pain (LBP) over one year in a working blue-collar population by examining (i) the incidence rate of LBP among...

  19. Cardiac Fibroblasts Aggravate Viral Myocarditis: Cell Specific Coxsackievirus B3 Replication

    Directory of Open Access Journals (Sweden)

    Diana Lindner

    2014-01-01

    Full Text Available Myocarditis is an inflammatory disease caused by viral infection. Different subpopulations of leukocytes enter the cardiac tissue and lead to severe cardiac inflammation associated with myocyte loss and remodeling. Here, we study possible cell sources for viral replication using three compartments of the heart: fibroblasts, cardiomyocytes, and macrophages. We infected C57BL/6j mice with Coxsackievirus B3 (CVB3 and detected increased gene expression of anti-inflammatory and antiviral cytokines in the heart. Subsequently, we infected cardiac fibroblasts, cardiomyocytes, and macrophages with CVB3. Due to viral infection, the expression of TNF-α, IL-6, MCP-1, and IFN-β was significantly increased in cardiac fibroblasts compared to cardiomyocytes or macrophages. We found that in addition to cardiomyocytes cardiac fibroblasts were infected by CVB3 and displayed a higher virus replication (132-fold increase compared to cardiomyocytes (14-fold increase between 6 and 24 hours after infection. At higher virus concentrations, macrophages are able to reduce the viral copy number. At low virus concentration a persistent virus infection was determined. Therefore, we suggest that cardiac fibroblasts play an important role in the pathology of CVB3-induced myocarditis and are another important contributor of virus replication aggravating myocarditis.

  20. Liver Cholesterol Overload Aggravates Obstructive Cholestasis by Inducing Oxidative Stress and Premature Death in Mice

    Science.gov (United States)

    Nuño-Lámbarri, Natalia; Domínguez-Pérez, Mayra; Baulies-Domenech, Anna; Monte, Maria J.; Marin, Jose J. G.; Rosales-Cruz, Patricia; Souza, Verónica; Miranda, Roxana U.; Bucio, Leticia; Montalvo-Jave, Eduardo E.; Concepción Gutiérrez-Ruiz, María; García-Ruiz, Carmen

    2016-01-01

    Nonalcoholic steatohepatitis is one of the leading causes of liver disease. Dietary factors determine the clinical presentation of steatohepatitis and can influence the progression of related diseases. Cholesterol has emerged as a critical player in the disease and hence consumption of cholesterol-enriched diets can lead to a progressive form of the disease. The aim was to investigate the impact of liver cholesterol overload on the progression of the obstructive cholestasis in mice subjected to bile duct ligation surgery. Mice were fed with a high cholesterol diet for two days and then were subjected to surgery procedure; histological, biochemical, and molecular analyses were conducted to address the effect of cholesterol in liver damage. Mice under the diet were more susceptible to damage. Results show that cholesterol fed mice exhibited increased apoptosis and oxidative stress as well as reduction in cell proliferation. Mortality following surgery was higher in HC fed mice. Liver cholesterol impairs the repair of liver during obstructive cholestasis and aggravates the disease with early fatal consequences; these effects were strongly associated with oxidative stress. PMID:27635189

  1. Cardiomyocyte Overexpression of FABP4 Aggravates Pressure Overload-Induced Heart Hypertrophy.

    Science.gov (United States)

    Zhang, Ji; Qiao, Congzhen; Chang, Lin; Guo, Yanhong; Fan, Yanbo; Villacorta, Luis; Chen, Y Eugene; Zhang, Jifeng

    2016-01-01

    Fatty acid binding protein 4 (FABP4) is a member of the intracellular lipid-binding protein family, responsible for the transportation of fatty acids. It is considered to express mainly in adipose tissues, and be strongly associated with inflammation, obesity, diabetes and cardiovasculardiseases. Here we report that FABP4 is also expressed in cardiomyocytes and plays an important role in regulating heart function under pressure overload. We generated heart-specific transgenic FABP4 (FABP4-TG) mice using α myosin-heavy chain (α-MHC) promoter and human FABP4 sequence, resulting in over-expression of FABP4 in cardiomyocytes. The FABP4-TG mice displayed normal cardiac morphology and contractile function. When they were subjected to the transverse aorta constriction (TAC) procedure, the FABP4-TG mice developed more cardiac hypertrophy correlated with significantly increased ERK phosphorylation, compared with wild type controls. FABP4 over-expression in cardiomyocytes activated phosphor-ERK signal and up-regulate the expression of cardiac hypertrophic marker genes. Conversely, FABP4 induced phosphor-ERK signal and hypertrophic gene expressions can be markedly inhibited by an ERK inhibitor PD098059 as well as the FABP4 inhibitor BMS309403. These results suggest that FABP4 over-expression in cardiomyocytes can aggravate the development of cardiac hypertrophy through the activation of ERK signal pathway. PMID:27294862

  2. Liver Cholesterol Overload Aggravates Obstructive Cholestasis by Inducing Oxidative Stress and Premature Death in Mice.

    Science.gov (United States)

    Nuño-Lámbarri, Natalia; Domínguez-Pérez, Mayra; Baulies-Domenech, Anna; Monte, Maria J; Marin, Jose J G; Rosales-Cruz, Patricia; Souza, Verónica; Miranda, Roxana U; Bucio, Leticia; Montalvo-Jave, Eduardo E; Concepción Gutiérrez-Ruiz, María; García-Ruiz, Carmen; Fernández-Checa, José C; Gomez-Quiroz, Luis Enrique

    2016-01-01

    Nonalcoholic steatohepatitis is one of the leading causes of liver disease. Dietary factors determine the clinical presentation of steatohepatitis and can influence the progression of related diseases. Cholesterol has emerged as a critical player in the disease and hence consumption of cholesterol-enriched diets can lead to a progressive form of the disease. The aim was to investigate the impact of liver cholesterol overload on the progression of the obstructive cholestasis in mice subjected to bile duct ligation surgery. Mice were fed with a high cholesterol diet for two days and then were subjected to surgery procedure; histological, biochemical, and molecular analyses were conducted to address the effect of cholesterol in liver damage. Mice under the diet were more susceptible to damage. Results show that cholesterol fed mice exhibited increased apoptosis and oxidative stress as well as reduction in cell proliferation. Mortality following surgery was higher in HC fed mice. Liver cholesterol impairs the repair of liver during obstructive cholestasis and aggravates the disease with early fatal consequences; these effects were strongly associated with oxidative stress. PMID:27635189

  3. Dietary fructose aggravates the pathobiology of traumatic brain injury by influencing energy homeostasis and plasticity.

    Science.gov (United States)

    Agrawal, Rahul; Noble, Emily; Vergnes, Laurent; Ying, Zhe; Reue, Karen; Gomez-Pinilla, Fernando

    2016-05-01

    Fructose consumption has been on the rise for the last two decades and is starting to be recognized as being responsible for metabolic diseases. Metabolic disorders pose a particular threat for brain conditions characterized by energy dysfunction, such as traumatic brain injury. Traumatic brain injury patients experience sudden abnormalities in the control of brain metabolism and cognitive function, which may worsen the prospect of brain plasticity and function. The mechanisms involved are poorly understood. Here we report that fructose consumption disrupts hippocampal energy homeostasis as evidenced by a decline in functional mitochondria bioenergetics (oxygen consumption rate and cytochrome C oxidase activity) and an aggravation of the effects of traumatic brain injury on molecular systems engaged in cell energy homeostasis (sirtuin 1, peroxisome proliferator-activated receptor gamma coactivator-1alpha) and synaptic plasticity (brain-derived neurotrophic factor, tropomyosin receptor kinase B, cyclic adenosine monophosphate response element binding, synaptophysin signaling). Fructose also worsened the effects of traumatic brain injury on spatial memory, which disruption was associated with a decrease in hippocampal insulin receptor signaling. Additionally, fructose consumption and traumatic brain injury promoted plasma membrane lipid peroxidation, measured by elevated protein and phenotypic expression of 4-hydroxynonenal. These data imply that high fructose consumption exacerbates the pathology of brain trauma by further disrupting energy metabolism and brain plasticity, highlighting the impact of diet on the resilience to neurological disorders. PMID:26661172

  4. [Relative increase and metacritic aggravation in the diagnosis of anicteric cholestasis].

    Science.gov (United States)

    Albot, G; Geraudias, P; Kind, M

    1975-02-14

    The authors report 3 cases and report the diagnostic usefulness of two signs of minor cholestasis described by one of them in 1966. A relative increase, in the absence of obvious virus hepatitis or cirrhosis, of the serum bilirubin, cholesterol, lipids and alkaline phosphatase, together with B.S.P. excretion. suggest minor cholestasis. The sign of "metacritical aggravation" when there is some suspicion of minor cholestasis, the supervision of the course of the disease, or a retrospective inquiry, permit, in the presence of minor symptoms, such as, pain, fever, jaundice, or pruritus, one to make the diagnosis of minor cholestasis. The latter is due either to the presence of small gall stones in the common bile duct, or to inflammation of the ampulla of Vater, or sphincter of Oddi, a Vaterian ampulloma, pancreatitis, or following damage to the common bile duct. In practice, liver biopsy confirms the diagnosis, and intravenous cholangiography, by the perfusion method, is usually able to demonstrate obstruction of the common bile duct. PMID:169583

  5. Absence of intestinal PPARγ aggravates acute infectious colitis in mice through a lipocalin-2-dependent pathway.

    Directory of Open Access Journals (Sweden)

    Parag Kundu

    2014-01-01

    Full Text Available To be able to colonize its host, invading Salmonella enterica serovar Typhimurium must disrupt and severely affect host-microbiome homeostasis. Here we report that S. Typhimurium induces acute infectious colitis by inhibiting peroxisome proliferator-activated receptor gamma (PPARγ expression in intestinal epithelial cells. Interestingly, this PPARγ down-regulation by S. Typhimurium is independent of TLR-4 signaling but triggers a marked elevation of host innate immune response genes, including that encoding the antimicrobial peptide lipocalin-2 (Lcn2. Accumulation of Lcn2 stabilizes the metalloproteinase MMP-9 via extracellular binding, which further aggravates the colitis. Remarkably, when exposed to S. Typhimurium, Lcn2-null mice exhibited a drastic reduction of the colitis and remained protected even at later stages of infection. Our data suggest a mechanism in which S. Typhimurium hijacks the control of host immune response genes such as those encoding PPARγ and Lcn2 to acquire residence in a host, which by evolution has established a symbiotic relation with its microbiome community to prevent pathogen invasion.

  6. Glucocorticoids aggravate retrograde memory deficiency associated with traumatic brain injury in rats.

    Science.gov (United States)

    Chen, Xin; Zhang, Ke-Li; Yang, Shu-Yuan; Dong, Jing-Fei; Zhang, Jian-Ning

    2009-02-11

    Administration of glucocorticoid to patients with head injury has previously been demonstrated to impair memory. We hypothesize that glucocorticoids promote post-traumatic hippocampal apoptosis, resulting in retrograde memory deficiency associated with traumatic brain injury (TBI). In the present study, we tested this hypothesis by measuring spatial memory deficiency in rats subjected to fluid percussion injury (FPI) and receiving dexamethasone (DXM at 0.5-10 mg/kg) or methylprednisolone (MP at 5-30 mg/kg); we also examined neuronal apoptosis in hippocampus. Adult male Wistar rats were trained for the acquisition of spatial memory, then subjected to FPI and tested for spatial reference memory on post-injury days 7 and 14 using the Morris Water Maze. Brain tissue from injured rats was examined 24 h to 2 weeks after injury. The percent time in the goal quadrant, which measures spatial reference memory, was significantly lower in injured rats receiving either high-dose DXM or MP than in control groups. TUNEL-positive cells in hippocampus were first detected 24 h post-injury, plateauing at 48h. The number of TUNEL-positive cells was significantly higher in injured rats treated with either DXM or MP. The data suggest that glucocorticoid therapy for TBI may increase neuronal apoptosis in hippocampus and, as a result, aggravate retrograde memory deficits induced by TBI.

  7. Feed exposure to FB1 can aggravate pneumonic damages in pigs provoked by P. multocida.

    Science.gov (United States)

    Kovács, Melinda; Pósa, Roland; Tuboly, Tamás; Donkó, Tamás; Repa, Imre; Tossenberger, János; Szabó-Fodor, Judit; Stoev, Stoycho; Magyar, Tibor

    2016-10-01

    The possible interaction between Pasteurella multocida and the mycotoxin fumonisin B1 (FB1), recognised as one of the most often food/feed contaminant, was studied with the aim to evaluate whether and how FB1 can influence and/or complicate the development and severity of various pathological damages provoked by Pasteurella multocida in some internal organs of pigs. Heavier lung pathology was seen in pigs experimentally infected with Pasteurella multocida, when the same were exposed to 20ppm dietary levels of fumonisin B1 (FB1) as was assessed by gross pathology, pathomorphological examinations, clinical biochemistry and some immunological investigations. The most typical damages in FB1 treated pigs were the strong oedema in the lung and the slight oedema in the other internal organs and mild degenerative changes in the kidneys, whereas the typical pathomorphological findings in pigs infected with Pasteurella multocida was broncho-interstitial pneumonia. FB1 was found to aggravate pneumonic changes provoked by P. multocida in the cranial lobes of the lung and to complicate pneumonic damages with interstitial oedema in the lung. No macroscopic damages were observed in the pigs infected only with Pasteurella multocida. It can be concluded that the feed intake of FB1 in pigs may complicate or exacerbate the course of P. multocida serotype A infection.

  8. Strenuous exercise aggravates MDMA-induced skeletal muscle damage in mice

    International Nuclear Information System (INIS)

    The aim of this study was to investigate the influence of ecstasy (MDMA) administration on body temperature and soleus muscle histology in exercised and non-exercised mice. Charles-River mice were distributed into four groups: Control (C), exercise (EX), MDMA treated (M), and M + EX. The treated animals received an i.p. injection (10 mg/kg) of MDMA (saline for C and EX), and the exercise consisted of a 90 min level run at a velocity of 900 m/h, immediately after the MDMA or saline administration. Body temperature was recorded every 30 min via subcutaneous implanted transponder. Animals were sacrificed 1.5, 25.5, and 49.5 h after i.p. injection and the soleus muscles were removed and processed for light and electron microscopy. The MDMA-treated animals showed a significant increase in body temperature (similar in M and M + EX groups), reaching the peak 90 min after i.p. administration; their temperature remained higher than control for more than 5 h. The EX group evidenced a similar and parallel, yet lower temperature increase during exercise and recovery. Morphological signs of damage were rarely encountered in the EX group; they were more pronounced in M group and even aggravated in M + EX group. In conclusion, MDMA and exercise per se increased body temperature but in conjunction did not have a cumulated effect. However, ecstasy and concomitant physical activity might severely accumulate with regard to skeletal muscle toxicity and may lead to rhabdomyolysis

  9. Feed exposure to FB1 can aggravate pneumonic damages in pigs provoked by P. multocida.

    Science.gov (United States)

    Kovács, Melinda; Pósa, Roland; Tuboly, Tamás; Donkó, Tamás; Repa, Imre; Tossenberger, János; Szabó-Fodor, Judit; Stoev, Stoycho; Magyar, Tibor

    2016-10-01

    The possible interaction between Pasteurella multocida and the mycotoxin fumonisin B1 (FB1), recognised as one of the most often food/feed contaminant, was studied with the aim to evaluate whether and how FB1 can influence and/or complicate the development and severity of various pathological damages provoked by Pasteurella multocida in some internal organs of pigs. Heavier lung pathology was seen in pigs experimentally infected with Pasteurella multocida, when the same were exposed to 20ppm dietary levels of fumonisin B1 (FB1) as was assessed by gross pathology, pathomorphological examinations, clinical biochemistry and some immunological investigations. The most typical damages in FB1 treated pigs were the strong oedema in the lung and the slight oedema in the other internal organs and mild degenerative changes in the kidneys, whereas the typical pathomorphological findings in pigs infected with Pasteurella multocida was broncho-interstitial pneumonia. FB1 was found to aggravate pneumonic changes provoked by P. multocida in the cranial lobes of the lung and to complicate pneumonic damages with interstitial oedema in the lung. No macroscopic damages were observed in the pigs infected only with Pasteurella multocida. It can be concluded that the feed intake of FB1 in pigs may complicate or exacerbate the course of P. multocida serotype A infection. PMID:27663368

  10. Cardiomyocyte Overexpression of FABP4 Aggravates Pressure Overload-Induced Heart Hypertrophy.

    Directory of Open Access Journals (Sweden)

    Ji Zhang

    Full Text Available Fatty acid binding protein 4 (FABP4 is a member of the intracellular lipid-binding protein family, responsible for the transportation of fatty acids. It is considered to express mainly in adipose tissues, and be strongly associated with inflammation, obesity, diabetes and cardiovasculardiseases. Here we report that FABP4 is also expressed in cardiomyocytes and plays an important role in regulating heart function under pressure overload. We generated heart-specific transgenic FABP4 (FABP4-TG mice using α myosin-heavy chain (α-MHC promoter and human FABP4 sequence, resulting in over-expression of FABP4 in cardiomyocytes. The FABP4-TG mice displayed normal cardiac morphology and contractile function. When they were subjected to the transverse aorta constriction (TAC procedure, the FABP4-TG mice developed more cardiac hypertrophy correlated with significantly increased ERK phosphorylation, compared with wild type controls. FABP4 over-expression in cardiomyocytes activated phosphor-ERK signal and up-regulate the expression of cardiac hypertrophic marker genes. Conversely, FABP4 induced phosphor-ERK signal and hypertrophic gene expressions can be markedly inhibited by an ERK inhibitor PD098059 as well as the FABP4 inhibitor BMS309403. These results suggest that FABP4 over-expression in cardiomyocytes can aggravate the development of cardiac hypertrophy through the activation of ERK signal pathway.

  11. GSN antibody pretreatment aggravates radiation-induced lung injury in mice

    International Nuclear Information System (INIS)

    Radiation-induced lung injury is one of the main dose limiting factors for thoracic radiation therapy. Gelsolin (GSN) is a widespread, multifunctional regulator of cellular structure and metabolism. In this work, the roles of GSN in radiation-induced lung injury in Balb/c mice were studied. The GSN levels in plasma reduced progressively in 72 hours after irradiation, and then increased gradually. GSN contents in the bronchoalveolar lavage (BAL) fluid increased after thoracic irradiation, whereas mRNA levels of GSN in the lung tissue decreased significantly within 24 hours after irradiation and then increased again. Mice were intravenously injected with 50 μg GSN antibody 0.5 hour before 20 Gy of thoracic irradiation. GSN antibody pretreatment increased lung inflammation, protein concentration in the BAL fluid and leukocytes infiltration in the irradiated mice. The activities of superoxidase dismutase (SOD) in the plasma and the BAL fluid in irradiated mice injected with GSN antibody were less than that of control groups, whereas the levels of malondialdehyde (MDA) increased. These results suggest that pretreatment of GSN antibody may aggravate radiation-induced pneumonitis. (authors)

  12. 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.

  13. Cobalamin inactivation by nitrous oxide produces severe neurological impairment in fruit bats: protection by methionine and aggravation by folates

    Energy Technology Data Exchange (ETDEWEB)

    van der Westhuyzen, J.; Fernandes-Costa, F.; Metz, J.

    1982-11-01

    Nitrous oxide, which inactivates cobalamin when administered to fruit bats, results in severe neurological impairment leading to ataxia, paralysis and death. This occurs after about 6 weeks in animals depleted of cobalamin by dietary restriction, and after about 10 weeks in cobalamin replete bats. Supplementation of the diet with pteroylglutamic acid caused acceleration of the neurological impairment--the first unequivocal demonstration of aggravation of the neurological lesion in cobalamin deficiency by pteroylglutamic acid. The administration of formyltetrahydropteroylglutamic acid produced similar aggravation of the neurological lesion. Supplementation of the diet with methionine protected the bats from neurological impairment, but failed to prevent death. Methionine supplementation protected against the exacerbating effect of folate, preventing the development of neurological changes. These findings lend support to the hypothesis that the neurological lesion in cobalamin deficiency may be related to a deficiency in the methyl donor S-adenosylmethionine which follows diminished synthesis of methionine.

  14. Charges for criminal exposure to HIV and aggravated prostitution filed in the Nashville, Tennessee Prosecutorial Region 2000-2010.

    Science.gov (United States)

    Galletly, Carol L; Lazzarini, Zita

    2013-10-01

    This paper examines comprehensive data on arrests for HIV-specific crimes within a single jurisdiction, the Nashville Tennessee prosecutorial region, over 11 years. There were 25 arrests for HIV exposure and 27 for aggravated prostitution. Eleven of the arrests for HIV exposure involved nonsexual behaviors; none alleged transmission. Sixteen of the arrests for HIV exposure involved sexual behavior; three alleged transmission. Aggravated prostitution cases (i.e. prostitution while knowing one has HIV) often involved solicitation of oral sex; none alleged transmission. Maximum sentences for HIV-specific crimes ranged from 5 to 8 years. We conclude that enforcement of US HIV-specific laws is underestimated. Fifty-two arrests over 11 years were recorded in one jurisdiction. Over half of the arrests involved behaviors posing minimal or no HIV transmission risk. Despite concerns about malicious, intentional HIV transmission, no cases alleged malice or intention.

  15. Chemerin aggravates DSS-induced colitis by suppressing M2 macrophage polarization.

    Science.gov (United States)

    Lin, Yuli; Yang, Xuguang; Yue, Wenjie; Xu, Xiaofei; Li, Bingji; Zou, Linlin; He, Rui

    2014-07-01

    Chemerin is present in various inflammatory sites and is closely involved in tissue inflammation. Recent studies have demonstrated that chemerin treatment can cause either anti-inflammatory or pro-inflammatory effects according to the disease model being investigated. Elevated circulating chemerin was recently found in patients with inflammatory bowel disease (IBD); however, the role of chemerin in intestinal inflammation remains unknown. In this study, we demonstrated that the administration of exogenous chemerin (aa17-156) aggravated the severity of dextran sulfate sodium (DSS)-induced colitis, which was characterized by higher clinical scores, extensive mucosal damage and significantly increased local and systemic production of pro-inflammatory cytokines, including IL-6, TNF-α and interferon (IFN-γ). Interestingly, chemerin did not appear to influence the magnitudes of inflammatory infiltrates in the colons, but did result in significantly decreased colonic expression of M2 macrophage-associated genes, including Arginase 1 (Arg-1), Ym1, FIZZ1 and IL-10, following DSS exposure, suggesting an impaired M2 macrophage skewing in vivo. Furthermore, an in vitro experiment showed that the addition of chemerin directly suppressed M2 macrophage-associated gene expression and STAT6 phosphorylation in IL-4-stimulated macrophages. Significantly elevated chemerin levels were found in colons from DSS-exposed mice and from ulcerative colitis (UC) patients and appeared to positively correlate with disease severity. Moreover, the in vivo administration of neutralizing anti-chemerin antibody significantly improved intestinal inflammation following DSS exposure. Taken together, our findings reveal a pro-inflammatory role for chemerin in DSS-induced colitis and the ability of chemerin to suppress the anti-inflammatory M2 macrophage response. Our study also suggests that upregulated chemerin in inflamed colons may contribute to the pathogenesis of IBD.

  16. High Potassium Aggravates the Oxidative Stress Inducedy by Magnesium Deficiency in Rice Leaves

    Institute of Scientific and Technical Information of China (English)

    DING Yu-Chuan; CHANG Chun-Rong; LUO Wen; WU Yan-Shou; REN Xiao-Li; WANG Ping; XU Guo-Hua

    2008-01-01

    Magnesium (Mg) deficiency in plant affects photosynthesis and many other metabolic processes.Rice (Oryza sativa L.cv.'Wuyunjing 7') plants were grown in hydroponics culture at three Mg and two potassium (K) levels under greenhouse conditions to examine the induction of oxidative stress and consequent antioxidant responses in rice leaves due to Mg deficiency.At low Mg (0.2 mmol L-1 Mg supply for two weeks after transplanting) and high K (6 mmol L-1) for 21days,the rice plants showed severe Mg deficiency and a significant decreases in the dry matter production. The Mg deficiency in leaves decreased chlorophyll concentrations,photosynthetic activity,and soluble protein,but significantly increased the concentrations of soluble sugars and malondialdehyde (MDA) and the activities of superoxide dismutase (SOD,EC 1.15.1.1),catalase (CAT,EC 1.11.1.6) and peroxidase (POD,EC 1.11.1.7).In addition,Mg concentrations in the leaves and in the shoot biomass were negatively related to the activities of the three antioxidative enzymes and the concentration of MDA in leaves.There were very significant interactive effects between Mg and K supplied in the culture solution on shoot biomass yield,chlorophyll content,photosynthesis rate,the activities of SOD,CAT and POD,and MDA content in the leaves of rice.It is suggested that the high K level in the nutrient solution aggravated the effect of low Mg supply-induced Mg deficiency and created the oxidative damage in rice plants.

  17. Ocean acidification may aggravate social-ecological trade-offs in coastal fisheries.

    Science.gov (United States)

    Voss, Rudi; Quaas, Martin F; Schmidt, Jörn O; Kapaun, Ute

    2015-01-01

    Ocean Acidification (OA) will influence marine ecosystems by changing species abundance and composition. Major effects are described for calcifying organisms, which are significantly impacted by decreasing pH values. Direct effects on commercially important fish are less well studied. The early life stages of fish populations often lack internal regulatory mechanisms to withstand the effects of abnormal pH. Negative effects can be expected on growth, survival, and recruitment success. Here we study Norwegian coastal cod, one of the few stocks where such a negative effect was experimentally quantified, and develop a framework for coupling experimental data on OA effects to ecological-economic fisheries models. In this paper, we scale the observed physiological responses to the population level by using the experimentally determined mortality rates as part of the stock-recruitment relationship. We then use an ecological-economic optimization model, to explore the potential effect of rising CO2 concentration on ecological (stock size), economic (profits), consumer-related (harvest) and social (employment) indicators, with scenarios ranging from present day conditions up to extreme acidification. Under the assumptions of our model, yields and profits could largely be maintained under moderate OA by adapting future fishing mortality (and related effort) to changes owing to altered pH. This adaptation comes at the costs of reduced stock size and employment, however. Explicitly visualizing these ecological, economic and social tradeoffs will help in defining realistic future objectives. Our results can be generalized to any stressor (or stressor combination), which is decreasing recruitment success. The main findings of an aggravation of trade-offs will remain valid. This seems to be of special relevance for coastal stocks with limited options for migration to avoid unfavorable future conditions and subsequently for coastal fisheries, which are often small scale local

  18. Ocean acidification may aggravate social-ecological trade-offs in coastal fisheries.

    Directory of Open Access Journals (Sweden)

    Rudi Voss

    Full Text Available Ocean Acidification (OA will influence marine ecosystems by changing species abundance and composition. Major effects are described for calcifying organisms, which are significantly impacted by decreasing pH values. Direct effects on commercially important fish are less well studied. The early life stages of fish populations often lack internal regulatory mechanisms to withstand the effects of abnormal pH. Negative effects can be expected on growth, survival, and recruitment success. Here we study Norwegian coastal cod, one of the few stocks where such a negative effect was experimentally quantified, and develop a framework for coupling experimental data on OA effects to ecological-economic fisheries models. In this paper, we scale the observed physiological responses to the population level by using the experimentally determined mortality rates as part of the stock-recruitment relationship. We then use an ecological-economic optimization model, to explore the potential effect of rising CO2 concentration on ecological (stock size, economic (profits, consumer-related (harvest and social (employment indicators, with scenarios ranging from present day conditions up to extreme acidification. Under the assumptions of our model, yields and profits could largely be maintained under moderate OA by adapting future fishing mortality (and related effort to changes owing to altered pH. This adaptation comes at the costs of reduced stock size and employment, however. Explicitly visualizing these ecological, economic and social tradeoffs will help in defining realistic future objectives. Our results can be generalized to any stressor (or stressor combination, which is decreasing recruitment success. The main findings of an aggravation of trade-offs will remain valid. This seems to be of special relevance for coastal stocks with limited options for migration to avoid unfavorable future conditions and subsequently for coastal fisheries, which are often small

  19. Aggravation of Allergic Airway Inflammation by Cigarette Smoke in Mice Is CD44-Dependent.

    Directory of Open Access Journals (Sweden)

    Smitha Kumar

    Full Text Available Although epidemiological studies reveal that cigarette smoke (CS facilitates the development and exacerbation of allergic asthma, these studies offer limited information on the mechanisms involved. The transmembrane glycoprotein CD44 is involved in cell adhesion and acts as a receptor for hyaluronic acid and osteopontin. We aimed to investigate the role of CD44 in a murine model of CS-facilitated allergic airway inflammation.Wild type (WT and CD44 knock-out (KO mice were exposed simultaneously to house dust mite (HDM extract and CS. Inflammatory cells, hyaluronic acid (HA and osteopontin (OPN levels were measured in bronchoalveolar lavage fluid (BALF. Proinflammatory mediators, goblet cell metaplasia and peribronchial eosinophilia were assessed in lung tissue. T-helper (Th 1, Th2 and Th17 cytokine production was evaluated in mediastinal lymph node cultures.In WT mice, combined HDM/CS exposure increased the number of inflammatory cells and the levels of HA and OPN in BALF and Th2 cytokine production in mediastinal lymph nodes compared to control groups exposed to phosphate buffered saline (PBS/CS, HDM/Air or PBS/Air. Furthermore, HDM/CS exposure significantly increased goblet cell metaplasia, peribronchial eosinophilia and inflammatory mediators in the lung. CD44 KO mice exposed to HDM/CS had significantly fewer inflammatory cells in BALF, an attenuated Th2 cytokine production, as well as decreased goblet cells and peribronchial eosinophils compared to WT mice. In contrast, the levels of inflammatory mediators were similar or higher than in WT mice.We demonstrate for the first time that the aggravation of pulmonary inflammation upon combined exposure to allergen and an environmental pollutant is CD44-dependent. Data from this murine model of concomitant exposure to CS and HDM might be of importance for smoking allergic asthmatics.

  20. Aggravated bone density decline following symptomatic osteonecrosis in children with acute lymphoblastic leukemia.

    Science.gov (United States)

    den Hoed, Marissa A H; Pluijm, Saskia M F; te Winkel, Mariël L; de Groot-Kruseman, Hester A; Fiocco, Martha; Hoogerbrugge, Peter; Leeuw, Jan A; Bruin, Marrie C A; van der Sluis, Inge M; Bresters, Dorien; Lequin, Maarten H; Roos, Jan C; Veerman, Anjo J P; Pieters, Rob; van den Heuvel-Eibrink, Marry M

    2015-12-01

    Osteonecrosis and decline of bone density are serious side effects during and after treatment of childhood acute lymphoblastic leukemia. It is unknown whether osteonecrosis and low bone density occur together in the same patients, or whether these two osteogenic side-effects can mutually influence each other's development. Bone density and the incidence of symptomatic osteonecrosis were prospectively assessed in a national cohort of 466 patients with acute lymphoblastic leukemia (4-18 years of age) who were treated according to the dexamethasone-based Dutch Child Oncology Group-ALL9 protocol. Bone mineral density of the lumbar spine (BMDLS) (n=466) and of the total body (BMDTB) (n=106) was measured by dual X-ray absorptiometry. Bone density was expressed as age- and gender-matched standard deviation scores. Thirty patients (6.4%) suffered from symptomatic osteonecrosis. At baseline, BMDLS and BMDTB did not differ between patients who did or did not develop osteonecrosis. At cessation of treatment, patients with osteonecrosis had lower mean BMDLS and BMDTB than patients without osteonecrosis (respectively, with osteonecrosis: -2.16 versus without osteonecrosis: -1.21, Pacute lymphoblastic leukemia does not seem to influence the occurrence of symptomatic osteonecrosis. Bone density declines from the time that osteonecrosis is diagnosed; this suggests that the already existing decrease in bone density during acute lymphoblastic leukemia therapy is further aggravated by factors such as restriction of weight-bearing activities and destruction of bone architecture due to osteonecrosis. Osteonecrosis can, therefore, be considered a risk factor for low bone density in children with acute lymphoblastic leukemia.

  1. Administration of Mycobacterium leprae rHsp65 aggravates experimental autoimmune uveitis in mice.

    Directory of Open Access Journals (Sweden)

    Eliana B Marengo

    Full Text Available The 60 kDa heat shock protein family, Hsp60, constitutes an abundant and highly conserved class of molecules that are highly expressed in chronic-inflammatory and autoimmune processes. Experimental autoimmune uveitis [EAU] is a T cell mediated intraocular inflammatory disease that resembles human uveitis. Mycobacterial and homologous Hsp60 peptides induces uveitis in rats, however their participation in aggravating the disease is poorly known. We here evaluate the effects of the Mycobacterium leprae Hsp65 in the development/progression of EAU and the autoimmune response against the eye through the induction of the endogenous disequilibrium by enhancing the entropy of the immunobiological system with the addition of homologous Hsp. B10.RIII mice were immunized subcutaneously with interphotoreceptor retinoid-binding protein [IRBP], followed by intraperitoneally inoculation of M. leprae recombinant Hsp65 [rHsp65]. We evaluated the proliferative response, cytokine production and the percentage of CD4(+IL-17(+, CD4(+IFN-gamma(+ and CD4(+Foxp3(+ cells ex vivo, by flow cytometry. Disease severity was determined by eye histological examination and serum levels of anti-IRBP and anti-Hsp60/65 measured by ELISA. EAU scores increased in the Hsp65 group and were associated with an expansion of CD4(+IFN-gamma(+ and CD4(+IL-17(+ T cells, corroborating with higher levels of IFN-gamma. Our data indicate that rHsp65 is one of the managers with a significant impact over the immune response during autoimmunity, skewing it to a pathogenic state, promoting both Th1 and Th17 commitment. It seems comprehensible that the specificity and primary function of Hsp60 molecules can be considered as a potential pathogenic factor acting as a whistleblower announcing chronic-inflammatory diseases progression.

  2. Intermittent hypoxia can aggravate motor neuronal loss and cognitive dysfunction in ALS mice.

    Directory of Open Access Journals (Sweden)

    Sung-Min Kim

    Full Text Available BACKGROUND: Patients with ALS may be exposed to variable degrees of chronic intermittent hypoxia. However, all previous experimental studies on the effects of hypoxia in ALS have only used a sustained hypoxia model and it is possible that chronic intermittent hypoxia exerts effects via a different molecular mechanism from that of sustained hypoxia. No study has yet shown that hypoxia (either chronic intermittent or sustained can affect the loss of motor neurons or cognitive function in an in vivo model of ALS. OBJECTIVE: To evaluate the effects of chronic intermittent hypoxia on motor and cognitive function in ALS mice. METHODS: Sixteen ALS mice and 16 wild-type mice were divided into 2 groups and subjected to either chronic intermittent hypoxia or normoxia for 2 weeks. The effects of chronic intermittent hypoxia on ALS mice were evaluated using the rotarod, Y-maze, and wire-hanging tests. In addition, numbers of motor neurons in the ventral horn of the spinal cord were counted and western blot analyses were performed for markers of oxidative stress and inflammatory pathway activation. RESULTS: Compared to ALS mice kept in normoxic conditions, ALS mice that experienced chronic intermittent hypoxia had poorer motor learning on the rotarod test, poorer spatial memory on the Y-maze test, shorter wire hanging time, and fewer motor neurons in the ventral spinal cord. Compared to ALS-normoxic and wild-type mice, ALS mice that experienced chronic intermittent hypoxia had higher levels of oxidative stress and inflammation. CONCLUSIONS: Chronic intermittent hypoxia can aggravate motor neuronal death, neuromuscular weakness, and probably cognitive dysfunction in ALS mice. The generation of oxidative stress with activation of inflammatory pathways may be associated with this mechanism. Our study will provide insight into the association of hypoxia with disease progression, and in turn, the rationale for an early non-invasive ventilation treatment in

  3. Vitamin D deficiency aggravates chronic kidney disease progression after ischemic acute kidney injury.

    Directory of Open Access Journals (Sweden)

    Janaína Garcia Gonçalves

    pathways and involvement of TGF-β1 growth factor, VDD could be considered as an aggravating factor for tubulointerstitial damage and fibrosis progression following acute kidney injury induced by ischemia/reperfusion.

  4. FR167653, a p38 mitogen-activated protein kinase inhibitor, aggravates experimental colitis in mice

    Institute of Scientific and Technical Information of China (English)

    Takashi Nishimura; Akira Andoh; Atsushi Nishida; Makoto Shioya; Yuhsuke Koizumi; Tomoyuki Tsujikawa; Yoshihide Fujiyama

    2008-01-01

    AIM: To investigate the effects of FR167653 on the development of dextran sulfate sodium (DSS)-induced colitis in mice.METHODS: BALB/c mice were fed rodent chow containing 3.5% (wt/wt) DSS. The recipient mice underwent intra-peritoneal injection of vehicles or FR167653 (30 mg/kg per day). The mice were sacrificed on day 14, and the degree of colitis was assessed. Immunohistochemical analyses for CD4+ T cell and F4/80+ macrophage infiltration were also performed. Mucosal o/tokine expression was analyzed by RT-PCR.RESULTS: The body weight loss was more apparent in the FR167653-treated DSS mice than in the vehicle-treated DSS mice. The colon length was shorter in the FR167653-treated DSS mice than in the vehicle-treated DSS mice. Disease activity index and histological colitis score were significantly higher in FR167653- than in vehicle-treated DSS animals. Microscopically, mucosal edema, cellular infiltration (CD4 T cells and F4/80 macrophages), and the disruption of the epithelium were much more severe in FR167653-treated mice than in controls. Mucosal mRNA expression for interleukin-1β (IL-1β) and tumor necrosis factor-α (TNF-α) were found to be markedly reduced in FR167653-treated DSS mice.CONCLUSION: Treatment with FR167653 aggravated DSS colitis in mice. This effect was accompanied by a reduction of mucosal IL-1β and TNF-α expression, suggesting a role of p38 mitogen-activated protein kinase (MAPK)-mediated proinflammatory cytokine induction in host defense mechanisms.

  5. MDA-5 activation by cytoplasmic double-stranded RNA impairs endothelial function and aggravates atherosclerosis.

    Science.gov (United States)

    Asdonk, Tobias; Steinmetz, Martin; Krogmann, Alexander; Ströcker, Christine; Lahrmann, Catharina; Motz, Inga; Paul-Krahe, Kathrin; Flender, Anna; Schmitz, Theresa; Barchet, Winfried; Hartmann, Gunther; Nickenig, Georg; Zimmer, Sebastian

    2016-09-01

    Recent studies have highlighted the relevance of viral nucleic acid immunorecognition by pattern recognition receptors in atherogenesis. Melanoma differentiation associated gene 5 (MDA-5) belongs to the intracellular retinoic acid inducible gene-I like receptors and its activation promotes pro-inflammatory mechanisms. Here, we studied the effect of MDA-5 stimulation in vascular biology. To gain insights into MDA-5 dependent effects on endothelial function, cultured human coronary artery endothelial cells (HCAEC) were transfected with the synthetic MDA-5 agonist polyIC (long double-stranded RNA). Human coronary endothelial cell expressed MDA-5 and reacted with receptor up-regulation upon stimulation. Reactive oxygen species formation, apoptosis and the release of pro-inflammatory cytokines was enhanced, whereas migration was significantly reduced in response to MDA-5 stimulation. To test these effects in vivo, wild-type mice were transfected with 32.5 μg polyIC/JetPEI or polyA/JetPEI as control every other day for 7 days. In polyIC-treated wild-type mice, endothelium-dependent vasodilation and re-endothelialization was significantly impaired, vascular oxidative stress significantly increased and circulating endothelial microparticles and circulating endothelial progenitor cells significantly elevated compared to controls. Importantly, these effects could be abrogated by MDA-5 deficiency in vivo. Finally, chronic MDA-5 stimulation in Apolipoprotein E/toll-like receptor 3 (TLR3) double(-) deficient (ApoE(-/-) /TLR3(-/-) ) mice-enhanced atherosclerotic plaque formation. This study demonstrates that MDA-5 stimulation leads to endothelial dysfunction, and has the potential to aggravate atherosclerotic plaque burden in murine atherosclerosis. Thus, the spectrum of relevant innate immune receptors in vascular diseases and atherogenesis might not be restricted to TLRs but also encompasses the group of RLRs including MDA-5. PMID:27130701

  6. Optimal cytoplasmatic density and flux balance model under macromolecular crowding effects.

    Science.gov (United States)

    Vazquez, Alexei

    2010-05-21

    Macromolecules occupy between 34% and 44% of the cell cytoplasm, about half the maximum packing density of spheres in three dimension. Yet, there is no clear understanding of what is special about this value. To address this fundamental question we investigate the effect of macromolecular crowding on cell metabolism. We develop a cell scale flux balance model capturing the main features of cell metabolism at different nutrient uptakes and macromolecular densities. Using this model we show there are two metabolic regimes at low and high nutrient uptakes. The latter regime is characterized by an optimal cytoplasmatic density where the increase of reaction rates by confinement and the decrease by diffusion slow-down balance. More important, the predicted optimal density is in the range of the experimentally determined density of Escherichia coli.

  7. (Questions)n on phloem biology. 2. Mass flow, molecular hopping, distribution patterns and macromolecular signalling.

    Science.gov (United States)

    van Bel, Aart J E; Furch, Alexandra C U; Hafke, Jens B; Knoblauch, Michael; Patrick, John W

    2011-10-01

    This review speculates on correlations between mass flow in sieve tubes and the distribution of photoassimilates and macromolecular signals. Since micro- (low-molecular compounds) and macromolecules are withdrawn from, and released into, the sieve-tube sap at various rates, distribution patterns of these compounds do not strictly obey mass-flow predictions. Due to serial release and retrieval transport steps executed by sieve tube plasma membranes, micromolecules are proposed to "hop" between sieve element/companion cell complexes and phloem parenchyma cells under source-limiting conditions (apoplasmic hopping). Under sink-limiting conditions, micromolecules escape from sieve tubes via pore-plasmodesma units and are temporarily stored. It is speculated that macromolecules "hop" between sieve elements and companion cells using plasmodesmal trafficking mechanisms (symplasmic hopping). We explore how differential tagging may influence distribution patterns of macromolecules and how their bidirectional movement could arise. Effects of exudation techniques on the macromolecular composition of sieve-tube sap are discussed. PMID:21889037

  8. PIMADb: A Database of Protein–Protein Interactions in Huge Macromolecular Assemblies

    Science.gov (United States)

    Mathew, Oommen K.; Sowdhamini, Ramanathan

    2016-01-01

    Protein–protein interactions play a very important role in the process of cellular functionality. Intricate details about the interactions between the proteins in a macromolecular assembly are important to understand the function and significance of protein complexes. We are reporting about a database of protein–protein interactions in huge macromolecular assemblies (PIMADb) that records the intrinsic details of 189,532 interchain interactions in 40,049 complexes from the Protein Data Bank. These details include the results of the quantification and analysis of all the interactions in the complex. The availability of interprotomer interaction networks can enable the design of point mutation experiments. PIMADb can be accessed from the URL: http://caps.ncbs.res.in/pimadb PMID:27478368

  9. Romp: The Method of Choice for Precise Macromolecular Engineering and Synthesis of Smart Materials

    Science.gov (United States)

    Khosravi, Ezat; Castle, Thomas C.; Kujawa, Margaret; Leejarkpai, Jan; Hutchings, Lian R.; Hine, Peter J.

    The recent advances in olefin metathesis highlight the impact of Ring Opening Metathesis Polymerisation (ROMP) as a powerful technique for macromolecular engineering and synthesis of smart materials with well-defined structures. ROMP has attracted a considerable research attention recently particularly by industry largely due to the development of well-defined metal complexes as initiators and also because of the award of the Noble Prize for Chemistry in 2005 to three scientists (Chauvin, Grubbs, Schrock) for their contributions in this area. This chapter discusses several interesting examples in order to demonstrate that ROMP is a power tool in macromolecular engineering and that it allows the design and synthesis of polymers with novel topologies.

  10. The macromolecular crystallography beamline I911-3 at the MAX IV laboratory

    Energy Technology Data Exchange (ETDEWEB)

    Ursby, Thomas, E-mail: thomas.ursby@maxlab.lu.se; Unge, Johan; Appio, Roberto [Lund University, POB 118, Lund SE-221 00 (Sweden); Logan, Derek T. [Lund University, POB 124, Lund SE-221 00 (Sweden); Fredslund, Folmer; Svensson, Christer; Larsson, Krister; Labrador, Ana [Lund University, POB 118, Lund SE-221 00 (Sweden); Thunnissen, Marjolein M. G. M. [Lund University, POB 124, Lund SE-221 00 (Sweden)

    2013-07-01

    The updated macromolecular crystallography beamline I911-3 at the MAX II storage ring is described. The macromolecular crystallography beamline I911-3, part of the Cassiopeia/I911 suite of beamlines, is based on a superconducting wiggler at the MAX II ring of the MAX IV Laboratory in Lund, Sweden. The beamline is energy-tunable within a range between 6 and 18 keV. I911-3 opened for users in 2005. In 2010–2011 the experimental station was completely rebuilt and refurbished such that it has become a state-of-the-art experimental station with better possibilities for rapid throughput, crystal screening and work with smaller samples. This paper describes the complete I911-3 beamline and how it is embedded in the Cassiopeia suite of beamlines.

  11. 3DEM Loupe: Analysis of macromolecular dynamics using structures from electron microscopy.

    Science.gov (United States)

    Nogales-Cadenas, R; Jonic, S; Tama, F; Arteni, A A; Tabas-Madrid, D; Vázquez, M; Pascual-Montano, A; Sorzano, C O S

    2013-07-01

    Electron microscopy (EM) provides access to structural information of macromolecular complexes in the 3-20 Å resolution range. Normal mode analysis has been extensively used with atomic resolution structures and successfully applied to EM structures. The major application of normal modes is the identification of possible conformational changes in proteins. The analysis can throw light on the mechanism following ligand binding, protein-protein interactions, channel opening and other functional macromolecular movements. In this article, we present a new web server, 3DEM Loupe, which allows normal mode analysis of any uploaded EM volume using a user-friendly interface and an intuitive workflow. Results can be fully explored in 3D through animations and movies generated by the server. The application is freely available at http://3demloupe.cnb.csic.es.

  12. Drug-Free Macromolecular Therapeutics--A New Paradigm in Polymeric Nanomedicines.

    Science.gov (United States)

    Chu, Te-Wei; Kopeček, Jindřich

    2015-07-01

    This review highlights a unique research area in polymer-based nanomedicine designs. Drug-free macromolecular therapeutics induce apoptosis of malignant cells by the crosslinking of surface non-internalizing receptors. The receptor crosslinking is mediated by the biorecognition of high-fidelity natural binding motifs (such as antiparallel coiled-coil peptides or complementary oligonucleotides) that are grafted to the side chains of polymers or attached to targeting moieties against cell receptors. This approach features the absence of low-molecular-weight cytotoxic compounds. Here, we summarize the rationales, different designs, and advantages of drug-free macromolecular therapeutics. Recent developments of novel therapeutic systems for B-cell lymphomas are discussed, as well as relevant approaches for other diseases. We conclude by pointing out various potential future directions in this exciting new field. PMID:26191406

  13. Amorphous silica nanoparticles size-dependently aggravate atopic dermatitis-like skin lesions following an intradermal injection

    Directory of Open Access Journals (Sweden)

    Hirai Toshiro

    2012-02-01

    Full Text Available Abstract Background Due to the rising use of nanomaterials (NMs, there is concern that NMs induce undesirable biological effects because of their unique physicochemical properties. Recently, we reported that amorphous silica nanoparticles (nSPs, which are one of the most widely used NMs, can penetrate the skin barrier and induce various biological effects, including an immune-modulating effect. Thus, it should be clarified whether nSPs can be a risk factor for the aggravation of skin immune diseases. Thus, in this study, we investigated the relationship between the size of SPs and adjuvant activity using a model for atopic dermatitis. Results We investigated the effects of nSPs on the AD induced by intradermaly injected-mite antigen Dermatophagoides pteronyssinus (Dp in NC/Nga mice. Ear thickness measurements and histopathological analysis revealed that a combined injection of amorphous silica particles (SPs and Dp induced aggravation of AD in an SP size-dependent manner compared to that of Dp alone. In particular, aggravation was observed remarkably in nSP-injected groups. Furthermore, these effects were correlated with the excessive induction of total IgE and a stronger systemic Th2 response. We demonstrated that these results are associated with the induction of IL-18 and thymic stromal lymphopoietin (TSLP in the skin lesions. Conclusions A particle size reduction in silica particles enhanced IL-18 and TSLP production, which leads to systemic Th2 response and aggravation of AD-like skin lesions as induced by Dp antigen treatment. We believe that appropriate regulation of nanoparticle physicochemical properties, including sizes, is a critical determinant for the design of safer forms of NMs.

  14. Cathepsin K Deficiency Prevents the Aggravated Vascular Remodeling Response to Flow Cessation in ApoE-/- Mice

    OpenAIRE

    Marjo M P C Donners; Bai, Lili; Lutgens, Suzanne P. M.; Wijnands, Erwin; Johnson, Jason; Schurgers, Leon J.; Liu, Cong-Lin; Daemen, Mat; Cleutjens, Kitty B.J.M.; Shi, Guo-Ping; BIESSEN, Erik; Heeneman, Sylvia

    2016-01-01

    Cathepsin K (catK) is a potent lysosomal cysteine protease involved in extracellular matrix (ECM) degradation and inflammatory remodeling responses. Here we have investigated the contribution of catK deficiency on carotid arterial remodeling in response to flow cessation in apoE-/- and wild type (wt) background. Ligation-induced hyperplasia is considerably aggravated in apoE-/- versus wt mice. CatK protein expression was significantly increased in neointimal lesions of apoE-/- compared with w...

  15. A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces

    OpenAIRE

    Y. C. ZHOU; Holst, Michael; McCammon, J. Andrew

    2010-01-01

    In this paper we propose a nonlinear elasticity model of macromolecular conformational change (deformation) induced by electrostatic forces generated by an implicit solvation model. The Poisson-Boltzmann equation for the electrostatic potential is analyzed in a domain varying with the elastic deformation of molecules, and a new continuous model of the electrostatic forces is developed to ensure solvability of the nonlinear elasticity equations. We derive the estimates of electrostatic forces ...

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

    OpenAIRE

    Kumar, Pramod; Satyam, Abhigyan; Fan, Xingliang; Rodriguez, Brian J.; et al

    2015-01-01

    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 regulate...

  17. From “Simple” DNA-Protein Interactions to the Macromolecular Machines of Gene Expression

    OpenAIRE

    von Hippel, Peter H.

    2007-01-01

    The physicochemical concepts that underlie our present ideas on the structure and assembly of the “macromolecular machines of gene expression” are developed, starting with the structure and folding of the individual protein and DNA components, the thermodynamics and kinetics of their conformational rearrangements during complex assembly, and the molecular basis of the sequence specificity and recognition interactions of the final assemblies that include the DNA genome. The role of diffusion i...

  18. STUDY ON HYDROLYSIS OF MACROMOLECULAR GELATIN WITH ENZYMES IN COMBINATION MODE

    Institute of Scientific and Technical Information of China (English)

    Ya-qin Huang; Rui Guan; Ming-zhi Huang

    2004-01-01

    The enzymatic hydrolysis of macromolecular gelatin with AS1.398 neutral protease, bromelain and their combinations was studied by estimating the molecular weights of their hydrolytic products. It was discovered that the products hydrolyzed by using combination enzymes had lower molecular weight than those obtained by using single ones,and the kind of enzymes, their combination mode and addition sequence are effective ways to control the molecular weights of gelatin hydrolyzates.

  19. Nur77 exacerbates PC12 cellular injury in vitro by aggravating mitochondrial impairment and endoplasmic reticulum stress

    Science.gov (United States)

    Gao, Huimin; Chen, Zhaoyu; Fu, Yongmei; Yang, Xiaoyan; Weng, Ruihui; Wang, Rui; Lu, Jianjun; Pan, Mengqiu; Jin, Kunlin; McElroy, Chris; Tang, Beisha; Xia, Ying; Wang, Qing

    2016-01-01

    The nuclear orphan receptor, Nur77 plays important roles in neuroimflammation, apoptosis, and dopaminergic neurodegeneration. We conducted a further mechanistic investigation into the association of Nur77 with cell death. Cytosporone B (Csn-B), an agonist for Nur77, and Nur77 knockdown were adopted in the 6-hydroxydopamine (OHDA)-lesioned PC12 cells to investigate the mechanisms underlying Nur77-mediated injury. The 6-OHDA incubation caused Nur77 translocation from the nucleus to cytosol and Endoplasm reticulum (ER) and induced co-localization of Tom20/Nur77 and Protein Disulfide Isomerase (PDI)/Nur77. Nur77 activation further decreased cell viability, aggravated intracellular LDH release, intracellular Ca2+, ROS levels, apoptosis, ER tress and, mitochondrial transmembrane potential (ΔΨm) decline. In addition, Nur77 activation significantly enhanced the efficiency of autophagy as indicated by an up-regulation of Beclin-1/LC-3 and downregulation of p62, and aggravated mitochondrial dysfunctions and ER stress as shown by increased HSP60/Cytochrome C (Cyt C) and CHOP-ATF3 levels respectively. These changes could be partially reversed by Nur77 knockdown. Moreover, Nur77 activation upregulated PINK1 and downregulated Parkin levels. We conclude that Nur77 exacerbates PC12 cell death at least partially by aggravating the mitochondrial impairment and ER stress and enhancing autophagy. We propose that Nur77 is likely a critical target in the PD therapy. PMID:27679973

  20. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination.

    Science.gov (United States)

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    2013-11-01

    The number of macromolecular structures deposited in the Protein Data Bank now approaches 100,000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation.

  1. A smooth and differentiable bulk-solvent model for macromolecular diffraction

    International Nuclear Information System (INIS)

    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, Rfree 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

  2. 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. PMID:27124275

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

    Directory of Open Access Journals (Sweden)

    Tatiana Maximova

    2016-04-01

    Full Text Available 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.

  4. Loss of p120 catenin aggravates alveolar edema of ventilation induced lung injury

    Institute of Scientific and Technical Information of China (English)

    DAI Chen-yang; DAI Guo-feng; SUN Yu; WANG Yue-lan

    2013-01-01

    Background p120 catenin (p120ctn) is an adheren junction protein that regulates barrier function,but its role has not been explored in alveolar edema induced by ventilation.We measured stretch-induced cell gap formation in MLE 12 cells due to the loss of p120.We hypothesized that alveolar permeability was increased by high lung inflation associated with alveolar epithelia cell tight junctions being destroyed,which resulted from the loss of p120.Methods Cultured MLE12 cells were subjected to being stretched or un-stretched (control) and some cells were pretreated with pp2 (c-src inhibitor).After the end of stretching for 0,1,2,and 4 hours,the cells were lysed,and p120 expression and c-src activation was determined by Western blotting analysis.In vivo,SD rats were taken to different tidal volumes (Vt 7 ml/kg or 40 ml/kg,PEEP=0,respiratory rate 30-40 betas/min) for 0,1,2,and 4 hour and some were pretreated with pp2,and alveolar edema was calculated.Rerults It was found that p120 expression was reduced and c-src activation increased in a time-dependent and strain-dependent manner due to cyclic-stretch of the alveolar epithelial cells.These changes could be reversed by inhibition of c-src.We obtained similar changes in rats when they were subjected to large tidal volumes and the alveolar edema increased more than in rats in the low Vt group.Pretreated the rats with inhibition of c-src had less pulmonary edema induced by the high tidal volume ventilation.Conclusions Cyclic stretch MLE 12 cells induced the loss of p120 and may be the same reason by high tidal volume ventilation in rats can aggravate alveolar edema.Maintenance of p120 expression may be a novel therapeutic strategy for the prevention and treatment of ventilation induced lung injury (VILI).

  5. RGD-tagged helical rosette nanotubes aggravate acute lipopolysaccharide-induced lung inflammation

    Directory of Open Access Journals (Sweden)

    Suri SS

    2011-12-01

    Full Text Available Sarabjeet Singh Suri1, Steven Mills1, Gurpreet Kaur Aulakh1, Felaniaina Rakotondradany2, Hicham Fenniri2, Baljit Singh11Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon; 2National Institute for Nanotechnology and Department of Chemistry, Edmonton, CanadaAbstract: Rosette nanotubes (RNT are a novel class of self-assembled biocompatible nanotubes that offer a built-in strategy for engineering structure and function through covalent tagging of synthetic self-assembling modules (G∧C motif. In this report, the G∧C motif was tagged with peptide Arg-Gly-Asp-Ser-Lys (RGDSK-G∧C and amino acid Lys (K-G∧C which, upon co-assembly, generate RNTs featuring RGDSK and K on their surface in predefined molar ratios. These hybrid RNTs, referred to as Kx/RGDSKy-RNT, where x and y refer to the molar ratios of K-G∧C and RGDSK–G∧C, were designed to target neutrophil integrins. A mouse model was used to investigate the effects of intravenous Kx/RGDSKy-RNT on acute lipopolysaccharide (LPS-induced lung inflammation. Healthy male C57BL/6 mice were treated intranasally with Escherichia coli LPS 80 µg and/or intravenously with K90/RGDSK10-RNT. Here we provide the first evidence that intravenous administration of K90/RGDSK10-RNT aggravates the proinflammatory effect of LPS in the mouse. LPS and K90/RGDSK10-RNT treatment groups showed significantly increased infiltration of polymorphonuclear cells in bronchoalveolar lavage fluid at all time points compared with the saline control. The combined effect of LPS and K90/RGDSK10-RNT was more pronounced than LPS alone, as shown by a significant increase in the expression of interleukin-1ß, MCP-1, MIP-1, and KC-1 in the bronchoalveolar lavage fluid and myeloperoxidase activity in the lung tissues. We conclude that K90/RGDSK10-RNT promotes acute lung inflammation, and when used along with LPS, leads to exaggerated immune response in the lung.Keywords: RGD peptide, helical rosette

  6. A case of aggravation of hemolytic anemia, elevated liver enzymes and low platelet count syndrome after delivery

    Institute of Scientific and Technical Information of China (English)

    JIANG Yuan-hui; WANG Yong-qing; WANG Jing; YE Rong-hua

    2011-01-01

    Background Hemolytic anemia, elevated liver enzymes and low platelet count (HELLP) syndrome is a severe obstetric complication which usually resolves in most patients after delivery.Methods We report a rare case of aggravation of HELLP syndrome after delivery.Results The patient underwent the treatment for HELLP syndrome,.including glucocorticoid therapy. The symptoms of HELLP syndrome reappeared and became more severe than before the termination of pregnancy. The patient also had severe and persistent hypoproteinemia, hyponatremia and hypocalcemia.Conclusions HELLP syndrome is an acute and critical obstetric syndrome which can have heterogeneous presentations and variable prognosis. We should be fully aware of the diverse clinical characteristics of this condition.

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

    Science.gov (United States)

    Coquel, Anne-Sophie; Jacob, Jean-Pascal; Primet, Mael; Demarez, Alice; Dimiccoli, Mariella; Julou, Thomas; Moisan, Lionel; Lindner, Ariel B; Berry, Hugues

    2013-04-01

    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 macromolecular

  8. 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

  9. D3, the new diffractometer for the macromolecular crystallography beamlines of the Swiss Light Source

    Energy Technology Data Exchange (ETDEWEB)

    Fuchs, Martin R., E-mail: mfuchs@bnl.gov [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Brookhaven National Laboratory, Mail Stop 745, Upton, NY 11973 (United States); Pradervand, Claude; Thominet, Vincent; Schneider, Roman; Panepucci, Ezequiel; Grunder, Marcel; Gabadinho, Jose; Dworkowski, Florian S. N.; Tomizaki, Takashi; Schneider, Jörg; Mayer, Aline; Curtin, Adrian; Olieric, Vincent; Frommherz, Uli; Kotrle, Goran; Welte, Jörg; Wang, Xinyu; Maag, Stephan [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland); Schulze-Briese, Clemens [DECTRIS Ltd, Neuenhoferstrasse 107, 5400 Baden (Switzerland); Wang, Meitian [Paul Scherrer Institute, 5232 Villigen PSI (Switzerland)

    2014-02-04

    A new diffractometer for microcrystallography has been developed for the three macromolecular crystallography beamlines of the Swiss Light Source. A new diffractometer for microcrystallography has been developed for the three macromolecular crystallography beamlines of the Swiss Light Source. Building upon and critically extending previous developments realised for the high-resolution endstations of the two undulator beamlines X06SA and X10SA, as well as the super-bend dipole beamline X06DA, the new diffractometer was designed to the following core design goals. (i) Redesign of the goniometer to a sub-micrometer peak-to-peak cylinder of confusion for the horizontal single axis. Crystal sizes down to at least 5 µm and advanced sample-rastering and scanning modes are supported. In addition, it can accommodate the new multi-axis goniometer PRIGo (Parallel Robotics Inspired Goniometer). (ii) A rapid-change beam-shaping element system with aperture sizes down to a minimum of 10 µm for microcrystallography measurements. (iii) Integration of the on-axis microspectrophotometer MS3 for microscopic sample imaging with 1 µm image resolution. Its multi-mode optical spectroscopy module is always online and supports in situ UV/Vis absorption, fluorescence and Raman spectroscopy. (iv) High stability of the sample environment by a mineral cast support construction and by close containment of the cryo-stream. Further features are the support for in situ crystallization plate screening and a minimal achievable detector distance of 120 mm for the Pilatus 6M, 2M and the macromolecular crystallography group’s planned future area detector Eiger 16M.

  10. 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.

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

    Science.gov (United States)

    Ó Conchúir, Shane; Barlow, Kyle A; Pache, Roland A; Ollikainen, Noah; Kundert, Kale; O'Meara, Matthew J; Smith, Colin A; Kortemme, Tanja

    2015-01-01

    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.

  12. The "macromolecular tourist": universal temperature dependence of thermal diffusion in aqueous colloidal suspensions.

    Science.gov (United States)

    Iacopini, S; Rusconi, R; Piazza, R

    2006-01-01

    By performing measurements on a large class of macromolecular and colloidal systems, we show that thermophoresis (particle drift induced by thermal gradients) in aqueous solvents displays a distinctive universal dependence on temperature. For systems of particles interacting via temperature-independent forces, this behavior is strictly related to the solvent thermal expansivity, while an additional, T-independent term is needed to account for the behavior of "thermophilic" (migrating to the warmth) particles. The former relation between thermophoresis and thermal expansion may be exploited to envisage other fruitful studies of colloidal diffusion in inhomogeneous fluids. PMID:16446985

  13. INFLUENCE OF THE SOLVENT SWELLING ON MACROMOLECULAR CHOLESTERIC LIQUID CRYSTALLINE STRUCTURE

    Institute of Scientific and Technical Information of China (English)

    Jia Zeng; Yong Huang

    1999-01-01

    Ethyl-cyanoethyl cellulose [(E-CE)C]/cross-linked polyacrylic acid [PAA] molecular composites with cholesteric order were prepared. It was found that the macromolecular cholesteric structure was changed with the swelling of PAA in the composites. The selective reflection of the cholesteric phase shifted to the longer wavelength and the X-ray diffraction angle shifted to the high angle direction during swelling, which suggested that the cholesteric pitch and the number of the layers of ordered (E-CE)C chains in the cholesteric phase were increased.

  14. Relations between functionality and macromolecular properties of alterated coals: the behaviour in solubility and swelling

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsov, P.N.; Gruber, R.; Bimer, J.; Salbut, P.D.; Djega-Mariadassou, G.; Kruchinin, A.V.; Kuznetsova, L.I. [Institute of Chemistry and Chemico-Metallurgical Processes, Krasnoyarsk (Russian Federation)

    1995-12-31

    Describes the study of the effects of chemical alteration of brown and bituminous coals on the solubility and swelling behaviour. A variety of chemical procedures such as ion-exchange with HCl, O-methylation and reductive methylation, reduction with LiAlH{sub 4} and with K/isopropanol in THF and oxidation with performic acid was applied in order to vary the oxygen functionality, the content of the alkyl substitutes and the proportion of aromatic to hydroaromatic rings. The extent of degradation of the macromolecular structure was evaluated as a function of chemical alteration. 6 refs., 2 tabs.

  15. Chirality as a physical aspect of structure formation in biological macromolecular systems

    Science.gov (United States)

    Malyshko, E. V.; Tverdislov, V. A.

    2016-08-01

    A novel regularity of hierarchical structures is found in the formation of chiral biological macromolecular systems. The formation of structures with alternating chirality (helical structures) serves as an instrument of stratification. The ability of a carbon atom to form chiral compounds is an important factor that determined the carbon basis of living systems on the Earth as well as their development through a series of chiral bifurcations. In the course of biological evolution, the helical structures became basic elements of the molecular machines in the cell. The discreteness of structural levels allowed the mechanical degrees of freedom formation in the molecular machines in the cell.

  16. Oral Candida as an aggravating factor of mucositis Induced by radiotherapy; Candida Oral como fator agravante da mucosite radioinduzida

    Energy Technology Data Exchange (ETDEWEB)

    Simoes, Cristiane Araujo; Castro, Jurema Freire Lisboa de; Cazal, Claudia [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil). Dept. de odontologia

    2011-07-01

    Antineoplastic treatment induces some undesirable consequences in head and neck cancer patients. Often, the emergence of major clinical manifestations, such as oral mucositis, results in temporary interruption of the treatment, decreasing the patients' quality of life, and increasing hospital costs. Radio-induced or chemo-induced oral mucositis is possibly aggravated by opportunist fungal infections, which turn the mucositis more resistant to the conventional treatments. Objective: this study aims to identify the presence of Candida sp. as a possible aggravating factor of oral mucositis in patients with head and neck cancer under antineoplastic treatment. Method: all patients with radio- or chemo-induced oral mucositis from the Cancer Hospital of Pernambuco, treated between October 2008 and April 2009, were selected for the study. The prevalence of Candida sp was measured through the cytological analysis of oral mucosa in patients with oral mucositis. The fungal presence was correlated with the mucositis severity. Results: the results showed a positive association between fungal colonization and more several lesions (degrees III and IV of mucositis). Conclusion: The outcomes shown may contribute to a solution for unconventional mucosites, which do not respond to the usual treatment. (author)

  17. Acrolein, a highly toxic aldehyde generated under oxidative stress in vivo, aggravates the mouse liver damage after acetaminophen overdose.

    Science.gov (United States)

    Arai, Tomoya; Koyama, Ryo; Yuasa, Makoto; Kitamura, Daisuke; Mizuta, Ryushin

    2014-01-01

    Although acetaminophen-induced liver injury in mice has been extensively studied as a model of human acute drug-induced hepatitis, the mechanism of liver injury remains unclear. Liver injury is believed to be initiated by metabolic conversion of acetaminophen to the highly reactive intermediate N-acetyl p-benzoquinoneimine, and is aggravated by subsequent oxidative stress via reactive oxygen species (ROS), including hydrogen peroxide (H2O2) and the hydroxyl radical (•OH). In this study, we found that a highly toxic unsaturated aldehyde acrolein, a byproduct of oxidative stress, has a major role in acetaminophen-induced liver injury. Acetaminophen administration in mice resulted in liver damage and increased acrolein-protein adduct formation. However, both of them were decreased by treatment with N-acetyl-L-cysteine (NAC) or sodium 2-mercaptoethanesulfonate (MESNA), two known acrolein scavengers. The specificity of NAC and MESNA was confirmed in cell culture, because acrolein toxicity, but not H2O2 or •OH toxicity, was inhibited by NAC and MESNA. These results suggest that acrolein may be more strongly correlated with acetaminophen-induced liver injury than ROS, and that acrolein produced by acetaminophen-induced oxidative stress can spread from dying cells at the primary injury site, causing damage to the adjacent cells and aggravating liver injury.

  18. Macromolecular liquids

    Energy Technology Data Exchange (ETDEWEB)

    Safinya, C.R.; Safran, S.A. (Exxon Research and Engineering Co., Annandale, NJ (US)); Pincus, P.A. (Univ. of California at Santa Barbara, Santa Barbara, CA (US))

    1990-01-01

    Liquids include a broad range of material systems which are of high scientific and technological interest. Generally speaking, these are partially ordered or disordered phases where the individual molecular species have organized themselves on length scales which are larger than simple fluids, typically between 10 Angstroms and several microns. The specific systems reported on in this book include membranes, microemulsions, micelles, liquid crystals, colloidal suspensions, and polymers. They have a major impact on a broad spectrum of technological industries such as displays, plastics, soap and detergents, chemicals and petroleum, and pharmaceuticals.

  19. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Amninder S Virk

    2015-02-01

    Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  20. 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.

  1. Influence of macromolecular architecture on necking in polymer extrusion film casting process

    International Nuclear Information System (INIS)

    Extrusion film casting (EFC) is an important polymer processing technique that is used to produce several thousand tons of polymer films/coatings on an industrial scale. In this research, we are interested in understanding quantitatively how macromolecular chain architecture (for example long chain branching (LCB) or molecular weight distribution (MWD or PDI)) influences the necking and thickness distribution of extrusion cast films. We have used different polymer resins of linear and branched molecular architecture to produce extrusion cast films under controlled experimental conditions. The necking profiles of the films were imaged and the velocity profiles during EFC were monitored using particle tracking velocimetry (PTV) technique. Additionally, the temperature profiles were captured using an IR thermography and thickness profiles were calculated. The experimental results are compared with predictions of one-dimensional flow model of Silagy et al1 wherein the polymer resin rheology is modeled using molecular constitutive equations such as the Rolie-Poly (RP) and extended Pom Pom (XPP). We demonstrate that the 1-D flow model containing the molecular constitutive equations provides new insights into the role of macromolecular chain architecture on film necking.1D. Silagy, Y. Demay, and J-F. Agassant, Polym. Eng. Sci., 36, 2614 (1996)

  2. Oral delivery of macromolecular drugs: Where we are after almost 100years of attempts.

    Science.gov (United States)

    Moroz, Elena; Matoori, Simon; Leroux, Jean-Christophe

    2016-06-01

    Since the first attempt to administer insulin orally in humans more than 90years ago, the oral delivery of macromolecular drugs (>1000g/mol) has been rather disappointing. Although several clinical pilot studies have demonstrated that the oral absorption of macromolecules is possible, the bioavailability remains generally low and variable. This article reviews the formulations and biopharmaceutical aspects of orally administered biomacromolecules on the market and in clinical development for local and systemic delivery. The most successful approaches for systemic delivery often involve a combination of enteric coating, protease inhibitors and permeation enhancers in relatively high amounts. However, some of these excipients have induced local or systemic adverse reactions in preclinical and clinical studies, and long-term studies are often missing. Therefore, strategies aimed at increasing the oral absorption of macromolecular drugs should carefully take into account the benefit-risk ratio. In the absence of specific uptake pathways, small and potent peptides that are resistant to degradation and that present a large therapeutic window certainly represent the best candidates for systemic absorption. While we acknowledge the need for systemically delivering biomacromolecules, it is our opinion that the oral delivery to local gastrointestinal targets is currently more promising because of their accessibility and the lacking requirement for intestinal permeability enhancement. PMID:26826437

  3. An Efficient Low Storage and Memory Treatment of Gridded Interaction Fields for Simulations of Macromolecular Association.

    Science.gov (United States)

    Ozboyaci, Musa; Martinez, Michael; Wade, Rebecca C

    2016-09-13

    Computer simulations of molecular systems often make use of regular rectangular grids with equidistant spacing to store information on their molecular interaction fields, e.g., electrostatic potential. These grids provide an easy way to store the data as they do not require any particular specification of the structure of the data. However, such grids may easily become large, and the storage and memory demands may become so high that calculations become infeasible. To overcome this problem, we show here how the data structure DT-Grid can be adapted and applied to efficiently represent macromolecular interaction grids by exploiting the nonuniformity of information on the grid; at the same time, this data structure ensures fast random data access. We demonstrate use of the DT-Grid data structure for potential of mean force and Brownian dynamics simulations of protein-surface binding and macromolecular association with the SDA software. We further demonstrate that the DT-Grid structure enables systems of large size, such as a viral capsid, and high resolution grids to be handled that are beyond current computational feasibility. PMID:27463233

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

    Science.gov (United States)

    Gabadinho, José; Beteva, Antonia; Guijarro, Matias; Rey-Bakaikoa, Vicente; Spruce, Darren; Bowler, Matthew W; Brockhauser, Sandor; Flot, David; Gordon, Elspeth J; Hall, David R; Lavault, Bernard; McCarthy, Andrew A; McCarthy, Joanne; Mitchell, Edward; Monaco, Stéphanie; Mueller-Dieckmann, Christoph; Nurizzo, Didier; Ravelli, Raimond B G; Thibault, Xavier; Walsh, Martin A; Leonard, Gordon A; McSweeney, Sean M

    2010-09-01

    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.

  5. Oral delivery of macromolecular drugs: Where we are after almost 100years of attempts.

    Science.gov (United States)

    Moroz, Elena; Matoori, Simon; Leroux, Jean-Christophe

    2016-06-01

    Since the first attempt to administer insulin orally in humans more than 90years ago, the oral delivery of macromolecular drugs (>1000g/mol) has been rather disappointing. Although several clinical pilot studies have demonstrated that the oral absorption of macromolecules is possible, the bioavailability remains generally low and variable. This article reviews the formulations and biopharmaceutical aspects of orally administered biomacromolecules on the market and in clinical development for local and systemic delivery. The most successful approaches for systemic delivery often involve a combination of enteric coating, protease inhibitors and permeation enhancers in relatively high amounts. However, some of these excipients have induced local or systemic adverse reactions in preclinical and clinical studies, and long-term studies are often missing. Therefore, strategies aimed at increasing the oral absorption of macromolecular drugs should carefully take into account the benefit-risk ratio. In the absence of specific uptake pathways, small and potent peptides that are resistant to degradation and that present a large therapeutic window certainly represent the best candidates for systemic absorption. While we acknowledge the need for systemically delivering biomacromolecules, it is our opinion that the oral delivery to local gastrointestinal targets is currently more promising because of their accessibility and the lacking requirement for intestinal permeability enhancement.

  6. Influence of macromolecular architecture on necking in polymer extrusion film casting process

    Energy Technology Data Exchange (ETDEWEB)

    Pol, Harshawardhan; Banik, Sourya; Azad, Lal Busher; Doshi, Pankaj; Lele, Ashish [CSIR-National Chemical Laboratory, Pune, Maharashtra (India); Thete, Sumeet [Purdue University, West Lafayette, Indiana (United States)

    2015-05-22

    Extrusion film casting (EFC) is an important polymer processing technique that is used to produce several thousand tons of polymer films/coatings on an industrial scale. In this research, we are interested in understanding quantitatively how macromolecular chain architecture (for example long chain branching (LCB) or molecular weight distribution (MWD or PDI)) influences the necking and thickness distribution of extrusion cast films. We have used different polymer resins of linear and branched molecular architecture to produce extrusion cast films under controlled experimental conditions. The necking profiles of the films were imaged and the velocity profiles during EFC were monitored using particle tracking velocimetry (PTV) technique. Additionally, the temperature profiles were captured using an IR thermography and thickness profiles were calculated. The experimental results are compared with predictions of one-dimensional flow model of Silagy et al{sup 1} wherein the polymer resin rheology is modeled using molecular constitutive equations such as the Rolie-Poly (RP) and extended Pom Pom (XPP). We demonstrate that the 1-D flow model containing the molecular constitutive equations provides new insights into the role of macromolecular chain architecture on film necking.{sup 1}D. Silagy, Y. Demay, and J-F. Agassant, Polym. Eng. Sci., 36, 2614 (1996)

  7. A NEW UNSTEADY THREE DIMENSIONAL MODEL FOR MACROMOLECULAR TRANSPORT AND WATER FILTRATION ACROSS THE ARTERIAL WALL

    Institute of Scientific and Technical Information of China (English)

    黄浩; 温功碧

    2001-01-01

    A new unsteady three-dimensional convective-diffusive mathematical model for the transportation of macromolecules and water across the arterial wall was proposed . After the formation of leaky junctions due to the mitosis of endothelial cell of the arterial wall, the macromolecular transport happens surrounding the leaky cells. The arterial wall was divided into four layers: the endothelial layer, the subendothelial intima, the internal elastic lamina and the media for the convenience of research. The time-dependent concentration growth,the effect of the shape of endothelial cell and the effect of physiological parameters were analyzed. The analytical solution of velocity field and pressure field of water flow across the arterial wall were obtained; and concentration distribution of three macromolecules ; LDL,HRP and Albumin, were calculated with numerical simulation method. The new theory predicts, the maximum and distribution areas of time dependent concentration with round shape endothelial cell are both larger than that with ellipse-shape endothelial cell. The model also predicts the concentration growth is much alike that of a two-dimensional model and it shows that the concentration reaches its peak at the leaky junction where atherosclerotic formation frequently occurs and falls down rapidly in a limited area beginning from its earlier time growth to the state when macromolecular transfer approaches steadily. These predictions of the new model are in agreement with the experimental observation for the growth and concentration distribution of LDL and Albumin.

  8. 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.

  9. Errors in macromolecular synthesis after stress : a study of the possible protective role of the small heat shock proteins

    OpenAIRE

    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, a phenomenon known as thermotolerance and attributed to the presence of the heat shock proteins. The question we asked first is whether the error rate in macromolecular synthesis (transcription, RN...

  10. The Vitamine D3 Analogue (1α Hydroxyvitamin D3) Aggravates Carbon Tetrachloride-Induced Hepatotoxicity In Albino Rats

    International Nuclear Information System (INIS)

    Provitamin D, cholecalciferol, undergoes hydroxylation at the 25 and the 1α position in the liver and the kidney, respectively, before it turns into a hormonally active form regulating calcium homeostasis. The main purpose of the present study is to assess the potential of the 1α hydroxyvitamin D3 analogue to aggravate the ability of carbon tetrachloride (CCl4) to cause hepatotoxicity in albino rats. For this purpose, four groups of male albino rats, each of five, were used as follow: control group (G 1) received no treatment, CCl4 treated group (G 2) received CCl4 at a dose of 0.2 ml/100 g body weight in sunflower oil (1/1) v/v ratio two times per week for three weeks subcutaneously, 1α hydroxyvitamin D3 treated group (G 3) received a total dose of 5 ng/g body weight of 1α hydroxyvitamin D3 dissolved in propyl alcohol divided into six doses each given twice weekly for three weeks via the subcutaneous route, and CCl4 + 1α hydroxyvitamin D3 treated group (G 4) received the same dose of CCl4 and 1α hydroxyvitamin D3 concomitantly as previously described. Liver tissues from sacrificed animals were fixed in 10% formalin before sectioning and stained with eosin and hematoxyline then were examined histopathologically. Sera from control and treated animals were separated from blood and examined for ALT, AST, alkaline phosphatase and LDH levels. Serum total protein, albumin, globulin, A/G, bilirubin, creatinine, phosphorous and Ca levels were also monitored. Data from the present study showed that administration of 1α hydroxyvitamin D3 aggravated CCl4-induced hepatotoxicity as evidenced by the exacerbation of the rise in serum ALT, AST, alkaline phosphatase levels. The analogue, however, had no effect on serum liver enzymes in CCl4 untreated rats. Though, CCl4 caused significant impairment of kidney function as shown by the rise in serum creatinine and urea levels which were differentially affected by the analogue. In conclusion, the 1α hydroxyvitamin D3 compound

  11. Errors in macromolecular synthesis after stress : a study of the possible protective role of the small heat shock proteins

    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,

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

    International Nuclear Information System (INIS)

    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

  13. Macromolecular crowding meets oxygen tension in human mesenchymal stem cell culture - A step closer to physiologically relevant in vitro organogenesis

    Science.gov (United States)

    Cigognini, Daniela; Gaspar, Diana; Kumar, Pramod; Satyam, Abhigyan; Alagesan, Senthilkumar; Sanz-Nogués, Clara; Griffin, Matthew; O’Brien, Timothy; Pandit, Abhay; Zeugolis, Dimitrios I.

    2016-08-01

    Modular tissue engineering is based on the cells’ innate ability to create bottom-up supramolecular assemblies with efficiency and efficacy still unmatched by man-made devices. Although the regenerative potential of such tissue substitutes has been documented in preclinical and clinical setting, the prolonged culture time required to develop an implantable device is associated with phenotypic drift and/or cell senescence. Herein, we demonstrate that macromolecular crowding significantly enhances extracellular matrix deposition in human bone marrow mesenchymal stem cell culture at both 20% and 2% oxygen tension. Although hypoxia inducible factor - 1α was activated at 2% oxygen tension, increased extracellular matrix synthesis was not observed. The expression of surface markers and transcription factors was not affected as a function of oxygen tension and macromolecular crowding. The multilineage potential was also maintained, albeit adipogenic differentiation was significantly reduced in low oxygen tension cultures, chondrogenic differentiation was significantly increased in macromolecularly crowded cultures and osteogenic differentiation was not affected as a function of oxygen tension and macromolecular crowding. Collectively, these data pave the way for the development of bottom-up tissue equivalents based on physiologically relevant developmental processes.

  14. Force Spectroscopy of Individual Stimulus-Responsive Poly(ferrocenyldimethylsilane) Chains: Towards a Redox-Driven Macromolecular Motor

    NARCIS (Netherlands)

    Zou, Shan; Hempenius, Mark A.; Schönherr, Holger; Vancso, G. Julius

    2006-01-01

    Progress in the development of a redox-driven macromolecular motor and the characterization of its redox-mechanical cycle using electrochemical AFM-based single-molecule force spectroscopy (SMFS) is described. The elasticities of individual neutral and oxidized poly(ferrocenyldimethylsilane) (PFS) m

  15. 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.

  16. A mixed method for measuring low-frequency acoustic properties of macromolecular materials

    Institute of Scientific and Technical Information of China (English)

    LIU; Hongwei; YAO; Lei; ZHAO; Hong; ZHANG; Jichuan; XUE; Zhaohong

    2006-01-01

    A mixed method for measuring low-frequency acoustic properties of macromolecular materials is presented.The dynamic mechanical parameters of materials are first measured by using Dynamic Mechanical Thermal Apparatus(DMTA) at low frequencies,usually less than 100 Hz; then based on the Principles of Time-Temperature Super position (TTS),these parameters are extended to the frequency range that acousticians are concerned about,usually from hundreds to thousands of hertz; finally the extended dynamic mechanical parameters are transformed into acoustic parameters with the help of acoustic measurement and inverse analysis.To test the feasibility and accuracy,we measure a kind of rubber sample in DMTA and acquire the basic acoustic parameters of the sample by using this method.While applying the basic parameters to calculating characteristics of the sample in acoustic pipe,a reasonable agreement of sound absorption coefficients is obtained between the calculations and measurements in the acoustic pipe.

  17. 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...... of around 32% is measured for a pure yeast cell suspension. Thus, EPS and BSA are "competing" in being transmitted which might explain the lowered BSA transmission in the presence of yeast cells. Additionally, EPS heavily foul the membranes, leading to a 86% permeability drop and a fouling resistance 6...

  18. Whole Cell Imprinting in Sol-Gel Thin Films for Bacterial Recognition in Liquids: Macromolecular Fingerprinting

    Directory of Open Access Journals (Sweden)

    Robert Armon

    2010-03-01

    Full Text Available Thin films of organically modified silica (ORMOSILS produced by a sol-gel method were imprinted with whole cells of a variety of microorganisms in order to develop an easy and specific probe to concentrate and specifically identify these microorganisms in liquids (e.g., water. Microorganisms with various morphology and outer surface components were imprinted into thin sol-gel films. Adsorption of target microorganism onto imprinted films was facilitated by these macromolecular fingerprints as revealed by various microscopical examinations (SEM, AFM, HSEM and CLSM. The imprinted films showed high selectivity toward each of test microorganisms with high adsorption affinity making them excellent candidates for rapid detection of microorganisms from liquids.

  19. Polymer segregation under confinement: Influences of macromolecular crowding and the interaction between the polymer and crowders

    Science.gov (United States)

    Chen, Yuhao; Yu, Wancheng; Wang, Jiajun; Luo, Kaifu

    2015-10-01

    Entropy driven polymer segregation in confinements as a model for chromosome separation in bacteria has attracted wide attention; however, the effects of macromolecular crowding and the interaction between the binding protein and the newly replicated DNA on the segregation dynamics are not clear. Using Langevin dynamics simulations, we investigate the influences of crowders and the attractive interaction between the polymer and a small number of crowders on segregation of two overlapping polymers under a cylindrical confinement. We find that the segregation time increases with increasing the volume fraction of crowders due to the slower chain diffusion in crowded environments. For a fixed volume fraction of crowders, the segregation time decreases with increasing the size of crowders. Moreover, the attractive interaction between the polymer and a small number of crowders can significantly facilitate the chain segregation. These results are important for understanding the chromosome segregation in living cells.

  20. 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 (PXD002319-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].

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

    Science.gov (United States)

    Phanse, Sadhna; Wan, Cuihong; Borgeson, Blake; Tu, Fan; Drew, Kevin; Clark, Greg; Xiong, Xuejian; Kagan, Olga; Kwan, Julian; Bezginov, Alexandr; Chessman, Kyle; Pal, Swati; Cromar, Graham; Papoulas, Ophelia; Ni, Zuyao; Boutz, Daniel R; Stoilova, Snejana; Havugimana, Pierre C; Guo, Xinghua; Malty, Ramy H; Sarov, Mihail; Greenblatt, Jack; Babu, Mohan; Derry, W Brent; Tillier, Elisabeth R; Wallingford, John B; Parkinson, John; Marcotte, Edward M; Emili, Andrew

    2016-03-01

    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 (PXD002319-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]. PMID:26870755

  2. Rasta silanes: new silyl resins with novel macromolecular architecture via living free radical polymerization

    Science.gov (United States)

    Lindsley; Hodges; Filzen; Watson; Geyer

    2000-09-01

    Heating TEMPO-methyl resin with dialkylsilane styrenes affords larger resin beads via living free radical polymerization. The new silyl resins prepared by this solvent-free suspension polymerization protocol have been coined "Rasta silanes". Rasta silanes have a novel macromolecular architecture typified by long straight chain polymers bearing the silanes which emanate from the phenyl rings of a cross-linked polystyrene core. By careful selection of comonomers during the polymerization step, loading capacity, silane spacing, and the relative distance of the silane moieties from the resin core can be controlled. The consistently high-loading Rasta silane resins produced can be easily converted into either a reactive silyl chloride or triflate to subsequently anchor alcohols and phenols to the solid phase. Cleavage from the resin can be mediated by treatment with HF.pyridine, TFA solutions, or TBAF.

  3. Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.

    Science.gov (United States)

    Goh, Boon Chong; Hadden, Jodi A; Bernardi, Rafael C; Singharoy, Abhishek; McGreevy, Ryan; Rudack, Till; Cassidy, C Keith; Schulten, Klaus

    2016-07-01

    The rise of the computer as a powerful tool for model building and refinement has revolutionized the field of structure determination for large biomolecular systems. Despite the wide availability of robust experimental methods capable of resolving structural details across a range of spatiotemporal resolutions, computational hybrid methods have the unique ability to integrate the diverse data from multimodal techniques such as X-ray crystallography and electron microscopy into consistent, fully atomistic structures. Here, commonly employed strategies for computational real-space structural refinement are reviewed, and their specific applications are illustrated for several large macromolecular complexes: ribosome, virus capsids, chemosensory array, and photosynthetic chromatophore. The increasingly important role of computational methods in large-scale structural refinement, along with current and future challenges, is discussed. PMID:27145875

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

    International Nuclear Information System (INIS)

    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)

  5. Phenix - a comprehensive python-based system for macromolecular structure solution

    Energy Technology Data Exchange (ETDEWEB)

    Terwilliger, Thomas C [Los Alamos National Laboratory; Hung, Li - Wei [Los Alamos National Laboratory; Adams, Paul D [UC BERKELEY; Afonine, Pavel V [UC BERKELEY; Bunkoczi, Gabor [UNIV OF CAMBRIDGE; Chen, Vincent B [DUKE UNIV; Davis, Ian [DUKE UNIV; Echols, Nathaniel [LBNL; Headd, Jeffrey J [DUKE UNIV; Grosse Kunstleve, Ralf W [LBNL; Mccoy, Airlie J [UNIV OF CAMBRIDGE; Moriarty, Nigel W [LBNL; Oeffner, Robert [UNIV OF CAMBRIDGE; Read, Randy J [UNIV OF CAMBRIDGE; Richardson, David C [DUKE UNIV; Richardson, Jane S [DUKE UNIV; Zwarta, Peter H [LBNL

    2009-01-01

    Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages, and the repeated use of interactive three-dimensional graphics. Phenix has been developed to provide a comprehensive system for crystallographic structure solution with an emphasis on automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand, and finally the development of a framework that allows a tight integration between the algorithms.

  6. 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.

  7. Parallel macromolecular delivery and biochemical/electrochemical interface to cells employing nanostructures

    Energy Technology Data Exchange (ETDEWEB)

    McKnight, Timothy E; Melechko, Anatoli V; Griffin, Guy D; Guillorn, Michael A; Merkulov, Vladimir L; Simpson, Michael L

    2015-03-31

    Systems and methods are described for parallel macromolecular delivery and biochemical/electrochemical interface to whole cells employing carbon nanostructures including nanofibers and nanotubes. A method includes providing a first material on at least a first portion of a first surface of a first tip of a first elongated carbon nanostructure; providing a second material on at least a second portion of a second surface of a second tip of a second elongated carbon nanostructure, the second elongated carbon nanostructure coupled to, and substantially parallel to, the first elongated carbon nanostructure; and penetrating a boundary of a biological sample with at least one member selected from the group consisting of the first tip and the second tip.

  8. 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.

  9. Phase transitions of macromolecular microsphere composite hydrogels based on the stochastic Cahn–Hilliard equation

    Energy Technology Data Exchange (ETDEWEB)

    Li, Xiao, E-mail: lixiao1228@163.com; Ji, Guanghua, E-mail: ghji@bnu.edu.cn; Zhang, Hui, E-mail: hzhang@bnu.edu.cn

    2015-02-15

    We use the stochastic Cahn–Hilliard equation to simulate the phase transitions of the macromolecular microsphere composite (MMC) hydrogels under a random disturbance. Based on the Flory–Huggins lattice model and the Boltzmann entropy theorem, we develop a reticular free energy suit for the network structure of MMC hydrogels. Taking the random factor into account, with the time-dependent Ginzburg-Landau (TDGL) mesoscopic simulation method, we set up a stochastic Cahn–Hilliard equation, designated herein as the MMC-TDGL equation. The stochastic term in the equation is constructed appropriately to satisfy the fluctuation-dissipation theorem and is discretized on a spatial grid for the simulation. A semi-implicit difference scheme is adopted to numerically solve the MMC-TDGL equation. Some numerical experiments are performed with different parameters. The results are consistent with the physical phenomenon, which verifies the good simulation of the stochastic term.

  10. PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

    Science.gov (United States)

    Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

    2008-11-01

    The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/.

  11. Macromolecular Stabilization by Excluded Cosolutes: Mean Field Theory of Crowded Solutions.

    Science.gov (United States)

    Sapir, Liel; Harries, Daniel

    2015-07-14

    We propose a mean field theory to account for the experimentally determined temperature dependence of protein stabilization that emerges in solutions crowded by preferentially excluded cosolutes. Based on regular solution theory and employing the Flory-Huggins approximation, our model describes cosolutes in terms of their size, and two temperature-dependent microscopic parameters that correspond to macromolecule-cosolute and bulk solution interactions. The theory not only predicts a "depletion force" that can account for the experimentally observed stabilization of protein folding or association in the presence of excluded cosolutes but also predicts the full range of associated entropic and enthalpic components. Remarkably, depending on cosolute identity and in accordance with experiments, the theory describes entropically as well as enthalpically dominated depletion forces, even those disfavored by entropy. This emerging depletion attraction cannot be simply linked to molecular volumes. Instead, the relevant parameter is an effective volume that represents an interplay between solvent, cosolute, and macromolecular interactions. We demonstrate that the apparent depletion free energy is often accompanied by significant yet compensating entropy and enthalpy terms that, although having a net zero contribution to stabilization, can obscure the underlying molecular mechanism. This study underscores the importance of including often-neglected free energy terms that correspond to solvent-cosolute and cosolute-macromolecule interactions, which for most typical cosolutes are expected to be temperature dependent. We propose that experiments specifically aimed at resolving the temperature-dependence of cosolute exclusion from macromolecular surfaces should help reveal the full range of the underlying molecular mechanisms of the depletion force.

  12. PURY: a database of geometric restraints of hetero compounds for refinement in complexes with macromolecular structures.

    Science.gov (United States)

    Andrejasic, Miha; Praaenikar, Jure; Turk, Dusan

    2008-11-01

    The number and variety of macromolecular structures in complex with ;hetero' ligands is growing. The need for rapid delivery of correct geometric parameters for their refinement, which is often crucial for understanding the biological relevance of the structure, is growing correspondingly. The current standard for describing protein structures is the Engh-Huber parameter set. It is an expert data set resulting from selection and analysis of the crystal structures gathered in the Cambridge Structural Database (CSD). Clearly, such a manual approach cannot be applied to the vast and ever-growing number of chemical compounds. Therefore, a database, named PURY, of geometric parameters of chemical compounds has been developed, together with a server that accesses it. PURY is a compilation of the whole CSD. It contains lists of atom classes and bonds connecting them, as well as angle, chirality, planarity and conformation parameters. The current compilation is based on CSD 5.28 and contains 1978 atom classes and 32,702 bonding, 237,068 angle, 201,860 dihedral and 64,193 improper geometric restraints. Analysis has confirmed that the restraints from the PURY database are suitable for use in macromolecular crystal structure refinement and should be of value to the crystallographic community. The database can be accessed through the web server http://pury.ijs.si/, which creates topology and parameter files from deposited coordinates in suitable forms for the refinement programs MAIN, CNS and REFMAC. In the near future, the server will move to the CSD website http://pury.ccdc.cam.ac.uk/. PMID:19020347

  13. Prostacyclin inhibition by indomethacin aggravates hepatic damage and encephalopathy in rats with thioacetamide-induced fulminant hepatic failure

    Institute of Scientific and Technical Information of China (English)

    Chi-Jen Chu; Shou-Dong Lee; Ching-Chin Hsiao; Teh-Fang Wang; Cho-Yu Chan; Fa-Yauh Lee; Full-Young Chang; Yi-Chou Chen; Hui-Chun Huang; Sun-Sang Wang

    2005-01-01

    AIM: Vasodilatation and increased capillary permeability have been proposed to be involved in the pathogenesis of acute and chronic form of hepatic encephalopathy.Prostacyclin (PGI2) and nitric oxide (NO) are important contributors to hyperdynamic circulation in portal hypertensive states. Our previous study showed that chronic inhibition of NO had detrimental effects on the severity of encephalopathy in thioacetamide (TAA)-treated rats due to aggravation of liver damage. To date, there are no detailed data concerning the effects of PGI2 inhibition on the severity of hepatic encephalopathy during fulminant hepatic failure.METHODS: Male Sprague-Dawley rats weighing 300-350 g were used. Fulminant hepatic failure was induced by were divided into two groups to receive intraperitoneal saline (N/S, n = 20) for 5 d, starting 2 d before TAA administration. Severity of encephalopathy was assessed by the counts of motor activity measured with Opto-Varimex animal activity meter. Plasma tumor necrosis factor-α(TNF-α, an index of liver injury) and 6-keto-PGF1α (a metabolite of PGI2) levels were measured by enzyme-linked immunosorbent assay.RESULTS: As compared with N/S-treated rats, the mortality rate was significantly higher in rats receiving indomethacin (20% vs5%, P<0.01). Inhibition of PGI2 created detrimental effects on total movement counts (indomethacin vs N/S:438±102 vs841±145 counts/30 min, P<0.05). Rats treated with indomethacin had significant higher plasma levels of TNF-α (indomethacin vsN/S: 22±5 vs 10±1 pg/mL, P<0.05)and lower plasma levels of 6-keto-PGF1α (P<0.001), but not total bilirubin or creatinine (P>0.05), as compared with rats treated with N/S.CONCLUSION: Chronic indomethacin administration has detrimental effects on the severity of encephalopathy in TAA-treated rats and this phenomenon may be attributed to the aggravation of liver injury. This study suggests that PGI2 may provide a protective role in the development of fulminant

  14. In vitro analysis of PDZ-dependent CFTR macromolecular signaling complexes.

    Science.gov (United States)

    Wu, Yanning; Wang, Shuo; Li, Chunying

    2012-08-13

    has been shown to be of functional significance, suggesting that PDZ scaffold proteins may facilitate formation of CFTR macromolecular signaling complexes for specific/selective and efficient signaling in cells(16-18). Multiple biochemical assays have been developed to study CFTR-involving protein interactions, such as co-immunoprecipitation, pull-down assay, pair-wise binding assay, colorimetric pair-wise binding assay, and macromolecular complex assembly assay(16-19,28,29). Here we focus on the detailed procedures of assembling a PDZ motif-dependent CFTR-containing macromolecular complex in vitro, which is used extensively by our laboratory to study protein-protein or domain-domain interactions involving CFTR(16-19,28,29).

  15. 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

  16. A higher oxidative status accelerates senescence and aggravates age-dependent disorders in SAMP strains of mice.

    Science.gov (United States)

    Hosokawa, Masanori

    2002-11-01

    The SAM strain of mice is actually a group of related inbred strains consisting of series of SAMP (accelerated senescence-prone, short-lived) and SAMR (accelerated senescence-resistant, longer-lived) strains. Comparing with the SAMR strains, the SAMP strains of mice show a more accelerated senescence process, shorter lifespan, and an earlier onset and more rapid progress of age-associated pathological phenotypes similar to several geriatric disorders observed in humans, including senile osteoporosis, degenerative joint disease, age-related deficits in learning and memory, olfactory bulb and forebrain atrophy, presbycusis and retinal atrophy, senile amyloidosis, immunosenescence, senile lungs, and diffuse medial thickening of the aorta. The higher oxidative stress observed in the SAMP strains of mice are partly caused by mitochondrial dysfunction, and may be one cause of the senescence acceleration and age-dependent alterations in cell structure and function, including neuronal cell degeneration. This senescence acceleration is also observed during senescence/crisis in cultures of isolated fibroblast-like cells from SAMP strains of mice, and was associated with a hyperoxidative status. These observations suggest that the SAM strains are useful tools in the attempt to understand the mechanisms of age-dependent degeneration of cells and tissues, and their aggravation, and to develop clinical interventions. PMID:12470893

  17. IL-33 Aggravates DSS-Induced Acute Colitis in Mouse Colon Lamina Propria by Enhancing Th2 Cell Responses.

    Science.gov (United States)

    Zhu, Junfeng; Yang, Fangli; Sang, Lixuan; Zhai, Jingbo; Zhang, Xiaoqing; Yue, Dan; Li, Shengjun; Li, Yan; Lu, Changlong; Sun, Xun

    2015-01-01

    Interleukin- (IL-) 33, a member of the IL-1 cytokine family, is an important modulator of the immune system associated with several immune-mediated diseases. IL-33 was expressed in high level on epithelial cells of intestinal tract. It suggested that IL-33 plays a potential role in inflammatory bowel diseases (IBD). We investigated the role of interleukin- (IL-) 33 in dextran sulphate sodium- (DSS-) induced acute colitis in mice using recombinant mouse IL-33 protein (rIL-33). We found that DSS-induced acute colitis was aggravated by rIL-33 treatment. rIL-33-treated DSS mice showed markedly reduced levels of interferon- (IFN-)γ and IL-17A in their colon lamina propria lymphocytes (LPL), but the levels of Th2 cytokines, such as IL-5 and IL-13, in these cells were significantly increased, compared to DSS mice treated with PBS. Our results suggested that IL-33 stimulated CD4(+)T cells and caused the cell to adopt a Th2-type response but at the same time suppressed Th17 and Th1 cell responses. Therefore, IL-33 may be involved in pathogenesis of DSS-induced acute colitis by promoting Th2 cell response in intestinal mucosa of mice. Modulation of IL-33/ST2 signaling by monoclonal antibody (mAb) could be a novel biological therapy in DSS-induced acute colitis.

  18. Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium.

    Science.gov (United States)

    Zhang, Qianpeng; Wu, Yanqiu; Wang, Jing; Wu, Guojun; Long, Wenmin; Xue, Zhengsheng; Wang, Linghua; Zhang, Xiaojun; Pang, Xiaoyan; Zhao, Yufeng; Zhao, Liping; Zhang, Chenhong

    2016-06-06

    Butyrate-producing bacteria (BPB) are potential probiotic candidates for inflammatory bowel diseases as they are often depleted in the diseased gut microbiota. However, here we found that augmentation of a human-derived butyrate-producing strain, Anaerostipes hadrus BPB5, significantly aggravated colitis in dextran sulphate sodium (DSS)-treated mice while exerted no detrimental effect in healthy mice. We explored how the interaction between BPB5 and gut microbiota may contribute to this differential impact on the hosts. Butyrate production and severity of colitis were assessed in both healthy and DSS-treated mice, and gut microbiota structural changes were analysed using high-throughput sequencing. BPB5-inoculated healthy mice showed no signs of colitis, but increased butyrate content in the gut. In DSS-treated mice, BPB5 augmentation did not increase butyrate content, but induced significantly more severe disease activity index and much higher mortality. BPB5 didn't induce significant changes of gut microbiota in healthy hosts, but expedited the structural shifts 3 days earlier toward the disease phase in BPB5-augmented than DSS-treated animals. The differential response of gut microbiota in healthy and DSS-treated mice to the same potentially beneficial bacterium with drastically different health consequences suggest that animals with dysbiotic gut microbiota should also be employed for the safety assessment of probiotic candidates.

  19. Continuing Exposure to Low-Dose Nonylphenol Aggravates Adenine-Induced Chronic Renal Dysfunction and Role of Rosuvastatin Therapy

    Directory of Open Access Journals (Sweden)

    Yen Chia-Hung

    2012-07-01

    Full Text Available Abstract Background Nonylphenol (NP, an environmental organic compound, has been demonstrated to enhance reactive-oxygen species (ROS synthesis. Chronic exposure to low-dose adenine (AD has been reported to induce chronic kidney disease (CKD. Methods In this study, we tested the hypothesis that chronic exposure to NP will aggravate AD-induced CKD through increasing generations of inflammation, ROS, and apoptosis that could be attenuated by rosuvastatin. Fifty male Wistar rats were equally divided into group 1 (control, group 2 (AD in fodder at a concentration of 0.25%, group 3 (NP: 2 mg/kg/day, group 4 (combined AD & NP, and group 5 (AD-NP + rosuvastatin: 20 mg/kg/day. Treatment was continued for 24 weeks for all animals before being sacrificed. Results By the end of 24 weeks, serum blood urea nitrogen (BUN and creatinine levels were increased in group 4 than in groups 1–3, but significantly reduced in group 5 as compared with group 4 (all p  Conclusion NP worsened AD-induced CKD that could be reversed by rosuvastatin therapy.

  20. Epiplakin deficiency aggravates murine caerulein-induced acute pancreatitis and favors the formation of acinar keratin granules.

    Directory of Open Access Journals (Sweden)

    Karl L Wögenstein

    Full Text Available Epiplakin, a member of the plakin protein family, is exclusively expressed in epithelial tissues and was shown to bind to keratins. Epiplakin-deficient (EPPK-/- mice showed no obvious spontaneous phenotype, however, EPPK-/- keratinocytes displayed faster keratin network breakdown in response to stress. The role of epiplakin in pancreas, a tissue with abundant keratin expression, was not yet known. We analyzed epiplakin's expression in healthy and inflamed pancreatic tissue and compared wild-type and EPPK-/- mice during caerulein-induced acute pancreatitis. We found that epiplakin was expressed primarily in ductal cells of the pancreas and colocalized with apicolateral keratin bundles in murine pancreatic acinar cells. Epiplakin's diffuse subcellular localization in keratin filament-free acini of K8-deficient mice indicated that its filament-associated localization in acinar cells completely depends on its binding partner keratin. During acute pancreatitis, epiplakin was upregulated in acinar cells and its redistribution closely paralleled keratin reorganization. EPPK-/- mice suffered from aggravated pancreatitis but showed no obvious regeneration phenotype. At the most severe stage of the disease, EPPK-/- acinar cells displayed more keratin aggregates than those of wild-type mice. Our data propose epiplakin to be a protective protein during acute pancreatitis, and that its loss causes impaired disease-associated keratin reorganization.

  1. Inhibition of catecholamine degradation ameliorates while chemical sympathectomy aggravates the severity of acute Friend retrovirus infection in mice.

    Science.gov (United States)

    Bloemker, Dominique; Mollerus, Sina; Gibbert, Kathrin; Dittmer, Ulf; del Rey, Adriana; Schedlowski, Manfred; Engler, Harald

    2016-05-01

    Several lines of evidence indicate that the sympathetic nervous system (SNS) might be involved in the pathogenesis and progression of retroviral infections. However, experimental data are scarce and findings inconsistent. Here, we investigated the role of the SNS during acute infection with Friend virus (FV), a pathogenic murine retrovirus that causes polyclonal proliferation of erythroid precursor cells and splenomegaly in adult mice. Experimental animals were infected with FV complex, and viral load, spleen weight, and splenic noradrenaline (NA) concentration was analyzed until 25 days post infection. Results show that FV infection caused a massive but transient depletion in splenic NA during the acute phase of the disease. At the peak of the virus-induced splenomegaly, splenic NA concentration was reduced by about 90% compared to naïve uninfected mice. Concurrently, expression of the catecholamine degrading enzymes monoamine oxidase A (MAO-A) and catechol-O-methyltransferase (COMT) was significantly upregulated in immune cells of the spleen. Pharmacological inhibition of MAO-A and COMT by the selective inhibitors clorgyline and 3,5-dinitrocatechol, respectively, efficiently blocked NA degradation and significantly reduced viral load and virus-induced splenomegaly. In contrast, chemical sympathectomy prior to FV inoculation aggravated the acute infection and extended the duration of the disease. Together these findings demonstrate that catecholamine availability at the site of viral replication is an important factor affecting the course of retroviral infections. PMID:26880342

  2. Partial Beclin 1 silencing aggravates doxorubicin- and Fas-induced apoptosis in HepG2 cells

    Institute of Scientific and Technical Information of China (English)

    Fanny Daniel; Agnès Legrand; Dominique Pessayre; Nathalie Vadrot; Véronique Descatoire; Dominique Bernuau

    2006-01-01

    AIM: To investigate the role of Beclin 1 on the susceptibility of HepG2 cells to undergo apoptosis after anti-Fas antibody or doxorubicin treatment.METHODS: Beclin 1 silencing was achieved using RNA interference. DNA ploidy, the percentage of apoptotic cells and the mitochondrial membrane potential were assessed by flow cytometry. Levels of Beclin 1, Bcl-XL and cytochrome c, and the cleavage of poly (ADP-ribose)polymerase (PARP) were assayed by using Western blots.RESULTS: Beclin 1 expression decreased by 75% 72 h after Beclin 1 siRNA transfection. Partial Beclin 1 silencing significantly increased the percentage of subG1 cells 24 and 40 h after treatment with doxorubicin or anti-Fas antibody, respectively, and this potentiation was abrogated by treatment with a pan-caspase inhibitor.Partial Beclin 1 silencing also increased PARP cleavage,mitochondrial membrane depolarization and cytosolic cytochrome c. The pro-apoptotic consequences of partial Beclin 1 silencing were not associated with a decline in Bcl-XL expression.CONCLUSION: Partial Beclin 1 silencing aggravates mitochondrial permeabilization and apoptosis in HepG2 cells treated with an anti-Fas antibody or with doxorubicin.

  3. Aggravation of brain infarction through an increase in acrolein production and a decrease in glutathione with aging.

    Science.gov (United States)

    Uemura, Takeshi; Watanabe, Kenta; Ishibashi, Misaki; Saiki, Ryotaro; Kuni, Kyoshiro; Nishimura, Kazuhiro; Toida, Toshihiko; Kashiwagi, Keiko; Igarashi, Kazuei

    2016-04-29

    We previously reported that tissue damage during brain infarction was mainly caused by inactivation of proteins by acrolein. This time, it was tested why brain infarction increases in parallel with aging. A mouse model of photochemically induced thrombosis (PIT) was studied using 2, 6, and 12 month-old female C57BL/6 mice. The size of brain infarction in the mouse PIT model increased with aging. The volume of brain infarction in 12 month-old mice was approximately 2-fold larger than that in 2 month-old mice. The larger brain infarction in 12 month-old mice was due to an increase in acrolein based on an increase in the activity of spermine oxidase, together with a decrease in glutathione (GSH), a major acrolein-detoxifying compound in cells, based on the decrease in one of the subunits of glutathione biosynthesizing enzymes, γ-glutamylcysteine ligase modifier subunit, with aging. The results indicate that aggravation of brain infarction with aging was mainly due to the increase in acrolein production and the decrease in GSH in brain.

  4. Accelerated dysbiosis of gut microbiota during aggravation of DSS-induced colitis by a butyrate-producing bacterium.

    Science.gov (United States)

    Zhang, Qianpeng; Wu, Yanqiu; Wang, Jing; Wu, Guojun; Long, Wenmin; Xue, Zhengsheng; Wang, Linghua; Zhang, Xiaojun; Pang, Xiaoyan; Zhao, Yufeng; Zhao, Liping; Zhang, Chenhong

    2016-01-01

    Butyrate-producing bacteria (BPB) are potential probiotic candidates for inflammatory bowel diseases as they are often depleted in the diseased gut microbiota. However, here we found that augmentation of a human-derived butyrate-producing strain, Anaerostipes hadrus BPB5, significantly aggravated colitis in dextran sulphate sodium (DSS)-treated mice while exerted no detrimental effect in healthy mice. We explored how the interaction between BPB5 and gut microbiota may contribute to this differential impact on the hosts. Butyrate production and severity of colitis were assessed in both healthy and DSS-treated mice, and gut microbiota structural changes were analysed using high-throughput sequencing. BPB5-inoculated healthy mice showed no signs of colitis, but increased butyrate content in the gut. In DSS-treated mice, BPB5 augmentation did not increase butyrate content, but induced significantly more severe disease activity index and much higher mortality. BPB5 didn't induce significant changes of gut microbiota in healthy hosts, but expedited the structural shifts 3 days earlier toward the disease phase in BPB5-augmented than DSS-treated animals. The differential response of gut microbiota in healthy and DSS-treated mice to the same potentially beneficial bacterium with drastically different health consequences suggest that animals with dysbiotic gut microbiota should also be employed for the safety assessment of probiotic candidates. PMID:27264309

  5. Absence of Intestinal PPARγ Aggravates Acute Infectious Colitis in Mice through a Lipocalin-2–Dependent Pathway

    Science.gov (United States)

    Kundu, Parag; Ling, Teo Wei; Korecka, Agata; Li, Yinghui; D'Arienzo, Rossana; Bunte, Ralph M.; Berger, Thorsten; Arulampalam, Velmurugesan; Chambon, Pierre; Mak, Tak Wah; Wahli, Walter; Pettersson, Sven

    2014-01-01

    To be able to colonize its host, invading Salmonella enterica serovar Typhimurium must disrupt and severely affect host-microbiome homeostasis. Here we report that S. Typhimurium induces acute infectious colitis by inhibiting peroxisome proliferator-activated receptor gamma (PPARγ) expression in intestinal epithelial cells. Interestingly, this PPARγ down-regulation by S. Typhimurium is independent of TLR-4 signaling but triggers a marked elevation of host innate immune response genes, including that encoding the antimicrobial peptide lipocalin-2 (Lcn2). Accumulation of Lcn2 stabilizes the metalloproteinase MMP-9 via extracellular binding, which further aggravates the colitis. Remarkably, when exposed to S. Typhimurium, Lcn2-null mice exhibited a drastic reduction of the colitis and remained protected even at later stages of infection. Our data suggest a mechanism in which S. Typhimurium hijacks the control of host immune response genes such as those encoding PPARγ and Lcn2 to acquire residence in a host, which by evolution has established a symbiotic relation with its microbiome community to prevent pathogen invasion. PMID:24465207

  6. Blockade of Wnt/β-Catenin Pathway Aggravated Silica-Induced Lung Inflammation through Tregs Regulation on Th Immune Responses

    Directory of Open Access Journals (Sweden)

    Wujing Dai

    2016-01-01

    Full Text Available CD4+ T cells play an important role in regulating silica-induced inflammation and fibrosis. Recent studies showed that Wnt/β-catenin pathway could modulate the function and the differentiation of CD4+ T cells. Therefore, Wnt/β-catenin pathway may participate in the development and progress of silicosis. To investigate the role of Wnt/β-catenin pathway, we used lentivirus expressing β-catenin shRNA to block the Wnt/β-catenin pathway by intratracheal instillation to the mice model of silicosis. Treatment of lentivirus could significantly aggravate the silica-induced lung inflammation and attenuated the fibrosis at the late stage. By analyzing CD4+ T cells, we found that blockade of Wnt/β-catenin pathway suppressed regulatory T cells (Tregs. Reciprocally, enhanced Th17 response was responsible for the further accumulation of neutrophils and production of proinflammatory cytokines. In addition, blockade of Wnt/β-catenin pathway delayed the Th1/Th2 polarization by inhibiting Tregs and Th2 response. These results indicated that Wnt/β-catenin pathway could regulate Tregs to modulate Th immune response, which finally altered the pathological character of silicosis. Our study suggested that Wnt/β-catenin pathway might be a potential target to treat the silica-induced inflammation and fibrosis.

  7. Make-up improves the quality of life of acne patients without aggravating acne eruptions during treatments.

    Science.gov (United States)

    Hayashi, Nobukazu; Imori, Mizuho; Yanagisawa, Midori; Seto, Yoko; Nagata, Osamu; Kawashima, Makoto

    2005-01-01

    Boehncke et al. suggested that decorative cosmetics can improve the quality of life (QOL) of skin diseases. But dermatologists sometimes discourage female acne patients from applying make-up since decorative cosmetics are considered one of the aggravating factors for acne eruptions. The purpose of this study is to assess whether make-up application interferes with acne treatments and how QOL changes when the make-up items are designed for acne patients and used in order to disguise acne eruptions. Eighteen female acne patients were trained by a make-up artist and advised to apply acne-designed basic and decorative cosmetics for 2 to 4 weeks while their acne was appropriately treated. The acne-severity and QOL of patients were assessed before and after the study. The results revealed that the number of acne eruptions decreased even though patients were applying make-up. The QOL scores of Skindex-16, GHQ30 and anxiety state index greatly improved. Our results suggest that dermatologists should encourage acne patients to utilize appropriate make-up to improve their QOL. PMID:16048760

  8. Solid-state NMR in macromolecular systems: insights on how molecular entities move.

    Science.gov (United States)

    Hansen, Michael Ryan; Graf, Robert; Spiess, Hans Wolfgang

    2013-09-17

    The function of synthetic and natural macromolecularsystems critically depends on the packing and dynamics of the individual components of a given system. Not only can solid-state NMR provide structural information with atomic resolution, but it can also provide a way to characterize the amplitude and time scales of motions over broad ranges of length and time. These movements include molecular dynamics, rotational and translational motions of the building blocks, and also the motion of the functional species themselves, such as protons or ions. This Account examines solid-state NMR methods for correlating dynamics and function in a variety of chemical systems. In the early days, scientists thought that the rotationalmotions reflected the geometry of the moving entities. They described these phenomena as jumps about well-defined axes, such as phenyl flips, even in amorphous polymers. Later, they realized that conformational transitions in macromolecules happen in a much more complex way. Because the individual entities do not rotate around well-defined axes, they require much less space. Only recently researchers have appreciated the relative importance of large angle fluctuations of polymers over rotational jumps. Researchers have long considered that cooperative motions might be at work, yet only recently they have clearly detected these motions by NMR in macromolecular and supramolecular systems. In correlations of dynamics and function, local motions do not always provide the mechanism of long-range transport. This idea holds true in ion conduction but also applies to chain transport in polymer melts and semicrystalline polymers. Similar chain motions and ion transport likewise occur in functional biopolymers, systems where solid-state NMR studies are also performed. In polymer science, researchers have appreciated the unique information on molecular dynamics available from advanced solid-state NMR at times, where their colleagues in the biomacromolecular

  9. DISTURBANCE OF THE CARDIOMYOCYTE’S MACROMOLECULAR STRUCTURE IN HEART ALLOGRAFTS AS A SIGN OF CHRONIC REJECTION

    Directory of Open Access Journals (Sweden)

    A. G. Kupriyanova

    2012-01-01

    Full Text Available Chronic rejection, especially cardiac allograft vasculopathy, is a major limiting factor for long-term transplant survival. This process affects not only the blood vessels, but also cardiomyocytes. However, there are extremely few reports on the evaluation of their macromolecular structure state. The aim of the study was to evaluate the structural proteins of cardiomyocytes (actin, myosin, troponin I, titin, desmin, vinculin of heart allografts in different periods after the operation (from 6 days to 15 years. Major changes of macromolecular structure were revealed in late period after transplantation (6 months – 15 years. The contribution of humoral immune response in the process of chronic cardiac allograft rejection was observed: in eight of twelve recipients episodes of acute humoral rejection had been repeatedly registered; disorders of the expression of 5 proteins out of 6 characterized were found in recipients with recurrent and persistent antibody-mediated rejection. 

  10. 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.

  11. 08B1-1: an automated beamline for macromolecular crystallography experiments at the Canadian Light Source.

    Science.gov (United States)

    Fodje, Michel; Grochulski, Pawel; Janzen, Kathryn; Labiuk, Shaunivan; Gorin, James; Berg, Russ

    2014-05-01

    Beamline 08B1-1 is a recently commissioned bending-magnet beamline at the Canadian Light Source. The beamline is designed for automation and remote access. Together with the undulator-based beamline 08ID-1, they constitute the Canadian Macromolecular Crystallography Facility. This paper describes the design, specifications, hardware and software of beamline 08B1-1. A few scientific results using data obtained at the beamline will be highlighted.

  12. DISTURBANCE OF THE CARDIOMYOCYTE’S MACROMOLECULAR STRUCTURE IN HEART ALLOGRAFTS AS A SIGN OF CHRONIC REJECTION

    OpenAIRE

    A. G. Kupriyanova; L. V. Beletskaya; I. M. Ilyinsky; V. A. Zaidenov; N. P. Mozeiko; R. S. Saitgareev; A. Y. Kormer; A. M. Golts; V. M. Zakharevich; S. V. Gautier

    2012-01-01

    Chronic rejection, especially cardiac allograft vasculopathy, is a major limiting factor for long-term transplant survival. This process affects not only the blood vessels, but also cardiomyocytes. However, there are extremely few reports on the evaluation of their macromolecular structure state. The aim of the study was to evaluate the structural proteins of cardiomyocytes (actin, myosin, troponin I, titin, desmin, vinculin) of heart allografts in different periods after the operation (from ...

  13. The influence of hyaluronic acid hydrogel crosslinking density and macromolecular diffusivity on human MSC chondrogenesis and hypertrophy

    OpenAIRE

    Bian, Liming; Hou, Chieh; Tous, Elena; Rai, Reena; Mauck, Robert L.; Burdick, Jason A.

    2012-01-01

    Hyaluronic acid (HA) hydrogels formed via photocrosslinking provide stable 3D hydrogel environments that support the chondrogenesis of mesenchymal stem cells (MSCs). Crosslinking density has a significant impact on the physical properties of hydrogels, including their mechanical stiffness and macromolecular diffusivity. Variations in the HA hydrogel crosslinking density can be obtained by either changes in the HA macromer concentration (1, 3, or 5% w/v at 15 min exposure) or the extent of rea...

  14. Impaired Macromolecular Protein Pools in Fronto-Striato-Thalamic Circuits in Type 2 Diabetes Revealed by Magnetization Transfer Imaging

    OpenAIRE

    Yang, Shaolin; Ajilore, Olusola; Wu, Minjie; Lamar, Melissa; Kumar, Anand

    2014-01-01

    Previous research has shown that type 2 diabetes mellitus (T2DM) is associated with white matter microstructural changes, cognitive impairment, and decreased resting-state functional connectivity and spontaneous brain activity. This study used magnetization transfer imaging to examine, for the first time, the integrity of macromolecular protein pools in fronto-striato-thalamic circuits and its clinical and cognitive correlates in patients with T2DM. T2DM patients without mood disorders (n = 2...

  15. 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.

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

    Science.gov (United States)

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

    2009-11-01

    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.

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

    Energy Technology Data Exchange (ETDEWEB)

    McCarthy, Andrew A., E-mail: andrewmc@embl.fr; Brockhauser, Sandor [European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble (France); Unit of Virus Host Cell Interactions, UJF-EMBL-CNRS, UMI 3265, 6 rue Jules Horowitz, 38042 Grenoble Cedex 9 (France); Nurizzo, Didier; Theveneau, Pascal; Mairs, Trevor; Spruce, Darren; Guijarro, Matias; Lesourd, Marc [European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38042 Grenoble (France); Ravelli, Raimond B. G. [European Molecular Biology Laboratory, 6 rue Jules Horowitz, BP 181, 38042 Grenoble (France); McSweeney, Sean [European Synchrotron Radiation Facility, 6 rue Jules Horowitz, BP 220, 38042 Grenoble (France)

    2009-11-01

    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.

  18. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  20. Optimizing the spatial distribution of dose in X-ray macromolecular crystallography.

    Science.gov (United States)

    Zeldin, Oliver B; Gerstel, Markus; Garman, Elspeth F

    2013-01-01

    X-ray data collection for macromolecular crystallography can lead to highly inhomogeneous distributions of dose within the crystal volume for cases when the crystal is larger than the beam or when the beam is non-uniform (gaussian-like), particularly when crystal rotation is fully taken into account. Here the spatial distribution of dose is quantitatively modelled in order to compare the effectiveness of two dose-spreading data-collection protocols: helical scanning and translational collection. Their effectiveness in reducing the peak dose per unit diffraction is investigated via simulations for four common crystal shapes (cube, plate, long and short needles) and beams with a wide range of full width half maximum values. By inspection of the chosen metric, it is concluded that the optimum strategy is always to use as flat (top-hat) a beam as possible and to either match the beam size in both dimensions to the crystal, or to perform a helical scan with a beam which is narrow along the rotation axis and matched to the crystal size along the perpendicular axis. For crystal shapes where this is not possible, the reduction in peak dose per unit diffraction achieved through dose spreading is quantified and tabulated as a reference for experimenters.

  1. Visualization of X-ray Beam Using CdWO4 Crystal for Macromolecular Crystallography

    Directory of Open Access Journals (Sweden)

    Kazimierz J. Gofron

    2011-12-01

    Full Text Available In synchrotron diffraction experiments, it is typically assumed that the X-ray beam at the sample position is uniform, stable and has dimensions that are controlled by the focus and slits settings. As might be expected, this process is much more complex. We present here an investigation of the properties of a synchrotron X-ray beam at the sample position. The X-ray beam is visualized with a single crystal scintillator that converts X-ray photons into visible light photons, which can be imaged using Structure Biology Center (SBC on-axis and off-axis microscope optics. The X-ray penetration is dependent on the composition of the scintillator (especially the effective Z, and X-ray energy. Several scintillators have been used to visualize X-ray beams. Here we compare CdWO4, PbWO4, Bi4Ge3O12, Y3Al5O12:Ce (YAG:Ce, and Gd2O2S:Tb (phosphor. We determined that scintillator crystals made of CdWO4 and similar high-Z materials are best suited for the energy range (7–20 keV and are most suitable for beam visualization for macromolecular crystallography applications. These scintillators show excellent absorption, optical, and mechanical properties.

  2. Tailoring Phase Behavior and Mechanical Properties in Thermoplastic Elastomers through Block Sequence and Macromolecular Architecture

    Science.gov (United States)

    Burns, Adam; Register, Richard

    2015-03-01

    Block copolymers exhibit unique properties which depend not only on the identities of the constituent blocks but also the block sequence and macromolecular architecture. Thermoplastic elastomers (TPEs) are a prime example. In TPEs the arrangement of glassy end blocks flanking a long rubbery midblock gives rise to a physically cross-linked, elastic solid. Exchanging the glassy blocks for crystalline blocks can improve the processability and solvent resistance, but adversely affects the mechanical performance. The block sequence crystalline-glassy-rubbery-glassy-crystalline has been developed to combine the advantages of both crystalline and glassy blocks. Careful selection of block lengths produces materials in which the order-disorder transition temperature lies below the melting point of the crystalline block, ensuring that the melt will be homogeneous above the melting point. Access to single-phase melts provides a large reduction in viscosity and elasticity over conventional TPEs, which remain microphase-separated in the melt. Inserting the glassy blocks between the crystalline and rubbery blocks produces a vitreous layer surrounding the crystalline domains, which improves the room-temperature mechanical performance. Incorporating the crystalline-glassy-rubbery motif into the arms of star block copolymers adds another level of control. The star architecture introduces a permanent cross-link at the center of the star without appreciably affecting the phase behavior.

  3. 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.

  4. ‘Broken symmetries’ in macromolecular crystallography: phasing from unmerged data

    International Nuclear Information System (INIS)

    Site-specific radiation damage and anisotropy of anomalous scattering can induce intensity differences in symmetry-related reflections. If the data are kept unmerged, these symmetry-breaking effects can become a source of phase information. The space-group symmetry of a crystal structure imposes a point-group symmetry on its diffraction pattern, giving rise to so-called symmetry-equivalent reflections. Instances in macromolecular crystallography are discussed in which the symmetry in reciprocal space is broken, i.e. where symmetry-related reflections are no longer equivalent. Such a situation occurs when the sample suffers from site-specific radiation damage during the X-ray measurements. Another example of broken symmetry arises from the polarization anisotropy of anomalous scattering. In these cases, the genuine intensity differences between symmetry-related reflections can be exploited to yield phase information in the structure-solution process. In this approach, the usual separation of the data merging and phasing steps is abandoned. The data are kept unmerged down to the Harker construction, where the symmetry-breaking effects are explicitly modelled and refined and become a source of supplementary phase information

  5. 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.

  6. Involvement of lysosomes in the uptake of macromolecular material by bloodstream forms of Trypanosoma brucei.

    Science.gov (United States)

    Opperdoes, F R; Van Roy, J

    1982-09-01

    To investigate whether the lysosomes of Trypanosoma brucei are capable of uptake of macromolecules after internalization by the cell, we used Triton WR-1339, a non-digestible macromolecular compound, which is known to cause a marked decrease in the density of hepatic lysosomes due to massive intralysosomal storage. Intraperitoneal administration of 0.4 g/kg Triton WR-1339 to rats infected with T. brucei led to the development of a large vacuole in the trypanosomes between nucleus and kinetoplast within 22 h. Higher doses (2 g/kg) led to the disappearance of the trypanosomes from the blood and resulted in permanent cures (greater than 100 days). Lysosomes isolated from the trypanosomes of animals treated with a sub-curative dose showed a decrease in equilibrium density of 0.03 g/cm3 in sucrose gradients. These lysosomes were partly damaged as evidenced by a reduction in latency and an increase in the non-sedimentable part of lysosomal enzymes. We conclude that acid proteinase and alpha-mannosidase-containing organelles of T. brucei take up exogenous macromolecules and must therefore be considered as true lysosomes and that Triton WR-1339 acts in T. brucei as a true lysosomotropic drug. Its trypanocidal action probably results from an interference with lysosomal function.

  7. MRI macromolecular contrast agents as indicators of changed tumor blood flow

    International Nuclear Information System (INIS)

    Background. A rapid mapping technique derived from dynamic contrast enhanced MRI data was used to identify and characterize reduction of blood flow in fibrosarcoma SA-1 tumors treated either by application of electric pulses or vinblastine. Materials and methods. Tissue permeability surface area product (PS) and fractional blood volume (BV) were calculated on a pixel-by-pixel basis using dynamic MRI intensity data after administration of gadomer- 17 or polylysine-Gd-DTPA; prototypic macromolecular contrast agents designed for blood pool enhancement. PS and BV values of untreated tumors were compared to those of tumors treated by local application of 8 electric pulses (amplitude/distance ratio, 1300 V/cm; duration, 100 μs, frequency, 1 Hz) percutaneously to the tumor or by systemic administration of vinblastine (2.5 mg/kg). Results. Both treatments transiently, but significantly reduced tumor blood flow, application of electric pulses to the tumors being by 40% more effective in reducing tumor blood flow than systemic administration of vinblastine. PS and BV values derived with polylysine-Gd-DTPA-enhanced MRI were lower compared to those with gadomer-17, due to larger molecular size. Interestingly, Gd-DTPA-enhanced MRI did not show any significant changes of PS and BV between untreated and treated tumors. Conclusion. This study demonstrates that dynamic contrast enhanced MRI can be effectively used to qualitatively monitor tumor blood flow, and quantitatively by means of BV and PS. (author)

  8. Effects of macromolecular crowding and DNA looping on gene regulation kinetics

    Science.gov (United States)

    Li, Gene-Wei; Berg, Otto G.; Elf, Johan

    2009-04-01

    DNA-binding proteins control how genomes function. The theory of facilitated diffusion explains how DNA-binding proteins can find targets apparently faster than the diffusion limit by using reduced dimensionality-combining three-dimensional (3D) diffusion through cytoplasm with 1D sliding along DNA (refs 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15). However, it does not include a description of macromolecular crowding on DNA as observed in living cells. Here, we show that such a physical constraint to sliding greatly reduces the search speed, in agreement with single-molecule measurements. Interestingly, the generalized theory also reveals significant insights into the design principles of biology. First, it places a hard constraint on the total number of DNA-binding proteins per cell. Remarkably, the number measured for Escherichia coli fits within the optimal range. Secondly, it defines a new role for DNA looping, a ubiquitous topological motif in genomes. DNA looping can speed up the search process by bypassing proteins that block the sliding track close to the target.

  9. IMAGINE: first neutron protein structure and new capabilities for neutron macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Munshi, Parthapratim [ORNL; Myles, Dean A A [ORNL; Robertson, Lee [ORNL; Stoica, Alexandru Dan [ORNL; Crow, Lowell [ORNL; Kovalevskyi, Andrii Y [ORNL; Koritsanszky, Tibor S [ORNL; Chakoumakos, Bryan C [ORNL; Blessing, Robert [Hauptman-Woodward Medical Research Institute; Meilleur, Flora [ORNL

    2013-01-01

    We report the first high resolution neutron protein structure of perdeuterated rubredoxin from Pyrococcus furiosus (PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory. Neutron diffraction data extending to 1.65 resolution were collected from a relatively small 0.7 mm3 PfRd crystal using 2.5 days (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the deuterium atoms of the protein, and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolutions (1.5 ) from crystals with volume < 1.0 mm3 and with unit cell edges < 100 . Beam line features include elliptical focusing mirrors that deliver 3x107 n s-1 cm-2 into a 3.5 x 2.0 mm2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations ( min=2.0 , 2.8 , 3.3 - max =3.0 , 4.0 , 4.5 , ~20 ). Notably, the crystal used to collect this PfRd data is 5-10 times smaller than has been previously reported.

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

    International Nuclear Information System (INIS)

    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 (201Tl) administration has been safely used to assess the direct pathway to the brain via the nose in healthy volunteers with a normal olfactory threshold. 201Tl 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 201Tl olfacto-scintigraphy for the exclusion of candidates in a clinical trial to assess the usefulness of nasal administration of IGF-I. (author)

  11. 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.

  12. Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration

    Science.gov (United States)

    Alster, Charlotte J.; Koyama, Akihiro; Johnson, Nels G.; Wallenstein, Matthew D.; Fischer, Joseph C.

    2016-06-01

    There is compelling evidence that microbial communities vary widely in their temperature sensitivity and may adapt to warming through time. To date, this sensitivity has been largely characterized using a range of models relying on versions of the Arrhenius equation, which predicts an exponential increase in reaction rate with temperature. However, there is growing evidence from laboratory and field studies that observe nonmonotonic responses of reaction rates to variation in temperature, indicating that Arrhenius is not an appropriate model for quantitatively characterizing temperature sensitivity. Recently, Hobbs et al. (2013) developed macromolecular rate theory (MMRT), which incorporates thermodynamic temperature optima as arising from heat capacity differences between isoenzymes. We applied MMRT to measurements of respiration from soils incubated at different temperatures. These soils were collected from three grassland sites across the U.S. Great Plains and reciprocally transplanted, allowing us to isolate the effects of microbial community type from edaphic factors. We found that microbial community type explained roughly 30% of the variation in the CO2 production rate from the labile C pool but that temperature and soil type were most important in explaining variation in labile and recalcitrant C pool size. For six out of the nine soil × inoculum combinations, MMRT was superior to Arrhenius. The MMRT analysis revealed that microbial communities have distinct heat capacity values and temperature sensitivities sometimes independent of soil type. These results challenge the current paradigm for modeling temperature sensitivity of soil C pools and understanding of microbial enzyme dynamics.

  13. RoboDiff: combining a sample changer and goniometer for highly automated macromolecular crystallography experiments

    Science.gov (United States)

    Nurizzo, Didier; Bowler, Matthew W.; Caserotto, Hugo; Dobias, Fabien; Giraud, Thierry; Surr, John; Guichard, Nicolas; Papp, Gergely; Guijarro, Matias; Mueller-Dieckmann, Christoph; Flot, David; McSweeney, Sean; Cipriani, Florent; Theveneau, Pascal; Leonard, Gordon A.

    2016-01-01

    Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically. PMID:27487827

  14. Diffraction cartography: applying microbeams to macromolecular crystallography sample evaluation and data collection.

    Science.gov (United States)

    Bowler, Matthew W; Guijarro, Matias; Petitdemange, Sebastien; Baker, Isabel; Svensson, Olof; Burghammer, Manfred; Mueller-Dieckmann, Christoph; Gordon, Elspeth J; Flot, David; McSweeney, Sean M; Leonard, Gordon A

    2010-08-01

    Crystals of biological macromolecules often exhibit considerable inter-crystal and intra-crystal variation in diffraction quality. This requires the evaluation of many samples prior to data collection, a practice that is already widespread in macromolecular crystallography. As structural biologists move towards tackling ever more ambitious projects, new automated methods of sample evaluation will become crucial to the success of many projects, as will the availability of synchrotron-based facilities optimized for high-throughput evaluation of the diffraction characteristics of samples. Here, two examples of the types of advanced sample evaluation that will be required are presented: searching within a sample-containing loop for microcrystals using an X-ray beam of 5 microm diameter and selecting the most ordered regions of relatively large crystals using X-ray beams of 5-50 microm in diameter. A graphical user interface developed to assist with these screening methods is also presented. For the case in which the diffraction quality of a relatively large crystal is probed using a microbeam, the usefulness and implications of mapping diffraction-quality heterogeneity (diffraction cartography) are discussed. The implementation of these techniques in the context of planned upgrades to the ESRF's structural biology beamlines is also presented.

  15. Effects of sound exposure on the growth and intracellular macromolecular synthesis of E. coli k-12.

    Science.gov (United States)

    Gu, Shaobin; Zhang, Yongzhu; Wu, Ying

    2016-01-01

    Microbes, as one of the primary producers of the biosphere, play an important role in ecosystems. Exploring the mechanism of adaptation and resistance of microbial population to various environmental factors has come into focus in the fields of modern microbial ecology and molecular ecology. However, facing the increasingly serious problem of acoustic pollution, very few efforts have been put forth into studying the relation of single cell organisms and sound field exposure. Herein, we studied the biological effects of sound exposure on the growth of E. coli K-12 with different acoustic parameters. The effects of sound exposure on the intracellular macromolecular synthesis and cellular morphology of E. coli K-12 were also analyzed and discussed. Experimental results indicated that E. coli K-12 exposed to sound waves owned a higher biomass and a faster specific growth rate compared to the control group. Also, the average length of E. coli K-12 cells increased more than 27.26%. The maximum biomass and maximum specific growth rate of the stimulation group by 8000 Hz, 80dB sound wave was about 1.7 times and 2.5 times that of the control group, respectively. Moreover, it was observed that E. coli K-12 can respond rapidly to sound stress at both the transcriptional and posttranscriptional levels by promoting the synthesis of intracellular RNA and total protein. Some potential mechanisms may be involved in the responses of bacterial cells to sound stress. PMID:27077011

  16. A test of macromolecular crystallization in microgravity: large well ordered insulin crystals.

    Science.gov (United States)

    Borgstahl, G E; Vahedi-Faridi, A; Lovelace, J; Bellamy, H D; Snell, E H

    2001-08-01

    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 phi slicing and unfocused synchrotron radiation. This experimental setup allowed hundreds of reflections to be precisely examined from each crystal in a short period of time. The microgravity crystals were on average 34 times larger, had sevenfold lower mosaicity, had 54-fold higher reflection peak heights and diffracted to significantly higher resolution than their earth-grown counterparts. A single mosaic domain model could account for the observed reflection profiles in microgravity crystals, whereas data 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 the resultant diffraction quality in insulin crystals and may be similarly useful for macromolecular crystals in general.

  17. Competitive interactions of ligands and macromolecular crowders with maltose binding protein.

    Directory of Open Access Journals (Sweden)

    Andrew C Miklos

    Full Text Available Cellular signaling involves a cascade of recognition events occurring in a complex environment with high concentrations of proteins, polysaccharides, and other macromolecules. The influence of macromolecular crowders on protein binding affinity through hard-core repulsion is well studied, and possible contributions of protein-crowder soft attraction have been implicated recently. Here we present direct evidence for weak association of maltose binding protein (MBP with a polysaccharide crowder Ficoll, and that this association effectively competes with the binding of the natural ligand, maltose. Titration data over wide ranges of maltose and Ficoll concentrations fit well with a three-state competitive binding model. Broadening of MBP (1H-(15N TROSY spectra by the addition of Ficoll indicates weak protein-crowder association, and subsequent recovery of sharp NMR peaks upon addition of maltose indicates that the interactions of the crowder and the ligand with MBP are competitive. We hypothesize that, in the Escherichia coli periplasm, the competitive interactions of polysaccharides and maltose with MBP could allow MBP to shuttle between the peptidoglycan attached to the outer membrane and the ATP-binding cassette transporter in the inner membrane.

  18. 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.

  19. RoboDiff: combining a sample changer and goniometer for highly automated macromolecular crystallography experiments.

    Science.gov (United States)

    Nurizzo, Didier; Bowler, Matthew W; Caserotto, Hugo; Dobias, Fabien; Giraud, Thierry; Surr, John; Guichard, Nicolas; Papp, Gergely; Guijarro, Matias; Mueller-Dieckmann, Christoph; Flot, David; McSweeney, Sean; Cipriani, Florent; Theveneau, Pascal; Leonard, Gordon A

    2016-08-01

    Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically. PMID:27487827

  20. A graph theoretical approach for assessing bio-macromolecular complex structural stability.

    Science.gov (United States)

    Del Carpio, Carlos Adriel; Iulian Florea, Mihai; Suzuki, Ai; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Ichiishi, Eiichiro; Miyamoto, Akira

    2009-11-01

    Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.

  1. SPring-8 BL41XU, a high-flux macromolecular crystallography beamline

    Energy Technology Data Exchange (ETDEWEB)

    Hasegawa, Kazuya [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Shimizu, Nobutaka [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); KEK-PF, 1-1 Oho, Tsukuba, Ibaraki 305-0801 (Japan); Okumura, Hideo; Mizuno, Nobuhiro; Baba, Seiki [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Hirata, Kunio [RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Takeuchi, Tomoyuki; Yamazaki, Hiroshi; Senba, Yasunori; Ohashi, Haruhiko [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan); Yamamoto, Masaki [RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148 (Japan); Kumasaka, Takashi, E-mail: kumasaka@spring8.or.jp [SPring-8/JASRI, 1-1-1 Kouto, Sayo, Hyogo 679-5198 (Japan)

    2013-11-01

    SPring-8 BL41XU provides a high-flux X-ray beam of size 10–50 µm, and enables high-quality diffraction data to be obtained from various types of protein crystals. Details of this beamline and an upgrade project are described. SPring-8 BL41XU is a high-flux macromolecular crystallography beamline using an in-vacuum undulator as a light source. The X-rays are monochromated by a liquid-nitrogen-cooling Si double-crystal monochromator, and focused by Kirkpatrick–Baez mirror optics. The focused beam size at the sample is 80 µm (H) × 22 µm (V) with a photon flux of 1.1 × 10{sup 13} photons s{sup −1}. A pinhole aperture is used to collimate the beam in the range 10–50 µm. This high-flux beam with variable size provides opportunities not only for micro-crystallography but also for data collection effectively making use of crystal volume. The beamline also provides high-energy X-rays covering 20.6–35.4 keV which allows ultra-high-resolution data to be obtained and anomalous diffraction using the K-edge of Xe and I. Upgrade of BL41XU for more rapid and accurate data collection is proceeding. Here, details of BL41XU are given and an outline of the upgrade project is documented.

  2. SCIENTIFIC PRINCIPLES FOR MODIFICATION OF WATER-SOLUBLE POLYMERS. FORMATION OF MACROMOLECULAR COMPLEXES

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    The study of nanosecond dynamics of macromolecules with the luminescent methods make it possible to investigate the formation and functioning of polymeric complexes, polymeric conjugates and macromolecular metal complexes, which are widely used for solving many practical tasks. The nanosecond dynamics of macromolecules are a highly sensitive indicator of interpolymer complexes (IPC) formation. It enables us to solve the problems of studying IPC formation and stability and to investigate the interpolymer reactions of exchange and substitution. The investigation of changes in the rotational mobility of globular protein molecules as a whole makes it possible to determine the complex composition and its stability, and to control the course of polymer-protein conjugate formstion reaction. The nanosecond dynamics of polymers interacting with surfacants' ions (S)are the sensitive indicator of the S-polymer complex formation. A method for determining the equilibrium constants of the S-polymer complex formation was developed on the basis of the study of polymer chains mobility. It is established that nanosecond dynamics influences the course of chemical reactions in polymer chains. Moreover, the marked effect of the nanosecond dynamics is also revealed in the study of photophysical processes (the formation of excimers and energy migration of electron excitation) in polymers with photoactive groups. It was found that the efficiency of both processes increases with increasing the mobility of side chains, the carriers of photoactive groups.

  3. Proteinase K activity determination with β-galactosidase as sensitive macromolecular substrate.

    Science.gov (United States)

    Ghéczy, Nicolas; Küchler, Andreas; Walde, Peter

    2016-11-15

    Proteinase K from Engyodontium album (proK) is a relatively unspecific serine endopeptidase which is known to attack proteins yet in their native states. If the attacked protein is an enzyme, even a partial hydrolysis by proK may lead to an inactivation of the enzyme, which can be monitored by measuring the loss of catalytic activity of the attacked enzyme. E. coli β-galactosidase (β-Gal) was used in this work as such enzyme. It was found to be a convenient and sensitive macromolecular model substrate for comparing the "native protein-attacking ability" of free and immobilized proK at pH = 7.0 and 23 °C. The β-Gal activity was measured spectrophotometrically with o-nitrophenyl-β-galactopyranoside. Reproducible proK determinations were possible for as little as 4.3 ng proK by using a proK analyte solution of 10 nM. Compared to free proK, immobilized proK was much less efficient in inactivating β-Gal, most likely due to a decreased mobility of immobilized proK and a restricted accessibility of β-Gal to the active site of proK. Worth noting is, that under conditions at which β-Gal was completely inactivated by proK, the activity of hen egg lysozyme, horseradish peroxidase, or Aspergillus sp. glucose oxidase remained unaltered. PMID:27594349

  4. Proteinase K activity determination with β-galactosidase as sensitive macromolecular substrate.

    Science.gov (United States)

    Ghéczy, Nicolas; Küchler, Andreas; Walde, Peter

    2016-11-15

    Proteinase K from Engyodontium album (proK) is a relatively unspecific serine endopeptidase which is known to attack proteins yet in their native states. If the attacked protein is an enzyme, even a partial hydrolysis by proK may lead to an inactivation of the enzyme, which can be monitored by measuring the loss of catalytic activity of the attacked enzyme. E. coli β-galactosidase (β-Gal) was used in this work as such enzyme. It was found to be a convenient and sensitive macromolecular model substrate for comparing the "native protein-attacking ability" of free and immobilized proK at pH = 7.0 and 23 °C. The β-Gal activity was measured spectrophotometrically with o-nitrophenyl-β-galactopyranoside. Reproducible proK determinations were possible for as little as 4.3 ng proK by using a proK analyte solution of 10 nM. Compared to free proK, immobilized proK was much less efficient in inactivating β-Gal, most likely due to a decreased mobility of immobilized proK and a restricted accessibility of β-Gal to the active site of proK. Worth noting is, that under conditions at which β-Gal was completely inactivated by proK, the activity of hen egg lysozyme, horseradish peroxidase, or Aspergillus sp. glucose oxidase remained unaltered.

  5. Native gel analysis of macromolecular protein complexes in cultured mammalian cells.

    Science.gov (United States)

    Munawar, Nayla; Olivero, Giorgio; Jerman, Emilia; Doyle, Benjamin; Streubel, Gundula; Wynne, Kieran; Bracken, Adrian; Cagney, Gerard

    2015-11-01

    Native gel electrophoresis enables separation of cellular proteins in their non-denatured state. In experiments aimed at analysing proteins in higher order or multimeric assemblies (i.e. protein complexes) it offers some advantages over rival approaches, particularly as an interface technology with mass spectrometry. Here we separated fractions from HEK293 cells by native electrophoresis in order to survey protein complexes in the cytoplasmic, nuclear and chromatin environments, finding 689 proteins distributed among 217 previously described complexes. As expected, different fractions contained distinct combinations of macromolecular complexes, with subunits of the same complex tending to co-migrate. Exceptions to this observation could often be explained by the presence of subunits shared among different complexes. We investigated one identified complex, the Polycomb Repressor Complex 2 (PRC2), in more detail following affinity purification of the EZH2 subunit. This approach resulted in the identification of all previously reported members of PRC2. Overall, this work demonstrates that the use of native gel electrophoresis as an upstream separating step is an effective approach for analysis of the components and cellular distribution of protein complexes. PMID:26223664

  6. RoboDiff: combining a sample changer and goniometer for highly automated macromolecular crystallography experiments.

    Science.gov (United States)

    Nurizzo, Didier; Bowler, Matthew W; Caserotto, Hugo; Dobias, Fabien; Giraud, Thierry; Surr, John; Guichard, Nicolas; Papp, Gergely; Guijarro, Matias; Mueller-Dieckmann, Christoph; Flot, David; McSweeney, Sean; Cipriani, Florent; Theveneau, Pascal; Leonard, Gordon A

    2016-08-01

    Automation of the mounting of cryocooled samples is now a feature of the majority of beamlines dedicated to macromolecular crystallography (MX). Robotic sample changers have been developed over many years, with the latest designs increasing capacity, reliability and speed. Here, the development of a new sample changer deployed at the ESRF beamline MASSIF-1 (ID30A-1), based on an industrial six-axis robot, is described. The device, named RoboDiff, includes a high-capacity dewar, acts as both a sample changer and a high-accuracy goniometer, and has been designed for completely unattended sample mounting and diffraction data collection. This aim has been achieved using a high level of diagnostics at all steps of the process from mounting and characterization to data collection. The RoboDiff has been in service on the fully automated endstation MASSIF-1 at the ESRF since September 2014 and, at the time of writing, has processed more than 20 000 samples completely automatically.

  7. Accreditation not Aggravation

    Science.gov (United States)

    Moss, Cath; Archer, Judith

    2014-01-01

    This paper describes an action research project that investigated a range of activities to improve learners' mathematical communication skills. It also gives details of a subsequent case study that illustrates how technology can provide a means of overcoming some of the difficulties learners and tutors face in communicating about numeracy, while…

  8. Erosive arthritis and hepatic granuloma formation induced by peptidoglycan polysaccharide in rats is aggravated by prasugrel treatment.

    Directory of Open Access Journals (Sweden)

    Analia E Garcia

    Full Text Available Administration of the thienopyridine P2Y12 receptor antagonist, clopidogrel, increased the erosive arthritis induced by peptidoglycan polysaccharide (PG-PS in rats or by injection of the arthritogenic K/BxN serum in mice. To determine if the detrimental effects are caused exclusively by clopidogrel, we evaluated prasugrel, a third-generation thienopyridine pro-drug, that contrary to clopidogrel is mostly metabolized into its active metabolite in the intestine. Prasugrel effects were examined on the PG-PS-induced arthritis rat model. Erosive arthritis was induced in Lewis rats followed by treatment with prasugrel for 21 days. Prasugrel treated arthritic animals showed a significant increase in the inflammatory response, compared with untreated arthritic rats, in terms of augmented macroscopic joint diameter associated with significant signs of inflammation, histomorphometric measurements of the hind joints and elevated platelet number. Moreover, fibrosis at the pannus, assessed by immunofluorescence of connective tissue growth factor, was increased in arthritic rats treated with prasugrel. In addition to the arthritic manifestations, hepatomegaly, liver granulomas and giant cell formation were observed after PG-PS induction and even more after prasugrel exposure. Cytokine plasma levels of IL-1 beta, IL-6, MIP1 alpha, MCP1, IL-17 and RANTES were increased in arthritis-induced animals. IL-10 plasma levels were significantly decreased in animals treated with prasugrel. Overall, prasugrel enhances inflammation in joints and liver of this animal model. Since prasugrel metabolites inhibit neutrophil function ex-vivo and the effects of both clopidogrel and prasugrel metabolites on platelets are identical, we conclude that the thienopyridines metabolites might exert non-platelet effects on other immune cells to aggravate inflammation.

  9. Inhibition of JNK aggravates the recovery of rat hearts after global ischemia: the role of mitochondrial JNK.

    Directory of Open Access Journals (Sweden)

    Sehwan Jang

    Full Text Available c-Jun N-terminal kinase (JNK, a stress-activated MAPK, is activated during cardiac ischemia-reperfusion (IR. The role of JNK inhibitors in cardioprotection against IR still remains controversial, in part, due to spill-over effects of non-specific inhibitors. In the present study, we sought to examine whether inhibition of JNK by SU3327, a specific JNK inhibitor that inhibits upstream JNK signaling rather than the kinase activity of JNK, improves cardiac function and reduces heart damage during IR. Hearts of male Sprague-Dawley rats perfused by Langendorff were subjected to 25 min of global ischemia followed by 30 min reperfusion in the presence or absence of SU3327. Cardiac function was monitored throughout the perfusion period. Myocardial damage was extrapolated from LDH activity in the coronary effluent. At the end of reperfusion, mitochondria were isolated and used to measure respiration rates and mitochondrial permeability transition pore opening. Protein analysis of mitochondria predictably revealed that SU3327 inhibited JNK phosphorylation. Although SU3327 significantly reduced cell damage during the first minutes of reperfusion, it did not improve cardiac function and, furthermore, reduced the mitochondrial respiratory control index. Interestingly, SU3327 activated the other stress-related MAPK, p38, and greatly increased its translocation to mitochondria. Mitochondrial P-JNK and P-p38 were co-immunoprecipitated with complex III of the electron transfer chain. Thus, JNK plays an essential role in cardiac signaling under both physiological and pathological conditions. Its inhibition by SU3327 during IR aggravates cardiac function. The detrimental effects of JNK inhibition are associated with reciprocal p38 activation and mitochondrial dysfunction.

  10. High-sodium intake aggravates myocardial injuriesinduced by aldosterone via oxidative stress inSprague-Dawley rats

    Institute of Scientific and Technical Information of China (English)

    Jing-yi LI; Shao-ling ZHANG; Meng REN; Yan-ling WEN; Li YAN; Hua CHENG

    2012-01-01

    To evaluate the effects of aldosterone with or without high sodium intake on blood pressure,myocardial structure and left ventricular function in rats,and to investigate the mechanisms underlying the effects.Methods:Eight-week-old male Sprague-Dawley rats were randomly divided into 3 groups:(1) control (CON) group fed a normal sodium diet,(2) aldosterone (ALD) group receiving aldosterone infusion and a normal sodium diet,and (3) high sodium plus aldosterone (HS-ALD) group receiving 1% NaCl diet in conjunction with aldosterone infusion.Aldosterone was administered through continuously subcutaneous infusion with osmotic minipump at the rate of 0.75 μg/h for 8 weeks.The myocardium structure was observed using transt-horacic echocardiography and transmission electron microscopy.The collagen deposition in left ventricle was evaluated with Masson'strichrome staining.The expression of IL-18,p22phox,and p47phox proteins was examined using Western blot analysis.Results:The systolic blood pressure in the ALD and HS-ALD groups was significantly higher than that in the CON group after 2-week treatment.But the blood pressure showed no significant difference between the HS-ALD and ALD groups.The left ventricular hyper-trophy,myocardial collagen deposition and oxidative stress were predominantly found in the HS-ALD and ALD group.Furthermore,the breakdown of myocardial structure and oxidative stress were more apparent in the HS-ALD group as compared with those in the ALDgroup.Conclusion:Long-term infusion of aldosterone results in hypertension and profibrotic cardiovascular responses in rats fed a normal sodium diet,which were mediated by oxidative stress.High-sodium intake could aggravate myocardial injuries induced by aldosterone.

  11. Extracellular heat-shock protein 70 aggravates cerulein-induced pancreatitis through toll-like receptor-4 in mice

    Institute of Scientific and Technical Information of China (English)

    SONG Jun-min; WANG Rong; LIU Hong-xiang; LI Yuan; ZENG Yu-jian; ZHOU Zong-guang; LIU Hai-yi; XU Bing; WANG Ling; ZHOU Bin

    2008-01-01

    Background In patients suffering from acute pancreatitis, the pathogenesis is not completely understood, and several recent studies in vitro suggested that heat shock proteins might play an important role in cell signaling. To investigate the possible role of extracellular heat shock protein 70 (Hsp70) in pancreatitis, toll-like receptor-4 (TLR4)-deficient and wild-type mice were administered with exogenous Hsp70 during the course of cerulein-induced pancreatitis (CIP).Methods Acute pancreatitis was induced by 5 intraperitoneal injections of cerulein at hourly intervals, and then treated with recombinant Hsp70 through the caudal vein 4 hours after the start of cerulein injections. Subsequently serum amylase and serum cytokines levels were detected. Histologic alteration of the pancreas was evaluated. Tumor necrosis factor alpha (TNF-a) concentrations and myeloperoxidase (MPO) activity in both pancreas and lungs were analyzed. The nuclear factor kappa B (NF-KB) activation in pancreatic tissue was measured using a sensitive RelA enzyme-linked immunosorbent assay.Results Treatment with recombinant Hsp70 to wild-type mice in CIP resulted in significant aggravation of inflammation in pancreas, elevated levels of serum cytokines, up-regulation of pulmonary MPO activity and increase of lung tissues TNF-α concentrations. In contrast, treatment with Hsp70 to TLR4-deficient mice had little effect on serum cytokines levels, pancreatic inflammation, pulmonary MPO activity and TNF-a concentrations.Conclusions The results suggest that extracellular HspTO might induce systemic inflammatory response syndrome (SIRS)-Iike response in vivo and TLR4 might be involved in the Hsp70-mediated activation of inflammatory reaction in the progression of CIP without infection.

  12. Iron as a possible aggravating factor for osteopathy in itai-itai disease, a disease associated with chronic cadmium intoxication

    Energy Technology Data Exchange (ETDEWEB)

    Noda, M.; Yasuda, M.; Kitagawa, M. (Toyama Medical and Pharmaceutical Univ. (Japan))

    1991-03-01

    Itai-itai disease is thought to be the result of chronic cadmium (Cd) intoxication. We examined 23 autopsy cases of itai-itai disease and 18 cases of sudden death as controls. Urine and blood samples from 10 patients were collected before they died and revealed the presence of severe anemia and renal tubular injuries. Undecalcified sections of iliac bone were stained with Aluminon reagent, and ammonium salt of aurintricarboxylic acid, and Prussian blue reagent in all cases of itai-itai disease. These two reagents reacted at the same mineralization fronts. X-ray microanalysis revealed the presence of iron at mineralization fronts in itai-itai disease. Five patients showed evidence of hemosiderosis in the liver, spleen, and pancreas, probably as a result of post transfusion iron overload. Renal calculi and calcified aortic walls were also stained with Prussian blue reagent in several patients. Neither ferritin nor transferrin were visualized at mineralization fronts in itai-itai disease by immunohistochemical staining. These results suggest that iron is bound to calcium or to calcium phosphate by a physicochemical reaction. A marked osteomalacia was observed in 10 cases of itai-itai disease by histomorphometry. Regression analyses of data from cases of itai-itai disease suggested that an Aluminon-positive metal inhibited mineralization and that renal tubules were injured. Since bone Cd levels were increased in itai-itai disease, it is likely that renal tubules were injured by exposure to Cd. Therefore, stainable bone iron is another possible aggravating factor for osteopathy in itai-itai disease, and a synergistic effect between iron and Cd on mineralization is proposed.

  13. Isolation and characterization of macromolecular protein R-Phycoerythrin from Portieria hornemannii.

    Science.gov (United States)

    Senthilkumar, Namasivayam; Suresh, Veeraperumal; Thangam, Ramar; Kurinjimalar, Chidambaram; Kavitha, Ganapathy; Murugan, Pitchai; Kannan, Soundarapandian; Rengasamy, Ramasamy

    2013-04-01

    R-Phycoerythrin (R-PE) is one of the three phycobiliproteins which are extensively used as fluorescent probes, and it is prepared from red macro-algae. This macromolecular protein has gained importance in many biotechnological applications in food science, immunodiagnostic, therapy, cosmetics, protein and cell labeling, and analytical processes. In the present investigation, R-PE was isolated and purified from a red alga Portieria hornemannii. R-PE extracted and purified through ammonium sulfate precipitation (55%) followed by Q-Sepharose column chromatography had yielded a maximum purity of 5.2%. R-PE exhibited a typical "three-peak" with absorption maxima at 499, 545 and 565 nm. CD spectrum of R-PE yielded the following secondary structure data: alpha helix (14.30%), beta helix (28.10%), turn helix (19.20%) and random coil helix (38.40%). The molecular mass of R-PE was 240 kDa under Native-PAGE. Three different subunits such as α, β and γ of 16 kDa, 21 kDa and 39 kDa were segregated under SDS-PAGE. On two dimensional gel electrophoresis, one basic and four acidic subunits were detected. Five different tryptic peptides were assigned under MALDI-TOF. The sequences of N-terminus of R-PE of 10 different amino acids are Met Lys Gln Met Trp Asp Arg Met Val Val. The preparative procedures of the R-PE extraction and purification established based on the experiments exhibit advantages and can offer a reference for R-PE preparation from other marine red macro-alga P. hornemannii.

  14. Prospects for Simulating Macromolecular Surfactant Chemistry at the Ocean-Atmosphere Boundary

    Energy Technology Data Exchange (ETDEWEB)

    Elliott, S.; Burrows, Susannah M.; Deal, C.; Liu, Xiaohong; Long, M.; Ogunro, O.; Russell, Lynn M.; Wingenter, O.

    2014-05-01

    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 in the surfactant logic 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.

  15. Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

    International Nuclear Information System (INIS)

    The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of Rfree or may leave it out completely

  16. X-ray detectors for soft X-ray macromolecular crystallography

    International Nuclear Information System (INIS)

    Full text: Modern protein crystallography ultimately makes use of the two-dimensional position - sensitive detectors such as Image Plates and CCD with scintillation convertors coupled with fiber optics for detection of X-Ray diffraction pictures taken from macromolecular crystals. These detectors have high efficiency for 1.5-1.0 A synchrotron radiation, special resolution ∼80-50 μm and large effective area (i.e. Σ 300 mm2 for large MAR Image Plate). Both of these types of detectors lack energy resolution. A major drawback of Image Plates is long read-out time (2.5-4 minutes). CCD based devices permit data collection in a real time, however at present they are much more expensive. One of the novel and very promising trends in protein crystallography is to use soft X-ray synchrotron radiation between 2.2 keV and 6 keV (5.6 to 2.5 A) and there is an urgent need to develop suitable detection system for these kinds of applications. It is to be two- dimensional positional sensitive detector with pitch of about 10 to 20 μm, high efficiency and real-time readout. An active area of the detector is to be at least 20 x 20 mm2. It seems to be the simplest solution to use conventional direct-illumination CCD detectors because absorption length of the 5 A radiation in silicon is about 3 μm. However they lack, for example, energy resolution and optimum solution of the problem has yet to come. (author)

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

    Science.gov (United States)

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

    2016-01-01

    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

  18. Electrostatic, elastic and hydration-dependent interactions in dermis influencing volume exclusion and macromolecular transport.

    Science.gov (United States)

    Øien, Alf H; Wiig, Helge

    2016-07-01

    Interstitial exclusion refers to the limitation of space available for plasma proteins and other macromolecules based on collagen and negatively charged glycosaminoglycans (GAGs) in the interstitial space. It is of particular importance to interstitial fluid and plasma volume regulation. Here we present a novel mechanical and mathematical model of the dynamic interactions of structural elements within the interstitium of the dermis at the microscopic level that may explain volume exclusion of charged and neutral macroparticles. At this level, the interstitium is considered to consist of elements called extracellular matrix (ECM) cells, again containing two main interacting structural components on a fluid background including anions and cations setting up osmotic forces: one smaller GAG component, having an intrinsic expansive electric force, and one bigger collagen component, having an intrinsic elastic force. Because of size differences, the GAG component interacts with a fraction of the collagen component only at normal hydration. This fraction, however, increases with rising hydration as a consequence of the modeled form of the interaction force between the GAGs and collagen. Collagen is locally displaced at variable degrees as hydration changes. Two models of GAGs are considered, having largely different geometries which demands different, but related, forms of GAG-collagen interaction forces. The effects of variable fixed charges on GAGs and of GAG density in tissue are evaluated taking into account observed volume exclusion properties of charged macromolecules as a function of tissue hydration. The presented models may improve our biophysical understanding of acting forces influencing tissue fluid dynamics. Such knowledge is significant when evaluating the transport of electrically charged and neutral macromolecules into and through the interstitium, and therefore to drug uptake and the therapeutic effects of macromolecular agents. PMID:27079466

  19. Room-temperature macromolecular crystallography using a micro-patterned silicon chip with minimal background scattering

    Science.gov (United States)

    Roedig, Philip; Duman, Ramona; Sanchez-Weatherby, Juan; Vartiainen, Ismo; Burkhardt, Anja; Warmer, Martin; David, Christian; Wagner, Armin; Meents, Alke

    2016-01-01

    Recent success at X-ray free-electron lasers has led to serial crystallography experiments staging a comeback at synchrotron sources as well. With crystal lifetimes typically in the millisecond range and the latest-generation detector technologies with high framing rates up to 1 kHz, fast sample exchange has become the bottleneck for such experiments. A micro-patterned chip has been developed from single-crystalline silicon, which acts as a sample holder for up to several thousand microcrystals at a very low background level. The crystals can be easily loaded onto the chip and excess mother liquor can be efficiently removed. Dehydration of the crystals is prevented by keeping them in a stream of humidified air during data collection. Further sealing of the sample holder, for example with Kapton, is not required. Room-temperature data collection from insulin crystals loaded onto the chip proves the applicability of the chip for macromolecular crystallography. Subsequent structure refinements reveal no radiation-damage-induced structural changes for insulin crystals up to a dose of 565.6 kGy, even though the total diffraction power of the crystals has on average decreased to 19.1% of its initial value for the same dose. A decay of the diffracting power by half is observed for a dose of D 1/2 = 147.5 ± 19.1 kGy, which is about 1/300 of the dose before crystals show a similar decay at cryogenic temperatures. PMID:27275143

  20. Connexin26 regulates assembly and maintenance of cochlear gap junction macromolecular complex for normal hearing

    Science.gov (United States)

    Kamiya, Kazusaku; Fukunaga, Ichiro; Hatakeyama, Kaori; Ikeda, Katsuhisa

    2015-12-01

    Hereditary deafness affects about 1 in 2000 children and GJB2 gene mutation is most frequent cause for this disease in the world. GJB2 encodes connexin26 (Cx26), a component in cochlear gap junction. Recently, we found macromolecular change of gap junction plaques with two different types of Cx26 mutation as major classification of clinical case, one is a model of dominant negative type, Cx26R75W+ and the other is conditional gene deficient mouse, Cx26f/fP0Cre as a model for insufficiency of gap junction protein [6]. Gap junction composed mainly of Cx26 and Cx30 in wild type mice formed large planar gap junction plaques (GJP). In contrast, Cx26R75W+ and Cx26f/fP0Cre showed fragmented small round GJPs around the cell border. In Cx26f/fP0Cre, some of the cells with Cx26 expression due to their cellular mosaicism showed normal large GJP with Cx26 and Cx30 only at the cell junction site between two Cx26 positive cells. These indicate that bilateral Cx26 expressions from both adjacent cells are essential for the formation of the cochlear linear GJP, and it is not compensated by other cochlear Connexins such as Connexin30. In the present study, we demonstrated a new molecular pathology in most common hereditary deafness with different types of Connexin26 mutations, and this machinery can be a new target for drag design of hereditary deafness.

  1. Anti-Fas mAb-induced apoptosis and cytolysis of airway tissue eosinophils aggravates rather than resolves established inflammation

    Directory of Open Access Journals (Sweden)

    Persson Carl GA

    2005-08-01

    eosinophils progressed into the pro-inflammatory cellular fate of secondary necrosis this may also explain the aggravated inflammation. Our data indicate that Fas receptor mediated eosinophil apoptosis in airway tissues in vivo may cause severe disease exacerbation due to direct cytolysis and secondary necrosis of eosinophils.

  2. Aging changes of macromolecular synthesis in the digestive organs of mice as revealed by microscopic radioautography and X-ray microanalysis

    Energy Technology Data Exchange (ETDEWEB)

    Nagata, Tetsuji [Shinshu Univ., Matsumoto (Japan). School of Medicine. Dept. of Anatomy and Cell Biology]. E-mail: nagatas@po.cnet.ne.jp

    2002-07-01

    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, we have studied the digestive organs of aging mice and rats as a series of systematic studies using light and electron microscopic radioautography after incorporations with macromolecular precursors. The experimental animals mainly used were ddY strain mice at various aging groups from embryo to postnatal days 1 and 3, weeks 1 and 2, months 1, 2, 6, 12 up to 2 year senescent stages as well as several groups of adult Wistar rats. The animals were injected with such macromolecular precursors as {sup 3}H - thymidine for DNA, {sup 3}H-uridine for RNA, {sup 3}H-leucine and {sup 3}H proline for proteins, {sup 35}SO{sub 4} for glycoproteins, {sup 3} H-glucosamine for glucides and {sup 3}H-glycerol for lipids. The results demonstrated that these precursors were incorporated into various cell types in the oral cavity, the salivary glands, the esophagus, the stomach, the small and large intestines, the liver and the pancreas at various ages from perinatal to juvenile, mature and senescent stages, showing specific patterns of macromolecular synthesis. It is concluded that these specific patterns of macromolecular synthesis in respective cell types demonstrated the organ specificity of aging of animals. (author)

  3. β-Cyclodextrin-Based Inclusion Complexation Bridged Biodegradable Self-Assembly Macromolecular Micelle for the Delivery of Paclitaxel.

    Directory of Open Access Journals (Sweden)

    Yanzuo Chen

    Full Text Available In this study, a novel adamantanamine-paclitaxel (AD-PTX incorporated oligochitosan- carboxymethyl-β-cyclodextrin (CSO-g-CM-β-CD self-assembly macromolecular (CSO-g-CM-β-CD@AD-PTX micelle was successfully prepared in water through sonication. The formed molecules were characterized by Fourier transform infrared spectroscopy, proton nuclear magnetic resonance (NMR spectroscopy, two-dimensional NMR, elemental analysis, and liquid chromatography-mass spectrometry, while the correspondent micelles were characterized by dynamic light scattering and transmission electron microscopy. We showed that the macromolecular micelle contained a spherical core-shell structure with a diameter of 197.1 ± 3.3 nm and zeta potential of -19.1 ± 4.3 mV. The CSO-g-CM-β-CD@AD-PTX micelle exhibited a high drug-loading efficacy up to 31.3%, as well as a critical micelle concentration of 3.4 × 10-7 M, which indicated good stability. Additionally, the in vitro release profile of the CSO-g-CM-β-CD@AD-PTX micelle demonstrated a long-term release pattern, 63.1% of AD-PTX was released from the micelle during a 30-day period. Moreover, the CSO-g-CM-β-CD@AD-PTX micelle displayed cytotoxicity at a sub-μM scale similar to PTX in U87 MG cells, and CSO-g-CM-β-CD exhibited a good safety profile by not manifesting significant toxicity at concentrations up to 100 μM. These results indicated that β-CD-based inclusion complexation resulting in biodegradable self-assembled macromolecular micelles can be utilized as nanocarrier, and may provide a promising platform for drug delivery in the future medical applications.

  4. 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)

    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 (KPS; μl/min × 100 cm3), obtained using a two-compartment kinetic model, were correlated with immunohistochemical measurements of VEGF in each tumor. Results: Mean KPS was 2.4 times greater in MDA-MB-231 tumors (KPS = 58 ± 30.9 μl/min × 100 cm3) than in MDA-MB-435 tumors (KPS = 24 ± 8.4 μl/min × 100 cm3) (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.

  5. β-Cyclodextrin-Based Inclusion Complexation Bridged Biodegradable Self-Assembly Macromolecular Micelle for the Delivery of Paclitaxel.

    Science.gov (United States)

    Chen, Yanzuo; Huang, Yukun; Qin, Dongdong; Liu, Wenchao; Song, Chao; Lou, Kaiyan; Wang, Wei; Gao, Feng

    2016-01-01

    In this study, a novel adamantanamine-paclitaxel (AD-PTX) incorporated oligochitosan- carboxymethyl-β-cyclodextrin (CSO-g-CM-β-CD) self-assembly macromolecular (CSO-g-CM-β-CD@AD-PTX) micelle was successfully prepared in water through sonication. The formed molecules were characterized by Fourier transform infrared spectroscopy, proton nuclear magnetic resonance (NMR) spectroscopy, two-dimensional NMR, elemental analysis, and liquid chromatography-mass spectrometry, while the correspondent micelles were characterized by dynamic light scattering and transmission electron microscopy. We showed that the macromolecular micelle contained a spherical core-shell structure with a diameter of 197.1 ± 3.3 nm and zeta potential of -19.1 ± 4.3 mV. The CSO-g-CM-β-CD@AD-PTX micelle exhibited a high drug-loading efficacy up to 31.3%, as well as a critical micelle concentration of 3.4 × 10-7 M, which indicated good stability. Additionally, the in vitro release profile of the CSO-g-CM-β-CD@AD-PTX micelle demonstrated a long-term release pattern, 63.1% of AD-PTX was released from the micelle during a 30-day period. Moreover, the CSO-g-CM-β-CD@AD-PTX micelle displayed cytotoxicity at a sub-μM scale similar to PTX in U87 MG cells, and CSO-g-CM-β-CD exhibited a good safety profile by not manifesting significant toxicity at concentrations up to 100 μM. These results indicated that β-CD-based inclusion complexation resulting in biodegradable self-assembled macromolecular micelles can be utilized as nanocarrier, and may provide a promising platform for drug delivery in the future medical applications. PMID:26964047

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

    International Nuclear Information System (INIS)

    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 14C 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

  7. Curcumin suppresses gastric NF-κB activation and macromolecular leakage in Helicobacter pylori-infected rats

    Institute of Scientific and Technical Information of China (English)

    Kawiya; Sintara; Duangporn; Thong-Ngam; Suthiluk; Patumraj; Naruemon; Klaikeaw; Tanittha; Chatsuwan

    2010-01-01

    AIM:To investigate whether curcumin could attenuate nuclear factor(NF)-κB p65 expression and macromolecular leakage in the gastric mucosa of Helicobacter pylori(H.pylori)-infected rats.METHODS:Twenty-five male Sprague-Dawley rats were equally divided into five groups:control rats(Control),control rats supplemented with 600 mg/kg curcumin,H.pylori-infected rats(Hp),H.pylori-infected rats supplemented with 200 mg/kg curcumin(Hp + curIn H.pylori-infected groups,rats were inoculated with H.pylori suspension twi...

  8. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Laurence, Ted Alfred

    2002-07-30

    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

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

    International Nuclear Information System (INIS)

    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

  11. 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

  12. Glucocerebrosidase deficiency accelerates the accumulation of proteinase K-resistant α-synuclein and aggravates neurodegeneration in a Drosophila model of Parkinson's disease.

    Science.gov (United States)

    Suzuki, Mari; Fujikake, Nobuhiro; Takeuchi, Toshihide; Kohyama-Koganeya, Ayako; Nakajima, Kazuki; Hirabayashi, Yoshio; Wada, Keiji; Nagai, Yoshitaka

    2015-12-01

    Alpha-synuclein (αSyn) plays a central role in the pathogenesis of Parkinson's disease (PD) and dementia with Lewy bodies (DLB). Recent multicenter genetic studies have revealed that mutations in the glucocerebrosidase 1 (GBA1) gene, which are responsible for Gaucher's disease, are strong risk factors for PD and DLB. However, the mechanistic link between the functional loss of glucocerebrosidase (GCase) and the toxicity of αSyn in vivo is not fully understood. In this study, we employed Drosophila models to examine the effect of GCase deficiency on the neurotoxicity of αSyn and its molecular mechanism. Behavioral and histological analyses showed that knockdown of the Drosophila homolog of GBA1 (dGBA1) exacerbates the locomotor dysfunction, loss of dopaminergic neurons and retinal degeneration of αSyn-expressing flies. This phenotypic aggravation was associated with the accumulation of proteinase K (PK)-resistant αSyn, rather than with changes in the total amount of αSyn, raising the possibility that glucosylceramide (GlcCer), a substrate of GCase, accelerates the misfolding of αSyn. Indeed, in vitro experiments revealed that GlcCer directly promotes the conversion of recombinant αSyn into the PK-resistant form, representing a toxic conformational change. Similar to dGBA1 knockdown, knockdown of the Drosophila homolog of β-galactosidase (β-Gal) also aggravated locomotor dysfunction of the αSyn flies, and its substrate GM1 ganglioside accelerated the formation of PK-resistant αSyn. Our findings suggest that the functional loss of GCase or β-Gal promotes the toxic conversion of αSyn via aberrant interactions between αSyn and their substrate glycolipids, leading to the aggravation of αSyn-mediated neurodegeneration.

  13. Slowed Diffusion and Excluded Volume Both Contribute to the Effects of Macromolecular Crowding on Alcohol Dehydrogenase Steady-State Kinetics.

    Science.gov (United States)

    Schneider, Samuel H; Lockwood, Schuyler P; Hargreaves, Dominique I; Slade, David J; LoConte, Micaela A; Logan, Bridget E; McLaughlin, Erin E; Conroy, Michael J; Slade, Kristin M

    2015-09-29

    To understand the consequences of macromolecular crowding, studies have largely employed in vitro experiments with synthetic polymers assumed to be both pure and "inert". These polymers alter enzyme kinetics by excluding volume that would otherwise be available to the enzymes, substrates, and products. Presented here is evidence that other factors, in addition to excluded volume, must be considered in the interpretation of crowding studies with synthetic polymers. Dextran has a weaker effect on the Michaelis-Menten kinetic parameters of yeast alcohol dehydrogenase (YADH) than its small molecule counterpart, glucose. For glucose, the decreased Vmax values directly correlate with slower translational diffusion and the decreased Km values likely result from enhanced substrate binding due to YADH stabilization. Because dextran is unable to stabilize YADH to the same extent as glucose, this polymer's ability to decrease Km is potentially due to the nonideality of the solution, a crowding-induced conformational change, or both. Chronoamperometry reveals that glucose and dextran have surprisingly similar ferricyanide diffusion coefficients. Thus, the reduction in Vmax values for glucose is partially offset by an additional macromolecular crowding effect with dextran. Finally, this is the first report that supplier-dependent impurities in dextran affect the kinetic parameters of YADH. Taken together, our results reveal that caution should be used when interpreting results obtained with inert synthetic polymeric agents, as additional effects from the underlying monomer need to be considered.

  14. SYNTHESIS OF STYRYL-CAPPED POLYPROPYLENE via METALLOCENE-MEDIATED COORDINATION POLYMERIZATION: APPLY TO POLYPROPYLENE MACROMOLECULAR ENGINEERING

    Institute of Scientific and Technical Information of China (English)

    Hua-hua Huang; Chuan-hui Zhang; Ya-wei Qin; Hui Niu; Jin-yong Dong

    2013-01-01

    In this paper,we review our recent progress in the synthesis and application of styryl-capped polypropylene (PP-tSt),an excellent reactive polyolefin that is both convenient and efficient in synthesis and facile and versatile in application for preparing advanced polypropylene materials via macromolecular engineering.The synthesis of PP-t-St is made possible by a unique chain transfer reaction coordinated by a bis-styrenic molecule,such as 1,4-divinylbenzene (DVB) and 1,2-bis(4-vinylphenyl)ethane (BVPE),and hydrogen in typical C2-symmetric metallocene (e.g.rac-Me2Si(2-Me-4-Ph-Ind)2ZrC12,in association with methylaluminocene,MAO) catalyzed propylene polymerization.The regio-selective 2,1-insertion of the styrenic double bond in DVB or BVPE into the overwhelmingly 1,2-fashioned Zr-PP propagating chain enables substantial dormancy of the catalyst active site,which triggers selective hydrogen chain transfer that,with the formed Zr-H species ultimately saturated by the insertion of propylene monomer,results in an exclusive capping of the afforded PP chains by styryl group at the termination end.With a highly reactive styryl group at chain end,PP-t-St has been used as a facile building block in PP macromolecular engineering together with the employment of state-of-the-art synthetic polymer chemistry to fabricate broad types of new polypropylene architectures.

  15. Lung surface-active fraction as a model system for macromolecular ultrastructural studies with Crotalus atrox venom.

    Science.gov (United States)

    Frosolono, M F; Pawlowski, R; Charms, B L; Corbusier, C; Abrams, M; Jones, J

    1973-01-01

    The dog lung surface-active fraction and phosphatidylcholine constituents were subjected to hydrolysis by Crotalus atrox phospholipase A(2). Relative rates of hydrolysis were: dipalmitoyl glycerophosphorylcholine > phosphatidylcholine isolated from the surface-active fraction > phosphatidylcholine as an integral component of the intact surface-active macromolecular structure. Cholesterol markedly inhibited, whereas tripalmitin increased, the rate of hydrolysis with both pure phosphatidylcholine substrates. The effect of temperature on the velocity indicated the enzyme was most active when the substrates were in the gel state. These kinetic results, in conjunction with surface chemistry studies, can be interpreted to indicate that the phosphatidylcholine in the intact surface-active macromolecular particle is liquid crystalline due to molecular interactions with other constituents. Gas-liquid chromatographic analysis of the 2-lysophosphatidylcholines and fatty acids produced from the enzymatic hydrolysis of the intact surface-active fraction indicated that palmitoyl residues were more accessible to the enzyme, perhaps because they occupied positions near the surface of the particle.

  16. Upgrade of IMCA-CAT Bending Magnet Beamline 17-BM for Macromolecular Crystallography at the Advanced Photon Source

    Energy Technology Data Exchange (ETDEWEB)

    Koshelev, I.; Huang, R.; Graber, T.; Meron, M.; Muir, J.L.; Lavender, W.; Battaile, K.; Mulichak, A.M.; Keefe, L.J. (UC)

    2007-05-15

    Pharmaceutical research depends on macromolecular crystallography as a tool in drug design and development. To solve the de novo three-dimensional atomic structure of a protein, it is essential to know the phases of the X-rays scattered by a protein crystal. Experimental phases can be obtained from multiwavelength anomalous dispersion (MAD) experiments. Dedicated to macromolecular crystallography, the IMCA-CAT bending magnet beamline at sector 17 of the Advanced Photon Source (APS) was upgraded to provide the energy resolution required to successfully perform synchrotron radiation-based MAD phasing of protein crystal structures. A collimating mirror was inserted into the beam path upstream of a double-crystal monochromator, thus increasing the monochromatic beam throughput in a particular bandwidth without sacrificing the energy resolution of the system. The beam is focused horizontally by a sagittally bent crystal and vertically by a cylindrically bent mirror, delivering a beam at the sample of 130 {micro}m (vertically) x 250 {micro}m (horizontally) FWHM. As a result of the upgrade, the beamline now operates with an energy range of 7.5 x 17.5 keV, delivers 8 x 10{sup +11} photons/sec at 12.398 keV at the sample, and has an energy resolution of {delta}E/E = 1.45 x 10{sup -4} at 10 keV, which is suitable for MAD experiments.

  17. Mass distributions of a macromolecular assembly based on electrospray ionization mass spectrometric masses of the constituent subunits

    Indian Academy of Sciences (India)

    Leonid Hanin; Brian Green; Franck Zal; Serge Vinogradov

    2003-09-01

    Macromolecular assemblies containing multiple protein subunits and having masses in the megadalton (MDa) range are involved in most of the functions of a living cell. Because of variation in the number and masses of subunits, macromolecular assemblies do not have a unique mass, but rather a mass distribution. The giant extracelular erythrocruorins (Ers), ∼ 3.5 MDa, comprized of at least 180 polypeptide chains, are one of the best characterized assemblies. Three-dimensional reconstructions from cryoelectron microscopic images show them to be hexagonal bilayer complexes of 12 subassemblies, each comprised of 12 globin chains, anchored to a subassembly of 36 nonglobin linker chains. We have calculated the most probable mass distributions for Lumbricus and Riftia assemblies and their globin and linker subassemblies, based on the Lumbricus Er stoichiometry and using accurate subunit masses obtained by electrospray ionization mass spectrometry. The expected masses of Lumbricus and Riftia Ers are 3.517 MDa and 3.284 MDa, respectively, with a possible variation of ∼ 9% due to the breadth of the mass distributions. The Lumbricus Er mass is in astonishingly good agreement with the mean of 23 known masses, 3.524 ± 0.481 MDa.

  18. Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.

    Science.gov (United States)

    Stark, Holger; Chari, Ashwin

    2016-02-01

    Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination. PMID:26671943

  19. Integration of imaging into clinical practice to assess the delivery and performance of macromolecular and nanotechnology-based oncology therapies.

    Science.gov (United States)

    Spence, Tara; De Souza, Raquel; Dou, Yannan; Stapleton, Shawn; Reilly, Raymond M; Allen, Christine

    2015-12-10

    Functional and molecular imaging has become increasingly used to evaluate interpatient and intrapatient tumor heterogeneity. Imaging allows for assessment of microenvironment parameters including tumor hypoxia, perfusion and proliferation, as well as tumor metabolism and the intratumoral distribution of specific molecular markers. Imaging information may be used to stratify patients for targeted therapies, and to define patient populations that may benefit from alternative therapeutic approaches. It also provides a method for non-invasive monitoring of treatment response at earlier time-points than traditional cues, such as tumor shrinkage. Further, companion diagnostic imaging techniques are becoming progressively more important for development and clinical implementation of targeted therapies. Imaging-based companion diagnostics are likely to be essential for the validation and FDA approval of targeted nanotherapies and macromolecular medicines. This review describes recent clinical advances in the use of functional and molecular imaging to evaluate the tumor microenvironment. Additionally, this article focuses on image-based assessment of distribution and anti-tumor effect of nano- and macromolecular systems.

  20. A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules.

    Science.gov (United States)

    Shan, Hong; Wang, Zihao; Zhang, Fa; Xiong, Yong; Yin, Chang-Cheng; Sun, Fei

    2016-01-01

    Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations.

  1. Vascular Endothelial Growth Factor-Receptor 1 Inhibition Aggravates Diabetic Nephropathy through eNOS Signaling Pathway in db/db Mice

    OpenAIRE

    Keun Suk Yang; Ji Hee Lim; Tae Woo Kim; Min Young Kim; Yaeni Kim; Sungjin Chung; Seok Joon Shin; Beom Soon Choi; Hyung Wook Kim; Yong-Soo Kim; Yoon Sik Chang; Hye Won Kim; Cheol Whee Park

    2014-01-01

    The manipulation of vascular endothelial growth factor (VEGF)-receptors (VEGFRs) in diabetic nephropathy is as controversial as issue as ever. It is known to be VEGF-A and VEGFR2 that regulate most of the cellular actions of VEGF in experimental diabetic nephropathy. On the other hand, such factors as VEGF-A, -B and placenta growth factor bind to VEGFR1 with high affinity. Such notion instigated us to investigate on whether selective VEGFR1 inhibition with GNQWFI hexamer aggravates the progre...

  2. A case of Long QT syndrome type 3 aggravated by beta-blockers and alleviated by mexiletine: the role of epinephrine provocation test.

    Science.gov (United States)

    Park, Junbeom; Kim, Sook Kyoung; Pak, Hui-Nam

    2013-03-01

    Long QT syndrome (LQTs) is an uncommon genetic disease causing sudden cardiac death with Torsade de Pointes (TdP). The first line drug treatment has been known to be β-blocker. We encountered a 15-year-old female student with LQTs who had prolonged QTc and multiple episodes of syncope or agonal respiration during sleep. Although her T wave morphology in surface electrocardiography resembled LQTs type 1, her clinical presentation was unusual. During the epinephrine test, TdP was aggravated during β-blocker medication, but alleviated by sodium channel blocker (mexiletine). Therefore, she underwent implantable cardioverter defibrillator implantation. PMID:23364992

  3. 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

  4. 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

  5. Carboxylated multi-walled carbon nanotubes aggravated biochemical and subcellular damages in leaves of broad bean (Vicia faba L.) seedlings under combined stress of lead and cadmium

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Chengrun, E-mail: chengrunwang@163.com [School of Life Science, Huainan Normal University, Huainan 232001 (China); Liu, Haitao; Chen, Jinyun [School of Life Science, Huainan Normal University, Huainan 232001 (China); Tian, Yuan [Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 (United States); Shi, Jian; Li, Dongdong; Guo, Chen; Ma, Qingping [School of Life Science, Huainan Normal University, Huainan 232001 (China)

    2014-06-01

    Highlights: • MWCNTs-COOH disturb mineral elements and cause oxidative damages in the leaves. • Cd and Pb combination result in reduction of mineral elements and enrichment of Na, involving in toxicity mechanisms. • MWCNTs-COOH facilitate Cd and Pb uptake, and aggravate biochemical and subcellular damages. - Abstract: Increasing industrialization of multi-walled carbon nanotubes (MWCNTs) would inevitably lead to their release into the environment and combination with heavy metals. However, studies concerning the combined effects of MWCNTs and heavy metals on agricultural crops are limited. Herein, effects and mechanisms of carboxylated MWCNTs (MWCNTs-COOH) (2.5, 5 and 10 mg/L) and their combination with 20 μM Pb and 5 μM Cd (shortened as Pb + Cd) on Vicia faba L. seedlings were investigated. The results showed that the MWCNTs-COOH disturbed the imbalance of nutrient elements, and caused oxidative stress and damages in the leaves. Additionally, the combination of MWCNTs-COOH with Pb + Cd resulted in enrichment of Pb and Cd, and deterioration of oxidative damages compared with the treatments of MWCNTs-COOH or Pb + Cd alone in the leaves. As the results, the concentrations of MWCNTs-COOH not only caused oxidative stress, but also exacerbated the biochemical and subcellular damages due to the treatment of Pb + Cd in the leaves. It also suggests that persistent release of MWCNTs-COOH into the environment may cause phytotoxicity and aggravate ecological risks due to combination of heavy metals.

  6. Effect of dopamine-related drugs on duodenal ulcer induced by cysteamine or propionitrile: prevention and aggravation may not be mediated by gastrointestinal secretory changes in the rat

    Energy Technology Data Exchange (ETDEWEB)

    Gallagher, G.; Brown, A.; Szabo, S.

    1987-03-01

    Dose- and time-response studies have been performed with dopamine agonists and antagonists using the cysteamine and propionitrile duodenal ulcer models in the rat. The experiments demonstrate that the chemically induced duodenal ulcer is prevented by bromocriptine, lergotrile and reduced by apomorphine or L-dopa. Aggravation of cysteamine-induced duodenal ulcer was seen especially after (-)-butaclamol, (-)-sulpiride, haloperidol and, less effectively, after other dopaminergic antagonists. The duodenal antiulcerogenic action of dopamine agonists was more prominent after chronic administration than after a single dose, whereas the opposite was found concerning the proulcerogenic effect of dopamine antagonists. In the chronic gastric fistula rat, both the antiulcerogens bromocriptine or lergotrile and the proulcerogens haloperidol, pimozide or (-)-N-(2-chlorethyl)-norapomorphine decreased the cysteamine- or propionitrile-induced gastric secretion. No correlation was apparent between the influence of these drugs on duodenal ulcer development and gastric and duodenal (pancreatic/biliary) secretions. In the chronic duodenal fistula rat, decreased acid content was measured in the proximal duodenum after haloperidol, and diminished duodenal pepsin exposure was recorded after bromocriptine. Furthermore, the aggravation by dopamine antagonists of experimental duodenal ulcer probably involves a peripheral component. The site of dopamine receptors and physiologic effects which modulate experimental duodenal ulcer remain to be identified, but their elucidation may prove to be an important element in the pathogenesis and treatment of duodenal ulcer.

  7. CaMKII binding to GluN2B is differentially affected by macromolecular crowding reagents.

    Directory of Open Access Journals (Sweden)

    Dayton J Goodell

    Full Text Available Binding of the Ca2+/calmodulin(CaM-dependent protein kinase II (CaMKII to the NMDA-type glutamate receptor (NMDAR subunit GluN2B controls long-term potentiation (LTP, a form of synaptic plasticity thought to underlie learning and memory. Regulation of this interaction is well-studied biochemically, but not under conditions that mimic the macromolecular crowding found within cells. Notably, previous molecular crowding experiments with lysozyme indicated an effect on the CaMKII holoenzyme conformation. Here, we found that the effect of molecular crowding on Ca2+/CaM-induced CaMKII binding to immobilized GluN2B in vitro depended on the specific crowding reagent. While binding was reduced by lysozyme, it was enhanced by BSA. The ATP content in the BSA preparation caused CaMKII autophosphorylation at T286 during the binding reaction; however, enhanced binding was also observed when autophosphorylation was blocked. Importantly, the positive regulation by nucleotide and BSA (as well as other macromolecular crowding reagents did not alleviate the requirement for CaMKII stimulation to induce GluN2B binding. The differential effect of lysozyme (14 kDa and BSA (66 kDa was not due to size difference, as both dextran-10 and dextran-70 enhanced binding. By contrast, crowding with immunoglobulin G (IgG reduced binding. Notably, lysozyme and IgG but not BSA directly bound to Ca2+/CaM in an overlay assay, suggesting a competition of lysozyme and IgG with the Ca2+/CaM-stimulus that induces CaMKII/GluN2B binding. However, lysozyme negatively regulated binding even when it was instead induced by CaMKII T286 phosphorylation. Alternative modes of competition would be with CaMKII or GluN2B, and the negative effects of lysozyme and IgG indeed also correlated with specific or non-specific binding to the immobilized GluN2B. Thus, the effect of any specific crowding reagent can differ, depending on its additional direct effects on CaMKII/GluN2B binding. However, the

  8. 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

    to a molecular sharing economy at a high level of competition inside the cell. Thus, the promoters compete with each other in the binding of a limited amount of free RNA polymerase and the ribosome binding sites on the mRNA chains compete with each other for the free ribosomes. The macromolecular chain...

  9. Effect of structural alteration on the macromolecular properties of brown and bituminous coals, quantitative relationships to the hydrogenation reactivity with tetralin

    Energy Technology Data Exchange (ETDEWEB)

    Kuznetsov, P.N.; Kuznetsova, L.I. [Inst. of Chemistry and Chemico-Metallurgical Processes, Krasnoyarsk (Russian Federation); Bimer, J.; Salbut, P.D. [Inst. of Organic Chemistry, Warszawa (Poland); Gruber, R. [Univ. de Metz (France)

    1996-12-31

    The mobility of macromolecular network has been found to be the fundamental property of both brown and bituminous coals governing the reactivity for hydrogenation with tetralin. In Kansk-Achinsk brown coal, this was primarily affected by carboxylate cross-linking via polyvalent cations like Ca.

  10. 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

  11. 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). [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

  12. Feasibility of macromolecular structure experiments operating at the 3W1 beamline of BSRF in the parasitic mode

    Institute of Scientific and Technical Information of China (English)

    X.Ju; D.C.Xian

    2001-01-01

    Parameters for the 3W1 source at BSRF were determined in both the dedicated and parasitic mode and their suitability for protein crystallography beamline at BSRF were realized.It is discussed that the physics motivation and the design of the 3W1 is compared with similar experimental stations at the Brazilian Light Sourec(1.37Gev) and Max-II in Sweden(1.5GeV).The photon flux from the 3W1 sourcd is about 2×1011 photon/smA in the wavelength range of 2.0-0.9A in parasitic mode and 50-80 times higher in the dedicated mode.Both the dedicated and parasitic modes are suitable for macromolecular structure experiments.2001 Elsevier Science B.V.All rights reserved.

  13. Nanometer-level axis of rotation metrology for a high-precision macromolecular X-ray diffractometer

    International Nuclear Information System (INIS)

    The availability of micro-focused beams at 3rd generation synchrotrons makes collecting X-ray data from macromolecular crystals down to a fraction of micron size possible. This requires using goniometers with nanometer-level errors. Crystal positioning is typically realized with a multi-axis goniometer designed to minimize error motion during rotation of the crystal by the data-collection axis. In this paper, five degree-of-freedom error motions of an air bearing diffractometer data-collection axis are evaluated using a multiprobe method. As spindle errors and artifact out-of-roundness approach equal magnitudes, techniques must be used to distinguish and separate each error. A purpose-built fixture orients a single capacitive sensor in three asymmetrical positions to separate artifact form error from spindle error motion. Metrology results of this air bearing Omega spindle demonstrate synchronous errors of 16 nm radial, 4 nm axial and 0.28 μrad tilt.

  14. Evolving Methods for Macromolecular Crystallography The Structural Path to the Understanding of the Mechanismof Action of CBRN Agents

    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.

  15. Synthesis and swelling peculiarities of new hydrogels based on the macromolecular reaction of anhydride copolymers with γ-aminopropyltriethoxysilane.

    Science.gov (United States)

    Timur, Mahir; Can, Hatice Kaplan

    2016-05-01

    This work describes the synthesis and macromolecular reactions of maleic anhydride (MA)-acrylamide (AAm) binary and MA-vinyl acetate (VA)- AAm ternary reactive copolymers with γ-aminopropyltriethoxysilane (APTS) as a polyfunctional crosslinker. Swelling parameters such as the start-time of the hydrogel-formation, initial rate of swelling, swelling rate constant, equilibrium swelling, and equilibrium water content (EWC) are determined for polymers/APTS/water systems with certain copolymer/crosslinker ratios (1.4/1 and 9/1). The formation of a hyperbranched network structure by the fragmentation of the side-chain reactive groups in the systems studied has also been confirmed by the Fourier Transform Infrared (FTIR) method. PMID:25761627

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

    Science.gov (United States)

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

    2016-03-01

    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.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. Multiscale modeling of metabolism and macromolecular synthesis in E. coli and its application to the evolution of codon usage.

    Directory of Open Access Journals (Sweden)

    Ines Thiele

    Full Text Available Biological systems are inherently hierarchal and multiscale in time and space. A major challenge of systems biology is to describe biological systems as a computational model, which can be used to derive novel hypothesis and drive experiments leading to new knowledge. The constraint-based reconstruction and analysis approach has been successfully applied to metabolism and to the macromolecular synthesis machinery assembly. Here, we present the first integrated stoichiometric multiscale model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655, which describes the sequence-specific synthesis and function of almost 2000 gene products at molecular detail. We added linear constraints, which couple enzyme synthesis and catalysis reactions. Comparison with experimental data showed improvement of growth phenotype prediction with the multiscale model over E. coli's metabolic model alone. Many of the genes covered by this integrated model are well conserved across enterobacters and other, less related bacteria. We addressed the question of whether the bias in synonymous codon usage could affect the growth phenotype and environmental niches that an organism can occupy. We created two classes of in silico strains, one with more biased codon usage and one with more equilibrated codon usage than the wildtype. The reduced growth phenotype in biased strains was caused by tRNA supply shortage, indicating that expansion of tRNA gene content or tRNA codon recognition allow E. coli to respond to changes in codon usage bias. Our analysis suggests that in order to maximize growth and to adapt to new environmental niches, codon usage and tRNA content must co-evolve. These results provide further evidence for the mutation-selection-drift balance theory of codon usage bias. This integrated multiscale reconstruction successfully demonstrates that the constraint-based modeling approach is well suited to whole-cell modeling endeavors.

  19. 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

  20. Effects of Kanlijian (坎离煎) on Exercise Tolerance, Quality of Life, and Frequency of Heart Failure Aggravation in Patients with Chronic Heart Failure

    Institute of Scientific and Technical Information of China (English)

    JIANG Mei-xian; RUAN Xiao-fen; XU Yan

    2006-01-01

    Objective: To observe the effects of conventional therapy combined with Kanlijian (坎离煎,KLJ) on exercise tolerance, quality of life and frequency of heart failure aggravation in patients with chronic heart failure(CHF). Methods: Sixty. CHF patients differentiated as sufferring from the syndrome of Xin-Shen Yang deficiency were included in the study and randomly assigned at the ratio of 2: 1 into the KLJ group (n=39) and the control group(n = 21). All the patients were treated with conventional therapy of Western medicine, but to those in the KLJ group, KLJ was medicated additionally one dose daily with 24 wks as one therapeutic course. The efficacy on TCM syndrome and changes of scores on TCM syndrome were observed after treatment. The indexes, including 6-minute walking distance (6MWD), quality of life (QOL, accessed by LHFQ scoring), NYHA grade, hemodynamic indexes and reducing/withdrawal rate of diuretic and digoxin before and after treatment were recorded and compared. Also the frequency of re-admission due to aggravation of heart failure in one year's time were observed. Results: ( 1 ) The efficacy on TCM syndrome, improvement on scores of TCM syndrome, therapeutic effects on 6MWD, QOL, and NYHA grade in the KLJ group were superior to those in the control group. (2) Hemodynamic indexes after treatment, left ventricular fractional shortening (LVFS) and E peak/A peak (E/A), between the two groups had no significant difference, while left ventricular ejection fraction (LVEF) was increased significantly in the KLJ group, but with no obvious change in the control group. (3) The reducing/withdrawal rate of diuretic and digoxin in the KLJ group was significantly higher than that in the control group. (4) The 1-year frequency of re-admission significantly decreased in the KLJ group. Conclusion: The adjuvant treatment of KLJ on the basis of Western conventional therapy can significantly improve CHF patients' exercise tolerance, quality of life and cardiac function

  1. Fentanyl-droperidol supplementation of rapid sequence induction in the presence of severe pregnancy-induced and pregnancy-aggravated hypertension.

    Science.gov (United States)

    Lawes, E G; Downing, J W; Duncan, P W; Bland, B; Lavies, N; Gane, G A

    1987-11-01

    Twenty-six patients manifesting severe pregnancy-induced (PIH) or pregnancy-aggravated (PAH) hypertension who presented for emergency Caesarean section under general anaesthesia were studied. All patients came from a previously identified high risk group--namely greater than 25 yr, multiparous and with diastolic arterial pressures sustained at greater than 120 mm Hg. Our standard accelerated induction technique for the management of severely hypertensive mothers was modified to include the use of fentanyl and droperidol before induction. This modification of the induction sequence produced a clinically significant amelioration of the reflex sympathetic hypertensive response to laryngoscopy and intubation in most mothers receiving antihypertensive therapy, without apparent deleterious effect in the immediate postoperative period to those neonates unaffected by intrauterine asphyxia. PMID:3689612

  2. Aggravation of atopic dermatitis in breast-fed infants by tree nut-related foods and fermented foods in breast milk.

    Science.gov (United States)

    Uenishi, Toshiaki; Sugiura, Hisashi; Tanaka, Toshihiro; Uehara, Masami

    2011-02-01

    Ninety-two exclusively breast-fed Japanese infants with atopic dermatitis were studied to see whether tree nut-related foods (chocolate and coffee) and fermented foods (cheese, yogurt, bread, soy sauce, miso soup and fermented soy beans) eaten by their mothers affected their skin condition. Of the 92 infants, 67 (73%) showed improvement of skin lesions when their mothers avoided these foods and showed aggravation of skin lesions when these foods were reintroduced. The predominant offending foods were chocolate, yogurt, soy sauce and miso soup. A long-term maternal exclusion of the trigger foods brought about progressive improvement of skin lesions in the majority of the infants. These findings suggest that tree nut-related foods and fermented foods are important offending foods of atopic dermatitis in breast-fed infants. PMID:21269309

  3. Chronic administration of recombinant IL-6 upregulates lipogenic enzyme expression and aggravates high-fat-diet-induced steatosis in IL-6-deficient mice

    Directory of Open Access Journals (Sweden)

    Margarita Vida

    2015-07-01

    Full Text Available Interleukin-6 (IL-6 has emerged as an important mediator of fatty acid metabolism with paradoxical effects in the liver. Administration of IL-6 has been reported to confer protection against steatosis, but plasma and tissue IL-6 concentrations are elevated in chronic liver diseases, including fatty liver diseases associated with obesity and alcoholic ingestion. In this study, we further investigated the role of IL-6 on steatosis induced through a high-fat diet (HFD in wild-type (WT and IL-6-deficient (IL-6−/− mice. Additionally, HFD-fed IL-6−/− mice were also chronically treated with recombinant IL-6 (rIL-6. Obesity in WT mice fed a HFD associated with elevated serum IL-6 levels, fatty liver, upregulation of carnitine palmitoyltransferase 1 (CPT1 and signal transducer and activator of transcription-3 (STAT3, increased AMP kinase phosphorylation (p-AMPK, and downregulation of the hepatic lipogenic enzymes fatty acid synthase (FAS and stearoyl-CoA desaturase 1 (SCD1. The HFD-fed IL-6−/− mice showed severe steatosis, no changes in CPT1 levels or AMPK activity, no increase in STAT3 amounts, inactivated STAT3, and marked downregulation of the expression of acetyl-CoA carboxylase (ACCα/β, FAS and SCD1. The IL-6 chronic replacement in HFD-fed IL-6−/− mice restored hepatic STAT3 and AMPK activation but also increased the expression of the lipogenic enzymes ACCα/β, FAS and SCD1. Furthermore, rIL-6 administration was associated with aggravated steatosis and elevated fat content in the liver. We conclude that, in the context of HFD-induced obesity, the administration of rIL-6 might contribute to the aggravation of fatty liver disease through increasing lipogenesis.

  4. Human Cytomegalovirus-Encoded miR-US25-1 Aggravates the Oxidised Low Density Lipoprotein-Induced Apoptosis of Endothelial Cells

    Directory of Open Access Journals (Sweden)

    Jianmin Fan

    2014-01-01

    Full Text Available Human cytomegalovirus (HCMV infection is linked to the development and severity of the cardiovascular disease atherosclerosis; however, there is little known about the promotion of atherosclerosis. miR-US25-1 is one of HCMV-encoded miRNAs and targets cellular genes that are essential for virus growth to control the life cycle of the virus and host cells. The prominent regulation on cell cycle genes of the miR-US25-1 attracts us to explore its role in the atherosclerosis promotion. It was indicated that miR-US25-1 level was upregulated in subjects or in endothelial cells with HCMV infection; and the miR-US25-1 downregulated the expression of BRCC 3 by targeting the 5′ UTR of BRCC 3. And a miR-US25-1 mimics transfection could reduce the EAhy926 cell viability but did not induce apoptosis in EAhy926 cells. And what is more, miR-US25-1 mimicis transfection deteriorated the ox-LDL-induced apoptosis and aggravated the upregulation of apoptosis-associated molecules by oxidised low density lipoprotein (ox-LDL in EAhy926 cells. And we have also confirmed the deregulation of BRCC 3 expression by miR-US25-1 by targeting the 5′ UTR of it. Given the vital role of BRCC 3 in DNA damage repairing, we speculated that the targeting inhibition of BRCC 3 by miR-US25-1 may contribute to the aggravation of ox-LDL-promoted apoptosis of endothelial EAhy926 cells.

  5. Chronic IL-6 Administration Desensitizes IL-6 Response in Liver, Causes Hyperleptinemia and Aggravates Steatosis in Diet-Induced-Obese Mice

    Science.gov (United States)

    Gavito, Ana Luisa; Bautista, Dolores; Suarez, Juan; Badran, Samir; Arco, Rocío; Pavón, Francisco Javier; Serrano, Antonia; Rivera, Patricia; Decara, Juan; Cuesta, Antonio Luis; Rodríguez-de-Fonseca, Fernando

    2016-01-01

    High-fat diet-induced obesity (DIO) is associated with fatty liver and elevated IL-6 circulating levels. IL-6 administration in rodents has yielded contradictory results regarding its effects on steatosis progression. In some models of fatty liver disease, high doses of human IL-6 ameliorate the liver steatosis, whereas restoration of IL-6 in DIO IL-6-/- mice up-regulates hepatic lipogenic enzymes and aggravates steatosis. We further examined the effects of chronic low doses of murine IL-6 on hepatic lipid metabolism in WT mice in DIO. IL-6 was delivered twice daily in C57BL/6J DIO mice for 15 days. The status and expression of IL-6-signalling mediators and targets were investigated in relation to the steatosis and lipid content in blood and in liver. IL-6 administration in DIO mice markedly raised circulating levels of lipids, glucose and leptin, elevated fat liver content and aggravated steatosis. Under IL-6 treatment there was hepatic Stat3 activation and increased gene expression of Socs3 and Tnf-alpha whereas the gene expression of endogenous IL-6, IL-6-receptor, Stat3, Cpt1 and the enzymes involved in lipogenesis was suppressed. These data further implicate IL-6 in fatty liver disease modulation in the context of DIO, and indicate that continuous stimulation with IL-6 attenuates the IL-6-receptor response, which is associated with high serum levels of leptin, glucose and lipids, the lowering levels of lipogenic and Cpt1 hepatic enzymes and with increased Tnf-alpha hepatic expression, a scenario evoking that observed in IL-6-/- mice exposed to DIO and in obese Zucker rats. PMID:27333268

  6. Nuevos métodos para el ajuste flexible de estructuras macromoleculares a distintas resoluciones empleando modos normales de vibración en coordenadas internas

    OpenAIRE

    López Blanco, José Ramón

    2012-01-01

    Los objetivos principales de esta tesis son el desarrollo e implementación de una nueva metodología bioinformática para el análisis de los modos normales de vibración (NMA) en coordenadas internas (CI) y su aplicación en el ajuste flexible de estructuras atómicas macromoleculares en mapas de densidad a media/baja resolución.

  7. Correlation of dynamic contrast-enhanced magnetic resonance imaging with histologic tumor grade: comparison of macromolecular and small-molecular contrast media

    International Nuclear Information System (INIS)

    Background. The endothelial integrity of microvessels is disrupted in malignant tumors. Quantitative assays of tumor microvascular characteristics based on dynamic magnetic resonance imaging (MRI) were correlated with histopathologic grade in mammary soft tissue tumors. Materials and methods. A spectrum of tumors, benign through highly malignant, was induced in 33 female rats by administration of N -ethyl-N -nitrosourea (ENU), a potent carcinogen. Dynamic contrast-enhanced MRI was performed using a small-molecular contrast medium [gadopentetate, MW = 0.5 kDa] and a macromolecular contrast medium [albumin-(Gd-DTPA)30, MW = 92 kDa] at an interval of 1-2 days. Permeability surface area product (PS), as estimated by the corresponding endothelial transfer coefficient (KPS), and fractional plasma volume (fPV) were calculated for each tumor and each contrast agent using a two-compartment bi-directional kinetic model. MRI microvascular characteristics were correlated with histopathologic tumor grade. Results. Tumor permeability to macromolecular contrast medium, characterized by KPS, showed a highly positive correlation with tumor grade (r 2 = 0.76, P -10). K PS values were zero for all benign and some low-grade carcinomas, greater than zero in all other carcinomas, and increased in magnitude with higher tumor grade. A considerably smaller but significantly positive correlation was found between fPV and tumor grade using macromolecular contrast medium (r 2 = 0.25, P PS or fPV values and tumor grade was found using gadopentetate (r 2 = 0.01, P > 0.95 and r 2 = 0.03, P > 0.15, respectively). Conclusion. Quantitative tumor microvascular permeability assays generated with macromolecular MRI contrast medium correlate closely with histologic tumor grade. No significant correlation is found using small-molecular gadopentetate. (orig.)

  8. Designs for the self-assembly of open and closed macromolecular structures and a molecular switch using DNA methyltransferases to order proteins on nucleic acid scaffolds

    Science.gov (United States)

    Smith, Steven S.

    2002-06-01

    The methyltransferase-directed addressing of fusion proteins to DNA scaffolds offers an approach to the construction of protein/nucleic acid biostructures with potential in a variety of applications. The technology is currently only limited by the yield of high occupancy structures. However, current evidence shows that DNA scaffolds that contain three or four targeted proteins can be reliably constructed. This permits a variety of macromolecular designs, several of which are given in this paper. Designs for open and closed two-dimensional and three-dimensional assemblies and a design for a molecular switch are discussed. The closed two-dimensional assembly takes the form of a square, and could find application as a component of other systems including a macromolecular rotaxane. The closed three-dimensional system takes the form of a trigonal bipyramid and could find application as a macromolecular carcerand. The molecular switch could find application as a peptide biosensor. Guidelines for the construction and structural verification of these designs are reported.

  9. Vascular endothelial growth factor-receptor 1 inhibition aggravates diabetic nephropathy through eNOS signaling pathway in db/db mice.

    Directory of Open Access Journals (Sweden)

    Keun Suk Yang

    Full Text Available The manipulation of vascular endothelial growth factor (VEGF-receptors (VEGFRs in diabetic nephropathy is as controversial as issue as ever. It is known to be VEGF-A and VEGFR2 that regulate most of the cellular actions of VEGF in experimental diabetic nephropathy. On the other hand, such factors as VEGF-A, -B and placenta growth factor bind to VEGFR1 with high affinity. Such notion instigated us to investigate on whether selective VEGFR1 inhibition with GNQWFI hexamer aggravates the progression of diabetic nephropathy in db/db mice. While diabetes suppressed VEGFR1, it did increase VEGFR2 expressions in the glomerulus. Db/db mice with VEGFR1 inhibition showed more prominent features with respect to, albuminuria, mesangial matrix expansion, inflammatory cell infiltration and greater numbers of apoptotic cells in the glomerulus, and oxidative stress than that of control db/db mice. All these changes were related to the suppression of diabetes-induced increases in PI3K activity and Akt phosphorylation as well as the aggravation of endothelial dysfunction associated with the inactivation of FoxO3a and eNOS-NOx. In cultured human glomerular endothelial cells (HGECs, high-glucose media with VEGFR1 inhibition induced more apoptotic cells and oxidative stress than did high-glucose media alone, which were associated with the suppression of PI3K-Akt phosphorylation, independently of the activation of AMP-activated protein kinase, and inactivation of FoxO3a and eNOS-NOx pathway. In addition, transfection with VEGFR1 siRNA in HGECs also suppressed PI3K-Akt-eNOS signaling. In conclusion, the specific blockade of VEGFR1 with GNQWFI caused severe renal injury related to profound suppression of the PI3K-Akt, FoxO3a and eNOS-NOx pathway, giving rise to the oxidative stress-induced apoptosis of glomerular cells in type 2 diabetic nephropathy.

  10. JBluIce-EPICS: a fast and flexible open-source beamline control system for macromolecular crystallography

    International Nuclear Information System (INIS)

    This paper overviews recent advances in the JBluIce-EPICS open-source control system designed at the macromolecular crystallography beamlines of the National Institute of General Medical Sciences and National Cancer Institute at the Advanced Photon Source (GM/CA-APS). We discuss some technical highlights of this system distinguishing it from the competition, such as reduction of software layers to only two, possibility to operate JBluIce in parallel with other beamline controls, plugin-enabled architecture where the plugins can be written in any programming language, and utilization of the whole power of the Java integrated development environment in the Graphical User Interface. Then, we demonstrate how these highlights help to make JBluIce fast, easily adaptable to new beamline developments, and intuitive for users. In particular, we discuss several recent additions to the system including a bridge between crystal rastering and data collection, automatic detection of raster polygons from optical crystal centering, background data processing, and a pathway to a fully automated pipeline from crystal screening to solving crystal structure.

  11. Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly.

    Science.gov (United States)

    Fadda, Elisa

    2016-01-01

    Lack of structure is often an essential functional feature of protein domains. The coordination of macromolecular assemblies in DNA repair pathways is yet another task disordered protein regions are highly implicated in. Here I review the available experimental and computational data and within this context discuss the functional role of structure and disorder in one of the essential scaffolding proteins in the nucleotide excision repair (NER) pathway, namely Xeroderma pigmentosum complementation group A (XPA). From the analysis of the current knowledge, in addition to protein-protein docking and secondary structure prediction results presented for the first time herein, a mechanistic framework emerges, where XPA builds the NER pre-incision complex in a modular fashion, as "beads on a string", where the protein-protein interaction "beads", or modules, are interconnected by disordered link regions. This architecture is ideal to avoid the expected steric hindrance constraints of the DNA expanded bubble. Finally, the role of the XPA structural disorder in binding affinity modulation and in the sequential binding of NER core factors in the pre-incision complex is also discussed. PMID:26865925

  12. Effects of macromolecular crowding on a small lipid binding protein probed at the single-amino acid level.

    Science.gov (United States)

    Pérez Santero, Silvia; Favretto, Filippo; Zanzoni, Serena; Chignola, Roberto; Assfalg, Michael; D'Onofrio, Mariapina

    2016-09-15

    Macromolecular crowding is a distinctive feature of the cellular interior, influencing the behaviour of biomacromolecules. Despite significant advancements in the description of the effects of crowding on global protein properties, the influence of cellular components on local protein attributes has received limited attention. Here, we describe a residue-level systematic interrogation of the structural, dynamic, and binding properties of the liver fatty acid binding protein (LFABP) in crowded solutions. Two-dimensional NMR spectral fingerprints and relaxation data were collected on LFABP in the presence of polymeric and biomolecular crowders. Non-interacting crowders produced minimal site-specific spectral perturbations on ligand-free and lipid-bound LFABP. Conformational adaptations upon ligand binding reproduced those observed in dilute solution, but a perturbation of the free oleate state resulted in less favorable uptake. When LFABP engaged in direct interactions with background molecules, changes in local chemical environments were detected for residues of the internal binding pocket and of the external surface. Enhanced complexity was introduced by investigating LFABP in cell lysates, and in membrane-bounded compartments. LFABP was able to capture ligands from prokaryotic and eukaryotic cell lysates, and from artificial cells (water-in-oil emulsion droplets). The data suggest that promiscuous interactions are a major factor influencing protein function in the cell. PMID:27457417

  13. A New Methodology for Assessing Macromolecular Click Reactions and Its Application to Amine--Tertiary Isocyanate Coupling for Polymer Ligation.

    Science.gov (United States)

    Gody, Guillaume; Roberts, Derrick A; Maschmeyer, Thomas; Perrier, Sébastien

    2016-03-30

    Click reactions have provided access to an array of remarkably complex polymer architectures. However, the term "click" is often applied inaccurately to polymer ligation reactions that fail to respect the criteria that typify a true "click" reaction. With the purpose of providing a universal way to benchmark polymer-polymer coupling efficiency at equimolarity and thus evaluate the fulfilment of click criteria, we report a simple one-pot methodology involving the homodicoupling of α-end-functionalized polymers using a small-molecule bifunctional linker. A combination of SEC analysis and chromatogram deconvolution enables straightforward quantification of the coupling efficiency. We subsequently employ this methodology to evaluate an overlooked candidate for the click reaction family: the addition of primary amines to α-tertiary isocyanates (α-(t)NCO). Using our bifunctional linker coupling strategy, we show that the amine-(t)NCO reaction fulfills the criteria for a polymer-polymer click reaction, achieving rapid, chemoselective, and quantitative coupling at room temperature without generating any byproducts. We demonstrate that amine-(t)NCO coupling is faster and more efficient than the more common amine-tertiary active ester coupling under equivalent conditions. Additionally, we show that the α-(t)NCO end group is unprecedentedly stable in aqueous media. Thus, we propose that the amine-(t)NCO ligation is a powerful new click reaction for efficient macromolecular coupling.

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

    Directory of Open Access Journals (Sweden)

    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.

  15. Protective effects of glutathione on bromodichloromethane in vivo toxicity and in vitro macromolecular binding in Fischer 344 rats.

    Science.gov (United States)

    Gao, P; Thornton-Manning, J R; Pegram, R A

    1996-10-11

    Bromodichloromethane (BDCM), a carcinogenic water disinfection by-product, has been shown to be metabolized to intermediates that covalently bind to lipids and proteins, and this binding has been associated with trihalomethane-induced renal and hepatic toxicity. In this study, the effects of glutathione (GSH) on in vivo BDCM toxicity and in vitro BDCM macromolecular binding were evaluated. The in vivo toxicity of BDCM in animals pretreated with buthionine sulfoximine (BSO, a glutathione synthesis inhibitor) and in untreated male Fischer 344 rats was investigated. In another experiment, covalent binding to protein and lipid was quantified after [14C]BDCM was incubated with hepatic microsomal and S9 fractions and renal microsomes from F344 rats, under aerobic and anaerobic conditions, with and without added GSH. After oral dosing with BDCM, the BSO-pretreated animals had greatly increased levels of serum indicators of hepatotoxicity and serum and urinary indicators of nephrotoxicity compared to those in animals dosed solely with BDCM. Histopathological examination revealed that hepatic necrosis was more severe than renal necrosis in the BSO-treated rats. When GSH was added to an aerobic incubation, protein binding was decreased in hepatic microsomal and S9 fractions by 92 and 83%, respectively. GSH also decreased lipid binding by 55% in hepatic microsomal incubations carried out under anaerobic conditions. Addition of GSH decreased renal microsomal protein (aerobic) and lipid binding (anaerobic) by 20 and 43%, respectively. These data indicate that GSH is an important protective factor in the toxicity associated with BDCM.

  16. NSLS-II Biomedical beamlines for macromolecular crystallography, FMX and AMX, and for X-ray scattering, LIX: current developments

    International Nuclear Information System (INIS)

    We present the current status of development of the two macromolecular crystallography (MX) beamlines, FMX and AMX, and the X-ray scattering beamline LIX, at the National Synchrotron Light Source-II (NSLS-II) [1]. Together, FMX and AMX will cover a broad range of use cases from serial crystallography on micron sized crystals, to very large unit cell complexes, to rapid sample screening, e.g. for the always-hard-to-grow membrane proteins and for ligand binding studies. The LIX beamline will support a variety of X-ray scattering measurements for studies on proteins in solution, lipid membranes and biological tissues. We have performed Synchrotron Radiation Workshop (SRW) [2] and Shadow[3] simulations to help select optimal methods to modify the size of the beam easily and smoothly at both FMX and AMX. The very low emittance of the NSLS-II storage ring and the resulting low divergence of the X-ray beam, as well as the long optical path lengths in the photon delivery systems lead to stringent requirements e.g. for vibrational stability and mirror quality. We discuss beamline design considerations addressing these challenges, such as combining mirror optics with compound refractive lenses (CRLs).

  17. JBluIce-EPICS: a fast and flexible open-source beamline control system for macromolecular crystallography

    Science.gov (United States)

    Stepanov, S.; Hilgart, M.; Makarov, O.; Pothineni, S. B.; Yoder, D.; Ogata, C.; Sanishvili, R.; Venugopalan, N.; Becker, M.; Clift, M.; Smith, J. L.; Fischetti, R. F.

    2013-03-01

    This paper overviews recent advances in the JBluIce-EPICS open-source control system designed at the macromolecular crystallography beamlines of the National Institute of General Medical Sciences and National Cancer Institute at the Advanced Photon Source (GM/CA@APS). We discuss some technical highlights of this system distinguishing it from the competition, such as reduction of software layers to only two, possibility to operate JBluIce in parallel with other beamline controls, plugin-enabled architecture where the plugins can be written in any programming language, and utilization of the whole power of the Java integrated development environment in the Graphical User Interface. Then, we demonstrate how these highlights help to make JBluIce fast, easily adaptable to new beamline developments, and intuitive for users. In particular, we discuss several recent additions to the system including a bridge between crystal rastering and data collection, automatic detection of raster polygons from optical crystal centering, background data processing, and a pathway to a fully automated pipeline from crystal screening to solving crystal structure.

  18. The Immediate Intramedullary Nailing Surgery Increased the Mitochondrial DNA Release That Aggravated Systemic Inflammatory Response and Lung Injury Induced by Elderly Hip Fracture

    Directory of Open Access Journals (Sweden)

    Li Gan

    2015-01-01

    Full Text Available Conventional concept suggests that immediate surgery is the optimal choice for elderly hip fracture patients; however, few studies focus on the adverse effect of immediate surgery. This study aims to examine the adverse effect of immediate surgery, as well as to explore the meaning of mtDNA release after trauma. In the experiment, elderly rats, respectively, received hip fracture operations or hip fracture plus intramedullary nail surgery. After fracture operations, the serum mtDNA levels as well as the related indicators of systemic inflammatory response and lung injury significantly increased in the rats. After immediate surgery, the above variables were further increased. The serum mtDNA levels were significantly related with the serum cytokine (TNF-α and IL-10 levels and pulmonary histological score. In order to identify the meaning of mtDNA release following hip fracture, the elderly rats received injections with mtDNA. After treatment, the related indicators of systemic inflammatory response and lung injury significantly increased in the rats. These results demonstrated that the immediate surgery increased the mtDNA release that could aggravate systemic inflammatory response and lung injury induced by elderly hip fracture; serum mtDNA might serve as a potential biomarker of systemic inflammatory response and lung injury following elderly hip fracture.

  19. New methodologies at PF AR-NW12A: the implementation of high-pressure macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Chavas, Leonard Michel Gabriel, E-mail: leonard.chavas@kek.jp [PF/IMSS/KEK, 1-1 Oho, Tsukuba, Ibaraki 300-0801 (Japan); Nagae, Tadayuki [Nagoya University, Nagoya, Aichi 464-8603 (Japan); Nagoya University, Nagoya, Aichi 464-8603 (Japan); Yamada, Hiroyuki [Nagoya University, Nagoya, Aichi 464-8603 (Japan); Watanabe, Nobuhisa [Nagoya University, Nagoya, Aichi 464-8603 (Japan); Nagoya University, Furo-cho Chikusa-ku, Nagoya, Aichi 464-8603 (Japan); Yamada, Yusuke; Hiraki, Masahiko; Matsugaki, Naohiro [PF/IMSS/KEK, 1-1 Oho, Tsukuba, Ibaraki 300-0801 (Japan)

    2013-11-01

    The evolution of AR-NW12A into a multi-purpose end-station with optional high-pressure crystallography is described. The macromolecular crystallography (MX) beamline AR-NW12A is evolving from its original design of high-throughput crystallography to a multi-purpose end-station. Among the various options to be implemented, great efforts were made in making available high-pressure MX (HPMX) at the beamline. High-pressure molecular biophysics is a developing field that attracts the interest of a constantly growing scientific community. A plethora of activities can benefit from high pressure, and investigations have been performed on its applicability to study multimeric complex assemblies, compressibility of proteins and their crystals, macromolecules originating from extremophiles, or even the trapping of higher-energy conformers for molecules of biological interest. Recent studies using HPMX showed structural hydrostatic-pressure-induced changes in proteins. The conformational modifications could explain the enzymatic mechanism differences between proteins of the same family, living at different environmental pressures, as well as the initial steps in the pressure-denaturation process that have been attributed to water penetration into the protein interior. To facilitate further HPMX, while allowing access to various individualized set-ups and experiments, the AR-NW12A sample environment has been revisited. Altogether, the newly added implementations will bring a fresh breath of life to AR-NW12A and allow the MX community to experiment in a larger set of fields related to structural biology.

  20. Metabolism and macromolecular covalent binding of [14C]-1-nitropyrene in isolated perfused and ventilated rat lungs

    International Nuclear Information System (INIS)

    The purpose of this study was to quantitate l-nitropyrene (1-NP) metabolism and macromolecular covalent binding in the isolated perfused rat lung. Rat lungs were perfused with 2, 5, or 24 microM [14C]-1-NP for 90 min. Tidal volume and dynamic lung compliance were monitored throughout the perfusion to document the ventilatory pattern and the decay of tissue elasticity. Perfusate was sampled periodically throughout the experiment and analyzed for 1-NP metabolites with high-performance liquid chromatography. In all experiments, both dynamic lung compliance and tidal volume declined in a nearly linear manner and were approximately 60% of the initial value at the end of 90 min of perfusion. At all concentrations of [14C]-1-NP tested, less than 5 to 6% of the total amount of [14C]-1-NP added was metabolized in lungs from control and phenobarbital (PB)-treated rats. Lungs from control and PB- and 3-methylcholanthrene (3-MC)-treated rats metabolized [14C]-1-NP to oxidized, reduced, and conjugated metabolites. The major metabolites were 3-, 6-, and 8-hydroxynitropyrene. Treatment of rats with PB resulted in a 60% increase in the total metabolism of [14C]-1-NP, whereas treatment of rats with 3-MC resulted in a 10-fold increase in the rate of metabolism of [14C]-1-NP when compared to controls. Conjugate hydrolysis studies indicated that the water-soluble metabolites from lungs of control and PB- and 3-MC-treated rats consisted of hydroxynitropyrene glucuronides and hydroxynitropyrene sulfate conjugates. Quantities of 14C covalently bound to lung macromolecules after 90 min of perfusion from lungs of control and PB-treated rats were 0.06 to 0.21 nmol equivalents/g lung. However, in lungs from 3-MC-treated rats, there was a 20-fold increase in quantities of 14C covalently bound when compared to lungs from either control or PB-treated rats

  1. Presence of circulating macromolecular IgA in patients with hematuria due to primary IgA nephropathy

    Energy Technology Data Exchange (ETDEWEB)

    Valentijn, R.M.; Kauffmann, R.H.; de la Riviere, G.B.; Daha, M.R.; Van, E.S.

    1983-03-01

    The relation between renal histologic features and the presence of circulating immune complexes was studied in 50 patients with hematuria. Primary IgA nephropathy was found in 25 patients, and various other forms of glomerulopathy were seen in the remaining 25 patients. Circulating immune complexes were detected with the 125I-C1q-binding assay, the conglutinin-binding assay, and the anti-IgA inhibition binding assay, the latter detecting specifically IgA-containing immune complex-like material. The 125I-C1q-binding assay gave negative findings for all patients except one. With the conglutinin-binding assay, immune complexes were found in a similar frequency for patients with and without IgA nephropathy. However, the anti-IgA inhibition binding assay gave positive results only in patients with primary IgA nephropathy (68 percent) and in none of the other patients. Sucrose density ultracentrifugation, as well as experiments in which the anti-IgA inhibition binding assay was performed with and without pretreatment of serum with polyethylene glycol, showed the presumed IgA immune complexes to have intermediate sedimentation coefficients (11 to 21S). The presence and level of this macromolecular IgA in the circulation correlated significantly (p less than 0.001) with the presence of hematuria in patients who had this clinical manifestation intermittently. Furthermore, a significant correlation (r . 0.69, p less than 0.0001) was found between the degree of hematuria and the degree of positive findings of the anti-IgA inhibition binding assay. This study shows that in patients presenting with hematuria, a positive finding on the anti-IgA inhibition binding assay is restricted to patients with primary IgA nephropathy and therefore could be of diagnostic value.

  2. A theory for water and macromolecular transport in the pulmonary artery wall with a detailed comparison to the aorta.

    Science.gov (United States)

    Zeng, Zhongqing; Jan, Kung-Ming; Rumschitzki, David S

    2012-04-15

    The pulmonary artery (PA) wall, which has much higher hydraulic conductivity and albumin void space and approximately one-sixth the normal transmural pressure of systemic arteries (e.g, aorta, carotid arteries), is rarely atherosclerotic, except under pulmonary hypertension. This study constructs a detailed, two-dimensional, wall-structure-based filtration and macromolecular transport model for the PA to investigate differences in prelesion transport processes between the disease-susceptible aorta and the relatively resistant PA. The PA and aorta models are similar in wall structure, but very different in parameter values, many of which have been measured (and therefore modified) since the original aorta model of Huang et al. (23). Both PA and aortic model simulations fit experimental data on transwall LDL concentration profiles and on the growth of isolated endothelial (horseradish peroxidase) tracer spots with circulation time very well. They reveal that lipid entering the aorta attains a much higher intima than media concentration but distributes better between these regions in the PA than aorta and that tracer in both regions contributes to observed tracer spots. Solutions show why both the overall transmural water flow and spot growth rates are similar in these vessels despite very different material transport parameters. Since early lipid accumulation occurs in the subendothelial intima and since (matrix binding) reaction kinetics depend on reactant concentrations, the lower intima lipid concentrations in the PA vs. aorta likely lead to slower accumulation of bound lipid in the PA. These findings may be relevant to understanding the different atherosusceptibilities of these vessels. PMID:22198178

  3. The influence of hyaluronic acid hydrogel crosslinking density and macromolecular diffusivity on human MSC chondrogenesis and hypertrophy.

    Science.gov (United States)

    Bian, Liming; Hou, Chieh; Tous, Elena; Rai, Reena; Mauck, Robert L; Burdick, Jason A

    2013-01-01

    Hyaluronic acid (HA) hydrogels formed via photocrosslinking provide stable 3D hydrogel environments that support the chondrogenesis of mesenchymal stem cells (MSCs). Crosslinking density has a significant impact on the physical properties of hydrogels, including their mechanical stiffness and macromolecular diffusivity. Variations in the HA hydrogel crosslinking density can be obtained by either changes in the HA macromer concentration (1, 3, or 5% w/v at 15 min exposure) or the extent of reaction through light exposure time (5% w/v at 5, 10, or 15 min). In this work, increased crosslinking by either method resulted in an overall decrease in cartilage matrix content and more restricted matrix distribution. Increased crosslinking also promoted hypertrophic differentiation of the chondrogenically induced MSCs, resulting in more matrix calcification in vitro. For example, type X collagen expression in the high crosslinking density 5% 15 min group was ~156 and 285% higher when compared to the low crosslinking density 1% 15 min and 5% 5 min groups on day 42, respectively. Supplementation with inhibitors of the small GTPase pathway involved in cytoskeletal tension or myosin II had no effect on hypertrophic differentiation and matrix calcification, indicating that the differential response is unlikely to be related to force-sensing mechanotransduction mechanisms. When implanted subcutaneously in nude mice, higher crosslinking density again resulted in reduced cartilage matrix content, restricted matrix distribution, and increased matrix calcification. This study demonstrates that hydrogel properties mediated through alterations in crosslinking density must be considered in the context of the hypertrophic differentiation of chondrogenically induced MSCs. PMID:23084553

  4. Davisson-Germer Prize in Atomic or Surface Physics Lecture: Line 'Em All Up: Macromolecular Assembly at Liquid Interfaces

    Science.gov (United States)

    Richmond, Geraldine

    2013-03-01

    Advances in our molecular level understanding of the ubiquitous fluid interface comprised of a hydrophobic fluid medium, and an aqueous solution of soluble ions and solutes has been slow until recently. This more recent upsurge in interest and progress comes from advances in both experimental and computational techniques as well as the increasingly important role that this interface is playing in such areas as green chemistry, nanoparticle synthesis, improved oil and mineral recovery and water purification. The presentation will focus on our most recent efforts in understanding (1) the molecular structure of the interface between two immiscible liquids, (2) the penetration of aqueous phase ions into the interfacial region and their effect on its properties, and (3) the structure and dynamics of the adsorption of surfactants, polymers and nanoparticles at this interface. To gain insights into these processes we use a combination of vibrational sum frequency spectroscopy, surface tension measurements using the pendant drop method, and molecular dynamics simulations. The results demonstrate that weak interactions between interfacial oil and water molecules create an interface that exhibits a high degree of molecular structuring and ordering, and with properties quite different than what is observed at the air-water interface. As a consequence of these interfacial oil-water interactions, the interface provides a unique environment for the adsorption and assembly of ions, polymers and nanoparticles that are drawn to its inner-most regions. Examples of our studies that provide new insights into the unique nature of adsorption, adsorption dynamics and macromolecular assembly at this interface will be provided.

  5. Does ageing aggravate parkinsonian disability?

    OpenAIRE

    Blin, J; DuBois, B; Bonnet, A M; Vidailhet, M; Brandabur, M; Agid, Y

    1991-01-01

    The influence of age of onset of Parkinson's disease on the severity and the pattern of motor symptoms was investigated by comparing the motor scores with and without levodopa therapy in two groups of patients divided according to age of onset (early less than 50, late greater than 60 years) and matched for disease duration (n = 69 in each group, Study I). The baseline score, that is, the motor disability of patients when off levodopa, was similar in the early- and late- onset groups. In cont...

  6. Are droughts occurrence and severity aggravating? A study on SPI drought class transitions using loglinear models and ANOVA-like inference

    Directory of Open Access Journals (Sweden)

    E. E. Moreira

    2011-12-01

    Full Text Available Long time series (95 to 135 yr of the Standardized Precipitation Index (SPI computed with the 12-month time scale relative to 10 locations across Portugal were studied with the aim of investigating if drought frequency and severity are changing through time. Considering four drought severity classes, time series of drought class transitions were computed and later divided into 4 or 5 sub-periods according to length of time series. Drought class transitions were calculated to form a 2-dimensional contingency table for each period. Two-dimensional loglinear models were fitted to these contingency tables and an ANOVA-like inference was then performed in order to investigate differences relative to drought class transitions among those sub-periods, which were considered as treatments of only one factor. The application of ANOVA-like inference to these data allowed to compare the four or five sub-periods in terms of probabilities of transition between drought classes, which were used to detect a possible trend in time evolution of droughts frequency and severity that could be related to climate change. Results for a number of locations show some similarity between the first, third and fifth period (or the second and the fourth if there were only 4 sub-periods regarding the persistency of severe/extreme and sometimes moderate droughts. In global terms, results do not support the assumption of a trend for progressive aggravation of droughts occurrence during the last century, but rather suggest the existence of long duration cycles.

  7. Reinjury risk of nano-calcium oxalate monohydrate and calcium oxalate dihydrate crystals on injured renal epithelial cells: aggravation of crystal adhesion and aggregation

    Science.gov (United States)

    Gan, Qiong-Zhi; Sun, Xin-Yuan; Bhadja, Poonam; Yao, Xiu-Qiong; Ouyang, Jian-Ming

    2016-01-01

    Background Renal epithelial cell injury facilitates crystal adhesion to cell surface and serves as a key step in renal stone formation. However, the effects of cell injury on the adhesion of nano-calcium oxalate crystals and the nano-crystal-induced reinjury risk of injured cells remain unclear. Methods African green monkey renal epithelial (Vero) cells were injured with H2O2 to establish a cell injury model. Cell viability, superoxide dismutase (SOD) activity, malonaldehyde (MDA) content, propidium iodide staining, hematoxylin–eosin staining, reactive oxygen species production, and mitochondrial membrane potential (Δψm) were determined to examine cell injury during adhesion. Changes in the surface structure of H2O2-injured cells were assessed through atomic force microscopy. The altered expression of hyaluronan during adhesion was examined through laser scanning confocal microscopy. The adhesion of nano-calcium oxalate monohydrate (COM) and calcium oxalate dihydrate (COD) crystals to Vero cells was observed through scanning electron microscopy. Nano-COM and COD binding was quantitatively determined through inductively coupled plasma emission spectrometry. Results The expression of hyaluronan on the cell surface was increased during wound healing because of Vero cell injury. The structure and function of the cell membrane were also altered by cell injury; thus, nano-crystal adhesion occurred. The ability of nano-COM to adhere to the injured Vero cells was higher than that of nano-COD crystals. The cell viability, SOD activity, and Δψm decreased when nano-crystals attached to the cell surface. By contrast, the MDA content, reactive oxygen species production, and cell death rate increased. Conclusion Cell injury contributes to crystal adhesion to Vero cell surface. The attached nano-COM and COD crystals can aggravate Vero cell injury. As a consequence, crystal adhesion and aggregation are enhanced. These findings provide further insights into kidney stone

  8. Analysis of Causes of Re-aggravation in the Process of Treatment of Cerebral Infarction%脑梗治疗过程中再次加重的原因分析

    Institute of Scientific and Technical Information of China (English)

    肖玲

    2016-01-01

    Objective To analyze the causes of re-aggravation in the process of treatment of cerebral infarction and research preventive measures. Methods 60 cases of patients whose disease was aggravated again after treatment in our hospital due to cerebral infarction from December 2010 to December 2015 were selected and the causes of them were retrospectively analyzed. Results Cerebral infarction occurred to 23 cases due to decreased blood pressure caused by cerebral infarction drugs, the disease of 12 cases was aggravated due to the intravenous infusion of glucose, cerebral infarction occurred to 13 cases due to cerebral hemorrhage, infusion reaction occurred to 12 cases. Conclusion The research shows that the re-aggravation can be totally avoided if the medical staff can pay attention to it in the process of treatment.%目的:对脑梗治疗过程中再次加重的原因分析,研究预防对策。方法选取2010年12月—2015年12月在该院因脑梗住院的进行治疗后病情再次加重的患者60例,对其因素进行回顾性分析。结果有23例患者是由于脑梗用药导致血压降低从而出现脑梗,有12例患者由于静脉输入葡萄糖后加重,有13例患者由于脑出血后导致,有12例患者出现输液反应。结论研究当中能够了解到,医护人员在治疗中重视,能够完全避免再次加重的情况出现。

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

    Science.gov (United States)

    Jensen, K F; Pedersen, S

    1990-06-01

    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 molecular sharing economy at a high level of competition inside the cell. Thus, the promoters compete with each other in the binding of a limited amount of free RNA polymerase and the ribosome binding sites on the mRNA chains compete with each other for the free ribosomes. The macromolecular chain elongation reactions sequester a considerable proportion of the total amount of RNA polymerase and ribosomes in the cells. We propose that the degree of subsaturation of the macromolecular biosynthetic apparatus renders a variable fraction of RNA polymerase and ribosomes unavailable for the initiation of new chain synthesis and that this, at least in part, determines the composition of the cell as a function of the growth rate. Thus, at rapid growth, the high speed of the elongation reactions enables the cell to increase the concentrations of free RNA polymerase and ribosomes for initiation purposes. Furthermore, it is proposed that the speed of RNA polymerase movement is adjusted to the performance speed of the ribosomes. Mechanistically, this adjustment of the coupling between transcription and translation involves transcriptional pause sites along the RNA chains, the adjustment of the saturation level of RNA polymerase with the nucleoside triphosphate substrates, and the concentration of ppGpp, which is known to inhibit RNA chain elongation. This model is able to explain the stringent response and the control of stable RNA and of ribosome synthesis in steady states and in shifts, as well as the rate of overall protein synthesis as a function of the growth rate. PMID:1694554

  10. The surface modification of TiN nano-particles using macromolecular coupling agents, and their resulting dispersibility

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Guojun, E-mail: chengguojun0436@126.com [School of Chemistry and Chemical Engineering, Anhui University, Hefei 230039 (China); School of Materials Science and Engineering, Anhui University of Science and Technology, Huainan 232001 (China); Qian, Jiasheng, E-mail: qianjs@ahu.edu.cn [School of Chemistry and Chemical Engineering, Anhui University, Hefei 230039 (China); Miao, Jibin; Yang, Bin; Xia, Ru; Chen, Peng [School of Chemistry and Chemical Engineering, Anhui University, Hefei 230039 (China)

    2014-05-01

    Graphical abstract: The hydroxyl groups on the surface of nano-TiN particles interacted with the silanol groups [-Si-OCH{sub 3}] of a F-MCA to form an organic coating layer that hindered the aggregation of the nano-TiN. The obvious agglomeration and homogeneous dispersion can be seen in TEM images. - Highlights: • The dispersible TiN nano-particles were prepared to increase its surface activity. • Surface hydrophobicity increased due to being modified by F-MCA. • TiN nano-particles modified with F-MCA shows good dispersion in anhydrous ethanol. • The coupling agents are tightly absorbed on the surface of particles by chemisorption. • Modified TiN nano-particles can be widely used in polymers with great compatibility. - Abstract: Titanium nitride (TiN) nano-particles were modified by the grafting of a random copolymerization functionalized macromolecular coupling agent (F-MCA) via a direct blending method. The hydroxyl groups on the surface of the nano-TiN particles interact with the silanol groups [-Si-OCH{sub 3}] of the F-MCA to form an organic coating layer. The formation of covalent bonds [Ti-O-Si] was verified using Fourier transform infrared spectroscopy. An X-ray diffraction analysis suggests that the presence of the F-MCA inhibited the growth of the crystal plane but did not change the crystal structure of the TiN. Thermogravimetric analysis and contact angle measurement indicated that the F-MCA molecules were adsorbed or anchored to the surface of the nano-TiN particles, which hindered their aggregation. Pristine nano-TiN particles are poorly dispersed in ethyl acetate. Compared with the pristine TiN particles, the modified TiN particles show good dispersibility and form a stable colloidal dispersion in ethyl acetate. The surface hydrophobicity of the modified TiN increases, and the F-MCA molecules are anchored on the surface of the TiN particles. TiN particles modified by a F-MCA can be used in polymer blends, thermoplastic elastomers and polymer

  11. Social Factors to Aggravate Disasters in Yunnan in Late Imperial China%清末民初云南灾荒加剧的社会因素

    Institute of Scientific and Technical Information of China (English)

    蒋立文

    2012-01-01

    云南的自然环境极具灾害性。明清以降至清末民初,由于人口急速膨胀、农田过度开垦和山林矿藏的掠夺式开发,云南生态环境迅速恶化,进而加速加剧了各类自然灾害的发生;农业与家庭手工业相结合的自然经济又从根本上限制了社会抗灾减荒能力的生成与提高。封建剥削、战乱兵祸及列强的经济掠夺、迷信赌毒等造成社会环境的全面恶化,各族民众极度贫困,加重了灾后饥荒疾疫的蔓延与流行。中央与地方政府的荒政长久缺失,导致云南赈灾救荒活动严重乏力。总之,清末民初的云南已完全陷入人为破坏生态环境加剧自然灾害频发、逢灾必荒的结果加速了社会环境的恶化、社会环境恶化又加重了饥荒的蔓延这一恶性循环过程。%Yunnan is prone to natural disasters due to its environment. From the Ming and Qing dynasties to late imperial China, population explosion, over-farming, predatory exploitation of forests and minerals, and ecological damages aggravated all kinds of natural disasters in Yunnan on one hand, and on the other hand, natural economy of agriculture and household handicrafts weakened the power of society to prevent and reduce disasters. Feudal exploitation, government's taxes, wars, bandits, economic plunder of imperialists, superstition, gambling and drugs deteriorated social environment, and extreme poverty of ethnic people speeded.up the wide spread of famine and epidemic after disasters. Neither the central government nor the local governments made policies to deal with natural disasters. As a result, disaster relief in Yunnan was seriously weak. All in all, Yunnan in late imperial China was ecological damages leading to frequent natural disasters which totally stuck into a vicious circle of man-made then would deteriorate social environment, and which in turn would result in prolonged famines.

  12. Single high-dose irradiation aggravates eosinophil-mediated fibrosis through IL-33 secreted from impaired vessels in the skin compared to fractionated irradiation

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Eun-Jung, E-mail: forejs2@yuhs.ac [Department of Radiation Oncology, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Kim, Jun Won, E-mail: JUNWON@yuhs.ac [Department of Radiation Oncology, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Yoo, Hyun, E-mail: gochunghee@yuhs.ac [Department of Radiation Oncology, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Kwak, Woori, E-mail: asleo02@snu.ac.kr [Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-747 (Korea, Republic of); Choi, Won Hoon, E-mail: wonhoon@yuhs.ac [Department of Radiation Oncology, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Cho, Seoae, E-mail: seoae@cnkgenomics.com [C& K Genomics, Seoul National University Mt.4-2, Main Bldg. #514, SNU Research Park, NakSeoungDae, Gwanakgu, Seoul 151-919 (Korea, Republic of); Choi, Yu Jeong, E-mail: yunk9275@daum.net [Department of Radiation Oncology, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of); Lee, Yoon-Jin, E-mail: yjlee8@kirams.re.kr [Division of Radiation Effects, Research Center for Radiotherapy, Korea Institute of Radiological & Medical Sciences, Seoul 139-760 (Korea, Republic of); Cho, Jaeho, E-mail: jjhmd@yuhs.ac [Department of Radiation Oncology, Yonsei University College of Medicine, Seoul 120-752 (Korea, Republic of)

    2015-08-14

    We have revealed in a porcine skin injury model that eosinophil recruitment was dose-dependently enhanced by a single high-dose irradiation. In this study, we investigated the underlying mechanism of eosinophil-associated skin fibrosis and the effect of high-dose-per-fraction radiation. The dorsal skin of a mini-pig was divided into two sections containing 4-cm{sup 2} fields that were irradiated with 30 Gy in a single fraction or 5 fractions and biopsied regularly over 14 weeks. Eosinophil-related Th2 cytokines such as interleukin (IL)-4, IL-5, and C–C motif chemokine-11 (CCL11/eotaxin) were evaluated by quantitative real-time PCR. RNA-sequencing using 30 Gy-irradiated mouse skin and functional assays in a co-culture system of THP-1 and irradiated-human umbilical vein endothelial cells (HUVECs) were performed to investigate the mechanism of eosinophil-mediated radiation fibrosis. Single high-dose-per-fraction irradiation caused pronounced eosinophil accumulation, increased profibrotic factors collagen and transforming growth factor-β, enhanced production of eosinophil-related cytokines including IL-4, IL-5, CCL11, IL-13, and IL-33, and reduced vessels compared with 5-fraction irradiation. IL-33 notably increased in pig and mouse skin vessels after single high-dose irradiation of 30 Gy, as well as in irradiated HUVECs following 12 Gy. Blocking IL-33 suppressed the migration ability of THP-1 cells and cytokine secretion in a co-culture system of THP-1 cells and irradiated HUVECs. Hence, high-dose-per-fraction irradiation appears to enhance eosinophil-mediated fibrotic responses, and IL-33 may be a key molecule operating in eosinophil-mediated fibrosis in high-dose-per fraction irradiated skin. - Highlights: • Single high-dose irradiation aggravates eosinophil-mediated fibrosis through IL-33. • Vascular endothelial cells damaged by high-dose radiation secrete IL-33. • Blocking IL-33 suppressed migration of inflammatory cells and cytokine secretion. • IL

  13. Drugs associated with the aggravation/induction of psoriasis: an update%药物诱发加重银屑病的研究进展

    Institute of Scientific and Technical Information of China (English)

    张冉; 杨森; 张学军

    2013-01-01

    银屑病是遗传、免疫和环境因素共同作用的结果,药物作为外因之一可诱发健康人群患病或恶化病情,如β肾上腺能受体阻滞剂、锂盐、抗疟药、四环素类抗生素等.药物按其与银屑病相关程度不同,可分为明确相关,有确切证据;可能相关,缺乏确切证据;偶有报道,有争议.按其后果不同可分为诱发银屑病的药物和恶化银屑病的药物.近年来发现诱发和加重银屑病的药物种类逐渐增多,有的药物本身可用于银屑病的临床治疗.了解这些药物的致病概况及致病机制,不仅有利于预防银屑病复发,而且对临床治疗有重要的指导意义.%Psoriasis is caused by a variety of internal and external paradoxical factorsincluding genetics,immunity and environment.Drugs,such as p-adrenergic receptor blockers,lithium,synthetic antimalarial drugs and tetracyclines,are an important external factor and can induce/aggravatepsoriasis.In view of their relationship to psoriasis,drugs can be classified into agents with evident relationshipsupported by strong evidence,agents with potential association supported by insufficient evidence,and agents with controversial relationship supported by occasional reports.According to their effects,drugs may beclassified into inducing agents and exacerbating agents.Recently,more and more drugs have been found to beassociated with the induction/aggravation of psoriasis,and some of them are used in the treatment of psoriasis.Understanding the effect and pathogenic mechanisms of the associated drugs not only helps to prevent psoriasisrelapse,but also is beneficial to the treatment of psoriasis.

  14. The in-vivo use of superparamagnetic iron oxide nanoparticles to detect inflammation elicits a cytokine response but does not aggravate experimental arthritis.

    Directory of Open Access Journals (Sweden)

    Eline A Vermeij

    -term effects were evident for gene expression, histology or serum cytokine concentrations.Injection of SPION, either locally or systemically, gives an acute inflammatory response. In the long term, up to 14 days after the injection, while the SPION reside in the joint, no further activating effects of SPION were observed. Hence, we conclude that SPION do not aggravate arthritis and can therefore be used safely to detect joint inflammation by MR imaging.

  15. Macromolecular crystallographic estructure refinement

    Directory of Open Access Journals (Sweden)

    Afonine, Pavel V.

    2015-04-01

    Full Text Available Model refinement is a key step in crystallographic structure determination that ensures final atomic structure of macromolecule represents measured diffraction data as good as possible. Several decades have been put into developing methods and computational tools to streamline this step. In this manuscript we provide a brief overview of major milestones of crystallographic computing and methods development pertinent to structure refinement.El refinamiento es un paso clave en el proceso de determinación de una estructura cristalográfica al garantizar que la estructura atómica de la macromolécula final represente de la mejor manera posible los datos de difracción. Han hecho falta varias décadas para poder desarrollar nuevos métodos y herramientas computacionales dirigidas a dinamizar esta etapa. En este artículo ofrecemos un breve resumen de los principales hitos en la computación cristalográfica y de los nuevos métodos relevantes para el refinamiento de estructuras.

  16. Macromolecular prodrugs of ribavirin

    DEFF Research Database (Denmark)

    Smith, Anton Allen Abbotsford; Zuwala, Kaja; Kryger, Mille;

    2015-01-01

    Human immunodeficiency virus (HIV) and hepatitis C virus (HCV) represent tremendous healthcare burdens with a large proportion of patients hosting the two viruses at the same time. An altered hepatic function and immunity as well as cross-interference of drugs make treatment of co-infection incre......Human immunodeficiency virus (HIV) and hepatitis C virus (HCV) represent tremendous healthcare burdens with a large proportion of patients hosting the two viruses at the same time. An altered hepatic function and immunity as well as cross-interference of drugs make treatment of co...... compositions were also potent in anti-inflammatory assays with relevance to viral hepatitis – thus making up formulations with potential for treatment of co-infection with HIV and HCV....

  17. Macromolecular Materials and Engineering

    Science.gov (United States)

    Cover: The image shows electrospun fibers based on poly(lactic acid)/polyaniline blends with diameters from 90 to 1000 nm. The structural characteristics of the fibers are compared to cast films by scanning electron microscopy, small-angle X-ray scattering, differential scanning calorimetry, and ato...

  18. 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

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

    Energy Technology Data Exchange (ETDEWEB)

    Pompidor, Guillaume; Dworkowski, Florian S. N.; Thominet, Vincent [Paul Scherrer Institut, CH-5232 Villigen (Switzerland); Schulze-Briese, Clemens [DECTRIS Ltd, CH-5400 Baden (Switzerland); Fuchs, Martin R., E-mail: mfuchs@bnl.gov [Paul Scherrer Institut, CH-5232 Villigen (Switzerland)

    2013-09-01

    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.

  20. Changes of macromolecular organizations in nonjunctional sarcolemmas after cross—innervation—a study of fast—and slow—twitch muscle fiberes in rats

    Institute of Scientific and Technical Information of China (English)

    LUJINANLI; TIEFENGZHANG; 等

    1995-01-01

    The purpose of the present study was to analyse the changes of macromolecular organizations in nonjunctional sarcolemmas of different types of skeletal muscle fibres after cross-innervation.In normal rate the mean density of square arrays(6nm particles organized in orthogonal of square arrays(6nm particles organized in othogonal arrays)was 9.02/μm2 for the nonjunctional sarcolemmas of fast-twitch extensor digitorum longus(control EDL,CE)muscle fibres and 0.34/μm2 for the nunjunctional sarcolemmas of slow-twitch soleus(control SOL,CS)muscle fibres.After cross-innervation between the fast-twitch EDL and slow-twitch SOL muscle fibres by slow and fast muscle nerves respectively for three months ,the mean density was 0.45/μm2 for the nonjunctional sarcolemmas of the operated EDL(OE)and 8.3/μm2 for the nonjunctional sarcolemmas of the operated SOL(OS).This indicates that the cross-innervation causes a reciprocal transformation of the number and distribution of such macromolecular organizations in the electrically excitable nonjunctional sarcolemmas.

  1. Cost-effective imprinting combining macromolecular crowding and a dummy template for the fast purification of punicalagin from pomegranate husk extract.

    Science.gov (United States)

    Sun, Guang-Ying; Wang, Chao; Luo, Yu-Qin; Zhao, Yong-Xin; Yang, Jian; Liu, Zhao-Sheng; Aisa, Haji Akber

    2016-05-01

    The combination of molecular crowding and virtual imprinting was employed to develop a cost-effective method to prepare molecularly imprinted polymers. By using linear polymer polystyrene as a macromolecular crowding agent, an imprinted polymer recognizable to punicalagin had been successfully synthesized with punicalin as the dummy template. The resulting punicalin-imprinted polymer presented a remarkable selectivity to punicalagin with an imprinting factor of 3.17 even at extremely low consumption of the template (template/monomer ratio of 1:782). In contrast, the imprinted polymer synthesized without crowding agent, did not show any imprinting effect at so low template amount. The imprinted polymers made by combination of molecular crowding and virtual imprinting can be utilized for the fast separation of punicalagin from pomegranate husk extract after optimizing the protocol of solid-phase extraction with the recovery of 85.3 ± 1.2%. PMID:27027975

  2. 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.

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

    Directory of Open Access Journals (Sweden)

    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

  4. 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

  5. Covalent Modification of SPI by Dextran in Macromolecular Crowding Conditions%大分子拥挤体系下葡聚糖对SPI的共价修饰

    Institute of Scientific and Technical Information of China (English)

    齐军茹; 卓秀英; 杨晓泉; 尹寿伟; 黄立新

    2011-01-01

    In order to explore the covalent modification of proteins by polysaccharide chains, soy protein isolate (SPI)-dextran conjugate (SDC) was prepared via the Maillard reaction in macromolecular crowding conditions. Then, the functions and conformation of the product were analyzed by means of the sodium dodecyl sulfate-polyac-rylamide gel electrophoresis, the fluorescence spectroscopy, the gel permeation chromatography and the circular di-chroism spectroscopy. The results show that ( 1) there occurs a covalent binding of dextran to SPI after the Maillard reaction best being carried out with a SPI-to-dextran mass ratio of 1:1 at 60℃ for 30h; (2) as compared with the SPI-dextran mixture without the Maillard reaction, SDC possesses less hydrophobic groups pn its surface and stronger emulsifying activity in macromolecular crowding conditions; (3 ) SDC is more thermally stable than SPI; and (4) the covalent binding of polysaccharides changes the structure of SPI and improves the structural flexibility, which benefits the function display of SPI.%为探讨糖链对蛋白质的共价修饰作用,在大分子拥挤体系中通过Maillard反应制备了大豆分离蛋白(SPI) -葡聚糖共价复合物(SDC),通过十二烷基磺酸钠二聚丙烯酰胺凝胶电泳、荧光光谱、凝胶渗透色谱、圆二色光谱等方法研究了葡聚糖共价键入后对SPI功能和构象的影响.结果表明,大豆分离蛋白和葡聚糖发生共价结合;Maillard反应的适宜条件为SPI/葡聚糖质量比1:1,温度60℃、反应时间30h;在大分子拥挤体系中,与未经Maillard反应的SPI/葡聚糖混合物相比,SDC表面的疏水基团减少,乳化活性较高;与SPI相比,SDC的热稳定性提高;糖链的键入使SPI的结构发生了变化,柔韧性有所增加,更有利于发挥其功能.

  6. 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

  7. 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)

    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

  8. Co-administration of α-lipoic acid and cyclosporine aggravates colon ulceration of acetic acid-induced ulcerative colitis via facilitation of NO/COX-2/miR-210 cascade.

    Science.gov (United States)

    El-Gowelli, Hanan M; Saad, Evan I; Abdel-Galil, Abdel-Galil A; Ibrahim, Einas R

    2015-11-01

    In this work, α-lipoic acid and cyclosporine demonstrated significant protection against acetic acid-induced ulcerative colitis in rats. We proposed that α-lipoic acid and cyclosporine co-administration might modulate their individual effects. Induction of ulcerative colitis in rats was performed by intra-rectal acetic acid (5% v/v) administration for 3 consecutive days. Effects of individual or combined used of α-lipoic acid (35 mg/kg ip) or cyclosporine (5mg/kg sc) for 6 days starting 2 days prior to acetic acid were assessed. Acetic acid caused colon ulceration, bloody diarrhea and weight loss. Histologically, there was mucosal atrophy and inflammatory cells infiltration in submucosa, associated with depletion of colon reduced glutathione, superoxide dismutase and catalase activities and elevated colon malondialdehyde, serum C-reactive protein (C-RP) and tumor necrosis factor-α (TNF-α). Colon gene expression of cyclooxygenase-2 and miR-210 was also elevated. These devastating effects of acetic acid were abolished upon concurrent administration of α-lipoic acid. Alternatively, cyclosporine caused partial protection against acetic acid-induced ulcerative colitis. Cyclosporine did not restore colon reduced glutathione, catalase activity, serum C-RP or TNF-α. Unexpectedly, co-administration of α-lipoic acid and cyclosporine aggravated colon ulceration. Concomitant use of α-lipoic acid and cyclosporine significantly increased nitric oxide production, cyclooxygenase-2 and miR-210 gene expression compared to all other studied groups. The current findings suggest that facilitation of nitric oxide/cyclooxygenase-2/miR-210 cascade constitutes, at least partially, the cellular mechanism by which concurrent use of α-lipoic acid and cyclosporine aggravates colon damage. Collectively, the present work highlights the probable risk of using α-lipoic acid/cyclosporine combination in ulcerative colitis patients.

  9. Research on Strategy of Foreign Trade Enterprises in Guangxi Based on the Aggravation of European Debt Crisis%欧债危机加剧下广西外贸企业对策探讨

    Institute of Scientific and Technical Information of China (English)

    林赵华

    2012-01-01

      The global economic, financial and trade situations deteriorate sharply with the European debt crisis erupting, spreading and upgrading. China's foreign trade is impacted tremendously and the development of foreign trade enterprises in Guangxi will inevitably be affected. In the paper, the aggravation of the European debt crisis is described. Its adverse effects on the development of foreign trade enterprises in Guangxi are analyzed through several aspects of the transmission mechanism in external demand, exchange rate fluctuations, exchange risk and trade frictions. And the development strategies coping with aggravation of the European debt crisis are proposed.%  欧债危机的爆发、蔓延和加剧,使全球经济、金融、贸易形势急剧恶化,我国外贸经济遭受巨大冲击,广西外贸企业的发展也不可避免地受到影响。文章就欧债危机加剧的态势,通过其外部需求、汇率变动、汇兑风险和贸易摩擦等几方面的传导机制,分析了欧债危机对广西对外贸易发展的不利影响,并相应地提出了外贸企业应对欧债危机日益加剧的策略。

  10. Effects of Macromolecular Emulsifiers on Double-emulsions Stability and Application%大分子乳化剂对复乳稳定性的影响及应用

    Institute of Scientific and Technical Information of China (English)

    徐成业; 陈亭亭; 陆伟根

    2011-01-01

    In this paper the mechanism of double-emulsions stability improved by macromolecular emulsifiers as well as the applications of macromolecular emulsifiers in the double-emulsions are reviewed. Double-emulsions are complex liquid dispersion systems, which are inherent thermodynamic unstable systems and tend to delaminate,flocculate and coalesce. Double-emulsions are usually stabilized by adding monomeric emulsifiers. In recently years,macromolecular emulsifiers such as biopolymers, block copolymers and polymeric emulsifies have obtained the widespread application in the double-emulsions, because these macromolecules can improve the stability of them.%综述了大分子乳化剂改善复乳稳定性的作用机制及其在复乳中的应用现状.复乳是复杂的液体分散体系,为热力学不稳定系统,易发生分层、絮凝和合并,通常加入单体乳化剂以提高其稳定性.近年来大分子乳化剂如生物聚合物、嵌段聚合物、高分子乳化剂因能较好地改善复乳稳定性,在复乳中得到广泛应用.

  11. Mutational interactions between near-UV radiation and DNA damaging agents in Escherichia coli: the role of near-UV-induced modifications in growth and macromolecular synthesis

    International Nuclear Information System (INIS)

    The mutational interactions between near-ultraviolet (334 nm, 365 nm) radiation and DNA damaging agents (far-UV (254 nm) and ethyl-methanesulphonate (EMS)) were studied in strains of Escherichia coli B/r trp thy with different susceptibilities to near-UV-induced growth delay (wild-type, rel and sr). Far-UV induced reversion to tryptophan independence is reduced while forward mutation to streptomycin is enhanced by prior exposure of the rel+ srd+ strains to near-UV radiation. The observed interactions are reduced (rel) or absent (srd) in the two mutant strains as are the corresponding growth and macromolecular synthesis delays normally observed after near-UV treatment. Quantitatively, the degree of interaction induced by near-UV pre-treatment correlates closely with the degree of protein synthesis inhibition. A mechanism is proposed for the contrasting interactions at the two genetic loci based on the different pathways by which pre-mutagenic lesions may be processed. The primary chromophore for the mutational interactions would appear to be 4-thiouracil-containing transfer RNA. (author)

  12. Effects of Opioids on Macromolecular Constituents of Animal Tissues%阿片对动物组织大分子成分的影响

    Institute of Scientific and Technical Information of China (English)

    李定健

    2012-01-01

    阿片系统是调节机体生理活动的系统之一。根据近几十年进行的调查,阿片被认为在控制家畜和其他种类动物生长中起着重要作用。然而有关阿片对家畜组织重量及组织DNA、RNA和蛋白质影响的研究甚少。阐述了阿片对豚鼠、负鼠以及真螈组织大分子成分的影响。虽然阿片是否影响组织功能尚不清楚,但是阿片可以抑制小白鼠和人类的免疫功能。%Opioid system is one of the systems to modulate physiological activities in the body. According to the investigations in recent decades, opioids are presumed to play a vital role in the control of growth in farm animals and other species. However little information is available regarding the effects of opioids on tissue weights and DNA, RNA and protein levels of tissues in farm animals. Effects of opioids on macromolecular constituents of tissues in guinea pigs, opossums and salamanders are described in the article. Although it is unclear whether opioids could affect the function of tissues or not, opioids can induce immunosuppression in mice and humans.

  13. 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.

  14. The Structure of Plant Cell Walls: I. The Macromolecular Components of the Walls of Suspension-cultured Sycamore Cells with a Detailed Analysis of the Pectic Polysaccharides.

    Science.gov (United States)

    Talmadge, K W; Keegstra, K; Bauer, W D; Albersheim, P

    1973-01-01

    This is the first in a series of papers dealing with the structure of cell walls isolated from suspension-cultured sycamore cells (Acer pseudoplatanus). These studies have been made possible by the availability of purified hydrolytic enzymes and by recent improvements in the techniques of methylation analysis. These techniques have permitted us to identify and quantitate the macromolecular components of sycamore cell walls. These walls are composed of 10% arabinan, 2% 3,6-linked arabinogalactan, 23% cellulose, 9% oligo-arabinosides (attached to hydroxyproline), 8% 4-linked galactan, 10% hydroxyproline-rich protein, 16% rhamnogalacturonan, and 21% xyloglucan.The structures of the pectic polymers (the neutral arabinan, the neutral galactan, and the acidic rhamnogalacturonan) were obtained, in part, by methylation analysis of fragments of these polymers which were released from the sycamore walls by the action of a highly purified endopolygalacturonase. The data suggest a branched arabinan and a linear 4-linked galactan occurring as side chains on the rhamnogalacturonan. Small amounts or pieces of a xyloglucan, the wall hemicellulose, appear to be covalently linked to some of the galactan chains. Thus, the galactan appears to serve as a bridge between the xyloglucan and rhamnogalacturonan components of the wall.The rhamnogalacturonan consists of an alpha-(1 --> 4)-linked galacturonan chain which is interspersed with 2-linked rhamnosyl residues. The rhamnosyl residues are not randomly distributed in the chain but probably occur in units of rhamnosyl- (1 --> 4)-galacturonosyl- (1 --> 2)-rhamnosyl. This sequence appears to alternate with a homogalacturonan sequence containing approximately 8 residues of 4-linked galacturonic acid. About half of the rhamnosyl residues are branched, having a substituent attached to carbon 4. This is likely to be the site of attachment of the 4-linked galactan.The hydroxyprolyl oligo-arabinosides of the hydroxyproline-rich glycoprotein

  15. Working at higher magnifications in scanning electron microscopy with secondary and backscattered electrons on metal coated biological specimens and imaging macromolecular cell membrane structures.

    Science.gov (United States)

    Peters, K R

    1985-01-01

    Membrane structures of macromolecular dimensions were imaged with high resolution secondary electron type I (SE-I) signal contrasts on metal coated biological specimens. The quality of the surface information was strongly dependent on the signal used for microscopy and on the properties of metal films, i.e., thickness, continuity, structure and decoration effects. Films of 10 nm thickness produced so much type II electrons that identical images were obtained with the conventional SE-II and BSE-II signals. In such images, the type I SE signal was so low that only very weak contrasts were recognizable. If the films--continuous or discontinuous--were composed of large metal aggregates (gold and platinum) a strong micro-roughness contrast was produced by the type II signal. At high magnifications (100,000 x) this background signal greatly reduced the S/N ratio of the SE-I signal. A similar effect was previously shown to be produced by the type III background signal. The type II background signal minimized when continuous films of small aggregates (tantalum and chromium) were applied. SE-I contrast dominated in the image if the film thickness was limited to 1 nm. Additionally, it was found that gold and platinum decorated membrane surface structures, less than 20 nm in size, and did not reveal all the topographic information available (size, shape, orientation spacing of small surface features) but merely displayed center-to-center distances. These decoration effects were avoided and extensive topographic information was obtained through surface coating with Ta or Cr. PMID:4095499

  16. Reaction Blending of PET with an Epoxy Macromolecular Chain Extender%大分子环氧扩链剂与PET的反应共混研究

    Institute of Scientific and Technical Information of China (English)

    刘世纯; 崔秀丽; 谭志勇

    2013-01-01

    采用连续自由基聚合法合成的大分子环氧扩链剂(聚甲基丙烯酸甲酯/甲基丙烯酸环氧丙酯)共聚物(PMMA-co-GMA)作为聚对苯二甲酸乙二酯(PET)的改性剂,考察了大分子环氧扩链剂的用量及聚合度对PET流变性能和结晶性能的影响。结果表明,随着扩链剂用量及聚合度的增加,PET共混物的扭矩和温度都明显提高,到达最大扭矩及温度的时间均提前;大分子环氧扩链剂的引入使PET共混物的结晶温度降低,结晶峰峰值降低,峰面积减小,PET的结晶度降低;PET共混物经热处理后结晶行为发生变化。%An epoxy macromolecular chain extender(PMMA-co-GMA) was synthesized by continuous random free radical polymerization,which was introduced into poly(ethylene terephthalate)(PET) and PET blends. Influences of the content and the polymerization degree of PMMA-co-GMA on rheological and crystallization properties of PET blends were investigated. The results show that the modiifed PET blends exhibited higher torque and temperature with increasing the content and the polymerization degree of PMMA-co-GMA. The time of reaching maximum torques and temperature are in advanced. The crystallization temperature, crystallization peak value and crystallization degree of PET blends decreased when adding PMMA-co-GMA. The crystallization behaviors of PET is effected by annealing.

  17. 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

    2007-12-01

    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). PMID

  18. The use of trimethylamine N-oxide as a primary precipitating agent and related methylamine osmolytes as cryoprotective agents for macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Marshall, Haley; Venkat, Murugappan; Hti Lar Seng, Nang San; Cahn, Jackson [Whitman College, Walla Walla, Washington (United States); Juers, Douglas H., E-mail: juersdh@whitman.edu [Whitman College, Walla Walla, Washington (United States); Whitman College, Walla Walla, Washington (United States)

    2012-01-01

    The stabilizing osmolyte trimethylamine N-oxide (TMAO) is shown to be an efficient primary precipitant for protein crystal growth. In addition to TMAO, two other methylamine osmolytes, sarcosine and betaine, are shown to be effective cryoprotective agents for protein crystal cooling. Both crystallization and cryoprotection are often bottlenecks for high-resolution X-ray structure determination of macromolecules. Methylamine osmolytes are known stabilizers of protein structure. One such osmolyte, trimethylamine N-oxide (TMAO), has seen occasional use as an additive to improve macromolecular crystal quality and has recently been shown to be an effective cryoprotective agent for low-temperature data collection. Here, TMAO and the related osmolytes sarcosine and betaine are investigated as primary precipitating agents for protein crystal growth. Crystallization experiments were undertaken with 14 proteins. Using TMAO, seven proteins crystallized in a total of 13 crystal forms, including a new tetragonal crystal form of trypsin. The crystals diffracted well, and eight of the 13 crystal forms could be effectively cryocooled as grown with TMAO as an in situ cryoprotective agent. Sarcosine and betaine produced crystals of four and two of the 14 proteins, respectively. In addition to TMAO, sarcosine and betaine were effective post-crystallization cryoprotective agents for two different crystal forms of thermolysin. Precipitation reactions of TMAO with several transition-metal ions (Fe{sup 3+}, Co{sup 2+}, Cu{sup 2+} and Zn{sup 2+}) did not occur with sarcosine or betaine and were inhibited for TMAO at lower pH. Structures of proteins from TMAO-grown crystals and from crystals soaked in TMAO, sarcosine or betaine were determined, showing osmolyte binding in five of the 12 crystals tested. When an osmolyte was shown to bind, it did so near the protein surface, interacting with water molecules, side chains and backbone atoms, often at crystal contacts.

  19. A rare aggravation of severe mucositis post chemotherapy in a child with acute lymphoblastic leukemia [v1; ref status: indexed, http://f1000r.es/1tf

    Directory of Open Access Journals (Sweden)

    Adlette Inati

    2013-09-01

    Full Text Available Oral mucositis is a debilitating manifestation in children undergoing chemotherapy and radiotherapy. Children with mucositis should be properly managed in order to prevent further exacerbation and adverse complications. We hereby present the first report of a severe chemotherapy-induced mucositis, plausibly aggravated by improper dental hygiene leading to shedding of the ventral part of the tongue in a child with pre-B acute lymphoblastic leukemia (ALL. The patient steadily and gradually recovered her oral maneuvers and ability to speak several months later. Her tongue underwent hypertrophy as a compensatory mechanism. We recommend that critical and regular assessment of the oral mucosa and proper dental care and oral hygiene be emphasized in all pediatric patients receiving chemotherapy. Families of affected children need to be educated about the benefits and modes of optimal oral hygiene for their children and the need to seek immediate care for mouth pain and or lesions. Optimal treatment for mucositis needs to be instituted without delay in this high risk pediatric population. Such a preventive and therapeutic approach may prevent associated life threatening oral and systemic complications, promote rapid and complete mucosal healing, alleviate pain and improve quality of life in children with cancer.

  20. Synthesis of novel complexing macromolecular surfactants and study of their interactions with cobalt for the development of a decontamination process of textiles in dense CO2 medium

    International Nuclear Information System (INIS)

    This study is about textile decontamination in dense CO2 (liquid CO2 or supercritical CO2). The study is carried out in the framework of decontamination of textile used in the nuclear industry. The dense CO2 offers an alternative to aqueous medium used in the current process which generates a huge quantity of contaminated aqueous effluent requiring a post-treatment. Cobalt is the targeted contamination and can be found as ionic species or particles. The cobalt extraction in dense CO2 is achieved with an additive: a complexing CO2-philic/CO2-phobic macromolecular surfactant. Several types of additives were synthesized by controlled free radical polymerization: gradient copolymers made with CO2-philic groups (silicone-based or fluorinated moieties) and CO2-phobic complexing groups (aceto acetoxy, di-ethylphosphonate or phosphonic acid moieties). The copolymer behavior in dense CO2 was determined by phase diagram measurements (cloud point method) and their self-assembly in dense CO2 was investigated by small angle neutron scattering. The fluorinated copolymers were found advantageous in terms of solubility. Nevertheless, the silicone-based copolymers showed solubilities which are compatible with the process, therefore they are a good alternative to avoid fluorinated compounds which are unwanted in the conditioning of nuclear wastes. The study of cobalt complexation by the copolymers (UV-vis spectroscopy and inductively coupled plasma-mass spectroscopy) established relations between the type of complexing group and the affinity with the cobalt. The solubility of copolymer-cobalt complexes in dense CO2 is similar to those of copolymers. Moreover, the self-assembly study of the complex revealed a low aggregation. Finally, the synthesized copolymers were used in particle or ionic decontamination processes. In the case of ionic decontamination process, a rate of 70% of decontamination was reached with the use of gradient copolymer poly(1,1,2,2-tetrahydroperfluoro

  1. The effect of thermal processing in oil on the macromolecular integrity and acrylamide formation from starch of three potato cultivars organically fertilized

    Directory of Open Access Journals (Sweden)

    Theo Varzakas

    2016-12-01

    Full Text Available Starches from three organically produced cultivars of potato tuber (Lady Rosetta, Spunta and Voyager have been studied in relation to (i acrylamide production (ii macromolecular integrity after frying with extra virgin olive oil, soybean oil and corn oil. During cultivation, a treatment involving the combination of nitrogen, phosphorus and potassium fertilization under organic farming was applied (N1, P2, K1 where Ν1 = 1.3 g Ν per plant, P2 = 5.2 g P2O5 per plant, Κ1 = 4.0 g K2O per plant. Potatoes fried in olive oil retained the highest glucose concentrations for all cultivars 0.85 ± 0.2 mmol/kg, followed by 0.48 ± 0.2 for those fried in corn oil and 0.40 ± 0.1 mmol/kg for those fried in soybean oil. The highest average fructose concentration was recorded for the samples fried in corn oil as 0.81 ± 0.2, followed by 0.80 ± 0.2 and 0.68 ± 0.3 mmol/kg for the samples fried in olive and soybean oils, respectively. Asparagine was the most abundant free amino acid in the three varieties tested, followed by glutamine and aspartic acid. The mean initial concentration of asparagine in raw potatoes tubers was 42.8 ± 1.6 mmoles kg−1 for Lady Rosetta, 34.6 ± 1.2 mmoles kg−1 (dry weight for Spunta and 36.2 ± 2.0 mmoles kg−1 for Voyager. Lady Rosetta contained a significantly higher concentration of asparagine compared to the other two varieties (p < 0.05. The greatest quantity of acrylamide was observed in French fries derived from the potato variety Lady Rosetta when fried in soybean oil and it was 2,600 ± 440 μg/kg, followed by Spunta which was 2,280 ± 340 μg/kg and Voyager 1,120 ± 220 μg/kg. There is a significant reduction in the formation of acrylamide in the variety Voyager compared to the others (p = 0.05.

  2. Asthma aggravation, combustion, and stagnant air

    OpenAIRE

    Norris, G; Larson, T; Koenig, J.; Claiborn, C.; Sheppard, L; D. Finn

    2000-01-01

    BACKGROUND—The relationship between current concentrations of ambient air pollution and adverse health effects is controversial. We report a meteorological index of air stagnation that is associated with daily visits to the emergency department for asthma in two urban areas.
METHODS—Data on daily values of a stagnation persistence index and visits to the emergency department for asthma were collected for approximately two years in Spokane, Washington, USA and for 15months...

  3. 高通量测序探讨胰腺炎加重肝损伤的研究%Through high-throughput sequencing technologies to explore the mechanism of pancreatitis aggravating liver damage

    Institute of Scientific and Technical Information of China (English)

    王谦; 白槟; 赵占伟; 余鹏飞; 郝一鸣; 邱兆岩; 郭敏; 冯全新; 刘朝旭

    2016-01-01

    目的 探讨急性胰腺炎(AP)加重肝脏损伤的机制.方法 将SD大鼠随机分为AP组和对照组(NC),采用牛磺胆酸钠逆行胰胆管注射的方法建立AP模型,造模后6h经下腔静脉采血,检测血清淀粉酶、脂肪酶水平、胰腺水含量,同时收集肝脏组织,用于提取RNA.通过转录组测序(RNA-seq)的方法分析AP加重肝损害的相关基因和通路改变.结果 AP组与NC组比,其血清淀粉酶[(8 964.65 ±401.23) U/L]和脂肪酶[(2350.00 ±201.90) U/L]含量明显上升(P<0.05);胰腺水含量AP组[(79.42±1.21)%]显著高于NC组[(70.14±1.02)%];RNA-seq结果显示两组间共有2 249个差异表达基因,其中564个表达上调,1 685个表达下调.京都基因与基因组百科全书(KEGG)通路富集结果由高到低为代谢通路、炎性因子通路、趋化因子通路、Toll样受体通路等.结论 AP可能通过炎性因子、Toll样受体(TLR)等通路介导了对肝脏的损伤.%Objective To explore the mechanism of acute pancrea titis (AP) aggravating liver damage.Methods SD rats were randomly divided into negative control (NC) and AP group.We use the method of sodium taurocholate retrograde pancreatic duct injection to establish the model of AP.After 6 h of anesthesia,the blood were collected from the inferior vena cava to detect the levels of serum amylase and lipase.The liver tissue was collected imnediately in order to extract total RNA.The genes and related pathways were analyzed by RNA-seq.Results Compared to NC group,the levels of serum amylase [(8 964.65 ±401.23) U/L] and lipase [(2 350.00 ± 201.90) U/L] were significantly higher in AP group (P <0.05);the pancreatic water content in AP group [(79.42 ± 1.21) %] were significantly higher than NC group [(70.14 ± 1.02) %];RNA-seq results showed that there were 2249 differently expressed genes between AP and NC group,among which 564 genes were up-regulated and 1685 genes were down-regulated.Kyoto gene and genome encyclopedia (KEGG

  4. A primer in macromolecular linguistics.

    Science.gov (United States)

    Searls, David B

    2013-03-01

    Polymeric macromolecules, when viewed abstractly as strings of symbols, can be treated in terms of formal language theory, providing a mathematical foundation for characterizing such strings both as collections and in terms of their individual structures. In addition this approach offers a framework for analysis of macromolecules by tools and conventions widely used in computational linguistics. This article introduces the ways that linguistics can be and has been applied to molecular biology, covering the relevant formal language theory at a relatively nontechnical level. Analogies between macromolecules and human natural language are used to provide intuitive insights into the relevance of grammars, parsing, and analysis of language complexity to biology.

  5. Advances in Macromolecular Data Storage

    CERN Document Server

    Mansuripur, Masud

    2014-01-01

    We propose to develop a new method of information storage to replace magnetic hard disk drives and other instruments of secondary/backup data storage. The proposed method stores petabytes of user-data in a sugar cube (1 cm3), and can read/write that information at hundreds of megabits/sec. Digital information is recorded and stored in the form of a long macromolecule consisting of at least two bases, A and B. (This would be similar to DNA strands constructed from the four nucleic acids G,C,A,T.) The macromolecules initially enter the system as blank slates. A macromolecule with, say, 10,000 identical bases in the form of AAAAA....AAA may be used to record a kilobyte block of user-data (including modulation and error-correction coding), although, in this blank state, it can only represent the null sequence 00000....000. Suppose this blank string of A's is dragged before an atomically-sharp needle of a scanning tunneling microscope (STM). When electric pulses are applied to the needle in accordance with the seq...

  6. A primer in macromolecular linguistics.

    Science.gov (United States)

    Searls, David B

    2013-03-01

    Polymeric macromolecules, when viewed abstractly as strings of symbols, can be treated in terms of formal language theory, providing a mathematical foundation for characterizing such strings both as collections and in terms of their individual structures. In addition this approach offers a framework for analysis of macromolecules by tools and conventions widely used in computational linguistics. This article introduces the ways that linguistics can be and has been applied to molecular biology, covering the relevant formal language theory at a relatively nontechnical level. Analogies between macromolecules and human natural language are used to provide intuitive insights into the relevance of grammars, parsing, and analysis of language complexity to biology. PMID:23034580

  7. 微通道中高分子溶液Poiseuille流的耗散粒子动力学模拟*%Dissipative particle dynamics simulation of macromolecular solutions under Poiseuille flow in microchannels∗

    Institute of Scientific and Technical Information of China (English)

    许少锋; 汪久根

    2013-01-01

      macromolecular solutions under Poiseuille flow in microchannels are investigated using the dissipative particle dynamics (DPD) approach. The results show that the macromolecular solutions are non-Newtonian fluids which can be described by power-law fluids, and the power-law index decreases with the increase of the macromolecular concentration. The DPD simulations show that the hydro-dynamic interaction between the macromolecular chains and the wall, and the gradient of Brownian diffusivity of the chains govern the cross-stream migration of the macromolecules. However, the chain-wall hydrodynamic interaction may not be fully developed and are partly screened in conventional DPD approach. Hence, the chains migrate toward the wall during flow. Simulation results also indicate that the migration toward the wall increases with the increase of the driving force. The competition between the unscreened chain-wall hydrodynamic interaction and Brownian diffusivity leads to two symmetric off-center peaks and a local minimum in the channel centerline in the chain center-of-mass distribution. Under strong confinement, the chain-wall hydrodynamic interaction may be fully screened and the Brownian motion is weak, thus the chains weakly move toward the wall for channel of small width.%  利用耗散粒子动力学(dissipative particle dynamics, DPD)方法模拟了微通道中高分子溶液的Poiseuille流动。研究表明,微通道中的高分子溶液呈现非牛顿流体特性,可以用幂律流体来描述流动行为,高分子浓度越大,幂律指数n越小。高分子链与壁面的流体动力学相互作用以及布朗扩散率梯度控制着高分子链的横向迁移。由于传统的DPD方法中壁面诱导的流体动力学作用部分被屏蔽,高分子链将向壁面方向迁移,并且随着流场增强,高分子链向壁面方向迁移越明显。未被屏蔽的流体动力学相互作用和布朗扩散率梯度相互竞争,使高分子链在微通道

  8. Hyperbaric oxygen therapy aggravates liver reperfusion injury in rats Oxigenoterapia hiperbárica agrava lesão de reperfusão hepática em ratos

    Directory of Open Access Journals (Sweden)

    Cristiano Xavier Lima

    2008-08-01

    Full Text Available PURPOSE: To evaluate the effects of hyperbaric oxygen (HO therapy in the protection against liver ischemia/reperfusion injury. METHODS: Thirty-two male Wistar rats were divided into four groups of eight animals each: group A - laparotomy and liver manipulation, group B - liver ischemia and reperfusion, group C - HO pretreatment for 60 min followed by liver ischemia and reperfusion, and group D - pretreatment with ambient air at 2.5 absolute atmospheres for 60 min followed by liver ischemia and reperfusion. Plasma was assayed for aspartate aminotransferase (AST, alanine aminotransferase (ALT and lactate dehydrogenase (LDH. Intra-arterial blood pressure was monitored continuously. Myeloperoxidase activity in the liver and lung was assessed 30 min after reperfusion. RESULTS: Plasma AST, ALT and LDH increased after reperfusion in all animals. Plasma ALT values and myeloperoxidase activity in the liver parenchyma were higher in HO-pretreated animals than in groups A, B and D. HO had a negative hemodynamic effect during liver reperfusion. CONCLUSION: Liver preconditioning with hyperbaric oxygen therapy aggravated liver ischemia/reperfusion injury in rats as demonstrated by plasma ALT and liver myeloperoxidase activity.OBJETIVO: Avaliar os efeitos da oxigenoterapia hiperbárica (OH como método preventivo da lesão de isquemia e reperfusão (LIR do fígado. MÉTODOS: Trinta e dois ratos machos Wistar foram distribuídos em quatro grupos de oito animais cada: A - laparotomia e manipulação hepática, B - isquemia e reperfusão hepática, C - pré-tratamento com OH por 60 minutos seguido de isquemia e reperfusão hepática e D - pré-tratamento com ar ambiente a 2,5 atmosferas absolutas por 60 minuto e isquemia e reperfusão hepática. Dosagens seriadas de AST, ALT e DHL foram realizadas. A pressão intra arterial foi monitorizada continuamente. O grau de infiltração leucocitária no fígado e pulmões foi inferido pela dosagem de mieloperoxidade

  9. Research Progress in Macromolecular Network Based on Cyclodextrin Inclusive Associations%基于环糊精包合作用的大分子网络研究进展

    Institute of Scientific and Technical Information of China (English)

    郭拥军; 王用良; 冯茹森; 乔智华; 钟金杭

    2011-01-01

    环糊精与客体分子的“锁一钥匙”包合作用,是一种纯粹的分子间非共价键作用力,利用这一超分子作用力可以构筑大分子网络体系。基于环糊精分子的包合选择性、可调控性等优势,该缔合体系在过去十多年里备受人们关注,已成为大分子组装研究的热点。本文对这种基于环糊精包合作用的分子间包结缔合型大分子网络的最新进展进行了综述,主要包括:(1)环糊精的二聚体、交联聚合物、线型聚合物、支化或星型聚合物分别与两亲聚合物自组装形成超分子聚合物、纳米粒子、缔合增稠流体、超分子水凝胶;(2)环糊精接枝新型无机功能分子进而与两亲性客体聚合物构建杂化水凝胶;(3)具有对pH、温度、光等敏感的智能凝胶的设计、设备及其在药物、基因传递与组织工程支架中的应用。%Based on the "lock-and-key" inclusion complexation between cyclodextrins and various guest molecules, which is strictly intermolekular non-covalent interaction, novel macromolecular networks can be formed. The novel networks have attracted much attention and have been the focus of macromolecular self-assembly in recent years due to the advantages of selectivity, regulating capability of cyclodextrins. In this paper, the recent progresses of macromolecular networks assembled by inclusive associations is reviewed, which mainly include. (1) supramolecular polymers, nanoparticles, association thickening fluid or supramolecular hydrogels induced by the complexation between cyclodextrin dimers,cyclodextrin crosslinked polymers, pendent cyclodextrin polymers, multi-arms star or hyperbranched polymers and the amphiphilic polymers; (2) hybrid organic-inorganic hydrogels prepared from CD-grafted new functional inorganic species and amphiphilic polymers; (3) the design and preparation of the supramolecular hydrogels with stimuli-responsive properties

  10. 高血糖通过抑制线粒体自噬加重大鼠脑缺血/再灌注损伤%Hyperglycemia aggravated cerebral ischemia/reperfusion injury by inhibiting mitophagy

    Institute of Scientific and Technical Information of China (English)

    左玮; 梅丹

    2016-01-01

    Aim Toinvestigatetheroleofhyperglyce-mia in cerebral ischemia/reperfusion(I/R)injury with a middle cerebral artery occlusion(MCAO)rat model anditsmechanism.Methods EightyhealthymaleSD rats were randomly assigned into sham group, I/R group (normoglycemia),hyperglycemic I/R groupⅠ(HG1 )and hyperglycemic I/R groupⅡ(HG2 ).The cerebral I/R model was established by occluding the middle cerebral artery(MCA)in rats.Hyperglycemia was induced by intraperitoneal injection of 50% glu-cose solution.Neurological deficit was determined by Ludmila Belayev test;infarct size and brain edema were measured by TTC staining;mitophagy was ob-served by double immunofluorescent staining and elec-tron microscope.The expressions of autophagy-related proteins(LC3 and Beclin-1 )and apoptosis-related pro-teins(Cyt-C,AIF,caspase-9 and caspase-3 )were ex-aminedbyWesternblotfurtherly.Results Bloodglu-cose level was controlled at 4 mmol·L-1 (normoglyce-mia),10 mmol · L-1 (HG1 ) and 20 mmol · L-1 (HG2)respectively.There were no significant differ-ences between model group and HG1 group in neuro-logical deficit scores,infarct volume and edema size(P>0. 05 ).However,these indications in HG2 group were significantly increased compared with model group (P<0. 05 ).After 3 days of reperfusion,the level of mitophagy was significantly reduced accompanied with increased mitochondria damages in HG 2 group (P <0. 05 ),and the expressions of mitochondrial related ap-optotic proteins(Cyt-C,AIF,caspase-9 and caspase-3 ) were significantly increased accordingly compared to modelgroup.Conclusions Mildhyperglycemiacan not intensify the cerebal ischemic injury.In contrast, severe hyperglycemia significantly aggravates the brain ischemic injury by inhibiting the removal of injured mi-tochondria in a manner of mitophagy,thus amplifying the mitochondrial mediated cascade damage responses.%目的探讨急性高血糖对局灶性脑缺血大鼠神经功能损伤的作用及机制。方

  11. 大分子乳化剂稳定的纳米乳中β-胡萝卜素的降解%Degradation of β-carotene in Nanoemulsions Stabilized by Macromolecular Emulsifiers

    Institute of Scientific and Technical Information of China (English)

    李燕; 刘成梅; 刘伟

    2012-01-01

    Macromolecular emulsifiers including whey protein isolate, heated whey isolate protein, mixture and maillard reaction products (MRPs) of whey protein isolate and maltodextrin were used to prepared β - carotene nanoemulsions. The particle size distribution as well as the β - carotene degradation at different temperatures of the obtained emulsions were investigated. The results showed that the average particle size of the nanoemulsions stabilized by MRPs was significantly lower and the β - carotene encapsulated in them degradated more rapidly than the other samples. Besides that,the heated whey isolate protein could effectively decrease the β-carotene degradation rate,which might be attributed to the protection effect of the protein aggregates formed during the heat process.%分别以乳清分离蛋白、热处理乳清分离蛋白、乳清分离蛋白与麦芽糖糊精的混合物和美拉德反应复合物为乳化剂,制备β-胡萝卜素纳米乳,并考察其乳滴粒径分布及β-胡萝卜素的降解.结果表明:乳清分离蛋白与麦芽糖糊精共价复合后,形成的纳米乳液平均粒径更小,但复合物加速纳米乳中β-胡萝卜素的降解.而热处理乳清分离蛋白能显著抑制纳米乳中β-胡萝卜素的降解,其机制可能是蛋白质大分子聚集体的形成对β-胡萝卜素起保护作用.

  12. 基于大分子拥挤原理的介孔二氧化硅中青霉素酰化酶的共价组装%Covalent Assembly of Penicillin Acylase in Mesoporous Silica Based on Macromolecular Crowding Theory

    Institute of Scientific and Technical Information of China (English)

    王安明; 周成; 王华; 沈树宝; 薛建跃; 欧阳平凯

    2007-01-01

    To improve the covalent immobilization of penicillin acylase (PA),macromolecular crowding theory was applied to its immobilization. Influence of mass ratio of enzyme to the silica,as well as,activation time with glutaraldehyde on the activity of assembled PA,was studied. In the mesopores,the effect of β-cyclodextrin (β-CD)on the immobilization of the enzyme was also investigated. It was remarkable that the coupled yield and relative activity reached 99.5% and 92.3%,respectively,when penicillin acylase assembled covalently in the mesopores. The results here indicate that mimicked macromolecule crowding could significantly ameliorate the performance of covalently immobilized PA.

  13. Does Population Ageing Aggravate Income Inequality? Evidence from China 1996 -2009%人口老龄化是否加剧收入不平等?——基于中国(1996~2009)的实证研究

    Institute of Scientific and Technical Information of China (English)

    董志强; 魏下海; 汤灿晴

    2012-01-01

    Since inequality differs cross population groups, changing population age structure may have an effect on overall income inequality. This paper develops an analytical (statistical) model to describe conditions under which population ageing could aggravate income inequality, and show theoretically and empirically that the conditions are true in China. Thus, it is hypothesized that population ageing aggravates inequality in China. With Gini coefficient as measurement of income inequality, and employing provincial level panel data over 1996 -2009, this paper confirms that population ageing (i. e. an increasing aged dependency ratio and a decreasing child dependency ratio) is a positive and significant factor contributing to income inequality. This suggests that inequality studies need to incorporate population ageing, as it conveys different policy implications as compared to other factors.%不同年龄群体内部的收入程度通常存在差异,因而人口年龄结构变迁会影响整个经济的收入不平等程度。文章建立了一个(统计性)分析框架,刻画出老龄化导致收入不平等加剧的条件,并从经济理论和经验证据上说明该条件在中国成立,从而提出假说:中国的老龄化加剧了经济中的收入不平等。运用1996—2009年省级面板数据,以基尼系数衡量收入不平等,从经验上证实老龄化(老年抚养比上升和少儿抚养比下降)对我国收入不平等有显著的正向影响。这一结论表明,研究收入不平等问题时,应注意老龄化这一长期被研究者们忽视的因素,因为它蕴含着与其他因素大不相同的政策含义。

  14. 高压喷射氧雾化吸入沐舒坦对慢性阻塞性肺疾病急性加重期痰液性状的影响%The Effects of Ambroxol Mucosolvan Inhalated by High-pressure Jet Oxygen Atomization to Sputum Properties in Patients with Chronic Obstructive Pulmonary Disease During Acute Aggravating Period

    Institute of Scientific and Technical Information of China (English)

    杨玉平; 周向东

    2014-01-01

    Objective To observe the effects of Ambroxol mucosolvan inhalated by High-pressure jet oxygen atomization to the physical and chemical properties of sputum in patients with chronic obstructive pulmonary disease during acute aggravating period. Method 72 cases of COPD patients with acute aggravating period to give an easy high-pressure jet oxygen atomization inhalation,bathing separately col ected before detect atomization,1 hours after atomization sputum volume,wet/dry weight and viscosity. Results After oxygen atomization,oxygen atomization before amount of sputum,sputum viscosity,sputum dry/wet weight had significant dif erence (p<0.05), and inflammatory biomarkers of neutrophil (PMN) combined with elastic enzyme membrane(HLE) has no obvious change. Conclusion High-pressure jet oxygen atomization inhalation of Ambroxol mucosolvan with dilute sputum and increased sputum volume effect,so as to ease of airway obstruction caused by high mucus secretion,relieve the patient's clinical symptoms,but the inhibition effect of the inflammatory response in the airways of has yet to be further research.%目的:观察高压喷射氧雾化吸入沐舒坦对慢性阻塞性肺疾病(COPD)急性加重期患者痰液理化性质的作用。方法72例COPD急性加重期患者给予沐舒坦高压喷射氧雾化吸入,分别收集检测雾化前、雾化后1h痰液量、干/湿重及黏度。结果氧雾化前与雾化后的痰液量、痰液黏度、痰液干/湿重均有明显差异(P<0.05)。而炎症指标中性粒细胞(PMN)膜结合弹力酶(HLE)无明显改变。结论高压喷射氧雾化吸入沐舒坦有稀释痰液、增加排痰量的作用。从而缓解黏液高分泌所致的气道阻塞、减轻患者的临床症状,但抑制气道炎症反应的作用尚无明确证据。

  15. Respiratory training and prompting effective discharging of sputum for COPD patients in acute aggravation period%呼吸训练和促进有效排痰应用于急性加重期慢性阻塞性肺疾病患者的效果观察

    Institute of Scientific and Technical Information of China (English)

    张洪; 邱丽清; 陈丽延

    2008-01-01

    Objective To discuss the influence of respiratory training and prompting effective discharging of sputum for chronic obstructive pulmonary disease (COPD) patients in acute aggravation period. Methods 50 patients were randomized into the intervention group and the control group with 25 cases in each group.The intervention group received respiratory training and prompting effective discharging of sputum while the control was only given routine treatment and nursing.The ratio of first second expiration volume to forced vital capacity, oxygen partial pressure (PaO2),carben dioxide partial pressure (PaCO2) ,blood oxygen saturation (SpO2)and the in-hospital days were compared between the two groups. Results The clinical effect in the intervention group was superior to that of the control group with shorter in-hospital days (P<0.01).Conclusion Better results could be obtained by application of respiratory training and prompting effective discharging of sputum for COPD patients in acute aggravation period.%目的 探讨呼吸训练和促进有效排痰对慢性阻塞性肺疾病(COPD)急性加重期患者康复的影响.方法 将50例患者随机分成干预组和对照组各25例,干预组由护士进行呼吸训练和促进有效排痰,对照组按常规进行治疗护理,比较2组患者第1秒用力呼气容积占用力肺活量百分比、氧分压、二氧化碳分压、血氧饱和度及2组患者住院天数.结果 干预组肺功能各项指标显著优于对照组,P<0.05,住院天数缩短,P<0.01. 结论呼吸训练和促进有效排痰对COPD急性加重期患者康复有较好的效果.

  16. Effects of organic macromolecular on sodium metasilicate fouling behavior of polyamide composite nanofiltration membrane%有机大分子对聚酰胺复合纳滤膜偏硅酸钠污染的影响

    Institute of Scientific and Technical Information of China (English)

    张晓婷; 王磊; 杨若松; 王佳璇

    2016-01-01

    选用腐殖酸(HA),海藻酸钠(SA),牛血清蛋白(BSA)和偏硅酸钠分别模拟水体中有机大分子和无机污染物对聚酰胺复合纳滤膜进行了膜污染试验.结合原子力显微镜(AFM)及自制的胶体探针定量测定了不同条件下,膜-偏硅酸钠以及偏硅酸钠-偏硅酸钠之间的作用力.分析了污染膜的表面结构特征及其通量恢复率,系统考察了膜表面吸附不同有机大分子后,对随后硅酸盐污染行为的影响.结果表明:膜表面吸附HA和SA后,膜面负电位增加,与偏硅酸钠之间静电斥力变大,导致其结合能力减弱,减缓了结垢污染.然而,吸附BSA后的膜与无有机条件膜相比,负电位基本一致,故对纳滤膜结垢过程几乎无影响.%The polyamide composite nanofiltration membrane fouling experiments were carried out by using humic acid (HA), sodium alginate (SA), bovine serum albumin (BSA) as model organic macromoleculars, sodium metasilicate as model inorganic foulant in natural water. The adhesion forces of membrane-sodium metasilicate and sodium metasilicate-sodium metasilicate under different conditions were tested by atomic force microscopy (AFM) in conjunction with self-made colloidal probe. The surface structural characteristics of the fouled membranes and flux recovery rates of the corresponding fouled membranes were analyzed. Besides, the effects of different membrane surface conditions on silicate scaling behavior were investigated. The results showed that the negative potential of the membrane surface increased after adsorption of HA or SA on membrane surface. Hence, the electrostatic repulsion between the membrane and sodium metasilicate increased. Therefore, the binding capacity between fouled membrane and sodium metasilicate was weakened and the scaling behavior was mitigated. However, compared with the membrane without organic conditioning, adsorption of BSA on the membrane surface had little influence on silicate scaling of nanofiltration

  17. CROW for large scale macromolecular simulations.

    Science.gov (United States)

    Hodoscek, Milan; Borstnik, Urban; Janezic, Dusanka

    2002-01-01

    CROW (Columns and Rows Of Workstations - http://www.sicmm.org/crow/) is a parallel computer cluster based on the Beowulf (http://www.beowulf.org/) idea, modified to support a larger number of processors. Its architecture is based on point-to-point network architecture, which does not require the use of any network switching equipment in the system. Thus, the cost is lower, and there is no degradation in network performance even for a larger number of processors.

  18. Macromolecular lesions and cellular radiation chemistry

    International Nuclear Information System (INIS)

    Our studies of the interaction of densely ionizing particles with macromolecules in the living cell may be divided into four parts: characterization of lesions to cellular DNA in the unmodified Bragg ionization curve; characterization of lesions to cellular DNA in the spread Bragg curve as used in radiation therapy; elucidation of the cellular radiation chemistry characteristic of high vs. low LET radiation qualities; and the introduction of novel techniques designed to give a better understanding of the fundamental properties of induction of lesions and their repair potentials in high LET radiation

  19. Liver-targeting macromolecular MRI contrast agents

    Institute of Scientific and Technical Information of China (English)

    XU; Mianyi

    2001-01-01

    Chitosans with various degrees of deacetylation (D.D.), which were used as standard sample for FTIR determination, were prepared from completely deacetylated chitosan by homogeneous N-acetylation reaction. By combining four probable probe bands, i.e. 1655, 1560, 1380 and 1320 cm-1, eight probable reference bands, i.e. 3430, 2920, 2880, 1425, 1155, 1070, 1030 and 895 cm-1 and two baseline methods, the most suitable ratios Aprobe band/Areference band from IR spectra to determine the degree of acetylation of chitosan were evaluated from 48 combinations to be A1560/A2880, A1560/A2920 and A1655/A3430(A1560/A2880 is mostly recommended). The second baseline method, i.e. linking between adjacent two valleys, was better for measuring the absorbances of 1560 and 1655 cm-1 bands. The determination range of the D.D. (1%-100%) covered almost the whole range. The standard curves with A1560/A2880 and A1655/A3430 were also suitable for the determination of degree of substitution of other N-acylated chitosan, such as N-propionyl chitosan, N-butyryl chitosan and N-hexanoyl chitosan.

  20. Computational Structural Biology of Macromolecular Interactions

    NARCIS (Netherlands)

    Garcia Lopes Maia Rodrigues, J.

    2014-01-01

    The living cell is a formidable entity kept intact and functioning by a network of interactions carried out by protein molecules. As such, understanding this network, the interactome, is key to understand the cell itself. To dissect the fundamental properties of protein interactions, researchers use

  1. Dynamics simulations for engineering macromolecular interactions

    Science.gov (United States)

    Robinson-Mosher, Avi; Shinar, Tamar; Silver, Pamela A.; Way, Jeffrey

    2013-06-01

    The predictable engineering of well-behaved transcriptional circuits is a central goal of synthetic biology. The artificial attachment of promoters to transcription factor genes usually results in noisy or chaotic behaviors, and such systems are unlikely to be useful in practical applications. Natural transcriptional regulation relies extensively on protein-protein interactions to insure tightly controlled behavior, but such tight control has been elusive in engineered systems. To help engineer protein-protein interactions, we have developed a molecular dynamics simulation framework that simplifies features of proteins moving by constrained Brownian motion, with the goal of performing long simulations. The behavior of a simulated protein system is determined by summation of forces that include a Brownian force, a drag force, excluded volume constraints, relative position constraints, and binding constraints that relate to experimentally determined on-rates and off-rates for chosen protein elements in a system. Proteins are abstracted as spheres. Binding surfaces are defined radially within a protein. Peptide linkers are abstracted as small protein-like spheres with rigid connections. To address whether our framework could generate useful predictions, we simulated the behavior of an engineered fusion protein consisting of two 20 000 Da proteins attached by flexible glycine/serine-type linkers. The two protein elements remained closely associated, as if constrained by a random walk in three dimensions of the peptide linker, as opposed to showing a distribution of distances expected if movement were dominated by Brownian motion of the protein domains only. We also simulated the behavior of fluorescent proteins tethered by a linker of varying length, compared the predicted Förster resonance energy transfer with previous experimental observations, and obtained a good correspondence. Finally, we simulated the binding behavior of a fusion of two ligands that could simultaneously bind to distinct cell-surface receptors, and explored the landscape of linker lengths and stiffnesses that could enhance receptor binding of one ligand when the other ligand has already bound to its receptor, thus, addressing potential mechanisms for improving targeted signal transduction proteins. These specific results have implications for the design of targeted fusion proteins and artificial transcription factors involving fusion of natural domains. More broadly, the simulation framework described here could be extended to include more detailed system features such as non-spherical protein shapes and electrostatics, without requiring detailed, computationally expensive specifications. This framework should be useful in predicting behavior of engineered protein systems including binding and dissociation reactions.

  2. Macromolecular structure phasing by neutron anomalous diffraction.

    Science.gov (United States)

    Cuypers, Maxime G; Mason, Sax A; Mossou, Estelle; Haertlein, Michael; Forsyth, V Trevor; Mitchell, Edward P

    2016-01-01

    In this report we show for the first time that neutron anomalous dispersion can be used in a practical manner to determine experimental phases of a protein crystal structure, providing a new tool for structural biologists. The approach is demonstrated through the use of a state-of-the-art monochromatic neutron diffractometer at the Institut Laue-Langevin (ILL) in combination with crystals of perdeuterated protein that minimise the level of hydrogen incoherent scattering and enhance the visibility of the anomalous signal. The protein used was rubredoxin in which cadmium replaced the iron at the iron-sulphur site. While this study was carried out using a steady-state neutron beam source, the results will be of major interest for capabilities at existing and emerging spallation neutron sources where time-of-flight instruments provide inherent energy discrimination. In particular this capability may be expected to offer unique opportunities to a rapidly developing structural biology community where there is increasing interest in the identification of protonation states, protein/water interactions and protein-ligand interactions - all of which are of central importance to a wide range of fundamental and applied areas in the biosciences. PMID:27511806

  3. Thermodynamics and Statistical Mechanics of Macromolecular Systems

    Science.gov (United States)

    Bachmann, Michael

    2014-04-01

    Preface and outline; 1. Introduction; 2. Statistical mechanics: a modern review; 3. The complexity of minimalistic lattice models for protein folding; 4. Monte Carlo and chain growth methods for molecular simulations; 5. First insights to freezing and collapse of flexible polymers; 6. Crystallization of elastic polymers; 7. Structural phases of semiflexible polymers; 8. Generic tertiary folding properties of proteins in mesoscopic scales; 9. Protein folding channels and kinetics of two-state folding; 10. Inducing generic secondary structures by constraints; 11. Statistical analyses of aggregation processes; 12. Hierarchical nature of phase transitions; 13. Adsorption of polymers at solid substrates; 14. Hybrid protein-substrate interfaces; 15. Concluding remarks and outlook; Notes; References; Index.

  4. Calorimetric studies of macromolecular aqueous solutions

    NARCIS (Netherlands)

    Blandamer, M.J; Cullis, P.M.; Engberts, J.B.F.N.

    1996-01-01

    Both titration and differential scanning microcalorimetric techniques are shown to yield important information concerning the properties of macromolecules in aqueous solution. Application of titration calorimetry is examined in me context of deaggregation of canonic micelles (e.g. hexadecyltrimethyl

  5. The Macromolecular Route to Chiral Amplification.

    Science.gov (United States)

    Green; Park; Sato; Teramoto; Lifson; Selinger; Selinger

    1999-11-01

    Cooperative phenomena, described by one-dimensional statistical physical methods, are observed between the enantiomeric characteristics of monomeric materials and the polymers they produce. The effect of minute energies associated with this amplified chirality, although currently not interpretable, can be easily measured. Nonlinear relationships between enantiomeric excess or enantiomeric content and polymer properties may offer the possibility of developing chiral catalysts and chiral chromatographic materials in which the burden of large enantiomeric excess or content may be considerably alleviated. New approaches to information and sensor technology may become possible. PMID:10556885

  6. Acute iron poisoning. Rescue with macromolecular chelators.

    OpenAIRE

    Mahoney, J R; Hallaway, P E; Hedlund, B E; Eaton, J. W.

    1989-01-01

    Acute iron intoxication is a frequent, sometimes life-threatening, form of poisoning. Present therapy, in severe cases, includes oral and intravenous administration of the potent iron chelator, deferoxamine. Unfortunately, high dose intravenous deferoxamine causes acute hypotension additive with that engendered by the iron poisoning itself. To obviate this problem, we have covalently attached deferoxamine to high molecular weight carbohydrates such as dextran and hydroxyethyl starch. These ma...

  7. Residential characteristics aggravating infestation by Culex quinquefasciatus in a region of Northeastern Brazil Características agravantes por infestación residencial de Culex quinquefasciatus, en una región del Noreste de Brasil Características agravantes por infestação residencial de Culex quinquefasciatus, em Olinda, PE

    Directory of Open Access Journals (Sweden)

    Juliana Cavalcanti Correia

    2012-12-01

    Full Text Available OBJECTIVE: Analyse how basic sanitation conditions, water supply and housing conditions affect the concentration of Culex quinquefasciatus METHODS: Populations of C. quinquefasciatus in 61 houses in the municipality of Olinda, PE, were monitored between October 2009 and October 2010. Observations were carried out in homes without the presence of preferred breeding sites in order to identify characteristics that may be aggravating factors for the development of the mosquito. Five aggravating factors were analysed: vegetation cover surrounding the home, number of residents/home, water storage, sewage drainage and water drainage. These characteristics were analysed in terms of presence or absence and as indicators of the degree of infestation, which was estimated through monitoring the concentration of eggs (oviposition traps - BR-OVT and adults (CDC light traps. RESULTS: Sewage drainage to a rudimentary septic tank or to the open air was the most frequent aggravating factor in the homes (91.8%, although the presence of vegetation was the only characteristic that significantly influenced the increase in the number of egg rafts (p = 0.02. The BR-OVT achieved positive results in 95.1% of the evaluations, with the presence of at least one egg raft per month. A total of 2,366 adults were caught, with a mosquito/room/night ratio of 32.9. No significant difference was found in the number of mosquitoes caught in the homes. CONCLUSIONS: Although the sanitation and water supply influence the population density of C. quinquefasciatus, residence features that are not usually considered in control measures can be aggravating factors in sustaining the mosquito population.OBJETIVO: Analizar como las condiciones de saneamiento básico, abastecimiento de agua y habitaciones afectan la densidad de Culex quinquefasciatus MÉTODOS: se monitoreó la población de C. quinquefasciatus en 61 residencias del municipio de Olinda, PE, Brasil, de octubre de 2009 a octubre de

  8. 抢劫罪中犯罪对象与加重情节定性之新思考——基于广义经济犯罪的视角%A New Think of Robbery Crime Object and Aggravating Circumstances——Based on the perspective of generalized economic Crimes

    Institute of Scientific and Technical Information of China (English)

    杨晓培

    2012-01-01

    伴随着现代化进程的加速,抢劫罪依然作为多发和高发的刑事犯罪危害着公众的生命财产安全与社会和谐。随着社会变迁,刑事法治下对抢劫罪的研究也须与社会需求和时代的进步相契合。当下,抢劫罪依然还是普遍,其社会危害性也仍然很大。文章基于广义经济犯罪的视角,通过对抢劫罪中犯罪对象与加重情节的重新审视和研究,期待可以更快更有效地打击犯罪,一定程度上为美丽中国与和谐社会的构建之秩序维护起到些许作用。%With the acceleration of modernization,the robbery as a criminal offence harms the life and property of the public as well as the social harmony.This paper,upon the perspective of generalized economic crimes,gives a new survey and study of the object in robbery crime and aggravating circumstances so as to provide a better or more effective crime fighting way.

  9. Synthesis of Macromolecular Crosslinker for Epoxy Cathodic Electrophoretic Paint Curable at Low Temperature%低温固化环氧阴极电泳涂料的大分子交联剂的制备

    Institute of Scientific and Technical Information of China (English)

    何煦; 戴晨伟; 管华平; 章于川

    2011-01-01

    首先以聚乙二醇200(PEG - 200)、异佛尔酮二异氰酸酯(IPDI)、二羟甲基丙酸(DMPA)为原料合成了末端为异氰酸根(-NCO)的预聚体,再以N-甲基二乙醇胺(MDEA)为封端剂对-NCO进行全封端反应.通过添加适量的亲水性DMPA,提高了封端大分子的自乳化性能,制备出全封闭型异氰酸酯大分子(P-M-I)乳液,以其作为环氧阴极电泳漆低温固化的交联剂.应用FT - IR、DSC、TG、TEM、粒径分析等检测手段对全封闭型大分子及其乳液进行了结构与性能表征.将其与胺化环氧树脂乳液进行共混,制备了低温固化环氧阴极电泳涂料.通过电泳涂装的金属样片在124~130℃烘烤30 min可完全固化成膜.实验结果表明:该大分子交联剂显著降低了电泳涂料的固化温度,涂膜外观平整光亮、附着力好、铅笔硬度达2H,综合性能良好.%A prepolymer terminated with isocyanate(NCO) was first synthesized with polyethylene glycol -200(PEG-200), isophorone diisocyanate(IPDI) and dimethylolpropionic acid(DMPA). Then methyl-diethanolamine ( MDEA) was used to block -NCO groups. In order to improve the self - emulsifying capability of the blocked macromolecule, a small amount of hydrophilic dimethylolpropionic acid ( DMPA) was added to prepare fully blocked isocyanate macromolecular (P - M - I) emulsion, which was used as the crosslinker for epoxy cathodic electrophoresis paint curable at low temperature. The performance of P - M - I and its emulsion were characterized by IR, DSC, TGA and Zetasizer. The P - M -1 emulsion and amine -epoxy resin emulsion were mixed by physical blending to prepare the epoxy cathodic electrophoretic coating curable at low temp. Under the baking schedure of 124 ~ 130 ℃/30 mins, the electrophoretic coatings on the metal panel can be cured completely. The results showed that the P - M - I could decrease the curing temperature of cathodic electrophoretic paint significantly. The coating film showed smooth

  10. Primary research on origins of the macromolecular organic matters in offshore sediments in Xiamen%厦门近海沉积物中高分子有机质的来源初探

    Institute of Scientific and Technical Information of China (English)

    陈衍婷; 赵金平; 尹丽倩; 陈进生; 袁东星; 胡恭任

    2012-01-01

    采用多步连续-湿法-化学方法,分离提纯了于2010年7月和12月在厦门近海采集的沉积物样品,获得3类高分子有机质,即腐殖酸(HA)、干酪根和碳黑(KB)和碳黑(BC).以扫描电镜(SEM)作为有效的辅助手段,观察沉积物原样及高分子有机质的形貌特征,结合稳定碳同位素(δ13C)的分析,初步探讨了厦门近海沉积物中高分子有机质的来源.扫描电镜观察发现,在原样沉积物中存在多种海源物质(如钙质硅藻和圆筛藻/冠盘藻);而在KB样品中同时发现类似于陆地植物的木质碎片以及来自海洋的藻胶鞘,暗示了其来源是海源与陆源共同作用的结果.稳定碳同位素研究表明厦门湾近海海域沉积物中有机质以陆源影响占优势,其比例在58.32%至84.45%之间;δ13C值整体上显示为夏季的贫于冬季的,这与研究区域的生态系统中陆源C3植被和海源水生植物的繁殖生长有关,同时还有排海污水及化石燃料煤燃烧后或者运煤船只洒落的碎屑的贡献.%A promoted comprehensive-wet-chemical procedure was performed to extract three Macromolecular Organic Matters (MOMs), including humic acid (HA), kerogen and black carbon (KB) and black carbon (BC), from marine sediments, which were collected in Xiamen Bay during July and December in 2010. The origins of three extractions were characterized by scanning electron microscopy (SEM) and stable carbon isotope (δ13C) analysis. The results of SEM showed that many of marine-derived materials were observed (eg: calcium diatoms, and coscinodiscus or stephanodiscus hantzschii). Wood debris and algaenan that origined from marine were discovered in KB samples, which indicated that the importance of the multiple sources. The δ13C analysis shown that the terrestrial contribution ranged from 58.32%~84.45%, which was the predominant contribution to the MOMs in the sediments. And the δ13C values in summer were lower than that in winter, which was

  11. Inflammation aggravates disease severity in Marfan syndrome patients.

    Directory of Open Access Journals (Sweden)

    Teodora Radonic

    Full Text Available BACKGROUND: Marfan syndrome (MFS is a pleiotropic genetic disorder with major features in cardiovascular, ocular and skeletal systems, associated with large clinical variability. Numerous studies reveal an involvement of TGF-β signaling. However, the contribution of tissue inflammation is not addressed so far. METHODOLOGY/PRINCIPAL FINDINGS: Here we showed that both TGF-β and inflammation are up-regulated in patients with MFS. We analyzed transcriptome-wide gene expression in 55 MFS patients using Affymetrix Human Exon 1.0 ST Array and levels of TGF-β and various cytokines in their plasma. Within our MFS population, increased plasma levels of TGF-β were found especially in MFS patients with aortic root dilatation (124 pg/ml, when compared to MFS patients with normal aorta (10 pg/ml; p = 8×10(-6, 95% CI: 70-159 pg/ml. Interestingly, our microarray data show that increased expression of inflammatory genes was associated with major clinical features within the MFS patients group; namely severity of the aortic root dilatation (HLA-DRB1 and HLA-DRB5 genes; r = 0.56 for both; False Discovery Rate(FDR = 0%, ocular lens dislocation (RAET1L, CCL19 and HLA-DQB2; Fold Change (FC = 1.8; 1.4; 1.5, FDR = 0% and specific skeletal features (HLA-DRB1, HLA-DRB5, GZMK; FC = 8.8, 7.1, 1.3; FDR = 0%. Patients with progressive aortic disease had higher levels of Macrophage Colony Stimulating Factor (M-CSF in blood. When comparing MFS aortic root vessel wall with non-MFS aortic root, increased numbers of CD4+ T-cells were found in the media (p = 0.02 and increased number of CD8+ T-cells (p = 0.003 in the adventitia of the MFS patients. CONCLUSION/SIGNIFICANCE: In conclusion, our results imply a modifying role of inflammation in MFS. Inflammation might be a novel therapeutic target in these patients.

  12. Fibrogenic Cell Plasticity Blunts Tissue Regeneration and Aggravates Muscular Dystrophy.

    Science.gov (United States)

    Pessina, Patrizia; Kharraz, Yacine; Jardí, Mercè; Fukada, So-ichiro; Serrano, Antonio L; Perdiguero, Eusebio; Muñoz-Cánoves, Pura

    2015-06-01

    Preservation of cell identity is necessary for homeostasis of most adult tissues. This process is challenged every time a tissue undergoes regeneration after stress or injury. In the lethal Duchenne muscular dystrophy (DMD), skeletal muscle regenerative capacity declines gradually as fibrosis increases. Using genetically engineered tracing mice, we demonstrate that, in dystrophic muscle, specialized cells of muscular, endothelial, and hematopoietic origins gain plasticity toward a fibrogenic fate via a TGFβ-mediated pathway. This results in loss of cellular identity and normal function, with deleterious consequences for regeneration. Furthermore, this fibrogenic process involves acquisition of a mesenchymal progenitor multipotent status, illustrating a link between fibrogenesis and gain of progenitor cell functions. As this plasticity also was observed in DMD patients, we propose that mesenchymal transitions impair regeneration and worsen diseases with a fibrotic component.

  13. Can pregnancy aggravate the course of non-Hodgkin's lymphoma?

    Science.gov (United States)

    Giovannini, M; Saccucci, P; Cannone, D; Damiani, G; Pomini, P

    1989-01-01

    The Authors present three cases of Non-Hodgkin's Lymphoma (NHL) in pregnancy and discuss about problem of diagnosis and management of NHL in this condition. They stress that the diagnosis of NHL in pregnancy is delayed and the clinical progression of lymphoma is probably influenced by hormonal and immunological changes occurring during pregnancy. On the other hand the management of NHL is problematic because radiotherapy is potentially teratogenic. (By editorial staff). PMID:2776787

  14. Therapy with Minocycline Aggravates Experimental Rabies in Mice▿

    OpenAIRE

    Jackson, Alan C.; Scott, Courtney A.; Owen, James; Weli, Simon C.; Rossiter, John P.

    2007-01-01

    Minocycline is a tetracycline derivative with antiapoptotic and anti-inflammatory properties, and the drug has been shown to have beneficial effects in a variety of models of neurological disorders. The potentially neuroprotective role of minocycline was assessed in experimental in vitro and in vivo models of rabies virus infection. In this study, 5 nM minocycline did not improve the viability of embryonic mouse cortical and hippocampal neurons infected in vitro with the attenuated SAD-D29 st...

  15. Fibrogenic Cell Plasticity Blunts Tissue Regeneration and Aggravates Muscular Dystrophy

    Directory of Open Access Journals (Sweden)

    Patrizia Pessina

    2015-06-01

    Full Text Available Preservation of cell identity is necessary for homeostasis of most adult tissues. This process is challenged every time a tissue undergoes regeneration after stress or injury. In the lethal Duchenne muscular dystrophy (DMD, skeletal muscle regenerative capacity declines gradually as fibrosis increases. Using genetically engineered tracing mice, we demonstrate that, in dystrophic muscle, specialized cells of muscular, endothelial, and hematopoietic origins gain plasticity toward a fibrogenic fate via a TGFβ-mediated pathway. This results in loss of cellular identity and normal function, with deleterious consequences for regeneration. Furthermore, this fibrogenic process involves acquisition of a mesenchymal progenitor multipotent status, illustrating a link between fibrogenesis and gain of progenitor cell functions. As this plasticity also was observed in DMD patients, we propose that mesenchymal transitions impair regeneration and worsen diseases with a fibrotic component.

  16. Rapidly aggravated Creutzfeldt-Jacob disease: autopsy-proven case

    Energy Technology Data Exchange (ETDEWEB)

    Park, Seung Hyun; Kang, Hyun Koo; Yu, Hyeon; Lee, Sang Chun [Seoul Veterans Hospital, Seoul (Korea, Republic of)

    2005-11-15

    Creutzfeldt-Jakob disease (DJD) is one of the transmissible spongiform encephalopathies, which is mediated by what has been known as 'prion'. It is a rare and fatal progressive neurodegenerative disease that affects the middle and old aged. There are a number of subtypes of CJD, one of which is the sporadic type characterized by rapidly progressing clinical symptoms, including progressive dementia, myoclonic jerk, and pyramidal or extrapyramidal syndrome. Patients usually end up dying within 1 to 2 years of contacting the disease. We report an autopsy-proven case of sporadic CJD with clinical symptoms that progressed within several days, along with dramatic changes on diffusion weighted magnetic resonance images.

  17. Inflammation Aggravates Disease Severity in Marfan Syndrome Patients

    NARCIS (Netherlands)

    Radonic, Teodora; de Witte, Piet; Groenink, Maarten; de Waard, Vivian; Lutter, Rene; van Eijk, Marco; Jansen, Marnix; Timmermans, Janneke; Kempers, Marlies; Scholte, Arthur J.; Hilhorst-Hofstee, Yvonne; van den Berg, Maarten P.; van Tintelen, J. Peter; Pals, Gerard; Baars, Marieke J. H.; Mulder, Barbara J. M.; Zwinderman, Aeilko H.

    2012-01-01

    Background: Marfan syndrome (MFS) is a pleiotropic genetic disorder with major features in cardiovascular, ocular and skeletal systems, associated with large clinical variability. Numerous studies reveal an involvement of TGF-beta signaling. However, the contribution of tissue inflammation is not ad

  18. Chronic kidney disease aggravates arteriovenous fistula damage in rats.

    Science.gov (United States)

    Langer, Stephan; Kokozidou, Maria; Heiss, Christian; Kranz, Jennifer; Kessler, Tina; Paulus, Niklas; Krüger, Thilo; Jacobs, Michael J; Lente, Christina; Koeppel, Thomas A

    2010-12-01

    Neointimal hyperplasia (NIH) and impaired dilatation are important contributors to arteriovenous fistula (AVF) failure. It is unclear whether chronic kidney disease (CKD) itself causes adverse remodeling in arterialized veins. Here we determined if CKD specifically triggers adverse effects on vascular remodeling and assessed whether these changes affect the function of AVFs. For this purpose, we used rats on a normal diet or on an adenine-rich diet to induce CKD and created a fistula between the right femoral artery and vein. Fistula maturation was followed noninvasively by high-resolution ultrasound (US), and groups of rats were killed on 42 and 84 days after surgery for histological and immunohistochemical analyses of the AVFs and contralateral femoral vessels. In vivo US and ex vivo morphometric analyses confirmed a significant increase in NIH in the AVFs of both groups with CKD compared to those receiving a normal diet. Furthermore, we found using histological evaluation of the fistula veins in the rats with CKD that the media shrank and their calcification increased significantly. Afferent artery dilatation was significantly impaired in CKD and the downstream fistula vein had delayed dilation after surgery. These changes were accompanied by significantly increased peak systolic velocity at the site of the anastomosis, implying stenosis. Thus, CKD triggers adverse effects on vascular remodeling in AVFs, all of which contribute to anatomical and/or functional stenosis.

  19. The proliferation of ballistic missiles: an aggravating factor of crises

    International Nuclear Information System (INIS)

    After a brief recall of the history of the development of ballistic missiles from World War II, the author discusses the various uses of these missiles, on the one hand by major powers, and on the other hand by other countries like Israel, Pakistan and India, and also Egypt and Iraq. He recalls the uses of these missiles during regional conflicts (Scuds by Iraq) and then discusses the issue of proliferation of ballistic missiles. He notices that most of these weapons are present in the arsenal of major powers under the form of intercontinental missiles, intermediate range weapons or theatre weapons. On the Third World side, proliferation concerns short- and medium-range missiles produced from technology transfers or national programmes. Mobile systems are now present in all conflicts (notably Libya, Syria) and are now based on more advanced technologies for propellers as well as for control and guidance systems. In the last part, the author discusses the perspectives associated with these missiles which are a strong offensive weapon, and are also modernised to carry nuclear warheads or multiple warheads. These evolutions could put the western superiority into question again

  20. Caffeine treatment aggravates secondary degeneration after spinal cord injury.

    Science.gov (United States)

    Yang, Cheng-Chang; Jou, I-Ming

    2016-03-01

    Spinal cord injury (SCI) often results in some form of paralysis. Recently, SCI therapy has been focused on preventing secondary injury to reduce both neuroinflammation and lesion size so that functional outcome after an SCI may be improved. Previous studies have shown that adenosine receptors (AR) are a major regulator of inflammation after an SCI. The current study was performed to examine the effect of caffeine, a pan-AR blocker, on spontaneous functional recovery after an SCI. Animals were assigned into 3 groups randomly, including sham, PBS and caffeine groups. The rat SCI was generated by an NYU impactor with a 10 g rod dropped from a 25 mm height at thoracic 9 spinal cord level. Caffeine and PBS were injected daily during the experiment period. Hind limb motor function was evaluated by the Basso, Beattie, Bresnahan (BBB) locomotor rating scale at 1 week and 4 weeks after the SCI. Spinal cord segments were collected after final behavior evaluation for morphological analysis. The tissue sparing was evaluated by luxol fast blue staining. Immunofluorescence stain was employed to assess astrocyte activation and neurofilament positioning, while microglia activation was examined by immunohistochemistry stain.The results showed that spontaneous functional recovery was blocked after the animals were subjected caffeine daily. Moreover, caffeine administration increased the demyelination area, promoted astrocyte and microglia activation and decreased the quantity of neurofilaments. These findings suggest that the neurotoxicity effect of caffeine may be associated with the inhibition of neural repair and the promotion of neuroinflammation. PMID:26746340

  1. Arteriovenous fistulas aggravate the hemodynamic effect of vein bypass stenoses

    DEFF Research Database (Denmark)

    Nielsen, T G; Djurhuus, C; Pedersen, Erik Morre;

    1996-01-01

    PURPOSE: The purpose of this study was to assess the impact of arteriovenous fistulas combined with varying degrees of stenosis on distal bypass hemodynamics and Doppler spectral parameters. METHODS: In an in vitro flow model bypass stenoses causing 30%, 55%, and 70% diameter reduction were induced...... hemodynamic conditions of a more severe stenosis. Assessment of the hemodynamic impact of fistulas must be undertaken in the evaluation of in situ vein bypass stenoses....

  2. NaCl胁迫加重强光胁迫下超大甜椒叶片的光系统Ⅱ和光系统Ⅰ的光抑制%NaCl stress aggravates photoinhibition of photosystem Ⅱ and photosystem Ⅰ in Capsicum annuum leaves under high irradiance stress

    Institute of Scientific and Technical Information of China (English)

    宋旭丽; 胡春梅; 孟静静; 侯喜林; 何启伟; 李新国

    2011-01-01

    快速叶绿素荧光动力学可以在无损情况下探知叶片光合机构的损伤程度,快速叶绿素荧光测定和分析技术(JIP-test)将测量值转化为多种具有生物学意义的参数,因而被广泛应用于植物光合机构对环境的响应机制研究.该文研究了超大甜椒(Capsicum annuum)幼苗在强光及不同NaCl浓度胁迫下的荧光响应情况.与单纯强光胁迫相比,NaCl胁迫引起了叶绿素荧光诱导曲线的明显改变,光系统Ⅱ(PSⅡ)光抑制加重,同时PSⅡ反应中心和受体侧受到明显影响,而且高NaCl浓度胁迫下PSⅡ供体侧受伤害明显,同时PSⅠ反应中心活性(P700+)在盐胁迫下明显降低.这些结果表明,NaCl胁迫会增强强光对超大甜椒光系统的光抑制,并且浓度越高抑制越明显,但对PSⅠ的抑制作用低于PSⅡ.高NaCl浓度胁迫易对PSⅡ供体侧造成破坏,且PSⅠ光抑制严重.%Aims Our aim was to study effects of salt stress and high irradiance on photoinhibition of photosystem Ⅱ (PSⅡ)and Ⅰ (PSⅠ) in leaves of sweet pepper (Capsicum annuum).Methods We used the chlorophyll a fluorescence technique and the JIP-test to study the responses of sweet pepper leaves to salt stress with different NaCl concentrations and under high irradiance (1 000 μmol.m-2·s-l).Important findings The chlorophyll a fluorescence induction curves changed greatly as induced by NaCI stress under high irradiance, and photoinhibition of PSⅡ was aggravated with apparent effects on PSⅡ reaction centers and the acceptor side. Also, the donor side of PSⅡ was damaged by high NaCl concentration under high irradiance. Additionally, the activity of PSⅠ reaction centers (P700+) was inhibited by NaCl stress under high irradiance.Therefore, NaCl stress could aggravate photoinhibition of sweet pepper photosystem under high irradiance, and photoinhibition was greater with higher NaCl concentration. However, PSI photoinhibition was less than PSⅡ photoinhibition

  3. Clinical Observation of Chronic Obstructive Pulmonary Disease at Acute Aggravation Stage Treated with Yiqi Huoxue Formula%益气活血方治疗急性加重期慢性阻塞性肺疾病临床观察

    Institute of Scientific and Technical Information of China (English)

    谭俊杰

    2011-01-01

    目的 观察益气活血方治疗急性加重期慢性阻塞性肺疾病(COPD)的临床疗效.方法 首先将符合诊断标准的患者分为男、女两组,每组60例,按照入组时间先后顺序,男、女两组中单号入治疗组,双号入对照组.对照组60例,采用吸氧联合西药治疗;治疗组60例,在对照组治疗基础上加用益气活血方治疗.两组均以治疗2周为1个疗程,比较两组治疗前后第一秒用力呼气容积占预计值百分比(FEV1%),并评价中医症状积分,判定疗效.结果 治疗后治疗组中医症状积分为(6.3± 5.3)分,对照组中医症状积分为(9.8±7.2)分,两组比较,差异有统计学意义(P<0.05);治疗组有效27例,对照组有效15例,两组比较,差异有统计学意义(P<0.01).结论 益气活血方治疗急性加重期慢性阻塞性肺疾病,针对病因病机,结合患者多为老年人的特点,遣方用药,取得了良好的临床疗效.%Objective To observe the clinical efficacy of yiqi huoxue formula on chronic obslruclive pulmonary disease ( COPD) at acute aggravation stage. Methods The palienls who were complied with the diagnostic criteria were divided into a male group and a female group, 60 cases in each one. In accordance with the inclusive sequence, of the cases in male group and female group, those with single number in the sequence were classified into a trial group and those with double number were into a control group. 60 cases in control group were treated with oxygen combined with western medicine therapy. 60 cases in trial group were treated with yiqi huoxue formula supplemented on the basis of the treatment as control group. The cases in either group were treated for 2 weeks as 1 session. The forced expiration volume in one second/predicted value (FEV1%)was compared before and after treatment between two groups. The symptom score of traditional Chinese medicine ( TCM ) and the efficacy were assessed. Results After treatment, the symptom score of TCM was(6

  4. 厦门市郊区降尘中大分子有机质化学特征浅析%Preliminary analysis on the characteristics of the macromolecular organic matters extracted from dust in the Suburban Xiamen

    Institute of Scientific and Technical Information of China (English)

    陈衍婷; 赵金平; 陈进生; 胡恭任

    2013-01-01

    以厦门市的降尘(包括一次沙尘天气)为研究对象,采用综合湿法-化学方法获得腐殖酸(HA)、干酪根+碳黑(KB)和碳黑(BC)3类大分子有机质,分析了两种天气情况下大分子有机质的形貌特征、官能团结构和来源,同时探讨沙尘天气条件下的影响.结果表明,大分子有机质的形貌特征为探讨其来源提供了丰富的信息,如呈大孔网状结构的干酪根样品可能源于植物,而呈球状结构的BC样品则可能源于煤或油的不完全燃烧.傅立叶红外光谱研究表明,降尘中的HA、KB和BC具有相似的结构组成和官能团信息,而受到沙尘天气及季节性的影响,官能团的含量存在差别.碳稳定同位素结合扫描电镜进一步研究大分子有机质来源表明,大分子有机质有明显的陆源C3植物的信息,且有部分化石燃料的信息.沙尘天气降尘中大分子有机质的δ13C值低于正常天气,这与植物的不同地域生长环境、沙尘暴携带的来自蒙古沙漠和中国西北部的沙尘及陆源有机质的δ13C值偏低区域的沙尘影响有关.KB和BC的相关性显著(r=0.964,p <0.01),表明干酪根(K)与BC有部分相似的生物质来源.%To investigate the morphological property, functional group and source of the macromolecular organic matters ( MOMs) in the dusts during dust storm (DS) and non-dust storm (n-DS) periods, three MOMs, i.e. humic acid (HA) , kerogen + black carbon (KB) and black carbon (BC) were extracted through a promoted comprehensive wet chemical procedure from these dust samples. The morphological properties of MOMs provided rich information for the sources, e. g. irregular macroporous network debris observed in kerogen samples might originate from vegetation, as well as the spherical BC particles might derive from coal or oil incomplete combustion. The analysis of fourier transform infrared spectroscopy (FT-IR) revealed that the MOMs had the similar functional group, but the contents

  5. The electroconvulsive shock can aggravate the cognitive impairment of the depression model rats though up-regulate the hyperphosphorylation of protein tau%电休克通过上调tau蛋白过度磷酸化程度加重抑郁模型大鼠认知障碍

    Institute of Scientific and Technical Information of China (English)

    陈安; 刘鸿章; 刘超

    2016-01-01

    indicate that the electroconvulsive shock reduce the impairment of learning-memory in depressed rats by aggravating the hyperphosphorylation of tau protein and up-regulating the content of glutamate.%目的 观察不同电量和不同时程电休克(ECT)对嗅球切除抑郁模型大鼠海马ECT后认知能力的变化.方法 建立大鼠嗅球切除抑郁模型,采用随机单位组3×3析因设计:将每只大鼠视为1个单位,对每个单位施加2个处理因素,即电流(25、50、75 mA)和时程(3次、6次、9次ECT)的所有组合(共9组,n=6).电休克结束24 h内行Morris水迷宫、高效液相色谱法测谷氨酸(Glu)在海马组织中含量,Western blot法测磷酸化tau蛋白(p-AT8Ser202)、糖原合成酶激酶-3β(GSK-3β1H8)表达.结果 随ECT电流加大,延长逃避潜伏期并缩短空间探索时间,随ECT时程延长,延长逃避潜伏期缩短空间探索时间,75 mA且行9次ECT组逃避潜伏期最长[(100.51±6.64)s]、空间探索时间最短[(10.02±1.20)s].随ECT电流加大,Glu浓度增加,随ECT时程延长,Glu浓度增加,75 mA且行9次ECT组Glu浓度最高[(184.39±20.86)μmol/gprot].随ECT电流加大,目标蛋白表达增加,随ECT时程延长,目标蛋白表达增加,75 mA且行9次ECT组目标蛋白表达最高(p-AT8Ser202:1771.50 ±278.26;GSK-3β1H8:1747.13±162.23).结论 ECT导致海马Glu浓度升高,加剧海马tau蛋白的磷酸化程度,诱发认知障碍.

  6. Method for removing atomic-model bias in macromolecular crystallography

    Science.gov (United States)

    Terwilliger, Thomas C.

    2006-08-01

    Structure factor bias in an electron density map for an unknown crystallographic structure is minimized by using information in a first electron density map to elicit expected structure factor information. Observed structure factor amplitudes are combined with a starting set of crystallographic phases to form a first set of structure factors. A first electron density map is then derived and features of the first electron density map are identified to obtain expected distributions of electron density. Crystallographic phase probability distributions are established for possible crystallographic phases of reflection k, and the process is repeated as k is indexed through all of the plurality of reflections. An updated electron density map is derived from the crystallographic phase probability distributions for each one of the reflections. The entire process is then iterated to obtain a final set of crystallographic phases with minimum bias from known electron density maps.

  7. The collection of MicroED data for macromolecular crystallography.

    Science.gov (United States)

    Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir

    2016-05-01

    The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

  8. Center for Macromolecular Crystallography, University of Alabama in Birmingham

    Science.gov (United States)

    Navia, Manuel A.

    1991-01-01

    Porcine pancreatic elastase (PPE) crystals grown under microgravity conditions on mission STS-26 of the Space Shuttle Discovery were shown to diffract to considerably higher resolution than the best PPE crystals grown by us on the ground. We have now independently refined both the microgravity and ground-based data. Preliminary results of these refinements are summarized. These results show nearly a doubling of experimental diffraction data for this structure, exceeding 1.3 A resolution. Improved phase information derived from the refined structure of PPE based on this microgravity data has allowed us to interpret previously-uninterpretable electron density obtained from ground-based crystals of a complex of PPE with a chemically-reactive inhibitor. Intermediate stages in the enzyme-inhibitor reaction mechanism in the crystal can now be directly observed. Further refinement of PPE structures is in progress.

  9. Deformable elastic network refinement for low-resolution macromolecular crystallography.

    Science.gov (United States)

    Schröder, Gunnar F; Levitt, Michael; Brunger, Axel T

    2014-09-01

    Crystals of membrane proteins and protein complexes often diffract to low resolution owing to their intrinsic molecular flexibility, heterogeneity or the mosaic spread of micro-domains. At low resolution, the building and refinement of atomic models is a more challenging task. The deformable elastic network (DEN) refinement method developed previously has been instrumental in the determinion of several structures at low resolution. Here, DEN refinement is reviewed, recommendations for its optimal usage are provided and its limitations are discussed. Representative examples of the application of DEN refinement to challenging cases of refinement at low resolution are presented. These cases include soluble as well as membrane proteins determined at limiting resolutions ranging from 3 to 7 Å. Potential extensions of the DEN refinement technique and future perspectives for the interpretation of low-resolution crystal structures are also discussed.

  10. Design Strategies of Fluorescent Biosensors Based on Biological Macromolecular Receptors

    Directory of Open Access Journals (Sweden)

    Takashi Morii

    2010-02-01

    Full Text Available Fluorescent biosensors to detect the bona fide events of biologically important molecules in living cells are increasingly demanded in the field of molecular cell biology. Recent advances in the development of fluorescent biosensors have made an outstanding contribution to elucidating not only the roles of individual biomolecules, but also the dynamic intracellular relationships between these molecules. However, rational design strategies of fluorescent biosensors are not as mature as they look. An insatiable request for the establishment of a more universal and versatile strategy continues to provide an attractive alternative, so-called modular strategy, which permits facile preparation of biosensors with tailored characteristics by a simple combination of a receptor and a signal transducer. This review describes an overview of the progress in design strategies of fluorescent biosensors, such as auto-fluorescent protein-based biosensors, protein-based biosensors covalently modified with synthetic fluorophores, and signaling aptamers, and highlights the insight into how a given receptor is converted to a fluorescent biosensor. Furthermore, we will demonstrate a significance of the modular strategy for the sensor design.

  11. Colorimetric determination of Boron-10 in macromolecular delivery agents

    Energy Technology Data Exchange (ETDEWEB)

    Camillo, Maria A.P.; Moura, Eduardo [Instituto de Pesquisas Energeticas e Nucleares (IPEN), Sao Paulo, SP (Brazil). Centro de Biologia Molecular]. E-mail: mcamillo@ipen.br; Queiroz, Alvaro A.A.A.de [Universidade Federal de Itajuba, MG (Brazil). Inst. de Ciencias Exatas. Dept. de Fisica e Quimica]. E-mail: alencar@unifei.edu.br

    2005-07-01

    A polyglycerol with dendritic structure (PGLD) was synthesized by the ring opening polymerization of deprotonated glycidol using a polyglycerol as core functionality in a step-growth process denominated divergent synthesis. After PGLD reaction with {sup 10}B-enriched boric acid there was a marked increase in the bulk viscosity of the PGLD dendrimer evidencing the polyester formation. Gel permeation chromatography (GPC) analysis was used to characterize the molecular weight and the polydispersivity of the synthesized PGLD dendrimer. A dendritic polyglycerol structure with M{sub n} value of 16.7 kDa and a narrow polydispersivity (M{sub w}/M{sub n} = 1.05) was obtained in this work. {sup 1}H-NMR and {sup 13}C-NMR measurements were employed to assess the degree of branching (DB) in PGLD. The DB of 0.85 indicates the tendency of a dentritic structure for the PGLD synthesized in this work. The boron-10 concentration was dependent of the PGLD generation. A selective reagent, curcumine, was studied for spectrophotometric determination of boron in polyglycerol dendrimers. Boron reacts with curcumine to form a complex, which has a maximum absorption peak at 552 nm. Under the optimal conditions, Beer's law was obeyed over the range 0{approx}20 {mu}g of boron in 25 mL of solution. The biological assays indicate the PGLD-B with boron-10 concentration of 25 mg{sup 10}B/gPGLD as the most promising macromolecule enriched with boron-10 for the BNCT therapy. (author)

  12. Colorimetric determination of Boron-10 in macromolecular delivery agents

    International Nuclear Information System (INIS)

    A polyglycerol with dendritic structure (PGLD) was synthesized by the ring opening polymerization of deprotonated glycidol using a polyglycerol as core functionality in a step-growth process denominated divergent synthesis. After PGLD reaction with 10B-enriched boric acid there was a marked increase in the bulk viscosity of the PGLD dendrimer evidencing the polyester formation. Gel permeation chromatography (GPC) analysis was used to characterize the molecular weight and the polydispersivity of the synthesized PGLD dendrimer. A dendritic polyglycerol structure with Mn value of 16.7 kDa and a narrow polydispersivity (Mw/Mn = 1.05) was obtained in this work. 1H-NMR and 13C-NMR measurements were employed to assess the degree of branching (DB) in PGLD. The DB of 0.85 indicates the tendency of a dentritic structure for the PGLD synthesized in this work. The boron-10 concentration was dependent of the PGLD generation. A selective reagent, curcumine, was studied for spectrophotometric determination of boron in polyglycerol dendrimers. Boron reacts with curcumine to form a complex, which has a maximum absorption peak at 552 nm. Under the optimal conditions, Beer's law was obeyed over the range 0∼20 μg of boron in 25 mL of solution. The biological assays indicate the PGLD-B with boron-10 concentration of 25 mg10B/gPGLD as the most promising macromolecule enriched with boron-10 for the BNCT therapy. (author)

  13. Macromolecular recognition: Recognition of polymer side chains by cyclodextrin

    Science.gov (United States)

    Hashidzume, Akihito; Harada, Akira

    2015-12-01

    The interaction of cyclodextrins (CD) with water soluble polymers possessing guest residues has been investigated as model systems in biological molecular recognition. The selectivity of interaction of CD with polymer-carrying guest residues is controlled by polymer chains, i.e., the steric effect of polymer main chain, the conformational effect of polymer main chain, and multi-site interaction. Macroscopic assemblies have been also realized based on molecular recognition using polyacrylamide-based gels possessing CD and guest residues.

  14. Polypeptoids: A perfect match for molecular definition and macromolecular engineering?

    KAUST Repository

    Luxenhofer, Robert

    2013-04-19

    Precision synthesis of polymers has been a hot topic in recent years. While this is notoriously difficult to address for polymers with a CC backbone, Merrifield has discovered a way many decades ago for polypeptides. Using a similar approach, N-substituted polypeptides, so-called polypeptoids have been synthesized and studied for about 20 years. In contrast, the living ring-opening polymerization (ROP) of N-substituted N-carboxyanhydrides was among the first living polymerizations to be discovered. More recently, a surge in new synthetic approaches led to the efficient synthesis of cyclic or linear multiblock copolypeptoids. Thus, polypeptoids can be synthesized either by solid phase synthesis to yield complex and exactly defined oligo- and small polymers or by ROP of appropriately N-substituted N-carboxyanhydrides (NNCA) to give linear, cyclic, or star-like polymers. Together with an excellent biocompatibility, this polymer family may have a bright future ahead as biomaterials. © 2013 Wiley Periodicals, Inc.

  15. Integration of macromolecular diffraction data using radial basis function networks.

    Science.gov (United States)

    Pokrić, B; Allinson, N M; Helliwell, J R

    2000-11-01

    This paper presents a novel approach for intensity calculation of X-ray diffraction spots based on a two-stage radial basis function (RBF) network. The first stage uses pre-determined reference profiles from a database as basis functions in order to locate the diffraction spots and identify any overlapping regions. The second-stage RBF network employs narrow basis functions capable of local modifications of the reference profiles leading to a more accurate observed diffraction spot approximation and therefore accurate determination of spot positions and integrated intensities.

  16. Topological Polymer Chemistry for Designing New Macromolecular Architectures

    Institute of Scientific and Technical Information of China (English)

    Y. Tezuka

    2005-01-01

    @@ 1Introduction The precise control in polymer architectures has been an ongoing challenge in synthetic polymer chemistry, since new polymer topologies will realize unprecedented properties and functions in polymeric materials.In particular, topologically unique macromolecules comprising single cyclic and multicyclic polymer units have gained growing interests due to their distinctive behaviors from linear and branched counterparts[1-4]. See Fig. 1.

  17. Characterization of cereulide synthetase, a toxin-producing macromolecular machine.

    Directory of Open Access Journals (Sweden)

    Diego A Alonzo

    Full Text Available Cereulide synthetase is a two-protein nonribosomal peptide synthetase system that produces a potent emetic toxin in virulent strains of Bacillus cereus. The toxin cereulide is a depsipeptide, as it consists of alternating aminoacyl and hydroxyacyl residues. The hydroxyacyl residues are derived from keto acid substrates, which cereulide synthetase selects and stereospecifically reduces with imbedded ketoreductase domains before incorporating them into the growing depsipeptide chain. We present an in vitro biochemical characterization of cereulide synthetase. We investigate the kinetics and side chain specificity of α-keto acid selection, evaluate the requirement of an MbtH-like protein for adenylation domain activity, assay the effectiveness of vinylsulfonamide inhibitors on ester-adding modules, perform NADPH turnover experiments and evaluate in vitro depsipeptide biosynthesis. This work also provides biochemical insight into depsipeptide-synthesizing nonribosomal peptide synthetases responsible for other bioactive molecules such as valinomycin, antimycin and kutzneride.

  18. Macromolecular sensing at the liquid-liquid interface

    Energy Technology Data Exchange (ETDEWEB)

    Herzog, Gregoire; Flynn, Shane [Tyndall National Institute, Lee Maltings, University College, Cork (Ireland); Arrigan, Damien W M, E-mail: gregoire.herzog@tyndall.ie [Nanochemistry Research Institute, Department of Chemistry, Curtin University, Perth (Australia)

    2011-08-17

    We report here the electrochemical sensing of macromolecules, such as polyLysine dendrimers, at the polarised liquid | liquid interface. Electrochemistry at the liquid | liquid interface is a powerful analytical technique which allows the detection of non-redox active molecules via ion transfer reactions at a polarised water - oil interface. We demonstrate here that different parameters of the polyLysine dendrimers (charge number, molecular weight) have a strong influence on the sensitivity and limit of detection of these macromolecules. This work will help to the development of sensors based on charge transfer at the liquid | liquid interface.

  19. 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.

  20. Towards the specification of consecutive steps in macromolecular lignin assembly

    Science.gov (United States)

    Nose, M.; Bernards, M. A.; Furlan, M.; Zajicek, J.; Eberhardt, T. L.; Lewis, N. G.

    1995-01-01

    When Pinus taeda cell suspension cultures are exposed to 8% sucrose solution, the cells undergo significant intracellular disruption, irregular wall thickening/lignification with concomitant formation of an 'extracellular lignin precipitate. However, addition of potassium iodide (KI), an H202 scavenger, inhibits this lignification response, while the ability to synthesize the monolignols, p-coumaryl and coniferyl alcohols, is retained. Lignin synthesis (i.e. polymerization) is thus temporarily correlated with H202 generation, strongly implying a regulatory role for the latter. Time course analyses of extracellular metabolites leading up to polymer formation reveal that coniferyl alcohol, but not p-coumaryl alcohol, undergoes substantial coupling reactions to give various lignans. Of these, the metabolites, dihydrodehydrodiconiferyl alcohol, shonanin (divanillyl tetrahydrofuran) and its apparent aryl tetralin derivative, cannot be explained simply on the basis of phenolic coupling. It is proposed that these moieties are the precursors of so-called reduced substructures in the lignin macromolecule. This adds a new perspective to the lignin assembly mechanism.

  1. KinImmerse: Macromolecular VR for NMR ensembles

    Directory of Open Access Journals (Sweden)

    Vinson E Claire

    2009-02-01

    Full Text Available Abstract Background In molecular applications, virtual reality (VR and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. Methods The Syzygy open-source toolkit for VR software was used to write the KinImmerse program, which translates the molecular capabilities of the kinemage graphics format into software for display and manipulation in the DiVE (Duke immersive Virtual Environment or other VR system. KinImmerse is supported by the flexible display construction and editing features in the KiNG kinemage viewer and it implements new forms of user interaction in the DiVE. Results In addition to molecular visualizations and navigation, KinImmerse provides a set of research tools for manipulation, identification, co-centering of multiple models, free-form 3D annotation, and output of results. The molecular research test case analyzes the local neighborhood around an individual atom within an ensemble of nuclear magnetic resonance (NMR models, enabling immersive visual comparison of the local conformation with the local NMR experimental data, including target curves for residual dipolar couplings (RDCs. Conclusion The promise of KinImmerse for production-level molecular research in the DiVE is shown by the locally co-centered RDC visualization developed there, which gave new insights now being pursued in wider data analysis.

  2. KinImmerse: Macromolecular VR for NMR ensembles

    OpenAIRE

    Vinson E Claire; Davis Ian W; Chen Vincent B; Zielinski David J; Block Jeremy N; Brady Rachael; Richardson Jane S; Richardson David C

    2009-01-01

    Abstract Background In molecular applications, virtual reality (VR) and immersive virtual environments have generally been used and valued for the visual and interactive experience – to enhance intuition and communicate excitement – rather than as part of the actual research process. In contrast, this work develops a software infrastructure for research use and illustrates such use on a specific case. Methods The Syzygy open-source toolkit for VR software was used to write the KinImmerse prog...

  3. The Differential Response of Proteins to Macromolecular Crowding

    Science.gov (United States)

    Candotti, Michela; Orozco, Modesto

    2016-01-01

    The habitat in which proteins exert their function contains up to 400 g/L of macromolecules, most of which are proteins. The repercussions of this dense environment on protein behavior are often overlooked or addressed using synthetic agents such as poly(ethylene glycol), whose ability to mimic protein crowders has not been demonstrated. Here we performed a comprehensive atomistic molecular dynamic analysis of the effect of protein crowders on the structure and dynamics of three proteins, namely an intrinsically disordered protein (ACTR), a molten globule conformation (NCBD), and a one-fold structure (IRF-3) protein. We found that crowding does not stabilize the native compact structure, and, in fact, often prevents structural collapse. Poly(ethylene glycol) PEG500 failed to reproduce many aspects of the physiologically-relevant protein crowders, thus indicating its unsuitability to mimic the cell interior. Instead, the impact of protein crowding on the structure and dynamics of a protein depends on its degree of disorder and results from two competing effects: the excluded volume, which favors compact states, and quinary interactions, which favor extended conformers. Such a viscous environment slows down protein flexibility and restricts the conformational landscape, often biasing it towards bioactive conformations but hindering biologically relevant protein-protein contacts. Overall, the protein crowders used here act as unspecific chaperons that modulate the protein conformational space, thus having relevant consequences for disordered proteins. PMID:27471851

  4. Identifying, studying and making good use of macromolecular crystals

    Energy Technology Data Exchange (ETDEWEB)

    Calero, Guillermo [University of Pittsburgh Medical School, Pittsburgh, PA 15261 (United States); Cohen, Aina E. [SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025 (United States); Luft, Joseph R. [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203 (United States); State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203 (United States); Newman, Janet [CSIRO Collaborative Crystallisation Centre, 343 Royal Parade, Parkville, Victoria 3052 (Australia); Snell, Edward H., E-mail: esnell@hwi.buffalo.edu [Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203 (United States); State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203 (United States); University of Pittsburgh Medical School, Pittsburgh, PA 15261 (United States)

    2014-07-25

    As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed.

  5. Macromolecular recognition directs calcium ions to coccolith mineralization sites.

    Science.gov (United States)

    Gal, Assaf; Wirth, Richard; Kopka, Joachim; Fratzl, Peter; Faivre, Damien; Scheffel, André

    2016-08-01

    Many organisms form elaborate mineralized structures, constituted of highly organized arrangements of crystals and organic macromolecules. The localization of crystals within these structures is presumably determined by the interaction of nucleating macromolecules with the mineral phase. Here we show that, preceding nucleation, a specific interaction between soluble organic molecules and an organic backbone structure directs mineral components to specific sites. This strategy underlies the formation of coccoliths, which are highly ordered arrangements of calcite crystals produced by marine microalgae. On combining the insoluble organic coccolith scaffold with coccolith-associated soluble macromolecules in vitro, we found a massive accretion of calcium ions at the sites where the crystals form in vivo. The in vitro process exhibits profound similarities to the initial stages of coccolith biogenesis in vivo. PMID:27493186

  6. Room-temperature macromolecular serial crystallography using synchrotron radiation.

    Science.gov (United States)

    Stellato, Francesco; Oberthür, Dominik; Liang, Mengning; Bean, Richard; Gati, Cornelius; Yefanov, Oleksandr; Barty, Anton; Burkhardt, Anja; Fischer, Pontus; Galli, Lorenzo; Kirian, Richard A; Meyer, Jan; Panneerselvam, Saravanan; Yoon, Chun Hong; Chervinskii, Fedor; Speller, Emily; White, Thomas A; Betzel, Christian; Meents, Alke; Chapman, Henry N

    2014-07-01

    A new approach for collecting data from many hundreds of thousands of microcrystals using X-ray pulses from a free-electron laser has recently been developed. Referred to as serial crystallography, diffraction patterns are recorded at a constant rate as a suspension of protein crystals flows across the path of an X-ray beam. Events that by chance contain single-crystal diffraction patterns are retained, then indexed and merged to form a three-dimensional set of reflection intensities for structure determination. This approach relies upon several innovations: an intense X-ray beam; a fast detector system; a means to rapidly flow a suspension of crystals across the X-ray beam; and the computational infrastructure to process the large volume of data. Originally conceived for radiation-damage-free measurements with ultrafast X-ray pulses, the same methods can be employed with synchrotron radiation. As in powder diffraction, the averaging of thousands of observations per Bragg peak may improve the ratio of signal to noise of low-dose exposures. Here, it is shown that this paradigm can be implemented for room-temperature data collection using synchrotron radiation and exposure times of less than 3 ms. Using lysozyme microcrystals as a model system, over 40 000 single-crystal diffraction patterns were obtained and merged to produce a structural model that could be refined to 2.1 Å resolution. The resulting electron density is in excellent agreement with that obtained using standard X-ray data collection techniques. With further improvements the method is well suited for even shorter exposures at future and upgraded synchrotron radiation facilities that may deliver beams with 1000 times higher brightness than they currently produce. PMID:25075341

  7. Room-temperature macromolecular serial crystallography using synchrotron radiation

    Directory of Open Access Journals (Sweden)

    Francesco Stellato

    2014-07-01

    Full Text Available A new approach for collecting data from many hundreds of thousands of microcrystals using X-ray pulses from a free-electron laser has recently been developed. Referred to as serial crystallography, diffraction patterns are recorded at a constant rate as a suspension of protein crystals flows across the path of an X-ray beam. Events that by chance contain single-crystal diffraction patterns are retained, then indexed and merged to form a three-dimensional set of reflection intensities for structure determination. This approach relies upon several innovations: an intense X-ray beam; a fast detector system; a means to rapidly flow a suspension of crystals across the X-ray beam; and the computational infrastructure to process the large volume of data. Originally conceived for radiation-damage-free measurements with ultrafast X-ray pulses, the same methods can be employed with synchrotron radiation. As in powder diffraction, the averaging of thousands of observations per Bragg peak may improve the ratio of signal to noise of low-dose exposures. Here, it is shown that this paradigm can be implemented for room-temperature data collection using synchrotron radiation and exposure times of less than 3 ms. Using lysozyme microcrystals as a model system, over 40 000 single-crystal diffraction patterns were obtained and merged to produce a structural model that could be refined to 2.1 Å resolution. The resulting electron density is in excellent agreement with that obtained using standard X-ray data collection techniques. With further improvements the method is well suited for even shorter exposures at future and upgraded synchrotron radiation facilities that may deliver beams with 1000 times higher brightness than they currently produce.

  8. Multiscale mechanics of macromolecular materials with unfolding domains

    Science.gov (United States)

    De Tommasi, D.; Puglisi, G.; Saccomandi, G.

    2015-05-01

    We propose a general multiscale approach for the mechanical behavior of three-dimensional networks of macromolecules undergoing strain-induced unfolding. Starting from a (statistically based) energetic analysis of the macromolecule unfolding strategy, we obtain a three-dimensional continuum model with variable natural configuration and an energy function analytically deduced from the microscale material parameters. The comparison with the experiments shows the ability of the model to describe the complex behavior, with residual stretches and unfolding effects, observed in different biological materials.

  9. L-canavanine incorporation into vitellogenin and macromolecular conformation.

    Science.gov (United States)

    Rosenthal, G A; Reichhart, J M; Hoffmann, J A

    1989-08-15

    L-Canavanine is a potentially deleterious arginine antimetabolite whose toxicity is expressed in canavanine-sensitive organisms ranging from viruses to humans. Canavanine, a substrate for arginyl-tRNA synthetase, is incorporated into nascent polypeptide chains in place of arginine. This substitution results in the production of structurally aberrant, canavanyl proteins. Chemical, physical, and immunological studies of native and canavanine-containing vitellogenin obtained from female migratory locusts (Locusta migratoria migratorioides (Orthoptera] provide the first experimental evidence that canavanine can disrupt the tertiary and/or quaternary structure that yields the three-dimensional conformation unique to the protein. These findings enhance our understanding of the biochemical basis for canavanine's antimetabolic and potent insecticidal properties. PMID:2760038

  10. Phasing macromolecular structures via structure-invariant algebra.

    Science.gov (United States)

    Hauptman, H; Han, F

    1993-01-01

    Owing to the breakdown of Friedel's law when anomalous scatterers are present, unique values of the three-phase structure invariants in the whole range from 0 to 2pi are determined by measured values of diffraction intensities alone. Two methods are described for going from presumed known values of these invariants to the values of the individual phases. The first, dependent on a scheme for resolving the 2pi ambiguity in the estimate omega(HK) of the triplet phi(H) + phi(K) + phi(-H-K), solves by least squares the resulting redundant system of linear equations phi(H) + phi(K) + phi(-H-K) = omega(HK). The second attempts to minimize the weighted sum of squares of differences between the true values of the cosine and sine invariants and their estimates. The latter method is closely related to one based on the 'minimal principle' which determines the values of a large set of phases as the constrained global minimum of a function of all the phases in the set. Both methods work in the sense that they yield values of the individual phases substantially better than the values of the initial estimates of the triplets. However, the second method proves to be superior to the first but requires, in addition to estimates of the triplets, initial estimates of the values of the individual phases. PMID:15299539

  11. The PDB_REDO server for macromolecular structure model optimization.

    Science.gov (United States)

    Joosten, Robbie P; Long, Fei; Murshudov, Garib N; Perrakis, Anastassis

    2014-07-01

    The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395-1412]. The PDB_REDO procedure aims for 'constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo-graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB. PMID:25075342

  12. The PDB_REDO server for macromolecular structure model optimization

    OpenAIRE

    Joosten, Robbie P.; Fei Long; Murshudov, Garib N.; Anastassis Perrakis

    2014-01-01

    The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395–1412]. The PDB_REDO procedure aims for ‘constructive valida...

  13. The PDB_REDO server for macromolecular structure model optimization

    Directory of Open Access Journals (Sweden)

    Robbie P. Joosten

    2014-07-01

    Full Text Available The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB. The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011, Structure, 19, 1395–1412]. The PDB_REDO procedure aims for `constructive validation', aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallographers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB.

  14. Identifying, studying and making good use of macromolecular crystals

    International Nuclear Information System (INIS)

    As technology advances, the crystal volume that can be used to collect useful X-ray diffraction data decreases. The technologies available to detect and study growing crystals beyond the optical resolution limit and methods to successfully place the crystal into the X-ray beam are discussed. Structural biology has contributed tremendous knowledge to the understanding of life on the molecular scale. The Protein Data Bank, a depository of this structural knowledge, currently contains over 100 000 protein structures, with the majority stemming from X-ray crystallography. As the name might suggest, crystallography requires crystals. As detectors become more sensitive and X-ray sources more intense, the notion of a crystal is gradually changing from one large enough to embellish expensive jewellery to objects that have external dimensions of the order of the wavelength of visible light. Identifying these crystals is a prerequisite to their study. This paper discusses developments in identifying these crystals during crystallization screening and distinguishing them from other potential outcomes. The practical aspects of ensuring that once a crystal is identified it can then be positioned in the X-ray beam for data collection are also addressed

  15. Macromolecular engineering of in-situ forming hydrogels

    NARCIS (Netherlands)

    Wang, Rong

    2016-01-01

    Surgery in our perspective generally requires an operation with a certain size of an incision, leaving wounds, which are painful, require a long time to heal and end up with the formation of scars. Advances in medical procedures and technologies have led to the development of minimally invasive surg

  16. Mobility fluctuations and electrophoretic light scattering from macromolecular solutions

    Energy Technology Data Exchange (ETDEWEB)

    Hubbard, J.B.; McQuarrie, D.A.

    1988-09-01

    We discuss the origins and the effects of mobility fluctuations of rigid, globular macromolecules on a solution's electrophoretic light scattering spectrum. Assuming a dilute solution, a modified van Hove self-correlation function is calculated via van Kampen's time-ordered cumulant method and the results are compared with less rigorous approaches. The consequences of generalizing to dynamic external fields are briefly considered.

  17. Addressable Macromolecular Architectures: Towards stimuli promoted motion at the nanoscale

    NARCIS (Netherlands)

    Kutnyanszky, Edit

    2012-01-01

    Addressable polymer structures play an increasingly important role in a variety of areas, such as surface engineering, drug delivery, and micro/nanofluidics. In these structures, addressability results from the sensitivity of incorporated polymer chains to variations in temperature, electric or magn

  18. Polyelectrolyte-mediated bridging interactions: columnar macromolecular phases

    Energy Technology Data Exchange (ETDEWEB)

    Licer, Matjaz [Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana (Slovenia); Podgornik, Rudolf [Department of Physics, Faculty of Mathematics and Physics, and Institute of Biophysics, School of Medicine, University of Ljubljana, SI-1000 Ljubljana (Slovenia)

    2010-10-20

    We present a mean-field theory for charged polymer chains in an external electrostatic field in the weak and strong coupling limits. We apply the theory to describe the statistical mechanics of flexible polyelectrolyte chains in a hexagonal columnar lattice of stiff cylindrical macroions, such as DNA, in a bathing solution of a uni-univalent salt (e.g. NaCl). The salt effects are first described in the Debye-Hueckel framework. This yields the macroion electrostatic field in the screened Coulomb form, which we take to represent the mean field into which the chains are immersed. We introduce the Green's function for the polyelectrolyte chains and derive the corresponding Edwards equation which we solve numerically in the Wigner-Seitz cylindrical cell using the ground state dominance ansatz. The solutions indicate the presence of polyelectrolyte bridging, which results in a like-charge attraction between stiff macroions. Then we reformulate the Edwards theory for the strong coupling case and use the standard Poisson-Boltzmann picture to describe the salt solution. We begin with the free energy which we minimize to obtain the Euler-Lagrange equations. The solutions yield self-consistently determined monomer density and electrostatic fields. We furthermore calculate the free energy density as well as the total osmotic pressure in the system. We again show that bridging implicates like-charge attractions of entropic origin between stiff cylindrical macroions. By analyzing the osmotic pressure we demonstrate that, in certain parts of the parameter space, a phase transition occurs between two phases of the same hexagonal symmetry.

  19. Macromolecular Chain at a Cellular Surface: a Computer Simulation Model

    Science.gov (United States)

    Xie, Jun; Pandey, Ras

    2001-06-01

    Computer simulations are performed to study conformation and dynamics of relatively large chain macromolecule at the surface of a model cell membrane - a preliminary attempt to ultimately realistic model for protein on a cell membrane. We use a discrete lattice of size Lx × L × L. The chain molecule of length Lc is modelled by consecutive nodes connected by bonds on the trail of a random walk with appropriate constraints such as excluded volume, energy dependent configurational bias, etc. Monte Carlo method is used to move chains via segmental dynamics, i.e., end-move, kink-jump, crank-shaft, reptation, etc. Membrane substrate is designed by an ensemble of short chains on a flat surface. Large chain molecule is then driven toward the membrane by a field. We plan to examine the dynamics of chain macromolecule, spread of its density, and its conformation.

  20. Macromolecular structure determination in the post-genome era

    International Nuclear Information System (INIS)

    Recent advances in genetics, molecular biology and crystallographic instrumentation and methodology have led to a revolution in the field of Structural Molecular Biology (SMB). These combined advances have paved the way to a more complete and detailed understanding of the biological macromolecules that make up an organism, both in terms of their individual functions and also the interactions between them. In this paper we describe a large-scale, genomic approach to the three-dimensional structure determination of macromolecules and their complexes, using high-throughput methodology to streamline all aspects of the process. This task requires the development of automated high-intensity synchrotron beam lines for X-ray diffraction data collection from single crystal samples. Furthermore, these beam lines must be operated within a sophisticated software and hardware environment, which is capable of delivering a completely automated structure determination pipeline. The SMB resource at SSRL is developing a system for the structure determination steps of this process, starting with the initial characterization of the frozen sample, followed by data collection, data reduction, phase determination, and model building. This paper focuses on the data collection elements of this high-throughput system