WorldWideScience

Sample records for macromolecular assemblage approach

  1. 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.

  2. Syntheses of Macromolecular Ruthenium Compounds: A New Approach for the Search of Anticancer Drugs

    Directory of Open Access Journals (Sweden)

    Andreia Valente

    2014-03-01

    Full Text Available The continuous rising of the cancer patient death rate undoubtedly shows the pressure to find more potent and efficient drugs than those in clinical use. These agents only treat a narrow range of cancer conditions with limited success and are associated with serious side effects caused by the lack of selectivity. In this frame, innovative syntheses approaches can decisively contribute to the success of “smart compounds” that might be only selective and/or active towards the cancer cells, sparing the healthy ones. In this scope, ruthenium chemistry is a rising field for the search of proficient metallodrugs by the use of macromolecular ruthenium complexes (dendrimers and dendronized polymers, coordination-cage and protein conjugates, nanoparticles and polymer-“ruthenium-cyclopentadienyl” conjugates that can take advantage of the singularities of tumor cells (vs. healthy cells.

  3. 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.

  4. A multi-scaled approach to evaluating the fish assemblage structure within southern Appalachian streams USA.

    Science.gov (United States)

    Kirsch, Joseph; Peterson, James T.

    2014-01-01

    There is considerable uncertainty about the relative roles of stream habitat and landscape characteristics in structuring stream-fish assemblages. We evaluated the relative importance of environmental characteristics on fish occupancy at the local and landscape scales within the upper Little Tennessee River basin of Georgia and North Carolina. Fishes were sampled using a quadrat sample design at 525 channel units within 48 study reaches during two consecutive years. We evaluated species–habitat relationships (local and landscape factors) by developing hierarchical, multispecies occupancy models. Modeling results suggested that fish occupancy within the Little Tennessee River basin was primarily influenced by stream topology and topography, urban land coverage, and channel unit types. Landscape scale factors (e.g., urban land coverage and elevation) largely controlled the fish assemblage structure at a stream-reach level, and local-scale factors (i.e., channel unit types) influenced fish distribution within stream reaches. Our study demonstrates the utility of a multi-scaled approach and the need to account for hierarchy and the interscale interactions of factors influencing assemblage structure prior to monitoring fish assemblages, developing biological management plans, or allocating management resources throughout a stream system.

  5. Environmental Quality Assessment of Bizerte Lagoon (Tunisia Using Living Foraminifera Assemblages and a Multiproxy Approach.

    Directory of Open Access Journals (Sweden)

    Maria Virgínia Alves Martins

    Full Text Available This study investigated the environmental quality of the Bizerte Lagoon (Tunisia through an integrated approach that combined environmental, biogeochemical, and living benthic foraminiferal analyses. Specifically, we analyzed the physicochemical parameters of the water and sediment. The textural, mineralogical, and geochemical characteristics of the sediment, including total organic carbon, total nitrogen, simultaneously extracted metals (SEM, acid volatile sulfides (AVS, chlorophyll a, CaCO3, and changes in bacterial populations and carbon isotopes were measured. The SEM/AVS values indicated the presence of relatively high concentrations of toxic metals in only some areas. Foraminiferal assemblages were dominated by species such as A. parkinsoniana (20-91%, Bolivina striatula (<40%, Hopkinsina atlantica (<17%, and Bolivina ordinaria (<15% that cannot be considered typical of impacted coastal lagoons both in Mediterranean and northeast Atlantic regions. The results of this work suggest that Bizerte Lagoon is a unique setting. This lagoon is populated by typical marine species that invaded this ecosystem, attracted not only by the prevailing favorable environmental conditions but also by the abundance and quality of food. The results indicate that the metal pollution found in some areas have a negative impact on the assemblages of foraminifera. At present, however, this negative impact is not highly alarming.

  6. Environmental Quality Assessment of Bizerte Lagoon (Tunisia) Using Living Foraminifera Assemblages and a Multiproxy Approach

    Science.gov (United States)

    Alves Martins, Maria Virgínia; Zaaboub, Noureddine; Aleya, Lotfi; Frontalini, Fabrizio; Pereira, Egberto; Miranda, Paulo; Mane, Miguel; Rocha, Fernando; Laut, Lazaro; El Bour, Monia

    2015-01-01

    This study investigated the environmental quality of the Bizerte Lagoon (Tunisia) through an integrated approach that combined environmental, biogeochemical, and living benthic foraminiferal analyses. Specifically, we analyzed the physicochemical parameters of the water and sediment. The textural, mineralogical, and geochemical characteristics of the sediment, including total organic carbon, total nitrogen, simultaneously extracted metals (SEM), acid volatile sulfides (AVS), chlorophyll a, CaCO3, and changes in bacterial populations and carbon isotopes were measured. The SEM/AVS values indicated the presence of relatively high concentrations of toxic metals in only some areas. Foraminiferal assemblages were dominated by species such as A. parkinsoniana (20–91%), Bolivina striatula (<40%), Hopkinsina atlantica (<17%), and Bolivina ordinaria (<15%) that cannot be considered typical of impacted coastal lagoons both in Mediterranean and northeast Atlantic regions. The results of this work suggest that Bizerte Lagoon is a unique setting. This lagoon is populated by typical marine species that invaded this ecosystem, attracted not only by the prevailing favorable environmental conditions but also by the abundance and quality of food. The results indicate that the metal pollution found in some areas have a negative impact on the assemblages of foraminifera. At present, however, this negative impact is not highly alarming. PMID:26372655

  7. Citizenship agendas, urban governance and social housing in the Netherlands: An assemblage approach

    NARCIS (Netherlands)

    Koster, M.

    2015-01-01

    This article combines recent conceptualizations of citizenship beyond the nation state with new perspectives on governance assemblages comprising both state and non-state actors. Focusing on Dutch social housing, this study explores how such governance assemblages produce agendas that attempt to sha

  8. Macromolecular Prodrugs of Ribavirin

    DEFF Research Database (Denmark)

    Riber, Camilla Frich; Hinton, Tracey M; Gajda, Paulina

    2017-01-01

    The requirement for new antiviral therapeutics is an ever present need. Particularly lacking are broad spectrum antivirals that have low toxicity. We develop such agents based on macromolecular prodrugs whereby both the polymer chain and the drug released from the polymer upon cell entry have ant...

  9. Macromolecular Crystallization in Microgravity

    Science.gov (United States)

    Snell, Edward H.; Helliwell, John R.

    2004-01-01

    The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. 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. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. 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 analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural

  10. Effects of macromolecular crowding on genetic networks.

    Science.gov (United States)

    Morelli, Marco J; Allen, Rosalind J; Wolde, Pieter Rein ten

    2011-12-21

    The intracellular environment is crowded with proteins, DNA, and other macromolecules. Under physiological conditions, macromolecular crowding can alter both molecular diffusion and the equilibria of bimolecular reactions and therefore is likely to have a significant effect on the function of biochemical networks. We propose a simple way to model the effects of macromolecular crowding on biochemical networks via an appropriate scaling of bimolecular association and dissociation rates. We use this approach, in combination with kinetic Monte Carlo simulations, to analyze the effects of crowding on a constitutively expressed gene, a repressed gene, and a model for the bacteriophage λ genetic switch, in the presence and absence of nonspecific binding of transcription factors to genomic DNA. Our results show that the effects of crowding are mainly caused by the shift of association-dissociation equilibria rather than the slowing down of protein diffusion, and that macromolecular crowding can have relevant and counterintuitive effects on biochemical network performance.

  11. Temporal Succession of Phytoplankton Assemblages in a Tidal Creek System of the Sundarbans Mangroves: An Integrated Approach

    Directory of Open Access Journals (Sweden)

    Dola Bhattacharjee

    2013-01-01

    Full Text Available Sundarbans, the world's largest mangrove ecosystem, is unique and biologically diverse. A study was undertaken to track temporal succession of phytoplankton assemblages at the generic level (≥10 µm encompassing 31 weeks of sampling (June 2010–May 2011 in Sundarbans based on microscopy and hydrological measurements. As part of this study, amplification and sequencing of type ID rbcL subunit of RuBisCO enzyme were also applied to infer chromophytic algal groups (≤10 µm size from one of the study points. We report the presence of 43 genera of Bacillariophyta, in addition to other phytoplankton groups, based on microscopy. Phytoplankton cell abundance, which was highest in winter and spring, ranged between 300 and 27,500 cells/L during this study. Cell biovolume varied between winter of 2010 (90–35281.04 µm3 and spring-summer of 2011 (52–33962.24 µm3. Winter supported large chain forming diatoms, while spring supported small sized diatoms, followed by other algal groups in summer. The clone library approach showed dominance of Bacillariophyta-like sequences, in addition to Cryptophyta-, Haptophyta-, Pelagophyta-, and Eustigmatophyta-like sequences which were detected for the first time highlighting their importance in mangrove ecosystem. This study clearly shows that a combination of microscopy and molecular tools can improve understanding of phytoplankton assemblages in mangrove environments.

  12. 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

  13. 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.

  14. Statistics of Multiscale Fluctuations in Macromolecular Systems

    CERN Document Server

    Yukalov, V I

    2012-01-01

    An approach is suggested for treating multiscale fluctuations in macromolecular systems. The emphasis is on the statistical properties of such fluctuations. The approach is illustrated by a macromolecular system with mesoscopic fluctuations between the states of atomic orbitals. Strong-orbital and weak-orbital couplings fluctuationally arise, being multiscale in space and time. Statistical properties of the system are obtained by averaging over the multiscale fluctuations. The existence of such multiscale fluctuations causes phase transitions between strong-coupling and weak-coupling states. These transitions are connected with structure and size transformations of macromolecules. An approach for treating density and size multiscale fluctuations by means of classical statistical mechanics is also advanced.

  15. A meta-analysis approach to the effects of fish farming on soft bottom polychaeta assemblages in temperate regions

    OpenAIRE

    Martinez-Garcia, Elena; Sanchez-Jerez, Pablo; Aguado Giménez, Felipe; Ávila, Pablo; Guerrero, Alejandro; Sánchez-Lizaso, José Luis; Fernandez-Gonzalez, Victoria; González, Nieves; Gairin Deulofeu, Joan Ignasi; Carballeira, Carlos; García García, Benjamín; Carreras, Jordi; Macías, José Carlos; Carballeira, Alejo; Collado, Cayetano

    2013-01-01

    Marine fish farms could cause environmental disturbances on the sediment due to uneaten food and fish faeces that impact the marine benthos. Polychaete assemblages are considered good indicators of environmental perturbations. The present study aimed to establish groups of polychaetes as potential indicators of fish farm pollution. This study was carried out in ten fish farms along the Spanish coast. Changes in polychaete assemblage were analyzed with meta-analysis and multivariate techniques...

  16. Strange Assemblage

    Directory of Open Access Journals (Sweden)

    David Robert Cole

    2014-08-01

    Full Text Available This paper contends that the power of Deleuze & Guattari’s (1988 notion of assemblage as theorised in 1000 Plateaus can be normalised and reductive with reference to its application to any social-cultural context where an open system of dynamic and fluid elements are located. Rather than determining the assemblage in this way, this paper argues for an alternative conception of ‘strange assemblage’ that must be deliberately and consciously created through rigorous and focused intellectual, creative and philosophical work around what makes assemblages singular. The paper will proceed with examples of ‘strange assemblage’ taken from a film by Peter Greenaway (A Zed and 2 Noughts; the film ‘Performance’; educational research with Sudanese families in Australia; the book, Bomb Culture by Jeff Nuttall (1970; and the band Hawkwind. Fittingly, these elements are themselves chosen to demonstrate the concept of ‘strange assemblage’, and how it can be presented. How exactly the elements of a ‘strange assemblage’ come together and work in the world is unknown until they are specifically elaborated and created ‘in the moment’. Such spontaneous methodology reminds us of the 1960s ‘Happenings’, the Situationist International and Dada/Surrealism. The difference that will be opened up by this paper is that all elements of this ‘strange assemblage’ cohere in terms of a rendering of ‘the unacceptable.'

  17. Phylogenetics and biogeographic approaches to the study of extinction: from timetrees to patterns of biotic assemblage

    Directory of Open Access Journals (Sweden)

    Isabel eSanmartin

    2016-03-01

    Full Text Available Global climate change and its impact on biodiversity levels have made extinction a relevant topic in biological research. Yet, until recently, extinction has received less attention in macroevolutionary studies than speciation; the reason is the difficulty to infer an event that actually eliminates rather than creates new taxa. For example, in biogeography, extinction has often been seen as noise, introducing homoplasy in biogeographic relationships, rather than a pattern-generating process. The molecular revolution and the possibility to integrate time into phylogenetic reconstructions have allowed studying extinction under different perspectives. Here, we review phylogenetic (temporal and biogeographic (spatial approaches to the inference of extinction and the challenges this process poses for reconstructing evolutionary history. Specifically, we focus on the problem of discriminating between alternative high extinction scenarios using time trees with only extant taxa, and on the confounding effect introduced by asymmetric spatial extinction – different rates of extinction across areas – in biogeographic inference. Finally, we identify the most promising avenues of research in both fields, which include the integration of additional sources of evidence such as the fossil record or environmental information in birth-death models and biogeographic reconstructions, the development of new models that tie extinction rates to phenotypic or environmental variation, or the implementation within a Bayesian framework of parametric non-stationary biogeographic models.

  18. 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.

  19. Influence of approach velocity and mesh size on the entrainment and contact of a lowland river fish assemblage at a screened irrigation pump.

    Directory of Open Access Journals (Sweden)

    Craig A Boys

    Full Text Available Fish screens can help prevent the entrainment or injury of fish at irrigation diversions, but only when designed appropriately. Design criteria cannot simply be transferred between sites or pump systems and need to be developed using an evidence-based approach with the needs of local species in mind. Laboratory testing is typically used to quantify fish responses at intake screens, but often limits the number of species that can studied and creates artificial conditions not directly applicable to screens in the wild. In this study a field-based approach was used to assess the appropriateness of different screen design attributes for the protection of a lowland river fish assemblage at an experimental irrigation pump. Direct netting of entrained fish was used along with sonar technology to quantify the probability of screen contact for a Murray-Darling Basin (Australia fish species. Two approach velocities (0.1 and 0.5 m.sec(-1 and different sizes of woven mesh (5, 10 and 20 mm were evaluated. Smaller fish (<150 mm in the assemblage were significantly more susceptible to entrainment and screen contact, especially at higher approach velocities. Mesh size appeared to have little impact on screen contact and entrainment, suggesting that approach velocity rather than mesh size is likely to be the primary consideration when developing screens. Until the effects of screen contacts on injury and survival of these species are better understood, it is recommended that approach velocities not exceed 0.1 m.sec(-1 when the desire is to protect the largest range of species and size classes for lowland river fish assemblages in the Murray-Darling Basin. The field method tested proved to be a useful approach that could compliment laboratory studies to refine fish screen design and facilitate field validation.

  20. A meta-analysis approach to the effects of fish farming on soft bottom polychaeta assemblages in temperate regions.

    Science.gov (United States)

    Martinez-Garcia, Elena; Sanchez-Jerez, Pablo; Aguado-Giménez, Felipe; Ávila, Pablo; Guerrero, Alejandro; Sánchez-Lizaso, Jose Luis; Fernandez-Gonzalez, Victoria; González, Nieves; Gairin, Joan Ignasi; Carballeira, Carlos; García-García, Benjamín; Carreras, Jordi; Macías, Jose Carlos; Carballeira, Alejo; Collado, Cayetano

    2013-04-15

    Marine fish farms could cause environmental disturbances on the sediment due to uneaten food and fish faeces that impact the marine benthos. Polychaete assemblages are considered good indicators of environmental perturbations. The present study aimed to establish groups of polychaetes as potential indicators of fish farm pollution. This study was carried out in ten fish farms along the Spanish coast. Changes in polychaete assemblage were analyzed with meta-analysis and multivariate techniques. Abundance, richness and diversity showed significant decreases under fish farm conditions. Distribution patterns of polychaetes responded to combinations of physicochemical variables. The main ones are sulfide concentration, silt and clays percentage, and stable nitrogen isotope ratio. The results showed that some families are tolerant, Capitellidae, Dorvilleidae, Glyceridae, Nereididae, Oweniidae and Spionidae; while others are sensitive to fish farm pollution, Magelonidae, Maldanidae, Nephtyidae, Onuphidae, Paralacydoniidae, Paraonide, Sabellidae and also Cirratulidae in spite of being reported as a tolerant family.

  1. Fashion, Mediations & Method Assemblages

    DEFF Research Database (Denmark)

    Sommerlund, Julie; Jespersen, Astrid Pernille

    , respectively. The paper thus takes on aesthetics and the social in a manner closely related to a core argument of STS - namely that the scientific fact, and the social processes of constructing, distributing, and using that fact, are co-constructed (Callon, 1986; Latour, 1993). The paper thus contributes......, it is an important ambition of this paper to go into a methodological discussion of how "that which effectively happens" can be approached. To this end, the paper will combine Hennion's term of the "mediator" with John Laws methodological term of "method assemblages". Method assemblages is a suggested as a way...... of handling multiple, fluid realities with multiple, fluid methods. Empirically, the paper works with mediation in fashion - that is efforts the active shaping of relations between producer and consumer through communication, marketing and PR. Fashion mediation is by no means simple, but organise complex...

  2. 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.

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

    Science.gov (United States)

    Bastard, Karine; Saladin, Adrien; Prévost, Chantal

    2011-01-01

    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. PMID:21541061

  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. Monitoring the Effects of Oil Sands Process-Affected Water (OSPW) on Thecamoebian Assemblages: An Experimental Approach

    Science.gov (United States)

    Christie, D. G.; McCarthy, F. F.; Penner, T.; MacKinnon, M. M.

    2009-05-01

    Thecamoebian (testate amoeba) assemblages have been shown to respond over short time periods to environmental conditions in aquatic reclamation options under development at oil sands operations in northeastern Alberta. This makes them a useful bio-monitoring tool for assessing reclamation success. Thecamoebian responses to Oil Sands Process Water (OSPW) have been monitored in the field at lacustrine and wetland test sites established by Syncrude Canada Ltd. and Suncor Energy Ltd. These field studies have confirmed that the generation times of testate amoebas is sufficiently rapid to permit the construction of a controlled laboratory experiment to be completed within one year, where controlled exposures of a natural assemblage of thecamoebians to OSPW can be undertaken to better understand the community responses to stressors We intend to culture these protists in the lab and monitor their response to different concentrations of OSPW in a controlled environment. Survival and changes in relative community composition (difflugiids vs. centropyxids) will be used to establish the dilution of OSPW in which thecameobians can survive and examine how a natural assemblage changes over time in response to increased concentrations of OSPW. This will assist in reclamation management in the Oil Sands region of Alberta.

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

    Science.gov (United States)

    Sarkar, Purbasha; Bosneaga, Elena; Yap, Edgar G; Das, Jyotirmoy; Tsai, Wen-Ting; Cabal, Angelo; Neuhaus, Erica; Maji, Dolonchampa; Kumar, Shailabh; Joo, Michael; Yakovlev, Sergey; Csencsits, Roseann; Yu, Zeyun; Bajaj, Chandrajit; Downing, Kenneth H; Auer, Manfred

    2014-01-01

    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 characterized the

  7. 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

  8. Rhythms and community dynamics of a hydrothermal tubeworm assemblage at main endeavour field - a multidisciplinary deep-sea observatory approach.

    Directory of Open Access Journals (Sweden)

    Daphne Cuvelier

    Full Text Available The NEPTUNE cabled observatory network hosts an ecological module called TEMPO-mini that focuses on hydrothermal vent ecology and time series, granting us real-time access to data originating from the deep sea. In 2011-2012, during TEMPO-mini's first deployment on the NEPTUNE network, the module recorded high-resolution imagery, temperature, iron (Fe and oxygen on a hydrothermal assemblage at 2186 m depth at Main Endeavour Field (North East Pacific. 23 days of continuous imagery were analysed with an hourly frequency. Community dynamics were analysed in detail for Ridgeia piscesae tubeworms, Polynoidae, Pycnogonida and Buccinidae, documenting faunal variations, natural change and biotic interactions in the filmed tubeworm assemblage as well as links with the local environment. Semi-diurnal and diurnal periods were identified both in fauna and environment, revealing the influence of tidal cycles. Species interactions were described and distribution patterns were indicative of possible microhabitat preference. The importance of high-resolution frequencies (<1 h to fully comprehend rhythms in fauna and environment was emphasised, as well as the need for the development of automated or semi-automated imagery analysis tools.

  9. Effects of reclamation on macrobenthic assemblages in the coastline of the Arabian Gulf: a microcosm experimental approach.

    Science.gov (United States)

    Naser, Humood A

    2011-03-01

    Coastal reclamation and modifications are extensively carried out in Bahrain, which may physically smother the coastal and subtidal habitats resulting in changes to abundance and distribution of macrobenthic assemblages. A microcosm laboratory experiment using three common macrobenthic invertebrates from a proposed reclaimed coastal area was preformed to examine their responses to mud burial using marine sediment collected from a designated borrow area. Significant difference in numbers of survived organisms between control and experimental treatments with a survival percentage of 41.8% for all of the selected species was observed. The polychaete Perinereis nuntia showed the highest percentage of survival (57.1%) followed by the bivalve Tellinavaltonis (42.3%) and the gastropod Cerithidea cingulata (24.0%). Quantifying species responses to sediment burial resulted from dredging and reclamation will aid in predicting the expected ecological impacts associated with coastal developments and subsequently minimizing these impacts and maintaining a sustainable use of coastal and marine ecosystems in the Arabian Gulf.

  10. Rotation-Induced Macromolecular Spooling of DNA

    Directory of Open Access Journals (Sweden)

    Tyler N. Shendruk

    2017-07-01

    Full Text Available Genetic information is stored in a linear sequence of base pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands, resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.

  11. Rotation-Induced Macromolecular Spooling of DNA

    Science.gov (United States)

    Shendruk, Tyler N.; Sean, David; Berard, Daniel J.; Wolf, Julian; Dragoman, Justin; Battat, Sophie; Slater, Gary W.; Leslie, Sabrina R.

    2017-07-01

    Genetic information is stored in a linear sequence of base pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that rotation-induced macromolecular spooling of DNA around a rotating microwire can monotonically order genomic bases, overcoming this challenge. We use single-molecule fluorescence microscopy to directly visualize long DNA strands deforming and elongating in shear flow near a rotating microwire, in agreement with numerical simulations. While untethered DNA is observed to elongate substantially, in agreement with our theory and numerical simulations, strong extension of DNA becomes possible by introducing tethering. For the case of tethered polymers, we show that increasing the rotation rate can deterministically spool a substantial portion of the chain into a fully stretched, single-file conformation. When applied to DNA, the fraction of genetic information sequentially ordered on the microwire surface will increase with the contour length, despite the increased entropy. This ability to handle long strands of DNA is in contrast to modern DNA sample preparation technologies for sequencing and mapping, which are typically restricted to comparatively short strands, resulting in challenges in reconstructing the genome. Thus, in addition to discovering new rotation-induced macromolecular dynamics, this work inspires new approaches to handling genomic-length DNA strands.

  12. The beginning of the Upper Paleolithic in the Iranian Zagros. A taphonomic approach and techno-economic comparison of Early Baradostian assemblages from Warwasi and Yafteh (Iran).

    Science.gov (United States)

    Tsanova, Tsenka

    2013-07-01

    Southwest Asia is a key region in current debates surrounding the appearance of the first cultures attributed to anatomically modern humans, particularly the Aurignacian and preceding cultural units of the Iranian Zagros, Levant, and the Balkans (Baradostian, Ahmarien, Kozarnikien, etc.). The Zagros mountain range encompasses an immense territory that remains understudied with regard to the Upper Paleolithic as well as the first bladelet industries traditionally presumed to be the work of anatomically modern humans. Concerning the emergence of the Aurignacian, the sites of Warwasi rockshelter and Yafteh cave in the central Zagros are considered to show evidence of in situ evolution of the Upper Paleolithic from the local Mousterian. This hypothesis is tested by way of a taphonomic, techno-typological and economic approach applied to the Upper Paleolithic levels of Warwasi (spits LL-AA) and Yafteh (the series from the lower part of the sequence). A comparison of the techno-economic features of both assemblages demonstrates a conceptual bond with contemporaneous techno-complexes from Levant and Europe (Ahmarian, Protoaurignacian, etc.). The techno-typological Middle Paleolithic character of the Warwasi lithic assemblage permits a discussion of a possible in situ dependence/continuum from the Mousterian or perhaps particular activities linked to the type of the occupation of the site. However, bladelet technology cannot be considered as rooted in the Zagros Mousterian. Consequently the origin of the Aurignacian sensu stricto has to be reconsidered.

  13. 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.

  14. Paleobathymetric reconstruction of the Miocene "Venetian foothills" (NE Italy): a multidisciplinary approach based on foraminiferal assemblages and rhodolith facies

    Science.gov (United States)

    Mancin, N.; Ventura, M.; Barbieri, C.

    2003-04-01

    A paleobathymetric reconstruction, based on the integrated study of both foraminiferal assemblages and red-algal concretions (rhodoliths), has been carried out for the Venetian Foothill succession cropping out along the southern border of the Alpine chain (Veneto-Friuli Foreland System, NE Italy). The studied succession, up to 500 m thick, has been deposited into a shallow to deep water marine environment during the Aquitanian to Langhian time-interval, due to the combined effect of the Dinaric and Alpine tectonics and the eustatic sea-level changes. The main goals of this work are: i) to reconstruct the paleobathymetry of the Venetian foothill succession and, tentatively, ii) to relate the bathymetric evolution of the studied areas to the sea-level changes and to the history of the vertical motion ("geohistory") of the underlying substratum in response to tectonics and sedimentary load. The detected time-interval (Aquitanian to Langhian) is particularly important as it embraces the transition between the Dinaric and South-Alpine orogenetic phases. The main results can be summarised as follows: a paleobathymetric evolution has been observed for the studied succession from the Aquitanian to the Langhian. In particular a 40--60 m paleodepth has been determined for the Calcareniti di Castelcucco Fm. Moreover a peculiar depositional environment, such as an outer-shelf incised by submarine canyons and characterised by a relatively high water hydrodynamism, has been proposed for this formation on the basis of the rhodolith size (5--6 cm). An upper to lower neritic depth (from 0--100 to 100--200 m) has been obtained for the Siltiti dei Casoni and Arenarie di Libano Formations and for the Marne di Monte Bolago Fm., respectively. An upper bathyal depth (200--600 m) has been determined for the lower-middle part of the Marne di Monfumo Fm. Finally a gradually decreasing in depth has been observed, in particular a lower to upper neritic paleodepth (from 200--100 to 100--0 m

  15. Environmental Quality Assessment of Bizerte Lagoon (Tunisia) Using Living Foraminifera Assemblages and a Multiproxy Approach: e0137250

    National Research Council Canada - National Science Library

    Maria Virgínia Alves Martins; Noureddine Zaaboub; Lotfi Aleya; Fabrizio Frontalini; Egberto Pereira; Paulo Miranda; Miguel Mane; Fernando Rocha; Lazaro Laut; Monia El Bour

    2015-01-01

      This study investigated the environmental quality of the Bizerte Lagoon (Tunisia) through an integrated approach that combined environmental, biogeochemical, and living benthic foraminiferal analyses...

  16. 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.

  17. 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.

  18. 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......, and gene regulation, at both transcriptional and translational levels. Udgivelsesdato: 1999-Jul...

  19. 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.

  20. 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.

  1. A Strategy for the Development of Macromolecular Nonlinear Optical Materials

    Science.gov (United States)

    1990-01-01

    obsolete. SECURITY CLASSIFICATION OF THIS PAGE STRATEGY FOR THE DEVELOPMENT OF MACROMOLECULAR NONLINEAR OPTICAL MATERIALS Braja K. Mandala , Jan-Chan...materials is significantly different from the conventional inorganic NLO materials. The extent of second order (quadratic) NLO effect such as second...is a criterion of paramount importance for a large second order electro-optic effect in organic materials 8 ,9 . The most common approach to obtain

  2. Affects and assemblages

    DEFF Research Database (Denmark)

    Samson, Kristine

    affects and assemblages produce subjective feelings and emotions (Pile 2009) Recently, urban experience designs and events aim at evoking affects through affects and assemblages. A Danish example is the Carlsberg city in Copenhagen another is The High line in Chelsea, New York (Samson 2011). Thus...

  3. 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.

  4. Analysis of Tagish Lake macromolecular organic material

    OpenAIRE

    Gilmour, I; Pearson, V. K.; Sephton, M.A.

    2001-01-01

    Macromolecular material is, by far, the major organic component of meteorites. Flash pyrolysis GCMS has been used to investigate this organic component in Tagish Lake. It is more condensed, less susbtituted than Murchson.

  5. Automated data collection for macromolecular crystallography.

    Science.gov (United States)

    Winter, Graeme; McAuley, Katherine E

    2011-09-01

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

  6. Macromolecular crowding: Macromolecules friend or foe.

    Science.gov (United States)

    Mittal, Shruti; Chowhan, Rimpy Kaur; Singh, Laishram Rajendrakumar

    2015-09-01

    Cellular interior is known to be densely crowded due to the presence of soluble and insoluble macromolecules, which altogether occupy ~40% of the total cellular volume. This results in altered biological properties of macromolecules. Macromolecular crowding is observed to have both positive and negative effects on protein folding, structure, stability and function. Significant data has been accumulated so far on both the aspects. However, most of the review articles so far have focused on the positive aspect of macromolecular crowding and not much attention has been paid on the deleterious aspect of crowding on macromolecules. In order to have a complete knowledge of the effect of macromolecular crowding on proteins and enzymes, it is important to look into both the aspects of crowding to determine its precise role under physiological conditions. To fill the gap in the understanding of the effect of macromolecular crowding on proteins and enzymes, this review article focuses on the deleterious influence of crowding on macromolecules. Macromolecular crowding is not always good but also has several deleterious effects on various macromolecular properties. Taken together, the properties of biological macromolecules in vivo appears to be finely regulated by the nature and level of the intracellular crowdedness in order to perform their biological functions appropriately. The information provided here gives an understanding of the role played by the nature and level of cellular crowdedness in intensifying and/or alleviating the burden of various proteopathies. Copyright © 2015 Elsevier B.V. All rights reserved.

  7. 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.

  8. 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.

  9. Fish assemblage in European Western Highlands and Western Plains: a type-specific approach to assess ecological quality of running waters

    NARCIS (Netherlands)

    Grenouillet, G.; Roset, N.; Goffaux, D.; Breine, J.; Leeuw, de J.J.

    2007-01-01

    After typological pre-classification of 398 calibration sites, fish-based metric models were used to predict the impact of human activities on river quality in European Western Highlands and Western Plains ecoregions. Calibration sites were grouped into six assemblage types and according to their ge

  10. Affects and assemblages

    DEFF Research Database (Denmark)

    Samson, Kristine

    the paper raises the questions where to locate aesthetics when planners and architects wishes to design for aesthetical experiences and sensations rather than formal objects. The paper will proceed through a brief outline of the recent notion of assemblage and affect in urban studies, planning theory...... as a ‘throwntogetherness’ (Massey 2005) or assemblage (Farias & Bender 2010) of perspectives bridging for instance the social and cultural experienced space investigated by the geographer and urban sociologist with the material and formal aesthetics of the architect and urban planner.......Affects and assemblages are Deleuzian Guattarian notions related to aesthetics and spatial territories. In recent urban geography and urban studies these notions are increasingly gaining more impact (Amin & Thrift 2002, Pile 2008, Farías & Bender 2010, Andersen & Harrison 2010, Thrift 2008). What...

  11. 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...

  12. The surveillant assemblage.

    Science.gov (United States)

    Haggerty, K D; Ericson, R V

    2000-12-01

    George Orwell's 'Big Brother' and Michel Foucault's 'panopticon' have dominated discussion of contemporary developments in surveillance. While such metaphors draw our attention to important attributes of surveillance, they also miss some recent dynamics in its operation. The work of Gilles Deleuze and Felix Guattari is used to analyse the convergence of once discrete surveillance systems. The resultant 'surveillant assemblage' operates by abstracting human bodies from their territorial settings, and separating them into a series of discrete flows. These flows are then reassembled in different locations as discrete and virtual 'data doubles'. The surveillant assemblage transforms the purposes of surveillance and the hierarchies of surveillance, as well as the institution of privacy.

  13. 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.

  14. Assemblages of Patient Safety

    DEFF Research Database (Denmark)

    Balatsas Lekkas, Angelos

    2016-01-01

    This thesis identifies how design processes emerge during the use of devices in healthcare, by attending to assemblages where contingencies of risk and harm co-exist with the contribution of healthcare professionals to the safe care of patients. With support from the field of Science and Technology...

  15. Phase Sensitive X-Ray Diffraction Imaging of Defects in Biological Macromolecular Crystals

    Science.gov (United States)

    Hu, Z. W.; Lai, B.; Chu, Y. S.; Cai, Z.; Mancini, D. C.; Thomas, B. R.; Chernov, A. A.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    Characterization of defects and/or disorder in biological macromolecular crystals presents much greater challenges than in conventional small-molecule crystals. The lack of sufficient contrast of defects is often a limiting factor in x-ray diffraction topography of protein crystals. This has seriously hampered efforts to understand mechanisms and origins of formation of imperfections, and the role of defects as essential entities in the bulk of macromolecular crystals. In this report, we employ a phase sensitive x-ray diffraction imaging approach for augmenting the contrast of defects in protein crystals.

  16. Poly(isophthalic acid)(ethylene oxide) as a Macromolecular Modulator for Metal-Organic Polyhedra.

    Science.gov (United States)

    Chen, Teng-Hao; Wang, Le; Trueblood, Jonathan V; Grassian, Vicki H; Cohen, Seth M

    2016-08-03

    A new strategy was developed by using a polymer ligand, poly(isophthalic acid)(ethylene oxide), to modulate the growth of metal-organic polyhedra (MOP) crystals. This macromolecular modulator can effectively control the crystal habit of several different Cu24L24 (L = isophthalic acid derivatives) MOPs. The polymer also directed the formation of MOP structures under reaction conditions that only produce metal-organic frameworks in the absence of modulator. Moreover, the polymer also enabled the deposition of MOP crystals on glass surfaces. This macromolecular modulator strategy provides an innovative approach to control the morphology and assembly of MOP particles.

  17. 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.

  18. Identifying and visualizing macromolecular flexibility in structural biology

    Directory of Open Access Journals (Sweden)

    Martina Palamini

    2016-09-01

    Full Text Available 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.

  19. Critical review and perspective of macromolecularly imprinted polymers.

    Science.gov (United States)

    Kryscio, David R; Peppas, Nicholas A

    2012-02-01

    Molecular recognition is a fundamental and ubiquitous process that is the driving force behind life. Natural recognition elements - including antibodies, enzymes, nucleic acids, and cells - exploit non-covalent interactions to bind to their targets with exceptionally strong affinities. Due to this unparalleled proficiency, scientists have long sought to mimic natural recognition pathways. One promising approach is molecularly imprinted polymers (MIPs), which are fully synthetic systems formed via the crosslinking of organic polymers in the presence of a template molecule, which results in stereo-specific binding sites for this analyte of interest. Macromolecularly imprinted polymers, those synthesized in the presence of macromolecule templates (>1500 Da), are of particular importance because they open up the field for a whole new set of robust diagnostic tools. Although the specific recognition of small-molecular-weight analytes is now considered routine, extension of these efficacious procedures to the protein regime has, thus far, proved challenging. This paper reviews the main approaches employed, highlights studies of interest with an emphasis on recent work, and offers suggestions for future success in the field of macromolecularly imprinted polymers.

  20. A kinetic type extended model for dense gases and macromolecular fluids

    Directory of Open Access Journals (Sweden)

    M. Cristina Carrisi

    2005-05-01

    Full Text Available Extended thermodynamics is an important theory which is appreciated from mathematicians and physicists. Following its ideas and considering the macroscopic approach with suggestions from the kinetic one, we find in this paper, the solution of an interesting model: the model for dense gases and macromolecular fluids.

  1. FCJ-177 Television Assemblages

    Directory of Open Access Journals (Sweden)

    Teresa Rizzo

    2015-06-01

    Full Text Available Television has become a multiplatform medium that houses content on a number of different sites and devices that encourage new forms of engagement. This new digital environment has transformed television from a closed system, where programmes are transmitted to a television set for viewers to tune into, to an open system that produces new television connections and configurations. Drawing on the work of Deleuze and Guattari, Latour and current media theorists, this essay turns to the concept of assemblages for theorising this new interactive multiplatform television environment. Thinking about multiplatform television through the concept of assemblages offers a means of exploring how television devices, texts and media are reconfigured or modified so as to display new functionalities and capacities. It also enables us to consider the way television culture can be deterritorialised and reterritorialised through new connections and in doing so introduce new qualities such as interactivity and reciprocal determination.

  2. Body size and geographic range do not explain long term variation in fish populations: a Bayesian phylogenetic approach to testing assembly processes in stream fish assemblages.

    Directory of Open Access Journals (Sweden)

    Stephen J Jacquemin

    Full Text Available We combine evolutionary biology and community ecology to test whether two species traits, body size and geographic range, explain long term variation in local scale freshwater stream fish assemblages. Body size and geographic range are expected to influence several aspects of fish ecology, via relationships with niche breadth, dispersal, and abundance. These traits are expected to scale inversely with niche breadth or current abundance, and to scale directly with dispersal potential. However, their utility to explain long term temporal patterns in local scale abundance is not known. Comparative methods employing an existing molecular phylogeny were used to incorporate evolutionary relatedness in a test for covariation of body size and geographic range with long term (1983 - 2010 local scale population variation of fishes in West Fork White River (Indiana, USA. The Bayesian model incorporating phylogenetic uncertainty and correlated predictors indicated that neither body size nor geographic range explained significant variation in population fluctuations over a 28 year period. Phylogenetic signal data indicated that body size and geographic range were less similar among taxa than expected if trait evolution followed a purely random walk. We interpret this as evidence that local scale population variation may be influenced less by species-level traits such as body size or geographic range, and instead may be influenced more strongly by a taxon's local scale habitat and biotic assemblages.

  3. In situ macromolecular crystallography using microbeams.

    Science.gov (United States)

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

    2012-05-01

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

  4. 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.

  5. Growth and Dissolution of Macromolecular Markov Chains

    Science.gov (United States)

    Gaspard, Pierre

    2016-07-01

    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.

  6. Macromolecular Hydrogen Sulfide Donors Trigger Spatiotemporally Confined Changes in Cell Signaling.

    Science.gov (United States)

    Ercole, Francesca; Mansfeld, Friederike M; Kavallaris, Maria; Whittaker, Michael R; Quinn, John F; Halls, Michelle L; Davis, Thomas P

    2016-01-11

    Hydrogen sulfide (H2S) is involved in a myriad of cell signaling processes that trigger physiological events ranging from vasodilation to cell proliferation. Moreover, disturbances to H2S signaling have been associated with numerous pathologies. As such, the ability to release H2S in a cellular environment and stimulate signaling events is of considerable interest. Herein we report the synthesis of macromolecular H2S donors capable of stimulating cell signaling pathways in both the cytosol and at the cell membrane. Specifically, copolymers having pendent oligo(ethylene glycol) and benzonitrile groups were synthesized, and the benzonitrile groups were subsequently transformed into primary aryl thioamide groups via thionation using sodium hydrosulfide. These thioamide moieties could be incorporated into a hydrophilic copolymer or a block copolymer (i.e., into either the hydrophilic or hydrophobic domain). An electrochemical sensor was used to demonstrate release of H2S under simulated physiological conditions. Subsequent treatment of HEK293 cells with a macromolecular H2S donor elicited a slow and sustained increase in cytosolic ERK signaling, as monitored using a FRET-based biosensor. The macromolecular donor was also shown to induce a small, fast and sustained increase in plasma membrane-localized PKC activity immediately following addition to cells. Studies using an H2S-selective fluorescent probe in live cells confirmed release of H2S from the macromolecular donor over physiologically relevant time scales consistent with the signaling observations. Taken together, these results demonstrate that by using macromolecular H2S donors it is possible to trigger spatiotemporally confined cell signaling events. Moreover, the localized nature of the observed signaling suggests that macromolecular donor design may provide an approach for selectively stimulating certain cellular biochemical pathways.

  7. 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.

  8. Revealing the macromolecular targets of complex natural products

    Science.gov (United States)

    Reker, Daniel; Perna, Anna M.; Rodrigues, Tiago; Schneider, Petra; Reutlinger, Michael; Mönch, Bettina; Koeberle, Andreas; Lamers, Christina; Gabler, Matthias; Steinmetz, Heinrich; Müller, Rolf; Schubert-Zsilavecz, Manfred; Werz, Oliver; Schneider, Gisbert

    2014-12-01

    Natural products have long been a source of useful biological activity for the development of new drugs. Their macromolecular targets are, however, largely unknown, which hampers rational drug design and optimization. Here we present the development and experimental validation of a computational method for the discovery of such targets. The technique does not require three-dimensional target models and may be applied to structurally complex natural products. The algorithm dissects the natural products into fragments and infers potential pharmacological targets by comparing the fragments to synthetic reference drugs with known targets. We demonstrate that this approach results in confident predictions. In a prospective validation, we show that fragments of the potent antitumour agent archazolid A, a macrolide from the myxobacterium Archangium gephyra, contain relevant information regarding its polypharmacology. Biochemical and biophysical evaluation confirmed the predictions. The results obtained corroborate the practical applicability of the computational approach to natural product ‘de-orphaning’.

  9. 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.

  10. Structuring factors of the spatio-temporal variability of macrozoobenthos assemblages in a southern Mediterranean lagoon: How useful for bioindication is a multi-biotic indices approach?

    Science.gov (United States)

    Khedhri, Ines; Afli, Ahmed; Aleya, Lotfi

    2017-01-15

    The authors investigated the impact of the extension of the El Kantra Channel on the composition and structure of macrobenthic assemblages in Boughrara Lagoon (Gulf of Gabes, Tunisia along with the use of 4 biotic indices (AMBI, BENTIX, M-AMBI and TUBI). Thirteen stations were sampled seasonally in 2012-2013. Forty-one species were found in 2012-2013 not recorded in 2009-2010, including 20 species of polychaetes belonging to the trophic groups of deposit-feeders and carnivores which are expected to increase in areas disturbed by organic pollution. During the survey, we recorded a high fish mortality, essentially caused by the development of harmful algal blooms (HAB) which increased organic matter deposition, thus inducing polychaete development. This seems to weaken the bio-indicating power of biotic indices used here which, paradoxically, classified all sampled stations at a high ecological status. A review of these indices and their applicability to all marine environments is recommended.

  11. Demersal Assemblages on the Soft Bottoms off the Catalan-Levante Coast of the Spanish Mediterranean

    Directory of Open Access Journals (Sweden)

    Mariano García-Rodríguez

    2011-01-01

    Full Text Available The analysis of 255 bottom trawl samples obtained in annual experimental surveys (2007–2010 along the western Mediterranean shows the existence of five well-defined demersal assemblages that follow a depth distribution: (a upper shelf assemblages, including two assemblages differentiated by the type of substrate (sand-muddy and terrigenous muddy bottoms; (b a middle shelf assemblage; (c an upper slope assemblage; (d a middle slope assemblage. Faunally, they are dominated by fish (37% of 452 total species, followed by crustaceans (22%, molluscs (17%, echinoderms (9%, and other invertebrates (15%. The assemblages identified showed major alterations on the shelf and shelf edge and less pronounced ones on the upper and middle slope. The average diversity values were more or less high, evidencing the high species richness in the western Mediterranean. The identified assemblages may facilitate future multispecies fisheries management based on an ecosystem approach.

  12. 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

  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. 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.

  15. NATO Advanced Study Institute on Evolving Methods for Macromolecular Gystallography

    CERN Document Server

    Read, Randy J

    2007-01-01

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

  16. 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.

  17. 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

  18. 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.

  19. Multiscale macromolecular simulation: role of evolving ensembles.

    Science.gov (United States)

    Singharoy, A; Joshi, H; Ortoleva, P J

    2012-10-22

    Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers.

  20. Macromolecular recognition in the Protein Data Bank

    Energy Technology Data Exchange (ETDEWEB)

    Janin, Joël, E-mail: joel.janin@ibbmc.u-psud.fr [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Rodier, Francis [Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France); Chakrabarti, Pinak [Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Bahadur, Ranjit P. [Institut de Biochimie et Biologie Moléculaire et Cellulaire, UMR8619, Bâtiment 430, Université Paris-Sud, 91405 Orsay (France); Department of Biochemistry, Bose Institute, P-1/12 CIT Scheme VIIM, Calcutta 700 054 (India); Laboratoire d’Enzymologie et de Biochimie Structurales, UPR9063, CNRS, 91198 Gif-sur-Yvette (France)

    2007-01-01

    X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts. Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein–protein and protein–DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200–2000 Å{sup 2} of protein surface occur in protease–inhibitor and antigen–antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.

  1. The role of macromolecular stability in desiccation tolerance

    NARCIS (Netherlands)

    Wolkers, W.F.

    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 st

  2. 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

  3. 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.

  4. Long-Wavelength X-Ray Diffraction and Its Applications in Macromolecular Crystallography.

    Science.gov (United States)

    Weiss, Manfred S

    2017-01-01

    For many years, diffraction experiments in macromolecular crystallography at X-ray wavelengths longer than that of Cu-K α (1.54 Å) have been largely underappreciated. Effects caused by increased X-ray absorption result in the fact that these experiments are more difficult than the standard diffraction experiments at short wavelengths. However, due to the also increased anomalous scattering of many biologically relevant atoms, important additional structural information can be obtained. This information, in turn, can be used for phase determination, for substructure identification, in molecular replacement approaches, as well as in structure refinement. This chapter reviews the possibilities and the difficulties associated with such experiments, and it provides a short description of two macromolecular crystallography synchrotron beam lines dedicated to long-wavelength X-ray diffraction experiments.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-01

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

  6. Effects of salinity on fish assemblage structure: An evaluation based on taxonomic and functional approaches in the Casamance estuary (Senegal, West Africa)

    Science.gov (United States)

    Kantoussan, Justin; Ecoutin, Jean Marc; Simier, Monique; Tito de Morais, Luis; Laë, Raymond

    2012-11-01

    The utility of taxonomic and functional approaches in assessing the structure of fish communities is tested in the hypersaline estuary of the Casamance river using data from surveys of commercial fisheries conducted between April and July of 2005. Both taxonomic and functional diversity decrease from downstream to upstream regions of the estuary. In terms of species composition, marine-estuarine species (33.3-46.3%, depending on the site) and estuarine species of marine origin (29.3-41.7%) dominate the exploited population in the Casamance estuary. In contrast, the proportion of strictly estuarine species observed upstream is twice that observed downstream. Quantitative analysis based on biomass landed distinguishes two groups in the population: (1) a group of species that is dominant downstream, containing primarily terminal predators and secondary consumers categorised as marine species that are occasional or accessory in estuaries, estuarine marine species, and estuarine species of marine origin; and (2) a group of species characteristic of the upstream region, dominated by a few species (Sarotherodon melanotheron, Tilapia guineensis, and Mugil cephalus) mainly of strictly estuarine and/or herbivorous categories and Elops lacerta, a carnivore fish. The outcomes of the two approaches are similar, and both indicate that the fish community in this estuary is under the influence of strong environmental disturbance. However, the scales at which the specific and functional approaches most reliably reflect environmental conditions are different. The taxonomic approach, i.e., the use of specific biomass is more appropriate at the ecosystem scale and therefore more accessible to local human communities, whereas the functional approach is better suited to regional and sub-regional studies because of the change in species composition from one environment to another.

  7. Macromolecular crowding for tailoring tissue-derived fibrillated matrices.

    Science.gov (United States)

    Magno, Valentina; Friedrichs, Jens; Weber, Heather M; Prewitz, Marina C; Tsurkan, Mikhail V; Werner, Carsten

    2017-06-01

    Tissue-derived fibrillated matrices can be instrumental for the in vitro reconstitution of multiphasic extracellular microenvironments. However, despite of several advantages, the obtained scaffolds so far offer a rather narrow range of materials characteristics only. In this work, we demonstrate how macromolecular crowding (MMC) - the supplementation of matrix reconstitution media with synthetic or natural macromolecules in ways to create excluded volume effects (EVE) - can be employed for tailoring important structural and biophysical characteristics of kidney-derived fibrillated matrices. Porcine kidneys were decellularized, ground and the obtained extracellular matrix (ECM) preparations were reconstituted under varied MMC conditions. We show that MMC strongly influences the fibrillogenesis kinetics and impacts the architecture and the elastic modulus of the reconstituted matrices, with diameters and relative alignment of fibrils increasing at elevated concentrations of the crowding agent Ficoll400, a nonionic synthetic polymer of sucrose. Furthermore, we demonstrate how MMC modulates the distribution of key ECM molecules within the reconstituted matrix scaffolds. As a proof of concept, we compared different variants of kidney-derived fibrillated matrices in cell culture experiments referring to specific requirements of kidney tissue engineering approaches. The results revealed that MMC-tailored matrices support the morphogenesis of human umbilical vein endothelial cells (HUVECs) into capillary networks and of murine kidney stem cells (KSCs) into highly branched aggregates. The established methodology is concluded to provide generally applicable new options for tailoring tissue-specific multiphasic matrices in vitro. Tissue-derived fibrillated matrices can be instrumental for the in vitro reconstitution of multiphasic extracellular microenvironments. However, despite of several advantages, the obtained scaffolds so far offer a rather narrow range of materials

  8. Macromolecular components of tomato fruit pectin.

    Science.gov (United States)

    Fishman, M L; Gross, K C; Gillespie, D T; Sondey, S M

    1989-10-01

    Chelate and alkaline-soluble pectin extracted from cell walls of pericarp tissue from mature green, turning, and red ripe (Lycopersicon esculentum Mill.) fruit (cv. Rutgers), were studied by high-performance size-exclusion chromatography. Computer-aided curve fitting of the chromatograms to a series of Gaussian-shaped components revealed that pectin from all fractions was composed of a linear combination of five macromolecular-sized species. The relative sizes of these macromolecules as obtained from their radii of gyration were 1:2:4:8:16. Dialysis against 0.05 M NaCl induced partial dissociation of the biopolymers. Apparently, the weight fraction of smaller sized species increased at the expense of larger ones. Also, the dissociation produced low-molecular-weight fragments. Behavior in the presence of 0.05 M NaCl led to the conclusion that cell wall pectin acted as if it were an aggregated mosaic, held together at least partially through noncovalent interactions.

  9. 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.

  10. 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.

  11. 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.

  12. Perturbation-based Markovian transmission model for probing allosteric dynamics of large macromolecular assembling: a study of GroEL-GroES.

    Directory of Open Access Journals (Sweden)

    Hsiao-Mei Lu

    2009-10-01

    Full Text Available Large macromolecular assemblies are often important for biological processes in cells. Allosteric communications between different parts of these molecular machines play critical roles in cellular signaling. Although studies of the topology and fluctuation dynamics of coarse-grained residue networks can yield important insights, they do not provide characterization of the time-dependent dynamic behavior of these macromolecular assemblies. Here we develop a novel approach called Perturbation-based Markovian Transmission (PMT model to study globally the dynamic responses of the macromolecular assemblies. By monitoring simultaneous responses of all residues (>8,000 across many (>6 decades of time spanning from the initial perturbation until reaching equilibrium using a Krylov subspace projection method, we show that this approach can yield rich information. With criteria based on quantitative measurements of relaxation half-time, flow amplitude change, and oscillation dynamics, this approach can identify pivot residues that are important for macromolecular movement, messenger residues that are key to signal mediating, and anchor residues important for binding interactions. Based on a detailed analysis of the GroEL-GroES chaperone system, we found that our predictions have an accuracy of 71-84% judged by independent experimental studies reported in the literature. This approach is general and can be applied to other large macromolecular machineries such as the virus capsid and ribosomal complex.

  13. Comics as Assemblage

    DEFF Research Database (Denmark)

    Cortsen, Rikke Platz

    This thesis examines the apparent simplicity of comics by exposing some of the layers in which meaning is created in a complex network; it approaches the complexity of comics from the angle of spatio-temporality and separates comics into several spatio-temporal levels that each interacts in the way...... representation, imagination and experience is renegotiated in comics. Another concern to the thesis is focus on how comics are structured in a network made up by individual elements and how these connect. The thesis uses various theoretical approaches in examining a wide range of comics across genres and formats...... to illuminate how time and space is constructed in comics. I argue that “time and space in comics” is too broad a notion and that we need to conceptualize a multiple spatio-temporal construction that takes into account the way spatio-temporality of diegesis is represented through the spatio...

  14. Macromolecular networks and intelligence in microorganisms

    Directory of Open Access Journals (Sweden)

    Hans V Westerhoff

    2014-07-01

    Full Text Available 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.

  15. 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

  16. Macromolecular Antioxidants and Dietary Fiber in Edible Seaweeds.

    Science.gov (United States)

    Sanz-Pintos, Nerea; Pérez-Jiménez, Jara; Buschmann, Alejandro H; Vergara-Salinas, José Rodrigo; Pérez-Correa, José Ricardo; Saura-Calixto, Fulgencio

    2017-02-01

    Seaweeds are rich in different bioactive compounds with potential uses in drugs, cosmetics and the food industry. The objective of this study was to analyze macromolecular antioxidants or nonextractable polyphenols, in several edible seaweed species collected in Chile (Gracilaria chilensis, Callophyllis concepcionensis, Macrocystis pyrifera, Scytosyphon lomentaria, Ulva sp. and Enteromorpha compressa), including their 1st HPLC characterization. Macromolecular antioxidants are commonly ignored in studies of bioactive compounds. They are associated with insoluble dietary fiber and exhibit significant biological activity, with specific features that are different from those of both dietary fiber and extractable polyphenols. We also evaluated extractable polyphenols and dietary fiber, given their relationship with macromolecular antioxidants. Our results show that macromolecular antioxidants are a major polyphenol fraction (averaging 42% to total polyphenol content), with hydroxycinnamic acids, hydroxybenzoic acids and flavonols being the main constituents. This fraction also showed remarkable antioxidant capacity, as determined by 2 complementary assays. The dietary fiber content was over 50% of dry weight, with some samples exhibiting the target proportionality between soluble and insoluble dietary fiber for adequate nutrition. Overall, our data show that seaweed could be an important source of commonly ignored macromolecular antioxidants. © 2017 Institute of Food Technologists®.

  17. Assessing the Mess: Challenges to Assemblage Theory and Teacher Education

    Science.gov (United States)

    Beighton, Chris

    2013-01-01

    This article examines the Deleuzian concept of "assemblage" in educational research in the context of Teacher Education (TE) for the "continuing education" or "Lifelong Learning" sector. Drawing on Deleuze's creative approach to analysis, it draws a portrait of practice which identifies problems and successes in…

  18. 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

  19. Influential environmental gradients and spatiotemporal patterns of fish assemblages in the unimpounded Upper Mississippi River

    Science.gov (United States)

    Barko, V.A.; Palmer, M.W.; Herzog, D.P.; Ickes, B.S.

    2004-01-01

    We investigated variation of fish assemblages in response to environmental factors using Long Term Resource Monitoring Program data. Data were collected from 1993 to 2000 from five physical habitats in the unimpounded upper Mississippi River. We captured 89 species composing 18 families. Of these, 26% were fluvial specialists, 25% were fluvial dependent and 49% were generalists. The numerically dominant component of the adult fish assemblage (species accounting for >10% of total catch) accounted for 50% of the assemblage and was comprised of only three species: gizzard shad (Dorosoma cepedianum; 25%), common carp (Cyprinus carpio, 15%) and channel catfish (Ictalurus punctatus, 10%). The dominant component of the YOY fish assemblage was comprised of only two species, which accounted for 76% of the total catch: freshwater drum (Aplodinotus grunniens; 39%) and gizzard shad (37%). We used a cross-validation multivariate approach to explore how adult and young-of-the-year (YOY) assemblages varied with respect. to physical habitat and environmental gradients. Furthermore, we were interested how the fish assemblages changed over time. Partial canonical correspondence analyses (pCCA) demonstrated significant effects of physical habitats. Such effects differed between young-of-the-year and adult fishes. The four main environmental gradients influencing overall assemblage structure for both age groups were river elevation, water velocity, conductivity, and depth of gear deployment. Morisita's index revealed similar adult assemblage structure over time. However, the YOY assemblage present in 1995 was dissimilar from assemblages present during the other years. We speculate this is a lag effect from the backwater spawning episodes (floodpulse) that occurred with the 500-y flood in 1993. Shannon-Weiner diversity and Camargo's evenness indices were low, but stable across years for the adult assemblage, but varied across years for the YOY assemblage.

  20. Public Sphere as Digital Assemblage

    DEFF Research Database (Denmark)

    Salovaara-Moring, Inka

    the 1990s onwards digitalization brought concepts of network and complexity into the theoretical discourse. This relational turn changed the social ontology of the public sphere into a dynamic and complex system, erasing the division between the fields of reality (the world), representation (discourse...... theories. Drawing from Deleuze & Guattari (1987), Bennett (2010), and Latour (2004) in order to imagine post-human assemblages of public sphere, this paper argues for a relational ontology that emphasizes the complex interactions of political assemblages. Empirically, it draws from the author’s studies......Normative theories of public sphere have struggled with the topic of materiality. The historical narrative of the ‘public sphere’ situated the phenomenon in specific spaces, where practices (public deliberation) and language (discourse) constructed political agencies, and further publics. From...

  1. 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.

  2. Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique

    Science.gov (United States)

    Peters, J. H.; Klein, R.; Delle Site, L.

    2016-08-01

    We extend the application of the adaptive resolution technique (AdResS) to liquid systems composed of alkane chains of different lengths. The aim of the study is to develop and test the modifications of AdResS required in order to handle the change of representation of large molecules. The robustness of the approach is shown by calculating several relevant structural properties and comparing them with the results of full atomistic simulations. The extended scheme represents a robust prototype for the simulation of macromolecular systems of interest in several fields, from material science to biophysics.

  3. Multi-regional synthesis of temporal trends in biotic assemblages in streams and rivers of the continental United States

    Science.gov (United States)

    Miller, Matthew P.; Brasher, Anne M.D.; Keenen, Jonathan G.

    2013-01-01

    Biotic assemblages in aquatic ecosystems are excellent integrators and indicators of changing environmental conditions within a watershed. Therefore, temporal changes in abiotic environmental variables often can be inferred from temporal changes in biotic assemblages. Algae, macroinvertebrate, and fish assemblage data were collected from 91 sampling sites in 4 geographic regions (northeastern/north-central, southeastern, south-central, and western), collectively encompassing the continental United States, from 1993 to 2009 as part of the U.S. Geological Survey National Water-Quality Assessment Program. This report uses a multivariate approach to synthesize temporal trends in biotic assemblages and correlations with relevant abiotic parameters as a function of biotic assemblage, geographic region, and land use. Of the three groups of biota, algal assemblages had temporal trends at the greatest percentage of sites. Of the regions, a greater percentage of sites in the northeastern/north-central and western regions had temporal trends in biotic assemblages. In terms of land use, a greater percentage of watersheds draining agricultural, urban, and undeveloped areas had significant temporal changes in biota, as compared to watersheds with mixed use. Correlations between biotic assemblages and abiotic variables indicate that, in general, macroinvertebrate assemblages correlated with water quality and fish assemblages correlated with physical habitat. Taken together, results indicate that there are regional differences in how individual biotic assemblages (algae, macroinvertebrates, and fish) respond to different abiotic drivers of change.

  4. On the vibron dressing in the one-dimensional macromolecular chains caused by the interaction with acoustic phonon modes

    CERN Document Server

    Cevizovic, Dalibor; Galovic, Slobodanka; Ivic, Zoran

    2012-01-01

    We present a study of the physical properties of the vibrational excitation in the one-dimensional macromolecular chains, caused by the interaction with acoustical phonon modes. The influence of the temperature and the basic system parameters on the vibron dressing has been analyzed by employing the simple mean--field approach based on the variational extension of the Lang--Firsov unitary transformation. Applied approach predicts a region in system parameter space where it is possible of the coexistence of the partially dressed (light and mobile) and fully dressed (immobile) vibron states. We found that the boundary of this region depends on system temperature and type of bond among structure elements in macromolecular chain.

  5. Viral assemblage composition in Yellowstone acidic hot springs assessed by network analysis.

    Science.gov (United States)

    Bolduc, Benjamin; Wirth, Jennifer F; Mazurie, Aurélien; Young, Mark J

    2015-10-01

    Understanding of viral assemblage structure in natural environments remains a daunting task. Total viral assemblage sequencing (for example, viral metagenomics) provides a tractable approach. However, even with the availability of next-generation sequencing technology it is usually only possible to obtain a fragmented view of viral assemblages in natural ecosystems. In this study, we applied a network-based approach in combination with viral metagenomics to investigate viral assemblage structure in the high temperature, acidic hot springs of Yellowstone National Park, USA. Our results show that this approach can identify distinct viral groups and provide insights into the viral assemblage structure. We identified 110 viral groups in the hot springs environment, with each viral group likely representing a viral family at the sub-family taxonomic level. Most of these viral groups are previously unknown DNA viruses likely infecting archaeal hosts. Overall, this study demonstrates the utility of combining viral assemblage sequencing approaches with network analysis to gain insights into viral assemblage structure in natural ecosystems.

  6. 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.

  7. 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...

  8. Lions as Bone Accumulators? Paleontological and Ecological Implications of a Modern Bone Assemblage from Olduvai Gorge

    Science.gov (United States)

    Arriaza, Mari Carmen; Domínguez-Rodrigo, Manuel; Yravedra, José; Baquedano, Enrique

    2016-01-01

    Analytic models have been developed to reconstruct early hominin behaviour, especially their subsistence patterns, revealed mainly through taphonomic analyses of archaeofaunal assemblages. Taphonomic research is used to discern which agents (carnivores, humans or both) generate the bone assemblages recovered at archaeological sites. Taphonomic frameworks developed during the last decades show that the only large-sized carnivores in African biomes able to create bone assemblages are leopards and hyenas. A carnivore-made bone assemblage located in the short-grassland ecological unit of the Serengeti (within Olduvai Gorge) was studied. Taphonomic analyses of this assemblage including skeletal part representation, bone density, breakage patterns and anatomical distribution of tooth marks, along with an ecological approach to the prey selection made by large carnivores of the Serengeti, were carried out. The results show that this bone assemblage may be the first lion-accumulated assemblage documented, although other carnivores (namely spotted hyenas) may have also intervened through postdepositional ravaging. This first faunal assemblage potentially created by lions constitutes a new framework for neotaphonomic studies. Since lions may accumulate carcasses under exceptional circumstances, such as those documented at the site reported here, this finding may have important consequences for interpretations of early archaeological and paleontological sites, which provide key information about human evolution. PMID:27144649

  9. 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

  10. 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

  11. SESAM – a new framework integrating macroecological and species distribution models for predicting spatio-temporal patterns of species assemblages

    DEFF Research Database (Denmark)

    Guisan, Antoine; Rahbek, Carsten

    2011-01-01

    , and ecological assembly rules to constrain predictions of the richness and composition of species assemblages obtained by stacking predictions of individual species distributions. We believe that such a framework could prove useful in many theoretical and applied disciplines of ecology and evolution, both......Two different approaches currently prevail for predicting spatial patterns of species assemblages. The first approach (macroecological modelling, MEM) focuses directly on realized properties of species assemblages, whereas the second approach (stacked species distribution modelling, S-SDM) starts...... with constituent species to approximate the properties of assemblages. Here, we propose to unify the two approaches in a single ‘spatially explicit species assemblage modelling’ (SESAM) framework. This framework uses relevant designations of initial species source pools for modelling, macroecological variables...

  12. 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.

  13. Controlled architecture for improved macromolecular memory within polymer networks.

    Science.gov (United States)

    DiPasquale, Stephen A; Byrne, Mark E

    2016-08-01

    This brief review analyzes recent developments in the field of living/controlled polymerization and the potential of this technique for creating imprinted polymers with highly structured architecture with macromolecular memory. As a result, it is possible to engineer polymers at the molecular level with increased homogeneity relating to enhanced template binding and transport. Only recently has living/controlled polymerization been exploited to decrease heterogeneity and substantially improve the efficiency of the imprinting process for both highly and weakly crosslinked imprinted polymers. Living polymerization can be utilized to create imprinted networks that are vastly more efficient than similar polymers produced using conventional free radical polymerization, and these improvements increase the role that macromolecular memory can play in the design and engineering of new drug delivery and sensing platforms.

  14. Temperature-dependent macromolecular X-ray crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Weik, Martin, E-mail: martin.weik@ibs.fr; Colletier, Jacques-Philippe [CEA, IBS, Laboratoire de Biophysique Moléculaire, F-38054 Grenoble (France); CNRS, UMR5075, F-38027 Grenoble (France); Université Joseph Fourier, F-38000 Grenoble (France)

    2010-04-01

    The dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100 K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15 K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography.

  15. Refinement of macromolecular structures against neutron data with SHELXL2013.

    Science.gov (United States)

    Gruene, Tim; Hahn, Hinrich W; Luebben, Anna V; Meilleur, Flora; Sheldrick, George M

    2014-02-01

    Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392-400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures.

  16. A macromolecular model for the endothelial surface layer

    Science.gov (United States)

    Harden, James; Danova-Okpetu, Darina; Grest, Gary

    2006-03-01

    The endothelial surface layer (ESL) is a micron-scale macromolecular lining of the luminal side of blood vessels composed of proteoglycans, glycoproteins, polysaccharides and associated plasma proteins all in dynamic equilibrium. It has numerous physiological roles including the regulation of blood flow and microvascular permeability, and active participation in mechanotransduction and stress regulation, coagulation, cell adhesion, and inflammatory response. The dynamic structure and the mechanical properties of the ESL are crucial for many of its physiological properties. We present a topological model for the ESL composed of three basic macromolecular elements: branched proteoglycans, linear polysaccharide chains, and small plasma proteins. The model was studied using non-equilibrium molecular dynamics simulations and compared with scaling theories for associating tethered polymers. We discuss the observed dynamical and mechanical properties of the ESL captured by this model, and the possible physical insight it provides into the physiological behavior of the ESL.

  17. 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.

  18. Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION.

    Science.gov (United States)

    Bharat, Tanmay A M; Scheres, Sjors H W

    2016-11-01

    Electron cryo-tomography (cryo-ET) is a technique that is used to produce 3D pictures (tomograms) of complex objects such as asymmetric viruses, cellular organelles or whole cells from a series of tilted electron cryo-microscopy (cryo-EM) images. Averaging of macromolecular complexes found within tomograms is known as subtomogram averaging, and this technique allows structure determination of macromolecular complexes in situ. Subtomogram averaging is also gaining in popularity for the calculation of initial models for single-particle analysis. We describe herein a protocol for subtomogram averaging from cryo-ET data using the RELION software (http://www2.mrc-lmb.cam.ac.uk/relion). RELION was originally developed for cryo-EM single-particle analysis, and the subtomogram averaging approach presented in this protocol has been implemented in the existing workflow for single-particle analysis so that users may conveniently tap into existing capabilities of the RELION software. We describe how to calculate 3D models for the contrast transfer function (CTF) that describe the transfer of information in the imaging process, and we illustrate the results of classification and subtomogram averaging refinement for cryo-ET data of purified hepatitis B capsid particles and Saccharomyces cerevisiae 80S ribosomes. Using the steps described in this protocol, along with the troubleshooting and optimization guidelines, high-resolution maps can be obtained in which secondary structure elements are resolved subtomogram.

  19. Facilitating structure determination: workshop on robotics andautomation in macromolecular crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Ralston, Corie; Cork, C.W.; McDermott, G.; Earnest, T.N.

    2006-03-28

    As part of the annual Advanced Light Source (ALS) andStanford Synchrotron Radiation Laboratory (SSRL) Users' Meeting inOctober of this year, the macromolecular crystallography staff at bothsynchrotrons held a joint hands-on workshop to address automation issuesin crystal mounting and data collection at the beamline. This paperdescribes the ALS portion of the workshop, while the accompanying paperreviews the SSRL workshop.

  20. 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...

  1. What Macromolecular Crowding Can Do to a Protein

    Science.gov (United States)

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

    2014-01-01

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

  2. REFMAC5 for the refinement of macromolecular crystal structures

    Energy Technology Data Exchange (ETDEWEB)

    Murshudov, Garib N., E-mail: garib@ysbl.york.ac.uk [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Skubák, Pavol [Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden (Netherlands); Lebedev, Andrey A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Pannu, Navraj S. [Biophysical Structural Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden (Netherlands); Steiner, Roberto A. [Randall Division of Cell and Molecular Biophysics, New Hunt’s House, King’s College London, London (United Kingdom); Nicholls, Robert A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom); Winn, Martyn D. [STFC Daresbury Laboratory, Warrington WA4 4AD (United Kingdom); Long, Fei; Vagin, Alexei A. [Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW (United Kingdom)

    2011-04-01

    The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described. This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.

  3. Macromolecular amplification of binding response in superaptamer hydrogels.

    Science.gov (United States)

    Bai, Wei; Gariano, Nicholas A; Spivak, David A

    2013-05-08

    It is becoming more important to detect ultralow concentrations of analytes for biomedical, environmental, and national security applications. Equally important is that new methods should be easy to use, inexpensive, portable, and if possible allow detection by the naked eye. By and large, detection of low concentrations of analytes cannot be achieved directly but requires signal amplification by catalysts, macromolecules, metal surfaces, or supramolecular aggregates. The rapidly progressing field of macromolecular signal amplification has been advanced using conjugated polymers, chirality in polymers, solvating polymers, and polymerization/depolymerization strategies. A new type of aptamer-based hydrogel with specific response to target proteins presented in this report demonstrates an additional category of macromolecular signal amplification. This superaptamer assembly provides the first example of using protein-specific aptamers to create volume-changing hydrogels with amplified response to the target protein. A remarkable aspect of these superaptamer hydrogels is that volume shrinking is visible to the naked eye down to femtomolar concentrations of protein. This extraordinary macromolecular amplification is attributed to a complex interplay between protein-aptamer supramolecular cross-links and the consequential reduction of excluded volume in the hydrogel. Specific recognition is even maintained in biological matrices such as urine and tears. Furthermore, the gels can be dried for long-term storage and regenerated for use without loss of activity. In practice, the ease of this biomarker detection method offers an alternative to traditional analytical techniques that require sophisticated instrumentation and highly trained personnel.

  4. 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.

  5. Fish assemblages in southern California kelp forests.

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This is a point file of fish assemblages calculated from diver surveys in kelp forests in Southern California. Visual census data was combined for two separate...

  6. Predictions of mineral assemblages in planetary interiors

    Science.gov (United States)

    Stolper, E.

    1980-01-01

    It is shown that mineral compatibilities in the model system CaO-MgO-Al2O3-SiO2 can be applied to deduce the mineral assemblages expected in planetary interiors and their variation with depth. In general, the available estimates of bulk composition of the terrestrial planets suggest that the terrestrial planets can be divided into two groups based on their predicted mineral assemblages. The terrestrial, Venusian, and lunar bulk compositions are expected to display the following sequence of mineral assemblages with increasing pressure: plagioclase lherzolite, spinel lherzolite, and garnet lherzolite. The sequences expected in Martian and Mercurian are different: spinel-plagioclase wehrlite, spinel lherzolite, and spinel-garnet wehrlite. These assemblages have a major influence on the compositions of liquids produced by melting of these planetary interiors, on the solidus temperatures, and thus on the nature of planetary differentiation and the types of magmas extruded at planetary surfaces.

  7. Giardia duodenalis genetic assemblages and hosts

    Directory of Open Access Journals (Sweden)

    Heyworth Martin F.

    2016-01-01

    Full Text Available Techniques for sub-classifying morphologically identical Giardia duodenalis trophozoites have included comparisons of the electrophoretic mobility of enzymes and of chromosomes, and sequencing of genes encoding β-giardin, triose phosphate isomerase, the small subunit of ribosomal RNA and glutamate dehydrogenase. To date, G. duodenalis organisms have been sub-classified into eight genetic assemblages (designated A–H. Genotyping of G. duodenalis organisms isolated from various hosts has shown that assemblages A and B infect the largest range of host species, and appear to be the main (or possibly only G. duodenalis assemblages that undeniably infect human subjects. In at least some cases of assemblage A or B infection in wild mammals, there is suggestive evidence that the infection had resulted from environmental contamination by G. duodenalis cysts of human origin.

  8. Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

    Science.gov (United States)

    Brenkman, Samuel J.; Connolly, Patrick J.

    2008-01-01

    movements and abundances in rivers. One underlying assumption is that the monitoring program is designed in perpetuity, and consequently our capability to detect trends substantially increases with time. The protocol describes sampling designs, methods, training procedures, safety considerations, data management, data analysis, and reporting. The allocation of sampling effort represents a balance between ecological considerations, a sound monitoring approach, and practical limitations caused by logistical constraints and a limited annual budget of $55,000. The widespread declines of native fish species in western North America highlights the importance and urgency of understanding trends in fish assemblages from undisturbed habitats. Seasonal and annual trends in fish assemblages will provide insights at the individual, population, and assemblage level. This protocol will allow managers to detect increases and decreases in abundance of priority management species, and occurrence of non-native, hatchery, and federally listed fish. The detection of trends in fish assemblages will allow for specific management actions that may include: implementation of more appropriate fishing regulations, evaluation of existing hatchery releases, control of non-native fish species, and prioritization of habitat restoration projects. Dissemination and communication of scientific findings on North Coast and Cascades Network fish assemblages will be a core product of this protocol, which will have much relevance to decision makers, park visitors, researchers, and educators.

  9. 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.

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

    CERN Document Server

    Stimson, L M

    2003-01-01

    Molecular simulations provide an increasingly useful insight into the static and dynamic characteristics of materials. In this thesis molecular simulations of macro-molecular liquid crystalline materials are reported. The first liquid crystalline material that has been investigated is a side chain liquid crystal polymer (SCLCP). In this study semi-atomistic molecular dynamics simulations have been conducted at a range of temperatures and an aligning potential has been applied to mimic the effect of a magnetic field. In cooling the SCLCP from an isotropic melt, microphase separation was observed yielding a domain structure. The application of a magnetic field to this structure aligns the domains producing a stable smectic mesophase. This is the first study in which mesophases have been observed using an off-lattice model of a SCLCP. The second material that has been investigated is a dendrimer with terminal mesogenic functionalization. Here, a multi-scale approach has been taken with Monte Carlo studies of a s...

  11. 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

  12. 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.

  13. BLOOD FLOW AND MACROMOLECULAR TRANSPORT IN CURVED BLOOD VESSELS

    Institute of Scientific and Technical Information of China (English)

    WEI Lan; WEN Gong-bi; TAN Wen-chang

    2006-01-01

    A numerical analysis of the steady/pulsatile flow and macromolecular (such as LDL and Albumin) transport in curved blood vessels was carried out. The computational results predict that the vortex of the secondary flow is time-dependent in the aortic arch.The concentration of macromolecule concentrates at the region of sharp curve, and the wall concentration at the outer part is higher than that at the inner part. Atherosclerosis and thrombosis are prone to develop in such regions with sharp flow.

  14. 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.

  15. The macromolecular crystallography facility at the advanced light source

    Science.gov (United States)

    Earnest, Thomas; Padmore, Howard; Cork, Carl; Behrsing, Rolf; Kim, Sung-Hou

    1996-10-01

    Synchrotron radiation offers several advantages over the use of rotating anode sources for biological crystallography, which allow for the collection of higher-resolution data, substantially more rapid data collection, phasing by multiwavelength anomalous diffraction (MAD) techniques, and time-resolved experiments using polychromatic radiation (Laue diffraction). The use of synchrotron radiation is often necessary to record useful data from crystals which diffract weakly or have very large unit cells. The high brightness and stability characteristics of the advanced light source (ALS) at Lawrence Berkeley National Laboratory, along with the low emittance and long straight sections to accommodate insertion devices present in third generation synchrotrons like the ALS, lead to several advantages in the field of macromolecular crystallography. We are presently constructing a macromolecular crystallography facility at the ALS which is optimized for user-friendliness and high-throughput data collection, with advanced capabilities for MAD and Laue experiments. The X-rays will be directed to three branchlines. A well-equipped support lab will be available for biochemistry, crystal mounting and sample storage, as well as computer hardware and software available, along with staff support, allowing for the complete processing of data on site.

  16. MMDB and VAST+: tracking structural similarities between macromolecular complexes.

    Science.gov (United States)

    Madej, Thomas; Lanczycki, Christopher J; Zhang, Dachuan; Thiessen, Paul A; Geer, Renata C; Marchler-Bauer, Aron; Bryant, Stephen H

    2014-01-01

    The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI's Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure.

  17. 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.

  18. 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.

  19. Enhancing Endosomal Escape for Intracellular Delivery of Macromolecular Biologic Therapeutics.

    Science.gov (United States)

    Lönn, Peter; Kacsinta, Apollo D; Cui, Xian-Shu; Hamil, Alexander S; Kaulich, Manuel; Gogoi, Khirud; Dowdy, Steven F

    2016-09-08

    Bioactive macromolecular peptides and oligonucleotides have significant therapeutic potential. However, due to their size, they have no ability to enter the cytoplasm of cells. Peptide/Protein transduction domains (PTDs), also called cell-penetrating peptides (CPPs), can promote uptake of macromolecules via endocytosis. However, overcoming the rate-limiting step of endosomal escape into the cytoplasm remains a major challenge. Hydrophobic amino acid R groups are known to play a vital role in viral escape from endosomes. Here we utilize a real-time, quantitative live cell split-GFP fluorescence complementation phenotypic assay to systematically analyze and optimize a series of synthetic endosomal escape domains (EEDs). By conjugating EEDs to a TAT-PTD/CPP spilt-GFP peptide complementation assay, we were able to quantitatively measure endosomal escape into the cytoplasm of live cells via restoration of GFP fluorescence by intracellular molecular complementation. We found that EEDs containing two aromatic indole rings or one indole ring and two aromatic phenyl groups at a fixed distance of six polyethylene glycol (PEG) units from the TAT-PTD-cargo significantly enhanced cytoplasmic delivery in the absence of cytotoxicity. EEDs address the critical rate-limiting step of endosomal escape in delivery of macromolecular biologic peptide, protein and siRNA therapeutics into cells.

  20. 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/.

  1. Application of “taxocene surrogation” and “taxonomic sufficiency” concepts to fish farming environmental monitoring. Comparison of BOPA index versus polychaete assemblage structure

    OpenAIRE

    Aguado Giménez, Felipe; Gairin Deulofeu, Joan Ignasi; Martinez-Garcia, Elena; Fernandez-Gonzalez, Victoria; Ballester-Moltó, Mateo; Cerezo-Valverde, Jesús; Sanchez-Jerez, Pablo

    2015-01-01

    “Taxocene surrogation” and “taxonomic sufficiency” concepts were applied to the monitoring of soft bottoms macrobenthic assemblages influenced by fish farming following two approaches. Polychaete assemblage evaluation through multivariate analysis and the benthic index BOPA were compared. Six fish farms along the Spanish Mediterranean coast were monitored. Polychaete assemblage provided a suitable picture of the impact gradient, being correlated with total free sulphides. BOPA did not support...

  2. Discovering free energy basins for macromolecular systems via guided multiscale simulation.

    Science.gov (United States)

    Sereda, Yuriy V; Singharoy, Abhishek B; Jarrold, Martin F; Ortoleva, Peter J

    2012-07-26

    An approach for the automated discovery of low free energy states of macromolecular systems is presented. The method does not involve delineating the entire free energy landscape but proceeds in a sequential free energy minimizing state discovery; i.e., it first discovers one low free energy state and then automatically seeks a distinct neighboring one. These states and the associated ensembles of atomistic configurations are characterized by coarse-grained variables capturing the large-scale structure of the system. A key facet of our approach is the identification of such coarse-grained variables. Evolution of these variables is governed by Langevin dynamics driven by thermal-average forces and mediated by diffusivities, both of which are constructed by an ensemble of short molecular dynamics runs. In the present approach, the thermal-average forces are modified to account for the entropy changes following from our knowledge of the free energy basins already discovered. Such forces guide the system away from the known free energy minima, over free energy barriers, and to a new one. The theory is demonstrated for lactoferrin, known to have multiple energy-minimizing structures. The approach is validated using experimental structures and traditional molecular dynamics. The method can be generalized to enable the interpretation of nanocharacterization data (e.g., ion mobility-mass spectrometry, atomic force microscopy, chemical labeling, and nanopore measurements).

  3. Microhabitat influence on larval fish assemblages within ...

    Science.gov (United States)

    We examined larval and juvenile fish assemblage structure in relation to microhabitat variables within the St. Louis River estuary, a drowned river mouth of Lake Superior. Fish were sampled in vegetated beds throughout the estuary, across a gradient of vegetation types and densities (including disturbed, preserved and post-restoration sites). Canonical correspondence analysis, relating species abundances to environmental variables revealed that plant species richness, turbidity and aquatic plant cover were most influential in structuring assemblages. Results from this microhabitat analysis at this crucial life stage has potential to inform wetland restoration efforts within the St. Louis River and other Great Lake coastal wetlands. not applicable

  4. PROFESSOR TEJ PAL SINGH: THE LEGEND OF INDIAN MACROMOLECULAR CRYSTALLOGRAPHY

    Directory of Open Access Journals (Sweden)

    Md. Imtaiyaz Hassan

    2013-12-01

    Full Text Available Professor Tej Pal Singh, an internationally recognized Indian scientist par excellence, is one of the pioneers of Indian macromolecular crystallography. He is a person of significant and enduring accomplishments as a teacher, scientist, administrator and family man. He has developed various methods to crystallize wide varieties of proteins. He has successfully determined crystal structures of lactoferrin, phospholipase A2, lactoperoxidase, peptidoglycan recognition proteins, disintegrin, zinc-α2-glycoprotein and several others including various protein-ligand and protein-protein complexes. He has a remarkably high number of structural entries in protein data bank. He received most of the prestigious awards and honors by Indian Government. This article covers most of his research and other achievements which will be a source of inspiration for young scientific community, motivation for peers and joy for his fellow colleagues and friends.

  5. Detecting stoichiometry of macromolecular complexes in live cells using FRET

    Science.gov (United States)

    Ben-Johny, Manu; Yue, Daniel N.; Yue, David T.

    2016-01-01

    The stoichiometry of macromolecular interactions is fundamental to cellular signalling yet challenging to detect from living cells. Fluorescence resonance energy transfer (FRET) is a powerful phenomenon for characterizing close-range interactions whereby a donor fluorophore transfers energy to a closely juxtaposed acceptor. Recognizing that FRET measured from the acceptor's perspective reports a related but distinct quantity versus the donor, we utilize the ratiometric comparison of the two to obtain the stoichiometry of a complex. Applying this principle to the long-standing controversy of calmodulin binding to ion channels, we find a surprising Ca2+-induced switch in calmodulin stoichiometry with Ca2+ channels—one calmodulin binds at basal cytosolic Ca2+ levels while two calmodulins interact following Ca2+ elevation. This feature is curiously absent for the related Na channels, also potently regulated by calmodulin. Overall, our assay adds to a burgeoning toolkit to pursue quantitative biochemistry of dynamic signalling complexes in living cells. PMID:27922011

  6. Macromolecularly "Caged" Carbon Nanoparticles for Intracellular Trafficking via Switchable Photoluminescence.

    Science.gov (United States)

    Misra, Santosh K; Srivastava, Indrajit; Tripathi, Indu; Daza, Enrique; Ostadhossein, Fatemeh; Pan, Dipanjan

    2017-02-08

    Reversible switching of photoluminescence (PL) of carbon nanoparticles (CNP) can be achieved with counterionic macromolecular caging and decaging at the nanoscale. A negatively charged uncoated, "bare" CNP with high luminescence loses its PL when positively charged macromolecules are wrapped around its surface. Prepared caged carbons could regain their emission only through interaction with anionic surfactant molecules, representing anionic amphiphiles of endocytic membranes. This process could be verified by gel electrophoresis, spectroscopically and in vitro confocal imaging studies. Results indicated for the first time that luminescence switchable CNPs can be synthesized for efficient intracellular tracking. This study further supports the origin of photoluminescence in CNP as a surface phenomenon correlated a function of characteristic charged macromolecules.

  7. On macromolecular refinement at subatomic resolution withinteratomic scatterers

    Energy Technology Data Exchange (ETDEWEB)

    Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Lunin, Vladimir Y.; Urzhumtsev, Alexandre

    2007-11-09

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

  8. Protein Coevolution and Isoexpression in Yeast Macromolecular Complexes

    Directory of Open Access Journals (Sweden)

    Laurence Ettwiller

    2007-01-01

    Full Text Available Previous studies in the yeast Saccharomyces cerevisiae have shown that genes encoding subunits of macromolecular complexes have similar evolutionary rates (K and expression levels (E. Besides, it is known that the expression of a gene is a strong predictor of its rate of evolution (i.e., E and K are correlated. Here we show that intracomplex variation of subunit expression correlates with intracomplex variation of their evolutionary rates (using two different measures of dispersion. However, a similar trend was observed for randomized complexes. Therefore, using a mathematical transformation, we created new variables capturing intracomplex variation of both E and K. The values of these new compound variables were smaller for real complexes than for randomized ones. This shows that proteins in complexes tend to have closer expressivities (E and K's simultaneously than in the randomly grouped genes. We speculate about the possible implications of this finding.

  9. [Progress in researches on synthetic antimicrobial macromolecular polymers].

    Science.gov (United States)

    Wei, Gang; Yang, Lihua; Chu, Liangyin

    2010-08-01

    Broad-spectrum antimicrobial peptides provide a new way to address the urgent growing problem of bacterial resistance. However, the limited natural resources and the high cost of extraction and purification of natural antimicrobial peptides can not meet the requirements of clinical application. In order to solve this problem, researchers have utilized two basic common structural features (amphiphilic and cationic) for designing and preparing synthetic antimicrobial macromolecular polymers. During the last decade, several kinds of amphiphilic polymers, including arylamide oligomers, phenylene ethynylenes, polymethacrylates, polynorbornenes as well as nylon-3 polymers have been synthesized. In this paper, the structures, antibacterial activities and selectivities of these polymers are reviewed, and the effects of molecular size, polarity and ratio of hydrophobic groups, positive charge density on antibacterial activity and selectivity are also summarized.

  10. 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.

  11. In-vacuum long-wavelength macromolecular crystallography.

    Science.gov (United States)

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

    2016-03-01

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

  12. Extracting trends from two decades of microgravity macromolecular crystallization history

    Science.gov (United States)

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

    2005-01-01

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

  13. 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

  14. 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.

  15. Morphological diversity at different spatial scales in a Neotropical bat assemblage.

    Science.gov (United States)

    Villalobos, Fabricio; Arita, Héctor T

    2014-10-01

    The morphology of species can be used to represent their ecological position and infer potential processes determining the structure of species assemblages. This ecomorphological approach has been widely applied to the study of bat assemblages which mainly focuses on a single spatial scale and particular guilds. We extended such an ecomorphological approach to a multi-scale analysis of a Neotropical bat assemblage and its constituent guilds (aerial and gleaning insectivores, frugivores, and nectarivores) to describe their structure at different spatial scales and determine the relative importance of inter-specific competition, habitat filtering, or stochastic processes shaping such structures. We measured the occupied morphological space (size) defined by wing and skull morphology independently and the nearest-neighbour distance (structure) among species within these spaces at each spatial scale. Observed patterns were compared with random expectations derived from null models for statistical inference. When controlling for species richness and regional sampling effects in the null models, we did not find a significant effect of spatial scale in the morphological structure of the studied bat assemblage and guilds. Morphological structure followed the same patterns across scales as those expected from random drawings of sample size alone. Similar results were obtained regardless of morphological complex (wing and skull) and guilds. At both the assemblage and guild levels, bat morphological structure seems to be determined by regional, abiotic processes (e.g. habitat filtering) shaping the composition and organization of the species pool.

  16. Factors influencing riverine fish assemblages in Massachusetts

    Science.gov (United States)

    Armstrong, David S.; Richards, Todd A.; Levin, Sara B.

    2011-01-01

    components analysis and Spearman rank correlation, was used to select a set of 15 non-redundant environmental and anthropogenic factors to test for use as explanatory variables in the regression analyses. Twenty-one fish species were used in a multivariate analysis of fish-assemblage patterns. Results of nonmetric multidimensional scaling and hierarchical cluster analysis were used to group fish species into fluvial and macrohabitat generalist habitat-use classes. Two analytical techniques, quantile regression and generalized linear modeling, were applied to characterize the association between fish-response variables and environmental and anthropogenic explanatory variables. Quantile regression demonstrated that as percent impervious cover and an indicator of percent alteration of August median flow from groundwater withdrawals increase, the relative abundance and species richness of fluvial fish decrease. The quantile regression plots indicate that (1) as many as seven fluvial fish species are expected in streams with little flow alteration or impervious cover, (2) no more than four fluvial fish species are expected in streams where flow alterations from groundwater withdrawals exceed 50 percent of the August median flow or the percent area of impervious cover exceeds 15 percent, and (3) few fluvial fish remain at high rates of withdrawal (approaching 100 percent) or high rates of impervious cover (between 25 and 30 percent). Three generalized linear models (GLMs) were developed to quantify the response of fluvial fish to multiple environmental and anthropogenic variables. All variables in the GLM equations were demonstrated to be significant (p less than 0.05, with most less than 0.01). Variables in the fluvial-fish relative-abundance model were channel slope, estimated percent alteration of August median flow from groundwater withdrawals, percent wetland in a 240-meter buffer strip, and percent impervious cover. Variables in the fluvial-fish species-richness model were

  17. Influence of landscape structure on reef fish assemblages

    Science.gov (United States)

    Grober-Dunsmore, R.; Frazer, T.K.; Beets, J.P.; Lindberg, W.J.; Zwick, P.; Funicelli, N.A.

    2008-01-01

    Management of tropical marine environments calls for interdisciplinary studies and innovative methodologies that consider processes occurring over broad spatial scales. We investigated relationships between landscape structure and reef fish assemblage structure in the US Virgin Islands. Measures of landscape structure were transformed into a reduced set of composite indices using principal component analyses (PCA) to synthesize data on the spatial patterning of the landscape structure of the study reefs. However, composite indices (e.g., habitat diversity) were not particularly informative for predicting reef fish assemblage structure. Rather, relationships were interpreted more easily when functional groups of fishes were related to individual habitat features. In particular, multiple reef fish parameters were strongly associated with reef context. Fishes responded to benthic habitat structure at multiple spatial scales, with various groups of fishes each correlated to a unique suite of variables. Accordingly, future experiments should be designed to test functional relationships based on the ecology of the organisms of interest. Our study demonstrates that landscape-scale habitat features influence reef fish communities, illustrating promise in applying a landscape ecology approach to better understand factors that structure coral reef ecosystems. Furthermore, our findings may prove useful in design of spatially-based conservation approaches such as marine protected areas (MPAs), because landscape-scale metrics may serve as proxies for areas with high species diversity and abundance within the coral reef landscape. ?? 2007 Springer Science+Business Media B.V.

  18. Mangrove macrobenthos: Assemblages, services, and linkages

    Science.gov (United States)

    Lee, S. Y.

    2008-02-01

    Macrobenthic assemblages are relatively poorly known compared to other components of the mangrove ecosystem. Tropical mangroves support macrobenthic biodiversity resources yet to be properly documented and interpreted. Some methodological challenges, such as the generally high spatial heterogeneity and complexity of the habitat, evidently reduce sampling efficiency and accuracy, while also leaving some microhabitats under-sampled. Macrobenthic assemblage structure seems to be influenced by local environmental conditions, such as hydroperiod, organic matter availability and sediment characteristics. Brachyurans, gastropods and oligochaetes dominate in the sediment, with the former two groups also common on hard surfaces provided by tree trunks, while insects and arachnids inhabit the canopy. Traditionally, studies of mangrove macrobenthos have focused on assemblage structure or the biology of individual species, but more complex inter-specific interactions and the inter-relationship between habitat and the biota are recently being addressed. Brachyuran crabs are the best-studied macrobenthos group, but many issues about their role in mangrove ecosystem dynamics are still controversial. Despite many species of mangrove macrobenthos being referred to as 'trophic dead ends', most serve as important links between recalcitrant mangrove organic matter and estuarine secondary production, through feeding excursion by mobile nekton during the high tide, and macrobenthos-mediated processing and exportation of organic matter. A significant difference in the standing crop biomass of forests between the Indo-west-Pacific (IWP)' and Atlantic-east-Pacific (AEP) mangroves may be related to the difference in species richness of mangrove as well as macrobenthos diversity in the two bioregions. Such differences in assemblage structure may also result in different ecosystem functioning, but the nature of the links is, however, yet to be explored. There is also a strong need for

  19. Hydrological controls on glacially exported microbial assemblages

    Science.gov (United States)

    Dubnick, Ashley; Kazemi, Sina; Sharp, Martin; Wadham, Jemma; Hawkings, Jon; Beaton, Alexander; Lanoil, Brian

    2017-05-01

    The Greenland Ice Sheet (GrIS) exports approximately 400 km3 of freshwater annually to downstream freshwater and marine ecosystems. These meltwaters originate in a wide range of well-defined habitats that can be associated with very different physical environments within the ice sheet, ranging from oxygenated surface environments that are exposed to light and supplied with nutrients from atmospheric/aeolian sources to subglacial environments that are permanently dark, isolated from the atmosphere, and potentially anoxic. Hydrological conditions in the latter likely favor prolonged rock-water contact. The seasonally evolving hydrological system that drains meltwaters from the GrIS connects these distinct microbial habitats and exports the microbes contained within them to downstream ecosystems. The microbial assemblages exported in glacier meltwater may have an impact on downstream ecosystem function and development. We explored how the seasonal development of a glacial drainage system influences the character of microbial assemblages exported from the GrIS by monitoring the seasonal changes in hydrology, water chemistry, and microbial assemblage composition of meltwaters draining from a glacier in southwest Greenland. We found that the microbial assemblages exported in meltwaters varied in response to glacier hydrological flow path characteristics. Whether or not meltwaters passed through the subglacial environment was the first-order control on the composition of the microbial assemblages exported from the glacier, while water source (i.e., supraglacial or extraglacial) and subglacial residence times were second-order controls. Glacier hydrology therefore plays a fundamental role in determining the microbial exports from glaciated watersheds.

  20. Diversity and biogeography of bacterial assemblages in surface sediments across the San Pedro Basin, Southern California Borderlands.

    Science.gov (United States)

    Hewson, Ian; Jacobson Meyers, Myrna E; Fuhrman, Jed A

    2007-04-01

    Sediment bacteria play important roles in the biogeochemistry of ocean sediments; however, factors influencing assemblage composition have not been extensively studied. We examined extractable sediment bacterial abundance, the composition of bacterial assemblages using a high-throughput molecular fingerprinting approach, and several sediment biogeochemical parameters (organic matter content and alkaline phosphatase activity), along a 35 km transect from Point Fermin, Southern California, to Santa Catalina Island, across the approximately 900-m-deep San Pedro Basin. Automated rRNA intergenic spacer analysis (ARISA) demonstrated that in two spatially isolated shallow (approximately < 60 m, on opposite sides of the channel) sediment environments, assemblages were more similar to each other than to deeper communities. Distinct communities existed in deeper and shallower sediments, and stations within the deep basin over 2 km apart contained remarkably similar assemblage fingerprints. The relative contribution to total amplified DNA fluorescence of operational taxonomic units (OTUs) was significantly correlated to that of other OTUs in few comparisons (2.7% of total), i.e. few bacterial types were found together or apart consistently. The relative proportions within assemblages of only a few OTU were significantly correlated to measured physicochemical parameters (organic matter content and wet/dry weight ratio of sediments) or enzyme (alkaline phosphatase) activities. A low percentage of shared OTU between shallow and deep sediments, and the presence of similar, but spatially isolated assemblages suggests that bacterial OTU may be widely dispersed over scales of a few kilometres, but that environmental conditions select for particular assemblages.

  1. Distinct Contribution of Electrostatics, Initial Conformational Ensemble, and Macromolecular Stability in RNA Folding

    Energy Technology Data Exchange (ETDEWEB)

    Laederach,A.; Shcherbakova, I.; Jonikas, M.; Altman, R.; Brenowitz, M.

    2007-01-01

    We distinguish the contribution of the electrostatic environment, initial conformational ensemble, and macromolecular stability on the folding mechanism of a large RNA using a combination of time-resolved 'Fast Fenton' hydroxyl radical footprinting and exhaustive kinetic modeling. This integrated approach allows us to define the folding landscape of the L-21 Tetrahymena thermophila group I intron structurally and kinetically from its earliest steps with unprecedented accuracy. Distinct parallel pathways leading the RNA to its native form upon its Mg2+-induced folding are observed. The structures of the intermediates populating the pathways are not affected by variation of the concentration and type of background monovalent ions (electrostatic environment) but are altered by a mutation that destabilizes one domain of the ribozyme. Experiments starting from different conformational ensembles but folding under identical conditions show that whereas the electrostatic environment modulates molecular flux through different pathways, the initial conformational ensemble determines the partitioning of the flux. This study showcases a robust approach for the development of kinetic models from collections of local structural probes.

  2. Connectedness of land use, nutrients, primary production, and fish assemblages in oxbow lakes

    Science.gov (United States)

    Miranda, Leandro E.; Andrews, Caroline S.; Kroger, Robert

    2013-01-01

    We explored the strength of connectedness among hierarchical system components associated with oxbow lakes in the alluvial valley of the Lower Mississippi River. Specifically, we examined the degree of canonical correlation between land use (agriculture and forests), lake morphometry (depth and size), nutrients (total nitrogen and total phosphorus), primary production (chlorophyll-a), and various fish assemblage descriptors. Watershed (p production (p production was associated with sunfish (Centrarchidae) assemblages (p hierarchical approach can be useful in developing management and conservation plans for oxbow lakes in a region impacted by widespread landscape changes due to agriculture.

  3. Variation in rocky shore assemblages and abundances of key taxa along gradients of stormwater input.

    Science.gov (United States)

    Kinsella, Chloe M; Crowe, Tasman P

    2015-04-01

    Stormwater brings freshwater and terrestrially derived contaminants into coastal systems and is predicted to increase with climate change. This study aimed to characterise variation in rocky shore assemblages in relation to stormwater pollution. Intertidal assemblages were sampled in similar habitats at a range of distances (0 m, 10 m, 20 m, 60 m, and 100 m) from stormwater outfalls on three rocky shores north of Dublin. In general, taxon richness and algal cover increased after 20 m from a stormwater outfall. Limpet population structure and condition index showed no consistent patterns among shores. Assemblage structure at or near stormwater sites differed from that at sites 100 m away. These findings, ideally supplemented by experimental research, may be used to inform stormwater management and remediation approaches.

  4. Climate change effects on North American inland fish populations and assemblages

    Science.gov (United States)

    Lynch, Abigail J.; Myers, Bonnie; Chu, Cindy; Eby, Lisa A.; Falke, Jeffrey A.; Kovach, Ryan P.; Krabbenhoft, Trevor J.; Kwak, Thomas J.; Lyons, John; Paukert, Craig P.; Whitney, James E.

    2016-01-01

    Climate is a critical driver of many fish populations, assemblages, and aquatic communities. However, direct observational studies of climate change impacts on North American inland fishes are rare. In this synthesis, we (1) summarize climate trends that may influence North American inland fish populations and assemblages, (2) compile 31 peer-reviewed studies of documented climate change effects on North American inland fish populations and assemblages, and (3) highlight four case studies representing a variety of observed responses ranging from warmwater systems in the southwestern and southeastern United States to coldwater systems along the Pacific Coast and Canadian Shield. We conclude by identifying key data gaps and research needs to inform adaptive, ecosystem-based approaches to managing North American inland fishes and fisheries in a changing climate.

  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. Protein-ion binding process on finite macromolecular concentration. A Poisson-Boltzmann and Monte Carlo study.

    Science.gov (United States)

    de Carvalho, Sidney Jurado; Fenley, Márcia O; da Silva, Fernando Luís Barroso

    2008-12-25

    Electrostatic interactions are one of the key driving forces for protein-ligands complexation. Different levels for the theoretical modeling of such processes are available on the literature. Most of the studies on the Molecular Biology field are performed within numerical solutions of the Poisson-Boltzmann Equation and the dielectric continuum models framework. In such dielectric continuum models, there are two pivotal questions: (a) how the protein dielectric medium should be modeled, and (b) what protocol should be used when solving this effective Hamiltonian. By means of Monte Carlo (MC) and Poisson-Boltzmann (PB) calculations, we define the applicability of the PB approach with linear and nonlinear responses for macromolecular electrostatic interactions in electrolyte solution, revealing some physical mechanisms and limitations behind it especially due the raise of both macromolecular charge and concentration out of the strong coupling regime. A discrepancy between PB and MC for binding constant shifts is shown and explained in terms of the manner PB approximates the excess chemical potentials of the ligand, and not as a consequence of the nonlinear thermal treatment and/or explicit ion-ion interactions as it could be argued. Our findings also show that the nonlinear PB predictions with a low dielectric response well reproduce the pK shifts calculations carried out with an uniform dielectric model. This confirms and completes previous results obtained by both MC and linear PB calculations.

  7. 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.

  8. 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.

  9. Preclinical imaging and translational animal models of cancer for accelerated clinical implementation of nanotechnologies and macromolecular agents.

    Science.gov (United States)

    De Souza, Raquel; Spence, Tara; Huang, Huang; Allen, Christine

    2015-12-10

    The majority of animal models of cancer have performed poorly in terms of predicting clinical performance of new therapeutics, which are most often first evaluated in patients with advanced, metastatic disease. The development and use of metastatic models of cancer may enhance clinical translatability of preclinical studies focused on the development of nanotechnology-based drug delivery systems and macromolecular therapeutics, potentially accelerating their clinical implementation. It is recognized that the development and use of such models are not without challenge. Preclinical imaging tools offer a solution by allowing temporal and spatial characterization of metastatic lesions. This paper provides a review of imaging methods applicable for evaluation of novel therapeutics in clinically relevant models of advanced cancer. An overview of currently utilized models of oncology in small animals is followed by image-based development and characterization of visceral metastatic cancer models. Examples of imaging tools employed for metastatic lesion detection, evaluation of anti-tumor and anti-metastatic potential and biodistribution of novel therapies, as well as the co-development and/or use of imageable surrogates of response, are also discussed. While the focus is on development of macromolecular and nanotechnology-based therapeutics, examples with small molecules are included in some cases to illustrate concepts and approaches that can be applied in the assessment of nanotechnologies or macromolecules.

  10. A versatile microparticle-based immunoaggregation assay for macromolecular biomarker detection and quantification.

    Directory of Open Access Journals (Sweden)

    Haiyan Wu

    Full Text Available The rapid, sensitive and low-cost detection of macromolecular biomarkers is critical in clinical diagnostics, environmental monitoring, research, etc. Conventional assay methods usually require bulky, expensive and designated instruments and relative long assay time. For hospitals and laboratories that lack immediate access to analytical instruments, fast and low-cost assay methods for the detection of macromolecular biomarkers are urgently needed. In this work, we developed a versatile microparticle (MP-based immunoaggregation method for the detection and quantification of macromolecular biomarkers. Antibodies (Abs were firstly conjugated to MP through streptavidin-biotin interaction; the addition of macromolecular biomarkers caused the aggregation of Ab-MPs, which were subsequently detected by an optical microscope or optical particle sizer. The invisible nanometer-scale macromolecular biomarkers caused detectable change of micrometer-scale particle size distributions. Goat anti-rabbit immunoglobulin and human ferritin were used as model biomarkers to demonstrate MP-based immunoaggregation assay in PBS and 10% FBS to mimic real biomarker assay in the complex medium. It was found that both the number ratio and the volume ratio of Ab-MP aggregates caused by biomarker to all particles were directly correlated to the biomarker concentration. In addition, we found that the detection range could be tuned by adjusting the Ab-MP concentration. We envision that this novel MP-based immunoaggregation assay can be combined with multiple detection methods to detect and quantify macromolecular biomarkers at the nanogram per milliliter level.

  11. Miura Tubes and Assemblages: Theory and Applications

    Science.gov (United States)

    Filipov, Evgueni; Paulino, Glaucio; Tachi, Tomohiro

    2015-03-01

    Origami systems inspired from the Miura-ori pattern are rigid and flat foldable meaning that they can fold completely by deforming only about prescribed fold lines. We investigate origami tubes and assemblages constructed from Miura-ori inspired sheets and use eigenvalue analyses to study their stiffness characteristics. A simplified bar model is used to model the stretching and shear of the flat panel segments and rotational hinges are used to simulate the bending stiffness of the panels and prescribed fold lines. We discuss the small to large deformation bending of thin sheets and show an improved method to estimate stiffness when modeling origami structures. The tube assemblages show interesting behaviors that make them suitable for applications in science and engineering.

  12. Consumer–brand assemblages in advertising

    DEFF Research Database (Denmark)

    Bjerrisgaard, Sofie Møller; Kjeldgaard, Dannie; Bengtson, Anders

    2013-01-01

    This paper discusses how the use of tattoos in advertising renders diverse brand–consumer assemblages visible. In considering advertising practitioners as professionals of entanglement, the paper emphasizes the embeddedness of practitioners’ use of tattoo symbolism in institutionalized marketing...... systems and in the cultural history of tattooing. In accordance with recent emphasis on the importance of material devices for understanding contemporary sociality, this paper presents a semiotic analysis of a convenience sample of advertisements depicting tattoos. Tattoos are productive for the study...... of brand–consumer assemblages because they are situated on the human skin, which is a mediator between the individual and the socio-material world. Furthermore, tattoos reproduce discourses of both mainstream fashion and deviant subcultural identification, which imbue tattoo symbolism with communicative...

  13. Teosinte inflorescence phytolith assemblages mirror Zea taxonomy.

    Directory of Open Access Journals (Sweden)

    John P Hart

    Full Text Available Molecular DNA analyses of the New World grass (Poaceae genus Zea, comprising five species, has resolved taxonomic issues including the most likely teosinte progenitor (Zea mays ssp. parviglumis of maize (Zea mays ssp. mays. However, archaeologically, little is known about the use of teosinte by humans both prior to and after the domestication of maize. One potential line of evidence to explore these relationships is opaline phytoliths produced in teosinte fruit cases. Here we use multidimensional scaling and multiple discriminant analyses to determine if rondel phytolith assemblages from teosinte fruitcases reflect teosinte taxonomy. Our results indicate that rondel phytolith assemblages from the various taxa, including subspecies, can be statistically discriminated. This indicates that it will be possible to investigate the archaeological histories of teosinte use pending the recovery of appropriate samples.

  14. Teosinte inflorescence phytolith assemblages mirror Zea taxonomy.

    Science.gov (United States)

    Hart, John P; Matson, R G; Thompson, Robert G; Blake, Michael

    2011-03-30

    Molecular DNA analyses of the New World grass (Poaceae) genus Zea, comprising five species, has resolved taxonomic issues including the most likely teosinte progenitor (Zea mays ssp. parviglumis) of maize (Zea mays ssp. mays). However, archaeologically, little is known about the use of teosinte by humans both prior to and after the domestication of maize. One potential line of evidence to explore these relationships is opaline phytoliths produced in teosinte fruit cases. Here we use multidimensional scaling and multiple discriminant analyses to determine if rondel phytolith assemblages from teosinte fruitcases reflect teosinte taxonomy. Our results indicate that rondel phytolith assemblages from the various taxa, including subspecies, can be statistically discriminated. This indicates that it will be possible to investigate the archaeological histories of teosinte use pending the recovery of appropriate samples.

  15. 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.

  16. 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

  17. Timely deposition of macromolecular structures is necessary for peer review

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-12-01

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

  18. 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.

  19. New concepts and applications in the macromolecular chemistry of fullerenes.

    Science.gov (United States)

    Giacalone, Francesco; Martín, Nazario

    2010-10-08

    A new classification on the different types of fullerene-containing polymers is presented according to their different properties and applications they exhibit in a variety of fields. Because of their interest and novelty, water-soluble and biodegradable C(60)-polymers are discussed first, followed by polyfullerene-based membranes where unprecedented supramolecular structures are presented. Next are compounds that involve hybrid materials formed from fullerenes and other components such as silica, DNA, and carbon nanotubes (CNTs) where the most recent advances have been achieved. A most relevant topic is still that of C(60)-based donor-acceptor (D-A) polymers. Since their application in photovoltaics D-A polymers are among the most realistic applications of fullerenes in the so-called molecular electronics. The most relevant aspects in these covalently connected fullerene/polymer hybrids as well as new concepts to improve energy conversion efficiencies are presented.The last topics disccused relate to supramolecular aspects that are in involved in C(60)-polymer systems and in the self-assembly of C(60)-macromolecular structures, which open a new scenario for organizing, by means of non-covalent interactions, new supramolecular structures at the nano- and micrometric scale, in which the combination of the hydrofobicity of fullerenes with the versatility of the noncovalent chemistry afford new and spectacular superstructures.

  20. 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.

  1. 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.

  2. Messy entanglements: research assemblages in heart transplantation discourses and practices.

    Science.gov (United States)

    Shildrick, Margrit; Carnie, Andrew; Wright, Alexa; McKeever, Patricia; Jan, Emily Huan-Ching; De Luca, Enza; Bachmann, Ingrid; Abbey, Susan; Dal Bo, Dana; Poole, Jennifer; El-Sheikh, Tammer; Ross, Heather

    2017-09-28

    The paper engages with a variety of data around a supposedly single biomedical event, that of heart transplantation. In conventional discourse, organ transplantation constitutes an unproblematised form of spare part surgery in which failing biological components are replaced by more efficient and enduring ones, but once that simple picture is complicated by employing a radically interdisciplinary approach, any biomedical certainty is profoundly disrupted. Our aim, as a cross-sectorial partnership, has been to explore the complexities of heart transplantation by explicitly entangling research from the arts, biosciences and humanities without privileging any one discourse. It has been no easy enterprise yet it has been highly productive of new insights. We draw on our own ongoing funded research with both heart donor families and recipients to explore our different perceptions of what constitutes data and to demonstrate how the dynamic entangling of multiple data produces a constitutive assemblage of elements in which no one can claim priority. Our claim is that the use of such research assemblages and the collaborations that we bring to our project breaks through disciplinary silos to enable a fuller comprehension of the significance and experience of heart transplantation in both theory and practice. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

  3. User Assemblages in Design: An Ethnographic Study

    OpenAIRE

    2010-01-01

    This thesis presents an ethnographic study of the role of users in user-centered design. It is written from the perspective of science and technology studies, in particular developments in actor-network theory, and draws on the notion of the assemblage from the work of Deleuze and Guattari. The data for this thesis derives from a six-month field study of the routine discourse and practices of user-centered designers working for a multinational microprocessor manufacturer. The central argument...

  4. Littoral zone fish assemblages of northern Cayuga Lake.

    Science.gov (United States)

    McKenna, James E.

    2001-01-01

    Fish assemblages from northern Cayuga Lake were examined for patterns in temporal structure. Fish assemblages changed significantly between seasons. Bluegill (Lepomis macrochirus), bluntnose minnow (Pimephales notatus), and smallmouth bass (Micropterus dolomieu) formed the basis for most assemblages, but the spring assemblage was dominated by common carp (Cyprinus carpio). Correlations between community structure and abiotic factors were identified. Ten abiotic factors strongly influenced species assemblages, including phosphorus concentration, but could not fully explain differences between assemblages. Results indicate that the seasonal pattern of fish assemblage structure and abundance of fish that tend to feed in the water column were related to the annual cycle of productivity in the lake and behavioral adaptations of the fish.

  5. PLEISTOCENE BATHYAL MOLLUSCAN ASSEMBLAGES FROM SOUTHERN ITALY

    Directory of Open Access Journals (Sweden)

    ITALO DI GERONIMO

    1997-11-01

    Full Text Available Four Pleistocene bathyal molluscan assemblages from southern Italy (Calabria and Messina area were studied. One hundred and thirty-six species were recorded. Twenty-four were classified and described in detail and thirty-five were illustrated. The following new combinations are pro posed: Solariella marginulata (Philippi, 1844, Iphitus tenuisculptus (Seguenza, 1876, Benthomangelia tenuicostata (Seguenza, 1879, Chrysallida microscalaria (Seguenza, 1876, Ennucula corbuloides (Seguenza, 1877, Ennucula rotundata (Seguenza, 1877, Thestyleda cuspidata (Philippi, 1844, Katadesmia confusa (Seguenza, 1877, Austrotindaria pusio (Philippi, 1844, Austrotindaria salicensis (Seguenza, 1877. Comments concerning the taxonomy of Fissurisepta Seguenza, 1862, Solariella Wood, 1842, Ennucula Iredale, 1931, Thestyleda Iredale, 1929, Ledella Verrill & Bush, 1897, Yoldiella Verrill & Bush, 1897, Bathyspinula Filatova, 1958, Katadesmia Dall, 1908, Austrotindaria Fleming, 1948 and Cadulus Philippi, 1844 are included. The assemblages are dominated by nuculoids and fit the general compositional pattern of the deep-sea molluscan communities. A paleodepth of 500-600 m is inferred for two assemblages, whereas a greater depth, pro bably not exceeding 1,000 m, is suggested for the other two. Taxonomic affinities with northeast Atlantic and more generally with World Ocean deep-sea molluscan faunas are remarkable. The Plio-Quaternary evolution of the deep Mediterranean benthos is discussed.    

  6. Combining projected changes in species richness and composition reveals climate change impacts on coastal Mediterranean fish assemblages

    DEFF Research Database (Denmark)

    Albouy, Camille; Guilhaumon, François; Bastos Araujo, Miguel;

    2012-01-01

    Species Temporal Turnover (STT) is one of the most familiar metrics to assess changes in assemblage composition as a consequence of climate change. However, STT mixes two components in one metric, changes in assemblage composition caused by a process of species loss or gain (i.e. the nestedness...... component) and changes in assemblage composition caused by a process of species replacement (i.e. the species replacement component). Drawing on previous studies investigating spatial patterns of beta diversity, we propose measures of STT that allow analysing each component (species replacement vs....... nestedness), separately. We also present a mapping strategy to simultaneously visualize changes in species richness and assemblage composition. To illustrate our approach, we used the Mediterranean coastal fish fauna as a case study. Using Bioclimatic Envelope Models (BEMs) we first projected the potential...

  7. 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.

  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

    sciences have emphasized structure. By contrast, following X-ray crystallographers, researchers studying proteins using solution NMR introduced the combination of NMR with computer simulation before that became common practice in solid-state NMR. Today's simulation methods can handle partially ordered or even disordered systems common in synthetic polymers. Thus, the multitechnique approaches employed in NMR of synthetic and biological macromolecules have converged. Therefore, this Account will be relevant to both researchers studying synthetic macromolecular and supramolecular systems and those studying biological complexes.

  9. 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.

  10. 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

  11. Larval assemblages of large and medium-sized pelagic species in the Straits of Florida

    Science.gov (United States)

    Richardson, David E.; Llopiz, Joel K.; Guigand, Cedric M.; Cowen, Robert K.

    2010-07-01

    Critical gaps in our understanding of the distributions, interactions, life histories and preferred habitats of large and medium-size pelagic fishes severely constrain the implementation of ecosystem-based, spatially structured fisheries management approaches. In particular, spawning distributions and the environmental characteristics associated with the early life stages are poorly documented. In this study, we consider the diversity, assemblages, and associated habitat of the larvae of large and medium-sized pelagic species collected during 2 years of monthly surveys across the Straits of Florida. In total, 36 taxa and 14,295 individuals were collected, with the highest diversity occurring during the summer and in the western, frontal region of the Florida Current. Only a few species (e.g. Thunnus obesus, T. alalunga, Tetrapturus pfluegeri) considered for this study were absent. Small scombrids (e.g. T. atlanticus, Katsuwonus pelamis, Auxis spp.) and gempylids dominated the catch and were orders of magnitude more abundant than many of the rare species (e.g. Thunnus thynnus,Kajikia albida). Both constrained (CCA) and unconstrained (NMDS) multivariate analyses revealed a number of species groupings including: (1) a summer Florida edge assemblage (e.g. Auxis spp., Euthynnus alleterattus, Istiophorus platypterus); (2) a summer offshore assemblage (e.g. Makaira nigricans, T. atlanticus, Ruvettus pretiosus, Lampris guttatus); (3) an ubiquitous assemblage (e.g. K. pelamis, Coryphaena hippurus, Xiphias gladius); and (4) a spring/winter assemblage that was widely dispersed in space (e.g. trachipterids). The primary environmental factors associated with these assemblages were sea-surface temperature (highest in summer-early fall), day length (highest in early summer), thermocline depth (shallowest on the Florida side) and fluorescence (highest on the Florida side). Overall, the results of this study provide insights into how a remarkable diversity of pelagic species

  12. Bird assemblage response to restoration of fire-suppressed longleaf pine sandhills.

    Science.gov (United States)

    Steen, David A; Conner, L M; Smith, Lora L; Provencher, Louis; Hiers, J Kevin; Pokswinski, Scott; Helms, Brian S; Guyer, Craig

    2013-01-01

    The ecological restoration of fire-suppressed habitats may require a multifaceted approach. Removal of hardwood trees together with reintroduction of fire has been suggested as a method of restoring fire-suppressed longleaf pine (Pinus palustris) forests; however, this strategy, although widespread, has not been evaluated on large spatial and temporal scales. We used a landscape-scale experimental design to examine how bird assemblages in fire-suppressed longleaf pine sandhills responded to fire alone or fire following mechanical removal or herbicide application to reduce hardwood levels. Individual treatments were compared to fire-suppressed controls and reference sites. After initial treatment, all sites were managed with prescribed fire, on an approximately two- to three-year interval, for over a decade. Nonmetric multidimensional scaling ordinations suggested that avian assemblages on sites that experienced any form of hardwood removal differed from assemblages on both fire-suppressed sites and reference sites 3-4 years after treatment (i.e., early posttreatment). After >10 years of prescribed burning on all sites (i.e., late posttreatment), only assemblages at sites treated with herbicide were indistinguishable from assemblages at reference sites. By the end of the study, individual species that were once indicators of reference sites no longer contributed to making reference sites unique. Occupancy modeling of these indicator species also demonstrated increasing similarity across treatments over time. Overall, although we documented long-term and variable assemblage-level change, our results indicate occupancy for birds considered longleaf pine specialists was similar at treatment and reference sites after over a decade of prescribed burning, regardless of initial method of hardwood removal. In other words, based on the response of species highly associated with the habitat, we found no justification for the added cost and effort of fire surrogates; fire

  13. Non-contact luminescence lifetime cryothermometry for macromolecular crystallography.

    Science.gov (United States)

    Mykhaylyk, V B; Wagner, A; Kraus, H

    2017-05-01

    Temperature is a very important parameter when aiming to minimize radiation damage to biological samples during experiments that utilize intense ionizing radiation. A novel technique for remote, non-contact, in situ monitoring of the protein crystal temperature has been developed for the new I23 beamline at the Diamond Light Source, a facility dedicated to macromolecular crystallography (MX) with long-wavelength X-rays. The temperature is derived from the temperature-dependent decay time constant of luminescence from a minuscule scintillation sensor (luminescence lifetime thermometry is presented, the features of the detection method and the choice of temperature sensor are discussed, and it is demonstrated how the temperature monitoring system was integrated within the viewing system of the endstation used for the visualization of protein crystals. The thermometry system was characterized using a Bi4Ge3O12 crystal scintillator that exhibits good responsivity of the decay time constant as a function of temperature over a wide range (8-270 K). The scintillation sensor was calibrated and the uncertainty of the temperature measurements over the primary operation temperature range of the beamline (30-150 K) was assessed to be ±1.6 K. It has been shown that the temperature of the sample holder, measured using the luminescence sensor, agrees well with the expected value. The technique was applied to characterize the thermal performance of different sample mounts that have been used in MX experiments at the I23 beamline. The thickness of the mount is shown to have the greatest impact upon the temperature distribution across the sample mount. Altogether, these tests and findings demonstrate the usefulness of the thermometry system in highlighting the challenges that remain to be addressed for the in-vacuum MX experiment to become a reliable and indispensable tool for structural biology.

  14. 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.

  15. 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.

  16. 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.

  17. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography

    Directory of Open Access Journals (Sweden)

    Julian C.-H. Chen

    2017-01-01

    Full Text Available The Protein Crystallography Station (PCS, located at the Los Alamos Neutron Scattering Center (LANSCE, was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER for 13 years (2002–2014. The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  18. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography.

    Science.gov (United States)

    Chen, Julian C-H; Unkefer, Clifford J

    2017-01-01

    The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  19. Detection of Macromolecular Fractions in HCN Polymers Using Electrophoretic and Ultrafiltration Techniques.

    Science.gov (United States)

    Marín-Yaseli, Margarita R; Cid, Cristina; Yagüe, Ana I; Ruiz-Bermejo, Marta

    2017-02-01

    Elucidating the origin of life involves synthetic as well as analytical challenges. Herein, for the first time, we describe the use of gel electrophoresis and ultrafiltration to fractionate HCN polymers. Since the first prebiotic synthesis of adenine by Oró, HCN polymers have gained much interest in studies on the origins of life due to the identification of biomonomers and related compounds within them. Here, we demonstrate that macromolecular fractions with electrophoretic mobility can also be detected within HCN polymers. The migration of polymers under the influence of an electric field depends not only on their sizes (one-dimensional electrophoresis) but also their different isoelectric points (two-dimensional electrophoresis, 2-DE). The same behaviour was observed for several macromolecular fractions detected in HCN polymers. Macromolecular fractions with apparent molecular weights as high as 250 kDa were detected by tricine-SDS gel electrophoresis. Cationic macromolecular fractions with apparent molecular weights as high as 140 kDa were also detected by 2-DE. The HCN polymers synthesized were fractionated by ultrafiltration. As a result, the molecular weight distributions of the macromolecular fractions detected in the HCN polymers directly depended on the synthetic conditions used to produce these polymers. The implications of these results for prebiotic chemistry will be discussed.

  20. Sothi-Siswal Ceramic Assemblage: A Reappraisal

    Directory of Open Access Journals (Sweden)

    Tejas Garge

    2010-12-01

    Full Text Available Harappan evidences in Chautan valley has a unique ceramic tradition. In the light of recent plethora of knowledge as well as against the background of the studies conducted by A. Ghosh, J.S. Nigam, Katy Frenchman, Suraj Bhan & Madhu Bala, we will have to not only reclassify the Sothi-Siswal ceramic assemblage but also alter basic nomenclatures and concepts involve in it. It will give us deep insight in to the process of evolution of Early Harappan cultures vis-à-vis the dynamic of regional cultural complexes.

  1. Nonlinear sequential laminates reproducing hollow sphere assemblages

    Science.gov (United States)

    Idiart, Martín I.

    2007-07-01

    A special class of nonlinear porous materials with isotropic 'sequentially laminated' microstructures is found to reproduce exactly the hydrostatic behavior of 'hollow sphere assemblages'. It is then argued that this result supports the conjecture that Gurson's approximate criterion for plastic porous materials, and its viscoplastic extension of Leblond et al. (1994), may actually yield rigorous upper bounds for the hydrostatic flow stress of porous materials containing an isotropic, but otherwise arbitrary, distribution of porosity. To cite this article: M.I. Idiart, C. R. Mecanique 335 (2007).

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

    Science.gov (United States)

    Knapp, B.; Marsh, E.; Cipriani, F.; Arneson, D.; Oss, D.; Liebers, M.; Keller, E.

    2013-03-01

    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.

  3. Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures

    Directory of Open Access Journals (Sweden)

    C. J. Friedline

    2012-06-01

    Full Text Available Microbial communities are recognized as major drivers of the biogeochemical processes in the oceans. However, the genetic diversity and composition of those communities is poorly understood. The aim of this study is to investigate the composition of bacterial assemblages in three different water layer habitats: surface (2–20 m, deep chlorophyll maximum (DCM; 28–90 m, and deep (100–4600 m at nine stations along the eastern Atlantic Ocean from 42.8° N to 23.7° S. The sampling of three discrete, predefined habitat types from different depths, Longhurstian provinces, and geographical locations allowed us to investigate whether marine bacterial assemblages show spatial variation and to determine if the observed spatial variation is influenced by current environmental conditions, historical/geographical contingencies, or both. The PCR amplicons of the V6 region of the 16S rRNA from 16 microbial assemblages were pyrosequenced, generating a total of 352 029 sequences; after quality filtering and processing, 257 260 sequences were clustered into 2871 normalized operational taxonomic units (OTU using a definition of 97% sequence identity. Community ecology statistical analyses demonstrate that the eastern Atlantic Ocean bacterial assemblages are vertically stratified and associated with water layers characterized by unique environmental signals (e.g., temperature, salinity, and nutrients. Genetic compositions of bacterial assemblages from the same water layer are more similar to each other than to assemblages from different water layers. The observed clustering of samples by water layer allows us to conclude that contemporary environments are influencing the observed biogeographic patterns. Moreover, the implementation of a novel Bayesian inference approach that allows a more efficient and explicit use of all the OTU abundance data shows a distance effect suggesting the influence of historical contingencies on the composition of bacterial

  4. Mammals of Australia's tropical savannas: a conceptual model of assemblage structure and regulatory factors in the Kimberley region.

    Directory of Open Access Journals (Sweden)

    Ian J Radford

    Full Text Available We construct a state-and-transition model for mammals in tropical savannas in northern Australia to synthesize ecological knowledge and understand mammalian declines. We aimed to validate the existence of alternative mammal assemblage states similar to those in arid Australian grasslands, and to speculate on transition triggers. Based on the arid grassland model, we hypothesized that assemblages are partitioned across rainfall gradients and between substrates. We also predicted that assemblages typical of arid regions in boom periods would be prevalent in savannas with higher and more regular rainfall. Data from eight mammal surveys from the Kimberley region, Western Australia (1994 to 2011 were collated. Survey sites were partitioned across rainfall zones and habitats. Data allowed us to identify three assemblage states: State 0:--low numbers of mammals, State II:--dominated by omnivorous rodents and State III:--dominated by rodents and larger marsupials. Unlike arid grasslands, assemblage dominance by insectivorous dasyurids (State I did not occur in savannas. Mammal assemblages were partitioned across rainfall zones and between substrates as predicted, but-unlike arid regions-were not related strongly to yearly rainfall. Mammal assemblage composition showed high regional stability, probably related to high annual rainfall and predictable wet season resource pulses. As a consequence, we speculate that perpetually booming assemblages in savannas allow top-down control of the ecosystem, with suppression of introduced cats by the dingo, the region's top predator. Under conditions of low or erratic productivity, imposed increasingly by intense fire regimes and introduced herbivore grazing, dingoes may not limit impacts of cats on native mammals. These interacting factors may explain contemporary declines of savanna mammals as well as historical declines in arid Australia. The cat-ecosystem productivity hypothesis raised here differs from the

  5. Mammals of Australia's Tropical Savannas: A Conceptual Model of Assemblage Structure and Regulatory Factors in the Kimberley Region

    Science.gov (United States)

    Radford, Ian J.; Dickman, Christopher R.; Start, Antony N.; Palmer, Carol; Carnes, Karin; Everitt, Corrin; Fairman, Richard; Graham, Gordon; Partridge, Thalie; Thomson, Allan

    2014-01-01

    We construct a state-and-transition model for mammals in tropical savannas in northern Australia to synthesize ecological knowledge and understand mammalian declines. We aimed to validate the existence of alternative mammal assemblage states similar to those in arid Australian grasslands, and to speculate on transition triggers. Based on the arid grassland model, we hypothesized that assemblages are partitioned across rainfall gradients and between substrates. We also predicted that assemblages typical of arid regions in boom periods would be prevalent in savannas with higher and more regular rainfall. Data from eight mammal surveys from the Kimberley region, Western Australia (1994 to 2011) were collated. Survey sites were partitioned across rainfall zones and habitats. Data allowed us to identify three assemblage states: State 0:- low numbers of mammals, State II:- dominated by omnivorous rodents and State III:- dominated by rodents and larger marsupials. Unlike arid grasslands, assemblage dominance by insectivorous dasyurids (State I) did not occur in savannas. Mammal assemblages were partitioned across rainfall zones and between substrates as predicted, but—unlike arid regions—were not related strongly to yearly rainfall. Mammal assemblage composition showed high regional stability, probably related to high annual rainfall and predictable wet season resource pulses. As a consequence, we speculate that perpetually booming assemblages in savannas allow top-down control of the ecosystem, with suppression of introduced cats by the dingo, the region's top predator. Under conditions of low or erratic productivity, imposed increasingly by intense fire regimes and introduced herbivore grazing, dingoes may not limit impacts of cats on native mammals. These interacting factors may explain contemporary declines of savanna mammals as well as historical declines in arid Australia. The cat-ecosystem productivity hypothesis raised here differs from the already

  6. Mammals of Australia's tropical savannas: a conceptual model of assemblage structure and regulatory factors in the Kimberley region.

    Science.gov (United States)

    Radford, Ian J; Dickman, Christopher R; Start, Antony N; Palmer, Carol; Carnes, Karin; Everitt, Corrin; Fairman, Richard; Graham, Gordon; Partridge, Thalie; Thomson, Allan

    2014-01-01

    We construct a state-and-transition model for mammals in tropical savannas in northern Australia to synthesize ecological knowledge and understand mammalian declines. We aimed to validate the existence of alternative mammal assemblage states similar to those in arid Australian grasslands, and to speculate on transition triggers. Based on the arid grassland model, we hypothesized that assemblages are partitioned across rainfall gradients and between substrates. We also predicted that assemblages typical of arid regions in boom periods would be prevalent in savannas with higher and more regular rainfall. Data from eight mammal surveys from the Kimberley region, Western Australia (1994 to 2011) were collated. Survey sites were partitioned across rainfall zones and habitats. Data allowed us to identify three assemblage states: State 0:--low numbers of mammals, State II:--dominated by omnivorous rodents and State III:--dominated by rodents and larger marsupials. Unlike arid grasslands, assemblage dominance by insectivorous dasyurids (State I) did not occur in savannas. Mammal assemblages were partitioned across rainfall zones and between substrates as predicted, but-unlike arid regions-were not related strongly to yearly rainfall. Mammal assemblage composition showed high regional stability, probably related to high annual rainfall and predictable wet season resource pulses. As a consequence, we speculate that perpetually booming assemblages in savannas allow top-down control of the ecosystem, with suppression of introduced cats by the dingo, the region's top predator. Under conditions of low or erratic productivity, imposed increasingly by intense fire regimes and introduced herbivore grazing, dingoes may not limit impacts of cats on native mammals. These interacting factors may explain contemporary declines of savanna mammals as well as historical declines in arid Australia. The cat-ecosystem productivity hypothesis raised here differs from the already-articulated cat

  7. Habitat Specialization in Tropical Continental Shelf Demersal Fish Assemblages

    OpenAIRE

    Ben M Fitzpatrick; Euan S Harvey; Heyward, Andrew J.; Twiggs, Emily J.; Jamie Colquhoun

    2012-01-01

    The implications of shallow water impacts such as fishing and climate change on fish assemblages are generally considered in isolation from the distribution and abundance of these fish assemblages in adjacent deeper waters. We investigate the abundance and length of demersal fish assemblages across a section of tropical continental shelf at Ningaloo Reef, Western Australia, to identify fish and fish habitat relationships across steep gradients in depth and in different benthic habitat types. ...

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

    Science.gov (United States)

    Thiele, Ines; Fleming, Ronan M T; Que, Richard; Bordbar, Aarash; Diep, Dinh; Palsson, Bernhard O

    2012-01-01

    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.

  9. 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.

  10. Techniques de formage et d'assemblage

    CERN Document Server

    Favre, G; CERN. Geneva. TS Department

    2004-01-01

    Les sections Techniques d'Assemblage du groupe EST/MF et Brasage du groupe EST/SM ont été groupées en un seul service dans un but de rationalisation accrue des ressources et méthodes. Ce service dispose de nombreux moyens : soudure et découpe LASER (YAG, 350 W), soudure par faisceau d'électrons (deux installations, 35 et 7.5 kW), équipements TIG orbital, jet line, MIG, soudure plasma, boîte à gants, portique de soudage trois axes multiprocédés, presses plieuses, rouleuses, moyens de repoussage, alimentation à induction 12 kW et divers fours sous vide et à air. Le service est composé de 17 personnes dont la polyvalence est encouragée. Les activités de la section seront décrites à travers quelques exemples significatifs récents, notamment : l'assemblage des amenées de courant HTS, la réalisation des chambres LSS, des tubes HET, d'enveloppes céramiques pour détecteurs PET-HPD, le brasage de RFQ, la soudure du Barrel d'ATLAS ou encore le soudage des lignes de thermalisation du toroïde d'AT...

  11. 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.

  12. Quantifying fish assemblages in large, offshore marine protected areas: an Australian case study.

    Directory of Open Access Journals (Sweden)

    Nicole A Hill

    Full Text Available As the number of marine protected areas (MPAs increases globally, so does the need to assess if MPAs are meeting their management goals. Integral to this assessment is usually a long-term biological monitoring program, which can be difficult to develop for large and remote areas that have little available fine-scale habitat and biological data. This is the situation for many MPAs within the newly declared Australian Commonwealth Marine Reserve (CMR network which covers approximately 3.1 million km2 of continental shelf, slope, and abyssal habitat, much of which is remote and difficult to access. A detailed inventory of the species, types of assemblages present and their spatial distribution within individual MPAs is required prior to developing monitoring programs to measure the impact of management strategies. Here we use a spatially-balanced survey design and non-extractive baited video observations to quantitatively document the fish assemblages within the continental shelf area (a multiple use zone, IUCN VI of the Flinders Marine Reserve, within the Southeast marine region. We identified distinct demersal fish assemblages, quantified assemblage relationships with environmental gradients (primarily depth and habitat type, and described their spatial distribution across a variety of reef and sediment habitats. Baited videos recorded a range of species from multiple trophic levels, including species of commercial and recreational interest. The majority of species, whilst found commonly along the southern or south-eastern coasts of Australia, are endemic to Australia, highlighting the global significance of this region. Species richness was greater on habitats containing some reef and declined with increasing depth. The trophic breath of species in assemblages was also greater in shallow waters. We discuss the utility of our approach for establishing inventories when little prior knowledge is available and how such an approach may inform future

  13. Prevalence of Giardia duodenalis assemblages and sub-assemblages in symptomatic patients from Damascus city and its suburbs.

    Science.gov (United States)

    Skhal, Dania; Aboualchamat, Ghalia; Al Mariri, Ayman; Al Nahhas, Samar

    2017-01-01

    Giardia duodenalis is one of the most important human enteric parasites worldwide and is endemic throughout the world with a vast range of mammalian hosts. However, there is limited information on the prevalent genetic variability of G. duodenalis in Syria. This study aimed to evaluate the predominance of G. duodenalis assemblages/sub-assemblages causing humans infection in the city of Damascus and its suburbs. 40 symptomatic giardiasis patients were recruited in this study. Fecal samples were genotyped using PCR/RFLP assay targeting the β-giardin and glutamate dehydrogenase (gdh) genes. HaeIII, BspL1 and RsaI restriction enzymes were used to differentiate between G. duodenalis assemblages/sub-assemblages. Our data showed that 65% of isolates were of assemblage A; 45% belonged to sub-assemblage AII and 20% to sub-assemblage AI. Assemblage B was detected in 27.5% of isolates; 12.5% fit in sub-assemblage BIV, 5% fit in sub-assemblage BIII and 10.5% fit in Discordant genotype BIII/BIV. Mixed genotypes (AII+BIII and AI+BIV) were identified in 3 isolates (7.5%). Significant correlation was found between Giardia AII sub-assemblage and weight loss symptom (P-value=0.05) as well as between contact with domestic animals (cats, P-value=0.027). Moreover, a significant correlation was found between sub-assemblage AI and livestock breeding (P-value=0.000). In conclusion genotyping of human Giardia duodenalis isolates suggests anthroponotic transmission for the route of infection in Damascus and its suburbs. Further studies are needed to screen a wide geographic areas in Syria and to estimate the prevalence of G. duodenalis infection in our population.

  14. Morphological assembly mechanisms in Neotropical bat assemblages and ensembles within a landscape.

    Science.gov (United States)

    Moreno, Claudia E; Arita, Héctor T; Solis, Leonor

    2006-08-01

    Empirical studies on bat assemblages have shown that richness is not appreciably influenced by local processes such as ecological interactions. However, most of these studies have been done in large areas that include high heterogeneity, and they analyse all bat species within such areas, and thus they may be not reflecting local but supra-community conditions. We followed an ecomorphological approach to assess how bat assemblages of species from the families Phyllostomidae and Mormoopidae, and ensembles of frugivorous bats, are assembled in local habitats within a single landscape. We measured the volume of the space defined by wing morphology and quantified the average distance between species within such a volume. Then, we related these measures to local richness. Such relationships were contrasted against relationships with random assemblages to test for statistical differences. At the ensemble level of organization, we found that the frugivorous bat morphological assembly mechanism is different from random patterns, and it corresponds to the volume-increasing model. On the other hand, bat assembly mechanisms may be ubiquitous at the assemblage level, because groups of species coexisting in a local habitat and delimited only by phylogeny include more than one ecological group with no potential to interact. Assembling processes are crucial to an understanding of species diversity in local communities, and ecomorphological analyses are very promising tools that may help in their study.

  15. Temporal trends in algae, benthic invertebrate, and fish assemblages in streams and rivers draining basins of varying land use in the south-central United States, 1993-2007

    Science.gov (United States)

    Miller, Matthew P.; Kennen, Jonathan G.; Mabe, Jeffrey A.; Mize, Scott V.

    2012-01-01

    Site-specific temporal trends in algae, benthic invertebrate, and fish assemblages were investigated in 15 streams and rivers draining basins of varying land use in the south-central United States from 1993–2007. A multivariate approach was used to identify sites with statistically significant trends in aquatic assemblages which were then tested for correlations with assemblage metrics and abiotic environmental variables (climate, water quality, streamflow, and physical habitat). Significant temporal trends in one or more of the aquatic assemblages were identified at more than half (eight of 15) of the streams in the study. Assemblage metrics and abiotic environmental variables found to be significantly correlated with aquatic assemblages differed between land use categories. For example, algal assemblages at undeveloped sites were associated with physical habitat, while algal assemblages at more anthropogenically altered sites (agricultural and urban) were associated with nutrient and streamflow metrics. In urban stream sites results indicate that streamflow metrics may act as important controls on water quality conditions, as represented by aquatic assemblage metrics. The site-specific identification of biotic trends and abiotic–biotic relations presented here will provide valuable information that can inform interpretation of continued monitoring data and the design of future studies. In addition, the subsets of abiotic variables identified as potentially important drivers of change in aquatic assemblages provide policy makers and resource managers with information that will assist in the design and implementation of monitoring programs aimed at the protection of aquatic resources.

  16. Seasonal variability of morphospaces in a subtropical fish assemblage

    Directory of Open Access Journals (Sweden)

    Carolina Correia Siliprandi

    2015-11-01

    Full Text Available Morphological characters of fishes are essential to evaluate the functional structure of assemblages, being morphological differences indicative of distinct ecological and adaptive strategies. The ecomorphology using morphospaces analyzes the structure of a fish assemblage through the values of intervals between homologous points positioned in anatomical structures of organisms phylogenetically related. These intervals can be quantified by morphogeometric and multivariate analyses. Seasonally during 2013-2014, standardized images were obtained from fishes sampled in Araça Bay, São Sebastião District, Brazil, using nine fishing gears which were grouped to verify the species occurrence variation. Qualitative approach (presence/absence data was used to carry out morphological analyses. A total of 27 landmarks and semilandmarks with anatomical, ecological and taxonomical meaning were positioned in species images of the left profile. Consensus figures were made embedding the intraspecific variability. Uniform components of the shape variation (RWs were generated. To build morphospaces, the first eight RWs were considered (explain more than 95% of the total morphological variability and were defined using Convex Hull. The RWs were also used to calculate the Morphological Richness (MR, Morphological Disparity (MD and Morphogeometric Index (EMI. The MD indicates the morphospace size and showed greater values in summer (0.051 and winter (0.047 as MR, related to the higher number of species (MRsummer=7.93; MRwinter=8.65. During all the year, the Araça Bay presents high diversity of fishes. Nevertheless, winter and summer seasons reached the highest diversity, periods when horizontal mobile fishes with elongated shapes arrive to the region, implying an increase of morphological diversity and shape’s redundancy (represented by the lowest values of EMI: winter=0.120; summer=0.123.

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

    CERN Document Server

    Mitchell, E P

    2001-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-07-01

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

  19. 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.

  20. Influence of protein crowder size on hydration structure and dynamics in macromolecular crowding

    Science.gov (United States)

    Wang, Po-hung; Yu, Isseki; Feig, Michael; Sugita, Yuji

    2017-03-01

    We investigate the effects of protein crowder sizes on hydration structure and dynamics in macromolecular crowded systems by all-atom MD simulations. The crowded systems consisting of only small proteins showed larger total surface areas than those of large proteins at the same volume fractions. As a result, more water molecules were trapped within the hydration shells, slowing down water diffusion. The simulation results suggest that the protein crowder size is another factor to determine the effect of macromolecular crowding and to explain the experimental kinetic data of proteins and DNAs in the presence of crowding agents.

  1. 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.

  2. Genetic exchange within and between assemblages of Giardia duodenalis.

    Science.gov (United States)

    Lasek-Nesselquist, Erica; Welch, David Mark; Thompson, Richard Christopher Andrew; Steuart, Robert F; Sogin, Mitchell L

    2009-01-01

    Meiotic sex evolved early in the history of eukaryotes. Giardia duodenalis (syn. Giardia lamblia, Giardia intestinalis), a parasitic protist belonging to an early diverging lineage of eukaryotes, shows no cytological or physiological evidence of meiotic or sexual processes. Recent molecular analyses challenge the idea that G. duodenalis is a strictly clonal organism by providing evidence of recombination between homologous chromosomes within one subgroup (Assemblage A) of this species as well as genetic transfer from one subgroup to another (Assemblage A-B). Because recombination is not well documented and because it is not known whether the observed inter-assemblage transfer represents true reciprocal genetic exchange or a non-sexual process, we analyzed genic sequences from all major subgroups (Assemblages A-G) of this species. For all assemblages, we detected molecular signatures consistent with meiotic sex or genetic exchange, including low levels of heterozygosity, as indicated by allelic sequence divergence within isolates, and intra- and inter-assemblage recombination. The identification of recombination between assemblages suggests a shared gene pool and calls into question whether it is appropriate to divide the genetically distinct assemblages of G. duodenalis into a species complex.

  3. RNA assemblages orchestrate complex cellular processes

    DEFF Research Database (Denmark)

    Nielsen, Finn Cilius; Hansen, Heidi Theil; Christiansen, Jan

    2016-01-01

    Eukaryotic mRNAs are monocistronic, and therefore mechanisms exist that coordinate the synthesis of multiprotein complexes in order to obtain proper stoichiometry at the appropriate intracellular locations. RNA-binding proteins containing low-complexity sequences are prone to generate liquid...... droplets via liquid-liquid phase separation, and in this way create cytoplasmic assemblages of functionally related mRNAs. In a recent iCLIP study, we showed that the Drosophila RNA-binding protein Imp, which exhibits a C-terminal low-complexity sequence, increases the formation of F-actin by binding to 3......' untranslated regions of mRNAs encoding components participating in F-actin biogenesis. We hypothesize that phase transition is a mechanism the cell employs to increase the local mRNA concentration considerably, and in this way synchronize protein production in cytoplasmic territories, as discussed...

  4. 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

  5. Phylogenetic and functional diversity in large carnivore assemblages.

    Science.gov (United States)

    Dalerum, F

    2013-06-07

    Large terrestrial carnivores are important ecological components and prominent flagship species, but are often extinction prone owing to a combination of biological traits and high levels of human persecution. This study combines phylogenetic and functional diversity evaluations of global and continental large carnivore assemblages to provide a framework for conservation prioritization both between and within assemblages. Species-rich assemblages of large carnivores simultaneously had high phylogenetic and functional diversity, but species contributions to phylogenetic and functional diversity components were not positively correlated. The results further provide ecological justification for the largest carnivore species as a focus for conservation action, and suggests that range contraction is a likely cause of diminishing carnivore ecosystem function. This study highlights that preserving species-rich carnivore assemblages will capture both high phylogenetic and functional diversity, but that prioritizing species within assemblages will involve trade-offs between optimizing contemporary ecosystem function versus the evolutionary potential for future ecosystem performance.

  6. Meiofaunal assemblages associated with native and non-indigenous macroalgae

    Science.gov (United States)

    Veiga, Puri; Sousa-Pinto, Isabel; Rubal, Marcos

    2016-07-01

    Meiofauna is a useful tool to detect effects of different disturbances; however, its relevance in the frame of biological invasions has been almost fully neglected. Meiofaunal assemblages associated with the invasive macroalga Sargassum muticum were studied and compared with those associated with two native macroalgae (Bifurcaria bifurcata and Chondrus crispus). We used a linear mixed model to determine the influence of habitat size (i.e. macroalgal biomass) in shaping meiofaunal assemblages. Results showed that habitat size (i.e. macroalgal biomass) shaped meiofaunal assemblages influencing its abundance, richness and structure. However, the identity of macroalga (i.e. species) appears also to play a significant role, particularly the differences of complexity among the studied species may shape their meiofaunal assemblages. Finally, the invasive macroalga appears to influence positively species richness. Our results highlight the need of including different faunal components to achieve a comprehensive knowledge on effects of invasive macroalgae and that meiofaunal assemblages may be a valuable tool to examine them.

  7. 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

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

    DEFF Research Database (Denmark)

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

    2017-01-01

    Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many...

  9. Isolation and chemical characterization of resistant macromolecular constituents in microalgae and marine sediments

    NARCIS (Netherlands)

    Gelin, F.

    1996-01-01

    The recognition of novel, insoluble and non-hydrolysable macromolecular constituents in protective tissues of fresh-water algae and higher plants has had a major impact on our understanding of the origin and fate of sedimentary organic matter (OM) in terrestrial and lacustrine deposits. The investig

  10. Researches, Publications and Achievements 2007-2011, Department of Macromolecular Science and Engineering

    OpenAIRE

    All teaching staffs at Department of Macromolecular Science and Engineering (19 members)

    2012-01-01

    Recent researches, publications and achievements are presented, which were made during these five years (2007-2011) by 19 members at Department of Macromolecular Science and Engineering. Listed publications include original papers, books, reviews and reports. Achievements such as invited lectures, patents, funds and financial supports, and awards are also listed.

  11. Synergy of DNA-bending nucleoid proteins and macromolecular crowd-condensing DNA

    NARCIS (Netherlands)

    Bessa Ramos, E.; Wintraecken, C.H.J.M.; Geerling, A.C.M.; Vries, de R.J.

    2007-01-01

    Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that

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

    Directory of Open Access Journals (Sweden)

    Kunst, B.

    2008-07-01

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

  13. Hydropyrolysis: A new technique for the analysis of macromolecular material in meteorites

    Science.gov (United States)

    Sephton, Mark A.; Love, Gordon D.; Meredith, Will; Snape, Colin E.; Sun, Cheng-Gong; Watson, Jonathan S.

    2005-10-01

    The carbonaceous chondrite meteorites are fragments of asteroids that have remained relatively unprocessed since the formation of the Solar System 4.56 billion years ago. The major organic component in these meteorites is a macromolecular phase that is resistant to solvent extraction. The information contained within macromolecular material can be accessed by degradative techniques such as pyrolysis. Hydropyrolysis refers to pyrolysis assisted by high hydrogen gas pressures and a dispersed sulphided molybdenum catalyst. Hydropyrolysis of the Murchison macromolecular material successfully releases much greater quantities of hydrocarbons than traditional pyrolysis techniques (twofold greater than hydrous pyrolysis) including significant amounts of high molecular weight polyaromatic hydrocarbons (PAH) such as phenanthrene, carbazole, fluoranthene, pyrene, chrysene, perylene, benzoperylene and coronene units with varying degrees of alkylation. When hydropyrolysis products are collected using a silica trap immersed in liquid nitrogen, the technique enables the solubilisation and retention of compounds with a wide range of volatilities (i.e. benzene to coronene). This report describes the hydropyrolysis method and the information it can provide about meteorite macromolecular material constitution.

  14. Can global weed assemblages be used to predict future weeds?

    Directory of Open Access Journals (Sweden)

    Louise Morin

    Full Text Available Predicting which plant taxa are more likely to become weeds in a region presents significant challenges to both researchers and government agencies. Often it is done in a qualitative or semi-quantitative way. In this study, we explored the potential of using the quantitative self-organising map (SOM approach to analyse global weed assemblages and estimate likelihoods of plant taxa becoming weeds before and after they have been moved to a new region. The SOM approach examines plant taxa associations by analysing where a taxon is recorded as a weed and what other taxa are recorded as weeds in those regions. The dataset analysed was extracted from a pre-existing, extensive worldwide database of plant taxa recorded as weeds or other related status and, following reformatting, included 187 regions and 6690 plant taxa. To assess the value of the SOM approach we selected Australia as a case study. We found that the key and most important limitation in using such analytical approach lies with the dataset used. The classification of a taxon as a weed in the literature is not often based on actual data that document the economic, environmental and/or social impact of the taxon, but mostly based on human perceptions that the taxon is troublesome or simply not wanted in a particular situation. The adoption of consistent and objective criteria that incorporate a standardized approach for impact assessment of plant taxa will be necessary to develop a new global database suitable to make predictions regarding weediness using methods like SOM. It may however, be more realistic to opt for a classification system that focuses on the invasive characteristics of plant taxa without any inference to impacts, which to be defined would require some level of research to avoid bias from human perceptions and value systems.

  15. Can Global Weed Assemblages Be Used to Predict Future Weeds?

    Science.gov (United States)

    Morin, Louise; Paini, Dean R.; Randall, Roderick P.

    2013-01-01

    Predicting which plant taxa are more likely to become weeds in a region presents significant challenges to both researchers and government agencies. Often it is done in a qualitative or semi-quantitative way. In this study, we explored the potential of using the quantitative self-organising map (SOM) approach to analyse global weed assemblages and estimate likelihoods of plant taxa becoming weeds before and after they have been moved to a new region. The SOM approach examines plant taxa associations by analysing where a taxon is recorded as a weed and what other taxa are recorded as weeds in those regions. The dataset analysed was extracted from a pre-existing, extensive worldwide database of plant taxa recorded as weeds or other related status and, following reformatting, included 187 regions and 6690 plant taxa. To assess the value of the SOM approach we selected Australia as a case study. We found that the key and most important limitation in using such analytical approach lies with the dataset used. The classification of a taxon as a weed in the literature is not often based on actual data that document the economic, environmental and/or social impact of the taxon, but mostly based on human perceptions that the taxon is troublesome or simply not wanted in a particular situation. The adoption of consistent and objective criteria that incorporate a standardized approach for impact assessment of plant taxa will be necessary to develop a new global database suitable to make predictions regarding weediness using methods like SOM. It may however, be more realistic to opt for a classification system that focuses on the invasive characteristics of plant taxa without any inference to impacts, which to be defined would require some level of research to avoid bias from human perceptions and value systems. PMID:23393591

  16. Faunal Assemblage Structure Suggests a Limited Impact of the Introduction of Domestic Stock on Later Stone Age Subsistence Economies in South Africa

    OpenAIRE

    Dusseldorp, G.L

    2016-01-01

    Livestock remains appear in the South African archaeological record around 2100 years ago. However, the economic importance of domestic animals in Later Stone Age subsistence is debated. This paper adopts an approach rooted in Optimal Foraging Theory to examine if the introduction of livestock is reflected in changing taxonomic diversity of faunal assemblages. Based on the analysis of a database of 300+ faunal assemblages, it is concluded that the economic importance of livestock during the f...

  17. No correlation between the diversity and productivity of assemblages: evidence from the phytophage and predator assemblages in various cotton agroecosystems.

    Science.gov (United States)

    Gao, Feng; Men, XingYuan; Ge, Feng

    2014-09-01

    Biodiversity research has shown that primary productivity increases with plant species number, especially in many experimental grassland systems. Here, we assessed the correlation between productivity and diversity of phytophages and natural enemy assemblages associated with planting date and intercropping in four cotton agroecosystems. Twenty-one pairs of data were used to determine Pearson correlations between species richness, total number of individuals, diversity indices and productivity for each assemblage every five days from 5 June to 15 September 2012. At the same trophic level, the productivity exhibited a significant positive correlation with species richness of the phytophage or predator assemblage. A significant correlation was found between productivity and total number of individuals in most cotton fields. However, no significant correlations were observed between productivity and diversity indices (including indices of energy flow diversity and numerical diversity) in most cotton fields for either the phytophage or the predator assemblages. Species richness of phytophage assemblage and total individual numbers were significantly correlated with primary productivity. Also, species richness of natural enemy assemblage and total number of individuals correlated with phytophage assemblage productivity. A negative but not significant correlation occurred between the indices of numerical diversity and energy flow diversity and lower trophic-level productivity in the cotton-phytophage and phytophage-predator assemblages for most intercropped cotton agroecosystems. Our results clearly showed that there were no correlations between diversity indices and productivity within the same or lower trophic levels within the phytophage and predator assemblages in cotton agroecosystems, and inter-cropped cotton fields had a stronger ability to support the natural enemy assemblage and potentially to reduce phytophages.

  18. Depth and medium-scale spatial processes influence fish assemblage structure of unconsolidated habitats in a subtropical marine park.

    Directory of Open Access Journals (Sweden)

    Arthur L Schultz

    Full Text Available Where biological datasets are spatially limited, abiotic surrogates have been advocated to inform objective planning for Marine Protected Areas. However, this approach assumes close correlation between abiotic and biotic patterns. The Solitary Islands Marine Park, northern NSW, Australia, currently uses a habitat classification system (HCS to assist with planning, but this is based only on data for reefs. We used Baited Remote Underwater Videos (BRUVs to survey fish assemblages of unconsolidated substrata at different depths, distances from shore, and across an along-shore spatial scale of 10 s of km (2 transects to examine how well the HCS works for this dominant habitat. We used multivariate regression modelling to examine the importance of these, and other environmental factors (backscatter intensity, fine-scale bathymetric variation and rugosity, in structuring fish assemblages. There were significant differences in fish assemblages across depths, distance from shore, and over the medium spatial scale of the study: together, these factors generated the optimum model in multivariate regression. However, marginal tests suggested that backscatter intensity, which itself is a surrogate for sediment type and hardness, might also influence fish assemblages and needs further investigation. Species richness was significantly different across all factors: however, total MaxN only differed significantly between locations. This study demonstrates that the pre-existing abiotic HCS only partially represents the range of fish assemblages of unconsolidated habitats in the region.

  19. 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.

  20. Faceless sex: glory holes and sexual assemblages.

    Science.gov (United States)

    Holmes, Dave; O'Byrne, Patrick; Murray, Stuart J

    2010-10-01

    According to our previous research, the use of glory holes in public venues such as saunas and bathhouses is very popular. The popularity of glory holes is due in part to the anonymous sex that these architectural elements allow. This post-structuralist theoretical reflection seeks to understand the specific nature of anonymous public sex among bathhouse patrons, focusing on the links between desire-architecture-place-sexual practices. Drawing on interviews with glory hole users gathered during an ethnographic research project in bathhouses, this essay goes beyond traditional public health discourse to offer an original perspective on anonymous public sex. Utilizing the philosophy of Deleuze and Guattari's concepts of assemblages and machines, we re-theorize glory hole sex--what we call 'faceless sex'--and rethink the ways that desire is imbricated with our understanding of architecture, place, and public. Finally, we reflect upon the particular ethical challenges that are posed by these particular sexual practices, and ask whether a post-structuralist ethic might be possible.

  1. Climatic influence on a marine fish assemblage.

    Science.gov (United States)

    Attrill, Martin J; Power, Michael

    2002-05-16

    Understanding the fluctuations in marine fish stocks is important for the management of fisheries, and attempts have been made to demonstrate links with oceanographic and climatic variability, including the North Atlantic Oscillation (NAO). The NAO has been correlated with a range of long-term ecological measures, including certain fish stocks. Such environmental influences are most likely to affect susceptible juveniles during estuarine residency, as estuaries are critical juvenile nursery or over-wintering habitats. Here we show that, during a 16-year period, climatic forcing (by means of the NAO) is consistently the most important parameter explaining variation in assemblage composition, abundance and growth of juvenile marine fish during estuarine residency. A possible mechanism for the effect of the NAO is a temperature differential between estuarine and marine waters that allows fish to facultatively exploit optimal thermal habitats. The connection has potentially important implications for the size and numbers of individuals recruited to the fishery, for understanding and predicting the composition of juvenile fish stocks using estuaries, and for the appropriate conservation of estuarine systems in relation to fish stocks.

  2. Coralligenous habitat: patterns of vertical distribution of macroalgal assemblages

    Directory of Open Access Journals (Sweden)

    Luigi Piazzi

    2011-06-01

    Full Text Available The present study investigates patterns of distribution of macroalgal coralligenous assemblages in relation to depth and evaluates the role of different environmental conditions on these patterns. Two depths (30 and 40 m were investigated off small islands and off continental coasts in order to select two different environmental conditions. Results showed differences between depths in the structure of assemblages around islands, while along the continental coasts these patterns were not evident. Moreover, differences between assemblages related to different environmental conditions were more evident in the shallower zone of distribution of the coralligenous habitat. This correlative study did not allow us to identify any cause-effect relationship, but patterns we detected agree with those of other studies, suggesting that alterations in the environmental conditions may be the cause of the decrease in differences among assemblages developing at different depths and may lead to a higher spatial homogenization and an impoverishment of the whole subtidal system.

  3. Large River Monitoring Forum Fish Assemblage Database 2016

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — The Large River Monitoring Forum compiled fish assemblage data for five large rivers in the U.S. as a part of a coordinated effort to compare and contract river...

  4. Global assemblages and structural models of International Relations

    DEFF Research Database (Denmark)

    Corry, Olaf

    2014-01-01

    Rather than consigning assemblages to the micro-politics of international relations, the chapter argues that assemblages can also be seen to play a role in the ‘grand’ structures of international relations. Structural IR theory normally only considers how subjects are ordered – hierarchically......, anarchically, in core-periphery relations or in terms of networks. However, not only subjects but also assemblages – the bringing together of previously unconnected elements into novel constellations – play a critical role in structuring international relations. More specifically, one sub......-category of assemblages – those constructed as malleable and governable which I call ‘governance-objects’ – is central to structure in international relations. The chapter begins with standard definitions of what structures are – patterns of interaction between elements – and briefly covers the range of models currently...

  5. Solidification in a Supercomputer: From Crystal Nuclei to Dendrite Assemblages

    Science.gov (United States)

    Shibuta, Yasushi; Ohno, Munekazu; Takaki, Tomohiro

    2015-08-01

    Thanks to the recent progress in high-performance computational environments, the range of applications of computational metallurgy is expanding rapidly. In this paper, cutting-edge simulations of solidification from atomic to microstructural levels performed on a graphics processing unit (GPU) architecture are introduced with a brief introduction to advances in computational studies on solidification. In particular, million-atom molecular dynamics simulations captured the spontaneous evolution of anisotropy in a solid nucleus in an undercooled melt and homogeneous nucleation without any inducing factor, which is followed by grain growth. At the microstructural level, the quantitative phase-field model has been gaining importance as a powerful tool for predicting solidification microstructures. In this paper, the convergence behavior of simulation results obtained with this model is discussed, in detail. Such convergence ensures the reliability of results of phase-field simulations. Using the quantitative phase-field model, the competitive growth of dendrite assemblages during the directional solidification of a binary alloy bicrystal at the millimeter scale is examined by performing two- and three-dimensional large-scale simulations by multi-GPU computation on the supercomputer, TSUBAME2.5. This cutting-edge approach using a GPU supercomputer is opening a new phase in computational metallurgy.

  6. Local and regional rarity in a diverse tropical fish assemblage.

    Science.gov (United States)

    Hercos, A P; Sobansky, M; Queiroz, H L; Magurran, A E

    2013-01-22

    Because most species in an ecological assemblage are rare, much of the species richness we value is due to taxa with few individuals or a restricted distribution. It has been apparent since the time of ecological pioneers such as Bates and Darwin that tropical systems have disproportionately large numbers of rare species, yet the distribution and abundance patterns of these species remain largely unknown. Here, we examine the diversity of freshwater fish in a series of lakes in the Amazonian várzea, and relate relative abundance, both as numbers of individuals and as biomass, to the occurrence of species in space and time. We find a bimodal relationship of occurrence that distinguishes temporally and spatially persistent species from those that are infrequent in both space and time. Logistic regression reveals that information on occurrence helps distinguish those species that are rare in this locality but abundant elsewhere, from those that are rare throughout the region. These results form a link between different approaches used to evaluate commonness and rarity. In doing so, they provide a tool for identifying species of high conservation priority in poorly documented but species rich localities.

  7. Benthic foraminiferal assemblages help to understand carbonate mound evolution

    Science.gov (United States)

    Rüggeberg, A.; Dorschel, B.; Dullo, C.; Hebbeln, D.; Freiwald, A.

    2003-04-01

    On- and off-mound sediment cores from Propeller Mound (Porcupine Seabight) were analysed for their benthic foraminiferal assemblages. Benthic foraminifera from the off-mound position show three different assemblages describing the Holocene, Oxygen Isotope Stage (OIS) 2 and late OIS 3. The Holocene assemblage is dominated by Uvigerina mediterranea, Trifarina angulosa, Melonis barleeanum, Hyalinea balthica, Bulimina marginata. These species are related to a higher supply of organic material. The glacial assemblage shows high abundances of Cassidulina teretis, C. reniforme, Globocassidulina subglobosa, and Cibicidoides kullenbergi, implying cold bottom waters and a reduced productivity. The lower part of late OIS 3 is dominated by Elphidium excavatum, which is displaced continuously by very high abundances of C. teretis towards the transition of OIS3/2. E. excavatum, a shallow shelf species generally reported from above 200 m water depth, and high amounts of sediment supplied to the core site points to shelf erosion related to sea level lowering (approx. 50 m). Towards OIS 2 the system returns to normal background sedimentation pattern. We transferred the established off-mound assemblages onto the on-mound core, in which the sediment sequence is incomplete characterised by numerous hiatuses. The Holocene assemblage describes almost the complete core with relative abundances of >20%, interrupted only by three sections with slightly higher amounts of the glacial assemblage, which are not comparable to abundances of >70% of the glacial assemblage found in the off-mound core. These results are in conjunction with stable oxygen isotope data indicating only interstadial values, assuming peak glacial and interglacial sediments to be removed from the mound. Another assemblage described for the on-mound core is dominated by Discanomalina coronata, Gavelinopsis translucens, Planulina ariminensis, Cibicides lobatulus and to a lower degree by Hyrrokkin sarcophaga. These species

  8. Quantifying Assemblage Turnover and Species Contributions at Ecologic Boundaries

    OpenAIRE

    Hayek,Lee-Ann C.; Brent Wilson

    2013-01-01

    Not all boundaries, whether stratigraphical or geographical, are marked by species-level changes in community composition. For example, paleodata for some sites do not show readily discernible glacial-interglacial contrasts. Rather, the proportional abundances of species can vary subtly between glacials and interglacials. This paper presents a simple quantitative measure of assemblage turnover (assemblage turnover index, ATI) that uses changes in species' proportional abundances to identify i...

  9. Copepod assemblages in a highly complex hydrographic region

    Science.gov (United States)

    Berasategui, A. D.; Menu Marque, S.; Gómez-Erache, M.; Ramírez, F. C.; Mianzan, H. W.; Acha, E. M.

    2006-02-01

    Community structure and diversity patterns of planktonic copepods were investigated for the Southwestern Atlantic Ocean between 34 and 41°S. Our objectives were (1) to define copepod assemblages, (2) to accurately identify their association to different water masses/hydrodynamic regimes, (3) to characterize the assemblages in terms of their community structure, and (4) to test if frontal boundaries between water masses separate copepod assemblages. Biogeographic patterns were investigated using multivariate analysis (cluster and ANOSIM analyses). Biodiversity patterns were examined using different univariate indexes (point species richness and taxonomic distinctness). Five regions of similar copepod assemblages were defined for our study area each one corresponding to different environments (freshwater, estuarine, continental shelf, Malvinas and Brazil current assemblages). These assemblages have major community structure differences. In spite of the complex oceanographic scenario of our study area, that can lead us to expect a pattern of copepod communities with diffuse boundaries, we found a strong spatial correspondence between these limits and the presence of permanent frontal structures.

  10. DETECTION AND COMPARISON OF GIARDIAVIRUS (GLV) FROM DIFFERENT ASSEMBLAGES OF GIARDIA DUODENALIS

    Science.gov (United States)

    Five assemblages of Giardia were identified from cysts in cattle, dog, cat, sheep, and reindeer feces using ribosomal DNA (rDNA) sequencing. Assemblage A was present in cattle and reindeer feces, Assemblages C and D were present in dog feces, Assemblage E was present in cattle and sheep feces, and ...

  11. The Miocene carnivore assemblage of Greece

    Directory of Open Access Journals (Sweden)

    Koufos, G. D.

    2011-12-01

    Full Text Available The Miocene carnivore assemblage of Greece includes a great number of taxa, described in numerous articles since the first decades of the 19th Century. The present article is a revision of all these taxa, providing information about their history, localities, age, as well as their stratigraphic distribution and palaeoenvironment. The Early/Middle Miocene carnivore record of Greece is poor as the available fossiliferous sites and material are rare. However, the Late Miocene one is quite rich, including numerous taxa. The Miocene localities with carnivores and their age are given in a stratigraphic table covering the European Mammal zones from MN 4 to MN 13. The type locality, holotype, and some historical and morphological remarks are given for each taxon. Several carnivore taxa were erected from Greek material and new photos of their holotypes are given. The stratigraphic distribution of the Greek carnivore taxa indicates that they are covering the time span from ~19.0-5.3Ma. The majority of the Miocene taxa (Adcrocuta, Hyaenictitherium, Plioviverrops, Protictitherium, Ictitherium, Indarctos, Dinocrocuta, Promephitis disappeared at the end of Miocene. The composition of the Early/Middle Miocene carnivore assemblage of Greece includes mainly viverrids (Lophocyon, Euboictis, while the hyaenids, percrocutids, felids and mustelids are very few. On the contrary the Late Miocene assemblage is richer, including more subfamilies and species; the hyaenids and mustelids dominate, while the viverrids are absent. The Late Miocene carnivore guild structure is similar to that of the modern Serengeti, indicating a relatively open, savannah-like environment.

    La asociación de carnívoros miocenos de Grecia incluye un gran número de taxones, descritos en numerosos artículos desde las primeras décadas del siglo XIX. El presente artículo supone un esfuerzo de síntesis de todos estos taxones, suministrando información sobre su

  12. Advances in electron microscopy: A qualitative view of instrumentation development for macromolecular imaging and tomography.

    Science.gov (United States)

    Schröder, Rasmus R

    2015-09-01

    Macromolecular imaging and tomography of ice embedded samples has developed into a mature imaging technology, in structural biology today widely referred to simply as cryo electron microscopy.(1) While the pioneers of the technique struggled with ill-suited instruments, state-of-the-art cryo microscopes are now readily available and an increasing number of groups are producing excellent high-resolution structural data of macromolecular complexes, of cellular organelles, or the morphology of whole cells. Instrumentation developers, however, are offering yet more novel electron optical devices, such as energy filters and monochromators, aberration correctors or physical phase plates. Here we discuss how current instrumentation has already changed cryo EM, and how newly available instrumentation - often developed in other fields of electron microscopy - may further develop the use and applicability of cryo EM to the imaging of single isolated macromolecules of smaller size or molecules embedded in a crowded cellular environment.

  13. 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.

  14. Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptive effect

    Energy Technology Data Exchange (ETDEWEB)

    Zimmerman, S.B.; Harrison, B.

    1987-05-01

    Macromolecular crowding extends the range of ionic conditions supporting high DNA polymerase reaction rates. Reactions tested were nick translation and gap-filling by DNA polymerase I of E. coli, nuclease and polymerase activities of the large fragment of that polymerase, and polymerization by the T4 DNA polymerase. For all of these reactions, high concentrations of nonspecific polymers increased enzymatic activity under otherwise inhibitory conditions resulting from relatively high ionic strength. The primary mechanism of the polymer effect seems to be to increase the binding of polymerase to DNA. They suggest that this effect of protein-DNA complexes is only one example of a general metabolic buffering action of crowded solutions on a variety of macromolecular interactions.

  15. 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.

  16. 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.

  17. 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.

  18. STUDIES ON PAN MACROMOLECULAR SEMICONDUCTING FIBER 1. PREPARATION OF PAN CONDUCTING FIBER TREATED BY STANNIC CHLORIDE AND ITS SEMICONDUCTING BEHAVIOUR

    Institute of Scientific and Technical Information of China (English)

    WANG Dexi; CUI Dayuan; LUO Boliang; WANG Xiugang; WU Renjie

    1984-01-01

    The PAN fiber treated by Lewis acid (e.g. stannic chloride) could be transformed into a macromolecular conducting fiber by further thermal treatment. Depending on thermal treatment condition the resistance of the fiber varied from 103 to 1012 Ω and kept stable after hydrolysis. The fiber has enough strength to be processed by various means. This is a new kind of macromolecular semiconducting fiber having some characteristics similar to those of organic semiconductors.

  19. Synthesis and application of water-soluble macromolecular derivatives of the redox coenzymes NAD(H), NADP(H) and FAD.

    Science.gov (United States)

    Bückmann, A F; Carrea, G

    1989-01-01

    During the past 15 years, the development of strategies to apply the catalytic potential of redox coenzyme-requiring enzymes has been a subject of intensive study; the main purpose of which has been to cut the cost of coenzyme to an economically acceptable level. One approach has been the utilization of isolated coenzyme-dependent enzyme systems with simultaneous enzymatic coenzyme regeneration (recycling). This has been used in conjugation with ultrafiltration reactor technology (enzyme membrane reactor), with coenzyme concentration being kept at a catalytic level. The concept implies confinement (immobilization) and practically 100% retention of both enzymes and coenzymes being dissolved in homogeneous solution within the reactor space that is closed off by an ultrafiltration membrane through which low-molecular-weight reactants (substrates and products) can freely pass. Since the problem of retaining nearly 100% native coenzymes of relatively low molecular weight by ultrafiltration membranes has not been satisfactorily solved, active macromolecular coenzyme derivatives are required. In this review, the syntheses, properties and merits of water-soluble macromolecular derivatives of NAD(H), NADP(H) and FAD are considered with respect to their biotechnological application.

  20. 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.

  1. Porphyrin-Cored Polymer Nanoparticles: Macromolecular Models for Heme Iron Coordination.

    Science.gov (United States)

    Rodriguez, Kyle J; Hanlon, Ashley M; Lyon, Christopher K; Cole, Justin P; Tuten, Bryan T; Tooley, Christian A; Berda, Erik B; Pazicni, Samuel

    2016-10-03

    Porphyrin-cored polymer nanoparticles (PCPNs) were synthesized and characterized to investigate their utility as heme protein models. Created using collapsible heme-centered star polymers containing photodimerizable anthracene units, these systems afford model heme cofactors buried within hydrophobic, macromolecular environments. Spectroscopic interrogations demonstrate that PCPNs display redox and ligand-binding reactivity similar to that of native systems and thus are potential candidates for modeling biological heme iron coordination.

  2. CplexA: a Mathematica package to study macromolecular-assembly control of gene expression

    OpenAIRE

    Vilar, J. M. G.; Saiz, L

    2010-01-01

    Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the en...

  3. Controlling Macromolecular Topology with Genetically Encoded SpyTag-SpyCatcher Chemistry

    OpenAIRE

    Zhang, Wen-Bin; Sun, Fei; Tirrell, David A.; Arnold, Frances H.

    2013-01-01

    Control of molecular topology constitutes a fundamental challenge in macromolecular chemistry. Here we describe the synthesis and characterization of artificial elastin-like proteins (ELPs) with unconventional nonlinear topologies including circular, tadpole, star, and H-shaped proteins using genetically encoded SpyTag–SpyCatcher chemistry. SpyTag is a short polypeptide that binds its protein partner SpyCatcher and forms isopeptide bonds under physiological conditions. Sequences encoding SpyT...

  4. Inter- and intra-estuarine fish assemblage variability patterns along the Portuguese coast

    Science.gov (United States)

    França, Susana; Costa, Maria José; Cabral, Henrique N.

    2011-01-01

    Estuaries along the Portuguese coast differ considerably in terms of their structure, geomorphologic and hydrologic characteristics. They play an important ecological role for different fish species, namely acting as important nursery areas. The fish assemblages of nine estuaries of the Portuguese coast were investigated in order to evaluate their main inter- and intra-estuarine variability patterns. Fish sampling surveys were conducted in May and July 2006, covering the full estuarine gradient. The different saline areas in each estuary were mapped using a Geographic Information System and fish assemblages' were described and compared using a functional guilds approach. Generalized linear models were used to relate fish species richness to geomorphologic, hydrologic and environmental characteristics of the estuaries considered and correspondence analyses were performed to evaluate similarities in fish assemblages' structure. At a large scale, river flow was the most important factor explaining the variability in species richness in estuaries along the Portuguese coast. At a regional scale, different abiotic factors explained the occurrence and abundance of fish species in the estuaries. Nonetheless, the overall role of the estuary was strongly related with the dominant saline zone within each estuary.

  5. Block copolymer libraries: modular versatility of the macromolecular Lego system.

    Science.gov (United States)

    Lohmeijer, Bas G G; Wouters, Daan; Yin, Zhihui; Schubert, Ulrich S

    2004-12-21

    The synthesis and characterization of a new 4 x 4 library of block copolymers based on polystyrene and poly(ethylene oxide) connected by an asymmetrical octahedral bis(terpyridine) ruthenium complex at the block junction are described, while initial studies on the thin film morphology of the components of the library are presented by the use of Atomic Force Microscopy, demonstrating the impact of a library approach to derive structure-property relationships.

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

    Directory of Open Access Journals (Sweden)

    Yoshiharu Machida

    2008-08-01

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

  7. Macromolecular (pro)drugs with concurrent direct activity against the hepatitis C virus and inflammation.

    Science.gov (United States)

    Wohl, Benjamin M; Smith, Anton A A; Jensen, Bettina E B; Zelikin, Alexander N

    2014-12-28

    Macromolecular prodrugs (MPs) are a powerful tool to alleviate side-effects and improve the efficacy of the broad-spectrum antiviral agent ribavirin. In this work, we sought an understanding of what makes an optimal formulation within the macromolecular parameter space--nature of the polymer carrier, average molar mass, drug loading, or a good combination thereof. A panel of MPs based on biocompatible synthetic vinylic and (meth)acrylic polymers was tested in an anti-inflammatory assay with relevance to alleviating inflammation in the liver during hepatitis C infection. Pristine polymer carriers proved to have a pronounced anti-inflammatory activity, a notion which may prove significant in developing MPs for antiviral and anticancer treatments. With conjugated ribavirin, MPs revealed enhanced activity but also higher toxicity. Therapeutic windows and therapeutic indices were determined and discussed to reveal the most potent formulation and those with optimized safety. Polymers were also tested as inhibitors of replication of the hepatitis C viral RNA using a subgenomic viral replicon system. For the first time, negatively charged polymers are revealed to have an intracellular activity against hepatitis C virus replication. Concerted activity of the polymer and ribavirin afforded MPs which significantly increased the therapeutic index of ribavirin-based treatment. Taken together, the systematic investigation of the macromolecular space identified lead candidates with high efficacy and concurrent direct activity against the hepatitis C virus and inflammation.

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

    Science.gov (United States)

    Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth

    2016-01-01

    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

  9. Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines

    Science.gov (United States)

    Yamada, Yusuke; pHonda, Nobuo; Matsugaki, Naohiro; Igarashi, Noriyuki; Hiraki, Masahiko; Wakatsuki, Soichi

    2008-01-01

    Owing to recent advances in high-throughput technology in macromolecular crystallography beamlines, such as high-brilliant X-ray sources, high-speed readout detectors and robotics, the number of samples that can be examined in a single visit to the beamline has increased dramatically. In order to make these experiments more efficient, two functions, remote monitoring and diffraction image evaluation, have been implemented in the macromolecular crystallography beamlines at the Photon Factory (PF). Remote monitoring allows scientists to participate in the experiment by watching from their laboratories, without having to come to the beamline. Diffraction image evaluation makes experiments easier, especially when using the sample exchange robot. To implement these two functions, two independent clients have been developed that work specifically for remote monitoring and diffraction image evaluation. In the macromolecular crystallography beamlines at PF, beamline control is performed using STARS (simple transmission and retrieval system). The system adopts a client–server style in which client programs communicate with each other through a server process using the STARS protocol. This is an advantage of the extension of the system; implementation of these new functions required few modifications of the existing system. PMID:18421163

  10. 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.

  11. 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.

  12. [Diversity and stability of arthropod assemblage in tea orchard].

    Science.gov (United States)

    Chen, Yigen; Xiong, Jinjun; Huang, Mingdu; Gu, Dejiu

    2004-05-01

    Two tea orchards, simplex tea orchard with weeds removed manually or by herbicides (STO) and complex tea orchard with the weed Hedyotis uncinella (CTO), each with an area of 0. 4 hm2, were established in 1995 in Yingde Hongxing Tea Plantation, Guangdong Province. The primary eigenvalues, species richness index (R), assemblage diversity index (H'), evenness index (J) and species concentration index (C) of arthropod assemblage were employed and compared to assess the efficacy of STO and CTO on the diversity and stabilityof arthropod assemblage. Stability indexes Ss/Si and Sn/Sp and variation coefficient of diversity index ds/dm were utilized as well. The results demonstrated that the R of arthropod assemblage in CTO ranged from 4 to 8, with the highest of 7.7403, while that in STO varied mainly between 4 to 6. The average R of arthropod assemblage in CTO was 5.4672 +/- 0.3483, higher than that in STO (4.8809 +/- 0.3175). The H' of arthropod in CTO (3.8535 +/- 0.1232) was higher, in contrast to the value in STO (3.4654 +/- 0.1856). The J in CTO was higher, while the species concentration index (C) was lower, in comparison to STO. The stability indexes Ss/Si and Sn/Sp of CTO were greater than those of STO, while the ds/dm in CTO (0.1107) was lower than that in STO (0.1855). All these indicated that the diversity of arthropod assemblage was better preserved in CTO, and the assemblage in CTO was more stable.

  13. 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.

  14. Operation of the Australian Store.Synchrotron for macromolecular crystallography.

    Science.gov (United States)

    Meyer, Grischa R; Aragão, David; Mudie, Nathan J; Caradoc-Davies, Tom T; McGowan, Sheena; Bertling, Philip J; Groenewegen, David; Quenette, Stevan M; Bond, Charles S; Buckle, Ashley M; Androulakis, Steve

    2014-10-01

    The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (∼1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

  15. 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.

  16. Macromolecular structure determination in the post-genome era

    CERN Document Server

    Kuhn, P

    2001-01-01

    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...

  17. 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.

  18. The effect of macromolecular crowding on the structure of the protein complex superoxide dismutase

    Science.gov (United States)

    Rajapaksha Mudalige, Ajith Rathnaweera

    Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied. We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using 400 MW polyethylene glycol (PEG), triethylene glycol (TEG), methyl-alpha-glucoside (alpha-MG) and trimethylamine N-oxide (TMAO). Parallel small angle neutron scattering (SANS) and small angle X-ray scattering (SAXS) allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. SAS coupled with osmotic pressure measurements allowed us to estimate a compressibility modulus for SOD. We believe this to be the first time the osmotic compressibility of a protein complex was measured. Molecular Dynamics (MD) simulations are widely used to obtain insights on biomolecular processes. However, it is not clear whether MD is capable of predicting subtle effects of macromolecular crowding. We used our experimentally observed compressibility of SOD to evaluate the ability of MD to predict macromolecular crowding. Effects of macromolecular crowding due to PEG on SOD were modeled using an all atom MD simulation with the CHARMM forcefield and the crystallographically resolved structures of SOD and PEG. Two parallel MD simulations were performed for SOD in water and SOD in 40% PEG for over 150~ns. Over the period of the simulation the SOD structure in 40

  19. Macromolecular fingerprinting of sulfolobus species in biofilm: a transcriptomic and proteomic approach combined with spectroscopic analysis.

    Science.gov (United States)

    Koerdt, Andrea; Orell, Alvaro; Pham, Trong Khoa; Mukherjee, Joy; Wlodkowski, Alexander; Karunakaran, Esther; Biggs, Catherine A; Wright, Phillip C; Albers, Sonja-Verena

    2011-09-02

    Microorganisms in nature often live in surface-associated sessile communities, encased in a self-produced matrix, referred to as biofilms. Biofilms have been well studied in bacteria but in a limited way for archaea. We have recently characterized biofilm formation in three closely related hyperthermophilic crenarchaeotes: Sulfolobus acidocaldarius, S. solfataricus, and S. tokodaii. These strains form different communities ranging from simple carpet structures in S. solfataricus to high density tower-like structures in S. acidocaldarius under static condition. Here, we combine spectroscopic, proteomic, and transcriptomic analyses to describe physiological and regulatory features associated with biofilms. Spectroscopic analysis reveals that in comparison to planktonic life-style, biofilm life-style has distinctive influence on the physiology of each Sulfolobus spp. Proteomic and transcriptomic data show that biofilm-forming life-style is strain specific (eg ca. 15% of the S. acidocaldarius genes were differently expressed, S. solfataricus and S. tokodaii had ~3.4 and ~1%, respectively). The -omic data showed that regulated ORFs were widely distributed in basic cellular functions, including surface modifications. Several regulated genes are common to biofilm-forming cells in all three species. One of the most striking common response genes include putative Lrs14-like transcriptional regulators, indicating their possible roles as a key regulatory factor in biofilm development.

  20. Spatio-Temporal Dynamics of Exploited Groundfish Species Assemblages Faced to Environmental and Fishing Forcings: Insights from the Mauritanian Exclusive Economic Zone

    Science.gov (United States)

    Kidé, Saïkou Oumar; Manté, Claude; Dubroca, Laurent; Demarcq, Hervé; Mérigot, Bastien

    2015-01-01

    Environmental changes and human activities can have strong impacts on biodiversity and ecosystem functioning. This study investigates how, from a quantitative point of view, simultaneously both environmental and anthropogenic factors affect species composition and abundance of exploited groundfish assemblages (i.e. target and non-target species) at large spatio-temporal scales. We aim to investigate (1) the spatial and annual stability of groundfish assemblages, (2) relationships between these assemblages and structuring factors in order to better explain the dynamic of the assemblages’ structure. The Mauritanian Exclusive Economic Zone (MEEZ) is of particular interest as it embeds a productive ecosystem due to upwelling, producing abundant and diverse resources which constitute an attractive socio-economic development. We applied the multi-variate and multi-table STATICO method on a data set consisting of 854 hauls collected during 14-years (1997–2010) from scientific trawl surveys (species abundance), logbooks of industrial fishery (fishing effort), sea surface temperature and chlorophyll a concentration as environmental variables. Our results showed that abiotic factors drove four main persistent fish assemblages. Overall, chlorophyll a concentration and sea surface temperature mainly influenced the structure of assemblages of coastal soft bottoms and those of the offshore near rocky bottoms where upwellings held. While highest levels of fishing effort were located in the northern permanent upwelling zone, effects of this variable on species composition and abundances of assemblages were relatively low, even if not negligible in some years and areas. The temporal trajectories between environmental and fishing conditions and assemblages did not match for all the entire time series analyzed in the MEEZ, but interestingly for some specific years and areas. The quantitative approach used in this work may provide to stakeholders, scientists and fishers a useful

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

    Science.gov (United States)

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

    2017-08-16

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

  2. A Review of Two Multiscale Methods for the Simulation of Macromolecular Assemblies: Multiscale Perturbation and Multiscale Factorization

    Directory of Open Access Journals (Sweden)

    Stephen Pankavich

    2015-02-01

    Full Text Available Many mesoscopic N-atom systems derive their structural and dynamical properties from processes coupled across multiple scales in space and time. That is, they simultaneously deform or display collective behaviors, while experiencing atomic scale vibrations and collisions. Due to the large number of atoms involved and the need to simulate over long time periods of biological interest, traditional computational tools, like molecular dynamics, are often infeasible for such systems. Hence, in the current review article, we present and discuss two recent multiscale methods, stemming from the N-atom formulation and an underlying scale separation, that can be used to study such systems in a friction-dominated regime: multiscale perturbation theory and multiscale factorization. These novel analytic foundations provide a self-consistent approach to yield accurate and feasible long-time simulations with atomic detail for a variety of multiscale phenomena, such as viral structural transitions and macromolecular self-assembly. As such, the accuracy and efficiency of the associated algorithms are demonstrated for a few representative biological systems, including satellite tobacco mosaic virus (STMV and lactoferrin.

  3. Public sphere as assemblage: the cultural politics of roadside memorialization.

    Science.gov (United States)

    Campbell, Elaine

    2013-09-01

    This paper investigates contemporary academic accounts of the public sphere. In particular, it takes stock of post-Habermasian public sphere scholarship, and acknowledges a lively and variegated debate concerning the multiple ways in which individuals engage in contemporary political affairs. A critical eye is cast over a range of key insights which have come to establish the parameters of what 'counts' as a/the public sphere, who can be involved, and where and how communicative networks are established. This opens up the conceptual space for re-imagining a/the public sphere as an assemblage. Making use of recent developments in Deleuzian-inspired assemblage theory - most especially drawn from DeLanda's (2006) 'new philosophy of society' - the paper sets out an alternative perspective on the notion of the public sphere, and regards it as a space of connectivity brought into being through a contingent and heterogeneous assemblage of discursive, visual and performative practices. This is mapped out with reference to the cultural politics of roadside memorialization. However, a/the public sphere as an assemblage is not simply a 'social construction' brought into being through a logic of connectivity, but is an emergent and ephemeral space which reflexively nurtures and assembles the cultural politics (and political cultures) of which it is an integral part. The discussion concludes, then, with a consideration of the contribution of assemblage theory to public sphere studies. (Also see Campbell 2009a). © London School of Economics and Political Science 2013.

  4. Quantifying assemblage turnover and species contributions at ecologic boundaries.

    Science.gov (United States)

    Hayek, Lee-Ann C; Wilson, Brent

    2013-01-01

    Not all boundaries, whether stratigraphical or geographical, are marked by species-level changes in community composition. For example, paleodata for some sites do not show readily discernible glacial-interglacial contrasts. Rather, the proportional abundances of species can vary subtly between glacials and interglacials. This paper presents a simple quantitative measure of assemblage turnover (assemblage turnover index, ATI) that uses changes in species' proportional abundances to identify intervals of community change. A second, functionally-related index (conditioned-on-boundary index, CoBI) identifies species contributions to the total assemblage turnover. With these measures we examine benthonic foraminiferal assemblages to assess glacial/interglacial contrasts at abyssal depths. Our results indicate that these measures, ATI and CoBI, have potential as sequence stratigraphic tools in abyssal depth deposits. Many peaks in the set of values of ATI coincide with terminations at the end of glaciations and delineate peak-bounded ATI intervals (PATIs) separated by boundaries that approximate to glacial terminations and to transgressions at neritic depths. These measures, however, can be used to evaluate the assemblage turnover and composition at any defined ecological or paleoecological boundary. The section used is from Ocean Drilling Program (OPD) Hole 994C, drilled on the Blake Ridge, offshore SE USA.

  5. Quantifying assemblage turnover and species contributions at ecologic boundaries.

    Directory of Open Access Journals (Sweden)

    Lee-Ann C Hayek

    Full Text Available Not all boundaries, whether stratigraphical or geographical, are marked by species-level changes in community composition. For example, paleodata for some sites do not show readily discernible glacial-interglacial contrasts. Rather, the proportional abundances of species can vary subtly between glacials and interglacials. This paper presents a simple quantitative measure of assemblage turnover (assemblage turnover index, ATI that uses changes in species' proportional abundances to identify intervals of community change. A second, functionally-related index (conditioned-on-boundary index, CoBI identifies species contributions to the total assemblage turnover. With these measures we examine benthonic foraminiferal assemblages to assess glacial/interglacial contrasts at abyssal depths. Our results indicate that these measures, ATI and CoBI, have potential as sequence stratigraphic tools in abyssal depth deposits. Many peaks in the set of values of ATI coincide with terminations at the end of glaciations and delineate peak-bounded ATI intervals (PATIs separated by boundaries that approximate to glacial terminations and to transgressions at neritic depths. These measures, however, can be used to evaluate the assemblage turnover and composition at any defined ecological or paleoecological boundary. The section used is from Ocean Drilling Program (OPD Hole 994C, drilled on the Blake Ridge, offshore SE USA.

  6. Crab death assemblages from Laguna Madre and vicinity, Texas

    Energy Technology Data Exchange (ETDEWEB)

    Plotnick, R.E.; McCarroll, S. (Univ. of Illinois, Chicago (USA)); Powell, E. (Texas A M Univ., College Station (USA))

    1990-02-01

    Crabs are a major component of modern marine ecosystems, but are only rarely described in fossil assemblages. Studies of brachyuran taphonomy have examined either the fossil end-products of the taphonomic process or the very earliest stages of decay and decomposition. The next logical step is the analysis of modern crab death assemblages; i.e., studies that examine taphonomic loss in areas where the composition of the living assemblage is known. The authors studied crab death assemblages in shallow water sediments at several localities in an near Laguna Madre, Texas. Nearly every sample examined contained some crab remains, most commonly in the form of isolated claws (dactyl and propodus). A crab fauna associated with a buried grass bed contained abundant remains of the xanthid crab Dyspanopeus texanus, including carapaces, chelipeds, and thoraxes, as well as fragments of the portunid Callinectes sapidus and the majiid Libinia dubia. Crab remains may be an overlooked portion of many preserved benthic assemblages, both in recent and modern sediments.

  7. Quantifying Assemblage Turnover and Species Contributions at Ecologic Boundaries

    Science.gov (United States)

    Hayek, Lee-Ann C.; Wilson, Brent

    2013-01-01

    Not all boundaries, whether stratigraphical or geographical, are marked by species-level changes in community composition. For example, paleodata for some sites do not show readily discernible glacial-interglacial contrasts. Rather, the proportional abundances of species can vary subtly between glacials and interglacials. This paper presents a simple quantitative measure of assemblage turnover (assemblage turnover index, ATI) that uses changes in species' proportional abundances to identify intervals of community change. A second, functionally-related index (conditioned-on-boundary index, CoBI) identifies species contributions to the total assemblage turnover. With these measures we examine benthonic foraminiferal assemblages to assess glacial/interglacial contrasts at abyssal depths. Our results indicate that these measures, ATI and CoBI, have potential as sequence stratigraphic tools in abyssal depth deposits. Many peaks in the set of values of ATI coincide with terminations at the end of glaciations and delineate peak-bounded ATI intervals (PATIs) separated by boundaries that approximate to glacial terminations and to transgressions at neritic depths. These measures, however, can be used to evaluate the assemblage turnover and composition at any defined ecological or paleoecological boundary. The section used is from Ocean Drilling Program (OPD) Hole 994C, drilled on the Blake Ridge, offshore SE USA. PMID:24130679

  8. 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.

  9. Fish stomach contents in benthic macroinvertebrate assemblage assessments

    Directory of Open Access Journals (Sweden)

    TH. Tupinambás

    for studies that only sample fish assemblages to evaluate aquatic ecosystem impacts. Therefore, this approach can be useful to amplify assessments of human impacts, and to incorporate additional bioindicators.

  10. Next generation sequencing reveals the hidden diversity of zooplankton assemblages.

    Directory of Open Access Journals (Sweden)

    Penelope K Lindeque

    Full Text Available BACKGROUND: Zooplankton play an important role in our oceans, in biogeochemical cycling and providing a food source for commercially important fish larvae. However, difficulties in correctly identifying zooplankton hinder our understanding of their roles in marine ecosystem functioning, and can prevent detection of long term changes in their community structure. The advent of massively parallel next generation sequencing technology allows DNA sequence data to be recovered directly from whole community samples. Here we assess the ability of such sequencing to quantify richness and diversity of a mixed zooplankton assemblage from a productive time series site in the Western English Channel. METHODOLOGY/PRINCIPLE FINDINGS: Plankton net hauls (200 µm were taken at the Western Channel Observatory station L4 in September 2010 and January 2011. These samples were analysed by microscopy and metagenetic analysis of the 18S nuclear small subunit ribosomal RNA gene using the 454 pyrosequencing platform. Following quality control a total of 419,041 sequences were obtained for all samples. The sequences clustered into 205 operational taxonomic units using a 97% similarity cut-off. Allocation of taxonomy by comparison with the National Centre for Biotechnology Information database identified 135 OTUs to species level, 11 to genus level and 1 to order, <2.5% of sequences were classified as unknowns. By comparison a skilled microscopic analyst was able to routinely enumerate only 58 taxonomic groups. CONCLUSIONS: Metagenetics reveals a previously hidden taxonomic richness, especially for Copepoda and hard-to-identify meroplankton such as Bivalvia, Gastropoda and Polychaeta. It also reveals rare species and parasites. We conclude that Next Generation Sequencing of 18S amplicons is a powerful tool for elucidating the true diversity and species richness of zooplankton communities. While this approach allows for broad diversity assessments of plankton it may

  11. Phytolith assemblages in grasses native to central Argentina.

    Science.gov (United States)

    Gallego, Lucrecia; Distel, Roberto A

    2004-12-01

    Phytolith reference collections are a prerequisite for accurate interpretation of soil phytolith assemblages aimed at reconstructing past vegetation. In this study a phytolith reference collection has been developed for several grasses native to central Argentina: Poa ligularis, Piptochaetium napostaense, Stipa clarazii, Stipa tenuis, Stipa tenuissima, Stipa eriostachya, Stipa ambigua, Stipa brachychaeta, Pappophorum subbulbosum, Digitaria californica, Bothriochloa edwardsiana and Aristida subulata. For each species, phytoliths present in the leaf blades were classified into 47 morphotypes, and their relative frequency determined by observing 300-400 phytoliths per sample (n = 5). Data were analyzed by complete linkage cluster analysis, using the Morisita Index as measure of association. The results showed differentiation among phytolith assemblages at species level or at plant functional type level. Cluster analysis separated C3 from C4 species and palatable from non-palatable species. This study highlights the possibility of reconstructing past vegetation in central Argentina grasslands through the analysis of soil phytolith assemblages.

  12. A common tendency for phylogenetic overdispersion in mammalian assemblages.

    Science.gov (United States)

    Cooper, Natalie; Rodríguez, Jesús; Purvis, Andy

    2008-09-07

    Competition has long been proposed as an important force in structuring mammalian communities. Although early work recognized that competition has a phylogenetic dimension, only with recent increases in the availability of phylogenies have true phylogenetic investigations of mammalian community structure become possible. We test whether the phylogenetic structure of 142 assemblages from three mammalian clades (New World monkeys, North American ground squirrels and Australasian possums) shows the imprint of competition. The full set of assemblages display a highly significant tendency for members to be more distantly related than expected by chance (phylogenetic overdispersion). The overdispersion is also significant within two of the clades (monkeys and squirrels) separately. This is the first demonstration of widespread overdispersion in mammal assemblages and implies an important role for either competition between close relatives where traits are conserved, habitat filtering where distant relatives share convergent traits, or both.

  13. Fuzzy electron density fragments in macromolecular quantum chemistry, combinatorial quantum chemistry, functional group analysis, and shape-activity relations.

    Science.gov (United States)

    Mezey, Paul G

    2014-09-16

    Conspectus Just as complete molecules have no boundaries and have "fuzzy" electron density clouds approaching zero density exponentially at large distances from the nearest nucleus, a physically justified choice for electron density fragments exhibits similar behavior. Whereas fuzzy electron densities, just as any fuzzy object, such as a thicker cloud on a foggy day, do not lend themselves to easy visualization, one may partially overcome this by using isocontours. Whereas a faithful representation of the complete fuzzy density would need infinitely many such isocontours, nevertheless, by choosing a selected few, one can still obtain a limited pictorial representation. Clearly, such images are of limited value, and one better relies on more complete mathematical representations, using, for example, density matrices of fuzzy fragment densities. A fuzzy density fragmentation can be obtained in an exactly additive way, using the output from any of the common quantum chemical computational techniques, such as Hartree-Fock, MP2, and various density functional approaches. Such "fuzzy" electron density fragments properly represented have proven to be useful in a rather wide range of applications, for example, (a) using them as additive building blocks leading to efficient linear scaling macromolecular quantum chemistry computational techniques, (b) the study of quantum chemical functional groups, (c) using approximate fuzzy fragment information as allowed by the holographic electron density theorem, (d) the study of correlations between local shape and activity, including through-bond and through-space components of interactions between parts of molecules and relations between local molecular shape and substituent effects, (e) using them as tools of density matrix extrapolation in conformational changes, (f) physically valid averaging and statistical distribution of several local electron densities of common stoichiometry, useful in electron density databank mining, for

  14. Spatial variation patterns of subtidal seaweed assemblages along a subtropical oceanic archipelago: Thermal gradient vs herbivore pressure

    Science.gov (United States)

    Sangil, Carlos; Sansón, Marta; Afonso-Carrillo, Julio

    2011-10-01

    The structure and composition of subtidal rocky seaweed assemblages were studied at 69 sites on the Canary Islands (northeastern Atlantic). This group of islands are situated at the southern boundary of the warm temperate region and adjacent to the cold waters from the northwest African coastal upwelling, which creates a difference of almost 2 °C in surface seawater temperature from the eastern to the western islands. This thermal variation allows an examination of the transition between the warm temperate and the tropical regions along this longitudinal gradient together with the hypothesised Fucales-dominated assemblages towards the eastern islands in contrast to the Dictyotales-dominated assemblages towards the western ones. Environmental and biological parameters were considered in order to investigate which were the main factors explaining spatial variation along the gradient in a multi-scaled approach. Although seventy-nine macroalgae were identified, 87.63% of the total mean cover was due to six taxa ( Lobophora variegata, nongeniculate corallines, Canistrocarpus cervicornis, Jania adhaerens, Cystoseira abies-marina and Pseudolithoderma adriaticum). At a large scale, sea urchin density explained the highest variation in seaweed assemblages (26.94%), and its pattern of distribution across the islands. The expected pattern of distribution according to the upwelling distance only occurred in restricted areas of the Canarian Archipelago in absence of herbivore pressure and habitat degradation. Spatial variations within islands (medium scale) were mainly related to wave exposure, while at a small scale these were mostly due to the degree of sedimentation.

  15. Habitat specialization in tropical continental shelf demersal fish assemblages.

    Directory of Open Access Journals (Sweden)

    Ben M Fitzpatrick

    Full Text Available The implications of shallow water impacts such as fishing and climate change on fish assemblages are generally considered in isolation from the distribution and abundance of these fish assemblages in adjacent deeper waters. We investigate the abundance and length of demersal fish assemblages across a section of tropical continental shelf at Ningaloo Reef, Western Australia, to identify fish and fish habitat relationships across steep gradients in depth and in different benthic habitat types. The assemblage composition of demersal fish were assessed from baited remote underwater stereo-video samples (n = 304 collected from 16 depth and habitat combinations. Samples were collected across a depth range poorly represented in the literature from the fringing reef lagoon (1-10 m depth, down the fore reef slope to the reef base (10-30 m depth then across the adjacent continental shelf (30-110 m depth. Multivariate analyses showed that there were distinctive fish assemblages and different sized fish were associated with each habitat/depth category. Species richness, MaxN and diversity declined with depth, while average length and trophic level increased. The assemblage structure, diversity, size and trophic structure of demersal fishes changes from shallow inshore habitats to deeper water habitats. More habitat specialists (unique species per habitat/depth category were associated with the reef slope and reef base than other habitats, but offshore sponge-dominated habitats and inshore coral-dominated reef also supported unique species. This suggests that marine protected areas in shallow coral-dominated reef habitats may not adequately protect those species whose depth distribution extends beyond shallow habitats, or other significant elements of demersal fish biodiversity. The ontogenetic habitat partitioning which is characteristic of many species, suggests that to maintain entire species life histories it is necessary to protect corridors of

  16. Environmental characteristics drive variation in Amazonian understorey bird assemblages.

    Science.gov (United States)

    Menger, Juliana; Magnusson, William E; Anderson, Marti J; Schlegel, Martin; Pe'er, Guy; Henle, Klaus

    2017-01-01

    Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical birds exhibit strong habitat specificity, their spatial distributions are generally assumed to be driven primarily by environmental heterogeneity and interspecific interactions. However, spatial distributions of some Amazonian forest birds are also often restricted by large rivers and other large-scale topographic features, suggesting that dispersal limitation may also play a role in driving species' turnover. In this study, we evaluated the effects of environmental characteristics, topographic and spatial variables on variation in local assemblage structure and diversity of birds in an old-growth forest in central Amazonia. Birds were mist-netted in 72 plots distributed systematically across a 10,000 ha reserve in each of three years. Alpha diversity remained stable through time, but species composition changed. Spatial variation in bird-assemblage structure was significantly related to environmental and topographic variables but not strongly related to spatial variables. At a broad scale, we found bird assemblages to be significantly distinct between two watersheds that are divided by a central ridgeline. We did not detect an effect of the ridgeline per se in driving these patterns, indicating that most birds are able to fly across it, and that differences in assemblage structure between watersheds may be due to unmeasured environmental variables or unique combinations of measured variables. Our study indicates that complex geography and landscape features can act together with environmental variables to drive changes in the diversity and composition of tropical bird assemblages at local scales, but highlights that we still know very little about what makes different parts of tropical forest suitable for different species.

  17. Habitat specialization in tropical continental shelf demersal fish assemblages.

    Science.gov (United States)

    Fitzpatrick, Ben M; Harvey, Euan S; Heyward, Andrew J; Twiggs, Emily J; Colquhoun, Jamie

    2012-01-01

    The implications of shallow water impacts such as fishing and climate change on fish assemblages are generally considered in isolation from the distribution and abundance of these fish assemblages in adjacent deeper waters. We investigate the abundance and length of demersal fish assemblages across a section of tropical continental shelf at Ningaloo Reef, Western Australia, to identify fish and fish habitat relationships across steep gradients in depth and in different benthic habitat types. The assemblage composition of demersal fish were assessed from baited remote underwater stereo-video samples (n = 304) collected from 16 depth and habitat combinations. Samples were collected across a depth range poorly represented in the literature from the fringing reef lagoon (1-10 m depth), down the fore reef slope to the reef base (10-30 m depth) then across the adjacent continental shelf (30-110 m depth). Multivariate analyses showed that there were distinctive fish assemblages and different sized fish were associated with each habitat/depth category. Species richness, MaxN and diversity declined with depth, while average length and trophic level increased. The assemblage structure, diversity, size and trophic structure of demersal fishes changes from shallow inshore habitats to deeper water habitats. More habitat specialists (unique species per habitat/depth category) were associated with the reef slope and reef base than other habitats, but offshore sponge-dominated habitats and inshore coral-dominated reef also supported unique species. This suggests that marine protected areas in shallow coral-dominated reef habitats may not adequately protect those species whose depth distribution extends beyond shallow habitats, or other significant elements of demersal fish biodiversity. The ontogenetic habitat partitioning which is characteristic of many species, suggests that to maintain entire species life histories it is necessary to protect corridors of connected habitats

  18. Environmental characteristics drive variation in Amazonian understorey bird assemblages

    Science.gov (United States)

    Magnusson, William E.; Anderson, Marti J.; Schlegel, Martin; Pe’er, Guy; Henle, Klaus

    2017-01-01

    Tropical bird assemblages display patterns of high alpha and beta diversity and, as tropical birds exhibit strong habitat specificity, their spatial distributions are generally assumed to be driven primarily by environmental heterogeneity and interspecific interactions. However, spatial distributions of some Amazonian forest birds are also often restricted by large rivers and other large-scale topographic features, suggesting that dispersal limitation may also play a role in driving species’ turnover. In this study, we evaluated the effects of environmental characteristics, topographic and spatial variables on variation in local assemblage structure and diversity of birds in an old-growth forest in central Amazonia. Birds were mist-netted in 72 plots distributed systematically across a 10,000 ha reserve in each of three years. Alpha diversity remained stable through time, but species composition changed. Spatial variation in bird-assemblage structure was significantly related to environmental and topographic variables but not strongly related to spatial variables. At a broad scale, we found bird assemblages to be significantly distinct between two watersheds that are divided by a central ridgeline. We did not detect an effect of the ridgeline per se in driving these patterns, indicating that most birds are able to fly across it, and that differences in assemblage structure between watersheds may be due to unmeasured environmental variables or unique combinations of measured variables. Our study indicates that complex geography and landscape features can act together with environmental variables to drive changes in the diversity and composition of tropical bird assemblages at local scales, but highlights that we still know very little about what makes different parts of tropical forest suitable for different species. PMID:28225774

  19. Light-dependant biostabilisation of sediments by stromatolite assemblages.

    Directory of Open Access Journals (Sweden)

    David M Paterson

    Full Text Available For the first time we have investigated the natural ecosystem engineering capacity of stromatolitic microbial assemblages. Stromatolites are laminated sedimentary structures formed by microbial activity and are considered to have dominated the shallows of the Precambrian oceans. Their fossilised remains are the most ancient unambiguous record of early life on earth. Stromatolites can therefore be considered as the first recognisable ecosystems on the planet. However, while many discussions have taken place over their structure and form, we have very little information on their functional ecology and how such assemblages persisted despite strong eternal forcing from wind and waves. The capture and binding of sediment is clearly a critical feature for the formation and persistence of stromatolite assemblages. Here, we investigated the ecosystem engineering capacity of stromatolitic microbial assemblages with respect to their ability to stabilise sediment using material from one of the few remaining living stromatolite systems (Highborne Cay, Bahamas. It was shown that the most effective assemblages could produce a rapid (12-24 h and significant increase in sediment stability that continued in a linear fashion over the period of the experimentation (228 h. Importantly, it was also found that light was required for the assemblages to produce this stabilisation effect and that removal of assemblage into darkness could lead to a partial reversal of the stabilisation. This was attributed to the breakdown of extracellular polymeric substances under anaerobic conditions. These data were supported by microelectrode profiling of oxygen and calcium. The structure of the assemblages as they formed was visualised by low-temperature scanning electron microscopy and confocal laser microscopy. These results have implications for the understanding of early stromatolite development and highlight the potential importance of the evolution of photosynthesis in the

  20. 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.

  1. Enhanced delivery of the RAPTA-C macromolecular chemotherapeutic by conjugation to degradable polymeric micelles.

    Science.gov (United States)

    Blunden, Bianca M; Lu, Hongxu; Stenzel, Martina H

    2013-12-09

    Macromolecular ruthenium complexes are a promising avenue to better and more selective chemotherapeutics. We have previously shown that RAPTA-C [RuCl2(p-cymene)(PTA)], with the water-soluble 1,3,5-phosphaadamantane (PTA) ligand, could be attached to a polymer moiety via nucleophilic substitution of an available iodide with an amide in the PTA ligand. To increase the cell uptake of this macromolecule, we designed an amphiphilic block copolymer capable of self-assembling into polymeric micelles. The block copolymer was prepared by ring-opening polymerization of d,l-lactide (3,6-dimethyl-1,4-dioxane-2,5-dione) using a RAFT agent with an additional hydroxyl functionality, followed by the RAFT copolymerization of 2-hydroxyethyl acrylate (HEA) and 2-chloroethyl methacrylate (CEMA). The Finkelstein reaction and reaction with PTA led to polymers that can readily react with the dimer of RuCl2(p-cymene) to create a macromolecular RAPTA-C drug. RAPTA-C conjugation, micellization, and subsequent cytotoxicity and cell uptake of these polymeric moieties was tested on ovarian cancer A2780, A2780cis, and Ovcar-3 cell lines. Confocal microscopy images confirmed cell uptake of the micelles into the lysosome of the cells, indicative of an endocytic pathway. On average, a 10-fold increase in toxicity was found for the macromolecular drugs when compared to the RAPTA-C molecule. Furthermore, the cell uptake of ruthenium was analyzed and a significant increase was found for the micelles compared to RAPTA-C. Notably, micelles prepared from the polymer containing fewer HEA units had the highest cytotoxicity, the best cell uptake of ruthenium and were highly effective in suppressing the colony-forming ability of cells.

  2. 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.

  3. 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.

  4. Optimized beamline design for macromolecular crystallography at the Cornell High Energy Synchrotron Source (CHESS) (abstract)

    Science.gov (United States)

    Schildkamp, Wilfried; Bilderback, Donald; Moffat, Keith

    1989-07-01

    The A1 station on the CHESS wiggler beamline has been the workhorse for most macromolecular crystallographic experiments. This station is equipped with a fixed energy focusing germanium (111) monochromator and a focusing total reflection mirror. Our macromolecular crystallographers made full use of the high flux of more than 1012 photons/s/mm2 and the stable beam conditions, both in position and energy resolution. As a result, the A1 station was heavily oversubscribed. CHESS is presently expanding its capabilities and a new diffraction station for macromolecular crystallography is under construction. This beamline will be powered by a 24-pole hybrid permanent magnet wiggler with a critical energy of 25 keV. A focusing monochromator, which handles a specific heat load of 10 W/mm2, will have a range of tunability which covers all relevant absorption edges from 7 to 15 keV using a Ge(111) crystal. The energy resolution and the focusing properties remain constant within a factor of 2 over the entire tunability range. We expect a brilliance of about 1013 photons/s/mm2/mrad2/0.1% bandpass. The diffraction station will be equipped with an oscillation camera which can be used with x-ray film of 5×5 or 8×10 in. size or alternatively with Kodak storage phosphors. A wide variety of clamp-on accessories, like crystal coolers, fast shutters, helium pathways, polarimeter, etc. are available. The station will contain a beampipe system, which can also be used for small angle scattering experiments with sample-to-detector distances of up to 3000 mm. The entire diffraction station, its control area, a biological preparation area, and a darkroom are to be embedded in a biological safety containment of the level BL3. This will allow diffraction studies of virulent strains of viruses and other biohazards, which could not previously be studied at synchrotron radiation sources before without causing major disruption to the normal laboratory procedure.

  5. 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.

  6. 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.

  7. 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...

  8. 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.

  9. Climate mediates the effects of disturbance on ant assemblage structure

    Science.gov (United States)

    Gibb, Heloise; Sanders, Nathan J.; Dunn, Robert R.; Watson, Simon; Photakis, Manoli; Abril, Silvia; Andersen, Alan N.; Angulo, Elena; Armbrecht, Inge; Arnan, Xavier; Baccaro, Fabricio B.; Bishop, Tom R.; Boulay, Raphael; Castracani, Cristina; Del Toro, Israel; Delsinne, Thibaut; Diaz, Mireia; Donoso, David A.; Enríquez, Martha L.; Fayle, Tom M.; Feener, Donald H.; Fitzpatrick, Matthew C.; Gómez, Crisanto; Grasso, Donato A.; Groc, Sarah; Heterick, Brian; Hoffmann, Benjamin D.; Lach, Lori; Lattke, John; Leponce, Maurice; Lessard, Jean-Philippe; Longino, John; Lucky, Andrea; Majer, Jonathan; Menke, Sean B.; Mezger, Dirk; Mori, Alessandra; Munyai, Thinandavha C.; Paknia, Omid; Pearce-Duvet, Jessica; Pfeiffer, Martin; Philpott, Stacy M.; de Souza, Jorge L. P.; Tista, Melanie; Vasconcelos, Heraldo L.; Vonshak, Merav; Parr, Catherine L.

    2015-01-01

    Many studies have focused on the impacts of climate change on biological assemblages, yet little is known about how climate interacts with other major anthropogenic influences on biodiversity, such as habitat disturbance. Using a unique global database of 1128 local ant assemblages, we examined whether climate mediates the effects of habitat disturbance on assemblage structure at a global scale. Species richness and evenness were associated positively with temperature, and negatively with disturbance. However, the interaction among temperature, precipitation and disturbance shaped species richness and evenness. The effect was manifested through a failure of species richness to increase substantially with temperature in transformed habitats at low precipitation. At low precipitation levels, evenness increased with temperature in undisturbed sites, peaked at medium temperatures in disturbed sites and remained low in transformed sites. In warmer climates with lower rainfall, the effects of increasing disturbance on species richness and evenness were akin to decreases in temperature of up to 9°C. Anthropogenic disturbance and ongoing climate change may interact in complicated ways to shape the structure of assemblages, with hot, arid environments likely to be at greatest risk. PMID:25994675

  10. Relationships between structural complexity, coral traits, and reef fish assemblages

    Science.gov (United States)

    Darling, Emily S.; Graham, Nicholas A. J.; Januchowski-Hartley, Fraser A.; Nash, Kirsty L.; Pratchett, Morgan S.; Wilson, Shaun K.

    2017-06-01

    With the ongoing loss of coral cover and the associated flattening of reef architecture, understanding the links between coral habitat and reef fishes is of critical importance. Here, we investigate whether considering coral traits and functional diversity provides new insights into the relationship between structural complexity and reef fish communities, and whether coral traits and community composition can predict structural complexity. Across 157 sites in Seychelles, Maldives, the Chagos Archipelago, and Australia's Great Barrier Reef, we find that structural complexity and reef zone are the strongest and most consistent predictors of reef fish abundance, biomass, species richness, and trophic structure. However, coral traits, diversity, and life histories provided additional predictive power for models of reef fish assemblages, and were key drivers of structural complexity. Our findings highlight that reef complexity relies on living corals—with different traits and life histories—continuing to build carbonate skeletons, and that these nuanced relationships between coral assemblages and habitat complexity can affect the structure of reef fish assemblages. Seascape-level estimates of structural complexity are rapid and cost effective with important implications for the structure and function of fish assemblages, and should be incorporated into monitoring programs.

  11. Learning in the "Platform Society": Disassembling an Educational Data Assemblage

    Science.gov (United States)

    Williamson, Ben

    2017-01-01

    Schools are increasingly involved in diverse forms of student data collection. This article provides a sociotechnical survey of a data assemblage used in education. ClassDojo is a commercial platform for tracking students' behaviour data in classrooms and a social media network for connecting teachers, students, and parents. The hybridization of…

  12. Nestedness of snake assemblages on islands of an inundated lake

    Institute of Scientific and Technical Information of China (English)

    Yanping WANG; Xi WANG; Ping DING

    2012-01-01

    Nestedness is a pattern frequently reported for faunal assemblages in fragmented systems.Although nestedness has been documented for a wide range of taxa,it is rarely tested in snake assemblages.To arrive at robust generalizations about processes and mechanisms structuring island biotas,it is important to examine under-represented taxa such as snakes for the insights they may offer.We tested for the existence of nestedness and underlying causal mechanisms using snake data collected on islands in the Thousand Island Lake,China.We used the line-transect method to survey snake occupancy and abundance on 20 islands during two breeding seasons in 2009 and 2010.We used the recently developed metric WNODF to estimate nestedness.We used Spearman rank correlations to examine the associations of nestedness and habitat variables (area,isolation,and habitat diversity) as well as life-history traits (body size,clutch size,geographical range size and area requirement) related to species extinction and immigration tendencies.Snake assemblages were significantly nested and were shaped by extinction processes mediated through area effects and habitat nestedness.The nestedness of snake assemblages was not due to passive sampling or selective colonization.From a conservation viewpoint,our results indicate that we should protect both the largest island with the most species-rich community and habitat-rich islands to maximize the number of species preserved.

  13. Elk herbivory alters small mammal assemblages in high elevation drainages

    Science.gov (United States)

    Parsons, Elliott W.R.; Maron, John L.; Martin, Thomas E.

    2012-01-01

    Heavy herbivory by ungulates can substantially alter habitat, but the indirect consequences of habitat modification for animal assemblages that rely on that habitat are not well studied. This is a particularly important topic given that climate change can alter plant–herbivore interactions.

  14. Temporal variability in epifaunal assemblages associated with temperate gorgonian gardens

    KAUST Repository

    Dias, I.M.

    2015-10-19

    The present study is one of the few that investigate the temporal variability of epifaunal assemblages associated with coral species, particularly the octocorals Eunicella gazella and Leptogorgia lusitanica in south Portugal. The results suggest time rather than colony size as a primary driver of the ecological patterns of these assemblages, which were dominated by amphipods, molluscs and polychaetes. Temporal variability was linked to changes in environmental parameters, namely temperature, chlorophyll a and particulate organic carbon. Hence, temporal variability must be taken into account for the design of future biodiversity assessment studies, as different patterns may be observed depending on the sampling time. Associated epifaunal assemblages were consistently dominated by resident species (i.e. species present in all sampling periods) and a peak of rare species was observed in the transition from spring to summer following the increase of seawater temperature. Turnover was particularly high in the transition between the spring and summer periods. In both hosts, turnover was higher in the small sized colonies, which generally harboured less diverse and less abundant assemblages which also differed from those inhabiting larger size colonies. The high levels of diversity associated with gorgonian colonies highlights the need for the conservation of this priority habitat.

  15. Temporal variability in epifaunal assemblages associated with temperate gorgonian gardens.

    Science.gov (United States)

    Dias, I M; Cúrdia, J; Cunha, M R; Santos, M N; Carvalho, S

    2015-12-01

    The present study is one of the few that investigate the temporal variability of epifaunal assemblages associated with coral species, particularly the octocorals Eunicella gazella and Leptogorgia lusitanica in south Portugal. The results suggest time rather than colony size as a primary driver of the ecological patterns of these assemblages, which were dominated by amphipods, molluscs and polychaetes. Temporal variability was linked to changes in environmental parameters, namely temperature, chlorophyll a and particulate organic carbon. Hence, temporal variability must be taken into account for the design of future biodiversity assessment studies, as different patterns may be observed depending on the sampling time. Associated epifaunal assemblages were consistently dominated by resident species (i.e. species present in all sampling periods) and a peak of rare species was observed in the transition from spring to summer following the increase in seawater temperature. Turnover was particularly high in the transition between the spring and summer periods. In both hosts, turnover was higher in the small sized colonies, which harboured less diverse and less abundant assemblages that also differed from those inhabiting larger size colonies. The high levels of diversity associated with gorgonian colonies highlight the need for the conservation of this priority habitat.

  16. The assemblage of compliance in psychiatric case management.

    Science.gov (United States)

    Brodwin, Paul

    2010-08-01

    In the post-asylum era, case managers perform much of the face-to-face work of pharmaceutical compliance for people with severe and persistent mental illness. Their work demands careful orchestration of the assemblage of compliance, including the actual medications, the ideology of biopsychiatry, the division of professional labor, and certain mundane tools. Ethnographic vignettes from an Assertive Community Treatment (ACT) team show how case managers use this assemblage in their everyday routines, but also how it undercuts key elements of the original ACT mission. Reflecting its roots in the deinstitutionalization movement, the ACT model gives case managers limitless responsibilities for clients' lives, but then narrowly defines their role as the prosthetic extension of psychiatric authority. To produce compliance, case managers depend on the medication cassette, analyzed here as a human/non-human hybrid woven into their ordinary work. The medication cassette has pre-scripted uses that enlist clinicians in biopsychiatric thinking and also silently impose compliant behavior on clients. The elements in the assemblage of compliance depend on each other, but they do not form a seamless whole, as evidenced by the dilemmas and micropolitics of the clinical front-line. Theoretical notions of assemblages and technologies of compliance, drawn from science and technology studies, illuminate a core conundrum of practice in psychiatric case management.

  17. Shikarpur lithic assemblage: New questions regarding Rohri chert blade production

    Directory of Open Access Journals (Sweden)

    Charusmita Gadekar

    2014-03-01

    Full Text Available Recent excavations at Shikarpur, a fortified Harappan site situated near the Gulf of Kuchchh in Gujarat, Western India, brought to light a large collection of Rohri chert blades.  Chert found in the Rohri hill near Sukkur in Sindh, central Pakistan is distinctive and easily identifiable. The wide distribution of standardized Rohri chert blades is often regarded as a testimony to the Harappan efficiency in long distance trade and craft production.  The possibility of localized production of Rohri chert blades in Gujarat is often negated due to the constraints of raw-material availability.  The absence of Rohri chert working debitage from most of the sites in Gujarat, has lent support to this position. The Shikarpur Rohri blade assemblage however incorporates more than 650 blades, a large fluted blade-core and a few Rohri chert debitage.  These have led the excavators to suggest that some of the blades found at Shikarpur were locally produced from raw materials brought to the site from the Rohri hills.  Typo-technological features of the Rohri chert assemblage from Shikarpur have been analysed in this background. These along with metrical features of the assemblage are compared with Rohri chert assemblages from other major Harappan sites in the region to check the validity of the proposed ‘limited local production’.

  18. The Liana assemblage of a Congolian rainforest : diversity, structure and dynamics

    NARCIS (Netherlands)

    Ewango Ekokinya, Corneille

    2010-01-01

    Key words: Liana assemblage, species composition, community, dynamics, canopy openness, Manniophyton fulvum, functional traits, population density, pervasive change. This study analyzes the diversity, composition, and dynamics of the liana assemblage of the Ituri rain forest in northeastern DR Con

  19. 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.

  20. Fast Method for Computing Chemical Potentials and Liquid-Liquid Phase Equilibria of Macromolecular Solutions.

    Science.gov (United States)

    Qin, Sanbo; Zhou, Huan-Xiang

    2016-08-25

    Chemical potential is a fundamental property for determining thermodynamic equilibria involving exchange of molecules, such as between two phases of molecular systems. Previously, we developed the fast Fourier transform (FFT)-based method for Modeling Atomistic Protein-crowder interactions (FMAP) to calculate excess chemical potentials according to the Widom insertion. Intermolecular interaction energies were expressed as correlation functions and evaluated via FFT. Here, we extend this method to calculate liquid-liquid phase equilibria of macromolecular solutions. Chemical potentials are calculated by FMAP over a wide range of molecular densities, and the condition for coexistence of low- and high-density phases is determined by the Maxwell equal-area rule. When benchmarked on Lennard-Jones fluids, our method produces an accurate phase diagram at 18% of the computational cost of the current best method. Importantly, the gain in computational speed increases dramatically as the molecules become more complex, leading to many orders of magnitude in speed up for atomistically represented proteins. We demonstrate the power of FMAP by reporting the first results for the liquid-liquid coexistence curve of γII-crystallin represented at the all-atom level. Our method may thus open the door to accurate determination of phase equilibria for macromolecular mixtures such as protein-protein mixtures and protein-RNA mixtures, that are known to undergo liquid-liquid phase separation, both in vitro and in vivo.

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

    Science.gov (United States)

    Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

    2014-09-01

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

  2. Force interacts with macromolecular structure in activation of TGF-β.

    Science.gov (United States)

    Dong, Xianchi; Zhao, Bo; Iacob, Roxana E; Zhu, Jianghai; Koksal, Adem C; Lu, Chafen; Engen, John R; Springer, Timothy A

    2017-02-02

    Integrins are adhesion receptors that transmit force across the plasma membrane between extracellular ligands and the actin cytoskeleton. In activation of the transforming growth factor-β1 precursor (pro-TGF-β1), integrins bind to the prodomain, apply force, and release the TGF-β growth factor. However, we know little about how integrins bind macromolecular ligands in the extracellular matrix or transmit force to them. Here we show how integrin αVβ6 binds pro-TGF-β1 in an orientation biologically relevant for force-dependent release of TGF-β from latency. The conformation of the prodomain integrin-binding motif differs in the presence and absence of integrin binding; differences extend well outside the interface and illustrate how integrins can remodel extracellular matrix. Remodelled residues outside the interface stabilize the integrin-bound conformation, adopt a conformation similar to earlier-evolving family members, and show how macromolecular components outside the binding motif contribute to integrin recognition. Regions in and outside the highly interdigitated interface stabilize a specific integrin/pro-TGF-β orientation that defines the pathway through these macromolecules which actin-cytoskeleton-generated tensile force takes when applied through the integrin β-subunit. Simulations of force-dependent activation of TGF-β demonstrate evolutionary specializations for force application through the TGF-β prodomain and through the β- and not α-subunit of the integrin.

  3. Importance of gastrointestinal ingestion and macromolecular antigens in the vein for oral tolerance induction

    Science.gov (United States)

    Wakabayashi, Ayako; Kumagai, Yoshihiro; Watari, Eiji; Shimizu, Masumi; Utsuyama, Masanori; Hirokawa, Katsuiku; Takahashi, Hidemi

    2006-01-01

    Oral administration of a certain dose of antigen can generally induce immunological tolerance against the same antigen. In this study, we showed the temporal appearance of ovalbumin (OVA) antigens in both portal and peripheral blood of mice after the oral administration of OVA. Furthermore, we detected 45 000 MW OVA in mouse serum 30 min after the oral administration of OVA. Based on this observation, we examined whether the injection of intact OVA into the portal or peripheral vein induces immunological tolerance against OVA. We found that the intravenous injection of intact OVA did not induce immunological tolerance but rather enhanced OVA-specific antibody production in some subclasses, suggesting that OVA antigens via the gastrointestinal tract but not intact OVA may contribute to establish immunological tolerance against OVA. Therefore, we examined the effects of digesting intact OVA in the gastrointestinal tract on the induction of oral tolerance. When mice were orally administered or injected into various gastrointestinal organs, such as the stomach, duodenum, ileum, or colon and boosted with intact OVA, OVA-specific antibody production and delayed-type hypersensitivity (DTH) response were significantly enhanced in mice injected into the ileum or colon, compared with orally administered mice. These results suggest that although macromolecular OVA antigens are detected after oral administration of OVA in tolerant-mouse serum, injection of intact OVA cannot contribute to tolerance induction. Therefore, some modification of macromolecular OVA in the gastrointestinal tract and ingestion may be essential for oral tolerance induction. PMID:16796692

  4. Assessing physio-macromolecular effects of lactic acid on Zygosaccharomyces bailii cells during microaerobic fermentation.

    Science.gov (United States)

    Kuanyshev, Nurzhan; Ami, Diletta; Signori, Lorenzo; Porro, Danilo; Morrissey, John P; Branduardi, Paola

    2016-08-01

    The ability of Zygosaccharomyces bailii to grow at low pH and in the presence of considerable amounts of weak organic acids, at lethal condition for Saccharomyces cerevisiae, increased the interest in the biotechnological potential of the yeast. To understand the mechanism of tolerance and growth effect of weak acids on Z. bailii, we evaluated the physiological and macromolecular changes of the yeast exposed to sub lethal concentrations of lactic acid. Lactic acid represents one of the important commodity chemical which can be produced by microbial fermentation. We assessed physiological effect of lactic acid by bioreactor fermentation using synthetic media at low pH in the presence of lactic acid. Samples collected from bioreactors were stained with propidium iodide (PI) which revealed that, despite lactic acid negatively influence the growth rate, the number of PI positive cells is similar to that of the control. Moreover, we have performed Fourier Transform Infra-Red (FTIR) microspectroscopy analysis on intact cells of the same samples. This technique has been never applied before to study Z. bailii under this condition. The analyses revealed lactic acid induced macromolecular changes in the overall cellular protein secondary structures, and alterations of cell wall and membrane physico-chemical properties.

  5. 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)

  6. X-ray Diffraction of Cotton Treated with Neutralized Vegetable Oil-based Macromolecular Crosslinkers

    Directory of Open Access Journals (Sweden)

    James W. Rawlins, Ph.D.

    2010-03-01

    Full Text Available Maleinized soybean oil (MSO has been investigated as a flexible, macromolecular crosslinker for cotton fabrics. The ability of MSO to penetrate crystalline cellulose and crosslink aligned cellulose chains upon cure has been in question. This study compares the penetration capability of MSO to dimethyloldihydroxyethyleneurea (DMDHEU, which is the commercial standard for durable press finishing and is an efficient cellulose crosslinker. X-ray diffraction was employed to characterize changes in the crystalline morphology upon heating un-mercerized cotton fabrics treated with aqueous DMDHEU and soybean oil derivatives. Displacement of characteristic interplanar spacings and the genesis/elimination of diffraction intensities from quintessential planes were evidence of structural modification. The penetration of ammonia neutralized MSO (acid value 230.00 mg KOH/g into the microstructure of cotton cellulose is similar to that of DMDHEU in terms of expanding the interplanar spacings of characteristic planes. Moreover, polymorphism of cotton and mercerized cotton occurred upon treatment with aqueous solutions of MSO. These findings suggest that macromolecular reagents can diffuse into cellulose fibrils if they are sufficiently hydrated or enshrouded by more favored penetrants.

  7. 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.

  8. Translational diffusion of macromolecular assemblies measured using transverse-relaxation-optimized pulsed field gradient NMR.

    Science.gov (United States)

    Horst, Reto; Horwich, Arthur L; Wüthrich, Kurt

    2011-10-19

    In structural biology, pulsed field gradient (PFG) NMR spectroscopy for the characterization of size and hydrodynamic parameters of macromolecular solutes has the advantage over other techniques that the measurements can be recorded with identical solution conditions as used for NMR structure determination or for crystallization trials. This paper describes two transverse-relaxation-optimized (TRO) (15)N-filtered PFG stimulated-echo (STE) experiments for studies of macromolecular translational diffusion in solution, (1)H-TRO-STE and (15)N-TRO-STE, which include CRINEPT and TROSY elements. Measurements with mixed micelles of the Escherichia coli outer membrane protein X (OmpX) and the detergent Fos-10 were used for a systematic comparison of (1)H-TRO-STE and (15)N-TRO-STE with conventional (15)N-filtered STE experimental schemes. The results provide an extended platform for evaluating the NMR experiments available for diffusion measurements in structural biology projects involving molecular particles with different size ranges. An initial application of the (15)N-TRO-STE experiment with very long diffusion delays showed that the tedradecamer structure of the 800 kDa Thermus thermophilus chaperonin GroEL is preserved in aqueous solution over the temperature range 25-60 °C.

  9. Translational diffusion of macromolecular assemblies measured using transverse relaxation-optimized PFG-NMR

    Science.gov (United States)

    Horst, Reto; Horwich, Arthur L.

    2012-01-01

    In structural biology, pulsed field gradient (PFG) NMR for characterization of size and hydrodynamic parameters of macromolecular solutes has the advantage over other techniques that the measurements can be recorded with identical solution conditions as used for NMR structure determination or for crystallization trials. This paper describes two transverse relaxation-optimized (TRO) 15N-filtered PFG stimulated-echo (STE) experiments for studies of macromolecular translational diffusion in solution, 1H-TRO-STE and 15N-TRO-STE, which include CRINEPT and TROSY elements. Measurements with mixed micelles of the Escherichia coli outer membrane protein X (OmpX) and the detergent Fos-10 were used for a systematic comparison of 1H-TRO-STE and 15N-TRO-STE with conventional 15N-filtered STE experimental schemes. The results provide an extended platform for evaluating the NMR experiments available for diffusion measurements in structural biology projects with molecular particles of different size ranges. An initial application of the 15N-TRO-STE experiment with very long diffusion delays showed that the tedradecamer structure of the 800 kDa Thermus thermophilus chaperonin GroEL is preserved in aqueous solution over the temperature range 25–60°C. PMID:21919531

  10. 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.

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

    Directory of Open Access Journals (Sweden)

    Iborra Francisco J

    2007-04-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Cowieson, Nathan Philip; Aragao, David; Clift, Mark; Ericsson, Daniel J.; Gee, Christine; Harrop, Stephen J.; Mudie, Nathan; Panjikar, Santosh; Price, Jason R.; Riboldi-Tunnicliffe, Alan; Williamson, Rachel; Caradoc-Davies, Tom, E-mail: tom.caradoc-davies@synchrotron.org.au [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia)

    2015-01-01

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

  13. Comparing amber fossil assemblages across the Cenozoic.

    Science.gov (United States)

    Penney, David; Langan, A Mark

    2006-06-22

    To justify faunistic comparisons of ambers that differ botanically, geographically and by age, we need to determine that resins sampled uniformly. Our pluralistic approach, analysing size distributions of 671 fossilized spider species from different behavioural guilds, demonstrates that ecological information about the communities of two well-studied ambers is retained. Several lines of evidence show that greater structural complexity of Baltic compared to Dominican amber trees explains the presence of larger web-spinners. No size differences occur in active hunters. Consequently, we demonstrate for the first time that resins were trapping organisms uniformly and that comparisons of amber palaeoecosystem structure across deep time are possible.

  14. Nematode assemblages in the rhizosphere of spring barley (Hordeum vulgare L.) depended on fertilisation and plant growth phase

    DEFF Research Database (Denmark)

    Madsen, Mette Vestergård

    2004-01-01

    rhizosphere; nitrogen and phosphorus fertilisation; nematode assemblages; plant parasites; barley......rhizosphere; nitrogen and phosphorus fertilisation; nematode assemblages; plant parasites; barley...

  15. Maintaining animal assemblages through single-species management: the case of threatened caribou in boreal forest.

    Science.gov (United States)

    Bichet, Orphé; Dupuch, Angélique; Hébert, Christian; Le Borgne, Hélène Le; Fortin, Daniel

    2016-03-01

    With the intensification of human activities, preserving animal populations is a contemporary challenge of critical importance. In this context, the umbrella species concept is appealing because preserving a single species should result in the protection of multiple co-occurring species. Practitioners, though, face the task of having to find suitable umbrellas to develop single-species management guidelines. In North America, boreal forests must be managed to facilitate the recovery of the threatened boreal caribou (Rangifer tarandus). Yet, the effect of caribou conservation on co-occurring animal species remains poorly documented. We tested if boreal caribou can constitute an effective umbrella for boreal fauna. Birds, small mammals, and insects were sampled along gradients of post-harvest and post-fire forest succession. Predictive models of occupancy were developed from the responses of 95 species to characteristics of forest stands and their surroundings. We then assessed the similarity of species occupancy expected between simulated harvested landscapes and a 90 000-km2 uncut landscape. Managed landscapes were simulated based on three levels of disturbance, two timber-harvest rotation cycles, and dispersed or aggregated cut-blocks. We found that management guidelines that were more likely to maintain caribou populations should also better preserve animal assemblages. Relative to fragmentation or harvest cycle, we detected a stronger effect of habitat loss on species assemblages. Disturbing 22%, 35%, and 45% of the landscape should result, respectively, in 80%, 60%, and 40% probability for caribou populations to be sustainable; in turn, this should result in regional species assemblages with Jaccard similarity indices of 0.86, 0.79, and 0.74, respectively, relative to the uncut landscape. Our study thus demonstrates the value of single-species management for animal conservation. Our quantitative approach allows for the evaluation of management guidelines prior

  16. Effects of competition and facilitation on species assemblage in two types of tropical cloud forest.

    Directory of Open Access Journals (Sweden)

    Wenxing Long

    Full Text Available Competition and facilitation between tree individuals are two kinds of non-random processes influencing the structure and functioning of forest communities, but how these two plant-plant interactions change along gradient of resources or environments remains very much a matter of debate. We developed a null model to test the size-distance regression, and assessed the effects of competition and facilitation (including interspecific interactions, intraspecific interactions and overall species interactions on each adult tree species assemblage [diameter at breast height (dbh ≥5 cm] across two types of tropical cloud forest with different environmental and resource regimes. The null model test revealed that 17% to 27% tree species had positive dbh-distance correlations while 11% to 19% tree species showed negative dbh-distance correlations within these two forest types, indicating that both competition and facilitation processes existed during the community assembly. The importance of competition for heterospecific species, and the intensity of competition for both heterospecific and overall species increased from high to low resources for all the shared species spanning the two forests. The importance of facilitation for conspecific and overall species, as well as that the intensity of facilitation for both heterospecific and conspecific species increased with increasing low air temperature stress for all the shared species spanning the two forests. Our results show that both competition and facilitation processes simultaneously affect parts of species assemblage in the tropical cloud forests. Moreover, the fact that nearly 50% species assemblage is not detected with our approaches suggest that tree species in these tropical forest systems are assembled with multiple ecological processes, and that there is a need to explore the processes other than the two biotic interactions in further researches.

  17. Changes in body size, abundance, and energy allocation in rockfish assemblages of the northeast Pacific.

    Science.gov (United States)

    Harvey, Chris J; Tolimieri, Nick; Levin, Phillip S

    2006-08-01

    Fish body size, a key driver of many aspects of fish population biology and ecology, is affected by fisheries that deplete the largest individuals. Rockfish (genus Sebastes) are a diverse group that has been heavily fished on the U.S. West Coast in recent decades. We examined trawl survey data from 1980 to 2001 to determine spatial and temporal trends in body size and density of 16 shelf rockfish species, including six that are considered overfished. Mean individual mass and maximum observed mass declined in the majority of species in one or more zoogeographic regions between central California and Washington. Density changes were far more variable in time and space, but in all regions, density declines were most often associated with large-bodied rockfish. We next estimated the impact of size and density changes on energy consumption and fecundity in a five-species rockfish assemblage that includes bocaccio (S. paucispinis), a large-bodied, overfished species. Indexes of both consumption and fecundity by the assemblage increased in the southern portion of the study area between 1980 and 2001 but decreased in the northern portion. Allocation of energy and reproductive potential within the assemblage shifted dramatically: relative to bocaccio, total energy consumption and fecundity indexes for the other four species increased by orders of magnitude from 1980 to 2001. These changes in community structure may affect the ability of bocaccio and other large rockfish species to recover from overfishing, especially in light of long-term declines in zooplankton production that may also be affecting rockfish size and production. Addressing these issues may require a regional, multispecies management approach.

  18. 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

  19. 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

  20. Source assemblage types for cratonic diamonds from X-ray synchrotron diffraction

    Science.gov (United States)

    Nestola, F.; Alvaro, M.; Casati, M. N.; Wilhelm, H.; Kleppe, A. K.; Jephcoat, A. P.; Domeneghetti, M. C.; Harris, J. W.

    2016-11-01

    Three single crystals of clinopyroxene trapped within three different gem-quality diamonds from the Udachnaya kimberlite (Siberia, Russia) were analysed in situ by single-crystal synchrotron X-ray diffraction in order to obtain information on their chemical composition and infer source assemblage type. A non-destructive approach was used with high-energy (≈ 60 keV; λ ≈ 0.206 Å) at I15, the extreme-conditions beamline at Diamond Light Source. A dedicated protocol was used to center the mineral inclusions located deep inside the diamonds in the X-ray beam. Our results reveal that two of the inclusions can be associated with peridotitic paragenesis whereas the third is eclogitic. This study also demonstrates that this non-destructive experimental approach is extremely efficient in evaluating the origin of minerals trapped in their diamond hosts.

  1. Assemblage time series reveal biodiversity change but not systematic loss.

    Science.gov (United States)

    Dornelas, Maria; Gotelli, Nicholas J; McGill, Brian; Shimadzu, Hideyasu; Moyes, Faye; Sievers, Caya; Magurran, Anne E

    2014-04-18

    The extent to which biodiversity change in local assemblages contributes to global biodiversity loss is poorly understood. We analyzed 100 time series from biomes across Earth to ask how diversity within assemblages is changing through time. We quantified patterns of temporal α diversity, measured as change in local diversity, and temporal β diversity, measured as change in community composition. Contrary to our expectations, we did not detect systematic loss of α diversity. However, community composition changed systematically through time, in excess of predictions from null models. Heterogeneous rates of environmental change, species range shifts associated with climate change, and biotic homogenization may explain the different patterns of temporal α and β diversity. Monitoring and understanding change in species composition should be a conservation priority.

  2. A new Lower Triassic ichthyopterygian assemblage from Fossil Hill, Nevada

    Directory of Open Access Journals (Sweden)

    Neil P. Kelley

    2016-01-01

    Full Text Available We report a new ichthyopterygian assemblage from Lower Triassic horizons of the Prida Formation at Fossil Hill in central Nevada. Although fragmentary, the specimens collected so far document a diverse fauna. One partial jaw exhibits isodont dentition with blunt tipped, mesiodistally compressed crowns and striated enamel. These features are shared with the Early Triassic genus Utatsusaurus known from coeval deposits in Japan and British Columbia. An additional specimen exhibits a different dentition characterized by relatively small, rounded posterior teeth resembling other Early Triassic ichthyopterygians, particularly Grippia. This Nevada assemblage marks a southward latitudinal extension for Early Triassic ichthyopterygians along the eastern margin of Panthalassa and indicates repeated trans-hemispheric dispersal events in Early Triassic ichthyopterygians.

  3. Hybrid carbon nanostructure assemblage for high performance pseudo-capacitors

    Directory of Open Access Journals (Sweden)

    A. K. Mishra

    2012-06-01

    Full Text Available Investigation of novel nanocomposites for pseudo-capacitors with high capacitance and energy density is the spotlight of current energy research. In the present work, hybrid carbon nanostructure assemblage of graphene and multiwalled carbon nanotubes has been used as carbon support to nanostructured RuO2 and polyaniline for high energy supercapacitors. Maximum specific capacitances of 110, 235 and 440 F g−1 at the voltage sweep rate of 10 mV s−1 and maximum energy densities of 7, 12.5 and 20.5 Wh kg−1 were observed for carbon assemblage and its RuO2 and polyanilne decorated nanocomposites, respectively, with 1M H2SO4 as electrolyte.

  4. Conceptualizing Autoethnography as Assemblage: Accounts of Occupational Therapy Practice

    Directory of Open Access Journals (Sweden)

    Sally Denshire PhD

    2013-02-01

    Full Text Available Drawing on theoretical work within ethnography and poststructuralism, this article discusses a conceptualization of autoethnography as assemblage. The concept of assemblage includes but goes beyond the literal bringing together of a range of heterogeneous elements in different modalities to offer different perspectives on a phenomenon. It challenges and displaces boundaries between the individual and the social through a focus on practice, which offers a new ontology of the social. These ideas are illustrated through excerpts from an autoethnographic study of an occupational therapist working with young people in a Sydney children's hospital in the mid-1980s. The article makes visible a material, relational, and affective landscape of remembered practice. Through successive displacements of the self as the primary site of experience and meaning, we seek to contribute new understandings about the potential for autoethnography to engage with professional practice as a space of multiplicity.

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

    Science.gov (United States)

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

    2010-01-01

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

  6. 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.

    2016-01-01

    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. PMID:27478033

  7. 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,

  8. An optimal strategy for X-ray data collection on macromolecular crystals with position-sensitive detectors

    NARCIS (Netherlands)

    Vicković, Ivan; Kalk, Kor H.; Drenth, Jan; Dijkstra, Bauke W.

    1994-01-01

    X-ray data collection on macromolecular crystals is preferably done with minimum exposure time and high completeness. A Fortran procedure - DCS - has been written in the environment of the MADNES program to predict the completeness of data before the start of actual data collection. In addition, the

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

    Science.gov (United States)

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

    2010-01-01

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

  10. 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.

  11. 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.

  12. Lipase-catalyzed Regioselective Synthesis of Vinyl Ester Derivatives of Thiamphenicol: Novel Thiamphenicol Monomers for Preparation of Macromolecular Antibiotic

    Institute of Scientific and Technical Information of China (English)

    Yu Zhen SHI; Zhi Chun CHEN; Na WANG; Qi WU; Xian Fu LIN

    2005-01-01

    Three polymerizable vinyl thiamphenicol esters with different acyl donor carbon chain length (C4, C6, C10) were regioselectivly synthesized by Lipozyme(R) (immobilized from mucor miehei) in acetone at 50 ℃ for 12 h to give 73%, 81%, 63% yield, respectively. The products were valuable monomers for preparation of macromolecular antibiotic.

  13. 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

  14. JMorph: Software for performing rapid morphometric measurements on digital images of fossil assemblages

    Science.gov (United States)

    Lelièvre, Peter G.; Grey, Melissa

    2017-08-01

    Quantitative morphometric analyses of form are widely used in palaeontology, especially for taxonomic and evolutionary research. These analyses can involve several measurements performed on hundreds or even thousands of samples. Performing measurements of size and shape on large assemblages of macro- or microfossil samples is generally infeasible or impossible with traditional instruments such as vernier calipers. Instead, digital image processing software is required to perform measurements via suitable digital images of samples. Many software packages exist for morphometric analyses but there is not much available for the integral stage of data collection, particularly for the measurement of the outlines of samples. Some software exists to automatically detect the outline of a fossil sample from a digital image. However, automatic outline detection methods may perform inadequately when samples have incomplete outlines or images contain poor contrast between the sample and staging background. Hence, a manual digitization approach may be the only option. We are not aware of any software packages that are designed specifically for efficient digital measurement of fossil assemblages with numerous samples, especially for the purposes of manual outline analysis. Throughout several previous studies, we have developed a new software tool, JMorph, that is custom-built for that task. JMorph provides the means to perform many different types of measurements, which we describe in this manuscript. We focus on JMorph's ability to rapidly and accurately digitize the outlines of fossils. JMorph is freely available from the authors.

  15. Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing.

    Science.gov (United States)

    Galand, Pierre E; Casamayor, Emilio O; Kirchman, David L; Potvin, Marianne; Lovejoy, Connie

    2009-07-01

    The Arctic Ocean plays a critical role in controlling nutrient budgets between the Pacific and Atlantic Ocean. Archaea are key players in the nitrogen cycle and in cycling nutrients, but their community composition has been little studied in the Arctic Ocean. Here, we characterize archaeal assemblages from surface and deep Arctic water masses using massively parallel tag sequencing of the V6 region of the 16S rRNA gene. This approach gave a very high coverage of the natural communities, allowing a precise description of archaeal assemblages. This first taxonomic description of archaeal communities by tag sequencing reported so far shows that it is possible to assign an identity below phylum level to most (95%) of the archaeal V6 tags, and shows that tag sequencing is a powerful tool for resolving the diversity and distribution of specific microbes in the environment. Marine group I Crenarchaeota was overall the most abundant group in the Arctic Ocean and comprised between 27% and 63% of all tags. Group III Euryarchaeota were more abundant in deep-water masses and represented the largest archaeal group in the deep Atlantic layer of the central Arctic Ocean. Coastal surface waters, in turn, harbored more group II Euryarchaeota. Moreover, group II sequences that dominated surface waters were different from the group II sequences detected in deep waters, suggesting functional differences in closely related groups. Our results unveiled for the first time an archaeal community dominated by group III Euryarchaeota and show biogeographical traits for marine Arctic Archaea.

  16. Giardia duodenalis sub-Assemblage of animal and human origin in horses.

    Science.gov (United States)

    Traversa, Donato; Otranto, Domenico; Milillo, Piermarino; Latrofa, Maria Stefania; Giangaspero, Annunziata; Di Cesare, Angela; Paoletti, Barbara

    2012-12-01

    In order to evaluate infection occurrence and the potential zoonotic role of horse isolates of Giardia duodenalis, 431 individual fecal samples were genetically characterized by PCR tests -coupled sequencing and phylogenetic analysis. Thirty-seven (8.6%) animals resulted infected by different Assemblage. The presence of sub-Assemblage was assessed by characterizing the β-giardin gene for 16 of the 37 positive horses. Ten isolates showed 99.6% to 100% homology with the sub-Assemblage described as B1-2 and B1-6, three Assemblage A showed 99.8% homology with sub-Assemblage A1, while one Assemblage E displayed 98.8% homology with sub-Assemblage E3. Furthermore, one isolate characterized as Assemblage A showed 99.6% homology with the sub-Assemblage B1-2 and one characterized as E was 100% identical with sub-Assemblage B1-6. These results demonstrate the presence of both animal and human sub-Assemblage of G. duodenalis in horses from Italy. Epidemiological and sanitary implications are discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Characterizing lentic freshwater fish assemblages using multiple sampling methods

    Science.gov (United States)

    Fischer, Jesse R.; Quist, Michael

    2014-01-01

    Characterizing fish assemblages in lentic ecosystems is difficult, and multiple sampling methods are almost always necessary to gain reliable estimates of indices such as species richness. However, most research focused on lentic fish sampling methodology has targeted recreationally important species, and little to no information is available regarding the influence of multiple methods and timing (i.e., temporal variation) on characterizing entire fish assemblages. Therefore, six lakes and impoundments (48–1,557 ha surface area) were sampled seasonally with seven gear types to evaluate the combined influence of sampling methods and timing on the number of species and individuals sampled. Probabilities of detection for species indicated strong selectivities and seasonal trends that provide guidance on optimal seasons to use gears when targeting multiple species. The evaluation of species richness and number of individuals sampled using multiple gear combinations demonstrated that appreciable benefits over relatively few gears (e.g., to four) used in optimal seasons were not present. Specifically, over 90 % of the species encountered with all gear types and season combinations (N = 19) from six lakes and reservoirs were sampled with nighttime boat electrofishing in the fall and benthic trawling, modified-fyke, and mini-fyke netting during the summer. Our results indicated that the characterization of lentic fish assemblages was highly influenced by the selection of sampling gears and seasons, but did not appear to be influenced by waterbody type (i.e., natural lake, impoundment). The standardization of data collected with multiple methods and seasons to account for bias is imperative to monitoring of lentic ecosystems and will provide researchers with increased reliability in their interpretations and decisions made using information on lentic fish assemblages.

  18. Temporal variation in fish assemblage composition on a tidal flat

    Directory of Open Access Journals (Sweden)

    Henry L. Spach

    2004-03-01

    Full Text Available Annual variation in the fish assemblage characteristics on a tidal flat was studied in coastal Paraná, in southern Brazil. Fish were collected between August 1998 and July 1999, during the diurnal high tide and diurnal and nocturnal low tide of the syzygial (full moon and quadrature (waning moon tides, to characterize temporal change in assemblage composition. A total of 64,265 fish in 133 species were collected. The average number of species and individuals, biomass, species richness, diversity (mass and equitability varied significantly over time . The dissimilarity of the assemblage was greatest in August, September and October in contrast with the period from November to January, with the lowest dissimilarity. The combined action of water temperature, salinity and wind intensity had a great influence over the structure of the fish assemblage.Os peixes de uma planície de maré da praia Balneário de Pontal do Sul, Paraná, foram coletados, na preamar diurna e na baixa-mar diurna e noturna das marés de sizígia e de quadratura, visando caracterizar as mudanças temporais entre agosto de 1998 e julho de 1999. As coletas totalizaram 64.265 peixes de 133 espécies. Foram observadas diferenças significativas na captura média em número de espécies e de peixes, peso total e nos índices de riqueza, diversidade (H' peso e eqüitatividade entre os meses de coleta. A dissimilaridade da ictiofauna foi maior entre os meses de agosto, setembro e outubro em comparação com o período de novembro a janeiro. A ação combinada da temperatura da água, salinidade e intensidade do vento, influenciaram mais sobre a estrutura da assembléia de peixes.

  19. A common tendency for phylogenetic overdispersion in mammalian assemblages

    OpenAIRE

    Cooper, Natalie; RODRIGUEZ, JESUS; Purvis, Andy

    2008-01-01

    PUBLISHED Competition has long been proposed as an important force in structuring mammalian communities. Although early work recognised that competition has a phylogenetic dimension, only with recent increases in the availability of phylogenies have true phylogenetic investigations of mammalian community structure become possible. We test whether the phylogenetic structure of 142 assemblages from three mammalian clades (New World monkeys, North American ground squirrels and Australasian po...

  20. Historic changes in fish assemblage structure in midwestern nonwadeable rivers

    Science.gov (United States)

    Parks, Timothy P.; Quist, Michael C.; Pierce, Clay L.

    2014-01-01

    Historical change in fish assemblage structure was evaluated in the mainstems of the Des Moines, Iowa, Cedar, Wapsipinicon, and Maquoketa rivers, in Iowa. Fish occurrence data were compared in each river between historical and recent time periods to characterize temporal changes among 126 species distributions and assess spatiotemporal patterns in faunal similarity. A resampling procedure was used to estimate species occurrences in rivers during each assessment period and changes in species occurrence were summarized. Spatiotemporal shifts in species composition were analyzed at the river and river section scale using cluster analysis, pairwise Jaccard's dissimilarities, and analysis of multivariate beta dispersion. The majority of species exhibited either increases or declines in distribution in all rivers with the exception of several “unknown” or inconclusive trends exhibited by species in the Maquoketa River. Cluster analysis identified temporal patterns of similarity among fish assemblages in the Des Moines, Cedar, and Iowa rivers within the historical and recent assessment period indicating a significant change in species composition. Prominent declines of backwater species with phytophilic spawning strategies contributed to assemblage changes occurring across river systems.

  1. Correspondence between zooplankton assemblages and the Estuary Environment Classification system

    Science.gov (United States)

    Lucena-Moya, Paloma; Duggan, Ian C.

    2017-01-01

    We tested whether variability in zooplankton assemblages was consistent with the categories of estuarine environments proposed by the 'Estuary Environment Classification' system (EEC) (Hume et al., 2007) across a variety of North Island, New Zealand, estuaries. The EEC classifies estuaries in to eight categories (A to F) based primarily on a combination of three abiotic controlling factors: ocean forcing, river forcing and basin morphometry. Additionally, we tested whether Remane's curve, which predicts higher diversities of benthic macrofauna and high and low salinities, can be applied to zooplankton assemblages. We focused on three of the eight EEC categories (B, D and F), which covered the range of estuaries with river inputs dominating (B) to ocean influence dominating (F). Additionally, we included samples from river (FW) and sea (MW) to encompass the entire salinity range. Zooplankton assemblages varied across the categories examined in accordance with a salinity gradient predicted by the EEC. Three groups of zooplankton were distinguishable: the first formed by the most freshwater categories, FW and B, and dominated by rotifers (primarily Bdelloidea) and estuarine copepods (Gladioferans pectinatus), a second group formed by categories D and F, of intermediate salinity, dominated by copepods (Euterpina acutifrons), and a final group including the purely marine category MW and dominated also by E. acutifrons along with other marine taxa. Zooplankton diversity responded to the salinity gradient in a manner expected from Remane's curve. The results of this study support others which have shown salinity to be the main factor driving zooplankton community composition and diversity.

  2. Effects of a brine discharge over soft bottom Polychaeta assemblage

    Energy Technology Data Exchange (ETDEWEB)

    Pilar-Ruso, Yoana del [Dpto. de Ciencias del Mar y Biologia Aplicada, Universidad de Alicante, Campus de San Vicente del Raspeig, Ap. 99, E-03080, Alicante (Spain)], E-mail: yoana.delpilar@ua.es; Ossa-Carretero, Jose Antonio de la; Gimenez-Casalduero, Francisca; Sanchez-Lizaso, Jose Luis [Dpto. de Ciencias del Mar y Biologia Aplicada, Universidad de Alicante, Campus de San Vicente del Raspeig, Ap. 99, E-03080, Alicante (Spain)

    2008-11-15

    Desalination is a growing activity that has introduced a new impact, brine discharge, which may affect benthic communities. Although the role of polychaetes as indicators to assess organic pollution is well known, their tolerance to salinity changes has not been examined to such a great extent. The aim of this study was to examine the effect of brine discharge over soft bottom polychaete assemblage along the Alicante coast (Southeast Spain) over a two year period. Changes in the polychaete assemblage was analysed using univariate and multivariate techniques. We compared a transect in front of the discharge with two controls. At each transect we sampled at three depths (4, 10 and 15 m) during winter and summer. We have observed different sensitivity of polychaete families to brine discharges, Ampharetidae being the most sensitive, followed by Nephtyidae and Spionidae. Syllidae and Capitellidae showed some resistance initially, while Paraonidae proved to be a tolerant family. - The Polychaete assemblage is affected by the brine discharge of the Alicante desalination plant and we detect different sensitivity levels in polychaete families to brine impact.

  3. PCBs in the fish assemblage of a southern European estuary

    Science.gov (United States)

    Baptista, Joana; Pato, Pedro; Pereira, Eduarda; Duarte, Armando C.; Pardal, Miguel A.

    2013-02-01

    The Mondego estuary fish assemblage was studied for the accumulation of PCBs. Three sampling stations were visited along an estuarine salinity gradient, and, in total, 15 species were collected. Analysis of PCBs revealed no significant differences among the sampling stations, although differences were observed among the fish assemblages. Fish assemblages could be divided into three groups. The first group comprised those with higher concentration (more than 10 ng g- 1, dw), included the species Gobius niger, Sardina pilchardus, Anguilla anguilla, Pomatoschistus microps, Chelidonichthys lucerna and Liza ramada; the second group with medium concentration (5-10 ng g- 1, dw), included the species Pomatoschistus minutus, Dicentrarchus labrax, Atherina presbyter, Chelon labrosus, Diplodus vulgaris, Platichthys flesus and Cilata mustela; and a third group with low concentration (less than 5 ng g- 1, dw), included the species Solea solea and Callionymus lyra. A positive correlation was found between lipid content and PCB concentrations. To evaluate the influence of the residence time of species on the accumulation of PCBs, species were divided into two groups: species that spend more than 3 years in the estuary, and species that spend less than 3 years in the estuary. Species that spend more than 3 years in the estuary presented higher concentrations than species that spend less than 3 years in the estuary. CBs 138 and 153 had higher concentration, and tended to increase with time spent in the estuary.

  4. Temporal changes of a macrobenthic assemblage in harsh lagoon sediments

    Science.gov (United States)

    Como, Serena; Magni, Paolo

    2009-08-01

    An opportunistic macrobenthic assemblage was studied from 2001 to 2003 in a central area of the Cabras lagoon (western Sardinia, Italy), known to be affected by environmental disturbances (i.e. organic over-enrichment of sediments, and episodic events of hypoxia/anoxia and sulphide development). We identified recurrent seasonal changes in this macrobenthic assemblage, with a general impoverishment in summer and a recovery in winter/spring. The nereids Neanthes succinea and Hediste diversicolor were found to replace the spionid Polydora ciliata as the most dominant species in the summer for 3 consecutive years. Occasional, unsynchronized appearances of small-sized deposit feeders, such as Tubificidae, Capitella cf. capitata, chironomid larvae and Hydrobia spp., were observed in winter/spring. We suggest that these changes are driven by the interplay of environmental conditions (worse in summer) with numerous biotic factors. This includes different tolerance levels of taxa to low oxygen concentrations and sulphides, variability in larval supply and post-larval transport, as well as competition for space and food between and within different functional groups, and facilitation through animal bioturbation and sediment reoxidation. A conceptual model is proposed to demonstrate how environmental conditions and biotic interactions may control the benthic assemblage in such a harsh lagoon environment.

  5. 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.

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

    Science.gov (United States)

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

    2010-12-01

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

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

    Science.gov (United States)

    Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.; Thiele, Ines; Palsson, Bernhard O.; Saunders, Michael A.

    2017-01-01

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

  8. 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.

  9. Recent Major Improvements to the ALS Sector 5 MacromolecularCrystallography Beamlines

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-07-01

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

  10. Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders

    Science.gov (United States)

    Mittal, Jeetain; Best, Robert B.

    2010-01-01

    We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the variation in folding stability with crowder size for typical α-, β-, and α/β-proteins is well described by an adaptation of the scaled particle theory. The native state, the transition state, and the unfolded protein are treated as effective hard spheres, with the folded and transition state radii independent of the size and concentration of the crowders. Remarkably, we find that, as the effective unfolded state radius is very weakly dependent on the crowder concentration, it can also be approximated by a single size. The same model predicts the effect of crowding on the folding barrier and therefore refolding rates with no adjustable parameters. A simple extension of the scaled-particle theory model, assuming additivity, can also describe the behavior of mixtures of crowding particles. PMID:20338853

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

    KAUST Repository

    Wang, De

    2017-05-09

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

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

    Directory of Open Access Journals (Sweden)

    Marius Schmidt

    2013-01-01

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

  13. 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.

  14. 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.

  15. Diatom assemblage responses to changing environment in the conspicuously eutrophic Kiuruvesi lake route, central-eastern Finland

    Science.gov (United States)

    Tammelin, Mira; Kauppila, Tommi

    2016-04-01

    Lakes and their water quality have been affected by anthropogenic actions for centuries. The most intensive changes have often occurred since the mid-19th century. Industrialization, modern agriculture, forest ditching and artificial lowering of water level are examples of these changes that have usually resulted in the deterioration of lake water quality. Many organisms, such as diatoms, are sensitive to these changes in their environmental conditions. Therefore, a marked species turnover is often seen between the pre and post human impact diatom assemblages. This turnover can be rapidly assessed simultaneously from many lakes by using multivariate methods and top-bottom sampling. Our study area consists of three adjacent lake routes in the grass cultivation and dairy production area of central-eastern Finland, where slash-and-burn cultivation and artificial water level lowering were common practice during the past centuries. The centermost Iisalmi lake route is particularly interesting because of the conspicuously eutrophic lakes in its Kiuruvesi subroute. We used the top-bottom approach to sample pre and post human impact samples from 47 lakes (50 sampling sites) located in the three lake routes. In addition, stratigraphic samples from the long cores of three lakes (one larger central basin and two small upstream lakes) in the Kiuruvesi subroute were studied in more detail. Multivariate methods were used to assess diatom assemblage change within the long cores and between the pre-disturbance and modern samples. The results indicate that most study lakes have undergone a marked shift in their diatom assemblages since the onset of human impact in the area. The lake routes are characterized by differing pre-impact diatom assemblages. However, human influence has reduced their natural variation. Similar diatom species are common in the modern samples of the heavily impacted lakes in all three lake routes. The detailed examination of the diatom assemblage turnover in

  16. Response of Tropical Stream Fish Assemblages to Small Hydropower Induced Flow Alteration in the Western Ghats of Karnataka, India.

    Science.gov (United States)

    Rao, S. T.

    2016-12-01

    Alteration of natural flow regime is considered as one of the major threats to tropical stream fish assemblages as it alters the physio-chemical and micro-habitat features of the river. Flow alteration induced by Small hydro-power (SHP) plants disrupts the flow regime by flow diversion and regulation. The effects of flow alteration on tropical stream fish assemblages, especially in the Western Ghats of India is largely understudied. Such a knowledge is imperative to set limits on flow alteration as SHPs in the Western Ghats are being planned at an unprecedented rate with exemption from environment impact assessments and backing in the form of government subsidies and carbon credits. This study aimed to understand the response of fish assemblages to SHP induced flow alteration in a regulated and unregulated tributary of the Yettinahole River in the Western Ghats of Karnataka. The study intended to quantify the natural and altered flow regime using automated periodic depth measurements, its effect on micro-habitats and environmental variables and finally, understand how fish assemblages respond to such changes. The response of fish assemblage was measured in terms of catch-per-site, species-regime associations and ecological distance between the regimes. The study used a space for time substitution approach and found that the altered flow regime dampened the diurnal and seasonal patterns of natural flow regime. The altered flow regime influenced variations in water quality, micro-habitat heterogeneity and fish assemblage response, each characteristic of the type of flow alteration. The natural flow regime was found to have a higher catch-per-site and strong associations with endemic and niche-specific taxa. Compositional dissimilarities, in terms of ecological distance were observed between the altered and the natural flow regime. Dewatered or flow diverted regime contained species with lentic affinities while an overall low catch-per-site and weak species

  17. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.

    Directory of Open Access Journals (Sweden)

    Rubbiya A Ali

    Full Text Available 3D image reconstruction of large cellular volumes by electron tomography (ET at high (≤ 5 nm resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters-the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms.

  18. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.

    Science.gov (United States)

    Ali, Rubbiya A; Landsberg, Michael J; Knauth, Emily; Morgan, Garry P; Marsh, Brad J; Hankamer, Ben

    2012-01-01

    3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤ 5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters-the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms.

  19. Transition modes in Ising networks: an approximate theory for macromolecular recognition.

    Science.gov (United States)

    Keating, S; Di Cera, E

    1993-07-01

    For a statistical lattice, or Ising network, composed of N identical units existing in two possible states, 0 and 1, and interacting according to a given geometry, a set of values can be found for the mean free energy of the 0-->1 transition of a single unit. Each value defines a transition mode in an ensemble of nu N = 3N - 2N possible values and reflects the role played by intermediate states in shaping the energetics of the system as a whole. The distribution of transition modes has a number of intriguing properties. Some of them apply quite generally to any Ising network, regardless of its dimension, while others are specific for each interaction geometry and dimensional embedding and bear on fundamental aspects of analytical number theory. The landscape of transition modes encapsulates all of the important thermodynamic properties of the network. The free energy terms defining the partition function of the system can be derived from the modes by simple transformations. Classical mean-field expressions can be obtained from consideration of the properties of transition modes in a rather straightforward way. The results obtained in the analysis of the transition mode distributions have been used to develop an approximate treatment of the problem of macromolecular recognition. This phenomenon is modeled as a cooperative process that involves a number of recognition subsites across an interface generated by the binding of two macromolecular components. The distribution of allowed binding free energies for the system is shown to be a superposition of Gaussian terms with mean and variance determined a priori by the theory. Application to the analysis of the biologically interaction of thrombin with hirudin has provided some useful information on basic aspects of the interaction, such as the number of recognition subsites involved and the energy balance for binding and cooperative coupling among them. Our results agree quite well with information derived independently

  20. Species traits and catchment-scale habitat factors influence the occurrence of freshwater mussel populations and assemblages

    Science.gov (United States)

    Pandolfo, Tamara J.; Kwak, Thomas J.; Cope, W. Gregory; Heise, Ryan J.; Nichols, Robert B.; Pacifici, Krishna

    2016-01-01

    Conservation of freshwater unionid mussels presents unique challenges due to their distinctive life cycle, cryptic occurrence and imperilled status. Relevant ecological information is urgently needed to guide their management and conservation.We adopted a modelling approach, which is a novel application to freshwater mussels to enhance inference on rare species, by borrowing data among species in a hierarchical framework to conduct the most comprehensive occurrence analysis for freshwater mussels to date. We incorporated imperfect detection to more accurately examine effects of biotic and abiotic factors at multiple scales on the occurrence of 14 mussel species and the entire assemblage of the Tar River Basin of North Carolina, U.S.A.The single assemblage estimate of detection probability for all species was 0.42 (95% CI, 0.36–0.47) with no species- or site-specific detection effects identified. We empirically observed 15 mussel species in the basin but estimated total species richness at 21 (95% CI, 16–24) when accounting for imperfect detection.Mean occurrence probability among species ranged from 0.04 (95% CI, 0.01–0.16) for Alasmidonta undulata, an undescribed Lampsilis sp., and Strophitus undulatus to 0.67 (95% CI, 0.42–0.86) for Elliptio icterina. Median occurrence probability among sites was <0.30 for all species with the exception of E. icterina. Site occurrence probability generally related to mussel conservation status, with reduced occurrence for endangered and threatened species.Catchment-scale abiotic variables (stream power, agricultural land use) and species traits (brood time, host specificity, tribe) influenced the occurrence of mussel assemblages more than reach- or microhabitat-scale features.Our findings reflect the complexity of mussel ecology and indicate that habitat restoration alone may not be adequate for mussel conservation. Catchment-scale management can benefit an entire assemblage, but species-specific strategies may be

  1. Giardia Assemblages A and B in Diarrheic Patients: A Comparative Study in Egyptian Children and Adults.

    Science.gov (United States)

    El Basha, Noussa R; Zaki, Mayssa M; Hassanin, Omayma M; Rehan, Mohamed K; Omran, Dalia

    2016-02-01

    Giardia duodenalis is considered the most common intestinal parasite in humans worldwide. Children are especially affected, with more severe consequences than adults. The present study was designed to determine the distribution of assemblages A and B Giardia infection in children and adults, with the use of light microscopy and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) as diagnostic procedures, and to investigate its associations with clinical and epidemiological data collected from children and adult groups. This cross-sectional study was conducted from October 2012 to October 2013 by collecting fecal samples from 200 children and 200 adults complaining of diarrhea. Samples were subjected to parasitological examination by direct wet smear and formol-ether methods. Genotyping of G. doudenalis samples was conducted by PCR-RFLP analysis. Giardia duodenalis infection caused by assemblages A and B was identified in 60 samples, 34 from children and 26 from adults. Assemblage B was detected in 38 patients (63.34%), and assemblage A was detected in 22 patients (36.66%). Assemblage A was significantly more frequent in children with age range 2-8 yr, and assemblage B was higher in children with age range 6-16 yr old. Diarrhea frequency/day and recurrences per month affected patients infected with assemblage A (P value Giardia assemblages A and B were identified in children and adults, assemblage A infected younger children more frequently and was more closely related to severe clinical manifestations than assemblage B.

  2. Small proportions of silt linked to distinct and predictable differences in marine macrofaunal assemblages on the continental shelf of the Pacific Northwest

    Science.gov (United States)

    Henkel, S. K.; Politano, K. K.

    2017-07-01

    Increasing interest in offshore development has motivated intensified efforts to map the seafloor for marine spatial planning. However, surficial geologic maps do not accurately represent habitats for various species groups of concern. This study used a bottom-up approach to integrate macrofaunal densities and benthic conditions on the Pacific Northwest shelf to identify macrofaunal assemblages and associated habitat features. Benthic cores and water-column profiles were collected from 137 stations from 50 to 110 m depth. Analyses grouping stations based on both similar species abundances and benthic conditions resulted in six broad habitats. Within the sampled depth and latitudinal range, sediment characteristics were the primary structuring variable. A major break in assemblages was detected between sediment that had less than 1% silt/clay and those containing more than 1% silt/clay. Assemblages differed primarily in the bivalve species present and secondarily in polychaete species. Within the greater than and less than 1% silt/clay habitats, further discretization of assemblages was based mostly on differing abundances of characteristic bivalves and polychaetes associated with differing median grain sizes, which did not correspond to traditional definitions of fine or medium sand. These data show that a bottom-up methodology is necessary to discern habitats for macrofauna and that site-specific physical sampling is necessary to predict macrofaunal assemblage composition. However, if detailed sediment characteristics are known, macrofaunal assemblages may be predicted without time-intensive biological sampling and processing. These results also indicate that seemingly small sedimentary changes due to offshore installations may have measureable effects on the relative abundances and even the species composition of macrofauna.

  3. Changes in mangrove species assemblages and future prediction of the Bangladesh Sundarbans using Markov chain model and cellular automata.

    Science.gov (United States)

    Mukhopadhyay, Anirban; Mondal, Parimal; Barik, Jyotiskona; Chowdhury, S M; Ghosh, Tuhin; Hazra, Sugata

    2015-06-01

    The composition and assemblage of mangroves in the Bangladesh Sundarbans are changing systematically in response to several environmental factors. In order to understand the impact of the changing environmental conditions on the mangrove forest, species composition maps for the years 1985, 1995 and 2005 were studied. In the present study, 1985 and 1995 species zonation maps were considered as base data and the cellular automata-Markov chain model was run to predict the species zonation for the year 2005. The model output was validated against the actual dataset for 2005 and calibrated. Finally, using the model, mangrove species zonation maps for the years 2025, 2055 and 2105 have been prepared. The model was run with the assumption that the continuation of the current tempo and mode of drivers of environmental factors (temperature, rainfall, salinity change) of the last two decades will remain the same in the next few decades. Present findings show that the area distribution of the following species assemblages like Goran (Ceriops), Sundari (Heritiera), Passur (Xylocarpus), and Baen (Avicennia) would decrease in the descending order, whereas the area distribution of Gewa (Excoecaria), Keora (Sonneratia) and Kankra (Bruguiera) dominated assemblages would increase. The spatial distribution of projected mangrove species assemblages shows that more salt tolerant species will dominate in the future; which may be used as a proxy to predict the increase of salinity and its spatial variation in Sundarbans. Considering the present rate of loss of forest land, 17% of the total mangrove cover is predicted to be lost by the year 2105 with a significant loss of fresh water loving mangroves and related ecosystem services. This paper describes a unique approach to assess future changes in species composition and future forest zonation in mangroves under the 'business as usual' scenario of climate change.

  4. Approaches to Pendent Groups' Functionalization of Polyimide

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Pendent groups' functionalization of polyimide is an optimum approach to improve its processability and achieve functionalized polyimide materials. There are two types of modification routes for pendent groups functionalization of polyimide: monomer route and macromolecular route. In this paper, various approaches for pendent groups' functionalization of polyimide are introduced. At the same time, a new method to achieve functional polyimide materials without decreasing its thermal stability and mechanical properties is mentioned.

  5. Spatialities of Hunger: Post-National Spaces, Assemblages and Fragmenting Liabilities

    Directory of Open Access Journals (Sweden)

    Jörg Gertel

    2015-11-01

    Full Text Available This contribution addresses the casual structure and spatialities of food insecurity. Drawing from scholarly debates on periphery, I illustrate the limited explana- tory range of state-centered periphery- approaches in order to comprehend the recent constellations of conflict and hunger. I argue that increasingly dynamic and post-national spaces of food insecurity emerge. Due to complex power geometries, these spaces are driven by realigning and territorially-stretched arrangements of action (e.g. global producer-consumer relations, by technologically enhanced new temporal config- urations (e.g. speculation and high frequency trade in food, by the performances of metrics (e.g. models of food price and value-constructions shaping food security, and by the reflexive effects of knowledge production. In order to comprehend these dynamics, concepts capable of cap- turing new assemblages are required.

  6. Requirements for representative sampling for fluvial fish assemblages – literary review

    Directory of Open Access Journals (Sweden)

    Potyó, I.

    2012-12-01

    Full Text Available Fish are good indicators of long-term changes of fluvial ecosystems therefore, assessment of fish assemblages is frequently used in evaluation of the ecological status of surface waters, especially since the implementation of the EU Water Framework Directive. Long-term changes of fish fauna and old-time abundance of fish populations in the Danube can be documented by historical data of fisheries. Direct detection of long-term changes of fish populations in large rivers is a difficult task due to large-scale temporal and spatial variability of fish distribution. The present study provides a review of river fish sampling methods, with special attention to approaches based on electrofishing. Our goal is to develop a standard monitoring method in large rivers to get more reliable and consistent data for description of long-term changes of fish populations.

  7. Temporal Assemblage Turnovers of Foraminiferal Communities from the Caribbean, United Kingdom and Mediterranean regions

    Science.gov (United States)

    Costelloe, Ashleigh; Wilson, Brent

    2016-04-01

    Temporal assemblage turnovers of intertidal foraminiferal communities were quantitatively determined using the assemblage turnover index (ATI), and contributing species were identified using the conditioned on-boundary index (CoBI). The live foraminiferal communities were examined as metacommunities (all stations) and assemblages (groups of stations defined by cluster analysis) over one and two year periods at Caroni Swamp, Claxton Bay (E Trinidad), Cowpen Marsh (NE England) and Bay of Cádiz (SW Spain). Major assemblage turnovers (when ATI > x + σ) of the Caroni Swamp metacommunity and assemblages coincided with seasonal changes from dry to wet conditions in 2011 and 2012. The abundant species (Ammonia tepida, Ammotium salsum, Arenoparella mexicana, Trochammina advena, Trochammina laevigata and Trochammina inflata) contributed the most to assemblage turnovers but showed no preference to either dry or wet conditions. At Claxton Bay major assemblage turnovers of the metacommunity and mid assemblage coincided with seasonal change and calcareous species (A. tepida and Triloculina oblonga) increased during wet conditions and decreased during dry conditions, while agglutinated species (T. advena and A. salsum) fluctuated oppositely. At Cowpen Marsh major assemblage turnovers of the metacommunity coincided with the start of summer and winter. Assemblages at higher elevations (mainly Jadammina macrescens and Haplophragmoides spp.) were responsible for the summer turnover, while the winter turnover was led by the assemblage at lower elevations (mainly Haynesina germanica, Elphidium earlandi, Elphidium williamsoni, Elphidium excavatum and Quinqueloculina spp.). At Bay of Cádiz, the foraminiferal assemblage at a tidal height of 1.5 to 1.7 m above the hydrographic zero was examined within three separate plots, and the seasonal occurrence of assemblage turnovers differed between plots. Thus, replicate samples and multiple plots may be necessary to overcome spatial

  8. ENVIRONMENTAL CONTROL OF NANNOPLANKTON AND FORAMINIFERA ASSEMBLAGES IN MADURA WATERS

    Directory of Open Access Journals (Sweden)

    Vijaya Isnaniawardhani

    2017-07-01

    Full Text Available Nannoplankton is widely used for determining age of sediments following the other microorganism foraminifera since the late 1960s; and it was started being used for marine geography study in the year of 1984. This topic interests to be done in Indonesia as one of the tropic region. The research covered a study about environment using nannoplankton and it is compared with the same study using foraminifera. Methods of the study include: (1 collecting secondary data and samples; (2 collecting field data record; (3 laboratory analyses upon sediment samples to determine the content of nannoplankton and foraminifera (micropaleontology analyses, the texture and composition of minerals (by means of grain size, petrology megascopic and microscopic analyses (4 intergrating all of the analyses result. Madura waters can be divided into four zones, among all : (I inner shelf (water depth less than 30 m in Madura Strait, (II inner shelf in open marine north of Madura, (III outer shelf (water depth 30 to 80 m in Madura Strait, and (IV outer shelf in open marine north of Madura. Inner shelf in the Madura Strait (Zone I is characterized by less than 1% sediment of nannoplankton (are made up of Gephyrocapsa oceanica; rare assemblages of benthic foraminifera only (Ammonia spp., arenaceous carbonate test taxa such as : Ammobaculites spp., Textularia agglutinans, Haplophragmoides spp., and milliolidae. Inner shelf open marine north of Madura (Zone II yielded few nannoplankton assemblages, dominated by Gephyrocapsa oceanica with low number of Emiliania huxleyi, Helicosphaera carteri, H. pavimentum, H. walichii and Pontosphaera spp; common foraminifera assemblages consist of rare planktic Globigerinoides ruber, G. trilobus sacculiferus, G. conglobatus with one or two dominant benthic (Elphidium spp, Ammonia spp., Pseudorotalia spp., Asterorotalia spp.. Outer shelf of Madura Strait (Zone III assigned by common nannoplankton assemblages, dominated by Gephyrocapsa

  9. Taming Distraction: The Second Screen Assemblage, Television and the Classroom

    Directory of Open Access Journals (Sweden)

    Markus Stauff

    2016-07-01

    Full Text Available This article argues that television’s resilience in the current media landscape can best be understood by analyzing its role in a broader quest to organize attention across different media. For quite a while, the mobile phone was considered to be a disturbance both for watching television and for classroom teaching. In recent years, however, strategies have been developed to turn the second screen’s distractive potential into a source for intensified, personalized and social attention. This has consequences for television’s position in a multimedia assemblage: television’s alleged specificities (e.g. liveness become mouldable features, which are selectively applied to guide the attention of users across different devices and platforms. Television does not end, but some of its traditional features do only persist because of its strategic complementarity with other media; others are re-adapted by new technologies thereby spreading televisual modes of attention across multiple screens. The article delineates the historical development of simultaneous media use as a ‘problematization’—from alternating (and competitive media use to multitasking and finally complementary use of different media. Additionally, it shows how similar strategies of managing attention are applied in the ‘digital classroom’. While deliberately avoiding to pin down, what television is, the analysis of the problem of attention allows for tracing how old and new media features are constantly reshuffled. This article combines three arguments: (1 the second screen is conceived of as both a danger to attention and a tool to manage attention. (2 To organize attention, the second screen assemblage modulates the specific qualities of television and all the other devices involved. (3 While being a fragile and often inconsistent assemblage, the second screen spreads its dynamics—and especially the problem of attention—far beyond television, e.g. into the realm of

  10. Variation in Symbiodinium ITS2 Sequence Assemblages among Coral Colonies

    Science.gov (United States)

    Stat, Michael; Bird, Christopher E.; Pochon, Xavier; Chasqui, Luis; Chauka, Leonard J.; Concepcion, Gregory T.; Logan, Dan; Takabayashi, Misaki; Toonen, Robert J.; Gates, Ruth D.

    2011-01-01

    Endosymbiotic dinoflagellates in the genus Symbiodinium are fundamentally important to the biology of scleractinian corals, as well as to a variety of other marine organisms. The genus Symbiodinium is genetically and functionally diverse and the taxonomic nature of the union between Symbiodinium and corals is implicated as a key trait determining the environmental tolerance of the symbiosis. Surprisingly, the question of how Symbiodinium diversity partitions within a species across spatial scales of meters to kilometers has received little attention, but is important to understanding the intrinsic biological scope of a given coral population and adaptations to the local environment. Here we address this gap by describing the Symbiodinium ITS2 sequence assemblages recovered from colonies of the reef building coral Montipora capitata sampled across Kāne'ohe Bay, Hawai'i. A total of 52 corals were sampled in a nested design of Coral Colony(Site(Region)) reflecting spatial scales of meters to kilometers. A diversity of Symbiodinium ITS2 sequences was recovered with the majority of variance partitioning at the level of the Coral Colony. To confirm this result, the Symbiodinium ITS2 sequence diversity in six M. capitata colonies were analyzed in much greater depth with 35 to 55 clones per colony. The ITS2 sequences and quantitative composition recovered from these colonies varied significantly, indicating that each coral hosted a different assemblage of Symbiodinium. The diversity of Symbiodinium ITS2 sequence assemblages retrieved from individual colonies of M. capitata here highlights the problems inherent in interpreting multi-copy and intra-genomically variable molecular markers, and serves as a context for discussing the utility and biological relevance of assigning species names based on Symbiodinium ITS2 genotyping. PMID:21246044

  11. Variation in Symbiodinium ITS2 sequence assemblages among coral colonies.

    Directory of Open Access Journals (Sweden)

    Michael Stat

    Full Text Available Endosymbiotic dinoflagellates in the genus Symbiodinium are fundamentally important to the biology of scleractinian corals, as well as to a variety of other marine organisms. The genus Symbiodinium is genetically and functionally diverse and the taxonomic nature of the union between Symbiodinium and corals is implicated as a key trait determining the environmental tolerance of the symbiosis. Surprisingly, the question of how Symbiodinium diversity partitions within a species across spatial scales of meters to kilometers has received little attention, but is important to understanding the intrinsic biological scope of a given coral population and adaptations to the local environment. Here we address this gap by describing the Symbiodinium ITS2 sequence assemblages recovered from colonies of the reef building coral Montipora capitata sampled across Kāne'ohe Bay, Hawai'i. A total of 52 corals were sampled in a nested design of Coral Colony(Site(Region reflecting spatial scales of meters to kilometers. A diversity of Symbiodinium ITS2 sequences was recovered with the majority of variance partitioning at the level of the Coral Colony. To confirm this result, the Symbiodinium ITS2 sequence diversity in six M. capitata colonies were analyzed in much greater depth with 35 to 55 clones per colony. The ITS2 sequences and quantitative composition recovered from these colonies varied significantly, indicating that each coral hosted a different assemblage of Symbiodinium. The diversity of Symbiodinium ITS2 sequence assemblages retrieved from individual colonies of M. capitata here highlights the problems inherent in interpreting multi-copy and intra-genomically variable molecular markers, and serves as a context for discussing the utility and biological relevance of assigning species names based on Symbiodinium ITS2 genotyping.

  12. Variation in Symbiodinium ITS2 sequence assemblages among coral colonies.

    Science.gov (United States)

    Stat, Michael; Bird, Christopher E; Pochon, Xavier; Chasqui, Luis; Chauka, Leonard J; Concepcion, Gregory T; Logan, Dan; Takabayashi, Misaki; Toonen, Robert J; Gates, Ruth D

    2011-01-05

    Endosymbiotic dinoflagellates in the genus Symbiodinium are fundamentally important to the biology of scleractinian corals, as well as to a variety of other marine organisms. The genus Symbiodinium is genetically and functionally diverse and the taxonomic nature of the union between Symbiodinium and corals is implicated as a key trait determining the environmental tolerance of the symbiosis. Surprisingly, the question of how Symbiodinium diversity partitions within a species across spatial scales of meters to kilometers has received little attention, but is important to understanding the intrinsic biological scope of a given coral population and adaptations to the local environment. Here we address this gap by describing the Symbiodinium ITS2 sequence assemblages recovered from colonies of the reef building coral Montipora capitata sampled across Kāne'ohe Bay, Hawai'i. A total of 52 corals were sampled in a nested design of Coral Colony(Site(Region)) reflecting spatial scales of meters to kilometers. A diversity of Symbiodinium ITS2 sequences was recovered with the majority of variance partitioning at the level of the Coral Colony. To confirm this result, the Symbiodinium ITS2 sequence diversity in six M. capitata colonies were analyzed in much greater depth with 35 to 55 clones per colony. The ITS2 sequences and quantitative composition recovered from these colonies varied significantly, indicating that each coral hosted a different assemblage of Symbiodinium. The diversity of Symbiodinium ITS2 sequence assemblages retrieved from individual colonies of M. capitata here highlights the problems inherent in interpreting multi-copy and intra-genomically variable molecular markers, and serves as a context for discussing the utility and biological relevance of assigning species names based on Symbiodinium ITS2 genotyping.

  13. Taming Distraction: The Second Screen Assemblage, Television and the Classroom

    Directory of Open Access Journals (Sweden)

    Markus Stauff

    2016-07-01

    Full Text Available This article argues that television’s resilience in the current media landscape can best be understood by analyzing its role in a broader quest to organize attention across different media. For quite a while, the mobile phone was considered to be a disturbance both for watching television and for classroom teaching. In recent years, however, strategies have been developed to turn the second screen’s distractive potential into a source for intensified, personalized and social attention. This has consequences for television’s position in a multimedia assemblage: television’s alleged specificities (e.g. liveness become mouldable features, which are selectively applied to guide the attention of users across different devices and platforms. Television does not end, but some of its traditional features do only persist because of its strategic complementarity with other media; others are re-adapted by new technologies thereby spreading televisual modes of attention across multiple screens. The article delineates the historical development of simultaneous media use as a ‘problematization’—from alternating (and competitive media use to multitasking and finally complementary use of different media. Additionally, it shows how similar strategies of managing attention are applied in the ‘digital classroom’. While deliberately avoiding to pin down, what television is, the analysis of the problem of attention allows for tracing how old and new media features are constantly reshuffled. This article combines three arguments: (1 the second screen is conceived of as both a danger to attention and a tool to manage attention. (2 To organize attention, the second screen assemblage modulates the specific qualities of television and all the other devices involved. (3 While being a fragile and often inconsistent assemblage, the second screen spreads its dynamics—and especially the problem of attention—far beyond television, e.g. into the realm of

  14. Mnemiopsis leidyi Gut Harbors Seasonally Variant and Commensal Microbial Assemblages

    Science.gov (United States)

    Mariita, R. M.; Hossain, M. J.; Liles, M. R.; Moss, A.

    2016-02-01

    Studies have shown that with widespread use of antibiotics in human and domestic animal populations, antibiotic resistance becomes increasingly common in the environment. Estuaries provide ideal conditions for acquisition and dissemination of drug resistance genes because they serve as sinks for pollution. This study aimed to identify M. leidyi microbial diversity and richness and their potential to act as vectors for antibiotic resistance determinants (ARDs). M. leidyi, although native to study area are highly invasive. Metagenomic analyses indicate that there are temporal variations of bacterioplankton assemblages in M. leidyi gut. Overall, Proteobacteria and Actinobacteria are the most abundant phyla. Despite the temporal dynamics in the microbial assemblages in M. leidyi gut, they seem to retain Propionibacterium acnes (gut microbiota in some insects) and select proteobacteria across all seasons. The results contradict previous studies that suggest that M. leidyi does not have constant a microbiota, but only seasonally variant microbial assemblages. Here we reveal the presence of M. leidyi gut ARDs in winter and summer, probably because of the ctenophores' positive geotaxis during rough surface conditions. Genes responsible for resistance to fluoroquinolones, multidrug resistance efflux pumps, mercuric reductase, copper homeostasis and blaR1 genes were observed. This is the first study to demonstrate that M. leidyi harbors constant microbiota and provides a baseline for understanding M. leidyi gut microbial and ARDs ecology. It also suggests that M. leidyi bacterial taxonomic and functional dynamics is influenced by season. Funding: Alabama EPSCoR GRSP fellowship, AU-CMB fellowship, NSF EPS-1158862, USDA-Hatch 370225-310100 (AGM, ML).

  15. Habitat relationships with fish assemblages in minimally disturbed Great Plains regions

    Science.gov (United States)

    Fischer, John R.; Paukert, C.P.

    2008-01-01

    Effects of local environmental influences on the structure of fish assemblages were evaluated from 159 sites in two regions of the Great Plains with limited anthropogenic disturbance. These regions offered an opportunity to evaluate the structure and variation of streams and fish assemblages within the Great Plains. We used canonical correspondence analyses to determine the influence of environmental conditions on species abundances, species occurrences and assemblage characteristics. Analysis of regions separately indicated that similar environmental factors structured streams and fish assemblages, despite differences in environmental conditions and species composition between regions. Variance in fish abundance and assemblage characteristics from both regions was best explained by metrics of stream size and associated metrics (width, depth, conductivity and instream cover). Our results provide a framework and reference for conditions and assemblage structure in North American prairie streams.

  16. Spatial and temporal variability of mobile macro-invertebrate assemblages associated to coralligenous habitat

    Directory of Open Access Journals (Sweden)

    R. BEDINI

    2014-03-01

    Full Text Available The study aimed to investigate patterns of spatial and temporal variability of mobile macroinvertebrate assemblages associated to coralligenous habitat. A multi-factorial sampling design was used to test the hypotheses that the structure of assemblages and their spatial and temporal variability changed in relation to substrate inclination. Moreover, macroalgae and sessile macro-invertebrates were also investigated in order to detect eventual relationship between sessile and mobile assemblages. A total of 236 mobile macro-invertebrate taxa were identified, among them 2 Platyhelminthes, 4 Sipuncula, 6 Nemertea, 27 Mollusca, 86 Annelida, 103 Arthropoda, 8 Echinodermata. Results of the study showed that mobile macro-invertebrate assemblages of coralligenous habitat were little influenced by the inclination of substrate and by the morphology of sessile organisms, as patterns of variation were different between the two assemblages. Mobile macro-invertebrate assemblages changed among sampling dates within one year period and they showed high variability at the spatial scale examined.

  17. Unbiased Cultural Transmission in Time-Averaged Archaeological Assemblages

    CERN Document Server

    Madsen, Mark E

    2012-01-01

    Unbiased models are foundational in the archaeological study of cultural transmission. Applications have as- sumed that archaeological data represent synchronic samples, despite the accretional nature of the archaeological record. I document the circumstances under which time-averaging alters the distribution of model predictions. Richness is inflated in long-duration assemblages, and evenness is "flattened" compared to unaveraged samples. Tests of neutrality, employed to differentiate biased and unbiased models, suffer serious problems with Type I error under time-averaging. Finally, the time-scale over which time-averaging alters predictions is determined by the mean trait lifetime, providing a way to evaluate the impact of these effects upon archaeological samples.

  18. 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).

  19. The succession of late Palaeozoic and Triassic plant assemblages of eastern China

    Science.gov (United States)

    Xingxue, Li; Xiuyuan, Wu

    This is a study dealing with the succession of the megafloras or plant assemblages of China's eastern part, ranging from the early Devonian to later Triassic. The plant assemblages in ascending order are as follows: 1. In the three floras formerly recognized for the early, middle and late Devonian, the latter two are here revised as the Protolepidodendron flora and the Leptophloeum-Archaeopteris flora, respectively. 2. Since the two-fold system of the Carboniferous has been currently accepted in China and the mid-Carboniferous boundary in NW China is drawn at the top of the Tsingyuan Formation (s.s.), the latest plant assemblage of the Lower Carboniferous is better named the Eleutherophyllum waldenburgense-Linopteris densissima-Pecopteris aspera Assemblage and its corresponding plant assemblage in SE China being tentatively named the Paripteris gigantea-Karinopteris acuta f. obtusa Assemblage. Moreover, recent studies on the Penchi flora of north China reveal that some typical Cathaysian elements, e.g. Lepidodendron posthumii, Tingia spp., occurred in the Penchi Formation, of which the plant assemblage is revised as the Paripteris gigantea-Linopteris neuropteroides-Conchophyllum richthofeni Assemblage, known probably as the first assemblage assigned to the early Cathaysian flora in east Asia. 3. The latest Permian (Tartarian) of north China is represented by the Ullmannia bronnii-Yuania magnifolia Assemblage based on recent studies of the flora of the Shihchienfeng (Sunjiagou) Formation. 4. Recent studies on the early Triassic flora in north China disclose that the flora may be named the Pleuromeia flora, which can be subdivided into the early Triassic Pl. jiaochengensis assemblage and the late early Triassic Pl. sternbergii Assemblage. In addition, problems about the correlation for some of the representative formations and their palaeophytogeographical regions are also discussed.

  20. Differences in stability of seed-associated microbial assemblages in response to invasion by phytopathogenic microorganisms

    OpenAIRE

    Samir Rezki; Claire Campion; Beatrice Iacomi-Vasilescu; Anne Preveaux; Youness Toualbia; Sophie Bonneau; Martial Briand; Emmanuelle Laurent; Gilles Hunault; Philippe Simoneau; Marie-Agnès Jacques; Matthieu Barret

    2016-01-01

    Seeds are involved in the vertical transmission of microorganisms from one plant generation to another and consequently act as reservoirs for the plant microbiota. However, little is known about the structure of seed-associated microbial assemblages and the regulators of assemblage structure. In this work, we have assessed the response of seed associated microbial assemblages of Raphanus sativus to invading phytopathogenic agents, the bacterial strain Xanthomonas campestris pv. campestris (Xc...

  1. Temporal changes in taxonomic and functional diversity of fish assemblages downstream from mountaintop mining

    Science.gov (United States)

    Hitt, Nathaniel P.; Chambers, Douglas B.

    2014-01-01

    Mountaintop mining (MTM) affects chemical, physical, and hydrological properties of receiving streams, but the long-term consequences for fish-assemblage structure and function are poorly understood. We sampled stream fish assemblages using electrofishing techniques in MTM exposure sites and reference sites within the Guyandotte River basin, USA, during 2010–2011. We calculated indices of taxonomic diversity (species richness, abundance, Shannon diversity) and functional diversity (functional richness, functional evenness, functional divergence) to compare exposure and reference assemblages between seasons (spring and autumn) and across years (1999–2011). We based temporal comparisons on 2 sites that were sampled during 1999–2001 by Stauffer and Ferreri (2002). Exposure assemblages had lower taxonomic and functional diversity than reference assemblages or simulated assemblages that accounted for random variation. Differences in taxonomic composition between reference and exposure assemblages were associated with conductivity and aqueous Se concentrations. Exposure assemblages had fewer species, lower abundances, and less biomass than reference assemblages across years and seasons. Green Sunfish (Lepomis cyanellus) and Creek Chub (Semotilus atromaculatus) became numerically dominant in exposure assemblages over time because of their persistence and losses of other taxa. In contrast, species richness increased over time in reference assemblages, a result that may indicate recovery from drought. Mean individual biomass increased as fish density decreased and most obligate invertivores were apparently extirpated at MTM exposure sites. Effects of MTM were not related to physical-habitat conditions but were associated with water-quality variables, which may limit quality and availability of benthic macroinvertebrate prey. Simulations revealed effects of MTM that could not be attributed to random variation in fish assemblage structure.

  2. Population-based analyses of Giardia duodenalis is consistent with the clonal assemblage structure

    OpenAIRE

    2012-01-01

    Abstract Background Giardia duodenalis is a common protozoan parasite of humans and animals. Genetic characterization of single loci indicates the existence of eight groups called assemblages, which differ in their host distribution. Molecular analyses challenged the idea that G. duodenalis is a strictly clonal diplomonad by providing evidence of recombination within and between assemblages. Particularly, inter-assemblage recombination events would complicate the interpretation of multi-locus...

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

    Science.gov (United States)

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

    2016-10-01

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

  4. Chemiluminescence-imaging detection of DNA on a solid-phase membrane by using a peroxidase-labeled macromolecular probe.

    Science.gov (United States)

    Azam, Md Golam; Yamasuji, Mutsumi; Krawczyk, Tomasz; Shibata, Takayuki; Kabashima, Tsutomu; Kai, Masaaki

    2015-07-01

    We have developed a novel method for sensitive chemiluminescence (CL)-imaging detection of DNA by using a macromolecular probe synthesized by attaching multiple molecules of horseradish peroxidase (HRP) and biotin in dextran backbone. The probe formed a macromolecular assembly by binding to streptavidin which specifically recognized biotinylated complementary DNA, which was hybridized to a target DNA on a solid-phase membrane. This methodology was applied to CL-imaging detection of a synthetic telomere DNA (TTAGGG)10 and human telomere DNA by using the CL probe comprising of dextranT2000 (MW=ca. 2000kDa) bonded to approximately 42 molecules of HRP and 210 molecules of biotin. The human telomere DNA in a small number of buccal mucous cells (ca. 70 cell numbers) of cheek tissue was quantitatively determined by the proposed CL detection method that afforded approximately 10 times higher sensitivity than that of the conventional CL method using commercially available HRP-avidin probe.

  5. 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.

  6. Seasonal dynamics of fish assemblages on breakwaters and natural rocky reefs in a temperate estuary: consistent assemblage differences driven by sub-adults.

    Science.gov (United States)

    Fowler, Ashley M; Booth, David J

    2013-01-01

    Development of infrastructure around cities is rapidly increasing the amount of artificial substrate (termed artificial reef, 'AR') in coastal marine habitats. However, effects of ARs on marine communities remain unknown, because it is unclear whether ARs can maintain similar communities to natural reefs. We investigated whether well-established (> 30 years old) breakwaters could consistently approximate fish assemblages on interspersed rocky reefs in a temperate estuary over 6 consecutive seasons using regular visual surveys between June 2009 (winter) and November 2010 (spring). We examined whether assemblage differences between reef types were driven by differences in juvenile recruitment, or were related to differences in older life-stages. Assemblages on both reef types were dominated by juveniles (61% of individuals) and sub-adults (34% of individuals). Seasonal fluctuations in assemblage parameters (species richness, diversity, sub-adult abundance) were similar between reef types, and levels of species diversity and assemblage composition were generally comparable. However, abundance and species richness were consistently higher (1.9-7.6 and 1.3-2.6 times, respectively) on breakwaters. These assemblage differences could not be explained by differences in juvenile recruitment, with seasonal patterns of recruitment and juvenile species found to be similar between reef types. In contrast, abundances of sub-adults were consistently higher (1.1-12 times) at breakwaters, and assemblage differences appeared to be driven by this life-stage. Our results indicate that breakwaters in temperate estuaries are capable of supporting abundant and diverse fish assemblages with similar recruitment process to natural reefs. However, breakwaters may not approximate all aspects of natural assemblage structure, with differences maintained by a single-life stage in some cases.

  7. Effects of hydrologic connectivity on aquatic macroinvertebrate assemblages in different marsh types

    Science.gov (United States)

    Kang, Sung-Ryong; King, Sammy L.

    2013-01-01

    Hydrologic connectivity can be an important driver of aquatic macroinvertebrate assemblages. Its effects on aquatic macroinvertebrate assemblages in coastal marshes, however, are relatively poorly studied. We evaluated the effects of lateral hydrologic connectivity (permanently connected ponds: PCPs; temporary connected ponds: TCPs), and other environmental variables on aquatic macroinvertebrate assemblages and functional feeding groups (FFGs) in freshwater, brackish, and saline marshes in Louisiana, USA. We hypothesized that (1) aquatic macroinvertebrate assemblages in PCPs would have higher assemblage metric values (density, biomass, Shannon-Wiener diversity) than TCPs and (2) the density and proportional abundance of certain FFGs (i.e. scrapers, shredders, and collectors) would be greater in freshwater marsh than brackish and saline marshes. The data in our study only partially supported our first hypothesis: while freshwater marsh PCPs had higher density and biomass than TCPs, assemblage metric values in saline TCPs were greater than saline PCPs. In freshwater TCPs, long duration of isolation limited access of macroinvertebrates from adjacent water bodies, which may have reduced assemblage metric values. However, the relatively short duration of isolation in saline TCPs provided more stable or similar habitat conditions, facilitating higher assemblage metric values. As predicted by our second hypothesis, freshwater PCPs and TCPs supported a greater density of scrapers, shredders, and collectors than brackish and saline ponds. Aquatic macroinvertebrate assemblages seem to be structured by individual taxa responses to salinity as well as pond habitat attributes.

  8. Effects of reef proximity on the structure of fish assemblages of unconsolidated substrata.

    Directory of Open Access Journals (Sweden)

    Arthur L Schultz

    Full Text Available Fish assemblages of unconsolidated sedimentary habitats on continental shelves are poorly described when compared to those of hard substrata. This lack of data restricts the objective management of these extensive benthic habitats. In the context of protecting representative areas of all community types, one important question is the nature of the transition from reefal to sedimentary fish assemblages. We addressed this question using Baited Remote Underwater Videos (BRUVs to assess fish assemblages of sedimentary habitats at six distances from rocky reefs (0, 25, 50, 100, 200, and 400 m at four sites in subtropical eastern Australia. Distance from reef was important in determining fish assemblage structure, and there was no overlap between reef sites and sedimentary sites 400 m from reef. While there was a gradient in assemblage structure at intermediate distances, this was not consistent across sites. All sites, however, supported a mixed 'halo' assemblage comprising both reef and sediment species at sampling stations close to reef. BRUVs used in conjunction with high-resolution bathymetric and backscatter spatial data can resolve differences in assemblage structure at small spatial scales (10s to 100s of metres, and has further application in unconsolidated habitats. Unless a 'reef halo' assemblage is being examined, a minimum of 200 m but preferably 400 m distance from any hard substrate is recommended when designing broader-scale assessments of fish assemblages of sedimentary habitats.

  9. Macroalgal assemblages of disturbed coastal detritic bottoms subject to invasive species

    Science.gov (United States)

    Klein, Judith C.; Verlaque, Marc

    2009-04-01

    Characteristic flora and fauna that are highly sensitive to disturbances colonize coastal detritic bottoms in the Mediterranean Sea. In the present study, a comparison of the assemblage composition and colonization by invasive macroalgae was made between two coastal detritic macrophyte assemblages, one dominated by rhodoliths (free-living non-geniculate Corallinales) and the other dominated by fleshy algae, in an area that has been exposed to important levels of anthropogenic disturbance, mainly pollution (including changed sedimentation regimes) in the recent past (bay of Marseilles, France). In comparison with less strongly impacted Mediterranean regions, the macrophyte assemblages in the bay of Marseilles were characteristic in terms of species identity and richness of coastal detritic macrophyte assemblages. However, extremely low species abundance (cover) was observed. As far as invasive species were concerned, Caulerpa racemosa var. cylindracea was only abundant in the rhodolith assemblage whereas the two invasive Rhodophyta Asparagopsis armata and Womersleyella setacea were mainly found in the fleshy algae assemblage. The seasonality observed in the Rhodolith assemblage seemed to be related to the development of C. racemosa var. cylindracea and did not follow the typical pattern of other Mediterranean assemblages. This study represents the first study of coastal detritic assemblages invaded by C. racemosa var. cylindracea.

  10. Autumn ichthyoplankton assemblage in the Yangtze Estuary shaped by environmental factors

    Directory of Open Access Journals (Sweden)

    Hui Zhang

    2016-04-01

    Full Text Available This study investigated the response of the ichthyoplankton community to environmental changes in the Yangtze Estuary using canonical correspondence analysis. Ichthyoplankton community and environmental data were recorded during the autumns of 1998, 2000, 2002, 2003, 2004, 2007 and 2009. Among the ichthyoplankton, the dominant larval and juvenile families were the Engraulidae, Gobiidae and Salangidae, and the most common eggs were from Trichiurus lepturus. The ichthyoplankton was identified via canonical correspondence analysis to three assemblages: an estuary assemblage dominated by Chaeturichthys stigmatias, a coastal assemblage dominated by Engraulis japonicus and Stolephorus commersonii, and an offshore assemblage dominated by Trichiurus lepturus. Regarding environmental factors in the Yangtze Estuary, suspended matter and surface seawater salinity were the main factors influencing the distributions of the different assemblages, while sediment from the Yangtze River during the rainy season and chlorophyll a were the principle drivers of the annual variances in the distribution of ichthyoplankton assemblages. Our aims in this study were to provide detailed characterizations of the ichthyoplankton assemblage in the autumns of seven years, examine the long-term dynamics of autumn ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary.

  11. Autumn ichthyoplankton assemblage in the Yangtze Estuary shaped by environmental factors

    Science.gov (United States)

    Liu, Shude

    2016-01-01

    This study investigated the response of the ichthyoplankton community to environmental changes in the Yangtze Estuary using canonical correspondence analysis. Ichthyoplankton community and environmental data were recorded during the autumns of 1998, 2000, 2002, 2003, 2004, 2007 and 2009. Among the ichthyoplankton, the dominant larval and juvenile families were the Engraulidae, Gobiidae and Salangidae, and the most common eggs were from Trichiurus lepturus. The ichthyoplankton was identified via canonical correspondence analysis to three assemblages: an estuary assemblage dominated by Chaeturichthys stigmatias, a coastal assemblage dominated by Engraulis japonicus and Stolephorus commersonii, and an offshore assemblage dominated by Trichiurus lepturus. Regarding environmental factors in the Yangtze Estuary, suspended matter and surface seawater salinity were the main factors influencing the distributions of the different assemblages, while sediment from the Yangtze River during the rainy season and chlorophyll a were the principle drivers of the annual variances in the distribution of ichthyoplankton assemblages. Our aims in this study were to provide detailed characterizations of the ichthyoplankton assemblage in the autumns of seven years, examine the long-term dynamics of autumn ichthyoplankton assemblages, and evaluate the influence of environmental factors on the spatial distribution and inter-annual variations of ichthyoplankton assemblages associated with the Yangtze Estuary. PMID:27114877

  12. Sporopollen Assemblages from the Cretaceous Yimin Formation of the Hailar Basin, Inner Mongolia, China

    Institute of Scientific and Technical Information of China (English)

    WAN Chuanbiao; QIAO Xiuyun; XU Yanbin; SUN Yuewu; REN Yanguang; JIN Yudong; GAO Ping; LIU Tongyan

    2005-01-01

    Three sporopollen assemblages are recognized for the first time from the Cretaceous Yimin Formation in the Hailar Basin of eastern Inner Mongolia.They are (in ascending order): the Impardecispora-AequitriraditesClavatipollenites assemblage; the Triporoletes-Pilosisporites-Asteropollis assemblage; and the AppendicisporitesAsteropollis-Tricolpites assemblage,distributed in Members 1,2 and 3 of the Yimin Formation respectively.Recognition of this biostratigraphic sequence is very important for the division and correlation of the Yimin Formation in the basin.Meanwhile,the age of the Yimin Formation is considered to be Barremian to Early Albian based on the palynological data.

  13. Identifying Shifts in Leaf-Litter Ant Assemblages (Hymenoptera: Formicidae) across Ecosystem Boundaries Using Multiple Sampling Methods

    Science.gov (United States)

    Wiezik, Michal; Svitok, Marek; Wieziková, Adela; Dovčiak, Martin

    2015-01-01

    Global or regional environmental changes in climate or land use have been increasingly implied in shifts in boundaries (ecotones) between adjacent ecosystems such as beech or oak-dominated forests and forest-steppe ecotones that frequently co-occur near the southern range limits of deciduous forest biome in Europe. Yet, our ability to detect changes in biological communities across these ecosystems, or to understand their environmental drivers, can be hampered when different sampling methods are required to characterize biological communities of the adjacent but ecologically different ecosystems. Ants (Hymenoptera: Formicidae) have been shown to be particularly sensitive to changes in temperature and vegetation and they require different sampling methods in closed vs. open habitats. We compared ant assemblages of closed-forests (beech- or oak-dominated) and open forest-steppe habitats in southwestern Carpathians using methods for closed-forest (litter sifting) and open habitats (pitfall trapping), and developed an integrated sampling approach to characterize changes in ant assemblages across these adjacent ecosystems. Using both methods, we collected 5,328 individual ant workers from 28 species. Neither method represented ant communities completely, but pitfall trapping accounted for more species (24) than litter sifting (16). Although pitfall trapping characterized differences in species richness and composition among the ecosystems better, with beech forest being most species poor and ecotone most species rich, litter sifting was more successful in identifying characteristic litter-dwelling species in oak-dominated forest. The integrated sampling approach using both methods yielded more accurate characterization of species richness and composition, and particularly so in species-rich forest-steppe habitat where the combined sample identified significantly higher number of species compared to either of the two methods on their own. Thus, an integrated sampling

  14. Identifying Shifts in Leaf-Litter Ant Assemblages (Hymenoptera: Formicidae) across Ecosystem Boundaries Using Multiple Sampling Methods.

    Science.gov (United States)

    Wiezik, Michal; Svitok, Marek; Wieziková, Adela; Dovčiak, Martin

    2015-01-01

    Global or regional environmental changes in climate or land use have been increasingly implied in shifts in boundaries (ecotones) between adjacent ecosystems such as beech or oak-dominated forests and forest-steppe ecotones that frequently co-occur near the southern range limits of deciduous forest biome in Europe. Yet, our ability to detect changes in biological communities across these ecosystems, or to understand their environmental drivers, can be hampered when different sampling methods are required to characterize biological communities of the adjacent but ecologically different ecosystems. Ants (Hymenoptera: Formicidae) have been shown to be particularly sensitive to changes in temperature and vegetation and they require different sampling methods in closed vs. open habitats. We compared ant assemblages of closed-forests (beech- or oak-dominated) and open forest-steppe habitats in southwestern Carpathians using methods for closed-forest (litter sifting) and open habitats (pitfall trapping), and developed an integrated sampling approach to characterize changes in ant assemblages across these adjacent ecosystems. Using both methods, we collected 5,328 individual ant workers from 28 species. Neither method represented ant communities completely, but pitfall trapping accounted for more species (24) than litter sifting (16). Although pitfall trapping characterized differences in species richness and composition among the ecosystems better, with beech forest being most species poor and ecotone most species rich, litter sifting was more successful in identifying characteristic litter-dwelling species in oak-dominated forest. The integrated sampling approach using both methods yielded more accurate characterization of species richness and composition, and particularly so in species-rich forest-steppe habitat where the combined sample identified significantly higher number of species compared to either of the two methods on their own. Thus, an integrated sampling

  15. 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.

  16. 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.

  17. "Controlling ourselves, by ourselves": risk assemblages on Malaysia's assembly lines.

    Science.gov (United States)

    Root, Robin

    2008-01-01

    Since the early 1990s, the Malaysian government has identified factories as high risk for HIV and AIDS. Signaling epidemiological concerns over the rising rates of HIV among factory workers, a significant proportion of whom are women, the label also appeared to reconstitute stereotypes of factory women as dangerously sexual and of factories as immoral spaces. Drawing on ethnographic research in the export processing zones of Penang, Malaysia in the mid-1990s, I examine the meanings and experiences of HIV risk among factory women themselves. Data were analyzed using discourse and grounded theory methods, the former to identify women's multiple modes of rationalizing HIV risks, and the latter to theorize the sources and significance of women's HIV risk assemblages. The heuristic of assemblages as localized knowledge spaces helped to show that biomedical and socioreligious risk lexica operated not as fixed epistemological categories but as situational resources in women's risk scripts. Overall, women desired multiple risk knowledges to help them "control themselves by themselves," a project of reflexive self-shaping mediated by the diverse and discordant discourses of gender, ethnicity, and modernity in Malaysia that shaped how HIV risks were engendered and experienced.

  18. Coastal Upwelling Drives Intertidal Assemblage Structure and Trophic Ecology.

    Directory of Open Access Journals (Sweden)

    Carl J Reddin

    Full Text Available Similar environmental driving forces can produce similarity among geographically distant ecosystems. Coastal oceanic upwelling, for example, has been associated with elevated biomass and abundance patterns of certain functional groups, e.g., corticated macroalgae. In the upwelling system of Northern Chile, we examined measures of intertidal macrobenthic composition, structure and trophic ecology across eighteen shores varying in their proximity to two coastal upwelling centres, in a hierarchical sampling design (spatial scales of >1 and >10 km. The influence of coastal upwelling on intertidal communities was confirmed by the stable isotope values (δ13C and δ15N of consumers, including a dominant suspension feeder, grazers, and their putative resources of POM, epilithic biofilm, and macroalgae. We highlight the utility of muscle δ15N from the suspension feeding mussel, Perumytilus purpuratus, as a proxy for upwelling, supported by satellite data and previous studies. Where possible, we used corrections for broader-scale trends, spatial autocorrelation, ontogenetic dietary shifts and spatial baseline isotopic variation prior to analysis. Our results showed macroalgal assemblage composition, and benthic consumer assemblage structure, varied significantly with the intertidal influence of coastal upwelling, especially contrasting bays and coastal headlands. Coastal topography also separated differences in consumer resource use. This suggested that coastal upwelling, itself driven by coastline topography, influences intertidal communities by advecting nearshore phytoplankton populations offshore and cooling coastal water temperatures. We recommend the isotopic values of benthic organisms, specifically long-lived suspension feeders, as in situ alternatives to offshore measurements of upwelling influence.

  19. Life history theory predicts fish assemblage response to hydrologic regimes.

    Science.gov (United States)

    Mims, Meryl C; Olden, Julian D

    2012-01-01

    The hydrologic regime is regarded as the primary driver of freshwater ecosystems, structuring the physical habitat template, providing connectivity, framing biotic interactions, and ultimately selecting for specific life histories of aquatic organisms. In the present study, we tested ecological theory predicting directional relationships between major dimensions of the flow regime and life history composition of fish assemblages in perennial free-flowing rivers throughout the continental United States. Using long-term discharge records and fish trait and survey data for 109 stream locations, we found that 11 out of 18 relationships (61%) tested between the three life history strategies (opportunistic, periodic, and equilibrium) and six hydrologic metrics (two each describing flow variability, predictability, and seasonality) were statistically significant (P history strategies, with 82% of all significant relationships observed supporting predictions from life history theory. Specifically, we found that (1) opportunistic strategists were positively related to measures of flow variability and negatively related to predictability and seasonality, (2) periodic strategists were positively related to high flow seasonality and negatively related to variability, and (3) the equilibrium strategists were negatively related to flow variability and positively related to predictability. Our study provides important empirical evidence illustrating the value of using life history theory to understand both the patterns and processes by which fish assemblage structure is shaped by adaptation to natural regimes of variability, predictability, and seasonality of critical flow events over broad biogeographic scales.

  20. Niche partitioning and species coexistence in a Neotropical felid assemblage

    Science.gov (United States)

    Di Bitetti, Mario S.; De Angelo, Carlos D.; Di Blanco, Yamil E.; Paviolo, Agustín

    2010-07-01

    Carnivores have been used as a model to understand the effects of competition in community structure. Behavioral mechanisms that facilitate species coexistence have been poorly explored and may explain the lack of community-wide morphological character displacement in some carnivore assemblages. We use the results of large-scale and intensive camera-trap surveys conducted in the Atlantic Forest of NE Argentina between 2003 and 2008 to describe the spatial patterns of detection and the daily pattern of records of the six wild cat species present in the region (jaguar Panthera onca, puma Puma concolor, ocelot Leopardus pardalis, jaguarundi Puma yagouaroundi, margay Leopardus wiedii, and oncilla Leopardus tigrinus). We use these patterns to generate hypotheses about behavioral differences that may facilitate species coexistence. The larger species were more frequently recorded in the better-protected areas, probably as a result of anthropogenic effects (poaching of cats and their prey). Competitive release from ocelots and jaguarundis may explain why the oncilla and the margay showed the opposite pattern. Morphologically similar species had the most contrasting activity patterns: the margay was exclusively nocturnal and the jaguarundi diurnal. The other species were cathemeral, but alternated their peaks of activity in relation to the relative order of their body weights. The contrasting temporal patterns observed and the ability of pumas and oncillas to adjust their activity patterns to local conditions may facilitate the coexistence of these cat species and explain the lack of character displacement in this assemblage.

  1. The effects of seasonally variable dragonfly predation on butterfly assemblages.

    Science.gov (United States)

    Tiitsaar, Anu; Kaasik, Ants; Teder, Tiit

    2013-01-01

    Where predation is seasonally variable, the potential impact of a predator on individual prey species will critically depend on phenological synchrony of the predator with the prey. Here we explored the effects of seasonally variable predation in multispecies assemblages of short-lived prey. The study was conducted in a landscape in which we had previously demonstrated generally high, but spatially and seasonally variable dragonfly-induced mortality in adult butterflies. In this system, we show that patterns of patch occupancy in butterfly species flying during periods of peak dragonfly abundance are more strongly associated with spatial variation in dragonfly abundance than patch occupancy of species flying when dragonfly density was low. We provide evidence indicating that this differential sensitivity of different butterfly species to between-habitat differences in dragonfly abundance is causally tied to seasonal variation in the intensity of dragonfly predation. The effect of dragonfly predation could also be measured at the level of whole local butterfly assemblages. With dragonfly density increasing, butterfly species richness decreased, and butterfly species composition tended to show a shift toward a greater proportion of species flying during periods of off-peak dragonfly abundance.

  2. Pollen assemblages as paleoenvironmental proxies in the Florida Everglades

    Science.gov (United States)

    Willard, D.A.; Weimer, L.M.; Riegel, W.L.

    2001-01-01

    Analysis of 170 pollen assemblages from surface samples in eight vegetation types in the Florida Everglades indicates that these wetland sub-environments are distinguishable from the pollen record and that they are useful proxies for hydrologic and edaphic parameters. Vegetation types sampled include sawgrass marshes, cattail marshes, sloughs with floating aquatics, wet prairies, brackish marshes, tree islands, cypress swamps, and mangrove forests. The distribution of these vegetation types is controlled by specific environmental parameters, such as hydrologic regime, nutrient availability, disturbance level, substrate type, and salinity; ecotones between vegetation types may be sharp. Using R-mode cluster analysis of pollen data, we identified diagnostic species groupings; Q-mode cluster analysis was used to differentiate pollen signatures of each vegetation type. Cluster analysis and the modern analog technique were applied to interpret vegetational and environmental trends over the last two millennia at a site in Water Conservation Area 3A. The results show that close modern analogs exist for assemblages in the core and indicate past hydrologic changes at the site, correlated with both climatic and land-use changes. The ability to differentiate marshes with different hydrologic and edaphic requirements using the pollen record facilitates assessment of relative impacts of climatic and anthropogenic changes on this wetland ecosystem on smaller spatial and temporal scales than previously were possible. ?? 2001 Elsevier Science B.V.

  3. Pollen assemblages as paleoenvironmental proxies in the Florida Everglades.

    Science.gov (United States)

    Willard, D A.; Weimer, L M.; Riegel, W L.

    2001-04-01

    Analysis of 170 pollen assemblages from surface samples in eight vegetation types in the Florida Everglades indicates that these wetland sub-environments are distinguishable from the pollen record and that they are useful proxies for hydrologic and edaphic parameters. Vegetation types sampled include sawgrass marshes, cattail marshes, sloughs with floating aquatics, wet prairies, brackish marshes, tree islands, cypress swamps, and mangrove forests. The distribution of these vegetation types is controlled by specific environmental parameters, such as hydrologic regime, nutrient availability, disturbance level, substrate type, and salinity; ecotones between vegetation types may be sharp. Using R-mode cluster analysis of pollen data, we identified diagnostic species groupings; Q-mode cluster analysis was used to differentiate pollen signatures of each vegetation type. Cluster analysis and the modern analog technique were applied to interpret vegetational and environmental trends over the last two millennia at a site in Water Conservation Area 3A. The results show that close modern analogs exist for assemblages in the core and indicate past hydrologic changes at the site, correlated with both climatic and land-use changes. The ability to differentiate marshes with different hydrologic and edaphic requirements using the pollen record facilitates assessment of relative impacts of climatic and anthropogenic changes on this wetland ecosystem on smaller spatial and temporal scales than previously were possible.

  4. Studies of Cystoseira assemblages in Northern Atlantic Iberia

    Directory of Open Access Journals (Sweden)

    García-Fernández, Alicia

    2016-06-01

    Full Text Available The Iberian Peninsula contains 24 specific and infraespecific taxa of the genus Cystoseira, but only 6 inhabit in Northern Iberia: C. baccata, C. foeniculacea, C. humilis var. myriophylloides, C. nodicaulis, C. tamariscifolia, and C. usneoides. The Cystoseira assemblages exhibit a complex structure and stratification that allows the presence of a large associate biota and a rich epiphytic flora. Although in the Mediterranean Sea several species have been analyzed in depth, the Atlantic ones are less studied. A revision of the literature (1931-2014 and grey information was made to know the diversity of the North Atlantic Iberian Cystoseira assemblages. The community of C. baccata harbors the biggest number of species (215, followed by C. tamariscifolia (162 and C. usneoides (126, whereas the community with fewest species was the C. foeniculacea one (34. More than 70 species were present in the majority of the Cystoseira assemblages. In this article, are revised also environmental issues in the Cystoseira assemblages, as pollution and anthropogenic pressures or disturbances that cause regression in their communities, and effects of biological invasions by non-native species. As a conclusion, it will necessary to study the Cystoseira assemblage in depth, starting by research of C. baccata along Northern Iberia, as it is an exclusive and widely distributed Atlantic species with very scarce information concerning its role in structuring the communities.La Península Ibérica contiene 24 táxones del género Cystoseira, pero sólo 6 habitan en las costas del norte: C. baccata, C. foeniculacea, C. humilis var. myriophylloides, C. nodicaulis, C. tamariscifolia y C. usneoides. Las comunidades de Cystoseira muestran una estructura compleja debido a su estratificación, lo que permite el desarrollo de una amplia biota asociada y una gran riqueza de flora epífita. Aunque diversas especies mediterráneas han sido analizadas en profundidad, las atl

  5. 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.

  6. 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.

  7. 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

  8. 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.

  9. Interaction of wall shear stress magnitude and gradient in the prediction of arterial macromolecular permeability.

    Science.gov (United States)

    LaMack, Jeffrey A; Himburg, Heather A; Li, Xue-Mei; Friedman, Morton H

    2005-04-01

    Large spatial shear stress gradients have anecdotally been associated with early atherosclerotic lesion susceptibility in vivo and have been proposed as promoters of endothelial cell dysfunction in vitro. Here, experiments are presented in which several measures of the fluid dynamic shear stress, including its gradient, at the walls of in vivo porcine iliac arteries, are correlated against the transendothelial macromolecular permeability of the vessels. The fluid dynamic measurements are based on postmortem vascular casts, and permeability is measured from Evans blue dye (EBD) uptake. Time-averaged wall shear stress (WSS), as well as a new parameter termed maximum gradient stress (MGS) that describes the spatial shear stress gradient due to flow acceleration at a given point, are mapped for each artery and compared on a point-by-point basis to the corresponding EBD patterns. While there was no apparent relation between MGS and EBD uptake, a composite parameter, WSS(-0.11) MGS(0.044), was highly correlated with permeability. Notwithstanding the small exponents, the parameter varied widely within the region of interest. The results suggest that sites exposed to low wall shear stresses are more likely to exhibit elevated permeability, and that this increase is exacerbated in the presence of large spatial shear stress gradients.

  10. Macromolecular crowding and the steady-state kinetics of malate dehydrogenase.

    Science.gov (United States)

    Poggi, Christopher G; Slade, Kristin M

    2015-01-20

    To understand how macromolecular crowding affects enzyme activity, we quantified the Michaelis-Menten kinetics of mitochondrial malate dehydrogenase (MDH) in the presence of hen egg white (HEW), lysozyme, bovine serum albumin (BSA), gum arabic, poly(vinylpyrrolidone) (PVP), and dextrans of various molecular weights. Although crowding tended to decrease Km and Vmax values, the magnitude depended on the crowding agent, reaction direction, and isozyme (mitochondrial porcine heart or thermophlic TaqMDH from Thermus flavus). Crowding slowed oxaloacetate reduction more significantly than malate oxidation, which may suggest that mitochondrial enzymes have evolved to function optimally under the crowded constraints in which they are immersed. Since direct comparisons of neutral to charged crowders are underrepresented in the literature, we performed these studies and found that neutral crowding agents lowered Vmax values more than charged crowders of similar size. The exception was hen egg white, a mixture of charged proteins that caused the largest observed decreases in both Km and Vmax. Finally, the data provide insight about the mechanism by corroborating MDH subunit dependence.

  11. Effect of the macromolecular architecture of biodegradable polyurethanes on the controlled delivery of ocular drugs.

    Science.gov (United States)

    da Silva, Gisele Rodrigues; da Silva Cunha, Armando; Ayres, Eliane; Oréfice, Rodrigo L

    2009-02-01

    Controlled delivery of drugs is a major issue in the treatment of ocular diseases, such as in the treatment of uveitis. In this study, dexamethasone acetate, an important type of corticoid used in the treatment of some uveitis, was incorporated into biodegradable polyurethanes (PU) having different macromolecular architectures. The biodegradable polyurethanes were obtained by preparing PU aqueous dispersions having poly(caprolactone) and/or poly(ethylene glycol) as soft segments. The drug was incorporated into the polymer by dissolving it in the PU aqueous dispersion. FTIR results showed the presence of the drug in the polymer with its original chemical structure. Small angle X-ray scattering (SAXS) results were explored to show that the incorporation of dexamethasone acetate led to the modification of the nanostructure of the polyurethane having only poly(caprolactone) as the soft segment, while the drug did not change significantly the microphase separated structure of PU having both poly(caprolactone) and poly(ethylene glycol) as soft segments. The evaluation of the release of the drug in vitro demonstrated that the obtained biodegradable polyurethanes were well succeeded in delivering dexamethasone acetate at an almost constant rate for 53 weeks. The presence of poly(ethylene glycol) together with poly(caprolactone) as soft segment in biodegradable PU was able to increase the rate of dexamethasone acetate release when compared to the rate of drug release from PU having only poly(caprolactone).

  12. Influence of temperature and macromolecular mobility on sorption of TCE on humic acid coated mineral surfaces.

    Science.gov (United States)

    Bell, Katherine Young; LeBoeuf, Eugene J

    2013-01-01

    This study demonstrates differences in sorptive capacity of volatile organic compound (VOC) trichloroethylene (TCE) onto natural organic matter (NOM) coated and uncoated mineral surfaces above and below the NOM glass transition temperature. TCE sorption isotherms for dry NOM-mineral systems below the NOM glass transition temperature (T(g)) demonstrated sorption behavior characteristic of micropore filling, with sorption capacities reduced relative to uncoated mineral matrices. Such differences were not entirely associated with differences in surface areas of the coated and uncoated mineral matrices, but were likely associated with either a blockage of pore space available to the VOC or a kinetic limitation that does not allow the VOC access to the internal porosity of the model soil within the time periods of the experiment. TCE sorption in dry NOM-mineral matrices above the T(g), however, was described in terms of sorption within a more fluid, macromolecular dissolution medium that does not hinder access to mineral surfaces. Such observations have potential important implications for modeling the fate and transport of VOCs in soils and sediment systems.

  13. 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.

  14. Enzyme activity determination on macromolecular substrates by isothermal titration calorimetry: application to mesophilic and psychrophilic chitinases.

    Science.gov (United States)

    Lonhienne, T; Baise, E; Feller, G; Bouriotis, V; Gerday, C

    2001-02-09

    Isothermal titration calorimetry has been applied to the determination of the kinetic parameters of chitinases (EC 3.2.1.14) by monitoring the heat released during the hydrolysis of chitin glycosidic bonds. Experiments were carried out using two different macromolecular substrates: a soluble polymer of N-acetylglucosamine and the insoluble chitin from crab shells. Different experimental temperatures were used in order to compare the thermodependence of the activity of two chitinases from the psychrophile Arthrobacter sp. TAD20 and of chitinase A from the mesophile Serratia marcescens. The method allowed to determine unequivocally the catalytic rate constant k(cat), the activation energy (E(a)) and the thermodynamic activation parameters (DeltaG(#), DeltaH(#), DeltaS(#)) of the chitinolytic reaction on the soluble substrate. The catalytic activity has also been determined on insoluble chitin, which displays an effect of substrate saturation by chitinases. On both substrates, the thermodependence of the activity of the psychrophilic chitinases was lower than that observed with the mesophilic counterpart.

  15. Chemical composition and structural features of the macromolecular components of plantation Acacia mangium wood.

    Science.gov (United States)

    Pinto, Paula C; Evtuguin, Dmitry V; Pascoal Neto, Carlos

    2005-10-05

    The wood of Acacia mangium, a prominent fast-growing plantation species used in the pulp-and-paper industry and, so far, poorly investigated for its chemical structure, was submitted to a detailed characterization of its main macromolecular components. Lignin (28% wood weight) isolated by mild acidolysis and characterized by permanganate oxidation, 1H and 13C NMR, and GPC, showed a very low content of syringylpropane-derived units (S:G:H of 48:49:3), a high degree of condensation, a low content of beta-O-4 ( approximately 0.40-0.43 per C6) structures, and a Mw of 2230. Glucuronoxylan (14% wood weight) isolated by alkaline (KOH) or by dimethyl sulfoxide extraction was characterized by methylation analysis, 1H NMR, and GPC. About 10% of the xylopyranose (Xylp) units constituting the linear backbone were substituted at O-2 with 4-O-methylglucuronic acid residues. Almost half of the Xylp units (45%) were O-2 (18%), O-3 (24%) or O-2,3 (3%) acetylated. X-ray diffraction analysis of cellulose (46% wood weight), isolated according to the Kürschner-Hoffer method, showed a degree of crystallinity of 67.6%.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. Large area high-resolution CCD-based X-ray detector for macromolecular crystallography

    CERN Document Server

    Pokric, M; Jorden, A R; Cox, M P; Marshall, A; Long, P G; Moon, K; Jerram, P A; Pool, P; Nave, C; Derbyshire, G E; Helliwell, J R

    2002-01-01

    An X-ray detector system for macromolecular crystallography based on a large area charge-coupled device (CCD) sensor has been developed as part of a large research and development programme for advanced X-ray sensor technology, funded by industry and the Particle Physics and Astronomy Research Council (PPARC) in the UK. The prototype detector consists of two large area three-sides buttable charge-coupled devices (CCD 46-62 EEV), where the single CCD area is 55.3 mmx41.5 mm. Overall detector imaging area is easily extendable to 85 mmx110 mm. The detector consists of an optically coupled X-ray sensitive phosphor, skewed fibre-optic studs and CCDs. The crystallographic measurement requirements at synchrotron sources are met through a high spatial resolution (2048x1536 pixel array), high dynamic range (approx 10 sup 5), a fast readout (approx 1 s), low noise (<10e sup -) and much reduced parallax error. Additionally, the prototype detector system has been optimised by increasing its efficiency at low X-ray ene...

  2. 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.

  3. 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.

  4. 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.

  5. The status of the macromolecular crystallography beamlines at the European Synchrotron Radiation Facility

    Science.gov (United States)

    Mueller-Dieckmann, Christoph; Bowler, Matthew W.; Carpentier, Philippe; Flot, David; McCarthy, Andrew A.; Nanao, Max H.; Nurizzo, Didier; Pernot, Petra; Popov, Alexander; Round, Adam; Royant, Antoine; de Sanctis, Daniele; von Stetten, David; Leonard, Gordon A.

    2015-04-01

    The European Synchrotron Radiation Facility (ESRF) is the oldest and most powerful 3rd generation synchrotron in Europe, providing X-rays to more than 40 experimental stations welcoming several thousand researchers per year. A major success story has been the ESRF's facilities for macromolecular crystallography (MX). These are grouped around 3 straight sections: On ID23 canted undulators accommodate ID23-1, a mini-focus tuneable energy end station and ID23-2, the world's first micro-focus beamline dedicated to MX; ID29 houses a single, mini-focus, tuneable energy end station; ID30 will provide three end stations for MX due in operation from mid-2014 to early 2015. Here, one branch of a canted X-ray source feeds two fixed-energy end stations (MASSIF-1, MASSIF-3). The second feeds ID30B, a variable focus, tuneable energy beamline. MASSIF-1 is optimised for automatic high-throughput experiments requiring a relatively large beam size at the sample position, MASSIF-3 is a high-intensity, micro-focus facility designed to complement ID23-2. All end stations are highly automated, equipped with sample mounting robots and large area, fast-readout photon-counting detectors. Experiment control and tracking is achieved via a combination of the MXCuBE2 graphical user interface and the ISPyB database, the former allowing user-friendly control of all beamline components, the latter providing data tracking before, after and during experiments.

  6. 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.

  7. 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.

  8. Characterization of PEG-Like Macromolecular Coatings on Plasma Modified NiTi Alloy

    Science.gov (United States)

    Yang, Jun; Gao, Jiacheng; Chang, Peng; Wang, Jianhua

    2008-04-01

    A poly (ethylene glycol) (PEG-like) coating was developed to improve the biocompatibility of Nickel-Titanium (NiTi) alloy implants. The PEG-like macromolecular coatings were deposited on NiTi substrates at a room temperature of 298 K through a ECR (electron-cyclotron resonance) cold-plasma enhanced chemical vapor deposition method using tetraglyme (CH3-O-(CH2-CH2-O)4-CH3) as a precursor. A power supply with a frequency of 2.45 GHz was applied to ignite the plasma with Ar(argon) used as the carrier gas. Based on the atomic force microscopy (AFM) studies, a thin smooth coating on NiTi substrates with highly amorphous functional groups on the modified NiTi surfaces were mainly the same accumulated stoichiometric ratio of C and O with PEG. The vitro studies showed that platelet-rich plasma (PRP) adsorption on the modified NiTi alloy surface was significantly reduced. This study indicated that plasma surface modification changes the surface components of NiTi alloy and subsequently improves its biocompatibility.

  9. Characterization of PEG-Like Macromolecular Coatings on Plasma Modified NiTi Alloy

    Institute of Scientific and Technical Information of China (English)

    YANG Jun; GAO Jiacheng; CHANG Peng; WANG Jianhua

    2008-01-01

    A poly(ethylene glycol) (PEG-like) coating was developed to improve the biocompatibility of Nickel-Titanium (NiTi) alloy implants. The PEG-like macromolecular coatings were deposited on NiTi substrates at a room temperature of 298 K through a ECR (electron-cyclotron resonance) cold-plasma .enhanced chemical vapor deposition method using tetraglyme (CH3-O(CH2-CH2-O)4-CH3) as a precursor. A power supply with a frequency of 2.45 GHz was applied to ignite the plasma with Ar(argon) used as the carrier gas. Based on the atomic force microscopy (AFM) studies, a thin smooth coating on NiTi substrates with highly amorphous functional groups on the modified NiTi surfaces were mainly the same accumulated stoichiometric ratio of C and O with PEG. The vitro studies showed that platelet-rich plasma (PRP) adsorption on the modified NiTi alloy surface was significantly reduced. This study indicated that plasma surface modification changes the surface components of NiTi alloy and subsequently improves its biocompatibility.

  10. Macromolecular depletion modulates the binding of red blood cells to activated endothelial cells.

    Science.gov (United States)

    Yang, Yang; Koo, Stephanie; Lin, Cheryl Shuyi; Neu, Björn

    2010-09-01

    Adhesion of red blood cells (RBCs) to endothelial cells (ECs) is usually insignificant but an enhanced adhesion has been observed in various diseases associated with vascular complications. This abnormal adhesion under pathological conditions such as sickle cell disease has been correlated with increased levels of various plasma proteins but the detailed underlying mechanism(s) remains unclear. Usually it is assumed that the proadhesive effects of plasma proteins originate from ligand interactions cross-linking receptors on adjacent cells, but explicit results detailing binding sites or receptors for some proteins (e.g., fibrinogen) on either RBC or EC surfaces that would support this model are missing. In this study, the authors tested whether there is an alternative mechanism. Their results demonstrate that dextran 2 MDa promotes the adhesion of normal RBCs to thrombin-activated ECs and that this effect becomes more pronounced with increasing thrombin concentration or with prolonged thrombin incubation time. It is concluded that depletion interaction originating from nonadsorbing macromolecules (i.e., dextran) can modulate the adhesion of red blood cells to thrombin-activated EC. This study thereby suggests macromolecular depletion as an alternative mechanism for the adhesion-promoting effects of nonadsorbing plasma proteins. These findings should not only aid in getting a better understanding of diseases associated with vascular complications but should also have many potential applications in biomedical or biotechnological areas that require the control of cell-cell or cell surface interactions.

  11. 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

  12. MetalPDB: a database of metal sites in biological macromolecular structures.

    Science.gov (United States)

    Andreini, Claudia; Cavallaro, Gabriele; Lorenzini, Serena; Rosato, Antonio

    2013-01-01

    We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner.

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

    Directory of Open Access Journals (Sweden)

    Shaobin Gu

    2016-04-01

    Full Text Available 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.

  14. 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.

  15. 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.

  16. 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.

  17. Effects of single-tree selection harvesting on hymenopteran and saproxylic insect assemblages in the canopy and understory of northern temperate forests

    Institute of Scientific and Technical Information of China (English)

    Sandy M.Smith; Nurul Islam; M.Isabel Bellocq

    2012-01-01

    Insects respond to changes in microhabitat caused by canopy disturbance,and thus can be used to examine the ecological impacts of harvesting.Single-tree selection harvesting is the most common silvicultural system used to emulate local small-scale natural disturbance and maintain uneven-aged forest structure in temperate forests.Here,we test for differences in richness,abundance,and composition of hymenopteran and saproxylic insect assemblages at four different taxon levels (selected insect orders; and all hymenopteran families,and braconid subfamilies and morphospecies) between the canopy and understory of unharvested and single-tree selection harvested sites in a northern temperate forest from central Canada.Harvesting had no effect on insect assemblage richness,composition or abundance at the three highest taxon levels (order,family and subfamily).Similarly,richness and abundance at the lowest-taxon level (braconid morphospecies) were similar,although composition differed slightly between unharvested and harvested stands.Insect assemblages were vertically stratified,with generally higher abundance (for Diptera,Hymenoptera,some hymenopteran families and braconid subfamilies) and richness (for braconid morphospecies) in the understory than the canopy.In particular,composition of the braconid morphospecies assemblage showed relatively low similarity between the understory and canopy.Single-tree selection harvesting appears to influence wood-associated insect taxa only subtly through small changes in community composition at the lowest taxon level,and thus is recommended as a conservative approach for managing these northern temperate forests.

  18. Rarefaction and Extrapolation: Making Fair Comparison of Abundance-Sensitive Phylogenetic Diversity among Multiple Assemblages.

    Science.gov (United States)

    Hsieh, T C; Chao, Anne

    2017-01-01

    Measures of phylogenetic diversity are basic tools in many studies of systematic biology. Faith’s PD (sum of branch lengths of a phylogenetic tree connecting all focal species) is the most widely used phylogenetic measure. Like species richness, Faith’s PD based on sampling data is highly dependent on sample size and sample completeness. The sample-size- and sample-coverage-based integration of rarefaction and extrapolation of Faith’s PD was recently developed to make fair comparison across multiple assemblages. However, species abundances are not considered in Faith’s PD. Based on the framework of Hill numbers, Faith’s PD was generalized to a class of phylogenetic diversity measures that incorporates species abundances. In this article, we develop both theoretical formulae and analytic estimators for seamless rarefaction and extrapolation for this class of abundance-sensitive phylogenetic measures, which includes simple transformations of phylogenetic entropy and of quadratic entropy. This work generalizes the previous rarefaction/extrapolation model of Faith’s PD to incorporate species abundance, and also extends the previous rarefaction/extrapolation model of Hill numbers to include phylogenetic differences among species. Thus a unified approach to assessing and comparing species/taxonomic diversity and phylogenetic diversity can be established. A bootstrap method is suggested for constructing confidence intervals around the phylogenetic diversity, facilitating the comparison of multiple assemblages. Our formulation and estimators can be extended to incidence data collected from multiple sampling units. We also illustrate the formulae and estimators using bacterial sequence data from the human distal esophagus and phyllostomid bat data from three habitats.

  19. Genetic diversity of eukaryotic plankton assemblages in Eastern Tibetan Lakes differing by their salinity and altitude.

    Science.gov (United States)

    Wu, Qinglong L; Chatzinotas, Antonis; Wang, Jianjun; Boenigk, Jens

    2009-10-01

    Eukaryotic plankton assemblages in 11 high-mountain lakes located at altitudes of 2,817 to 5,134 m and over a total area of ca. one million square kilometers on the Eastern Tibet Plateau, spanning a salinity gradient from 0.2 (freshwater) to 187.1 g l(-1) (hypersaline), were investigated by cultivation independent methods. Two 18S rRNA gene-based fingerprint approaches, i.e., the terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing were applied. Samples of the same lake type (e.g., freshwater) generally shared more of the same bands or T-RFs than samples of different types (e.g., freshwater versus saline). However, a certain number of bands or T-RFs among the samples within each lake were distinct, indicating the potential presence of significant genetic diversity within each lake. PCA indicated that the most significant environmental gradient among the investigated lakes was salinity. The observed molecular profiles could be further explained (17-24%) by ion percentage of chloride, carbonate and bicarbonate, and sulfate, which were also covaried with change of altitude and latitude. Sequence analysis of selected major DGGE bands revealed many sequences (largely protist) that are not related to any known cultures but to uncultured eukaryotic picoplankton and unidentified eukaryotes. One fourth of the retrieved sequences showed eukaryotic plankton, which were found worldwide and detected in low land lakes, were also detected in habitats located above 4,400 m, suggesting a cosmopolitan distribution of these phylotypes. Collectively, our study suggests that there was a high beta-diversity of eukaryotic plankton assemblages in the investigated Tibetan lakes shaped by multiple geographic and environmental factors.

  20. Recovery of macrobenthic assemblages following experimental sand burial

    Directory of Open Access Journals (Sweden)

    José J. Barrón

    2008-09-01

    Full Text Available This research was supported by a fund provided by the Instituto de Ciencias del Mar y Limnología (UNAM and a fund provided to Celia Olabarria in 2004 and 2005 by the University of Vigo for overseas short stays.AbstractPeriodic inundation by sand is a very common feature of rocky coasts throughout the world. Even so, there have been few direct observations or experiments to investigate the role of sediments on intertidal rocky shores. We designed a field experiment in Mazatlán Bay, Mexico, to test the initial impact and subsequent recovery of intertidal macrobenthic assemblages exposed to sand burial at two sites of varying wave exposure. Both sites supported different natural assemblages. Treatment plots for the addition of sediment and control plots (50 × 50 cm, separated by at least 1.5 m, were randomly placed across the mid-water tidal level. The initial response of the resident macrobenthos and the subsequent recolonization was monitored over a period of 95 days. The main effect of sediment deposition at both sites was mortality and removal of biota due to smothering. The recovery process was rapid and may in part have been the result of the mechanism by which the small, disturbed patches were recolonized. Most of the invertebrates colonized the patches as adults; several seaweeds exhibited vegetative growth as the major mechanism of colonization (e.g., Ulva lactuca Linnaeus, 1753, Amphiroa valonioides Yendo, 1902 and Chaetomorpha antennina (Borgensen Kutzing, 1849. The rate of recovery varied between the sites, however. Recovery of species numbers proceeded quickly at the sheltered site (day 7, but took 95 days at the exposed site. In contrast, biomass reached control levels by day 45 at the sheltered site, but already by day 15 at the exposed site. By day 95, the assemblages recovered to 83.5% and 81% similarity with the controls at the sheltered and exposed sites respectively. Although differences in wave exposure could be very

  1. Isotopic characteristics of canopies in simulated leaf assemblages

    Science.gov (United States)

    Graham, Heather V.; Patzkowsky, Mark E.; Wing, Scott L.; Parker, Geoffrey G.; Fogel, Marilyn L.; Freeman, Katherine H.

    2014-11-01

    The geologic history of closed-canopy forests is of great interest to paleoecologists and paleoclimatologists alike. Closed canopies have pronounced effects on local, continental and global rainfall and temperature patterns. Although evidence for canopy closure is difficult to reconstruct from the fossil record, the characteristic isotope gradients of the "canopy effect" could be preserved in leaves and proxy biomarkers. To assess this, we employed new carbon isotopic data for leaves collected in diverse light environments within a deciduous, temperate forest (Maryland, USA) and for leaves from a perennially closed canopy, moist tropical forest (Bosque Protector San Lorenzo, Panamá). In the tropical forest, leaf carbon isotope values range 10‰, with higher δ13Cleaf values occurring both in upper reaches of the canopy, and with higher light exposure and lower humidity. Leaf fractionation (Δleaf) varied negatively with height and light and positively with humidity. Vertical 13C enrichment in leaves largely reflects changes in Δleaf, and does not trend with δ13C of CO2 within the canopy. At the site in Maryland, leaves express a more modest δ13C range (∼6‰), with a clear trend that follows both light and leaf height. Using a model we simulate leaf assemblage isotope patterns from canopy data binned by elevation. The re-sampling (bootstrap) model determined both the mean and range of carbon isotope values for simulated leaf assemblages ranging in size from 10 to over 1000 leaves. For the tropical forest data, the canopy's isotope range is captured with 50 or more randomly sampled leaves. Thus, with a sufficient number of fossil leaves it is possible to distinguish isotopic gradients in an ancient closed canopy forest from those in an open forest. For very large leaf assemblages, mean isotopic values approximate the δ13C of carbon contributed by leaves to soil and are similar to observed δ13Clitter values at forested sites within Panamá, including the

  2. Identification and mapping of bottom fish assemblages in Davis Strait and southern Baffin Bay

    DEFF Research Database (Denmark)

    Jørgensen, Ole A; Hvingel, Carsten; Møller, P. R.;

    2005-01-01

    multinomial logit model was then applied to calculate vectors of probabilities defining the likelihood of each haul belonging to each of the seven clusters. The spatial distribution of the conditional probabilities for each cluster (assemblage) was mapped by means of a geostatistical tool. Each assemblage...

  3. Assemblage Organization in Stream Fishes: Effects of Enviromental Variation and Interspecific Interactions

    Science.gov (United States)

    Gary D. Grossman; Robert E. Ratajczak; Maurice Crawford; Mary C. Freeman

    1998-01-01

    We assessed the relative importance of environmental variation, interspecific competition for space, and predator abundance on assemblage structure and microhabitat use in a stream fish assemblage inhabiting Coweeta Creek, North Carolina, USA. Our study encompassed a l0-yr time span (1983-1992) and included some of the highest and lowest flows in the last 58 years. We...

  4. Changes in dominance patterns in upper Carboniferous plant-fossil assemblages

    Science.gov (United States)

    Pfefferkorn, Hermann W.; Thomson, Margaret C.

    1982-12-01

    Upper Carboniferous (Pennsylvanian) terrestrial clastic rocks from North America and Europe contain compression-impression plant-fossil assemblages that represent the remains of plant communities that grew on floodplains, levees, and other clastic facies of fluvial and deltaic lowlands. Quantitative analysis of 66 plant-fossil assemblages spanning the entire late Carboniferous demonstrates that before the middle of the Westphalian D Stage the majority of plant-fossil assemblages are dominated by pteridosperms and sphenopsids. Lycopods and cordaites dominate only a few assemblages counted. Ferns do not dominate any assemblages. These findings contrast sharply with the dominance of lycopods reported by others from coal swamps of the same time interval. Above the middle of the Westphalian D, however, one-third of the compression-impression assemblages counted are dominated by ferns. The change in dominance pattern in compression-impression plant-fossil assemblages occurs half a stage earlier than the previously reported change from lycopod-dominated to fern-dominated assemblages at the Westphalian-Stephanian boundary in coal swamps. A trend toward dryer climate during Westphalian D apparently influenced plants growing on better-drained alluvial soils earlier than those growing on water-logged soils of contemporaneous coal swamps. *Present address: Room 108 Math.-Geology Building, University of Minnesota, Duluth, Minnesota 55812

  5. Lunch Time at the Child Care Centre: Neoliberal Assemblages in Early Childhood Education

    Science.gov (United States)

    Nxumalo, Fikile; Pacini-Ketchabaw, Veronica; Rowan, Mary Caroline

    2011-01-01

    In this article we interrogate neoliberal assemblages within the context of eating and feeding practices in early childhood education. We consider how neoliberal assemblages are enacted and created through multiple linkages between micro and macro regulations and policies, and everyday food routines. We attend to the embodied intensities, desires…

  6. Intra-Diegetic Cameras as Cinematic Actor Assemblages in Found Footage Horror Cinema

    DEFF Research Database (Denmark)

    Rødje, Kjetil

    2017-01-01

    This article proposes a reconceptualization of the term “actor” within motion pictures and presents the argument that “acting” is a matter of distributed agency performed by heterogeneous assemblages. What constitutes an actor is what I will label as a “cinematic actor assemblage,” a term that co...

  7. THE SEVEN PRINCIPELS OF USEFUL INNOVATION OF SOCIO-MATERIAL ASSEMBLAGES

    DEFF Research Database (Denmark)

    Tjørnehøj, Gitte; Nicolajsen, Hanne Westh

    2017-01-01

    . That the need for innovations now extends beyond administration into more complex social areas, calls for taking the theory of technology as social-material assemblages serious, and ponder; how can innovation towards these assemblages be understood and what aspects characterizes this innovation in complex...

  8. Petrogenesis of opaque assemblages in the Ningqiang carbonaceous chondrite

    Institute of Scientific and Technical Information of China (English)

    HSU; WeiBiao

    2007-01-01

    Numerous round to oblate opaque assemblages (OAs) are found in chondrules and matrix of the Ningqiang carbonaceous chondrite. They are mainly composed of Ni-rich metal,magnetite,Fe,Ni-sulfides,with minor amounts of phosphate,phosphoran-olivine,pyroxene and trace amounts of nano-sized platinum-group metal alloys. The mineralogy of Ningqiang OAs is very similar to that of OAs previously reported in Ca,Al-rich inclusions of CV chondrites. Being a rare mineral phase in nature,phosphoran-olivine is thought to form by nonequilibrium reactions between P-bearing molten metal and olivine crystals during rapid cooling. Its occurrence in Ningqiang OAs indicates that the precursor of OAs was locally produced during chondrule formation,rather than directly condensed from the solar nebula as previously thought. The petrographic and mineralogical characteristics of Ningqiang OAs reveal that OAs formed by low temperature alterations of pre-existing homogeneous alloys within chondrules on a planetary body.

  9. Description of viral assemblages associated with the Gorgonia ventalina holobiont

    Science.gov (United States)

    Hewson, I.; Brown, J. M.; Burge, C. A.; Couch, C. S.; LaBarre, B. A.; Mouchka, M. E.; Naito, M.; Harvell, C. D.

    2012-06-01

    The diversity and function of viruses in coral holobionts has only recently received attention. The non-reef building gorgonian octocoral, Gorgonia ventalina, is a major constituent of Caribbean reefs. We investigated viral communities associated with G. ventalina tissues to understand their role in gorgonian ecology. Pyrosequencing was used to prepare a total of 514,632 sequence reads of DNA- and RNA-based mixed-community viral genomes (metaviromes). RNA viral assemblages were comprised of primarily unidentifiable reads, with most matching host transcripts and other RNA metaviromes. DNA metaviromes were similar between healthy and diseased tissues and comprised of contiguous sequences (contigs) that matched primarily metazoan and bacterial proteins. Only ~5% of contigs matched viral proteins that were primarily cyanophage and viruses of Chlorella and Ostreococcus. Our results confirm that DNA and RNA viruses comprise a component of the gorgonian holobiont, suggesting that they may play a role in the ecology of G. ventalina.

  10. Petrogenesis of opaque assemblages in the Ningqiang carbonaceous chondrite

    Institute of Scientific and Technical Information of China (English)

    WANG Ying; HUA Xin; HSU WeiBiao

    2007-01-01

    Numerous round to oblate opaque assemblages (OAs) are found in chondrules and matrix of the Ningqiang carbonaceous chondrite. They are mainly composed of Ni-rich metal, magnetite, Fe,Ni-sulfides, with minor amounts of phosphate, phosphoran-olivine, pyroxene and trace amounts of nano-sized platinum-group metal alloys. The mineralogy of Ningqiang OAs is very similar to that of OAs previously reported in Ca, Al-rich inclusions of CV chondrites. Being a rare mineral phase in nature,phosphoran-olivine is thought to form by nonequilibrium reactions between P-bearing molten metal and olivine crystals during rapid cooling. Its occurrence in Ningqiang OAs indicates that the precursor of OAs was locally produced during chondrule formation, rather than directly condensed from the solar nebula as previously thought. The petrographic and mineralogical characteristics of Ningqiang OAs reveal that OAs formed by low temperature alterations of pre-existing homogeneous alloys within chondrules on a planetary body.

  11. The (Big Data-security assemblage: Knowledge and critique

    Directory of Open Access Journals (Sweden)

    Claudia Aradau

    2015-10-01

    Full Text Available The Snowden revelations and the emergence of ‘Big Data’ have rekindled questions about how security practices are deployed in a digital age and with what political effects. While critical scholars have drawn attention to the social, political and legal challenges to these practices, the debates in computer and information science have received less analytical attention. This paper proposes to take seriously the critical knowledge developed in information and computer science and reinterpret their debates to develop a critical intervention into the public controversies concerning data-driven security and digital surveillance. The paper offers a two-pronged contribution: on the one hand, we challenge the credibility of security professionals’ discourses in light of the knowledge that they supposedly mobilize; on the other, we argue for a series of conceptual moves around data, human–computer relations, and algorithms to address some of the limitations of existing engagements with the Big Data-security assemblage.

  12. Identification of Giardia lamblia Assemblage E in Humans Points to a New Anthropozoonotic Cycle.

    Science.gov (United States)

    Fantinatti, Maria; Bello, Alexandre R; Fernandes, Octavio; Da-Cruz, Alda M

    2016-10-15

    Giardia lamblia is a pathogen transmitted by water and food that causes infection worldwide. Giardia genotypes are classified into 8 assemblages (A-H). Assemblages A and B are detected in humans, but they are potentially zoonotic because they infect other mammalian hosts. Giardia in samples from 44 children was genotyped. Conserved fragments of the genes encoding β-giardin and glutamate dehydrogenase were sequenced and their alignment were carried out with sequences deposited in GenBank. As expected for Rio de Janeiro, the majority of samples were related to assemblage A. Surprisingly, assemblage E was detected in 15 samples. Detection of assemblage E in humans suggests a new zoonotic route of Giardia transmission. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  13. Bleaching response of coral species in the context of assemblage response

    Science.gov (United States)

    Swain, Timothy D.; DuBois, Emily; Goldberg, Scott J.; Backman, Vadim; Marcelino, Luisa A.

    2017-06-01

    Caribbean coral reefs are declining due to a mosaic of local and global stresses, including climate change-induced thermal stress. Species and assemblage responses differ due to factors that are not easily identifiable or quantifiable. We calculated a novel species-specific metric of coral bleaching response, taxon- α and - β, which relates the response of a species to that of its assemblages for 16 species over 18 assemblages. By contextualizing species responses within the response of their assemblages, the effects of environmental factors are removed and intrinsic differences among taxa are revealed. Most corals experience either a saturation response, overly sensitive to weak stress ( α > 0) but under-responsive compared to assemblage bleaching ( β bleaching ( β > 1). This metric may help reveal key factors of bleaching susceptibility and identify species as targets for conservation.

  14. Genome-wide analyses of recombination suggest that Giardia intestinalis assemblages represent different species.

    Science.gov (United States)

    Xu, Feifei; Jerlström-Hultqvist, Jon; Andersson, Jan O

    2012-10-01

    Giardia intestinalis is a major cause of waterborne enteric disease in humans. The species is divided into eight assemblages suggested to represent separate Giardia species based on host specificities and the genetic divergence of marker genes. We have investigated whether genome-wide recombination occurs between assemblages using the three available G. intestinalis genomes. First, the relative nonsynonymous substitution rates of the homologs were compared for 4,009 positional homologs. The vast majority of these comparisons indicate genetic isolation without interassemblage recombinations. Only a region of 6 kbp suggests genetic exchange between assemblages A and E, followed by gene conversion events. Second, recombination-detecting software fails to identify within-gene recombination between the different assemblages for most of the homologs. Our results indicate very low frequency of recombination between the syntenic core genes, suggesting that G. intestinalis assemblages are genetically isolated lineages and thus should be viewed as separated Giardia species.

  15. The role of depth in regulating water quality and fish assemblages in oxbow lakes

    Science.gov (United States)

    Goetz, Daniel B.; Miranda, Leandro E.; Kroger, Robert; Andrews, Caroline S.

    2015-01-01

    We evaluated water quality and fish assemblages in deep (> 3.0 m; N = 7) and shallow (water temperatures. Conversely, deeper lakes were represented by higher visibility, stable oxygen levels, and cooler water temperatures. Fish assemblages in shallow lakes were dominated by tolerant, small-bodied fishes and those able to breathe atmospheric oxygen. Deeper lakes had a greater representation of predators and other large-bodied fishes. Our evaluation suggests fish assemblages are reflective of oxbow lakes water quality, which is shaped by depth. Understanding the interactions between depth, water quality, and fish assemblages may facilitate development of effective management plans for improving conditions necessary to sustain diverse fish assemblages in agriculturally dominated basins.

  16. Different processes lead to similar patterns: a test of codivergence and the role of sea level and climate changes in shaping a southern temperate freshwater assemblage

    Directory of Open Access Journals (Sweden)

    Barber Brian R

    2011-11-01

    Full Text Available Abstract Background Understanding how freshwater assemblages have been formed and maintained is a fundamental goal in evolutionary and ecological disciplines. Here we use a historical approach to test the hypothesis of codivergence in three clades of the Chilean freshwater species assemblage. Molecular studies of freshwater crabs (Aegla: Aeglidae: Anomura and catfish (Trichomycterus arealatus: Trichomycteridae: Teleostei exhibited similar levels of genetic divergences of mitochondrial lineages between species of crabs and phylogroups of the catfish, suggesting a shared evolutionary history among the three clades in this species assemblage. Results A phylogeny was constructed for Trichomycterus areolatus under the following best-fit molecular models of evolution GTR + I + R, HKY + I, and HKY for cytochrome b, growth hormone, and rag 1 respectively. A GTR + I + R model provided the best fit for both 28S and mitochondrial loci and was used to construct both Aegla phylogenies. Three different diversification models were observed and the three groups arose during different time periods, from 2.25 to 5.05 million years ago (Ma. Cladogenesis within Trichomycterus areolatus was initiated roughly 2.25 Ma (Late Pliocene - Early Pleistocene some 1.7 - 2.8 million years after the basal divergences observed in both Aegla clades. These results reject the hypothesis of codivergence. Conclusions The similar genetic distances between terminal sister-lineages observed in these select taxa from the freshwater Chilean species assemblage were formed by different processes occurring over the last ~5.0 Ma. Dramatic changes in historic sea levels documented in the region appear to have independently shaped the evolutionary history of each group. Our study illustrates the important role that history plays in shaping a species assemblage and argues against assuming similar patterns equal a shared evolutionary history.

  17. Evaluating habitat associations of a fish assemblage at multiple spatial scales in a minimally disturbed stream using low-cost remote sensing

    Science.gov (United States)

    Cheek, Brandon D.; Grabowski, Timothy B.; Bean, Preston T.; Groeschel, Jillian R.; Magnelia, Stephan J.

    2016-01-01

    Habitat heterogeneity at multiple scales is a major factor affecting fish assemblage structure. However, assessments that examine these relationships at multiple scales concurrently are lacking. The lack of assessments at these scales is a critical gap in understanding as conservation and restoration efforts typically work at these levels.A combination of low-cost side-scan sonar surveys, aerial imagery using an unmanned aerial vehicle, and fish collections were used to evaluate the relationship between physicochemical and landscape variables at various spatial scales (e.g. micro-mesohabitat, mesohabitat, channel unit, stream reach) and stream–fish assemblage structure and habitat associations in the South Llano River, a spring-fed second-order stream on the Edwards Plateau in central Texas during 2012–2013.Low-cost side-scan sonar surveys have not typically been used to generate data for riverscape assessments of assemblage structure, thus the secondary objective was to assess the efficacy of this approach.The finest spatial scale (micro-mesohabitat) and the intermediate scale (channel unit) had the greatest explanatory power for variation in fish assemblage structure.Many of the fish endemic to the Edwards Plateau showed similar associations with physicochemical and landscape variables suggesting that conservation and restoration actions targeting a single endemic species may provide benefits to a large proportion of the endemic species in this system.Low-cost side-scan sonar proved to be a cost-effective means of acquiring information on the habitat availability of the entire river length and allowed the assessment of how a full suite of riverscape-level variables influenced local fish assemblage structure.

  18. An empirical, hierarchical typology of tree species assemblages for assessing forest dynamics under global change scenarios.

    Science.gov (United States)

    Costanza, Jennifer K; Coulston, John W; Wear, David N

    2017-01-01

    The composition of tree species occurring in a forest is important and can be affected by global change drivers such as climate change. To inform assessment and projection of global change impacts at broad extents, we used hierarchical cluster analysis and over 120,000 recent forest inventory plots to empirically define forest tree assemblages across the U.S., and identified the indicator and dominant species associated with each. Cluster typologies in two levels of a hierarchy of forest assemblages, with 29 and 147 groups respectively, were supported by diagnostic criteria. Groups in these two levels of the hierarchy were labeled based on the top indicator species in each, and ranged widely in size. For example, in the 29-cluster typology, the sugar maple-red maple assemblage contained the largest number of plots (30,068), while the butternut-sweet birch and sourwood-scarlet oak assemblages were both smallest (6 plots each). We provide a case-study demonstration of the utility of the typology for informing forest climate change impact assessment. For five assemblages in the 29-cluster typology, we used existing projections of changes in importance value (IV) for the dominant species under one low and one high climate change scenario to assess impacts to the assemblages. Results ranged widely for each scenario by the end of the century, with each showing an average decrease in IV for dominant species in some assemblages, including the balsam fir-quaking aspen assemblage, and an average increase for others, like the green ash-American elm assemblage. Future work should assess adaptive capacity of these forest assemblages and investigate local population- and community-level dynamics in places where dominant species may be impacted. This typology will be ideal for monitoring, assessing, and projecting changes to forest communities within the emerging framework of macrosystems ecology, which emphasizes hierarchies and broad extents.

  19. 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.

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

    Science.gov (United States)

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

    2013-11-01

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

  1. Prospects for simulating macromolecular surfactant chemistry at the ocean-atmosphere boundary

    Science.gov (United States)

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

  2. 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.

  3. Structure of metaphase chromosomes: a role for effects of macromolecular crowding.

    Science.gov (United States)

    Hancock, Ronald

    2012-01-01

    In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll) in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

  4. Macromolecular interactions of triterpenoids and targeted toxins: role of saponins charge.

    Science.gov (United States)

    Thakur, Mayank; Weng, Alexander; Pieper, Alexandra; Mergel, Katharina; von Mallinckrodt, Benedicta; Gilabert-Oriol, Roger; Görick, Cornelia; Wiesner, Burkhard; Eichhorst, Jenny; Melzig, Matthias F; Fuchs, Hendrik

    2013-10-01

    Macromolecular interaction of protein toxins with certain plant triterpenoids holds potential for application in tumor therapy. The ability of only certain saponins to enhance the endosomal escape of toxins specifically in tumor cells was evaluated and set into correlation with the electrophoretic mobility. Saponins from Saponaria officinalis Linn, were selected as a lead to understand this evolutionarily conserved principle in detail. Agarose gel electrophoresis was utilized to procure pure saponin fractions with different electrophoretic mobility, which were tested for their ability to enhance the toxicity by live cell monitoring. Five fractions (SOG1-SOG5) were isolated with a relative electrophoretic mobility of (-0.05, 0.41, 0.59, 0.75 and 1.00) and evaluated using thin layer chromatography, HPLC, and mass spectroscopic analysis. Cytotoxicity experiments revealed highest effectiveness with SOG3. Live cell imaging experiments with SOG3 revealed that this saponin with a specific REM of 0.59 could assist in the lyso/endosomal release of the toxic payload without affecting the integrity of plasma membrane and could lead to the induction of apoptosis. This charge dependent enhancement was also found to be highly specific to type I ribosome inactivating proteins compared to bacterial toxins. Charge interaction of plant toxins and saponins with tumor cells, plays a major role in toxin specific modulation of response. The finding opens up newer ways of finding protein saponin interaction conserved evolutionarily and to test their role in endosomal escape of therapeutic molecules. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. 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

  6. Temperature Sensitivity as a Microbial Trait Using Parameters from Macromolecular Rate Theory

    Directory of Open Access Journals (Sweden)

    Charlotte Jean Alster

    2016-11-01

    Full Text Available The activity of soil microbial extracellular enzymes is strongly controlled by temperature, yet the degree to which temperature sensitivity varies by microbe and enzyme type is unclear. Such information would allow soil microbial enzymes to be incorporated in a traits-based framework to improve prediction of ecosystem response to global change. If temperature sensitivity varies for specific soil enzymes, then determining the underlying causes of variation in temperature sensitivity of these enzymes will provide fundamental insights for predicting nutrient dynamics belowground. In this study, we characterized how both microbial taxonomic variation as well as substrate type affects temperature sensitivity. We measured β-glucosidase, leucine aminopeptidase, and phosphatase activities at six temperatures: 4, 11, 25, 35, 45, and 60°C, for seven different soil microbial isolates. To calculate temperature sensitivity, we employed two models, Arrhenius, which predicts an exponential increase in reaction rate with temperature, and Macromolecular Rate Theory (MMRT, which predicts rate to peak and then decline as temperature increases. We found MMRT provided a more accurate fit and allowed for more nuanced interpretation of temperature sensitivity in all of the enzyme × isolate combinations tested. Our results revealed that both the enzyme type and soil isolate type explain variation in parameters associated with temperature sensitivity. Because we found temperature sensitivity to be an inherent and variable property of an enzyme, we argue that it can be incorporated as a microbial functional trait, but only when using the MMRT definition of temperature sensitivity. We show that the Arrhenius metrics of temperature sensitivity are overly sensitive to test conditions, with activation energy changing depending on the temperature range it was calculated within. Thus, we propose the use of the MMRT definition of temperature sensitivity for accurate

  7. Temperature Sensitivity as a Microbial Trait Using Parameters from Macromolecular Rate Theory.

    Science.gov (United States)

    Alster, Charlotte J; Baas, Peter; Wallenstein, Matthew D; Johnson, Nels G; von Fischer, Joseph C

    2016-01-01

    The activity of soil microbial extracellular enzymes is strongly controlled by temperature, yet the degree to which temperature sensitivity varies by microbe and enzyme type is unclear. Such information would allow soil microbial enzymes to be incorporated in a traits-based framework to improve prediction of ecosystem response to global change. If temperature sensitivity varies for specific soil enzymes, then determining the underlying causes of variation in temperature sensitivity of these enzymes will provide fundamental insights for predicting nutrient dynamics belowground. In this study, we characterized how both microbial taxonomic variation as well as substrate type affects temperature sensitivity. We measured β-glucosidase, leucine aminopeptidase, and phosphatase activities at six temperatures: 4, 11, 25, 35, 45, and 60°C, for seven different soil microbial isolates. To calculate temperature sensitivity, we employed two models, Arrhenius, which predicts an exponential increase in reaction rate with temperature, and Macromolecular Rate Theory (MMRT), which predicts rate to peak and then decline as temperature increases. We found MMRT provided a more accurate fit and allowed for more nuanced interpretation of temperature sensitivity in all of the enzyme × isolate combinations tested. Our results revealed that both the enzyme type and soil isolate type explain variation in parameters associated with temperature sensitivity. Because we found temperature sensitivity to be an inherent and variable property of an enzyme, we argue that it can be incorporated as a microbial functional trait, but only when using the MMRT definition of temperature sensitivity. We show that the Arrhenius metrics of temperature sensitivity are overly sensitive to test conditions, with activation energy changing depending on the temperature range it was calculated within. Thus, we propose the use of the MMRT definition of temperature sensitivity for accurate interpretation of

  8. Structure of metaphase chromosomes: a role for effects of macromolecular crowding.

    Directory of Open Access Journals (Sweden)

    Ronald Hancock

    Full Text Available In metaphase chromosomes, chromatin is compacted to a concentration of several hundred mg/ml by mechanisms which remain elusive. Effects mediated by the ionic environment are considered most frequently because mono- and di-valent cations cause polynucleosome chains to form compact ~30-nm diameter fibres in vitro, but this conformation is not detected in chromosomes in situ. A further unconsidered factor is predicted to influence the compaction of chromosomes, namely the forces which arise from crowding by macromolecules in the surrounding cytoplasm whose measured concentration is 100-200 mg/ml. To mimic these conditions, chromosomes were released from mitotic CHO cells in solutions containing an inert volume-occupying macromolecule (8 kDa polyethylene glycol, 10.5 kDa dextran, or 70 kDa Ficoll in 100 µM K-Hepes buffer, with contaminating cations at only low micromolar concentrations. Optical and electron microscopy showed that these chromosomes conserved their characteristic structure and compaction, and their volume varied inversely with the concentration of a crowding macromolecule. They showed a canonical nucleosomal structure and contained the characteristic proteins topoisomerase IIα and the condensin subunit SMC2. These observations, together with evidence that the cytoplasm is crowded in vivo, suggest that macromolecular crowding effects should be considered a significant and perhaps major factor in compacting chromosomes. This model may explain why ~30-nm fibres characteristic of cation-mediated compaction are not seen in chromosomes in situ. Considering that crowding by cytoplasmic macromolecules maintains the compaction of bacterial chromosomes and has been proposed to form the liquid crystalline chromosomes of dinoflagellates, a crowded environment may be an essential characteristic of all genomes.

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

    Science.gov (United States)

    Mueller, Uwe; Darowski, Nora; Fuchs, Martin R; Förster, Ronald; Hellmig, Michael; Paithankar, Karthik S; Pühringer, Sandra; Steffien, Michael; Zocher, Georg; Weiss, Manfred S

    2012-05-01

    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.

  10. The High Mosaicity Illusion: Revealing the True Physical Characteristics of Macromolecular Crystals

    Science.gov (United States)

    Bellamy, Henry; Snell, Edward H.; Borgstahl, Gloria

    2000-01-01

    An experimental system and software have been developed for simultaneously measuring the diffraction resolution and mosaic spread of macromolecular crystals. Hundreds of reflection profiles over a wide resolution range were rapidly measured by using a charge coupled device (CCD) area detector in combination with superfine phi slicing data collection. The contributions of the X-ray beam to the reflection widths were minimized by using a highly-parallel, highly-monochromatic synchrotron source. These contributions and Lorentz effects were evaluated and deconvoluted from the recorded data. Data collection and processing is described. From one degree of superfine phi slice data collected on a crystal of manganese superoxide dismutase the mosaicity of 261 reflections were measured. The average mosaicity was 0.0101 degrees (0.0035) at the full-width-at-half-maximum (FWHM) and ranged from 0.0011 degrees to 0.0188 degrees. Each reflection profile was individually fit with two gaussian profiles with the first gaussian contributing 55% and the second contributing 35% of the reflection. On average, the mosaicity of the first gaussian was 0.0054 degrees (0.0015) and the second was 0.0061 degrees (0.0023). The mosaicity of the crystal was anisotropic with fh, f k, and fl values of 0.0068 degrees, 0.0140 degrees and 0.0046 degrees, respectively at the FWHM. The anisotropic mosaicity analysis indicates that the crystal is the most perfect in the I direction which corresponds to the favored growth direction of the crystal.

  11. Role of solvent properties of aqueous media in macromolecular crowding effects.

    Science.gov (United States)

    Ferreira, Luisa A; Madeira, Pedro P; Breydo, Leonid; Reichardt, Christian; Uversky, Vladimir N; Zaslavsky, Boris Y

    2016-01-01

    Analysis of the macromolecular crowding effects in polymer solutions show that the excluded volume effect is not the only factor affecting the behavior of biomolecules in a crowded environment. The observed inconsistencies are commonly explained by the so-called soft interactions, such as electrostatic, hydrophobic, and van der Waals interactions, between the crowding agent and the protein, in addition to the hard nonspecific steric interactions. We suggest that the changes in the solvent properties of aqueous media induced by the crowding agents may be the root of these "soft" interactions. To check this hypothesis, the solvatochromic comparison method was used to determine the solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity of aqueous solutions of different polymers (dextran, poly(ethylene glycol), Ficoll, Ucon, and polyvinylpyrrolidone) with the polymer concentration up to 40% typically used as crowding agents. Polymer-induced changes in these features were found to be polymer type and concentration specific, and, in case of polyethylene glycol (PEG), molecular mass specific. Similarly sized polymers PEG and Ucon producing different changes in the solvent properties of water in their solutions induced morphologically different α-synuclein aggregates. It is shown that the crowding effects of some polymers on protein refolding and stability reported in the literature can be quantitatively described in terms of the established solvent features of the media in these polymers solutions. These results indicate that the crowding agents do induce changes in solvent properties of aqueous media in crowded environment. Therefore, these changes should be taken into account for crowding effect analysis.

  12. 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.

  13. Low frequency sound scattering from spherical assemblages of bubbles using effective medium theory.

    Science.gov (United States)

    Hahn, Thomas R

    2007-12-01

    The determination of the acoustic field scattered by an underwater assembly of gas bubbles or similar resonant monopole scatterers is of considerable theoretical and practical interest. This problem is addressed from a theoretical point of view within the framework of the effective medium theory for the case of spherically shaped assemblages. Although being valid more generally, the effective medium theory is an ideal instrument to study multiple scattering effects such as low frequency collective resonances, acoustically coupled breathing modes of the entire assembly. Explicit expressions for the scattering amplitude and cross sections are derived, as well as closed form expressions for the resonance frequency and spectral shape of the fundamental collective mode utilizing analytical S-matrix methods. This approach allows, in principle, a simultaneous inversion for the assembly radius and void fraction directly from the scattering cross sections. To demonstrate the validity of the approach, the theory is applied to the example of idealized, spherically shaped schools of swim bladder bearing fish. The analytic results of the theory are compared to numerical first-principle benchmark computations and excellent agreement is found, even for densely packed schools and frequencies across the bladder resonance.

  14. A general thermodynamic analysis and treatment of phases and components in the analysis of phase assemblages in multicomponent systems

    Institute of Scientific and Technical Information of China (English)

    HU JiaWen

    2012-01-01

    Systematic thermodynamic analysis reveals that an essential condition for the thermodynamically valid chemographic projections proposed by Greenwood is completely excessive.In other words,the phases or components from which the projection is made need not be pure,nor have their chemical potentials fixed over the whole chemographic diagram.To facilitate the analysis of phase assemblages in multicomponent systems,all phases and components in the system are divided into internal and external ones in terms of their thermodynamic features and roles,where the external phases are those common to all assemblages in the system,and the external components include excess components and the components whose chemical potentials (or relevant intensive properties of components) are used to define the thermodynamic conditions of the system.This general classification overcomes the difficulties and defects in the previous classifications,and is easier to use than the previous ones.According to the above classification,the phase rule is transformed into a new form.This leads to two findings:(1) the degree of freedom of the system under the given conditions is only determined by the internal components and phases; (2) different external phases can be identified conveniently according to the conditions of the system before knowing the real phase relations.Based on the above results,a simple but general approach is proposed for the treatment of phases and components:all external phases and components can be eliminated from the system without affecting the phase relations,where the external components can be eliminated by appropriate chemographic projections.The projections have no restriction on the states of the phases or the chemical potentials of components from which the projections are made.Th e present work can give a unified explanation of the previous treatments of phases and components in the analysis of phase assemblages under various specific conditions.It helps to avoid

  15. An altitudinal cline in UV floral pattern corresponds with a behavioral change of a generalist pollinator assemblage.

    Science.gov (United States)

    Koski, Matthew H; Ashman, Tia-Lynn

    2015-12-01

    Spatial variation in pollinator communities or behaviors can underlie floral diversification. Floral traits in the UV spectrum are common and mediate plant-pollinator interactions, but the role of pollinators in driving or maintaining their geographic variation has not been fully explored. We identify an altitudinal cline of increasing relative size of the UV bullseye pattern in Argentina anserina (Rosaceae) flowers, and assess whether pollination context contributes to clinal variation. At four sites that varied in altitude, we document the pollinator assemblage, and pollinator preference and visitation behavior. We then determine how pollinator visits affected pollen receipt and export. Finally, we describe how the functional relationship between UV floral phenotype and pollen receipt changed with altitude. Floral UV bullseye size increased with altitude, which corresponded with a change from a hymenopteran- to a dipteran-dominated pollinator assemblage. While dipteran and hymenopteran preferences for bullseye size were similar, flowers with large bullseyes received more foraging visits than those with small bullseyes at higher altitude. The reverse was observed at the lower altitudes; pollinators approached large-bullseye flowers often but rarely foraged. These differences are expected to affect fitness because foraging visits increased pollen export and receipt. Indeed, when natural variation in bullseye size was considered, it had a stronger effect on pollen receipt than other traits (flower size, display, or color). Plants with larger bullseyes tended to receive more pollen at the highest-altitude site, while those with smaller ones received more pollen at the lowest-altitude site. Results suggest that altitudinal changes in preference and behavior of the overall pollinator assemblage, but not differential preferences of pollinator taxonomic groups, could contribute to clinal variation in a UV floral trait for a generalist-pollinated plant.

  16. 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)

  17. 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