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Sample records for area protein patterning

  1. Geometry-induced protein pattern formation.

    Science.gov (United States)

    Thalmeier, Dominik; Halatek, Jacob; Frey, Erwin

    2016-01-19

    Protein patterns are known to adapt to cell shape and serve as spatial templates that choreograph downstream processes like cell polarity or cell division. However, how can pattern-forming proteins sense and respond to the geometry of a cell, and what mechanistic principles underlie pattern formation? Current models invoke mechanisms based on dynamic instabilities arising from nonlinear interactions between proteins but neglect the influence of the spatial geometry itself. Here, we show that patterns can emerge as a direct result of adaptation to cell geometry, in the absence of dynamical instability. We present a generic reaction module that allows protein densities robustly to adapt to the symmetry of the spatial geometry. The key component is an NTPase protein that cycles between nucleotide-dependent membrane-bound and cytosolic states. For elongated cells, we find that the protein dynamics generically leads to a bipolar pattern, which vanishes as the geometry becomes spherically symmetrical. We show that such a reaction module facilitates universal adaptation to cell geometry by sensing the local ratio of membrane area to cytosolic volume. This sensing mechanism is controlled by the membrane affinities of the different states. We apply the theory to explain AtMinD bipolar patterns in [Formula: see text] EcMinDE Escherichia coli. Due to its generic nature, the mechanism could also serve as a hitherto-unrecognized spatial template in many other bacterial systems. Moreover, the robustness of the mechanism enables self-organized optimization of protein patterns by evolutionary processes. Finally, the proposed module can be used to establish geometry-sensitive protein gradients in synthetic biological systems.

  2. Protein patterning by a DNA origami framework.

    Science.gov (United States)

    Aslan, Hüsnü; Krissanaprasit, Abhichart; Besenbacher, Flemming; Gothelf, Kurt V; Dong, Mingdong

    2016-08-18

    A spatial arrangement of proteins provides structural and functional advantages in vast technological applications as well as fundamental research. Most protein patterning procedures employ complicated, time consuming and very costly nanofabrication techniques. As an alternative route, we developed a fully biomolecular self-assembly method using DNA Origami Frames (DOF) as a template for both small and large scale protein patterning. We employed a triangular DOF (tDOF) to arrange the Bovine Serum Albumin (BSA) protein. Our in situ protein patterning strategy provides a novel, fully organic platform using a fast and low-cost surface approach with possible utilization in fundamental science and technological applications.

  3. Pattern Recognition of Adsorbing HP Lattice Proteins

    Science.gov (United States)

    Wilson, Matthew S.; Shi, Guangjie; Wüst, Thomas; Landau, David P.; Schmid, Friederike

    2015-03-01

    Protein adsorption is relevant in fields ranging from medicine to industry, and the qualitative behavior exhibited by course-grained models could shed insight for further research in such fields. Our study on the selective adsorption of lattice proteins utilizes the Wang-Landau algorithm to simulate the Hydrophobic-Polar (H-P) model with an efficient set of Monte Carlo moves. Each substrate is modeled as a square pattern of 9 lattice sites which attract either H or P monomers, and are located on an otherwise neutral surface. The fully enumerated set of 102 unique surfaces is simulated with each protein sequence. A collection of 27-monomer sequences is used- each of which is non-degenerate and protein-like. Thermodynamic quantities such as the specific heat and free energy are calculated from the density of states, and are used to investigate the adsorption of lattice proteins on patterned substrates. Research supported by NSF.

  4. Discovering functional interaction patterns in protein-protein interaction networks

    Directory of Open Access Journals (Sweden)

    Can Tolga

    2008-06-01

    Full Text Available Abstract Background In recent years, a considerable amount of research effort has been directed to the analysis of biological networks with the availability of genome-scale networks of genes and/or proteins of an increasing number of organisms. A protein-protein interaction (PPI network is a particular biological network which represents physical interactions between pairs of proteins of an organism. Major research on PPI networks has focused on understanding the topological organization of PPI networks, evolution of PPI networks and identification of conserved subnetworks across different species, discovery of modules of interaction, use of PPI networks for functional annotation of uncharacterized proteins, and improvement of the accuracy of currently available networks. Results In this article, we map known functional annotations of proteins onto a PPI network in order to identify frequently occurring interaction patterns in the functional space. We propose a new frequent pattern identification technique, PPISpan, adapted specifically for PPI networks from a well-known frequent subgraph identification method, gSpan. Existing module discovery techniques either look for specific clique-like highly interacting protein clusters or linear paths of interaction. However, our goal is different; instead of single clusters or pathways, we look for recurring functional interaction patterns in arbitrary topologies. We have applied PPISpan on PPI networks of Saccharomyces cerevisiae and identified a number of frequently occurring functional interaction patterns. Conclusion With the help of PPISpan, recurring functional interaction patterns in an organism's PPI network can be identified. Such an analysis offers a new perspective on the modular organization of PPI networks. The complete list of identified functional interaction patterns is available at http://bioserver.ceng.metu.edu.tr/PPISpan/.

  5. Complex protein nanopatterns over large areas via colloidal lithography

    DEFF Research Database (Denmark)

    Kristensen, Stine H; Pedersen, Gitte Albinus; Ogaki, Ryosuke;

    2013-01-01

    are used to generate complex protein nanopatterns over large areas. Simple circular patches or more complex ring structures are produced in addition to hierarchical patterns of smaller patches. The gold regions are modified through alkanethiol chemistry, which enables the preparation of extracellular......The patterning of biomolecules at the nanoscale provides a powerful method to investigate cellular adhesion processes. A novel method for patterning is presented that is based on colloidal monolayer templating combined with multiple and angled deposition steps. Patterns of gold and SiO2 layers...... for using sets of systematically varied samples with simpler or more complex patterns for studies of cellular adhesive behavior and reveal that the local distribution of proteins within a simple patch critically influences cell adhesion....

  6. A Versatile Method of Patterning Proteins and Cells.

    Science.gov (United States)

    Shrirao, Anil B; Kung, Frank H; Yip, Derek; Firestein, Bonnie L; Cho, Cheul H; Townes-Anderson, Ellen

    2017-02-26

    Substrate and cell patterning techniques are widely used in cell biology to study cell-to-cell and cell-to-substrate interactions. Conventional patterning techniques work well only with simple shapes, small areas and selected bio-materials. This article describes a method to distribute cell suspensions as well as substrate solutions into complex, long, closed (dead-end) polydimethylsiloxane (PDMS) microchannels using negative pressure. This method enables researchers to pattern multiple substrates including fibronectin, collagen, antibodies (Sal-1), poly-D-lysine (PDL), and laminin. Patterning of substrates allows one to indirectly pattern a variety of cells. We have tested C2C12 myoblasts, the PC12 neuronal cell line, embryonic rat cortical neurons, and amphibian retinal neurons. In addition, we demonstrate that this technique can directly pattern fibroblasts in microfluidic channels via brief application of a low vacuum on cell suspensions. The low vacuum does not significantly decrease cell viability as shown by cell viability assays. Modifications are discussed for application of the method to different cell and substrate types. This technique allows researchers to pattern cells and proteins in specific patterns without the need for exotic materials or equipment and can be done in any laboratory with a vacuum.

  7. Understanding Road Usage Patterns in Urban Areas

    CERN Document Server

    Wang, Pu; Bayen, Alexandre M; Schechtner, Katja; González, Marta C; 10.1038/srep01001

    2012-01-01

    In this paper, we combine the most complete record of daily mobility, based on large-scale mobile phone data, with detailed Geographic Information System (GIS) data, uncovering previously hidden patterns in urban road usage. We find that the major usage of each road segment can be traced to its own - surprisingly few - driver sources. Based on this finding we propose a network of road usage by defining a bipartite network framework, demonstrating that in contrast to traditional approaches, which define road importance solely by topological measures, the role of a road segment depends on both: its betweeness and its degree in the road usage network. Moreover, our ability to pinpoint the few driver sources contributing to the major traffic flow allows us to create a strategy that achieves a significant reduction of the travel time across the entire road system, compared to a benchmark approach.

  8. DETECTION OF TOPOLOGICAL PATTERNS IN PROTEIN NETWORKS.

    Energy Technology Data Exchange (ETDEWEB)

    MASLOV,S.SNEPPEN,K.

    2003-11-17

    interesting property of many biological networks that was recently brought to attention of the scientific community [3, 4, 5] is an extremely broad distribution of node connectivities defined as the number of immediate neighbors of a given node in the network. While the majority of nodes have just a few edges connecting them to other nodes in the network, there exist some nodes, that we will refer to as ''hubs'', with an unusually large number of neighbors. The connectivity of the most connected hub in such a network is typically several orders of magnitude larger than the average connectivity in the network. Often the distribution of connectivities of individual nodes can be approximated by a scale-free power law form [3] in which case the network is referred to as scale-free. Among biological networks distributions of node connectivities in metabolic [4], protein interaction [5], and brain functional [6] networks can be reasonably approximated by a power law extending for several orders of magnitude. The set of connectivities of individual nodes is an example of a low-level (single-node) topological property of a network. While it answers the question about how many neighbors a given node has, it gives no information about the identity of those neighbors. It is clear that most functional properties of networks are defined at a higher topological level in the exact pattern of connections of nodes to each other. However, such multi-node connectivity patterns are rather difficult to quantify and compare between networks. In this work we concentrate on multi-node topological properties of protein networks. These networks (as any other biological networks) lack the top-down design. Instead, selective forces of biological evolution shape them from raw material provided by random events such as mutations within individual genes, and gene duplications. As a result their connections are characterized by a large degree of randomness. One may wonder which

  9. DETECTION OF TOPOLOGICAL PATTERNS IN PROTEIN NETWORKS.

    Energy Technology Data Exchange (ETDEWEB)

    MASLOV,S.SNEPPEN,K.

    2003-11-17

    interesting property of many biological networks that was recently brought to attention of the scientific community [3, 4, 5] is an extremely broad distribution of node connectivities defined as the number of immediate neighbors of a given node in the network. While the majority of nodes have just a few edges connecting them to other nodes in the network, there exist some nodes, that we will refer to as ''hubs'', with an unusually large number of neighbors. The connectivity of the most connected hub in such a network is typically several orders of magnitude larger than the average connectivity in the network. Often the distribution of connectivities of individual nodes can be approximated by a scale-free power law form [3] in which case the network is referred to as scale-free. Among biological networks distributions of node connectivities in metabolic [4], protein interaction [5], and brain functional [6] networks can be reasonably approximated by a power law extending for several orders of magnitude. The set of connectivities of individual nodes is an example of a low-level (single-node) topological property of a network. While it answers the question about how many neighbors a given node has, it gives no information about the identity of those neighbors. It is clear that most functional properties of networks are defined at a higher topological level in the exact pattern of connections of nodes to each other. However, such multi-node connectivity patterns are rather difficult to quantify and compare between networks. In this work we concentrate on multi-node topological properties of protein networks. These networks (as any other biological networks) lack the top-down design. Instead, selective forces of biological evolution shape them from raw material provided by random events such as mutations within individual genes, and gene duplications. As a result their connections are characterized by a large degree of randomness. One may wonder which

  10. Protein surface patterning using nanoscale PEG hydrogels.

    Science.gov (United States)

    Hong, Ye; Krsko, Peter; Libera, Matthew

    2004-12-01

    We have used focused electron-beam cross-linking to create nanosized hydrogels and thus present a new method with which to bring the attractive biocompatibility associated with macroscopic hydrogels into the submicron length-scale regime. Using amine-terminated poly(ethylene glycol) thin films on silicon substrates, we generate nanohydrogels with lateral dimensions of order 200 nm which can swell by a factor of at least five, depending on the radiative dose. With the focused electron beam, high-density arrays of such nanohydrogels can be flexibly patterned onto silicon surfaces. Significantly, the amine groups remain functional after e-beam exposure, and we show that they can be used to covalently bind proteins and other molecules. We use bovine serum albumin to amplify the number of amine groups, and we further demonstrate that different proteins can be covalently bound to different hydrogel pads on the same substrate to create multifunctional surfaces useful in emerging bio/proteomic and sensor technologies.

  11. Regular Nanoscale Protein Patterns via Directed Adsorption through Self-Assembled DNA Origami Masks.

    Science.gov (United States)

    Ramakrishnan, Saminathan; Subramaniam, Sivaraman; Stewart, A Francis; Grundmeier, Guido; Keller, Adrian

    2016-11-16

    DNA origami has become a widely used method for synthesizing well-defined nanostructures with promising applications in various areas of nanotechnology, biophysics, and medicine. Recently, the possibility to transfer the shape of single DNA origami nanostructures into different materials via molecular lithography approaches has received growing interest due to the great structural control provided by the DNA origami technique. Here, we use ordered monolayers of DNA origami nanostructures with internal cavities on mica surfaces as molecular lithography masks for the fabrication of regular protein patterns over large surface areas. Exposure of the masked sample surface to negatively charged proteins results in the directed adsorption of the proteins onto the exposed surface areas in the holes of the mask. By controlling the buffer and adsorption conditions, the protein coverage of the exposed areas can be varied from single proteins to densely packed monolayers. To demonstrate the versatility of this approach, regular nanopatterns of four different proteins are fabricated: the single-strand annealing proteins Redβ and Sak, the iron-storage protein ferritin, and the blood protein bovine serum albumin (BSA). We furthermore demonstrate the desorption of the DNA origami mask after directed protein adsorption, which may enable the fabrication of hierarchical patterns composed of different protein species. Because selectivity in adsorption is achieved by electrostatic interactions between the proteins and the exposed surface areas, this approach may enable also the large-scale patterning of other charged molecular species or even nanoparticles.

  12. Network based approaches reveal clustering in protein point patterns

    Science.gov (United States)

    Parker, Joshua; Barr, Valarie; Aldridge, Joshua; Samelson, Lawrence E.; Losert, Wolfgang

    2014-03-01

    Recent advances in super-resolution imaging have allowed for the sub-diffraction measurement of the spatial location of proteins on the surfaces of T-cells. The challenge is to connect these complex point patterns to the internal processes and interactions, both protein-protein and protein-membrane. We begin analyzing these patterns by forming a geometric network amongst the proteins and looking at network measures, such the degree distribution. This allows us to compare experimentally observed patterns to models. Specifically, we find that the experimental patterns differ from heterogeneous Poisson processes, highlighting an internal clustering structure. Further work will be to compare our results to simulated protein-protein interactions to determine clustering mechanisms.

  13. Chromosome driven spatial patterning of proteins in bacteria.

    Directory of Open Access Journals (Sweden)

    Saeed Saberi

    Full Text Available The spatial patterning of proteins in bacteria plays an important role in many processes, from cell division to chemotaxis. In the asymmetrically dividing bacteria Caulobacter crescentus, a scaffolding protein, PopZ, localizes to both poles and aids the differential patterning of proteins between mother and daughter cells during division. Polar patterning of misfolded proteins in Escherichia coli has also been shown, and likely plays an important role in cellular ageing. Recent experiments on both of the above systems suggest that the presence of chromosome free regions along with protein multimerization may be a mechanism for driving the polar localization of proteins. We have developed a simple physical model for protein localization using only these two driving mechanisms. Our model reproduces all the observed patterns of PopZ and misfolded protein localization--from diffuse, unipolar, and bipolar patterns and can also account for the observed patterns in a variety of mutants. The model also suggests new experiments to further test the role of the chromosome in driving protein patterning, and whether such a mechanism is responsible for helping to drive the differentiation of the cell poles.

  14. Adsorption of HP Lattice Proteins on Patterned Surfaces

    Science.gov (United States)

    Wilson, Matthew; Shi, Guangjie; Landau, David P.; Li, Ying Wai; Wuest, Thomas

    2014-03-01

    The HP lattice model[2] is a course-grained, yet useful tool for modeling protein sequences where amino acids are treated as either hydrophobic (H) or polar (P) monomers. With the use of Wang-Landau sampling and an efficient set of Monte-Carlo moves[3], HP lattice proteins adsorbed on patterned surfaces are studied. Each substrate is modeled as a periodically bounded pattern of lattice sites that interact with either H or P monomers in the lattice protein, where the energy contributions of the surface are determined by assigned coupling strengths. By analyzing energy degeneracies, along with the thermodynamic and structural quantities of the protein, both the protein folding and surface adsorption can be observed. The adsorption behavior of the lattice proteins on patterned surfaces will be compared to those interacting with uniform surfaces. Research supported by NSF.

  15. Spontaneous pattern formation in broad-area lasers

    Science.gov (United States)

    Krents, Anton; Anchikov, Dmitry; Molevich, Nonna; Pakhomov, Anton

    2016-10-01

    The paper studies the spontaneous formation of nonlinear optical patterns in broad area lasers. Spatiotemporal transverse dynamics of the laser is described by the Maxwell-Bloch equations (MBE). The instability of the steady-state solution leads to pattern formation. Two different types of instabilities were observed analytically (Hopf and wave). 2D numerical simulation of the MBE with the random initial conditions has been performed using a split-step Fourier method and periodic boundary conditions. Hopf instability leads to homogeneous oscillations, spatiotemporal chaos and spiral waves. In the case of wave instability, the direct numerical simulation showed that space-time (periodic, quasi-periodic, or chaotic) modulation of the uniform profile is observed. The characteristic sizes of excited patterns are in good agreement with analytical predictions. The nonlinear interaction of four travelling waves forms a square optical vortex lattice similar to the vortex lattices observed in superconductors and Bose Einstein condensate.

  16. Characterization of white grub (Melolonthidae; Coleoptera in salak plantation based on morphology and protein banding pattern

    Directory of Open Access Journals (Sweden)

    SUGIYARTO

    2009-07-01

    Full Text Available Maryati KT, Sugiyarto. 2010. Characterization of white grub (Melolonthidae; Coleoptera in salak plantation based on morphology and protein banding pattern. Nusantara Bioscience 1: 72-77. This research aims to find out the white grub (Melolonthidae; Coleoptera variability based on the morphological characteristic and protein banding pattern found in ”salak pondoh” farm in Regencies of Sleman, Yogyakarta and Magelang, Central Java. Each area has five sampling points. Morphological analysis on white grub was conducted using descriptive method and analysis on protein banding pattern was conducted using qualitative analysis based on the presence or absent of band pattern on the gel, and qualitatively based on the relative mobility value (Rf of protein. The result indicated that the white grub in Sleman and Magelang, based on morphology characteristic is only one species, namely Holothricia sp. Based on the protein banding pattern, the white grub sample have differences of protein band number and protein molecular weight. Key words: Salacca zalacca, white grub, morphology, protein banding pattern.Abstrak. Maryati KT, Sugiyarto. 2010. Karakterisasi lundi putih (Melolonthidae: Coleoptera pada pertanaman salak berdasarkan ciri morfologi dan pola pita protein. Nusantara Bioscience 1: 72-77. Penelitian ini bertujuan untuk mengetahui keanekaragaman lundi putih (Melolonthidae; Coleoptera berdasarkan ciri morfologi dan pola pita protein yang ditemukan di lahan pertanaman salak pondoh di Kabupaten Sleman, Yogyakarta dan Kabupaten Magelang, Jawa Tengah. Pada masing-masing wilayah diambil lima titik sampling. Analisis morfologi lundi putih digunakan metode deskriptif, dan analisis pola pita protein digunakan analisis kualitatif berdasarkan muncul tidaknya pola pita pada gel, dan secara kuantitatif berdasarkan nilai mobilitas relatif protein (RF. Hasil penelitian menunjukkan bahwa sampel lundi putih di Kabupaten Sleman dan Magelang, berdasar karakter

  17. Elastohydrodynamics and kinetics of protein patterning in the immunological synapse

    CERN Document Server

    Carlson, Andreas

    2015-01-01

    The cellular basis for the adaptive immune response during antigen recognition relies on a specialized protein interface known as the immunological synapse (IS). Understanding the biophysical basis for protein patterning by deciphering the quantitative rules for their formation and motion is an important aspect of characterizing immune cell recognition and thence the rules for immune system activation. We propose a minimal mathematical model for the physical basis of membrane protein patterning in the IS, which encompass membrane mechanics, protein binding kinetics and motion, and fluid flow in the synaptic cleft. Our theory leads to simple predictions for the spatial and temporal scales of protein cluster formation, growth and arrest as a function of membrane stiffness, rigidity and kinetics of the adhesive proteins, and the fluid in the synaptic cleft. Numerical simulations complement these scaling laws by quantifying the nucleation, growth and stabilization of proteins domains on the size of the cell. Dire...

  18. Characterization of oligopeptide patterns in large protein sets

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    Persson Bengt

    2007-10-01

    Full Text Available Abstract Background Recent sequencing projects and the growth of sequence data banks enable oligopeptide patterns to be characterized on a genome or kingdom level. Several studies have focused on kingdom or habitat classifications based on the abundance of short peptide patterns. There have also been efforts at local structural prediction based on short sequence motifs. Oligopeptide patterns undoubtedly carry valuable information content. Therefore, it is important to characterize these informational peptide patterns to shed light on possible new applications and the pitfalls implicit in neglecting bias in peptide patterns. Results We have studied four classes of pentapeptide patterns (designated POP, NEP, ORP and URP in the kingdoms archaea, bacteria and eukaryotes. POP are highly abundant patterns statistically not expected to exist; NEP are patterns that do not exist but are statistically expected to; ORP are patterns unique to a kingdom; and URP are patterns excluded from a kingdom. We used two data sources: the de facto standard of protein knowledge Swiss-Prot, and a set of 386 completely sequenced genomes. For each class of peptides we looked at the 100 most extreme and found both known and unknown sequence features. Most of the known sequence motifs can be explained on the basis of the protein families from which they originate. Conclusion We find an inherent bias of certain oligopeptide patterns in naturally occurring proteins that cannot be explained solely on the basis of residue distribution in single proteins, kingdoms or databases. We see three predominant categories of patterns: (i patterns widespread in a kingdom such as those originating from respiratory chain-associated proteins and translation machinery; (ii proteins with structurally and/or functionally favored patterns, which have not yet been ascribed this role; (iii multicopy species-specific retrotransposons, only found in the genome set. These categories will affect the

  19. Patterns of fluorescent protein expression in Scleractinian corals.

    Science.gov (United States)

    Gruber, David F; Kao, Hung-Teh; Janoschka, Stephen; Tsai, Julia; Pieribone, Vincent A

    2008-10-01

    Biofluorescence exists in only a few classes of organisms, with Anthozoa possessing the majority of species known to express fluorescent proteins. Most species within the Anthozoan subgroup Scleractinia (reef-building corals) not only express green fluorescent proteins, they also localize the proteins in distinct anatomical patterns.We examined the distribution of biofluorescence in 33 coral species, representing 8 families, from study sites on Australia's Great Barrier Reef. For 28 of these species, we report the presence of biofluorescence for the first time. The dominant fluorescent emissions observed were green (480-520 nm) and red (580-600 nm). Fluorescent proteins were expressed in three distinct patterns (highlighted, uniform, and complementary) among specific anatomical structures of corals across a variety of families. We report no significant overlap between the distribution of fluorescent proteins and the distribution of zooxanthellae. Analysis of the patterns of fluorescent protein distribution provides evidence that the scheme in which fluorescent proteins are distributed among the anatomical structures of corals is nonrandom. This targeted expression of fluorescent proteins in corals produces contrast and may function as a signaling mechanism to organisms with sensitivity to specific wavelengths of light.

  20. Collective human mobility pattern from taxi trips in urban area

    KAUST Repository

    Peng, Chengbin

    2012-04-18

    We analyze the passengers\\' traffic pattern for 1.58 million taxi trips of Shanghai, China. By employing the non-negative matrix factorization and optimization methods, we find that, people travel on workdays mainly for three purposes: commuting between home and workplace, traveling from workplace to workplace, and others such as leisure activities. Therefore, traffic flow in one area or between any pair of locations can be approximated by a linear combination of three basis flows, corresponding to the three purposes respectively. We name the coefficients in the linear combination as traffic powers, each of which indicates the strength of each basis flow. The traffic powers on different days are typically different even for the same location, due to the uncertainty of the human motion. Therefore, we provide a probability distribution function for the relative deviation of the traffic power. This distribution function is in terms of a series of functions for normalized binomial distributions. It can be well explained by statistical theories and is verified by empirical data. These findings are applicable in predicting the road traffic, tracing the traffic pattern and diagnosing the traffic related abnormal events. These results can also be used to infer land uses of urban area quite parsimoniously. 2012 Peng et al.

  1. Multistability and dynamic transitions of intracellular Min protein patterns.

    Science.gov (United States)

    Wu, Fabai; Halatek, Jacob; Reiter, Matthias; Kingma, Enzo; Frey, Erwin; Dekker, Cees

    2016-06-08

    Cells owe their internal organization to self-organized protein patterns, which originate and adapt to growth and external stimuli via a process that is as complex as it is little understood. Here, we study the emergence, stability, and state transitions of multistable Min protein oscillation patterns in live Escherichia coli bacteria during growth up to defined large dimensions. De novo formation of patterns from homogenous starting conditions is observed and studied both experimentally and in simulations. A new theoretical approach is developed for probing pattern stability under perturbations. Quantitative experiments and simulations show that, once established, Min oscillations tolerate a large degree of intracellular heterogeneity, allowing distinctly different patterns to persist in different cells with the same geometry. Min patterns maintain their axes for hours in experiments, despite imperfections, expansion, and changes in cell shape during continuous cell growth. Transitions between multistable Min patterns are found to be rare events induced by strong intracellular perturbations. The instances of multistability studied here are the combined outcome of boundary growth and strongly nonlinear kinetics, which are characteristic of the reaction-diffusion patterns that pervade biology at many scales.

  2. Self medication pattern in rural areas in Pune, India

    Directory of Open Access Journals (Sweden)

    Yogendra Keche

    2012-10-01

    Full Text Available Objective: This study was carried to analyze the self medication pattern in rural areas of Pune. Method: Semi-structured questionnaire was used for collection of data. Information about age, sex, name of the self medication, diagnosis for the use of self medication, source of information about the self medication and adverse effects reported to self medications was collected. Results: NSAIDs (33.33, antibiotics (10.32, vitamins (14.08 and GIT ailment drugs (13.61 are most commonly used as self medication in rural areas. Other drugs that self medicated are: drugs for upper respiratory tract infection, antibiotics, antihypertensives, anticonvulsants and diuretics. Information about the self medication was predominantly obtained from previous prescription of doctors (64.32% and from chemists (23%. Antibiotics like macrolides, fluoroquinolones, cephalosporins, antihelminthics, and furazolidine were taken as self medication in rural areas. 50% of antibiotics used as self medication was associated with development of ADRs. The adverse effects reported with antibiotics self medication were: vomiting, hyperacidity, gastrointestinal discomfort. 21.13% of persons reported adverse effects with NSAIDs self medication. Adverse effects reported with analgesic use in this study were: hyperacidity, skin rashes, nausea. Conclusions: NSAIDs, antibiotics, vitamins and GIT ailment drugs are commonly self medicated in rural areas of Pune. The self medication of antibiotics is disturbing, as these are liable for drug resistance and severe ADRs and hence should be taken under supervision only. Pharmacists, key person in rural areas, can provide information about adverse effects of self medicated drugs and also can guide about proper precautions to be taken for self medication.

  3. Pattern of occurrence and occupancy of carbonylation sites in proteins

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Møller, Ian Max

    2011-01-01

    Proteins are targets for modification by reactive oxygen species, and carbonylation is an important irreversible modification that increases during oxidative stress. While information on protein carbonylation is accumulating, its pattern is not yet understood. We have made a meta......-analysis of the available literature data (456 carbonylation sites on 208 proteins) to appreciate the nature of carbonylation sites in proteins. Of the carbonylated (Arg, Lys, Pro, and Thr – RKPT) amino acids, Lys is the most abundant, whereas Pro is the most susceptible and Thr is the least susceptible. The incidence...... of carbonylation is lower in the N-terminal part of the protein primary sequence. Although a significantly higher number of carbonylated sites occur in Arg-, Lys-, Pro- and Thr-rich regions of proteins, the hydropathy environment of carbonylated sites is not significantly different from potential carbonylation...

  4. Large-area settlement pattern recognition from Landsat-8 data

    Science.gov (United States)

    Wieland, Marc; Pittore, Massimiliano

    2016-09-01

    The study presents an image processing and analysis pipeline that combines object-based image analysis with a Support Vector Machine to derive a multi-layered settlement product from Landsat-8 data over large areas. 43 image scenes are processed over large parts of Central Asia (Southern Kazakhstan, Kyrgyzstan, Tajikistan and Eastern Uzbekistan). The main tasks tackled by this work include built-up area identification, settlement type classification and urban structure types pattern recognition. Besides commonly used accuracy assessments of the resulting map products, thorough performance evaluations are carried out under varying conditions to tune algorithm parameters and assess their applicability for the given tasks. As part of this, several research questions are being addressed. In particular the influence of the improved spatial and spectral resolution of Landsat-8 on the SVM performance to identify built-up areas and urban structure types are evaluated. Also the influence of an extended feature space including digital elevation model features is tested for mountainous regions. Moreover, the spatial distribution of classification uncertainties is analyzed and compared to the heterogeneity of the building stock within the computational unit of the segments. The study concludes that the information content of Landsat-8 images is sufficient for the tested classification tasks and even detailed urban structures could be extracted with satisfying accuracy. Freely available ancillary settlement point location data could further improve the built-up area classification. Digital elevation features and pan-sharpening could, however, not significantly improve the classification results. The study highlights the importance of dynamically tuned classifier parameters, and underlines the use of Shannon entropy computed from the soft answers of the SVM as a valid measure of the spatial distribution of classification uncertainties.

  5. Modeling associated protein-DNA pattern discovery with unified scores.

    Science.gov (United States)

    Chan, Tak-Ming; Lo, Leung-Yau; Sze-To, Ho-Yin; Leung, Kwong-Sak; Xiao, Xinshu; Wong, Man-Hon

    2013-01-01

    Understanding protein-DNA interactions, specifically transcription factor (TF) and transcription factor binding site (TFBS) bindings, is crucial in deciphering gene regulation. The recent associated TF-TFBS pattern discovery combines one-sided motif discovery on both the TF and the TFBS sides. Using sequences only, it identifies the short protein-DNA binding cores available only in high-resolution 3D structures. The discovered patterns lead to promising subtype and disease analysis applications. While the related studies use either association rule mining or existing TFBS annotations, none has proposed any formal unified (both-sided) model to prioritize the top verifiable associated patterns. We propose the unified scores and develop an effective pipeline for associated TF-TFBS pattern discovery. Our stringent instance-level evaluations show that the patterns with the top unified scores match with the binding cores in 3D structures considerably better than the previous works, where up to 90 percent of the top 20 scored patterns are verified. We also introduce extended verification from literature surveys, where the high unified scores correspond to even higher verification percentage. The top scored patterns are confirmed to match the known WRKY binding cores with no available 3D structures and agree well with the top binding affinities of in vivo experiments.

  6. Multivariate analysis of 2-DE protein patterns - Practical approaches

    DEFF Research Database (Denmark)

    Jacobsen, Charlotte; Jacobsen, Susanne; Grove, H.;

    2007-01-01

    Practical approaches to the use of multivariate data analysis of 2-DE protein patterns are demonstrated by three independent strategies for the image analysis and the multivariate analysis on the same set of 2-DE data. Four wheat varieties were selected on the basis of their baking quality. Two...

  7. Isozyme patterns and protein profiles in neuromuscular disorders.

    Science.gov (United States)

    Edwards, Y H; Tipler, T D; Morgan-Hughes, J A; Neerunjun, J S; Hopkinson, D A

    1982-06-01

    The isozyme patterns of six different enzymes and the polypeptide profiles of soluble proteins have been examined in muscle biopsy specimens from 74 patients with a wide variety of neuromuscular disorders. About half of the samples showed unusual features in at least one, and often several, of the enzymes and proteins tested. The extent of the biochemical abnormalities was roughly proportional to the severity of the disorders. In all cases the unusual isozymes and polypeptide profiles seemed to reflect a reversion to the fetal pattern of gene expression. However, this change appeared to occur in extant muscle and was not dependent on the appearance of new muscle fibres. Among the enzymes, phosphoglycerate mutase followed by creatine kinase appeared to be the most sensitive index of muscle disorder. The extent of the change in the muscle creatine kinase isozyme pattern was not correlated with the levels of serum creatine kinase activity.

  8. Lifestyle pattern in selected slums in Mymensingh Municipal area.

    Science.gov (United States)

    Basher, M S; Haque, M M; Ullah, M S; Nasreen, S A; Begum, A A; Islam, M N; Akhter, S; Haque, M S

    2012-04-01

    Lifestyle is composed of cultural and behavioural patterns and lifelong personal habits that developed through processes of socialization. Lifestyle may be health promotive or detrimental to health. Health requires the promotion of healthy lifestyle. Many current day health problems are associated with lifestyle changes. Because of rising urban population, the number of slum dwellers is rising. The mobility of people from rural to urban areas is the main reason of the growing slum population in cities. This Descriptive, cross-sectional study was directed to assess lifestyle pattern in four purposively selected slums in Mymensingh Municipal area. Non-Probability purposive type of sampling technique was used for selecting the study unit. Sample size was one hundred and twenty-three (123) families. Data were collected by interview with one of the adult family members, preferably with the head of the family, with mixed type of interviewer administered questionnaire. There were 494 family members with an average family size of 4.02, while mean age was 24.58 years with a standard deviation (SD) of 17.79 years. Male-female ratio was 103:100. Of 409 members over 5 years, 174(42.54%) did not have schooling and were illiterate. At least 105(33.02%) members were house-wives, and 99(81.15%) members were smokers. An overwhelming majority (79, 64.23%) families had monthly income between 2000 to 4999 taka. As many as 55(44.72%) families lived in kaccha house, while 40(32.52%) had to live in "Jhupree". In cent per cent families, tube well was the source of water for drinking and other household purposes. A highest majority 121(98.37%) of the families had latrine, while the remaining 2(1.63%) did not have any latrine, and defecate in open air. Of 121 families, 78(64.46%) families had sanitary latrine, while 43(37.54%) did not have sanitary latrine. It was revealed that 86(69.92%) families had cell-phone, while 65(52.85%) families had television, 10(8.13%) families had radio, and 5

  9. Protein pattern of Xenopus laevis embryos grown in simulated microgravity.

    Science.gov (United States)

    Tedeschi, Gabriella; Pagliato, Lara; Negroni, Manuela; Montorfano, Gigliola; Corsetto, Paola; Nonnis, Simona; Negri, Armando; Rizzo, Angela Maria

    2011-03-01

    Numerous studies indicate that microgravity affects cell growth and differentiation in many living organisms, and various processes are modified when cells are placed under conditions of weightlessness. However, until now, there is no coherent explanation for these observations, and little information is available concerning the biomolecules involved. Our aim has been to investigate the protein pattern of Xenopus laevis embryos exposed to simulated microgravity during the first 6 days of development. A proteomic approach was applied to compare the protein profiles of Xenopus embryos developed in simulated microgravity and in normal conditions. Attention was focused on embryos that do not present visible malformations in order to investigate if weightlessness has effects at protein level in the absence of macroscopic alterations. The data presented strongly suggest that some of the major components of the cytoskeleton vary in such conditions. Three major findings are described for the first time: (i) the expression of important factors involved in the organization and stabilization of the cytoskeleton, such as Arp (actin-related protein) 3 and stathmin, is heavily affected by microgravity; (ii) the amount of the two major cytoskeletal proteins, actin and tubulin, do not change in such conditions; however, (iii) an increase in the tyrosine nitration of these two proteins can be detected. The data suggest that, in the absence of morphological alterations, simulated microgravity affects the intracellular movement system of cells by altering cytoskeletal proteins heavily involved in the regulation of cytoskeleton remodelling.

  10. Continuities in Delinquency and Riot Patterns in Black Residential Areas

    Science.gov (United States)

    Kapsis, Robert E.

    1976-01-01

    Presents evidence that patterns of neighborhood involvement during a 1968 racial disturbance resembled prior neighborhood delinquency patterns, and suggests that riots represent a direct continuity rather than a sharp discontinuity with pre-existing social conditions. The adequacy of a social control model to explain similarities between…

  11. Analysis on Residents’ Travel Activity Pattern in Historic Urban Areas: A Case Study of Historic Urban Area of Yangzhou, China

    Directory of Open Access Journals (Sweden)

    Mao Ye

    2013-01-01

    Full Text Available Travel behaviors and activity patterns in the historic urban area of a city are expected to be different from the overall situations in the city area. The primary objective of this study is to analyze the residents’ travel activity patterns in historic urban area. Based on survey data conducted in the historic urban area of Yangzhou, the travel activities of local residents in a whole day were classified into five types of patterns. The multinomial logit (MNL model was developed to evaluate the impacts of explanatory variables on the choices of activity patterns. The results showed that the choice of activity pattern was significantly impacted by five contributing factors including the gender, age, occupation, car ownership, and number of electric bikes in household. The other variables, which were the family population, preschoolers, number of conventional bikes in household, motorcycle ownership, and income, were found to be not significantly related to the choice of activities. The results of this study from historic urban area were compared to findings of previous studies from overall urban area. The comparison showed that the impacts of factors on activity pattern in the historic urban area were different from those in the overall area. Findings of this study provide important suggestions for the policy makings to improve the traffic situations in historic urban areas of cities.

  12. Pbx homeodomain proteins pattern both the zebrafish retina and tectum

    Directory of Open Access Journals (Sweden)

    Stout Jennifer

    2007-07-01

    Full Text Available Abstract Background Pbx genes encode TALE class homeodomain transcription factors that pattern the developing neural tube, pancreas, and blood. Within the hindbrain, Pbx cooperates with Hox proteins to regulate rhombomere segment identity. Pbx cooperates with Eng to regulate midbrain-hindbrain boundary maintenance, and with MyoD to control fast muscle cell differentiation. Although previous results have demonstrated that Pbx is required for proper eye size, functions in regulating retinal cell identity and patterning have not yet been examined. Results Analysis of retinal ganglion cell axon pathfinding and outgrowth in pbx2/4 null embryos demonstrated a key role for pbx genes in regulating neural cell behavior. To identify Pbx-dependent genes involved in regulating retino-tectal pathfinding, we conducted a microarray screen for Pbx-dependent transcripts in zebrafish, and detected genes that are specifically expressed in the eye and tectum. A subset of Pbx-dependent retinal transcripts delineate specific domains in the dorso-temporal lobe of the developing retina. Furthermore, we determined that some Pbx-dependent transcripts also require Meis1 and Gdf6a function. Since gdf6a expression is also dependent on Pbx, we propose a model in which Pbx proteins regulate expression of the growth factor gdf6a, which in turn regulates patterning of the dorso-temporal lobe of the retina. This, in concert with aberrant tectal patterning in pbx2/4 null embryos, may lead to the observed defects in RGC outgrowth. Conclusion These data define a novel role for Pbx in patterning the vertebrate retina and tectum in a manner required for proper retinal ganglion cell axon outgrowth.

  13. Pattern Formation by Electrostatic Self-Organization of Membrane Proteins

    Science.gov (United States)

    Boedec, G.; Jaeger, M.; Homble, F.; Leonetti, M.

    2012-07-01

    The electric activity of biological cells and organs such as heart for example is at the origin of various phenomena of pattern formation. The electric membrane potential appears as the order parameter to characterize these spatiotemporal dynamics. A kind of patterns is characterized by a stationary spatial modulation of membrane potential along the cell, breaking a symmetry of the system. They are associated to transcellular currents. A mechanism proposed in literature is based on the coupling of the electric current produced by membrane proteins and their electrophoretic mobilities. Beyond its classical linear stability analysis, the numerical and theoretical analysis of this model offers a variety of spatiotemporal dynamics. Firstly, the background in the modelization of electric phenomena is recalled. Secondly, the analysis is focused on two nonlinear dynamics.

  14. Recognition of higher order patterns in proteins: immunologic kernels.

    Directory of Open Access Journals (Sweden)

    Robert D Bremel

    Full Text Available By applying analysis of the principal components of amino acid physical properties we predicted cathepsin cleavage sites, MHC binding affinity, and probability of B-cell epitope binding of peptides in tetanus toxin and in ten diverse additional proteins. Cross-correlation of these metrics, for peptides of all possible amino acid index positions, each evaluated in the context of a ±25 amino acid flanking region, indicated that there is a strongly repetitive pattern of short peptides of approximately thirty amino acids each bounded by cathepsin cleavage sites and each comprising B-cell linear epitopes, MHC-I and MHC-II binding peptides. Such "immunologic kernel" peptides comprise all signals necessary for adaptive immunologic cognition, response and recall. The patterns described indicate a higher order spatial integration that forms a symbolic logic coordinating the adaptive immune system.

  15. Novel technique sheds new light on protein colocalization patterns

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ The potential of MELC, a brand-new and highly efficient technique for studying the temporal and spatial distribution of proteins in living tissue,has been explored jointly over the last years by Walter Schubert, its inventor from the Molecular Pattern-Recognition Research Group at the Institute of Medical Neurobiology, Otto-von-Guericke University (Magdeburg, Germany),and his collaborators including Andreas Dress from the CAS-MPG Partner Institute for Computational Biology (PICB), the Shanghai Institutes for Biological Sciences (SIBS).

  16. Morphology and protein patterns of honey bee drone accessory glands.

    Science.gov (United States)

    Cruz-Landim, Carminda da; Dallacqua, Rodrigo Pires

    2005-09-30

    We used light and transmission electron microscopy to examine the morphology of the accessory glands of immature and mature adult males of Apis mellifera L. We also made an electrophoretic analysis of the protein content of the mature gland. The glands of the immature male actively secrete a mucous substance that can be seen in the lumen of the gland of the mature male. This secretion stains with mercury bromophenol blue and with periodic acid-Schiff reaction, which stain glyconjugates. The protein content was higher in the lumen secretion than in the gland wall extracts. The electrophoresis patterns of the wall extracts were different from those of the secretion found in the gland lumen.

  17. The E4 protein; structure, function and patterns of expression

    Energy Technology Data Exchange (ETDEWEB)

    Doorbar, John, E-mail: jdoorba@nimr.mrc.ac.uk

    2013-10-15

    }E4, these kinases regulate one of the E1{sup ∧}E4 proteins main functions, the association with the cellular keratin network, and eventually also its cleavage by the protease calpain which allows assembly into amyloid-like fibres and reorganisation of the keratin network. Although the E4 proteins of different HPV types appear divergent at the level of their primary amino acid sequence, they share a recognisable modular organisation and pattern of expression, which may underlie conserved functions and regulation. Assembly into higher-order multimers and suppression of cell proliferation are common to all E4 proteins examined. Although not yet formally demonstrated, a role in virus release and transmission remains a likely function for E4. - Highlights: • E4 gene products have a modular structure, and are expressed from the E1{sup ∧}E4 spliced mRNA. • E4 proteins are modified during epithelial differentiation by phosphorylation and proteolysis. • The E4 proteins contribute to genome amplification-efficiency and virus synthesis. • E4 proteins are abundantly expressed and may facilitate efficient virus release and transmission. • High-risk E4 proteins are deposited as amyloid fibres and can be used as infection biomarkers.

  18. Fragile X mental retardation protein (FMRP) interacting proteins exhibit different expression patterns during development.

    Science.gov (United States)

    Bonaccorso, C M; Spatuzza, M; Di Marco, B; Gloria, A; Barrancotto, G; Cupo, A; Musumeci, S A; D'Antoni, S; Bardoni, B; Catania, M V

    2015-05-01

    Fragile X syndrome is caused by the lack of expression of fragile X mental retardation protein (FMRP), an RNA-binding protein involved in mRNA transport and translation. FMRP is a component of mRNA ribonucleoprotein complexes and it can interact with a range of proteins either directly or indirectly, as demonstrated by two-hybrid selection and co-immunoprecipitation, respectively. Most of FMRP-interacting proteins are RNA-binding proteins such as FXR1P, FXR2P and 82-FIP. Interestingly, FMRP can also interact directly with the cytoplasmic proteins CYFIP1 and CYFIP2, which do not bind RNA and link FMRP to the RhoGTPase pathway. The interaction with these different proteins may modulate the functions of FMRP by influencing its affinity to RNA and by affecting the FMRP ability of cytoskeleton remodeling through Rho/Rac GTPases. To better define the relationship of FMRP with its interacting proteins during brain development, we have analyzed the expression pattern of FMRP and its interacting proteins in the cortex, striatum, hippocampus and cerebellum at different ages in wild type (WT) mice. FMRP and FXR2P were strongly expressed during the first week and gradually decreased thereafter, more rapidly in the cerebellum than in the cortex. FXR1P was also expressed early and showed a reduction at later stages of development with a similar developmental pattern in these two regions. CYFIP1 was expressed at all ages and peaked in the third post-natal week. In contrast, CYFIP2 and 82-FIP (only in forebrain regions) were moderately expressed at P3 and gradually increased after P7. In general, the expression pattern of each protein was similar in the regions examined, except for 82-FIP, which exhibited a strong expression at P3 and low levels at later developmental stages in the cerebellum. Our data indicate that FMRP and its interacting proteins have distinct developmental patterns of expression and suggest that FMRP may be preferentially associated to certain proteins in

  19. Concentration Dependent Ion-Protein Interaction Patterns Underlying Protein Oligomerization Behaviours

    Science.gov (United States)

    Batoulis, Helena; Schmidt, Thomas H.; Weber, Pascal; Schloetel, Jan-Gero; Kandt, Christian; Lang, Thorsten

    2016-04-01

    Salts and proteins comprise two of the basic molecular components of biological materials. Kosmotropic/chaotropic co-solvation and matching ion water affinities explain basic ionic effects on protein aggregation observed in simple solutions. However, it is unclear how these theories apply to proteins in complex biological environments and what the underlying ionic binding patterns are. Using the positive ion Ca2+ and the negatively charged membrane protein SNAP25, we studied ion effects on protein oligomerization in solution, in native membranes and in molecular dynamics (MD) simulations. We find that concentration-dependent ion-induced protein oligomerization is a fundamental chemico-physical principle applying not only to soluble but also to membrane-anchored proteins in their native environment. Oligomerization is driven by the interaction of Ca2+ ions with the carboxylate groups of aspartate and glutamate. From low up to middle concentrations, salt bridges between Ca2+ ions and two or more protein residues lead to increasingly larger oligomers, while at high concentrations oligomers disperse due to overcharging effects. The insights provide a conceptual framework at the interface of physics, chemistry and biology to explain binding of ions to charged protein surfaces on an atomistic scale, as occurring during protein solubilisation, aggregation and oligomerization both in simple solutions and membrane systems.

  20. Dynamic expression pattern of kinesin accessory protein in Drosophila

    Indian Academy of Sciences (India)

    Ritu Sarpal; Krishanu Ray

    2002-09-01

    We have identified the Drosophila homologue of the non-motor accessory subunit of kinesin-II motor complex. It is homologous to the SpKAP115 of the sea urchin, KAP3A and KAP3B of the mouse, and SMAP protein in humans. In situ hybridization using a DmKAP specific cRNA probe has revealed a dynamic pattern of expression in the developing nervous system. The staining first appears in a subset of cells in the embryonic central nervous system at stage 13 and continues till the first instar larva stage. At the third instar larva stage the staining gets restricted to a few cells in the optic lobe and in the ventral ganglion region. It has also stained a subset of sensory neurons from late stage 13 and till the first instar larva stage. The DmKAP expression pattern in the nervous system corresponds well with that of Klp64D and Klp68D as reported earlier. In addition, we have found that the DmKAP gene is constitutively expressed in the germline cells and in follicle cells during oogenesis. These cells are also stained using an antibody to KLP68D protein, but mRNA in situ hybridization using KLP64D specific probe has not stained these cells. Together these results proved a basis for further analysis of tissue specific function of DmKAP in future.

  1. Protein patterning on polycrystalline silicon-germanium via standard UV lithography for bioMEMS applications

    Energy Technology Data Exchange (ETDEWEB)

    Lenci, S., E-mail: silvia.lenci@gmail.com [Dipartimento di Ingegneria dell' Informazione, University of Pisa, Via G. Caruso 16, I-56122 Pisa (Italy); imec, Kapeldreef 75, Leuven B-3001 (Belgium); Tedeschi, L.; Domenici, C.; Lande, C. [Istituto di Fisiologia Clinica, CNR, via G. Moruzzi 1, Pisa I-56124 (Italy); Nannini, A.; Pennelli, G.; Pieri, F. [Dipartimento di Ingegneria dell' Informazione, University of Pisa, Via G. Caruso 16, I-56122 Pisa (Italy); Severi, S. [imec, Kapeldreef 75, Leuven B-3001 (Belgium)

    2010-10-12

    Polycrystalline silicon-germanium (poly-SiGe) is a promising structural material for the post-processing of micro electro-mechanical systems (MEMS) on top of complementary metal-oxide-semiconductor (CMOS) substrates. Combining MEMS and CMOS allows for the development of high-performance devices. We present for the first time selective protein immobilization on top of poly-SiGe surfaces, an enabling technique for the development of novel poly-SiGe based MEMS biosensors. Active regions made of 3-aminopropyl-triethoxysilane (APTES) were defined using silane deposition onto photoresist patterns followed by lift-off in organic solvents. Subsequently, proteins were covalently bound on the created APTES patterns. Fluorescein-labeled human serum albumin (HSA) was used to verify the immobilization procedure while the binding capability of the protein layer was tested by an antigen-labeled antibody pair. Inspection by fluorescence microscopy showed protein immobilization inside the desired bioactive areas and low non-specific adsorption outside the APTES pattern. Furthermore, the quality of the silane patches was investigated by treatment with 30 nm-diameter gold nanoparticles and scanning electron microscope observation. The developed technique is therefore a promising first step towards the realization of poly-SiGe based biosensors.

  2. Changing industrial patterns in the metroplitan Chicago area

    Energy Technology Data Exchange (ETDEWEB)

    Allardice, D.

    1994-12-31

    The industrial base of Chicago, and most Midwestern cities, continues to change. These changes are particularly visible in the manufacturing sector where the exodus of companies has left behind abandoned factories and industrial sites that now blight the urban landscape. As urban centers have seen a steady decline in their ability to attract and maintain their manufacturing base, great interest has been placed in seeing what can be done to attract economic activity back into the urban center. For most Midwestern cities, this often means trying to either replace or stem the tide of manufacturing facilities that have left the city for {open_quotes}greenfields{close_quotes} in suburban or rural locations or have simply moved overseas. On the replacement front, to compensate for the loss of manufacturing, some cities such as Chicago have managed to expand other areas of their economies, such as business services, finance, and tourism and recreation to maintain their vitality. This paper discusses three aspects of the changing economic landscape of Chicago and other Midwestern urban areas. First, some historical perspective will be provided on how Chicago came to be a manufacturing center and what factors since World War II have led manufacturing facilities to move away from the urban center. Second, the future prospects for manufacturing in the central city will be examined. Finally, what policies may help increase (or at the very least maintain) the concentration of manufacturing in Chicago will be discussed.

  3. Reducing contact resistance in graphene devices through contact area patterning.

    Science.gov (United States)

    Smith, Joshua T; Franklin, Aaron D; Farmer, Damon B; Dimitrakopoulos, Christos D

    2013-04-23

    Performance of graphene electronics is limited by contact resistance associated with the metal-graphene (M-G) interface, where unique transport challenges arise as carriers are injected from a 3D metal into a 2D-graphene sheet. In this work, enhanced carrier injection is experimentally achieved in graphene devices by forming cuts in the graphene within the contact regions. These cuts are oriented normal to the channel and facilitate bonding between the contact metal and carbon atoms at the graphene cut edges, reproducibly maximizing "edge-contacted" injection. Despite the reduction in M-G contact area caused by these cuts, we find that a 32% reduction in contact resistance results in Cu-contacted, two-terminal devices, while a 22% reduction is achieved for top-gated graphene transistors with Pd contacts as compared to conventionally fabricated devices. The crucial role of contact annealing to facilitate this improvement is also elucidated. This simple approach provides a reliable and reproducible means of lowering contact resistance in graphene devices to bolster performance. Importantly, this enhancement requires no additional processing steps.

  4. The use of protein patterns in genetic diversity analysis in some Brassica napus cultivars

    Directory of Open Access Journals (Sweden)

    Roya Razavizadeh

    2013-11-01

    Full Text Available In this study, protein variations of seeds and five-day old cotyledonal leaves of four selected Brassica napus cultivars including Elite, Ocapy, Tasilo and Zarfam were analyzed by SDS-PAGE to identify protein markers. The amount of total soluble protein of seed storage proteins did not show significant differences in all cultivars whereas it was different in cotyledonal leaves. Protein patterns of seeds and cotyledonal leaves showed significant differences using SDS-PAGE and consequence analysis of bands by ImageJ program. Relative expression of six protein bands in seeds and five-day old cotyledonal leaves were significantly different. Three protein markers were identified by protein patterns of seed and cotyledonal leaves. The results of relationship analysis based on presence and absence of the specific protein bands in protein pattern of seed storage proteins showed that Tasilo and Elite cultivars had the highest similarities.

  5. A truncation method for modelling effective antenna patterns in urban areas

    NARCIS (Netherlands)

    Mantel, O.C.; Rijken, M.; Matic, D.; Mawira, A.

    2004-01-01

    Signal level predictions for sector antennas in mobile networks strongly depend on the antenna pattern used in the prediction tool. For built-up areas, reflections and scattering often lead to a significant energy component at the back of the antenna, and the theoretical antenna pattern does not acc

  6. Areas of cat auditory cortex as defined by neurofilament proteins expressing SMI-32.

    Science.gov (United States)

    Mellott, Jeffrey G; Van der Gucht, Estel; Lee, Charles C; Carrasco, Andres; Winer, Jeffery A; Lomber, Stephen G

    2010-08-01

    The monoclonal antibody SMI-32 was used to characterize and distinguish individual areas of cat auditory cortex. SMI-32 labels non-phosphorylated epitopes on the high- and medium-molecular weight subunits of neurofilament proteins in cortical pyramidal cells and dendritic trees with the most robust immunoreactivity in layers III and V. Auditory areas with unique patterns of immunoreactivity included: primary auditory cortex (AI), second auditory cortex (AII), dorsal zone (DZ), posterior auditory field (PAF), ventral posterior auditory field (VPAF), ventral auditory field (VAF), temporal cortex (T), insular cortex (IN), anterior auditory field (AAF), and the auditory field of the anterior ectosylvian sulcus (fAES). Unique patterns of labeling intensity, soma shape, soma size, layers of immunoreactivity, laminar distribution of dendritic arbors, and labeled cell density were identified. Features that were consistent in all areas included: layers I and IV neurons are immunonegative; nearly all immunoreactive cells are pyramidal; and immunoreactive neurons are always present in layer V. To quantify the results, the numbers of labeled cells and dendrites, as well as cell diameter, were collected and used as tools for identifying and differentiating areas. Quantification of the labeling patterns also established profiles for ten auditory areas/layers and their degree of immunoreactivity. Areal borders delineated by SMI-32 were highly correlated with tonotopically-defined areal boundaries. Overall, SMI-32 immunoreactivity can delineate ten areas of cat auditory cortex and demarcate topographic borders. The ability to distinguish auditory areas with SMI-32 is valuable for the identification of auditory cerebral areas in electrophysiological, anatomical, and/or behavioral investigations.

  7. Symmetry and scale orient Min protein patterns in shaped bacterial sculptures

    Science.gov (United States)

    Wu, Fabai; van Schie, Bas G. C.; Keymer, Juan E.; Dekker, Cees

    2015-08-01

    The boundary of a cell defines the shape and scale of its subcellular organization. However, the effects of the cell's spatial boundaries as well as the geometry sensing and scale adaptation of intracellular molecular networks remain largely unexplored. Here, we show that living bacterial cells can be ‘sculpted’ into defined shapes, such as squares and rectangles, which are used to explore the spatial adaptation of Min proteins that oscillate pole-to-pole in rod-shaped Escherichia coli to assist cell division. In a wide geometric parameter space, ranging from 2 × 1 × 1 to 11 × 6 × 1 μm3, Min proteins exhibit versatile oscillation patterns, sustaining rotational, longitudinal, diagonal, stripe and even transversal modes. These patterns are found to directly capture the symmetry and scale of the cell boundary, and the Min concentration gradients scale with the cell size within a characteristic length range of 3-6 μm. Numerical simulations reveal that local microscopic Turing kinetics of Min proteins can yield global symmetry selection, gradient scaling and an adaptive range, when and only when facilitated by the three-dimensional confinement of the cell boundary. These findings cannot be explained by previous geometry-sensing models based on the longest distance, membrane area or curvature, and reveal that spatial boundaries can facilitate simple molecular interactions to result in far more versatile functions than previously understood.

  8. Fabrication and characterization of mesoscale protein patterns using atomic force microscopy (AFM)

    Science.gov (United States)

    Gao, Pei

    2011-07-01

    A versatile AFM local oxidation lithography was developed for fabricating clean protein patterns ranging from nanometer to sub-millimeter scale on octadecyltrichlorosilane (OTS) layer of Si (100) wafer. This protein patterning method can generate bio-active protein pattern with a clean background without the need of the anti-fouling the surface or repetitive rinsing. As a model system, lysozyme protein patterns were investigated through their binding reactions with antibodies and aptamers by AFM. Polyclonal anti-lysozyme antibodies and anti-lysozyme aptamer are found to preferentially bind to the lysozyme molecules on the edge of a protein pattern before their binding to the interior ones. It was also demonstrated that the topography of the immobilized protein pattern affects the antibody binding direction. We found that the anti-lysozyme antibodies binding to the edge lysozyme molecules on the half-buried pattern started from the top but the binding on the extruded pattern started from the side because of their different spatial accessibility. In addition, after incubating lysozyme pattern with anti-lysozyme aptamer in buffer solution for enough long time, some fractal-shaped aptamer fibers with 1-6nm high and up to tens of micrometers long were formed by the self-assembling of aptamer molecules on the surface. The aptamer fibers anchor specifically on the edge of protein patterns, which originates from the biospecific recognition between the aptamer and its target protein. Once these edge-bound fibers have formed, they can serve as scaffolds for further assembly processes. We used these aptamer fibers as templates to fabricate palladium and streptavidin nanowires, which anchored on the pattern edges and never cross over or collapse over each other. The aptamer fiber scaffold potentially can lead to an effective means to fabricate and interface nanowires to existing surface patterns. KEYWORDS: Atomic Force Microscopy (AFM), Protein Patterns, Lysozyme, Aptamer

  9. Trehalose glycopolymer resists allow direct writing of protein patterns by electron-beam lithography

    Science.gov (United States)

    Bat, Erhan; Lee, Juneyoung; Lau, Uland Y.; Maynard, Heather D.

    2015-03-01

    Direct-write patterning of multiple proteins on surfaces is of tremendous interest for a myriad of applications. Precise arrangement of different proteins at increasingly smaller dimensions is a fundamental challenge to apply the materials in tissue engineering, diagnostics, proteomics and biosensors. Herein, we present a new resist that protects proteins during electron-beam exposure and its application in direct-write patterning of multiple proteins. Polymers with pendant trehalose units are shown to effectively crosslink to surfaces as negative resists, while at the same time providing stabilization to proteins during the vacuum and electron-beam irradiation steps. In this manner, arbitrary patterns of several different classes of proteins such as enzymes, growth factors and immunoglobulins are realized. Utilizing the high-precision alignment capability of electron-beam lithography, surfaces with complex patterns of multiple proteins are successfully generated at the micrometre and nanometre scale without requiring cleanroom conditions.

  10. Measurements of area and the (island) species-area relationship: new directions for an old pattern

    DEFF Research Database (Denmark)

    Triantis, K.A.; Nogues-Bravo, D.; Hortal, J.;

    2008-01-01

    of environmental heterogeneity (in the form of the so-called choros model), can substantially improve the descriptive power of models of island species number. We suggest that quantification of other variables, apart from area, that are also critical for the establishment of biodiversity and at the same time have...... high explanatory power (such as island age, distance, productivity, energy, and environmental heterogeneity), is necessary if we are to build up a more predictive science of species richness variation across island systems...

  11. Expression Patterns of Extracellular Matrix Proteins during Posterior Commissure Development

    Directory of Open Access Journals (Sweden)

    Karen Stanic

    2016-09-01

    Full Text Available Extracellular matrix (ECM molecules are pivotal for central nervous system development, facilitating cell migration, axonal growth, myelination, dendritic spine formation, and synaptic plasticity, among other processes. During axonal guidance, the ECM not only acts as a permissive or non-permissive substrate for navigating axons, but also modulates the effects of classical guidance cues, such as netrin or Eph/ephrin family members. Despite being highly important, little is known about the expression of ECM molecules during central nervous system development. Therefore, this study assessed the molecular expression patterns of tenascin, HNK-1, laminin, fibronectin, perlecan, decorin, and osteopontin along chick embryo prosomere 1 during posterior commissure development. The posterior commissure is the first transversal axonal tract of the embryonic vertebrate brain. Located in the dorso-caudal portion of prosomere 1, posterior commissure axons primarily arise from the neurons of basal pretectal nuclei that run dorsally to the roof plate midline, where some turn towards the ipsilateral side. Expressional analysis of ECM molecules in this area these revealed to be highly arranged, and molecule interactions with axon fascicles suggested involvement in processes other than structural support. In particular, tenascin and the HNK-1 epitope extended in ventro-dorsal columns and enclosed axons during navigation to the roof plate. Laminin and osteopontin were expressed in the midline, very close to axons that at this point must decide between extending to the contralateral side or turning to the ipsilateral side. Finally, fibronectin, decorin, and perlecan appeared unrelated to axonal pathfinding in this region and were instead restricted to the external limiting membrane. In summary, the present report provides evidence for an intricate expression of different extracellular molecules that may cooperate in guiding posterior commissure axons.

  12. Expression Patterns of Extracellular Matrix Proteins during Posterior Commissure Development

    Science.gov (United States)

    Stanic, Karen; Saldivia, Natalia; Förstera, Benjamín; Torrejón, Marcela; Montecinos, Hernán; Caprile, Teresa

    2016-01-01

    Extracellular matrix (ECM) molecules are pivotal for central nervous system (CNS) development, facilitating cell migration, axonal growth, myelination, dendritic spine formation, and synaptic plasticity, among other processes. During axon guidance, the ECM not only acts as a permissive or non-permissive substrate for navigating axons, but also modulates the effects of classical guidance cues, such as netrin or Eph/ephrin family members. Despite being highly important, little is known about the expression of ECM molecules during CNS development. Therefore, this study assessed the molecular expression patterns of tenascin, HNK-1, laminin, fibronectin, perlecan, decorin, and osteopontin along chick embryo prosomere 1 during posterior commissure development. The posterior commissure is the first transversal axonal tract of the embryonic vertebrate brain. Located in the dorso-caudal portion of prosomere 1, posterior commissure axons primarily arise from the neurons of basal pretectal nuclei that run dorsally to the roof plate midline, where some turn toward the ipsilateral side. Expressional analysis of ECM molecules in this area these revealed to be highly arranged, and molecule interactions with axon fascicles suggested involvement in processes other than structural support. In particular, tenascin and the HNK-1 epitope extended in ventro-dorsal columns and enclosed axons during navigation to the roof plate. Laminin and osteopontin were expressed in the midline, very close to axons that at this point must decide between extending to the contralateral side or turning to the ipsilateral side. Finally, fibronectin, decorin, and perlecan appeared unrelated to axonal pathfinding in this region and were instead restricted to the external limiting membrane. In summary, the present report provides evidence for an intricate expression of different extracellular molecules that may cooperate in guiding posterior commissure axons. PMID:27733818

  13. Valley Density Evaluation and Typical Development Pattern in Mountainous Areas of Beijing

    Institute of Scientific and Technical Information of China (English)

    MU Song-lin; ZHANG Yi-feng; WANG Kai-yong; TANG Cheng-cai; WANG Ling-en; LIU Yu

    2012-01-01

    Based on geographical differences and space differentiation, valley economy is a new pattern and new perspective for the development of mountainous areas, integrating ecological protection, industrial nurture, and village integration. On the basis of natural and geographical differentiation of valley, we give an overview of the spatial distribution of valley in mountainous areas of Beijing and spatial difference in valley density, and sum up the typical development pattern of valley economy, using DEM data. The results show that the spatial distribution of valley presents an asymmetric shape of inverted V or branch; Miyun, Yanqing, and Changping have high valley density, while Pinggu, Fangshan and Mentougou have low valley density; there is a significant positive relationship between valley density and the spatial distribution of river and reservoir. The development pattern of valley economy is divided into five types: leisure and high-end upgrade-based pattern, ecological development and transition demonstration-based pattern, folk culture and creation-driven pattern, scenic spots-driven and valley-linked pattern and leisure agriculture and specialty-led pattern.

  14. Easy fabrication of thin membranes with through holes. Application to protein patterning.

    Directory of Open Access Journals (Sweden)

    Thomas Masters

    Full Text Available Since protein patterning on 2D surfaces has emerged as an important tool in cell biology, the development of easy patterning methods has gained importance in biology labs. In this paper we present a simple, rapid and reliable technique to fabricate thin layers of UV curable polymer with through holes. These membranes are as easy to fabricate as microcontact printing stamps and can be readily used for stencil patterning. We show how this microfabrication scheme allows highly reproducible and highly homogeneous protein patterning with micron sized resolution on surfaces as large as 10 cm(2. Using these stencils, fragile proteins were patterned without loss of function in a fully hydrated state. We further demonstrate how intricate patterns of multiple proteins can be achieved by stacking the stencil membranes. We termed this approach microserigraphy.

  15. Periodic nanoscale patterning of polyelectrolytes over square centimeter areas using block copolymer templates.

    Science.gov (United States)

    Oded, Meirav; Kelly, Stephen T; Gilles, Mary K; Müller, Axel H E; Shenhar, Roy

    2016-05-18

    Nano-patterned materials are beneficial for applications such as solar cells, opto-electronics, and sensing owing to their periodic structure and high interfacial area. Here, we present a non-lithographic approach for assembling polyelectrolytes into periodic nanoscale patterns over cm(2)-scale areas. Chemically modified block copolymer thin films featuring alternating charged and neutral domains are used as patterned substrates for electrostatic self-assembly. In-depth characterization of the deposition process using spectroscopy and microscopy techniques, including the state-of-the-art scanning transmission X-ray microscopy (STXM), reveals both the selective deposition of the polyelectrolyte on the charged copolymer domains as well as gradual changes in the film topography that arise from further penetration of the solvent molecules and possibly also the polyelectrolyte into these domains. Our results demonstrate the feasibility of creating nano-patterned polyelectrolyte layers, which opens up new opportunities for structured functional coating fabrication.

  16. Assessment of forest geospatial patterns over the three giant forest areas of China

    Institute of Scientific and Technical Information of China (English)

    LI Ming-shi; ZHU Zhi-liang; LU Heng; XU Da; LIU An-xing; PENG Shi-kui

    2008-01-01

    Geospatial patterns of forest fragmentation over the three traditional giant forested areas of China (Northeastern, southwestern and Southern China) were analyzed comparatively and reported based on a 250-m resolution land cover dataset. Specifically, the spatial patterns of forest fragmentation were characterized by combining geospatial metrics and forest fragmentation models. The driving forces resulting in the differences of the forest spatial patterns were also investigated. Results suggested that forests in southwest China had the highest severity of forest fragmentation, followed by south region and northeast region. The driving forces of forest fragmentation in China were primarily the giant population and improper exploitation of forests. In conclusion, the generated information in the study provided valuable insights and implications as to the fragmentation patterns and the conservation of biodiversity or genes, and the use of the chosen geospatial metrics and forest fragmentation models was quite useful for depicting forest fragmentation patterns.

  17. Identification of seismically susceptible areas in western Himalaya using pattern recognition

    Indian Academy of Sciences (India)

    Mridula; Amita Sinvhal; Hans Raj Wason

    2016-06-01

    Seismicity in the western Himalayas is highly variable. Several historical and instrumentally recordeddevastating earthquakes originated in the western Himalayas which are part of the Alpine–Himalayanbelt. Earthquakes cause tremendous loss of life and to the built environment. The amount of loss interms of life and infrastructure has been rising continuously due to significant increase in population andinfrastructure. This study is an attempt to identify seismically susceptible areas in western Himalaya,using pattern recognition technique. An area between latitude 29◦–36◦N and longitude 73◦–80◦E wasconsidered for this study. Pattern recognition starts with identification, selection and extraction of featuresfrom seismotectonic data. These features are then subjected to discriminant analysis and the studyarea was classified into three categories, viz., Area A: most susceptible area, Area B: moderately susceptiblearea, and Area C: least susceptible area. Results show that almost the entire states of HimachalPradesh and Uttarakhand and a portion of Jammu & Kashmir are classified as Area A, while most ofJammu & Kashmir is classified as Area B and the Indo-Gangetic plains are classified as Area C.

  18. In various protein complexes, disordered protomers have large per-residue surface areas and area of protein-, DNA- and RNA-binding interfaces.

    Science.gov (United States)

    Wu, Zhonghua; Hu, Gang; Yang, Jianyi; Peng, Zhenling; Uversky, Vladimir N; Kurgan, Lukasz

    2015-09-14

    We provide first large scale analysis of the peculiarities of surface areas of 5658 dissimilar (below 50% sequence similarity) proteins with known 3D-structures that bind to proteins, DNA or RNAs. We show here that area of the protein surface is highly correlated with the protein length. The size of the interface surface is only modestly correlated with the protein size, except for RNA-binding proteins where larger proteins are characterized by larger interfaces. Disordered proteins with disordered interfaces are characterized by significantly larger per-residue areas of their surfaces and interfaces when compared to the structured proteins. These result are applicable for proteins involved in interaction with DNA, RNA, and proteins and suggest that disordered proteins and binding regions are less compact and more likely to assume extended shape. We demonstrate that disordered protein binding residues in the interfaces of disordered proteins drive the increase in the per residue area of these interfaces. Our results can be used to predict in silico whether a given protomer from the DNA, RNA or protein complex is likely to be disordered in its unbound form.

  19. [Regional ecosecurity pattern in urban area based on land use analysis: a case study in Lanzhou].

    Science.gov (United States)

    Fang, Shubo; Xiao, Dunin; An, Shuqing

    2005-12-01

    Mid-scale regional ecosecurity, which takes practical ecosecurity issues as its priority, should be viewed as the core of the multi-scale concept of ecosecurity. For urban area, a special region taking ecological infrastructure as its core mission, the construction of regional ecosecurity pattern may provide a good chance to realize its sustainable development. Based on land use analysis, a qualitative and quantitative research on the landscape pattern, ecovalue evaluation, and driving force analysis of social economy could provide an effective approach to construct the ecosecurity pattern in urban area. This study showed that in Lanzhou, the ecosecurity pattern consisted of three parts, i.e., eco-safeguarding system, eco-buffering system and eco-percolating system, among which, eco-buffering system was the decisive part determining ecosecurity pattern construction. The quantitative analysis of urban spatial expansion pattern was taken as the decisive function to determine the security level of the ecosecurity pattern, which was divided into low, middle and high levels.

  20. Influence of Exterior Space to Linkage and Tourist Movement Pattern in Losari Coastal Area

    Directory of Open Access Journals (Sweden)

    Nur Adyla Suriadi

    2015-07-01

    Full Text Available Makassar City has a strategic location because located at the crossroads of good traffic from north to south and from west to east, from these advantages so Makassar City eligible to be a tourism destination. One of the hallmarks quality tourism destination is Losari Coastal Area, which is a tourist area that became an icon of the city of Makassar and has many tourist attractions i.e. Reclamation Losari Beach, Fort Rotterdam, Somba Opu Shopping Centre and Culinary Tourism Area. However, tourist movement patterns who concentrated only in Reclamation Losari Beach needs for development of linkage at tourist attractions based on tourist movement patterns. Research method used is descriptive qualitative method with cognitive mapping technique to identify of tourist movement patterns characteristic in visiting tourist attractions at Losari Coastal Area and influence of exterior space to linkage among tourist attractions. Results from this research is determine influence of exterior space to connectivity linkage and tourist movement patterns among tourist attractions and find local criteria of exterior space which can be applied in Losari Coastal Area.

  1. Honeycomb-patterned films of polystyrene/poly(ethylene glycol): Preparation, surface aggregation and protein adsorption

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Highly ordered honeycomb-patterned polystyrene (PS)/poly(ethylene glycol) (PEG) films were prepared by a water-assisted method using an improved setup, which facilitated the formation of films with higher regularity, better reproducibility, and larger area of honeycomb structures. Surface aggregation of hydrophilic PEG and adsorption of bovine serum albumin (BSA) on the honeycomb-patterned films were investigated. Field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM) were used to observe the surface morphologies of the films before and after being rinsed with water. As confirmed by the FESEM images and the AFM phase images, PEG was enriched in the pores and could be gradually removed by water. The adsorption of fluorescence-labeled BSA on the films was studied in visual form using laser scanning confocal microscopy. Results clearly demonstrated that the protein-resistant PEG was selectively enriched in the pores. This water-assisted method may be a latent tool to prepare honeycomb-patterned biofunctional surfaces.

  2. Sustainable development pattern and strategy in the Three Gorges Reservoir Areas

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The development pattern, development situation, and existing problems of land exploitation in Zigui County, Three Gorges Reservoir Areas of China were presented. The sustainable development mode and its strategy in the Three Gorges Reservoir Areas was also discussed. A sustainable development framework for low mountain regions, middle mountain regions and high mountain regions was developed, and management countermeasures for structural optimization of complex ecosystems were advanced.

  3. Malaria Transmission Pattern in an Area Selected for Clinical Trials in the Sudanian Area of Senegal (West Africa

    Directory of Open Access Journals (Sweden)

    El Hadji Amadou Niang

    2013-01-01

    Full Text Available Malaria transmission pattern was studied in 3 villages (Toubanding, Daga Ndoup, and Keur Samba Guèye situated within an area selected for clinical trials. The study was conducted in the rainy season from July to December 2011. The main objective of this work was to gather baseline data on malaria transmission intensity and other entomological parameters before the advent of clinical trials. Mosquitoes were collected by Human-Landing Collections (HLCs and by pyrethrum spray catches (PSCs. Five anopheline species were collected, namely, An. arabiensis, An. gambiae, An. funestus, An. pharoensis, and An. rufipes, giving a heterogeneous distribution within the study area. The populations dynamics of the vectors varied temporarily in each village depending on the pattern of the rainy season. Transmission intensity estimated by the entomological inoculation rate (EIR was measured in each of the three villages with the variations linked to the microecological differences between the villages. Measurements were calculated for August, September, and October and were found to vary between 4 and 30 infected bites per person over the study period with a peak intensity observed in September. These results indicate that epidemiological field trials on malaria could be conducted in this area on the basis of the differences observed with transmission intensity, micro-ecological variations, and the objectives of the trials.

  4. Spatial and temporal patterns of air pollutants in rural and urban areas of India.

    Science.gov (United States)

    Sharma, Disha; Kulshrestha, U C

    2014-12-01

    In this study, we analysed spatial and temporal patterns of Suspended Particulate Matter (SPM) concentrations across India. We have also assessed MODIS-derived aerosol optical depth (AOD) variations to characterize the air quality and relate it to SPM, NO2 and SO2 in different areas. In addition, the pollutant concentrations have been mapped using geospatial techniques. The results indicated significant differences in air pollutant levels across rural and urban areas. In general, districts of central and northern India had relatively higher SPM concentrations compared to southern India. Out of the top ten SPM polluted districts in India, nine were located in the state of Uttar Pradesh (UP). We observed significant correlations between the SPM and AOD at different sites. Although spatial and temporal patterns of NO2 and SO2 matched AOD patterns, the correlation strength (r2) varied based on location. The causes and implications of these findings are presented.

  5. Invariant patterns in crystal lattices: Implications for protein folding algorithms

    Energy Technology Data Exchange (ETDEWEB)

    HART,WILLIAM E.; ISTRAIL,SORIN

    2000-06-01

    Crystal lattices are infinite periodic graphs that occur naturally in a variety of geometries and which are of fundamental importance in polymer science. Discrete models of protein folding use crystal lattices to define the space of protein conformations. Because various crystal lattices provide discretizations of the same physical phenomenon, it is reasonable to expect that there will exist invariants across lattices related to fundamental properties of the protein folding process. This paper considers whether performance-guaranteed approximability is such an invariant for HP lattice models. The authors define a master approximation algorithm that has provable performance guarantees provided that a specific sublattice exists within a given lattice. They describe a broad class of crystal lattices that are approximable, which further suggests that approximability is a general property of HP lattice models.

  6. Patterns of molecular evolution in pathogenesis-related proteins

    OpenAIRE

    Scherer,Nicole M.; Thompson,Claudia E.; Freitas,Loreta B.; Bonatto, Sandro L.; Salzano,Francisco M.

    2005-01-01

    The genes encoding 13 classes of pathogenesis-related (PR) proteins were examined for positive selection using maximum-likelihood (ML) models of codon substitution. The study involved 194 sequences from 54 species belonging to 37 genera. Although the sizes of the sequences examined varied from 237 bp for PR12 to 1,110 bp for PR7, most classes (9 out of 13) contained sequences made up of more than 400 nucleotides. Signs of positive selection were obtained for sites in PR proteins 4, 6, 8, 9 an...

  7. Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site

    Energy Technology Data Exchange (ETDEWEB)

    Valley, Cary T.; Porter, Douglas F.; Qiu, Chen; Campbell, Zachary T.; Tanaka Hall, Traci M.; Wickens, Marvin (NIEHS); (UW)

    2012-06-28

    mRNA control hinges on the specificity and affinity of proteins for their RNA binding sites. Regulatory proteins must bind their own sites and reject even closely related noncognate sites. In the PUF [Pumilio and fem-3 binding factor (FBF)] family of RNA binding proteins, individual proteins discriminate differences in the length and sequence of binding sites, allowing each PUF to bind a distinct battery of mRNAs. Here, we show that despite these differences, the pattern of RNA interactions is conserved among PUF proteins: the two ends of the PUF protein make critical contacts with the two ends of the RNA sites. Despite this conserved 'two-handed' pattern of recognition, the RNA sequence is flexible. Among the binding sites of yeast Puf4p, RNA sequence dictates the pattern in which RNA bases are flipped away from the binding surface of the protein. Small differences in RNA sequence allow new modes of control, recruiting Puf5p in addition to Puf4p to a single site. This embedded information adds a new layer of biological meaning to the connections between RNA targets and PUF proteins.

  8. Topographic patterns of vascular disease: HOX proteins as determining factors?

    Institute of Scientific and Technical Information of China (English)

    Richard; P; Visconti; Alexander; Awgulewitsch

    2015-01-01

    Steadily increasing evidence supports the idea that genetic diversities in the vascular bed are, in addition to hemodynamic influences, a major contributing factor in determining region-specific cardiovascular disease susceptibility. Members of the phylogenetically highly conserved Hox gene family of developmental regulators have to be viewed as prime candidates for determining these regional genetic differences in the vasculature. During embryonic patterning, the regionally distinct and precisely choreographed expression patterns of HOX transcription factors are essential for the correct specification of positional identities. Apparently, these topographic patterns are to some degree retained in certain adult tissues, including the circulatory system. While an understanding of the functional significance of these localized Hox activities in adult blood vessels is only beginning to emerge, an argument can be made for a role of Hox genes in the maintenance of vessel wall homeostasis and functional integrity on the one hand, and in regulating the development and progression of regionally restricted vascular pathologies, on the other. Initial functional studies in animal models, as well as data from clinical studies provide some level of support for this view. The data suggest that putative genetic regulatory networks of Hox-dependent cardiovascular disease processes include genes of diverse functional categories(extracellular matrix remodeling, transmembrane signaling, cell cycle control, inflammatory response, transcriptional control, etc.), as potential targets in both vascular smooth muscle and endothelial cells, as well as cell populations residing in the adventitia.

  9. Protein patterns of black fungi under simulated Mars-like conditions

    Science.gov (United States)

    Zakharova, Kristina; Marzban, Gorji; de Vera, Jean-Pierre; Lorek, Andreas; Sterflinger, Katja

    2014-05-01

    Two species of microcolonial fungi - Cryomyces antarcticus and Knufia perforans - and a species of black yeasts-Exophiala jeanselmei - were exposed to thermo-physical Mars-like conditions in the simulation chamber of the German Aerospace Center. In this study the alterations at the protein expression level from various fungi species under Mars-like conditions were analyzed for the first time using 2D gel electrophoresis. Despite of the expectations, the fungi did not express any additional proteins under Mars simulation that could be interpreted as stress induced HSPs. However, up-regulation of some proteins and significant decreasing of protein number were detected within the first 24 hours of the treatment. After 4 and 7 days of the experiment protein spot number was increased again and the protein patterns resemble the protein patterns of biomass from normal conditions. It indicates the recovery of the metabolic activity under Martian environmental conditions after one week of exposure.

  10. Interaction of Hepatitis C virus proteins with pattern recognition receptors

    Directory of Open Access Journals (Sweden)

    Imran Muhammad

    2012-06-01

    Full Text Available Abstract Hepatitis C virus (HCV is an important human pathogen that causes acute and chronic hepatitis, cirrhosis and hepatocellular carcinoma worldwide. This positive stranded RNA virus is extremely efficient in establishing persistent infection by escaping immune detection or hindering the host immune responses. Recent studies have discovered two important signaling pathways that activate the host innate immunity against viral infection. One of these pathways utilizes members of Toll-like receptor (TLR family and the other uses the RNA helicase retinoic acid inducible gene I (RIG-I as the receptors for intracellular viral double stranded RNA (dsRNA, and activation of transcription factors. In this review article, we summarize the interaction of HCV proteins with various host receptors/sensors through one of these two pathways or both, and how they exploit these interactions to escape from host defense mechanisms. For this purpose, we searched data from Pubmed and Google Scholar. We found that three HCV proteins; Core (C, non structural 3/4 A (NS3/4A and non structural 5A (NS5A have direct interactions with these two pathways. Core protein only in the monomeric form stimulates TLR2 pathway assisting the virus to evade from the innate immune system. NS3/4A disrupts TLR3 and RIG-1 signaling pathways by cleaving Toll/IL-1 receptor domain-containing adapter inducing IFN-beta (TRIF and Cardif, the two important adapter proteins of these signaling cascades respectively, thus halting the defense against HCV. NS5A downmodulates the expressions of NKG2D on natural killer cells (NK cells via TLR4 pathway and impairs the functional ability of these cells. TLRs and RIG-1 pathways have a central role in innate immunity and despite their opposing natures to HCV proteins, when exploited together, HCV as an ever developing virus against host immunity is able to accumulate these mechanisms for near unbeatable survival.

  11. Dispersal patterns of coastal fish: implications for designing networks of marine protected areas.

    Directory of Open Access Journals (Sweden)

    Antonio Di Franco

    Full Text Available Information about dispersal scales of fish at various life history stages is critical for successful design of networks of marine protected areas, but is lacking for most species and regions. Otolith chemistry provides an opportunity to investigate dispersal patterns at a number of life history stages. Our aim was to assess patterns of larval and post-settlement (i.e. between settlement and recruitment dispersal at two different spatial scales in a Mediterranean coastal fish (i.e. white sea bream, Diplodus sargus sargus using otolith chemistry. At a large spatial scale (∼200 km we investigated natal origin of fish and at a smaller scale (∼30 km we assessed "site fidelity" (i.e. post-settlement dispersal until recruitment. Larvae dispersed from three spawning areas, and a single spawning area supplied post-settlers (proxy of larval supply to sites spread from 100 to 200 km of coastline. Post-settlement dispersal occurred within the scale examined of ∼30 km, although about a third of post-settlers were recruits in the same sites where they settled. Connectivity was recorded both from a MPA to unprotected areas and vice versa. The approach adopted in the present study provides some of the first quantitative evidence of dispersal at both larval and post-settlement stages of a key species in Mediterranean rocky reefs. Similar data taken from a number of species are needed to effectively design both single marine protected areas and networks of marine protected areas.

  12. Dispersal patterns of coastal fish: implications for designing networks of marine protected areas.

    Science.gov (United States)

    Di Franco, Antonio; Gillanders, Bronwyn M; De Benedetto, Giuseppe; Pennetta, Antonio; De Leo, Giulio A; Guidetti, Paolo

    2012-01-01

    Information about dispersal scales of fish at various life history stages is critical for successful design of networks of marine protected areas, but is lacking for most species and regions. Otolith chemistry provides an opportunity to investigate dispersal patterns at a number of life history stages. Our aim was to assess patterns of larval and post-settlement (i.e. between settlement and recruitment) dispersal at two different spatial scales in a Mediterranean coastal fish (i.e. white sea bream, Diplodus sargus sargus) using otolith chemistry. At a large spatial scale (∼200 km) we investigated natal origin of fish and at a smaller scale (∼30 km) we assessed "site fidelity" (i.e. post-settlement dispersal until recruitment). Larvae dispersed from three spawning areas, and a single spawning area supplied post-settlers (proxy of larval supply) to sites spread from 100 to 200 km of coastline. Post-settlement dispersal occurred within the scale examined of ∼30 km, although about a third of post-settlers were recruits in the same sites where they settled. Connectivity was recorded both from a MPA to unprotected areas and vice versa. The approach adopted in the present study provides some of the first quantitative evidence of dispersal at both larval and post-settlement stages of a key species in Mediterranean rocky reefs. Similar data taken from a number of species are needed to effectively design both single marine protected areas and networks of marine protected areas.

  13. Assessing dispersal patterns of fish propagules from an effective mediterranean marine protected area.

    Directory of Open Access Journals (Sweden)

    Antonio Di Franco

    Full Text Available Successfully enforced marine protected areas (MPAs have been widely demonstrated to allow, within their boundaries, the recovery of exploited species and beyond their boundaries, the spillover of juvenile and adult fish. Little evidence is available about the so-called 'recruitment subsidy', the augmented production of propagules (i.e. eggs and larvae due to the increased abundance of large-sized spawners hosted within effective MPAs. Once emitted, propagules can be locally retained and/or exported elsewhere. Patterns of propagule retention and/or export from MPAs have been little investigated, especially in the Mediterranean. This study investigated the potential for propagule production and retention/export from a Mediterranean MPA (Torre Guaceto, SW Adriatic Sea using the white sea bream, Diplodus sargus sargus, as a model species. A multidisciplinary approach was used combining 1 spatial distribution patterns of individuals (post-settlers and adults assessed through visual census within Torre Guaceto MPA and in northern and southern unprotected areas, 2 Lagrangian simulations of dispersal based on an oceanographic model of the region and data on early life-history traits of the species (spawning date, pelagic larval duration and 3 a preliminary genetic study using microsatellite loci. Results show that the MPA hosts higher densities of larger-sized spawners than outside areas, potentially guaranteeing higher propagule production. Model simulations and field observation suggest that larval retention within and long-distance dispersal across MPA boundaries allow the replenishment of the MPA and of exploited populations up to 100 km down-current (southward from the MPA. This pattern partially agrees with the high genetic homogeneity found in the entire study area (no differences in genetic composition and diversity indices, suggesting a high gene flow. By contributing to a better understanding of propagule dispersal patterns, these findings

  14. Assessing dispersal patterns of fish propagules from an effective mediterranean marine protected area.

    Science.gov (United States)

    Di Franco, Antonio; Coppini, Giovanni; Pujolar, José Martin; De Leo, Giulio A; Gatto, Marino; Lyubartsev, Vladyslav; Melià, Paco; Zane, Lorenzo; Guidetti, Paolo

    2012-01-01

    Successfully enforced marine protected areas (MPAs) have been widely demonstrated to allow, within their boundaries, the recovery of exploited species and beyond their boundaries, the spillover of juvenile and adult fish. Little evidence is available about the so-called 'recruitment subsidy', the augmented production of propagules (i.e. eggs and larvae) due to the increased abundance of large-sized spawners hosted within effective MPAs. Once emitted, propagules can be locally retained and/or exported elsewhere. Patterns of propagule retention and/or export from MPAs have been little investigated, especially in the Mediterranean. This study investigated the potential for propagule production and retention/export from a Mediterranean MPA (Torre Guaceto, SW Adriatic Sea) using the white sea bream, Diplodus sargus sargus, as a model species. A multidisciplinary approach was used combining 1) spatial distribution patterns of individuals (post-settlers and adults) assessed through visual census within Torre Guaceto MPA and in northern and southern unprotected areas, 2) Lagrangian simulations of dispersal based on an oceanographic model of the region and data on early life-history traits of the species (spawning date, pelagic larval duration) and 3) a preliminary genetic study using microsatellite loci. Results show that the MPA hosts higher densities of larger-sized spawners than outside areas, potentially guaranteeing higher propagule production. Model simulations and field observation suggest that larval retention within and long-distance dispersal across MPA boundaries allow the replenishment of the MPA and of exploited populations up to 100 km down-current (southward) from the MPA. This pattern partially agrees with the high genetic homogeneity found in the entire study area (no differences in genetic composition and diversity indices), suggesting a high gene flow. By contributing to a better understanding of propagule dispersal patterns, these findings provide

  15. Assessing Dispersal Patterns of Fish Propagules from an Effective Mediterranean Marine Protected Area

    Science.gov (United States)

    Di Franco, Antonio; Coppini, Giovanni; Pujolar, José Martin; De Leo, Giulio A.; Gatto, Marino; Lyubartsev, Vladyslav; Melià, Paco; Zane, Lorenzo; Guidetti, Paolo

    2012-01-01

    Successfully enforced marine protected areas (MPAs) have been widely demonstrated to allow, within their boundaries, the recovery of exploited species and beyond their boundaries, the spillover of juvenile and adult fish. Little evidence is available about the so-called ‘recruitment subsidy’, the augmented production of propagules (i.e. eggs and larvae) due to the increased abundance of large-sized spawners hosted within effective MPAs. Once emitted, propagules can be locally retained and/or exported elsewhere. Patterns of propagule retention and/or export from MPAs have been little investigated, especially in the Mediterranean. This study investigated the potential for propagule production and retention/export from a Mediterranean MPA (Torre Guaceto, SW Adriatic Sea) using the white sea bream, Diplodus sargus sargus, as a model species. A multidisciplinary approach was used combining 1) spatial distribution patterns of individuals (post-settlers and adults) assessed through visual census within Torre Guaceto MPA and in northern and southern unprotected areas, 2) Lagrangian simulations of dispersal based on an oceanographic model of the region and data on early life-history traits of the species (spawning date, pelagic larval duration) and 3) a preliminary genetic study using microsatellite loci. Results show that the MPA hosts higher densities of larger-sized spawners than outside areas, potentially guaranteeing higher propagule production. Model simulations and field observation suggest that larval retention within and long-distance dispersal across MPA boundaries allow the replenishment of the MPA and of exploited populations up to 100 km down-current (southward) from the MPA. This pattern partially agrees with the high genetic homogeneity found in the entire study area (no differences in genetic composition and diversity indices), suggesting a high gene flow. By contributing to a better understanding of propagule dispersal patterns, these findings provide

  16. Quantity of dietary protein intake, but not pattern of intake, affects net protein balance primarily through differences in protein synthesis in older adults.

    Science.gov (United States)

    Kim, Il-Young; Schutzler, Scott; Schrader, Amy; Spencer, Horace; Kortebein, Patrick; Deutz, Nicolaas E P; Wolfe, Robert R; Ferrando, Arny A

    2015-01-01

    To examine whole body protein turnover and muscle protein fractional synthesis rate (MPS) following ingestions of protein in mixed meals at two doses of protein and two intake patterns, 20 healthy older adult subjects (52-75 yr) participated in one of four groups in a randomized clinical trial: a level of protein intake of 0.8 g (1RDA) or 1.5 g·kg(-1)·day(-1) (∼2RDA) with uneven (U: 15/20/65%) or even distribution (E: 33/33/33%) patterns of intake for breakfast, lunch, and dinner over the day (1RDA-U, 1RDA-E, 2RDA-U, or 2RDA-E). Subjects were studied with primed continuous infusions of L-[(2)H5]phenylalanine and L-[(2)H2]tyrosine on day 4 following 3 days of diet habituation. Whole body protein kinetics [protein synthesis (PS), breakdown, and net balance (NB)] were expressed as changes from the fasted to the fed states. Positive NB was achieved at both protein levels, but NB was greater in 2RDA vs. 1RDA (94.8 ± 6.0 vs. 58.9 ± 4.9 g protein/750 min; P = 0.0001), without effects of distribution on NB. The greater NB was due to the higher PS with 2RDA vs. 1RDA (15.4 ± 4.8 vs. -18.0 ± 8.4 g protein/750 min; P = 0.0018). Consistent with PS, MPS was greater with 2RDA vs. 1RDA, regardless of distribution patterns. In conclusion, whole body net protein balance was greater with protein intake above recommended dietary allowance (0.8 g protein·kg(-1)·day(-1)) in the context of mixed meals, without demonstrated effects of protein intake pattern, primarily through higher rates of protein synthesis at whole body and muscle levels.

  17. Direct Laser Interference Patterning: Tailoring of Contact Area for Frictional and Antibacterial Properties

    Directory of Open Access Journals (Sweden)

    Andreas Rosenkranz

    2016-01-01

    Full Text Available Surface functionalization by topographic micro- and nano-structures in order to achieve unique properties, like super-hydrophobicity or ultrahigh light absorption, is a common strategy in nature. In this paper, direct laser interference patterning (DLIP is presented as a promising tool allowing for the generation of such surface patterns on technical surfaces in order to mimic these biological surfaces and effects. Friction optimization and antibacterial effects by DLIP are exemplarily described. Topographic surface patterns on the micro- and nano-scale demonstrated a significant reduction in the coefficient of friction and bacterial adhesion. It was shown that in both cases, the control of the contact area between surfaces or between surface and bacteria is of utmost importance.

  18. Creating two-dimensional patterned substrates for protein and cell confinement.

    Science.gov (United States)

    Johnson, Dawn M; LaFranzo, Natalie A; Maurer, Joshua A

    2011-01-01

    Microcontact printing provides a rapid, highly reproducible method for the creation of well-defined patterned substrates.(1) While microcontact printing can be employed to directly print a large number of molecules, including proteins,(2) DNA,(3) and silanes,(4) the formation of self-assembled monolayers (SAMs) from long chain alkane thiols on gold provides a simple way to confine proteins and cells to specific patterns containing adhesive and resistant regions. This confinement can be used to control cell morphology and is useful for examining a variety of questions in protein and cell biology. Here, we describe a general method for the creation of well-defined protein patterns for cellular studies.(5) This process involves three steps: the production of a patterned master using photolithography, the creation of a PDMS stamp, and microcontact printing of a gold-coated substrate. Once patterned, these cell culture substrates are capable of confining proteins and/or cells (primary cells or cell lines) to the pattern. The use of self-assembled monolayer chemistry allows for precise control over the patterned protein/cell adhesive regions and non-adhesive regions; this cannot be achieved using direct protein stamping. Hexadecanethiol, the long chain alkane thiol used in the microcontact printing step, produces a hydrophobic surface that readily adsorbs protein from solution. The glycol-terminated thiol, used for backfilling the non-printed regions of the substrate, creates a monolayer that is resistant to protein adsorption and therefore cell growth.(6) These thiol monomers produce highly structured monolayers that precisely define regions of the substrate that can support protein adsorption and cell growth. As a result, these substrates are useful for a wide variety of applications from the study of intercellular behavior(7) to the creation of microelectronics.(8) While other types of monolayer chemistry have been used for cell culture studies, including work from

  19. Distribution Patterns of Human Elephant Conflict in Areas Adjacent to Rungwa Game Reserve, Tanzania

    OpenAIRE

    Munuo, Wilbright

    2016-01-01

    Abstract Human pressure on terrestrial ecosystems has caused loss and fragmentation of habitats for wildlife species. That has brought humans and wildlife in close proximity intensifying human wildlife conflicts, especially when wild animals with wide home ranges, such as African and Asian elephants, are involved. This study assesses distribution patterns of human elephant conflict (HEC) in areas adjacent to Rungwa Game Reserve (RGR) in Tanzania. Questionnaire survey was used as a tool fo...

  20. [Altitudinal richness patterns of Papilionidae, Pieridae and Nymphalidae (Lepidoptera) in Mexican mountain areas].

    Science.gov (United States)

    Monteagudo Sabaté, David; Luis Martínez, Moisés Armando

    2013-09-01

    Altitudinal richness patterns of Papilionidae, Pieridae and Nymphalidae (Lepidoptera) in Mexican mountain areas. Butterflies constitute an useful group to investigate biodiversity patterns in specific geographic areas. The aim of this study was to describe the altitudinal patterns distribution and to recognize the main grouping factors of these families. We conducted a comparative study between the butterfly fauna (Papilionidae, Pieridae and Nymphalidae) of five Mexican mountain ranges (Sierra de Manantlán, Sierra de Atoyac de Alvarez, Loxicha Region, Teocelo-Xalapa and Sierra de Juárez), that included 34 sites of altitudinal ranges from 100 to 2 820m. Data was obtained from the Zoology Museum of the National University of Mexico, and comprised more than 60 000 butterfly records of 398 taxa (subspecies level) proceeding during the last 35 years. Fauna similarity between localities were analyzed using a cluster analysis by Sorensen similarity coefficient. Species richness showed a general tendency to decrease with altitude; the main difference was found between the locality with higher altitude and the rest of the sites. The principal factors affecting the identified clusters followed this order: the location in Pacific or Atlantic slope, and location on a particular mountain range. Three altitudinal levels (low elevations, up to 1 200m; intermediate elevations, from 1200 to 1800 m; and high elevations, from 1800 to 2500 m) were described in accordance to their main characteristic taxa. While Neartic elements were common in the highest altitudinal floor, Neotropical taxa were common in the lowest one. It was more difficult to characterize the intermediate level in which a high number of localities were clustered; this intermediate level was characterized by the presence of some endemic species. The results suggest that historical factors are preeminent in butterfly fauna composition in these areas. Future studies may include other Mexican mountain areas to obtain

  1. Fluorescent Biotin Analogues for Microstructure Patterning and Selective Protein Immobilization.

    Science.gov (United States)

    Krishna, K Vijaya; Ghosh, Subhadip; Sharma, Bikramjit; Singh, Leeju; Mukherjee, Saptarshi; Verma, Sandeep

    2015-11-24

    Benzyl substitution on ureido nitrogens of biotin led to manifestation of aggregation-induced emission, which was studied by steady-state fluorescence, microscopy, and TD-DFT, providing a rationale into the observed photophysical behavior. Besides exhibiting solvatochromism, the biotin derivatives revealed emission peaks centered at ∼430 and 545 nm, which has been attributed to the π-π stacking interactions. Our TD-DFT results also correlate the spectroscopic data and quantify the nature of transitions involved. The isothermal titration calorimetry data substantiates that the binding of the biotin derivatives with avidin are pretty strong. These derivatives on lithographic patterning present a platform for site specific strept(avidin) immobilization, thus opening avenues for potential applications exploiting these interactions. The fluorescent biotin derivatives can thus find applications in cellular biology and imaging.

  2. UV lithography-based protein patterning on silicon: Towards the integration of bioactive surfaces and CMOS electronics

    Energy Technology Data Exchange (ETDEWEB)

    Lenci, S., E-mail: silvia.lenci@iet.unipi.it [Dipartimento di Ingegneria dell' Informazione, via G.Caruso 16, Pisa I-56122 (Italy); Tedeschi, L. [Istituto di Fisiologia Clinica - CNR, via G. Moruzzi 1, Pisa I-56124 (Italy); Pieri, F. [Dipartimento di Ingegneria dell' Informazione, via G.Caruso 16, Pisa I-56122 (Italy); Domenici, C. [Istituto di Fisiologia Clinica - CNR, via G. Moruzzi 1, Pisa I-56124 (Italy)

    2011-08-01

    A simple and fast methodology for protein patterning on silicon substrates is presented, providing an insight into possible issues related to the interaction between biological and microelectronic technologies. The method makes use of standard photoresist lithography and is oriented towards the implementation of biosensors containing Complementary Metal-Oxide-Semiconductor (CMOS) conditioning circuitry. Silicon surfaces with photoresist patterns were prepared and hydroxylated by means of resist- and CMOS backend-compatible solutions. Subsequent aminosilane deposition and resist lift-off in organic solvents resulted into well-controlled amino-terminated geometries. The discussion is focused on resist- and CMOS-compatibility problems related to the used chemicals. Some samples underwent gold nanoparticle (Au NP) labeling and Scanning Electron Microscopy (SEM) observation, in order to investigate the quality of the silane layer. Antibodies were immobilized on other samples, which were subsequently exposed to a fluorescently labeled antigen. Fluorescence microscopy observation showed that this method provides spatially selective immobilization of protein layers onto APTES-patterned silicon samples, while preserving protein reactivity inside the desired areas and low non-specific adsorption elsewhere. Strong covalent biomolecule binding was achieved, giving stable protein layers, which allows stringent binding conditions and a good binding specificity, really useful for biosensing.

  3. Selective Area Growth of GaAs on Si Patterned Using Nanoimprint Lithography

    Energy Technology Data Exchange (ETDEWEB)

    Warren, Emily L.; Makoutz, Emily A.; Horowitz, Kelsey A. W.; Dameron, Arrelaine; Norman, Andrew G.; Stradins, Paul; Zimmerman, Jeramy D.; Tamboli, Adele C.

    2016-11-21

    Heteroepitaxial selective area growth (SAG) of GaAs on patterned Si substrates is a potential low-cost approach to integrate III-V and Si materials for tandem or multijunction solar cells. The use of nanoscale openings in a dielectric material can minimize nucleation-related defects and allow thinner buffer layers to be used to accommodate lattice mismatch between Si and an epitaxial III-V layer. For photovoltaic applications, the cost of patterning and growth, as well as the impact on the performance of the Si bottom cell must be considered. We present preliminary results on the use of soft nanoimprint lithography (SNIL) to create patterned nucleation templates for the heteroepitaxial SAG of GaAs on Si. We demonstrate that SNIL patterning of passivating layers on the Si substrate improves measured minority carrier properties relative to unprotected Si. Cost modeling of the SNIL process shows that adding a patterning step only adds a minor contribution to the overall cost of a tandem III-V/Si solar cell, and can enable significant savings if it enables thinner buffer layers.

  4. Patterns and variability of projected bioclimatic habitat for Pinus albicaulis in the Greater Yellowstone Area.

    Science.gov (United States)

    Chang, Tony; Hansen, Andrew J; Piekielek, Nathan

    2014-01-01

    Projected climate change at a regional level is expected to shift vegetation habitat distributions over the next century. For the sub-alpine species whitebark pine (Pinus albicaulis), warming temperatures may indirectly result in loss of suitable bioclimatic habitat, reducing its distribution within its historic range. This research focuses on understanding the patterns of spatiotemporal variability for future projected P.albicaulis suitable habitat in the Greater Yellowstone Area (GYA) through a bioclimatic envelope approach. Since intermodel variability from General Circulation Models (GCMs) lead to differing predictions regarding the magnitude and direction of modeled suitable habitat area, nine bias-corrected statistically down-scaled GCMs were utilized to understand the uncertainty associated with modeled projections. P.albicaulis was modeled using a Random Forests algorithm for the 1980-2010 climate period and showed strong presence/absence separations by summer maximum temperatures and springtime snowpack. Patterns of projected habitat change by the end of the century suggested a constant decrease in suitable climate area from the 2010 baseline for both Representative Concentration Pathways (RCPs) 8.5 and 4.5 climate forcing scenarios. Percent suitable climate area estimates ranged from 2-29% and 0.04-10% by 2099 for RCP 8.5 and 4.5 respectively. Habitat projections between GCMs displayed a decrease of variability over the 2010-2099 time period related to consistent warming above the 1910-2010 temperature normal after 2070 for all GCMs. A decreasing pattern of projected P.albicaulis suitable habitat area change was consistent across GCMs, despite strong differences in magnitude. Future ecological research in species distribution modeling should consider a full suite of GCM projections in the analysis to reduce extreme range contractions/expansions predictions. The results suggest that restoration strageties such as planting of seedlings and controlling

  5. Patterns and variability of projected bioclimatic habitat for Pinus albicaulis in the Greater Yellowstone Area.

    Directory of Open Access Journals (Sweden)

    Tony Chang

    Full Text Available Projected climate change at a regional level is expected to shift vegetation habitat distributions over the next century. For the sub-alpine species whitebark pine (Pinus albicaulis, warming temperatures may indirectly result in loss of suitable bioclimatic habitat, reducing its distribution within its historic range. This research focuses on understanding the patterns of spatiotemporal variability for future projected P.albicaulis suitable habitat in the Greater Yellowstone Area (GYA through a bioclimatic envelope approach. Since intermodel variability from General Circulation Models (GCMs lead to differing predictions regarding the magnitude and direction of modeled suitable habitat area, nine bias-corrected statistically down-scaled GCMs were utilized to understand the uncertainty associated with modeled projections. P.albicaulis was modeled using a Random Forests algorithm for the 1980-2010 climate period and showed strong presence/absence separations by summer maximum temperatures and springtime snowpack. Patterns of projected habitat change by the end of the century suggested a constant decrease in suitable climate area from the 2010 baseline for both Representative Concentration Pathways (RCPs 8.5 and 4.5 climate forcing scenarios. Percent suitable climate area estimates ranged from 2-29% and 0.04-10% by 2099 for RCP 8.5 and 4.5 respectively. Habitat projections between GCMs displayed a decrease of variability over the 2010-2099 time period related to consistent warming above the 1910-2010 temperature normal after 2070 for all GCMs. A decreasing pattern of projected P.albicaulis suitable habitat area change was consistent across GCMs, despite strong differences in magnitude. Future ecological research in species distribution modeling should consider a full suite of GCM projections in the analysis to reduce extreme range contractions/expansions predictions. The results suggest that restoration strageties such as planting of seedlings and

  6. Expression patterns of protein kinase D 3 during mouse development

    Directory of Open Access Journals (Sweden)

    Lutz Sylke

    2008-04-01

    Full Text Available Abstract Background The PKD family of serine/threonine kinases comprises a single member in Drosophila (dPKD, two isoforms in C. elegans (DKF-1 and 2 and three members, PKD1, PKD2 and PKD3 in mammals. PKD1 and PKD2 have been the focus of most studies up to date, which implicate these enzymes in very diverse cellular functions, including Golgi organization and plasma membrane directed transport, immune responses, apoptosis and cell proliferation. Concerning PKD3, a role in the formation of vesicular transport carriers at the trans-Golgi network (TGN and in basal glucose transport has been inferred from in vitro studies. So far, however, the physiological functions of the kinase during development remain unknown. Results We have examined the expression pattern of PKD3 during the development of mouse embryos by immunohistochemistry. Using a PKD3 specific antibody we demonstrate that the kinase is differentially expressed during organogenesis. In the developing heart a strong PKD3 expression is constantly detected from E10 to E16.5. From E12.5 on PKD3 is increasingly expressed in neuronal as well as in the supporting connective tissue and in skeletal muscles. Conclusion The data presented support an important role for PKD3 during development of these tissues.

  7. Simultaneous formation of fine and large-area electrode patterns using screen-offset printing and its application to the patterning on adhesive materials

    Science.gov (United States)

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

    2016-03-01

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

  8. Unsupervised clustering of subcellular protein expression patterns in high-throughput microscopy images reveals protein complexes and functional relationships between proteins.

    Directory of Open Access Journals (Sweden)

    Louis-François Handfield

    Full Text Available Protein subcellular localization has been systematically characterized in budding yeast using fluorescently tagged proteins. Based on the fluorescence microscopy images, subcellular localization of many proteins can be classified automatically using supervised machine learning approaches that have been trained to recognize predefined image classes based on statistical features. Here, we present an unsupervised analysis of protein expression patterns in a set of high-resolution, high-throughput microscope images. Our analysis is based on 7 biologically interpretable features which are evaluated on automatically identified cells, and whose cell-stage dependency is captured by a continuous model for cell growth. We show that it is possible to identify most previously identified localization patterns in a cluster analysis based on these features and that similarities between the inferred expression patterns contain more information about protein function than can be explained by a previous manual categorization of subcellular localization. Furthermore, the inferred cell-stage associated to each fluorescence measurement allows us to visualize large groups of proteins entering the bud at specific stages of bud growth. These correspond to proteins localized to organelles, revealing that the organelles must be entering the bud in a stereotypical order. We also identify and organize a smaller group of proteins that show subtle differences in the way they move around the bud during growth. Our results suggest that biologically interpretable features based on explicit models of cell morphology will yield unprecedented power for pattern discovery in high-resolution, high-throughput microscopy images.

  9. The simulation of cropping pattern to improve the performance of irrigation network in Cau irrigation area

    Science.gov (United States)

    Wahyuningsih, Retno; Rintis Hadiani, RR; Sobriyah

    2017-01-01

    Cau irrigation area located in Madiun district, East Java Province, irrigates 1.232 Ha of land which covers Cau primary channel irrigation network, Wungu Secondary channel irrigation network, and Grape secondary channel irrigation network. The problems in Cau irrigation area are limited availability of water especially during the dry season (planting season II and III) and non-compliance to cropping patterns. The evaluation of irrigation system performance of Cau irrigation area needs to be done in order to know how far the irrigation system performance is, especially based on planting productivity aspect. The improvement of irrigation network performance through cropping pattern optimization is based on the increase of water necessity fulfillment (k factor), the realization of planting area and rice productivity. The research method of irrigation system performance is by analyzing the secondary data based on the Regulation of Ministry of Public Work and State Minister for Public Housing Number: 12/PRT/M/2015. The analysis of water necessity fulfillment (k factor) uses Public Work Plan Criteria Method. The performance level of planting productivity aspect in existing condition is 87.10%, alternative 1 is 93.90% dan alternative 2 is 96.90%. It means that the performance of the irrigation network from productivity aspect increases 6.80% for alternative 1 and 9.80% for alternative 2.

  10. Determining the area of convergence in Bloodstain Pattern Analysis: a probabilistic approach

    CERN Document Server

    Camana, Francesco

    2013-01-01

    A complete procedure for identifying the area of convergence of blood drops originated from a single static source is presented. Both for bloodstains lying on an horizontal and on a vertical plane a complete study is developed, based on error analysis and on an opportunely defined joint probability density for the orientation of the horizontal projections of the trajectories of the drops. The method generates a probabilistic map for the area of convergence, directly linking the angles of impact, and their uncertainties, to the projection on the ground of the point of origin. One of the objectives consists in providing a statistical definition of area of convergence, extending to this topic the mathematical accuracy of the calculation of the angle of impact in bloodstain pattern analysis (BPA).

  11. Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein

    Energy Technology Data Exchange (ETDEWEB)

    Buffalo, Cosmo Z.; Bahn-Suh, Adrian J.; Hirakis, Sophia P.; Biswas, Tapan; Amaro, Rommie E.; Nizet, Victor; Ghosh, Partho

    2016-09-05

    No vaccine exists against group A Streptococcus (GAS), a leading cause of worldwide morbidity and mortality. A severe hurdle is the hypervariability of its major antigen, the M protein, with >200 different M types known. Neutralizing antibodies typically recognize M protein hypervariable regions (HVRs) and confer narrow protection. In stark contrast, human C4b-binding protein (C4BP), which is recruited to the GAS surface to block phagocytic killing, interacts with a remarkably large number of M protein HVRs (apparently ∼90%). Such broad recognition is rare, and we discovered a unique mechanism for this through the structure determination of four sequence-diverse M proteins in complexes with C4BP. The structures revealed a uniform and tolerant ‘reading head’ in C4BP, which detected conserved sequence patterns hidden within hypervariability. Our results open up possibilities for rational therapies that target the M–C4BP interaction, and also inform a path towards vaccine design.

  12. Groundwater occurrence and flow patterns in the Ishiagu mining area of southeastern Nigeria

    Institute of Scientific and Technical Information of China (English)

    I.C.EZEKWE; E.ODUBO; G.N.CHIMA; I.S.ONWUCHEKWA

    2012-01-01

    The Ishiagu area is a water scarce region and has played host to mining activities for more than four decades.Mining-related activities have become a threat to potable water supply in the area.This paper is an attempt to show the extent of this threat and in particular,investigate the regional groundwater occurrence and flow pattern based on GPS,water well and geological data.This basinwide model can be used for further groundwater assessment,pollution control and contaminant management.Groundwater occurs between 2.4 and 9 m in the Lekwesi-Lokpaukwu area; 1.5-3.7 m in the Ndi-Ugbugbor-Ayaragu axis and 1.2-4.6 m in the Ishiagu area.Recharge areas include the Leru-Amaubiri-Lekwesi sandstone hills and the lhetutu-Ugwuajirija mine field.While the ultimate sink of contamiants is the Ivo River system,other discharge axis is the Ishiagu-Ayaragu axis and the Ogwor Ndi-Ugbugbor zone.An unconfined and a confined (> 10)circulation groundwater system was inferred,and flow model reveals that a large part of Ishiag-Ayaragu and NdiUgbugbor part of the study area suffer polluted recharge from the Pb/Zn mining area.Groundwater was also subjected to hierarchical cluster analysis and the existence of 3-4 hydrological regimes,which revealed:Unpolluted recharge areas,areas affected by polluted recharge,a deep water and shallow water circulation and mine effluents.

  13. Neurofilament protein defines regional patterns of cortical organization in the macaque monkey visual system: a quantitative immunohistochemical analysis

    Science.gov (United States)

    Hof, P. R.; Morrison, J. H.; Bloom, F. E. (Principal Investigator)

    1995-01-01

    Visual function in monkeys is subserved at the cortical level by a large number of areas defined by their specific physiological properties and connectivity patterns. For most of these cortical fields, a precise index of their degree of anatomical specialization has not yet been defined, although many regional patterns have been described using Nissl or myelin stains. In the present study, an attempt has been made to elucidate the regional characteristics, and to varying degrees boundaries, of several visual cortical areas in the macaque monkey using an antibody to neurofilament protein (SMI32). This antibody labels a subset of pyramidal neurons with highly specific regional and laminar distribution patterns in the cerebral cortex. Based on the staining patterns and regional quantitative analysis, as many as 28 cortical fields were reliably identified. Each field had a homogeneous distribution of labeled neurons, except area V1, where increases in layer IVB cell and in Meynert cell counts paralleled the increase in the degree of eccentricity in the visual field representation. Within the occipitotemporal pathway, areas V3 and V4 and fields in the inferior temporal cortex were characterized by a distinct population of neurofilament-rich neurons in layers II-IIIa, whereas areas located in the parietal cortex and part of the occipitoparietal pathway had a consistent population of large labeled neurons in layer Va. The mediotemporal areas MT and MST displayed a distinct population of densely labeled neurons in layer VI. Quantitative analysis of the laminar distribution of the labeled neurons demonstrated that the visual cortical areas could be grouped in four hierarchical levels based on the ratio of neuron counts between infragranular and supragranular layers, with the first (areas V1, V2, V3, and V3A) and third (temporal and parietal regions) levels characterized by low ratios and the second (areas MT, MST, and V4) and fourth (frontal regions) levels characterized by

  14. Exploring Urbanization Patterns for Counties in Underdeveloped Mountainous Areas: A Case Study of Hubei, China

    Institute of Scientific and Technical Information of China (English)

    Lin; Xiaoru

    2015-01-01

    In the present work, features of urbanization of 24 underdeveloped mountainous counties(UMCs) in Hubei Province are analyzed and summarized, which includes low rates of urbanization, signifi cant nonlocal urbanization, undeveloped three industries, and a homogeneous spatial layout of underdeveloped towns. Moreover, our analysis reveals that driving forces originating from favorable macro policies, medium economy, and micro elements are needed to speed up the urbanization in such areas. Based on the case study, we proposes a new path pattern for urbanization of these UMCs in western & central China. In principle, this pattern mainly consists of two important strategies which are driven by a simultaneous development of industry and trade and the exploitation of local characteristics in both economics and culture. In addition, the practice of such a new urbanization path should be carried out through incremental development together with the construction of node-centralizing towns.

  15. Numerical comparison of coal spontaneous combustion danger influenced by different methane drainage patterns in gob area

    Institute of Scientific and Technical Information of China (English)

    ZHU Hong-qing; LIU Xing-kui; ZHANG Ru-ming; ZHANG Sheng-zhu

    2011-01-01

    The influence of gas drainage on float coal spontaneous combustion in the work face with "U" style ventilation was studied. Numerical simulation was used to compare the mutative law of steady flow and density field in the gob area under different drainage conditions by solving the equation set, including mass, momentum, and component transition. Consequently, the sequence of drainage effect and safety was obtained. The result manifests that the more effective the drainage pattern is, the easier float coal spontaneous combustion is caused due to air being guided into the depth of the gob area when the drainage position is arranged in the gas accumulation area. If the widened scope of oxidation zone exceeds the upper limit of the work face advancing speed, nitrogen injection should be applied to decrease the probability of spontaneous combustion. Then, the pipe laying drainage in the upper angle is most economical and safe compared with other drainage patterns when only the situation of gas accumulation is controlled in the upper angle. Finally, drainage pressure must not be too great. Otherwise the drainage density will decrease even if hazard is caused by back flow possibly happening in the return outlet when the drainage position is arranged near the work face.

  16. Disordered patterns in clustered Protein Data Bank and in eukaryotic and bacterial proteomes.

    Directory of Open Access Journals (Sweden)

    Michail Yu Lobanov

    Full Text Available We have constructed the clustered Protein Data Bank and obtained clusters of chains of different identity inside each cluster, http://bioinfo.protres.ru/st_pdb/. We have compiled the largest database of disordered patterns (141 from the clustered PDB where identity between chains inside of a cluster is larger or equal to 75% (version of 28 June 2010 by using simple rules of selection. The results of these analyses would help to further our understanding of the physicochemical and structural determinants of intrinsically disordered regions that serve as molecular recognition elements. We have analyzed the occurrence of the selected patterns in 97 eukaryotic and in 26 bacterial proteomes. The disordered patterns appear more often in eukaryotic than in bacterial proteomes. The matrix of correlation coefficients between numbers of proteins where a disordered pattern from the library of 141 disordered patterns appears at least once in 9 kingdoms of eukaryota and 5 phyla of bacteria have been calculated. As a rule, the correlation coefficients are higher inside of the considered kingdom than between them. The patterns with the frequent occurrence in proteomes have low complexity (PPPPP, GGGGG, EEEED, HHHH, KKKKK, SSTSS, QQQQQP, and the type of patterns vary across different proteomes, http://bioinfo.protres.ru/fp/search_new_pattern.html.

  17. Proteomic analysis of cow, yak, buffalo, goat and camel milk whey proteins: quantitative differential expression patterns.

    Science.gov (United States)

    Yang, Yongxin; Bu, Dengpan; Zhao, Xiaowei; Sun, Peng; Wang, Jiaqi; Zhou, Lingyun

    2013-04-05

    To aid in unraveling diverse genetic and biological unknowns, a proteomic approach was used to analyze the whey proteome in cow, yak, buffalo, goat, and camel milk based on the isobaric tag for relative and absolute quantification (iTRAQ) techniques. This analysis is the first to produce proteomic data for the milk from the above-mentioned animal species: 211 proteins have been identified and 113 proteins have been categorized according to molecular function, cellular components, and biological processes based on gene ontology annotation. The results of principal component analysis showed significant differences in proteomic patterns among goat, camel, cow, buffalo, and yak milk. Furthermore, 177 differentially expressed proteins were submitted to advanced hierarchical clustering. The resulting clustering pattern included three major sample clusters: (1) cow, buffalo, and yak milk; (2) goat, cow, buffalo, and yak milk; and (3) camel milk. Certain proteins were chosen as characterization traits for a given species: whey acidic protein and quinone oxidoreductase for camel milk, biglycan for goat milk, uncharacterized protein (Accession Number: F1MK50 ) for yak milk, clusterin for buffalo milk, and primary amine oxidase for cow milk. These results help reveal the quantitative milk whey proteome pattern for analyzed species. This provides information for evaluating adulteration of specific specie milk and may provide potential directions for application of specific milk protein production based on physiological differences among animal species.

  18. Multitemporal analysis of landscape metrics for monitoring forested patterns in coastal and mountainous areas

    Science.gov (United States)

    Carone, M. T.; Imbrenda, V.; Lanfredi, M.; Macchiato, M.; Simoniello, T.

    2009-04-01

    The role of forested areas for the maintaining of an acceptable landscape balance is crucial. As an example, they contribute to higher biodiversity levels directly and to cleaner fluvial waters indirectly, thus, the degradation of such ecosystems has strong repercussions on many ecological processes. In order to preserve their natural stability, monitoring forest temporal dynamics is very important for a correct management, particularly, in fragile Mediterranean environments that are highly vulnerable to both natural and human-induced perturbations. For analysing the evolution of forested patterns, especially in areas with a strong human presence, landscape metrics are a basilar tool since they allow for evaluating the structure of landscape patterns at different spatio-temporal scales and the relationship between natural environment and human environment. Starting from this premise, we selected a set of Landscape Metrics to evaluate the temporal dynamics of forested covers in two different environments (coastal and mountainous) located in Basilicata Region, Southern Italy. The first one (area A) is located along the Ionian coast and is largely characterized by evergreen forests; in such an area, even if many sites are protected by the European Community (SCI), forests are subjected to a strong incidence of human activities mainly linked to agriculture and tourism as well as to frequent fire events and coastal erosion processes that favour salt-water intrusion. The second one (area B) is a high heterogeneous mountainous area, which also comprehends alluvial planes. The particular configuration of the territory allows for the presence of a very rich faunal and vegetation biodiversity; thus, it is partially under the protection of a National Park, but there are also many critical anthropical activities (e.g. oil drilling, agriculture, etc.). The landscape ecology analyses were performed on multi temporal land cover maps, obtained from hybrid classifications of a time

  19. Evolutionary Pattern of N-Glycosylation Sequon Numbers in Eukaryotic ABC Protein Superfamilies

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Buus, Ole Thomsen; Wollenweber, Bernd

    2010-01-01

    Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underly......Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins...... and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average......-against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly...

  20. Regular patterns for proteome-wide distribution of protein abundance across species.

    Directory of Open Access Journals (Sweden)

    Fan Zhong

    Full Text Available A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category are more abundant than those that act on information modulation (information category. Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function.

  1. Inference of Hopfield-Potts patterns from covariation in protein families: calculation and statistical error bars

    Science.gov (United States)

    Cocco, Simona; Monasson, Rémi; Weigt, Martin

    2013-12-01

    We consider the Hopfield-Potts model for the covariation between residues in protein families recently introduced in Cocco, Monasson, Weigt (2013). The patterns of the model are inferred from the data within a new gauge, more symmetric in the residues. We compute the statistical error bars on the pattern components. Results are illustrated on real data for a response regulator receiver domain (Pfam ID PF00072) family.

  2. Area-Efficient Low Power CMOS Image Sensor Readout Circuit with Fixed Pattern Noise Cancellation

    Institute of Scientific and Technical Information of China (English)

    赵士彬; 姚素英; 聂凯明; 徐江涛

    2010-01-01

    A low cost of die area and power consumption CMOS image sensor readout circuit with fixed pattern noise(FPN) cancellation is proposed.By using only one coupling capacitor and switch in the double FPN cancelling correlative double sampling(CDS),pixel FPN is cancelled and column FPN is stored and eliminated by the sampleand-hold operation of digitally programmable gain amplifier(DPGA).The bandwidth balance technology based on operational amplifier(op-amp) sharing is also introduced to decrease the power dissi...

  3. Variation of morphology, karyotype and protein band pattern of adenium (Adenium obesum varieties

    Directory of Open Access Journals (Sweden)

    PRABANG SETYONO

    2009-07-01

    Full Text Available Hastuti D, Suranto, Setyono P. 2009. Variation of morphology, karyotype and protein band pattern of adenium (Adenium obesum varieties. Nusantara Bioscience 1: 78-83. The aim of this research to find out the Adenium obesum variation from six varieties, namely: obesum, cery, red lucas, red fanta , white bigben and harry potter based on morphology, karyotype, as well as protein banding pattern. The chromosome preparation was made using semi-permanent squash method from the tip of root plant; while protein banding pattern was made using SDS-PAGE method. Qualitative data included shape and color of the leave and flower described from each variety. Data were presented in morphometry and analyzed using ANOVA and then followed by DMRT with 5% of confidence levels, indicated significance difference. Protein banding pattern, the root, stem, leave and all organs were analyzed using Hierarchical Cluster Analysis method with Average Linkage (between Groups using SPSS 10.0. The result of research shows that the six A. obesum varieties have morphological character with no variation of light green to dark green leave, not hairy, smooth leave bone, meanwhile for light red to dark red flower crown color although some of them are white and the same funnel color, yellow. All varieties of A. obesum have same number of chromosome, 2n = 22 and shows the difference ranging from 2.56 to 5.13 um. In the banding pattern formed qualitatively, there is variation among the six varieties.

  4. Small proteins: untapped area of potential biological importance.

    Science.gov (United States)

    Su, Mingming; Ling, Yunchao; Yu, Jun; Wu, Jiayan; Xiao, Jingfa

    2013-12-16

    Polypeptides containing ≤100 amino acid residues (AAs) are generally considered to be small proteins (SPs). Many studies have shown that some SPs are involved in important biological processes, including cell signaling, metabolism, and growth. SP generally has a simple domain and has an advantage to be used as model system to overcome folding speed limits in protein folding simulation and drug design. But SPs were once thought to be trivial molecules in biological processes compared to large proteins. Because of the constraints of experimental methods and bioinformatics analysis, many genome projects have used a length threshold of 100 amino acid residues to minimize erroneous predictions and SPs are relatively under-represented in earlier studies. The general protein discovery methods have potential problems to predict and validate SPs, and very few effective tools and algorithms were developed specially for SPs identification. In this review, we mainly consider the diverse strategies applied to SPs prediction and discuss the challenge for differentiate SP coding genes from artifacts. We also summarize current large-scale discovery of SPs in species at the genome level. In addition, we present an overview of SPs with regard to biological significance, structural application, and evolution characterization in an effort to gain insight into the significance of SPs.

  5. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution.

    Directory of Open Access Journals (Sweden)

    Nelle Lambert

    Full Text Available The developmental mechanisms through which the cerebral cortex increased in size and complexity during primate evolution are essentially unknown. To uncover genetic networks active in the developing cerebral cortex, we combined three-dimensional reconstruction of human fetal brains at midgestation and whole genome expression profiling. This novel approach enabled transcriptional characterization of neurons from accurately defined cortical regions containing presumptive Broca and Wernicke language areas, as well as surrounding associative areas. We identified hundreds of genes displaying differential expression between the two regions, but no significant difference in gene expression between left and right hemispheres. Validation by qRTPCR and in situ hybridization confirmed the robustness of our approach and revealed novel patterns of area- and layer-specific expression throughout the developing cortex. Genes differentially expressed between cortical areas were significantly associated with fast-evolving non-coding sequences harboring human-specific substitutions that could lead to divergence in their repertoires of transcription factor binding sites. Strikingly, while some of these sequences were accelerated in the human lineage only, many others were accelerated in chimpanzee and/or mouse lineages, indicating that genes important for cortical development may be particularly prone to changes in transcriptional regulation across mammals. Genes differentially expressed between cortical regions were also enriched for transcriptional targets of FoxP2, a key gene for the acquisition of language abilities in humans. Our findings point to a subset of genes with a unique combination of cortical areal expression and evolutionary patterns, suggesting that they play important roles in the transcriptional network underlying human-specific neural traits.

  6. The Kinase Regulator Mob1 Acts as a Patterning Protein for Stentor Morphogenesis

    Science.gov (United States)

    Slabodnick, Mark M.; Ruby, J. Graham; Dunn, Joshua G.; Feldman, Jessica L.; DeRisi, Joseph L.; Marshall, Wallace F.

    2014-01-01

    Morphogenesis and pattern formation are vital processes in any organism, whether unicellular or multicellular. But in contrast to the developmental biology of plants and animals, the principles of morphogenesis and pattern formation in single cells remain largely unknown. Although all cells develop patterns, they are most obvious in ciliates; hence, we have turned to a classical unicellular model system, the giant ciliate Stentor coeruleus. Here we show that the RNA interference (RNAi) machinery is conserved in Stentor. Using RNAi, we identify the kinase coactivator Mob1—with conserved functions in cell division and morphogenesis from plants to humans—as an asymmetrically localized patterning protein required for global patterning during development and regeneration in Stentor. Our studies reopen the door for Stentor as a model regeneration system. PMID:24823688

  7. Characterization of a nanoscale S-layer protein based template for biomolecular patterning.

    Science.gov (United States)

    Wong, Wing Sze; Yung, Pun To

    2014-01-01

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

  8. Protein-protein interactions: general trends in the relationship between binding affinity and interfacial buried surface area.

    Science.gov (United States)

    Chen, Jieming; Sawyer, Nicholas; Regan, Lynne

    2013-04-01

    Protein-protein interactions play key roles in many cellular processes and their affinities and specificities are finely tuned to the functions they perform. Here, we present a study on the relationship between binding affinity and the size and chemical nature of protein-protein interfaces. Our analysis focuses on heterodimers and includes curated structural and thermodynamic data for 113 complexes. We observe a direct correlation between binding affinity and the amount of surface area buried at the interface. For a given amount of surface area buried, the binding affinity spans four orders of magnitude in terms of the dissociation constant (Kd ). Across the entire dataset, we observe no obvious relationship between binding affinity and the chemical composition of the interface. We also calculate the free energy per unit surface area buried, or "surface energy density," of each heterodimer. For interfacial surface areas between 500 and 2000 Å(2) , the surface energy density decreases as the buried surface area increases. As the buried surface area increases beyond about 2000 Å(2) , the surface energy density levels off to a constant value. We believe that these analyses and data will be useful for researchers with an interest in understanding, designing or inhibiting protein-protein interfaces.

  9. Morbidity Pattern Among Elderly Population In A Rural Area Of Dehradun In Uttaranchal

    Directory of Open Access Journals (Sweden)

    K S Negi

    2004-06-01

    Full Text Available Research Question : What is the morbidity pattern among elderly people in rural area of Dehradun?Objectives :(1     To assess the morbidity pattern among elderly population.(2     To assess the psycho-social problems among elderly people.(3     To assess the relationship between addiction and hypertension among them.Study design : Cross-Sectional.Setting : Atturwala - a rural area of district Dehradun in Uttaranchal.Participants : 332 elderly people aged 60 years and above.Statistical Analysis : Proportions, Chi-Square test.Results ; It was observed that 78.3% elderly had ophthalmic problem, 69.3% elderly had psycho-social problems followed by hypertension (49.1%, Chronic bronchitis (22% and asthma (12%. A significant relation was found between hypertention and addiction i. e. smoking and / or alcohol (p<.001. Respiratory diseases were found in 47.3% elderly persons. Depression was highly dominating problem among elderly (59.6%.

  10. Pattern of protein retention in growing boars of different breeds, and estimation of maximum protein retention

    DEFF Research Database (Denmark)

    Tauson, A H; Chwalibog, André; Jakobsen, K

    1998-01-01

    Protein and energy metabolism in boars of different breeds, 10 each of Hampshire, Duroc and Danish Landrace was measured in balance and respiration experiments by means of indirect calorimetry in an open-air circulation system. Measurements were performed in four periods (Period I-IV) covering...... the body weight range from 25 to 100 kg. In order to achieve maximum protein retention (RP) a daily intake of digestible protein > 12 g/kg0.75 and metabolisable energy > 1100 kJ/kg0.75 was assumed to be necessary. Protein retention of Danish Landrace boars was inferior to that of Hampshire and Duroc boars...... in Periods III and IV, and therefore, 55 measurements on Hampshire and Duroc boars fulfilling the chosen criteria for digested protein and ME intake were used for calculation of maximum protein retention, giving the following significant quadratic relationship: RP [g/d] = 11.43.W0.75-0.144.W1.50 (n = 55, RSD...

  11. PREVALENCE AND PATTERN OF ALCOHOL ABUSE IN A RURAL AREA OF PUNJAB

    Directory of Open Access Journals (Sweden)

    Salil

    2015-03-01

    Full Text Available INTRODUCTION: “Drug abuse” is defined as self - administration of a drug for non - medical reasons, in quantities and frequencies which may impair an individual’s ability to function effectively and which may result in social, physical, or emotional harm. About 190 million people all over the world consume one drug or the other. Drug abuse causes immense human distress and the illegal production and distribution of drugs have spawned crime and violence worldwide. According to World Drug Report (2009 there were 25,71,52582 alcohol users , alcohol dependents were 8,22,88826 . Cannabis users were 82,28,883 and Opiate users were 2,057,221 in India. Alcohol is one of the leading causes of death and disability globally. Overall, 3.5% of the global burden of disease is attributable to alcohol, which accounts for as much death and disability as tobacco and hypertension. As lot of changes have occurred in the last two decades and variations in consumption patterns is present in different regions, thus the findings of studies conducted earlier and at distant places may not be of much interest in the present scenario. Hence the present study was carried out to assess the prevalence and pattern of alcohol abuse in a rural area of Ludhiana, Punjab. OBJECTIVES: a To find out the prevalence of alcohol abuse in a rural area of Punjab; b To assess pattern of alcohol abuse in a rural area of Punjab. MATERIALS AND METHODS : Community based cross - sectional study done in t he field practice area of Department of Community Medicine, Dayanand Medical College and Hospital, Ludhiana (i.e. Rural Health Training Center (RHTC located at village Pohir, Block Dehlon, District Ludhiana, Punjab. One thousand seven hundred thirty two study subjects of fifteen years and above were part of study. Primary tools in this study were predesigned and pretested interview schedule and Alcohol, Smoking and Substance Involvement Screening Test V3 (ASSIST V3 questioner, to collect

  12. Water supply patterns in two agricultural areas of Central Germany under climate change conditions

    Directory of Open Access Journals (Sweden)

    M. H. Tölle

    2012-04-01

    Full Text Available Increasing emissions of greenhouse gases and increasing prices for fossil fuels have highlighted the demand for CO2 "neutral" renewable energy sources, e.g. short rotation forestry systems used for bioenergy. These systems might be vulnerable to changes in temperature, precipitation and occurrence of extreme weather events. To estimate success or failure of such short rotation coppices in a certain area we need regional climate projections and risk assessment. Changes of water supply patterns in two agriculturally extensively used regions in Central Germany (around Göttingen and Großfahner with different climate conditions but both in the temperate climate zone are explored. The study is carried out under present conditions as well as under projected climate change conditions (1971–2100 using A1B and B1 climate scenarios downscaled for Europe. Analysis of precipitation bias shows regional differences: a strong bias in Göttingen area and a weaker bias in the Großfahner area. A bias correction approach, Quantile mapping, is applied to the ensemble results for both areas for winter and summer seasons. By using quantile regression on the seasonal Standardized Precipitation Indices (SPIs as indicator for water supply conditions we found that precipitation is expected to increase in winter in all quantiles of the distribution for Göttingen area during the 21th century. Heavy precipitation is also expected to increase for Großfahner area suggesting a trend to wetter extremes in winter for the future. This winter precipitation increase could trigger runoff and soil erosion risk enhancing the severity of floods. Increasing winter availability of water could enhance local water supply in spring. For both areas no significant change in summer was found over the whole time period. Although the climate change signal of the SPI indicate mild dryer conditions in summer at the end of the 21st century which may trigger water shortage and

  13. Water supply patterns in two agricultural areas of Central Germany under climate change conditions

    Science.gov (United States)

    Tölle, M. H.; Moseley, C.; Panferov, O.; Busch, G.; Knohl, A.

    2012-04-01

    Increasing emissions of greenhouse gases and increasing prices for fossil fuels have highlighted the demand for CO2 "neutral" renewable energy sources, e.g. short rotation forestry systems used for bioenergy. These systems might be vulnerable to changes in temperature, precipitation and occurrence of extreme weather events. To estimate success or failure of such short rotation coppices in a certain area we need regional climate projections and risk assessment. Changes of water supply patterns in two agriculturally extensively used regions in Central Germany (around Göttingen and Großfahner) with different climate conditions but both in the temperate climate zone are explored. The study is carried out under present conditions as well as under projected climate change conditions (1971-2100) using A1B and B1 climate scenarios downscaled for Europe. Analysis of precipitation bias shows regional differences: a strong bias in Göttingen area and a weaker bias in the Großfahner area. A bias correction approach, Quantile mapping, is applied to the ensemble results for both areas for winter and summer seasons. By using quantile regression on the seasonal Standardized Precipitation Indices (SPIs) as indicator for water supply conditions we found that precipitation is expected to increase in winter in all quantiles of the distribution for Göttingen area during the 21th century. Heavy precipitation is also expected to increase for Großfahner area suggesting a trend to wetter extremes in winter for the future. This winter precipitation increase could trigger runoff and soil erosion risk enhancing the severity of floods. Increasing winter availability of water could enhance local water supply in spring. For both areas no significant change in summer was found over the whole time period. Although the climate change signal of the SPI indicate mild dryer conditions in summer at the end of the 21st century which may trigger water shortage and summer drying associated with above

  14. Versatile functional microstructured polystyrene-based platforms for protein patterning and recognition.

    Science.gov (United States)

    Palacios-Cuesta, Marta; Cortajarena, Aitziber L; García, Olga; Rodríguez-Hernández, Juan

    2013-09-09

    We report the preparation of different functional surface patterns based on the optimization of the photo-cross-linking/degradation kinetics of polystyrene (PS) upon exposure to UV-light. We employed a PS-b-PGA (polystyrene-block-poly(l-glutamic acid)) block copolymer that will, in addition to the surface pattern, provide functionality. By using short irradiation times, PS can be initially cross-linked, whereas an excess of the exposure time provokes the degradation of the material. As a result of the optimization of time of exposure, the use of an appropriate cover, or the incorporation of an appropriate amount of absorbing active species (photoinitiator), different tailor-made surface patterns can be obtained, from boxes to needles. Moreover, in addition to the surface pattern, we introduced changes on the chemical composition of the polystyrene using an amphiphilic block copolymer (for instance, we employ PS-b-PGA) that will provide functional surfaces with major advantages. In particular, the presence of carboxylic functional groups provides a unique opportunity to anchor, for instance polypeptide sequences. We describe the immobilization of polypeptide sequences in precise surface positions that allows the use of the surfaces for protein recognition purposes. The immobilization of the proteins evidence the success of the recognition and opens a new alternative for protein patterning on surfaces for many biotechnological and biomedical applications.

  15. Multivariate data analysis of two-dimensional gel electrophoresis protein patterns from few samples

    DEFF Research Database (Denmark)

    Jensen, Kristina Nedenskov; Jessen, Flemming; Jørgensen, Bo

    2008-01-01

    One application of 2D gel electrophoresis is to reveal differences in protein pattern between two or more groups of individuals, attributable to their group membership. Multivariate data analytical methods are useful in pinpointing the spots relevant for discrimination by focusing not only...

  16. Protein Adsorption Patterns and Analysis on IV Nanoemulsions—The Key Factor Determining the Organ Distribution

    Directory of Open Access Journals (Sweden)

    Mirko Jansch

    2012-12-01

    Full Text Available Intravenous nanoemulsions have been on the market for parenteral nutrition since the 1950s; meanwhile, they have also been used successfully for IV drug delivery. To be well tolerable, the emulsions should avoid uptake by the MPS cells of the body; for drug delivery, they should be target-specific. The organ distribution is determined by the proteins adsorbing them after injection from the blood (protein adsorption pattern, typically analyzed by two-dimensional polyacrylamide gel electrophoresis, 2-D PAGE. The article reviews the 2-D PAGE method, the analytical problems to be faced and the knowledge available on how the composition of emulsions affects the protein adsorption patterns, e.g., the composition of the oil phase, stabilizer layer and drug incorporation into the interface or oil core. Data were re-evaluated and compared, and the implications for the in vivo distribution are discussed. Major results are that the interfacial composition of the stabilizer layer is the main determining factor and that this composition can be modulated by simple processes. Drug incorporation affects the pattern depending on the localization of the drug (oil core versus interface. The data situation regarding in vivo effects is very limited; mainly, it has to be referred to in the in vivo data of polymeric nanoparticles. As a conclusion, determination of the protein adsorption patterns can accelerate IV nanoemulsion formulation development regarding optimized organ distribution and related pharmacokinetics.

  17. Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: A computational study

    Indian Academy of Sciences (India)

    Piyali Ganguli; Saikat Chowdhury; Rupa Bhowmick; Ram Rup Sarkar

    2015-10-01

    Various T-cell co-receptor molecules and calcium channel CRAC play a pivotal role in the maintenance of cell’s functional responses by regulating the production of effector molecules (mostly cytokines) that aids in immune clearance and also maintaining the cell in a functionally active state. Any defect in these co-receptor signalling pathways may lead to an altered expression pattern of the effector molecules. To study the propagation of such defects with time and their effect on the intracellular protein expression patterns, a comprehensive and largest pathway map of T-cell activation network is reconstructed manually. The entire pathway reactions are then translated using logical equations and simulated using the published time series microarray expression data as inputs. After validating the model, the effect of in silico knock down of co-receptor molecules on the expression patterns of their downstream proteins is studied and simultaneously the changes in the phenotypic behaviours of the T-cell population are predicted, which shows significant variations among the proteins expression and the signalling routes through which the response is propagated in the cytoplasm. This integrative computational approach serves as a valuable technique to study the changes in protein expression patterns and helps to predict variations in the cellular behaviour.

  18. Frequency of metabolic syndrome and the food intake patterns in adults living in a rural area of Brazil

    Directory of Open Access Journals (Sweden)

    Karine Fedrigo Silva

    2011-08-01

    Full Text Available INTRODUCTION: Metabolic syndrome (MetS, a risk factor for atherosclerosis and coronary heart disease, is related to an inadequate food intake pattern. Its incidence is increasing among Brazilian adults, including those living in rural areas. Our aim was not only to describe the frequency of MetS in adults with or without MetS but also to compare their food intake pattern as assessed by the healthy eating index (HEI and serum albumin and C reactive protein (CRP levels. METHODS: Men and women (n = 246 living in a small village in Brazil were included. MetS was characterized according to the adult treatment panel (ATP III criteria. Groups were compared by chi-square, student t or Mann-Whitney tests. RESULTS: MetS was diagnosed in 15.4% of the cases. The MetS group showed higher CRP (1.8±1.2 vs. 1.0±0.9 mg/dl and lower albumin (4.3±0.3 vs. 4.4±0.3 g/dl serum levels compared to the control group. Additionally, the MetS group showed lower scores (median[range] in the HEI compared to the control group (53.5[31.2-78.1] vs 58[29.7-89.5], respectively. The MetS group also had decreased scores for total fat and daily variety of food intake. CONCLUSIONS: The results suggest that adults with MetS displayed chronic mild inflammation and a poorer food intake pattern than the control group.

  19. Seasonal Variability in Boreal Wildfire Activity Associated with Landscape Patterns of Burned Area

    Science.gov (United States)

    Barrett, K. M.; Kasischke, E. S.

    2012-12-01

    Wildfire is the most prominent disturbance in the boreal forest, effecting changes in stand age and vegetation composition often over thousands of square kilometers. The effect of wildfire on ecosystem structure and function depends heavily on the seasonality of the burn, and periods of seasonally high fire activity are highly sporadic. The majority of area in Alaska that burns in a fire season does so during relatively short periods of high fire activity. These periods, which can be determined from active fire detections or fire management agency data records, are caused by elevated air temperatures and low precipitation which decrease fuel moisture and encourage the spread of fire. While fire fronts dominate during periods of low fire activity, more active periods have a higher proportion of residual burning which remains after a front has passed through. Residual burning is likely responsible for the extensive combustion of surface organic materials in the boreal forest, which can lead to post-fire changes in dominant vegetation type. Seasonal variations in fire activity are therefore an important factor in the mosaic of severity conditions across large burned areas and shifts in land cover over successional time scales. The purpose of this study is to characterize the temporal and spatial variability in periods of seasonal high fire activity that influence patterns of burned area. In large burns, unburned areas within a fire scar may serve as an important seed stock during post-fire recruitment. These areas may also feedback to future fire regimes through the preservation of more fire-resistant vegetation in unburned "islands".

  20. Mapping regional patterns of large forest fires in Wildland-Urban Interface areas in Europe.

    Science.gov (United States)

    Modugno, Sirio; Balzter, Heiko; Cole, Beth; Borrelli, Pasquale

    2016-05-01

    Over recent decades, Land Use and Cover Change (LUCC) trends in many regions of Europe have reconfigured the landscape structures around many urban areas. In these areas, the proximity to landscape elements with high forest fuels has increased the fire risk to people and property. These Wildland-Urban Interface areas (WUI) can be defined as landscapes where anthropogenic urban land use and forest fuel mass come into contact. Mapping their extent is needed to prioritize fire risk control and inform local forest fire risk management strategies. This study proposes a method to map the extent and spatial patterns of the European WUI areas at continental scale. Using the European map of WUI areas, the hypothesis is tested that the distance from the nearest WUI area is related to the forest fire probability. Statistical relationships between the distance from the nearest WUI area, and large forest fire incidents from satellite remote sensing were subsequently modelled by logistic regression analysis. The first European scale map of the WUI extent and locations is presented. Country-specific positive and negative relationships of large fires and the proximity to the nearest WUI area are found. A regional-scale analysis shows a strong influence of the WUI zones on large fires in parts of the Mediterranean regions. Results indicate that the probability of large burned surfaces increases with diminishing WUI distance in touristic regions like Sardinia, Provence-Alpes-Côte d'Azur, or in regions with a strong peri-urban component as Catalunya, Comunidad de Madrid, Comunidad Valenciana. For the above regions, probability curves of large burned surfaces show statistical relationships (ROC value > 0.5) inside a 5000 m buffer of the nearest WUI. Wise land management can provide a valuable ecosystem service of fire risk reduction that is currently not explicitly included in ecosystem service valuations. The results re-emphasise the importance of including this ecosystem service

  1. Protein synthesis patterns of Paracoccidiodes brasiliensis isolates in stage-specific forms and during cellular differentiation.

    Science.gov (United States)

    Salem-Izacc, S M; Jesuino, R S; Brito, W A; Pereira, M; Felipe, M S; Soares, C M

    1997-01-01

    In this paper we compared the protein synthesis patterns of Paracoccidioides brasiliensis isolates. The protein profiles were compared for both yeast and mycelial forms and similarity analysis among them was performed by calculating similarity matrices and grouping the isolates in dendrograms. The examined isolates exhibited highly variable cellular morphology at 36 degrees C, when typical yeast cells were expected. On the other hand, at 26 degrees C all the isolates showed mycelial morphology. The analysis of protein synthesis profiles made it possible to cluster the P. brasiliensis isolates into groups that correlated with the morphological data. Interestingly, growth at 36 degrees C strongly decreased the heterogeneity of protein synthesis patterns seen in mycelial isolates. It was possible to cluster the isolates grown at 36 degrees C in three groups based on their two-dimensional protein synthesis analysis. The similarity index observed among the mycelial isolates was lower than that obtained with yeast cells, suggesting a more homogenous gene expression pattern in the host-adapted form than in the saprobic phase.

  2. Compare local pocket and global protein structure models by small structure patterns

    KAUST Repository

    Cui, Xuefeng

    2015-09-09

    Researchers proposed several criteria to assess the quality of predicted protein structures because it is one of the essential tasks in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competitions. Popular criteria include root mean squared deviation (RMSD), MaxSub score, TM-score, GDT-TS and GDT-HA scores. All these criteria require calculation of rigid transformations to superimpose the the predicted protein structure to the native protein structure. Yet, how to obtain the rigid transformations is unknown or with high time complexity, and, hence, heuristic algorithms were proposed. In this work, we carefully design various small structure patterns, including the ones specifically tuned for local pockets. Such structure patterns are biologically meaningful, and address the issue of relying on a sufficient number of backbone residue fragments for existing methods. We sample the rigid transformations from these small structure patterns; and the optimal superpositions yield by these small structures are refined and reported. As a result, among 11; 669 pairs of predicted and native local protein pocket models from the CASP10 dataset, the GDT-TS scores calculated by our method are significantly higher than those calculated by LGA. Moreover, our program is computationally much more efficient. Source codes and executables are publicly available at http://www.cbrc.kaust.edu.sa/prosta/

  3. Gradient analysis of landscape spatial and temporal pattern changes in Beijing metropolitan area

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The gradient based landscape metrics analysis is now widely used to study the landscape pattern changes in respond to the urbanization.In order to discover the trend of spatio-temporal changes in Beijing metropolitan area during the past 15 years,several landscape metrics are computed using a moving window along a 96 km long transect across Beijing metropolitan area from west to east.Specially,the spatial extent of sub-landscape,which is determined by the moving window’s size,is profoundly examined.The results show that the metrics varies smoothly and regularly along the selected transect when the window size is greater than 6 km×6 km,and irregularly fluctuated for the smaller window size,that the spatial and temporal landscape characteristics of Beijing city match the hypothetical framework of spatio-temporal urban sprawl in the form of alternating processes of diffusion and coalescence well,and that some new trends of the urban sprawl style in Beijing metropolitan area,such as leap-frog manner,are also detected by the gradient landscape analysis.

  4. Chewing side, bite force symmetry, and occlusal contact area of subjects with different facial vertical patterns

    Directory of Open Access Journals (Sweden)

    Simone Guimarães Farias Gomes

    2011-10-01

    Full Text Available Craniofacial dimensions influence oral functions; however, it is not known whether they are associated with function asymmetry. The objective of this study was to evaluate chewing side preference and lateral asymmetry of occlusal contact area and bite force of individuals with different craniofacial patterns. Seventy-eight dentate subjects were divided into 3 groups according to the VERT index as follows: (1 mesofacial, (2 brachyfacial and (3 dolichofacial. Chewing side preference was evaluated using jaw tracking equipment, occlusal contact area was measured by silicon registration of posterior teeth, and bite force was measured unilaterally on molar regions using 2.25 mm-thick sensors. Statistical analysis was performed using ANOVA on Ranks, Student's t-test, and Mann-Whitney tests at a 5% significance level. Mesofacial, brachyfacial, and dolichofacial subjects presented more occlusal contact area on the left side. Only dolichofacial subjects showed lateral asymmetry for bite force, presenting higher force on the left side. No statistically significant differences were found for chewing side preference among all groups. Within the limitations of this study, it can be concluded that craniofacial dimensions play a role in asymmetry of bite force. ClinicalTrials.gov ID: NCT01286363.

  5. Distinct expression patterns of ICK/MAK/MOK protein kinases in the intestine implicate functional diversity.

    Directory of Open Access Journals (Sweden)

    Tufeng Chen

    Full Text Available ICK/MRK (intestinal cell kinase/MAK-related kinase, MAK (male germ cell-associated kinase, and MOK (MAPK/MAK/MRK-overlapping kinase are closely related serine/threonine protein kinases in the protein kinome. The biological functions and regulatory mechanisms of the ICK/MAK/MOK family are still largely elusive. Despite significant similarities in their catalytic domains, they diverge markedly in the sequence and structural organization of their C-terminal non-catalytic domains, raising the question as to whether they have distinct, overlapping, or redundant biological functions. In order to gain insights into their biological activities and lay a fundamental groundwork for functional studies, we investigated the spatio-temporal distribution patterns and the expression dynamics of ICK/MAK/MOK protein kinases in the intestine. We found that ICK/MAK/MOK proteins display divergent expression patterns along the duodenum-to-colon axis and during postnatal murine development. Furthermore, they are differentially partitioned between intestinal epithelium and mesenchyme. A significant increase in the protein level of ICK, but not MAK, was induced in human primary colon cancer specimens. ICK protein level was up-regulated whereas MOK protein level was down-regulated in mouse intestinal adenomas as compared with their adjacent normal intestinal mucosa. These data suggest distinct roles for ICK/MAK/MOK protein kinases in the regulation of intestinal neoplasia. Taken together, our findings demonstrate that the expressions of ICK/MAK/MOK proteins in the intestinal tract can be differentially and dynamically regulated, implicating a significant functional diversity within this group of protein kinases.

  6. Seismic hazard assessment and pattern recognition of earthquake prone areas in the Po Plain (Italy)

    Science.gov (United States)

    Gorshkov, Alexander; Peresan, Antonella; Soloviev, Alexander; Panza, Giuliano F.

    2014-05-01

    A systematic and quantitative assessment, capable of providing first-order consistent information about the sites where large earthquakes may occur, is crucial for the knowledgeable seismic hazard evaluation. The methodology for the pattern recognition of areas prone to large earthquakes is based on the morphostructural zoning method (MSZ), which employs topographic data and present-day tectonic structures for the mapping of earthquake-controlling structures (i.e. the nodes formed around lineaments intersections) and does not require the knowledge about past seismicity. The nodes are assumed to be characterized by a uniform set of topographic, geologic, and geophysical parameters; on the basis of such parameters the pattern recognition algorithm defines a classification rule to discriminate seismogenic and non-seismogenic nodes. This methodology has been successfully applied since the early 1970s in a number of regions worldwide, including California, where it permitted the identification of areas that have been subsequently struck by strong events and that previously were not considered prone to strong earthquakes. Recent studies on the Iberian Peninsula and the Rhone Valley, have demonstrated the applicability of MSZ to flat basins, with a relatively flat topography. In this study, the analysis is applied to the Po Plain (Northern Italy), an area characterized by a flat topography, to allow for the systematic identification of the nodes prone to earthquakes with magnitude larger or equal to M=5.0. The MSZ method differs from the standard morphostructural analysis where the term "lineament" is used to define the complex of alignments detectable on topographic maps or on satellite images. According to that definition the lineament is locally defined and the existence of the lineament does not depend on the surrounding areas. In MSZ, the primary element is the block - a relatively homogeneous area - while the lineament is a secondary element of the morphostructure

  7. Zif268 mRNA Expression Patterns Reveal a Distinct Impact of Early Pattern Vision Deprivation on the Development of Primary Visual Cortical Areas in the Cat.

    Science.gov (United States)

    Laskowska-Macios, Karolina; Zapasnik, Monika; Hu, Tjing-Tjing; Kossut, Malgorzata; Arckens, Lutgarde; Burnat, Kalina

    2015-10-01

    Pattern vision deprivation (BD) can induce permanent deficits in global motion perception. The impact of timing and duration of BD on the maturation of the central and peripheral visual field representations in cat primary visual areas 17 and 18 remains unknown. We compared early BD, from eye opening for 2, 4, or 6 months, with late onset BD, after 2 months of normal vision, using the expression pattern of the visually driven activity reporter gene zif268 as readout. Decreasing zif268 mRNA levels between months 2 and 4 characterized the normal maturation of the (supra)granular layers of the central and peripheral visual field representations in areas 17 and 18. In general, all BD conditions had higher than normal zif268 levels. In area 17, early BD induced a delayed decrease, beginning later in peripheral than in central area 17. In contrast, the decrease occurred between months 2 and 4 throughout area 18. Lack of pattern vision stimulation during the first 4 months of life therefore has a different impact on the development of areas 17 and 18. A high zif268 expression level at a time when normal vision is restored seems to predict the capacity of a visual area to compensate for BD.

  8. Exploiting pattern and sustainable development of marginal lands in the Three Gorge Reservoir Areas

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    This paper studied the distribution and utilization status,reasonable exploitation patterns and potential productivity, and sustainable development of marginal lands in the Three Gorge Reservoir Areas. It has been pointed that problems of the soil fertility degradation, poor productivity in crop lands, natural disasters and environmental deterioration existed in all the exploited marginal lands. In order to maintain the sustainability of the marginal lands, following measure have been proposed: prohibiting cultivation in the crop lands with a slope more than 25°, restoring vegetation in the slope more than 25°, strengthening the basic agricultural construction, establishing the production base of woody feeds and oils, establishing a multi-dimensional management model with reasonable structure and optimumfunction for forestry, agriculture and fishing.

  9. The pattern of fibrosis in the acinar zone 3 areas in early alcoholic liver disease

    DEFF Research Database (Denmark)

    Junge, Jette; Horn, T; Vyberg, M;

    1991-01-01

    The degree of fibrosis and the pattern of collagen distribution in the acinar zone 3, as well as the thickness of the terminal hepatic vein walls (THV) were analyzed in 48 consecutive liver needle biopsies from 48 alcoholics with preserved liver architecture. The fibrosis occurred to more or less....... No relationship was found between TTHV and PSF. The results were compared to similar data obtained in liver biopsies from 117 non-alcoholics with normal morphology or slight non-specific changes. No significant difference concerning TTHV and THV diameter was found between alcoholic and non-alcoholic patients....... The results suggest that the initial liver fibrosis in alcoholics is slightly asymmetrical distributed in each acinar zone 3 area. With progression, the fibrosis tends to be more uniformly distributed and septa appear, eventually linking THV with portal tracts. Apparently, thickening of the THV walls does...

  10. Persistence of self-recruitment and patterns of larval connectivity in a marine protected area network

    KAUST Repository

    Berumen, Michael L.

    2012-02-01

    The use of marine protected area (MPA) networks to sustain fisheries and conserve biodiversity is predicated on two critical yet rarely tested assumptions. Individual MPAs must produce sufficient larvae that settle within that reserve\\'s boundaries to maintain local populations while simultaneously supplying larvae to other MPA nodes in the network that might otherwise suffer local extinction. Here, we use genetic parentage analysis to demonstrate that patterns of self-recruitment of two reef fishes (Amphiprion percula and Chaetodon vagabundus) in an MPA in Kimbe Bay, Papua New Guinea, were remarkably consistent over several years. However, dispersal from this reserve to two other nodes in an MPA network varied between species and through time. The stability of our estimates of self-recruitment suggests that even small MPAs may be self-sustaining. However, our results caution against applying optimization strategies to MPA network design without accounting for variable connectivity among species and over time. 2012 The Authors.

  11. Persistence of self-recruitment and patterns of larval connectivity in a marine protected area network.

    Science.gov (United States)

    Berumen, Michael L; Almany, Glenn R; Planes, Serge; Jones, Geoffrey P; Saenz-Agudelo, Pablo; Thorrold, Simon R

    2012-02-01

    The use of marine protected area (MPA) networks to sustain fisheries and conserve biodiversity is predicated on two critical yet rarely tested assumptions. Individual MPAs must produce sufficient larvae that settle within that reserve's boundaries to maintain local populations while simultaneously supplying larvae to other MPA nodes in the network that might otherwise suffer local extinction. Here, we use genetic parentage analysis to demonstrate that patterns of self-recruitment of two reef fishes (Amphiprion percula and Chaetodon vagabundus) in an MPA in Kimbe Bay, Papua New Guinea, were remarkably consistent over several years. However, dispersal from this reserve to two other nodes in an MPA network varied between species and through time. The stability of our estimates of self-recruitment suggests that even small MPAs may be self-sustaining. However, our results caution against applying optimization strategies to MPA network design without accounting for variable connectivity among species and over time.

  12. Protein coverage on polymer nanolayers leading to mesenchymal stem cell patterning.

    Science.gov (United States)

    You, Jungmok; Yoshida, Akihito; Heo, June Seok; Kim, Han-Soo; Kim, Hyun Ok; Tamada, Kaoru; Kim, Eunkyoung

    2011-10-21

    Interactions of gelatin and albumin with a photo-reactive diphenylamino-s-triazine bridged p-phenylene vinylene polymer (DTOPV) were examined by using surface plasmon resonance (SPR) spectroscopy to explore the effect of the polymer structure on protein coverage of DTOPV nanofilms. The SPR data revealed a significant increase of gelatin adsorption on UV-DTOPV nanofilms, while the adsorption of albumin was decreased by UV exposure in the time frame of the experiment. We also found that the selective adsorption of these proteins was highly dependent on the protein concentration; the highest selectivity of protein adsorption was obtained at the lowest concentration (3.5 μg ml(-1)), while no selective adsorption was confirmed at high concentrations (350 and 1000 μg ml(-1)). The selective attachment of mesenchymal stem cells (MSCs) was directly correlated with the selective adsorption of these proteins onto DTOPV nanofilms. The MSCs attachment onto UV-DTOPV films was promoted with only small mass coverage of gelatin, which led to MSC patterning onto the patterned DTOPV nanofilms successfully. The role of cell adhesion proteins that we found in this study will be a clue to elucidate the complex response of biomolecules on functional polymer nanolayers, and contribute to build up biocompatible surfaces on various advanced materials for the sake of cell engineering and medical implants.

  13. Pattern separation and synchronization in spiking associative memories and visual areas.

    Science.gov (United States)

    Knoblauch, A; Palm, G

    2001-01-01

    Scene analysis in the mammalian visual system, conceived as a distributed and parallel process, faces the so-called binding problem. As a possible solution, the temporal correlation hypothesis has been suggested and implemented in phase-coding models. We propose an alternative model that reproduces experimental findings of synchronized and desynchronized fast oscillations more closely. This model is based on technical considerations concerning improved pattern separation in associative memories on the one hand, and on known properties of the visual cortex on the other. It consists of two reciprocally connected areas, one corresponding to a peripheral visual area (P), the other a central association area (C). P implements the orientation-selective subsystem of the primary visual cortex, while C was modeled as an associative memory with connections formed by Hebbian learning of all assemblies corresponding to stimulus objects. Spiking neurons including habituation and correlated noise were incorporated as well as realistic synaptic delays. Three learned stimuli were presented simultaneously and correlation analysis was performed on spike recordings. Generally, we found two states of activity: (i) relatively slow and unordered oscillations at about 20-25 Hz, synchronized only within small regions; and (ii) faster and more precise oscillations around 50-60 Hz, synchronized over the whole simulated area. The neuron groups representing one stimulus tended to be simultaneously in either the slow or the fast state. At each particular time, only one assembly was found to be in the fast state. Activation of the three assemblies switched on a time scale of 100 ms. This can be interpreted as self-generated attention switching. On the time scale corresponding to gamma oscillations, cross correlations between local neuron groups were either modulated or flat. Modulated correlograms resulted if the groups coded features corresponding to a common object. Otherwise, the

  14. Flood warnings in coastal areas: how do social and behavioural patterns influence alert services?

    Science.gov (United States)

    Pescaroli, G.; Magni, M.

    2015-01-01

    Many studies discuss the economic and technical aspects of flood warnings. Less attention has been given to the social and psychological patterns that affect alert services. In particular, the literature focuses on warnings activated in river basins or marine environments without providing clear evidence of relevance to Mediterranean coastal areas, even though these are subjected to growing flood risk related to climate change. This paper is a first attempt to bridge this gap. Our research develops an in- depth analysis of the village of Cesenatico on the Adriatic Sea coast. Here the municipality adopted two complementary warning systems: a siren and an alert via Short Message Service (SMS). The analysis focuses on a survey conducted in 2011 and 2012 with 228 participants. The relationships between social and behavioural variables and warning services are investigated, and so are flood preparedness and information dissemination. Qualitative evidence from informal interviews is used to support the understanding of key responses. The conclusions show how different social and behavioural patterns can influence the effectiveness and use of warning systems, regardless of the technology adopted and the structural mitigation measures implemented. Education, training and accountability are seen to be critical elements for improvement. Finally, the statistical output is used to suggest new questions and new directions for research.

  15. Seasonal Abundance and Host-Feeding Patterns of Anopheline Vectors in Malaria Endemic Area of Iran

    Directory of Open Access Journals (Sweden)

    Hamidreza Basseri

    2010-01-01

    Full Text Available Seasonal abundance and tendency to feed on humans are important parameters to measure for effective control of malaria vectors. The objective of this study was to describe relation between feeding pattern, abundance, and resting behavior of four malaria vectors in southern Iran. This study was conducted in ten indicator villages (based on malaria incidence and entomological indices in mountainous/hilly and plain regions situated south and southeastern Iran. Mosquito vectors were collected from indoor as well as outdoor shelters and the blood meals were examined by ELISA test. Over all 7654 female Anopheles spp. were captured, the most common species were Anopheles stephensi, An. culicifacies, An. fluviatilis, and An. d'thali. The overall human blood index was 37.50%, 19.83%, 16.4%, and 30.1% for An. fluviatilis, An. stephensi, An. culicifacies, and An. d'thali, respectively. In addition, An. fluviatilis fed on human blood during the entire year but the feeding behavior of An. stephensi and An. culicifacies varied according to seasons. Overall, the abundance of the female mosquito positive to human blood was 4.25% per human shelter versus 17.5% per animal shelter. This result indicates that the vectors had tendency to rest in animal shelters after feeding on human. Therefore, vector control measure should be planned based on such as feeding pattern, abundance, and resting behavior of these vectors in the area.

  16. Ultrathin coatings from isocyanate terminated star PEG prepolymers: patterning of proteins on the layers.

    Science.gov (United States)

    Groll, Juergen; Haubensak, Wulf; Ameringer, Thomas; Moeller, Martin

    2005-03-29

    This study presents the easy and fast patterning of low molecular weight molecules that act as binding partners for proteins on Star PEG coatings. These coatings are prepared from isocyanate terminated star shaped prepolymers and form a highly cross-linked network on the substrate in which the stars are connected via urea groups and free amino groups are present. Streptavidin has been patterned on these layers by microcontact printing (muCP) of an amino reactive biotin derivative and consecutive binding of streptavidin to the biotin. Patterns of Ni(2+)-nitriltriacetic acid (NTA) receptors have been prepared by printing amino functional NTA molecules in freshly prepared Star PEG layers that still contain amino reactive isocyanate groups. Complexation of the NTA groups with Ni(II) ions enabled the binding of His-tag enhanced green fluorescent protein (EGFP) in the desired pattern on the substrates. Since the unmodified Star PEG layers prevent unspecific protein adsorption, His-EGFP could selectively be bound to the sample by immersion into crude, nonpurified His-tag EGFP containing cell lysate.

  17. Biased inheritance of the protein PatN frees vegetative cells to initiate patterned heterocyst differentiation.

    Science.gov (United States)

    Risser, Douglas D; Wong, Francis C Y; Meeks, John C

    2012-09-18

    Heterocysts, cells specialized for nitrogen fixation in certain filamentous cyanobacteria, appear singly in a nonrandom spacing pattern along the chain of vegetative cells. A two-stage, biased initiation and competitive resolution model has been proposed to explain the establishment of this spacing pattern. There is substantial evidence that competitive resolution of a subset of cells initiating differentiation occurs by interactions between a self-enhancing activator protein, HetR, and a diffusible pentapeptide inhibitor PatS-5 (RGSGR). Results presented here show that the absence of a unique membrane protein, PatN, in Nostoc punctiforme strain ATCC 29133 leads to a threefold increase in heterocyst frequency and a fourfold decrease in the vegetative cell interval between heterocysts. A PatN-GFP translational fusion shows a pattern of biased inheritance in daughter vegetative cells of ammonium-grown cultures. Inactivation of another heterocyst patterning gene, patA, is epistatic to inactivation of patN, and transcription of patA increases in a patN-deletion strain, implying that patN may function by modulating levels of patA. The presence of PatN is hypothesized to decrease the competency of a vegetative cell to initiate heterocyst differentiation, and the cellular concentration of PatN is dependent on cell division that results in cells transiently depleted of PatN. We suggest that biased inheritance of cell-fate determinants is a phylogenetic domain-spanning paradigm in the development of biological patterns.

  18. Electrophoretic separation of purified myelin: a method to improve the protein pattern resolving.

    Science.gov (United States)

    Ravera, Silvia; Bartolucci, Martina; Barbarito, Giulia; Calzia, Daniela; Panfoli, Isabella

    2013-01-01

    Myelin sheath is a lipid-rich membrane, consisting of 70% lipid and 30% proteins, that is involved in physiological and pathological processes. For this reason its protein composition has been often investigated, principally by two-dimensional electrophoresis; however, the consistent lipid content makes it difficult to obtain good proteins separation. To improve the resolution of myelin proteins in a denaturing monodimensional gel electrophoresis, we examined several mixtures for the denaturation of the sample, utilizing different detergents and reducing agents. The definition of the protein pattern was analyzed by both "Blue Silver" Coomassie staining and Western Blot analysis against myelin basic protein, one of the most represented myelin proteins. The best resolution is observed when the sample was incubated with a mixture containing 1.25% dithiothreitol, 4 M urea, and 1% dodecyl maltoside or 1 % 3-[(3-cholamidopropyl)-dimethylammonio]-1-propanesulfonate, prior to addition of denaturing agents. In conclusion, this work describes a novel method to improve the separation of myelin proteins in a monodimensional gel electrophoresis. It may be also useful for investigating other lipid-rich samples.

  19. Automated classification of immunostaining patterns in breast tissue from the human protein Atlas

    Directory of Open Access Journals (Sweden)

    Issac Niwas Swamidoss

    2013-01-01

    Full Text Available Background: The Human Protein Atlas (HPA is an effort to map the location of all human proteins (http://www.proteinatlas.org/. It contains a large number of histological images of sections from human tissue. Tissue micro arrays (TMA are imaged by a slide scanning microscope, and each image represents a thin slice of a tissue core with a dark brown antibody specific stain and a blue counter stain. When generating antibodies for protein profiling of the human proteome, an important step in the quality control is to compare staining patterns of different antibodies directed towards the same protein. This comparison is an ultimate control that the antibody recognizes the right protein. In this paper, we propose and evaluate different approaches for classifying sub-cellular antibody staining patterns in breast tissue samples. Materials and Methods: The proposed methods include the computation of various features including gray level co-occurrence matrix (GLCM features, complex wavelet co-occurrence matrix (CWCM features, and weighted neighbor distance using compound hierarchy of algorithms representing morphology (WND-CHARM-inspired features. The extracted features are used into two different multivariate classifiers (support vector machine (SVM and linear discriminant analysis (LDA classifier. Before extracting features, we use color deconvolution to separate different tissue components, such as the brownly stained positive regions and the blue cellular regions, in the immuno-stained TMA images of breast tissue. Results: We present classification results based on combinations of feature measurements. The proposed complex wavelet features and the WND-CHARM features have accuracy similar to that of a human expert. Conclusions: Both human experts and the proposed automated methods have difficulties discriminating between nuclear and cytoplasmic staining patterns. This is to a large extent due to mixed staining of nucleus and cytoplasm. Methods for

  20. Micro patterning of cell and protein non-adhesive plasma polymerized coatings for biochip applications

    DEFF Research Database (Denmark)

    Bouaidat, Salim; Berendsen, C.; Thomsen, P.;

    2004-01-01

    Micro scale patterning of bioactive surfaces is desirable for numerous biochip applications. Polyethyleneoxide-like (PEO-like) coating with non-fouling functionality has been deposited using low frequency AC plasma polymerization. The non-fouling properties of the coating were tested with human...... cells ( HeLa) and fluorescence labeled proteins (isothiocyanate-labeled bovine serum albumin, i.e. FITC-BSA). The PEO-like coatings were fabricated by plasma polymerization of 12-crown-4 (ppCrown) with plasma polymerized hexene (ppHexene) as adhesion layer. The coatings were micro patterned using...

  1. Protein micro patterned lattices to probe a fundamental lengthscale involved in cell adhesion

    CERN Document Server

    Guillou, Herve; Chaussy, Jacques; Block, Marc R

    2009-01-01

    Cell adhesion, a fundamental process of cell biology is involved in the embryo development and in numerous pathologies especially those related to cancers. We constrained cells to adhere on extracellular matrix proteins patterned in a micro lattices. The actin cytoskeleton is particularly sensitive to this constraint and reproducibly self organizes in simple geometrical patterns. Such highly organized cells are functional and proliferate. We performed statistical analysis of spread cells morphologies and discuss the existence of a fundamental lengthscale associated with active processes required for spreading.

  2. Seasonal patterns of aflatoxin M1 contamination in commercial pasteurised milk from different areas in Thailand.

    Science.gov (United States)

    Suriyasathaporn, Witaya; Nakprasert, Watinee

    2012-01-01

    Aflatoxin M1 (AFM1) levels were determined in pasteurised milk from five commercial trademarks produced in different areas in Thailand. One hundred and twenty milk samples were collected from local markets in Chiang Mai province, Thailand, to evaluate AFM1 concentrations using immunoaffinity columns and high-performance liquid chromatography with fluorescence detection. The overall median AFM1 level was 0.023 µg L(-1) ranging from 0.004 to 0.293 µg L(-1). All trademarks had average AFM1 concentrations lower than 0.05 µg L(-1), with those in Trademarks 3 to 5 being higher than Trademarks 1 and 2 (P < 0.01). All trademarks had different seasonal patterns of AFM1, even though operating in the same area. However, only Trademark 3 showed significant differences of AFM1 levels between seasons. The results suggested that farm management factors, rather than environment factors, were likely to be the main cause of AFM1 contamination in dairy products.

  3. Prevalence and Pattern of Self-medication Practices in Urban area of Southern Rajasthan

    Directory of Open Access Journals (Sweden)

    Manish Jain, Rahul Prakash, Dhriti Bapna, Rohit Jain

    2015-01-01

    Full Text Available Background: Self-medications is widely practiced in both developed and developing countries. Inappropriate self-medication results in increases resistance of pathogens, wastage of resources, and serious health hazards. Objectives: Present study was conducted to determine the prevalence, pattern and factors associated with self-medication among general population of an urban area of Sothern Rajasthan. Materials and Methods: A cross sectional community based study was conducted among general population in urban field practice area of Department of community medicine, RNT Medical College, Udaipur, Rajasthan from May 2015 to August 2015. Individuals aged 18 years and above were included as study participants using Simple random method of sampling. Results: Out of total 440 study participants, 324 (73.6% had used self-medication within last three months recall period. The practice of self-medication was more common among younger age groups, male gender and higher levels of education. Paracetamol (73.77% and other analgesics (41.98% were most commonly used drugs. Most common symptoms warranting self-medication were fever (75.31% and headache (62.04%. Conclusion: Rising prevalence of self-medication is a matter of serious concern. IEC activities should be strengthened among general population to minimize the practice of self-medication.

  4. Spatial Patterns and Temporal Variability of Drought in Beijing-Tianjin-Hebei Metropolitan Areas in China

    Directory of Open Access Journals (Sweden)

    Wanyuan Cai

    2015-01-01

    Full Text Available Drought identification and assessment are essential for regional water resources management. In this paper, the spatiotemporal characteristics of drought were evaluated based on monthly precipitation data from 33 synoptic stations during the period of 1960–2010. The percent of normal precipitation was applied to illustrate the driest years in Beijing-Tianjin-Hebei metropolitan areas (BTHMA (1965, 1997, and 2002. The modified Reconnaissance Drought Index (RDI was applied to capture the drought patterns and to estimate the drought severity at 33 meteorological stations. Agglomerative hierarchical cluster analysis (AHCA and principal component analysis (PCA were used to identify three different drought subregions R1, R2, and R3 based on the monthly precipitation values in BTHMA, which is located in southeast, north, and south of BTHMA, respectively. The year 1965 was the driest and 1964 was the wettest during the observed period. The characteristics of drought were analyzed in terms of the temporal evolution of the RDI-12 values and the frequency of drought for the three identified regions. The percentage of years characterized by drought was 13.73% for R1, 16.50% for R2, and 15.53% for R3. 66.91% of drought belongs to the near normal drought category. The obtained results can aid to improve water resources management in the area.

  5. Area-Efficient Low Power CMOS Image Sensor Readout Circuit with Fixed Pattern Noise Cancellation

    Institute of Scientific and Technical Information of China (English)

    ZHAO Shibin; YAO Suying; NIE Kaiming; XU Jiangtao

    2010-01-01

    A low cost of die area and power consumption CMOS image sensor readout circuit with fixed pattern noise(FPN)cancellation is proposed.By using only one coupling capacitor and switch in the double FPN cancelling correlative double sampling(CDS),pixel FPN is cancelled and column FPN is stored and eliminated by the sample-and-hold operation of digitally programmable gain amplifier(DPGA).The bandwidth balance technology based on operational amplifier(op-amp)sharing is also introduced to decrease the power dissipation of traditional multi-stage switched capacitor DPGA.The circuit is designed and simulated using 1P6M 0.18 μm 1.8 V/3.3 V process.Simulation results indicate that the proposed CDS scheme can achieve an FPN of less than 1 mV.The total sampling capacitor per column is 0.9 pF and no column-wise power is dissipated.The die area and FPN value are cut by 70% and 41% respectively compared with amplifier-based CDS.The op-amp sharing gain stage can achieve a 12-bit precision and also implement an 8-bit gain controlling within a gain range of 24 dB.Its power consumption is 1.4 mW,which is reduced by 57% compared with traditional schemes.The proposed readout circuit is suitable for the application of low power cost-sensitive imaging systems.

  6. Large-scale patterns of turnover and Basal area change in Andean forests.

    Directory of Open Access Journals (Sweden)

    Selene Báez

    Full Text Available General patterns of forest dynamics and productivity in the Andes Mountains are poorly characterized. Here we present the first large-scale study of Andean forest dynamics using a set of 63 permanent forest plots assembled over the past two decades. In the North-Central Andes tree turnover (mortality and recruitment and tree growth declined with increasing elevation and decreasing temperature. In addition, basal area increased in Lower Montane Moist Forests but did not change in Higher Montane Humid Forests. However, at higher elevations the lack of net basal area change and excess of mortality over recruitment suggests negative environmental impacts. In North-Western Argentina, forest dynamics appear to be influenced by land use history in addition to environmental variation. Taken together, our results indicate that combinations of abiotic and biotic factors that vary across elevation gradients are important determinants of tree turnover and productivity in the Andes. More extensive and longer-term monitoring and analyses of forest dynamics in permanent plots will be necessary to understand how demographic processes and woody biomass are responding to changing environmental conditions along elevation gradients through this century.

  7. Geographic patterns of vertebrate diversity and identification of relevant areas for conservation in Europe

    Directory of Open Access Journals (Sweden)

    Assunção–Albuquerque, M. J. T.

    2012-06-01

    Full Text Available The ‘EU Council conclusions on biodiversity post–2010′ re–enforced Europe’s commitment to halt biodiversity loss by 2020. Identifying areas of high–value for biodiversity conservation is an important issue to meet this target. We investigated the geographic pattern of terrestrial vertebrate diversity status in Europe by assessing the species richness, rarity, vulnerability (according to IUCN criteria, and a combined index of the three former for the amphibians, reptiles, bird and mammals of this region. We also correlated the value of all indices with climate and human influence variables. Overall, clear geographic gradients of species diversity were found. The combined biodiversity index indicated that high–value biodiversity areas were mostly located in the Mediterranean basin and the highest vulnerability was found in the Iberian peninsula for most taxa. Across all indexes, the proportion of variance explained by climate and human influence factors was moderate to low. The results obtained in this study have the potential to provide valuable support for nature conservation policies in Europe and, consequently, might contribute to mitigate biodiversity decline in this region.

  8. Large-Scale Patterns of Turnover and Basal Area Change in Andean Forests

    Science.gov (United States)

    Blundo, Cecilia; Aguilar, Manuel; Aguirre, Nikolay; Aquirre, Zhofre; Álvarez, Esteban; Cuesta, Francisco; Farfán-Ríos, William; García-Cabrera, Karina; Grau, Ricardo; Linares-Palomino, Reynaldo; Malizia, Lucio R.; Cruz, Omar Melo; Osinaga, Oriana; Reynel, Carlos; Silman, Miles R.

    2015-01-01

    General patterns of forest dynamics and productivity in the Andes Mountains are poorly characterized. Here we present the first large-scale study of Andean forest dynamics using a set of 63 permanent forest plots assembled over the past two decades. In the North-Central Andes tree turnover (mortality and recruitment) and tree growth declined with increasing elevation and decreasing temperature. In addition, basal area increased in Lower Montane Moist Forests but did not change in Higher Montane Humid Forests. However, at higher elevations the lack of net basal area change and excess of mortality over recruitment suggests negative environmental impacts. In North-Western Argentina, forest dynamics appear to be influenced by land use history in addition to environmental variation. Taken together, our results indicate that combinations of abiotic and biotic factors that vary across elevation gradients are important determinants of tree turnover and productivity in the Andes. More extensive and longer-term monitoring and analyses of forest dynamics in permanent plots will be necessary to understand how demographic processes and woody biomass are responding to changing environmental conditions along elevation gradients through this century. PMID:25973977

  9. Movement patterns and study area boundaries: Influences on survival estimation in capture-mark-recapture studies

    Science.gov (United States)

    Horton, G.E.; Letcher, B.H.

    2008-01-01

    The inability to account for the availability of individuals in the study area during capture-mark-recapture (CMR) studies and the resultant confounding of parameter estimates can make correct interpretation of CMR model parameter estimates difficult. Although important advances based on the Cormack-Jolly-Seber (CJS) model have resulted in estimators of true survival that work by unconfounding either death or recapture probability from availability for capture in the study area, these methods rely on the researcher's ability to select a method that is correctly matched to emigration patterns in the population. If incorrect assumptions regarding site fidelity (non-movement) are made, it may be difficult or impossible as well as costly to change the study design once the incorrect assumption is discovered. Subtleties in characteristics of movement (e.g. life history-dependent emigration, nomads vs territory holders) can lead to mixtures in the probability of being available for capture among members of the same population. The result of these mixtures may be only a partial unconfounding of emigration from other CMR model parameters. Biologically-based differences in individual movement can combine with constraints on study design to further complicate the problem. Because of the intricacies of movement and its interaction with other parameters in CMR models, quantification of and solutions to these problems are needed. Based on our work with stream-dwelling populations of Atlantic salmon Salmo salar, we used a simulation approach to evaluate existing CMR models under various mixtures of movement probabilities. The Barker joint data model provided unbiased estimates of true survival under all conditions tested. The CJS and robust design models provided similarly unbiased estimates of true survival but only when emigration information could be incorporated directly into individual encounter histories. For the robust design model, Markovian emigration (future

  10. Abnormal Brain Areas Common to the Focal Epilepsies: Multivariate Pattern Analysis of fMRI.

    Science.gov (United States)

    Pedersen, Mangor; Curwood, Evan K; Vaughan, David N; Omidvarnia, Amir H; Jackson, Graeme D

    2016-04-01

    Individuals with focal epilepsy have heterogeneous sites of seizure origin. However, there may be brain regions that are common to most cases of intractable focal epilepsy. In this study, we aim to identify these using multivariate analysis of task-free functional MRI. Fourteen subjects with extratemporal focal epilepsy and 14 healthy controls were included in the study. Task-free functional MRI data were used to calculate voxel-wise regional connectivity with regional homogeneity (ReHo) and weighted degree centrality (DCw), in addition to regional activity using fraction of amplitude of low-frequency fluctuations (fALFF). Multivariate pattern analysis was applied to each of these metrics to discriminate brain areas that differed between focal epilepsy subjects and healthy controls. ReHo and DCw classified focal epilepsy subjects from healthy controls with high accuracy (89.3% and 75%, respectively). However, fALFF did not significantly classify patients from controls. Increased regional network activity in epilepsy subjects was seen in the ipsilateral piriform cortex, insula, and thalamus, in addition to the dorsal anterior cingulate cortex and lateral frontal cortices. Decreased regional connectivity was observed in the ventromedial prefrontal cortex, as well as lateral temporal cortices. Patients with extratemporal focal epilepsy have common areas of abnormality (ReHo and DCw measures), including the ipsilateral piriform cortex, temporal neocortex, and ventromedial prefrontal cortex. ReHo shows additional increase in the "salience network" that includes anterior insula and anterior cingulate cortex. DCw showed additional effects in the ipsilateral thalamus and striatum. These brain areas may represent key regional network properties underlying focal epilepsy.

  11. Automatic classification and pattern discovery in high-throughput protein crystallization trials.

    Science.gov (United States)

    Cumbaa, Christian; Jurisica, Igor

    2005-01-01

    Conceptually, protein crystallization can be divided into two phases search and optimization. Robotic protein crystallization screening can speed up the search phase, and has a potential to increase process quality. Automated image classification helps to increase throughput and consistently generate objective results. Although the classification accuracy can always be improved, our image analysis system can classify images from 1,536-well plates with high classification accuracy (85%) and ROC score (0.87), as evaluated on 127 human-classified protein screens containing 5,600 crystal images and 189,472 non-crystal images. Data mining can integrate results from high-throughput screens with information about crystallizing conditions, intrinsic protein properties, and results from crystallization optimization. We apply association mining, a data mining approach that identifies frequently occurring patterns among variables and their values. This approach segregates proteins into groups based on how they react in a broad range of conditions, and clusters cocktails to reflect their potential to achieve crystallization. These results may lead to crystallization screen optimization, and reveal associations between protein properties and crystallization conditions. We also postulate that past experience may lead us to the identification of initial conditions favorable to crystallization for novel proteins.

  12. Abundantly and rarely expressed Lhc protein genes exhibit distinct regulation patterns in plants.

    Science.gov (United States)

    Klimmek, Frank; Sjödin, Andreas; Noutsos, Christos; Leister, Dario; Jansson, Stefan

    2006-03-01

    We have analyzed gene regulation of the Lhc supergene family in poplar (Populus spp.) and Arabidopsis (Arabidopsis thaliana) using digital expression profiling. Multivariate analysis of the tissue-specific, environmental, and developmental Lhc expression patterns in Arabidopsis and poplar was employed to characterize four rarely expressed Lhc genes, Lhca5, Lhca6, Lhcb7, and Lhcb4.3. Those genes have high expression levels under different conditions and in different tissues than the abundantly expressed Lhca1 to 4 and Lhcb1 to 6 genes that code for the 10 major types of higher plant light-harvesting proteins. However, in some of the datasets analyzed, the Lhcb4 and Lhcb6 genes as well as an Arabidopsis gene not present in poplar (Lhcb2.3) exhibited minor differences to the main cooperative Lhc gene expression pattern. The pattern of the rarely expressed Lhc genes was always found to be more similar to that of PsbS and the various light-harvesting-like genes, which might indicate distinct physiological functions for the rarely and abundantly expressed Lhc proteins. The previously undetected Lhcb7 gene encodes a novel plant Lhcb-type protein that possibly contains an additional, fourth, transmembrane N-terminal helix with a highly conserved motif. As the Lhcb4.3 gene seems to be present only in Eurosid species and as its regulation pattern varies significantly from that of Lhcb4.1 and Lhcb4.2, we conclude it to encode a distinct Lhc protein type, Lhcb8.

  13. Mathematical Characterization of Protein Sequences Using Patterns as Chemical Group Combinations of Amino Acids

    Science.gov (United States)

    Choudhury, Pabitra Pal; Jana, Siddhartha Sankar

    2016-01-01

    Comparison of amino acid sequence similarity is the fundamental concept behind the protein phylogenetic tree formation. By virtue of this method, we can explain the evolutionary relationships, but further explanations are not possible unless sequences are studied through the chemical nature of individual amino acids. Here we develop a new methodology to characterize the protein sequences on the basis of the chemical nature of the amino acids. We design various algorithms for studying the variation of chemical group transitions and various chemical group combinations as patterns in the protein sequences. The amino acid sequence of conventional myosin II head domain of 14 family members are taken to illustrate this new approach. We find two blocks of maximum length 6 aa as ‘FPKATD’ and ‘Y/FTNEKL’ without repeating the same chemical nature and one block of maximum length 20 aa with the repetition of chemical nature which are common among all 14 members. We also check commonality with another motor protein sub-family kinesin, KIF1A. Based on our analysis we find a common block of length 8 aa both in myosin II and KIF1A. This motif is located in the neck linker region which could be responsible for the generation of mechanical force, enabling us to find the unique blocks which remain chemically conserved across the family. We also validate our methodology with different protein families such as MYOI, Myosin light chain kinase (MLCK) and Rho-associated protein kinase (ROCK), Na+/K+-ATPase and Ca2+-ATPase. Altogether, our studies provide a new methodology for investigating the conserved amino acids’ pattern in different proteins. PMID:27930687

  14. Expression Pattern of Fatty Acid Binding Proteins in Celiac Disease Enteropathy

    Directory of Open Access Journals (Sweden)

    Natalia M. Bottasso Arias

    2015-01-01

    Full Text Available Celiac disease (CD is an immune-mediated enteropathy that develops in genetically susceptible individuals following exposure to dietary gluten. Severe changes at the intestinal mucosa observed in untreated CD patients are linked to changes in the level and in the pattern of expression of different genes. Fully differentiated epithelial cells express two isoforms of fatty acid binding proteins (FABPs: intestinal and liver, IFABP and LFABP, respectively. These proteins bind and transport long chain fatty acids and also have other important biological roles in signaling pathways, particularly those related to PPARγ and inflammatory processes. Herein, we analyze the serum levels of IFABP and characterize the expression of both FABPs at protein and mRNA level in small intestinal mucosa in severe enteropathy and normal tissue. As a result, we observed higher levels of circulating IFABP in untreated CD patients compared with controls and patients on gluten-free diet. In duodenal mucosa a differential FABPs expression pattern was observed with a reduction in mRNA levels compared to controls explained by the epithelium loss in severe enteropathy. In conclusion, we report changes in FABPs’ expression pattern in severe enteropathy. Consequently, there might be alterations in lipid metabolism and the inflammatory process in the small intestinal mucosa.

  15. [Spatiotemporal patterns and driving forces of land use change in industrial relocation area: a case study of old industrial area in Tiexi of Shenyang, Northeast China].

    Science.gov (United States)

    Wang, Mei-Ling; Bing, Long-Fei; Xi, Feng-Ming; Wu, Rui; Geng, Yong

    2013-07-01

    Based on the QuickBird remote sensing images and with the support of GIS, this paper analyzed the spatiotemporal characteristics of land use change and its driving forces in old industrial area of Tiexi, Shenyang City of Liaoning Province in 2000-2010. During the study period, the industrial and mining warehouse land pattern had the greatest change, evolving from the historical pattern of residential land in the south and of industrial land in the north into residential land as the dominant land use pattern. In the last decade, the residential land area increased by 9%, mainly transferred from the industrial and mining warehouse land located in the north of Jianshe Road, while the industrial and mining warehouse land area decreased by 20%. The land areas for the commercial service and for the administrative and public services were increased by 1.3% and 3.1%, respectively. The land area for construction had a greater change, with an overall change rate being 76.9%. The land use change rate in 2000-2005 was greater than that in 2005-2010. National development strategies and policies, regional development planning, administrative reform, and industrial upgrading were the main driving forces of the land use change in old industrial area of Tiexi.

  16. Nanoscale programmable sequence-specific patterning of DNA scaffolds using RecA protein

    Science.gov (United States)

    Sharma, R.; Davies, A. G.; Wälti, C.

    2012-09-01

    Molecular self-assembly inherent to many biological molecules, in conjunction with suitable molecular scaffolds to facilitate programmable positioning of nanoscale objects, offers a promising approach for the integration of functional nanoscale complexes into macroscopic host devices. Here, we report the use of the protein RecA as a means of highly efficient programmable patterning of double-stranded (ds)DNA molecules with molecular-scale precision at specific locations along the DNA strand. RecA proteins form nucleoprotein filaments with single-stranded (ss)DNA molecules, which are chosen to be of sequence homologous to the desired binding region on the dsDNA scaffold. We show that the patterning yield can be in excess of 85% and we demonstrate that concurrent patterning of multiple locations on the same dsDNA scaffold can be achieved with separation between the assembled nucleoprotein filaments of less than 4 nm. This is an important prerequisite for this programmable and flexible DNA scaffold patterning technique to be employed in molecular- and nanoscale assembly applications.

  17. Land Use of the Three Gorges Reservoir Area and the Effect on Its Landscape Pattern in the Recent 50 Years

    Institute of Scientific and Technical Information of China (English)

    HUANG Zhiqin; ZHOU Wancun; ZHOU Jieming; ZHU Mingcang

    2006-01-01

    The paper makes detailed analysis on the changing processes of the main types of land use in Three Gorges Reservoir Area through the techniques of RS (Remote Sense) and GIS (Geography Information System). Based on the theory of landscape ecology, many types of landscape pattern indexes are calculated and made correlation analysis. The results indicate that: in 1995 the ecological environment of Three Gorges Reservoir Area was the most vulnerable in the recent 50 years, but resumed in 2002; the landscape pattern diversity index, fractal dimension index and fragmentation index has close correlation with the area of land use/cover change (LUCC). The research also releases that the increase of the cultivated land, grassland and construction land deteriorates the landscape ecological pattern, while the increase of forest land area will help restore the landscape ecological pattern to its original state. The rapid change of grassland is an important index of the change of landscape pattern, because it has the most effect on change of landscape pattern index.

  18. Mapping burned areas and burn severity patterns across the Mediterranean region

    Science.gov (United States)

    Kalogeropoulos, Christos; Amatulli, Giuseppe; Kempeneers, Pieter; Sedano, Fernando; San Miguel-Ayanz, Jesus; Camia, Andrea

    2010-05-01

    The Mediterranean region is highly susceptible to wildfires. On average, about 60,000 fires take place in this region every year, burning on average half a million hectares of forests and natural vegetation. Wildfires cause environmental degradation and affect the lives of thousands of people in the region. In order to minimize the consequences of these catastrophic events, fire managers and national authorities need to have in their disposal accurate and updated spatial information concerning the size of the burned area as well as the burn severity patterns. Mapping burned areas and burn severity patterns is necessary to effectively support the decision-making process in what concerns strategic (long-term) planning with the definition of post-fire actions at European and national scales. Although a comprehensive archive of burnt areas exists at the European Forest Fire Information System, the analysis of the severity of the areas affected by forest fires in the region is not yet available. Fire severity is influenced by many variables, including fuel type, topography and meteorological conditions before and during the fire. The analysis of fire severity is essential to determine the socio-economic impact of forest fires, to assess fire impacts, and to determine the need of post-fire rehabilitation measures. Moreover, fire severity is linked to forest fire emissions and determines the rate of recovery of the vegetation after the fire. Satellite imagery can give important insights about the conditions of the live fuel moisture content and can be used to assess changes on vegetation structure and vitality after forest fires. Fire events occurred in Greece, Portugal and Spain during the fire season of 2009 were recorded and analyzed in a GIS environment. The Normalized Difference Vegetation Index (NDVI), the Enhanced Vegetation Index (EVI) and the Normalized Burn Ratio (NBR) were calculated from 8-days composites MODIS/TERRA imagery from March to October 2009. In

  19. Development pattern of the industry form in mountains area:Case study of the Three Gorges Reservoir area

    Institute of Scientific and Technical Information of China (English)

    Feng Quanguang

    2008-01-01

    The mountainous areas (mountain,plateau and hilly area) cover more than 85% of the total land territory of China.Nature and humanity in very mountainous area has its own geographic characteristics.In the process of industrialization and urbanization in China realizing the sustainable development of the mountainous areas optiinizing man-land system,and adopting and continuously developing corresponding economic modes of the mountainous areas with mulli-functiorns of economy,ecology,culture and society to charactertze production content,mode of production,mode of operation is not only helpful to economy,society and ecological value and is of great aesthetic value,but also solve the technological problems of the subject of starting undertaking to finally transform the region al resource advantage of the mountainous area into the advantage of capital and technology for economic develop ment and to get rid of the contradiction between underdeveloped economy,and abundant resources.This paper takes the Three Gorges Reservoir (TGR) area for example to show that it's of great practical and theoretical significance to develop"Five Types of Agriculture" and to optimize eco-environment,industrial structure,department structure regional distribution,variety structure and quality structure.

  20. Climatic patterns and extreme rainfalls on coastal areas in Central Italy

    Science.gov (United States)

    Bramati, M. C.; Tarragoni, C.

    2012-04-01

    In this paper we focus on the extreme values analysis to estimate the rainfall return levels for some Adriatic and Tyrrhenian coastal areas in central Italy. Two approaches are mainly considered: the first one is based on the maximum annual daily rainfall series (1-day, 2-day and 3-day) for which suitable probability distributions are fitted, whereas the second one is based on the series of peaks over annual thresholds (POT) for which the best fitting Generalized Pareto distribution is identified. Spectral analysis and appropriate tests for stationarity and homogeneity are run in order to verify the hypothesis under which the analysis performed is valid. From the density plots and the parameter estimates of the fitted distributions to the various annual maximum rainfall series we can conclude that there is a different pattern in the occurrence of extreme events for the western coast with respect to the eastern coast. Specifically, on the Tyrrhenian side extreme rainfalls are more likely to happen in correspondence of longer time spans (i.e. 3-day series) as the effect of cumulated stable rainfalls over time. On the opposite, for the Adriatic coast extremes are more frequent in shorter time spans (1-day). A vector autoregressive model is then estimated and through a causal ordering the identifying restrictions are set. The impulse response analysis shows a lag in the transmission of rainfall shocks of the central Adriatic coast to the Tyrrhenian one. This paper is prepared as a background paper to the SECOA N1.2 Report: Assessment of frequency-magnitude of extreme rainfall events and flooding. Project SECOA (Solutions for Environmental contrast in Coastal Areas) is funded by the EU Commission within the 7th Framework Programme (2007-2013).

  1. Regulation of gene expression in prediapausing embryos of the silkworm, Bombyx mori: pattern of protein synthesis.

    Science.gov (United States)

    Dorel, C; Coulon, M

    1988-03-01

    Specific qualitative and quantitative changes in protein synthesis occur from the fertilization to the onset of diapause in the silkworm. We have used two-dimensional gel electrophoresis to analyse the patterns of proteins synthesized in prediapausing eggs of Bombyx. This analysis has been carried out with in vivo labelled polypeptides and with proteins synthesized in vitro by RNA isolated at different stages. The oocyte contains an abundant supply of diverse mRNA which are translatable in vitro. A set of proteins with molecular weight range of 68,000 to 74,000 and isoelectric points of 5.85-5.95 (hereafter referred to as No. 30) is specific of the germ-anlage stage. Transcripts encoding the No. 30 proteins are not detectable in oocytes, and inhibition of transcription by actinomycin D indicates that No. 30 mRNA are synthesized de novo. Treating eggs at the germ-anlage stage with 4 N HCl at 46 degrees C prevents diapause and is accompanied by overproduction of No. 30 protein. The induction of No. 30 synthesis is also the main event of the heat shock response. The implications of these findings in relation to early embryonic development and prevention of diapause are discussed.

  2. Transparent self-cleaning lubricant-infused surfaces made with large-area breath figure patterns

    Science.gov (United States)

    Zhang, Pengfei; Chen, Huawei; Zhang, Liwen; Ran, Tong; Zhang, Deyuan

    2015-11-01

    Nepenthes pitcher inspired slippery lubricant-infused porous surfaces greatly impact the understanding of liquid-repellent surfaces construction and have attracted extensive attention in recent years due to their potential applications in self-cleaning, anti-fouling, anti-icing, etc. In this work, we have successfully fabricated transparent slippery lubricant-infused surfaces based on breath figure patterns (BFPs). Large-area BFPs with interconnected pores were initially formed on the glass substrate and then a suitable lubricant was added onto the surfaces. The interconnected pores in BFPs were able to hold the lubricant liquid in place and form a stable liquid/solid composite surface capable of repelling a variety of liquids. The liquid-repellent surfaces show extremely low critical sliding angles for various liquids, thus providing the surfaces with efficient self-cleaning property. It was also found that the liquid droplets' sliding behaviors on the surfaces were significantly influenced by the tilting angle of the substrate, liquid volume, liquid chemical properties, and pore sizes of the surfaces.

  3. Effect of Perforation Area and Arrangement Pattern on Structural Behaviour of Nature Inspired Perforated Hollow Structure

    Directory of Open Access Journals (Sweden)

    Woo Yian Peen

    2013-01-01

    Full Text Available The Cholla cactus skeleton has been the inspiration source for this study, in our effort to search forlight and more structural effective structures. This woody skeleton of Cholla with oval shaped perforationsarranged in spiral pattern is found strong enough to support the cactus self weight. This research has beencarried out to investigate the effects of percentage of perforations and perforations arrangements on structuralbehaviour of cylindrical hollow section. A total of eleven models consisting of one cylindrical hollow sectionwithout perforation as the control model and ten simplified perforated cylindrical hollow sections have beenconstructed using a finite element method software. The perforated models have been assigned with 10 to 50percent of perforations area by fixing the number of perforations to twenty and altering the perforation size toachieve the percentage variable. Computational analyses have been carried out for three loading conditions:compressive, flexural and torsional. Findings have shown that the increment in percentage of perforationsproduces higher stresses to the cylindrical hollow section. This has effects on the structural capacity of thecylindrical hollow section. Array arrangement of the perforations shows better structural performance incompression and flexural loading conditions while spiral arrangement exhibits better structural performanceunder torsional loading condition.

  4. High-resolution functional epoxysilsesquioxane-based patterning layers for large-area nanoimprinting.

    Science.gov (United States)

    Pina-Hernandez, Carlos; Guo, L Jay; Fu, Peng-Fei

    2010-08-24

    Epoxysilsesquioxane (SSQ)-based materials have been developed as patterning layers for large-area and high-resolution nanoimprinting. The SSQ polymers, poly(methyl-co-3-glycidoxypropyl) silsesquioxanes (T(Me)T(Ep)), poly(phenyl-co-3-glycidoxypropyl) silsesquioxanes (T(Ph)T(Ep)), and poly(phenyl-co-3-glycidoxypropyl-co-perfluorooctyl) silsesquioxanes (T(Ph)T(Ep)T(Fluo)), were precisely designed and synthesized by incorporating the necessary functional groups onto the SSQ backbone. The materials possess a variety of characteristics desirable for NIL, such as great coatability, high modulus, good mold release, and excellent dry etch resistance. In particular, the presence of epoxy functional groups allows the resists to be solidified within seconds under UV exposure at room temperature, and the presence of the fluoroalkyl groups in the SSQ resins greatly facilitate mold release after the imprint process. In addition, the absence of metal in the resins makes the materials highly compatible with applications involving Si CMOS integrated circuits fabrication.

  5. Patterns and socioeconomic influences of tobacco exposure in tobacco cultivating rural areas of Yunnan Province, China

    Directory of Open Access Journals (Sweden)

    Cai Le

    2012-10-01

    Full Text Available Abstract Background This study describes the patterns and socioeconomic influences of tobacco use among adults in tobacco-cultivating regions of rural southwest China. Methods A cross-sectional survey was conducted in 8681 adults aged ≥18 years in rural areas of Yunnan Province, China from 2010 to 2011. A standardized questionnaire was administered to obtain data about participants’ demographic characteristics, individual socioeconomic status, ethnicity, self-reported smoking habits, and exposure to secondhand smoke (SHS. The socioeconomic predictors of current smoking, nicotine addiction, and SHS exposure were analyzed using multivariate logistic regression. Results The prevalence rates of tobacco use were much higher in men compared with women (current smoking 68.5% vs. 1.3%; and nicotine dependence 85.2% vs. 72.7%. However, the rate of SHS exposure was higher in women compared with men (76.6% vs. 70.5%. Tobacco farmers had higher prevalence rates of current smoking, nicotine dependence, and SHS exposure compared with participants not engaged in tobacco farming (P Conclusions This study suggests that tobacco control efforts in rural southwest China must be tailored to address tobacco-cultivating status and socioeconomic factors.

  6. Evolutionarily Conserved Pattern of Interactions in a Protein Revealed by Local Thermal Expansion Properties.

    Science.gov (United States)

    Dellarole, Mariano; Caro, Jose A; Roche, Julien; Fossat, Martin; Barthe, Philippe; García-Moreno E, Bertrand; Royer, Catherine A; Roumestand, Christian

    2015-07-29

    The way in which the network of intramolecular interactions determines the cooperative folding and conformational dynamics of a protein remains poorly understood. High-pressure NMR spectroscopy is uniquely suited to examine this problem because it combines the site-specific resolution of the NMR experiments with the local character of pressure perturbations. Here we report on the temperature dependence of the site-specific volumetric properties of various forms of staphylococcal nuclease (SNase), including three variants with engineered internal cavities, as measured with high-pressure NMR spectroscopy. The strong temperature dependence of pressure-induced unfolding arises from poorly understood differences in thermal expansion between the folded and unfolded states. A significant inverse correlation was observed between the global thermal expansion of the folded proteins and the number of strong intramolecular hydrogen bonds, as determined by the temperature coefficient of the backbone amide chemical shifts. Comparison of the identity of these strong H-bonds with the co-evolution of pairs of residues in the SNase protein family suggests that the architecture of the interactions detected in the NMR experiments could be linked to a functional aspect of the protein. Moreover, the temperature dependence of the residue-specific volume changes of unfolding yielded residue-specific differences in expansivity and revealed how mutations impact intramolecular interaction patterns. These results show that intramolecular interactions in the folded states of proteins impose constraints against thermal expansion and that, hence, knowledge of site-specific thermal expansivity offers insight into the patterns of strong intramolecular interactions and other local determinants of protein stability, cooperativity, and potentially also of function.

  7. Vertical profiles and enrichment pattern of natural radionuclides in monazite areas of coastal Kerala

    Energy Technology Data Exchange (ETDEWEB)

    Shetty, P.K. [Department of Studies in Physics, Mangalore University, Mangalagangothri, Mangalore, Karnataka 574199 (India); Narayana, Y. [Department of Studies in Physics, Mangalore University, Mangalagangothri, Mangalore, Karnataka 574199 (India)]. E-mail: narayanay@yahoo.com; Siddappa, K. [Department of Studies in Physics, Mangalore University, Mangalagangothri, Mangalore, Karnataka 574199 (India)

    2006-07-01

    Detailed studies on radionuclides concentration in different environmental matrices of high background areas were undertaken in the coastal areas of Karunagapalli, Chavara, Neendakara and Kollam to study the distribution and enrichment of the radionuclides in the region. The sand samples collected at different distances from sea waterline and at different depths, were analysed for primordial radionuclides by gamma spectrometry. The activity of primordial radionuclides was determined for the different size fractions of sand to study the enrichment pattern. The highest activity was found confined in 125-63 {mu}m particle size fraction in sand. The minimum {sup 232}Th activity was 9.4 Bq kg{sup -1}, found in Kollam at a depth of 10-20 cm, 40 m away from waterline in 500-250 {mu}m particle size fraction and maximum activity of 136,811.2 Bq kg{sup -1} was observed in Chavara in grains of size 125-63 {mu}m at a depth of 0-10 cm for a sample collected 20 m away from waterline. The lowest {sup 226}Ra activity observed was 29.6 Bq kg{sup -1} at Kollam beach for a sample 40 m away from waterline in grains of size 1000-500 {mu}m and at a depth of 20-30 cm and the highest activity observed was 10,309 Bq kg{sup -1} in grains of size 125-63 {mu}m for a sample collected at a distance 20 m away from waterline and at a depth of 0-10 cm. The activity of {sup 4}K was below detectable level in most of the samples collected from the high background monazite area. The {sup 232}Th, {sup 226}Ra activities decrease with depth for the samples collected 20 m away from the waterline and increase with depth for the samples collected 40 m away from the waterline at Chavara and Kollam beaches. No definite correlation was found between variation of the concentrations of {sup 232}Th and {sup 226}Ra with depth at Karunagapalli and Neendakara beach sands. There exists a strong correlation between {sup 226}Ra and {sup 232}Th activities in the region. The results of these investigations are presented

  8. Pattern recognition analysis and classification modeling of selenium-producing areas

    Science.gov (United States)

    Naftz, D.L.

    1996-01-01

    Established chemometric and geochemical techniques were applied to water quality data from 23 National Irrigation Water Quality Program (NIWQP) study areas in the Western United States. These techniques were applied to the NIWQP data set to identify common geochemical processes responsible for mobilization of selenium and to develop a classification model that uses major-ion concentrations to identify areas that contain elevated selenium concentrations in water that could pose a hazard to water fowl. Pattern recognition modeling of the simple-salt data computed with the SNORM geochemical program indicate three principal components that explain 95% of the total variance. A three-dimensional plot of PC 1, 2 and 3 scores shows three distinct clusters that correspond to distinct hydrochemical facies denoted as facies 1, 2 and 3. Facies 1 samples are distinguished by water samples without the CaCO3 simple salt and elevated concentrations of NaCl, CaSO4, MgSO4 and Na2SO4 simple salts relative to water samples in facies 2 and 3. Water samples in facies 2 are distinguished from facies 1 by the absence of the MgSO4 simple salt and the presence of the CaCO3 simple salt. Water samples in facies 3 are similar to samples in facies 2, with the absence of both MgSO4 and CaSO4 simple salts. Water samples in facies 1 have the largest selenium concentration (10 ??gl-1), compared to a median concentration of 2.0 ??gl-1 and less than 1.0 ??gl-1 for samples in facies 2 and 3. A classification model using the soft independent modeling by class analogy (SIMCA) algorithm was constructed with data from the NIWQP study areas. The classification model was successful in identifying water samples with a selenium concentration that is hazardous to some species of water-fowl from a test data set comprised of 2,060 water samples from throughout Utah and Wyoming. Application of chemometric and geochemical techniques during data synthesis analysis of multivariate environmental databases from other

  9. PATTERNS OF MULTIMORBIDITY AMONG ELDERLY IN AN URBAN AREA OF NORTH INDIA

    Directory of Open Access Journals (Sweden)

    Akriti

    2016-03-01

    Full Text Available BACKGROUND Ageing is a natural process. By 2020, the number of people aged 60 years and older will outnumber children younger than 5 years in the entire world. This natural phenomenon of population ageing is rampant in developing countries like India while data and studies regarding health conditions and prevalence of multimorbidity is lacking. AIMS AND OBJECTIVES This cross sectional study was conducted to determine the morbidity pattern and health care seeking behaviour of elderly in North India. SETTINGS AND DESIGN Community based Cross-sectional study in Urban Field Practice Area, Shimlapuri. MATERIALS AND METHODS A Community based cross-sectional study was conducted in Urban field practice area, Shimlapuri under the Department of Community Medicine of Dayanand Medical College and hospital, Ludhiana, Punjab, India from June 2014 to December 2014. The study population comprised of 534 elderlies above 60 years of age, both males and females residing in the area. The subjects were interviewed and examined in accordance with a pre-structured proforma by field workers, medical interns and faculty members. Majority of the morbidity profile was obtained through history. Information on diseases including visual impairment, respiratory diseases, musculoskeletal disorder, acid peptic disease, deafness and stroke were based on history given by the participants. The association of multimorbidity with socio demographic variables was studied. STATISTICAL ANALYSIS Percentages and Chi Square Test. RESULTS The mean age of the participants was 66.27 ± 6.26 years. Majority of the subjects belonged to age group of 60-69 years (70%. Morbidity was observed in 99.5% subjects. The most common chronic condition was eye problem (68.5% including visual impairment and refractive error. Hypertension and acid peptic disease were found to be significantly higher among females (p<0.01. A total of 352 study subjects (65.9% were found to be suffering from multimorbidity

  10. Assembly of transmembrane helices of simple polytopic membrane proteins from sequence conservation patterns.

    Science.gov (United States)

    Park, Yungki; Helms, Volkhard

    2006-09-01

    The transmembrane (TM) domains of most membrane proteins consist of helix bundles. The seemingly simple task of TM helix bundle assembly has turned out to be extremely difficult. This is true even for simple TM helix bundle proteins, i.e., those that have the simple form of compact TM helix bundles. Herein, we present a computational method that is capable of generating native-like structural models for simple TM helix bundle proteins having modest numbers of TM helices based on sequence conservation patterns. Thus, the only requirement for our method is the presence of more than 30 homologous sequences for an accurate extraction of sequence conservation patterns. The prediction method first computes a number of representative well-packed conformations for each pair of contacting TM helices, and then a library of tertiary folds is generated by overlaying overlapping TM helices of the representative conformations. This library is scored using sequence conservation patterns, and a subsequent clustering analysis yields five final models. Assuming that neighboring TM helices in the sequence contact each other (but not that TM helices A and G contact each other), the method produced structural models of Calpha atom root-mean-square deviation (CA RMSD) of 3-5 A from corresponding crystal structures for bacteriorhodopsin, halorhodopsin, sensory rhodopsin II, and rhodopsin. In blind predictions, this type of contact knowledge is not available. Mimicking this, predictions were made for the rotor of the V-type Na(+)-adenosine triphosphatase without such knowledge. The CA RMSD between the best model and its crystal structure is only 3.4 A, and its contact accuracy reaches 55%. Furthermore, the model correctly identifies the binding pocket for sodium ion. These results demonstrate that the method can be readily applied to ab initio structure prediction of simple TM helix bundle proteins having modest numbers of TM helices.

  11. Site-selective adsorption of protein induced by a metal pattern on a poly(ethylene terephthalate) surface.

    Science.gov (United States)

    Cao, Jiali; Wu, Zhongkui; Li, Shaoying; Tang, Hongxiao; Mei, Qilin

    2013-11-01

    A novel technique for inducing site-selective adsorption of protein through constructing metal patterns on flexible poly(ethylene terephthalate) surfaces is presented. The substrates were first modified by vacuum ultraviolet (VUV) irradiation through a photomask to introduce regions with different functional groups. Then the designed metal patterns were constructed on the surfaces of VUV-treated substrates. The surface rearrangement was effectively prevented by constructing silver patterns on poly(ethylene terephthalate) surfaces, thus significantly improving the stability and selectivity of protein adsorption on the surfaces. Moreover, the protein-repulsive layer further reinforced the effect. Finally, protein patterns were successfully obtained. As confirmed by fluorescence microscope, field emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS), and static water contact angle measurement, the protein patterns possess both excellent selectivity and high fidelity. Feature size of the protein patterns surrounded by a protein-repulsive layer was exactly the same as that of the photomask. And the grain sizes of silver particles were approximately 50 nm. This work could potentially be used in various fields such as biomedicine, bioelectronic components, and tissue repair and replacement, where selective adsorption of protein is desired.

  12. Solution processed large area fabrication of Ag patterns as electrodes for flexible heaters, electrochromics and organic solar cells

    DEFF Research Database (Denmark)

    Gupta, Ritu; Walia, Sunil; Hösel, Markus

    2014-01-01

    A simple method for producing patterned Ag electrodes on transparent and flexible substrates is reported. The process makes use of laser printed toner as a sacrificial template for an organic precursor, which upon thermolysis and toner lift off produced highly conducting Ag electrodes. Thus, the ...... solar cells have been demonstrated. The method is extendable to produce defect-free patterns over large areas as demonstrated by roll coating.......A simple method for producing patterned Ag electrodes on transparent and flexible substrates is reported. The process makes use of laser printed toner as a sacrificial template for an organic precursor, which upon thermolysis and toner lift off produced highly conducting Ag electrodes. Thus...

  13. Factors controlling spatial distribution patterns of biocrusts in a heterogeneous and topographically complex semiarid area

    Science.gov (United States)

    Chamizo, Sonia; Rodríguez-Caballero, Emilio; Roncero, Beatriz; Raúl Román, José; Cantón, Yolanda

    2016-04-01

    Biocrusts are widespread soil components in drylands all over the world. They are known to play key roles in the functioning of these regions by fixing carbon and nitrogen, regulating hydrological processes, and preventing from water and wind erosion, thus reducing the loss of soil resources and increasing soil fertility. The rate and magnitude of services provided by biocrusts greatly depend on their composition and developmental stage. Late-successional biocrusts such as lichens and mosses have higher carbon and nitrogen fixation rates, and confer greater protection against erosion and the loss of sediments and nutrients than early-successional algae and cyanobacteria biocrusts. Knowledge of spatial distribution patterns of different biocrust types and the factors that control their distribution is important to assess ecosystem services provided by biocrusts at large spatial scales and to improve modelling of biogeochemical processes and water and carbon balance in drylands. Some of the factors that condition biocrust cover and composition are incoming solar radiation, terrain attributes, vegetation distribution patterns, microclimatic variables and soil properties such as soil pH, texture, soil organic matter, soil nutrients and gypsum and CaCO3 content. However, the factors that govern biocrust distribution may vary from one site to another depending on site characteristics. In this study, we examined the influence of abiotic attributes on the spatial distribution of biocrust types in a complex heterogeneous badland system (Tabernas, SE Spain) where biocrust cover up to 50% of the soil surface. From the analysis of relationships between terrain attributes and proportional abundance of biocrust types, it was found that topography exerted a main control on the spatial distribution of biocrust types in this area. SW-facing slopes were dominated by physical soil crusts and were practically devoid of vegetation and biocrusts. Biocrusts mainly occupied the pediments

  14. Mapping functional group free energy patterns at protein occluded sites: nuclear receptors and G-protein coupled receptors.

    Science.gov (United States)

    Lakkaraju, Sirish Kaushik; Yu, Wenbo; Raman, E Prabhu; Hershfeld, Alena V; Fang, Lei; Deshpande, Deepak A; MacKerell, Alexander D

    2015-03-23

    Occluded ligand-binding pockets (LBP) such as those found in nuclear receptors (NR) and G-protein coupled receptors (GPCR) represent a significant opportunity and challenge for computer-aided drug design. To determine free energies maps of functional groups of these LBPs, a Grand-Canonical Monte Carlo/Molecular Dynamics (GCMC/MD) strategy is combined with the Site Identification by Ligand Competitive Saturation (SILCS) methodology. SILCS-GCMC/MD is shown to map functional group affinity patterns that recapitulate locations of functional groups across diverse classes of ligands in the LBPs of the androgen (AR) and peroxisome proliferator-activated-γ (PPARγ) NRs and the metabotropic glutamate (mGluR) and β2-adreneric (β2AR) GPCRs. Inclusion of protein flexibility identifies regions of the binding pockets not accessible in crystal conformations and allows for better quantitative estimates of relative ligand binding affinities in all the proteins tested. Differences in functional group requirements of the active and inactive states of the β2AR LBP were used in virtual screening to identify high efficacy agonists targeting β2AR in Airway Smooth Muscle (ASM) cells. Seven of the 15 selected ligands were found to effect ASM relaxation representing a 46% hit rate. Hence, the method will be of use for the rational design of ligands in the context of chemical biology and the development of therapeutic agents.

  15. Overlapping functions of argonaute proteins in patterning and morphogenesis of Drosophila embryos.

    Directory of Open Access Journals (Sweden)

    Wibke J Meyer

    2006-08-01

    Full Text Available Argonaute proteins are essential components of the molecular machinery that drives RNA silencing. In Drosophila, different members of the Argonaute family of proteins have been assigned to distinct RNA silencing pathways. While Ago1 is required for microRNA function, Ago2 is a crucial component of the RNA-induced silencing complex in siRNA-triggered RNA interference. Drosophila Ago2 contains an unusual amino-terminus with two types of imperfect glutamine-rich repeats (GRRs of unknown function. Here we show that the GRRs of Ago2 are essential for the normal function of the protein. Alleles with reduced numbers of GRRs cause specific disruptions in two morphogenetic processes associated with the midblastula transition: membrane growth and microtubule-based organelle transport. These defects do not appear to result from disruption of siRNA-dependent processes but rather suggest an interference of the mutant Ago2 proteins in an Ago1-dependent pathway. Using loss-of-function alleles, we further demonstrate that Ago1 and Ago2 act in a partially redundant manner to control the expression of the segment-polarity gene wingless in the early embryo. Our findings argue against a strict separation of Ago1 and Ago2 functions and suggest that these proteins act in concert to control key steps of the midblastula transition and of segmental patterning.

  16. Dewetting of polystyrene thin films on poly(ethylene glycol)-modified surfaces as a simple approach for patterning proteins.

    Science.gov (United States)

    Cai, Yangjun; Newby, Bi-min Zhang

    2008-05-20

    A simple technique for patterning proteins utilizing dewetted polystyrene (PS) droplets is demonstrated. A polystyrene thin film was spin coated on a poly(ethylene glycol) (PEG) silane-modified surface. As the PS film dewets from the surface, upon annealing, to form droplets, the PEG-silane-modified surface is exposed, which retains its capability to resist protein adsorption, and the PS droplets allow the selective adsorption of proteins. In contrast to the undewetted flat PS film, the droplet surface had a greater amount of adsorbed proteins. Atomic force microscopy scans reveal that the roughness of the droplet surface is higher, and a multilayer of proteins results on the droplet surface. Moreover, micro- and nanoscale droplet patterns can easily be achieved by tuning the thickness of PS thin films. Because dewetting approaches for generating ordered dewetting droplets have been successfully generated by others, those approaches could be easily combined with this technique to fabricate ordered protein patterns.

  17. Early, nonciliary role for microtubule proteins in left-right patterning is conserved across kingdoms.

    Science.gov (United States)

    Lobikin, Maria; Wang, Gang; Xu, Jingsong; Hsieh, Yi-Wen; Chuang, Chiou-Fen; Lemire, Joan M; Levin, Michael

    2012-07-31

    Many types of embryos' bodyplans exhibit consistently oriented laterality of the heart, viscera, and brain. Errors of left-right patterning present an important class of human birth defects, and considerable controversy exists about the nature and evolutionary conservation of the molecular mechanisms that allow embryos to reliably orient the left-right axis. Here we show that the same mutations in the cytoskeletal protein tubulin that alter asymmetry in plants also affect very early steps of left-right patterning in nematode and frog embryos, as well as chirality of human cells in culture. In the frog embryo, tubulin α and tubulin γ-associated proteins are required for the differential distribution of maternal proteins to the left or right blastomere at the first cell division. Our data reveal a remarkable molecular conservation of mechanisms initiating left-right asymmetry. The origin of laterality is cytoplasmic, ancient, and highly conserved across kingdoms, a fundamental feature of the cytoskeleton that underlies chirality in cells and multicellular organisms.

  18. Polymorphism patterns in Duffy-binding protein among Thai Plasmodium vivax isolates

    Directory of Open Access Journals (Sweden)

    Schaecher Kurt E

    2008-06-01

    Full Text Available Abstract Background The Duffy-binding protein II of Plasmodium vivax (PvDBPII has been considered as an attractive target for vaccine-mediated immunity despite a possible highly polymorphic nature. Among seven PvDBP domains, domain II has been shown to exhibit a high rate of nonsynonymous polymorphism, which has been suggested to be a potential immune (antibody binding evasion mechanism. This study aimed to determine the extent of genetic polymorphisms and positive natural selection at domain II of the PvDBP gene among a sampling of Thai P. vivax isolates. Methods The PvDBPII gene was PCR amplified and the patterns of polymorphisms were characterized from 30 Thai P. vivax isolates using DNA cloning and sequencing. Phylogenetic analysis of the sequences and positive selection were done using DnaSP ver 4.0 and MEGA ver 4.0 packages. Results This study demonstrated a high rate of nonsynonymous polymorphism. Using Sal I as the reference strain, a total of 30 point-mutations were observed in the PvDBPII gene among the set of Thai P. vivax isolates, of which 25 nonsynonymous and five synonymous were found. The highest frequency of polymorphism was found in five variant amino acids (residues D384G, R390H, L424I, W437R, I503K with the variant L424I having the highest frequency. The difference between the rates of nonsynonymous and synonymous mutations estimated by the Nei and Gojobori's method suggested that PvDBPII antigen appears to be under selective pressure. Phylogenetic analysis of PvDBPII Thai P. vivax isolates to others found internationally demonstrated six distinct allele groups. Allele groups 4 and 6 were unique to Thailand. Conclusion Polymorphisms within PvDBPII indicated that Thai vivax malaria parasites are genetically diverse. Phylogenetic analysis of DNA sequences using the Neighbour-Joining method demonstrated that Thai isolates shared distinct alleles with P. vivax isolates from different geographical areas. The study reported here

  19. Changing Pattern of Hepatitis A Virus Epidemiology in an Area of High Endemicity

    Directory of Open Access Journals (Sweden)

    Marcello Campagna

    2012-06-01

    Full Text Available Background: Continuous assessment of hepatitis A virus (HAV seroepidemiology is a useful tool to control the risk of infection.Objectives:This study aimed to evaluate the changing patterns of anti-HAV seroprevalence in a population,which isgenerally considered to be anarea ofhigh endemicity.Patients and Methods: Overall, the results of 3349 sera collected during the period 2005-2008 from patients attending the University Hospital of Cagliari, Italy were studied; their mean age was 52.7 years, (s + 16.22. Patients with liver disease were excluded from the study. Age specific seroprevalence results were compared with those observed in similar previous studies carried out in the same area.Results: The overall prevalence of anti-HAV was 74.6% with consistently lower values in subjects younger than 40 years (17.5%; P < 0.0001 particularly in those under 30 years of age (8.9%, CI 5.8-11.9. A significant declining trend in age specific seroprevalence has been foundin people under 30 years;61% in 1988, 33% in 1995 and 8.9% in 2005-2008.Conclusions: Our findings show that a significant decline inherd immunity has occurred in the last 20 years as a consequence of lower HAV circulation due to improvementsin socio-economical and hygienic conditions. Adolescents and young adults are becoming increasingly susceptible to HAV infections, as recent outbreaks of acute HAV hepatitis have occurred. Persistent environmental monitoring and the implementation of prevention measures must be considered in order to contain the risk related to this epidemiological shift..

  20. Improved Discriminability of Spatiotemporal Neural Patterns in Rat Motor Cortical Areas as Directional Choice Learning Progresses

    Directory of Open Access Journals (Sweden)

    Hongwei eMao

    2015-03-01

    Full Text Available Animals learn to choose a proper action among alternatives to improve their odds of success in food foraging and other activities critical for survival. Through trial-and-error, they learn correct associations between their choices and external stimuli. While a neural network that underlies such learning process has been identified at a high level, it is still unclear how individual neurons and a neural ensemble adapt as learning progresses. In this study, we monitored the activity of single units in the rat medial and lateral agranular (AGm and AGl, respectively areas as rats learned to make a left or right side lever press in response to a left or right side light cue. We noticed that rat movement parameters during the performance of the directional choice task quickly became stereotyped during the first 2-3 days or sessions. But learning the directional choice problem took weeks to occur. Accompanying rats’ behavioral performance adaptation, we observed neural modulation by directional choice in recorded single units. Our analysis shows that ensemble mean firing rates in the cue-on period did not change significantly as learning progressed, and the ensemble mean rate difference between left and right side choices did not show a clear trend of change either. However, the spatiotemporal firing patterns of the neural ensemble exhibited improved discriminability between the two directional choices through learning. These results suggest a spatiotemporal neural coding scheme in a motor cortical neural ensemble that may be responsible for and contributing to learning the directional choice task.

  1. Seasonal patterns of tropical forest leaf area index and CO2 exchange

    Science.gov (United States)

    Doughty, Christopher E.; Goulden, Michael L.

    2008-03-01

    We used in situ and satellite measurements to investigate the seasonal patterns of leaf area index (LAI) and gross ecosystem CO2 exchange (GEE) by an evergreen tropical forest. The forest experienced a dry season from June through November. The rates of light-saturated CO2 uptake (GEE) were comparatively high from December through March and low from May through July. In situ measurements showed that LAI varied seasonally, with a minimum from May through September. Leaf production and leaf abscission were reduced from December through April. Leaf abscission increased in May, which reduced LAI. High rates of leaf abscission and production occurred from July through September associated with leaf turnover. Leaf abscission decreased abruptly in October, while production continued, which rapidly increased LAI. Leaf phenology was not directly correlated with changes in soil water. The seasonal cycle of in situ LAI differed markedly from the seasonal cycles of in situ normalized difference vegetation index (NDVI) and the Moderate Resolution Imaging Spectroradiometer (MODIS) MOD15 LAI product. We hypothesize that the NDVI and MOD15 seasonality at the site is driven partly by seasonal changes in leaf age and leaf reflectance. We developed three simple models to investigate the causes of GEE seasonality. The first two models showed that the seasonal changes in LAI alone, and the effects of leaf age on leaf-level photosynthesis alone, could not account for the observed GEE seasonality. The third model showed that the combined effect of seasonal changes in LAI and seasonal changes in leaf age and leaf photosynthesis was sufficient to account for the observed GEE seasonality.

  2. An LRR-only protein representing a new type of pattern recognition receptor in Chlamys farreri.

    Science.gov (United States)

    Wang, Mengqiang; Wang, Lingling; Guo, Ying; Yi, Qilin; Song, Linsheng

    2016-01-01

    Accumulating evidence has demonstrated that leucine-rich repeat (LRR)-only proteins could mediate protein-ligand and protein-protein interactions and were involved in the immune response. In the present study, an LRR-only protein (designed as CfLRRop-1) was cloned from Zhikong scallop Chlamys farreri. The complete cDNA sequence of CfLRRop-1 contained an open reading frame (ORF) of 1377 bp, which encoded a protein of 458 amino acids. An LRRNT motif, an LRR_7 motif and seven LRR motifs were found in the deduced amino acid sequence of CfLRRop-1. And these seven LRR motifs contained a conserved signature sequence LxxLxLxxNxL. The mRNA transcripts of CfLRRop-1 were constitutively expressed in all the tested tissues, including haemocytes, muscle, mantle, gill, hepatopancreas and gonad, with the highest expression level in hepatopancreas. After the stimulation of lipopolysaccharide (LPS), peptidoglycan (PGN), glucan (GLU) and polyinosinic-polycytidylic acid (poly I:C), the mRNA transcripts of CfLRRop-1 in haemocytes all increased firstly within the first 6 h and secondly during 12-24 h post stimulation. The mRNA expression level of CfLRRop-1 was continuously up-regulated, after the expression of CfTLR (previously identified Toll-like receptor in C. farreri) was suppressed via RNA interference (RNAi). The recombinant CfLRRop-1 protein could directly bind LPS, PGN, GLU and poly I:C, and induce the release of TNF-α in mixed primary cultured scallop haemocytes. These results collectively indicated that CfLRRop-1 would function as a powerful pattern recognition receptor (PRR) and play a pivotal role in the immune response of scallops.

  3. Developmentally regulated epitopes of cell surface arabinogalactan proteins and their relation to root tissue pattern formation.

    Science.gov (United States)

    Knox, J P; Linstead, P J; Peart, J; Cooper, C; Roberts, K

    1991-11-01

    Two polymorphic forms of an extracellular arabinogalactan protein (AGP1 and AGP2), obtained from the conditioned media of two carrot suspension-cultured cell lines, have been identified in terms of binding of the anti-plasma membrane antibodies JIM4 and MAC207. AGP1 and AGP2 have been used as immunogens to generate further anti-AGP monoclonal antibodies. JIM14 identified an epitope carried by AGP2 and also by glycoproteins of low molecular weight localized to the plant cell wall. In addition, further antibodies (JIM13 and JIM15) identified carbohydrate epitopes of the AGPs that also occur on plasma membrane glycoproteins and are expressed by patterns of cells that reflect cell position at the carrot root apex. Indirect immunofluorescence microscopy indicated that JIM13 recognized the surface of cells forming the epidermis and cells marking the region and axis of the future xylem. JIM15 recognized a pattern of cells directly complementary to the JIM13 pattern. The panel of anti-AGP monoclonal antibodies now available indicates groups of cells within the root meristem that may reflect an early pre-pattern of the tissues of the mature root structure and suggests extensive modulation of cell surface AGPs during cell development and the positioning of cells within the apex.

  4. Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves.

    Science.gov (United States)

    Guo, Feng; Zhou, Weijie; Li, Peng; Mao, Zhangming; Yennawar, Neela H; French, Jarrod B; Huang, Tony Jun

    2015-06-01

    Advances in modern X-ray sources and detector technology have made it possible for crystallographers to collect usable data on crystals of only a few micrometers or less in size. Despite these developments, sample handling techniques have significantly lagged behind and often prevent the full realization of current beamline capabilities. In order to address this shortcoming, a surface acoustic wave-based method for manipulating and patterning crystals is developed. This method, which does not damage the fragile protein crystals, can precisely manipulate and pattern micrometer and submicrometer-sized crystals for data collection and screening. The technique is robust, inexpensive, and easy to implement. This method not only promises to significantly increase efficiency and throughput of both conventional and serial crystallography experiments, but will also make it possible to collect data on samples that were previously intractable.

  5. Light at night alters daily patterns of cortisol and clock proteins in female Siberian hamsters.

    Science.gov (United States)

    Bedrosian, T A; Galan, A; Vaughn, C A; Weil, Z M; Nelson, R J

    2013-06-01

    Humans and other organisms have adapted to a 24-h solar cycle in response to life on Earth. The rotation of the planet on its axis and its revolution around the sun cause predictable daily and seasonal patterns in day length. To successfully anticipate and adapt to these patterns in the environment, a variety of biological processes oscillate with a daily rhythm of approximately 24 h in length. These rhythms arise from hierarchally-coupled cellular clocks generated by positive and negative transcription factors of core circadian clock gene expression. From these endogenous cellular clocks, overt rhythms in activity and patterns in hormone secretion and other homeostatic processes emerge. These circadian rhythms in physiology and behaviour can be organised by a variety of cues, although they are most potently entrained by light. In recent history, there has been a major change from naturally-occurring light cycles set by the sun, to artificial and sometimes erratic light cycles determined by the use of electric lighting. Virtually every individual living in an industrialised country experiences light at night (LAN) but, despite its prevalence, the biological effects of such unnatural lighting have not been fully considered. Using female Siberian hamsters (Phodopus sungorus), we investigated the effects of chronic nightly exposure to dim light on daily rhythms in locomotor activity, serum cortisol concentrations and brain expression of circadian clock proteins (i.e. PER1, PER2, BMAL1). Although locomotor activity remained entrained to the light cycle, the diurnal fluctuation of cortisol concentrations was blunted and the expression patterns of clock proteins in the suprachiasmatic nucleus and hippocampus were altered. These results demonstrate that chronic exposure to dim LAN can dramatically affect fundamental cellular function and emergent physiology.

  6. Distinct protein domains and expression patterns confer divergent axon guidance functions for Drosophila Robo receptors.

    Science.gov (United States)

    Spitzweck, Bettina; Brankatschk, Marko; Dickson, Barry J

    2010-02-05

    The orthogonal array of axon pathways in the Drosophila CNS is constructed in part under the control of three Robo family axon guidance receptors: Robo1, Robo2 and Robo3. Each of these receptors is responsible for a distinct set of guidance decisions. To determine the molecular basis for these functional specializations, we used homologous recombination to create a series of 9 "robo swap" alleles: expressing each of the three Robo receptors from each of the three robo loci. We demonstrate that the lateral positioning of longitudinal axon pathways relies primarily on differences in gene regulation, not distinct combinations of Robo proteins as previously thought. In contrast, specific features of the Robo1 and Robo2 proteins contribute to their distinct functions in commissure formation. These specializations allow Robo1 to prevent crossing and Robo2 to promote crossing. These data demonstrate how diversification of expression and structure within a single family of guidance receptors can shape complex patterns of neuronal wiring.

  7. Landscape pattern and its restoration for coal mine subsidence area in southern part of Tangshan in China

    Institute of Scientific and Technical Information of China (English)

    CHEN Ying; ZHANG Tie-min; BIAN Lu-feng; BO Li-jie; CUI Jian-yu; HU Lin

    2009-01-01

    To investigate the ecosystem damage and environment pollution resulted from coal resources exploitation, based on remote sensing image, the landscape pattern was quantitatively analyzed with GIS and landscape pattern analysis software FRAGSTATS by utilizing multiform landscape pattern indexes, such as patch area,patch circumference, patch number, fractal dimension, fragmentation index, connectivity index and so on. Resuits indicate that the restored landscape type occupies the control status and accounts for the majority of the whole area, and needs to be further restored and adjusted because of its internal body with smaller patches,lower fractal dimension and better connectivity. The landscape type without restoration has destroyed the ecology and beauty of the whole landscape. In addition, some suggestive instructions for restoring various kinds of patches are put forward according to the quantitative analysis.

  8. Differential expression patterns of arabinogalactan proteins in Arabidopsis thaliana reproductive tissues

    Science.gov (United States)

    Pereira, Ana Marta; Masiero, Simona; Nobre, Margarida Sofia; Costa, Mário Luís; Solís, María-Teresa; Testillano, Pilar S.; Sprunck, Stefanie; Coimbra, Sílvia

    2014-01-01

    Arabinogalactan proteins (AGPs) are heavily glycosylated proteins existing in all members of the plant kingdom and are differentially distributed through distinctive developmental stages. Here, we showed the individual distributions of specific Arabidopsis AGPs: AGP1, AGP9, AGP12, AGP15, and AGP23, throughout reproductive tissues and indicated their possible roles in several reproductive processes. AGP genes specifically expressed in female tissues were identified using available microarray data. This selection was confirmed by promoter analysis using multiple green fluorescent protein fusions to a nuclear localization signal, β-glucuronidase fusions, and in situ hybridization as approaches to confirm the expression patterns of the AGPs. Promoter analysis allowed the detection of a specific and differential presence of these proteins along the pathway followed by the pollen tube during its journey to reach the egg and the central cell inside the embryo sac. AGP1 was expressed in the stigma, style, transmitting tract, and the chalazal and funiculus tissues of the ovules. AGP9 was present along the vasculature of the reproductive tissues and AGP12 was expressed in the stigmatic cells, chalazal and funiculus cells of the ovules, and in the septum. AGP15 was expressed in all pistil tissues, except in the transmitting tract, while AGP23 was specific to the pollen grain and pollen tube. The expression pattern of these AGPs provides new evidence for the detection of a subset of specific AGPs involved in plant reproductive processes, being of significance for this field of study. AGPs are prominent candidates for male–female communication during reproduction. PMID:25053647

  9. Sex hormones and expression pattern of cytoskeletal proteins in the rat brain throughout pregnancy.

    Science.gov (United States)

    González-Arenas, Aliesha; Piña-Medina, Ana Gabriela; González-Flores, Oscar; Galván-Rosas, Agustín; Porfirio Gómora-Arrati; Camacho-Arroyo, Ignacio

    2014-01-01

    Pregnancy involves diverse changes in brain function that implicate a re-organization in neuronal cytoskeleton. In this physiological state, the brain is in contact with several hormones that it has never been exposed, as well as with very high levels of hormones that the brain has been in touch throughout life. Among the latter hormones are progesterone and estradiol which regulate several brain functions, including learning, memory, neuroprotection, and the display of sexual and maternal behavior. These functions involve changes in the structure and organization of neurons and glial cells that require the participation of cytoskeletal proteins whose expression and activity is regulated by estradiol and progesterone. We have found that the expression pattern of Microtubule Associated Protein 2, Tau, and Glial Fibrillary Acidic Protein changes in a tissue-specific manner in the brain of the rat throughout gestation and the start of lactation, suggesting that these proteins participate in the plastic changes observed in the brain during pregnancy. This article is part of a Special Issue entitled 'Pregnancy and Steroids'.

  10. Aligning protein sequence and analysing substitution pattern using a class-specific matrix

    Indian Academy of Sciences (India)

    Hai Song Xu; Wen Ke Ren; Xiao Hui Liu; Xiao Qin Li

    2010-06-01

    Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in the ‘twilight zone’ remains an open issue. It is feasible and necessary to construct a new score matrix as more protein structures are resolved. Three structural class-specific score matrices (all-alpha, all-beta and alpha/beta) were constructed based on the structure alignment of low identity proteins of the corresponding structural classes. The class-specific score matrices were significantly better than a structure-derived matrix (HSDM) and three other generalized matrices (BLOSUM30, BLOSUM60 and Gonnet250) in alignment performance tests. The optimized gap penalties presented here also promote alignment performance. The results indicate that different protein classes have distinct amino acid substitution patterns, and an amino acid score matrix should be constructed based on different structural classes. The class-specific score matrices could also be used in profile construction to improve homology detection.

  11. Studying the expression patterns of OCT4 and SOX2 proteins in regenerating rabbit ear tissue

    Directory of Open Access Journals (Sweden)

    A. S. Javanmard

    2016-06-01

    Full Text Available Epimorphic regeneration in New Zealand rabbit ear is an interesting example of mammalian wound healing in which blastema formation is involved in replacement of injured tissues. It has been suggested that isolated cells from regenerating rabbit ear possess stem-like properties. In this study, we aimed to determine the expression of stemness markers, OCT4 and SOX2 proteins, in regenerating rabbit tissues by immunohistochemistry. Results indicated that both proteins could be detected in epithelial cells, hair follicle cells and perichondrium cells. Expression pattern analysis of OCT4 and SOX2 proteins showed no clear differences between regenerative and non-regenerative control tissues. According to several reports of OCT4 and SOX2 proteins expression in adult stem cells, it could be proposed that OCT4 and SOX2 expressing cells in regenerating rabbit ear tissues are progenitor/adult stem cells which are resident in these tissues, and other markers should be used for detection of blastema cells.

  12. Protein profiles of field isolates ofBacillus anthracis from different endemic areas of Indonesia

    Directory of Open Access Journals (Sweden)

    M Bhakti Poerwadikarta

    1998-03-01

    Full Text Available Sonicated cell-free extract proteins of 14 field isolates ofBacillus anthracis from six different endemic areas of Indonesia were analyzed by the use of sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE methods . The protein profiles of each field isolate tested demonstrated slightly different at the protein bands with molecular weights of 18, 37, 52, 65 and 70 kDa, and varied between the field isolates and vaccine strains. The variation could provide clues to the source of anthrax transmission whether it was originated from similar strain or not.

  13. Maintaining solvent accessible surface area under rotamer substitution for protein design.

    Science.gov (United States)

    Leaver-Fay, Andrew; Butterfoss, Glenn L; Snoeyink, Jack; Kuhlman, Brian

    2007-06-01

    Although quantities derived from solvent accessible surface areas (SASA) are useful in many applications in protein design and structural biology, the computational cost of accurate SASA calculation makes SASA-based scores difficult to integrate into commonly used protein design methodologies. We demonstrate a method for maintaining accurate SASA during a Monte Carlo search of sequence and rotamer space for a fixed protein backbone. We extend the fast Le Grand and Merz algorithm (Le Grand and Merz, J Comput Chem, 14, 349), which discretizes the solvent accessible surface for each atom by placing dots on a sphere and combines Boolean masks to determine which dots are exposed. By replacing semigroup operations with group operations (from Boolean logic to counting dot coverage) we support SASA updates. Our algorithm takes time proportional to the number of atoms affected by rotamer substitution, rather than the number of atoms in the protein. For design simulations with a one hundred residue protein our approach is approximately 145 times faster than performing a Le Grand and Merz SASA calculation from scratch following each rotamer substitution. To demonstrate practical effectiveness, we optimize a SASA-based measure of protein packing in the complete redesign of a large set of proteins and protein-protein interfaces.

  14. A pairwise residue contact area-based mean force potential for discrimination of native protein structure

    Directory of Open Access Journals (Sweden)

    Pezeshk Hamid

    2010-01-01

    Full Text Available Abstract Background Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed. Results We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets. Conclusions This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield

  15. Pattern of distribution and cycling of SLOB, Slowpoke channel binding protein, in Drosophila

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    Sheldon Amanda

    2004-01-01

    Full Text Available Abstract Background SLOB binds to and modulates the activity of the Drosophila Slowpoke (dSlo calcium activated potassium channel. Recent microarray analyses demonstrated circadian cycling of slob mRNA. Results We report the mRNA and protein expression pattern of slob in Drosophila heads. slob transcript is present in the photoreceptors, optic lobe, pars intercerebralis (PI neurons and surrounding brain cortex. SLOB protein exhibits a similar distribution pattern, and we show that it cycles in Drosophila heads, in photoreceptor cells and in neurosecretory cells of the PI. The cycling of SLOB is altered in various clock gene mutants, and SLOB is expressed in ectopic locations in tim01 flies. We also demonstrate that SLOB no longer cycles in the PI neurons of Clkjrk flies, and that SLOB expression is reduced in the PI neurons of flies that lack pigment dispersing factor (PDF, a neuropeptide secreted by clock cells. Conclusions These data are consistent with the idea that SLOB may participate in one or more circadian pathways in Drosophila.

  16. Discovering approximate-associated sequence patterns for protein-DNA interactions

    KAUST Repository

    Chan, Tak Ming

    2010-12-30

    Motivation: The bindings between transcription factors (TFs) and transcription factor binding sites (TFBSs) are fundamental protein-DNA interactions in transcriptional regulation. Extensive efforts have been made to better understand the protein-DNA interactions. Recent mining on exact TF-TFBS-associated sequence patterns (rules) has shown great potentials and achieved very promising results. However, exact rules cannot handle variations in real data, resulting in limited informative rules. In this article, we generalize the exact rules to approximate ones for both TFs and TFBSs, which are essential for biological variations. Results: A progressive approach is proposed to address the approximation to alleviate the computational requirements. Firstly, similar TFBSs are grouped from the available TF-TFBS data (TRANSFAC database). Secondly, approximate and highly conserved binding cores are discovered from TF sequences corresponding to each TFBS group. A customized algorithm is developed for the specific objective. We discover the approximate TF-TFBS rules by associating the grouped TFBS consensuses and TF cores. The rules discovered are evaluated by matching (verifying with) the actual protein-DNA binding pairs from Protein Data Bank (PDB) 3D structures. The approximate results exhibit many more verified rules and up to 300% better verification ratios than the exact ones. The customized algorithm achieves over 73% better verification ratios than traditional methods. Approximate rules (64-79%) are shown statistically significant. Detailed variation analysis and conservation verification on NCBI records demonstrate that the approximate rules reveal both the flexible and specific protein-DNA interactions accurately. The approximate TF-TFBS rules discovered show great generalized capability of exploring more informative binding rules. © The Author 2010. Published by Oxford University Press. All rights reserved.

  17. Notch-mediated post-translational control of Ngn3 protein stability regulates pancreatic patterning and cell fate commitment

    DEFF Research Database (Denmark)

    Qu, Xiaoling; Afelik, Solomon; Jensen, Jan Nygaard

    2013-01-01

    protein stabilization in the normal mouse pancreas explants. We conclude that the mutually exclusive expression pattern of Ngn3/Hes1 proteins in the mammalian pancreas is partially controlled through Notch-mediated post-translational regulation and we demonstrate that the formation of insulin...

  18. Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design

    Directory of Open Access Journals (Sweden)

    Bathelt Christine

    2008-03-01

    Full Text Available Abstract Background Protein structure prediction and computational protein design require efficient yet sufficiently accurate descriptions of aqueous solvent. We continue to evaluate the performance of the Coulomb/Accessible Surface Area (CASA implicit solvent model, in combination with the Charmm19 molecular mechanics force field. We test a set of model parameters optimized earlier, and we also carry out a new optimization in this work, using as a target a set of experimental stability changes for single point mutations of various proteins and peptides. The optimization procedure is general, and could be used with other force fields. The computation of stability changes requires a model for the unfolded state of the protein. In our approach, this state is represented by tripeptide structures of the sequence Ala-X-Ala for each amino acid type X. We followed an iterative optimization scheme which, at each cycle, optimizes the solvation parameters and a set of tripeptide structures for the unfolded state. This protocol uses a set of 140 experimental stability mutations and a large set of tripeptide conformations to find the best tripeptide structures and solvation parameters. Results Using the optimized parameters, we obtain a mean unsigned error of 2.28 kcal/mol for the stability mutations. The performance of the CASA model is assessed by two further applications: (i calculation of protein-ligand binding affinities and (ii computational protein design. For these two applications, the previous parameters and the ones optimized here give a similar performance. For ligand binding, we obtain reasonable agreement with a set of 55 experimental mutation data, with a mean unsigned error of 1.76 kcal/mol with the new parameters and 1.47 kcal/mol with the earlier ones. We show that the optimized CASA model is not inferior to the Generalized Born/Surface Area (GB/SA model for the prediction of these binding affinities. Likewise, the new parameters perform

  19. Proteome analysis of tobacco leaves reveals dynamic changes in protein expression among different cultivation areas.

    Science.gov (United States)

    Lu, L M; Ye, K Y; Tang, Z X; Liu, L; Chen, Y; Luo, J; Huang, Y B

    2015-11-30

    The leaves of tobacco plants were used to analyze differences in protein content of tobacco grown in the four main flue-cured tobacco-producing areas of Sichuan Province, China. An improved protein extraction method, isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis two-dimensional gel electrophoretic separation, was used to extract and separate total protein from tobacco leaves. Proteomic maps with relatively high resolution and repeatability were produced. At isoelectric points 4 to 7 and molecular weight ranging from 20-100 kDa, we detected 1032, 1030, 1019, and 1011 clearly visible protein spots in tobacco leaves from the four study areas. Proteome comparison between these protein spots showed that 119 spots with a greater than 2-fold change in expression quantity contributed to the variation in expression. Of which, 115 were successfully identified and annotated. According to the annotation results, these proteins participate in photosynthesis, energy metabolism, mineral nutrition, terpene metabolism, defensive reaction, and other physiological and biochemical processes. This study preliminarily explains the effects of ecological conditions on the physiological metabolism of tobacco leaves and how such effects directly or indirectly contribute to tobacco leaf quality.

  20. Expression Pattern Analysis of Zinc Finger Protein Genes in Wheat (Triticum aestivum L.) Under Phosphorus Deprivation

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-juan; GUO Cheng-jin; LU Wen-jing; DUAN Wei-wei; ZHAO Miao; MA Chun-ying; GU Jun-tao; XIAO Kai

    2014-01-01

    Zinc ifnger protein (ZFP) genes comprise a large and diverse gene family, and are involved in biotic and abiotic stress responses in plants. In this study, a total of 126 ZFP genes classiifed into various types in wheat were characterized and subjected to expression pattern analysis under inorganic phosphate (Pi) deprivation. The wheat ZFP genes and their corresponding GenBank numbers were obtained from the information of a 4×44K wheat gene expression microarray chip. They were conifrmed by sequence similarity analysis and named based on their homologs in Brachypodium distachyon or Oriza sativa. Expression analysis based on the microarray chip revealed that these ZFP genes are categorized into 11 classes according to their gene expression patterns in a 24-h of Pi deprivation regime. Among them, ten genes were differentially up-regulated, ten genes differentially down-regulated, and two genes both differentially up-and down-regulated by Pi deprivation. The differentially up-or down-regulated genes exhibited signiifcantly more or less transcripts at one, two, or all of the checking time points (1, 6, and 24 h) of Pi stress in comparison with those of normal growth, respectively. The both differentially up-and down-regulated genes exhibited contrasting expression patterns, of these, TaWRKY70;5 showed significantly up-regulated at 1 and 6 h and down-regulated at 24 h whereas TaAN1AN20-8;2 displayed signiifcantly upregulated at 1 h and downregulated at 6 h under deprivation Pi condition. Real time PCR analysis conifrmed the expression patterns of the differentially expressed genes obtained by the microarray chip. Our results indicate that numerous ZFP genes in wheat respond to Pi deprivation and have provided further insight into the molecular basis that plants respond to Pi deprivation mediated by the ZFP gene family.

  1. Conservation and divergence of plant LHP1 protein sequences and expression patterns in angiosperms and gymnosperms.

    Science.gov (United States)

    Guan, Hexin; Zheng, Zhengui; Grey, Paris H; Li, Yuhua; Oppenheimer, David G

    2011-05-01

    Floral transition is a critical and strictly regulated developmental process in plants. Mutations in Arabidopsis LIKE HETEROCHROMATIN PROTEIN 1 (AtLHP1)/TERMINAL FLOWER 2 (TFL2) result in early and terminal flowers. Little is known about the gene expression, function and evolution of plant LHP1 homologs, except for Arabidopsis LHP1. In this study, the conservation and divergence of plant LHP1 protein sequences was analyzed by sequence alignments and phylogeny. LHP1 expression patterns were compared among taxa that occupy pivotal phylogenetic positions. Several relatively conserved new motifs/regions were identified among LHP1 homologs. Phylogeny of plant LHP1 proteins agreed with established angiosperm relationships. In situ hybridization unveiled conserved expression of plant LHP1 in the axillary bud/tiller, vascular bundles, developing stamens, and carpels. Unlike AtLHP1, cucumber CsLHP1-2, sugarcane SoLHP1 and maize ZmLHP1, rice OsLHP1 is not expressed in the shoot apical meristem (SAM) and the OsLHP1 transcript level is consistently low in shoots. "Unequal crossover" might have contributed to the divergence in the N-terminal and hinge region lengths of LHP1 homologs. We propose an "insertion-deletion" model for soybean (Glycine max L.) GmLHP1s evolution. Plant LHP1 homologs are more conserved than previously expected, and may favor vegetative meristem identity and primordia formation. OsLHP1 may not function in rice SAM during floral induction.

  2. Zebrafish Thsd7a is a neural protein required for angiogenic patterning during development.

    Science.gov (United States)

    Wang, Chieh-Huei; Chen, I-Hui; Kuo, Meng-Wei; Su, Pei-Tsu; Lai, Zih-Yin; Wang, Chian-Huei; Huang, Wei-Chang; Hoffman, Jana; Kuo, Calvin J; You, May-Su; Chuang, Yung-Jen

    2011-06-01

    Angiogenesis is a highly organized process under the control of guidance cues that direct endothelial cell (EC) migration. Recently, many molecules that were initially described as regulators of neural guidance were subsequently shown to also direct EC migration. Here, we report a novel protein, thrombospondin type I domain containing 7A (Thsd7a), that is a neural molecule required for directed EC migration during embryonic angiogenesis in zebrafish. Thsd7a is a vertebrate conserved protein. Zebrafish thsd7a transcript was detected along the ventral edge of the neural tube in the developing zebrafish embryos, correlating with the growth path of angiogenic intersegmental vessels (ISVs). Morpholino-knockdown of Thsd7a caused a lateral deviation of angiogenic ECs below the thsd7a-expressing sites, resulting in aberrant ISV patterning. Collectively, our study shows that zebrafish Thsd7a is a neural protein required for ISV angiogenesis, and suggests an important role of Thsd7a in the neurovascular interaction during zebrafish development.

  3. Low Temperature Stress Induced Changes in Biochemical Parameters, Protein Banding Pattern and Expression of Zat12 and Myb Genes in Rice Seedling

    Directory of Open Access Journals (Sweden)

    Salma Perveen

    2013-11-01

    Full Text Available Low temperature stress is one of the main abiotic factors that reduce the productivity of many crops in hilly areas around the world. In this study, rice seedling were exposed to low temperature stress (control, 0°C, -2°C, -4°C and -6°C for 2 hr to observe its effect on two rice varieties (Basmati-385 and Shaheen Basmati through ion and proline contents, photosynthetic pigments, total protein content, protein banding pattern and expression of Zat12 and Myb genes. Resulted showed different patterns of accumulation of Na+ K+ and Ca+2 ions with the decrease in temperature in both varieties. Proline accumulation was gradually increased in both varieties with the decrease in temperature. Photosynthetic pigments (Chlorophyll (Chl a, b and carotene were negatively affected by low temperature stress in both varieties, however, carotene content was much affected than Chl a and b. Nonsignificant variation in protein contents was observed at all levels of low temperature, but the effects of low temperature stress on protein banding pattern of Basmti-385 and Shaheen Basmati were different at different treatments. RT-PCR results indicated that ZAT12 was upregulated by short term low temperature stress while OsMYB show slight upregulation at -2°C as compared to the other treatments. This study identified that ZAT12 and OsMYB function as a positive regulator to mediate tolerance of rice seedlings at low temperature stress.

  4. [FOOD CONSUMPTION PATTERN AT A FAMILY LEVEL OF URBAN AREAS OF ANZOÁTEGUI, VENEZUELA].

    Science.gov (United States)

    Ekmeiro Salvador, Jesús; Moreno Rojas, Rafael; García Lorenzo, María; Cámara Martos, Fernando

    2015-10-01

    In order to assess the qualitative pattern of food consumption in urban families of Anzoátegui, Venezuela, 300 domestic groups that combined a total of 1 163 people were studied. The domestic dietary pattern was addressed by the method of qualitative frequency of food consumption, which applied a structured survey that yielded the usual frequency of intake of a food or food group over a given period. The information was obtained through an interview with the person responsible for the procurement of food in every home, and included basic data for the socioeconomic and nutritional profile of the families studied. The qualitative analysis of the diet was obtained by comparing the different food groups that constitute the actual consumption pattern of the population studied, with official feeding guidelines suggested for the Venezuelan population. The present study showed that the qualitative pattern of food consumption in the urban population evaluated is characterized by slightly adjusted to the promotion of health and control of diet-related diseases. The family food proved to be far from the guidelines established by the dietary guidelines for Venezuela and consumption patterns are fairly homogeneous in the different socioeconomic strata. The foods most consumed daily were salt, coffee, dressing and precooked corn flour as well as beef, chicken and the higher weekly food consumption pastas. 90% of the food consumed daily is technologically processed. The results contribute to increase knowledge about the food situation of the Venezuelan population, and technically could direct the efforts of the authorities to reconcile the development of the productive sector and food supply, whereas a pattern qualitatively inadequate intake directly affects the individual biological functioning, and results in the collective conditioning of unfavorable health states.

  5. Nanostructured grating patterns over a large area fabricated by optically directed assembly

    Science.gov (United States)

    Huang, Xiaoping; Chen, Kai; Qi, Mingxi; Li, Yu; Hou, Yumeng; Wang, Ying; Zhao, Qing; Luo, Xiangang; Xu, Qingyu

    2016-07-01

    Optical trapping and manipulation of nanoparticles (NPs) have been widely used in nanotechnology and biology. Here, we demonstrate an optically directed assembly (ODA) route for bottom-up fabrication of stable nanostructured grating patterns in solution using laser standing evanescent wave (LSEW) fields. The control mechanism is the intriguing cooperative action of the periodically line-centered attractive optical gradient force and the near field dipolar coupling force induced by LSEW, which leads to assembly of the colloidal silver NPs into robust grating patterns within minutes. The anisotropic polarization nature of the grating patterns was studied further by examining the morphology correlation of the surface-enhanced Raman scattering (SERS)-based signal amplification. We show the LSEW ODA method can optimize and stabilize the strongest dipolar coupling style among the NPs during pattern assembly. These results advance the further understanding of ODA of colloid NPs and might have many potential applications in SERS, catalysis, nanophotonics and nano-fabrication.Optical trapping and manipulation of nanoparticles (NPs) have been widely used in nanotechnology and biology. Here, we demonstrate an optically directed assembly (ODA) route for bottom-up fabrication of stable nanostructured grating patterns in solution using laser standing evanescent wave (LSEW) fields. The control mechanism is the intriguing cooperative action of the periodically line-centered attractive optical gradient force and the near field dipolar coupling force induced by LSEW, which leads to assembly of the colloidal silver NPs into robust grating patterns within minutes. The anisotropic polarization nature of the grating patterns was studied further by examining the morphology correlation of the surface-enhanced Raman scattering (SERS)-based signal amplification. We show the LSEW ODA method can optimize and stabilize the strongest dipolar coupling style among the NPs during pattern assembly

  6. Two different immunostaining patterns of beta-amyloid precursor protein (APP) may distinguish traumatic from nontraumatic axonal injury.

    Science.gov (United States)

    Hayashi, Takahito; Ago, Kazutoshi; Nakamae, Takuma; Higo, Eri; Ogata, Mamoru

    2015-09-01

    Immunostaining for beta-amyloid precursor protein (APP) is recognized as an effective tool for detecting traumatic axonal injury, but it also detects axonal injury due to ischemic or other metabolic causes. Previously, we reported two different patterns of APP staining: labeled axons oriented along with white matter bundles (pattern 1) and labeled axons scattered irregularly (pattern 2) (Hayashi et al. (Leg Med (Tokyo) 11:S171-173, 2009). In this study, we investigated whether these two patterns are consistent with patterns of trauma and hypoxic brain damage, respectively. Sections of the corpus callosum from 44 cases of blunt head injury and equivalent control tissue were immunostained for APP. APP was detected in injured axons such as axonal bulbs and varicose axons in 24 of the 44 cases of head injuries that also survived for three or more hours after injury. In 21 of the 24 APP-positive cases, pattern 1 alone was observed in 14 cases, pattern 2 alone was not observed in any cases, and both patterns 1 and 2 were detected in 7 cases. APP-labeled injured axons were detected in 3 of the 44 control cases, all of which were pattern 2. These results suggest that pattern 1 indicates traumatic axonal injury, while pattern 2 results from hypoxic insult. These patterns may be useful to differentiate between traumatic and nontraumatic axonal injuries.

  7. Review of Distance Education Research (2000 to 2008): Analysis of Research Areas, Methods, and Authorship Patterns

    Science.gov (United States)

    Zawacki-Richter, Olaf; Backer, Eva Maria; Vogt, Sebastian

    2009-01-01

    This paper presents a review of distance education literature to describe the status thereof and to identify gaps and priority areas in distance education research based on a validated classification of research areas. The articles (N = 695) published in five prominent distance education journals between 2000 and 2008 were reviewed for this study.…

  8. Automated Learning of Subcellular Variation among Punctate Protein Patterns and a Generative Model of Their Relation to Microtubules.

    Directory of Open Access Journals (Sweden)

    Gregory R Johnson

    2015-12-01

    Full Text Available Characterizing the spatial distribution of proteins directly from microscopy images is a difficult problem with numerous applications in cell biology (e.g. identifying motor-related proteins and clinical research (e.g. identification of cancer biomarkers. Here we describe the design of a system that provides automated analysis of punctate protein patterns in microscope images, including quantification of their relationships to microtubules. We constructed the system using confocal immunofluorescence microscopy images from the Human Protein Atlas project for 11 punctate proteins in three cultured cell lines. These proteins have previously been characterized as being primarily located in punctate structures, but their images had all been annotated by visual examination as being simply "vesicular". We were able to show that these patterns could be distinguished from each other with high accuracy, and we were able to assign to one of these subclasses hundreds of proteins whose subcellular localization had not previously been well defined. In addition to providing these novel annotations, we built a generative approach to modeling of punctate distributions that captures the essential characteristics of the distinct patterns. Such models are expected to be valuable for representing and summarizing each pattern and for constructing systems biology simulations of cell behaviors.

  9. Ownership structure of protected areas influences the patterns of seed removal by mammals

    NARCIS (Netherlands)

    Martínez-Sánchez, J.L.; Kampichler, C.

    2011-01-01

    In Mexico, nature reserves vary greatly in the size of the property, administration, financial budget and measures to protect against land use change and illegal hunting. We compared two private and two public reserves and observed an influence between the ownership structure and the patterns of rem

  10. A Comparative Study on the Selected Area Electron Diffraction Pattern of Fe Oxide/Au Core-shell Structured Nanoparticles

    Institute of Scientific and Technical Information of China (English)

    Qianghua LU; Kailun YAO; Dong XI; Zuli LIU; Xiaoping LUO; Qin NING

    2007-01-01

    The selected area electron diffraction (SAED) pattern of magnetic iron oxide core/gold shell nanoparticles has been studied. For the composite particles with mean size less than 10 nm, their SAED pattern is found to be different from either the pattern of pure Fe oxide nanoparticles or that of pure Au particles. Based on the fact that the ring diameters of these composite particles fit the characteristic relation for the fcc structure, the Au atoms on surfaces of the concerned particles are supposed to pack in a way more tightly than they usually do in pure Au nanoparticles. The driving force for this is the coherency strain which enables the shell material at the heterostructured interface to adapt the lattice parameters of the core.

  11. Antigen sequence typing of outer membrane protein (fetA gene of Neisseria meningitidis serogroup A from Delhi & adjoining areas

    Directory of Open Access Journals (Sweden)

    S Dwivedi

    2014-01-01

    Full Text Available Background & objectives: Meningitis caused by Neisseria meningitidis is a fatal disease. Meningococcal meningitis is an endemic disease in Delhi and irregular pattern of outbreaks has been reported in India. All these outbreaks were associated with serogroup A. Detailed molecular characterization of N. meningitidis is required for the management of this fatal disease. In this study, we characterized antigenic diversity of surface exposed outer membrane protein (OMP FetA antigen of N. meningitidis serogroup A isolates obtained from cases of invasive meningococcal meningitis in Delhi, India. Methods: Eight isolates of N. meningitidis were collected from cerebrospinal fluid during October 2008 to May 2011 from occasional cases of meningococcal meningitis. Seven isolates were from outbreaks of meningococcal meningitis in 2005-2006 in Delhi and its adjoining areas. These were subjected to molecular typing of fetA gene, an outer membrane protein gene. Results: All 15 N. meningitides isolates studied were serogroup A. This surface exposed porin is putatively under immune pressure. Hence as a part of molecular characterization, genotyping was carried out to find out the diversity in outer membrane protein (FetA gene among the circulating isolates of N. meningitidis. All 15 isolates proved to be of the same existing allele type of FetA variable region (VR when matched with global database. The allele found was F3-1 for all the isolates. Interpretation & conclusions: There was no diversity reported in the outer membrane protein FetA in the present study and hence this protein appeared to be a stable molecule. More studies on molecular characterization of FetA antigen are required from different serogroups circulating in different parts of the world.

  12. Large-area alignment of tungsten oxide nanowires over flat and patterned substrates for room-temperature gas sensing.

    Science.gov (United States)

    Cheng, Wei; Ju, Yanrui; Payamyar, Payam; Primc, Darinka; Rao, Jingyi; Willa, Christoph; Koziej, Dorota; Niederberger, Markus

    2015-01-02

    Alignment of nanowires over a large area of flat and patterned substrates is a prerequisite to use their collective properties in devices such as gas sensors. In this work, uniform single-crystalline ultrathin W18 O49 nanowires with diameters less than 2 nm and aspect ratios larger than 100 have been synthesized, and, despite their flexibility, assembled into thin films with high orientational order over a macroscopic area by the Langmuir-Blodgett technique. Alignment of the tungsten oxide nanowires was also possible on top of sensor substrates equipped with electrodes. Such sensor devices were found to exhibit outstanding sensitivity to H2 at room temperature.

  13. Relative importance of habitat area and isolation for bird occurrence patterns in a naturally patchy landscape

    Science.gov (United States)

    Wilson, T.L.; Johnson, E.J.; Bissonette, J.A.

    2009-01-01

    There is debate among ecologists about whether total habitat area or patch arrangement contributes most to population and/or community responses to fragmented or patchy landscapes. We tested the relative effects of patch area and isolation for predicting bird occurrence in a naturally patchy landscape in the Bear River Mountains of Northern Utah, USA. We selected focal patches (mountain meadows) ranging in elevation from 1,920 to 2,860 m and in size from 0.6 to 182 ha. Breeding birds were sampled in each focal meadow during the summers of 2003 and 2004 using variable-distance point transects. Logistic regression and likelihood-based model selection were used to determine the relationship between likelihood of occurrence of three bird species (Brewer's sparrow, vesper sparrow, and white-crowned sparrow) and area, isolation, and proximity metrics. We used model weights and model-averaged confidence intervals to assess the importance of each predictor variable. Plots of area versus isolation were used to evaluate complex relationships between the variables. We found that meadow area was the most important variable for explaining occurrence for two species, and that isolation was the most important for the other. We also found that the absolute distance was more appropriate for evaluating isolation responses than was the species-specific proximity metric. Our findings add clarity to the debate between ecologists regarding the relative importance of area and isolation in species responses to patchy landscapes.

  14. Spatial patterns of large natural fires in Sierra Nevada wilderness areas

    Science.gov (United States)

    Collins, B.M.; Kelly, M.; van Wagtendonk, J.W.; Stephens, S.L.

    2007-01-01

    The effects of fire on vegetation vary based on the properties and amount of existing biomass (or fuel) in a forest stand, weather conditions, and topography. Identifying controls over the spatial patterning of fire-induced vegetation change, or fire severity, is critical in understanding fire as a landscape scale process. We use gridded estimates of fire severity, derived from Landsat ETM+ imagery, to identify the biotic and abiotic factors contributing to the observed spatial patterns of fire severity in two large natural fires. Regression tree analysis indicates the importance of weather, topography, and vegetation variables in explaining fire severity patterns between the two fires. Relative humidity explained the highest proportion of total sum of squares throughout the Hoover fire (Yosemite National Park, 2001). The lowest fire severity corresponded with increased relative humidity. For the Williams fire (Sequoia/Kings Canyon National Parks, 2003) dominant vegetation type explains the highest proportion of sum of squares. Dominant vegetation was also important in determining fire severity throughout the Hoover fire. In both fires, forest stands that were dominated by lodgepole pine (Pinus contorta) burned at highest severity, while red fir (Abies magnifica) stands corresponded with the lowest fire severities. There was evidence in both fires that lower wind speed corresponded with higher fire severity, although the highest fire severity in the Williams fire occurred during increased wind speed. Additionally, in the vegetation types that were associated with lower severity, burn severity was lowest when the time since last fire was fewer than 11 and 17 years for the Williams and Hoover fires, respectively. Based on the factors and patterns identified, managers can anticipate the effects of management ignited and naturally ignited fires at the forest stand and the landscape levels. ?? 2007 Springer Science+Business Media, Inc.

  15. Spinal cord injury markedly altered protein expression patterns in the affected rat urinary bladder during healing stages.

    Science.gov (United States)

    Lee, Ji-Young; Kim, Bong Jo; Sim, Gyujin; Kim, Gyu-Tae; Kang, Dawon; Jung, Jae Hun; Hwa, Jeong Seok; Kwak, Yeon Ju; Choi, Yeon Jin; Park, Young Sook; Han, Jaehee; Lee, Cheol Soon; Kang, Kee Ryeon

    2011-06-01

    The influence of spinal cord injury (SCI) on protein expression in the rat urinary bladder was assessed by proteomic analysis at different time intervals post-injury. After contusion SCI between T9 and T10, bladder tissues were processed by 2-DE and MALDI-TOF/MS at 6 hr to 28 days after SCI to identify proteins involved in the healing process of SCI-induced neurogenic bladder. Approximately 1,000 spots from the bladder of SCI and sham groups were visualized and identified. At one day after SCI, the expression levels of three protein were increased, and seven spots were down-regulated, including heat shock protein 27 (Hsp27) and heat shock protein 20 (Hsp20). Fifteen spots such as S100-A11 were differentially expressed seven days post-injury, and seven proteins including transgelin had altered expression patterns 28 days after injury. Of the proteins with altered expression levels, transgelin, S100-A11, Hsp27 and Hsp20 were continuously and variably expressed throughout the entire post-SCI recovery of the bladder. The identified proteins at each time point belong to eight functional categories. The altered expression patterns identified by 2-DE of transgelin and S100-A11 were verified by Western blot. Transgelin and protein S100-A11 may be candidates for protein biomarkers in the bladder healing process after SCI.

  16. Stem fasciation in cacti and succulent species--tissue anatomy, protein pattern and RAPD polymorphisms.

    Science.gov (United States)

    El-Banna, A N; El-Nady, M F; Dewir, Y H; El-Mahrouk, M E

    2013-09-01

    Fasciated and normal stem segments of Opuntia microdasys, Opuntia cylindrica, Huernia primulina and Euphorbia lactea were collected from the same plant and compared for their anatomy, water relations and genetic variations. Anatomical differences in terms of thickness of cuticle, vascular bundle, xylem and phloem were analyzed in both normal and fasciated stems. The mucilage cells were higher in the fasciated form of Opuntia microdasys than that in the normal form. Water status in terms of total water content (TWC), water deficit and relative water content (RWC) was influenced by fasciation. Genetic variations were tested in normal and fasciated stems using randomly amplified polymorphic DNA (RAPD) fingerprints and SDS-PAGE of soluble protein extracts. SDS-PAGE protein and RAPD analysis confirmed that normal and fasciated tissues were genetically different. Polymerase chain reaction (PCR) yielded different polymorphic banding patterns that were unique to each primer and distinguishable over all samples. The PCR results of normal and fasciated samples were significantly different in cases of primers P1, P2 and P3. These results indicate that occurrence of fasciation in Opuntia microdasys, Opuntia cylindrica, Huernia primulina and Euphorbia lactea is an epigenetic mutation of tissues.

  17. Using phylogenomic patterns and gene ontology to identify proteins of importance in plant evolution.

    Science.gov (United States)

    Cibrián-Jaramillo, Angélica; De la Torre-Bárcena, Jose E; Lee, Ernest K; Katari, Manpreet S; Little, Damon P; Stevenson, Dennis W; Martienssen, Rob; Coruzzi, Gloria M; DeSalle, Rob

    2010-07-12

    We use measures of congruence on a combined expressed sequenced tag genome phylogeny to identify proteins that have potential significance in the evolution of seed plants. Relevant proteins are identified based on the direction of partitioned branch and hidden support on the hypothesis obtained on a 16-species tree, constructed from 2,557 concatenated orthologous genes. We provide a general method for detecting genes or groups of genes that may be under selection in directions that are in agreement with the phylogenetic pattern. Gene partitioning methods and estimates of the degree and direction of support of individual gene partitions to the overall data set are used. Using this approach, we correlate positive branch support of specific genes for key branches in the seed plant phylogeny. In addition to basic metabolic functions, such as photosynthesis or hormones, genes involved in posttranscriptional regulation by small RNAs were significantly overrepresented in key nodes of the phylogeny of seed plants. Two genes in our matrix are of critical importance as they are involved in RNA-dependent regulation, essential during embryo and leaf development. These are Argonaute and the RNA-dependent RNA polymerase 6 found to be overrepresented in the angiosperm clade. We use these genes as examples of our phylogenomics approach and show that identifying partitions or genes in this way provides a platform to explain some of the more interesting organismal differences among species, and in particular, in the evolution of plants.

  18. Patterns of Lynx Predation at the Interface between Protected Areas and Multi-Use Landscapes in Central Europe.

    Directory of Open Access Journals (Sweden)

    Elisa Belotti

    Full Text Available In Central Europe, protected areas are too small to ensure survival of populations of large carnivores. In the surrounding areas, these species are often persecuted due to competition with game hunters. Therefore, understanding how predation intensity varies spatio-temporally across areas with different levels of protection is fundamental. We investigated the predation patterns of Eurasian lynx (Lynx lynx on roe deer (Capreolus capreolus and red deer (Cervus elaphus in both protected areas and multi-use landscapes of the Bohemian Forest Ecosystem. Based on 359 roe and red deer killed by 10 GPS-collared lynx, we calculated the species-specific annual kill rates and tested for effects of season and lynx age, sex and reproductive status. Because roe and red deer in the study area concentrate in unprotected lowlands during winter, we modeled spatial distribution of kills separately for summer and winter and calculated-the probability of a deer killed by lynx and-the expected number of kills for areas with different levels of protection. Significantly more roe deer (46.05-74.71/year/individual lynx were killed than red deer (1.57-9.63/year/individual lynx, more deer were killed in winter than in summer, and lynx family groups had higher annual kill rates than adult male, single adult female and subadult female lynx. In winter the probability of a deer killed and the expected number of kills were higher outside the most protected part of the study area than inside; in summer, this probability did not differ between areas, and the expected number of kills was slightly larger inside than outside the most protected part of the study area. This indicates that the intensity of lynx predation in the unprotected part of the Bohemian Forest Ecosystem increases in winter, thus mitigation of conflicts in these areas should be included as a priority in the lynx conservation strategy.

  19. Multiplex protein pattern unmixing using a non-linear variable-weighted support vector machine as optimized by a particle swarm optimization algorithm.

    Science.gov (United States)

    Yang, Qin; Zou, Hong-Yan; Zhang, Yan; Tang, Li-Juan; Shen, Guo-Li; Jiang, Jian-Hui; Yu, Ru-Qin

    2016-01-15

    Most of the proteins locate more than one organelle in a cell. Unmixing the localization patterns of proteins is critical for understanding the protein functions and other vital cellular processes. Herein, non-linear machine learning technique is proposed for the first time upon protein pattern unmixing. Variable-weighted support vector machine (VW-SVM) is a demonstrated robust modeling technique with flexible and rational variable selection. As optimized by a global stochastic optimization technique, particle swarm optimization (PSO) algorithm, it makes VW-SVM to be an adaptive parameter-free method for automated unmixing of protein subcellular patterns. Results obtained by pattern unmixing of a set of fluorescence microscope images of cells indicate VW-SVM as optimized by PSO is able to extract useful pattern features by optimally rescaling each variable for non-linear SVM modeling, consequently leading to improved performances in multiplex protein pattern unmixing compared with conventional SVM and other exiting pattern unmixing methods.

  20. Direct detection of x-rays for protein crystallography employing a thick, large area CCD

    Science.gov (United States)

    Atac, Muzaffer; McKay, Timothy

    1999-01-01

    An apparatus and method for directly determining the crystalline structure of a protein crystal. The crystal is irradiated by a finely collimated x-ray beam. The interaction of the x-ray beam with the crystal produces scattered x-rays. These scattered x-rays are detected by means of a large area, thick CCD which is capable of measuring a significant number of scattered x-rays which impact its surface. The CCD is capable of detecting the position of impact of the scattered x-ray on the surface of the CCD and the quantity of scattered x-rays which impact the same cell or pixel. This data is then processed in real-time and the processed data is outputted to produce a image of the structure of the crystal. If this crystal is a protein the molecular structure of the protein can be determined from the data received.

  1. Complement activating soluble pattern recognition molecules with collagen-like regions, mannan-binding lectin, ficolins and associated proteins

    DEFF Research Database (Denmark)

    Thiel, Steffen

    2007-01-01

    Mannan-binding lectin (MBL), L-ficolin, M-ficolin and H-ficolin are all complement activating soluble pattern recognition molecules with recognition domains linked to collagen-like regions. All four may form complexes with four structurally related proteins, the three MBL-associated serine...... proteases (MASPs), MASP-1, MASP-2 and MASP-3, and a smaller MBL-associated protein (MAp19). The four recognition molecules recognize patterns of carbohydrate or acetyl-group containing ligands. After binding to the relevant targets all four are able to activate the complement system. We thus have a system...... where four different and/or overlapping patterns of microbial origin or patterns of altered-self may be recognized, but in all cases the signalling molecules, the MASPs, are shared. MASP-1 and MASP-3 are formed from one gene, MASP1/3, by alternative splicing generating two different mRNAs from a single...

  2. [Feeding pattern of Triatoma rubrovaria (Blanchard, 1843) (Hemiptera, Triatominae) in peridomiciliary habitats, of a rural area of Uruguay].

    Science.gov (United States)

    Salvatella, R; Calegari, L; Puime, A; Basmadjian, Y; Rosa, R; Guerrero, J; Martinez, M; Mendaro, G; Briano, D; Montero, C

    1994-01-01

    It has been studied the feeding patterns of Triatoma rubrovaria (wild triatominae bug, and intradomiciliary secondary vector of T. cruzi) in a rural area of "La Bolsa" (Department of Artigas). Agar double diffusion test were used for analyze the blood meal, from 120 insects, which were confronted to 13 antisera. It has 251 identify blood meals, and the most frequently was mammalian host (73%), but it has a variable source of feeding (mammals, birds, reptiles and cockroach), including humans rate 8% of the total. The identify of haemolimphe as feed, place this triatominae bug as an intermediary vector between predator and haematophagous. The most usual mammals are dasypodides and bovines. The frequence of human blood meal near the dwellings, shows its potentiality as vectors. Therefore, the peridomicile is an area of interaction between, domestic, wild and sinantropic host. The trypanosomic infection's rate at peridomiciles was lesser those at wild areas.

  3. Annual Rainfall and Seasonality Predict Pan-tropical Patterns of Liana Density and Basal Area

    NARCIS (Netherlands)

    DeWalt, S.J.; Schnitzer, S.A.; Chave, J.; Bongers, F.; Cai, Z.Q.; Ewango, C.E.N.; Parren, M.P.E.

    2010-01-01

    We test the hypotheses proposed by Gentry and Schnitzer that liana density and basal area in tropical forests vary negatively with mean annual precipitation (MAP) and positively with seasonality. Previous studies correlating liana abundance with these climatic variables have produced conflicting res

  4. Patterns, rates and possible causes of saltmarsh erosion in the Greater Thames area (UK)

    NARCIS (Netherlands)

    Van der Wal, D.; Pye, K.

    2004-01-01

    The estuary-dominated coast of the Greater Thames in England has experienced rapid lateral erosion and internal dissection of saltmarshes. This paper provides an overview of saltmarsh development in this area, and re-examines the role of environmental and human forcing factors. It draws on documenta

  5. A Study on Energy Consumption Pattern in Developing Areas of Western Himalayan State

    Directory of Open Access Journals (Sweden)

    Lalit Kumar

    2015-12-01

    Full Text Available A study was carried out on energy consumption and carbon emission in growth oriented Dharmpur block of Solan district of Himachal Pradesh. The energy consumption pattern revealed that fuelwood consumption contributed highest (80.43% proportion of total energy mix followed by electricity (11.55%, kerosene (2.87%, dung cake (2.79%, LPG (2.31% and diesel (0.08%. The daily energy consumption pattern in kg of coal equivalent for fuelwood, electricity, kerosene, dung cake, LPG and diesel was worked to be as 10.09, 1.45, 0.36, 0.35, 0.29 and 0.01, respectively. The per capita annual energy consumption of electricity was estimated to be 160 kWh, kerosene (1.29 liters, dung cake (0.07 tonnes and fuelwood (0.76 tonnes. Annual CO2 emission from households in Dharmpur block was estimated as 86,603 tonnes out of which 74,275 tonnes (80.64% was emitted from the fuelwood consumption only. The annual per capita energy consumption from all sources for Dharmpur block was estimated to be 12.5 tonnes of coal equivalent. The per capita CO2 emission from different energy sources in Dharmpur block was 1.1 tonnes.

  6. Antimicrobial susceptibility pattern of Staphylococcus aureus isolated from clinical specimens in Northern area of Jordan

    Directory of Open Access Journals (Sweden)

    Mazhar Salim Al Zoubi

    2015-12-01

    Full Text Available Background and Objectives: The global spread of methicillin resistant Staphylococcus aureus (MRSA constitutes one of the most serious contemporary challenges to the treatment of hospital-acquired infections. We aimed to screen and assess the antibiotic susceptibility pattern of Staphylococcus aureus isolated from clinical specimens in local hospitals of Northern province in Jordan.Materials and Methods: Staphylococcus aureus was isolated and identified using standard methods from various clinical specimens of different infected body sites from 358 patients during the period from January 2005 to November 2008.Results: Our analysis showed that 31.6% of S. aureus infections were MRSA, while 31% were multidrug resistance (MDR and 42.7% were Oxacillin-resistant (ORSA. Most of these strains were isolated from wound specimens. All isolates were susceptible to vancomycin (100%. They were also susceptible to chloramphenicol, linezolid, nitrofurantoin, rifampicin and teicoplanin (>80%, but showed resistance to erythromycin and penicillin.Conclusion: Vancomycin was the most effective antimicrobial agent against S. aureus. We recommend regular surveillance of hospital associated infections and monitoring antibiotic sensitivity pattern and strict drug policy for antibiotics used within and outside the hospital environments. Keywords: Staphylococcus aureus, MRSA, MDR

  7. Sound production patterns from humpback whales in a high latitude foraging area

    Science.gov (United States)

    Stimpert, Alison K.; Wiley, David N.; Barton, Kira L.; Johnson, Mark P.; Lammers, Marc O.; Au, Whitlow W. L.

    2005-09-01

    Numerous studies have been conducted on humpback whale song, but substantially fewer have focused on the acoustic properties of non-song sound production (i.e., feeding and social sounds). Non-invasive digital acoustic recording tags (DTAGS) were attached to humpback whales on the western North Atlantics Great South Channel feeding grounds during July 2004. Acoustic records totaling 48.4 data hours from four of these attachments were aurally analyzed for temporal trends in whale signal production. A custom automatic detection function was also used to identify occurrences of specific signals and evaluate their temporal consistency. Patterns in sound usage varied by stage of foraging dive and by time of day. Amount of time with signals present was greater at the bottom of dives than during surface periods, indicating that sounds are probably related to foraging at depth. For the two tags that recorded at night, signals were present during a greater proportion of daylight hours than night hours. These results will be compared with previously published trends describing diel patterns in male humpback whale song chorusing on the breeding grounds. Data from the continuation of this research during the summer of 2005 will also be included.

  8. Colonization pattern of the biocontrol strain Pseudomonas chlororaphis MA 342 on barley seeds visualized by using green fluorescent protein.

    Science.gov (United States)

    Tombolini, R; van der Gaag, D J; Gerhardson, B; Jansson, J K

    1999-08-01

    Pseudomonas chlororaphis MA 342 is a potent biocontrol agent that can be used against several seed-borne diseases of cereal crops, including net blotch of barley caused by the fungus Drechslera teres. In this study, strain MA 342 was tagged with the gfp gene (encoding the green fluorescent protein) in order to study the fate of cells after seed inoculation. The gfp-tagged strain, MA 342G2, had the same biocontrol efficacy as the wild type when it was applied at high cell concentrations to seeds but was less effective at lower cell concentrations. By comparing cell counts determined by microscopy to the number of CFU, we found that the number of culturable cells was significantly lower than the total number of bacteria on seeds which were inoculated and dried for 20 h. Confocal microscopy and epifluorescence stereomicroscopy were used to determine the pattern of MA 342G2 colonization and cell aggregation on barley seeds. Immediately after inoculation of seeds, bacteria were found mainly under the seed glume, and there was no particular aggregation pattern. However, after the seeds were sown, irregularly distributed areas of bacterial aggregation were found, which reflected epiphytic colonization of glume cells. There was a trend towards bacterial aggregation near the embryo but never within the embryo. Bacterial aggregates were regularly found in the groove of each seed formed by the base of the coleoptile and the scutellum. Based on these results, we suggest that MA 342 colocalizes with the pathogen D. teres, which facilitates the action of the fungistatic compound(s) produced by this strain.

  9. Small ICBM Area Narrowing Report. Volume 3: Hard Silo in Patterned Array Basing Mode

    Science.gov (United States)

    1986-01-01

    mission. Existing peak electrical power usage is 50 percent below a maximum rated capacity of 12.5 MW. Heating is provided primarily by fuel oil, but the...ACTIVITY NAVY 5 FL JACKSONVILLE FUEL DEPOT NAVY 5 FL JACKSONVILLE NAVAL AIR STATION NAVY 5 FL KEY WEST NAVAL AIR STATION NAVY 4 FL MACDILL’ AIR FORCE BASE...Maximize Main Operating Base Effectiveness OBJECTIVE 2.3.4: Consider Transportation Availabilty LEVEL OF APPLICATION: B - Area Evaluative CRITERION

  10. MIGRATION PATTERNS, USE OF STOPOVER AREAS, AND AUSTRAL SUMMER MOVEMENTS OF SWAINSON’S HAWKS

    Science.gov (United States)

    Kochert, Michael N.; Fuller, Mark R.; Schueck, Linda S.; Bond, Laura; Bechard, Marc J.; Woodbridge, Brian; Holroyd, Geoff; Martell, Mark; Banasch, Ursula

    2015-01-01

    From 1995–1998, we tracked movements of adult Swainson’s Hawks (Buteo swainsoni) using satellite telemetry to characterize migration, important stopover areas, and austral summer movements. We tagged 46 hawks from July - September on their nesting grounds in seven U.S. states and two Canadian provinces. Swainson’s Hawks basically followed three routes south on a broad front, converged along the east coast of central Mexico, and followed a concentrated corridor to a communal austral summer area in central Argentina. North of 20° N, southward and northward tracks differed little for individuals from east of the Continental Divide but differed greatly (up to 1700 km) for individuals from west of the Continental Divide. Hawks left the breeding grounds mid-August to mid-October; departure dates did not differ by location, year, or sex. South migration lasted 42 to 98 days, and north migration took 51 to 82 days. On south migration, 36% of the Swainson’s Hawks departed the nesting grounds nearly 3 weeks earlier than the other radio marked hawks and made stopovers 9.0 – 26.0 days long in seven separate areas, mainly in the southern Great Plains, southern Arizona and New Mexico, and north-central Mexico. The austral period lasted 76 to 128 days. All Swainson’s Hawks used a core area in central Argentina within 23% of the 738800 km2 austral summer range where they frequently moved long distances (up to 1600 km). Conservation of Swainson’s Hawks must be an international effort that considers habitats used during nesting and non-nesting seasons including migration stopovers. PMID:26380528

  11. MIGRATION PATTERNS, USE OF STOPOVER AREAS, AND AUSTRAL SUMMER MOVEMENTS OF SWAINSON'S HAWKS.

    Science.gov (United States)

    Kochert, Michael N; Fuller, Mark R; Schueck, Linda S; Bond, Laura; Bechard, Marc J; Woodbridge, Brian; Holroyd, Geoff; Martell, Mark; Banasch, Ursula

    From 1995-1998, we tracked movements of adult Swainson's Hawks (Buteo swainsoni) using satellite telemetry to characterize migration, important stopover areas, and austral summer movements. We tagged 46 hawks from July - September on their nesting grounds in seven U.S. states and two Canadian provinces. Swainson's Hawks basically followed three routes south on a broad front, converged along the east coast of central Mexico, and followed a concentrated corridor to a communal austral summer area in central Argentina. North of 20° N, southward and northward tracks differed little for individuals from east of the Continental Divide but differed greatly (up to 1700 km) for individuals from west of the Continental Divide. Hawks left the breeding grounds mid-August to mid-October; departure dates did not differ by location, year, or sex. South migration lasted 42 to 98 days, and north migration took 51 to 82 days. On south migration, 36% of the Swainson's Hawks departed the nesting grounds nearly 3 weeks earlier than the other radio marked hawks and made stopovers 9.0 - 26.0 days long in seven separate areas, mainly in the southern Great Plains, southern Arizona and New Mexico, and north-central Mexico. The austral period lasted 76 to 128 days. All Swainson's Hawks used a core area in central Argentina within 23% of the 738800 km(2) austral summer range where they frequently moved long distances (up to 1600 km). Conservation of Swainson's Hawks must be an international effort that considers habitats used during nesting and non-nesting seasons including migration stopovers.

  12. Modeling of debris flow depositional patterns according to the catchments and sediment source areas characteristics

    Science.gov (United States)

    Tiranti, Davide; Deangeli, Chiara

    2015-03-01

    A method to predict the most probable flow rheology in Alpine debris flows is presented. The methods classifies outcropping rock masses in catchments on the basis of the type of resulting unconsolidated deposits. The grain size distribution of the debris material and the depositional style of past debris flow events are related to the dominant flow processes: viscoplastic and frictional/collisional. Three catchments in the upper Susa Valley (Western Alps), characterized by different lithologies, were selected for numerical analysis carried out with a Cellular Automata code with viscoplastic and frictional/collisional rheologies. The obtained numerical results are in good agreement with in site evidences in terms of depositional patterns, confirming the possibility of choosing the rheology of the debris flow based on the source material within the catchment.

  13. Laterally Stitched Heterostructures of Transition Metal Dichalcogenide: Chemical Vapor Deposition Growth on Lithographically Patterned Area

    KAUST Repository

    Li, Henan

    2016-10-31

    Two-dimensional transition metal dichalcogenides (TMDCs) have shown great promise in electronics and optoelectronics due to their unique electrical and optical properties. Heterostructured TMDC layers such as the laterally stitched TMDCs offer the advantages of better electronic contact and easier band offset tuning. Here, we demonstrate a photoresist-free focused ion beam (FIB) method to pattern as-grown TMDC monolayers by chemical vapor deposition, where the exposed edges from FIB etching serve as the seeds for growing a second TMDC material to form desired lateral heterostructures with arbitrary layouts. The proposed lithographic and growth processes offer better controllability for fabrication of the TMDC heterostrucuture, which enables the construction of devices based on heterostructural monolayers. © 2016 American Chemical Society.

  14. Investigation on Reflection of Tectonic Pattern in ASG EUPOS Data in the Sudetes and Adjacent Areas

    Directory of Open Access Journals (Sweden)

    Szczerbowski Zbigniew

    2016-12-01

    Full Text Available The GNSS data evaluated from on observation of ASG EUPOS stations in the Sudety Mts. and in adjacent areas is analyzed by the author in the scope of disturbances in daily solutions that can be induced by tectonics stress. The daily position changes derived from GNSS data demonstrate the long or short term trends, which are affected by offsets of different nature. Author presents an analysis based on frequency of parameter – displacement vector azimuth. The aim of the analysis is to show statistical significance of observed small values of temporal displacements, which values are not normally distributed. There are “outliers” of the normal distribution of displacement azimuths, which values show a certain reproducibility, which corresponds to orientations of tectonic lines. That suggests small, short time movements along boundaries of horsts and grabens – a crustal-extension structure of the area. However derived results (values of displacements are less than a limitation error, temporal distributions of coordinates are not random as usually data errors. So in author’s opinion the spatial-temporal evolution of horizontal displacements of ASG EUPOS stations in the Sudety Mts. and in adjacent areas are determined by expressions of underlying geological structures.

  15. Disease patterns in pediatric classical Hodgkin lymphoma: a report from a developing area in Brazil.

    Science.gov (United States)

    Barros, Mário Henrique M; Hassan, Rocio; Niedobitek, Gerald

    2011-12-01

    Epidemiological patterns established about 20 years ago, divided classical Hodgkin lymphoma (cHL) in three entities with regard to Epstein-Barr virus (EBV) status and histological subtypes and suggested different epidemiological patterns associated with degree of economic development. Here, we investigated histopathological features and EBV association in 100 consecutive pediatric cHL cases occurring in Rio de Janeiro (Brazil). Age at diagnosis ranged from 3 to 18 years (median 14 years) with 27% of cases ≤10 years. Unexpectedly, we did not observe an early childhood peak with most cases occurring in the >10 years age group. Nodular sclerosis (NS) was the most frequent subtype (69%) and was more frequently observed in the >10 years age group, followed by mixed cellularity (MC, 23%) which was distributed equally between age groups. EBV was identified in 44.8% of cases, without preferential association with age groups (≤10 years vs. >10 years). MC cases were independently associated with EBV infection of tumour cells (p = 0.045) and with a CD4/CD20 ratio <1 in the microenvironment (p = 0.014). Our results suggest that a gradual shift from childhood peak to early adulthood peak may be observed in developing regions. The development of MC subtype may result from early exposure to EBV in the context of an impaired immune system reflected by a CD4/CD20 ratio <1. Conversely, it is possible that NS originates predominantly in the context of a better immune response against EBV and/or tumour antigens expressed in the neoplastic cells.

  16. ASSESSMENT OF PATTERN OF ANTIMICROBIAL RESISTANCE OF HELICOBACTER PYLORI IN PATIENTS OF DYSPEPSIA OF RURAL AREA

    Directory of Open Access Journals (Sweden)

    Yogendra

    2015-08-01

    Full Text Available BACKGROUND : Helicobacter Pylori is a gastric pathogen that chronically infects more than half of the world's population. Unless treated, colonization usually persists lifelong. H. pylori infection represents a key factor in the etiology of various gastrointestinal diseases, ranging from chronic active gastritis without clinical symptoms to peptic ulceration, gastric adenocarcinoma, and gastric mucosa - associated lymphoid tissue lymphoma. Helicobacter pylori eradication rate varies in different parts of the world. This may be related to the regional difference in anti - microbial resistance that affects the outcome of therapy, genetic difference in the metabolism of the proton pump inhibitor, which can also alter the availability of anti - microbial in the stomach. The pattern of antimicrobial resistant of Helicobacter pylori has not been tested in this part of central India. In present study we have assessed the pattern of anti - microbial resistance of Helicobacter Pylori in patients of dyspepsia attending medicine opd , Department of Medicine, Dr. BRAM Hospital, Raipur (Chhattisgarh, India. METHODS: The present study was conducted in the Department of Medicine, Pt . J. N. M. Medical College, and Dr . BRAM Hospital Raipur (C.G. 60 patients attending medicine opd were subjected to upper gastrointestinal endoscopy. Multiple biopsy specimens taken from the gastric antrum. Rapid urease test were done. The biopsy specimen was inoculated in to culture media. The strains were subjected to antibiotic sensitivity test by disk diffusion method for metronidazole, tinidazole, Ornidazole, Clarithromycin, amoxicillin, tetracycline, furazolidone, ofloxacin and ciprofl oxacin. RESULT : The antibiotic resistance of H. Pylori in culture positive cases in our study showed 84.6%o of cases were resistant to Metronidazole, 38.5% to Tinidazole, 7.6%o to Ornidazole, 32.8% to Amoxicillin, 3.8% to Tetracycline, 19.2% to Clarithromycin, 11.5% to furazolidone, and 3

  17. Cooking Banana Consumption Patterns in the Plantain-growing Area of Southeastern Nigeria

    Directory of Open Access Journals (Sweden)

    Tshiunza, M.

    2001-01-01

    Full Text Available Cooking bananas (Musa spp., ABB genome were intro-duced into Southeastern Nigeria by the International Institute of Tropical Agriculture (IITA in the mid-1980s as an interim measure to reduce the incidence of black sigatoka disease (caused by the fungus Mycosphaerel-la fijiensis Morelet on plantain. However, the people of this region were not familiar with their utilisation methods. To address this lack of the knowledge and thereby sustain cooking banana cultivation, IITA, in collaboration with the Shell Petroleum Development Company (SPDC and the Nigeria Agip OU Company (NAOC commenced a training campaign on cooking banana processing methods. This study examined the patterns of utilisation of cooking bananas ten years after the training took place and compared them with plantain. About 95 % of the households interviewed are consuming cooking banana, indicating a broad acceptance of the crop in the region. Overall, two ripening stages termed green and ripe are the most popular ripening stages for the consumption of both plantain and cooking banana, followed by partially ripe maturity stage. The most common forms of consumption for green plantain are, in decreasing order of importance, pottage, boiled, roasted, and fried. Green cooking banana is also mostly eaten in pottage and boiled forms, and less frequently in fried and pounded forms. Ripe plantain is mostly eaten in fried and pottage forms, while ripe cooking banana is mostly eaten in fried and raw forms. Partially ripe plantain is mostly eaten in pottage, fried, boiled, and roasted forms, while partially ripe cooking banana is eaten in fried, pottage and boiled forms. These results indicate that the consumption patterns of plantain and cooking banana are very similar. This similarity has greatly contributed to the rapid integration of cooking banana within the existing plantain consumption and cropping systems.

  18. Distribution patterns and sources of metals and PAHs in an intensely urbanized area: The Acerra-Pomigliano-Marigliano conurbation (Italy)

    Science.gov (United States)

    Albanese, Stefano; Lima, Annamaria; Rezza, Carmela; Ferullo, Giampiero; De Vivo, Benedetto; Chen, Wei; Qi, Shihua

    2014-05-01

    The main objective of the URGE (URban GEochemistry) project is to define, map and interpretate the geochemical baseline patterns of potentially harmful elements and compounds in the soils of 12 european urban areas using shared procedures for both sampling and analytical techniques. In Italy, in the framework of the URGE project, the north-eastern sector of the Napoli metropolitan area, namely the Acerra-Pomigliano-Marigliano conurbation, has undergone a geochemical characterization based on 145 soil samples collected over an area of 90 sq km. This area has been selected on the basis of the results obtained from previous regional studies [1, 2, 3] and because of the presence on its territory of an historical industrial settlement (formerly devoted to plastic materials and synthetic fibres production) which was partly dismantled and party converted to a power plant fuelled by palm oil. Furthermore, in March 2009 also an incinerator came into operation in the northern sector of the study area. The main objective of the study carried out for the Acerra-Pomigliano-Marigliano conurbation was to define the local geochemical baselines for both 53 elements (among which the toxic ones) and some organic compounds, including PAHs and OCPs. The study also aimed at supporting epidemiological researches at local scale and at establishing a record of the actual environmental conditions to evaluate the future impact of the incinerator on both the territory and the public health. Results obtained showed that Pb, Zn and V exceed the trigger limits established by the Italian Environmental law (D.Lgs. 152/2006) especially in correspondence with the most densely populated areas of the conurbation and where the traffic load is higher (Road junctions and fast lanes). Furthermore, most of the soils collected in the surroundings of the urbanized areas resulted to be generally enriched in Cu, Co, Cd, Be, Ni and P suggesting the presence of a relevant influence on their chemistry of an

  19. Terminal sequence importance of de novo proteins from binary-patterned library: stable artificial proteins with 11- or 12-amino acid alphabet.

    Science.gov (United States)

    Okura, Hiromichi; Takahashi, Tsuyoshi; Mihara, Hisakazu

    2012-06-01

    Successful approaches of de novo protein design suggest a great potential to create novel structural folds and to understand natural rules of protein folding. For these purposes, smaller and simpler de novo proteins have been developed. Here, we constructed smaller proteins by removing the terminal sequences from stable de novo vTAJ proteins and compared stabilities between mutant and original proteins. vTAJ proteins were screened from an α3β3 binary-patterned library which was designed with polar/ nonpolar periodicities of α-helix and β-sheet. vTAJ proteins have the additional terminal sequences due to the method of constructing the genetically repeated library sequences. By removing the parts of the sequences, we successfully obtained the stable smaller de novo protein mutants with fewer amino acid alphabets than the originals. However, these mutants showed the differences on ANS binding properties and stabilities against denaturant and pH change. The terminal sequences, which were designed just as flexible linkers not as secondary structure units, sufficiently affected these physicochemical details. This study showed implications for adjusting protein stabilities by designing N- and C-terminal sequences.

  20. Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI) from the Class Arachnida.

    Science.gov (United States)

    Young, Monica R; Hebert, Paul D N

    2015-01-01

    Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI) from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625). It examines divergences at three taxonomic levels-among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10-0.39), while the mean of the Family Distances for the ten orders ranges fivefold (0.07-0.35). BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is 'locked down' in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in 'locked down' taxa.

  1. Patterns of Protein Evolution in Cytochrome c Oxidase 1 (COI from the Class Arachnida.

    Directory of Open Access Journals (Sweden)

    Monica R Young

    Full Text Available Because sequence information is now available for the 648bp barcode region of cytochrome c oxidase 1 (COI from more than 400,000 animal species, this gene segment can be used to probe patterns of mitochondrial evolution. The present study examines levels of amino acid substitution and the frequency of indels in COI from 4177 species of arachnids, including representatives from all 16 orders and 43% of its families (267/625. It examines divergences at three taxonomic levels-among members of each order to an outgroup, among families in each order and among BINs, a species proxy, in each family. Order Distances vary fourfold (0.10-0.39, while the mean of the Family Distances for the ten orders ranges fivefold (0.07-0.35. BIN Distances show great variation, ranging from 0.01 or less in 12 families to more than 0.25 in eight families. Patterns of amino acid substitution in COI are generally congruent with previously reported variation in nucleotide substitution rates in arachnids, but provide some new insights, such as clear rate acceleration in the Opiliones. By revealing a strong association between elevated rates of nucleotide and amino acid substitution, this study builds evidence for the selective importance of the rate variation among arachnid lineages. Moreover, it establishes that groups whose COI genes have elevated levels of amino acid substitution also regularly possess indels, a dramatic form of protein reconfiguration. Overall, this study suggests that the mitochondrial genome of some arachnid groups is dynamic with high rates of amino acid substitution and frequent indels, while it is 'locked down' in others. Dynamic genomes are most prevalent in arachnids with short generation times, but the possible impact of breeding system deserves investigation since many of the rapidly evolving lineages reproduce by haplodiploidy, a mode of reproduction absent in 'locked down' taxa.

  2. Spatio-temporal patterns and environmental controls of small pelagic fish body condition from contrasted Mediterranean areas

    Science.gov (United States)

    Brosset, Pablo; Fromentin, Jean-Marc; Van Beveren, Elisabeth; Lloret, Josep; Marques, Virginie; Basilone, Gualtiero; Bonanno, Angelo; Carpi, Piera; Donato, Fortunata; Čikeš Keč, Vanja; De Felice, Andrea; Ferreri, Rosalia; Gašparević, Denis; Giráldez, Ana; Gücü, Ali; Iglesias, Magdalena; Leonori, Iole; Palomera, Isabel; Somarakis, Stylianos; Tičina, Vjekoslav; Torres, Pedro; Ventero, Ana; Zorica, Barbara; Ménard, Frédéric; Saraux, Claire

    2017-02-01

    Small pelagic fish are among the most ecologically and economically important marine fish species and are characterized by large fluctuations all over the world. In the Mediterranean Sea, low catches and biomass of anchovies and sardines have been described in some areas during the last decade, resulting in important fisheries crises. Therefore, we studied anchovy and sardine body condition variability, a key index of population health and its response to environmental and anthropogenic changes. Wide temporal and spatial patterns were investigated by analyzing separately data from scientific surveys and fisheries in eight Mediterranean areas between 1975 and 2015. Results showed that anchovy and sardine body condition as well as maximum size in some areas sharply decreased in most Mediterranean areas along years (except in the Northern Alboran Sea). Despite this general pattern, well-marked environmental differences between sub-regions were highlighted by several analyses and variations in body condition were not found to be homogeneous over all the Mediterranean Sea. Further, other analyses revealed that except for the Adriatic where major changes towards a lower body condition were concomitant with a decrease in river runoffs and chl-a concentration, no concomitant environmental regime shift was detected in other areas. Together, these analyses highlighted the current poor body condition of almost all small pelagic fish populations in the Mediterranean. Yet, global environmental indices could not explain the observed changes and the general decrease in condition might more likely come from regional environmental and/or anthropogenic (fishing) effects. A prolonged state of poor fish body condition, together with an observed reduced size and early age-at-maturity may have strong ecological, economic and social consequences all around the Mediterranean Sea.

  3. Proline content and protein patterns in Eucalyptus grandis shoots submitted to high and low temperature shocks

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    Gustavo M. Souza

    2004-07-01

    Full Text Available Proline content and protein patterns changes in response to temperature shocks of both acclimated and non acclimated E. grandis shoots cultivated in vitro were investigated. Analysis of soluble proteins through SDS-PAGE and proline were carried out after 12h at 12ºC (cold acclimation or 33ºC (heat acclimation, and immediately after temperature shocks at 41ºC and 0ºC. Analyses were also performed 24h after the temperature shocks (recovery period. Temperature treatment at 0ºC did not change soluble protein patterns both in acclimatized and non acclimatized plants, whereas cold temperature induced high proline levels, which kept relatively high after recovery period. Three novel, probably HSPs, proteins (90.5, 75 and 39 kDa were observed in both acclimated and non acclimated plants submitted to high temperatures. Plants exposed at 41ºC were able to recover from heat shocks after 24h, whereas they did not recover completely from cold shocks. The effect of the acclimation period on the recovering (homeostasis varied depending on the parameter evaluated, and type and duration of the temperature shock.As respostas às mudanças de temperatura de plantas aclimatadas e não aclimatadas de E. grandis cultivadas in vitro foram avaliadas considerando alterações dos níveis de prolina e proteínas solúveis totais. Análises de proteínas solúveis através de SDS-PAGE e prolina foram realizadas após 12h a 12ºC (aclimatação ao frio ou a 33ºC (aclimatação ao calor, e imediatamente depois dos choques térmicos a 41ºC e 0ºC. Análises também foram realizadas após um período de 24h depois dos choques térmicos (período de recuperação. O tratamento de temperatura a 0ºC não alterou o padrão de proteínas nas plantas aclimatadas e não aclimatadas, entretanto a temperatura baixa induziu altos níveis de prolina, que se mantiveram relativamente altos após o período de recuperação. Três novas proteínas (90,5, 75 e 39 kDa, provavelmente

  4. Phenols content and 2-D electrophoresis protein pattern: a promising tool to monitor Posidonia meadows health state

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    Randazzo Davide

    2007-07-01

    Full Text Available Abstract Background The endemic seagrass Posidonia oceanica (L. Delile colonizes soft bottoms producing highly productive meadows that play a crucial role in coastal ecosystems dynamics. Human activities and natural events are responsible for a widespread meadows regression; to date the identification of "diagnostic" tools to monitor conservation status is a critical issue. In this study the feasibility of a novel tool to evaluate ecological impacts on Posidonia meadows has been tested. Quantification of a putative stress indicator, i.e. phenols content, has been coupled to 2-D electrophoretic protein analysis of rhizome samples. Results The overall expression pattern from Posidonia rhizome was determined using a preliminary proteomic approach, 437 protein spots were characterized by pI and molecular weight. We found that protein expression differs in samples belonging to sites with high or low phenols: 22 unique protein spots are peculiar of "low phenols" and 27 other spots characterize "high phenols" samples. Conclusion Posidonia showed phenols variations within the meadow, that probably reflect the heterogeneity of environmental pressures. In addition, comparison of the 2-D electrophoresis patterns allowed to highlight qualitative protein expression differences in response to these pressures. These differences may account for changes in metabolic/physiological pathways as adaptation to stress. A combined approach, based on phenols content determination and 2-D electrophoresis protein pattern, seems a promising tool to monitor Posidonia meadows health state.

  5. Multiligand Specificity of Pathogen-associated Molecular Pattern-binding Site in Peptidoglycan Recognition Protein*

    Science.gov (United States)

    Sharma, Pradeep; Dube, Divya; Sinha, Mau; Mishra, Biswajit; Dey, Sharmistha; Mal, Gorakh; Pathak, Krishan M. L.; Kaur, Punit; Sharma, Sujata; Singh, Tej P.

    2011-01-01

    The peptidoglycan recognition protein PGRP-S is an innate immunity molecule that specifically interacts with microbial peptidoglycans and other pathogen-associated molecular patterns. We report here two structures of the unique tetrameric camel PGRP-S (CPGRP-S) complexed with (i) muramyl dipeptide (MDP) at 2.5 Å resolution and (ii) GlcNAc and β-maltose at 1.7Å resolution. The binding studies carried out using surface plasmon resonance indicated that CPGRP-S binds to MDP with a dissociation constant of 10−7 m, whereas the binding affinities for GlcNAc and β-maltose separately are in the range of 10−4 m to 10−5 m, whereas the dissociation constant for the mixture of GlcNAc and maltose was estimated to be 10−6 m. The data from bacterial suspension culture experiments showed a significant inhibition of the growth of Staphylococcus aureus cells when CPGRP-S was added to culture medium. The ELISA experiment showed that the amount of MDP-induced production of TNF-α and IL-6 decreased considerably after the introduction of CPGRP-S. The crystal structure determinations of (i) a binary complex with MDP and (ii) a ternary complex with GlcNAc and β-maltose revealed that MDP, GlcNAc, and β-maltose bound to CPGRP-S in the ligand binding cleft, which is situated at the interface of molecules C and D of the homotetramer formed by four protein molecules A, B, C, and D. In the binary complex, the muramyl moiety of MDP is observed at the C-D interface, whereas the peptide chain protrudes into the center of tetramer. In the ternary complex, GlcNAc and β-maltose occupy distinct non-overlapping positions belonging to different subsites. PMID:21784863

  6. Influence of protein source on amino acid uptake patterns and protein utilization in rainbow trout Oncorhynchus mykiss

    DEFF Research Database (Denmark)

    Rolland, Marine; Holm, Jørgen; Dalsgaard, Anne Johanne Tang

    Matrixes of different protein sources (fish and plant products) combined with the use of crystalline amino acids allow for formulation of diets that meet fish requirements with little or no effect on protein digestibility and/or feed intake. Despite this, a total or partial replacement of fish meal...... induces reduced growth performances that remain partly unexplained. The aim of the current study was to investigate the effect of exchanging the protein source on protein utilization. Marine (fish meal) and vegetable (pea protein) sources were used with or without supplementation of crystalline amino...

  7. DETERMINATION OF SPACE-TIME PATTERNS AND RAINFALL HOMOGENEOUS AREAS AT MINAS GERAIS STATE

    Directory of Open Access Journals (Sweden)

    Leandro Rodrigues Souza

    2011-07-01

    Full Text Available The present study aimed to determine the spatial and temporal rainfall in Minas Gerais State relating to their respective rainfall weather systems and to identify homogeneous regions. The method of Factorial Analysis in Principal Components and Hierarchical Grouping were used to determine the seasonal and spatial patterns and homogeneous groups of rainfall. It was observed that the three first principal components describe 80.4% of the total variance of rainfall observed, in that the first factor explains 34.3% of the variance and showed high correlations with the rains from December to April in the southern State, which is influenced, mainly by the performance of frontal systems. The second factor explains 26.6% of data variance and showed significant correlations with rainfall from May to September in the northwest and southwest, and is possibly related to cold fronts and the South Atlantic Convergence Zone. Finally, the relative contributions to the third factor, with 19.5% of data variance accounted for the months of October and November, and are associated with mesoscale and microscale systems. Four homogeneous regions in relation to seasonal and interannual variability of rainfall were found. It concludes that statistical methods tested showed satisfactory results for this type of analyze, corroborates previous studies.

  8. Patterns and Determinants of Essential Newborn Care Practices in Rural Areas of Northern Ghana

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    Mahama Saaka

    2014-01-01

    Full Text Available Background. This study was designed to understand the patterns and determinants of three essential newborn care practices: safe cord care, optimal thermal care, and neonatal feeding practices. Methods. A community-based cross-sectional study was carried out on a sample of 404 lactating mothers who have delivered a live baby at home within the past one year prior to the study. Results. Overall, the prevalence of essential newborn practices on safe cord care and optimal thermal care was exceptionally low. Of the 404 newborns, only 0.2% (1 had safe cord care, 5.2% (21 optimal thermal care, and 50.2% (203 were considered to have had adequate neonatal feeding. In logistic regression analysis, the main predictors of good neonatal feeding were maternal age, timing of the first antenatal care (ANC, and maternal knowledge of newborn danger signs. Women who could mention at least 4 danger signs of the neonate were 4 times more likely to give good neonatal feeding to their babies (AOR = 4.7, Cl: 2.43–9.28, P<0.001. Conclusion. Evidence from this study strongly suggests that the expected essential newborn care practices are not available to a substantial number of the newborns. Efforts should therefore be made by the Ghana Health Service (GHS to expand essential newborn care interventions beyond institutional level into the communities.

  9. Changing pattern of the subcellular distribution of erythroblast macrophage protein (Emp) during macrophage differentiation.

    Science.gov (United States)

    Soni, Shivani; Bala, Shashi; Kumar, Ajay; Hanspal, Manjit

    2007-01-01

    Erythroblast macrophage protein (Emp) mediates the attachment of erythroid cells to macrophages and is required for normal differentiation of both cell lineages. In erythroid cells, Emp is believed to be involved in nuclear extrusion, however, its role in macrophage differentiation is unknown. Information on the changes in the expression level and subcellular distribution of Emp in differentiating macrophages is essential for understanding the function of Emp. Macrophages of varying maturity were examined by immunofluorescence microscopy and biochemical methods. Our data show that Emp is expressed in all stages of maturation, but its localization pattern changes dramatically during maturation: in immature macrophages, a substantial fraction of Emp is associated with the nuclear matrix, whereas in more mature cells, Emp is expressed largely at cell surface. Pulse-chase experiments show that nascent Emp migrates intracellularly from the cytoplasm to the plasma membrane more efficiently in mature macrophages than in immature cells. Incubation of erythroid cells with macrophages in culture shows that erythroid cells attach to mature macrophages but not to immature macrophage precursors. Together, our data show that the temporal and spatial expression of Emp correlates with its role in erythroblastic island formation and suggest that Emp may be involved in multiple cellular functions.

  10. Alterations in the protein pattern of subcellular fractions isolated from Paramecium cells suppressed in phagocytosis.

    Science.gov (United States)

    Surmacz, L; Wiejak, J; Wyroba, E

    2001-01-01

    SDS-PAGE and quantitative densitometric analysis revealed alterations in the protein pattern of subcellular fractions (100,000 x g) isolated from Paramecium aurelia (299s axenic) cells suppressed in phagocytosis as compared with the control. Two different agents were used to block phagocytosis: the beta-adrenergic antagonist-1-propranolol (200 microM) and inhibitor of calmodulin-dependent processes--trifluoperazine (20 microM). More than 40 polypeptides were identified in the cytosolic (soluble) fractions S1 and S2. A considerable decrease in band intensity was found for three polypeptides: by 60% for 87 kDa band, 52% for 75 kDa and 37% for 42 kDa in comparison to the control, when S2 fractions from propranolol-treated cells of equal load were quantified. TFP treatment evoked only a small decrease in the intensity of the same bands: 9%, 10% and 6%, respectively. The 42 kDa band was identified by Western blot analysis and chemiluminiscent detection to be actin. This result suggests that actin may be a primary target of pharmacological agents used in this study to inhibit Paramecium phagocytic activity.

  11. Expression pattern of the CsPK3 auxin-responsive protein kinase gene.

    Science.gov (United States)

    Chono, M; Suzuki, Y; Nemoto, K; Yamane, H; Murofushi, N; Yamaguchi, I

    2001-03-01

    We have previously cloned a cDNA of a putative serine/threonine protein kinase gene named CsPK3 from cucumber, the mRNA level of which was up-regulated by auxin and down-regulated by light irradiation. To examine the CsPK3 gene expression in detail, we cloned a genomic DNA of CsPK3 gene and made transgenic tobacco (Nicotiana tabacum L. cv. Petit Havana SR1) plants containing the fused CsPK3 promoter-beta-glucuronidase gene. The beta-glucuronidase expression was detected in the shoot apex, vascular tissues, and the outermost layer of cortex. The histological distribution of CsPK3 mRNA in cucumber seedlings was supported by in situ hybridization, where the positive signals were observed in similar tissues as those observed by beta-glucuronidase staining. The responsiveness of the CsPK3 gene to auxin and light was also confirmed for beta-glucuronidase activity. The pattern of beta-glucuronidase staining changed during the development of the tobacco seedlings. The results of our experiment showed that CsPK3 was expressed in a wide variety of tissues and cells in which the developmental and growth controls by auxin are suggested.

  12. Beyond breeding area management: Population specific migration patterns of a European-Afrotropical songbird

    DEFF Research Database (Denmark)

    Pedersen, Lykke; Tøttrup, Anders P.; Thorup, Kasper

    species migration systems is thus still limited. In this study, we analysed the spatio-temporal migration schedule of Red-backed Shrikes, Lanius collurio, using tracking data from individuals originating from geographically distinct breeding populations (Scandinavia, the Netherlands, Spain and Greece......Every year, billions of songbirds migrate thousands of kilometres between their European breeding grounds and African overwintering area. As migratory birds are dependent on resources at a number of sites varying in both space and time, they are likely to be more vulnerable to environmental change....... Perhaps as a consequence, long-distance migratory songbirds are declining rapidly compared to their sedentary counterparts. To understand what is driving these declines in European-Afrotropical migratory bird populations we need to understand the full annual migration cycle of these birds. Recent...

  13. Assessing patterns of human-wildlife conflicts and compensation around a Central Indian protected area.

    Directory of Open Access Journals (Sweden)

    Krithi K Karanth

    Full Text Available Mitigating crop and livestock loss to wildlife and improving compensation distribution are important for conservation efforts in landscapes where people and wildlife co-occur outside protected areas. The lack of rigorously collected spatial data poses a challenge to management efforts to minimize loss and mitigate conflicts. We surveyed 735 households from 347 villages in a 5154 km(2 area surrounding Kanha Tiger Reserve in India. We modeled self-reported household crop and livestock loss as a function of agricultural, demographic and environmental factors, and mitigation measures. We also modeled self-reported compensation received by households as a function of demographic factors, conflict type, reporting to authorities, and wildlife species involved. Seventy-three percent of households reported crop loss and 33% livestock loss in the previous year, but less than 8% reported human injury or death. Crop loss was associated with greater number of cropping months per year and proximity to the park. Livestock loss was associated with grazing animals inside the park and proximity to the park. Among mitigation measures only use of protective physical structures were associated with reduced livestock loss. Compensation distribution was more likely for tiger related incidents, and households reporting loss and located in the buffer. Average estimated probability of crop loss was 0.93 and livestock loss was 0.60 for surveyed households. Estimated crop and livestock loss and compensation distribution were higher for households located inside the buffer. Our approach modeled conflict data to aid managers in identifying potential conflict hotspots, influential factors, and spatially maps risk probability of crop and livestock loss. This approach could help focus allocation of conservation efforts and funds directed at conflict prevention and mitigation where high densities of people and wildlife co-occur.

  14. Assessing patterns of human-wildlife conflicts and compensation around a Central Indian protected area.

    Science.gov (United States)

    Karanth, Krithi K; Gopalaswamy, Arjun M; DeFries, Ruth; Ballal, Natasha

    2012-01-01

    Mitigating crop and livestock loss to wildlife and improving compensation distribution are important for conservation efforts in landscapes where people and wildlife co-occur outside protected areas. The lack of rigorously collected spatial data poses a challenge to management efforts to minimize loss and mitigate conflicts. We surveyed 735 households from 347 villages in a 5154 km(2) area surrounding Kanha Tiger Reserve in India. We modeled self-reported household crop and livestock loss as a function of agricultural, demographic and environmental factors, and mitigation measures. We also modeled self-reported compensation received by households as a function of demographic factors, conflict type, reporting to authorities, and wildlife species involved. Seventy-three percent of households reported crop loss and 33% livestock loss in the previous year, but less than 8% reported human injury or death. Crop loss was associated with greater number of cropping months per year and proximity to the park. Livestock loss was associated with grazing animals inside the park and proximity to the park. Among mitigation measures only use of protective physical structures were associated with reduced livestock loss. Compensation distribution was more likely for tiger related incidents, and households reporting loss and located in the buffer. Average estimated probability of crop loss was 0.93 and livestock loss was 0.60 for surveyed households. Estimated crop and livestock loss and compensation distribution were higher for households located inside the buffer. Our approach modeled conflict data to aid managers in identifying potential conflict hotspots, influential factors, and spatially maps risk probability of crop and livestock loss. This approach could help focus allocation of conservation efforts and funds directed at conflict prevention and mitigation where high densities of people and wildlife co-occur.

  15. Data on the role of accessible surface area on osmolytes-induced protein stabilization

    Directory of Open Access Journals (Sweden)

    Safikur Rahman

    2017-02-01

    Full Text Available This paper describes data related to the research article “Testing the dependence of stabilizing effect of osmolytes on the fractional increase in the accessible surface area on thermal and chemical denaturations of proteins” [1]. Heat- and guanidinium chloride (GdmCl-induced denaturation of three disulfide free proteins (bovine cytochrome c (b-cyt-c, myoglobin (Mb and barstar in the presence of different concentrations of methylamines (sarcosine, glycine-betaine (GB and trimethylamine-N-oxide (TMAO was monitored by [ϴ]222, the mean residue ellipticity at 222 nm at pH 7.0. Methylamines belong to a class of osmolytes known to protect proteins from deleterious effect of urea. This paper includes comprehensive thermodynamic data obtained from the heat- and GdmCl-induced denaturations of barstar, b-cyt-c and Mb.

  16. Anthelmintic prescribing patterns of a sample of general practitioners from selected areas in the Colombo district of Sri Lanka

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    Gunawardena GSA

    2008-01-01

    Full Text Available General Practitioners (GPs provide first contact care of children and pregnant mothers in the community. This study ascertained the prescribing pattern of anthelmintics to children and pregnant women by a sample of GPs from the district of Colombo. Two hundred medical practitioners engaged in full-time General Practice (100 urban and 100 rural, were selected randomly. A pre-tested interviewer-administered questionnaire was used to collect data. A total of 183 GPs aged between 26 and 72 years (median 38 participated with 94 coming from urban areas. Seventy percent of the GPs were male. Almost 13% of GPs from urban areas had a Postgraduate degree in comparison to 4.5% from the rural areas ( P < 0.05. Over 50% of GPs had 6-20 years of service and over 30% treated 16-30 patients daily. Seventy-three percent of GPs from rural areas accessed health-related reading material either daily or weekly in contrast to only 40% from urban areas ( P < 0.001. All GPs prescribed anthelmintics to children. Pyrantel pamoate was the preferred anthelmintic used for children by both groups. Approximately 55% and 64% of GPs from urban and rural areas, respectively, prescribed anthelmintics during pregnancy. A majority of GPs prescribed drugs after the first trimester. However, 25% from urban areas gave drugs during any trimester ( P < 0.001. Regression analysis revealed that GPs with postgraduate qualifications, those having frequent access to health-related material and those seeing more than 30 patients daily, prescribed anthelmintics to pregnant women more often. Although routine de-worming of pregnant women and children should occur through government antenatal and well-baby clinics, and through the schools de-worming programme, it may not happen due to various reasons. Thus, GPs play a vital role in achieving good coverage of anthelmintics among children and pregnant women. Making available clear national guidelines on prescribing anthelmintics in Sri Lanka would

  17. WEREWOLF, a MYB-related protein in Arabidopsis, is a position-dependent regulator of epidermal cell patterning.

    Science.gov (United States)

    Lee, M M; Schiefelbein, J

    1999-11-24

    The formation of the root epidermis of Arabidopsis provides a simple and elegant model for the analysis of cell patterning. A novel gene, WEREWOLF (WER), is described here that is required for position-dependent patterning of the epidermal cell types. The WER gene encodes a MYB-type protein and is preferentially expressed within cells destined to adopt the non-hair fate. Furthermore, WER is shown to regulate the position-dependent expression of the GLABRA2 homeobox gene, to interact with a bHLH protein, and to act in opposition to the CAPRICE MYB. These results suggest a simple model to explain the specification of the two root epidermal cell types, and they provide insight into the molecular mechanisms used to control cell patterning.

  18. Ozone Concentrations Patterns over the Metropolitan Area of São Paulo, Brazil

    Science.gov (United States)

    Mazzoli, C. R.; Carvalho, V. S.; Martins, L. D.; Freitas, E. D.; Andrade, M.

    2009-05-01

    Eleven years of ozone concentrations were analyzed in order to characterize the tropospheric ozone behavior since 1996 up to 2006 over the Metropolitan Area of São Paulo (MASP). MASP covers an area of 8.051 square kilometers, where approximately 19 million people live, and represents the most important economic region of Brazil. The main sources of pollutants in the MASP are the vehicles, which are responsible for more than 95% of CO, NOX and HC emission according to the São Paulo State Environmental Agency (CETESB). These pollutants are strictly correlated with ozone formation through a complex mechanism that depends mainly on a nonlinear mixture of volatile organic compounds (VOC) and nitrogen oxides (NOx). The ozone concentrations are also affected by meteorological conditions, as solar radiation that will be important for the photolysis, and by transport processes from/to other regions. The established maximum hourly National Air Quality Standard (NAAQS) for ozone is frequently violated in the MASP. According to CETESB, during the last five years the annual average of NAAQS violations was 65 days. It is important to emphasize that during this period a substantial increase in the number of vehicles was observed. So far, there is no study available in the literature which evaluates the complete historical time series of the ozone concentration data collected in the air quality monitoring network of the MASP. In this study, data from 12 air quality monitoring stations distributed over the MASP were evaluated. In general, annual mean concentrations of primary pollutants decreased on the last two decades mostly due to the Brazilian Vehicular Emission Control Program (PROCONVE). The program by itself was responsible for a drop of almost 70% of vehicular emissions. However, ozone annual mean concentrations do not reveal the same trend. Among 10 air quality monitoring sites four of it presented a reduction of ozone concentration values while the others six presented

  19. Short-term low-protein diet during pregnancy alters islet area and protein content of phosphatidylinositol 3-kinase pathway in rats

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    CRISTIANA S.B. SALVATIERRA

    2015-06-01

    Full Text Available The phosphatidylinositol 3-kinase and mitogen-activated protein kinase pathways mediate β cell growth, proliferation, survival and death. We investigated whether protein restriction during pregnancy alters islet morphometry or the expression and phosphorylation of several proteins involved in the phosphatidylinositol 3-kinase and mitogen-activated protein kinase pathways. As controls, adult pregnant and non-pregnant rats were fed a normal-protein diet (17%. Pregnant and non-pregnant rats in the experimental groups were fed a low-protein diet (6% for 15 days. Low protein diet during pregnancy increased serum prolactin level, reduced serum corticosterone concentration and the expression of both protein kinase B/AKT1 (AKT1 and p70 ribosomal protein S6 kinase (p70S6K, as well as the islets area, but did not alter the insulin content of pancreatic islets. Pregnancy increased the expression of the Src homology/collagen (SHC protein and the extracellular signal-regulated kinases 1/2 (ERK1/2 independent of diet. ERK1/2 phosphorylation (pERK1/2 was similar in islets from pregnant and non-pregnant rats fed a low-protein diet, and was higher in islets from pregnant rats than in islets from non-pregnant rats fed a normal-protein diet. Thus, a short-term, low-protein diet during pregnancy was sufficient to reduce the levels of proteins in the phosphatidylinositol 3-kinase pathway and affect islet morphometry.

  20. Resting Energy Expenditure and Its Relationship With Patterns of Obesity and Visceral Fat Area in Chinese Adults

    Institute of Scientific and Technical Information of China (English)

    WEI-PING JIA; MING YANG; XIN-YU SHAO; YU-QIAN BAO; JUN-XI LU; KUN-SAN XIANG

    2005-01-01

    Objective To investigate the relationship between resting energy expenditure (REE) and patterns of obesity/regional fat parameters in Chinese adults. Methods Body mass index (BMI), fat mass (FM), fat-free mass (FFM) were assessed in 109 Chinese adults (52 men and 57 women), and their abdominal visceral adipose tissue area (VA) and subcutaneous fat area (SA) were measured using magnetic resonance imaging (MRI) measurements. REE was measured with indirect calorimetry and compared with normal and obese subjects. Multivariate analysis was used to study the factors related to REE. Results The resting energy expenditure per kilogram of body weight (REE/kg) was closely related with the area of abdominal visceral fat measured with MRI. REE/kg was significantly lower in overweight/obesity subjects than in normal-weighted subjects, and significantly lower in subjects with abdominal obesity (VA≥100 cm2) than in subjects with non-abdominal obesity (VA< 100 cm2, BMI≥25 kg/m2). In the stepwise regression analysis of REE/kg on regional fat parameters, VA in men and women and SA in women were independent factors reversely related to REE/kg. Conclusion REE/kg is associated with the visceral fat area and more prominent in men. REE/kg can be used as an index in the pathophysiology of intra-abdominal obesity.

  1. Temporal patterns in the soundscape of the shallow waters of a Mediterranean marine protected area

    Science.gov (United States)

    Buscaino, Giuseppa; Ceraulo, Maria; Pieretti, Nadia; Corrias, Valentina; Farina, Almo; Filiciotto, Francesco; Maccarrone, Vincenzo; Grammauta, Rosario; Caruso, Francesco; Giuseppe, Alonge; Mazzola, Salvatore

    2016-09-01

    The study of marine soundscapes is an emerging field of research that contributes important information about biological compositions and environmental conditions. The seasonal and circadian soundscape trends of a marine protected area (MPA) in the Mediterranean Sea have been studied for one year using an autonomous acoustic recorder. Frequencies less than 1 kHz are dominated by noise generated by waves and are louder during the winter; conversely, higher frequencies (4–96 kHz) are dominated by snapping shrimp, which increase their acoustic activity at night during the summer. Fish choruses, below 2 kHz, characterize the soundscape at sunset during the summer. Because there are 13 vessel passages per hour on average, causing acoustic interference with fish choruses 46% of the time, this MPA cannot be considered to be protected from noise. On the basis of the high seasonal variability of the soundscape components, this study proposes a one-year acoustic monitoring protocol using the soundscape methodology approach and discusses the concept of MPA size.

  2. Annual pattern of sulphur content in spruce needles from heavily and less polluted areas

    Energy Technology Data Exchange (ETDEWEB)

    Simoncic, P.; Kalan, P. [Slovenia Forestry Institute, Ljubljana (Slovenia)

    1996-12-31

    Needles of twenty years old spruces from Prednji vrh, an area affected by the Sostanj power station (Slovenia) and from Pojljuka, Alps region, with a relatively unpolluted environment, were analysed for total sulphur (S-t) and total nitrogen content (N-t). Sulphur measurements were taken in a period between April and August twice monthly, and in the period from August to April every four weeks (May 1993-June 1994). Sulphur content in the current and one year old spruce needles from Prednji vrh were much higher (current year needles, 2.06-2.50 mg/m dry weight, 1993) than in needles from Pokljuka (current year needles 1.05-1.25 mg/g dry weight, 1993). Nitrogen contents and ratio N-t/S-t for current year needles from Pokljuka were higher (12.3 mg/g dry weight, N-t/S-t 10.2, November 1993) than in needles from Prednji vrh (10.8 mg/g dry weight, N-t/S-t 5.3, November 1993).

  3. Protein patterns of brush-border fragments in congenital lactose malabsorption and in specific hypolactasia of the adult.

    Science.gov (United States)

    Freiburghaus, A U; Schmitz, J; Schindler, M; Rotthauwe, H W; Kuitunen, P; Launiala, K; Hadorn, B

    1976-05-06

    Brush-border membrane proteins of the small-bowel mucosa were separated on polyacrylamide gels from intestinal biopsy specimens obtained from four children with congenital lactose malabsorption and from two adults with specific hypolactasia. In three patients with the congenital type of lactase deficiency the protein band corresponding to brush-border lactase was reduced in intensity, but was never completely absent. No difference in gel patterns was detected when this pattern in congenital deficiency was compared to that obtained from the two patients with adult-type selective hypolactasia. In one patient with congenital lactose malabsorption the protein band corresponding to lactase activity was not detectable. The findings suggest that the mechanisms leading to low lactase activity in the congenital and adult forms of lactose intolerance are similar.

  4. Diagenetic Pattern in the Citarate Carbonate Rocks, Cilograng Area, Lebak Regency, Banten Province

    Directory of Open Access Journals (Sweden)

    N. I. Basuki

    2014-06-01

    Full Text Available DOI: 10.17014/ijog.v7i3.142The carbonate sequence overlies conformably the tuffaceous sandstone unit, and in turn is conformably underlain by the tuff-sandstone unit, both of which are members of the Citarate Formation. The Citarate carbonate rocks were deposited in an open platform back reef environment, which was temporarily drowned by local sea level rise. Regional Middle Miocene deformation formed NNE-WSW trend faults and E-W trend folds in the researched area. This paper discusses the nature of diagenetic alteration of the Citarate carbonate rocks based on petrographic analyses of twenty surface samples. Carbonate rocks from bottom to top comprise algae packstone, packstone-grainstone, coral-algae packstone, and foraminifer wackestone-packstone. Fragments of coral, coralline red algae, and large foraminifera are the dominant bioclasts in most of the observed samples, whereas echinoids and bivalves are less abundant; they are set in a recrystallized micrite matrix. Planktonic foraminifera are abundant only in few samples. Fragments of plagioclase, igneous volcanic rocks, pyroclastic rocks (tuff, and much less abundant quartz are commonly present in all the studied samples. A generalized diagenesis includes early marine cementation by fibrous aragonite, compaction, aragonite dissolution and/or neomorphism, precipitation of equant-grained calcite cement in a phreatic environment, dissolution to form moldic porosities, dolomitization, the formation of stylolites and fractures, and precipitation of late ferroan calcite during burial. Multiple carbonate cements occur as pore-filling phases, with ferroan calcite cementation taking place during later-stage burial. Secondary porosities were formed during different stages in diagenetic processes, such as dissolution, dolomitization, and stylolite and fracture formations. Although precipitation of nonferroan and ferroan calcite cement occluded porosities, porosity enhancement during early selective

  5. Prevalence and pattern of self-medication practices in an urban area of Delhi, India

    Directory of Open Access Journals (Sweden)

    Varun Kumar

    2015-01-01

    Full Text Available Background: Self-medication is one of the major health concerns worldwide and World Health Organization has laid emphasis on correctly investigating and controlling it. There is much public and professional concern regarding self-medication practices, which has dramatically increased in the last few decades, especially in the developing countries. Hence, this study was designed to study the prevalence and practice of self-medication practices in an urban area of Delhi, India. Materials and Methods: A cross-sectional study was conducted in March 2013 and data were collected by personal interviews using pretested questionnaires. An urban colony in the south district of Delhi was chosen and the eldest member of the family, present at the time of the visit was interviewed. Data were collected from 236 persons and analyzed using SPSS version 21. Results: The prevalence of self-medication was 92.8% (95 confidence interval: 66.5-79.4. 74.9% preferred allopathic medicines. Self-medication was found to be practiced more among younger persons than older age group persons (P = 0.000. Graduates and postgraduates practiced self-medication more than others (P = 0.002. Common cold (61.6% and fever (51.8% were the most common ailments for which self-medication were practiced. Paracetamol and cough syrups were the most commonly used class of drugs. Conclusion: The prevalence of self-medication in this study was high. Drugs especially antimicrobials were not taken for the proper length of time. Awareness regarding self-medication practices to help patients decide on the appropriateness of self-medication is required.

  6. Polymer blend lithography for metal films: large-area patterning with over 1 billion holes/inch2

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    Cheng Huang

    2015-05-01

    Full Text Available Polymer blend lithography (PBL is a spin-coating-based technique that makes use of the purely lateral phase separation between two immiscible polymers to fabricate large area nanoscale patterns. In our earlier work (Huang et al. 2012, PBL was demonstrated for the fabrication of patterned self-assembled monolayers. Here, we report a new method based on the technique of polymer blend lithography that allows for the fabrication of metal island arrays or perforated metal films on the nanometer scale, the metal PBL. As the polymer blend system in this work, a mixture of polystyrene (PS and poly(methyl methacrylate (PMMA, dissolved in methyl ethyl ketone (MEK is used. This system forms a purely lateral structure on the substrate at controlled humidity, which means that PS droplets are formed in a PMMA matrix, whereby both phases have direct contact both to the substrate and to the air interface. Therefore, a subsequent selective dissolution of either the PS or PMMA component leaves behind a nanostructured film which can be used as a lithographic mask. We use this lithographic mask for the fabrication of metal patterns by thermal evaporation of the metal, followed by a lift-off process. As a consequence, the resulting metal nanostructure is an exact replica of the pattern of the selectively removed polymer (either a perforated metal film or metal islands. The minimum diameter of these holes or metal islands demonstrated here is about 50 nm. Au, Pd, Cu, Cr and Al templates were fabricated in this work by metal PBL. The wavelength-selective optical transmission spectra due to the localized surface plasmonic effect of the holes in perforated Al films were investigated and compared to the respective hole diameter histograms.

  7. Scaling properties of the radius of gyration and surface area for EF-hand calcium binding proteins

    Energy Technology Data Exchange (ETDEWEB)

    Pitulice, L. [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania); Isvoran, A. [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania)], E-mail: aisvoran@cbg.uvt.ro; Craescu, C.T. [INSERM U759/Institute Curie-Recherche, Centre Universitaire Paris-Sud, Batiment 112, 91405 Orsay (France); Chiriac, A. [West University of Timisoara, Department of Chemistry, Pestalozzi 16, 300115 Timisoara (Romania)

    2009-04-30

    In this paper, we analyze the scaling properties of both the radius of gyration and the surface area for EF-hand calcium binding proteins. These properties are different for two conformational subfamilies: proteins with extended and compact structures, respectively. The radius of gyration is a measure of the shape of protein, whereas its surface fractal dimension is a measure of its interatomic packing. Different scaling properties for the radius of gyration underline that these two subfamilies present different shapes whilst different scaling properties for the surface area reveal different strengths of their intermolecular forces. All these data suggest different mechanisms responsible for the global folding of proteins belonging to these two subfamilies.

  8. Human cellular protein patterns and their link to genome DNA sequence data: usefulness of two-dimensional gel electrophoresis and microsequencing

    DEFF Research Database (Denmark)

    Celis, J E; Rasmussen, H H; Leffers, H;

    1991-01-01

    Analysis of cellular protein patterns by computer-aided 2-dimensional gel electrophoresis together with recent advances in protein sequence analysis have made possible the establishment of comprehensive 2-dimensional gel protein databases that may link protein and DNA information and that offer a...

  9. Long-term and wide-area subsidence pattern from time series of Envisat Asar Data in Konya Basin, Turkey

    Science.gov (United States)

    Ustun, Aydin

    2016-04-01

    Konya Basin as a sub-part of Konya Closed Basin is dominated by the Neogene and Quaternary sediments that are largely fluvial and lacustrine characteristic. The wide plains cultivated over the last 10000 years are the remnants of the Pluvial lake basin during wet and humid climate environment after the last glacial period. With the form of isolated depression-block, the geomorphological landscape has been mainly driven by the neotectonic activity of striking normal fault systems of the region. Konya that has doubled in size over the last two and half decades is both expanding into the agricultural areas and increasing its building expansion in the city center. The level observations recorded at the monitoring stations indicate that groundwater resources have been exploited permanently or seasonally in some parts where water demand exceeds supply. In this study, a long-term and wide area subsidence pattern in Konya Basin has been analyzed by stacking the deformation interferograms for time series. The study area that covers approximately 7500 km squared was investigated through a large number of the raw images of Asar sensor onboard Envisat from December 2002 to October 2010. Almost a hundred SAR scenes imaged over three tracks in both ascending and descending modes have been used to create a set of 127 differential interferograms using GMTSAR processing system. A continuous deformation map on the basinwide scale has been produced by combining the stacked interferograms. The average contour map shows that the DInSAR detected line of sight subsidence (or uplift) rates vary between 0.6 and -3.3 cm/yr throughout 8 years. The subsidence pattern significantly is correlated with the land and groundwater use within the basin and it states that the anthropogenic effect is much greater than the identified geological and hydrogeological processes.

  10. Connectivity patterns and key non–breeding areas of white–throated bluethroat (Luscinia svecica European populations

    Directory of Open Access Journals (Sweden)

    Arizaga, J.

    2013-01-01

    Full Text Available Using ring recovery data from the EURING databank, the aims of this study were: (1 to identify the chief migration and wintering areas of white–throated bluethroat European subspecies, L. s. namnetum, L. s. cyanecula and L. s. azuricollis, (2 to evaluate the degree of connectivity between breeding and non–breeding regions and determine the migration patterns of each subspecies, and (3 to evaluate whether recovery data are sufficient to answer the previous questions adequately. Most of the recoveries were obtained during the autumn migration period (n = 155, 68.9%, followed by winter (n = 49, 21.8% and spring (n = 21, 9.3%. For L. s. azuricollis, we did not find any ring recoveries at more than 100 km in autumn or spring, and there were none at all in winter. All analyses thus relate to L. s. cyanecula and L. s. namnetum. Both subspecies move across a NE–SW axis from their breeding to their wintering areas within the circum–Mediterranean region, mainly in Iberia, following population–specific parallel migration routes. L. s. namnetum mainly uses the Atlantic coastal marshes from France to south–western Iberia, where the chief wintering areas are found. L. s. cyanecula, however, uses both Atlantic and Mediterranean wetlands in autumn, but only those in the Mediterranean in spring, thus giving rise to a loop–migration pattern. Telescopic migration was demonstrated for L. s. cyanecula. Recovery data were insufficient to identify in detail the entire wintering range for all white–throated bluethroat European populations. Technologies such as the use of geolocators will play a relevant role in this scenario

  11. Comparison of expression patterns of fibroblast growth factor 8, bone morphogenetic protein 4 and sonic hedgehog in jaw development of the house shrew, Suncus murinus.

    Science.gov (United States)

    Ogi, Hidenao; Tabata, Makoto J; Yamanaka, Atsushi; Yasui, Kinya; Uemura, Masanori

    2002-01-01

    To elucidate the mechanism underlying jaw development in mammals, we used a new laboratory animal, Suncus murinus (house shrew, an insectivore) as the subject for the investigation, because Suncus has all types of teeth (incisor, canine, premolar and molar) in its upper and lower jaws and is thought to be a good model animal having a general mammalian tooth pattern. At the start, by use of degenerate primers we cloned Suncus homologues of fibroblast growth factor 8 (sFgf8), bone morphogenetic protein 4 (sBmp4) and sonic hedgehog (sShh) genes from cDNA library derived from whole Suncus embryos at day 12 (E12). Thereafter, we examined the expression patterns of these genes in the jaw development of Suncus E11-16 embryos (for mouse E9.5-12 embryos). sFgf8 and sBmp4 were expressed in E11 but not in E15 and onward during orofacial development. sShh was expressed from E11 onward, and its expression was increased in the orofacial area. The expression pattern of sFgf8 in the maxillary and mandibular arches of E14 coincided with the area of the presumptive tooth arch. However, sShh and sBmp4 were expressed only in the outer area (= buccal/labial side) of presumptive tooth arch. Thus, these 3 genes showed specific expression pattern in jaw development of Suncus, and their distributions did not overlap each other except in a few regions. These findings suggest that sFgf8, sBmp4 and sShh have a specific function respectively during jaw development in Suncus murinus.

  12. NMR spin relaxation in proteins: The patterns of motion that dissipate power to the bath

    Energy Technology Data Exchange (ETDEWEB)

    Shapiro, Yury E., E-mail: eva.meirovitch@biu.ac.il, E-mail: yuryeshapiro@gmail.com; Meirovitch, Eva, E-mail: eva.meirovitch@biu.ac.il, E-mail: yuryeshapiro@gmail.com [The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900-02 (Israel)

    2014-04-21

    We developed in recent years the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for the analysis of NMR relaxation in proteins. The two bodies/rotators are the protein (diffusion tensor D{sub 1}) and the spin-bearing probe, e.g., the {sup 15}N−{sup 1}H bond (diffusion tensor, D{sub 2}), coupled by a local potential (u). A Smoluchowski equation is solved to yield the generic time correlation functions (TCFs), which are sums of weighted exponentials (eigenmodes). By Fourier transformation one obtains the generic spectral density functions (SDFs) which underlie the experimental relaxation parameters. The typical paradigm is to characterize structural dynamics in terms of the best-fit values of D{sub 1}, D{sub 2}, and u. Additional approaches we pursued employ the SRLS TCFs, SDFs, or eigenmodes as descriptors. In this study we develop yet another perspective. We consider the SDF as function of the angular velocity associated with the fluctuating fields underlying NMR relaxation. A parameter called j-fraction, which represents the relative contribution of eigenmode, i, to a given value of the SDF function at a specific frequency, ω, is defined. j-fraction profiles of the dominant eigenmodes are derived for 0 ≤ ω ≤ 10{sup 12} rad/s. They reveal which patterns of motion actuate power dissipation at given ω-values, what are their rates, and what is their relative contribution. Simulations are carried out to determine the effect of timescale separation, D{sub 1}/D{sub 2}, axial potential strength, and local diffusion axiality. For D{sub 1}/D{sub 2} ≤ 0.01 and strong local potential of 15 k{sub B}T, power is dissipated by global diffusion, renormalized (by the strong potential) local diffusion, and probe diffusion on the surface of a cone (to be called cone diffusion). For D{sub 1}/D{sub 2} = 0.1, power is dissipated by mixed eigenmodes largely of a global-diffusion-type or cone-diffusion-type, and a nearly bare renormalized

  13. Pattern recognition in pulmonary tuberculosis defined by high content peptide microarray chip analysis representing 61 proteins from M. tuberculosis.

    Directory of Open Access Journals (Sweden)

    Simani Gaseitsiwe

    Full Text Available BACKGROUND: Serum antibody-based target identification has been used to identify tumor-associated antigens (TAAs for development of anti-cancer vaccines. A similar approach can be helpful to identify biologically relevant and clinically meaningful targets in M. tuberculosis (MTB infection for diagnosis or TB vaccine development in clinically well defined populations. METHOD: We constructed a high-content peptide microarray with 61 M. tuberculosis proteins as linear 15 aa peptide stretches with 12 aa overlaps resulting in 7446 individual peptide epitopes. Antibody profiling was carried with serum from 34 individuals with active pulmonary TB and 35 healthy individuals in order to obtain an unbiased view of the MTB epitope pattern recognition pattern. Quality data extraction was performed, data sets were analyzed for significant differences and patterns predictive of TB+/-. FINDINGS: Three distinct patterns of IgG reactivity were identified: 89/7446 peptides were differentially recognized (in 34/34 TB+ patients and in 35/35 healthy individuals and are highly predictive of the division into TB+ and TB-, other targets were exclusively recognized in all patients with TB (e.g. sigmaF but not in any of the healthy individuals, and a third peptide set was recognized exclusively in healthy individuals (35/35 but no in TB+ patients. The segregation between TB+ and TB- does not cluster into specific recognition of distinct MTB proteins, but into specific peptide epitope 'hotspots' at different locations within the same protein. Antigen recognition pattern profiles in serum from TB+ patients from Armenia vs. patients recruited in Sweden showed that IgG-defined MTB epitopes are very similar in individuals with different genetic background. CONCLUSIONS: A uniform target MTB IgG-epitope recognition pattern exists in pulmonary tuberculosis. Unbiased, high-content peptide microarray chip-based testing of clinically well-defined populations allows to visualize

  14. Interaction of gold and silver nanoparticles with human plasma: Analysis of protein corona reveals specific binding patterns.

    Science.gov (United States)

    Lai, Wenjia; Wang, Qingsong; Li, Lumeng; Hu, Zhiyuan; Chen, Jiankui; Fang, Qiaojun

    2017-04-01

    Determining how nanomaterials interact with plasma will assist in understanding their effects on the biological system. This work presents a systematic study of the protein corona formed from human plasma on 20nm silver and gold nanoparticles with three different surface modifications, including positive and negative surface charges. The results show that all nanoparticles, even those with positive surface modifications, acquire negative charges after interacting with plasma. Approximately 300 proteins are identified on the coronas, while 99 are commonly found on each nanomaterial. The 20 most abundant proteins account for over 80% of the total proteins abundance. Remarkably, the surface charge and core of the nanoparticles, as well as the isoelectric point of the plasma proteins, are found to play significant roles in determining the nanoparticle coronas. Albumin and globulins are present at levels of less than 2% on these nanoparticle coronas. Fibrinogen, which presents in the plasma but not in the serum, preferably binds to negatively charged gold nanoparticles. These observations demonstrate the specific plasma protein binding pattern of silver and gold nanoparticles, as well as the importance of the surface charge and core in determining the protein corona compositions. The potential downstream biological impacts of the corona proteins were also investigated.

  15. New algorithmic approaches to protein spot detection and pattern matching in two-dimensional electrophoresis gel databases.

    Science.gov (United States)

    Pleissner, K P; Hoffmann, F; Kriegel, K; Wenk, C; Wegner, S; Sahlström, A; Oswald, H; Alt, H; Fleck, E

    1999-01-01

    Protein spot identification in two-dimensional electrophoresis gels can be supported by the comparison of gel images accessible in different World Wide Web two-dimensional electrophoresis (2-DE) gel protein databases. The comparison may be performed either by visual cross-matching between gel images or by automatic recognition of similar protein spot patterns. A prerequisite for the automatic point pattern matching approach is the detection of protein spots yielding the x(s),y(s) coordinates and integrated spot intensities i(s). For this purpose an algorithm is developed based on a combination of hierarchical watershed transformation and feature extraction methods. This approach reduces the strong over-segmentation of spot regions normally produced by watershed transformation. Measures for the ellipticity and curvature are determined as features of spot regions. The resulting spot lists containing x(s),y(s),i(s)-triplets are calculated for a source as well as for a target gel image accessible in 2-DE gel protein databases. After spot detection a matching procedure is applied. Both the matching of a local pattern vs. a full 2-DE gel image and the global matching between full images are discussed. Preset slope and length tolerances of pattern edges serve as matching criteria. The local matching algorithm relies on a data structure derived from the incremental Delaunay triangulation of a point set and a two-step hashing technique. For the incremental construction of triangles the spot intensities are considered in decreasing order. The algorithm needs neither landmarks nor an a priori image alignment. A graphical user interface for spot detection and gel matching is written in the Java programming language for the Internet. The software package called CAROL (http://gelmatching.inf.fu-berlin.de) is realized in a client-server architecture.

  16. Comparison of protein patterns after two-dimensional gel electrophoresis from leaves of in vitro cultures and seedlings of Rubus chamaemorus L.

    Directory of Open Access Journals (Sweden)

    Barbara Thiem

    2014-01-01

    Full Text Available Proteins from leaves of Rubus chamaemorus propagated in vitro were subjected to miniaturized 2-D electrophoresis. The 2-DE patterns of proteins showed qualitative differences between plants propagated in vitro and control seedlings. More proteins of a high molecular weight were observed in leaves of plants from in vitro culture. A two-dimensional map of proteins from leaves provides detailed data concerning both polymorphism and protein patterns of this species. This makes it possible to start constructing a protein map of R. chamaemorus. The reasons for qualitative differences are discussed.

  17. SDS-PAGE analysis of whole cell protein and outer memr-bane protein patterns of clinical isolates of Burkholderia pseud-omallei

    Institute of Scientific and Technical Information of China (English)

    Apichart Nontprasert; Cheeraratana Cheeramakara; Sasithon Pukrittayakamee; David AB Dance; Ty L Pitt; Michael D Smith; Sirivan Vanijanonta; Nicholas J White

    2009-01-01

    Objective:To investigate the banding patterns of whole cell protein (WCP)and outer membrane protein (OMP)of Burkholderia pseudomallei (B.pseudomallei)in clinical isolates from patients with melioidosis. Methods:WCP and OMP of of B.pseudomallei in 50 clinical isolates,from 47 patients with melioidosis were prepared and separated by polyacrylamide gel electrophoresis (SDS-PAGE)using 10% gels and stained with Coomassie brilliant blue.The banding patterns were compared by using a laser densitometer and dendrogram. Results:There were 6 different banding patterns of WCP and 2 types of OMP.Type 1-5 WCP had 8 common protein bands at 19.0 -45.0 kDa with identical OMP pattern.The banding patterns of WCP in type 6 were distinct from the others and also its OMP profile.The majority of clinical isolates (37 /50,74%)were in type 1 WCP.Of the remaining isolates,8 were in type 2,2 in type 3,and one each was in type 4 to 6.There was no significant association between the WCP typing and the demographic or clinical features of the investigated patients.Conclusion:Despite the wide variation of clinical features of melioidosis,the results of this study show that B.pseudomallei had a few differences in the WCP and OMP profiles.Therefore typing of WCP and OMP,using SDS-PAGE analysis,could be an alternative method for phenotypic differentiation in clinical iso-lates of B.pseudomallei.

  18. Analysis of Aggregation Delay for Multisource Sensor Data with On-Off Traffic Pattern in Wireless Body Area Networks

    Science.gov (United States)

    Kim, Un-Ha; Kong, Eutteum; Choi, Hyun-Ho; Lee, Jung-Ryun

    2016-01-01

    Data aggregation plays an important role to improve the transmission efficiency in wireless body area networks (WBANs); however, it inherently induces additional aggregation delay. Therefore, the effect of packet aggregation on WBAN applications, which are vulnerable to delay, must be analyzed rigorously. In this paper, we analyze the packet aggregation delay for multisource sensor data with an on-off traffic pattern in WBANs. Considering two operational parameters of the aggregation threshold and aggregation timer, we calculate the probability that a packet aggregation occurs during a unit time and then derive the average aggregation delay in closed-form. The analysis results show that the aggregation delay increases as the aggregation timer or aggregation threshold increases, but is bounded below a certain level according to the number of active sensors and their on-off traffic attribute. This implies that the data aggregation technique can maximize the transmission efficiency while satisfying a given delay requirement in the WBAN system. PMID:27706029

  19. Using advanced dispersion models and mobile monitoring to characterize spatial patterns of ultrafine particles in an urban area

    Science.gov (United States)

    Zwack, Leonard M.; Hanna, Steven R.; Spengler, John D.; Levy, Jonathan I.

    2011-09-01

    data and the advanced dispersion model QUIC provide insight about source contributions above background levels and spatiotemporal air pollution patterns in urban areas.

  20. Activity patterns and diet of the howler monkey Alouatta belzebul in areas of logged and unlogged forest in Eastern Amazonia

    Directory of Open Access Journals (Sweden)

    Pinto, A. C. B.

    2003-12-01

    Full Text Available This work compared the activity patterns and diet of a group of Alouatta belzebul in areas of logged and unlogged forest in eastern Amazonia. An instantaneous scan sampling procedure was used for the behavioral study (9.3 ± 1.9 complete observation days/month from February to November 2000. Fruit availability was estimated monthly. Activity budgets were not significantly different between sites. Rest was the predominant activity in both sites (53.6 % and 48.7 %, respectively. Average daily path length was 683.5 ± 215.1 m (n = 93, and the home range was 17.8 ha, including 7 ha in unlogged forest and 10.8 ha in the logged forest. Neither fruit availability nor diet varied significantly between sites. The diet was predominantly folivorous (43.4 % and 46.6 % in unlogged and logged forest, respectively and frugivorous (43.9 % and 42.8 %. The spatial use by the group was positively related to fruit sources. This study documented the ability of a ranging group of A. belzebul to survive in a habitat influenced by reduced impact logging without dramatically influencing its activity patterns and diet

  1. Classification, expression pattern and comparative analysis of sugarcane expressed sequences tags (ESTs encoding glycine-rich proteins (GRPs

    Directory of Open Access Journals (Sweden)

    Fusaro Adriana

    2001-01-01

    Full Text Available Since the isolation of the first glycine-rich proteins (GRPs in plants a wealth of new GRPs have been identified. The highly specific but diverse expression pattern of grp genes, taken together with the distinct sub-cellular localization of some GRP groups, clearly indicate that these proteins are involved in several independent physiological processes. Notwithstanding the absence of a clear definition of the role of GRPs in plant cells, studies conducted with these proteins have provided new and interesting insights into the molecular biology and cell biology of plants. Complexly regulated promoters and distinct mechanisms for the regulation of gene expression have been demonstrated and new protein targeting pathways, as well as the exportation of GRPs from different cell types have been discovered. These data show that GRPs can be useful as markers and/or models to understand distinct aspects of plant biology. In this paper, the structural and functional features of these proteins in sugarcane (Saccharum officinarum L. are summarized. Since this is the first description of GRPs in sugarcane, special emphasis has been given to the expression pattern of these GRP genes by studying their abundance and prevalence in the different cDNA-libraries of the Sugarcane Expressed Sequence Tag (SUCEST project . The comparison of sugarcane GRPs with GRPs from other species is also discussed.

  2. Tissue distribution and deposition pattern of a cellulosic parenchyma-specific protein from cassava roots

    Directory of Open Access Journals (Sweden)

    Petrônio A.S. Souza

    1998-06-01

    Full Text Available A protein with a molecular mass of 22kDa was purified from the cellulosic parenchyma of cassava roots. The amino acid composition of the protein was determined and antibodies generated against the purified protein were used to show that the concentration of the protein remains unchanged during root "tuber" formation. By using a tissue printing technique, as well as western blot, it was shown that the cellulosic parenchyma was the only root tissue in which the protein was deposited.

  3. New multi protein patterns differentiate liver fibrosis stages and hepatocellular carcinoma in chronic hepatitis C serum samples

    Institute of Scientific and Technical Information of China (English)

    Thomas G(o)bel; Sonja Vorderwülbecke; Katarzyna Hauck; Holger Fey; Dieter H(a)ussinger; Andreas Erhardt

    2006-01-01

    AIM: To identify a multi serum protein pattern as well as single protein markers using surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF-MS) for detection and differentiation of liver fibrosis (F1-F2), liver cirrhosis (F4) and hepatocellular carcinoma (HCC) in patients with chronic hepatitis C virus (HCV).METHODS: Serum samples of 39 patients with F1/F2 fibrosis, 44 patients with F4 fibrosis, 34 patients with HCC were applied to CM10 arrays and analyzed using the SELDI-TOF ProteinChip System (PBS-Ⅱ c; Ciphergen Biosystems) after anion-exchange fractionation. All patients had chronic hepatitis C and histologically confirmed fibrosis stage/HCC. Data were analyzed for protein patterns by multivariate statistical techniques and artificial neural networks.RESULTS: A 4 peptide/protein multimarker panel (7486,12843, 44293 and 53598 Da) correctly identified HCCs with a sensitivity of 100% and specificity of 85% in a two way-comparison of HCV-cirrhosis versus HCV-HCC training samples (AUROC 0.943). Sensitivity and specificity for identification of HCC were 68% and 80% for random test samples. Cirrhotic patients could be discriminated against patients with F1 or F2 fibrosisusing a 5 peptide/protein multimarker pattern (2873,6646, 7775, 10525 and 67867 Da) with a specificity of 100% and a sensitivity of 85% in training samples (AUROC 0.976) and a sensitivity and specificity of 80% and 67% for random test samples. Combination of the biomarker classifiers with APRI score and alfa-fetopotein (AFP) improved the diagnostic performance. The 6646 Da marker protein for liver fibrosis was identified as apolipoprotein C-Ⅰ.CONCLJSION: SELDI-TOF-MS technology combined with protein pattern analysis seems a valuable approach for the identification of liver cirrhosis and hepatocellular carcinoma in patients with chronic hepatitis C. Most probably a combination of different serum markers will help to identify liver cirrhosis and early

  4. Distinct contractile and cytoskeletal protein patterns in the Antarctic midge are elicited by desiccation and rehydration.

    Science.gov (United States)

    Li, Aiqing; Benoit, Joshua B; Lopez-Martinez, Giancarlo; Elnitsky, Michael A; Lee, Richard E; Denlinger, David L

    2009-05-01

    Desiccation presents a major challenge for the Antarctic midge, Belgica antarctica. In this study, we use proteomic profiling to evaluate protein changes in the larvae elicited by dehydration and rehydration. Larvae were desiccated at 75% relative humidity (RH) for 12 h to achieve a body water loss of 35%, approximately half of the water that can be lost before the larvae succumb to dehydration. To evaluate the rehydration response, larvae were first desiccated, then rehydrated for 6 h at 100% RH and then in water for 6 h. Controls were held continuously at 100% RH. Protein analysis was performed using 2-DE and nanoscale capillary LC/MS/MS. Twenty-four identified proteins changed in abundance in response to desiccation: 16 were more abundant and 8 were less abundant; 84% of these proteins were contractile or cytoskeletal proteins. Thirteen rehydration-regulated proteins were identified: 8 were more abundant and 5 were less abundant, and 69% of these proteins were also contractile or cytoskeletal proteins. Additional proteins responsive to desiccation and rehydration were involved in functions including stress responses, energy metabolism, protein synthesis, glucogenesis and membrane transport. We conclude that the major protein responses elicited by both desiccation and rehydration are linked to body contraction and cytoskeleton rearrangements.

  5. Microcystin-Bound Protein Patterns in Different Cultures of Microcystis aeruginosa and Field Samples

    Science.gov (United States)

    Wei, Nian; Hu, Lili; Song, Lirong; Gan, Nanqin

    2016-01-01

    Micocystin (MC) exists in Microcystis cells in two different forms, free and protein-bound. We examined the dynamic change in extracellular free MCs, intracellular free MCs and protein-bound MCs in both batch cultures and semi-continuous cultures, using high performance liquid chromatography and Western blot. The results showed that the free MC per cell remained constant, while the quantity of protein-bound MCs increased with the growth of Microcystis cells in both kinds of culture. Significant changes in the dominant MC-bound proteins occurred in the late exponential growth phase of batch cultures, while the dominant MC-bound proteins in semi-continuous cultures remained the same. In field samples collected at different months in Lake Taihu, the dominant MC-bound proteins were shown to be similar, but the amount of protein-bound MC varied and correlated with the intracellular MC content. We identified MC-bound proteins by two-dimensional electrophoresis immunoblots and mass spectrometry. The 60 kDa chaperonin GroEL was a prominent MC-bound protein. Three essential glycolytic enzymes and ATP synthase alpha subunit were also major targets of MC-binding, which might contribute to sustained growth in semi-continuous culture. Our results indicate that protein-bound MC may be important for sustaining growth and adaptation of Microcystis sp. PMID:27754336

  6. Focused ion beam patterned Fe thin films A study by selective area Stokes polarimetry and soft x-Ray microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Cook, P. J.; Shen, T. H.; Grundy, P. J.; Im, M.-Y.; Fischer, P.; Morton, S. A.; Kilcoyne, A. L. D.

    2010-11-14

    We demonstrate the potential to modify the magnetic behavior and structural properties of ferromagnetic thin films using focused ion beam 'direct-write' lithography. Patterns inspired by the split-ring resonators often used as components in meta-materials were defined upon 15 nm Fe films using a 30 keV Ga{sup +} focused ion beam at a dose of 2 x 10{sup 16} ions cm{sup -2}. Structural, chemical and magnetic changes to the Fe were studied using transmission soft X-ray microscopy at the ALS, Berkeley CA. X-ray absorption spectra showed a 23% reduction in the thickness of the film in the Ga irradiated areas, but no chemical change to the Fe was evident. X-ray images of the magnetic reversal process show domain wall pinning around the implanted areas, resulting in an overall increase in the coercivity of the film. Transmission electron microscopy showed significant grain growth in the implanted regions.

  7. Testing promotes long-term learning via stabilizing activation patterns in a large network of brain areas.

    Science.gov (United States)

    Keresztes, Attila; Kaiser, Daniel; Kovács, Gyula; Racsmány, Mihály

    2014-11-01

    The testing effect refers to the phenomenon that repeated retrieval of memories promotes better long-term retention than repeated study. To investigate the neural correlates of the testing effect, we used event-related functional magnetic resonance imaging methods while participants performed a cued recall task. Prior to the neuroimaging experiment, participants learned Swahili-German word pairs, then half of the word pairs were repeatedly studied, whereas the other half were repeatedly tested. For half of the participants, the neuroimaging experiment was performed immediately after the learning phase; a 1-week retention interval was inserted for the other half of the participants. We found that a large network of areas identified in a separate 2-back functional localizer scan were active during the final recall of the word pair associations. Importantly, the learning strategy (retest or restudy) of the word pairs determined the manner in which the retention interval affected the activations within this network. Recall of previously restudied memories was accompanied by reduced activation within this network at long retention intervals, but no reduction was observed for previously retested memories. We suggest that retrieval promotes learning via stabilizing cue-related activation patterns in a network of areas usually associated with cognitive and attentional control functions.

  8. Spatial patterns and movements of red king and Tanner crabs: Implications for the design of marine protected areas

    Science.gov (United States)

    Taggart, S.J.; Mondragon, J.; Andrews, A.G.; Nielsen, J.K.

    2008-01-01

    Most examples of positive population responses to marine protected areas (MPAs) have been documented for tropical reef species with very small home ranges; the utility of MPAs for commercially harvested temperate species that have large movement patterns remains poorly tested. We measured the distribution and abundance of red king Paralithodes camtschaticus and Tanner Chionoecetes bairdi crabs inside and outside of MPAs in Glacier Bay National Park, Alaska, USA. By tagging a sub-sample of crabs with sonic tags, we estimated the movement of adult crabs from one of the MPAs (Muir Inlet) into the central portion of Glacier Bay where fishing still occurs. Tanner crabs and red king crabs moved similar average distances per day, although Tanner crabs had a higher transfer out of the Muir Inlet MPA into the central bay. Tanner crab movements were characterized by large variation among individual crabs, both in distance and direction traveled, while red king crabs migrated seasonally between 2 specific areas. Although Tanner crabs exhibited relatively large movements, distribution and abundance data suggest that they may be restricted at large spatial scales by habitat barriers. MPAs that are effective at protecting king and especially Tanner crab brood stock from fishing mortality will likely need to be larger than is typical of MPAs worldwide. However, by incorporating information on the seasonal movements of red king crabs and the location of habitat barriers for Tanner crabs, MPAs could likely be designed that would effectively protect adults from fishing mortality. ?? Inter-Research 2008.

  9. Lipid transfer protein-linked hazelnut allergy in children from a non-Mediterranean birch-endemic area

    NARCIS (Netherlands)

    Flinterman, Annebeth E.; Akkerdaas, Jaap H.; Jager, Constance F. den Hartog; Rigby, Neil M.; Fernandez-Rivas, Montserrat; Hoekstra, Maarten O.; Bruijnzeel-Koomen, Carla A.; Knuist, Andr C.; van Ree, Ronald; Pasmans, Suzanne G.

    2008-01-01

    Background: Hazelnut allergy in birch pollen-exposed areas is usually due to cross-reactivity (Cor a 1 and 2) and is usually mild in nature (oral allergy). In areas without birches, severe reactions are more prevalent and linked to sensitization to the lipid transfer protein (LTP) Cor a 8. Objective

  10. The identification of global patterns and unique signatures of proteins across 14 environments using outer membrane proteomics of bacteria.

    Science.gov (United States)

    Schliep, Martin; Ryall, Ben; Ferenci, Thomas

    2012-11-01

    We test the hypothesis that organisms sourced from different environments exhibit unique fingerprints in macromolecular composition. Experimentally, we followed proteomic changes with 14 different sub-lethal environmental stimuli in Escherichia coli at controlled growth rates. The focus was on the outer membrane sub-proteome, which is known to be extremely sensitive to environmental controls. The analyses surprisingly revealed that pairs of proteins belonging to very different regulons, such as Slp and OmpX or FadL and OmpF, have the closest patterns of change with the 14 conditions. Fe-limited and cold-cultured bacteria have the most distinct global patterns of spot changes, but the patterns with fast growth and oxygen limitation are the closest amongst the 14 environments. These unexpected but statistically robust results suggest that we have an incomplete picture of bacterial regulation across different stress responses; baseline choices and growth-rate influences are probably underestimated factors in such systems-level analysis. In terms of our aim of getting a unique profile for each of the 14 investigated environments, we find that it is unnecessary to compare all the proteins in a proteome and that a panel of five proteins is sufficient for identification of environmental fingerprints. This demonstrates the future feasibility of tracing the history of contaminating bacteria in hospitals, foods or industrial settings as well as for released organisms and biosecurity purposes.

  11. Ultrasound Technologies for the Spatial Patterning of Cells and Extracellular Matrix Proteins and the Vascularization of Engineered Tissue

    Science.gov (United States)

    Garvin, Kelley A.

    Technological advancements in the field of tissue engineering could save the lives of thousands of organ transplant patients who die each year while waiting for donor organs. Currently, two of the primary challenges preventing tissue engineers from developing functional replacement tissues and organs are the need to recreate complex cell and extracellular microenvironments and to vascularize the tissue to maintain cell viability and function. Ultrasound is a form of mechanical energy that can noninvasively and nondestructively interact with tissues at the cell and protein level. In this thesis, novel ultrasound-based technologies were developed for the spatial patterning of cells and extracellular matrix proteins and the vascularization of three-dimensional engineered tissue constructs. Acoustic radiation forces associated with ultrasound standing wave fields were utilized to noninvasively control the spatial organization of cells and cell-bound extracellular matrix proteins within collagen-based engineered tissue. Additionally, ultrasound induced thermal mechanisms were exploited to site-specifically pattern various extracellular matrix collagen microstructures within a single engineered tissue construct. Finally, ultrasound standing wave field technology was used to promote the rapid and extensive vascularization of three-dimensional tissue constructs. As such, the ultrasound technologies developed in these studies have the potential to provide the field of tissue engineering with novel strategies to spatially pattern cells and extracellular matrix components and to vascularize engineered tissue, and thus, could advance the fabrication of functional replacement tissues and organs in the field of tissue engineering.

  12. Gene expression profiles and phosphorylation patterns of AMP-activated protein kinase subunits in various mesenchymal cell types

    Institute of Scientific and Technical Information of China (English)

    Wang Yugang; Fan Qiming; Ma Rui; Lin Wentao; Tang Tingting

    2014-01-01

    Background Recent studies on bone have shown an endocrine role of the skeleton,which could be impaired in various human diseases,including osteoporosis,obesity,and diabetes-associated bone diseases.As a sensor and regulator of energy metabolism,AMP-activated protein kinase (AMPK) may also play an important role in the regulation of bone metabolism.The current study aimed to establish the expression profiles and phosphorylation patterns of AMPK subunits in several mesenchymal cell types.Methods Reverse transcription-polymerase chain reaction (PCR) for relative quantification,real-time PCR for absolute quantification,and Western blotting were used to investigate the gene expression profiles and phosphorylation patterns of AMPK subunits in several mesenchymal cell types,including primary human mesenchymal stem cells (hMSCs) and hFOB,Saos-2,C3H/10T1/2,MC3T3-E1,3T3-L1,and C2C12 cells.Results AMPKα1 and AMPKβ1 mRNAs were abundantly expressed in all cell types.AMPKY1 mRNA was abundantly expressed in C3H/10T1/2,MC3T3-E1,3T3-L1,and C2C12 but not detected in human-derived cell types.AMPKY2 mRNA was mildly expressed in all cell types.AMPKα1 protein was highly expressed in all cell types and AMPKα2 protein was highly expressed only in hFOB and Saos-2 cells.AMPKβ1 protein was abundantly expressed in all cell types except for Saos-2,in which AMPKβ2 protein overwhelmed AMPKβ1 expression.AMPKy1 and AMPKY2 proteins were expressed in C3H/10T1/2,MC3T3-E1,3T3-L1,and C2C12 cells and only AMPKY2 protein was expressed in hMSCs,hFOB and Saos2 cells.AMPKα was phosphorylated at Thr172 and Ser485 and AMPKβ1 was phosphorylated at Ser108 and Ser182 in all cell types with a specific pattern in each cell type.Conclusion The combination of AMPK α,β,and Y subunits and phosphorylation of AMPKα (Thr172 and Ser485) and AMPKβ1 (Ser108 and Ser182) showed a specific pattern in each cell type.

  13. Changes in expression pattern of selected endometrial proteins following mesenchymal stem cells infusion in mares with endometrosis.

    Directory of Open Access Journals (Sweden)

    Lisley I Mambelli

    Full Text Available Mesenchymal stem cells (MSCs due to their self-renewal potential and differentiation capacity are useful for tissue regeneration. Immunomodulatory and trophic properties of MSCs were demonstrated suggesting their use as medicinal signaling cells able to positively change local environment in injured tissue. Equine endometrosis is a progressive degenerative disease responsible for glandular alterations and endometrial fibrosis which causes infertility in mares. More precisely, this disease is characterized by phenotypic changes in the expression pattern of selected endometrial proteins. Currently, no effective treatment is available for endometrosis. Herein, we aimed at the evaluation of expression pattern of these proteins after allogeneic equine adipose tissue-derived multipotent mesenchymal stem cells (eAT-MSCs infusion as well as at testing the capacity of these cells to promote endometrial tissue remodeling in mares with endometrosis. eAT-MSC (2 × 10(7/animal were transplanted into mares' uterus and control animals received only placebo. Uterine biopsies were collected before (day 0 and after (days 7, 21 and 60 cells transplantation. Conventional histopathology as well as expression analysis of such proteins as laminin, vimentin, Ki-67-antigen, α-smooth muscle actin (α-SMA and cytokeratin 18 (CK18 have been performed before and after eAT-MSCs transplantation. We demonstrated that eAT-MSCs induced early (at day 7 remodeling of endometrial tissue microenvironment through changes observed in intra cellular and intra glandular localization of aforementioned proteins. We demonstrated that eAT-MSCs were able to positively modulate the expression pattern of studied secretory proteins as well as, to promote the induction of glandular epithelial cells proliferation suggesting local benefits to committed endometrial tissue environment after eAT-MSCs transplantation.

  14. Diversity in transcripts and translational pattern of stress proteins in marine extremophiles

    Digital Repository Service at National Institute of Oceanography (India)

    Nath, I.V.A.; LokaBharathi, P.A.

    in the cell under normal conditions, but at very low concentrations. When a cell undergoes stress above their physiological tolerance level, stress proteins are produced in greater quantities. They help the defective-shaped proteins to acquire proper.... Identical protein profiles were also produced in P. abyssi (Marteinsson et al., 1999). Mesophiles In deep sea habitat, the interactions of different parameters like pressure and cold produce complex stress response in mesophiles and it is practically...

  15. High-resolution spatial patterns of long-term mean concentrations of air pollutants in Haifa Bay area

    Science.gov (United States)

    Yuval; Broday, David M.

    High-resolution maps of the mean concentrations of SO2, NO, NO2, O3, and PM10 in the period 2002-2004 were produced using half-hourly data from the local air quality monitoring network in Haifa Bay area, Israel. The network consists of 20 monitoring stations within an area of 206km2, which encompasses a major industrial and power generation centre in the midst of a population of about 500 000. The pollutants' spatial features agree well with their known sources and the expected dispersion by the prevailing meteorology. The ranking of their spatial variations agree with published observations on larger spatial scales. The high-resolution maps capture in a small spatial scale the NOx and O3 cycle relationships expected by theory, and previously observed by analyses of monitoring time series. High correlation was found between the spatial patterns of the PM10, NOx and O3, whereas the correlation between the spatial features of the PM10 and SO2 is low. This suggests that the traffic, a major source of NOx, rather than industry, the major source of SO2, is the main contributor to the anthropogenic PM10 in the study area. This inference is corroborated by the low sulphur to nitrogen ratio throughout the region, which is typical of traffic-dominated pollution. A general conclusion drawn from this study is that high-resolution monitoring and mapping can significantly contribute to air quality management programmes in terms of both pollution abatement and exposure and risk assessment.

  16. Distinct MRI pattern in lesional and perilesional area after traumatic brain injury in rat--11 months follow-up.

    Science.gov (United States)

    Immonen, Riikka J; Kharatishvili, Irina; Niskanen, Juha-Pekka; Gröhn, Heidi; Pitkänen, Asla; Gröhn, Olli H J

    2009-01-01

    To understand the dynamics of progressive brain damage after lateral fluid-percussion induced traumatic brain injury (TBI) in rat, which is the most widely used animal model of closed head TBI in humans, MRI follow-up of 11 months was performed. The evolution of tissue damage was quantified using MRI contrast parameters T(2), T(1rho), diffusion (D(av)), and tissue atrophy in the focal cortical lesion and adjacent areas: the perifocal and contralateral cortex, and the ipsilateral and contralateral hippocampus. In the primary cortical lesion area, which undergoes remarkable irreversible pathologic changes, MRI alterations start at 3 h post-injury and continue to progress for up to 6 months. In more mildly affected perifocal and hippocampal regions, the robust alterations in T(2), T(1rho), and D(av) at 3 h to 3 d post-injury normalize within the next 9-23 d, and thereafter, progressively increase for several weeks. The severity of damage in the perifocal and hippocampal areas 23 d post-injury appeared independent of the focal lesion volume. Magnetic resonance spectroscopy (MRS) performed at 5 and 10 months post-injury detected metabolic alterations in the ipsilateral hippocampus, suggesting ongoing neurodegeneration and inflammation. Our data show that TBI induced by lateral fluid-percussion injury triggers long-lasting alterations with region-dependent temporal profiles. Importantly, the temporal pattern in MRI parameters during the first 23 d post-injury can indicate the regions that will develop secondary damage. This information is valuable for targeting and timing interventions in studies aiming at alleviating or reversing the molecular and/or cellular cascades causing the delayed injury.

  17. SHH Protein Variance in the Limb Bud Is Constrained by Feedback Regulation and Correlates with Altered Digit Patterning

    Directory of Open Access Journals (Sweden)

    Rui Zhang

    2017-03-01

    Full Text Available mRNA variance has been proposed to play key roles in normal development, population fitness, adaptability, and disease. While variance in gene expression levels may be beneficial for certain cellular processes, for example in a cell’s ability to respond to external stimuli, variance may be detrimental for the development of some organs. In the bilaterally symmetric vertebrate limb buds, the amount of Sonic Hedgehog (SHH protein present at specific stages of development is essential to ensure proper patterning of this structure. To our surprise, we found that SHH protein variance is present during the first 10 hr of limb development. The variance is virtually eliminated after the first 10 hr of limb development. By examining mutant animals, we determined that the ability of the limb bud apical ectodermal ridge (AER to respond to SHH protein was required for reducing SHH variance during limb formation. One consequence of the failure to eliminate variance in SHH protein was the presence of polydactyly and an increase in digit length. These data suggest a potential novel mechanism in which alterations in SHH variance during evolution may have driven changes in limb patterning and digit length.

  18. A novel C1qDC protein acting as pattern recognition receptor in scallop Argopecten irradians.

    Science.gov (United States)

    Wang, Leilei; Wang, Lingling; Kong, Pengfei; Yang, Jialong; Zhang, Huan; Wang, Mengqiang; Zhou, Zhi; Qiu, Limei; Song, Linsheng

    2012-08-01

    The C1q domain containing (C1qDC) proteins refer to a family of proteins containing the versatile charge pattern recognition globular C1q domain in the C-terminus, which could bind various ligands including PAMPs and trigger a serial of immune response. In this study, a novel C1qDC protein was identified from Argopecten irradians (designated as AiC1qDC-2). Its full-length cDNA was of 1062 bp with an open reading frame of 720 bp encoding a polypeptide of 240 amino acids containing a typical gC1q domain. This gC1q domain possessed the typical 10-stranded β-sandwich fold with a jelly-roll topology common to all C1q family members, and shared high homology with most of the other identified gC1q domains. The mRNA transcripts of AiC1qDC-2 were mainly detected in hepatopancreas, and also marginally detectable in mantle, gonad, adductor, gill and hemocytes. Its relative expression level in hemocytes was significantly up-regulated after challenges of fungi Pichia pastoris GS115 (P pattern recognition receptor to recognize various PAMPs on different pathogens in the innate immune responses of scallop, and provided new clues to understand the role of invertebrate C1qDC proteins in the ancient complement system.

  19. C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability.

    Science.gov (United States)

    Kumar, Manjeet; Balaji, Petety V

    2014-02-01

    C-H…pi interactions are a class of non-covalent interactions found in different molecular systems including organic crystals, proteins and nucleic acids. High-resolution protein structures have been analyzed in the present study to delineate various aspects of C-H…pi interactions. Additionally, to determine the extent to which redundancy of a database biases the outcome, two datasets differing from each other in the level of redundancy have been analyzed. On average, only one out of six {with C-H(Aro) group} or eight {with C-H(Ali) group} residues in a protein participate as C-H group donors. Neither the frequency of occurrence in proteins nor the number of C-H groups present in it is correlated to the propensity of an amino acid to participate in C-H…pi interactions. Most of the residues that participate in C-H…pi interactions are solvent-shielded. Solvent shielded nature of most of the C-H…pi interactions and prevalence of intra- as well as inter-secondary structural element C-H…pi interactions suggest that the contribution of these interactions to the enthalpy of folded form will be significant. The separation in the primary structure between donor and acceptor residues is found to be correlated to secondary structure type. Other insights obtained from this study include the presence of networks of C-H…pi interactions spanning multiple secondary structural elements. To our knowledge this has not been reported so far. A substantial number of residues involved in C-H…pi interactions are found in catalytic and ligand binding sites suggesting their possible role in maintaining active site geometry. No significant differences of C-H…pi interactions in the two datasets are found for any of the parameters/features analyzed.

  20. Analysis of the Protein Electrophoresis Patterns of Curvularia Lunata in Maize and Immunological Detection of the Pathogenic Culture

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Twelve isolates of Curvularia lunata and six related species from maize or other host plants are examined for the analysis of polyacrylamide gel electrophores is(SDS-PAGE)patterns of their soluble proteins. Differences exist significantly among different species and the same species.There is a special protein band for Curvularia at relative mobility value 0.177 (Rf 0.177)and a special protein band for C.lunata at Rf 0.225.Two kinds of primary antibodies to C.lunata are used to indirect ELISA and Avidin Biotinperoxidase Complex (ABC) immun oassay to evaluate their detecting sensitivity and specificity.The sensitivity of ABC immuno-assay is higher than indirectELISA.APAbs to C.lunata is special to C.lunata.

  1. CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.

    Science.gov (United States)

    Carrillo-Tripp, Mauricio; Montiel-García, Daniel Jorge; Brooks, Charles L; Reddy, Vijay S

    2015-04-01

    Structural analysis and visualization of protein-protein interactions is a challenging task since it is difficult to appreciate easily the extent of all contacts made by the residues forming the interfaces. In the case of viruses, structural analysis becomes even more demanding because several interfaces coexist and, in most cases, these are formed by hundreds of contacting residues that belong to multiple interacting coat proteins. CapsidMaps is an interactive analysis and visualization tool that is designed to benefit the structural virology community. Developed as an improved extension of the φ-ψ Explorer, here we describe the details of its design and implementation. We present results of analysis of a spherical virus to showcase the features and utility of the new tool. CapsidMaps also facilitates the comparison of quaternary interactions between two spherical virus particles by computing a similarity (S)-score. The tool can also be used to identify residues that are solvent exposed and in the process of locating antigenic epitope regions as well as residues forming the inside surface of the capsid that interact with the nucleic acid genome. CapsidMaps is part of the VIPERdb Science Gateway, and is freely available as a web-based and cross-browser compliant application at http://viperdb.scripps.edu.

  2. Protein pattern of canola (Brassica napus L. changes in response to salt and salicylic acid in vitro

    Directory of Open Access Journals (Sweden)

    Razavizadeh Roya

    2015-12-01

    Full Text Available The effect of salicylic acid (SA on the salt (NaCl tolerance mechanism was studied in canola plants (oilseed rape, Brassica napus L. by molecular and physiological experiments in plant tissue culture. Seeds of B. napus ‘Ocapy’ were germinated at 0, 50, and 100 mM NaCl on Murashige and Skoog (MS medium containing different levels (0, 2, and 5 μM of SA for 4 weeks. Total chlorophyll, carotenoid, and flavonoid content increased in response to interactive effects of SA and NaCl treatments at some concentrations. Proline content was increased under salt and SA treatments in shoot and root tissues. Salt alone and in combination with SA increased the total soluble protein content of shoots only, while the different concentrations of SA in the culture media affected variously the total soluble protein content. Protein patterns of shoots and roots showed some remarkable differences, based on gel electrophoresis and the consequent analysis of bands by ImageJ program. The relative expression of 15 and 12 protein bands in shoots and roots, respectively, differed under the applied treatments. In addition, the protein profile indicated that salinity and SA regulate the expression of salt-stress-inducible proteins as well as induced de novo synthesis of specific polypeptides. The findings may help to explain the salt tolerance mechanisms and to produce salt-tolerant canola plants.

  3. The Disulfide Bond Pattern of Transforming Growth Factor Beta-Induced protein

    DEFF Research Database (Denmark)

    Lukassen, Marie V; Scavenius, Carsten; Thøgersen, Ida B;

    2016-01-01

    Transforming growth factor beta-induced protein (TGFBIp) is an extracellular matrix protein composed of an NH2-terminal cysteine-rich domain (CRD) annotated as an emilin (EMI) domain, and four fasciclin-1 (FAS1-1 to FAS1-4) domains. Mutations in the gene cause corneal dystrophies, a group...

  4. Spatial and temporal patterns of burned area over Brazilian Cerrado from 2005 to 2015 using remote sensing data

    Science.gov (United States)

    Libonati, Renata; DaCamara, Carlos; Setzer, Alberto

    2016-04-01

    Although Cerrado is a fire-dependent biome, current agriculture practices have significantly modified the native fire regime. Moreover, over the last decades, climate conditions, such as intensive droughts, have contributed to enhance the effects of anthropogenic activities, and consequently fire, over the region. For instance, during the 2010 extreme drought there was an increase of 100% in the number of fire pixels detected by just one polar orbiting satellite (information online at http://www.cptec.inpe.br/queimadas). A better characterization of spatial and temporal fire patterns over Cerrado is therefore crucial to uncover both climate and anthropogenic influences in this ecosystem. Additionally, information about the extent, location and time of burned areas (BA) over Cerrado is especially useful to a wide range of users, from government agencies, research groups and ecologists, to fire managers and NGOs. Instruments on-board satellites are the only available operational means to collect BA data at appropriated spatial and temporal scales and in a cost-effective way. Several global BA products derived from remote sensed information have been developed over the last years using a variety of techniques based on different spatial, spectral and temporal resolutions. Although presenting similar inter-annual variability, there are marked differences among the products both in magnitude and location of the area burnt. The development of regional algorithms which take into account local characteristics such as vegetation type, soil and climate is therefore an added value to the existing information. We present a monthly BA product (AQM) for Brazil based on information from MODIS 1km. The algorithm was specifically designed for ecosystems in Brazil and the procedure represents the first initiative of an automated method for BA monitoring using remote sensing information in the country. The product relies on an algorithm that takes advantage of the ability of MIR

  5. Enhanced protein adsorption and patterning on nanostructured latex-coated paper.

    Science.gov (United States)

    Juvonen, Helka; Määttänen, Anni; Ihalainen, Petri; Viitala, Tapani; Sarfraz, Jawad; Peltonen, Jouko

    2014-06-01

    Specific interactions of extracellular matrix proteins with cells and their adhesion to the substrate are important for cell growth. A nanopatterned latex-coated paper substrate previously shown to be an excellent substrate for cell adhesion and 2D growth was studied for directed immobilization of proteins. The nanostructured latex surface was formed by short-wavelength IR irradiation of a two-component latex coating consisting of a hydrophilic film-forming styrene butadiene acrylonitrile copolymer and hydrophobic polystyrene particles. The hydrophobic regions of the IR-treated latex coating showed strong adhesion of bovine serum albumin (cell repelling protein), fibronectin (cell adhesive protein) and streptavidin. Opposite to the IR-treated surface, fibronectin and streptavidin had a poor affinity toward the untreated pristine latex coating. Detailed characterization of the physicochemical surface properties of the latex-coated substrates revealed that the observed differences in protein affinity were mainly due to the presence or absence of the protein repelling polar and charged surface groups. The protein adsorption was assisted by hydrophobic (dehydration) interactions.

  6. Different zinc sensitivity of Brassica organs is accompanied by distinct responses in protein nitration level and pattern.

    Science.gov (United States)

    Feigl, Gábor; Kolbert, Zsuzsanna; Lehotai, Nóra; Molnár, Árpád; Ördög, Attila; Bordé, Ádám; Laskay, Gábor; Erdei, László

    2016-03-01

    Zinc is an essential microelement, but its excess exerts toxic effects in plants. Heavy metal stress can alter the metabolism of reactive oxygen (ROS) and nitrogen species (RNS) leading to oxidative and nitrosative damages; although the participation of these processes in Zn toxicity and tolerance is not yet known. Therefore this study aimed to evaluate the zinc tolerance of Brassica organs and the putative correspondence of it with protein nitration as a relevant marker for nitrosative stress. Both examined Brassica species (B. juncea and B. napus) proved to be moderate Zn accumulators; however B. napus accumulated more from this metal in its organs. The zinc-induced damages (growth diminution, altered morphology, necrosis, chlorosis, and the decrease of photosynthetic activity) were slighter in the shoot system of B. napus than in B. juncea. The relative zinc tolerance of B. napus shoot was accompanied by moderate changes of the nitration pattern. In contrast, the root system of B. napus suffered more severe damages (growth reduction, altered morphology, viability loss) and slighter increase in nitration level compared to B. juncea. Based on these, the organs of Brassica species reacted differentially to excess zinc, since in the shoot system modification of the nitration pattern occurred (with newly appeared nitrated protein bands), while in the roots, a general increment in the nitroproteome could be observed (the intensification of the same protein bands being present in the control samples). It can be assumed that the significant alteration of nitration pattern is coupled with enhanced zinc sensitivity of the Brassica shoot system and the general intensification of protein nitration in the roots is attached to relative zinc endurance.

  7. Patterns of benthic bacterial diversity in coastal areas contaminated by heavy metals, Polycyclic Aromatic Hydrocarbons (PAHs and Polychlorinated Biphenyls (PCBs

    Directory of Open Access Journals (Sweden)

    Grazia Marina eQuero

    2015-10-01

    Full Text Available Prokaryotes in coastal sediments are fundamental players in the ecosystem functioning and regulate processes relevant in the global biogeochemical cycles. Nevertheless, knowledge on benthic microbial diversity patterns across spatial scales, or as function to anthropogenic influence, is still limited. We investigated the microbial diversity in two of the most chemically polluted sites along the coast of Italy. One site is the Po River Prodelta (Northern Adriatic Sea, which receives contaminant discharge from one of the largest rivers in Europe. The other site, the Mar Piccolo of Taranto (Ionian Sea, is a chronically-polluted area due to steel production plants, oil refineries, and intense maritime traffic. We collected sediments from 30 stations along gradients of contamination, and studied prokaryotic diversity using Illumina sequencing of amplicons of a 16S rDNA gene fragment. The main sediment variables and the concentration of eleven metals, PCBs and PAHs were measured. Chemical analyses confirmed the high contamination in both sites, with concentrations of PCBs particularly high and often exceeding the sediment guidelines. The analysis of more than 3 millions 16S rDNA sequences showed that richness decreased with higher contamination levels. Multivariate analyses showed that contaminants significantly shaped community composition. Assemblages differed significantly between the two sites, but showed wide within-site variations related with spatial gradients in the chemical contamination, and the presence of a core set of OTUs shared by the two geographically distant sites. A larger importance of PCB-degrading taxa was observed in the Mar Piccolo, suggesting their potential selection in this historically-polluted site. Our results indicate that sediment contamination by multiple contaminants significantly alter benthic prokaryotic diversity in coastal areas, and suggests considering the potential contribution of the resident microbes to

  8. Identification of Methanococcus Jannaschii Proteins in 2-D Gel Electrophoresis Patterns by Mass Spectrometry

    Science.gov (United States)

    Liang, X.

    1998-06-10

    The genome of Methanococcus jannaschii has been sequenced completely and has been found to contain approximately 1,770 predicted protein-coding regions. When these coding regions are expressed and how their expression is regulated, however, remain open questions. In this work, mass spectrometry was combined with two-dimensional gel electrophoresis to identify which proteins the genes produce under different growth conditions, and thus investigate the regulation of genes responsible for functions characteristic of this thermophilic representative of the methanogenic Archaea.

  9. Thermodynamic instability of viral proteins is a pathogen-associated molecular pattern targeted by human defensins.

    Science.gov (United States)

    Kudryashova, Elena; Koneru, Pratibha C; Kvaratskhelia, Mamuka; Strömstedt, Adam A; Lu, Wuyuan; Kudryashov, Dmitri S

    2016-09-01

    Human defensins are innate immune defense peptides with a remarkably broad repertoire of anti-pathogen activities. In addition to modulating immune response, inflammation, and angiogenesis, disintegrating bacterial membranes, and inactivating bacterial toxins, defensins are known to intercept various viruses at different stages of their life cycles, while remaining relatively benign towards human cells and proteins. Recently we have found that human defensins inactivate proteinaceous bacterial toxins by taking advantage of their low thermodynamic stability and acting as natural "anti-chaperones", i.e. destabilizing the native conformation of the toxins. In the present study we tested various proteins produced by several viruses (HIV-1, PFV, and TEV) and found them to be susceptible to destabilizing effects of human α-defensins HNP-1 and HD-5 and the synthetic θ-defensin RC-101, but not β-defensins hBD-1 and hBD-2 or structurally related plant-derived peptides. Defensin-induced unfolding promoted exposure of hydrophobic groups otherwise confined to the core of the viral proteins. This resulted in precipitation, an enhanced susceptibility to proteolytic cleavage, and a loss of viral protein activities. We propose, that defensins recognize and target a common and essential physico-chemical property shared by many bacterial toxins and viral proteins - the intrinsically low thermodynamic protein stability.

  10. Comprehensive Investigation of Areae Gastricae Pattern in Gastric Corpus using Magnifying Narrow Band Imaging Endoscopy in Patients with Chronic Atrophic Fundic Gastritis

    Science.gov (United States)

    Kanzaki, Hiromitsu; Uedo, Noriya; Ishihara, Ryu; Nagai, Kengo; Matsui, Fumi; Ohta, Takashi; Hanafusa, Masao; Hanaoka, Noboru; Takeuchi, Yoji; Higashino, Koji; Iishi, Hiroyasu; Tomita, Yasuhiko; Tatsuta, Masaharu; Yamamoto, Kazuhide

    2012-01-01

    Background: Barium radiographic studies have suggested the importance of evaluating areae gastricae pattern for the diagnosis of gastritis. Significance of endoscopic appearance of areae gastricae in the diagnosis of chronic atrophic fundic gastritis (CAFG) was investigated by image-enhanced endoscopy. Materials and Methods: Endoscopic images of the corpus lesser curvature were studied in 50 patients with CAFG. Extent of CAFG was evaluated with autofluorescence imaging endoscopy. The areae gastricae pattern was evaluated with 0.2% indigo carmine chromoendoscopy. Micro-mucosal structure was examined with magnifying chromoendoscopy and narrow band imaging. Results: In patients with small extent of CAFG, polygonal areae gastricae separated by a narrow intervening part of areae gastricae was observed, whereas in patients with wide extent of CAFG, the size of the areae gastricae decreased and the width of the intervening part of areae gastricae increased (p < 0.001). Most areae gastricae showed a foveola-type micro-mucosal structure (82.7%), while intervening part of areae gastricae had a groove-type structure (98.0%, p < 0.001). Groove-type mucosa had a higher grade of atrophy (p < 0.001) and intestinal metaplasia (p < 0.001) compared with foveola type. Conclusions: As extent of CAFG widened, multifocal groove-type mucosa that had high-grade atrophy and intestinal metaplasia developed among areae gastricae and increased along the intervening part of areae gastricae. Our observations facilitate our understanding of the development and progression of CAFG. PMID:22515361

  11. Dispersal pattern of the sand fly Lutzomyia neivai (Diptera: Psychodidae in a cutaneous leishmaniasis endemic rural area in Southeastern Brazil

    Directory of Open Access Journals (Sweden)

    Cláudio Casanova

    2005-11-01

    Full Text Available The dispersal pattern of the sand fly Lutzomyia neivai was studied through mark-release-recapture experiments in an American cutaneous leishmaniasis endemic rural area in Southeastern Brazil. Over 6500 specimens were marked with fluorescent powder and released in forest edge and peridomicile habitats from August to November 1999, February and April 2000. Recapture attempts were made using Shannon and CDC traps up to eight successive nights after releases. A total of 493 (7.58% specimens were recaptured. The number of recaptured males and females of L. neivai in CDC traps was not affected by the distance between the trap and the release points. Approximately 90% of males and females recaptured in CDC traps were caught up to 70 m from the release points. The maximum female flight range recorded was 128 m. The average flight range per day was less than 60 m for males and females. Of the flies released in forest edge, approximately 16% of the recaptured females were caught in Shannon traps in the peridomicile habitat. The results indicate that the movements of L. neivai are spatially focal and the possibility of dispersion from forest to peridomicile habitat may be an important way of contracting leishmaniasis in dwellings.

  12. Temporal patterns of domestic and wildlife rabies in central Namibia stock-ranching area, 1986-1996.

    Science.gov (United States)

    Courtin, F; Carpenter, T E; Paskin, R D; Chomel, B B

    2000-01-05

    Eleven years (1986-1996) of wildlife- and domestic-rabies data from the agriculture stock-ranching area of central Namibia were studied using time-series analysis. Nine hundred and sixty three rabies cases were observed in domestic ruminants (5.4 cases/mo), black-backed jackals (Canis mesomelas, 1.3 cases/mo), domestic dogs (0.5 case/mo), and bat-eared foxes (Otocyon megalotis, 0.1 case/mo). The incidence of rabies for all species did not change significantly over the whole study period. However, seasonal variations with an increase in the number of cases between June and November of each year, as well as 34 yr cyclical fluctuations were identified in domestic ruminants and black-backed jackals. The black-backed jackal time-series variable was a significant predictor of the domestic-ruminant and dog time-series variables. The rainfall seasonality combined with the seasonal reproductive pattern of the black-backed jackal appeared to be plausible explanations for the seasonal variations of rabies. However, there was no overall significant correlation between the cyclical weather fluctuations and the 3-4 yr cyclical rabies variations.

  13. Fructose-bisphosphate aldolase and enolase from Echinococcus granulosus: genes, expression patterns and protein interactions of two potential moonlighting proteins.

    Science.gov (United States)

    Lorenzatto, Karina Rodrigues; Monteiro, Karina Mariante; Paredes, Rodolfo; Paludo, Gabriela Prado; da Fonsêca, Marbella Maria; Galanti, Norbel; Zaha, Arnaldo; Ferreira, Henrique Bunselmeyer

    2012-09-10

    Glycolytic enzymes, such as fructose-bisphosphate aldolase (FBA) and enolase, have been described as complex multifunctional proteins that may perform non-glycolytic moonlighting functions, but little is known about such functions, especially in parasites. We have carried out in silico genomic searches in order to identify FBA and enolase coding sequences in Echinococcus granulosus, the causative agent of cystic hydatid disease. Four FBA genes and 3 enolase genes were found, and their sequences and exon-intron structures were characterized and compared to those of their orthologs in Echinococcus multilocularis, the causative agent of alveolar hydatid disease. To gather evidence of possible non-glycolytic functions, the expression profile of FBA and enolase isoforms detected in the E. granulosus pathogenic larval form (hydatid cyst) (EgFBA1 and EgEno1) was assessed. Using specific antibodies, EgFBA1 and EgEno1 were detected in protoscolex and germinal layer cells, as expected, but they were also found in the hydatid fluid, which contains parasite's excretory-secretory (ES) products. Besides, both proteins were found in protoscolex tegument and in vitro ES products, further suggesting possible non-glycolytic functions in the host-parasite interface. EgFBA1 modeled 3D structure predicted a F-actin binding site, and the ability of EgFBA1 to bind actin was confirmed experimentally, which was taken as an additional evidence of FBA multifunctionality in E. granulosus. Overall, our results represent the first experimental evidences of alternative functions performed by glycolytic enzymes in E. granulosus and provide relevant information for the understanding of their roles in host-parasite interplay.

  14. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

    Science.gov (United States)

    Shi, Tujin; Niepel, Mario; McDermott, Jason E; Gao, Yuqian; Nicora, Carrie D; Chrisler, William B; Markillie, Lye M; Petyuk, Vladislav A; Smith, Richard D; Rodland, Karin D; Sorger, Peter K; Qian, Wei-Jun; Wiley, H Steven

    2016-07-12

    Various genetic mutations associated with cancer are known to alter cell signaling, but it is not clear whether they dysregulate signaling pathways by altering the abundance of pathway proteins. Using a combination of RNA sequencing and ultrasensitive targeted proteomics, we defined the primary components-16 core proteins and 10 feedback regulators-of the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway in normal human mammary epithelial cells and then quantified their absolute abundance across a panel of normal and breast cancer cell lines as well as fibroblasts. We found that core pathway proteins were present at very similar concentrations across all cell types, with a variance similar to that of proteins previously shown to display conserved abundances across species. In contrast, EGFR and transcriptionally controlled feedback regulators were present at highly variable concentrations. The absolute abundance of most core proteins was between 50,000 and 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower amounts (2000 to 5000 copies per cell). MAPK signaling showed saturation in all cells between 3000 and 10,000 occupied EGFRs, consistent with the idea that adaptors limit signaling. Our results suggest that the relative stoichiometry of core MAPK pathway proteins is very similar across different cell types, with cell-specific differences mostly restricted to variable amounts of feedback regulators and receptors. The low abundance of adaptors relative to EGFR could be responsible for previous observations that only a fraction of total cell surface EGFR is capable of rapid endocytosis, high-affinity binding, and mitogenic signaling.

  15. "Hot cores" in proteins: Comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms

    Directory of Open Access Journals (Sweden)

    Bossa Francesco

    2008-02-01

    Full Text Available Abstract Background A wide variety of stabilizing factors have been invoked so far to elucidate the structural basis of protein thermostability. These include, amongst the others, a higher number of ion-pairs interactions and hydrogen bonds, together with a better packing of hydrophobic residues. It has been frequently observed that packing of hydrophobic side chains is improved in hyperthermophilic proteins, when compared to their mesophilic counterparts. In this work, protein crystal structures from hyper/thermophilic organisms and their mesophilic homologs have been compared, in order to quantify the difference of apolar contact area and to assess the role played by the hydrophobic contacts in the stabilization of the protein core, at high temperatures. Results The construction of two datasets was carried out so as to satisfy several restrictive criteria, such as minimum redundancy, resolution and R-value thresholds and lack of any structural defect in the collected structures. This approach allowed to quantify with relatively high precision the apolar contact area between interacting residues, reducing the uncertainty due to the position of atoms in the crystal structures, the redundancy of data and the size of the dataset. To identify the common core regions of these proteins, the study was focused on segments that conserve a similar main chain conformation in the structures analyzed, excluding the intervening regions whose structure differs markedly. The results indicated that hyperthermophilic proteins underwent a significant increase of the hydrophobic contact area contributed by those residues composing the alpha-helices of the structurally conserved regions. Conclusion This study indicates the decreased flexibility of alpha-helices in proteins core as a major factor contributing to the enhanced termostability of a number of hyperthermophilic proteins. This effect, in turn, may be due to an increased number of buried methyl groups in

  16. Correlation of acidic and basic carrier ampholyte and immobilized pH gradient two-dimensional gel electrophoresis patterns based on mass spectrometric protein identification

    DEFF Research Database (Denmark)

    Nawrocki, A; Larsen, Martin Røssel; Podtelejnikov, A V;

    1998-01-01

    Separation of proteins on either carrier ampholyte-based or immobilized pH gradient-based two-dimensional (2-D) gels gives rise to electrophoretic patterns that are difficult to compare visually. In this paper we have used matrix-assisted laser desorption/ionization mass spectrometry (MALDI......-MS) to determine the identities of 335 protein spots in these two 2-D gel systems, including a substantial number of basic proteins which had never been identified before. Proteins that were identified in both gel systems allowed us to cross-reference the gel patterns. Vector analysis of these cross...

  17. JUNK FOOD CONSUMPTION PATTERN AND OBESITY AMONG SCHOOL GOING CHILDREN IN AN URBAN FIELD PRACTICE AREA: A CROSS SECTIONAL STUDY

    Directory of Open Access Journals (Sweden)

    Vidya

    2015-03-01

    Full Text Available BACKGROUND: Junk food simply means an empty calorie food; it lacks in micronutrients such as vitamins, minerals, or amino acids, and fibre but has high energy (calories. During school - age years, children begin to establish habits for eating and exercise that stick w ith them for their entire lives. If children establish healthy habits, their risk for developing many chronic diseases will be greatly decreased. The family, friends, schools, and community resources in a child’s environment reinforce lifestyle habits rega rding diet and activity. OBJECTIVES: To study the fast food consumptions pattern and fast food preferences among the school going children (9 - 13yrs and some of the determinants related to fast food consumption . STUDY SETTING: Department of Community Medic ine in an Urban field practice area of Rajarajeswari Medical College & Hospital, Bangalore. STUDY DESIGN: Cross - sectional study. STUDY DURATION: Three months duration ( Oct – Dec 2014. STUDY POPULATION: school students studying in V th standard to X th standar d. SAMPLE SIZE : The selected school had a strength of 200 students. Hence complete enumeration of the students was considered for this study. DATA COLLECTION : by using pre - structured questionnaire by interview method. The variables included were socio - demographic profile, measurement of height, weight and questions related to junk food consumption and its patterns. DATA ANALYSIS: using statistics software SPSS 20. Mean and standard deviation was calculated for anthropometric measurements. Test of significance for proportions was done by Chi - square test. RESULTS: Among 200 study subjects, 107 were male (53.5% and 93 females (46.5%. Majority of the students wer e in the age group of 12 - 15 years ( 66% and 9 - 11 years ( 34%. Snacks (41%, Fast food (25.50%, soft drinks (17.50% and candies (16% were the favourite junk foods among the study subjects. Taste and time factors, watching television while consuming

  18. Distinct Patterns of Gene and Protein Expression Elicited by Organophosphorus Pesticides in Caenorhabditis elegans

    Science.gov (United States)

    2009-01-01

    triglyceride transfer protein, large subunit -1.7 1 3 -1.3 -2.4 -2.0 pmt-1 NP_494990.2 NP_494991.1 NP_871997.1 phosphoethanolamine N...www.biomedcentral.com/1471-2164/10/202 Page 15 of 21 (page number not for citation purposes) hydrolysis of the phosphate [73]. However, as many car...particular interest because this enzyme is a known tar- get for OP inhibition. The NTE protein affects lipid metab- olism, and its inhibition causes

  19. Phylogenetic relationships among wine yeast strains based on electrophoretic whole-cell protein patterns.

    Science.gov (United States)

    Guillamón, J M; Querol, A; Jiménez, M; Huerta, T

    1993-04-01

    In the present work, a phylogenetic study based on protein electrophoretic profiles of Saccharomyces strains isolated from different Spanish wine regions has been carried out. Qualitative differences between the protein electrophoregrams were found at inter- and intraspecific level, but not between electrophoregrams of strains isolated at the same ecosystem. The numerical analysis of these results allowed us to conclude that intraspecific relationships are determined by ecological factors, as well as human influences (dispersion and artificial selection). A correlation between ecological and/or geographical origin and the relationships among strains was observed.

  20. Rapid photochemical surface patterning of proteins in thiol-ene based microfluidic devices

    DEFF Research Database (Denmark)

    Lafleur, Josiane P.; Kwapiszewski, Radoslaw; Jensen, Thomas Glasdam;

    2013-01-01

    The suitable optical properties of thiol–ene polymers combined with the ease of modifying their surface for the attachment of recognition molecules make them ideal candidates in many biochip applications. This paper reports the rapid one-step photochemical surface patterning of biomolecules...... in microfluidic thiol–ene chips. This work focuses on thiol–ene substrates featuring an excess of thiol groups at their surface. The thiol–ene stoichiometric composition can be varied to precisely control the number of surface thiol groups available for surface modification up to an average surface density of 136...... ! 17 SH nm"2. Biotin alkyne was patterned directly inside thiol–ene microchannels prior to conjugation with fluorescently labelled streptavidin. The surface bound conjugates were detected by evanescent waveinduced fluorescence (EWIF), demonstrating the success of the grafting procedure and its...

  1. Expression Pattern of Lysosomal Protective Protein/Cathepsin A: Implications for the analysis of hnman galactosialidosis

    NARCIS (Netherlands)

    R.J. Rottier (Robbert)

    1998-01-01

    textabstractThe lysosome represents a well characterized, membrane-contained intracellular digestive system. Iu this important organelle a battery of lysosomal hydro lases and accessory proteins work in concert on the step-wise conversion of macromolecular substrates into small biological building b

  2. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway

    Energy Technology Data Exchange (ETDEWEB)

    Shi, T.; Niepel, M.; McDermott, J. E.; Gao, Y.; Nicora, C. D.; Chrisler, W. B.; Markillie, L. M.; Petyuk, V. A.; Smith, R. D.; Rodland, K. D.; Sorger, P. K.; Qian, W. -J.; Wiley, H. S.

    2016-07-12

    It is not known whether cancer cells generally show quantitative differences in the expression of signaling pathway proteins that could dysregulate signal transduction. To explore this issue, we first defined the primary components of the EGF-MAPK pathway in normal human mammary epithelial cells, identifying 16 core proteins and 10 feedback regulators. We then quantified their absolute abundance across a panel of normal and cancer cell lines. We found that core pathway proteins were expressed at very similar levels across all cell types. In contrast, the EGFR and transcriptionally controlled feedback regulators were expressed at highly variable levels. The absolute abundance of most core pathway proteins was between 50,000- 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower levels (2,000-5,000 per cell). MAPK signaling showed saturation in all cells between 3,000-10,000 occupied EGFR, consistent with the idea that low adaptor levels limit signaling. Our results suggest that the core MAPK pathway is essentially invariant across different cell types, with cell- specific differences in signaling likely due to variable levels of feedback regulators. The low abundance of adaptors relative to the EGFR could be responsible for previous observation of saturable signaling, endocytosis, and high affinity EGFR.

  3. Brain inflammation in a chronic epilepsy model : Evolving pattern of the translocator protein during epileptogenesis

    NARCIS (Netherlands)

    Amhaoul, Halima; Hamaide, Julie; Bertoglio, Daniele; Reichel, Stephanie Nadine; Verhaeghe, Jeroen; Geerts, Elly; Dam, van Debby; De Deyn, Peter Paul; Kumar-Singh, Samir; Katsifis, Andrew; Van der Linden, Annemie; Staelens, Steven; Dedeurwaerdere, Stefanie

    2015-01-01

    Aims: A hallmark in the neuropathology of temporal lobe epilepsy is brain inflammation which has been suggested as both a biomarker and a new mechanistic target for treatments. The translocator protein (TSPO), due to its high upregulation under neuroinflammatory conditions and the availability of se

  4. Raft protein clustering alters N-Ras membrane interactions and activation pattern

    NARCIS (Netherlands)

    Eisenberg, Sharon; Beckett, Alison J; Prior, Ian A; Dekker, Frank J; Hedberg, Christian; Waldmann, Herbert; Ehrlich, Marcelo; Henis, Yoav I; Dekker, Frank

    2011-01-01

    The trafficking, membrane localization, and lipid raft association of Ras proteins, which are crucial oncogenic mediators, dictate their isoform-specific biological responses. Accordingly, their spatiotemporal dynamics are tightly regulated. While extensively studied for H- and K-Ras, such informati

  5. Electron transfer patterns of the di-heme protein cytochrome c(4) from Pseudomonas stutzeri

    DEFF Research Database (Denmark)

    Raffalt, Anders Christer; Schmidt, L.; Christensen, Hans Erik Mølager;

    2009-01-01

    We report kinetic data for the two-step electron transfer (ET) oxidation and reduction of the two-domain di-heme redox protein Pseudomonas stutzeri cytochrome (cyt) c(4) by [Co(bipy)(3)](2- 3-) (bipy = 2,2'-bipyridine). Following earlier reports, the data accord with both bi- and tri-exponential ...

  6. The pattern of protein retention in pigs from 2 to 120 kg live weight

    DEFF Research Database (Denmark)

    Chwalibog, André; Jakobsen, K; Thorbek, G

    1996-01-01

    1. Data from experiments with growing pigs of Danish Landrace (n = 782) including measurements of nitrogen and energy balances were scrutinized in order to select observations in which maximum protein retention (RP) were expected. 2. The criterions for selection were based on intake of metaboliza...

  7. Expression patterns of glial fibrillary acidic protein (GFAP)-delta in epilepsy-associated lesional pathologies

    NARCIS (Netherlands)

    L. Martinian; K. Boer; J. Middeldorp; E.M. Hol; S.M. Sisodiya; W. Squier; E.M.A. Aronica; M. Thom

    2009-01-01

    Aims: Glial fibrillary acidic protein (GFAP)-delta is a novel isoform that differs in its C-terminal sequence from other GFAP isoforms. Previous studies suggest restriction of expression to the subpial layer, subventricular zone and the subgranular zone astrocytes, with an absence in pathological co

  8. Protein metabolism, feed energy partitioning, behavior patterns and plasma cortisol in Nellore steers with high and low residual feed intake

    Directory of Open Access Journals (Sweden)

    Rodrigo da Costa Gomes

    2013-01-01

    Full Text Available The objective was to evaluate protein turnover, nitrogen balance, feed energy partitioning, behavior patterns and plasma cortisol in Nellore (B. indicus cattle with high and low residual feed intake (RFI = actual minus expected dry matter intake. Seventy-two Nellore steers (16 to 21 months-old, 334±19 kg initial body weight were fed a feedlot diet for 70 days ad libitum. Daily dry matter intake (DMI and average daily gain (ADG were recorded individually and RFI was calculated. The 12 steers of lowest (Low-RFI, most efficient RFI and the 12 ones of highest RFI (High-RFI, least efficient were evaluated with respect to their behavior patterns and plasma cortisol concentration. Urine was collected for determination of daily 3-methylhistidine excretion (3MH and myofibrillar protein breakdown rates. Urinary, gaseous and fecal energy losses were determined as well as the N retention and excretion. High-RFI steers tended to have shorter lying and idle periods and greater feeding time and plasma cortisol levels than low-RFI cattle. No RFI effects were seen for urine 3MH excretion and for rates of protein degradation and synthesis. No effects of efficiency class were observed for N excretion or N retention. No RFI effects were observed for dry matter digestibility, digestible energy (DE and metabolizable energy (ME content and DE/ME ratio. Methane energy losses were lower for low-compared with high-RFI steers. Protein turnover seems not to affect feed efficiency in Nellore steers. Improved RFI in Nellore steers is probably associated with lower degrees of activity and responsiveness to stress and lower losses of dietary energy as methane.

  9. Application of SAIL phenylalanine and tyrosine with alternative isotope-labeling patterns for protein structure determination

    Energy Technology Data Exchange (ETDEWEB)

    Takeda, Mitsuhiro [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan); Ono, Akira M.; Terauchi, Tsutomu [SAIL Technologies Co., Inc. (Japan); Kainosho, Masatsune, E-mail: kainosho@nmr.chem.metro-u.ac.j [Nagoya University, Structural Biology Research Center, Graduate School of Science (Japan)

    2010-01-15

    The extensive collection of NOE constraint data involving the aromatic ring signals is essential for accurate protein structure determination, although it is often hampered in practice by the pervasive signal overlapping and tight spin couplings for aromatic rings. We have prepared various types of stereo-array isotope labeled phenylalanines ({epsilon}- and {zeta}-SAIL Phe) and tyrosine ({epsilon}-SAIL Tyr) to overcome these problems (Torizawa et al. 2005), and proven that these SAIL amino acids provide dramatic spectral simplification and sensitivity enhancement for the aromatic ring NMR signals. In addition to these SAIL aromatic amino acids, we recently synthesized {delta}-SAIL Phe and {delta}-SAIL Tyr, which allow us to observe and assign {delta}-{sup 13}C/{sup 1}H signals very efficiently. Each of the various types of SAIL Phe and SAIL Tyr yields well-resolved resonances for the {delta}-, {epsilon}- or {zeta}-{sup 13}C/{sup 1}H signals, respectively, which can readily be assigned by simple and robust pulse sequences. Since the {delta}-, {epsilon}-, and {zeta}-proton signals of Phe/Tyr residues give rise to complementary NOE constraints, the concomitant use of various types of SAIL-Phe and SAIL-Tyr would generate more accurate protein structures, as compared to those obtained by using conventional uniformly {sup 13}C, {sup 15}N-double labeled proteins. We illustrated this with the case of an 18.2 kDa protein, Escherichia coli peptidyl-prolyl cis-trans isomerase b (EPPIb), and concluded that the combined use of {zeta}-SAIL Phe and {epsilon}-SAIL Tyr would be practically the best choice for protein structural determinations.

  10. Prevalence and pattern of birth defects in a tertiary health facility in the Niger Delta area of Nigeria

    Science.gov (United States)

    Abbey, Mkpe; Oloyede, Olufemi A; Bassey, Goddy; Kejeh, Benjamin M; Otaigbe, Barbara E; Opara, Peace I; Eneh, Austa U; Akani, Chris I

    2017-01-01

    Objective To ascertain the prevalence and pattern of congenital abnormalities that are peculiar to the Niger Delta area of Nigeria. Methods This is a descriptive retrospective cross-sectional study. It involved data from the labor ward and neonatal birth registers of the University of Port Harcourt Teaching Hospital on the total number of births and the babies that were delivered with major birth defects between August 2011 and December 2014. We also conducted a statistical comparison of the prevalence of congenital abnormalities in the Niger Delta with that in other regions of Nigeria and the developed world of Europe. Results Out of the 7,670 deliveries that occurred, 159 maternities had babies with major birth defects giving a prevalence of 20.73 cases per 1,000 live births. This figure is far more than that which was obtained in other regions of Nigeria −4.15:cases per 1,000 live births in the South East (P51:1,000 in the North East (P<0.001). Eighty-five (53.46%) of the defects occurred in 1,681 unbooked patients, while 74 (46.54%) happened in 5,989 booked maternities (P<0.001). The predominant abnormalities were those of the central nervous system at 27.0%, gastrointestinal system 11.95%, cardiovascular system 10.69%, anterior abdominal wall 8.18%, skeleton 6.29%, and chromosomal abnormalities at 5.66%. Conclusion The prevalence of major birth defects at the University of Port Harcourt Teaching Hospital was 20.73 cases per 1,000 live births and it was more in the unbooked than the booked maternities. All body systems were affected with those of the central nervous system predominating at 27.0% of the total diagnosed defects.

  11. Human Social Behavior and Demography Drive Patterns of Fine-Scale Dengue Transmission in Endemic Areas of Colombia.

    Directory of Open Access Journals (Sweden)

    Harish Padmanabha

    Full Text Available Dengue is known to transmit between humans and A. aegypti mosquitoes living in neighboring houses. Although transmission is thought to be highly heterogeneous in both space and time, little is known about the patterns and drivers of transmission in groups of houses in endemic settings. We carried out surveys of PCR positivity in children residing in 2-block patches of highly endemic cities of Colombia. We found high levels of heterogeneity in PCR positivity, varying from less than 30% in 8 of the 10 patches to 56 and 96%, with the latter patch containing 22 children simultaneously PCR positive (PCR22 for DEN2. We then used an agent-based model to assess the likely eco-epidemiological context of this observation. Our model, simulating daily dengue dynamics over a 20 year period in a single two block patch, suggests that the observed heterogeneity most likely derived from variation in the density of susceptible people. Two aspects of human adaptive behavior were critical to determining this density: external social relationships favoring viral introduction (by susceptible residents or infectious visitors and immigration of households from non-endemic areas. External social relationships generating frequent viral introduction constituted a particularly strong constraint on susceptible densities, thereby limiting the potential for explosive outbreaks and dampening the impact of heightened vectorial capacity. Dengue transmission can be highly explosive locally, even in neighborhoods with significant immunity in the human population. Variation among neighborhoods in the density of local social networks and rural-to-urban migration is likely to produce significant fine-scale heterogeneity in dengue dynamics, constraining or amplifying the impacts of changes in mosquito populations and cross immunity between serotypes.

  12. Localization and expression pattern of amelotin, odontogenic ameloblast-associated protein and follicular dendritic cell-secreted protein in the junctional epithelium of inflamed gingiva.

    Science.gov (United States)

    Nakayama, Yohei; Kobayashi, Ryoki; Matsui, Sari; Matsumura, Hiroyoshi; Iwai, Yasunobu; Noda, Keisuke; Yamazaki, Mizuho; Kurita-Ochiai, Tomoko; Yoshimura, Atsutoshi; Shinomura, Tamayuki; Ganss, Bernhard; Ogata, Yorimasa

    2016-11-02

    The purpose of this study is to elucidate the localization of amelotin (AMTN), odontogenic ameloblast-associated protein (ODAM) and follicular dendritic cell-secreted protein (FDC-SP) at the junctional epithelium (JE) in Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans infected mice and inflamed and non-inflamed human gingiva. We performed immunostaining to determine the localization and expression pattern of AMTN, ODAM and FDC-SP. AMTN, ODAM and FDC-SP in A. actinomycetemcomitans infected mice did not change dramatically compared with non-infected mice. AMTN and FDC-SP expressions were observed stronger in P. gingivalis infected mice at early stage. However, at the following stage, the coronal part of the AMTN expression disappeared from the JE, and FDC-SP expression decreased due to severe inflammation by P. gingivalis. ODAM expressed internal and external basal lamina, and the expression increased not only at early stage but also at the following stage in the inflammatory JE induced by P. gingivalis. In the human gingival tissues, AMTN was detected at the surface of the sulcular epithelium and JE in the non-inflamed and inflamed gingiva, and the localization did not change the process of inflammation. ODAM and FDC-SP were more widely detected at the sulcular epithelium and JE in the non-inflamed gingiva. In the inflamed gingiva, localization of ODAM and FDC-SP was spread into the gingival epithelium, compared to AMTN. These studies demonstrated that the expression pattern of AMTN, ODAM and FDC-SP at the JE were changed during inflammation process and these three proteins might play an important role in the resistance to inflammation.

  13. Localisation of nursery areas based on comparative analyses of the horizontal and vertical distribution patterns of juvenile Baltic cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Nielsen, J. Rasmus; Lundgren, Bo; Kristensen, Kasper

    2013-01-01

    ) are present in all areas of the central Baltic Sea (CBS), showing broad dispersal. However, their highest density in the Baltic Basins is found at localities with a 40–70 m bottom depth in waters with oxygen concentrations above 2 ml O2.l−1 and temperatures above 5°C. The smallest juveniles are also found......Knowledge of the spatial distribution of juvenile cod is essential for obtaining precise recruitment data to conduct sustainable management of the eastern and western Baltic cod stocks. In this study, the horizontal and vertical distribution and density patterns of settled juvenile 0- and 1-group...... patterns related to the seabed topography, water layer depth, and the presence of hydrographic frontal zones (pycnoclines) as well as intraspecific patterns in relation to the presence of adult cod. The extent of the nursery areas also depends on the cod year class strength. Juvenile cod (≥3 cm...

  14. Study on the Comprehensive Tourism Development Pattern in Periphery Minority Area:A Case Study of Gannan Tibetan Autonomous Prefecture of Gansu Province,China

    Institute of Scientific and Technical Information of China (English)

    Xu Lin; Li Yu; Wang Lili

    2007-01-01

    The paper took the human-land relations as a basic point,and the theories of tourism industry system and sustainable development as the guidance,with Gannan Tibetan Autonomous Prefecture(Gannan)as the case study area.From microcosmic and macroscopic viewpoints,the author carried out function orientation and evaluation to the tourism industry development,and research on the comprehensive tourism industry development pattern of Gannan.Results show that the fragile ecological environment and the traditional economic growth pattern have restricted regional sustainable development,and made Gannan to bocome a representative of the periphery minonty areas in Northwest China.Tourism development of Gannan is at the primary phase,with the characteristics of short industry chain and low economic efficiency.It iS an inevitable choice to transform the way of regional economic growth and the development pattern of tourism industry from the traditional pattern to the pattern of snstainable development.Simultaneously,Gannan's natural,uational and religious culture makes Gannan a broad prospect on the comprehensive tourism development.Gannan should choose the comprehensive tourism industry as its scientific pattern to realize sustainable development,promote harmonious social,economic and ecological development,alleviate the human-land contradictory,and realize dual goals in terms of ecology construction and economical development. For Gannan and the similar areas in China,studies on the sustainable development pattern of tourism have extremely important strategic sense with respect to tourism development and the sustainable development of regional economy.

  15. Development-related expression patterns of protein-coding and miRNA genes involved in porcine muscle growth.

    Science.gov (United States)

    Wang, F J; Jin, L; Guo, Y Q; Liu, R; He, M N; Li, M Z; Li, X W

    2014-01-01

    Muscle growth and development is associated with remarkable changes in protein-coding and microRNA (miRNA) gene expression. To determine the expression patterns of genes and miRNAs related to muscle growth and development, we measured the expression levels of 25 protein-coding and 16 miRNA genes in skeletal and cardiac muscles throughout 5 developmental stages by quantitative reverse transcription-polymerase chain reaction. The Short Time-Series Expression Miner (STEM) software clustering results showed that growth-related genes were downregulated at all developmental stages in both the psoas major and longissimus dorsi muscles, indicating their involvement in early developmental stages. Furthermore, genes related to muscle atrophy, such as forkhead box 1 and muscle ring finger, showed unregulated expression with increasing age, suggesting a decrease in protein synthesis during the later stages of skeletal muscle development. We found that development of the cardiac muscle was a complex process in which growth-related genes were highly expressed during embryonic development, but they did not show uniform postnatal expression patterns. Moreover, the expression level of miR-499, which enhances the expression of the β-myosin heavy chain, was significantly different in the psoas major and longissimus dorsi muscles, suggesting the involvement of miR-499 in the determination of skeletal muscle fiber types. We also performed correlation analyses of messenger RNA and miRNA expression. We found negative relationships between miR-486 and forkhead box 1, and miR-133a and serum response factor at all developmental stages, suggesting that forkhead box 1 and serum response factor are potential targets of miR-486 and miR-133a, respectively.

  16. Cloning, tissue expression pattern, and chromosome localization of human protein kinase Bγ gene

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Protein kinase B (PKB) is a member of the second messenger-regulated subfamily of protein kinases, and plays a key role in cell-cycle regulation, glucose uptake and promotion of cell differentiation. Evidence shows that PKB undergoes activation in some human tumors and is involved in Ras pathway, which implies that PKB can trigger a pathway to induce oncogenic transformation. A nucleotide sequence of mouse Pkb? was used as a probe to screen homolog in a human liver cDNA library. A fragment of 1998 bp containing a 1440 bp ORF encoding 479 amino acid residues was obtained. Then the 3'-terminal of this fragment was extended to 2788 bp by 'electronic walking' screening, and the extended fragment was confirmed by PCR amplification. The protein deduced by the gene had a high identity of 83% and 78% to the human PKBγ and γ, respectively, and was designated as human PKB?. Northern hybridization detected two equally expressed transcripts of 8.5 and 6.5 kb in length in all 16 human tissues tested, with the highest expression level in brain, and lower levels with variation in the other tissues. By RH mapping, the PKBγ was placed on chromosome 1q43, between markers D1S304 and D1S2693. It is a valuable clue for cloning the candidate genes related to prostate cancer; Arrhythmogenic Right Ventricular Dysplasia (ARVD); Chediak-Higashi, NK cell Deficiency (CHS); and Hypoparathyrodism with Short Stature, Mental Retardation and Seizures which have already been mapped in this chromosomal region.

  17. Automated extraction of precise protein expression patterns in lymphoma by text mining abstracts of immunohistochemical studies

    Directory of Open Access Journals (Sweden)

    Jia-Fu Chang

    2013-01-01

    Full Text Available Background: In general, surgical pathology reviews report protein expression by tumors in a semi-quantitative manner, that is, -, -/+, +/-, +. At the same time, the experimental pathology literature provides multiple examples of precise expression levels determined by immunohistochemical (IHC tissue examination of populations of tumors. Natural language processing (NLP techniques enable the automated extraction of such information through text mining. We propose establishing a database linking quantitative protein expression levels with specific tumor classifications through NLP. Materials and Methods: Our method takes advantage of typical forms of representing experimental findings in terms of percentages of protein expression manifest by the tumor population under study. Characteristically, percentages are represented straightforwardly with the % symbol or as the number of positive findings of the total population. Such text is readily recognized using regular expressions and templates permitting extraction of sentences containing these forms for further analysis using grammatical structures and rule-based algorithms. Results: Our pilot study is limited to the extraction of such information related to lymphomas. We achieved a satisfactory level of retrieval as reflected in scores of 69.91% precision and 57.25% recall with an F-score of 62.95%. In addition, we demonstrate the utility of a web-based curation tool for confirming and correcting our findings. Conclusions: The experimental pathology literature represents a rich source of pathobiological information, which has been relatively underutilized. There has been a combinatorial explosion of knowledge within the pathology domain as represented by increasing numbers of immunophenotypes and disease subclassifications. NLP techniques support practical text mining techniques for extracting this knowledge and organizing it in forms appropriate for pathology decision support systems.

  18. DNA methylation patterns of protein coding genes and long noncoding RNAs in female schizophrenic patients.

    Science.gov (United States)

    Liao, Qi; Wang, Yunliang; Cheng, Jia; Dai, Dongjun; Zhou, Xingyu; Zhang, Yuzheng; Gao, Shugui; Duan, Shiwei

    2015-02-01

    Schizophrenia (SCZ) is a complex mental disorder contributed by both genetic and epigenetic factors. Long noncoding RNAs (lncRNAs) was recently found playing an important regulatory role in mental disorders. However, little was known about the DNA methylation of lncRNAs, although numerous SCZ studies have been performed on genetic polymorphisms or epigenetic marks in protein coding genes. We presented a comprehensive genome wide DNA methylation study of both protein coding genes and lncRNAs in female patients with paranoid and undifferentiated SCZ. Using the methyl-CpG binding domain (MBD) protein-enriched genome sequencing (MBD-seq), 8,163 and 764 peaks were identified in paranoid and undifferentiated SCZ, respectively (p Gene ontology analysis showed that the hypermethylated regions were enriched in the genes related to neuron system and brain for both paranoid and undifferentiated SCZ (p gene promoter regions that might affect gene expression and influence the SCZ related pathways. Interestingly, DNA methylation of 136 and 23 known lncRNAs in Refseq database were identified in paranoid and undifferentiated SCZ, respectively. In addition, ∼20% of intergenic peaks annotated based on Refseq genes were overlapped with lncRNAs in UCSC and gencode databases. In order to show the results well for most biological researchers, we created an online database to display and visualize the information of DNA methyation peaks in both types of SCZ (http://www.bioinfo.org/scz/scz.htm). Our results showed that the aberrant DNA methylation of lncRNAs might be another important epigenetic factor for SCZ.

  19. Expression patterns of CREB binding protein (CREBBP) and its methylated species during zebrafish development.

    Science.gov (United States)

    Batut, Julie; Duboé, Carine; Vandel, Laurence

    2015-01-01

    Proper embryonic development requires a fine-tuned control of gene expression, which is achieved in part through the activity of transcription coactivators or corepressors. The nuclear coactivator cAMP-response element-binding protein (CREB) binding protein (CREBBP or CBP) interacts with numerous transcription factors and thereby plays a key role in various signaling pathways. Interestingly, in cell-based studies CREBBP activity is modulated by post-translational modifications such as methylation on arginine residues which is catalyzed by coactivator-associated arginine methyltransferase 1 (CARM1). However, whether and where CREBBP, and in particular its methylated forms, are expressed during development in vertebrates has not been addressed so far. Here, we analyzed the expression of the two crebbp genes (crebbpa & crebbpb) during zebrafish development using both RT-qPCR and in situ hybridization. We found that while crebbpa expression is higher in posterior, caudal nascent somites during somitogenesis, crebbpb accumulates in anterior, rostral, and more mature somites. In addition, crebbpa mRNA is enriched in the central myotome at 24 hpf indicating that its expression is spatially and temporally controlled. We next characterized the expression of CREBBP protein from blastula to gastrula stages by immunohistochemistry. We found that while CREBBP is clearly cytoplasmic in the early blastula, it becomes both cytoplasmic and nuclear at 30% epiboly before turning mainly nuclear during gastrulation. Of interest, CREBBP methylated species appear to be mainly nuclear from 30% epiboly to 6-somite stage. This suggests that methylation may regulate CREBBP import to the nucleus during zebrafish development and could therefore participate in the control of early developmental processes.

  20. Tetranectin, a plasminogen kringle 4-binding protein. Cloning and gene expression pattern in human colon cancer

    DEFF Research Database (Denmark)

    Wewer, U M; Albrechtsen, R

    1992-01-01

    BACKGROUND: Tetranectin is a recently discovered protein that binds to kringle 4 region of plasminogen (Clemmensen I, Petersen LC, Kluft C. Eur J Biochem 1986; 156:327. EXPERIMENTAL DESIGN: The mRNA encoding human tetranectin was cloned by using degenerate primers in a reverse transcriptase...... reaction followed by polymerase chain reaction amplification. The resulting polymerase chain reaction product was examined by DNA sequencing and subsequently used as probe for screening a human placental cDNA library. A full length cDNA clone (TET-1) was isolated, characterized, and used for Northern blot...

  1. Expression patterns of Wnt signaling component, secreted frizzled-related protein 3 in astrocytoma and glioblastoma

    Science.gov (United States)

    PEĆINA-ŠLAUS, NIVES; KAFKA, ANJA; VAROŠANEC, ANA MARIA; MARKOVIĆ, LEON; KRSNIK, ŽELJKA; NJIRIĆ, NIKO; MRAK, GORAN

    2016-01-01

    Secreted frizzled-related protein 3 (SFRP3) is a member of the family of soluble proteins, which modulate the Wnt signaling cascade. Novel research has identified aberrant expression of SFRPs in different types of cancer. In the present study the expression intensities and localizations of the SFRP3 protein across different histopathological grades of astrocytic brain tumors were investigated by immunohistochemistry, digital scanning and image analysis. The results demonstrated that the differences between expression levels and malignancy grades were statistically significant. Tumors were classified into four malignancy grades according to the World Health Organization guidelines. Moderate (P=0.014) and strong (P=0.028) nuclear expression levels were significantly different in pilocytic (grade I) and diffuse (grade II) astrocytomas demonstrating higher expression values, as compared with anaplastic astrocytoma (grade III) and glioblastoma (grade IV). When the sample was divided into two groups, the moderate and high cytoplasmic expression levels were observed to be significantly higher in glioblastomas than in the group comprising astrocytoma II and III. Furthermore, the results indicated that high grade tumors were associated with lower values of moderate (P=0.002) and strong (P=0.018) nuclear expression in comparison to low grade tumors. Analysis of cytoplasmic staining demonstrated that strong cytoplasmic expression was significantly higher in the astrocytoma III and IV group than in the astrocytoma I and II group (P=0.048). Furthermore, lower grade astrocytomas exhibited reduced membranous SFRP3 staining when compared with higher grade astrocytomas and this difference was statistically significant (P=0.036). The present results demonstrated that SFRP3 protein expression levels were decreased in the nucleus in higher grade astrocytoma (indicating the expected behavior of an antagonist of Wnt signaling), whereas when the SFRP3 was located in the cytoplasm an

  2. Expression patterns of Wnt signaling component, secreted frizzled‑related protein 3 in astrocytoma and glioblastoma.

    Science.gov (United States)

    Pećina-Šlaus, Nives; Kafka, Anja; Varošanec, Ana Maria; Marković, Leon; Krsnik, Željka; Njirić, Niko; Mrak, Goran

    2016-05-01

    Secreted frizzled-related protein 3 (SFRP3) is a member of the family of soluble proteins, which modulate the Wnt signaling cascade. Novel research has identified aberrant expression of SFRPs in different types of cancer. In the present study the expression intensities and localizations of the SFRP3 protein across different histopathological grades of astrocytic brain tumors were investigated by immunohistochemistry, digital scanning and image analysis. The results demonstrated that the differences between expression levels and malignancy grades were statistically significant. Tumors were classified into four malignancy grades according to the World Health Organization guidelines. Moderate (P=0.014) and strong (P=0.028) nuclear expression levels were significantly different in pilocytic (grade I) and diffuse (grade II) astrocytomas demonstrating higher expression values, as compared with anaplastic astrocytoma (grade III) and glioblastoma (grade IV). When the sample was divided into two groups, the moderate and high cytoplasmic expression levels were observed to be significantly higher in glioblastomas than in the group comprising astrocytoma II and III. Furthermore, the results indicated that high grade tumors were associated with lower values of moderate (P=0.002) and strong (P=0.018) nuclear expression in comparison to low grade tumors. Analysis of cytoplasmic staining demonstrated that strong cytoplasmic expression was significantly higher in the astrocytoma III and IV group than in the astrocytoma I and II group (P=0.048). Furthermore, lower grade astrocytomas exhibited reduced membranous SFRP3 staining when compared with higher grade astrocytomas and this difference was statistically significant (P=0.036). The present results demonstrated that SFRP3 protein expression levels were decreased in the nucleus in higher grade astrocytoma (indicating the expected behavior of an antagonist of Wnt signaling), whereas when the SFRP3 was located in the

  3. [Landscape pattern changes at village scale using high resolution satellite images: A case study in low-slope hilly area of Dali City, Northwestern Yunnan Province].

    Science.gov (United States)

    Zhao, Ming-yue; Peng, Jian; Liu, Yan-xu; Zhang, Tian

    2015-12-01

    Human activity is the main driving force of the change of land cover and landscape patterns. However, there are few studies focusing on the mechanism of human-induced change of land cover and landscape patterns at village scale. In this study, taking low-slope hilly area of Dali City, Northwestern Yunnan Province as a case study area, high resolution satellite images were introduced to find out the rules of land cover and landscape pattern changes, i.e. GeoEye-1 of 2009 and World- View-3 of 2014. The object-oriented and human-computer-interaction approaches were applied to interpret the images using ArcGIS 10.2 and ENVI 5.2. The results showed that, the main land cover types in the study area were forest land, paddy field and dry land in 2009, with forest, bulldozed unbuilt ground and paddy field in 2014, accounting for 82.8% and 70.9% of the total area, respectively. The land cover transition showed that, during 2009-2014, the main land cover change flows were from forest land, paddy field and dry land, to bulldozed unbuilt ground and construction land. Furthermore, the area of bulldozed but unbuilt land had increased to be 531.57 hm² in 2014, which mainly came from forest land (42.8%), dry land (21.7%), and paddy field (14.2%). Landscape pattern change was characterized as the increase of patch quantity and density, the decrease of mean patch size, the complication of patch shape, the fragmentation of landscape patches, and the diversification of landscape patterns.

  4. Hepatic DNA Damage and Abnormality in Serum Protein Pattern Due to Long Term Use of Tramadol in Rats

    Directory of Open Access Journals (Sweden)

    Laila Abd El kawy

    2012-10-01

    Full Text Available Tramadol is a widely used analgesic that stimulates the μ opioid receptor and inhibits serotonin and noradrenalin reuptake. In this study, we investigate the effect of chronic administration of 200 and 400mg of tramal for 15,30 ,45 days followed by withdrawal periods(w15 on protein activity in male rats as manifested by changes in electrophoretic serum protein patterns and gene expression manifested by DNA damage, measured by Comet Assay . Materials and methods:100 male Wistar rats (100-150 g were included and divided into three groups, control group (n = 20, Tramal(I group (n = 40, received the drug orally at doses of 200mg/kg/day for 15,30,45 days of the study, respectively(10 rats for each subgroup.TR45 group was followed by 15 withdrawal period(W15 ,Tramal(II group (n = 40, received the drug orally at doses of400mg/kg/day for 15,30,45 days of the study, respectively. TR45 group was followed by 15 withdrawal period (W15. Results:Results exhibited major changes in the protein pattern which included changes in the molecular weight of the control bands and the relative percentage of protein fraction as well as the total number of bands, as a result of disappearance of some original bands and appearance of other new one. Serum protein fraction revealed an increase in total number of protein fractions being in Tr200mg (14 and 16 bands, whileTR400mg revealed a decrease in total number of bands (except TR15 which exhibited an increase in bands (14. The changes were observed all over the treated groups as well as in the withdrawal groups In this study, the alkaline version of the comet assay has been used to determine the effect of tramal administration (200 and 400mg/Kg on peroxide-initiated free radical-mediated DNA damage in rat liver cells. Indeed, levels of strand breaks in rat liver cell exposed to tramal400mg/Kg were significantly higher than in cells exposed to 200mg/Kg, especially after a long administration period (TR45 days. The intensity

  5. Skeletal Muscle Regeneration on Protein-Grafted and Microchannel-Patterned Scaffold for Hypopharyngeal Tissue Engineering

    Directory of Open Access Journals (Sweden)

    Zhisen Shen

    2013-01-01

    Full Text Available In the field of tissue engineering, polymeric materials with high biocompatibility like polylactic acid and polyglycolic acid have been widely used for fabricating living constructs. For hypopharynx tissue engineering, skeletal muscle is one important functional part of the whole organ, which assembles the unidirectionally aligned myotubes. In this study, a polyurethane (PU scaffold with microchannel patterns was used to provide aligning guidance for the seeded human myoblasts. Due to the low hydrophilicity of PU, the scaffold was grafted with silk fibroin (PU-SF or gelatin (PU-Gel to improve its cell adhesion properties. Scaffolds were observed to degrade slowly over time, and their mechanical properties and hydrophilicities were improved through the surface grafting. Also, the myoblasts seeded on PU-SF had the higher proliferative rate and better differentiation compared with those on the control or PU-Gel. Our results demonstrate that polyurethane scaffolds seeded with myoblasts hold promise to guide hypopharynx muscle regeneration.

  6. Skeletal muscle regeneration on protein-grafted and microchannel-patterned scaffold for hypopharyngeal tissue engineering.

    Science.gov (United States)

    Shen, Zhisen; Guo, Shanshan; Ye, Dong; Chen, Jingjing; Kang, Cheng; Qiu, Shejie; Lu, Dakai; Li, Qun; Xu, Kunjie; Lv, Jingjing; Zhu, Yabin

    2013-01-01

    In the field of tissue engineering, polymeric materials with high biocompatibility like polylactic acid and polyglycolic acid have been widely used for fabricating living constructs. For hypopharynx tissue engineering, skeletal muscle is one important functional part of the whole organ, which assembles the unidirectionally aligned myotubes. In this study, a polyurethane (PU) scaffold with microchannel patterns was used to provide aligning guidance for the seeded human myoblasts. Due to the low hydrophilicity of PU, the scaffold was grafted with silk fibroin (PU-SF) or gelatin (PU-Gel) to improve its cell adhesion properties. Scaffolds were observed to degrade slowly over time, and their mechanical properties and hydrophilicities were improved through the surface grafting. Also, the myoblasts seeded on PU-SF had the higher proliferative rate and better differentiation compared with those on the control or PU-Gel. Our results demonstrate that polyurethane scaffolds seeded with myoblasts hold promise to guide hypopharynx muscle regeneration.

  7. DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

    Directory of Open Access Journals (Sweden)

    Masudur Rahman

    2016-10-01

    Full Text Available Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.

  8. Electrophoretic and spectroscopic characterization of the protein patterns formed in different surfactant solutions.

    Science.gov (United States)

    Blanco, Elena; Ruso, Juan M; Prieto, Gerardo; Sarmiento, Félix

    2008-01-01

    The complexations between catalase and the sodium perfluorooctanoate/sodium octanoate and sodium perfluorooctanoate/sodium dodecanoate systems have been studied by a combination of electrophoresis and spectroscopy measurements. The numbers of adsorption sites on the protein were determined from the observed increases of the zeta-potential as a function of surfactant concentration in the regions where the adsorption was a consequence of the hydrophobic effect. The Gibbs energies of adsorption of the surfactants onto the protein were evaluated and the results show that for all systems, Gibbs energies are negative and larger, in absolute values, at low values of surfactant concentration where binding to the high energy sites takes place, and become less negative as more surfactant molecules bind, suggesting a saturation process. The role of hydrophobic interactions in these systems has been demonstrated to be the predominant. Spectroscopy measurements suggest conformational changes on catalase depending on the surfactant mixture as well as the mixed ratio. No isosbestic point or shifts have been found showing that catalase has spectrophotometrically one kind of binding site for these surfactant mixtures.

  9. GLIMPSE ON PROTEIN DRUG DELIVERY: AN UTMOST RESEARCH AREA FOR BIOPHARMACEUTICALS

    Directory of Open Access Journals (Sweden)

    YAGNESH A BHATT

    2010-06-01

    Full Text Available A major challenge confronting pharmaceutical scientists in the future will be to design successful dosage forms for the next generation of drugs. Many of these drugs will be complex polymers of amino acids (e.g., peptides, proteins, nucleosides (e.g., antisense molecules, carbohydrates (e.g., polysaccharides, or complex lipids. Protein and peptide therapeutics currently represent eight of the top 100 prescription pharmaceuticals in the US, and biotechnology products are projected to account for 15% of the total US Prescription drug market by 2003. Conventional drug formulation has the same focus but, due to the unique structures of peptide and protein molecules, formulation of these compounds is more complex and challenging. Therapeutic peptides and proteins always enjoyed unique place in pharmaceutical biotechnology. Peptides and proteins are expected to mitigate suffering in coming years as anticancer, hormones, analgesic antihypertensive, thrombolytics, growth factors, and many others. This review represents outstanding contributions in the field of biopharmaceuticals.

  10. Two novel LRR-only proteins in Chlamys farreri: Similar in structure, yet different in expression profile and pattern recognition.

    Science.gov (United States)

    Wang, Mengqiang; Wang, Lingling; Xin, Lusheng; Wang, Xiudan; Wang, Lin; Xu, Jianchao; Jia, Zhihao; Yue, Feng; Wang, Hao; Song, Linsheng

    2016-06-01

    Leucine-rich repeat (LRR)-only proteins could mediate protein-ligand and protein-protein interactions and be involved in the immune response. In the present study, two novel LRR-only proteins, CfLRRop-2 and CfLRRop-3, were identified and characterized from scallop Chlamys farreri. They both contained nine LRR motifs with the consensus signature sequence LxxLxLxxNxL and formed typical horseshoe structure. The CfLRRop-2 and CfLRRop-3 mRNA transcripts were constitutively expressed in haemocytes, muscle, mantle, gill, haepatopancreas and gonad, with the highest expression level in haepatopancreas and gill, respectively. During the ontogenesis of scallop, the mRNA transcripts of CfLRRop-2 were kept at a high level in oocytes and embryos, while those of CfLRRop-3 were expressed at a rather low level from oocytes to blastula. Their mRNA transcripts were significantly increased after the stimulation of lipopolysaccharide (LPS), peptidoglycan (PGN), glucan (GLU) and polyinosinic-polycytidylic acid (poly I:C), and the mRNA expression of CfLRRop-2 rose more intensely than that of CfLRRop-3. After the suppression of CfTLR (previously identified Toll-like receptor in C. farreri) via RNA interference (RNAi), CfLRRop-3 mRNA transcripts increased more intensely and lastingly than those of CfLRRop-2. The rCfLRRop-3 protein could bind LPS, PGN, GLU and poly I:C, while rCfLRRop-2 exhibited no significant binding activity to them. Additionally, rCfLRRop-2 could significantly induce the release of TNF-α from the mixed primary cultured scallop haemocytes, but rCfLRRop-3 failed. These results collectively indicated that CfLRRop-2 might act as an immune effector or pro-inflammatory factor, while CfLRRop-3 would function as a pattern recognition receptor (PRR), suggesting the function of LRR-only protein family has differentiated in scallop.

  11. Heavy metal accumulation, heat shock protein expression and cytogenetic changes in Tetrix tenuicornis (L.) (Tetrigidae, Orthoptera) from polluted areas

    Energy Technology Data Exchange (ETDEWEB)

    Warchalowska-Sliwa, E. [Institute of Systematics and Evolution of Animals, Polish Academy of Sciences, Slawkowska 17, 31-016 Cracow (Poland)]. E-mail: warchalowska@isez.pan.krakow.pl; Niklinska, M. [Department of Ecotoxicology, Institute of Environmental Studies, Jagiellonian University, Gronostajowa 3, 30-387 Cracow (Poland); Goerlich, A. [Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, Ingardena 6, 30-060 Cracow (Poland); Michailova, P. [Institute of Zoology, Bulgarian Academy of Sciences, 1 Tzar Osvoboditiel Boulevard, Sofia 1000 (Bulgaria); Pyza, E. [Department of Cytology and Histology, Institute of Zoology, Jagiellonian University, Ingardena 6, 30-060 Cracow (Poland)

    2005-01-01

    The orthopteran insect Tetrix tenuicornis, collected from polluted and unpolluted areas, was used to study heavy metal accumulation and its impact on stress protein levels and on changes in the number and morphology of chromosomes in mitotic and meiotic cells. During two consecutive years, insects were collected from polluted areas of zinc-lead mine spoils near Boleslaw (Poland) and from unpolluted areas near Busko and Staszow (Poland). T. tenuicornis from the polluted area showed 1.5, 4.03, 4.32 and 41.73 times higher concentrations of copper (Cu), zinc (Zn), lead (Pb) and cadmium (Cd), respectively, than insects of the same species collected from unpolluted areas. Insects exposed to heavy metals showed only small changes, and rather a decrease in the concentration of constitutive and inducible heat shock proteins Hsp70, the level of which increases under stress conditions. A cytogenetic study of T. tenuicornis revealed intra-population anomalies in chromosome number and morphology in mitotic and meiotic cells and the presence of an additional B chromosome in germinal cells. In 50% of females collected from polluted areas, mosaic oogonial mitotic chromosome sets and diploid, hypo- or hypertetraploid, tetraploid, and octoploid chromosome numbers were detected. In turn, 14.6% of males showed a heterozygous deficiency of chromatin in L{sub 2} and M{sub 3} bivalents in addition to the presence of B chromosomes. - Metals accumulation caused genotoxicity in insects.

  12. Neighborhood Landscape Spatial Patterns and Land Surface Temperature: An Empirical Study on Single-Family Residential Areas in Austin, Texas.

    Science.gov (United States)

    Kim, Jun-Hyun; Gu, Donghwan; Sohn, Wonmin; Kil, Sung-Ho; Kim, Hwanyong; Lee, Dong-Kun

    2016-09-02

    Rapid urbanization has accelerated land use and land cover changes, and generated the urban heat island effect (UHI). Previous studies have reported positive effects of neighborhood landscapes on mitigating urban surface temperatures. However, the influence of neighborhood landscape spatial patterns on enhancing cooling effects has not yet been fully investigated. The main objective of this study was to assess the relationships between neighborhood landscape spatial patterns and land surface temperatures (LST) by using multi-regression models considering spatial autocorrelation issues. To measure the influence of neighborhood landscape spatial patterns on LST, this study analyzed neighborhood environments of 15,862 single-family houses in Austin, Texas, USA. Using aerial photos, geographic information systems (GIS), and remote sensing, FRAGSTATS was employed to calculate values of several landscape indices used to measure neighborhood landscape spatial patterns. After controlling for the spatial autocorrelation effect, results showed that larger and better-connected landscape spatial patterns were positively correlated with lower LST values in neighborhoods, while more fragmented and isolated neighborhood landscape patterns were negatively related to the reduction of LST.

  13. Neighborhood Landscape Spatial Patterns and Land Surface Temperature: An Empirical Study on Single-Family Residential Areas in Austin, Texas

    Directory of Open Access Journals (Sweden)

    Jun-Hyun Kim

    2016-09-01

    Full Text Available Rapid urbanization has accelerated land use and land cover changes, and generated the urban heat island effect (UHI. Previous studies have reported positive effects of neighborhood landscapes on mitigating urban surface temperatures. However, the influence of neighborhood landscape spatial patterns on enhancing cooling effects has not yet been fully investigated. The main objective of this study was to assess the relationships between neighborhood landscape spatial patterns and land surface temperatures (LST by using multi-regression models considering spatial autocorrelation issues. To measure the influence of neighborhood landscape spatial patterns on LST, this study analyzed neighborhood environments of 15,862 single-family houses in Austin, Texas, USA. Using aerial photos, geographic information systems (GIS, and remote sensing, FRAGSTATS was employed to calculate values of several landscape indices used to measure neighborhood landscape spatial patterns. After controlling for the spatial autocorrelation effect, results showed that larger and better-connected landscape spatial patterns were positively correlated with lower LST values in neighborhoods, while more fragmented and isolated neighborhood landscape patterns were negatively related to the reduction of LST.

  14. Proteomic analyses of human cytomegalovirus strain AD169 derivatives reveal highly conserved patterns of viral and cellular proteins in infected fibroblasts.

    Science.gov (United States)

    Reyda, Sabine; Büscher, Nicole; Tenzer, Stefan; Plachter, Bodo

    2014-01-07

    Human cytomegalovirus (HCMV) particle morphogenesis in infected cells is an orchestrated process that eventually results in the release of enveloped virions. Proteomic analysis has been employed to reveal the complexity in the protein composition of these extracellular particles. Only limited information is however available regarding the proteome of infected cells preceding the release of HCMV virions. We used quantitative mass spectrometry to address the pattern of viral and cellular proteins in cells, infected with derivatives of the AD169 laboratory strain. Our analyses revealed a remarkable conservation in the patterns of viral and of abundant cellular proteins in cells, infected for 2 hours, 2 days, or 4 days. Most viral proteins increased in abundance as the infection progressed over time. Of the proteins that were reliably detectable by mass spectrometry, only IE1 (pUL123), pTRS1, and pIRS1 were downregulated at 4 days after infection. In addition, little variation of viral proteins in the virions of the different viruses was detectable, independent of the expression of the major tegument protein pp65. Taken together these data suggest that there is little variation in the expression program of viral and cellular proteins in cells infected with related HCMVs, resulting in a conserved pattern of viral proteins ultimately associated with extracellular virions.

  15. Active machine learning-driven experimentation to determine compound effects on protein patterns.

    Science.gov (United States)

    Naik, Armaghan W; Kangas, Joshua D; Sullivan, Devin P; Murphy, Robert F

    2016-02-03

    High throughput screening determines the effects of many conditions on a given biological target. Currently, to estimate the effects of those conditions on other targets requires either strong modeling assumptions (e.g. similarities among targets) or separate screens. Ideally, data-driven experimentation could be used to learn accurate models for many conditions and targets without doing all possible experiments. We have previously described an active machine learning algorithm that can iteratively choose small sets of experiments to learn models of multiple effects. We now show that, with no prior knowledge and with liquid handling robotics and automated microscopy under its control, this learner accurately learned the effects of 48 chemical compounds on the subcellular localization of 48 proteins while performing only 29% of all possible experiments. The results represent the first practical demonstration of the utility of active learning-driven biological experimentation in which the set of possible phenotypes is unknown in advance.

  16. RNA-binding protein VICKZ is expressed in a germinal center associated pattern among lymphoma subtypes

    DEFF Research Database (Denmark)

    Natkunam, Y.; Vainer, G.; Zhao, S.C.;

    2005-01-01

    to the cytoplasm. Among 868 non-Hodgkin and Hodgkin lymphomas tested by immunohistochemistry on tissue microarrays, staining for VICKZ protein was present in 76% (126/165) of follicular lymphoma, 78% (155/200) of DLBCL, 90% (9/10) of mediastinal large B-cell lymphoma, and 100% (2/2) of Burkitt lymphoma. A subset...... of mantle cell lymphoma (11%, 2/19), extranodal (8%, 2/25), and nodal (20%, 1/5) marginal zone lymphoma and lymphoblastic lymphoma (25%, 4/13), showed VICKZ staining. The majority of lymphocyte predominant Hodgkin (92%, 12/13) and classical Hodgkin (94%, 101/108) lymphoma were found to be positive. Among T......Recent effort in the molecular characterization of diffuse large B-cell lymphoma (DLBCL) has led to the recognition that patients with DLBCL of germinal center origin exhibit a better overall survival. Thus, identification and characterization of markers of germinal center derivation...

  17. Evaluation of opening pattern and bone neoformation at median palatal suture area in patients submitted to surgically assisted rapid maxillary expansion (SARME through cone beam computed tomography

    Directory of Open Access Journals (Sweden)

    Daniel Gomes SALGUEIRO

    2015-08-01

    Full Text Available AbstractSurgically assisted rapid maxillary expansion (SARME is the treatment of choice to adult patients even with severe transversal maxillary discrepancies. However, the adequate retention period to achieve the bone remodeling, thus assuring treatment stability, is controversial.Objective To evaluate the opening pattern and bone neoformation process at the midpalatal suture in patients submitted to surgically assisted (SARME through cone beam computed tomography (CBCT.Material and Methods Fourteen patients were submitted to SARME through subtotal Le Fort I osteotomy. Both the opening pattern and the mean bone density at midpalatal suture area to evaluate bone formation were assessed pre- and post-operatively (15, 60 and 180 days through CBCT.Results Type I opening pattern (from anterior to posterior nasal spine occurred in 12 subjects while type II opening pattern (from anterior nasal spine to transverse palatine suture occurred in 2 individuals. The 180-day postoperative mean (PO 180 of bone density value was 49.9% of the preoperative mean (Pre value.Conclusions The opening pattern of midpalatal suture is more related to patients’ age (23.9 years in type I and 33.5 years in type II and surgical technique. It was not possible to observe complete bone formation at midpalatal suture area at the ending of the retention period studied (180 days.

  18. Nep1-like proteins from three kingdoms of life act as a microbe-associated molecular pattern in Arabidopsis.

    Science.gov (United States)

    Oome, Stan; Raaymakers, Tom M; Cabral, Adriana; Samwel, Simon; Böhm, Hannah; Albert, Isabell; Nürnberger, Thorsten; Van den Ackerveken, Guido

    2014-11-25

    Necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLPs) are secreted by a wide range of plant-associated microorganisms. They are best known for their cytotoxicity in dicot plants that leads to the induction of rapid tissue necrosis and plant immune responses. The biotrophic downy mildew pathogen Hyaloperonospora arabidopsidis encodes 10 different noncytotoxic NLPs (HaNLPs) that do not cause necrosis. We discovered that these noncytotoxic NLPs, however, act as potent activators of the plant immune system in Arabidopsis thaliana. Ectopic expression of HaNLP3 in Arabidopsis triggered resistance to H. arabidopsidis, activated the expression of a large set of defense-related genes, and caused a reduction of plant growth that is typically associated with strongly enhanced immunity. N- and C-terminal deletions of HaNLP3, as well as amino acid substitutions, pinpointed to a small central region of the protein that is required to trigger immunity, indicating the protein acts as a microbe-associated molecular pattern (MAMP). This was confirmed in experiments with a synthetic peptide of 24 aa, derived from the central part of HaNLP3 and corresponding to a conserved region in type 1 NLPs that induces ethylene production, a well-known MAMP response. Strikingly, corresponding 24-aa peptides of fungal and bacterial type 1 NLPs were also able to trigger immunity in Arabidopsis. The widespread phylogenetic distribution of type 1 NLPs makes this protein family (to our knowledge) the first proteinaceous MAMP identified in three different kingdoms of life.

  19. G-protein-coupled receptors and localized signaling in the primary cilium during ventral neural tube patterning.

    Science.gov (United States)

    Hwang, Sun-Hee; Mukhopadhyay, Saikat

    2015-01-01

    The primary cilium is critical in sonic hedgehog (Shh)-dependent ventral patterning of the vertebrate neural tube. Most mutants that cause disruption of the cilium result in decreased Shh signaling in the neural tube. In contrast, mutations in the intraflagellar complex A (IFT-A) and the tubby family protein, Tulp3, result in increased Shh signaling in the neural tube. Proteomic analysis of Tulp3-binding proteins first pointed to the role of the IFT-A complex in trafficking Tulp3 into the cilia. Tulp3 directs trafficking of rhodopsin family G-protein-coupled receptors (GPCRs) to the cilia, suggesting the role of a GPCR in mediating the paradoxical effects of the Tulp3/IFT-A complex in causing increased Shh signaling. Gpr161 has recently been identified as a Tulp3/IFT-A-regulated GPCR that localizes to the primary cilium. A null knock-out mouse model of Gpr161 phenocopies Tulp3 and IFT-A mutants, and causes increased Shh signaling throughout the neural tube. In the absence of Shh, the bifunctional Gli transcription factors are proteolytically processed into repressor forms in a protein kinase A (PKA) -dependent and cilium-dependent manner. Gpr161 activity results in increased cAMP levels in a Gαs -coupled manner, and determines processing of Gli3. Shh signaling also results in removal of Gpr161 from the cilia, suggesting that Gpr161 functions in a positive feedback loop in the Shh pathway. As PKA-null and Gαs mutant embryos also exhibit increased Shh signaling in the neural tube, Gpr161 is a strong candidate for a GPCR that regulates ciliary cAMP levels, and activates PKA in close proximity to the cilia.

  20. Cytophilic antibodies to Plasmodium falciparum glutamate rich protein are associated with malaria protection in an area of holoendemic transmission

    DEFF Research Database (Denmark)

    Lusingu, John P A; Vestergaard, Lasse S; Alifrangis, Michael;

    2005-01-01

    BACKGROUND: Several studies conducted in areas of medium or low malaria transmission intensity have found associations between malaria immunity and plasma antibody levels to glutamate rich protein (GLURP). This study was conducted to analyse if a similar relationship could be documented in an area...... of intense malaria transmission. METHODS: A six month longitudinal study was conducted in an area of holoendemic malaria transmission in north-eastern Tanzania, where the incidence of febrile malaria decreased sharply by the age of three years, and anaemia constituted a significant part of the malaria...... density. Similarly, antibody levels were not associated with haemoglobin levels or anaemia risk. CONCLUSION: Cytophilic IgG1 and IgG3 antibodies against R0-GLURP may contribute to the control of parasite multiplication and reduction in febrile malaria incidence in children living in an area of intense...

  1. Diversity and above-ground biomass patterns of vascular flora induced by flooding in the drawdown area of China's Three Gorges Reservoir.

    Science.gov (United States)

    Wang, Qiang; Yuan, Xingzhong; Willison, J H Martin; Zhang, Yuewei; Liu, Hong

    2014-01-01

    Hydrological alternation can dramatically influence riparian environments and shape riparian vegetation zonation. However, it was difficult to predict the status in the drawdown area of the Three Gorges Reservoir (TGR), because the hydrological regime created by the dam involves both short periods of summer flooding and long-term winter impoundment for half a year. In order to examine the effects of hydrological alternation on plant diversity and biomass in the drawdown area of TGR, twelve sites distributed along the length of the drawdown area of TGR were chosen to explore the lateral pattern of plant diversity and above-ground biomass at the ends of growing seasons in 2009 and 2010. We recorded 175 vascular plant species in 2009 and 127 in 2010, indicating that a significant loss of vascular flora in the drawdown area of TGR resulted from the new hydrological regimes. Cynodon dactylon and Cyperus rotundus had high tolerance to short periods of summer flooding and long-term winter flooding. Almost half of the remnant species were annuals. Species richness, Shannon-Wiener Index and above-ground biomass of vegetation exhibited an increasing pattern along the elevation gradient, being greater at higher elevations subjected to lower submergence stress. Plant diversity, above-ground biomass and species distribution were significantly influenced by the duration of submergence relative to elevation in both summer and previous winter. Several million tonnes of vegetation would be accumulated on the drawdown area of TGR in every summer and some adverse environmental problems may be introduced when it was submerged in winter. We conclude that vascular flora biodiversity in the drawdown area of TGR has dramatically declined after the impoundment to full capacity. The new hydrological condition, characterized by long-term winter flooding and short periods of summer flooding, determined vegetation biodiversity and above-ground biomass patterns along the elevation gradient in

  2. Specificity patterns indicate that auxin exporters and receptors are the same proteins.

    Science.gov (United States)

    Hössel, D; Schmeiser, C; Hertel, R

    2005-01-01

    A study of transport and action of synthetic auxin analogues can help to identify transporters and receptors of this plant hormone. Both aspects--transportability and action on growth--were tested with 2-naphthoxyacetic acid (2-NOA) and compared across several plant species. 2-NOA stimulates elongation effectively at low concentrations in petioles of the gymnosperm Ginkgo biloba L., in hypocotyls or internodes of the dicot legumes, mung bean (Vigna mungo L.) and pea (Pisum sativum L.), in cotyledons of onion (Allium cepa L.) and in leaf bases of chive (Allium schoenoprasum L.), the latter two of the monocot order Asparagales. In contrast, elongation of coleoptile segments of maize (Zea mays L.) is poorly responsive to 2-NOA. Significant auxin-like transport of 2-NOA was observed in segments of mung bean hypocotyls, pea internodes, and chive leaf bases, but not in segments of the grass coleoptiles. Thus, for the two assays, elongation and polar transportability, the same difference in ligand specificity was observed between the grass and all other species assayed. This finding supports the hypothesis that a common protein mediates auxin efflux as well as auxin action on elongation.

  3. C4b-binding protein is present in affected areas of myocardial infarction during the acute inflammatory phase and covers a larger area than C3.

    Directory of Open Access Journals (Sweden)

    Leendert A Trouw

    Full Text Available BACKGROUND: During myocardial infarction reduced blood flow in the heart muscle results in cell death. These dying/dead cells have been reported to bind several plasma proteins such as IgM and C-reactive protein (CRP. In the present study we investigated whether fluid-phase complement inhibitor C4b-binding protein (C4BP would also bind to the infarcted heart tissue. METHODS AND FINDINGS: Initial studies using immunohistochemistry on tissue arrays for several cardiovascular disorders indicated that C4BP can be found in heart tissue in several cardiac diseases but that it is most abundantly found in acute myocardial infarction (AMI. This condition was studied in more detail by analyzing the time window and extent of C4BP positivity. The binding of C4BP correlates to the same locations as C3b, a marker known to correlate to the patterns of IgM and CRP staining. Based on criteria that describe the time after infarction we were able to pinpoint that C4BP binding is a relatively early marker of tissue damage in myocardial infarction with a peak of binding between 12 hours and 5 days subsequent to AMI, the phase in which infiltration of neutrophilic granulocytes in the heart is the most extensive. CONCLUSIONS: C4BP, an important fluid-phase inhibitor of the classical and lectin pathway of complement activation binds to jeopardized cardiomyocytes early after AMI and co-localizes to other well known markers such as C3b.

  4. Structural factors influencing patterns of drug selling and use and HIV risk in the San Salvador metropolitan area.

    Science.gov (United States)

    Dickson-Gomez, Julia

    2010-06-01

    This article explores differences in the social context in which crack sales and use and HIV risk take place in seven low-income communities in San Salvador, and structural factors that may influence these differences. The organization of drug selling varied among the communities on a number of dimensions including: whether drug sales were open or closed systems; the type of drug-selling site; and the participation of drug users in drug-distribution roles. Drug-use sites also varied according to whether crack was used in private, semiprivate, or public spaces, and whether individuals used drugs alone or with other drug users. Three patterns of drug use and selling were identified based on the dimensions outlined above. Structural factors that influenced these patterns included the geographic location of the communities, their physical layout, gang involvement in drug sales, and police surveillance. Implications for HIV risk and prevention are explored for each pattern.

  5. Alterations in penicillin binding protein gene of Streptococcus pneumoniae and their correlation with susceptibility patterns.

    Science.gov (United States)

    Ohsaki, Yoshinobu; Tachibana, Mineji; Nakanishi, Kyoko; Nakao, Shoko; Saito, Kumiko; Toyoshima, Eri; Sato, Maki; Takahashi, Toru; Osanai, Shinobu; Itoh, Yoshihisa; Kikuchi, Kenjiro

    2003-08-01

    Penicillin binding protein (pbp) gene alterations of 328 clinical isolates of Streptococcus pneumoniae were examined for a correlation with their antibiotic-resistance. The frequency of penicillin G (PEN-G) resistance was determined to clarify susceptibility to several antibiotics, namely PEN-G, ampicillin, sulbactam/ampicillin, cefozopram, panipenem (PAPM), clarithromycin (CLR), azithromycin (AZM) and levofloxacin (LVX). Oligonucleotide primers for three pbp genes (pbp1a, pbp2x and pbp2b) were used to detect mutations in pbp. Of the strains, 25.9% were classified as Pen-Gs, 68.0% as Pen-Gir and 6.1% as Pen-Gr. The polymerase chain reaction product for wild-type pbp1a was found in 185 isolates, that for wild-type pbp2x was found in 66 isolates and that for wild-type pbp2b was found in 213 isolates. None of these three genes was detectable in 100 isolates while all of them were detected in 64 isolates (1aw/2xw/2bw). Of those 64 isolates with 1aw/2xw/2bw, the minimum inhibitory concentration (MIC) of PEN-G was or =4.0 mg/l included one Pen-Gs and two Pen-Gir isolates. The MICs of CLR correlated significantly with those of AZM. The MIC of CLR was > or =1 mg/l for 216 isolates, and the MIC of AZM was > or =1 mg/l for 244 of them. These data suggested that PAPM may be effective against S. pneumoniae infection, although acquisition of resistance should be considered. LVX also seemed to be effective against S. pneumoniae.

  6. Applying of hierarchical clustering to analysis of protein patterns in the human cancer-associated liver.

    Directory of Open Access Journals (Sweden)

    Natalia A Petushkova

    Full Text Available There are two ways that statistical methods can learn from biomedical data. One way is to learn classifiers to identify diseases and to predict outcomes using the training dataset with established diagnosis for each sample. When the training dataset is not available the task can be to mine for presence of meaningful groups (clusters of samples and to explore underlying data structure (unsupervised learning.We investigated the proteomic profiles of the cytosolic fraction of human liver samples using two-dimensional electrophoresis (2DE. Samples were resected upon surgical treatment of hepatic metastases in colorectal cancer. Unsupervised hierarchical clustering of 2DE gel images (n = 18 revealed a pair of clusters, containing 11 and 7 samples. Previously we used the same specimens to measure biochemical profiles based on cytochrome P450-dependent enzymatic activities and also found that samples were clearly divided into two well-separated groups by cluster analysis. It turned out that groups by enzyme activity almost perfectly match to the groups identified from proteomic data. Of the 271 reproducible spots on our 2DE gels, we selected 15 to distinguish the human liver cytosolic clusters. Using MALDI-TOF peptide mass fingerprinting, we identified 12 proteins for the selected spots, including known cancer-associated species.Our results highlight the importance of hierarchical cluster analysis of proteomic data, and showed concordance between results of biochemical and proteomic approaches. Grouping of the human liver samples and/or patients into differing clusters may provide insights into possible molecular mechanism of drug metabolism and creates a rationale for personalized treatment.

  7. MODELING FLOW PATTERNS IN A SMALL VEGETATED AREA IN THE NORTHERN CHICHUAHUAN DESERT USING QUIC ( QUIC URBAN AND INDUSTRIAL COMPLEX )

    Science.gov (United States)

    Sandstorms are frequent in the northern Chihuahuan Desert in New Mexico, an area characterized by open areas lacking vegetation, individual mesquite bushes, and mesquite coppice dunes. Field measurements of sand fluxes and wind velocities over a two year period provided a descri...

  8. Design and Implementation of Integrated Solid Wastes Management Pattern in Industrial areas, Case Study of Shahroud, Iran

    Directory of Open Access Journals (Sweden)

    Kamiar Yaghmaeian

    2014-03-01

    Conclusion: Results showed that implementation of this pattern, i.e. running source separation, training programs, capacity building, providing technical services, completing chain of industries and strengthening the cooperation between industrial estate management and industrial units could greatly reduce the waste management problems.

  9. Intraspecific variation in protein pattern of red scorpion (Mesobuthus tamulus, coconsis, pocock venoms from Western and Southern India

    Directory of Open Access Journals (Sweden)

    R. V. Badhe

    2006-01-01

    Full Text Available Red scorpions Mesobuthus tamulus (Coconsis, Pocock were obtained from different regions of West and South India (Ratnagiri, Chiplun and Ahmednagar from Maharashtra and Chennai from Tamil Nadu, respectively. Their venoms composition was analyzed using gel electrophoresis (SDS-PAGE. All venom samples shared six bands of 170, 80, 60, 57, 43, and 38 kDa molecular weights. Bands of 115 kDa and 51.5 kDa were characteristic of venoms obtained from red scorpions of Chiplun region, and the 26kDa band was absent in scorpion venom from Tamil Nadu. The separated protein band patterns suggest that the venoms from Ratnagiri, Ahmednagar and Tamil Nadu had high similarities in their biochemical composition but differed from that of Chiplun region. These data were also supported by the Jaccard (J index. The J value was 0.33 for venom obtained from Ratnagiri-Ahmednagar, 0.31 for venom from Ratnagiri-Tamil Nadu, and 0.3 for venom from Ratnagiri-Chiplun region. This suggests the existence of genetic variation among the different strains of red scorpion in western and southern India. The antiserum produced by Haffkine Biopharmaceuticals Corporation Ltd. completely neutralized proteins of venoms from all the regions studied.

  10. Patterns of mouse reticulon 3 mRNA and protein expression in the mouse central nervous system

    Institute of Scientific and Technical Information of China (English)

    LIU Jin; QIANG Boqin; YUAN Jiangang; HUANG Xiaowei; PENG Xiaozhong; YANG Hongbo; YIN Bin; TAN Xinyu; FAN Ming; FAN Wenhong; LIU Bingyan

    2003-01-01

    Reticulons (RTN) are endoplasmic reticulumassociated protein complexes, which are localized in the endoplasmic reticulum (ER) and identified as markers for neuroendocrine differentiation. At least four different RTN genes have been identified in mammals, but in most cases,the functions of the encoded proteins except mammalian RTN4-A and RTN4-B are still elusive. In the present study,mouse reticulon 3 (mRTN3) is cloned and its expression pattern in a variety of tissues is investigated. Three alternatively spliced transcripts of 1.8, 2.8 and 4.2 kb are revealed by Northern blotting hybridization. The 1.8 and 2.8 kb transcripts are expressed in many tissues. The 2.8 kb transcript has a high level in brain and the 4.2 kb transcript is only found in brain. In situ hybridization and immunohistochemical analysis indicated its high expression in non-glial cells in some particular region of mouse central nervous system, such as hippocampus, sub-thalamus nucleus, thalamus nucleus and cerebrum cortex.

  11. Application of power spectra patterns in Fourier transform square wave voltammetry to evaluate electrode kinetics of surface-confined proteins.

    Science.gov (United States)

    Fleming, Barry D; Barlow, Nicola L; Zhang, Jie; Bond, Alan M; Armstrong, Fraser A

    2006-05-01

    This paper describes an application of Fourier transform (FT) voltammetry that provides a quantitative evaluation of the electron-transfer kinetics of protein molecules attached to electrode surfaces. The potential waveform applied in these experiments consists of a large-amplitude square wave of frequency f superimposed onto the traditional triangular voltage used in dc cyclic voltammetry. The resultant current-time response, when Fourier transformed into the frequency domain, provides patterns of data at the even harmonic frequencies that arise from nonlinearity in the Faradaic response. These even harmonic contributions are ideally suited for kinetic evaluation of electron-transfer processes because they are highly selective to quasi-reversible behavior (insensitive to reversible or irreversible processes) and almost devoid of background charging current. Inverse FT methods can then be used to provide the wave shapes of the dc as well as the ac voltammetric components and other characteristics employed to detect the level of nonideality present relative to theoretical models based upon noninteracting surface-confined molecules. The new form of data evaluation has been applied to the electron-transfer properties of a typical biological electron carrier, the blue copper protein azurin, immobilized on polycrystalline gold electrodes modified with self-assembled monolayers of different length alkanethiols. Details of the electrode kinetics (rates of electron transfer, dispersion, and charge-transfer coefficients) as a function of alkanethiol, apparent surface coverage, and capacitance are all deduced from the square wave (FT-inverse FT) protocol, and the implications of these findings are considered.

  12. Divide and Conquer Approach to Contact Map Overlap Problem Using 2D-Pattern Mining of Protein Contact Networks.

    Science.gov (United States)

    Koneru, Suvarna Vani; Bhavani, Durga S

    2015-01-01

    A novel approach to Contact Map Overlap (CMO) problem is proposed using the two dimensional clusters present in the contact maps. Each protein is represented as a set of the non-trivial clusters of contacts extracted from its contact map. The approach involves finding matching regions between the two contact maps using approximate 2D-pattern matching algorithm and dynamic programming technique. These matched pairs of small contact maps are submitted in parallel to a fast heuristic CMO algorithm. The approach facilitates parallelization at this level since all the pairs of contact maps can be submitted to the algorithm in parallel. Then, a merge algorithm is used in order to obtain the overall alignment. As a proof of concept, MSVNS, a heuristic CMO algorithm is used for global as well as local alignment. The divide and conquer approach is evaluated for two benchmark data sets that of Skolnick and Ding et al. It is interesting to note that along with achieving saving of time, better overlap is also obtained for certain protein folds.

  13. Fasciola hepatica phenotypic characterization in Andean human endemic areas: valley versus altiplanic patterns analysed in liver flukes from sheep from Cajamarca and Mantaro, Peru.

    Science.gov (United States)

    Valero, M Adela; Perez-Crespo, Ignácio; Khoubbane, Messaoud; Artigas, Patricio; Panova, Miroslava; Ortiz, Pedro; Maco, Vicente; Espinoza, José R; Mas-Coma, Santiago

    2012-03-01

    Fascioliasis is a zoonotic parasitic disease caused by Fasciola hepatica and Fasciola gigantica. Of both species, F. hepatica is the only one described in the Americas, mainly transmitted by lymnaeid snail vectors of the Galba/Fossaria group. Human fascioliasis endemic areas are mainly located in high altitude areas of Andean countries. Given the necessity to characterize F. hepatica populations involved, the phenotypic features of fasciolid adults infecting sheep present in human fascioliasis endemic areas were analysed in the Cajamarca Valley and Mantaro Valley (valley transmission patterns) and the northern Bolivian Altiplano (altiplanic transmission pattern). A computer image analysis system (CIAS) was applied on the basis of standardized measurements. The aforementioned highland populations were compared to standard lowland natural and experimental populations of European origin. Liver fluke size was studied by multivariate analyses. Two phenotypic patterns could be distinguished in F. hepatica adult size: the valley pattern (Cajamarca and Mantaro, Peru) and the altiplanic pattern (northern Altiplano, Bolivia). Results showed that the Andean valley population and European standard populations presented a phenotypic homogeneity. The Altiplano population showed a large size range with a pronouncedly lower minimum size indicating that uterus gravidity is reached at a smaller size than in valley populations. The results of this study demonstrate that there is no apparent relationship between the shape of fasciolid adults with regard to altitudinal difference or geographical origin and that allometry-free shape appears as a more stable trait than size in fasciolid species. Results are analysed in terms of intensity/crowding effect aspects and permanent/seasonal transmission characteristics.

  14. Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

    Directory of Open Access Journals (Sweden)

    Warwicker Jim

    2008-10-01

    Full Text Available Abstract Background Empirical binding models have previously been investigated for the energetics of protein complexation (ΔG models and for the influence of mutations on complexation (i.e. differences between wild-type and mutant complexes, ΔΔG models. We construct binding models to directly compare these processes, which have generally been studied separately. Results Although reasonable fit models were found for both ΔG and ΔΔG cases, they differ substantially. In a dataset curated for the absence of mainchain rearrangement upon binding, non-polar area burial is a major determinant of ΔG models. However this ΔG model does not fit well to the data for binding differences upon mutation. Burial of non-polar area is weighted down in fitting of ΔΔG models. These calculations were made with no repacking of sidechains upon complexation, and only minimal packing upon mutation. We investigated the consequences of more extensive packing changes with a modified mean-field packing scheme. Rather than emphasising solvent exposure with relatively extended sidechains, rotamers are selected that exhibit maximal packing with protein. This provides solvent accessible areas for proteins that are much closer to those of experimental structures than the more extended sidechain regime. The new packing scheme increases changes in non-polar burial for mutants compared to wild-type proteins, but does not substantially improve agreement between ΔG and ΔΔG binding models. Conclusion We conclude that solvent accessible area, based on modelled mutant structures, is a poor correlate for ΔΔG upon mutation. A simple volume-based, rather than solvent accessibility-based, model is constructed for ΔG and ΔΔG systems. This shows a more consistent behaviour. We discuss the efficacy of volume, as opposed to area, approaches to describe the energetic consequences of mutations at interfaces. This knowledge can be used to develop simple computational screens for

  15. Dataset on outdoor behavior-system and spatial-pattern in the third place in cold area-based on the perspective of new energy structure

    Directory of Open Access Journals (Sweden)

    Kai Ren

    2017-02-01

    Full Text Available The data presented in this paper are related to the research article entitled “Exploration of Outdoor Behavior System and Spatial Pattern in the Third Place in Cold Area- based on the perspective of new energy structure” (Ren, 2016 [1]. The dataset was from a field sub-time extended investigation to residents of Power Home Community in Inner Mongolia of China that belongs to cold region of ID area according to Chinese design code for buildings. This filed data provided descriptive statistics about environment-behavior symbiosis system, environment loading, behavior system, spatial demanding and spatial pattern for all kinds of residents (Older, younger, children. The field data set is made publicly available to enable critical or extended analyzes.

  16. Dataset on outdoor behavior-system and spatial-pattern in the third place in cold area-based on the perspective of new energy structure.

    Science.gov (United States)

    Ren, Kai; Wang, Yuan; Liu, Tingxi; Wang, Guanli

    2017-02-01

    The data presented in this paper are related to the research article entitled "Exploration of Outdoor Behavior System and Spatial Pattern in the Third Place in Cold Area- based on the perspective of new energy structure" (Ren, 2016) [1]. The dataset was from a field sub-time extended investigation to residents of Power Home Community in Inner Mongolia of China that belongs to cold region of ID area according to Chinese design code for buildings. This filed data provided descriptive statistics about environment-behavior symbiosis system, environment loading, behavior system, spatial demanding and spatial pattern for all kinds of residents (Older, younger, children). The field data set is made publicly available to enable critical or extended analyzes.

  17. CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.

    Science.gov (United States)

    Terashi, Genki; Takeda-Shitaka, Mayuko

    2015-01-01

    Proteins are flexible, and this flexibility has an essential functional role. Flexibility can be observed in loop regions, rearrangements between secondary structure elements, and conformational changes between entire domains. However, most protein structure alignment methods treat protein structures as rigid bodies. Thus, these methods fail to identify the equivalences of residue pairs in regions with flexibility. In this study, we considered that the evolutionary relationship between proteins corresponds directly to the residue-residue physical contacts rather than the three-dimensional (3D) coordinates of proteins. Thus, we developed a new protein structure alignment method, contact area-based alignment (CAB-align), which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment. We evaluated the performance and advantages of CAB-align based on four main points: (1) agreement with the gold standard alignment, (2) alignment quality based on an evolutionary relationship without 3D coordinate superposition, (3) consistency of the multiple alignments, and (4) classification agreement with the gold standard classification. Comparisons of CAB-align with other state-of-the-art protein structure alignment methods (TM-align, FATCAT, and DaliLite) using our benchmark dataset showed that CAB-align performed robustly in obtaining high-quality alignments and generating consistent multiple alignments with high coverage and accuracy rates, and it performed extremely well when discriminating between homologous and nonhomologous pairs of proteins in both

  18. Landscape pattern and its effect on ecosystem functions in Seoul Metropolitan area: Urban ecology on distribution of the naturalized plant species

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    During land transformation process in the human history, naturalized plants were introduced to several land use patterns by thedifferent ways of plant itself.Including some naturalized plants that had been contribute to land restoration, many naturalized plants have beeninvaded to original habitat or landscape for native plants.Once the plants were colonized, they extend their area and population size.Urbandeveloped areas often give an important role of source habitat for naturalized plants and expanding their population size.In recent, this situationis appearing as one of environmental problems about the urban landscape management controlling the naturalized plants that invaded in thedeveloped area and conserving the native vegetation.This paper is focusing on relationships between distribution of habitat of naturalized plantsand landscape patch in urban area in Seoul.Gangdong-Gu, one of the administrative areas in Seoul was selected for this study.We examinedthe recent land use change using LANDSAT TM data and spreading of the representative naturalized plants ( Robinia pseudoacacia andEupatorium rugosum) by Seoul Biotope Mapping Project and field survey in 1999.As a result, these two species were often occurred in thesame habitat and distributed in forest edge disturbed by man.Their distribution patterns were related to landscape indices (patch size andshape) in the forest edge.

  19. Blood pressure patterns in relation to geographic area of residence: a cross-sectional study of adolescents in Kogi state, Nigeria

    Directory of Open Access Journals (Sweden)

    Ugwu Chidi E

    2008-12-01

    Full Text Available Abstract Background The prevalence of hypertension, an important risk factor for cardiovascular disease (CVD, is increasing in the developing countries and this may be connected with the economic transition in those countries. Adult hypertension is thought to be related to childhood and adolescent increases in blood pressure, and hence the need to monitor patterns in early life. This study investigates the BP patterns, and their correlates, of adolescents from different geographic areas of residence in Nigeria. Methods A total of 1,088 Nigerian adolescents from different geographic areas of residence were recruited for the study. Their blood pressures and anthropometric indices were measured using standard procedures. The association of blood pressure with height, weight, body mass index (BMI and geographic area of residence was assessed. Results Male and female urban-dwelling adolescents had significantly (p 2 for males and 21.35 ± 3.37 kg/m2 for females than those in the non-urban areas (20.33 ± 3.11 kg/m2 for males and 21.35 ± 3.37 kg/m2 for females though the difference was significant (p Conclusion These findings underscore the need for efforts to be made towards addressing adolescent blood pressure elevation (in both urban and non-urban areas as they are a reflection of adult morbidity and mortality from hypertension and the associated disorders.

  20. Flow pattern and related chemical quality of ground water in the "500-foot" sand in the Memphis area, Tennessee

    Science.gov (United States)

    Bell, Edwin Allen; Nyman, Dale J.

    1968-01-01

    The '500-foot' sand is the major source of water supply for the Memphis area. Thick layers of impervious clay above and below the sand confine the water in the aquifer under artesian pressure and also protect the aquifer from contamination. Recharge from rainfall enters the '500-foot' sand in the outcrop, or intake area south and east of Memphis. Recharge from other aquifers enters the sand wherever the confining beds are breached or absent. Some of the recharge that enters the '500-foot' sand in eastern Arkansas moves down the gradients created by pumping in the Memphis area. All discharge from the '500-foot' sand in the Memphis area results from well pumping. Since 1886 continuous withdrawals at gradually increasing rates of pumping have lowered water levels and altered hydraulic gradients in the area. These withdrawals have resulted in changes in direction and velocity of movement of water through the '500-foot' sand. Water in the sand in the southeaster n part of the Memphis area normally moves from the (outcrop area east and south of Memphis northwestward toward points of withdrawal. In the northwestern part of the area, water moves southeastward toward points of withdrawal. A flow-net analysis of the aquifer shows that the rate of water movement through the '500-foot' sand in 1964, toward the major cones of depression in the Memphis area, was about 350 feet per year, or 1 mile in 15 years. A flow-net analysis projected for the year 1975 indicates the rate will increase by about 20 percent in the 12-year period 1964-75. Water in the '500-foot' sand in the Memphis area is generally a calcium magnesium sodium bicarbonate type. It is soft, low in dissolved solids, high in concentrations of iron and carbon dioxide, and slightly to moderately corrosive. The softest and least mineralized water occurs in the southeastern part of the area, and the water becomes slightly harder and more mineralized as it moves downdip toward Memphis. The hardest and most mineralized

  1. Nutritional Status and Daytime Pattern of Protein Intake on Match, Post-Match, Rest and Training Days in Senior Professional and Youth Elite Soccer Players.

    Science.gov (United States)

    Bettonviel A, E O; Brinkmans N, Y J; Russcher, Kris; Wardenaar, Floris C; Witard, Oliver C

    2016-06-01

    The nutritional status of elite soccer players across match, postmatch, training and rest days has not been defined. Recent evidence suggests the pattern of dietary protein intake impacts the daytime turnover of muscle proteins and, as such, influences muscle recovery. We assessed the nutritional status and daytime pattern of protein intake in senior professional and elite youth soccer players and compared findings against published recommendations. Fourteen senior professional (SP) and 15 youth elite (YP) soccer players from the Dutch premier division completed nutritional assessments using a 24-hr web-based recall method. Recall days consisted of a match, postmatch, rest, and training day. Daily energy intake over the 4-day period was similar between SP (2988 ± 583 kcal/day) and YP (2938 ± 465 kcal/day; p = .800). Carbohydrate intake over the combined 4-day period was lower in SP (4.7 ± 0.7 g·kg-1 BM·day-1) vs. YP (6.0 ± 1.5 g·kg-1 BM·day-1, p = .006) and SP failed to meet recommended carbohydrate intakes on match and training days. Conversely, recommended protein intakes were met for SP (1.9 ± 0.3 g·kg-1 BM·day-1) and YP (1.7 ± 0.4 g·kg-1 BM·day-1), with no differences between groups (p = .286). Accordingly, both groups met or exceeded recommended daily protein intakes on individual match, postmatch, rest and training days. A similar "balanced" daytime pattern of protein intake was observed in SP and YP. To conclude, SP increased protein intake on match and training days to a greater extent than YP, however at the expense of carbohydrate intake. The daytime distribution of protein intake for YP and SP aligned with current recommendations of a balanced protein meal pattern.

  2. Diversity, distribution pattern and seasonal variation in moth assemblages along altitudinal gradient in Gangotri landscape area, Western Himalaya, Uttarakhand, India

    Directory of Open Access Journals (Sweden)

    A.K. Sanyal

    2013-02-01

    Full Text Available Field survey was conducted at different altitudes and land-use areas in the two protected areas, viz., Gangotri National Park and Govind National Park of Uttarkashi District, Uttarakhand, India. A total of 475 specimens of moth representing 436 morphospecies were collected using light trap method during the survey conducted between September 2008-May 2010. Preliminary findings show a decreasing diversity with increasing altitude. Subalpine areas were least diverse and subtropical areas had the highest diversity of moths. The greatest number of specimens were collected during the summer and post-monsoon period. The lunar phase had a significant effect on catch success with new moon days resulting in the largest catches and full moon days resulting in the least number of species as well as individuals. Of the thirty two species mentioned in Appendix 1, nine species are first time record from the state Uttarakhand. Four species are new record from Western Himalaya within Indian Territory, and also first time recorded from entire Himalayan landscape. As there was no previous comprehensive study on the moth diversity of Gangotri landscape area, all the 32 species described could be regarded as new record from these two protected areas.

  3. Dietary patterns in the population living in the Sami core areas of Norway--the SAMINOR study

    OpenAIRE

    Brustad, Magritt; Parr, Christine L; Melhus, Marita; Lund, Eiliv

    2008-01-01

    OBJECTIVES: To identify dietary patterns and to investigate their association with selected life-style and demographic factors, ethnicity and self-perceived health. Study design. Population-based cross-sectional design, using food frequency questionnaires. METHODS: A total of 12,811 subjects aged 36-79 years participated from the municipalities in Norway where more than 5-10% of the population reported to be Simi in the 1970 Census, in addition to some selected districts. The data were colle...

  4. Selective-area catalyst-free MBE growth of GaN nanowires using a patterned oxide layer.

    Science.gov (United States)

    Schumann, T; Gotschke, T; Limbach, F; Stoica, T; Calarco, R

    2011-03-04

    GaN nanowires (NWs) were grown selectively in holes of a patterned silicon oxide mask, by rf-plasma-assisted molecular beam epitaxy (PAMBE), without any metal catalyst. The oxide was deposited on a thin AlN buffer layer previously grown on a Si(111) substrate. Regular arrays of holes in the oxide layer were obtained using standard e-beam lithography. The selectivity of growth has been studied varying the substrate temperature, gallium beam equivalent pressure and patterning layout. Adjusting the growth parameters, GaN NWs can be selectively grown in the holes of the patterned oxide with complete suppression of the parasitic growth in between the holes. The occupation probability of a hole with a single or multiple NWs depends strongly on its diameter. The selectively grown GaN NWs have one common crystallographic orientation with respect to the Si(111) substrate via the AlN buffer layer, as proven by x-ray diffraction (XRD) measurements. Based on the experimental data, we present a schematic model of the GaN NW formation in which a GaN pedestal is initially grown in the hole.

  5. [C and N allocation patterns in planted forests and their release patterns during leaf litter decomposition in subalpine area of west Sichuan].

    Science.gov (United States)

    Liu, Zeng-wen; Duan, Er-jun; Pan, Kai-wen; Zhang, Li-ping; Du, Hong-xia

    2009-01-01

    With the planted forest ecosystems of Cercidiphyllum japonicum, Betula utilis, Pinus yunnansinsis, and Picea asperata in subalpine area of west Sichuan as test objects, their total biomass and the C and N contents in soils and tree organs were determined. The results showed that the allocation of C in tree organs had less correlation with the age of the organs, while that of N and C/N ratio had closer relationship with the age. The N content in young organs was higher than that in aged ones, whereas the C/N ratio was higher in aged organs than in young organs, and higher in the leaf litters of needle-leaved forests than in those of broad-leaved forests. There was an obvious enrichment of C and N in the topsoil of test forests. The accumulated amounts of C and N in the whole planted forest ecosystem, including tree, litter, and 0-40 cm soil layer, were 176.75-228.05 t x hm(-2) and 11.06-16.54 t x hm(-2), respectively, and the nutrients allocation ratio between soil-litter and tree was (1.9-3.3):1 for C and (15.6-41.5):1 for N. Needle-leaved forests functioned as a stronger "C-sink" than broad-leaved forests. The decomposition rate of the leaf litters in needle-leaved forests was larger than that in broad-leaved forests, with the turnover rate being 2.2-3.7 years and 3.9-4.2 years, respectively. During the decomposition of leaf litter, the C in all of the four forests released at super-speed, with the turnover rate being 1.9-3.4 years. As for N, it also released at super-speed in C. japonicum and B. utilis forests, with the turnover rate being 1.9-3.2 years, but released at low speed in P. yunnansinsis and P. asperata forests, with the turnover rate being 6.7-8.5 years.

  6. Alternative mRNA Splicing from the Glial Fibrillary Acidic Protein (GFAP) Gene Generates Isoforms with Distinct Subcellular mRNA Localization Patterns in Astrocytes

    DEFF Research Database (Denmark)

    Thomsen, Rune; Daugaard, Tina Fuglsang; Holm, Ida E;

    2013-01-01

    The intermediate filament network of astrocytes includes Glial fibrillary acidic protein (Gfap) as a major component. Gfap mRNA is alternatively spliced resulting in generation of different protein isoforms where Gfapa is the most predominant isoform. The Gfapd isoform is expressed in proliferating......RNA localization patterns were dependent on the different 39-exon sequences included in Gfapd and Gfapa mRNA. The presented results show that alternative Gfap mRNA splicing results in isoform-specific mRNA localization patterns with resulting different local mRNA concentration ratios which have potential...

  7. The Change of Land Use/Cover and Characteristics of Landscape Pattern in Arid Areas Oasis: An Application in Jinghe, Xinjiang

    Institute of Scientific and Technical Information of China (English)

    ZHANG Fei; TASHPOLAT·Tiyip; Hsiang-te KUNG; DING Jianli

    2010-01-01

    This paper uses 3S technology in macroscopic. Combining the integrated technology of ecological quantity analytical method with GIS technology through ArcGIS and Fragstats, the authors study the images of 1972, 1990, 2001, and 2005 and obtained land use data in Jinghe County. Then, the change of land use/cover and landscape pattern had been analyzed in the Jinghe County of Xinjiang. The conclusions were as follows: (1) The trend of LUCC is that the area of oasis expands slowly in nearly 33years between 1972 to 2005 in Jinghe County. (2) The water area is mainly influenced by Ebinur Lake, so the area expands a little in this period. (3) The area of salinization-land expands at first and reduces later. The area of sand land decreases and the other land class increases, while the probability of transfer is always high. (4) Landscape change is also obvious throughout the decades.Overall, landscape density increases, the largest path index decreases at first and expends later, the weight area index decreases, and the shape of landscape becomes regulated. The nearest distances, the degrees of reunite, and outspread decreases. It shows that the connection of the main path in 1972 is better than 2005, wherein the patch becomes more complex. From the changes of Shannon's Diversity Index and Shannon's Evenness Index, we know that the diversity of landscape and the Interspersion Juxtaposition Index increase. The degree of diversity landscape and fragmentation increase also shows that the land uses become more complex. All in all, it is essential to intensify the spatial relationships among landscape elements and to maintain the continuity of landscape ecological process and pattern in the course of area expansion.

  8. Protein

    Science.gov (United States)

    ... Food Service Resources Additional Resources About FAQ Contact Protein Protein is found throughout the body—in muscle, ... the heart and respiratory system, and death. All Protein Isn’t Alike Protein is built from building ...

  9. Atmospheric chemistry of mercury in Antarctica and the role of cryptogams to assess deposition patterns in coastal ice-free areas.

    Science.gov (United States)

    Bargagli, R

    2016-11-01

    Mercury in the Antarctic troposphere has a distinct chemistry and challenging long-term measurements are needed for a better understanding of the atmospheric Hg reactions with oxidants and the exchanges of the various mercury forms among air-snow-sea and biota. Antarctic mosses and lichens are reliable biomonitors of airborne metals and in short time they can give useful information about Hg deposition patterns. Data summarized in this review show that although atmospheric Hg concentrations in the Southern Hemisphere are lower than those in the Northern Hemisphere, Antarctic cryptogams accumulate Hg at levels in the same range or higher than those observed for related cryptogam species in the Arctic, suggesting an enhanced deposition of bioavailable Hg in Antarctic coastal ice-free areas. In agreement with the newest findings in the literature, the Hg bioaccumulation in mosses and lichens from a nunatak particularly exposed to strong katabatic winds can be taken as evidence for a Hg contribution to coastal ecosystems by air masses from the Antarctic plateau. Human activities on the continent are mostly concentrated in coastal ice-free areas, and the deposition in these areas of Hg from the marine environment, the plateau and anthropogenic sources raises concern. The use of Antarctic cryptogams as biomonitors will be very useful to map Hg deposition patterns in costal ice-free areas and will contribute to a better understanding of Hg cycling in Antarctica and its environmental fate in terrestrial ecosystems.

  10. The impact of endemic and epidemic malaria on the risk of stillbirth in two areas of Tanzania with different malaria transmission patterns

    Directory of Open Access Journals (Sweden)

    Mutabingwa TK

    2006-10-01

    Full Text Available Abstract Background The impact of malaria on the risk of stillbirth is still under debate. The aim of the present analysis was to determine comparative changes in stillbirth prevalence between two areas of Tanzania with different malaria transmission patterns in order to estimate the malaria attributable component. Methods A retrospective analysis was completed of stillbirth differences between primigravidae and multigravidae in relation to malaria cases and transmission patterns for two different areas of Tanzania with a focus on the effects of the El Niño southern climatic oscillation (ENSO. One area, Kagera, experiences outbreaks of malaria, and the other area, Morogoro, is holoendemic. Delivery and malaria data were collected over a six year period from records of the two district hospitals in these locations. Results There was a significantly higher prevalence of low birthweight in primigravidae compared to multigravidae for both data sets. Low birthweight and stillbirth prevalence (17.5% and 4.8% were significantly higher in Kilosa compared to Ndolage (11.9% and 2.4%. There was a significant difference in stillbirth prevalence between Ndolage and Kilosa between malaria seasons (2.4% and 5.6% respectively, p Conclusion Malaria exposure during pregnancy has a delayed effect on birthweight outcomes, but a more acute effect on stillbirth risk.

  11. Structural Basis of Recognition of Pathogen-associated Molecular Patterns and Inhibition of Proinflammatory Cytokines by Camel Peptidoglycan Recognition Protein*

    Science.gov (United States)

    Sharma, Pradeep; Dube, Divya; Singh, Amar; Mishra, Biswajit; Singh, Nagendra; Sinha, Mau; Dey, Sharmistha; Kaur, Punit; Mitra, Dipendra K.; Sharma, Sujata; Singh, Tej P.

    2011-01-01

    Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated molecular patterns. The well known pathogen-associated molecular patterns include LPS from Gram-negative bacteria and lipoteichoic acid (LTA) from Gram-positive bacteria. In this work, the crystal structures of two complexes of the short form of camel PGRP (CPGRP-S) with LPS and LTA determined at 1.7- and 2.1-Å resolutions, respectively, are reported. Both compounds were held firmly inside the complex formed with four CPGRP-S molecules designated A, B, C, and D. The binding cleft is located at the interface of molecules C and D, which is extendable to the interface of molecules A and C. The interface of molecules A and B is tightly packed, whereas that of molecules B and D forms a wide channel. The hydrophilic moieties of these compounds occupy a common region, whereas hydrophobic chains interact with distinct regions in the binding site. The binding studies showed that CPGRP-S binds to LPS and LTA with affinities of 1.6 × 10−9 and 2.4 × 10−8 m, respectively. The flow cytometric studies showed that both LPS- and LTA-induced expression of the proinflammatory cytokines TNF-α and IL-6 was inhibited by CPGRP-S. The results of animal studies using mouse models indicated that both LPS- and LTA-induced mortality rates decreased drastically when CPGRP-S was administered. The recognition of both LPS and LTA, their high binding affinities for CPGRP-S, the significant decrease in the production of LPS- and LTA-induced TNF-α and IL-6, and the drastic reduction in the mortality rates in mice by CPGRP-S indicate its useful properties as an antibiotic agent. PMID:21454594

  12. Structural basis of recognition of pathogen-associated molecular patterns and inhibition of proinflammatory cytokines by camel peptidoglycan recognition protein.

    Science.gov (United States)

    Sharma, Pradeep; Dube, Divya; Singh, Amar; Mishra, Biswajit; Singh, Nagendra; Sinha, Mau; Dey, Sharmistha; Kaur, Punit; Mitra, Dipendra K; Sharma, Sujata; Singh, Tej P

    2011-05-06

    Peptidoglycan recognition proteins (PGRPs) are involved in the recognition of pathogen-associated molecular patterns. The well known pathogen-associated molecular patterns include LPS from Gram-negative bacteria and lipoteichoic acid (LTA) from Gram-positive bacteria. In this work, the crystal structures of two complexes of the short form of camel PGRP (CPGRP-S) with LPS and LTA determined at 1.7- and 2.1-Å resolutions, respectively, are reported. Both compounds were held firmly inside the complex formed with four CPGRP-S molecules designated A, B, C, and D. The binding cleft is located at the interface of molecules C and D, which is extendable to the interface of molecules A and C. The interface of molecules A and B is tightly packed, whereas that of molecules B and D forms a wide channel. The hydrophilic moieties of these compounds occupy a common region, whereas hydrophobic chains interact with distinct regions in the binding site. The binding studies showed that CPGRP-S binds to LPS and LTA with affinities of 1.6 × 10(-9) and 2.4 × 10(-8) M, respectively. The flow cytometric studies showed that both LPS- and LTA-induced expression of the proinflammatory cytokines TNF-α and IL-6 was inhibited by CPGRP-S. The results of animal studies using mouse models indicated that both LPS- and LTA-induced mortality rates decreased drastically when CPGRP-S was administered. The recognition of both LPS and LTA, their high binding affinities for CPGRP-S, the significant decrease in the production of LPS- and LTA-induced TNF-α and IL-6, and the drastic reduction in the mortality rates in mice by CPGRP-S indicate its useful properties as an antibiotic agent.

  13. Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning.

    Science.gov (United States)

    Heffernan, Rhys; Paliwal, Kuldip; Lyons, James; Dehzangi, Abdollah; Sharma, Alok; Wang, Jihua; Sattar, Abdul; Yang, Yuedong; Zhou, Yaoqi

    2015-01-01

    Direct prediction of protein structure from sequence is a challenging problem. An effective approach is to break it up into independent sub-problems. These sub-problems such as prediction of protein secondary structure can then be solved independently. In a previous study, we found that an iterative use of predicted secondary structure and backbone torsion angles can further improve secondary structure and torsion angle prediction. In this study, we expand the iterative features to include solvent accessible surface area and backbone angles and dihedrals based on Cα atoms. By using a deep learning neural network in three iterations, we achieved 82% accuracy for secondary structure prediction, 0.76 for the correlation coefficient between predicted and actual solvent accessible surface area, 19° and 30° for mean absolute errors of backbone φ and ψ angles, respectively, and 8° and 32° for mean absolute errors of Cα-based θ and τ angles, respectively, for an independent test dataset of 1199 proteins. The accuracy of the method is slightly lower for 72 CASP 11 targets but much higher than those of model structures from current state-of-the-art techniques. This suggests the potentially beneficial use of these predicted properties for model assessment and ranking.

  14. Patterns of use of the Mar Chiquita lagoon (Buenos Aires, Argentina) and adjacent coastal area by fish early life stages.

    OpenAIRE

    Bruno, Daniel O.

    2014-01-01

    The role of the Mar Chiquita lagoon and its adjacent coastal area as nursery ground for fish larvae and juveniles and the factors which regulate their recruitment process, was evaluated. To do so, we analyzed the fish early life stages composition and spatio-temporal variation over the marine-estuarine gradient of the lagoon and its relationship with environmental factors; the diel variation of these stages in the immediate area at the mouth of the lagoon; and the source of the organic carbon...

  15. Human salivary gland acinar cells spontaneously form three-dimensional structures and change the protein expression patterns.

    Science.gov (United States)

    Chan, Yen-Hui; Huang, Tsung-Wei; Young, Tai-Horng; Lou, Pei-Jen

    2011-11-01

    Applying tissue engineering principles to design an auto-secretory device is a potential solution for patients suffering loss of salivary gland function. However, the largest challenge in implementing this solution is the primary culture of human salivary gland cells, because the cells are highly differentiated and difficult to expand in vitro. This situation leads to the lack of reports on the in vitro cell biology and physiology of human salivary gland cells. This study used a low-calcium culture system to selectively cultivate human parotid gland acinar (PGAC) cells from tissues with high purity in cell composition. This condition enables PGAC cells to continuously proliferate and retain the phenotypes of epithelial acinar cells to express secreting products (α-amylase) and function-related proteins (aquaporin-3, aquaporin-5, and ZO-1). Notably, when the cells reached confluence, three-dimensional (3D) cell aggregates were observed in crowded regions. These self-formed cell spheres were termed post-confluence structures (PCSs). Unexpectedly, despite being cultured in the same media, cells in PCSs exhibited higher expression levels and different expression patterns of function-related proteins compared to the two-dimensional (2D) cells. Translocation of aquoporin-3 from cytosolic to alongside the cell boundaries, and of ZO-1 molecules to the boundary of the PCSs were also observed. These observations suggest that when PGAC cells cultured on the 2D substrate would form PCSs without the help of 3D scaffolds and retain certain differentiation and polarity. This phenomenon implies that it is possible to introduce 2D substrates instead of 3D scaffolds into artificial salivary gland tissue engineering.

  16. Patterns of structural dynamics in RACK1 protein retained throughout evolution: A hydrogen-deuterium exchange study of three orthologs

    Science.gov (United States)

    Tarnowski, Krzysztof; Fituch, Kinga; Szczepanowski, Roman H; Dadlez, Michal; Kaus-Drobek, Magdalena

    2014-01-01

    RACK1 is a member of the WD repeat family of proteins and is involved in multiple fundamental cellular processes. An intriguing feature of RACK1 is its ability to interact with at least 80 different protein partners. Thus, the structural features enabling such interactomic flexibility are of great interest. Several previous studies of the crystal structures of RACK1 orthologs described its detailed architecture and confirmed predictions that RACK1 adopts a seven-bladed β-propeller fold. However, this did not explain its ability to bind to multiple partners. We performed hydrogen-deuterium (H-D) exchange mass spectrometry on three orthologs of RACK1 (human, yeast, and plant) to obtain insights into the dynamic properties of RACK1 in solution. All three variants retained similar patterns of deuterium uptake, with some pronounced differences that can be attributed to RACK1's divergent biological functions. In all cases, the most rigid structural elements were confined to B-C turns and, to some extent, strands B and C, while the remaining regions retained much flexibility. We also compared the average rate constants for H-D exchange in different regions of RACK1 and found that amide protons in some regions exchanged at least 1000-fold faster than in others. We conclude that its evolutionarily retained structural architecture might have allowed RACK1 to accommodate multiple molecular partners. This was exemplified by our additional analysis of yeast RACK1 dimer, which showed stabilization, as well as destabilization, of several interface regions upon dimer formation. PMID:24591271

  17. Patterns of structural dynamics in RACK1 protein retained throughout evolution: a hydrogen-deuterium exchange study of three orthologs.

    Science.gov (United States)

    Tarnowski, Krzysztof; Fituch, Kinga; Szczepanowski, Roman H; Dadlez, Michal; Kaus-Drobek, Magdalena

    2014-05-01

    RACK1 is a member of the WD repeat family of proteins and is involved in multiple fundamental cellular processes. An intriguing feature of RACK1 is its ability to interact with at least 80 different protein partners. Thus, the structural features enabling such interactomic flexibility are of great interest. Several previous studies of the crystal structures of RACK1 orthologs described its detailed architecture and confirmed predictions that RACK1 adopts a seven-bladed β-propeller fold. However, this did not explain its ability to bind to multiple partners. We performed hydrogen-deuterium (H-D) exchange mass spectrometry on three orthologs of RACK1 (human, yeast, and plant) to obtain insights into the dynamic properties of RACK1 in solution. All three variants retained similar patterns of deuterium uptake, with some pronounced differences that can be attributed to RACK1's divergent biological functions. In all cases, the most rigid structural elements were confined to B-C turns and, to some extent, strands B and C, while the remaining regions retained much flexibility. We also compared the average rate constants for H-D exchange in different regions of RACK1 and found that amide protons in some regions exchanged at least 1000-fold faster than in others. We conclude that its evolutionarily retained structural architecture might have allowed RACK1 to accommodate multiple molecular partners. This was exemplified by our additional analysis of yeast RACK1 dimer, which showed stabilization, as well as destabilization, of several interface regions upon dimer formation.

  18. Remapping annual precipitation in mountainous areas based on vegetation patterns: a case study in the Nu River basin

    Science.gov (United States)

    Zhou, Xing; Ni, Guang-Heng; Shen, Chen; Sun, Ting

    2017-02-01

    Accurate high-resolution estimates of precipitation are vital to improving the understanding of basin-scale hydrology in mountainous areas. The traditional interpolation methods or satellite-based remote sensing products are known to have limitations in capturing the spatial variability of precipitation in mountainous areas. In this study, we develop a fusion framework to improve the annual precipitation estimation in mountainous areas by jointly utilizing the satellite-based precipitation, gauge measured precipitation, and vegetation index. The development consists of vegetation data merging, vegetation response establishment, and precipitation remapping. The framework is then applied to the mountainous areas of the Nu River basin for precipitation estimation. The results demonstrate the reliability of the framework in reproducing the high-resolution precipitation regime and capturing its high spatial variability in the Nu River basin. In addition, the framework can significantly reduce the errors in precipitation estimates as compared with the inverse distance weighted (IDW) method and the TRMM (Tropical Rainfall Measuring Mission) precipitation product.

  19. Carbon Storage Patterns of Caragana korshinskii in Areas of Reduced Environmental Moisture on the Loess Plateau, China

    Science.gov (United States)

    Gong, Chunmei; Bai, Juan; Wang, Junhui; Zhou, Yulu; Kang, Tai; Wang, Jiajia; Hu, Congxia; Guo, Hongbo; Chen, Peilei; Xie, Pei; Li, Yuanfeng

    2016-07-01

    Precipitation patterns are influenced by climate change and profoundly alter the carbon sequestration potential of ecosystems. Carbon uptake by shrubbery alone accounts for approximately one-third of the total carbon sink; however, whether such uptake is altered by reduced precipitation is unclear. In this study, five experimental sites characterised by gradual reductions in precipitation from south to north across the Loess Plateau were used to evaluate the Caragana korshinskii’s functional and physiological features, particularly its carbon fixation capacity, as well as the relationships among these features. We found the improved net CO2 assimilation rates and inhibited transpiration at the north leaf were caused by lower canopy stomatal conductance, which enhanced the instantaneous water use efficiency and promoted plant biomass as well as carbon accumulation. Regional-scale precipitation reductions over a certain range triggered a distinct increase in the shrub’s organic carbon storage with an inevitable decrease in the soil’s organic carbon storage. Our results confirm C. korshinskii is the optimal dominant species for the reconstruction of fragile dryland ecosystems. The patterns of organic carbon storage associated with this shrub occurred mostly in the soil at wetter sites, and in the branches and leaves at drier sites across the arid and semi-arid region.

  20. Patterns of Distribution of Macro-fauna in Different Types of Estuarine, Soft Sediment Habitats Adjacent to Urban and Non-urban Areas

    Science.gov (United States)

    Lindegarth, M.; Hoskin, M.

    2001-02-01

    Urban development typically creates a large number of potentially interacting disturbances that may cause impacts on assemblages of animals and plans in estuarine habitats. We tested predictions from the general model that intertidal areas exposed to different types of disturbances have different types of assemblages of benthic macrofauna. Different parts of the Port Hacking Estuary (New South Wales, Australia) are exposed to varying degrees of disturbance by human activities. We predicted that the average structure of assemblages of intertidal animals, and patterns of variability would differ between urban and non-urban areas of Port Hacking. Consistent with previous observations from the literature, there were differences in average structure between urban and non-urban sandy areas. Qualitative differences between abundances of individual taxa in urban and non-urban areas were generally not consistent with previous observations. Differences between assemblages in urban and non-urban areas were not observed in muddy sediments, nor in sediments among mangroves and seagrass. No significant differences in variability was observed between urban and non-urban areas. Two general models may be proposed to explain the observed differences in response to urbanization in different habitats: (1) animals are exposed to different levels or combinations of disturbances in different habitats; or (2) assemblages of animals differ in sensitivity to disturbances among habitats.

  1. A Study Of Protein Calorie Malnutrition Amongst Under Six Children In Slum Area Of Kanpur

    Directory of Open Access Journals (Sweden)

    S C Saxena

    2003-12-01

    Full Text Available Objective To assess the nutritional profile amongst under six children in slum area of Kanpur.Study Design Door to door survey by collecting relevent information from head of household on a pretested questionaire. Study UnitEach of household having any child in the age group less than 6 years.Study Area The study was conducted in Katari slum area of Kalyanpur, Kanpur.Study Variable Grades of PCM as per recommendation of nutrition sub-committee of paediatrics (ICMR-1972 Statistical analysis:- By chi-square test of significance.Results The highest percentage of PCM was observed amongst 0-1 year and boys of single families whose parents were illiterate and unemployed or labourers belonging mainly to lower socio-economic class.Conclusions:- To reduce childhood mortality with reference to PCM, die literacy status of parents especially of mothers should be increased and social reform measures to be taken for engaging them in some income generating jobs/business, agriculture etc.

  2. Cloned s-Lap Gene Coding Area, Expression and Localizationof s-Lap/GFP Fusion Protein in Mammal Cells

    Institute of Scientific and Technical Information of China (English)

    SONG Yi-shu; SONG Zhi-yu; LI Hong-jun; Wu Yin; BAO Yong-li; TAN Da-peng; LI Yu-xin

    2005-01-01

    s-Lap is a new gene sequence from pig retinal pigment epithelial(RPE) cells, which was found and cloned in the early period of apoptosis of RPE cells damaged with visible light. We cloned the coding area sequence of the novel gene of s-Lap and constructed its recombinant eukaryotic plasmid pcDNA3.1-GFP/s-lap with the recombinant DNA technique. The expression and localization of s-lap/GFP fusion protein in CHO and B16 cell lines were studied with the instantaneously transfected pcDNA3.1-GFP/s-lap recombinant plasmid. s-Lap/GFP fusion protein can be expressed in CHO and B16 cells with a high rate expression in the nuclei.

  3. Next generation non-vacuum, maskless, low temperature nanoparticle ink laser digital direct metal patterning for a large area flexible electronics.

    Directory of Open Access Journals (Sweden)

    Junyeob Yeo

    Full Text Available Flexible electronics opened a new class of future electronics. The foldable, light and durable nature of flexible electronics allows vast flexibility in applications such as display, energy devices and mobile electronics. Even though conventional electronics fabrication methods are well developed for rigid substrates, direct application or slight modification of conventional processes for flexible electronics fabrication cannot work. The future flexible electronics fabrication requires totally new low-temperature process development optimized for flexible substrate and it should be based on new material too. Here we present a simple approach to developing a flexible electronics fabrication without using conventional vacuum deposition and photolithography. We found that direct metal patterning based on laser-induced local melting of metal nanoparticle ink is a promising low-temperature alternative to vacuum deposition- and photolithography-based conventional metal patterning processes. The "digital" nature of the proposed direct metal patterning process removes the need for expensive photomask and allows easy design modification and short turnaround time. This new process can be extremely useful for current small-volume, large-variety manufacturing paradigms. Besides, simple, scalable, fast and low-temperature processes can lead to cost-effective fabrication methods on a large-area polymer substrate. The developed process was successfully applied to demonstrate high-quality Ag patterning (2.1 µΩ·cm and high-performance flexible organic field effect transistor arrays.

  4. Next generation non-vacuum, maskless, low temperature nanoparticle ink laser digital direct metal patterning for a large area flexible electronics.

    Science.gov (United States)

    Yeo, Junyeob; Hong, Sukjoon; Lee, Daehoo; Hotz, Nico; Lee, Ming-Tsang; Grigoropoulos, Costas P; Ko, Seung Hwan

    2012-01-01

    Flexible electronics opened a new class of future electronics. The foldable, light and durable nature of flexible electronics allows vast flexibility in applications such as display, energy devices and mobile electronics. Even though conventional electronics fabrication methods are well developed for rigid substrates, direct application or slight modification of conventional processes for flexible electronics fabrication cannot work. The future flexible electronics fabrication requires totally new low-temperature process development optimized for flexible substrate and it should be based on new material too. Here we present a simple approach to developing a flexible electronics fabrication without using conventional vacuum deposition and photolithography. We found that direct metal patterning based on laser-induced local melting of metal nanoparticle ink is a promising low-temperature alternative to vacuum deposition- and photolithography-based conventional metal patterning processes. The "digital" nature of the proposed direct metal patterning process removes the need for expensive photomask and allows easy design modification and short turnaround time. This new process can be extremely useful for current small-volume, large-variety manufacturing paradigms. Besides, simple, scalable, fast and low-temperature processes can lead to cost-effective fabrication methods on a large-area polymer substrate. The developed process was successfully applied to demonstrate high-quality Ag patterning (2.1 µΩ·cm) and high-performance flexible organic field effect transistor arrays.

  5. [Effect of freezing and cooking on the texture and electrophoretic pattern of the proteins of octopus arms (Octopus vulgaris)].

    Science.gov (United States)

    Reyes, Genara; Nirchio, Mauro; Bello, Rafael; Borderías, Javier

    2014-09-01

    Texture is the most valuable feature in cephalopods. Factors that mainly affect the texture of octopus are: freezing, scalding and cooking. The aim of this study was to assess the effect of freezing, scalding and length of cooking time on the texture and electrophoretic pattern of proteins of octopus arms. Octopuses were trapped near Margarita Island and carried with ice to the laboratory where they were packed and subjected to: a) freezing at -27 degrees C or at -20 degrees C b) scalding c) cooking for 25 min, 35 min or 45 min. Shear force was determined by Kramer cell on strips of octopus arms. SDS-PAGE was done according to the Laemmli method with 12% polyacrilamide gels. A sensory evaluation of the preference of texture was carried out using a hedonic scale of 7-points and a non-trained panel. Octopus texture was not affected by freezing temperature or scalding. Frozen octopus was softer after cooking than fresh. The longer the cooking time was, the softer the octopus was. Myosin heavy chain (MHC) was not significantly affected by scalding or cooking; however large aggregates heavier than MHC, new bands and loss of resolution of the bands appeared. Myosin and paramyosin bands were more affected by freezing prior to cooking.

  6. Activity patterns and use of microhabitat in lizards of the genus Tropidurus in a urbanized area of Natal, Brazil

    Directory of Open Access Journals (Sweden)

    Felipe Pernambuco da Costa

    2016-06-01

    Full Text Available This study analyzed sun exposure, substrate type selected, and various behaviors exhibited by the lizard Tropidurus during thermoregulation. Observation entailed thirty days in an urbanized area of Centro de Biociências/ Universidade Federal do Rio Grande do Norte. Their behavior was recorded using a scan sampling route and an instantaneous record method at three different time intervals (9am to 10am, 12am to 1pm, and 3pm to 4pm. Significant differences were seen with sun exposure (p = 0.027, with most lizards remaining in shadowed areas, where the animals preferentially remained standing (p < 0.001. We were also able to observe more lizards in the following substrates: tile, wall, rocks, and bricks (p < 0.001. In addition, the animals were in these substrates more frequently from 12am to 1pm (p = 0.004.

  7. Physical and Verbal Aggressive Behaviour Pattern Among School Children in Urban Area of North Karnataka: A Cross Sectional Study

    OpenAIRE

    Fawwad Shaikh; R. G. Viveki; A.B. Halappanavar

    2014-01-01

    Background: There is growing concern with student conflict, aggression, and violence in the schools, and anger is an important contributing factor which can damage school climate. Aims and Objectives: To elucidate the differentials of aggressive behaviour among high school students and to recognize the influence of age and sex on aggressive behaviour. Material and Methods: The present cross sectional study was conducted in one of the high school in urban area, which...

  8. Influence of biological oxygen demand degradation patterns on water-quality modeling for rivers running through urban areas.

    Science.gov (United States)

    Fan, Chihhao; Wang, Wei-Shen

    2008-10-01

    Water-quality modeling has been used as a support tool for water-resources management. The Streeter-Phelps (SP) equation is one often-used algorithm in river water-quality simulation because of its simplicity and ease in use. To characterize the river dissolved oxygen (DO) sag profile, it only considers that the first-order biological oxygen demand (BOD) degradation and atmospheric reaeration are the sink and source in a river, respectively. In the river water-quality calculation, the assumption may not always provide satisfactory simulation due to an inappropriate description of BOD degradation. In the study, various patterns of BOD degradation were combined with the oxygen reaeration to simulate the DO sag profile in a river. Different BOD degradation patterns used include the first-order decay, mixed second-order decay, and oxygen-inhibition decay. The results shows that the oxygen-inhibition SP equation calculates higher BOD and DO concentration, while the mixed second SP equation calculates the least among the three tested models. In river-water calculation of Keelung River, the SP and oxygen-inhibition SP equations calculate similar BOD and DO concentrations, and the mixed second SP equation calculates the least BOD and DO concentration. The pollution loading of BOD and atmospheric reaeration constant are the two important factors that have significant impacts on aqueous DO concentration. In the field application, it is suggested that the mixed second SP equation be employed in water-quality simulation when the monitoring data exhibits a faster trend in BOD decay. The oxygen-inhibition SP equation may calculate the water quality more accurately when BOD decay is slower.

  9. AN EVEN ODD MULTIPLE PATTERN MATCHING ALGORITHM

    OpenAIRE

    Raju Bhukya; DVLN Somayajulu

    2011-01-01

    Pattern matching plays an important role in various applications ranging from text searching in word processors to identification of functional and structural behavior in proteins and genes. Pattern matching is one of the fundamental areas in the field of computational biology. Currently research in life science area is producing large amount of genetic data. Due to this large and use full information can be gained by finding valuable information available from the genomic sequences. Many alg...

  10. Patterns of diversity, areas of endemism, and multiple glacial refuges for freshwater crabs of the genus Sinopotamon in China (Decapoda: Brachyura: Potamidae).

    Science.gov (United States)

    Fang, Fang; Sun, Hongying; Zhao, Qiang; Lin, Congtian; Sun, Yufang; Gao, Wei; Xu, Juanjuan; Zhou, Junying; Ge, Feng; Liu, Naifa

    2013-01-01

    Previous research has shown that the geographical distribution patterns of freshwater fishes and amphibians have been influenced by past climatic oscillations in China resulting from Pleistocene glacial activity. However, it remains unknown how these past changes have impacted the present-day distribution of Chinese freshwater crabs. This work describes the diversity and endemism of freshwater crabs belonging to Sinopotamon, a highly speciose genus endemic to China, and evaluates its distribution in terms of topography and past climatic fluctuations. Species diversity within Sinopotamon was found to be concentrated in an area from the northeastern edge of the Yunnan-Guizhou Plateau to the Jiangnan Hills, and three areas of endemism were identified. Multiple regression analysis between current climatic variables and Sinopotamon diversity suggested that regional annual precipitation, minimum temperature in the coldest month, and annual temperature range significantly influenced species diversity and may explain the diversity patterns of Sinopotamon. A comparison of ecological niche models (ENMs) between current conditions and the last glacial maximum (LGM) showed that suitable habitat for Sinopotamon in China severely contracted during the LGM. The coincidence of ENMs and the areas of endemism indicated that southeast of the Daba Mountains, and central and southeastern China, are potential Pleistocene refuges for Sinopotamon. The presence of multiple Pleistocene refuges within the range of this genus could further promote inter- and intraspecific differentiations, and may have led to high Sinopotamon species diversity, a high endemism rate and widespread distribution.

  11. Land use pattern, socio-economic development, and assessment of their impacts on ecosystem service value: study on natural wetlands distribution area (NWDA) in Fuzhou city, southeastern China.

    Science.gov (United States)

    Cai, Yuan-Bin; Zhang, Hao; Pan, Wen-Bin; Chen, Yan-Hong; Wang, Xiang-Rong

    2013-06-01

    This paper quantifies the allocation of ecosystem services value (ESV) associated with land use pattern and qualitatively examined impacts of land use changes and socio-economic factors on spatiotemporal variation of ESV in the Natural Wetland Distribution Area (NWDA), Fuzhou city, China. The results showed that total ESV of the study area decreased from 4,332.16 × 10(6) RMB Yuan in 1989 to 3,697.42 × 10(6) RMB Yuan in 2009, mainly due to the remarkable decreases in cropland (decreased by 55.3 %) and wetland (decreased by 74.2 %). Forest, water, and wetland played major roles in providing ecosystem services, accounting for over 90 % of the total ESV. Based on time series Landsat TM/ETM+ imagery, geographic information system, and historical data, analysis of the spatiotemporal variation of ESV from 1989 to 2009 was performed. It indicated that rapid expansion of urban areas along the Minjiang River resulted in significant changes in land use types, leading to a dramatic decline in ecosystem services. Meanwhile, because of land scarcity and unique ecosystem functions, the emergency of wetland and cropland protection in built-up area has become an urgent task of local authorities to the local government. Furthermore, there was still a significant negative correlation between ESV of cropland and wetland and the GDP. The results suggest that future planning of land use pattern should control encroachment of urban areas into cropland and wetland in addition to scientific and rational policies towards minimizing the adverse effects of urbanization.

  12. Hyporheic flow pattern based on the coupling of regional and stream scales: Case of Krycklan Catchment area

    Science.gov (United States)

    Mojarrad, Morteza; Wörman, Anders; Riml, Joakim

    2016-04-01

    Water resources intense development within the past century has had an enormous impact on hydrological systems especially on rivers and groundwater resources. A river basin is a flow system involving the interaction between surface water and groundwater. This interaction occurs in terrestrial and coastal zone and even in arid and semi-arid areas, where surface water overlie on a permeable sediment. A key zone for the interaction between surface water and groundwater is the hyporheic zone, which forms by stream water that in- and exfiltrating in the permeable sediments surrounding the river corridor. Groundwater and hyporheic flows arise due to different range of topographical scales and their relative importance is investigated in this study. Krycklan is a well-monitored research catchment in which the data collection for more than 90 years has comprised hydrology, biochemistry, and aquatic ecology. The catchment is located in a boreal area of northern Sweden. The head-water streams begin in mountainous area and fall to the Baltic Sea near the city of Umea. In this paper, COMSOL Multi-physics simulation software has been used to model the subsurface flow of the whole Krycklan catchment in order to reach a comprehensive understanding of large-scale groundwater circulation and its impact of the stream hyporheic flows. The model statement is based on the 3D Laplace equation, which has been applied independently on two ranges of topographical scales to obtain a superimposed solution. Steady state simulation has been done based on the simplified assumption of constant boundary conditions of the groundwater surface and otherwise non-flow boundaries. The hydraulic head of the groundwater surface was taken as the topography, which apply as an approximation in wet climate with shallow soil layers. The results demonstrated how the ratio of the topographical amplitudes on different scales affect the size (depth) and fragmentation of the hyporheic zone. "Fragmentation" was

  13. SEDIMENTARY PATTERN OF PROTOTYPE BASIN IN THE DEPOSITION PERIOD OF LAIYANG FORMATION AND THE ADVANTAGEOUS AREAS FOR OIL AND GAS EXPLORATION OF JIAOLAI BASIN

    Institute of Scientific and Technical Information of China (English)

    WU Zhiping; LI Ling; LI Wei; ZHOU Yaoqi

    2004-01-01

    Laiyang formation of Jiaolai Basin is the target stratum for oil and gas exploration. By measuring several field sections, the authors find that Laiyang formation reveals the whole processes from development to death of the lake basin and its sedimentary facies differ in different structural locations.Analyses about sedimentary facies and paleocurrent orientations in association with researches about the positive tectonic units such as Dayetou horseback and Chaigou horst indicate that Laiyang sag is a relatively independent sedimentary unit that shows great water depth typical of deep lake or semideep lake and was controlled by Wulongcun fault during the deposition period of Laiyang formation. Its sediments mainly originated from Jiaobei uplift area and Dayetou horseback. Gaomi-Zhucheng sag was a fast-filled basin controlled by Wurong fault and Yishu fault zone, being high in the northeast and low in the northwest and characterized by the development of pluvial facies and fluvial facies in most areas, and with the development of lake facies being limited to local low-lying regions. Selection of advantageous hydrocarbon reservoir areas for exploration purpose mainly relies on the sedimentation pattern of prototype basin and conservation conditions. The central-west area of Laiyang sag covered by overlying Laiyang formation is the most advantageous exploration area.

  14. 面向城市导游的无缝服务研究%Study on Seamless Service Pattern of Tour Guide for City Tourist Scenic Areas

    Institute of Scientific and Technical Information of China (English)

    史永; 龙毅; 许越; 郑星雨

    2015-01-01

    Nowdays, intelligent tour guide system is not only providing services for single tourist scenic area any more, and it is now developing into providing services for many tourist scenic areas in cities, so the service pattern is usually consist of both tour guide in scenic area(tour guide)and tour guide on routes which link scenic areas(road guide), and what's more, the city tour guide porvides services to individual tourist futher, and it can runs on any mobile terminal as an application(App). But in general, tour guide system and road guide system are self-contained, so there would be an unavoidable transfer between these two guide systems when a visitor entering and leaving a scenic area and the progress of transfer is mainly manually operated, and cannot realize automatic, seamless transfer. In order to solve this problem, this paper designs a seamless service pattern for any scenic area in one city, analyses the architecture and work manchmain mechanism of the pattern, and then discusses these key technologies such as conforming tourist enteriing or leaving a scenic area, which are as triggers for the automatic seamless switching between applications, and seamless integrating tour guide status on the level of content, such as designing data structure, transfering of the seamless integration of tourist status. Through the instances test, it proves that the pattern can realize switch automaticlly between Apps and city road navigation and seamless tour guide process with dynamic status transfering, and can be seen as a new service pattern. It is also a solution to integrate existing tour guide Apps.%智能导游服务已从传统的单一景区导游发展为城市多景区导游,因此包含了景区间导游和景区内导游两大部分;表现为更加注重面向散客服务、兼容多移动智能终端以应用程序(App)的方式运行。由于景区间导游和景区内导游往往自成系统,在游客进出景区的过程中存在着两种系统的

  15. 面向城市导游的无缝服务研究%Study on Seamless Service Pattern of Tour Guide for City Tourist Scenic Areas

    Institute of Scientific and Technical Information of China (English)

    史永; 龙毅; 许越; 郑星雨

    2014-01-01

    Nowadays, intelligent tour guide system is not only providing services for single tourist scenic area any more, and it is now developing into providing services for many tourist scenic areas in cities, so the service pattern is usually consisted of both tour guide in scenic area (tour guide) and tour guide on routes which link scenic areas (road guide), and what's more, the city tour guide provides services to individual tourist further, and can runs on any mobile terminal as an application(App). But in general, tour guide system and road guide system are self-contained, so there would be an unavoidable transfer between these two guide systems when a visitor entering and leaving a scenic area, and the progress of transfer is mainly manually operated, which cannot realize automatic and seamless transfer. In order to solve this problem, this paper designs a seamless service pattern for any scenic area in one city, and analyses the architecture and work ranchman of the pattern, and then discusses these key technologies such as conforming tourist entering or leaving a scenic area, which is as a trigger for the automatic seamless switching between applications, and seamless integrating tour guide status on the level of content, such as designing data structure, transferring of the seamless integration of tourist status. The instances tests prove that the pattern can realize switch automatically between Apps and city road navigation, and can realize seamless tour guide process with dynamic status transferring, and can be seen as a new service pattern, also a solution to integrate exited tour guide Apps.%智能导游服务已从传统的单一景区导游发展为城市多景区导游,因此,包含了景区间导游和景区内导游两大部分;表现为更加注重面向散客服务、兼容多移动智能终端以应用程序(App)的方式运行。由于景区间导游和景区内导游往往自成系统,在游客进出景区的过程中存在着两种系统

  16. Helminths infection patterns in a lizard (Tropidurus hispidus) population from a semiarid neotropical area: associations between female reproductive allocation and parasite loads.

    Science.gov (United States)

    Galdino, Conrado A B; Ávila, Robson W; Bezerra, Castiele H; Passos, Daniel C; Melo, Gabriela C; Zanchi-Silva, Djan

    2014-12-01

    This study reports helminth infection patterns of the lizard Tropidurus hispidus from an area of semiarid caatinga in northeastern Brazil (Ceará state). The lizard population was parasitized by 8 helminth species, and the species composition of the component community resembles that found for other Neotropical lizards. The prevalence of parasites was higher for males compared with females, whereas no relation was found between intensity of infection of 2 parasites (Parapharyngodon alvarengai and Physaloptera lutzi) and the lizards body size. For reproductive females, parasite infection intensity was negatively correlated to reproductive investment.

  17. A simple process for the fabrication of large-area CVD graphene based devices via selective in situ functionalization and patterning

    Science.gov (United States)

    Alexeev, Arseny M.; Barnes, Matthew D.; Karthik Nagareddy, V.; Craciun, Monica F.; Wright, C. David

    2017-03-01

    We report a novel approach for the fabrication of micro- and nano-scale graphene devices via the in situ plasma functionalization and in situ lithographic patterning of large-area graphene directly on CVD catalytic metal (Cu) substrates. This enables us to create graphene-based devices in their entirety prior to any transfer processes, simplifying very significantly the device fabrication process and potentially opening up the route to the use of a wider range of target substrates. We demonstrate the capabilities of our technique via the fabrication of a flexible, transparent, graphene/graphene oxide humidity sensor that outperforms a conventional commercial sensor.

  18. Activation and connectivity patterns of the presupplementary and dorsal premotor areas during free improvisation of melodies and rhythms.

    Science.gov (United States)

    de Manzano, Örjan; Ullén, Fredrik

    2012-10-15

    Free, i.e. non-externally cued generation of movement sequences is fundamental to human behavior. We have earlier hypothesized that the dorsal premotor cortex (PMD), which has been consistently implicated in cognitive aspects of planning and selection of spatial motor sequences may be particularly important for the free generation of spatial movement sequences, whereas the pre-supplementary motor area (pre-SMA), which shows increased activation during perception, learning and reproduction of temporal sequences, may contribute more to the generation of temporal structures. Here we test this hypothesis using fMRI and musical improvisation in professional pianists as a model behavior. We employed a 2 × 2 factorial design with the factors Melody (Specified/Improvised) and Rhythm (Specified/Improvised). The main effect analyses partly confirmed our hypothesis: there was a main effect of Melody in the PMD; the pre-SMA was present in the main effect of Rhythm, as predicted, as well as in the main effect of Melody. A psychophysiological interaction analysis of functional connectivity demonstrated that the correlation in activity between the pre-SMA and cerebellum was higher during rhythmic improvisation than during the other conditions. In summary, there were only subtle differences in activity level between the pre-SMA and PMD during improvisation, regardless of condition. Consequently, the free generation of rhythmic and melodic structures, appears to be largely integrated processes but the functional connectivity between premotor areas and other regions may change during free generation in response to sequence-specific spatiotemporal demands.

  19. Crustal thickening and attenuation as revealed by regional fold interference patterns: Ciudad Rodrigo basement area (Salamanca, Spain)

    Science.gov (United States)

    Díez Fernández, Rubén; Gómez Barreiro, Juan; Martínez Catalán, José R.; Ayarza, Puy

    2013-01-01

    The structure of the Ciudad Rodrigo area (Iberian Massif, Central Iberian Zone) has been revisited in order to integrate new geological data with recent models of the evolution of the Iberian Massif. Detailed mapping of fold structures along with a compilation of field data have been used to constrain the geometry and relative timing of ductile deformation events in this section of the hinterland of the Variscan belt. The structural evolution shows, in the first place, the development of a regional train of overturned folds with associated axial planar foliation (D1). Towards the lower structural levels, the deflection of the fold limbs and a subhorizontal crenulation cleavage depict the upper structural boundary of a superimposed low angle shear zone (D2), which extends at least to the deepest parts of the basement exposed in the study area. The amplification and rotation of D1 folds about a horizontal axis also occurred within this shear zone. The flat-lying character of the D2 structures accounts for the attenuation of the previously thickened crust, which developed following gravity gradients during thermal re-equilibration. Subsequent deformation led to the formation of two orthogonal sets of upright folds (D3), representing a new shift between crustal thinning and crustal thickening in the region.

  20. Late Holocene spatial patterns of coseismic land level changes and earthquake rupture areas, south-central Alaska

    Science.gov (United States)

    Shennan, I.; Barlow, N.; Watcham, E.

    2010-12-01

    Previous investigations of multiple late Holocene earthquake events in Cook Inlet suggest different spatial patterns of co-seismic subsidence for the 1964, ~900 BP and ~1500 BP great earthquakes . One hypothesis to explain these differences is that they record variations in the location, extent or depth of the rupture zone. Testing this hypothesis is important if we are to reduce uncertainties regarding the nature of future earthquake hazard in south central Alaska and improve our understanding of the nature of past earthquake ruptures in this region. Here we study sites beyond Cook Inlet to address the issue of spatial variability; Copper River Delta and Cape Suckling record coseismic uplift, Middle Bay and Anton Larson Bay, Kodiak Island, record coseismic subsidence. The 1964 rupture involved two segments (Kodiak and Prince William Sound) of the Aleutian Megathrust. We aim to quantify coseismic deformation for three Late Holocene earthquakes: ~500BP, a single segment rupture of the Kodiak segment; and ~900 and ~1500BP earthquakes that we consider involved simultaneous rupturing of three segments. These are the Kodiak and Prince William Sound segments and the adjacent segment extending to the Pamplona - Malaspina thrust front in the east. In this scenario, the Yakataga seismic gap ruptures in conjunction with the Aleutian megathrust.

  1. Association between atmospheric circulation patterns and firn-ice core records from the Inilchek glacierized area, central Tien Shan, Asia

    Science.gov (United States)

    Aizen, V.B.; Aizen, E.M.; Melack, J.M.; Kreutz, K.J.; Cecil, L.D.

    2004-01-01

    Glacioclimatological research in the central Tien Shan was performed in the summers of 1998 and 1999 on the South Inilchek Glacier at 5100-5460 m. A 14.36 m firn-ice core and snow samples were collected and used for stratigraphic, isotopic, and chemical analyses. The firn-ice core and snow records were related to snow pit measurements at an event scale and to meteorological data and synoptic indices of atmospheric circulation at annual and seasonal scales. Linear relationships between the seasonal air temperature and seasonal isotopic composition in accumulated precipitation were established. Changes in the ??18O air temperature relationship, in major ion concentration and in the ratios between chemical species, were used to identify different sources of moisture and investigate changes in atmospheric circulation patterns. Precipitation over the central Tien Shan is characterized by the lowest ionic content among the Tien Shan glaciers and indicates its mainly marine origin. In seasons of minimum precipitation, autumn and winter, water vapor was derived from the and and semiarid regions in central Eurasia and contributed annual maximal solute content to snow accumulation in Tien Shan. The lowest content of major ions was observed in spring and summer layers, which represent maximum seasonal accumulation when moisture originates over the Atlantic Ocean and Mediterranean and Black Seas. Copyright 2004 by the American Geophysical Union.

  2. Study on contamination of sheep meat in Shahrekord area with Listeria ivanovii and determination its antibiotic resistance pattern

    Directory of Open Access Journals (Sweden)

    Farid Khalili Borujeni

    2013-06-01

    Full Text Available Background and objectives: Listeria monocytogenes and Listeria ivanovii are two pathogenic species of Listeria. The role of Listeria ivanovii is important in abortion, stillbirth, septicemia in animals and this bacterium sometimes is pathogenic in humans. Contamination of ovine carcasses during the slaughter and processing can cause foodborne infections in humans. In this study we examined the contamination of sheep meat in slaughter house of Shahrekord city to Listeria ivanovii and determined its antibiotic resistance pattern.Material and Methods: A total 200 samples of sheep meat were collected from abattoir and processed by use of two enrichment method. After doing specific biochemical tests and PCR, Listeria spp was identified and antibiotic resistance of isolated Listeria were tested by the agar disc diffusion method. Results: The contamination of sheep carcasses with listeria was 2.5% (5 out of 200 samples. All five isolates (2.5% were recognized as Listeria ivanovii and were resistant to four antibiotics, sensitive to six antibiotics and intermediate to other antibiotics.  Conclusion: According to the contamination rate in sheep carcasses with Listeria ivanovii and the relatively high antibiotic resistance specified in this bacteria, the role of red meat in transmission of Listeria spp. and appropriate use of antibiotics against this bacteria should be considered.

  3. Achieving single-lobed far-field patterns of broad area laser diode with external cavity feedback

    Institute of Scientific and Technical Information of China (English)

    Jianhong Ge(葛剑虹); Jun Chen(陈军); Andreas Hermerschmidt; H.J.Eichler

    2003-01-01

    We demonstrate a technique for single transverse mode operation of high-power broad area laser diode(BAL). In the experiment, the HR mirror is used as an external cavity mirror and the grating is used as a wavelength selective component. By tiling the HR mirror and the grating, the number of transverse modes oscillating in the cavity can be limited and the spectral bandwidth of the laser diode can be reduced. A single-lobed near diffraction-limited laser beam with the beam divergence (FWHM) of 0.43°, the spectral line-width of 0.7 nm and the output power of 350 mW are obtained. With the feedback, the power density of the output laser beam is increased 6 times in comparison with the free running.

  4. Focal cerebral ischemia induces increased myelin basic protein and growth-associated protein-43 gene transcription in peri-infarct areas in the rat brain

    DEFF Research Database (Denmark)

    Gregersen, R; Christensen, Thomas; Lehrmann, E;

    2001-01-01

    , in peri-infarct areas in adult rat brain after transient middle cerebral artery occlusion (MCAO) and correlated it to the expression of the growth-associated protein-43 (GAP-43), a marker for axonal regeneration and sprouting, using non-radioactive in situ hybridization techniques. Within the infarct, MBP......, corresponding to the appearance of process-bearing MBP and occasional MOG-immunoreactive oligodendrocytes in parallel sections. Quantitative analysis revealed significant increases in the density of oligodendrocytes (up to 7.6-fold) and in the level of MBP mRNA expressed by individual cells. Parallel sections...... showed that increased expression of GAP-43 mRNA in neurons was concomitant to MBP mRNA upregulation in oligodendrocytes. While the mechanisms regulating oligodendrocyte survival and myelination signals are not clear at this point, axonal sprouting could putatively serve as a stimulus for the upregulation...

  5. Association of rearing patterns with diet and temperament traits among infants in urban areas%城市地区抚养模式与幼儿饮食特征及气质的关联研究

    Institute of Scientific and Technical Information of China (English)

    鲁影; 朱鹏; 高荣; 梁贞贞; 黄文; 陶芳标

    2012-01-01

    cereals-based food pattern, with relatively poor rhythmicity; infants in Group C tended to adopt aquatic products and fruit/vegetable-based food pattern, with good rhythmicity and adaptability. Linear regression model showed that infants who consumed more aquatic products, high-protein food, and fruits/vegetables had more positive temperamental traits, whereas infants who consumed more processed foods had more negative temperamental traits. Conclusions A joint rearing pattern may be a favorable rearing style for infants aged 25-30 months in urban areas in terms of diet and temperament traits.

  6. Relationship between Individual External Doses, Ambient Dose Rates and Individuals' Activity-Patterns in Affected Areas in Fukushima following the Fukushima Daiichi Nuclear Power Plant Accident.

    Science.gov (United States)

    Naito, Wataru; Uesaka, Motoki; Yamada, Chie; Kurosawa, Tadahiro; Yasutaka, Tetsuo; Ishii, Hideki

    2016-01-01

    The accident at Fukushima Daiichi Nuclear Power Plant on March 11, 2011, released radioactive material into the atmosphere and contaminated the land in Fukushima and several neighboring prefectures. Five years after the nuclear disaster, the radiation levels have greatly decreased due to physical decay, weathering, and decontamination operations in Fukushima. The populations of 12 communities were forced to evacuate after the accident; as of March 2016, the evacuation order has been lifted in only a limited area, and permanent habitation is still prohibited in most of the areas. In order for the government to lift the evacuation order and for individuals to return to their original residential areas, it is important to assess current and future realistic individual external doses. Here, we used personal dosimeters along with the Global Positioning System and Geographic Information System to understand realistic individual external doses and to relate individual external doses, ambient doses, and activity-patterns of individuals in the affected areas in Fukushima. The results showed that the additional individual external doses were well correlated to the additional ambient doses based on the airborne monitoring survey. The results of linear regression analysis suggested that the additional individual external doses were on average about one-fifth that of the additional ambient doses. The reduction factors, which are defined as the ratios of the additional individual external doses to the additional ambient doses, were calculated to be on average 0.14 and 0.32 for time spent at home and outdoors, respectively. Analysis of the contribution of various activity patterns to the total individual external dose demonstrated good agreement with the average fraction of time spent daily in each activity, but the contribution due to being outdoors varied widely. These results are a valuable contribution to understanding realistic individual external doses and the corresponding

  7. Relationship between Individual External Doses, Ambient Dose Rates and Individuals’ Activity-Patterns in Affected Areas in Fukushima following the Fukushima Daiichi Nuclear Power Plant Accident

    Science.gov (United States)

    Kurosawa, Tadahiro; Yasutaka, Tetsuo; Ishii, Hideki

    2016-01-01

    The accident at Fukushima Daiichi Nuclear Power Plant on March 11, 2011, released radioactive material into the atmosphere and contaminated the land in Fukushima and several neighboring prefectures. Five years after the nuclear disaster, the radiation levels have greatly decreased due to physical decay, weathering, and decontamination operations in Fukushima. The populations of 12 communities were forced to evacuate after the accident; as of March 2016, the evacuation order has been lifted in only a limited area, and permanent habitation is still prohibited in most of the areas. In order for the government to lift the evacuation order and for individuals to return to their original residential areas, it is important to assess current and future realistic individual external doses. Here, we used personal dosimeters along with the Global Positioning System and Geographic Information System to understand realistic individual external doses and to relate individual external doses, ambient doses, and activity-patterns of individuals in the affected areas in Fukushima. The results showed that the additional individual external doses were well correlated to the additional ambient doses based on the airborne monitoring survey. The results of linear regression analysis suggested that the additional individual external doses were on average about one-fifth that of the additional ambient doses. The reduction factors, which are defined as the ratios of the additional individual external doses to the additional ambient doses, were calculated to be on average 0.14 and 0.32 for time spent at home and outdoors, respectively. Analysis of the contribution of various activity patterns to the total individual external dose demonstrated good agreement with the average fraction of time spent daily in each activity, but the contribution due to being outdoors varied widely. These results are a valuable contribution to understanding realistic individual external doses and the corresponding

  8. Consumption of a healthy dietary pattern results in significant reductions in C-reactive protein levels in adults: a meta-analysis.

    Science.gov (United States)

    Neale, E P; Batterham, M J; Tapsell, L C

    2016-05-01

    Consumption of healthy dietary patterns has been associated with reduced risk of cardiovascular disease and metabolic syndrome. Dietary intervention targets disease prevention, so studies increasingly use biomarkers of underlying inflammation and metabolic syndrome progression to examine the diet-health relationship. The extent to which these biomarkers contribute to the body of evidence on healthy dietary patterns is unknown. The aim of this meta-analysis was to determine the effect of healthy dietary patterns on biomarkers associated with adiposity, insulin resistance, and inflammation in adults. A systematic search of Scopus, PubMed, Web of Science, and Cochrane Central Register of Controlled Trials (all years to April 2015) was conducted. Inclusion criteria were randomized controlled trials; effects of dietary patterns assessed on C-reactive protein (CRP), total adiponectin, high-molecular-weight adiponectin, tumor necrosis factor-α, adiponectin:leptin, resistin, or retinol binding protein 4. Random effects meta-analyses were conducted to assess the weighted mean differences in change or final mean values for each outcome. Seventeen studies were included in the review. These reflected research on dietary patterns associated with the Mediterranean diet, Nordic diet, Tibetan diet, and the Dietary Approaches to Stop Hypertension diet. Consumption of a healthy dietary pattern was associated with significant reductions in CRP (weighted mean difference, -0.75 [-1.16, -0.35]; P = .0003). Non-significant changes were found for all other biomarkers. This analysis found evidence for favorable effects of healthy dietary patterns on CRP, with limited evidence for other biomarkers. Future research should include additional randomized controlled trials incorporating a greater range of dietary patterns and biomarkers.

  9. Corridor effect of the spatial changes of landscape patterns in arid areas: A case study of the river corridor areas in the middle and lower reaches of Tarim River

    Institute of Scientific and Technical Information of China (English)

    ZHOU Huarong; XIAO Duning; ZHOU Kefa

    2006-01-01

    The river corridor areas in the middle and lower reaches of the Tarim River are dominated by the traditional green corridors along the river section from the Qara Reservoir in Yuli County to the Taitema Lake in Ruoqiang County, which plays an important role in the social and economic development in the Tarim River Watershed with a extremely significant ecological functions. The buffer zones perpendicular to the watercourse were defined along both riversides at a 5-km interval beginning from the watercourse (10 km wider) using the method of the buffer zone analysis. The landscape pattern indexes of each buffer zone were calculated, and the indexes of the main landscape patterns were analyzed so as to reveal the radiative effect and the characteristics of the river corridors on landscape and patch levels.The results show that the radiative width is generally 30 km in the study area, and can be up to 50-70 km in sub- region FG1 because the study area is located in two drainage basins, with an ecological interstitial zone between them. The landscapes of woodlands and wetlands are generally distributed within the 10km buffer zone (it means that the buffer zone is 5 km away from the watercourse; the same hereafter)along both riversides. Moreover, the closer the buffer zone is to the watercourse, the higher the patch density and the largest patch index are. In the ecological and environmental regeneration for the study area,the extent of ecological effect of the river corridors 82must be fully considered, and the projects must be scientifically and rationally planned and designed.

  10. MORBIDITY PATTERN AMO NG THE ELDERLY POPULATION IN AN URBAN FIELD PRACTICE AREA OF GUNTUR MEDICAL COLLEGE, GUNTUR

    Directory of Open Access Journals (Sweden)

    K.V. Phan

    2013-12-01

    Full Text Available INTRODUCTION: India, the world’s second most populous country, has experienced a dramatic demographic transition in the past 50 years, entailing almost a tripling of the population over the age of 60 years (i.e., the elderly (Gove rnment of India, 2011.Discoveries in medical science and improved social conditions during past few decades have increased the life span of man. The ageing population is both a medical and sociological problem. It creates a greater demand on the health se rvices of a community. In rapidly graying world, healthy aging is vital for countries. The Predicted explosion of non - communicable diseases like cardiovascular diseases, cancer, and depression in the ever increasing number of older persons globally, will r esult in enormous human and social costs unless preventive action is taken. 1 Morbidity among elderly people has an important influence on their physical functioning and psychological well - being. This study was undertaken to know the prevalence of various mo rbidities among the elderly patients. OBJECTIVE : To assess the morbidity profile of geriatric population . METHODOLOGY : A cross sectional study was conducted in Mallikarjun pet which is in theurban field practice area of Guntur medical college, Guntur. Mallik arjun pet consists of 1156 families with a population of 4114.The study was conducted to assess the health status of elderly population during October 2012 – November 2012. Study has included all the households and residents of the study area who were abov e 60 years of age.Outof 297elderly persons, 283participated in the study and data were collected using pretested questionnaire followed by physical examination. Data was analyzed using SPSS Version 21.0. RESULTS : Out of 283 study participants, 76(26.9% are males and 207(73.1% are females with a mean age of 70 + 6.8 yrs. Majority of them are living with spouse 225(79.5% whereas 53(18.7% are widows, 5(1.8% are widowers. About 133(47% belong to

  11. Patterns of Social Marginalization and its Spatial Expression in the Urban Area of Râmnicu Vâlcea: Preventing vs. Controlling the Outcomes

    Directory of Open Access Journals (Sweden)

    SIMONA MĂLĂESCU

    2015-12-01

    Full Text Available This paper aims to underline the dynamic patterns of social marginalization, which ultimately leads to social exclusion within the urban area of Râmnicu Vâlcea from the communist period to present. Conclusions were drawn from field observations, semi-structural interviews conducted with the guaranteed minimum income (GMI beneficiaries (according to the Law no. 416/2001, the meta-analysis of the statistical data collected by the Directorate for Labour and Social Protection, content analysis of the local press and cartographic and historical materials. Data confirm the clustering of the GMI beneficiaries, mostly in the peripheral areas (Nuci Colony, Morilor-Izvorului, Alunului-Poienari and Gib Mihăescu colonies, as well as the ethnic fingerprint of the urban poverty along with the absence of the spatial concentration of the ethnic majority, only the areas with a high rate of marginalization (social as well as spatial making an exception. In areas with concentrated social dwellings such as Nuci Colony, the effects of the intensive social contamination and disorganization emphasize that once installed, the social disorganization is much more difficult to eradicate or even to control the sprawl than to prevent the social disorganization, conflicts and increasing crime.

  12. Spatial-temporal Patterns of Land-use Change in Typical Transect Area Along China National Highway 106 During 1996-2008

    Institute of Scientific and Technical Information of China (English)

    LIU Yu; LIU Yansui; GUO Liying; LU Shasha

    2011-01-01

    Based on land-use database updated with the survey of 1996, 2000, 2004 and 2008, this paper analyzed the land-use changes in the typical transect area along National Highway 106 with the aid of GIS technology and quantitative models. The results showed that arable land had been continuously decreased from 1996 to 2008, with a loss of 65.85× 10^3 hm2 and an average decrement of 5.49×10^3 hm^2 per year, and the loss in northern areas was larger; garden land and woodland were gradually centralized to the predominance area with an increment of 25.73×10^3 hm2 and 22.37×10^3 hm2, respectively; residential and industrial land increased year after year, and the transportation land showed the equalized developing spatial pattern; the increment of construction land and encroachment on arable land in the area were deeply influenced by the national macroscopic land-use policies, the rapid advance of urbanization and the development level of the regional economy. Through this case study, it is suggested that differential land- use policies should be adopted to create good environmental conditions to guarantee food security and to promote the economic development.

  13. Changing patterns of malaria during 1996-2010 in an area of moderate transmission in Southern Senegal

    Directory of Open Access Journals (Sweden)

    Vaillant Michel T

    2011-07-01

    Full Text Available Abstract Background Malaria is reportedly receding in different epidemiological settings, but local long-term surveys are limited. At Mlomp dispensary in south-western Senegal, an area of moderate malaria transmission, year-round, clinically-suspected malaria was treated with monotherapy as per WHO and national policy in the 1990s. Since 2000, there has been a staggered deployment of artesunate-amodiaquine after parasitological confirmation; this was adopted nationally in 2006. Methods Data were extracted from clinic registers for the period between January 1996 and December 2010, analysed and modelled. Results Over the 15-year study period, the risk of malaria decreased about 32-times (from 0.4 to 0.012 episodes person-year, while anti-malarial treatments decreased 13-times (from 0.9 to 0.07 treatments person-year and consultations for fever decreased 3-times (from 1.8 to 0.6 visits person-year. This was paralleled by changes in the age profile of malaria patients so that the risk of malaria is now almost uniformly distributed throughout life, while in the past malaria used to concern more children below 16 years of age. Conclusions This study provides direct evidence of malaria risk receding between 1996-2010 and becoming equal throughout life where transmission used to be moderate. Infection rates are no longer enough to sustain immunity. Temporally, this coincides with deploying artemisinin combinations on parasitological confirmation, but other contributing causes are unclear.

  14. Pattern of Survival and Mortality of Mangrove Populations Grown at Al-Jubail Area (Saudi Arabia of the Arabian Gulf

    Directory of Open Access Journals (Sweden)

    Akram Ali

    2008-01-01

    Full Text Available The life table and fecundity schedule were produced for [Avicennia marina (Forsk. Vierh] populations of four habitat types at Al-Jubail area, KSA. These types are sand mounds, salt flats, shoreline and intertidal sites. Survivorship (lx was least in sand mounds and similar in all other sites. Age-specific-mortality rates (qx where parallel in the flower bud, flower, fruiting and seedling stages in all sites, while demonstrated site-specific variations in adult stages with highest values in the shoreline and salt flat sites. The killing power (kx values were parallel in all sites except for the sand mounds. The expectations of future life (ex were variable at different age classes and sites with highest values attained in the intertidal and shoreline sites. Plants in the sand mounds and salt flats showed lower expectations for future life than in the other habitats. The reproductive values were close to zero in all age classes of the salt flats site. The net reproduction rate (R0 ranged from 0.023 to 0.4 with negative or close to zero intrinsic rate of increase per capita (r. The generation time (T ranged from 25.6 years in the sand flats to 53.75 years in the sand mounds. This study supported that the conservation of Avicennia marina may allow for continued dynamic adaptation to different habitat types in the Arabian Gulf coast.

  15. Evidence that local land use practices influence regional climate, vegetation, and stream flow patterns in adjacent natural areas

    Science.gov (United States)

    Stohlgren, T.J.; Chase, T.N.; Pielke, R.A.; Kittel, T.G.F.; Baron, J.S.

    1998-01-01

    We present evidence that land use practices in the plains of Colorado influence regional climate and vegetation in adjacent natural areas in the Rocky Mountains in predictable ways. Mesoscale climate model simulations using the Colorado State University Regional Atmospheric Modelling System (RAMS) projected that modifications to natural vegetation in the plains, primarily due to agriculture and urbanization, could produce lower summer temperatures in the mountains. We corroborate the RAMS simulations with three independent sets of data: (i) climate records from 16 weather stations, which showed significant trends of decreasing July temperatures in recent decades; (ii) the distribution of seedlings of five dominant conifer species in Rocky Mountain National Park, Colorado, which suggested that cooler, wetter conditions occurred over roughly the same time period; and (iii) increased stream flow, normalized for changes in precipitation, during the summer months in four river basins, which also indicates cooler summer temperatures and lower transpiration at landscape scales. Combined, the mesoscale atmospheric/land-surface model, short-term in regional temperatures, forest distribution changes, and hydrology data indicate that the effects of land use practices on regional climate may overshadow larger-scale temperature changes commonly associated with observed increases in CO2 and other greenhouse gases.

  16. Pattern of Tobacco and Alcohol Use among Elderly Population in a Rural Area of Andhra Pradesh, India

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    Sharvanan E Udayar, Praveen B Ashok, Arun D , Sai Sravan

    2015-01-01

    Full Text Available "Background: Tobacco and alcohol consumption are the leading cause of preventable death. Fewer studies have focused on tobacco and alcohol use among rural elderly. Objective of the study was to find out the prevalence of tobacco and alcohol use among rural elderly population and its association with various sociodemographic factors. Methods: Cross-sectional community based study was conducted in the rural area of V.Kota mandal of Chittoor district, Andhra Pradesh. Studyparticipants were selected using multistage random sampling method. Results: The prevalence of current tobacco users was 40.5%, among them 37.2% men and 1.4% women were current smokers. Among tobacco chewers 37.3% were women and 17.3% were men.Alcohol consumption was seen in 28.7% of the men compared with 0.9% of the women.Tobacco and alcohol use was significantly associated with age, education, economic status, marital status and living arrangements. Conclusion: There is a high prevalence of smoking and alcohol consumption among men in this rural elderly population which needs to addressed immediately to prolong health living years."

  17. Anemia plus hypoproteinemia in dogs; various proteins in diet show various patterns in blood protein production; beef muscle,. egg, lactalbumin, fibrin, viscera, and supplements.

    Science.gov (United States)

    WHIPPLE, G H; ROBSCHEIT-ROBBINS, F S

    1951-09-01

    Dogs with sustained anemia plus hypoproteinemia due to bleeding and a continuing low protein or protein-free diet containing abundant iron have been used in the present work to test food proteins and supplements as to their See PDF for Structure capacity to produce new hemoglobin and plasma proteins. The reserve stores of blood protein-producing materials are thus largely depleted in such animals and sustained levels of 6 to 8 gm. per cent hemoglobin and 4 to 5 gm. per cent plasma protein can be maintained for considerable periods of time. The stimulus of double depletion drives the body to use all protein building materials with the utmost conservation. This represents a severe biological test for food and body proteins and its assay value must have significance. Measured by this biological test in these experiments, casein stands well up among the best food proteins. The ratio of plasma protein to hemoglobin is about 40 to 50 per cent, which emphasizes the fact that these dogs produce on most diets about 2 gm. hemoglobin to 1 gm. plasma protein. The reason for this preference for hemoglobin production is obscure. The mass of circulating hemoglobin is greater even in this degree of anemia and the life cycle of hemoglobin is much longer than that of the plasma protein. Egg protein, egg albumin, and lactalbumin all favor the production of more plasma protein and less hemoglobin as compared with casein. The plasma protein to hemoglobin ratio is increased, sometimes above 100 per cent. Supplements to the above proteins of casein digests or several amino acids may return the response toward that which is standard for casein. Histidine as a supplement to egg protein increases the total blood protein output and brings the ratio of plasma protein to hemoglobin toward that of casein. Beef muscle goes to the other extreme and favors new hemoglobin production up to 4 gm. hemoglobin to 1 gm. plasma protein-a ratio of 25 per cent. The total amounts of new blood proteins are

  18. Assessment of the immigration effect and choice of development pattern for scenic areas:a case study of Wuyi Mountain,China

    Institute of Scientific and Technical Information of China (English)

    Wang Peixian; Dong Suocheng; Zhang Yuanyuan; Xu Lin; Yan Shenghu

    2008-01-01

    Mountainous regions face a series of conflicts between the natural resources conservation and the economic development,especially in protected areas,where are the home to some of the poorest people in the world.In China,the Protected Areas Authorities(such as Protected Areas Authorities of Wuyi Mountain) transferred the mountainous people out of the protected areas.We found that it is not a good approach of immigration project,as far as economic and ecological effect is concerned.Although remote and mahestic beauty attracted many tourists,mass tourism is not a good approach to solve the development prohlem in mountainous areas because it can not provide enough opportunities to make local people live a comfortable life,and the high volume of tourists indicates that the resources face significant threats.Because many,landscapes are run by private enterprises,local residents and government only get limited benefus.Although ecotourism principles expatiate on economic development and resources conservation,local people income and tourists feelings,it has discordance between the theory and the practice Therefore,the term of"integrated ecotourism"was coined in the paper based on the ecotourism theory.Integrated ecotourism means a broadly tourism resources and pendulum spatial pattern which will come into being with the movement of local people and tourists from protected areas to the nearby town or city,and it also tries to soh,e the property right conflict of mountain land between the local people and the private enterprises according to property right theory.

  19. Variations in the polar cap area during intervals of substorm activity on 20-21 March 1990 deduced from AMIE convection patterns

    Directory of Open Access Journals (Sweden)

    J. R. Taylor

    Full Text Available The dynamic behaviour of the northern polar cap area is studied employing Northern Hemisphere electric potential patterns derived by the Assimilative Mapping of Ionospheric Electrodynamics (AMIE procedure. The rate of change in area of the polar cap, which can be defined as the region of magnetospheric field lines open to the interplanetary magnetic field (IMF, has been calculated during two intervals when the IMF had an approximately constant southward component (1100–2200 UT, 20 March 1990 and 1300–2100 UT, 21 March 1990. The estimates of the polar cap area are based on the approximation of the polar cap boundary by the flow reversal boundary. The change in the polar cap area is then compared to the predicted expansion rate based on a simple application of Faraday's Law. Furthermore, timings of magnetospheric substorms are also related to changes in the polar cap area. Once the convection electric field reconfigures following a southward turning of the IMF, the growth rate of the observed polar cap boundary is consistent with that predicted by Faraday's Law. A delay of typically 20 min to 50 min is observed between a substorm expansion phase onset and a reduction in the polar cap area. Such a delay is consistent with a synthesis between the near Earth neutral line and current disruption models of magnetospheric substorms in which the dipolarisation in the magnetotail may act as a trigger for reconnection. These delays may represent a propagation time between near geosynchronous orbit dipolarisation and subsequent reconnection further down tail. We estimate, from these delays, that the neutral X line occurs between ~35RE and ~75RE downstream in the tail.

  20. The UNUSUAL FLORAL ORGANS gene of Arabidopsis thaliana is an F-box protein required for normal patterning and growth in the floral meristem.

    Science.gov (United States)

    Samach, A; Klenz, J E; Kohalmi, S E; Risseeuw, E; Haughn, G W; Crosby, W L

    1999-11-01

    Genetic and molecular studies have suggested that the UNUSUAL FLORAL ORGANS (UFO) gene, from Arabidopsis thaliana, is expressed in all shoot apical meristems, and is involved in the regulation of a complex set of developmental events during floral development, including floral meristem and floral organ identity. Results from in situ hybridization using genes expressed early in floral development as probes indicate that UFO controls growth of young floral primordia. Transgenic constructs were used to provide evidence that UFO regulates floral organ identity by activating or maintaining transcription of the class B organ-identity gene APETALA 3, but not PISTILLATA. In an attempt to understand the biochemical mode of action of the UFO gene product, we show here that UFO is an F-box protein that interacts with Arabidopsis SKP1-like proteins, both in the yeast two-hybrid system and in vitro. In yeast and other organisms both F-box proteins and SKP1 homologues are subunits of specific ubiquitin E3 enzyme complexes that target specific proteins for degradation. The protein selected for degradation by the complex is specified by the F-box proteins. It is therefore possible that the role of UFO is to target for degradation specific proteins controlling normal growth patterns in the floral primordia, as well as proteins that negatively regulate APETALA 3 transcription.

  1. Seasonal and diurnal pattern of CH4 and CO2 fluxes from the reed area of a fen in South-West Germany

    Science.gov (United States)

    van den Berg, Merit; Lamers, Marc; Streck, Thilo

    2014-05-01

    About 45 million tons of CO2 equivalents are emitted yearly from peat soils in Germany, making it the second largest source of greenhouse gases after the energy sector. A large part of the emission consists of CH4. Nevertheless, carbon budgets of peatlands are not well represented in the National Greenhouse Gas Inventory of Germany, required by the Kyoto Protocol. To fill this gap, we measure CO2 and CH4 fluxes in the reed area of the minerotrophic peatland 'Federseemoor' (3500 ha) in South-West Germany, by means of the Eddy Covariance method. It is expected that this reed area will release high emissions of CH4, due to the anoxic conditions in general and the capacity of reed vegetation to transport gas actively between soil and atmosphere in particular. The results of 2013 show that both CO2 and CH4 fluxes exhibit a distinct seasonal pattern. A clear diurnal pattern is visible for both CO2 and CH4 fluxes during the vegetation period. Overall, this fen system appears to be a sink for carbon dioxide (-4.7 tCO2 ha-1 yr-1), and a source for CH4 (0.3 tCH4 ha-1 yr-1). Although the site is a carbon sink, the GWP100 is slightly positive (1.9 tCO2eq ha-1 yr-1), considering CH4 as a 25 times stronger greenhouse gas than CO2. In our presentation, we will (i) introduce the experimental set up, (ii) summarize the key measurement results from 2013 and (iii) evaluate the main environmental variables affecting the temporal pattern of CH4 and CO2 fluxes.

  2. Antibody responses to Rhoptry-Associated Protein-1 (RAP-1) of Plasmodium falciparum parasites in humans from areas of different malaria endemicity

    DEFF Research Database (Denmark)

    Jakobsen, P H; Kurtzhals, J A; Riley, E M;

    1997-01-01

    Plasma IgM and IgG antibody reactivities against the recombinant Plasmodium falciparum protein, Rhoptry Associated Protein-1 (rRAP-1) were measured by ELISA in individuals from Sudan, Indonesia, Kenya and The Gambia living in areas of different malaria endemicity. IgG and IgM reactivities to rRAP-1...

  3. Physical and Verbal Aggressive Behaviour Pattern Among School Children in Urban Area of North Karnataka: A Cross Sectional Study

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    Fawwad Shaikh

    2014-07-01

    Full Text Available Background: There is growing concern with student conflict, aggression, and violence in the schools, and anger is an important contributing factor which can damage school climate. Aims and Objectives: To elucidate the differentials of aggressive behaviour among high school students and to recognize the influence of age and sex on aggressive behaviour. Material and Methods: The present cross sectional study was conducted in one of the high school in urban area, which included all 347 students (199 boys and 148 girls of classes VII to X. The students were asked to answer, by recall method, a self-administered, pre tested, structured questionnaire indicating the types of aggressive behaviour by them in the previous month and to assess themselves with reference to the statements regarding physical / verbal aggression, after taking their consent. Results: Majority of the students (58.8% were from nuclear families and 26.2% students experienced aggressive behaviour in the family. Role models for aggressive behaviour were parents (42.3% and TV / Cinema actors (39.0%. Overall, 241 (69.5% children were physically aggressive in the previous month. Physical active direct and indirect aggression was significantly more common among boys than among girls. 248 (71.5% children were verbally aggressive in the previous month. Physical aggression increased substantially from VII standard (56.9% to X standard (84.6%. Conclusion: Aggressive behaviour was common among both boys and girls, with increasing trend of physical aggression from VII standard to X standard. Classroom management, counseling and life skills education strategies are recommended for channelizing the aggressive behaviour among school children.

  4. Development of electrical-erosion instrument for direct write micro-patterning on large area conductive thin films.

    Science.gov (United States)

    Álvarez, Ángel Luis; Coya, Carmen; García-Vélez, Miguel

    2015-08-01

    We have developed a complete instrument to perform direct, dry, and cost-effective lithography on conductive materials, based on localized electrical discharges, which avoids using masks or chemicals typical of conventional photolithography. The technique is considered fully compatible with substrate transport based systems, like roll-to-roll technology. The prototype is based on two piezo nano-steppers coupled to three linear micro-stages to cover a large scale operation from micrometers to centimeters. The operation mode consists of a spring probe biased at low DC voltage with respect to a grounded conductive layer. The tip slides on the target layer keeping contact with the material in room conditions, allowing continuous electric monitoring of the process, and also real-time tilt correction via software. The sliding tip leaves an insulating path (limited by the tip diameter) along the material, enabling to draw electrically insulated tracks and pads. The physical principle of operation is based in the natural self-limitation of the discharge due to material removal or insulation. The so produced electrical discharges are very fast, in the range of μs, so features may be performed at speeds of few cm/s, enabling scalability to large areas. The instrument has been tested on different conducting materials as gold, indium tin oxide, and aluminum, allowing the fabrication of alphanumeric displays based on passive matrix of organic light emitting diodes without the use of masks or photoresists. We have verified that the highest potential is achieved on graphene, where no waste material is detected, producing excellent well defined edges. This allows manufacturing graphene micro-ribbons with a high aspect ratio up to 1200:1.

  5. Development of electrical-erosion instrument for direct write micro-patterning on large area conductive thin films

    Energy Technology Data Exchange (ETDEWEB)

    Álvarez, Ángel Luis; Coya, Carmen; García-Vélez, Miguel [Departamento Teoría de la Señal y Comunicaciones, Sistemas Telemáticos y Computación, Escuela Técnica Superior de Ingeniería de Telecomunicación, Universidad Rey Juan Carlos, Fuenlabrada, Madrid 28943 (Spain)

    2015-08-15

    We have developed a complete instrument to perform direct, dry, and cost-effective lithography on conductive materials, based on localized electrical discharges, which avoids using masks or chemicals typical of conventional photolithography. The technique is considered fully compatible with substrate transport based systems, like roll-to-roll technology. The prototype is based on two piezo nano-steppers coupled to three linear micro-stages to cover a large scale operation from micrometers to centimeters. The operation mode consists of a spring probe biased at low DC voltage with respect to a grounded conductive layer. The tip slides on the target layer keeping contact with the material in room conditions, allowing continuous electric monitoring of the process, and also real-time tilt correction via software. The sliding tip leaves an insulating path (limited by the tip diameter) along the material, enabling to draw electrically insulated tracks and pads. The physical principle of operation is based in the natural self-limitation of the discharge due to material removal or insulation. The so produced electrical discharges are very fast, in the range of μs, so features may be performed at speeds of few cm/s, enabling scalability to large areas. The instrument has been tested on different conducting materials as gold, indium tin oxide, and aluminum, allowing the fabrication of alphanumeric displays based on passive matrix of organic light emitting diodes without the use of masks or photoresists. We have verified that the highest potential is achieved on graphene, where no waste material is detected, producing excellent well defined edges. This allows manufacturing graphene micro-ribbons with a high aspect ratio up to 1200:1.

  6. Exposures of Sus scrofa to a TASER(®) conducted electrical weapon: no effects on 2-dimensional gel electrophoresis patterns of plasma proteins.

    Science.gov (United States)

    Jauchem, James R; Cerna, Cesario Z; Lim, Tiffany Y; Seaman, Ronald L

    2014-12-01

    In an earlier study, we found significant changes in red-blood-cell, leukocyte, and platelet counts, and in red-blood-cell membrane proteins, following exposures of anesthetized pigs to a conducted electrical weapon. In the current study, we examined potential changes in plasma proteins [analyzed via two-dimensional gel electrophoresis (2-DGE)] following two 30 s exposures of anesthetized pigs (Sus scrofa) to a TASER (®) C2 conducted electrical weapon. Patterns of proteins, separated by 2-DGE, were consistent and reproducible between animals and between times of sampling. We determined that the blood plasma collection, handling, storage, and processing techniques we used are suitable for swine blood. There were no statistically significant changes in plasma proteins following the conducted-electrical-weapon exposures. Overall gel patterns of fibrinogen were similar to results of other studies of both pigs and humans (in control settings, not exposed to conducted electrical weapons). The lack of significant changes in plasma proteins may be added to the body of evidence regarding relative safety of TASER C2 device exposures.

  7. Partial Sequence Analysis of Merozoite Surface Proteine-3α Gene in Plasmodium vivax Isolates from Malarious Areas of Iran

    Directory of Open Access Journals (Sweden)

    H Mirhendi

    2008-12-01

    Full Text Available Background: Approximately 85-90% of malaria infections in Iran are attributed to Plasmodium vivax, while little is known about the genetic of the parasite and its strain types in this region. This study was designed and performed for describing genetic characteristics of Plasmodium vivax population of Iran based on the merozoite surface protein-3α gene sequence. Methods: Through a descriptive study we analyzed partial P. vivax merozoite surface protein-3α gene sequences from 17 clinical P. vivax isolates collected from malarious areas of Iran. Genomic DNA was extracted by Q1Aamp® DNA blood mini kit, amplified through nested PCR for a partial nucleotide sequence of PvMSP-3 gene in P. vivax. PCR-amplified products were sequenced with an ABI Prism Perkin-Elmer 310 sequencer machine and the data were analyzed with clustal W software. Results: Analysis of PvMSP-3 gene sequences demonstrated extensive polymorphisms, but the sequence identity between isolates of same types was relatively high. We identified specific insertions and deletions for the types A, B and C variants of P. vivax in our isolates. In phylogenetic comparison of geographically separated isolates, there was not a significant geo­graphical branching of the parasite populations. Conclusion: The highly polymorphic nature of isolates suggests that more investigations of the PvMSP-3 gene are needed to explore its vaccine potential.

  8. Protein feeding pattern, casein feeding, or milk-soluble protein feeding did not change the evolution of body composition during a short-term weight loss program.

    Science.gov (United States)

    Adechian, Solange; Balage, Michèle; Remond, Didier; Migné, Carole; Quignard-Boulangé, Annie; Marset-Baglieri, Agnès; Rousset, Sylvie; Boirie, Yves; Gaudichon, Claire; Dardevet, Dominique; Mosoni, Laurent

    2012-10-15

    Studies have shown that timing of protein intake, leucine content, and speed of digestion significantly affect postprandial protein utilization. Our aim was to determine if one can spare lean body mass during energy restriction by varying the quality and the timing of protein intake. Obese volunteers followed a 6-wk restricted energy diet. Four groups were compared: casein pulse, casein spread, milk-soluble protein (MSP, = whey) pulse, and MSP spread (n = 10-11 per group). In casein groups, caseins were the only protein source; it was MSP in MSP groups. Proteins were distributed in four meals per day in the proportion 8:80:4:8% in the pulse groups; it was 25:25:25:25% in the spread groups. We measured weight, body composition, nitrogen balance, 3-methylhistidine excretion, perception of hunger, plasma parameters, adipose tissue metabolism, and whole body protein metabolism. Volunteers lost 7.5 ± 0.4 kg of weight, 5.1 ± 0.2 kg of fat, and 2.2 ± 0.2 kg of lean mass, with no difference between groups. In adipose tissue, cell size and mRNA expression of various genes were reduced with no difference between groups. Hunger perception was also never different between groups. In the last week, due to a higher inhibition of protein degradation and despite a lower stimulation of protein synthesis, postprandial balance between whole body protein synthesis and degradation was better with caseins than with MSP. It seems likely that the positive effect of caseins on protein balance occurred only at the end of the experiment.

  9. Short-term low-protein diet during pregnancy alters islet area and protein content of phosphatidylinositol 3-kinase pathway in rats

    OpenAIRE

    CRISTIANA S.B. SALVATIERRA; REIS,SÍLVIA R.L.; ANA F.M. PESSOA; LETÍCIA M.I. DE SOUZA; Luiz F. Stoppiglia; Veloso, Roberto V; REIS,MARISE A.B.; Everardo M Carneiro; Boschero, Antonio C.; Edson M. Colodel; ARANTES,VANESSA C.; Latorraca, Márcia Q.

    2015-01-01

    The phosphatidylinositol 3-kinase and mitogen-activated protein kinase pathways mediate β cell growth, proliferation, survival and death. We investigated whether protein restriction during pregnancy alters islet morphometry or the expression and phosphorylation of several proteins involved in the phosphatidylinositol 3-kinase and mitogen-activated protein kinase pathways. As controls, adult pregnant and non-pregnant rats were fed a normal-protein diet (17%). Pregnant and non-pregnant rats in ...

  10. Short-term low-protein diet during pregnancy alters islet area and protein content of phosphatidylinositol 3-kinase pathway in rats

    OpenAIRE

    CRISTIANA S.B. SALVATIERRA; REIS,SÍLVIA R.L.; ANA F.M. PESSOA; LETÍCIA M.I. DE SOUZA; Luiz F. Stoppiglia; Veloso, Roberto V; REIS,MARISE A.B.; Everardo M Carneiro; Boschero, Antonio C.; Edson M. Colodel; ARANTES,VANESSA C.; Latorraca, Márcia Q.

    2015-01-01

    The phosphatidylinositol 3-kinase and mitogen-activated protein kinase pathways mediate β cell growth, proliferation, survival and death. We investigated whether protein restriction during pregnancy alters islet morphometry or the expression and phosphorylation of several proteins involved in the phosphatidylinositol 3-kinase and mitogen-activated protein kinase pathways. As controls, adult pregnant and non-pregnant rats were fed a normal-protein diet (17%). Pregnant and non-pregnant rat...

  11. Characterization of Personal Privacy Devices (PPD) radiation pattern impact on the ground and airborne segments of the local area augmentation system (LAAS) at GPS L1 frequency

    Science.gov (United States)

    Alkhateeb, Abualkair M. Khair

    Personal Privacy Devices (PPDs) are radio-frequency transmitters that intentionally transmit in a frequency band used by other devices for the intent purpose of denying service to those devices. These devices have shown the potential to interfere with the ground and air sub-systems of the Local Area Augmentation Systems (LAAS), a GPS-based navigation aids at commercial airports. The Federal Aviation Administration (FAA) is concerned by the potential impact of these devices to GPS navigation aids at airports and has commenced an activity to determine the severity of this threat. In support of this situation, the research in this dissertation has been conducted under (FAA) Cooperative Agreement 2011-G-012, to investigate the impact of these devices on the LAAS. In order to investigate the impact of PPDs Radio Frequency Interference (RFI) on the ground and air sub-systems of the LAAS, the work presented in phase one of this research is intended to characterize the vehicle's impact on the PPD's Effective Isotropic Radiated Power (EIRP). A study was conceived in this research to characterize PPD performance by examining the on-vehicle radiation patterns as a function of vehicle type, jammer type, jammer location inside a vehicle and jammer orientation at each location. Phase two was to characterize the GPS Radiation Pattern on Multipath Limiting Antenna. MLA has to meet stringent requirements for acceptable signal detection and multipath rejection. The ARL-2100 is the most recent MLA antenna proposed to be used in the LAAS ground segment. The ground-based antenna's radiation pattern was modeled. This was achieved via (HFSS) a commercial-off the shelf CAD-based modeling code with a full-wave electromagnetic software simulation package that uses the Finite Element Analysis. Phase three of this work has been conducted to study the characteristics of the GPS Radiation Pattern on Commercial Aircraft. The airborne GPS antenna was modeled and the resulting radiation pattern on

  12. Comparison of Elementary Educational Facility Allocation Patterns and Planning Strategies in Rural Areas:Case Studies of Central and Eastern China

    Institute of Scientific and Technical Information of China (English)

    Zhao; Min; Shao; Lin; Li; Wei; Qian; Fang

    2016-01-01

    Elementary educational facilities are one of the essential public service facilities in rural China. Based on case studies of two countylevel cities in central and eastern China, this paper explores issues regarding a rational allocation of elementary educational facilities in rural areas, including different allocation patterns and effects, and rural residents’ views on elementary educational facilities, as well as their preference when choosing schools. This paper, on the basis of empirical studies, concludes that relevant policies and planning strategies should be adjusted in accordance with the general trends of rural population being decreasing continuously and the student pool concentrating toward towns, so as to achieve an efficient and fair allocation of elementary educational facilities.

  13. Direct Host Plasminogen Binding to Bacterial Surface M-protein in Pattern D Strains of Streptococcus pyogenes Is Required for Activation by Its Natural Coinherited SK2b Protein.

    Science.gov (United States)

    Chandrahas, Vishwanatha; Glinton, Kristofor; Liang, Zhong; Donahue, Deborah L; Ploplis, Victoria A; Castellino, Francis J

    2015-07-24

    Streptokinase (SK), secreted by Group A Streptococcus (GAS), is a single-chain ∼47-kDa protein containing three consecutive primary sequence regions that comprise its α, β, and γ modules. Phylogenetic analyses of the variable β-domain sequences from different GAS strains suggest that SKs can be arranged into two clusters, SK1 and SK2, with a subdivision of SK2 into SK2a and SK2b. SK2b is secreted by skin-tropic Pattern D M-protein strains that also express plasminogen (human Pg (hPg)) binding Group A streptococcal M-protein (PAM) as its major cell surface M-protein. SK2a-expressing strains are associated with nasopharynx tropicity, and many of these strains express human fibrinogen (hFg) binding Pattern A-C M-proteins, e.g. M1. PAM interacts with hPg directly, whereas M1 binds to hPg indirectly via M1-bound hFg. Subsequently, SK is secreted by GAS and activates hPg to plasmin (hPm), thus generating a proteolytic surface on GAS that enhances its dissemination. Due to these different modes of hPg/hPm recognition by GAS, full characterizations of the mechanisms of activation of hPg by SK2a and SK2b and their roles in GAS virulence are important topics. To more fully examine these subjects, isogenic chimeric SK- and M-protein-containing GAS strains were generated, and the virulence of these chimeric strains were analyzed in mice. We show that SK and M-protein alterations influenced the virulence of GAS and were associated with the different natures of hPg activation and hPm binding. These studies demonstrate that GAS virulence can be explained by disparate hPg activation by SK2a and SK2b coupled with the coinherited M-proteins of these strains.

  14. Adjustment of Daily Activities: the Influence of Smartphone Adoption on the Travel Pattern of Mobile Professionals in the Greater Jakarta Area

    Directory of Open Access Journals (Sweden)

    Gloriani Novita Christin

    2014-12-01

    Full Text Available The swift augmentation in the adoption of smartphones, the gadget that resulted from the convergence of Information and Communication Technology (ICT, potentially transforms people's life in myriad dimensions. One potential change induced by smartphones, is how people restructure their daily agenda and consecutively influence their travel pattern. To understand it, this study theoretically reviews mobile professional work, smartphone adoption, and how people conduct their mobile interaction, planni