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Sample records for reveals exchange patterns

  1. Effects of Externalities on Patterns of Exchange

    NARCIS (Netherlands)

    Dijkstra, J.; van Assen, M.A.L.M.

    Many real−life examples of exchanges with externalities exist. Externalities of exchange are defined as direct consequences of exchanges for the payoff of actors who are not involved in the exchange. This paper focuses on how externalities influence the partner choice in exchange networks. In an

  2. Social patterns revealed through random matrix theory

    Science.gov (United States)

    Sarkar, Camellia; Jalan, Sarika

    2014-11-01

    Despite the tremendous advancements in the field of network theory, very few studies have taken weights in the interactions into consideration that emerge naturally in all real-world systems. Using random matrix analysis of a weighted social network, we demonstrate the profound impact of weights in interactions on emerging structural properties. The analysis reveals that randomness existing in particular time frame affects the decisions of individuals rendering them more freedom of choice in situations of financial security. While the structural organization of networks remains the same throughout all datasets, random matrix theory provides insight into the interaction pattern of individuals of the society in situations of crisis. It has also been contemplated that individual accountability in terms of weighted interactions remains as a key to success unless segregation of tasks comes into play.

  3. Metabolism and gas exchange patterns in Rhodnius prolixus.

    Science.gov (United States)

    Schilman, Pablo E

    Insect's metabolic rate and patterns of gas-exchange varies according to different factors such as: species, activity, mass, and temperature among others. One particular striking pattern of gas-exchange in insects is discontinuous gas-exchange cycles, for which many different hypotheses regarding their evolution have been stated. This article does not pretend to be an extensive review on the subject, rather to focus on the work performed on the haematophagous bug Rhodnius prolixus, a model organism used from the mid XX century until present days, with the great influence of Wigglesworth and his students/collaborator's work. I have no doubt that the renovated field of insect gas-exchange has a bright future and will advance at large gaits thank to the help of this model organism, R. prolixus, whose entire genome has recently being unraveled. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. CRISPR loci reveal networks of gene exchange in archaea

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    Brodt Avital

    2011-12-01

    Full Text Available Abstract Background CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism. Results Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention. Conclusions CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense. Open peer review This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten

  5. CRISPR loci reveal networks of gene exchange in archaea.

    Science.gov (United States)

    Brodt, Avital; Lurie-Weinberger, Mor N; Gophna, Uri

    2011-12-21

    CRISPR (Clustered, Regularly, Interspaced, Short, Palindromic Repeats) loci provide prokaryotes with an adaptive immunity against viruses and other mobile genetic elements. CRISPR arrays can be transcribed and processed into small crRNA molecules, which are then used by the cell to target the foreign nucleic acid. Since spacers are accumulated by active CRISPR/Cas systems, the sequences of these spacers provide a record of the past "infection history" of the organism. Here we analyzed all currently known spacers present in archaeal genomes and identified their source by DNA similarity. While nearly 50% of archaeal spacers matched mobile genetic elements, such as plasmids or viruses, several others matched chromosomal genes of other organisms, primarily other archaea. Thus, networks of gene exchange between archaeal species were revealed by the spacer analysis, including many cases of inter-genus and inter-species gene transfer events. Spacers that recognize viral sequences tend to be located further away from the leader sequence, implying that there exists a selective pressure for their retention. CRISPR spacers provide direct evidence for extensive gene exchange in archaea, especially within genera, and support the current dogma where the primary role of the CRISPR/Cas system is anti-viral and anti-plasmid defense. This article was reviewed by: Profs. W. Ford Doolittle, John van der Oost, Christa Schleper (nominated by board member Prof. J Peter Gogarten).

  6. Using register data to deduce patterns of social exchange.

    Science.gov (United States)

    Jansson, Fredrik

    2017-07-01

    This paper presents a novel method for deducting propensities for social exchange between individuals based on the choices they make, and based on factors such as country of origin, sex, school grades and socioeconomic background. The objective here is to disentangle the effect of social ties from the other factors, in order to find patterns of social exchange. This is done through a control-treatment design on analysing available data, where the 'treatment' is similarity of choices between socially connected individuals, and the control is similarity of choices between non-connected individuals. Structural dependencies are controlled for and effects from different classes are pooled through a mix of methods from network and meta-analysis. The method is demonstrated and tested on Swedish register data on students at upper secondary school. The results show that having similar grades is a predictor of social exchange. Also, previous results from Norwegian data are replicated, showing that students cluster based on country of origin.

  7. Exchange bias of patterned systems: Model and numerical simulation

    International Nuclear Information System (INIS)

    Garcia, Griselda; Kiwi, Miguel; Mejia-Lopez, Jose; Ramirez, Ricardo

    2010-01-01

    The magnitude of the exchange bias field of patterned systems exhibits a notable increase in relation to the usual bilayer systems, where a continuous ferromagnetic film is deposited on an antiferromagnet insulator. Here we develop a model, and implement a Monte Carlo calculation, to interpret the experimental observations which is consistent with experimental results, on the basis of assuming a small fraction of spins pinned ferromagnetically in the antiferromagnetic interface layer.

  8. King Lear Reveals the Tragic Pattern of Shakespeare

    Directory of Open Access Journals (Sweden)

    Salim Eflih Al-Ibia

    2017-04-01

    Full Text Available Rather than focusing on the obvious traditions of evaluating Shakespearean tragic heroes, this paper presents a groundbreaking approach to unfold the pattern William Shakespeare follows as he designed his unique characters. This pattern applies to most, if not all, Shakespearean tragic heroes. I argue that Shakespeare himself reveals a great portion of this pattern on the tongue of Lear as the latter disowns Goneril and Regan promising to have “such revenges on [them] both” in King Lear. Lear’s threats bestow four unique aspects that apply not only to his character but they also apply to Shakespearean tragic heroes. Lear’s speech tells us that he is determined to have an awful type of revenge on his daughters. However, the very same speech tells us that he seems uncertain about the method through which he should carry out this revenge. Lear does not express any type of remorse as he pursues his vengeful plans nor should he aim at amnesty. He also admits his own madness as he closes his revealing speech. This research develops these facts about Lear to unfold the unique pattern Shakespeare follows as he portrayed his major tragic figures. This pattern is examined, described and analyzed in King Lear, Othello, and Hamlet. We will find out that the pattern suggested in this study helps us better understand Shakespeare’s tragedies and enables us to provide better explanations for some controversial scenes in the tragedies discussed.

  9. Inheritance Patterns in Citation Networks Reveal Scientific Memes

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    Tobias Kuhn

    2014-11-01

    Full Text Available Memes are the cultural equivalent of genes that spread across human culture by means of imitation. What makes a meme and what distinguishes it from other forms of information, however, is still poorly understood. Our analysis of memes in the scientific literature reveals that they are governed by a surprisingly simple relationship between frequency of occurrence and the degree to which they propagate along the citation graph. We propose a simple formalization of this pattern and validate it with data from close to 50 million publication records from the Web of Science, PubMed Central, and the American Physical Society. Evaluations relying on human annotators, citation network randomizations, and comparisons with several alternative approaches confirm that our formula is accurate and effective, without a dependence on linguistic or ontological knowledge and without the application of arbitrary thresholds or filters.

  10. Inheritance Patterns in Citation Networks Reveal Scientific Memes

    Science.gov (United States)

    Kuhn, Tobias; Perc, Matjaž; Helbing, Dirk

    2014-10-01

    Memes are the cultural equivalent of genes that spread across human culture by means of imitation. What makes a meme and what distinguishes it from other forms of information, however, is still poorly understood. Our analysis of memes in the scientific literature reveals that they are governed by a surprisingly simple relationship between frequency of occurrence and the degree to which they propagate along the citation graph. We propose a simple formalization of this pattern and validate it with data from close to 50 million publication records from the Web of Science, PubMed Central, and the American Physical Society. Evaluations relying on human annotators, citation network randomizations, and comparisons with several alternative approaches confirm that our formula is accurate and effective, without a dependence on linguistic or ontological knowledge and without the application of arbitrary thresholds or filters.

  11. Facilitators on networks reveal optimal interplay between information exchange and reciprocity.

    Science.gov (United States)

    Szolnoki, Attila; Perc, Matjaž; Mobilia, Mauro

    2014-04-01

    Reciprocity is firmly established as an important mechanism that promotes cooperation. An efficient information exchange is likewise important, especially on structured populations, where interactions between players are limited. Motivated by these two facts, we explore the role of facilitators in social dilemmas on networks. Facilitators are here mirrors to their neighbors-they cooperate with cooperators and defect with defectors-but they do not participate in the exchange of strategies. As such, in addition to introducing direct reciprocity, they also obstruct information exchange. In well-mixed populations, facilitators favor the replacement and invasion of defection by cooperation as long as their number exceeds a critical value. In structured populations, on the other hand, there exists a delicate balance between the benefits of reciprocity and the deterioration of information exchange. Extensive Monte Carlo simulations of social dilemmas on various interaction networks reveal that there exists an optimal interplay between reciprocity and information exchange, which sets in only when a small number of facilitators occupy the main hubs of the scale-free network. The drawbacks of missing cooperative hubs are more than compensated for by reciprocity and, at the same time, the compromised information exchange is routed via the auxiliary hubs with only marginal losses in effectivity. These results indicate that it is not always optimal for the main hubs to become leaders of the masses, but rather to exploit their highly connected state to promote tit-for-tat-like behavior.

  12. Influence of ion bombardment induced patterning of exchange bias in pinned artificial ferrimagnets on the interlayer exchange coupling

    Energy Technology Data Exchange (ETDEWEB)

    Schmalhorst, Jan; Reiss, Guenter; Hoenik, V. [Thin Films and Nanostructures, Department of Physics, Univ. Bielefeld (Germany); Weis, Tanja; Engel, Dieter; Ehresmann, Arno [Institute of Physics and Center for Interdisciplinary Nanostructure Science and Technology, Kassel Univ. (Germany)

    2007-07-01

    Artificial ferrimagnets (AFi) have many applications as, e.g., pinned reference electrodes in magnetic tunnel junctions. It is known that the application of ion bombardment induced magnetic patterning with He ions on a single layer reference electrode of magnetic tunnel junctions is possible. For some applications a combination of ion bombardment induced magnetic patterning and artificial ferrimagnets as a reference electrode is desirable. The effect of ion bombardment induced magnetic patterning on pinned artificial ferrimagnets with a Ru interlayer which is frequently used in magnetic tunnel junctions as well as pinned AFis with a Cu interlayer has been tested. Special attention has been given to the question whether the antiferromagnetic interlayer exchange coupling can withstand the ion dose necessary to turn the exchange bias.

  13. A Network Based Methodology to Reveal Patterns in Knowledge Transfer

    Directory of Open Access Journals (Sweden)

    Orlando López-Cruz

    2015-12-01

    Full Text Available This paper motivates, presents and demonstrates in use a methodology based in complex network analysis to support research aimed at identification of sources in the process of knowledge transfer at the interorganizational level. The importance of this methodology is that it states a unified model to reveal knowledge sharing patterns and to compare results from multiple researches on data from different periods of time and different sectors of the economy. This methodology does not address the underlying statistical processes. To do this, national statistics departments (NSD provide documents and tools at their websites. But this proposal provides a guide to model information inferences gathered from data processing revealing links between sources and recipients of knowledge being transferred and that the recipient detects as main source to new knowledge creation. Some national statistics departments set as objective for these surveys the characterization of innovation dynamics in firms and to analyze the use of public support instruments. From this characterization scholars conduct different researches. Measures of dimensions of the network composed by manufacturing firms and other organizations conform the base to inquiry the structure that emerges from taking ideas from other organizations to incept innovations. These two sets of data are actors of a two- mode-network. The link between two actors (network nodes, one acting as the source of the idea. The second one acting as the destination comes from organizations or events organized by organizations that “provide” ideas to other group of firms. The resulting demonstrated design satisfies the objective of being a methodological model to identify sources in knowledge transfer of knowledge effectively used in innovation.

  14. Use patterns of health information exchange through a multidimensional lens: conceptual framework and empirical validation.

    Science.gov (United States)

    Politi, Liran; Codish, Shlomi; Sagy, Iftach; Fink, Lior

    2014-12-01

    Insights about patterns of system use are often gained through the analysis of system log files, which record the actual behavior of users. In a clinical context, however, few attempts have been made to typify system use through log file analysis. The present study offers a framework for identifying, describing, and discerning among patterns of use of a clinical information retrieval system. We use the session attributes of volume, diversity, granularity, duration, and content to define a multidimensional space in which each specific session can be positioned. We also describe an analytical method for identifying the common archetypes of system use in this multidimensional space. We demonstrate the value of the proposed framework with a log file of the use of a health information exchange (HIE) system by physicians in an emergency department (ED) of a large Israeli hospital. The analysis reveals five distinct patterns of system use, which have yet to be described in the relevant literature. The results of this study have the potential to inform the design of HIE systems for efficient and effective use, thus increasing their contribution to the clinical decision-making process. Copyright © 2014 Elsevier Inc. All rights reserved.

  15. Geometric Mechanics Reveals Optimal Complex Terrestrial Undulation Patterns

    Science.gov (United States)

    Gong, Chaohui; Astley, Henry; Schiebel, Perrin; Dai, Jin; Travers, Matthew; Goldman, Daniel; Choset, Howie; CMU Team; GT Team

    Geometric mechanics offers useful tools for intuitively analyzing biological and robotic locomotion. However, utility of these tools were previously restricted to systems that have only two internal degrees of freedom and in uniform media. We show kinematics of complex locomotors that make intermittent contacts with substrates can be approximated as a linear combination of two shape bases, and can be represented using two variables. Therefore, the tools of geometric mechanics can be used to analyze motions of locomotors with many degrees of freedom. To demonstrate the proposed technique, we present studies on two different types of snake gaits which utilize combinations of waves in the horizontal and vertical planes: sidewinding (in the sidewinder rattlesnake C. cerastes) and lateral undulation (in the desert specialist snake C. occipitalis). C. cerastes moves by generating posteriorly traveling body waves in the horizontal and vertical directions, with a relative phase offset equal to +/-π/2 while C. occipitalismaintains a π/2 offset of a frequency doubled vertical wave. Geometric analysis reveals these coordination patterns enable optimal movement in the two different styles of undulatory terrestrial locomotion. More broadly, these examples demonstrate the utility of geometric mechanics in analyzing realistic biological and robotic locomotion.

  16. High porewater exchange in a mangrove-dominated estuary revealed from short-lived radium isotopes

    Science.gov (United States)

    Sadat-Noori, Mahmood; Santos, Isaac R.; Tait, Douglas R.; Reading, Michael J.; Sanders, Christian J.

    2017-10-01

    We hypothesise that mangroves play an important role in groundwater exchange processes in sub-tropical and tropical estuarine waters. To investigate this, multiple high resolution time series measurements of radium across a tidal estuary (Coffs Creek, NSW, Australia) were performed as well as a spatial survey in both bottom and surface layers. Results from the spatial survey revealed increasing radium concentrations in parts of the estuary surrounded by mangroves. The average radium concentration in estuary areas lined with mangroves was 2.5 times higher than the average concentration at the mouth of the estuary and 6.5-fold higher than upstream freshwater areas. Additionally, the area enriched in radium coincided with low dissolved oxygen concentrations, implying that porewater exchange may drive anoxia. A radium mass balance model based on 223Ra and 224Ra isotopes at different sections of the estuary confirmed higher porewater exchange rates from areas fringed with mangrove vegetation. Estimated porewater exchange rates were 27.8 ± 5.3 and 13.6 ± 2.1 cm d-1 (0.8 ± 0.1 and 0.4 ± 0.1 m3 s-1) based on 223Ra and 224Ra isotopes, respectively. The average saline porewater exchange was ∼ 10-fold larger than the upstream surface freshwater inputs to the estuary. We suggest that mangrove environments within subtropical estuaries are hotspots for porewater exchange due to the complex belowground structure of crab burrows and the effect of tidal pumping. Because porewater exchange releases carbon and nitrogen from coastal sediments, development and modification of mangrove areas in subtropical estuaries have a significant effect on coastal biogeochemical cycles.

  17. Social support and employee well-being: the conditioning effect of perceived patterns of supportive exchange.

    Science.gov (United States)

    Nahum-Shani, Inbal; Bamberger, Peter A; Bacharach, Samuel B

    2011-03-01

    Seeking to explain divergent empirical findings regarding the direct effect of social support on well-being, the authors posit that the pattern of supportive exchange (i.e., reciprocal, under-, or over-reciprocating) determines the impact of receiving support on well-being. Findings generated on the basis of longitudinal data collected from a sample of older blue-collar workers support the authors' predictions, indicating that receiving emotional support is associated with enhanced well-being when the pattern of supportive exchange is perceived by an individual as being reciprocal (support received equals support given), with this association being weaker when the exchange of support is perceived as being under-reciprocating (support given exceeds support received). Moreover, receiving support was found to adversely affect well-being when the pattern of exchange was perceived as being over-reciprocating (support received exceeds support given). Theoretical and practical implications of these findings are discussed.

  18. Gas exchange patterns and water loss rates in the Table Mountain cockroach, Aptera fusca (Blattodea: Blaberidae).

    Science.gov (United States)

    Groenewald, Berlizé; Bazelet, Corinna S; Potter, C Paige; Terblanche, John S

    2013-10-15

    The importance of metabolic rate and/or spiracle modulation for saving respiratory water is contentious. One major explanation for gas exchange pattern variation in terrestrial insects is to effect a respiratory water loss (RWL) saving. To test this, we measured the rates of CO2 and H2O release ( and , respectively) in a previously unstudied, mesic cockroach, Aptera fusca, and compared gas exchange and water loss parameters among the major gas exchange patterns (continuous, cyclic, discontinuous gas exchange) at a range of temperatures. Mean , and per unit did not differ among the gas exchange patterns at all temperatures (P>0.09). There was no significant association between temperature and gas exchange pattern type (P=0.63). Percentage of RWL (relative to total water loss) was typically low (9.79±1.84%) and did not differ significantly among gas exchange patterns at 15°C (P=0.26). The method of estimation had a large impact on the percentage of RWL, and of the three techniques investigated (traditional, regression and hyperoxic switch), the traditional method generally performed best. In many respects, A. fusca has typical gas exchange for what might be expected from other insects studied to date (e.g. , , RWL and cuticular water loss). However, we found for A. fusca that expressed as a function of metabolic rate was significantly higher than the expected consensus relationship for insects, suggesting it is under considerable pressure to save water. Despite this, we found no consistent evidence supporting the conclusion that transitions in pattern type yield reductions in RWL in this mesic cockroach.

  19. Time-series analysis of multiple foreign exchange rates using time-dependent pattern entropy

    Science.gov (United States)

    Ishizaki, Ryuji; Inoue, Masayoshi

    2018-01-01

    Time-dependent pattern entropy is a method that reduces variations to binary symbolic dynamics and considers the pattern of symbols in a sliding temporal window. We use this method to analyze the instability of daily variations in multiple foreign exchange rates. The time-dependent pattern entropy of 7 foreign exchange rates (AUD/USD, CAD/USD, CHF/USD, EUR/USD, GBP/USD, JPY/USD, and NZD/USD) was found to be high in the long period after the Lehman shock, and be low in the long period after Mar 2012. We compared the correlation matrix between exchange rates in periods of high and low of the time-dependent pattern entropy.

  20. 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.

  1. High Pressure ZZ-Exchange NMR Reveals Key Features of Protein Folding Transition States.

    Science.gov (United States)

    Zhang, Yi; Kitazawa, Soichiro; Peran, Ivan; Stenzoski, Natalie; McCallum, Scott A; Raleigh, Daniel P; Royer, Catherine A

    2016-11-23

    Understanding protein folding mechanisms and their sequence dependence requires the determination of residue-specific apparent kinetic rate constants for the folding and unfolding reactions. Conventional two-dimensional NMR, such as HSQC experiments, can provide residue-specific information for proteins. However, folding is generally too fast for such experiments. ZZ-exchange NMR spectroscopy allows determination of folding and unfolding rates on much faster time scales, yet even this regime is not fast enough for many protein folding reactions. The application of high hydrostatic pressure slows folding by orders of magnitude due to positive activation volumes for the folding reaction. We combined high pressure perturbation with ZZ-exchange spectroscopy on two autonomously folding protein domains derived from the ribosomal protein, L9. We obtained residue-specific apparent rates at 2500 bar for the N-terminal domain of L9 (NTL9), and rates at atmospheric pressure for a mutant of the C-terminal domain (CTL9) from pressure dependent ZZ-exchange measurements. Our results revealed that NTL9 folding is almost perfectly two-state, while small deviations from two-state behavior were observed for CTL9. Both domains exhibited large positive activation volumes for folding. The volumetric properties of these domains reveal that their transition states contain most of the internal solvent excluded voids that are found in the hydrophobic cores of the respective native states. These results demonstrate that by coupling it with high pressure, ZZ-exchange can be extended to investigate a large number of protein conformational transitions.

  2. Control rod pattern exchange in a BWR/6 utilizing gang mode withdrawal

    International Nuclear Information System (INIS)

    Auvil, A.B. Jr.; Aldemir, T.; Hajek, B.K.

    1986-01-01

    The use of checkerboard pattern of alternating inserted and fully withdrawn control rods and the uneven void distribution in boiling water reactor (BWR) cores can cause large burnup gradients even after a short time of operation. To compensate for these effects, power has to be reshaped periodically (typically every two full-power months) by individually manipulating the control rods. During this manipulation process (called the control rod pattern exchange), the core power is reduced to 60% of nominal power by means of flow reduction to limit power swings to tolerable levels and to ensure that fuel thermal limits are not exceeded. A control rod pattern exchange by individual rod manipulation typically takes 4 to 8 h and represents a large cost burden to the utility in terms of reduced system output. The latest generation of BWRs, the BWR/6, possesses the capability to simultaneously move up to four symmetrically located control rods. The rods corresponding to a given gang may have rotational symmetry, mirror symmetry, or a combination of the two. This paper presents a pattern exchange procedure that exploits the capability of gang mode rod withdrawal to reduce the pattern exchange execution time and radial power distribution asymmetry associated with individual rod manipulation. The working model used in the study is the Perry Nuclear Power Plant Unit 1, located in Perry, Ohio, and owned by the Cleveland Electric Illuminating Company

  3. Spectro-temporal modulation masking patterns reveal frequency selectivity.

    Science.gov (United States)

    Oetjen, Arne; Verhey, Jesko L

    2015-02-01

    The present study investigated the possibility that the human auditory system demonstrates frequency selectivity to spectro-temporal amplitude modulations. Threshold modulation depth for detecting sinusoidal spectro-temporal modulations was measured using a generalized masked threshold pattern paradigm with narrowband masker modulations. Four target spectro-temporal modulations were examined, differing in their temporal and spectral modulation frequencies: a temporal modulation of -8, 8, or 16 Hz combined with a spectral modulation of 1 cycle/octave and a temporal modulation of 4 Hz combined with a spectral modulation of 0.5 cycles/octave. The temporal center frequencies of the masker modulation ranged from 0.25 to 4 times the target temporal modulation. The spectral masker-modulation center-frequencies were 0, 0.5, 1, 1.5, and 2 times the target spectral modulation. For all target modulations, the pattern of average thresholds for the eight normal-hearing listeners was consistent with the hypothesis of a spectro-temporal modulation filter. Such a pattern of modulation-frequency sensitivity was predicted on the basis of psychoacoustical data for purely temporal amplitude modulations and purely spectral amplitude modulations. An analysis of separability indicates that, for the present data set, selectivity in the spectro-temporal modulation domain can be described by a combination of a purely spectral and a purely temporal modulation filter function.

  4. Segmentation and Time-of-Day Patterns in Foreign Exchange Markets

    OpenAIRE

    Angelo Ranaldo

    2007-01-01

    This paper sheds light on a puzzling pattern in foreign exchange markets: Domestic currencies appreciate (depreciate) systematically during foreign (domestic) working hours. These time-of-day patterns are statistically and economically highly significant. They pervasively persist across many years, even after accounting for calendar effects. This phenomenon is difficult to reconcile with the random walk and market efficiency hypothesis. Microstructural and behavioural explanations suggest tha...

  5. Time-series analysis of foreign exchange rates using time-dependent pattern entropy

    Science.gov (United States)

    Ishizaki, Ryuji; Inoue, Masayoshi

    2013-08-01

    Time-dependent pattern entropy is a method that reduces variations to binary symbolic dynamics and considers the pattern of symbols in a sliding temporal window. We use this method to analyze the instability of daily variations in foreign exchange rates, in particular, the dollar-yen rate. The time-dependent pattern entropy of the dollar-yen rate was found to be high in the following periods: before and after the turning points of the yen from strong to weak or from weak to strong, and the period after the Lehman shock.

  6. Bibliometric Analyses Reveal Patterns of Collaboration between ASMS Members

    Science.gov (United States)

    Palmblad, Magnus; van Eck, Nees Jan

    2018-03-01

    We have explored the collaborative network of the current American Society for Mass Spectrometry (ASMS) membership using bibliometric methods. The analysis shows that 4249 members are connected in a single, large, co-authorship graph, including the majority of the most published authors in the field of mass spectrometry. The map reveals topographical differences between university groups and national laboratories, and that the co-authors with the strongest links have long worked together at the same location. We have collected and summarized information on the geographical distribution of members, showing a high coverage of active researchers in North America and Western Europe. Looking at research fields, we could also identify a number of new or `hot' topics among ASMS members. Interactive versions of the maps are available on-line at https://goo.gl/UBNFMQ (collaborative network) and https://goo.gl/WV25vm (research topics). [Figure not available: see fulltext.

  7. Tyrannosauroid integument reveals conflicting patterns of gigantism and feather evolution.

    Science.gov (United States)

    Bell, Phil R; Campione, Nicolás E; Persons, W Scott; Currie, Philip J; Larson, Peter L; Tanke, Darren H; Bakker, Robert T

    2017-06-01

    Recent evidence for feathers in theropods has led to speculations that the largest tyrannosaurids, including Tyrannosaurus rex , were extensively feathered. We describe fossil integument from Tyrannosaurus and other tyrannosaurids ( Albertosaurus, Daspletosaurus, Gorgosaurus and Tarbosaurus ), confirming that these large-bodied forms possessed scaly, reptilian-like skin. Body size evolution in tyrannosauroids reveals two independent occurrences of gigantism; specifically, the large sizes in Yutyrannus and tyrannosaurids were independently derived. These new findings demonstrate that extensive feather coverings observed in some early tyrannosauroids were lost by the Albian, basal to Tyrannosauridae. This loss is unrelated to palaeoclimate but possibly tied to the evolution of gigantism, although other mechanisms exist. © 2017 The Author(s).

  8. Patterned ion exchange membranes for improved power production in microbial reverse-electrodialysis cells

    KAUST Repository

    Liu, Jia

    2014-12-01

    Power production in microbial reverse-electrodialysis cells (MRCs) can be limited by the internal resistance of the reverse electrodialysis stack. Typical MRC stacks use non-conductive spacers that block ion transport by the so-called spacer shadow effect. These spacers can be relatively thick compared to the membrane, and thus they increase internal stack resistance due to high solution (ohmic) resistance associated with a thick spacer. New types of patterned anion and cation exchange membranes were developed by casting membranes to create hemispherical protrusions on the membranes, enabling fluid flow between the membranes without the need for a non-conductive spacer. The use of the patterned membrane decreased the MRC stack resistance by ∼22 Ω, resulting in a 38% increase in power density from 2.50 ± 0.04 W m-2 (non-patterned membrane with a non-conductive spacer) to 3.44 ± 0.02 W m-2 (patterned membrane). The COD removal rate, coulombic efficiency, and energy efficiency of the MRC also increased using the patterned membranes compared to the non-patterned membranes. These results demonstrate that these patterned ion exchange membranes can be used to improve performance of an MRC. © 2014 Elsevier B.V. All rights reserved.

  9. Regional Atmospheric CO2 Inversion Reveals Seasonal and Geographic Differences in Amazon Net Biome Exchange

    Science.gov (United States)

    Alden, Caroline B.; Miller, John B.; Gatti, Luciana V.; Gloor, Manuel M.; Guan, Kaiyu; Michalak, Anna M.; van der Laan-Luijkx, Ingrid; Touma, Danielle; Andrews, Arlyn; Basso, Luana G.; hide

    2016-01-01

    Understanding tropical rainforest carbon exchange and its response to heat and drought is critical for quantifying the effects of climate change on tropical ecosystems, including global climate carbon feedbacks. Of particular importance for the global carbon budget is net biome exchange of CO2 with the atmosphere (NBE), which represents nonfire carbon fluxes into and out of biomass and soils. Subannual and sub-Basin Amazon NBE estimates have relied heavily on process-based biosphere models, despite lack of model agreement with plot-scale observations. We present a new analysis of airborne measurements that reveals monthly, regional-scale (Approx.1-8 x 10(exp -6) km2) NBE variations. We develop a regional atmospheric CO2 inversion that provides the first analysis of geographic and temporal variability in Amazon biosphere-atmosphere carbon exchange and that is minimally influenced by biosphere model-based first guesses of seasonal and annual mean fluxes. We find little evidence for a clear seasonal cycle in Amazon NBE but do find NBE sensitivity to aberrations from long-term mean climate. In particular, we observe increased NBE (more carbon emitted to the atmosphere) associated with heat and drought in 2010, and correlations between wet season NBE and precipitation (negative correlation) and temperature (positive correlation). In the eastern Amazon, pulses of increased NBE persisted through 2011, suggesting legacy effects of 2010 heat and drought. We also identify regional differences in postdrought NBE that appear related to long-term water availability. We examine satellite proxies and find evidence for higher gross primary productivity (GPP) during a pulse of increased carbon uptake in 2011, and lower GPP during a period of increased NBE in the 2010 dry season drought, but links between GPP and NBE changes are not conclusive. These results provide novel evidence of NBE sensitivity to short-term temperature and moisture extremes in the Amazon, where monthly and sub

  10. Prediction of ion-exchange column breakthrough curves by constant-pattern wave approach.

    Science.gov (United States)

    Lee, I-Hsien; Kuan, Yu-Chung; Chern, Jia-Ming

    2008-03-21

    The release of heavy metals from industrial wastewaters represents one of major threats to environment. Compared with chemical precipitation method, fixed-bed ion-exchange process can effectively remove heavy metals from wastewaters and generate no hazardous sludge. In order to design and operate fixed-bed ion-exchange processes successfully, it is very important to understand the column dynamics. In this study, the column experiments for Cu2+/H+, Zn2+/H+, and Cd2+/H+ systems using Amberlite IR-120 were performed to measure the breakthrough curves under varying operating conditions. The experimental results showed that total cation concentration in the mobile-phase played a key role on the breakthrough curves; a higher feed concentration resulted in an earlier breakthrough. Furthermore, the column dynamics was also predicted by self-sharpening and constant-pattern wave models. The self-sharpening wave model assuming local ion-exchange equilibrium could provide a simple and quick estimation for the breakthrough volume, but the predicted breakthrough curves did not match the experimental data very well. On the contrary, the constant-pattern wave model using a constant driving force model for finite ion-exchange rate provided a better fit to the experimental data. The obtained liquid-phase mass transfer coefficient was correlated to the flow velocity and other operating parameters; the breakthrough curves under varying operating conditions could thus be predicted by the constant-pattern wave model using the correlation.

  11. Reciprocal Exchange Patterned by Market Forces Helps Explain Cooperation in a Small-Scale Society.

    Science.gov (United States)

    Jaeggi, Adrian V; Hooper, Paul L; Beheim, Bret A; Kaplan, Hillard; Gurven, Michael

    2016-08-22

    Social organisms sometimes depend on help from reciprocating partners to solve adaptive problems [1], and individual cooperation strategies should aim to offer high supply commodities at low cost to the donor in exchange for high-demand commodities with large return benefits [2, 3]. Although such market dynamics have been documented in some animals [4-7], naturalistic studies of human cooperation are often limited by focusing on single commodities [8]. We analyzed cooperation in five domains (meat sharing, produce sharing, field labor, childcare, and sick care) among 2,161 household dyads of Tsimane' horticulturalists, using Bayesian multilevel models and information-theoretic model comparison. Across domains, the best-fit models included kinship and residential proximity, exchanges in kind and across domains, measures of supply and demand and their interactions with exchange, and household-specific exchange slopes. In these best models, giving, receiving, and reciprocating were to some extent shaped by market forces, and reciprocal exchange across domains had a strong partial effect on cooperation independent of more exogenous factors like kinship and proximity. Our results support the view that reciprocal exchange can provide a reliable solution to adaptive problems [8-11]. Although individual strategies patterned by market forces may generate gains from trade in any species [3], humans' slow life history and skill-intensive foraging niche favor specialization and create interdependence [12, 13], thus stabilizing cooperation and fostering divisions of labor even in informal economies [14, 15]. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

    Science.gov (United States)

    Alshamsi, Aamena; Pianesi, Fabio; Lepri, Bruno; Pentland, Alex; Rahwan, Iyad

    2015-01-01

    Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional) states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported) face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people) cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits) of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

  13. Beyond Contagion: Reality Mining Reveals Complex Patterns of Social Influence.

    Directory of Open Access Journals (Sweden)

    Aamena Alshamsi

    Full Text Available Contagion, a concept from epidemiology, has long been used to characterize social influence on people's behavior and affective (emotional states. While it has revealed many useful insights, it is not clear whether the contagion metaphor is sufficient to fully characterize the complex dynamics of psychological states in a social context. Using wearable sensors that capture daily face-to-face interaction, combined with three daily experience sampling surveys, we collected the most comprehensive data set of personality and emotion dynamics of an entire community of work. From this high-resolution data about actual (rather than self-reported face-to-face interaction, a complex picture emerges where contagion (that can be seen as adaptation of behavioral responses to the behavior of other people cannot fully capture the dynamics of transitory states. We found that social influence has two opposing effects on states: adaptation effects that go beyond mere contagion, and complementarity effects whereby individuals' behaviors tend to complement the behaviors of others. Surprisingly, these effects can exhibit completely different directions depending on the stable personality or emotional dispositions (stable traits of target individuals. Our findings provide a foundation for richer models of social dynamics, and have implications on organizational engineering and workplace well-being.

  14. Investigation of material efficient fin patterns for cost-effective operation of fin and tube heat exchanger

    DEFF Research Database (Denmark)

    Singh, Shobhana; Sørensen, Kim; Condra, Thomas Joseph

    2017-01-01

    Design management of a thermal energy system is a critical part of identifying basic designs that meet large scale user demand under certain operating characteristics. Fin and tube heat exchangers are among the most commonly used thermal energy systems which are generating considerable interest...... and tube heat exchanger. Computational fluid dynamic models of fin and tube heat exchanger with different fin patterns are developed to investigate the fin pattern behavior on heat transfer and pressure loss performance data. In addition, the numerical results are utilized to analyze the engineering design...... scale-up heat exchanger configurations with each fin pattern focusing on the application of chosen fin and tube heat exchanger in marine exhaust gas boiler. The analysis highlights the impact of material efficient fin patterns investigated and predicts that the polynomial and sinusoidal fin patterns...

  15. Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation

    Directory of Open Access Journals (Sweden)

    Hines Heather M

    2012-06-01

    Full Text Available Abstract Background Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying over 140 transcriptome microarrays to assay gene expression in dissected wing pattern elements across a range of developmental stages and wing pattern morphs of Heliconius erato. Results We identified a number of putative early prepattern genes with color-pattern related expression domains. We also identified 51 genes differentially expressed in association with natural color pattern variation. Of these, the previously identified color pattern “switch gene” optix was recovered as the first transcript to show color-specific differential expression. Most differentially expressed genes were transcribed late in pupal development and have roles in cuticle formation or pigment synthesis. These include previously undescribed transporter genes associated with ommochrome pigmentation. Furthermore, we observed upregulation of melanin-repressing genes such as ebony and Dat1 in non-melanic patterns. Conclusions This study identifies many new genes implicated in butterfly wing pattern development and provides a glimpse into the number and types of genes affected by variation in genes that drive color pattern evolution.

  16. Revealing the surface pattern of medieval pattern welded iron objects - etching tests conducted on reconstructed composites

    Czech Academy of Sciences Publication Activity Database

    Thiele, Á.; Hošek, Jiří; Haramza, M.; Török, B.

    2014-01-01

    Roč. 25, č. 1 (2014), s. 18-24 ISSN 1805-7241 R&D Projects: GA ČR GAP405/12/2289 Institutional support: RVO:67985912 Keywords : etching * pattern welding * phosphoric iron * archaeometallurgy Subject RIV: AC - Archeology, Anthropology, Ethnology

  17. Vascular patterns in the heads of crocodilians: blood vessels and sites of thermal exchange.

    Science.gov (United States)

    Porter, William Ruger; Sedlmayr, Jayc C; Witmer, Lawrence M

    2016-12-01

    Extant crocodilians are a highly apomorphic archosaur clade that is ectothermic, yet often achieve large body sizes that can be subject to higher heat loads. Therefore, the anatomical and physiological roles that blood vessels play in crocodilian thermoregulation need further investigation to better understand how crocodilians establish and maintain cephalic temperatures and regulate neurosensory tissue temperatures during basking and normal activities. The cephalic vascular anatomy of extant crocodilians, particularly American alligator (Alligator mississippiensis) was investigated using a differential-contrast, dual-vascular injection technique and high resolution X-ray micro-computed tomography (μCT). Blood vessels were digitally isolated to create representations of vascular pathways. The specimens were then dissected to confirm CT results. Sites of thermal exchange, consisting of the oral, nasal, and orbital regions, were given special attention due to their role in evaporative cooling and cephalic thermoregulation in other diapsids. Blood vessels to and from sites of thermal exchange were studied to detect conserved vascular patterns and to assess their ability to deliver cooled blood to neurosensory tissues. Within the orbital region, both the arteries and veins demonstrated consistent branching patterns, with the supraorbital, infraorbital, and ophthalmotemporal vessels supplying and draining the orbit. The venous drainage of the orbital region showed connections to the dural sinuses via the orbital veins and cavernous sinus. The palatal region demonstrated a vast plexus that comprised both arteries and veins. The most direct route of venous drainage of the palatal plexus was through the palatomaxillary veins, essentially bypassing neurosensory tissues. Anastomotic connections with the nasal region, however, may provide an alternative route for palatal venous blood to reach neurosensory tissues. The nasal region in crocodilians is probably the most

  18. Design of flow-field patterns for proton exchange membrane fuel cell application

    International Nuclear Information System (INIS)

    Rosli, M.I.; Wan Ramli Wan Daud; Kamaruzzaman Sopian; Jaafar Sahari

    2006-01-01

    Fuel cells are electrochemical devices that produce electricity at high efficiency without combustion. Fuel cells are emerging as viable candidates as power sources in many applications, including road vehicles, small-scale power stations, and possibly even portable electronics. This paper addresses the design of flow-field patterns for proton exchange membrane fuel cell (PEMFC). The PEMFC is a low-temperature fuel cell, in which a proton conductive polymer membrane is used as the electrolyte. In PEMFC, flow-field pattern is one important thing that effects the performance of PEMFC. This paper present three types of flow-field pattern that will be consider to be testing using CFD analysis and by experimental. The design look detail on to their shape and dimension to get the best pattern in term of more active electrode area compare to electrode area that will be used. Another advantage and disadvantage for these three type of flow-field patterns from literature also compared in this paper

  19. Integration of computational modeling with membrane transport studies reveals new insights into amino acid exchange transport mechanisms

    Science.gov (United States)

    Widdows, Kate L.; Panitchob, Nuttanont; Crocker, Ian P.; Please, Colin P.; Hanson, Mark A.; Sibley, Colin P.; Johnstone, Edward D.; Sengers, Bram G.; Lewis, Rohan M.; Glazier, Jocelyn D.

    2015-01-01

    Uptake of system L amino acid substrates into isolated placental plasma membrane vesicles in the absence of opposing side amino acid (zero-trans uptake) is incompatible with the concept of obligatory exchange, where influx of amino acid is coupled to efflux. We therefore hypothesized that system L amino acid exchange transporters are not fully obligatory and/or that amino acids are initially present inside the vesicles. To address this, we combined computational modeling with vesicle transport assays and transporter localization studies to investigate the mechanisms mediating [14C]l-serine (a system L substrate) transport into human placental microvillous plasma membrane (MVM) vesicles. The carrier model provided a quantitative framework to test the 2 hypotheses that l-serine transport occurs by either obligate exchange or nonobligate exchange coupled with facilitated transport (mixed transport model). The computational model could only account for experimental [14C]l-serine uptake data when the transporter was not exclusively in exchange mode, best described by the mixed transport model. MVM vesicle isolates contained endogenous amino acids allowing for potential contribution to zero-trans uptake. Both L-type amino acid transporter (LAT)1 and LAT2 subtypes of system L were distributed to MVM, with l-serine transport attributed to LAT2. These findings suggest that exchange transporters do not function exclusively as obligate exchangers.—Widdows, K. L., Panitchob, N., Crocker, I. P., Please, C. P., Hanson, M. A., Sibley, C. P., Johnstone, E. D., Sengers, B. G., Lewis, R. M., Glazier, J. D. Integration of computational modeling with membrane transport studies reveals new insights into amino acid exchange transport mechanisms. PMID:25761365

  20. Vascular Patterns in Iguanas and Other Squamates: Blood Vessels and Sites of Thermal Exchange.

    Directory of Open Access Journals (Sweden)

    William Ruger Porter

    Full Text Available Squamates use the circulatory system to regulate body and head temperatures during both heating and cooling. The flexibility of this system, which possibly exceeds that of endotherms, offers a number of physiological mechanisms to gain or retain heat (e.g., increase peripheral blood flow and heart rate, cooling the head to prolong basking time for the body as well as to shed heat (modulate peripheral blood flow, expose sites of thermal exchange. Squamates also have the ability to establish and maintain the same head-to-body temperature differential that birds, crocodilians, and mammals demonstrate, but without a discrete rete or other vascular physiological device. Squamates offer important anatomical and phylogenetic evidence for the inference of the blood vessels of dinosaurs and other extinct archosaurs in that they shed light on the basal diapsid condition. Given this basal positioning, squamates likewise inform and constrain the range of physiological thermoregulatory mechanisms that may have been found in Dinosauria. Unfortunately, the literature on squamate vascular anatomy is limited. Cephalic vascular anatomy of green iguanas (Iguana iguana was investigated using a differential-contrast, dual-vascular injection (DCDVI technique and high-resolution X-ray microcomputed tomography (μCT. Blood vessels were digitally segmented to create a surface representation of vascular pathways. Known sites of thermal exchange, consisting of the oral, nasal, and orbital regions, were given special attention due to their role in brain and cephalic thermoregulation. Blood vessels to and from sites of thermal exchange were investigated to detect conserved vascular patterns and to assess their ability to deliver cooled blood to the dural venous sinuses. Arteries within sites of thermal exchange were found to deliver blood directly and through collateral pathways. The venous drainage was found to have multiple pathways that could influence neurosensory

  1. Vascular Patterns in Iguanas and Other Squamates: Blood Vessels and Sites of Thermal Exchange.

    Science.gov (United States)

    Porter, William Ruger; Witmer, Lawrence M

    2015-01-01

    Squamates use the circulatory system to regulate body and head temperatures during both heating and cooling. The flexibility of this system, which possibly exceeds that of endotherms, offers a number of physiological mechanisms to gain or retain heat (e.g., increase peripheral blood flow and heart rate, cooling the head to prolong basking time for the body) as well as to shed heat (modulate peripheral blood flow, expose sites of thermal exchange). Squamates also have the ability to establish and maintain the same head-to-body temperature differential that birds, crocodilians, and mammals demonstrate, but without a discrete rete or other vascular physiological device. Squamates offer important anatomical and phylogenetic evidence for the inference of the blood vessels of dinosaurs and other extinct archosaurs in that they shed light on the basal diapsid condition. Given this basal positioning, squamates likewise inform and constrain the range of physiological thermoregulatory mechanisms that may have been found in Dinosauria. Unfortunately, the literature on squamate vascular anatomy is limited. Cephalic vascular anatomy of green iguanas (Iguana iguana) was investigated using a differential-contrast, dual-vascular injection (DCDVI) technique and high-resolution X-ray microcomputed tomography (μCT). Blood vessels were digitally segmented to create a surface representation of vascular pathways. Known sites of thermal exchange, consisting of the oral, nasal, and orbital regions, were given special attention due to their role in brain and cephalic thermoregulation. Blood vessels to and from sites of thermal exchange were investigated to detect conserved vascular patterns and to assess their ability to deliver cooled blood to the dural venous sinuses. Arteries within sites of thermal exchange were found to deliver blood directly and through collateral pathways. The venous drainage was found to have multiple pathways that could influence neurosensory tissue temperature

  2. Electron self-exchange in hemoglobins revealed by deutero-hemin substitution.

    Science.gov (United States)

    Athwal, Navjot Singh; Alagurajan, Jagannathan; Sturms, Ryan; Fulton, D Bruce; Andreotti, Amy H; Hargrove, Mark S

    2015-09-01

    Hemoglobins (phytoglobins) from rice plants (nsHb1) and from the cyanobacterium Synechocystis (PCC 6803) (SynHb) can reduce hydroxylamine with two electrons to form ammonium. The reaction requires intermolecular electron transfer between protein molecules, and rapid electron self-exchange might play a role in distinguishing these hemoglobins from others with slower reaction rates, such as myoglobin. A relatively rapid electron self-exchange rate constant has been measured for SynHb by NMR, but the rate constant for myoglobin is equivocal and a value for nsHb1 has not yet been measured. Here we report electron self-exchange rate constants for nsHb1 and Mb as a test of their role in hydroxylamine reduction. These proteins are not suitable for analysis by NMR ZZ exchange, so a method was developed that uses cross-reactions between each hemoglobin and its deutero-hemin substituted counterpart. The resulting electron transfer is between identical proteins with low driving forces and thus closely approximates true electron self-exchange. The reactions can be monitored spectrally due to the distinct spectra of the prosthetic groups, and from this electron self-exchange rate constants of 880 (SynHb), 2900 (nsHb1), and 0.05M(-1) s(-1) (Mb) have been measured for each hemoglobin. Calculations of cross-reactions using these values accurately predict hydroxylamine reduction rates for each protein, suggesting that electron self-exchange plays an important role in the reaction. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. A Filtering Method to Reveal Crystalline Patterns from Atom Probe Microscopy Desorption Maps

    Science.gov (United States)

    2016-03-26

    reveal crystalline patterns from atom probe microscopy desorption maps Lan Yao Department of Materials Science and Engineering, University of Michigan, Ann...reveal the crystallographic information present in Atom Probe Microscopy (APM) data is presented. Themethod filters atoms based on the time difference...between their evaporation and the evaporation of the previous atom . Since this time difference correlates with the location and the local structure of

  4. Working in Separate Silos? What Citation Patterns Reveal about Higher Education Research Internationally

    Science.gov (United States)

    Tight, Malcolm

    2014-01-01

    Higher education research is a growing, inter-disciplinary and increasingly international field of study. This article examines the citation patterns of articles published in six leading higher education journals--three published in the United States and three published elsewhere in the world--for what they reveal about the development of this…

  5. Manipulation of Superparamagnetic Beads on Patterned Exchange-Bias Layer Systems for Biosensing Applications.

    Science.gov (United States)

    Ehresmann, Arno; Koch, Iris; Holzinger, Dennis

    2015-11-13

    A technology platform based on a remotely controlled and stepwise transport of an array arrangement of superparamagnetic beads (SPB) for efficient molecular uptake, delivery and accumulation in the context of highly specific and sensitive analyte molecule detection for the application in lab-on-a-chip devices is presented. The near-surface transport of SPBs is realized via the dynamic transformation of the SPBs' magnetic potential energy landscape above a magnetically stripe patterned Exchange-Bias (EB) thin film layer systems due to the application of sub-mT external magnetic field pulses. In this concept, the SPB velocity is dramatically influenced by the magnitude and gradient of the magnetic field landscape (MFL) above the magnetically stripe patterned EB substrate, the SPB to substrate distance, the magnetic properties of both the SPBs and the EB layer system, respectively, as well as by the properties of the external magnetic field pulses and the surrounding fluid. The focus of this review is laid on the specific MFL design in EB layer systems via light-ion bombardment induced magnetic patterning (IBMP). A numerical approach is introduced for the theoretical description of the MFL in comparison to experimental characterization via scanning Hall probe microscopy. The SPB transport mechanism will be outlined in terms of the dynamic interplay between the EB substrate's MFL and the pulse scheme of the external magnetic field.

  6. Manipulation of Superparamagnetic Beads on Patterned Exchange-Bias Layer Systems for Biosensing Applications

    Directory of Open Access Journals (Sweden)

    Arno Ehresmann

    2015-11-01

    Full Text Available A technology platform based on a remotely controlled and stepwise transport of an array arrangement of superparamagnetic beads (SPB for efficient molecular uptake, delivery and accumulation in the context of highly specific and sensitive analyte molecule detection for the application in lab-on-a-chip devices is presented. The near-surface transport of SPBs is realized via the dynamic transformation of the SPBs’ magnetic potential energy landscape above a magnetically stripe patterned Exchange-Bias (EB thin film layer systems due to the application of sub-mT external magnetic field pulses. In this concept, the SPB velocity is dramatically influenced by the magnitude and gradient of the magnetic field landscape (MFL above the magnetically stripe patterned EB substrate, the SPB to substrate distance, the magnetic properties of both the SPBs and the EB layer system, respectively, as well as by the properties of the external magnetic field pulses and the surrounding fluid. The focus of this review is laid on the specific MFL design in EB layer systems via light-ion bombardment induced magnetic patterning (IBMP. A numerical approach is introduced for the theoretical description of the MFL in comparison to experimental characterization via scanning Hall probe microscopy. The SPB transport mechanism will be outlined in terms of the dynamic interplay between the EB substrate’s MFL and the pulse scheme of the external magnetic field.

  7. Health information exchange technology on the front lines of healthcare: workflow factors and patterns of use

    Science.gov (United States)

    Johnson, Kevin B; Lorenzi, Nancy M

    2011-01-01

    Objective The goal of this study was to develop an in-depth understanding of how a health information exchange (HIE) fits into clinical workflow at multiple clinical sites. Materials and Methods The ethnographic qualitative study was conducted over a 9-month period in six emergency departments (ED) and eight ambulatory clinics in Memphis, Tennessee, USA. Data were collected using direct observation, informal interviews during observation, and formal semi-structured interviews. The authors observed for over 180 h, during which providers used the exchange 130 times. Results HIE-related workflow was modeled for each ED site and ambulatory clinic group and substantial site-to-site workflow differences were identified. Common patterns in HIE-related workflow were also identified across all sites, leading to the development of two role-based workflow models: nurse based and physician based. The workflow elements framework was applied to the two role-based patterns. An in-depth description was developed of how providers integrated HIE into existing clinical workflow, including prompts for HIE use. Discussion Workflow differed substantially among sites, but two general role-based HIE usage models were identified. Although providers used HIE to improve continuity of patient care, patient–provider trust played a significant role. Types of information retrieved related to roles, with nurses seeking to retrieve recent hospitalization data and more open-ended usage by nurse practitioners and physicians. User and role-specific customization to accommodate differences in workflow and information needs may increase the adoption and use of HIE. Conclusion Understanding end users' perspectives towards HIE technology is crucial to the long-term success of HIE. By applying qualitative methods, an in-depth understanding of HIE usage was developed. PMID:22003156

  8. Oligomerization interface of RAGE receptor revealed by MS-monitored hydrogen deuterium exchange.

    Directory of Open Access Journals (Sweden)

    Ewa Sitkiewicz

    Full Text Available Activation of the receptor for advanced glycation end products (RAGE leads to a chronic proinflammatory signal, affecting patients with a variety of diseases. Potentially beneficial modification of RAGE activity requires understanding the signal transduction mechanism at the molecular level. The ligand binding domain is structurally uncoupled from the cytoplasmic domain, suggesting receptor oligomerization is a requirement for receptor activation. In this study, we used hydrogen-deuterium exchange and mass spectrometry to map structural differences between the monomeric and oligomeric forms of RAGE. Our results indicated the presence of a region shielded from exchange in the oligomeric form of RAGE and led to the identification of a new oligomerization interface localized at the linker region between domains C1 and C2. Based on this finding, a model of a RAGE dimer and higher oligomeric state was constructed.

  9. Ultrafast hydrogen exchange reveals specific structural events during the initial stages of folding of cytochrome c.

    Science.gov (United States)

    Fazelinia, Hossein; Xu, Ming; Cheng, Hong; Roder, Heinrich

    2014-01-15

    Many proteins undergo a sharp decrease in chain dimensions during early stages of folding, prior to the rate-limiting step in folding. However, it remains unclear whether compact states are the result of specific folding events or a general hydrophobic collapse of the poly peptide chain driven by the change in solvent conditions. To address this fundamental question, we extended the temporal resolution of NMR-detected H/D exchange labeling experiments into the microsecond regime by adopting a microfluidics approach. By observing the competition between H/D exchange and folding as a function of labeling pH, coupled with direct measurement of exchange rates in the unfolded state, we were able to monitor hydrogen-bond formation for over 50 individual backbone NH groups within the initial 140 microseconds of folding of horse cytochrome c. Clusters of solvent-shielded amide protons were observed in two α-helical segments in the C-terminal half of the protein, while the N-terminal helix remained largely unstructured, suggesting that proximity in the primary structure is a major factor in promoting helix formation and association at early stages of folding, while the entropically more costly long-range contacts between the N- and C-terminal helices are established only during later stages. Our findings clearly indicate that the initial chain condensation in cytochrome c is driven by specific interactions among a subset of α-helical segments rather than a general hydrophobic collapse.

  10. Instantaneous, Simple, and Reversible Revealing of Invisible Patterns Encrypted in Robust Hollow Sphere Colloidal Photonic Crystals.

    Science.gov (United States)

    Zhong, Kuo; Li, Jiaqi; Liu, Liwang; Van Cleuvenbergen, Stijn; Song, Kai; Clays, Koen

    2018-05-04

    The colors of photonic crystals are based on their periodic crystalline structure. They show clear advantages over conventional chromophores for many applications, mainly due to their anti-photobleaching and responsiveness to stimuli. More specifically, combining colloidal photonic crystals and invisible patterns is important in steganography and watermarking for anticounterfeiting applications. Here a convenient way to imprint robust invisible patterns in colloidal crystals of hollow silica spheres is presented. While these patterns remain invisible under static environmental humidity, even up to near 100% relative humidity, they are unveiled immediately (≈100 ms) and fully reversibly by dynamic humid flow, e.g., human breath. They reveal themselves due to the extreme wettability of the patterned (etched) regions, as confirmed by contact angle measurements. The liquid surface tension threshold to induce wetting (revealing the imprinted invisible images) is evaluated by thermodynamic predictions and subsequently verified by exposure to various vapors with different surface tension. The color of the patterned regions is furthermore independently tuned by vapors with different refractive indices. Such a system can play a key role in applications such as anticounterfeiting, identification, and vapor sensing. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Patterns of exchange of forensic DNA data in the European Union through the Pr?m system

    OpenAIRE

    Santos, Filipe; Machado, Helena

    2017-01-01

    Article in press This paper presents a study of the 5-year operation (2011–2015) of the transnational exchange of forensic DNA data between Member States of the European Union (EU) for the purpose of combating cross-border crime and terrorism within the so-called Prüm system. This first systematisation of the full official statistical dataset provides an overall assessment of the match figures and patterns of operation of the Prüm system for DNA exchange. These figures and patterns are ana...

  12. Effect of induced cross flow on flow pattern and performance of proton exchange membrane fuel cell

    International Nuclear Information System (INIS)

    Jiao, Kui; Bachman, John; Zhou, Yibo; Park, Jae Wan

    2014-01-01

    Highlights: • 3D numerical works to study the effect of cross flow on the PEMFC performance. • The cross flow ensure more evenly distributed water and oxygen in the CL. • The optimal net power output can be identified by controlling the back pressure. • Results confirm that present design is effective in improving performance. - Abstract: The cross flow in proton exchange membrane fuel cells (PEMFCs) plays an important role in changing the transport pattern and performance. In this study, three-dimensional numerical simulations are carried out to investigate the effect of induced cross flow on the flow pattern and performance of a PEMFC with a previously proposed and experimentally studied novel parallel flow channel design. The numerical results indicate that the liquid water and oxygen become more evenly distributed in the catalyst layer (CL) as the pressure difference between the low-pressure and high-pressure flow channels increases. It has been found that, in the low-pressure channels, the cross flow drives a convective flow from the CL to the flow channel resulting in improved liquid water removal. The optimal net power output can be identified by controlling the back pressure on the high-pressure flow channels. The numerical results confirm that this novel parallel flow channel design is effective in improving PEMFC performance

  13. Feeding and stocking up: radio-labelled food reveals exchange patterns in ants.

    Science.gov (United States)

    Buffin, Aurélie; Denis, Damien; Van Simaeys, Gaetan; Goldman, Serge; Deneubourg, Jean-Louis

    2009-06-17

    Food sharing is vital for a large number of species, either solitary or social, and is of particular importance within highly integrated societies, such as in colonial organisms and in social insects. Nevertheless, the mechanisms that govern the distribution of food inside a complex organizational system remain unknown. Using scintigraphy, a method developed for medical imaging, we were able to describe the dynamics of food-flow inside an ant colony. We monitored the sharing process of a radio-labelled sucrose solution inside a nest of Formica fusca. Our results show that, from the very first load that enters the nest, food present within the colony acts as negative feedback to entering food. After one hour of the experiments, 70% of the final harvest has already entered the nest. The total foraged quantity is almost four times smaller than the expected storage capacity. A finer study of the spatial distribution of food shows that although all ants have been fed rapidly (within 30 minutes), a small area representing on average 8% of the radioactive surface holds more than 25% of the stored food. Even in rather homogeneous nests, we observed a strong concentration of food in few workers. Examining the position of these workers inside the nest, we found heavily loaded ants in the centre of the aggregate. The position of the centre of this high-intensity radioactive surface remained stable for the three consecutive hours of the experiments. We demonstrate that the colony simultaneously managed to rapidly feed all workers (200 ants fed within 30 minutes) and build up food stocks to prevent food shortage, something that occurs rather often in changing environments. Though we expected the colony to forage to its maximum capacity, the flow of food entering the colony is finely tuned to the colony's needs. Indeed the food-flow decreases proportionally to the food that has already been harvested, liberating the work-force for other tasks.

  14. Feeding and stocking up: radio-labelled food reveals exchange patterns in ants.

    OpenAIRE

    Aurélie Buffin; Damien Denis; Gaetan Van Simaeys; Serge Goldman; Jean-Louis Deneubourg

    2009-01-01

    Food sharing is vital for a large number of species, either solitary or social, and is of particular importance within highly integrated societies, such as in colonial organisms and in social insects. Nevertheless, the mechanisms that govern the distribution of food inside a complex organizational system remain unknown. Using scintigraphy, a method developed for medical imaging, we were able to describe the dynamics of food-flow inside an ant colony. We monitored the sharing process of a radi...

  15. Structure of the cold-shock domain protein from Neisseria meningitidis reveals a strand-exchanged dimer

    Energy Technology Data Exchange (ETDEWEB)

    Ren, Jingshan [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Division of Structural Biology, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Nettleship, Joanne E.; Sainsbury, Sarah [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom); Saunders, Nigel J. [Bacterial Pathogenesis and Functional Genomics Group, Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE (United Kingdom); Owens, Raymond J., E-mail: ray@strubi.ox.ac.uk [The Oxford Protein Production Facility, Henry Wellcome Building for Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN (United Kingdom)

    2008-04-01

    The X-ray crystal structure of the cold-shock domain protein from N. meningitidis reveals a strand-exchanged dimer. The structure of the cold-shock domain protein from Neisseria meningitidis has been solved to 2.6 Å resolution and shown to comprise a dimer formed by the exchange of two β-strands between protein monomers. The overall fold of the monomer closely resembles those of other bacterial cold-shock proteins. The neisserial protein behaved as a monomer in solution and was shown to bind to a hexathymidine oligonucleotide with a stoichiometry of 1:1 and a K{sub d} of 1.25 µM.

  16. Heat exchange from the toucan bill reveals a controllable vascular thermal radiator.

    Science.gov (United States)

    Tattersall, Glenn J; Andrade, Denis V; Abe, Augusto S

    2009-07-24

    The toco toucan (Ramphastos toco), the largest member of the toucan family, possesses the largest beak relative to body size of all birds. This exaggerated feature has received various interpretations, from serving as a sexual ornament to being a refined adaptation for feeding. However, it is also a significant surface area for heat exchange. Here we show the remarkable capacity of the toco toucan to regulate heat distribution by modifying blood flow, using the bill as a transient thermal radiator. Our results indicate that the toucan's bill is, relative to its size, one of the largest thermal windows in the animal kingdom, rivaling elephants' ears in its ability to radiate body heat.

  17. Distribution patterns of firearm discharge residues as revealed by neutron activation analysis

    International Nuclear Information System (INIS)

    Pillay, K.K.S.; Driscoll, D.C.; Jester, W.A.

    1975-01-01

    A systematic investigation using a variety of handguns has revealed the existence of distinguisable distribution patterns of firearm discharge residues on surfaces below the flight path of a bullet. The residues are identificable even at distances of 12 meters from the gun using nondestructive neutron activation analysis. The results of these investigations show that the distribution pattern for a gun is reproducible using similar ammunition and that there exist two distinct regions to the patterns developed between the firearm and the target-one with respect to the position of the gun and the other in the vicinity of the target. The judicious applications of these findings could be of significant value in criminal investigations. (T.G.)

  18. [The conformational dynamics of the tetramer hemoglobin molecule as revealed by hydrogen exchange. III. Influence of the heme removal].

    Science.gov (United States)

    Abaturov, L V; Nosova, N G; Shliapnikova, S V

    2006-01-01

    Two main types of conformational fluctuations--local and global are characteristic of the native protein structure and revealed by hydrogen exchange. The probability of those fluctuations changes to a different extent upon hemoglobin oxygenation, changing of pH, splitting of the intersubunit contacts. To compare with the influence of the heme removal the rate of the H-D exchange of the peptide NH atoms of the human apoHb was studied at the pH range 5.5-9.0 and temperature 10-38 degrees C by the IR spectroscopy. The removal of the heme increases the rate of the H-D exchange of the 80% peptide NH atoms with the factor retardation of the exchange rate (P) in the range approximately 10(2)-10(8). For the most of the peptide NH atoms the probability of the local fluctuations weakly depends on the temperature, the enthalpy changes upon all such local conformational transitions deltaH(op) degrees are 0-15 kcal/M. Characterized by the stronger temperature dependence the global fluctuations are not arised upon the temperature increases up to 38 degrees C at pH 7.0 inspite of in these conditions the slow denaturation and aggregation of apoHb begin to occur. Upon the destabilization of the apoHb structure by the simultaneous decreasing of pH to 5.5 and temperature to 10 degrees C the global fluctuations of the apoHb native structure described by deltaH(op)o < 0 begin to intensify. The mechanism of the overall intensification of the local fluctuations upon the heme removal, the peculiarity of the heat denaturation of apoHb in conditions, close to that existing upon the selfassembly of Hb in vivo, and analogy between low temperature global fluctuations and cold denaturation of globular proteins are discussed.

  19. Movement patterns and dispersal potential of Pecos bluntnose shiner (Notropis simus pecosensis) revealed using otolith microchemistry

    Science.gov (United States)

    Chase, Nathan M.; Caldwell, Colleen A.; Carleton, Scott A.; Gould, William R.; Hobbs, James A.

    2015-01-01

    Natal origin and dispersal potential of the federally threatened Pecos bluntnose shiner (Notropis simus pecosensis) were successfully characterized using otolith microchemistry and swimming performance trials. Strontium isotope ratios (87Sr:86Sr) of otoliths within the resident plains killifish (Fundulus zebrinus) were successfully used as a surrogate for strontium isotope ratios in water and revealed three isotopically distinct reaches throughout 297 km of the Pecos River, New Mexico, USA. Two different life history movement patterns were revealed in Pecos bluntnose shiner. Eggs and fry were either retained in upper river reaches or passively dispersed downriver followed by upriver movement during the first year of life, with some fish achieving a minimum movement of 56 km. Swimming ability of Pecos bluntnose shiner confirmed upper critical swimming speeds (Ucrit) as high as 43.8 cm·s−1 and 20.6 body lengths·s−1 in 30 days posthatch fish. Strong swimming ability early in life supports our observations of upriver movement using otolith microchemistry and confirms movement patterns that were previously unknown for the species. Understanding patterns of dispersal of this and other small-bodied fishes using otolith microchemistry may help redirect conservation and management efforts for Great Plains fishes.

  20. Multivariate pattern classification reveals autonomic and experiential representations of discrete emotions.

    Science.gov (United States)

    Kragel, Philip A; Labar, Kevin S

    2013-08-01

    Defining the structural organization of emotions is a central unresolved question in affective science. In particular, the extent to which autonomic nervous system activity signifies distinct affective states remains controversial. Most prior research on this topic has used univariate statistical approaches in attempts to classify emotions from psychophysiological data. In the present study, electrodermal, cardiac, respiratory, and gastric activity, as well as self-report measures were taken from healthy subjects during the experience of fear, anger, sadness, surprise, contentment, and amusement in response to film and music clips. Information pertaining to affective states present in these response patterns was analyzed using multivariate pattern classification techniques. Overall accuracy for classifying distinct affective states was 58.0% for autonomic measures and 88.2% for self-report measures, both of which were significantly above chance. Further, examining the error distribution of classifiers revealed that the dimensions of valence and arousal selectively contributed to decoding emotional states from self-report, whereas a categorical configuration of affective space was evident in both self-report and autonomic measures. Taken together, these findings extend recent multivariate approaches to study emotion and indicate that pattern classification tools may improve upon univariate approaches to reveal the underlying structure of emotional experience and physiological expression. PsycINFO Database Record (c) 2013 APA, all rights reserved.

  1. Master stability functions reveal diffusion-driven pattern formation in networks

    Science.gov (United States)

    Brechtel, Andreas; Gramlich, Philipp; Ritterskamp, Daniel; Drossel, Barbara; Gross, Thilo

    2018-03-01

    We study diffusion-driven pattern formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing random walks, while they can be created or destroyed by reactions between or within a layer. We show that the stability of homogeneous steady states can be analyzed with a master stability function approach that reveals a deep analogy between pattern formation in networks and pattern formation in continuous space. For illustration, we consider a generalized model of ecological meta-food webs. This fairly complex model describes the dispersal of many different species across a region consisting of a network of individual habitats while subject to realistic, nonlinear predator-prey interactions. In this example, the method reveals the intricate dependence of the dynamics on the spatial structure. The ability of the proposed approach to deal with this fairly complex system highlights it as a promising tool for ecology and other applications.

  2. Foreign exchange market data analysis reveals statistical features that predict price movement acceleration.

    Science.gov (United States)

    Nacher, Jose C; Ochiai, Tomoshiro

    2012-05-01

    Increasingly accessible financial data allow researchers to infer market-dynamics-based laws and to propose models that are able to reproduce them. In recent years, several stylized facts have been uncovered. Here we perform an extensive analysis of foreign exchange data that leads to the unveiling of a statistical financial law. First, our findings show that, on average, volatility increases more when the price exceeds the highest (or lowest) value, i.e., breaks the resistance line. We call this the breaking-acceleration effect. Second, our results show that the probability P(T) to break the resistance line in the past time T follows power law in both real data and theoretically simulated data. However, the probability calculated using real data is rather lower than the one obtained using a traditional Black-Scholes (BS) model. Taken together, the present analysis characterizes a different stylized fact of financial markets and shows that the market exceeds a past (historical) extreme price fewer times than expected by the BS model (the resistance effect). However, when the market does, we predict that the average volatility at that time point will be much higher. These findings indicate that any Markovian model does not faithfully capture the market dynamics.

  3. Angiogenesis interactome and time course microarray data reveal the distinct activation patterns in endothelial cells.

    Directory of Open Access Journals (Sweden)

    Liang-Hui Chu

    Full Text Available Angiogenesis involves stimulation of endothelial cells (EC by various cytokines and growth factors, but the signaling mechanisms are not completely understood. Combining dynamic gene expression time-course data for stimulated EC with protein-protein interactions associated with angiogenesis (the "angiome" could reveal how different stimuli result in different patterns of network activation and could implicate signaling intermediates as points for control or intervention. We constructed the protein-protein interaction networks of positive and negative regulation of angiogenesis comprising 367 and 245 proteins, respectively. We used five published gene expression datasets derived from in vitro assays using different types of blood endothelial cells stimulated by VEGFA (vascular endothelial growth factor A. We used the Short Time-series Expression Miner (STEM to identify significant temporal gene expression profiles. The statistically significant patterns between 2D fibronectin and 3D type I collagen substrates for telomerase-immortalized EC (TIME show that different substrates could influence the temporal gene activation patterns in the same cell line. We investigated the different activation patterns among 18 transmembrane tyrosine kinase receptors, and experimentally measured the protein level of the tyrosine-kinase receptors VEGFR1, VEGFR2 and VEGFR3 in human umbilical vein EC (HUVEC and human microvascular EC (MEC. The results show that VEGFR1-VEGFR2 levels are more closely coupled than VEGFR1-VEGFR3 or VEGFR2-VEGFR3 in HUVEC and MEC. This computational methodology can be extended to investigate other molecules or biological processes such as cell cycle.

  4. Multivoxel Patterns Reveal Functionally Differentiated Networks Underlying Auditory Feedback Processing of Speech

    DEFF Research Database (Denmark)

    Zheng, Zane Z.; Vicente-Grabovetsky, Alejandro; MacDonald, Ewen N.

    2013-01-01

    The everyday act of speaking involves the complex processes of speech motor control. An important component of control is monitoring, detection, and processing of errors when auditory feedback does not correspond to the intended motor gesture. Here we show, using fMRI and converging operations...... within a multivoxel pattern analysis framework, that this sensorimotor process is supported by functionally differentiated brain networks. During scanning, a real-time speech-tracking system was used to deliver two acoustically different types of distorted auditory feedback or unaltered feedback while...... human participants were vocalizing monosyllabic words, and to present the same auditory stimuli while participants were passively listening. Whole-brain analysis of neural-pattern similarity revealed three functional networks that were differentially sensitive to distorted auditory feedback during...

  5. Complex (Nonstandard) Six-Layer Polytypes of Lizardite Revealed from Oblique-Texture Electron Diffraction Patterns

    International Nuclear Information System (INIS)

    Zhukhlistov, A.P.; Zinchuk, N.N.; Kotel'nikov, D.D.

    2004-01-01

    Association of simple (1T and 3R) and two complex (nonstandard) orthogonal polytypes of the serpentine mineral lizardite from the Catoca kimberlite pipe (West Africa) association is revealed from oblique-texture electron diffraction patterns. A six-layer polytype with an ordered superposition of equally oriented layers (notation 3 2 3 2 3 4 3 4 3 6 3 6 or ++ - -00) belonging to the structural group A and a three-layer (336 or I,I,II) or a six-layer (336366 or I,I,II,I,II,II) polytype with alternating oppositely oriented layers and semi-disordered structure are identified using polytype analysis

  6. Multiple oxygen tension environments reveal diverse patterns of transcriptional regulation in primary astrocytes.

    Directory of Open Access Journals (Sweden)

    Wayne Chadwick

    Full Text Available The central nervous system normally functions at O(2 levels which would be regarded as hypoxic by most other tissues. However, most in vitro studies of neurons and astrocytes are conducted under hyperoxic conditions without consideration of O(2-dependent cellular adaptation. We analyzed the reactivity of astrocytes to 1, 4 and 9% O(2 tensions compared to the cell culture standard of 20% O(2, to investigate their ability to sense and translate this O(2 information to transcriptional activity. Variance of ambient O(2 tension for rat astrocytes resulted in profound changes in ribosomal activity, cytoskeletal and energy-regulatory mechanisms and cytokine-related signaling. Clustering of transcriptional regulation patterns revealed four distinct response pattern groups that directionally pivoted around the 4% O(2 tension, or demonstrated coherent ascending/decreasing gene expression patterns in response to diverse oxygen tensions. Immune response and cell cycle/cancer-related signaling pathway transcriptomic subsets were significantly activated with increasing hypoxia, whilst hemostatic and cardiovascular signaling mechanisms were attenuated with increasing hypoxia. Our data indicate that variant O(2 tensions induce specific and physiologically-focused transcript regulation patterns that may underpin important physiological mechanisms that connect higher neurological activity to astrocytic function and ambient oxygen environments. These strongly defined patterns demonstrate a strong bias for physiological transcript programs to pivot around the 4% O(2 tension, while uni-modal programs that do not, appear more related to pathological actions. The functional interaction of these transcriptional 'programs' may serve to regulate the dynamic vascular responsivity of the central nervous system during periods of stress or heightened activity.

  7. TreeNetViz: revealing patterns of networks over tree structures.

    Science.gov (United States)

    Gou, Liang; Zhang, Xiaolong Luke

    2011-12-01

    Network data often contain important attributes from various dimensions such as social affiliations and areas of expertise in a social network. If such attributes exhibit a tree structure, visualizing a compound graph consisting of tree and network structures becomes complicated. How to visually reveal patterns of a network over a tree has not been fully studied. In this paper, we propose a compound graph model, TreeNet, to support visualization and analysis of a network at multiple levels of aggregation over a tree. We also present a visualization design, TreeNetViz, to offer the multiscale and cross-scale exploration and interaction of a TreeNet graph. TreeNetViz uses a Radial, Space-Filling (RSF) visualization to represent the tree structure, a circle layout with novel optimization to show aggregated networks derived from TreeNet, and an edge bundling technique to reduce visual complexity. Our circular layout algorithm reduces both total edge-crossings and edge length and also considers hierarchical structure constraints and edge weight in a TreeNet graph. These experiments illustrate that the algorithm can reduce visual cluttering in TreeNet graphs. Our case study also shows that TreeNetViz has the potential to support the analysis of a compound graph by revealing multiscale and cross-scale network patterns. © 2011 IEEE

  8. Using biological markets principles to examine patterns of grooming exchange in Macaca thibetana.

    Science.gov (United States)

    Balasubramaniam, K N; Berman, C M; Ogawa, H; Li, J

    2011-12-01

    Biological markets principles offer testable hypotheses to explain variation in grooming exchange patterns among nonhuman primates. They predict that when within-group contest competition (WGC) is high and dominance hierarchies steep, grooming interchange with other "commodity" behaviors (such as agonistic support) should prevail. In contrast, when WGC is low and gradients shallow, market theory predicts that grooming reciprocity should prevail. We tested these predictions in a wild, provisioned Tibetan macaque (Macaca thibetana) group across six time periods during which the group had been subjected to varying degrees of range restriction. Data on female-female aggression, grooming, and support were collected using all-occurrences and focal animal sampling techniques, and analyzed using ANCOVA methods and correlation analyses. We found that hierarchical steepness varied significantly across periods, but did not correlate with two indirect indicators of WGC (group size and range restriction) in predicted directions. Contrary to expectations, we found a negative correlation between steepness and group size, perhaps because the responses of group members to external risks (i.e. prolonged and unavoidable exposure to humans) may have overshadowed the effects of WGC. As predicted, grooming reciprocity was significant in each period and negatively correlated with steepness, even after we controlled group size, kinship, rank differences, and proximity. In contrast, there was no evidence for grooming interchange with agonistic support or for a positive relationship between interchange and steepness. We hypothesize that stressful conditions and/or the presence of stable hierarchies during each period may have led to a greater market demand for grooming than support. We suggest that future studies testing these predictions consider more direct measures of WGC and commodities in addition to support, such as feeding tolerance and access to infants. © 2011 Wiley Periodicals

  9. Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse.

    Science.gov (United States)

    Ning, T; Li, J; Lin, K; Xiao, H; Wylie, S; Hua, S; Li, H; Zhang, Y-P

    2014-01-01

    The domestic horse is the most widely used and important stock and recreational animal, valued for its strength and endurance. The energy required by the domestic horse is mainly supplied by mitochondria via oxidative phosphorylation. Thus, selection may have played an essential role in the evolution of the horse mitochondria. Besides, demographic events also affect the DNA polymorphic pattern on mitochondria. To understand the evolutionary patterns of the mitochondria of the domestic horse, we used a deep sequencing approach to obtain the complete sequences of 15 mitochondrial genomes, and four mitochondrial gene sequences, ND6, ATP8, ATP6 and CYTB, collected from 509, 363, 363 and 409 domestic horses, respectively. Evidence of strong substitution rate heterogeneity was found at nonsynonymous sites across the genomes. Signatures of recent positive selection on mtDNA of domestic horse were detected. Specifically, five amino acids in the four mitochondrial genes were identified as the targets of positive selection. Coalescentbased simulations imply that recent population expansion is the most probable explanation for the matrilineal population history for domestic horse. Our findings reveal a complex pattern of non-neutral evolution of the mitochondrial genome in the domestic horses.

  10. Expression Pattern and Localization Dynamics of Guanine Nucleotide Exchange Factor RIC8 during Mouse Oogenesis.

    Directory of Open Access Journals (Sweden)

    Merly Saare

    Full Text Available Targeting of G proteins to the cell cortex and their activation is one of the triggers of both asymmetric and symmetric cell division. Resistance to inhibitors of cholinesterase 8 (RIC8, a guanine nucleotide exchange factor, activates a certain subgroup of G protein α-subunits in a receptor independent manner. RIC8 controls the asymmetric cell division in Caenorhabditis elegans and Drosophila melanogaster, and symmetric cell division in cultured mammalian cells, where it regulates the mitotic spindle orientation. Although intensely studied in mitosis, the function of RIC8 in mammalian meiosis has remained unknown. Here we demonstrate that the expression and subcellular localization of RIC8 changes profoundly during mouse oogenesis. Immunofluorescence studies revealed that RIC8 expression is dependent on oocyte growth and cell cycle phase. During oocyte growth, RIC8 is abundantly present in cytoplasm of oocytes at primordial, primary and secondary preantral follicle stages. Later, upon oocyte maturation RIC8 also populates the germinal vesicle, its localization becomes cell cycle dependent, and it associates with chromatin and the meiotic spindle. After fertilization, RIC8 protein converges to the pronuclei and is also detectable at high levels in the nucleolus precursor bodies of both maternal and paternal pronucleus. During first cleavage of zygote RIC8 localizes in the mitotic spindle and cell cortex of forming blastomeres. In addition, we demonstrate that RIC8 co-localizes with its interaction partners Gαi1/2:GDP and LGN in meiotic/mitotic spindle, cell cortex and polar bodies of maturing oocytes and zygotes. Downregulation of Ric8 by siRNA leads to interferred translocation of Gαi1/2 to cortical region of maturing oocytes and reduction of its levels. RIC8 is also expressed at high level in female reproductive organs e.g. oviduct. Therefore we suggest a regulatory function for RIC8 in mammalian gametogenesis and fertility.

  11. Potential for tree rings to reveal spatial patterns of past drought variability across western Australia

    Science.gov (United States)

    O'Donnell, Alison J.; Cook, Edward R.; Palmer, Jonathan G.; Turney, Chris S. M.; Grierson, Pauline F.

    2018-02-01

    Proxy records have provided major insights into the variability of past climates over long timescales. However, for much of the Southern Hemisphere, the ability to identify spatial patterns of past climatic variability is constrained by the sparse distribution of proxy records. This is particularly true for mainland Australia, where relatively few proxy records are located. Here, we (1) assess the potential to use existing proxy records in the Australasian region—starting with the only two multi-century tree-ring proxies from mainland Australia—to reveal spatial patterns of past hydroclimatic variability across the western third of the continent, and (2) identify strategic locations to target for the development of new proxy records. We show that the two existing tree-ring records allow robust reconstructions of past hydroclimatic variability over spatially broad areas (i.e. > 3° × 3°) in inland north- and south-western Australia. Our results reveal synchronous periods of drought and wet conditions between the inland northern and southern regions of western Australia as well as a generally anti-phase relationship with hydroclimate in eastern Australia over the last two centuries. The inclusion of 174 tree-ring proxy records from Tasmania, New Zealand and Indonesia and a coral record from Queensland did not improve the reconstruction potential over western Australia. However, our findings suggest that the addition of relatively few new proxy records from key locations in western Australia that currently have low reconstruction skill will enable the development of a comprehensive drought atlas for the region, and provide a critical link to the drought atlases of monsoonal Asia and eastern Australia and New Zealand.

  12. Long-term acoustical observations of the mesopelagic fish Maurolicus muelleri reveal novel and varied vertical migration patterns

    KAUST Repository

    Staby, A; Rø stad, Anders; Kaartvedt, Stein

    2011-01-01

    . The data revealed known patterns as normal diel vertical migration (DVM), midnight sinking between dusk and dawn, and periods without migrations, as well as novel behaviours consisting of early morning ascents, reverse diel vertical migrations

  13. Patterned biofilm formation reveals a mechanism for structural heterogeneity in bacterial biofilms.

    Science.gov (United States)

    Gu, Huan; Hou, Shuyu; Yongyat, Chanokpon; De Tore, Suzanne; Ren, Dacheng

    2013-09-03

    Bacterial biofilms are ubiquitous and are the major cause of chronic infections in humans and persistent biofouling in industry. Despite the significance of bacterial biofilms, the mechanism of biofilm formation and associated drug tolerance is still not fully understood. A major challenge in biofilm research is the intrinsic heterogeneity in the biofilm structure, which leads to temporal and spatial variation in cell density and gene expression. To understand and control such structural heterogeneity, surfaces with patterned functional alkanthiols were used in this study to obtain Escherichia coli cell clusters with systematically varied cluster size and distance between clusters. The results from quantitative imaging analysis revealed an interesting phenomenon in which multicellular connections can be formed between cell clusters depending on the size of interacting clusters and the distance between them. In addition, significant differences in patterned biofilm formation were observed between wild-type E. coli RP437 and some of its isogenic mutants, indicating that certain cellular and genetic factors are involved in interactions among cell clusters. In particular, autoinducer-2-mediated quorum sensing was found to be important. Collectively, these results provide missing information that links cell-to-cell signaling and interaction among cell clusters to the structural organization of bacterial biofilms.

  14. A second life for old data: Global patterns in pollution ecology revealed from published observational studies

    Energy Technology Data Exchange (ETDEWEB)

    Kozlov, Mikhail V., E-mail: mikoz@utu.fi [Section of Ecology, University of Turku, 20014 Turku (Finland); Zvereva, Elena L. [Section of Ecology, University of Turku, 20014 Turku (Finland)

    2011-05-15

    A synthesis of research on the responses of terrestrial biota (1095 effect sizes) to industrial pollution (206 point emission sources) was conducted to reveal regional and global patterns from small-scale observational studies. A meta-analysis, in combination with other statistical methods, showed that the effects of pollution depend on characteristics of the specific polluter (type, amount of emission, duration of impact on biota), the affected organism (trophic group, life history), the level at which the response was measured (organism, population, community), and the environment (biome, climate). In spite of high heterogeneity in responses, we have detected several general patterns. We suggest that the development of evolutionary adaptations to pollution is a common phenomenon and that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms. We argue that community- and ecosystem-level responses to pollution should be explored directly, rather than deduced from organism-level studies. - Research synthesis demonstrated that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms.

  15. A second life for old data: Global patterns in pollution ecology revealed from published observational studies

    International Nuclear Information System (INIS)

    Kozlov, Mikhail V.; Zvereva, Elena L.

    2011-01-01

    A synthesis of research on the responses of terrestrial biota (1095 effect sizes) to industrial pollution (206 point emission sources) was conducted to reveal regional and global patterns from small-scale observational studies. A meta-analysis, in combination with other statistical methods, showed that the effects of pollution depend on characteristics of the specific polluter (type, amount of emission, duration of impact on biota), the affected organism (trophic group, life history), the level at which the response was measured (organism, population, community), and the environment (biome, climate). In spite of high heterogeneity in responses, we have detected several general patterns. We suggest that the development of evolutionary adaptations to pollution is a common phenomenon and that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms. We argue that community- and ecosystem-level responses to pollution should be explored directly, rather than deduced from organism-level studies. - Research synthesis demonstrated that the harmful effects of pollution on terrestrial ecosystems are likely to increase as the climate warms.

  16. Quantifying relief on alluvial fans using airborne lidar to reveal patterns of sediment accumulation

    Science.gov (United States)

    Morelan, A. E., III; Oskin, M. E.

    2017-12-01

    We present a method of quantifying detailed surface relief on alluvial fans from high-resolution topography. Average slope and curvature of the fan are used together to empirically derive an idealized, radially symmetric fan surface, from which we compute residual topography. Maps produced using this technique highlight spatial patterns of fan deposition and avulsion. Regions of high residual topography reveal active and abandoned sediment lobes accumulated from recent depositional events, often with well-defined channels at their apex. Preliminary observations suggest that surface relief is uniform across a collection of fans in a given region and source lithology. Alluvial fans with granitic catchment lithologies in eastern California (n=12), each with varying source catchment size and mean fan slope, all show relief of around 4 meters. A collection of fans from the Carrizo Plain in central California (n=12), with source catchments set within Miocene marine and nonmarine sedimentary rocks, show significantly lower relief values around 2 meters. We hypothesize that particle grain size determines this contrasting relief through its control on the thickness of fan-building debris flows. In both settings we find that sediment lobes tend to extend toward the fan toe. This pattern supports a process, observed in analog experiments, of fan deposition dominated by back-filling and overtopping of distributary channels by debris-flows.

  17. Ocean time-series reveals recurring seasonal patterns of virioplankton dynamics in the northwestern Sargasso Sea.

    Science.gov (United States)

    Parsons, Rachel J; Breitbart, Mya; Lomas, Michael W; Carlson, Craig A

    2012-02-01

    There are an estimated 10(30) virioplankton in the world oceans, the majority of which are phages (viruses that infect bacteria). Marine phages encompass enormous genetic diversity, affect biogeochemical cycling of elements, and partially control aspects of prokaryotic production and diversity. Despite their importance, there is a paucity of data describing virioplankton distributions over time and depth in oceanic systems. A decade of high-resolution time-series data collected from the upper 300 m in the northwestern Sargasso Sea revealed recurring temporal and vertical patterns of virioplankton abundance in unprecedented detail. An annual virioplankton maximum developed between 60 and 100 m during periods of summer stratification and eroded during winter convective mixing. The timing and vertical positioning of this seasonal pattern was related to variability in water column stability and the dynamics of specific picophytoplankton and heterotrophic bacterioplankton lineages. Between 60 and 100 m, virioplankton abundance was negatively correlated to the dominant heterotrophic bacterioplankton lineage SAR11, as well as the less abundant picophytoplankton, Synechococcus. In contrast, virioplankton abundance was positively correlated to the dominant picophytoplankton lineage Prochlorococcus, and the less abundant alpha-proteobacteria, Rhodobacteraceae. Seasonally, virioplankton abundances were highly synchronous with Prochlorococcus distributions and the virioplankton to Prochlorococcus ratio remained remarkably constant during periods of water column stratification. The data suggest that a significant fraction of viruses in the mid-euphotic zone of the subtropical gyres may be cyanophages and patterns in their abundance are largely determined by Prochlorococcus dynamics in response to water column stability. This high-resolution, decadal survey of virioplankton abundance provides insight into the possible controls of virioplankton dynamics in the open ocean.

  18. A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets.

    Science.gov (United States)

    Ritchie, Scott C; Watts, Stephen; Fearnley, Liam G; Holt, Kathryn E; Abraham, Gad; Inouye, Michael

    2016-07-01

    Network modules-topologically distinct groups of edges and nodes-that are preserved across datasets can reveal common features of organisms, tissues, cell types, and molecules. Many statistics to identify such modules have been developed, but testing their significance requires heuristics. Here, we demonstrate that current methods for assessing module preservation are systematically biased and produce skewed p values. We introduce NetRep, a rapid and computationally efficient method that uses a permutation approach to score module preservation without assuming data are normally distributed. NetRep produces unbiased p values and can distinguish between true and false positives during multiple hypothesis testing. We use NetRep to quantify preservation of gene coexpression modules across murine brain, liver, adipose, and muscle tissues. Complex patterns of multi-tissue preservation were revealed, including a liver-derived housekeeping module that displayed adipose- and muscle-specific association with body weight. Finally, we demonstrate the broader applicability of NetRep by quantifying preservation of bacterial networks in gut microbiota between men and women. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

  19. Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain.

    Science.gov (United States)

    Li, Jing; Rodnin, Mykola V; Ladokhin, Alexey S; Gross, Michael L

    2014-11-04

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our "standard condition" (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W(+)-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8-9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8-9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain.

  20. Hydrogen–Deuterium Exchange and Mass Spectrometry Reveal the pH-Dependent Conformational Changes of Diphtheria Toxin T Domain

    Science.gov (United States)

    2015-01-01

    The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membrane form. High-resolution structural studies are only applicable to the static T-domain structure at physiological pH, and studies of the T-domain translocation pathway are hindered by the simultaneous presence of multiple conformations. Here, we report the application of hydrogen–deuterium exchange mass spectrometry (HDX-MS) for the study of the pH-dependent conformational changes of the T domain in solution. Effects of pH on intrinsic HDX rates were deconvolved by converting the on-exchange times at low pH into times under our “standard condition” (pH 7.5). pH-Dependent HDX kinetic analysis of T domain clearly reveals the conformational transition from the native state (W-state) to a membrane-competent state (W+-state). The initial transition occurs at pH 6 and includes the destabilization of N-terminal helices accompanied by the separation between N- and C-terminal segments. The structural rearrangements accompanying the formation of the membrane-competent state expose a hydrophobic hairpin (TH8–9) to solvent, prepare it to insert into the membrane. At pH 5.5, the transition is complete, and the protein further unfolds, resulting in the exposure of its C-terminal hydrophobic TH8–9, leading to subsequent aggregation in the absence of membranes. This solution-based study complements high resolution crystal structures and provides a detailed understanding of the pH-dependent structural rearrangement and acid-induced oligomerization of T domain. PMID:25290210

  1. Lactose Binding Induces Opposing Dynamics Changes in Human Galectins Revealed by NMR-Based Hydrogen-Deuterium Exchange.

    Science.gov (United States)

    Chien, Chih-Ta Henry; Ho, Meng-Ru; Lin, Chung-Hung; Hsu, Shang-Te Danny

    2017-08-16

    Galectins are β-galactoside-binding proteins implicated in a myriad of biological functions. Despite their highly conserved carbohydrate binding motifs with essentially identical structures, their affinities for lactose, a common galectin inhibitor, vary significantly. Here, we aimed to examine the molecular basis of differential lactose affinities amongst galectins using solution-based techniques. Consistent dissociation constants of lactose binding were derived from nuclear magnetic resonance (NMR) spectroscopy, intrinsic tryptophan fluorescence, isothermal titration calorimetry and bio-layer interferometry for human galectin-1 (hGal1), galectin-7 (hGal7), and the N-terminal and C-terminal domains of galectin-8 (hGal8 NTD and hGal8 CTD , respectively). Furthermore, the dissociation rates of lactose binding were extracted from NMR lineshape analyses. Structural mapping of chemical shift perturbations revealed long-range perturbations upon lactose binding for hGal1 and hGal8 NTD . We further demonstrated using the NMR-based hydrogen-deuterium exchange (HDX) that lactose binding increases the exchange rates of residues located on the opposite side of the ligand-binding pocket for hGal1 and hGal8 NTD , indicative of allostery. Additionally, lactose binding induces significant stabilisation of hGal8 CTD across the entire domain. Our results suggested that lactose binding reduced the internal dynamics of hGal8 CTD on a very slow timescale (minutes and slower) at the expense of reduced binding affinity due to the unfavourable loss of conformational entropy.

  2. Gas-exchange patterns of Mediterranean fruit fly Pupae (Diptera: Tephritidae): A tool to forecast developmental stage

    International Nuclear Information System (INIS)

    Nestel, D.; Nemny-Lavy, E.; Alchanatis, V.

    2007-01-01

    The pattern of gas-exchange (CO 2 emission) was investigated for developing Mediterranean fruit fly (medfly) Ceratitis capitata (Wiedemann) pupae incubated at different temperatures. This study was undertaken to explore the usefulness of gas-exchange systems in the determination of physiological age in developing pupae that are mass produced for sterile insect technique projects. The rate of CO 2 emission was measured in a closed flow-through system connected to commercial infrared gas analysis equipment. Metabolic activity (rate of CO 2 emission) was related to pupal eye-color, which is the current technique used to determine physiological age. Eye-color was characterized digitally with 3 variables (Hue, Saturation and Intensity), and color separated by discriminant analysis. The rate of CO 2 emission throughout pupal development followed a U-shape, with high levels of emission during pupariation, pupal transformation and final pharate adult stages. Temperature affected the development time of pupae, but not the basic CO 2 emission patterns during development. In all temperatures, rates of CO 2 emission 1 and 2 d before adult emergence were very similar. After mid larval-adult transition (e.g., phanerocephalic pupa), digital eye-color was significantly correlated with CO 2 emission. Results support the suggestion that gas-exchange should be explored further as a system to determine pupal physiological age in mass production of fruit flies. (author) [es

  3. Range-wide multilocus phylogeography of the red fox reveals ancient continental divergence, minimal genomic exchange and distinct demographic histories.

    Science.gov (United States)

    Statham, Mark J; Murdoch, James; Janecka, Jan; Aubry, Keith B; Edwards, Ceiridwen J; Soulsbury, Carl D; Berry, Oliver; Wang, Zhenghuan; Harrison, David; Pearch, Malcolm; Tomsett, Louise; Chupasko, Judith; Sacks, Benjamin N

    2014-10-01

    Widely distributed taxa provide an opportunity to compare biogeographic responses to climatic fluctuations on multiple continents and to investigate speciation. We conducted the most geographically and genomically comprehensive study to date of the red fox (Vulpes vulpes), the world's most widely distributed wild terrestrial carnivore. Analyses of 697 bp of mitochondrial sequence in ~1000 individuals suggested an ancient Middle Eastern origin for all extant red foxes and a 400 kya (SD = 139 kya) origin of the primary North American (Nearctic) clade. Demographic analyses indicated a major expansion in Eurasia during the last glaciation (~50 kya), coinciding with a previously described secondary transfer of a single matriline (Holarctic) to North America. In contrast, North American matrilines (including the transferred portion of Holarctic clade) exhibited no signatures of expansion until the end of the Pleistocene (~12 kya). Analyses of 11 autosomal loci from a subset of foxes supported the colonization time frame suggested by mtDNA (and the fossil record) but, in contrast, reflected no detectable secondary transfer, resulting in the most fundamental genomic division of red foxes at the Bering Strait. Endemic continental Y-chromosome clades further supported this pattern. Thus, intercontinental genomic exchange was overall very limited, consistent with long-term reproductive isolation since the initial colonization of North America. Based on continental divergence times in other carnivoran species pairs, our findings support a model of peripatric speciation and are consistent with the previous classification of the North American red fox as a distinct species, V. fulva. © 2014 John Wiley & Sons Ltd.

  4. Multivariate pattern analysis reveals anatomical connectivity differences between the left and right mesial temporal lobe epilepsy

    Directory of Open Access Journals (Sweden)

    Peng Fang

    2015-01-01

    Full Text Available Previous studies have demonstrated differences of clinical signs and functional brain network organizations between the left and right mesial temporal lobe epilepsy (mTLE, but the anatomical connectivity differences underlying functional variance between the left and right mTLE remain uncharacterized. We examined 43 (22 left, 21 right mTLE patients with hippocampal sclerosis and 39 healthy controls using diffusion tensor imaging. After the whole-brain anatomical networks were constructed for each subject, multivariate pattern analysis was applied to classify the left mTLE from the right mTLE and extract the anatomical connectivity differences between the left and right mTLE patients. The classification results reveal 93.0% accuracy for the left mTLE versus the right mTLE, 93.4% accuracy for the left mTLE versus controls and 90.0% accuracy for the right mTLE versus controls. Compared with the right mTLE, the left mTLE exhibited a different connectivity pattern in the cortical-limbic network and cerebellum. The majority of the most discriminating anatomical connections were located within or across the cortical-limbic network and cerebellum, thereby indicating that these disease-related anatomical network alterations may give rise to a portion of the complex of emotional and memory deficit between the left and right mTLE. Moreover, the orbitofrontal gyrus, cingulate cortex, hippocampus and parahippocampal gyrus, which exhibit high discriminative power in classification, may play critical roles in the pathophysiology of mTLE. The current study demonstrated that anatomical connectivity differences between the left mTLE and the right mTLE may have the potential to serve as a neuroimaging biomarker to guide personalized diagnosis of the left and right mTLE.

  5. Multivariate pattern analysis reveals anatomical connectivity differences between the left and right mesial temporal lobe epilepsy.

    Science.gov (United States)

    Fang, Peng; An, Jie; Zeng, Ling-Li; Shen, Hui; Chen, Fanglin; Wang, Wensheng; Qiu, Shijun; Hu, Dewen

    2015-01-01

    Previous studies have demonstrated differences of clinical signs and functional brain network organizations between the left and right mesial temporal lobe epilepsy (mTLE), but the anatomical connectivity differences underlying functional variance between the left and right mTLE remain uncharacterized. We examined 43 (22 left, 21 right) mTLE patients with hippocampal sclerosis and 39 healthy controls using diffusion tensor imaging. After the whole-brain anatomical networks were constructed for each subject, multivariate pattern analysis was applied to classify the left mTLE from the right mTLE and extract the anatomical connectivity differences between the left and right mTLE patients. The classification results reveal 93.0% accuracy for the left mTLE versus the right mTLE, 93.4% accuracy for the left mTLE versus controls and 90.0% accuracy for the right mTLE versus controls. Compared with the right mTLE, the left mTLE exhibited a different connectivity pattern in the cortical-limbic network and cerebellum. The majority of the most discriminating anatomical connections were located within or across the cortical-limbic network and cerebellum, thereby indicating that these disease-related anatomical network alterations may give rise to a portion of the complex of emotional and memory deficit between the left and right mTLE. Moreover, the orbitofrontal gyrus, cingulate cortex, hippocampus and parahippocampal gyrus, which exhibit high discriminative power in classification, may play critical roles in the pathophysiology of mTLE. The current study demonstrated that anatomical connectivity differences between the left mTLE and the right mTLE may have the potential to serve as a neuroimaging biomarker to guide personalized diagnosis of the left and right mTLE.

  6. Functional redundancy patterns reveal non-random assembly rules in a species-rich marine assemblage.

    Directory of Open Access Journals (Sweden)

    Nicolas Guillemot

    Full Text Available The relationship between species and the functional diversity of assemblages is fundamental in ecology because it contains key information on functional redundancy, and functionally redundant ecosystems are thought to be more resilient, resistant and stable. However, this relationship is poorly understood and undocumented for species-rich coastal marine ecosystems. Here, we used underwater visual censuses to examine the patterns of functional redundancy for one of the most diverse vertebrate assemblages, the coral reef fishes of New Caledonia, South Pacific. First, we found that the relationship between functional and species diversity displayed a non-asymptotic power-shaped curve, implying that rare functions and species mainly occur in highly diverse assemblages. Second, we showed that the distribution of species amongst possible functions was significantly different from a random distribution up to a threshold of ∼90 species/transect. Redundancy patterns for each function further revealed that some functions displayed fast rates of increase in redundancy at low species diversity, whereas others were only becoming redundant past a certain threshold. This suggested non-random assembly rules and the existence of some primordial functions that would need to be fulfilled in priority so that coral reef fish assemblages can gain a basic ecological structure. Last, we found little effect of habitat on the shape of the functional-species diversity relationship and on the redundancy of functions, although habitat is known to largely determine assemblage characteristics such as species composition, biomass, and abundance. Our study shows that low functional redundancy is characteristic of this highly diverse fish assemblage, and, therefore, that even species-rich ecosystems such as coral reefs may be vulnerable to the removal of a few keystone species.

  7. Patterns of hybrid loss of imprinting reveal tissue- and cluster-specific regulation.

    Directory of Open Access Journals (Sweden)

    Christopher D Wiley

    Full Text Available Crosses between natural populations of two species of deer mice, Peromyscus maniculatus (BW, and P. polionotus (PO, produce parent-of-origin effects on growth and development. BW females mated to PO males (bwxpo produce growth-retarded but otherwise healthy offspring. In contrast, PO females mated to BW males (POxBW produce overgrown and severely defective offspring. The hybrid phenotypes are pronounced in the placenta and include POxBW conceptuses which lack embryonic structures. Evidence to date links variation in control of genomic imprinting with the hybrid defects, particularly in the POxBW offspring. Establishment of genomic imprinting is typically mediated by gametic DNA methylation at sites known as gDMRs. However, imprinted gene clusters vary in their regulation by gDMR sequences.Here we further assess imprinted gene expression and DNA methylation at different cluster types in order to discern patterns. These data reveal POxBW misexpression at the Kcnq1ot1 and Peg3 clusters, both of which lose ICR methylation in placental tissues. In contrast, some embryonic transcripts (Peg10, Kcnq1ot1 reactivated the silenced allele with little or no loss of DNA methylation. Hybrid brains also display different patterns of imprinting perturbations. Several cluster pairs thought to use analogous regulatory mechanisms are differentially affected in the hybrids.These data reinforce the hypothesis that placental and somatic gene regulation differs significantly, as does that between imprinted gene clusters and between species. That such epigenetic regulatory variation exists in recently diverged species suggests a role in reproductive isolation, and that this variation is likely to be adaptive.

  8. Magnetic charge distribution and stray field landscape of asymmetric néel walls in a magnetically patterned exchange bias layer system

    Science.gov (United States)

    Zingsem, Norbert; Ahrend, Florian; Vock, Silvia; Gottlob, Daniel; Krug, Ingo; Doganay, Hatice; Holzinger, Dennis; Neu, Volker; Ehresmann, Arno

    2017-12-01

    The 3D stray field landscape above an exchange bias layer system with engineered domain walls has been fully characterized by quantitative magnetic force microscopy (qMFM) measurements. This method is based on a complete quantification of the MFM tip’s imaging properties and the subtraction of its contribution from the measured MFM data by deconvolution in Fourier space. The magnetically patterned Ir17Mn83/Co70Fe30-exchange-bias-multilayers have been designed to contain asymmetric head-to-head (hh)/tail-to-tail (tt) Néel walls between domains of different magnetic anisotropies for potential use in guided particle transport. In the current application, qMFM reveals the effective magnetic charge profile on the surface of the sample—with high spatial resolution and in an absolute quantitative manner. These data enable to calculate the magnetostatic potential and the full stray field landscape above the sample surface. It has been successfully tested against: (i) micromagnetic simulations of the magnetization structure of a comparable exchange-bias layer system, (ii) measurements of the magnetization profile across the domain boundary with x-ray photoemission electron microscopy, and (iii) direct stray field measurements obtained by scanning Hall probe microscopy at elevated scan heights. This approach results in a quantitative determination of the stray field landscape at close distances to the sample surface, which will be of importance for remote magnetic particle transport applications in lab-on-a-chip devices. Furthermore, the highly resolving and quantitative MFM approach reveals details of the domain transition across the artificially structured phase boundary, which have to be attributed to a continuous change in the materials parameters across this boundary, rather than an abrupt one.

  9. Label-free proteome profiling reveals developmental-dependent patterns in young barley grains.

    Science.gov (United States)

    Kaspar-Schoenefeld, Stephanie; Merx, Kathleen; Jozefowicz, Anna Maria; Hartmann, Anja; Seiffert, Udo; Weschke, Winfriede; Matros, Andrea; Mock, Hans-Peter

    2016-06-30

    Due to its importance as a cereal crop worldwide, high interest in the determination of factors influencing barley grain quality exists. This study focusses on the elucidation of protein networks affecting early grain developmental processes. NanoLC-based separation coupled to label-free MS detection was applied to gain insights into biochemical processes during five different grain developmental phases (pre-storage until storage phase, 3days to 16days after flowering). Multivariate statistics revealed two distinct developmental patterns during the analysed grain developmental phases: proteins showed either highest abundance in the middle phase of development - in the transition phase - or at later developmental stages - within the storage phase. Verification of developmental patterns observed by proteomic analysis was done by applying hypothesis-driven approaches, namely Western Blot analysis and enzyme assays. High general metabolic activity of the grain with regard to protein synthesis, cell cycle regulation, defence against oxidative stress, and energy production via photosynthesis was observed in the transition phase. Proteins upregulated in the storage phase are related towards storage protein accumulation, and interestingly to the defence of storage reserves against pathogens. A mixed regulatory pattern for most enzymes detected in our study points to regulatory mechanisms at the level of protein isoforms. In-depth understanding of early grain developmental processes of cereal caryopses is of high importance as they influence final grain weight and quality. Our knowledge about these processes is still limited, especially on proteome level. To identify key mechanisms in early barley grain development, a label-free data-independent proteomics acquisition approach has been applied. Our data clearly show, that proteins either exhibit highest expression during cellularization and the switch to the storage phase (transition phase, 5-7 DAF), or during storage

  10. A study of flow patterns in a thermosyphon for compact heat exchanger applications

    NARCIS (Netherlands)

    Grooten, M.H.M.; Geld, van der C.W.M.; Deursen, van L.G.M.

    2008-01-01

    Recently, thermosyphons have attracted interest in the design of smaller, lighter and cheaper heat exchangers, because of their compactness, low thermal resistance, high heat recovery effectiveness, safety and reliability. In order to understand the effects of the angle of inclination on heat

  11. Partitioning of the net CO2 exchange using an automated chamber system reveals plant phenology as key control of production and respiration fluxes in a boreal peatland.

    Science.gov (United States)

    Järveoja, Järvi; Nilsson, Mats B; Gažovič, Michal; Crill, Patrick M; Peichl, Matthias

    2018-04-30

    The net ecosystem CO 2 exchange (NEE) drives the carbon (C) sink-source strength of northern peatlands. Since NEE represents a balance between various production and respiration fluxes, accurate predictions of its response to global changes require an in depth understanding of these underlying processes. Currently, however, detailed information of the temporal dynamics as well as the separate biotic and abiotic controls of the NEE component fluxes is lacking in peatland ecosystems. In this study, we address this knowledge gap by using an automated chamber system established across natural and trenching-/vegetation removal plots to partition NEE into its production (i.e. gross and net primary production; GPP and NPP) and respiration (i.e. ecosystem, heterotrophic and autotrophic respiration; ER, Rh and Ra) fluxes in a boreal peatland in northern Sweden. Our results showed that daily NEE patterns were driven by GPP while variations in ER were governed by Ra rather than Rh. Moreover, we observed pronounced seasonal shifts in the Ra/Rh and above-/belowground NPP ratios throughout the main phenological phases. Generalized linear model analysis revealed that the greenness index derived from digital images (as a proxy for plant phenology) was the strongest control of NEE, GPP and NPP while explaining considerable fractions also in the variations of ER and Ra. In addition, our data exposed greater temperature sensitivity of NPP compared to Rh resulting in enhanced C sequestration with increasing temperature. Overall, our study suggests that the temporal patterns in NEE and its component fluxes are tightly coupled to vegetation dynamics in boreal peatlands and thus challenges previous studies that commonly identify abiotic factors as key drivers. These findings further emphasize the need for integrating detailed information on plant phenology into process-based models to improve predictions of global change impacts on the peatland C cycle. This article is protected by

  12. Descriptive parameters for revealing substitution patterns of sugar beet pectins using pectolytic enzymes.

    Science.gov (United States)

    Remoroza, C; Buchholt, H C; Gruppen, H; Schols, H A

    2014-01-30

    Enzymatic fingerprinting was applied to sugar beet pectins (SBPs) modified by either plant or fungal pectin methyl esterases and alkali catalyzed de-esterification to reveal the ester distributions over the pectin backbone. A simultaneous pectin lyase (PL) treatment to the commonly used endo-polygalacturonase (endo-PG) degradation showed to be effective in degrading both high and low methylesterified and/or acetylated homogalaturonan regions of SBP simultaneously. Using LC-HILIC-MS/ELSD, we studied in detail all the diagnostic oligomers present, enabling us to discriminate between differently prepared sugar beet pectins having various levels of methylesterification and acetylation. Furthermore, distinction between commercially extracted and de-esterified sugar beet pectin having different patterns of substitution was achieved by using novel descriptive pectin parameters. In addition to DBabs approach for nonmethylesterified sequences degradable by endo-PG, the "degree of hydrolysis" (DHPG) representing all partially saturated methylesterified and/or acetylated galacturonic acid (GalA) moieties was introduced as a new parameter. Consequently, the description DHPL has been introduced to quantify all esterified unsaturated GalA oligomers. Copyright © 2013 Elsevier Ltd. All rights reserved.

  13. Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure.

    Directory of Open Access Journals (Sweden)

    Amira Amrani

    Full Text Available RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HPt that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria.

  14. Integrated Analysis of Alzheimer's Disease and Schizophrenia Dataset Revealed Different Expression Pattern in Learning and Memory.

    Science.gov (United States)

    Li, Wen-Xing; Dai, Shao-Xing; Liu, Jia-Qian; Wang, Qian; Li, Gong-Hua; Huang, Jing-Fei

    2016-01-01

    Alzheimer's disease (AD) and schizophrenia (SZ) are both accompanied by impaired learning and memory functions. This study aims to explore the expression profiles of learning or memory genes between AD and SZ. We downloaded 10 AD and 10 SZ datasets from GEO-NCBI for integrated analysis. These datasets were processed using RMA algorithm and a global renormalization for all studies. Then Empirical Bayes algorithm was used to find the differentially expressed genes between patients and controls. The results showed that most of the differentially expressed genes were related to AD whereas the gene expression profile was little affected in the SZ. Furthermore, in the aspects of the number of differentially expressed genes, the fold change and the brain region, there was a great difference in the expression of learning or memory related genes between AD and SZ. In AD, the CALB1, GABRA5, and TAC1 were significantly downregulated in whole brain, frontal lobe, temporal lobe, and hippocampus. However, in SZ, only two genes CRHBP and CX3CR1 were downregulated in hippocampus, and other brain regions were not affected. The effect of these genes on learning or memory impairment has been widely studied. It was suggested that these genes may play a crucial role in AD or SZ pathogenesis. The different gene expression patterns between AD and SZ on learning and memory functions in different brain regions revealed in our study may help to understand the different mechanism between two diseases.

  15. Reliable and rapid characterization of functional FCN2 gene variants reveals diverse geographical patterns

    Directory of Open Access Journals (Sweden)

    Ojurongbe Olusola

    2012-05-01

    Full Text Available Abstract Background Ficolin-2 coded by FCN2 gene is a soluble serum protein and an innate immune recognition element of the complement system. FCN2 gene polymorphisms reveal distinct geographical patterns and are documented to alter serum ficolin levels and modulate disease susceptibility. Methods We employed a real-time PCR based on Fluorescence Resonance Energy Transfer (FRET method to genotype four functional SNPs including -986 G > A (#rs3124952, -602 G > A (#rs3124953, -4A > G (#rs17514136 and +6424 G > T (#rs7851696 in the ficolin-2 (FCN2 gene. We characterized the FCN2 variants in individuals representing Brazilian (n = 176, Nigerian (n = 180, Vietnamese (n = 172 and European Caucasian ethnicity (n = 165. Results We observed that the genotype distribution of three functional SNP variants (−986 G > A, -602 G > A and -4A > G differ significantly between the populations investigated (p p  Conclusions The observed distribution of the FCN2 functional SNP variants may likely contribute to altered serum ficolin levels and this may depend on the different disease settings in world populations. To conclude, the use of FRET based real-time PCR especially for FCN2 gene will benefit a larger scientific community who extensively depend on rapid, reliable method for FCN2 genotyping.

  16. Proteomic Analysis of Lysine Acetylation Sites in Rat Tissues Reveals Organ Specificity and Subcellular Patterns

    Directory of Open Access Journals (Sweden)

    Alicia Lundby

    2012-08-01

    Full Text Available Lysine acetylation is a major posttranslational modification involved in a broad array of physiological functions. Here, we provide an organ-wide map of lysine acetylation sites from 16 rat tissues analyzed by high-resolution tandem mass spectrometry. We quantify 15,474 modification sites on 4,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals that the subcellular acetylation distribution is tissue-type dependent and that acetylation targets tissue-specific pathways involved in fundamental physiological processes. We compare lysine acetylation patterns for rat as well as human skeletal muscle biopsies and demonstrate its general involvement in muscle contraction. Furthermore, we illustrate that acetylation of fructose-bisphosphate aldolase and glycerol-3-phosphate dehydrogenase serves as a cellular mechanism to switch off enzymatic activity.

  17. Transcriptomics Reveal Several Gene Expression Patterns in the Piezophile Desulfovibrio hydrothermalis in Response to Hydrostatic Pressure

    Science.gov (United States)

    Amrani, Amira; Bergon, Aurélie; Holota, Hélène; Tamburini, Christian; Garel, Marc; Ollivier, Bernard; Imbert, Jean; Dolla, Alain; Pradel, Nathalie

    2014-01-01

    RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HPt) that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria. PMID:25215865

  18. How They Move Reveals What Is Happening: Understanding the Dynamics of Big Events from Human Mobility Pattern

    Directory of Open Access Journals (Sweden)

    Jean Damascène Mazimpaka

    2017-01-01

    Full Text Available The context in which a moving object moves contributes to the movement pattern observed. Likewise, the movement pattern reflects the properties of the movement context. In particular, big events influence human mobility depending on the dynamics of the events. However, this influence has not been explored to understand big events. In this paper, we propose a methodology for learning about big events from human mobility pattern. The methodology involves extracting and analysing the stopping, approaching, and moving-away interactions between public transportation vehicles and the geographic context. The analysis is carried out at two different temporal granularity levels to discover global and local patterns. The results of evaluating this methodology on bus trajectories demonstrate that it can discover occurrences of big events from mobility patterns, roughly estimate the event start and end time, and reveal the temporal patterns of arrival and departure of event attendees. This knowledge can be usefully applied in transportation and event planning and management.

  19. Simulating carbon dioxide exchange rates of deciduous tree species: evidence for a general pattern in biochemical changes and water stress response.

    Science.gov (United States)

    Reynolds, Robert F; Bauerle, William L; Wang, Ying

    2009-09-01

    Deciduous trees have a seasonal carbon dioxide exchange pattern that is attributed to changes in leaf biochemical properties. However, it is not known if the pattern in leaf biochemical properties - maximum Rubisco carboxylation (V(cmax)) and electron transport (J(max)) - differ between species. This study explored whether a general pattern of changes in V(cmax), J(max), and a standardized soil moisture response accounted for carbon dioxide exchange of deciduous trees throughout the growing season. The model MAESTRA was used to examine V(cmax) and J(max) of leaves of five deciduous trees, Acer rubrum 'Summer Red', Betula nigra, Quercus nuttallii, Quercus phellos and Paulownia elongata, and their response to soil moisture. MAESTRA was parameterized using data from in situ measurements on organs. Linking the changes in biochemical properties of leaves to the whole tree, MAESTRA integrated the general pattern in V(cmax) and J(max) from gas exchange parameters of leaves with a standardized soil moisture response to describe carbon dioxide exchange throughout the growing season. The model estimates were tested against measurements made on the five species under both irrigated and water-stressed conditions. Measurements and modelling demonstrate that the seasonal pattern of biochemical activity in leaves and soil moisture response can be parameterized with straightforward general relationships. Over the course of the season, differences in carbon exchange between measured and modelled values were within 6-12 % under well-watered conditions and 2-25 % under water stress conditions. Hence, a generalized seasonal pattern in the leaf-level physiological change of V(cmax) and J(max), and a standardized response to soil moisture was sufficient to parameterize carbon dioxide exchange for large-scale evaluations. Simplification in parameterization of the seasonal pattern of leaf biochemical activity and soil moisture response of deciduous forest species is demonstrated. This

  20. Contrasting patterns of evolutionary constraint and novelty revealed by comparative sperm proteomic analysis in Lepidoptera.

    Science.gov (United States)

    Whittington, Emma; Forsythe, Desiree; Borziak, Kirill; Karr, Timothy L; Walters, James R; Dorus, Steve

    2017-12-02

    Rapid evolution is a hallmark of reproductive genetic systems and arises through the combined processes of sequence divergence, gene gain and loss, and changes in gene and protein expression. While studies aiming to disentangle the molecular ramifications of these processes are progressing, we still know little about the genetic basis of evolutionary transitions in reproductive systems. Here we conduct the first comparative analysis of sperm proteomes in Lepidoptera, a group that exhibits dichotomous spermatogenesis, in which males produce a functional fertilization-competent sperm (eupyrene) and an incompetent sperm morph lacking nuclear DNA (apyrene). Through the integrated application of evolutionary proteomics and genomics, we characterize the genomic patterns potentially associated with the origination and evolution of this unique spermatogenic process and assess the importance of genetic novelty in Lepidopteran sperm biology. Comparison of the newly characterized Monarch butterfly (Danaus plexippus) sperm proteome to those of the Carolina sphinx moth (Manduca sexta) and the fruit fly (Drosophila melanogaster) demonstrated conservation at the level of protein abundance and post-translational modification within Lepidoptera. In contrast, comparative genomic analyses across insects reveals significant divergence at two levels that differentiate the genetic architecture of sperm in Lepidoptera from other insects. First, a significant reduction in orthology among Monarch sperm genes relative to the remainder of the genome in non-Lepidopteran insect species was observed. Second, a substantial number of sperm proteins were found to be specific to Lepidoptera, in that they lack detectable homology to the genomes of more distantly related insects. Lastly, the functional importance of Lepidoptera specific sperm proteins is broadly supported by their increased abundance relative to proteins conserved across insects. Our results identify a burst of genetic novelty

  1. A global analysis of bird plumage patterns reveals no association between habitat and camouflage

    Directory of Open Access Journals (Sweden)

    Marius Somveille

    2016-11-01

    Full Text Available Evidence suggests that animal patterns (motifs function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types—mottled (irregular, scales, bars and spots (regular—and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species’ geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world’s birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world’s eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

  2. A global analysis of bird plumage patterns reveals no association between habitat and camouflage.

    Science.gov (United States)

    Somveille, Marius; Marshall, Kate L A; Gluckman, Thanh-Lan

    2016-01-01

    Evidence suggests that animal patterns (motifs) function in camouflage. Irregular mottled patterns can facilitate concealment when stationary in cluttered habitats, whereas regular patterns typically prevent capture during movement in open habitats. Bird plumage patterns have predominantly converged on just four types-mottled (irregular), scales, bars and spots (regular)-and habitat could be driving convergent evolution in avian patterning. Based on sensory ecology, we therefore predict that irregular patterns would be associated with visually noisy closed habitats and that regular patterns would be associated with open habitats. Regular patterns have also been shown to function in communication for sexually competing males to stand-out and attract females, so we predict that male breeding plumage patterns evolved in both open and closed habitats. Here, taking phylogenetic relatedness into account, we investigate ecological selection for bird plumage patterns across the class Aves. We surveyed plumage patterns in 80% of all avian species worldwide. Of these, 2,756 bird species have regular and irregular plumage patterns as well as habitat information. In this subset, we tested whether adult breeding/non-breeding plumages in each sex, and juvenile plumages, were associated with the habitat types found within the species' geographical distributions. We found no evidence for an association between habitat and plumage patterns across the world's birds and little phylogenetic signal. We also found that species with regular and irregular plumage patterns were distributed randomly across the world's eco-regions without being affected by habitat type. These results indicate that at the global spatial and taxonomic scale, habitat does not predict convergent evolution in bird plumage patterns, contrary to the camouflage hypothesis.

  3. Extracting gene expression patterns and identifying co-expressed genes from microarray data reveals biologically responsive processes

    Directory of Open Access Journals (Sweden)

    Paules Richard S

    2007-11-01

    Full Text Available Abstract Background A common observation in the analysis of gene expression data is that many genes display similarity in their expression patterns and therefore appear to be co-regulated. However, the variation associated with microarray data and the complexity of the experimental designs make the acquisition of co-expressed genes a challenge. We developed a novel method for Extracting microarray gene expression Patterns and Identifying co-expressed Genes, designated as EPIG. The approach utilizes the underlying structure of gene expression data to extract patterns and identify co-expressed genes that are responsive to experimental conditions. Results Through evaluation of the correlations among profiles, the magnitude of variation in gene expression profiles, and profile signal-to-noise ratio's, EPIG extracts a set of patterns representing co-expressed genes. The method is shown to work well with a simulated data set and microarray data obtained from time-series studies of dauer recovery and L1 starvation in C. elegans and after ultraviolet (UV or ionizing radiation (IR-induced DNA damage in diploid human fibroblasts. With the simulated data set, EPIG extracted the appropriate number of patterns which were more stable and homogeneous than the set of patterns that were determined using the CLICK or CAST clustering algorithms. However, CLICK performed better than EPIG and CAST with respect to the average correlation between clusters/patterns of the simulated data. With real biological data, EPIG extracted more dauer-specific patterns than CLICK. Furthermore, analysis of the IR/UV data revealed 18 unique patterns and 2661 genes out of approximately 17,000 that were identified as significantly expressed and categorized to the patterns by EPIG. The time-dependent patterns displayed similar and dissimilar responses between IR and UV treatments. Gene Ontology analysis applied to each pattern-related subset of co-expressed genes revealed underlying

  4. Nanoparticle Photoresists: Ligand Exchange as a New, Sensitive EUV Patterning Mechanism

    KAUST Repository

    Kryask, Marie; Trikeriotis, Markos; Ouyang, Christine; Chakrabarty, Sovik; Giannelis, Emmanuel P.; Ober, Christopher K.

    2013-01-01

    compared to other standard photoresists. The current study aims at investigating and establishing the underlying mechanism for dual tone patterning of these nanoparticle photoresist systems. Infrared spectroscopy and UV absorbance studies supported by mass

  5. Nanoparticle Photoresists: Ligand Exchange as a New, Sensitive EUV Patterning Mechanism

    KAUST Repository

    Kryask, Marie

    2013-01-01

    Hybrid nanoparticle photoresists and their patterning using DUV, EUV, 193 nm lithography and e-beam lithography has been investigated and reported earlier. The nanoparticles have demonstrated very high EUV sensitivity and significant etch resistance compared to other standard photoresists. The current study aims at investigating and establishing the underlying mechanism for dual tone patterning of these nanoparticle photoresist systems. Infrared spectroscopy and UV absorbance studies supported by mass loss and dissolution studies support the current model. © 2013SPST.

  6. Hydrogen-Deuterium Exchange Mass Spectrometry Reveals Calcium Binding Properties and Allosteric Regulation of Downstream Regulatory Element Antagonist Modulator (DREAM).

    Science.gov (United States)

    Zhang, Jun; Li, Jing; Craig, Theodore A; Kumar, Rajiv; Gross, Michael L

    2017-07-18

    Downstream regulatory element antagonist modulator (DREAM) is an EF-hand Ca 2+ -binding protein that also binds to a specific DNA sequence, downstream regulatory elements (DRE), and thereby regulates transcription in a calcium-dependent fashion. DREAM binds to DRE in the absence of Ca 2+ but detaches from DRE under Ca 2+ stimulation, allowing gene expression. The Ca 2+ binding properties of DREAM and the consequences of the binding on protein structure are key to understanding the function of DREAM. Here we describe the application of hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis to investigate the Ca 2+ binding properties and the subsequent conformational changes of full-length DREAM. We demonstrate that all EF-hands undergo large conformation changes upon calcium binding even though the EF-1 hand is not capable of binding to Ca 2+ . Moreover, EF-2 is a lower-affinity site compared to EF-3 and -4 hands. Comparison of HDX profiles between wild-type DREAM and two EF-1 mutated constructs illustrates that the conformational changes in the EF-1 hand are induced by long-range structural interactions. HDX analyses also reveal a conformational change in an N-terminal leucine-charged residue-rich domain (LCD) remote from Ca 2+ -binding EF-hands. This LCD domain is responsible for the direct interaction between DREAM and cAMP response element-binding protein (CREB) and regulates the recruitment of the co-activator, CREB-binding protein. These long-range interactions strongly suggest how conformational changes transmit the Ca 2+ signal to CREB-mediated gene transcription.

  7. Rapid fabrication of microfluidic polymer electrolyte membrane fuel cell in PDMS by surface patterning of perfluorinated ion-exchange resin

    Energy Technology Data Exchange (ETDEWEB)

    Song, Yong-Ak; Han, Jongyoon [Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139 (United States); Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139 (United States); Batista, Candy [Roxbury Community College, 1234 Columbus Ave., Roxbury Crossing, MA 02120 (United States); Sarpeshkar, Rahul [Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA 02139 (United States)

    2008-09-01

    In this paper we demonstrate a simple and rapid fabrication method for a microfluidic polymer electrolyte membrane (PEM) fuel cell using polydimethylsiloxane (PDMS), which has become the de facto standard material in BioMEMS. Instead of integrating a Nafion sheet film between two layers of a PDMS device in a traditional ''sandwich format,'' we pattern a perfluorinated ion-exchange resin such as a Nafion resin on a glass substrate using a reversibly bonded PDMS microchannel to generate an ion-selective membrane between the fuel-cell electrodes. After this patterning step, the assembly of the microfluidic fuel cell is accomplished by simple oxygen plasma bonding between the PDMS chip and the glass substrate. In an example implementation, the planar PEM microfluidic fuel cell generates an open circuit voltage of 600-800 mV and delivers a maximum current output of nearly 4 {mu}A. To enhance the power output of the fuel cell we utilize self-assembled colloidal arrays as a support matrix for the Nafion resin. Such arrays allow us to increase the thickness of the ion-selective membrane to 20 {mu}m and increase the current output by 166%. Our novel fabrication method enables rapid prototyping of microfluidic fuel cells to study various ion-exchange resins for the polymer electrolyte membrane. Our work will facilitate the development of miniature, implantable, on-chip power sources for biomedical applications. (author)

  8. Patterns of exchange of forensic DNA data in the European Union through the Prüm system.

    Science.gov (United States)

    Santos, Filipe; Machado, Helena

    2017-07-01

    This paper presents a study of the 5-year operation (2011-2015) of the transnational exchange of forensic DNA data between Member States of the European Union (EU) for the purpose of combating cross-border crime and terrorism within the so-called Prüm system. This first systematisation of the full official statistical dataset provides an overall assessment of the match figures and patterns of operation of the Prüm system for DNA exchange. These figures and patterns are analysed in terms of the differentiated contributions by participating EU Member States. The data suggest a trend for West and Central European countries to concentrate the majority of Prüm matches, while DNA databases of Eastern European countries tend to contribute with profiles of people that match stains in other countries. In view of the necessary transparency and accountability of the Prüm system, more extensive and informative statistics would be an important contribution to the assessment of its functioning and societal benefits. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

  9. Exchange pattern of gaseous elemental mercury in an active urban landfill facility.

    Science.gov (United States)

    Nguyen, Hang Thi; Kim, Ki-Hyun; Kim, Min-Young; Shon, Zang-Ho

    2008-01-01

    The environmental behavior of gaseous elemental mercury (Hg) in the ambient air was investigated from the center of a municipal landfill site (area approximately 0.6km(2)) located in Dae Gu, Korea in the winter of 2004. In order to provide insight on the Hg exchange processes in strong source areas, we continuously analyzed Hg concentration gradients developed across two heights between 1m and 5m over soil surfaces at hourly intervals. The results displayed Hg concentrations in the lower and upper levels in the range of 1.46-13.1ngm(-3) (3.33+/-1.29ngm(-3): N=139) and 1.20-13.7ngm(-3) (3.27+/-1.23ngm(-3): N=139), respectively. The results of our analysis, when divided separately into emission and dry deposition, showed that emission of Hg was fairly dominant in frequency (up to 58%) over dry deposition. By multiplying our Hg gradient data with the K-values predicted indirectly from the results of previous studies, the emission and deposition fluxes of Hg were estimated as 39.0+/-43.3ngm(-2)h(-1) (N=80) and -60.0+/-80.2ngm(-2)h(-1) (N=59), respectively. Although the magnitudes of exchange were moderately lower than previously investigated anthropogenic sources, the overall results of this study suggest that an active landfill site can act as an important source of Hg in an urban environment along with other man-made activities.

  10. Biological invasion hotspots: a trait-based perspective reveals new sub-continental patterns

    Science.gov (United States)

    Basil V. Iannone III; Kevin M. Potter; Qinfeng Guo; Andrew M. Liebhold; Bryan C. Pijanowski; Christopher M. Oswalt; Songlin Fei

    2015-01-01

    Invader traits (including plant growth form) may play an important, and perhaps overlooked, role in determining macroscale patterns of biological invasions and therefore warrant greater consideration in future investigations aimed at understanding these patterns. To assess this need, we used empirical data from a national-level survey of forest in the contiguous 48...

  11. Clustering Patterns of Engagement in Massive Open Online Courses (MOOCs): The Use of Learning Analytics to Reveal Student Categories

    Science.gov (United States)

    Khalil, Mohammad; Ebner, Martin

    2017-01-01

    Massive Open Online Courses (MOOCs) are remote courses that excel in their students' heterogeneity and quantity. Due to the peculiarity of being massiveness, the large datasets generated by MOOC platforms require advanced tools and techniques to reveal hidden patterns for purposes of enhancing learning and educational behaviors. This publication…

  12. Big data analyses reveal patterns and drivers of the movements of southern elephant seals

    KAUST Repository

    Rodrí guez, J. P.; Ferná ndez-Gracia, Juan; Thums, Michele; Hindell, Mark A.; Sequeira, Ana M. M.; Meekan, Mark G.; Costa, Daniel P.; Guinet, Christophe; Harcourt, R.; McMahon, Clive R.; Muelbert, Monica; Duarte, Carlos M.; Eguí luz, V. M.

    2017-01-01

    The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

  13. Big data analyses reveal patterns and drivers of the movements of southern elephant seals

    KAUST Repository

    Rodríguez, Jorge P.

    2017-03-02

    The growing number of large databases of animal tracking provides an opportunity for analyses of movement patterns at the scales of populations and even species. We used analytical approaches, developed to cope with

  14. An ancestral stomatal patterning module revealed in the non-vascular land plant Physcomitrella patens

    Science.gov (United States)

    Chater, Caspar C.; Kamisugi, Yasuko

    2016-01-01

    The patterning of stomata plays a vital role in plant development and has emerged as a paradigm for the role of peptide signals in the spatial control of cellular differentiation. Research in Arabidopsis has identified a series of epidermal patterning factors (EPFs), which interact with an array of membrane-localised receptors and associated proteins (encoded by ERECTA and TMM genes) to control stomatal density and distribution. However, although it is well-established that stomata arose very early in the evolution of land plants, until now it has been unclear whether the established angiosperm stomatal patterning system represented by the EPF/TMM/ERECTA module reflects a conserved, universal mechanism in the plant kingdom. Here, we use molecular genetics to show that the moss Physcomitrella patens has conserved homologues of angiosperm EPF, TMM and at least one ERECTA gene that function together to permit the correct patterning of stomata and that, moreover, elements of the module retain function when transferred to Arabidopsis. Our data characterise the stomatal patterning system in an evolutionarily distinct branch of plants and support the hypothesis that the EPF/TMM/ERECTA module represents an ancient patterning system. PMID:27407102

  15. Conformations of cationized linear oligosaccharides revealed by FTMS combined with in-ESI H/D exchange.

    Science.gov (United States)

    Kostyukevich, Yury; Kononikhin, Alexey; Popov, Igor; Nikolaev, Eugene

    2015-10-01

    Previously (Kostyukevich et al. Anal Chem 2014, 86, 2595), we have reported that oligosaccharides anions are produced in the electrospray in two different conformations, which differ by the rate of gas phase hydrogen/deuterium (H/D) exchange reaction. In the present paper, we apply the in-electrospray ionization (ESI) source H/D exchange approach for the investigation of the oligosaccharides cations formed by attaching of metal ions (Na, K) to the molecule. It was observed that the formation of different conformers can be manipulated by varying the temperature of the desolvating capillary of the ESI interphase. Separation of the conformers was performed using gas phase H/D approach. Because the conformers have different rates of the H/D exchange reaction, the deuterium distribution spectrum becomes bimodal. It was found that the conformation corresponding to the slow H/D exchange rate dominates in the spectrum when the capillary temperature is low (~200 °C), and the conformation corresponding to the fast H/D exchange rate dominates at high (~400 °C) temperatures. In the intermediate temperature region, two conformers are present simultaneously. It was also observed that large oligosaccharide requires higher temperature for the formation of another conformer. It was found that the presence of the conformers considerably depends on the solvent used for ESI and the pH. We have compared these results with the previously performed in-ESI source H/D exchange experiments with peptides and proteins. Copyright © 2015 John Wiley & Sons, Ltd.

  16. Interaction patterns of nurturant support exchanged in online health social networking.

    Science.gov (United States)

    Chuang, Katherine Y; Yang, Christopher C

    2012-05-03

    Expressing emotion in online support communities is an important aspect of enabling e-patients to connect with each other and expand their social resources. Indirectly it increases the amount of support for coping with health issues. Exploring the supportive interaction patterns in online health social networking would help us better understand how technology features impacts user behavior in this context. To build on previous research that identified different types of social support in online support communities by delving into patterns of supportive behavior across multiple computer-mediated communication formats. Each format combines different architectural elements, affecting the resulting social spaces. Our research question compared communication across different formats of text-based computer-mediated communication provided on the MedHelp.org health social networking environment. We identified messages with nurturant support (emotional, esteem, and network) across three different computer-mediated communication formats (forums, journals, and notes) of an online support community for alcoholism using content analysis. Our sample consisted of 493 forum messages, 423 journal messages, and 1180 notes. Nurturant support types occurred frequently among messages offering support (forum comments: 276/412 messages, 67.0%; journal posts: 65/88 messages, 74%; journal comments: 275/335 messages, 82.1%; and notes: 1002/1180 messages, 84.92%), but less often among messages requesting support. Of all the nurturing supports, emotional (ie, encouragement) appeared most frequently, with network and esteem support appearing in patterns of varying combinations. Members of the Alcoholism Community appeared to adapt some traditional face-to-face forms of support to their needs in becoming sober, such as provision of encouragement, understanding, and empathy to one another. The computer-mediated communication format may have the greatest influence on the supportive interactions

  17. Correlations between human mobility and social interaction reveal general activity patterns.

    Science.gov (United States)

    Mollgaard, Anders; Lehmann, Sune; Mathiesen, Joachim

    2017-01-01

    A day in the life of a person involves a broad range of activities which are common across many people. Going beyond diurnal cycles, a central question is: to what extent do individuals act according to patterns shared across an entire population? Here we investigate the interplay between different activity types, namely communication, motion, and physical proximity by analyzing data collected from smartphones distributed among 638 individuals. We explore two central questions: Which underlying principles govern the formation of the activity patterns? Are the patterns specific to each individual or shared across the entire population? We find that statistics of the entire population allows us to successfully predict 71% of the activity and 85% of the inactivity involved in communication, mobility, and physical proximity. Surprisingly, individual level statistics only result in marginally better predictions, indicating that a majority of activity patterns are shared across our sample population. Finally, we predict short-term activity patterns using a generalized linear model, which suggests that a simple linear description might be sufficient to explain a wide range of actions, whether they be of social or of physical character.

  18. Correlations between human mobility and social interaction reveal general activity patterns

    DEFF Research Database (Denmark)

    Mollgaard, Anders; Jørgensen, Sune Lehmann; Mathiesen, Joachim

    2017-01-01

    activity types, namely communication, motion, and physical proximity by analyzing data collected from smartphones distributed among 638 individuals. We explore two central questions: Which underlying principles govern the formation of the activity patterns? Are the patterns specific to each individual...... or shared across the entire population? We find that statistics of the entire population allows us to successfully predict 71% of the activity and 85% of the inactivity involved in communication, mobility, and physical proximity. Surprisingly, individual level statistics only result in marginally better...... they be of social or of physical character....

  19. What Do Citation Patterns Reveal about the Outdoor Education Field? A Snapshot 2000-2013

    Science.gov (United States)

    Brookes, Andrew; Stewart, Alistair

    2016-01-01

    This study considered what insights into outdoor education (OE) research and scholarship could be gleaned from citation indices and patterns. Citation indices have long been used as ranking tools in the physical sciences, and more recently have been used in humanities and social sciences. High citation measures indicate high research impact,…

  20. Correlations between human mobility and social interaction reveal general activity patterns

    DEFF Research Database (Denmark)

    Mollgaard, Anders; Jørgensen, Sune Lehmann; Mathiesen, Joachim

    2017-01-01

    A day in the life of a person involves a broad range of activities which are common across many people. Going beyond diurnal cycles, a central question is: to what extent do individuals act according to patterns shared across an entire population? Here we investigate the interplay between differe...... they be of social or of physical character....

  1. Genome sequence of the pattern forming Paenibacillus vortex bacterium reveals potential for thriving in complex environments

    NARCIS (Netherlands)

    Sirota-Madi, A.; Olender, T.; Helman, Y.; Ingham, C.; Brainis, I.; Roth, D.; Hagi, E.; Brodsky, L.; Leshkowitz, D.; Galatenko, V.; Nikolaev, V.; Mugasimangalam, R.C.; Bransburg-Zabary, S.; Gutnick, D.L.; Lancet, D.; Ben-Jacob, E.

    2010-01-01

    Background: The pattern-forming bacterium Paenibacillus vortex is notable for its advanced social behavior, which is reflected in development of colonies with highly intricate architectures. Prior to this study, only two other Paenibacillus species (Paenibacillus sp. JDR-2 and Paenibacillus larvae)

  2. Activity patterns of free-ranging koalas (Phascolarctos cinereus revealed by accelerometry.

    Directory of Open Access Journals (Sweden)

    Michelle A Ryan

    Full Text Available An understanding of koala activity patterns is important for measuring the behavioral response of this species to environmental change, but to date has been limited by the logistical challenges of traditional field methodologies. We addressed this knowledge gap by using tri-axial accelerometer data loggers attached to VHF radio collars to examine activity patterns of adult male and female koalas in a high-density population at Cape Otway, Victoria, Australia. Data were obtained from 27 adult koalas over two 7-d periods during the breeding season: 12 in the early-breeding season in November 2010, and 15 in the late-breeding season in January 2011. Multiple 15 minute observation blocks on each animal were used for validation of activity patterns determined from the accelerometer data loggers. Accelerometry was effective in distinguishing between inactive (sleeping, resting and active (grooming, feeding and moving behaviors. Koalas were more active during the early-breeding season with a higher index of movement (overall dynamic body acceleration [ODBA] for both males and females. Koalas showed a distinct temporal pattern of behavior, with most activity occurring from mid-afternoon to early morning. Accelerometry has potential for examining fine-scale behavior of a wide range of arboreal and terrestrial species.

  3. Activity patterns of free-ranging koalas (Phascolarctos cinereus) revealed by accelerometry.

    Science.gov (United States)

    Ryan, Michelle A; Whisson, Desley A; Holland, Greg J; Arnould, John P Y

    2013-01-01

    An understanding of koala activity patterns is important for measuring the behavioral response of this species to environmental change, but to date has been limited by the logistical challenges of traditional field methodologies. We addressed this knowledge gap by using tri-axial accelerometer data loggers attached to VHF radio collars to examine activity patterns of adult male and female koalas in a high-density population at Cape Otway, Victoria, Australia. Data were obtained from 27 adult koalas over two 7-d periods during the breeding season: 12 in the early-breeding season in November 2010, and 15 in the late-breeding season in January 2011. Multiple 15 minute observation blocks on each animal were used for validation of activity patterns determined from the accelerometer data loggers. Accelerometry was effective in distinguishing between inactive (sleeping, resting) and active (grooming, feeding and moving) behaviors. Koalas were more active during the early-breeding season with a higher index of movement (overall dynamic body acceleration [ODBA]) for both males and females. Koalas showed a distinct temporal pattern of behavior, with most activity occurring from mid-afternoon to early morning. Accelerometry has potential for examining fine-scale behavior of a wide range of arboreal and terrestrial species.

  4. Growth patterns of an intertidal gastropod as revealed by oxygen isotope analysis

    Science.gov (United States)

    Bean, J. R.; Hill, T. M.; Guerra, C.

    2007-12-01

    The size and morphology of mollusk shells are affected by environmental conditions. As a result, it is difficult to assess growth rate, population age structure, shell morphologies associated with ontogenetic stages, and to compare life history patterns across various environments. Oxygen isotope analysis is a useful tool for estimating minimum ages and growth rates of calcium carbonate secreting organisms. Calcite shell material from members of two northern California populations of the intertidal muricid gastropod Acanthinucella spirata was sampled for isotopic analysis. Individual shells were sampled from apex to margin, thus providing a sequential record of juvenile and adult growth. A. spirata were collected from a sheltered habitat in Tomales Bay and from an exposed reef in Bolinas. Abiotic factors, such as temperature, wave exposure, and substrate consistency, and biotic composition differ significantly between these sites, possibly resulting in local adaptations and variation in life history and growth patterns. Shell morphology of A. spirata changes with age as internal shell margin thickenings of denticle rows associated with external growth bands are irregularly accreted. It is not known when, either seasonally and/or ontogentically, these thickenings and bands form or whether inter or intra-populational variation exists. Preliminary results demonstrate the seasonal oxygen isotopic variability present at the two coastal sites, indicating 5-6 degC changes from winter to summertime temperatures; these data are consistent with local intertidal temperature records. Analysis of the seasonal patterns indicate that: 1) differences in growth rate and seasonal growth patterns at different ontogenetic stages within populations, and 2) differences in growth patterns and possibly age structure between the two A. spirata populations. These findings indicate that isotopic analyses, in addition to field observations and morphological measurements, are necessary to

  5. Chronic malaria revealed by a new fluorescence pattern on the antinuclear autoantibodies test.

    Directory of Open Access Journals (Sweden)

    Benjamin Hommel

    Full Text Available BACKGROUND: Several clinical forms of malaria such as chronic carriage, gestational malaria or hyper-reactive malarial splenomegaly may follow a cryptic evolution with afebrile chronic fatigue sometimes accompanied by anemia and/or splenomegaly. Conventional parasitological tests are often negative or not performed, and severe complications may occur. Extensive explorations of these conditions often include the search for antinuclear autoantibodies (ANA. METHODS: We analysed fluorescence patterns in the ANA test in patients with either chronic cryptic or acute symptomatic malaria, then conducted a one-year prospective study at a single hospital on all available sera drawn for ANA detections. We then identified autoantibodies differentially expressed in malaria patients and in controls using human protein microarray. RESULTS: We uncovered and defined a new, malaria-related, nucleo-cytoplasmic ANA pattern displaying the specific association of a nuclear speckled pattern with diffuse cytoplasmic perinuclearly-enhanced fluorescence. In the one-year prospective analysis, 79% of sera displaying this new nucleo-cytoplasmic fluorescence were from patients with malaria. This specific pattern, not seen in other parasitic diseases, allowed a timely reorientation of the diagnosis toward malaria. To assess if the autoantibody immune response was due to autoreactivity or molecular mimicry we isolated 42 autoantigens, targets of malarial autoantibodies. BLAST analysis indicated that 23 of recognized autoantigens were homologous to plasmodial proteins suggesting autoimmune responses directly driven by the plasmodial infection. CONCLUSION: In patients with malaria in whom parasitological tests have not been performed recognition of this new, malaria-related fluorescence pattern on the ANA test is highly suggestive of the diagnosis and triggers immediate, easy confirmation and adapted therapy.

  6. Visual guidance of forward flight in hummingbirds reveals control based on image features instead of pattern velocity.

    Science.gov (United States)

    Dakin, Roslyn; Fellows, Tyee K; Altshuler, Douglas L

    2016-08-02

    Information about self-motion and obstacles in the environment is encoded by optic flow, the movement of images on the eye. Decades of research have revealed that flying insects control speed, altitude, and trajectory by a simple strategy of maintaining or balancing the translational velocity of images on the eyes, known as pattern velocity. It has been proposed that birds may use a similar algorithm but this hypothesis has not been tested directly. We examined the influence of pattern velocity on avian flight by manipulating the motion of patterns on the walls of a tunnel traversed by Anna's hummingbirds. Contrary to prediction, we found that lateral course control is not based on regulating nasal-to-temporal pattern velocity. Instead, birds closely monitored feature height in the vertical axis, and steered away from taller features even in the absence of nasal-to-temporal pattern velocity cues. For vertical course control, we observed that birds adjusted their flight altitude in response to upward motion of the horizontal plane, which simulates vertical descent. Collectively, our results suggest that birds avoid collisions using visual cues in the vertical axis. Specifically, we propose that birds monitor the vertical extent of features in the lateral visual field to assess distances to the side, and vertical pattern velocity to avoid collisions with the ground. These distinct strategies may derive from greater need to avoid collisions in birds, compared with small insects.

  7. Evapotranspiration patterns in complex upland forests reveal contrasting topographic thresholds of non-linearity

    Science.gov (United States)

    Metzen, D.; Sheridan, G. J.; Benyon, R. G.; Bolstad, P. V.; Nyman, P.; Lane, P. N. J.

    2017-12-01

    Large areas of forest are often treated as being homogeneous just because they fall in a single climate category. However, we observe strong vegetation patterns in relation to topography in SE Australian forests and thus hypothesise that ET will vary spatially as well. Spatial heterogeneity evolves over different temporal scales in response to climatic forcing with increasing time lag from soil moisture (sub-yearly), to vegetation (10s -100s of years) to soil properties and topography (>100s of years). Most importantly, these processes and time scales are not independent, creating feedbacks that result in "co-evolved stable states" which yield the current spatial terrain, vegetation and ET patterns. We used up-scaled sap flux and understory ET measurements from water-balance plots, as well as LiDAR derived terrain and vegetation information, to infer links between spatio-temporal energy and water fluxes, topography and vegetation patterns at small catchment scale. Topography caused variations in aridity index between polar and equatorial-facing slopes (1.3 vs 1.8), which in turn manifested in significant differences in sapwood area index (6.9 vs 5.8), overstory LAI (3.0 vs 2.3), understory LAI (0.5 vs 0.4), sub-canopy radiation load (4.6 vs 6.8 MJ m-2 d-1), overstory transpiration (501 vs 347 mm a-1) and understory ET (79 vs 155 mm a-1). Large spatial variation in overstory transpiration (195 to 891 mm a-1) was observed over very short distances (100s m); a range representative of diverse forests such as arid open woodlands and wet mountain ash forests. Contrasting, non-linear overstory and understory ET patterns were unveiled between aspects, and topographic thresholds were lower for overstory than understory ET. While ET partitioning remained stable on polar-facing slopes regardless of slope position, overstory contribution gradually decreased with increasing slope inclination on equatorial aspects. Further, we show that ET patterns and controls underlie strong

  8. Generalised power graph compression reveals dominant relationship patterns in complex networks.

    Science.gov (United States)

    Ahnert, Sebastian E

    2014-03-25

    We introduce a framework for the discovery of dominant relationship patterns in complex networks, by compressing the networks into power graphs with overlapping power nodes. When paired with enrichment analysis of node classification terms, the most compressible sets of edges provide a highly informative sketch of the dominant relationship patterns that define the network. In addition, this procedure also gives rise to a novel, link-based definition of overlapping node communities in which nodes are defined by their relationships with sets of other nodes, rather than through connections within the community. We show that this completely general approach can be applied to undirected, directed, and bipartite networks, yielding valuable insights into the large-scale structure of real-world networks, including social networks and food webs. Our approach therefore provides a novel way in which network architecture can be studied, defined and classified.

  9. High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.

    Science.gov (United States)

    Anandapadamanaban, Madhanagopal; Andresen, Cecilia; Helander, Sara; Ohyama, Yoshifumi; Siponen, Marina I; Lundström, Patrik; Kokubo, Tetsuro; Ikura, Mitsuhiko; Moche, Martin; Sunnerhagen, Maria

    2013-08-01

    The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 Å) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBP's concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.

  10. Use-Wear Patterns on Wild Macaque Stone Tools Reveal Their Behavioural History

    OpenAIRE

    Haslam, Michael; Gumert, Michael D.; Biro, Dora; Carvalho, Susana; Malaivijitnond, Suchinda

    2013-01-01

    Burmese long-tailed macaques (Macaca fascicularis aurea) are one of a limited number of wild animal species to use stone tools, with their tool use focused on pounding shelled marine invertebrates foraged from intertidal habitats. These monkeys exhibit two main styles of tool use: axe hammering of oysters, and pound hammering of unattached encased foods. In this study, we examined macroscopic use-wear patterns on a sample of 60 wild macaque stone tools from Piak Nam Yai Island, Thailand, that...

  11. Cardiovascular magnetic resonance imaging (CMR) reveals characteristic pattern of myocardial damage in patients with mitochondrial myopathy.

    Science.gov (United States)

    Yilmaz, Ali; Gdynia, Hans-Jürgen; Ponfick, Matthias; Rösch, Sabine; Lindner, Alfred; Ludolph, Albert C; Sechtem, Udo

    2012-04-01

    Mitochondrial myopathy comprises various clinical subforms of neuromuscular disorders that are characterised by impaired mitochondrial energy metabolism due to dysfunction of the mitochondrial respiratory chain. No comprehensive and targeted cardiovascular magnetic resonance (CMR) studies have been performed so far in patients with mitochondrial disorders. The present study aimed at characterising cardiac disease manifestations in patients with mitochondrial myopathy and elucidating the in vivo cardiac damage pattern of patients with different subforms of mitochondrial disease by CMR studies. In a prospective study, 37 patients with mitochondrial myopathy underwent comprehensive neurological and cardiac evaluations including physical examination, resting ECG and CMR. The CMR studies comprised cine-CMR, T2-weighted "edema" imaging and T1-weighted late-gadolinium-enhancement (LGE) imaging. Various patterns and degrees of skeletal myopathy were present in the participants of this study, whereas clinical symptoms such as chest pain symptoms (in eight (22%) patients) and various degrees of dyspnea (in 16 (43%) patients) were less frequent. Pathological ECG findings were documented in eight (22%) patients. T2-weighted "edema" imaging was positive in one (3%) patient with MELAS (mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes) only. LGE imaging demonstrated the presence of non-ischemic LGE in 12 (32%) patients: 10 out of 24 (42%) patients with CPEO (chronic progressive external ophthalmoplegia) or KSS (Kearns-Sayre syndrome) and 2 of 3 (67%) patients with MELAS were LGE positive. All 10 LGE-positive patients with CPEO or KSS demonstrated a potentially typical pattern of diffuse intramural LGE in the left-ventricular (LV) inferolateral segments. Cardiac involvement is a frequent finding in patients with mitochondrial myopathy. A potentially characteristic pattern of diffuse intramural LGE in the LV inferolateral segments was identified in

  12. A reflective discussion: questions about globalization and multiculturalism in nursing as revealed during a student/staff exchange programme.

    Science.gov (United States)

    Graham, Iain; Norman, Linda

    2008-06-01

    The purpose of this paper is to present elements of a discussion on the discipline of nursing that arose from a student-faculty exchange programme, as a reflection of the experiences the students and faculty had during the 3-year exchange. It suggests that the globalization of health and the international migration of nurses might prove to be an opportunity for nurses to learn more about nursing practice. It became apparent to the participants that the phenomenon of nursing, although understood by them all, was not easy to describe, and words used in Swedish, Finnish or British or American English were often not easy to interpret or explain. These reflections were noted by the authors when the group came together to plan the programme and design experiences for the participants. We were concerned how nursing could contribute to health-care improvement globally if it wasn't universally understood within the four countries concerned.

  13. Revealing patterns of cultural transmission from frequency data: equilibrium and non-equilibrium assumptions

    Science.gov (United States)

    Crema, Enrico R.; Kandler, Anne; Shennan, Stephen

    2016-12-01

    A long tradition of cultural evolutionary studies has developed a rich repertoire of mathematical models of social learning. Early studies have laid the foundation of more recent endeavours to infer patterns of cultural transmission from observed frequencies of a variety of cultural data, from decorative motifs on potsherds to baby names and musical preferences. While this wide range of applications provides an opportunity for the development of generalisable analytical workflows, archaeological data present new questions and challenges that require further methodological and theoretical discussion. Here we examine the decorative motifs of Neolithic pottery from an archaeological assemblage in Western Germany, and argue that the widely used (and relatively undiscussed) assumption that observed frequencies are the result of a system in equilibrium conditions is unwarranted, and can lead to incorrect conclusions. We analyse our data with a simulation-based inferential framework that can overcome some of the intrinsic limitations in archaeological data, as well as handle both equilibrium conditions and instances where the mode of cultural transmission is time-variant. Results suggest that none of the models examined can produce the observed pattern under equilibrium conditions, and suggest. instead temporal shifts in the patterns of cultural transmission.

  14. Dynamics of metal-humate complexation equilibria as revealed by isotope exchange studies - a matter of concentration and time

    Science.gov (United States)

    Lippold, Holger; Eidner, Sascha; Kumke, Michael U.; Lippmann-Pipke, Johanna

    2017-01-01

    Complexation with dissolved humic matter can be crucial in controlling the mobility of toxic or radioactive contaminant metals. For speciation and transport modelling, a dynamic equilibrium process is commonly assumed, where association and dissociation run permanently. This is, however, questionable in view of reported observations of a growing resistance to dissociation over time. In this study, the isotope exchange principle was employed to gain direct insight into the dynamics of the complexation equilibrium, including kinetic inertisation phenomena. Terbium(III), an analogue of trivalent actinides, was used as a representative of higher-valent metals. Isotherms of binding to (flocculated) humic acid, determined by means of 160Tb as a radiotracer, were found to be identical regardless of whether the radioisotope was introduced together with the bulk of stable 159Tb or subsequently after pre-equilibration for up to 3 months. Consequently, there is a permanent exchange of free and humic-bound Tb since all available binding sites are occupied in the plateau region of the isotherm. The existence of a dynamic equilibrium was thus evidenced. There was no indication of an inertisation under these experimental conditions. If the small amount of 160Tb was introduced prior to saturation with 159Tb, the expected partial desorption of 160Tb occurred at much lower rates than observed for the equilibration process in the reverse procedure. In addition, the rates decreased with time of pre-equilibration. Inertisation phenomena are thus confined to the stronger sites of humic molecules (occupied at low metal concentrations). Analysing the time-dependent course of isotope exchange according to first-order kinetics indicated that up to 3 years are needed to attain equilibrium. Since, however, metal-humic interaction remains reversible, exchange of metals between humic carriers and mineral surfaces cannot be neglected on the long time scale to be considered in predictive

  15. Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns

    DEFF Research Database (Denmark)

    Lundby, Alicia; Hansen, Kasper Lage; Weinert, Brian Tate

    2012-01-01

    ,541 proteins and provide the data set as a web-based database. We demonstrate that lysine acetylation displays site-specific sequence motifs that diverge between cellular compartments, with a significant fraction of nuclear sites conforming to the consensus motifs G-AcK and AcK-P. Our data set reveals...

  16. Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses

    Science.gov (United States)

    Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from UK, South Korea, Brazil and USA revealed four novel large-scale structural variations of at least 2,000...

  17. Dynamic studies of H-Ras•GTPγS interactions with nucleotide exchange factor Sos reveal a transient ternary complex formation in solution.

    Science.gov (United States)

    Vo, Uybach; Vajpai, Navratna; Embrey, Kevin J; Golovanov, Alexander P

    2016-07-14

    The cycling between GDP- and GTP- bound forms of the Ras protein is partly regulated by the binding of Sos. The structural/dynamic behavior of the complex formed between activated Sos and Ras at the point of the functional cycle where the nucleotide exchange is completed has not been described to date. Here we show that solution NMR spectra of H-Ras∙GTPγS mixed with a functional fragment of Sos (Sos(Cat)) at a 2:1 ratio are consistent with the formation of a rather dynamic assembly. H-Ras∙GTPγS binding was in fast exchange on the NMR timescale and retained a significant degree of molecular tumbling independent of Sos(Cat), while Sos(Cat) also tumbled largely independently of H-Ras. Estimates of apparent molecular weight from both NMR data and SEC-MALS revealed that, at most, only one H-Ras∙GTPγS molecule appears stably bound to Sos. The weak transient interaction between Sos and the second H-Ras∙GTPγS may provide a necessary mechanism for complex dissociation upon the completion of the native GDP → GTP exchange reaction, but also explains measurable GTP → GTP exchange activity of Sos routinely observed in in vitro assays that use fluorescently-labelled analogs of GTP. Overall, the data presents the first dynamic snapshot of Ras functional cycle as controlled by Sos.

  18. Analysis of image versus position, scale and direction reveals pattern texture anisotropy

    Directory of Open Access Journals (Sweden)

    Roland eLehoucq

    2015-01-01

    Full Text Available Pattern heterogeneities and anisotropies often carry significant physical information. We provide a toolbox which: (i cumulates analysis in terms of position, direction and scale; (ii is as general as possible; (iii is simple and fast to understand, implement, execute and exploit.It consists in dividing the image into analysis boxes at a chosen scale; in each box an ellipse (the inertia tensor is fitted to the signal and thus determines the direction in which the signal is more present. This tensor can be averaged in position and/or be used to study the dependence with scale. This choice is formally linked with Leray transforms and anisotropic wavelet analysis. Such protocol is intutively interpreted and consistent with what the eye detects: relevant scales, local variations in space, priviledged directions. It is fast and parallelizable.Its several variants are adaptable to the user's data and needs. It is useful to statistically characterize anisotropies of 2D or 3D patterns in which individual objects are not easily distinguished, with only minimal pre-processing of the raw image, and more generally applies to data in higher dimensions.It is less sensitive to edge effects, and thus better adapted for a multiscale analysis down to small scale boxes, than pair correlation function or Fourier transform.Easy to understand and implement,it complements more sophisticated methods such as Hough transform or diffusion tensor imaging.We use it on various fracture patterns (sea ice cover, thin sections of granite, granular materials, to pinpoint the maximal anisotropy scales. The results are robust to noise and to user choices. This toolbox could turn also useful for granular materials, hard condensed matter, geophysics, thin films, statistical mechanics, characterisation of networks, fluctuating amorphous systems, inhomogeneous and disordered systems, or medical imaging, among others.

  19. Pattern Analyses Reveal Separate Experience-Based Fear Memories in the Human Right Amygdala.

    Science.gov (United States)

    Braem, Senne; De Houwer, Jan; Demanet, Jelle; Yuen, Kenneth S L; Kalisch, Raffael; Brass, Marcel

    2017-08-23

    Learning fear via the experience of contingencies between a conditioned stimulus (CS) and an aversive unconditioned stimulus (US) is often assumed to be fundamentally different from learning fear via instructions. An open question is whether fear-related brain areas respond differently to experienced CS-US contingencies than to merely instructed CS-US contingencies. Here, we contrasted two experimental conditions where subjects were instructed to expect the same CS-US contingencies while only one condition was characterized by prior experience with the CS-US contingency. Using multivoxel pattern analysis of fMRI data, we found CS-related neural activation patterns in the right amygdala (but not in other fear-related regions) that dissociated between whether a CS-US contingency had been instructed and experienced versus merely instructed. A second experiment further corroborated this finding by showing a category-independent neural response to instructed and experienced, but not merely instructed, CS presentations in the human right amygdala. Together, these findings are in line with previous studies showing that verbal fear instructions have a strong impact on both brain and behavior. However, even in the face of fear instructions, the human right amygdala still shows a separable neural pattern response to experience-based fear contingencies. SIGNIFICANCE STATEMENT In our study, we addressed a fundamental problem of the science of human fear learning and memory, namely whether fear learning via experience in humans relies on a neural pathway that can be separated from fear learning via verbal information. Using two new procedures and recent advances in the analysis of brain imaging data, we localized purely experience-based fear processing and memory in the right amygdala, thereby making a direct link between human and animal research. Copyright © 2017 the authors 0270-6474/17/378116-15$15.00/0.

  20. Phylogeny of bent-toed geckos (Cyrtodactylus) reveals a west to east pattern of diversification.

    Science.gov (United States)

    Wood, Perry L; Heinicke, Matthew P; Jackman, Todd R; Bauer, Aaron M

    2012-12-01

    The Asian/Pacific genus Cyrtodactylus is the most diverse and among the most widely distributed genera of geckos, and more species are continually being discovered. Major patterns in the evolutionary history of Cyrtodactylus have remained largely unknown because no published study has broadly sampled across the geographic range and morphological diversity of the genus. We assembled a data set including sequences from one mitochondrial and three nuclear loci for 68 Cyrtodactylus and 20 other gekkotan species to infer phylogenetic relationships within the genus and identify major biogeographic patterns. Our results indicate that Cyrtodactylus is monophyletic, but only if the Indian/Sri Lankan species sometimes recognized as Geckoella are included. Basal divergences divide Cyrtodactylus into three well-supported groups: the single species C. tibetanus, a clade of Myanmar/southern Himalayan species, and a large clade including all other Cyrtodactylus plus Geckoella. Within the largest major clade are several well-supported subclades, with separate subclades being most diverse in Thailand, Eastern Indochina, the Sunda region, the Papuan region, and the Philippines, respectively. The phylogenetic results, along with molecular clock and ancestral area analyses, show Cyrtodactylus to have originated in the circum-Himalayan region just after the Cretaceous/Paleogene boundary, with a generally west to east pattern of colonization and diversification progressing through the Cenozoic. Wallacean species are derived from within a Sundaland radiation, the Philippines were colonized from Borneo, and Australia was colonized twice, once via New Guinea and once via the Lesser Sundas. Overall, these results are consistent with past suggestions of a Palearctic origin for Cyrtodactylus, and highlight the key role of geography in diversification of the genus. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Genome-Wide Methylome Analyses Reveal Novel Epigenetic Regulation Patterns in Schizophrenia and Bipolar Disorder

    Science.gov (United States)

    Li, Yongsheng; Camarillo, Cynthia; Xu, Juan; Arana, Tania Bedard; Xiao, Yun; Zhao, Zheng; Chen, Hong; Ramirez, Mercedes; Zavala, Juan; Escamilla, Michael A.; Armas, Regina; Mendoza, Ricardo; Ontiveros, Alfonso; Nicolini, Humberto; Jerez Magaña, Alvaro Antonio; Rubin, Lewis P.; Li, Xia; Xu, Chun

    2015-01-01

    Schizophrenia (SZ) and bipolar disorder (BP) are complex genetic disorders. Their appearance is also likely informed by as yet only partially described epigenetic contributions. Using a sequencing-based method for genome-wide analysis, we quantitatively compared the blood DNA methylation landscapes in SZ and BP subjects to control, both in an understudied population, Hispanics along the US-Mexico border. Remarkably, we identified thousands of differentially methylated regions for SZ and BP preferentially located in promoters 3′-UTRs and 5′-UTRs of genes. Distinct patterns of aberrant methylation of promoter sequences were located surrounding transcription start sites. In these instances, aberrant methylation occurred in CpG islands (CGIs) as well as in flanking regions as well as in CGI sparse promoters. Pathway analysis of genes displaying these distinct aberrant promoter methylation patterns showed enhancement of epigenetic changes in numerous genes previously related to psychiatric disorders and neurodevelopment. Integration of gene expression data further suggests that in SZ aberrant promoter methylation is significantly associated with altered gene transcription. In particular, we found significant associations between (1) promoter CGIs hypermethylation with gene repression and (2) CGI 3′-shore hypomethylation with increased gene expression. Finally, we constructed a specific methylation analysis platform that facilitates viewing and comparing aberrant genome methylation in human neuropsychiatric disorders. PMID:25734057

  2. Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes

    Science.gov (United States)

    Fournier, David; Redl, Stefan; Best, Gerrit; Borsos, Máté; Tiwari, Vijay K.; Tachibana-Konwalski, Kikuë; Ketting, René F.; Parekh, Sapun H.; Cremer, Christoph; Birk, Udo J.

    2015-01-01

    During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated. PMID:26561583

  3. Migration history of air-breathing fishes reveals Neogene atmospheric circulation patterns

    Science.gov (United States)

    Böhme, M.

    2004-05-01

    The migration history of an air-breathing fish group (Channidae; snakehead fishes) is used for reconstructing Neogene Eurasian precipitation and atmospheric circulation patterns. The study shows that snakeheads are sensitive indicators of summer precipitation maxima in subtropical and temperate regions, and are present regularly if the wettest month exceeds 150 mm precipitation and 20 °C mean temperature. The analysis of 515 fossil freshwater fish deposits of the past 50 m.y. from Africa and Eurasia shows two continental-scale migration events from the snakeheads' center of origin in the south Himalayan region, events that can be related to changes in the Northern Hemisphere circulation pattern. The first migration, ca. 17.5 Ma, into western and central Eurasia may have been caused by a northward shift of the Intertropical Convergence Zone that brought western Eurasia under the influence of trade winds that produced a zonal and meridional precipitation gradient in Europe. During the second migration, between 8 and 4 Ma, into Africa and East Asia, snakeheads reached their present-day distribution. This migration could have been related to the intensification of the Asian monsoon that brought summer precipitation to their migratory pathways in East Africa Arabia and East Asia.

  4. Analysis of chlorophyll fluorescence reveals stage specific patterns of chloroplast-containing cells during Arabidopsis embryogenesis

    Directory of Open Access Journals (Sweden)

    RICARDO I TEJOS

    2010-01-01

    Full Text Available The basic body plan of a plant is established early in embryogenesis when cells differentiate, giving rise to the apical and basal regions of the embryo. Using chlorophyll fluorescence as a marker for chloroplasts, we have detected specific patterns of chloroplast-containing cells at specific stages of embryogenesis. Non-randomly distributed chloroplast-containing cells are seen as early as the globular stage of embryogenesis in Arabidopsis. In the heart stage of embryogenesis, chloroplast containing cells are detected in epidermal cells as well as a central region of the heart stage embryo, forming a triangular septum of chloroplast-containing cells that divides the embryo into three equal sectors. Torpedo stage embryos have chloroplast-containing epidermal cells and a central band of chloroplast-containing cells in the cortex layer, just below the shoot apical meristem. In the walking-stick stage of embryogenesis, chloroplasts are present in the epidermal, cortex and endodermal cells. The chloroplasts appear reduced or absent from the provascular and columella cells of walking-stick stage embryos. These results suggest that there is a tight regulation of plastid differentiation during embryogenesis that generates specific patterns of chloroplast-containing cells in specific cell layers at specific stages of embryogenesis.

  5. Patterns in stream longitudinal profiles and implications for hyporheic exchange flow at the H.J. Andrews Experimental Forest, Oregon, USA.

    Science.gov (United States)

    Justin K. Anderson; Steven M. Wondzell; Michael N. Gooseff; Roy. Haggerty

    2005-01-01

    There is a need to identify measurable characteristics of stream channel morphology that vary predictably throughout stream networks and that influence patterns of hyporheic exchange flow in mountain streams. In this paper we characterize stream longitudinal profiles according to channel unit spacing and the concavity of the water surface profile. We demonstrate that...

  6. Different patterns of auditory cortex activation revealed by functional magnetic resonance imaging

    Energy Technology Data Exchange (ETDEWEB)

    Formisano, E; Pepino, A; Bracale, M [Department of Electronic Engineering, Biomedical Unit, Universita di Napoli, Federic II, Italy, Via Claudio 21, 80125 Napoli (Italy); Di Salle, F [Department of Biomorphological and Functional Sciences, Radiologucal Unit, Universita di Napoli, Federic II, Italy, Via Claudio 21, 80125 Napoli (Italy); Lanfermann, H; Zanella, F E [Department of Neuroradiology, J.W. Goethe Universitat, Frankfurt/M. (Germany)

    1999-12-31

    In the last few years, functional Magnetic Resonance Imaging (fMRI) has been widely accepted as an effective tool for mapping brain activities in both the sensorimotor and the cognitive field. The present work aims to assess the possibility of using fMRI methods to study the cortical response to different acoustic stimuli. Furthermore, we refer to recent data collected at Frankfurt University on the cortical pattern of auditory hallucinations. Healthy subjects showed broad bilateral activation, mostly located in the transverse gyrus of Heschl. The analysis of the cortical activation induced by different stimuli has pointed out a remarkable difference in the spatial and temporal features of the auditory cortex response to pulsed tones and pure tones. The activated areas during episodes of auditory hallucinations match the location of primary auditory cortex as defined in control measurements with the same patients and in the experiments on healthy subjects. (authors) 17 refs., 4 figs.

  7. A diminutive perinate European Enantiornithes reveals an asynchronous ossification pattern in early birds.

    Science.gov (United States)

    Knoll, Fabien; Chiappe, Luis M; Sanchez, Sophie; Garwood, Russell J; Edwards, Nicholas P; Wogelius, Roy A; Sellers, William I; Manning, Phillip L; Ortega, Francisco; Serrano, Francisco J; Marugán-Lobón, Jesús; Cuesta, Elena; Escaso, Fernando; Sanz, Jose Luis

    2018-03-05

    Fossils of juvenile Mesozoic birds provide insight into the early evolution of avian development, however such fossils are rare. The analysis of the ossification sequence in these early-branching birds has the potential to address important questions about their comparative developmental biology and to help understand their morphological evolution and ecological differentiation. Here we report on an early juvenile enantiornithine specimen from the Early Cretaceous of Europe, which sheds new light on the osteogenesis in this most species-rich clade of Mesozoic birds. Consisting of a nearly complete skeleton, it is amongst the smallest known Mesozoic avian fossils representing post-hatching stages of development. Comparisons between this new specimen and other known early juvenile enantiornithines support a clade-wide asynchronous pattern of osteogenesis in the sternum and the vertebral column, and strongly indicate that the hatchlings of these phylogenetically basal birds varied greatly in size and tempo of skeletal maturation.

  8. Different patterns of auditory cortex activation revealed by functional magnetic resonance imaging

    International Nuclear Information System (INIS)

    Formisano, E.; Pepino, A.; Bracale, M.; Di Salle, F.; Lanfermann, H.; Zanella, F.E.

    1998-01-01

    In the last few years, functional Magnetic Resonance Imaging (fMRI) has been widely accepted as an effective tool for mapping brain activities in both the sensorimotor and the cognitive field. The present work aims to assess the possibility of using fMRI methods to study the cortical response to different acoustic stimuli. Furthermore, we refer to recent data collected at Frankfurt University on the cortical pattern of auditory hallucinations. Healthy subjects showed broad bilateral activation, mostly located in the transverse gyrus of Heschl. The analysis of the cortical activation induced by different stimuli has pointed out a remarkable difference in the spatial and temporal features of the auditory cortex response to pulsed tones and pure tones. The activated areas during episodes of auditory hallucinations match the location of primary auditory cortex as defined in control measurements with the same patients and in the experiments on healthy subjects. (authors)

  9. SMRT Sequencing Revealed Mitogenome Characteristics and Mitogenome-Wide DNA Modification Pattern in Ophiocordyceps sinensis.

    Science.gov (United States)

    Kang, Xincong; Hu, Liqin; Shen, Pengyuan; Li, Rui; Liu, Dongbo

    2017-01-01

    Single molecule, real-time (SMRT) sequencing was used to characterize mitochondrial (mt) genome of Ophiocordyceps sinensis and to analyze the mt genome-wide pattern of epigenetic DNA modification. The complete mt genome of O. sinensis , with a size of 157,539 bp, is the fourth largest Ascomycota mt genome sequenced to date. It contained 14 conserved protein-coding genes (PCGs), 1 intronic protein rps3 , 27 tRNAs and 2 rRNA subunits, which are common characteristics of the known mt genomes in Hypocreales. A phylogenetic tree inferred from 14 PCGs in Pezizomycotina fungi supports O. sinensis as most closely related to Hirsutella rhossiliensis in Ophiocordycipitaceae. A total of 36 sequence sites in rps3 were under positive selection, with dN/dS >1 in the 20 compared fungi. Among them, 16 sites were statistically significant. In addition, the mt genome-wide base modification pattern of O. sinensis was determined in this study, especially DNA methylation. The methylations were located in coding and uncoding regions of mt PCGs in O. sinensis , and might be closely related to the expression of PCGs or the binding affinity of transcription factor A to mtDNA. Consequently, these methylations may affect the enzymatic activity of oxidative phosphorylation and then the mt respiratory rate; or they may influence mt biogenesis. Therefore, methylations in the mitogenome of O. sinensis might be a genetic feature to adapt to the cold and low PO 2 environment at high altitude, where O. sinensis is endemic. This is the first report on epigenetic modifications in a fungal mt genome.

  10. Molecular genetic features of polyploidization and aneuploidization reveal unique patterns for genome duplication in diploid Malus.

    Directory of Open Access Journals (Sweden)

    Michael J Considine

    Full Text Available Polyploidization results in genome duplication and is an important step in evolution and speciation. The Malus genome confirmed that this genus was derived through auto-polyploidization, yet the genetic and meiotic mechanisms for polyploidization, particularly for aneuploidization, are unclear in this genus or other woody perennials. In fact the contribution of aneuploidization remains poorly understood throughout Plantae. We add to this knowledge by characterization of eupolyploidization and aneuploidization in 27,542 F₁ seedlings from seven diploid Malus populations using cytology and microsatellite markers. We provide the first evidence that aneuploidy exceeds eupolyploidy in the diploid crosses, suggesting aneuploidization is a leading cause of genome duplication. Gametes from diploid Malus had a unique combinational pattern; ova preserved euploidy exclusively, while spermatozoa presented both euploidy and aneuploidy. All non-reduced gametes were genetically heterozygous, indicating first-division restitution was the exclusive mode for Malus eupolyploidization and aneuploidization. Chromosome segregation pattern among aneuploids was non-uniform, however, certain chromosomes were associated for aneuploidization. This study is the first to provide molecular evidence for the contribution of heterozygous non-reduced gametes to fitness in polyploids and aneuploids. Aneuploidization can increase, while eupolyploidization may decrease genetic diversity in their newly established populations. Auto-triploidization is important for speciation in the extant Malus. The features of Malus polyploidization confer genetic stability and diversity, and present heterozygosity, heterosis and adaptability for evolutionary selection. A protocol using co-dominant markers was proposed for accelerating apple triploid breeding program. A path was postulated for evolution of numerically odd basic chromosomes. The model for Malus derivation was considerably revised

  11. Molecular genetic features of polyploidization and aneuploidization reveal unique patterns for genome duplication in diploid Malus.

    Science.gov (United States)

    Considine, Michael J; Wan, Yizhen; D'Antuono, Mario F; Zhou, Qian; Han, Mingyu; Gao, Hua; Wang, Man

    2012-01-01

    Polyploidization results in genome duplication and is an important step in evolution and speciation. The Malus genome confirmed that this genus was derived through auto-polyploidization, yet the genetic and meiotic mechanisms for polyploidization, particularly for aneuploidization, are unclear in this genus or other woody perennials. In fact the contribution of aneuploidization remains poorly understood throughout Plantae. We add to this knowledge by characterization of eupolyploidization and aneuploidization in 27,542 F₁ seedlings from seven diploid Malus populations using cytology and microsatellite markers. We provide the first evidence that aneuploidy exceeds eupolyploidy in the diploid crosses, suggesting aneuploidization is a leading cause of genome duplication. Gametes from diploid Malus had a unique combinational pattern; ova preserved euploidy exclusively, while spermatozoa presented both euploidy and aneuploidy. All non-reduced gametes were genetically heterozygous, indicating first-division restitution was the exclusive mode for Malus eupolyploidization and aneuploidization. Chromosome segregation pattern among aneuploids was non-uniform, however, certain chromosomes were associated for aneuploidization. This study is the first to provide molecular evidence for the contribution of heterozygous non-reduced gametes to fitness in polyploids and aneuploids. Aneuploidization can increase, while eupolyploidization may decrease genetic diversity in their newly established populations. Auto-triploidization is important for speciation in the extant Malus. The features of Malus polyploidization confer genetic stability and diversity, and present heterozygosity, heterosis and adaptability for evolutionary selection. A protocol using co-dominant markers was proposed for accelerating apple triploid breeding program. A path was postulated for evolution of numerically odd basic chromosomes. The model for Malus derivation was considerably revised. Impacts of

  12. Patterns of hypothalamic regionalization in amphibians and reptiles: common traits revealed by a genoarchitectonic approach

    Directory of Open Access Journals (Sweden)

    Laura eDominguez

    2015-02-01

    Full Text Available Most studies in mammals and birds have demonstrated common patterns of hypothalamic development highlighted by the combination of developmental regulatory genes (genoarchitecture, supporting the notion of the hypothalamus as a component of the secondary prosencephalon, topologically rostral to the diencephalon. In our comparative analysis we have summarized the data on the expression patterns of different transcription factors and neuroactive substances, used as anatomical markers, in the developing hypothalamus of the amphibian Xenopus laevis and the juvenile turtle Pseudemys scripta. This analysis served to highlight the organization of the hypothalamus in the anamniote/amniotic transition. We have identified supraoptoparaventricular and the suprachiasmatic regions in the alar part of the hypothalamus, and tuberal and mammillary regions in the basal hypothalamus. Shared features in the two species are: 1 The supraoptoparaventricular region is defined by the expression of Otp and the lack of Nkx2.1/Isl1. It is subdivided into rostral, rich in Otp and Nkx2.2, and caudal, only Otp-positive, portions. 2 The suprachiasmatic area contains catecholaminergic cell groups and lacks Otp, and can be further divided into rostral (rich in Nkx2.1 and Nkx2.2 and a caudal (rich in Isl1 and devoid of Nkx2.1 portions. 3 Expression of Nkx2.1 and Isl1 define the tuberal hypothalamus and only the rostral portion expresses Otp. 4 Its caudal boundary is evident by the lack of Isl1 in the adjacent mammillary region, which expresses Nkx2.1 and Otp. Differences in the anamnio-amniote transition were noted since in the turtle, like in other amniotes, the boundary between the alar hypothalamus and the telencephalic preoptic area shows distinct Nkx2.2 and Otp expressions but not in the amphibian (anamniote, and the alar supraoptoparaventricular region is defined by the expression of Otp/Pax6, whereas in Xenopus only Otp is expressed.

  13. An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns.

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    Murray P Cox

    2014-03-01

    Full Text Available Polyploidy, a state in which the chromosome complement has undergone an increase, is a major force in evolution. Understanding the consequences of polyploidy has received much attention, and allopolyploids, which result from the union of two different parental genomes, are of particular interest because they must overcome a suite of biological responses to this merger, known as "genome shock." A key question is what happens to gene expression of the two gene copies following allopolyploidization, but until recently the tools to answer this question on a genome-wide basis were lacking. Here we utilize high throughput transcriptome sequencing to produce the first genome-wide picture of gene expression response to allopolyploidy in fungi. A novel pipeline for assigning sequence reads to the gene copies was used to quantify their expression in a fungal allopolyploid. We find that the transcriptional response to allopolyploidy is predominantly conservative: both copies of most genes are retained; over half the genes inherit parental gene expression patterns; and parental differential expression is often lost in the allopolyploid. Strikingly, the patterns of gene expression change are highly concordant with the genome-wide expression results of a cotton allopolyploid. The very different nature of these two allopolyploids implies a conserved, eukaryote-wide transcriptional response to genome merger. We provide evidence that the transcriptional responses we observe are mostly driven by intrinsic differences between the regulatory systems in the parent species, and from this propose a mechanistic model in which the cross-kingdom conservation in transcriptional response reflects conservation of the mutational processes underlying eukaryotic gene regulatory evolution. This work provides a platform to develop a universal understanding of gene expression response to allopolyploidy and suggests that allopolyploids are an exceptional system to investigate gene

  14. Multilocus sequence analysis of nectar pseudomonads reveals high genetic diversity and contrasting recombination patterns.

    Science.gov (United States)

    Alvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas 'sensu stricto' isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria.

  15. Multilocus Sequence Analysis of Nectar Pseudomonads Reveals High Genetic Diversity and Contrasting Recombination Patterns

    Science.gov (United States)

    Álvarez-Pérez, Sergio; de Vega, Clara; Herrera, Carlos M.

    2013-01-01

    The genetic and evolutionary relationships among floral nectar-dwelling Pseudomonas ‘sensu stricto’ isolates associated to South African and Mediterranean plants were investigated by multilocus sequence analysis (MLSA) of four core housekeeping genes (rrs, gyrB, rpoB and rpoD). A total of 35 different sequence types were found for the 38 nectar bacterial isolates characterised. Phylogenetic analyses resulted in the identification of three main clades [nectar groups (NGs) 1, 2 and 3] of nectar pseudomonads, which were closely related to five intrageneric groups: Pseudomonas oryzihabitans (NG 1); P. fluorescens, P. lutea and P. syringae (NG 2); and P. rhizosphaerae (NG 3). Linkage disequilibrium analysis pointed to a mostly clonal population structure, even when the analysis was restricted to isolates from the same floristic region or belonging to the same NG. Nevertheless, signatures of recombination were observed for NG 3, which exclusively included isolates retrieved from the floral nectar of insect-pollinated Mediterranean plants. In contrast, the other two NGs comprised both South African and Mediterranean isolates. Analyses relating diversification to floristic region and pollinator type revealed that there has been more unique evolution of the nectar pseudomonads within the Mediterranean region than would be expected by chance. This is the first work analysing the sequence of multiple loci to reveal geno- and ecotypes of nectar bacteria. PMID:24116076

  16. Large-area imaging reveals biologically driven non-random spatial patterns of corals at a remote reef

    Science.gov (United States)

    Edwards, Clinton B.; Eynaud, Yoan; Williams, Gareth J.; Pedersen, Nicole E.; Zgliczynski, Brian J.; Gleason, Arthur C. R.; Smith, Jennifer E.; Sandin, Stuart A.

    2017-12-01

    For sessile organisms such as reef-building corals, differences in the degree of dispersion of individuals across a landscape may result from important differences in life-history strategies or may reflect patterns of habitat availability. Descriptions of spatial patterns can thus be useful not only for the identification of key biological and physical mechanisms structuring an ecosystem, but also by providing the data necessary to generate and test ecological theory. Here, we used an in situ imaging technique to create large-area photomosaics of 16 plots at Palmyra Atoll, central Pacific, each covering 100 m2 of benthic habitat. We mapped the location of 44,008 coral colonies and identified each to the lowest taxonomic level possible. Using metrics of spatial dispersion, we tested for departures from spatial randomness. We also used targeted model fitting to explore candidate processes leading to differences in spatial patterns among taxa. Most taxa were clustered and the degree of clustering varied by taxon. A small number of taxa did not significantly depart from randomness and none revealed evidence of spatial uniformity. Importantly, taxa that readily fragment or tolerate stress through partial mortality were more clustered. With little exception, clustering patterns were consistent with models of fragmentation and dispersal limitation. In some taxa, dispersion was linearly related to abundance, suggesting density dependence of spatial patterning. The spatial patterns of stony corals are non-random and reflect fundamental life-history characteristics of the taxa, suggesting that the reef landscape may, in many cases, have important elements of spatial predictability.

  17. Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents

    Energy Technology Data Exchange (ETDEWEB)

    Bendell, L.I., E-mail: bendell@sfu.ca

    2011-02-15

    Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of 'pulse' toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a 'snap-shot' of soil, plant or avian tissue trace metal analysis post-mining activity. - Research Highlights: {yields} Archived gizzard samples reveals mining history. {yields} Grit ingestion exposes grouse to cadmium and lead. {yields} Grit selection includes particles enriched in cadmium. {yields} Cadmium enriched particles are of toxicological significance.

  18. Neuronal generator patterns at scalp elicited by lateralized aversive pictures reveal consecutive stages of motivated attention.

    Science.gov (United States)

    Kayser, Jürgen; Tenke, Craig E; Abraham, Karen S; Alschuler, Daniel M; Alvarenga, Jorge E; Skipper, Jamie; Warner, Virginia; Bruder, Gerard E; Weissman, Myrna M

    2016-11-15

    Event-related potential (ERP) studies have provided evidence for an allocation of attentional resources to enhance perceptual processing of motivationally salient stimuli. Emotional modulation affects several consecutive components associated with stages of affective-cognitive processing, beginning as early as 100-200ms after stimulus onset. In agreement with the notion that the right parietotemporal region is critically involved during the perception of arousing affective stimuli, some ERP studies have reported asymmetric emotional ERP effects. However, it is difficult to separate emotional from non-emotional effects because differences in stimulus content unrelated to affective salience or task demands may also be associated with lateralized function or promote cognitive processing. Other concerns pertain to the operational definition and statistical independence of ERP component measures, their dependence on an EEG reference, and spatial smearing due to volume conduction, all of which impede the identification of distinct scalp activation patterns associated with affective processing. Building on prior research using a visual half-field paradigm with highly controlled emotional stimuli (pictures of cosmetic surgery patients showing disordered [negative] or healed [neutral] facial areas before or after treatment), 72-channel ERPs recorded from 152 individuals (ages 13-68years; 81 female) were transformed into reference-free current source density (CSD) waveforms and submitted to temporal principal components analysis (PCA) to identify their underlying neuronal generator patterns. Using both nonparametric randomization tests and repeated measures ANOVA, robust effects of emotional content were found over parietooccipital regions for CSD factors corresponding to N2 sink (212ms peak latency), P3 source (385ms) and a late centroparietal source (630ms), all indicative of greater positivity for negative than neutral stimuli. For the N2 sink, emotional effects were

  19. Naming patterns reveal cultural values: patronyms, matronyms, and the U.S. culture of honor.

    Science.gov (United States)

    Brown, Ryan P; Carvallo, Mauricio; Imura, Mikiko

    2014-02-01

    Four studies examined the hypothesis that honor norms would be associated with a pronounced use of patronyms, but not matronyms, for naming children. Study 1 shows that men who endorse honor values expressed a stronger desire to use patronyms (but not matronyms) for future children, an association that was mediated by patriarchal attitudes. Study 2 presents an indirect method for assessing state patronym and matronym levels. As expected, patronym scores were significantly higher in honor states and were associated with a wide range of variables linked previously to honor-related dynamics. Study 3a shows that following the terrorist attacks of 9/11, patronyms increased in honor states, but not in non-honor states. Likewise, priming men with a fictitious terrorist attack (Study 3b) increased the association between honor ideology and patronym preferences. Together, these studies reveal a subtle social signal that reflects the masculine values of an honor culture.

  20. Sex differences in functional activation patterns revealed by increased emotion processing demands.

    Science.gov (United States)

    Hall, Geoffrey B C; Witelson, Sandra F; Szechtman, Henry; Nahmias, Claude

    2004-02-09

    Two [O(15)] PET studies assessed sex differences regional brain activation in the recognition of emotional stimuli. Study I revealed that the recognition of emotion in visual faces resulted in bilateral frontal activation in women, and unilateral right-sided activation in men. In study II, the complexity of the emotional face task was increased through tje addition of associated auditory emotional stimuli. Men again showed unilateral frontal activation, in this case to the left; whereas women did not show bilateral frontal activation, but showed greater limbic activity. These results suggest that when processing broader cross-modal emotional stimuli, men engage more in associative cognitive strategies while women draw more on primary emotional references.

  1. New patterns in human biogeography revealed by networks of contacts between linguistic groups.

    Science.gov (United States)

    Capitán, José A; Bock Axelsen, Jacob; Manrubia, Susanna

    2015-03-07

    Human languages differ broadly in abundance and are distributed highly unevenly on the Earth. In many qualitative and quantitative aspects, they strongly resemble biodiversity distributions. An intriguing and previously unexplored issue is the architecture of the neighbouring relationships between human linguistic groups. Here we construct and characterize these networks of contacts and show that they represent a new kind of spatial network with uncommon structural properties. Remarkably, language networks share a meaningful property with food webs: both are quasi-interval graphs. In food webs, intervality is linked to the existence of a niche space of low dimensionality; in language networks, we show that the unique relevant variable is the area occupied by the speakers of a language. By means of a range model analogous to niche models in ecology, we show that a geometric restriction of perimeter covering by neighbouring linguistic domains explains the structural patterns observed. Our findings may be of interest in the development of models for language dynamics or regarding the propagation of cultural innovations. In relation to species distribution, they pose the question of whether the spatial features of species ranges share architecture, and eventually generating mechanism, with the distribution of human linguistic groups. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  2. Network Analysis Reveals a Common Host–Pathogen Interaction Pattern in Arabidopsis Immune Responses

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    Hong Li

    2017-05-01

    Full Text Available Many plant pathogens secrete virulence effectors into host cells to target important proteins in host cellular network. However, the dynamic interactions between effectors and host cellular network have not been fully understood. Here, an integrative network analysis was conducted by combining Arabidopsis thaliana protein–protein interaction network, known targets of Pseudomonas syringae and Hyaloperonospora arabidopsidis effectors, and gene expression profiles in the immune response. In particular, we focused on the characteristic network topology of the effector targets and differentially expressed genes (DEGs. We found that effectors tended to manipulate key network positions with higher betweenness centrality. The effector targets, especially those that are common targets of an individual effector, tended to be clustered together in the network. Moreover, the distances between the effector targets and DEGs increased over time during infection. In line with this observation, pathogen-susceptible mutants tended to have more DEGs surrounding the effector targets compared with resistant mutants. Our results suggest a common plant–pathogen interaction pattern at the cellular network level, where pathogens employ potent local impact mode to interfere with key positions in the host network, and plant organizes an in-depth defense by sequentially activating genes distal to the effector targets.

  3. We'll meet again: revealing distributional and temporal patterns of social contact.

    Directory of Open Access Journals (Sweden)

    Thorsten Pachur

    Full Text Available What are the dynamics and regularities underlying social contact, and how can contact with the people in one's social network be predicted? In order to characterize distributional and temporal patterns underlying contact probability, we asked 40 participants to keep a diary of their social contacts for 100 consecutive days. Using a memory framework previously used to study environmental regularities, we predicted that the probability of future contact would follow in systematic ways from the frequency, recency, and spacing of previous contact. The distribution of contact probability across the members of a person's social network was highly skewed, following an exponential function. As predicted, it emerged that future contact scaled linearly with frequency of past contact, proportionally to a power function with recency of past contact, and differentially according to the spacing of past contact. These relations emerged across different contact media and irrespective of whether the participant initiated or received contact. We discuss how the identification of these regularities might inspire more realistic analyses of behavior in social networks (e.g., attitude formation, cooperation.

  4. Shotgun Bisulfite Sequencing of the Betula platyphylla Genome Reveals the Tree’s DNA Methylation Patterning

    Directory of Open Access Journals (Sweden)

    Chang Su

    2014-12-01

    Full Text Available DNA methylation plays a critical role in the regulation of gene expression. Most studies of DNA methylation have been performed in herbaceous plants, and little is known about the methylation patterns in tree genomes. In the present study, we generated a map of methylated cytosines at single base pair resolution for Betula platyphylla (white birch by bisulfite sequencing combined with transcriptomics to analyze DNA methylation and its effects on gene expression. We obtained a detailed view of the function of DNA methylation sequence composition and distribution in the genome of B. platyphylla. There are 34,460 genes in the whole genome of birch, and 31,297 genes are methylated. Conservatively, we estimated that 14.29% of genomic cytosines are methylcytosines in birch. Among the methylation sites, the CHH context accounts for 48.86%, and is the largest proportion. Combined transcriptome and methylation analysis showed that the genes with moderate methylation levels had higher expression levels than genes with high and low methylation. In addition, methylated genes are highly enriched for the GO subcategories of binding activities, catalytic activities, cellular processes, response to stimulus and cell death, suggesting that methylation mediates these pathways in birch trees.

  5. Diurnal patterns of productivity of arbuscular mycorrhizal fungi revealed with the Soil Ecosystem Observatory.

    Science.gov (United States)

    Hernandez, Rebecca R; Allen, Michael F

    2013-10-01

    Arbuscular mycorrhizal (AM) fungi are the most abundant plant symbiont and a major pathway of carbon sequestration in soils. However, their basic biology, including their activity throughout a 24-h day : night cycle, remains unknown. We employed the in situ Soil Ecosystem Observatory to quantify the rates of diurnal growth, dieback and net productivity of extra-radical AM fungi. AM fungal hyphae showed significantly different rates of growth and dieback over a period of 24 h and paralleled the circadian-driven photosynthetic oscillations observed in plants. The greatest rates (and incidences) of growth and dieback occurred between noon and 18:00 h. Growth and dieback events often occurred simultaneously and were tightly coupled with soil temperature and moisture, suggesting a rapid acclimation of the external phase of AM fungi to the immediate environment. Changes in the environmental conditions and variability of the mycorrhizosphere may alter the diurnal patterns of productivity of AM fungi, thereby modifying soil carbon sequestration, nutrient cycling and host plant success. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.

  6. Neighbor Detection Induces Organ-Specific Transcriptomes, Revealing Patterns Underlying Hypocotyl-Specific Growth.

    Science.gov (United States)

    Kohnen, Markus V; Schmid-Siegert, Emanuel; Trevisan, Martine; Petrolati, Laure Allenbach; Sénéchal, Fabien; Müller-Moulé, Patricia; Maloof, Julin; Xenarios, Ioannis; Fankhauser, Christian

    2016-12-01

    In response to neighbor proximity, plants increase the growth of specific organs (e.g., hypocotyls) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing these bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we separately analyzed gene expression patterns in the major light-sensing organ (cotyledons) and in rapidly elongating hypocotyls of Arabidopsis thaliana PIFs initiate transcriptional reprogramming in both organs within 15 min, comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. We show that cotyledon-derived auxin is both necessary and sufficient to initiate hypocotyl growth, but we also provide evidence for the functional importance of the local PIF-induced response. With time, the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between different developmentally regulated growth processes and responses to the environment in different organs. © 2016 American Society of Plant Biologists. All rights reserved.

  7. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer.

    Science.gov (United States)

    Kim, Jung H; Dhanasekaran, Saravana M; Prensner, John R; Cao, Xuhong; Robinson, Daniel; Kalyana-Sundaram, Shanker; Huang, Christina; Shankar, Sunita; Jing, Xiaojun; Iyer, Matthew; Hu, Ming; Sam, Lee; Grasso, Catherine; Maher, Christopher A; Palanisamy, Nallasivam; Mehra, Rohit; Kominsky, Hal D; Siddiqui, Javed; Yu, Jindan; Qin, Zhaohui S; Chinnaiyan, Arul M

    2011-07-01

    Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified ∼68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from ~12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.

  8. Participatory Boat Tracking Reveals Spatial Fishing Patterns in an Indonesian Artisanal Fishery

    Directory of Open Access Journals (Sweden)

    Gabriela Navarrete Forero

    2017-12-01

    Full Text Available The Spermonde Archipelago holds one of the largest artisanal fisheries in Indonesia, providing livelihoods for local communities and many other people involved in international trade networks of seafood. High demand and a lack of enforcement of existing fisheries regulations turn into high pressure for the coral reef ecosystem, contributing to its overall degradation. Estimations on the ecological impacts of different levels of fishing pressure, as well as fisheries stock assessments and marine resource management require precise information of the spatial distribution of fishing effort, which involves great uncertainty when only anecdotal information is considered. We explored the feasibility of applying participatory boat tracking to complement fisheries data during the NW monsoon season 2014–2015. We conducted interviews, measured catch landings, and distributed GPS data loggers among hook and line fishermen to identify fishing grounds by gear-dependent patterns of boat movement. Most of the fishing activities involved two gears (octopus bait and trolling line for live groupers and three fishing grounds. The mass of catch landings was dominated by Octopoda (CPUE = 10.1 kg boatday−1 while the most diverse group was the fish family Serranidae, with Plectropomus leopardus being the main target species. In conclusion, boat tracking combined with interviews and catch surveys has proven a useful tool to reduce uncertainty in information on spatial resource use, while allowing a high level of participation by fishermen.

  9. Monitoring of Water Spectral Pattern Reveals Differences in Probiotics Growth When Used for Rapid Bacteria Selection.

    Directory of Open Access Journals (Sweden)

    Aleksandar Slavchev

    Full Text Available Development of efficient screening method coupled with cell functionality evaluation is highly needed in contemporary microbiology. The presented novel concept and fast non-destructive method brings in to play the water spectral pattern of the solution as a molecular fingerprint of the cell culture system. To elucidate the concept, NIR spectroscopy with Aquaphotomics were applied to monitor the growth of sixteen Lactobacillus bulgaricus one Lactobacillus pentosus and one Lactobacillus gasseri bacteria strains. Their growth rate, maximal optical density, low pH and bile tolerances were measured and further used as a reference data for analysis of the simultaneously acquired spectral data. The acquired spectral data in the region of 1100-1850nm was subjected to various multivariate data analyses - PCA, OPLS-DA, PLSR. The results showed high accuracy of bacteria strains classification according to their probiotic strength. Most informative spectral fingerprints covered the first overtone of water, emphasizing the relation of water molecular system to cell functionality.

  10. Secondary analysis of a marketing research database reveals patterns in dairy product purchases over time.

    Science.gov (United States)

    Van Wave, Timothy W; Decker, Michael

    2003-04-01

    Development of a method using marketing research data to assess food purchase behavior and consequent nutrient availability for purposes of nutrition surveillance, evaluation of intervention effects, and epidemiologic studies of diet-health relationships. Data collected on household food purchases accrued over a 13-week period were selected by using Universal Product Code numbers and household characteristics from a marketing research database. Universal Product Code numbers for 39,408 dairy product purchases were linked to a standard reference for food composition to estimate the nutrient content of foods purchased over time. Two thousand one hundred sixty-one households located in Victoria, Texas, and surrounding communities who were active members of a frequent shopper program. Demographic characteristics of sample households and the nutrient content of their dairy product purchases were analyzed using frequency distribution, cross tabulation, analysis of variance, and t test procedures. A method for using marketing research data was successfully used to estimate household purchases of specific foods and their nutrient content from a marketing database containing hundreds of thousands of records. Distribution of dairy product purchases and their concomitant nutrients between Hispanic and non-Hispanic households were significant (P<.01, P<.001, respectively) and sustained over time. Purchase records from large, nationally representative panels of shoppers, such as those maintained by major market research companies, might be used to accomplish detailed longitudinal epidemiologic studies or surveillance of national food- and nutrient-purchasing patterns within and between countries and segments of their respective populations.

  11. Fibrillar organization in tendons: A pattern revealed by percolation characteristics of the respective geometric network

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    Daniel Andres Dos Santos

    2014-06-01

    Full Text Available Since the tendon is composed by collagen fibrils of various sizes connected between them through molecular cross-links, it sounds logical to model it via a heterogeneous network of fibrils. Using cross sectional images, that network is operatively inferred from the respective Gabriel graph of the fibril mass centers. We focus on network percolation characteristics under an ordered activation of fibrils (progressive recruitment going from the smallest to the largest fibril. Analyses of percolation were carried out on a repository of images of digital flexor tendons obtained from samples of lizards and frogs. Observed percolation thresholds were compared against values derived from hypothetical scenarios of random activation of nodes. Strikingly, we found a significant delay for the occurrence of percolation in actual data. We interpret this finding as the consequence of some non-random packing of fibrillar units into a size-constrained geometric pattern. We erect an ideal geometric model of balanced interspersion of polymorphic units that accounts for the delayed percolating instance. We also address the circumstance of being percolation curves mirrored by the empirical curves of stress-strain obtained from the same studied tendons. By virtue of this isomorphism, we hypothesize that the inflection points of both curves are different quantitative manifestations of a common transitional process during mechanical load transference.

  12. Evolution in the lineament patterns associated to strong earthquakes revealed by satellite observations

    Science.gov (United States)

    Soto-Pinto, C. A.; Arellano-Baeza, A. A.; Ouzounov, D. P.

    2011-12-01

    We study the temporal evolution of the stress patterns in the crust by using high-resolution (10-300 m) satellite images from MODIS and ASTER satellite sensors. We are able to detect some changes in density and orientation of lineaments preceding earthquake events. A lineament is generally defined as a straight or a somewhat curved feature in the landscape visible in a satellite image as an aligned sequence of pixels of a contrasting intensity compared to the background. The system of lineaments extracted from the satellite images is not identical to the geological lineaments; nevertheless, it generally reflects the structure of the faults and fractures in the Earth's crust. Our analysis has shown that the system of lineaments is very dynamical, and the significant number of lineaments appeared approximately one month before an earthquake, while one month after the earthquake the lineament configuration returned to its initial state. These features were not observed in the test areas that are free of any seismic activity in that period (null hypothesis). We have designed a computational prototype capable to detect lineament evolution and to utilize both ASTER and MODIS satellite L1/L2. We will demonstrate the first successful test results for several Mw> 5 earthquakes in Chile, Peru, China, and California (USA).

  13. Expression pattern of glycoside hydrolase genes in Lutzomyia longipalpis reveals key enzymes involved in larval digestion

    Directory of Open Access Journals (Sweden)

    Caroline da Silva Moraes

    2014-08-01

    Full Text Available The sand fly Lutzomyia longipalpis is the most important vector of American Visceral Leishmaniasis. Adults are phytophagous (males and females or blood feeders (females only, and larvae feed on solid detritus. Digestion in sand fly larvae has scarcely been studied, but some glycosidase activities putatively involved in microorganism digestion were already described. Nevertheless, the molecular nature of these enzymes, as the corresponding genes and transcripts, were not explored yet. Catabolism of microbial carbohydrates in insects generally involves β-1,3-glucanases, chitinases and digestive lysozymes. In this work, the transcripts of digestive β-1,3-glucanase and chitinases were identified in the L. longipalpis larvae throughout analysis of sequences and expression patterns of glycoside hydrolases families 16, 18 and 22. The activity of one i-type lysozyme was also registered. Interestingly, this lysozyme seems to play a role in immunity, rather than digestion. This is the first attempt to identify the molecular nature of sand fly larval digestive enzymes.

  14. Expression pattern of glycoside hydrolase genes in Lutzomyia longipalpis reveals key enzymes involved in larval digestion

    Science.gov (United States)

    Moraes, Caroline da Silva; Diaz-Albiter, Hector M.; Faria, Maiara do Valle; Sant'Anna, Maurício R. V.; Dillon, Rod J.; Genta, Fernando A.

    2014-01-01

    The sand fly Lutzomyia longipalpis is the most important vector of American Visceral Leishmaniasis. Adults are phytophagous (males and females) or blood feeders (females only), and larvae feed on solid detritus. Digestion in sand fly larvae has scarcely been studied, but some glycosidase activities putatively involved in microorganism digestion were already described. Nevertheless, the molecular nature of these enzymes, as the corresponding genes and transcripts, were not explored yet. Catabolism of microbial carbohydrates in insects generally involves β-1,3-glucanases, chitinases, and digestive lysozymes. In this work, the transcripts of digestive β-1,3-glucanase and chitinases were identified in the L. longipalpis larvae throughout analysis of sequences and expression patterns of glycoside hydrolases families 16, 18, and 22. The activity of one i-type lysozyme was also registered. Interestingly, this lysozyme seems to play a role in immunity, rather than digestion. This is the first attempt to identify the molecular nature of sand fly larval digestive enzymes. PMID:25140153

  15. Different gene expression patterns between leaves and flowers in Lonicera japonica revealed by transcriptome analysis

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    Libin eZhang

    2016-05-01

    Full Text Available The perennial and evergreen twining vine, Lonicera japonica is an important herbal medicine with great economic value. However, gene expression information for flowers and leaves of L. japonica remains elusive, which greatly impedes functional genomics research on this species. In this study, transcriptome profiles from leaves and flowers of L. japonica were examined using next-generation sequencing technology. A total of 239.41 million clean reads were used for de novo assembly with Trinity software, which generated 150,523 unigenes with N50 containing 947 bp. All the unigenes were annotated using Nr, SwissProt, COGs (Clusters of Orthologous Groups, GO (Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes databases. A total of 35,327 differentially expressed genes (DEGs, P≤0.05 between leaves and flowers were detected. Among them, a total of 6,602 DEGs were assigned with important biological processes including Metabolic process, Response to stimulus, Cellular process and etc. KEGG analysis showed that three possible enzymes involved in the biosynthesis of chlorogenic acid were up-regulated in flowers. Furthermore, the TF-based regulation network in L. japonica identified three differentially expressed transcription factors between leaves and flowers, suggesting distinct regulatory roles in L. japonica. Taken together, this study has provided a global picture of differential gene expression patterns between leaves and flowers in L japonica, providing a useful genomic resource that can also be used for functional genomics research on L. japonica in the future.

  16. CO I barcoding reveals new clades and radiation patterns of Indo-Pacific sponges of the family Irciniidae (Demospongiae: Dictyoceratida.

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    Judith Pöppe

    2010-04-01

    Full Text Available DNA barcoding is a promising tool to facilitate a rapid and unambiguous identification of sponge species. Demosponges of the order Dictyoceratida are particularly challenging to identify, but are of ecological as well as biochemical importance.Here we apply DNA barcoding with the standard CO1-barcoding marker on selected Indo-Pacific specimens of two genera, Ircinia and Psammocinia of the family Irciniidae. We show that the CO1 marker identifies several species new to science, reveals separate radiation patterns of deep-sea Ircinia sponges and indicates dispersal patterns of Psammocinia species. However, some species cannot be unambiguously barcoded by solely this marker due to low evolutionary rates.We support previous suggestions for a combination of the standard CO1 fragment with an additional fragment for sponge DNA barcoding.

  17. RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats.

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    B Alex Merrick

    Full Text Available Deep sequencing was used to investigate the subchronic effects of 1 ppm aflatoxin B1 (AFB1, a potent hepatocarcinogen, on the male rat liver transcriptome prior to onset of histopathological lesions or tumors. We hypothesized RNA-Seq would reveal more differentially expressed genes (DEG than microarray analysis, including low copy and novel transcripts related to AFB1's carcinogenic activity compared to feed controls (CTRL. Paired-end reads were mapped to the rat genome (Rn4 with TopHat and further analyzed by DESeq and Cufflinks-Cuffdiff pipelines to identify differentially expressed transcripts, new exons and unannotated transcripts. PCA and cluster analysis of DEGs showed clear separation between AFB1 and CTRL treatments and concordance among group replicates. qPCR of eight high and medium DEGs and three low DEGs showed good comparability among RNA-Seq and microarray transcripts. DESeq analysis identified 1,026 differentially expressed transcripts at greater than two-fold change (p<0.005 compared to 626 transcripts by microarray due to base pair resolution of transcripts by RNA-Seq, probe placement within transcripts or an absence of probes to detect novel transcripts, splice variants and exons. Pathway analysis among DEGs revealed signaling of Ahr, Nrf2, GSH, xenobiotic, cell cycle, extracellular matrix, and cell differentiation networks consistent with pathways leading to AFB1 carcinogenesis, including almost 200 upregulated transcripts controlled by E2f1-related pathways related to kinetochore structure, mitotic spindle assembly and tissue remodeling. We report 49 novel, differentially-expressed transcripts including confirmation by PCR-cloning of two unique, unannotated, hepatic AFB1-responsive transcripts (HAfT's on chromosomes 1.q55 and 15.q11, overexpressed by 10 to 25-fold. Several potentially novel exons were found and exon refinements were made including AFB1 exon-specific induction of homologous family members, Ugt1a6 and Ugt1a7c

  18. RNA-Seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats.

    Science.gov (United States)

    Merrick, B Alex; Phadke, Dhiral P; Auerbach, Scott S; Mav, Deepak; Stiegelmeyer, Suzy M; Shah, Ruchir R; Tice, Raymond R

    2013-01-01

    Deep sequencing was used to investigate the subchronic effects of 1 ppm aflatoxin B1 (AFB1), a potent hepatocarcinogen, on the male rat liver transcriptome prior to onset of histopathological lesions or tumors. We hypothesized RNA-Seq would reveal more differentially expressed genes (DEG) than microarray analysis, including low copy and novel transcripts related to AFB1's carcinogenic activity compared to feed controls (CTRL). Paired-end reads were mapped to the rat genome (Rn4) with TopHat and further analyzed by DESeq and Cufflinks-Cuffdiff pipelines to identify differentially expressed transcripts, new exons and unannotated transcripts. PCA and cluster analysis of DEGs showed clear separation between AFB1 and CTRL treatments and concordance among group replicates. qPCR of eight high and medium DEGs and three low DEGs showed good comparability among RNA-Seq and microarray transcripts. DESeq analysis identified 1,026 differentially expressed transcripts at greater than two-fold change (p<0.005) compared to 626 transcripts by microarray due to base pair resolution of transcripts by RNA-Seq, probe placement within transcripts or an absence of probes to detect novel transcripts, splice variants and exons. Pathway analysis among DEGs revealed signaling of Ahr, Nrf2, GSH, xenobiotic, cell cycle, extracellular matrix, and cell differentiation networks consistent with pathways leading to AFB1 carcinogenesis, including almost 200 upregulated transcripts controlled by E2f1-related pathways related to kinetochore structure, mitotic spindle assembly and tissue remodeling. We report 49 novel, differentially-expressed transcripts including confirmation by PCR-cloning of two unique, unannotated, hepatic AFB1-responsive transcripts (HAfT's) on chromosomes 1.q55 and 15.q11, overexpressed by 10 to 25-fold. Several potentially novel exons were found and exon refinements were made including AFB1 exon-specific induction of homologous family members, Ugt1a6 and Ugt1a7c. We find the

  19. Mantle convection patterns reveal the enigma of the Red Sea rifting

    Science.gov (United States)

    Petrunin, Alexey; Kaban, Mikhail; El Khrepy, Sami; Al-Arifi, Nassir

    2017-04-01

    Initiation and further development of the Red Sea rift (RSR) is usually associated with the Afar plume at the Oligocene-Miocene separating the Arabian plate from the rest of the continent. Usually, the RSR is divided into three parts with different geological, tectonic and geophysical characteristics, but the nature of this partitioning is still debatable. To understand origin and driving forces responsible for the tectonic partitioning of the RSR, we have developed a global mantle convection model based on the refined density model and viscosity distribution derived from tectonic, rheological and seismic data. The global density model of the upper mantle is refined for the Middle East based on the high-resolution 3D model (Kaban et al., 2016). This model based on a joint inversion of the residual gravity and residual topography provides much better constraints on the 3D density structure compared to the global model based on seismic tomography. The refined density model and the viscosity distribution based on a homologous temperature approach provide an initial setup for further numerical calculations. The present-day snapshot of the mantle convection is calculated by using the code ProSpher 3D that allows for strong lateral variations of viscosity (Petrunin et al., 2013). The setup includes weak plate boundaries, while the measured GPS velocities are used to constrain the solution. The resulting mantle flow patterns show clear distinctions among the mantle flow patterns below the three parts of the RSR. According to the modeling results, tectonics of the southern part of the Red Sea is mainly determined by the Afar plume and the Ethiopian rift opening. It is characterized by a divergent mantle flow, which is connected to the East African Rift activity. The rising mantle flow is traced down to the transition zone and continues in the lower mantle for a few thousand kilometers south-west of Afar. The hot mantle anomaly below the central part of the RSR can be

  20. Estimates of connectivity reveal non-equilibrium epiphyte occurrence patterns almost 180 years after habitat decline.

    Science.gov (United States)

    Johansson, Victor; Snäll, Tord; Ranius, Thomas

    2013-06-01

    Habitat loss is a major cause of species decline and extinction. Immediately after habitat loss, species occurrences are not in equilibrium with the new landscape and more closely reflect the previous landscape structure. Species with slow colonisation-extinction dynamics may display long time-lags before reaching a new equilibrium. We investigated the importance of connectivity to current and historical dispersal sources with the aim of explaining the occurrence pattern of epiphytic lichens with different traits among 104 old oaks. We used oak survey data collected from 1830 and 2009 for a Swedish landscape where oak densities declined drastically shortly after 1830. We fitted a commonly used connectivity measure and estimated the confidence interval for the spatial scale parameter. Small differences in the spatial scale parameter resulted in large differences in model fit. Connectivity to trees in 1830 better explained the occurrence of three of the four species compared to the connectivity in 2009. The explanatory power of the historical landscape structure was highest for the species with traits that may result in a low colonisation rate--both a narrow niche (here few suitable trees) and large dispersal propagules. The results suggest that oak-dependent epiphytic lichens have not reached equilibrium with the spatial landscape structure 180 years after the drastic decline in habitat. For the long-term persistence of epiphytes associated with old trees, conservation efforts should focus on (1) protecting and restoring stands where specialised species with large dispersal propagules (i.e. with low colonisation rates) occur today and (2) promoting tree regeneration in their near vicinity.

  1. Risk and Ambiguity in Information Seeking: Eye Gaze Patterns Reveal Contextual Behavior in Dealing with Uncertainty.

    Science.gov (United States)

    Wittek, Peter; Liu, Ying-Hsang; Darányi, Sándor; Gedeon, Tom; Lim, Ik Soo

    2016-01-01

    Information foraging connects optimal foraging theory in ecology with how humans search for information. The theory suggests that, following an information scent, the information seeker must optimize the tradeoff between exploration by repeated steps in the search space vs. exploitation, using the resources encountered. We conjecture that this tradeoff characterizes how a user deals with uncertainty and its two aspects, risk and ambiguity in economic theory. Risk is related to the perceived quality of the actually visited patch of information, and can be reduced by exploiting and understanding the patch to a better extent. Ambiguity, on the other hand, is the opportunity cost of having higher quality patches elsewhere in the search space. The aforementioned tradeoff depends on many attributes, including traits of the user: at the two extreme ends of the spectrum, analytic and wholistic searchers employ entirely different strategies. The former type focuses on exploitation first, interspersed with bouts of exploration, whereas the latter type prefers to explore the search space first and consume later. Our findings from an eye-tracking study of experts' interactions with novel search interfaces in the biomedical domain suggest that user traits of cognitive styles and perceived search task difficulty are significantly correlated with eye gaze and search behavior. We also demonstrate that perceived risk shifts the balance between exploration and exploitation in either type of users, tilting it against vs. in favor of ambiguity minimization. Since the pattern of behavior in information foraging is quintessentially sequential, risk and ambiguity minimization cannot happen simultaneously, leading to a fundamental limit on how good such a tradeoff can be. This in turn connects information seeking with the emergent field of quantum decision theory.

  2. The spatiotemporal pattern of Src activation at lipid rafts revealed by diffusion-corrected FRET imaging.

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    Shaoying Lu

    2008-07-01

    Full Text Available Genetically encoded biosensors based on fluorescence resonance energy transfer (FRET have been widely applied to visualize the molecular activity in live cells with high spatiotemporal resolution. However, the rapid diffusion of biosensor proteins hinders a precise reconstruction of the actual molecular activation map. Based on fluorescence recovery after photobleaching (FRAP experiments, we have developed a finite element (FE method to analyze, simulate, and subtract the diffusion effect of mobile biosensors. This method has been applied to analyze the mobility of Src FRET biosensors engineered to reside at different subcompartments in live cells. The results indicate that the Src biosensor located in the cytoplasm moves 4-8 folds faster (0.93+/-0.06 microm(2/sec than those anchored on different compartments in plasma membrane (at lipid raft: 0.11+/-0.01 microm(2/sec and outside: 0.18+/-0.02 microm(2/sec. The mobility of biosensor at lipid rafts is slower than that outside of lipid rafts and is dominated by two-dimensional diffusion. When this diffusion effect was subtracted from the FRET ratio images, high Src activity at lipid rafts was observed at clustered regions proximal to the cell periphery, which remained relatively stationary upon epidermal growth factor (EGF stimulation. This result suggests that EGF induced a Src activation at lipid rafts with well-coordinated spatiotemporal patterns. Our FE-based method also provides an integrated platform of image analysis for studying molecular mobility and reconstructing the spatiotemporal activation maps of signaling molecules in live cells.

  3. Analysis of patterns of bushmeat consumption reveals extensive exploitation of protected species in eastern Madagascar.

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    Richard K B Jenkins

    Full Text Available Understanding the patterns of wild meat consumption from tropical forests is important for designing approaches to address this major threat to biodiversity and mitigate potential pathways for transmission of emerging diseases. Bushmeat consumption has been particularly poorly studied in Madagascar, one of the world's hottest biodiversity hotspots. Studying bushmeat consumption is challenging as many species are protected and researchers must consider the incentives faced by informants. Using interviews with 1154 households in 12 communes in eastern Madagascar, as well as local monitoring data, we investigated the importance of socio-economic variables, taste preference and traditional taboos on consumption of 50 wild and domestic species. The majority of meals contain no animal protein. However, respondents consume a wide range of wild species and 95% of respondents have eaten at least one protected species (and nearly 45% have eaten more than 10. The rural/urban divide and wealth are important predictors of bushmeat consumption, but the magnitude and direction of the effect varies between species. Bushmeat species are not preferred and are considered inferior to fish and domestic animals. Taboos have provided protection to some species, particularly the Endangered Indri, but we present evidence that this taboo is rapidly eroding. By considering a variety of potential influences on consumption in a single study we have improved understanding of who is eating bushmeat and why. Evidence that bushmeat species are not generally preferred meats suggest that projects which increase the availability of domestic meat and fish may have success at reducing demand. We also suggest that enforcement of existing wildlife and firearm laws should be a priority, particularly in areas undergoing rapid social change. The issue of hunting as an important threat to biodiversity in Madagascar is only now being fully recognised. Urgent action is required to ensure

  4. A tobacco cDNA reveals two different transcription patterns in vegetative and reproductive organs

    Directory of Open Access Journals (Sweden)

    I. da Silva

    2002-08-01

    Full Text Available In order to identify genes expressed in the pistil that may have a role in the reproduction process, we have established an expressed sequence tags project to randomly sequence clones from a Nicotiana tabacum stigma/style cDNA library. A cDNA clone (MTL-8 showing high sequence similarity to genes encoding glycine-rich RNA-binding proteins was chosen for further characterization. Based on the extensive identity of MTL-8 to the RGP-1a sequence of N. sylvestris, a primer was defined to extend the 5' sequence of MTL-8 by RT-PCR from stigma/style RNAs. The amplification product was sequenced and it was confirmed that MTL-8 corresponds to an mRNA encoding a glycine-rich RNA-binding protein. Two transcripts of different sizes and expression patterns were identified when the MTL-8 cDNA insert was used as a probe in RNA blots. The largest is 1,100 nucleotides (nt long and markedly predominant in ovaries. The smaller transcript, with 600 nt, is ubiquitous to the vegetative and reproductive organs analyzed (roots, stems, leaves, sepals, petals, stamens, stigmas/styles and ovaries. Plants submitted to stress (wounding, virus infection and ethylene treatment presented an increased level of the 600-nt transcript in leaves, especially after tobacco necrosis virus infection. In contrast, the level of the 1,100-nt transcript seems to be unaffected by the stress conditions tested. Results of Southern blot experiments have suggested that MTL-8 is present in one or two copies in the tobacco genome. Our results suggest that the shorter transcript is related to stress while the larger one is a flower predominant and nonstress-inducible messenger.

  5. Polarization-dependent Imaging Contrast (PIC) mapping reveals nanocrystal orientation patterns in carbonate biominerals

    Energy Technology Data Exchange (ETDEWEB)

    Gilbert, Pupa U.P.A., E-mail: pupa@physics.wisc.edu [University of Wisconsin-Madison, Departments of Physics and Chemistry, Madison, WI 53706 (United States)

    2012-10-15

    Highlights: Black-Right-Pointing-Pointer Nanocrystal orientation shown by Polarization-dependent Imaging Contrast (PIC) maps. Black-Right-Pointing-Pointer PIC-mapping of carbonate biominerals reveals their ultrastructure at the nanoscale. Black-Right-Pointing-Pointer The formation mechanisms of biominerals is discovered by PIC-mapping using PEEM. -- Abstract: Carbonate biominerals are one of the most interesting systems a physicist can study. They play a major role in the CO{sub 2} cycle, they master templation, self-assembly, nanofabrication, phase transitions, space filling, crystal nucleation and growth mechanisms. A new imaging modality was introduced in the last 5 years that enables direct observation of the orientation of carbonate single crystals, at the nano- and micro-scale. This is Polarization-dependent Imaging Contrast (PIC) mapping, which is based on X-ray linear dichroism, and uses PhotoElectron Emission spectroMicroscopy (PEEM). Here we present PIC-mapping results from biominerals, including the nacre and prismatic layers of mollusk shells, and sea urchin teeth. We describe various PIC-mapping approaches, and show that these lead to fundamental discoveries on the formation mechanisms of biominerals.

  6. Migrating pattern of deformation prior to the Tohoku-Oki earthquake revealed by GRACE data

    Science.gov (United States)

    Panet, Isabelle; Bonvalot, Sylvain; Narteau, Clément; Remy, Dominique; Lemoine, Jean-Michel

    2018-05-01

    Understanding how and when far-field continuous motions lead to giant subduction earthquakes remains a challenge. An important limitation comes from an incomplete description of aseismic mass fluxes at depth along plate boundaries. Here we analyse Earth's gravity field variations derived from GRACE satellite data in a wide space-time domain surrounding the Mw 9.0 2011 Tohoku-Oki earthquake. We show that this earthquake is the extreme expression of initially silent deformation migrating from depth to the surface across the entire subduction system. Our analysis indeed reveals large-scale gravity and mass changes throughout three tectonic plates and connected slabs, starting a few months before March 2011. Before the Tohoku-Oki earthquake rupture, the gravity variations can be explained by aseismic extension of the Pacific plate slab at mid-upper mantle depth, concomitant with increasing seismicity in the shallower slab. For more than two years after the rupture, the deformation propagated far into the Pacific and Philippine Sea plate interiors, suggesting that subduction accelerated along 2,000 km of the plate boundaries in March 2011. This gravitational image of the earthquake's long-term dynamics provides unique information on deep and crustal processes over intermediate timescales, which could be used in seismic hazard assessment.

  7. Different migration patterns of sea urchin and mouse sperm revealed by a microfluidic chemotaxis device.

    Directory of Open Access Journals (Sweden)

    Haixin Chang

    Full Text Available Chemotaxis refers to a process whereby cells move up or down a chemical gradient. Sperm chemotaxis is known to be a strategy exploited by marine invertebrates such as sea urchins to reach eggs efficiently in moving water. Less is understood about how or whether chemotaxis is used by mammalian sperm to reach eggs, where fertilization takes place within the confinement of a reproductive tract. In this report, we quantitatively assessed sea urchin and mouse sperm chemotaxis using a recently developed microfluidic model and high-speed imaging. Results demonstrated that sea urchin Arbacia punctulata sperm were chemotactic toward the peptide resact with high chemotactic sensitivity, with an average velocity Vx up the chemical gradient as high as 20% of its average speed (238 μm/s, while mouse sperm displayed no statistically significant chemotactic behavior in progesterone gradients, which had been proposed to guide mammalian sperm toward eggs. This work demonstrates the validity of a microfluidic model for quantitative sperm chemotaxis studies, and reveals a biological insight that chemotaxis up a progesterone gradient may not be a universal strategy for mammalian sperm to reach eggs.

  8. The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau.

    Science.gov (United States)

    Zeng, Xingquan; Long, Hai; Wang, Zhuo; Zhao, Shancen; Tang, Yawei; Huang, Zhiyong; Wang, Yulin; Xu, Qijun; Mao, Likai; Deng, Guangbing; Yao, Xiaoming; Li, Xiangfeng; Bai, Lijun; Yuan, Hongjun; Pan, Zhifen; Liu, Renjian; Chen, Xin; WangMu, QiMei; Chen, Ming; Yu, Lili; Liang, Junjun; DunZhu, DaWa; Zheng, Yuan; Yu, Shuiyang; LuoBu, ZhaXi; Guang, Xuanmin; Li, Jiang; Deng, Cao; Hu, Wushu; Chen, Chunhai; TaBa, XiongNu; Gao, Liyun; Lv, Xiaodan; Abu, Yuval Ben; Fang, Xiaodong; Nevo, Eviatar; Yu, Maoqun; Wang, Jun; Tashi, Nyima

    2015-01-27

    The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called "Qingke" in Chinese and "Ne" in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.

  9. Temporal motifs reveal collaboration patterns in online task-oriented networks

    Science.gov (United States)

    Xuan, Qi; Fang, Huiting; Fu, Chenbo; Filkov, Vladimir

    2015-05-01

    Real networks feature layers of interactions and complexity. In them, different types of nodes can interact with each other via a variety of events. Examples of this complexity are task-oriented social networks (TOSNs), where teams of people share tasks towards creating a quality artifact, such as academic research papers or software development in commercial or open source environments. Accomplishing those tasks involves both work, e.g., writing the papers or code, and communication, to discuss and coordinate. Taking into account the different types of activities and how they alternate over time can result in much more precise understanding of the TOSNs behaviors and outcomes. That calls for modeling techniques that can accommodate both node and link heterogeneity as well as temporal change. In this paper, we report on methodology for finding temporal motifs in TOSNs, limited to a system of two people and an artifact. We apply the methods to publicly available data of TOSNs from 31 Open Source Software projects. We find that these temporal motifs are enriched in the observed data. When applied to software development outcome, temporal motifs reveal a distinct dependency between collaboration and communication in the code writing process. Moreover, we show that models based on temporal motifs can be used to more precisely relate both individual developer centrality and team cohesion to programmer productivity than models based on aggregated TOSNs.

  10. Internal Acoustic Transceivers Reveal the Annual Social Network Patterns in a Coastal Top Predator

    Science.gov (United States)

    Haulsee, D.; Fox, D. A.; Breece, M.; Wetherbee, B.; Brown, L.; Kneebone, J.; Skomal, G.; Oliver, M. J.

    2016-02-01

    Sand Tigers (Carcharias taurus) are large apex predators resident in the coastal ocean along the Eastern US Coast. Although Delaware Bay and surrounding coastal waters are known summer "hot spots" for Sand Tigers, our understanding of their seasonal movements is less well known. Since 2007, we have implanted more than 300 VEMCO acoustic transmitters in Sand Tigers, which have been detected from Cape Canaveral, Florida to Long Island, New York by collaborators in the Atlantic Cooperative Telemetry (ACT) Network. During the summer of 2012, 20 Sand Tigers were implanted with VEMCO Mobile Transceivers (VMTs), which are capable of both transmitting and receiving coded acoustic pings. To date, two of the 20 sharks have been recaptured, and their VMTs recovered. VMTs recorded detections of 350 individuals, from 8 different species. We analyzed their intra- and interspecific social network, which allowed us to reconstruct the approximate locations of Sand Tigers throughout the year. Changes in the interspecific population dynamics throughout the year revealed evidence of fission-fusion social behavior, which is common in mammals, but rarely documented in non-mammalian species. This project is a unique look at the social network of an apex predator and is a useful model for studies quantifying the social structures of marine animals. In addition, understanding how the aggregations of this species changes (in terms of sex and size class segregation) on spatiotemporal scales is critical for effective protection of the species and will be useful as managers develop conservation plans along the East Coast.

  11. Glycogen distribution in the microwave-fixed mouse brain reveals heterogeneous astrocytic patterns.

    Science.gov (United States)

    Oe, Yuki; Baba, Otto; Ashida, Hitoshi; Nakamura, Kouichi C; Hirase, Hajime

    2016-09-01

    In the brain, glycogen metabolism has been implied in synaptic plasticity and learning, yet the distribution of this molecule has not been fully described. We investigated cerebral glycogen of the mouse by immunohistochemistry (IHC) using two monoclonal antibodies that have different affinities depending on the glycogen size. The use of focused microwave irradiation yielded well-defined glycogen immunoreactive signals compared with the conventional periodic acid-Schiff method. The IHC signals displayed a punctate distribution localized predominantly in astrocytic processes. Glycogen immunoreactivity (IR) was high in the hippocampus, striatum, cortex, and cerebellar molecular layer, whereas it was low in the white matter and most of the subcortical structures. Additionally, glycogen distribution in the hippocampal CA3-CA1 and striatum had a 'patchy' appearance with glycogen-rich and glycogen-poor astrocytes appearing in alternation. The glycogen patches were more evident with large-molecule glycogen in young adult mice but they were hardly observable in aged mice (1-2 years old). Our results reveal brain region-dependent glycogen accumulation and possibly metabolic heterogeneity of astrocytes. GLIA 2016;64:1532-1545. © 2016 The Authors. Glia Published by Wiley Periodicals, Inc.

  12. Glycogen distribution in the microwave‐fixed mouse brain reveals heterogeneous astrocytic patterns

    Science.gov (United States)

    Baba, Otto; Ashida, Hitoshi; Nakamura, Kouichi C.

    2016-01-01

    In the brain, glycogen metabolism has been implied in synaptic plasticity and learning, yet the distribution of this molecule has not been fully described. We investigated cerebral glycogen of the mouse by immunohistochemistry (IHC) using two monoclonal antibodies that have different affinities depending on the glycogen size. The use of focused microwave irradiation yielded well‐defined glycogen immunoreactive signals compared with the conventional periodic acid‐Schiff method. The IHC signals displayed a punctate distribution localized predominantly in astrocytic processes. Glycogen immunoreactivity (IR) was high in the hippocampus, striatum, cortex, and cerebellar molecular layer, whereas it was low in the white matter and most of the subcortical structures. Additionally, glycogen distribution in the hippocampal CA3‐CA1 and striatum had a ‘patchy’ appearance with glycogen‐rich and glycogen‐poor astrocytes appearing in alternation. The glycogen patches were more evident with large‐molecule glycogen in young adult mice but they were hardly observable in aged mice (1–2 years old). Our results reveal brain region‐dependent glycogen accumulation and possibly metabolic heterogeneity of astrocytes. GLIA 2016;64:1532–1545 PMID:27353480

  13. Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.

    Directory of Open Access Journals (Sweden)

    Johannes Asplund-Samuelsson

    Full Text Available Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18% were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota. Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse sub-groups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

  14. Sleep-dependent consolidation patterns reveal insights into episodic memory structure.

    Science.gov (United States)

    Oyanedel, Carlos N; Sawangjit, Anuck; Born, Jan; Inostroza, Marion

    2018-05-18

    Episodic memory formation is considered a genuinely hippocampal function. Its study in rodents has relied on two different task paradigms, i.e. the so called "what-where-when" (WW-When) task and "what-where-which" (WW-Which) task. The WW-When task aims to assess the memory for an episode as an event bound into its context defined by spatial and distinct temporal information, the WW-Which task lacks the temporal component and introduces, instead, an "occasion setter" marking the broader contextual configuration in which the event occurred. Whether both tasks measure episodic memory in an equivalent manner in terms of recollection has been controversially discussed. Here, we compared in two groups of rats the consolidating effects of sleep on episodic-like memory between both task paradigms. Sampling and test phases were separated by a 90-min morning retention interval which did or did not allow for spontaneous sleep. Results show that sleep is crucial for the consolidation of the memory on both tasks. However, consolidating effects of sleep were stronger for the WW-Which than WW-When task. Comparing performance during the post-sleep test phase revealed that WW-When memory only gradually emerged during the 3-min test period whereas WW-Which memory was readily expressed already from the first minute onward. Separate analysis of the temporal and spatial components of WW-When performance showed that the delayed episodic memory on this task originated from the temporal component which also did not emerge until the third minute of the test phase, whereas the spatial component already showed up in the first minute. In conclusion, sleep differentially affects consolidation on the two episodic-like memory tasks, with the delayed expression of WW-When memory after sleep resulting from preferential coverage of temporal aspects by this task. Copyright © 2018. Published by Elsevier Inc.

  15. Genetic patterns in European geometrid moths revealed by the Barcode Index Number (BIN system.

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    Axel Hausmann

    Full Text Available BACKGROUND: The geometrid moths of Europe are one of the best investigated insect groups in traditional taxonomy making them an ideal model group to test the accuracy of the Barcode Index Number (BIN system of BOLD (Barcode of Life Datasystems, a method that supports automated, rapid species delineation and identification. METHODOLOGY/PRINCIPAL FINDINGS: This study provides a DNA barcode library for 219 of the 249 European geometrid moth species (88% in five selected subfamilies. The data set includes COI sequences for 2130 specimens. Most species (93% were found to possess diagnostic barcode sequences at the European level while only three species pairs (3% were genetically indistinguishable in areas of sympatry. As a consequence, 97% of the European species we examined were unequivocally discriminated by barcodes within their natural areas of distribution. We found a 1:1 correspondence between BINs and traditionally recognized species for 67% of these species. Another 17% of the species (15 pairs, three triads shared BINs, while specimens from the remaining species (18% were divided among two or more BINs. Five of these species are mixtures, both sharing and splitting BINs. For 82% of the species with two or more BINs, the genetic splits involved allopatric populations, many of which have previously been hypothesized to represent distinct species or subspecies. CONCLUSIONS/SIGNIFICANCE: This study confirms the effectiveness of DNA barcoding as a tool for species identification and illustrates the potential of the BIN system to characterize formal genetic units independently of an existing classification. This suggests the system can be used to efficiently assess the biodiversity of large, poorly known assemblages of organisms. For the moths examined in this study, cases of discordance between traditionally recognized species and BINs arose from several causes including overlooked species, synonymy, and cases where DNA barcodes revealed

  16. Genetic networking of the Bemisia tabaci cryptic species complex reveals pattern of biological invasions.

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    Paul De Barro

    Full Text Available BACKGROUND: A challenge within the context of cryptic species is the delimitation of individual species within the complex. Statistical parsimony network analytics offers the opportunity to explore limits in situations where there are insufficient species-specific morphological characters to separate taxa. The results also enable us to explore the spread in taxa that have invaded globally. METHODOLOGY/PRINCIPAL FINDINGS: Using a 657 bp portion of mitochondrial cytochrome oxidase 1 from 352 unique haplotypes belonging to the Bemisia tabaci cryptic species complex, the analysis revealed 28 networks plus 7 unconnected individual haplotypes. Of the networks, 24 corresponded to the putative species identified using the rule set devised by Dinsdale et al. (2010. Only two species proposed in Dinsdale et al. (2010 departed substantially from the structure suggested by the analysis. The analysis of the two invasive members of the complex, Mediterranean (MED and Middle East - Asia Minor 1 (MEAM1, showed that in both cases only a small number of haplotypes represent the majority that have spread beyond the home range; one MEAM1 and three MED haplotypes account for >80% of the GenBank records. Israel is a possible source of the globally invasive MEAM1 whereas MED has two possible sources. The first is the eastern Mediterranean which has invaded only the USA, primarily Florida and to a lesser extent California. The second are western Mediterranean haplotypes that have spread to the USA, Asia and South America. The structure for MED supports two home range distributions, a Sub-Saharan range and a Mediterranean range. The MEAM1 network supports the Middle East - Asia Minor region. CONCLUSION/SIGNIFICANCE: The network analyses show a high level of congruence with the species identified in a previous phylogenetic analysis. The analysis of the two globally invasive members of the complex support the view that global invasion often involve very small portions of

  17. Hydrogen exchange mass spectrometry of bacteriorhodopsin reveals light-induced changes in the structural dynamics of a biomolecular machine.

    Science.gov (United States)

    Pan, Yan; Brown, Leonid; Konermann, Lars

    2011-12-21

    Many proteins act as molecular machines that are fuelled by a nonthermal energy source. Examples include transmembrane pumps and stator-rotor complexes. These systems undergo cyclic motions (CMs) that are being driven along a well-defined conformational trajectory. Superimposed on these CMs are thermal fluctuations (TFs) that are coupled to stochastic motions of the solvent. Here we explore whether the TFs of a molecular machine are affected by the occurrence of CMs. Bacteriorhodopsin (BR) is a light-driven proton pump that serves as a model system in this study. The function of BR is based on a photocycle that involves trans/cis isomerization of a retinal chromophore, as well as motions of transmembrane helices. Hydrogen/deuterium exchange (HDX) mass spectrometry was used to monitor the TFs of BR, focusing on the monomeric form of the protein. Comparative HDX studies were conducted under illumination and in the dark. The HDX kinetics of BR are dramatically accelerated in the presence of light. The isotope exchange rates and the number of backbone amides involved in EX2 opening transitions increase roughly 2-fold upon illumination. In contrast, light/dark control experiments on retinal-free protein produced no discernible differences. It can be concluded that the extent of TFs in BR strongly depends on photon-driven CMs. The light-induced differences in HDX behavior are ascribed to protein destabilization. Specifically, the thermodynamic stability of the dark-adapted protein is estimated to be 5.5 kJ mol(-1) under the conditions of our work. This value represents the free energy difference between the folded state F and a significantly unfolded conformer U. Illumination reduces the stability of F by 2.2 kJ mol(-1). Mechanical agitation caused by isomerization of the chromophore is transferred to the surrounding protein scaffold, and subsequently, the energy dissipates into the solvent. Light-induced retinal motions therefore act analogously to an internal heat

  18. Multichannel detrended fluctuation analysis reveals synchronized patterns of spontaneous spinal activity in anesthetized cats.

    Directory of Open Access Journals (Sweden)

    Erika E Rodríguez

    .924. In contrast to the classical methods, such as correlation and coherence quantification that define a relation between two sets of data, the mDFA method properly reveals the synchronization of multiple groups of neurons in several segments of the spinal cord. This method is envisaged as a useful tool to characterize the structure of higher order ensembles of cord dorsum spontaneous potentials after spinal cord or peripheral nerve lesions.

  19. Structure of the nucleotide exchange factor eIF2B reveals mechanism of memory-enhancing molecule.

    Science.gov (United States)

    Tsai, Jordan C; Miller-Vedam, Lakshmi E; Anand, Aditya A; Jaishankar, Priyadarshini; Nguyen, Henry C; Renslo, Adam R; Frost, Adam; Walter, Peter

    2018-03-30

    Regulation by the integrated stress response (ISR) converges on the phosphorylation of translation initiation factor eIF2 in response to a variety of stresses. Phosphorylation converts eIF2 from a substrate to a competitive inhibitor of its dedicated guanine nucleotide exchange factor, eIF2B, thereby inhibiting translation. ISRIB, a drug-like eIF2B activator, reverses the effects of eIF2 phosphorylation, and in rodents it enhances cognition and corrects cognitive deficits after brain injury. To determine its mechanism of action, we solved an atomic-resolution structure of ISRIB bound in a deep cleft within decameric human eIF2B by cryo-electron microscopy. Formation of fully active, decameric eIF2B holoenzyme depended on the assembly of two identical tetrameric subcomplexes, and ISRIB promoted this step by cross-bridging a central symmetry interface. Thus, regulation of eIF2B assembly emerges as a rheostat for eIF2B activity that tunes translation during the ISR and that can be further modulated by ISRIB. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

  20. Patterns of Storage, Synthesis and Changing Light Levels Revealed by Carbon Isotope Microsampling within Eocene Metasequoia Tree Rings

    Science.gov (United States)

    Jahren, H.; Sternberg, L.

    2005-12-01

    Fossil tree rings from Axel Heiberg Island were microanalyzed for δ13C value in order to assess patterns of tree growth and carbon storage within the Middle Eocene (~45 Ma) Arctic paleoenvironment. Wood from four Metasequoia-type individuals was subsampled for analysis: each individual fossil consisted of between 4 and 10 large (~1 cm thick) consecutive tree rings. One of the fossils displayed an obvious concentric pattern, allowing for the determination of the direction of growth with isotopic pattern. Each ring was divided into ~1 mm thick subsamples, resulting in 5-10 δ13C value determinations per period of ring growth (i.e., growing season). All rings revealed a distinct pattern that was characteristic across growing seasons and across individual fossils. Early in the season, δ13C was at its highest value but descended systematically and sharply to its lowest value at the end of the growing season. Total decrease ranged between 3 and 5 ‰ over the course of each growing season. Identical patterns were observed in the δ13C value of alpha-cellulose isolated from each subsample, indicating that the trends observed did not represent changing levels of secondary metabolites, but rather a seasonal adjustment in the bulk source of carbon used during biosynthesis. Our results are consistent with the following annual pattern of wood synthesis 1.) complete dependence on the mobilization of stored carbon compounds early in the growing season; 2.) systematically increasing use of actively-acquired photosynthate during the growing season; 3.) complete reliance on active photosynthate by the end of the growing season. An additional and significant source of 13C discrimination is declining light levels late in the growing season, and likely contributes to the extreme pattern of δ13C decrease seen across each ring. Our results mimic those seen from modern broadleaf deciduous trees (Helle & Schlesser 2004), but differ from those seen in modern conifers (Barbour et al 2002

  1. Trace metal depositional patterns from an open pit mining activity as revealed by archived avian gizzard contents.

    Science.gov (United States)

    Bendell, L I

    2011-02-15

    Archived samples of blue grouse (Dendragapus obscurus) gizzard contents, inclusive of grit, collected yearly between 1959 and 1970 were analyzed for cadmium, lead, zinc, and copper content. Approximately halfway through the 12-year sampling period, an open-pit copper mine began activities, then ceased operations 2 years later. Thus the archived samples provided a unique opportunity to determine if avian gizzard contents, inclusive of grit, could reveal patterns in the anthropogenic deposition of trace metals associated with mining activities. Gizzard concentrations of cadmium and copper strongly coincided with the onset of opening and the closing of the pit mining activity. Gizzard zinc and lead demonstrated significant among year variation; however, maximum concentrations did not correlate to mining activity. The archived gizzard contents did provide a useful tool for documenting trends in metal depositional patterns related to an anthropogenic activity. Further, blue grouse ingesting grit particles during the time of active mining activity would have been exposed to toxicologically significant levels of cadmium. Gizzard lead concentrations were also of toxicological significance but not related to mining activity. This type of "pulse" toxic metal exposure as a consequence of open-pit mining activity would not necessarily have been revealed through a "snap-shot" of soil, plant or avian tissue trace metal analysis post-mining activity. Copyright © 2010 Elsevier B.V. All rights reserved.

  2. Seasonal patterns of leaf gas exchange and water relations in dry rain forest trees of contrasting leaf phenology.

    Science.gov (United States)

    Choat, Brendan; Ball, Marilyn C; Luly, Jon G; Donnelly, Christine F; Holtum, Joseph A M

    2006-05-01

    Diurnal and seasonal patterns of leaf gas exchange and water relations were examined in tree species of contrasting leaf phenology growing in a seasonally dry tropical rain forest in north-eastern Australia. Two drought-deciduous species, Brachychiton australis (Schott and Endl.) A. Terracc. and Cochlospermum gillivraei Benth., and two evergreen species, Alphitonia excelsa (Fenzal) Benth. and Austromyrtus bidwillii (Benth.) Burret. were studied. The deciduous species had higher specific leaf areas and maximum photosynthetic rates per leaf dry mass in the wet season than the evergreens. During the transition from wet season to dry season, total canopy area was reduced by 70-90% in the deciduous species and stomatal conductance (g(s)) and assimilation rate (A) were markedly lower in the remaining leaves. Deciduous species maintained daytime leaf water potentials (Psi(L)) at close to or above wet season values by a combination of stomatal regulation and reduction in leaf area. Thus, the timing of leaf drop in deciduous species was not associated with large negative values of daytime Psi(L) (greater than -1.6 MPa) or predawn Psi(L) (greater than -1.0 MPa). The deciduous species appeared sensitive to small perturbations in soil and leaf water status that signalled the onset of drought. The evergreen species were less sensitive to the onset of drought and g(s) values were not significantly lower during the transitional period. In the dry season, the evergreen species maintained their canopies despite increasing water-stress; however, unlike Eucalyptus species from northern Australian savannas, A and g(s) were significantly lower than wet season values.

  3. Machine learning methods reveal the temporal pattern of dengue incidence using meteorological factors in metropolitan Manila, Philippines.

    Science.gov (United States)

    Carvajal, Thaddeus M; Viacrusis, Katherine M; Hernandez, Lara Fides T; Ho, Howell T; Amalin, Divina M; Watanabe, Kozo

    2018-04-17

    Several studies have applied ecological factors such as meteorological variables to develop models and accurately predict the temporal pattern of dengue incidence or occurrence. With the vast amount of studies that investigated this premise, the modeling approaches differ from each study and only use a single statistical technique. It raises the question of whether which technique would be robust and reliable. Hence, our study aims to compare the predictive accuracy of the temporal pattern of Dengue incidence in Metropolitan Manila as influenced by meteorological factors from four modeling techniques, (a) General Additive Modeling, (b) Seasonal Autoregressive Integrated Moving Average with exogenous variables (c) Random Forest and (d) Gradient Boosting. Dengue incidence and meteorological data (flood, precipitation, temperature, southern oscillation index, relative humidity, wind speed and direction) of Metropolitan Manila from January 1, 2009 - December 31, 2013 were obtained from respective government agencies. Two types of datasets were used in the analysis; observed meteorological factors (MF) and its corresponding delayed or lagged effect (LG). After which, these datasets were subjected to the four modeling techniques. The predictive accuracy and variable importance of each modeling technique were calculated and evaluated. Among the statistical modeling techniques, Random Forest showed the best predictive accuracy. Moreover, the delayed or lag effects of the meteorological variables was shown to be the best dataset to use for such purpose. Thus, the model of Random Forest with delayed meteorological effects (RF-LG) was deemed the best among all assessed models. Relative humidity was shown to be the top-most important meteorological factor in the best model. The study exhibited that there are indeed different predictive outcomes generated from each statistical modeling technique and it further revealed that the Random forest model with delayed meteorological

  4. Pattern analysis approach reveals restriction enzyme cutting abnormalities and other cDNA library construction artifacts using raw EST data

    Directory of Open Access Journals (Sweden)

    Zhou Sun

    2012-05-01

    or filtered by AFST. Conclusions cDNA terminal pattern analysis, as implemented in the AFST software tool, can be utilized to reveal wet-lab errors such as restriction enzyme cutting abnormities and chimeric EST sequences, detect various data abnormalities embedded in existing Sanger EST datasets, improve the accuracy of identifying and extracting bona fide cDNA inserts from raw ESTs, and therefore greatly benefit downstream EST-based applications.

  5. Comparative genome analysis of Pseudogymnoascus spp. reveals primarily clonal evolution with small genome fragments exchanged between lineages.

    Science.gov (United States)

    Leushkin, Evgeny V; Logacheva, Maria D; Penin, Aleksey A; Sutormin, Roman A; Gerasimov, Evgeny S; Kochkina, Galina A; Ivanushkina, Natalia E; Vasilenko, Oleg V; Kondrashov, Alexey S; Ozerskaya, Svetlana M

    2015-05-21

    Pseudogymnoascus spp. is a wide group of fungi lineages in the family Pseudorotiaceae including an aggressive pathogen of bats P. destructans. Although several lineages of P. spp. were shown to produce ascospores in culture, the vast majority of P. spp. demonstrates no evidence of sexual reproduction. P. spp. can tolerate a wide range of different temperatures and salinities and can survive even in permafrost layer. Adaptability of P. spp. to different environments is accompanied by extremely variable morphology and physiology. We sequenced genotypes of 14 strains of P. spp., 5 of which were extracted from permafrost, 1 from a cryopeg, a layer of unfrozen ground in permafrost, and 8 from temperate surface environments. All sequenced genotypes are haploid. Nucleotide diversity among these genomes is very high, with a typical evolutionary distance at synonymous sites dS ≈ 0.5, suggesting that the last common ancestor of these strains lived >50 Mya. The strains extracted from permafrost do not form a separate clade. Instead, each permafrost strain has close relatives from temperate environments. We observed a strictly clonal population structure with no conflicting topologies for ~99% of genome sequences. However, there is a number of short (~100-10,000 nt) genomic segments with the total length of 67.6 Kb which possess phylogenetic patterns strikingly different from the rest of the genome. The most remarkable case is a MAT-locus, which has 2 distinct alleles interspersed along the whole-genome phylogenetic tree. Predominantly clonal structure of genome sequences is consistent with the observations that sexual reproduction is rare in P. spp. Small number of regions with noncanonical phylogenies seem to arise due to some recombination events between derived lineages of P. spp., with MAT-locus being transferred on multiple occasions. All sequenced strains have heterothallic configuration of MAT-locus.

  6. Abnormal patterns of cerebral lateralisation as revealed by the Universal Chimeric Faces Task in individuals with autistic disorder.

    Science.gov (United States)

    Taylor, Sandie; Workman, Lance; Yeomans, Heather

    2012-01-01

    A previous study by Workman, Chilvers, Yeomans, and Taylor (2006), using the "Universal" Chimeric Faces Task (UCFT) for six emotional expressions, demonstrated that an overall left hemispatial/right hemisphere (RH) advantage has begun to develop by the age of 7-8. Moreover, the development of this left hemispatial advantage was observed to correlate positively with the ability to read emotions in the faces of others. Adopting the UCFT, the current study compared autistic children (11-15) with unimpaired children of two age groups (5-6 and 7-8) from this previous study. The autistic children showed a left hemispatial/RH advantage only for the two emotional expressions of "happiness" and "anger". Results for the autistic children revealed a similar overall pattern of lateralisation to the 5-6-year-olds and one that is less lateralised than the pattern for the 7-8-year-olds. Autistic children appear to show a developmental deficit for left hemispatial/RH advantage for emotional expression with the exception of "happiness" and "anger." The findings are discussed in terms of role hemisphericity and an approach-avoidance model.

  7. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador

    Science.gov (United States)

    Pyron, R. Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H.; Guayasamin, Juan M.

    2016-01-01

    Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history. PMID:27120100

  8. Different localization patterns of anthocyanin species in the pericarp of black rice revealed by imaging mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Yukihiro Yoshimura

    Full Text Available Black rice (Oryza sativa L. Japonica contains high levels of anthocyanins in the pericarp and is considered an effective health-promoting food. Several studies have identified the molecular species of anthocyanins in black rice, but information about the localization of each anthocyanin species is limited because methodologies for investigating the localization such as determining specific antibodies to anthocyanin, have not yet been developed Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS is a suitable tool for investigating the localization of metabolites. In this study, we identified 7 species of anthocyanin monoglycosides and 2 species of anthocyanin diglycosides in crude extracts from black rice by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS analysis. We also analyzed black rice sections by MALDI-IMS and found 2 additional species of anthocyanin pentosides and revealed different localization patterns of anthocyanin species composed of different sugar moieties. Anthocyanin species composed of a pentose moiety (cyanidin-3-O-pentoside and petunidin-3-O-pentoside were localized in the entire pericarp, whereas anthocyanin species composed of a hexose moiety (cyanidin-3-O-hexoside and peonidin-3-O-hexoside were focally localized in the dorsal pericarp. These results indicate that anthocyanin species composed of different sugar moieties exhibit different localization patterns in the pericarp of black rice. This is the first detailed investigation into the localization of molecular species of anthocyanins by MALDI-IMS.

  9. Comparative Phylogeography Reveals Cryptic Diversity and Repeated Patterns of Cladogenesis for Amphibians and Reptiles in Northwestern Ecuador.

    Science.gov (United States)

    Arteaga, Alejandro; Pyron, R Alexander; Peñafiel, Nicolás; Romero-Barreto, Paulina; Culebras, Jaime; Bustamante, Lucas; Yánez-Muñoz, Mario H; Guayasamin, Juan M

    2016-01-01

    Comparative phylogeography allow us to understand how shared historical circumstances have shaped the formation of lineages, by examining a broad spectrum of co-distributed populations of different taxa. However, these types of studies are scarce in the Neotropics, a region that is characterized by high diversity, complex geology, and poorly understood biogeography. Here, we investigate the diversification patterns of five lineages of amphibians and reptiles, co-distributed across the Choco and Andes ecoregions in northwestern Ecuador. Mitochondrial DNA and occurrence records were used to determine the degree of geographic genetic divergence within species. Our results highlight congruent patterns of parapatric speciation and common geographical barriers for distantly related taxa. These comparisons indicate similar biological and demographic characteristics for the included clades, and reveal the existence of two new species of Pristimantis previously subsumed under P. walkeri, which we describe herein. Our data supports the hypothesis that widely distributed Chocoan taxa may generally experience their greatest opportunities for isolation and parapatric speciation across thermal elevational gradients. Finally, our study provides critical information to predict which unstudied lineages may harbor cryptic diversity, and how geology and climate are likely to have shaped their evolutionary history.

  10. Cross-shelf investigation of coral reef cryptic benthic organisms reveals diversity patterns of the hidden majority

    KAUST Repository

    Pearman, John K.

    2018-05-18

    Coral reefs harbor diverse assemblages of organisms yet the majority of this diversity is hidden within the three dimensional structure of the reef and neglected using standard visual surveys. This study uses Autonomous Reef Monitoring Structures (ARMS) and amplicon sequencing methodologies, targeting mitochondrial cytochrome oxidase I and 18S rRNA genes, to investigate changes in the cryptic reef biodiversity. ARMS, deployed at 11 sites across a near- to off-shore gradient in the Red Sea were dominated by Porifera (sessile fraction), Arthropoda and Annelida (mobile fractions). The two primer sets detected different taxa lists, but patterns in community composition and structure were similar. While the microhabitat of the ARMS deployment affected the community structure, a clear cross-shelf gradient was observed for all fractions investigated. The partitioning of beta-diversity revealed that replacement (i.e. the substitution of species) made the highest contribution with richness playing a smaller role. Hence, different reef habitats across the shelf are relevant to regional diversity, as they harbor different communities, a result with clear implications for the design of Marine Protected Areas. ARMS can be vital tools to assess biodiversity patterns in the generally neglected but species-rich cryptic benthos, providing invaluable information for the management and conservation of hard-bottomed habitats over local and global scales.

  11. Segment polarity gene expression in a myriapod reveals conserved and diverged aspects of early head patterning in arthropods.

    Science.gov (United States)

    Janssen, Ralf

    2012-09-01

    Arthropods show two kinds of developmental mode. In the so-called long germ developmental mode (as exemplified by the fly Drosophila), all segments are formed almost simultaneously from a preexisting field of cells. In contrast, in the so-called short germ developmental mode (as exemplified by the vast majority of arthropods), only the anterior segments are patterned similarly as in Drosophila, and posterior segments are added in a single or double segmental periodicity from a posterior segment addition zone (SAZ). The addition of segments from the SAZ is controlled by dynamic waves of gene activity. Recent studies on a spider have revealed that a similar dynamic process, involving expression of the segment polarity gene (SPG) hedgehog (hh), is involved in the formation of the anterior head segments. The present study shows that in the myriapod Glomeris marginata the early expression of hh is also in a broad anterior domain, but this domain corresponds only to the ocular and antennal segment. It does not, like in spiders, represent expression in the posterior adjacent segment. In contrast, the anterior hh pattern is conserved in Glomeris and insects. All investigated myriapod SPGs and associated factors are expressed with delay in the premandibular (tritocerebral) segment. This delay is exclusively found in insects and myriapods, but not in chelicerates, crustaceans and onychophorans. Therefore, it may represent a synapomorphy uniting insects and myriapods (Atelocerata hypothesis), contradicting the leading opinion that suggests a sister relationship of crustaceans and insects (Pancrustacea hypothesis). In Glomeris embryos, the SPG engrailed is first expressed in the mandibular segment. This feature is conserved in representatives of all arthropod classes suggesting that the mandibular segment may have a special function in anterior patterning.

  12. Explaining the Variable Effects of Social Support on Work-Based Stressor-Strain Relations: The Role of Perceived Pattern of Support Exchange

    Science.gov (United States)

    Nahum-Shani, Inbal; Bamberger, Peter A.

    2010-01-01

    Seeking to explain mixed empirical findings regarding the buffering effect of social support on work-based stress-strain relations, we posit that whether an increase in the level of support received buffers or exacerbates the harmful effects of workload on employee health and well-being is contingent upon the general pattern characterizing an employee supportive exchanges across his/her close relationships. Specifically, we propose that the buffering effect of receiving social support depends on whether the employee perceives his/her social exchanges as reciprocal (support given equals support received), under-reciprocating (support given exceeds support received), or over-reciprocating (support received exceeds support given). Based on longitudinal data collected from a random sample of blue-collar workers, our findings support our predictions, indicating that the buffering effect of social support on the relationship between work hours (on the one hand) and employee health and well-being (on the other) varies as a function of the pattern of exchange relations between an employee and his/her close support providers. PMID:21152110

  13. Explaining the Variable Effects of Social Support on Work-Based Stressor-Strain Relations: The Role of Perceived Pattern of Support Exchange.

    Science.gov (United States)

    Nahum-Shani, Inbal; Bamberger, Peter A

    2011-01-01

    Seeking to explain mixed empirical findings regarding the buffering effect of social support on work-based stress-strain relations, we posit that whether an increase in the level of support received buffers or exacerbates the harmful effects of workload on employee health and well-being is contingent upon the general pattern characterizing an employee supportive exchanges across his/her close relationships. Specifically, we propose that the buffering effect of receiving social support depends on whether the employee perceives his/her social exchanges as reciprocal (support given equals support received), under-reciprocating (support given exceeds support received), or over-reciprocating (support received exceeds support given). Based on longitudinal data collected from a random sample of blue-collar workers, our findings support our predictions, indicating that the buffering effect of social support on the relationship between work hours (on the one hand) and employee health and well-being (on the other) varies as a function of the pattern of exchange relations between an employee and his/her close support providers.

  14. The Slow:Fast substitution ratio reveals changing patterns of natural selection in gamma-proteobacterial genomes

    Energy Technology Data Exchange (ETDEWEB)

    Alm, Eric; Shapiro, B. Jesse

    2009-04-15

    Different microbial species are thought to occupy distinct ecological niches, subjecting each species to unique selective constraints, which may leave a recognizable signal in their genomes. Thus, it may be possible to extract insight into the genetic basis of ecological differences among lineages by identifying unusual patterns of substitutions in orthologous gene or protein sequences. We use the ratio of substitutions in slow versus fast-evolving sites (nucleotides in DNA, or amino acids in protein sequence) to quantify deviations from the typical pattern of selective constraint observed across bacterial lineages. We propose that elevated S:F in one branch (an excess of slow-site substitutions) can indicate a functionally-relevant change, due to either positive selection or relaxed evolutionary constraint. In a genome-wide comparative study of gamma-proteobacterial proteins, we find that cell-surface proteins involved with motility and secretion functions often have high S:F ratios, while information-processing genes do not. Change in evolutionary constraints in some species is evidenced by increased S:F ratios within functionally-related sets of genes (e.g., energy production in Pseudomonas fluorescens), while other species apparently evolve mostly by drift (e.g., uniformly elevated S:F across most genes in Buchnera spp.). Overall, S:F reveals several species-specific, protein-level changes with potential functional/ecological importance. As microbial genome projects yield more species-rich gene-trees, the S:F ratio will become an increasingly powerful tool for uncovering functional genetic differences among species.

  15. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    Science.gov (United States)

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2016-02-01

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments. Copyright © 2016, American Society for Microbiology. All Rights

  16. Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns

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    Alexander H. Li

    2017-10-01

    Full Text Available Abstract Background Left-sided lesions (LSLs account for an important fraction of severe congenital cardiovascular malformations (CVMs. The genetic contributions to LSLs are complex, and the mutations that cause these malformations span several diverse biological signaling pathways: TGFB, NOTCH, SHH, and more. Here, we use whole exome sequence data generated in 342 LSL cases to identify likely damaging variants in putative candidate CVM genes. Methods Using a series of bioinformatics filters, we focused on genes harboring population-rare, putative loss-of-function (LOF, and predicted damaging variants in 1760 CVM candidate genes constructed a priori from the literature and model organism databases. Gene variants that were not observed in a comparably sequenced control dataset of 5492 samples without severe CVM were then subjected to targeted validation in cases and parents. Whole exome sequencing data from 4593 individuals referred for clinical sequencing were used to bolster evidence for the role of candidate genes in CVMs and LSLs. Results Our analyses revealed 28 candidate variants in 27 genes, including 17 genes not previously associated with a human CVM disorder, and revealed diverse patterns of inheritance among LOF carriers, including 9 confirmed de novo variants in both novel and newly described human CVM candidate genes (ACVR1, JARID2, NR2F2, PLRG1, SMURF1 as well as established syndromic CVM genes (KMT2D, NF1, TBX20, ZEB2. We also identified two genes (DNAH5, OFD1 with evidence of recessive and hemizygous inheritance patterns, respectively. Within our clinical cohort, we also observed heterozygous LOF variants in JARID2 and SMAD1 in individuals with cardiac phenotypes, and collectively, carriers of LOF variants in our candidate genes had a four times higher odds of having CVM (odds ratio = 4.0, 95% confidence interval 2.5–6.5. Conclusions Our analytical strategy highlights the utility of bioinformatic resources, including human

  17. "Contrasting patterns of selection at Pinus pinaster Ait. Drought stress candidate genes as revealed by genetic differentiation analyses".

    Science.gov (United States)

    Eveno, Emmanuelle; Collada, Carmen; Guevara, M Angeles; Léger, Valérie; Soto, Alvaro; Díaz, Luis; Léger, Patrick; González-Martínez, Santiago C; Cervera, M Teresa; Plomion, Christophe; Garnier-Géré, Pauline H

    2008-02-01

    The importance of natural selection for shaping adaptive trait differentiation among natural populations of allogamous tree species has long been recognized. Determining the molecular basis of local adaptation remains largely unresolved, and the respective roles of selection and demography in shaping population structure are actively debated. Using a multilocus scan that aims to detect outliers from simulated neutral expectations, we analyzed patterns of nucleotide diversity and genetic differentiation at 11 polymorphic candidate genes for drought stress tolerance in phenotypically contrasted Pinus pinaster Ait. populations across its geographical range. We compared 3 coalescent-based methods: 2 frequentist-like, including 1 approach specifically developed for biallelic single nucleotide polymorphisms (SNPs) here and 1 Bayesian. Five genes showed outlier patterns that were robust across methods at the haplotype level for 2 of them. Two genes presented higher F(ST) values than expected (PR-AGP4 and erd3), suggesting that they could have been affected by the action of diversifying selection among populations. In contrast, 3 genes presented lower F(ST) values than expected (dhn-1, dhn2, and lp3-1), which could represent signatures of homogenizing selection among populations. A smaller proportion of outliers were detected at the SNP level suggesting the potential functional significance of particular combinations of sites in drought-response candidate genes. The Bayesian method appeared robust to low sample sizes, flexible to assumptions regarding migration rates, and powerful for detecting selection at the haplotype level, but the frequentist-like method adapted to SNPs was more efficient for the identification of outlier SNPs showing low differentiation. Population-specific effects estimated in the Bayesian method also revealed populations with lower immigration rates, which could have led to favorable situations for local adaptation. Outlier patterns are discussed

  18. Phylogeny and patterns of diversity of goat mtDNA haplogroup A revealed by resequencing complete mitogenomes.

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    Maria Grazia Doro

    Full Text Available We sequenced to near completion the entire mtDNA of 28 Sardinian goats, selected to represent the widest possible diversity of the most widespread mitochondrial evolutionary lineage, haplogroup (Hg A. These specimens were reporters of the diversity in the island but also elsewhere, as inferred from their affiliation to each of 11 clades defined by D-loop variation. Two reference sequences completed the dataset. Overall, 206 variations were found in the full set of 30 sequences, of which 23 were protein-coding non-synonymous single nucleotide substitutions. Many polymorphic sites within Hg A were informative for the reconstruction of its internal phylogeny. Bayesian and network clustering revealed a general similarity over the entire molecule of sequences previously assigned to the same D-loop clade, indicating evolutionarily meaningful lineages. Two major sister groupings emerged within Hg A, which parallel distinct geographical distributions of D-loop clades in extant stocks. The pattern of variation in protein-coding genes revealed an overwhelming role of purifying selection, with the quota of surviving variants approaching neutrality. However, a simple model of relaxation of selection for the bulk of variants here reported should be rejected. Non-synonymous diversity of Hg's A, B and C denoted that a proportion of variants not greater than that allowed in the wild was given the opportunity to spread into domesticated stocks. Our results also confirmed that a remarkable proportion of pre-existing Hg A diversity became incorporated into domestic stocks. Our results confirm clade A11 as a well differentiated and ancient lineage peculiar of Sardinia.

  19. Characterization of WRKY transcription factors in Solanum lycopersicum reveals collinearity and their expression patterns under cold treatment.

    Science.gov (United States)

    Chen, Lin; Yang, Yang; Liu, Can; Zheng, Yanyan; Xu, Mingshuang; Wu, Na; Sheng, Jiping; Shen, Lin

    2015-08-28

    WRKY transcription factors play an important role in cold defense of plants. However, little information is available about the cold-responsive WRKYs in tomato (Solanum lycopersicum). In the present study, a complete characterization of this gene family was described. Eighty WRKY genes in the tomato genome were identified. Almost all WRKY genes contain putative stress-responsive cis-elements in their promoter regions. Segmental duplications contributed significantly to the expansion of the SlWRKY gene family. Transcriptional analysis revealed notable differential expression in tomato tissues and expression patterns under cold stress, which indicated wide functional divergence in this family. Ten WRKYs in tomato were strongly induced more than 2-fold during cold stress. These genes represented candidate genes for future functional analysis of WRKYs involved in the cold-related signal pathways. Our data provide valuable information about tomato WRKY proteins and form a foundation for future studies of these proteins, especially for those that play an important role in response to cold stress. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Long-term acoustical observations of the mesopelagic fish Maurolicus muelleri reveal novel and varied vertical migration patterns

    KAUST Repository

    Staby, A

    2011-11-15

    We studied the temporal dynamics in the vertical distribution of Maurolicus muelleri scattering layers (SL) by examining continuous acoustic recordings over a 15 mo period in Masfjorden, Norway, complemented by intermittent sampling campaigns. The data revealed known patterns as normal diel vertical migration (DVM), midnight sinking between dusk and dawn, and periods without migrations, as well as novel behaviours consisting of early morning ascents, reverse diel vertical migrations, and interrupted ascents in the evening. During the first autumn of the study, adult fish modified their normal DVM behaviour by suspending their migration in the evening, yet ascending toward the surface in the later part of the night to reach upper layers during dawn. This behaviour was not observed during the second autumn of the study. By mid- to end of November (1st autumn), adult fish had suspended the nocturnal ascent entirely, and in the subsequent period until the end of January, a fraction of the population rather performed limited reverse migrations, slightly shifting their vertical distribution upwards during the first part of the day. From January to March 2008, fish interrupted their evening ascent at apparently random intervals and returned to deeper waters, instead of completing a full ascent to the surface. Our study underlines the value of long-term recordings, with the results suggesting that M. muelleri has the capability of changing its behaviour in response to ontogeny and internal state (satiation and hunger) as well as to external stimuli.

  1. Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern.

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    Fatou Diouf

    Full Text Available Acacia senegal (L Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60% clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4. We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T, one in MSP1 (STM8789, MSP2 (ORS3359 and MSP3 (ORS3324. The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.

  2. Genetic and genomic diversity studies of Acacia symbionts in Senegal reveal new species of Mesorhizobium with a putative geographical pattern.

    Science.gov (United States)

    Diouf, Fatou; Diouf, Diegane; Klonowska, Agnieszka; Le Queré, Antoine; Bakhoum, Niokhor; Fall, Dioumacor; Neyra, Marc; Parrinello, Hugues; Diouf, Mayecor; Ndoye, Ibrahima; Moulin, Lionel

    2015-01-01

    Acacia senegal (L) Willd. and Acacia seyal Del. are highly nitrogen-fixing and moderately salt tolerant species. In this study we focused on the genetic and genomic diversity of Acacia mesorhizobia symbionts from diverse origins in Senegal and investigated possible correlations between the genetic diversity of the strains, their soil of origin, and their tolerance to salinity. We first performed a multi-locus sequence analysis on five markers gene fragments on a collection of 47 mesorhizobia strains of A. senegal and A. seyal from 8 localities. Most of the strains (60%) clustered with the M. plurifarium type strain ORS 1032T, while the others form four new clades (MSP1 to MSP4). We sequenced and assembled seven draft genomes: four in the M. plurifarium clade (ORS3356, ORS3365, STM8773 and ORS1032T), one in MSP1 (STM8789), MSP2 (ORS3359) and MSP3 (ORS3324). The average nucleotide identities between these genomes together with the MLSA analysis reveal three new species of Mesorhizobium. A great variability of salt tolerance was found among the strains with a lack of correlation between the genetic diversity of mesorhizobia, their salt tolerance and the soils samples characteristics. A putative geographical pattern of A. senegal symbionts between the dryland north part and the center of Senegal was found, reflecting adaptations to specific local conditions such as the water regime. However, the presence of salt does not seem to be an important structuring factor of Mesorhizobium species.

  3. Molecular characterization of HCV in a Swedish county over 8 years (2002–2009 reveals distinct transmission patterns

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    Josefine Ederth

    2016-02-01

    Full Text Available Background: Hepatitis C virus (HCV is a major public health concern and data on its molecular epidemiology in Sweden is scarce. We carried out an 8-year population-based study of newly diagnosed HCV cases in one of Sweden's centrally situated counties, Södermanland (D-county. The aim was to characterize the HCV strains circulating, analyze their genetic relatedness to detect networks, and in combination with demographic data learn more about transmission. Methods: Molecular analyses of serum samples from 91% (N=557 of all newly notified cases in D-county, 2002–2009, were performed. Phylogenetic analysis (NS5B gene, 300 bp was linked to demographic data from the national surveillance database, SmiNet, to characterize D-county transmission clusters. The linear-by-linear association test (LBL was used to analyze trends over time. Results: The most prevalent subtypes were 1a (38% and 3a (34%. Subtype 1a was most prevalent among cases transmitted via sexual contact, via contaminated blood, or blood products, while subtype 3a was most prevalent among people who inject drugs (PWIDs. Phylogenetic analysis revealed that the subtype 3a sequences formed more and larger transmission clusters (50% of the sequences clustered, while the 1a sequences formed smaller clusters (19% of the sequences clustered, possibly suggesting different epidemics. Conclusion: We found different transmission patterns in D-county which may, from a public health perspective, have implications for how to control virus infections by targeted interventions.

  4. Surface- vs Diffusion-Limited Mechanisms of Anion Exchange in CsPbBr3 Nanocrystal Cubes Revealed through Kinetic Studies.

    Science.gov (United States)

    Koscher, Brent A; Bronstein, Noah D; Olshansky, Jacob H; Bekenstein, Yehonadav; Alivisatos, A Paul

    2016-09-21

    Ion-exchange transformations allow access to nanocrystalline materials with compositions that are inaccessible via direct synthetic routes. However, additional mechanistic insight into the processes that govern these reactions is needed. We present evidence for the presence of two distinct mechanisms of exchange during anion exchange in CsPbX3 nanocrystals (NCs), ranging in size from 6.5 to 11.5 nm, for transformations from CsPbBr3 to CsPbCl3 or CsPbI3. These NCs exhibit bright luminescence throughout the exchange, allowing their optical properties to be observed in real time, in situ. The iodine exchange presents surface-reaction-limited exchanges allowing all anionic sites within the NC to appear chemically identical, whereas the chlorine exchange presents diffusion-limited exchanges proceeding through a more complicated exchange mechanism. Our results represent the first steps toward developing a microkinetic description of the anion exchange, with implications not only for understanding the lead halide perovskites but also for nanoscale ion exchange in general.

  5. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice

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    Riaño-Pachón Diego

    2007-08-01

    Full Text Available Abstract Background In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs, ABRE and CE3, in thale cress (Arabidopsis thaliana and rice (Oryza sativa. Results Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Conclusion Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of

  6. Genome-wide analysis of ABA-responsive elements ABRE and CE3 reveals divergent patterns in Arabidopsis and rice.

    Science.gov (United States)

    Gómez-Porras, Judith L; Riaño-Pachón, Diego Mauricio; Dreyer, Ingo; Mayer, Jorge E; Mueller-Roeber, Bernd

    2007-08-01

    In plants, complex regulatory mechanisms are at the core of physiological and developmental processes. The phytohormone abscisic acid (ABA) is involved in the regulation of various such processes, including stomatal closure, seed and bud dormancy, and physiological responses to cold, drought and salinity stress. The underlying tissue or plant-wide control circuits often include combinatorial gene regulatory mechanisms and networks that we are only beginning to unravel with the help of new molecular tools. The increasing availability of genomic sequences and gene expression data enables us to dissect ABA regulatory mechanisms at the individual gene expression level. In this paper we used an in-silico-based approach directed towards genome-wide prediction and identification of specific features of ABA-responsive elements. In particular we analysed the genome-wide occurrence and positional arrangements of two well-described ABA-responsive cis-regulatory elements (CREs), ABRE and CE3, in thale cress (Arabidopsis thaliana) and rice (Oryza sativa). Our results show that Arabidopsis and rice use the ABA-responsive elements ABRE and CE3 distinctively. Earlier reports for various monocots have identified CE3 as a coupling element (CE) associated with ABRE. Surprisingly, we found that while ABRE is equally abundant in both species, CE3 is practically absent in Arabidopsis. ABRE-ABRE pairs are common in both genomes, suggesting that these can form functional ABA-responsive complexes (ABRCs) in Arabidopsis and rice. Furthermore, we detected distinct combinations, orientation patterns and DNA strand preferences of ABRE and CE3 motifs in rice gene promoters. Our computational analyses revealed distinct recruitment patterns of ABA-responsive CREs in upstream sequences of Arabidopsis and rice. The apparent absence of CE3s in Arabidopsis suggests that another CE pairs with ABRE to establish a functional ABRC capable of interacting with transcription factors. Further studies will be

  7. Hydrogen/deuterium exchange mass spectrometry and computational modeling reveal a discontinuous epitope of an antibody/TL1A Interaction.

    Science.gov (United States)

    Huang, Richard Y-C; Krystek, Stanley R; Felix, Nathan; Graziano, Robert F; Srinivasan, Mohan; Pashine, Achal; Chen, Guodong

    2018-01-01

    TL1A, a tumor necrosis factor-like cytokine, is a ligand for the death domain receptor DR3. TL1A, upon binding to DR3, can stimulate lymphocytes and trigger secretion of proinflammatory cytokines. Therefore, blockade of TL1A/DR3 interaction may be a potential therapeutic strategy for autoimmune and inflammatory diseases. Recently, the anti-TL1A monoclonal antibody 1 (mAb1) with a strong potency in blocking the TL1A/DR3 interaction was identified. Here, we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) to obtain molecular-level details of mAb1's binding epitope on TL1A. HDX coupled with electron-transfer dissociation MS provided residue-level epitope information. The HDX dataset, in combination with solvent accessible surface area (SASA) analysis and computational modeling, revealed a discontinuous epitope within the predicted interaction interface of TL1A and DR3. The epitope regions span a distance within the approximate size of the variable domains of mAb1's heavy and light chains, indicating it uses a unique mechanism of action to block the TL1A/DR3 interaction.

  8. Genome-wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress.

    Science.gov (United States)

    Huang, Xiaosan; Li, Kongqing; Xu, Xiaoyong; Yao, Zhenghong; Jin, Cong; Zhang, Shaoling

    2015-12-24

    WRKY transcription factors (TFs) constitute one of the largest protein families in higher plants, and its members contain one or two conserved WRKY domains, about 60 amino acid residues with the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif. WRKY proteins play significant roles in plant development, and in responses to biotic and abiotic stresses. Pear (Pyrus bretschneideri) is one of the most important fruit crops in the world and is frequently threatened by abiotic stress, such as drought, affecting growth, development and productivity. Although the pear genome sequence has been released, little is known about the WRKY TFs in pear, especially in respond to drought stress at the genome-wide level. We identified a total of 103 WRKY TFs in the pear genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the pear WRKY (PbWRKY) family was classified into seven groups (Groups 1, 2a-e, and 3). The microsyteny analysis indicated that 33 (32%) PbWRKY genes were tandemly duplicated and 57 genes (55.3%) were segmentally duplicated. RNA-seq experiment data and quantitative real-time reverse transcription PCR revealed that PbWRKY genes in different groups were induced by drought stress, and Group 2a and 3 were mainly involved in the biological pathways in response to drought stress. Furthermore, adaptive evolution analysis detected a significant positive selection for Pbr001425 in Group 3, and its expression pattern differed from that of other members in this group. The present study provides a solid foundation for further functional dissection and molecular evolution of WRKY TFs in pear, especially for improving the water-deficient resistance of pear through manipulation of the PbWRKYs.

  9. High-density SNP genotyping of tomato (Solanum lycopersicum L. reveals patterns of genetic variation due to breeding.

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    Sung-Chur Sim

    Full Text Available The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids and over 97% of the markers were polymorphic in the entire collection. Principal component analysis (PCA and pairwise estimates of F(st supported that the inbred accessions represented seven sub-populations including processing, large-fruited fresh market, large-fruited vintage, cultivated cherry, landrace, wild cherry, and S. pimpinellifolium. Further divisions were found within both the contemporary processing and fresh market sub-populations. These sub-populations showed higher levels of genetic diversity relative to the vintage sub-population. The array provided a large number of polymorphic SNP markers across each sub-population, ranging from 3,159 in the vintage accessions to 6,234 in the cultivated cherry accessions. Visualization of minor allele frequency revealed regions of the genome that distinguished three representative sub-populations of cultivated tomato (processing, fresh market, and vintage, particularly on chromosomes 2, 4, 5, 6, and 11. The PCA loadings and F(st outlier analysis between these three sub-populations identified a large number of candidate loci under positive selection on chromosomes 4, 5, and 11. The extent of linkage disequilibrium (LD was examined within each chromosome for these sub-populations. LD decay varied between chromosomes and sub-populations, with large differences reflective of breeding history. For example, on chromosome 11, decay occurred over 0.8 cM for processing accessions and over 19.7 cM for fresh market accessions. The observed SNP variation and LD decay suggest that different patterns of genetic variation in cultivated tomato are due to introgression from wild species and selection for market specialization.

  10. Salmon migration patterns revealed the temporal and spatial fluctuations of the radiocesium levels in terrestrial and ocean environments.

    Science.gov (United States)

    Arai, Takaomi

    2014-01-01

    The disabling of the Fukushima Daiichi Nuclear Power Plant (F1NPP) resulted in the release of radionuclides, including 134Cs and 137Cs, into the air and the ocean. The unpredicted nuclear accident is of global concern for human health and the ecosystem. Although investigations of radionuclides in environments were performed shortly after the accident started, the temporal and spatial impacts and fluctuations on the releasing radionuclides to natural environment remain unclear. I focused on salmon, which migrate from inland to the open ocean globally, to reveal the three-year (May 2011 to February 2014) fluctuations and accumulations of 134Cs and 137Cs from terrestrial to open ocean environments after the F1NPP accident. The 134Cs and 137Cs concentrations in six salmonids exhibited lower temporal variations for three years after the F1NPP accident, suggesting that these radionuclides are widely distributed and these radionuclides remain in the natural environment globally with less convergence. The accumulation patterns were significantly different among the different salmon species. Fluvial (freshwater residence) type salmons exhibited significantly higher accumulation in 134Cs (25.3-40.2 Bq kg(-1) in mean) and 137Cs (41.4-51.7 Bq kg(-1) in mean) than did the anadromous (sea-run) type salmons (0.64-8.03 Bq kg(-1) in mean 134Cs and 0.42-10.2 Bq kg(-1) in mean 137Cs) suggesting widespread contamination in terrestrial environments versus the coastal and open ocean environments. Salmonids are the most highly migratory animals and are characterised by their strong tendency to return home to their natal site for reproduction. Salmonids have a potential to be a good indicator as an effective monitoring animal.

  11. Patterns of Limnohabitans Microdiversity across a Large Set of Freshwater Habitats as Revealed by Reverse Line Blot Hybridization

    Science.gov (United States)

    Jezbera, Jan; Jezberová, Jitka; Kasalický, Vojtěch; Šimek, Karel; Hahn, Martin W.

    2013-01-01

    Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization) probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S–23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus) patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of these bacteria

  12. Patterns of Limnohabitans microdiversity across a large set of freshwater habitats as revealed by Reverse Line Blot Hybridization.

    Directory of Open Access Journals (Sweden)

    Jan Jezbera

    Full Text Available Among abundant freshwater Betaproteobacteria, only few groups are considered to be of central ecological importance. One of them is the well-studied genus Limnohabitans and mainly its R-BT subcluster, investigated previously mainly by fluorescence in situ hybridization methods. We designed, based on sequences from a large Limnohabitans culture collection, 18 RLBH (Reverse Line Blot Hybridization probes specific for different groups within the genus Limnohabitans by targeting diagnostic sequences on their 16 S-23 S rRNA ITS regions. The developed probes covered in sum 92% of the available isolates. This set of probes was applied to environmental DNA originating from 161 different European standing freshwater habitats to reveal the microdiversity (intra-genus patterns of the Limnohabitans genus along a pH gradient. Investigated habitats differed in various physicochemical parameters, and represented a very broad range of standing freshwater habitats. The Limnohabitans microdiversity, assessed as number of RLBH-defined groups detected, increased significantly along the gradient of rising pH of habitats. 14 out of 18 probes returned detection signals that allowed predictions on the distribution of distinct Limnohabitans groups. Most probe-defined Limnohabitans groups showed preferences for alkaline habitats, one for acidic, and some seemed to lack preferences. Complete niche-separation was indicated for some of the probe-targeted groups. Moreover, bimodal distributions observed for some groups of Limnohabitans, suggested further niche separation between genotypes within the same probe-defined group. Statistical analyses suggested that different environmental parameters such as pH, conductivity, oxygen and altitude influenced the distribution of distinct groups. The results of our study do not support the hypothesis that the wide ecological distribution of Limnohabitans bacteria in standing freshwater habitats results from generalist adaptations of

  13. Design and Micromagnetic Simulation of Fe/L10-FePt/Fe Trilayer for Exchange Coupled Composite Bit Patterned Media at Ultrahigh Areal Density

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    Warunee Tipcharoen

    2015-01-01

    Full Text Available Exchange coupled composite bit patterned media (ECC-BPM are one candidate to solve the trilemma issues, overcome superparamagnetic limitations, and obtain ultrahigh areal density. In this work, the ECC continuous media and ECC-BPM of Fe/L10-FePt/Fe trilayer schemes are proposed and investigated based on the Landau-Lifshitz-Gilbert equation. The switching field, Hsw, of the hard phase in the proposed continuous ECC trilayer media structure is reduced below the maximum write head field at interlayer exchange coupling between hard and soft phases, Aex, higher than 20 pJ/m and its value is lower than that for continuous L10-FePt single layer media and L10-FePt/Fe bilayer. Furthermore, the Hsw of the proposed ECC-BPM is lower than the maximum write head field with exchange coupling coefficient between neighboring dots of 5 pJ/m and Aex over 10 pJ/m. Therefore, the proposed ECC-BPM trilayer has the highest potential and is suitable for ultrahigh areal density magnetic recording technology at ultrahigh areal density. The results of this work may be gainful idea for nanopatterning in magnetic media nanotechnology.

  14. Investigation of patterned and non-patterned poly(2,6-dimethyl 1,4-phenylene) oxide based anion exchange membranes for enhanced desalination and power generation in a microbial desalination cell.

    Science.gov (United States)

    Moruno, Francisco Lopez; Rubio, Juan E; Santoro, Carlo; Atanassov, Plamen; Cerrato, José M; Arges, Christopher G

    2018-01-01

    Quaternary ammonium poly(2,6-dimethyl 1,4-phenylene oxide) (QAPPO) anion exchange membranes (AEMs) with topographically patterned surfaces were assessed in a microbial desalination cell (MDC) system. The MDC results with these QAPPO AEMs were benchmarked against a commercially available AEM. The MDC with the non-patterned QAPPO AEM (Q1) displayed the best desalination rate (a reduction of salinity by 53 ± 2.7%) and power generation (189 ± 5 mW m - 2 ) when compared against the commercially available AEM and the patterned AEMs. The enhanced performance with the Q1 AEM was attributed to its higher ionic conductivity and smaller thickness leading to a reduced area specific resistance. It is important to note that Real Pacific Ocean seawater and activated sludge were used into the desalination chamber and anode chamber respectively for the MDC - which mimicked realistic conditions. Although the non-patterned QAPPO AEM displayed better performance over the patterned QAPPO AEMs, it was observed that the anodic overpotential was smaller when the MDCs featured QAPPO AEMs with larger lateral feature sizes. The results from this study have important implications for the continuous improvements necessary for developing cheaper and better performing membranes in order to optimize the MDC.

  15. Whole genome sequencing reveals complex evolution patterns of multidrug-resistant Mycobacterium tuberculosis Beijing strains in patients.

    Directory of Open Access Journals (Sweden)

    Matthias Merker

    Full Text Available Multidrug-resistant (MDR Mycobacterium tuberculosis complex (MTBC strains represent a major threat for tuberculosis (TB control. Treatment of MDR-TB patients is long and less effective, resulting in a significant number of treatment failures. The development of further resistances leads to extensively drug-resistant (XDR variants. However, data on the individual reasons for treatment failure, e.g. an induced mutational burst, and on the evolution of bacteria in the patient are only sparsely available. To address this question, we investigated the intra-patient evolution of serial MTBC isolates obtained from three MDR-TB patients undergoing longitudinal treatment, finally leading to XDR-TB. Sequential isolates displayed identical IS6110 fingerprint patterns, suggesting the absence of exogenous re-infection. We utilized whole genome sequencing (WGS to screen for variations in three isolates from Patient A and four isolates from Patient B and C, respectively. Acquired polymorphisms were subsequently validated in up to 15 serial isolates by Sanger sequencing. We determined eight (Patient A and nine (Patient B polymorphisms, which occurred in a stepwise manner during the course of the therapy and were linked to resistance or a potential compensatory mechanism. For both patients, our analysis revealed the long-term co-existence of clonal subpopulations that displayed different drug resistance allele combinations. Out of these, the most resistant clone was fixed in the population. In contrast, baseline and follow-up isolates of Patient C were distinguished each by eleven unique polymorphisms, indicating an exogenous re-infection with an XDR strain not detected by IS6110 RFLP typing. Our study demonstrates that intra-patient microevolution of MDR-MTBC strains under longitudinal treatment is more complex than previously anticipated. However, a mutator phenotype was not detected. The presence of different subpopulations might confound phenotypic and

  16. Hidden Markov model analysis reveals the advantage of analytic eye movement patterns in face recognition across cultures.

    Science.gov (United States)

    Chuk, Tim; Crookes, Kate; Hayward, William G; Chan, Antoni B; Hsiao, Janet H

    2017-12-01

    It remains controversial whether culture modulates eye movement behavior in face recognition. Inconsistent results have been reported regarding whether cultural differences in eye movement patterns exist, whether these differences affect recognition performance, and whether participants use similar eye movement patterns when viewing faces from different ethnicities. These inconsistencies may be due to substantial individual differences in eye movement patterns within a cultural group. Here we addressed this issue by conducting individual-level eye movement data analysis using hidden Markov models (HMMs). Each individual's eye movements were modeled with an HMM. We clustered the individual HMMs according to their similarities and discovered three common patterns in both Asian and Caucasian participants: holistic (looking mostly at the face center), left-eye-biased analytic (looking mostly at the two individual eyes in addition to the face center with a slight bias to the left eye), and right-eye-based analytic (looking mostly at the right eye in addition to the face center). The frequency of participants adopting the three patterns did not differ significantly between Asians and Caucasians, suggesting little modulation from culture. Significantly more participants (75%) showed similar eye movement patterns when viewing own- and other-race faces than different patterns. Most importantly, participants with left-eye-biased analytic patterns performed significantly better than those using either holistic or right-eye-biased analytic patterns. These results suggest that active retrieval of facial feature information through an analytic eye movement pattern may be optimal for face recognition regardless of culture. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. H/D exchange mass spectrometry and statistical coupling analysis reveal a role for allostery in a ferredoxin-dependent bifurcating transhydrogenase catalytic cycle.

    Science.gov (United States)

    Berry, Luke; Poudel, Saroj; Tokmina-Lukaszewska, Monika; Colman, Daniel R; Nguyen, Diep M N; Schut, Gerrit J; Adams, Michael W W; Peters, John W; Boyd, Eric S; Bothner, Brian

    2018-01-01

    Recent investigations into ferredoxin-dependent transhydrogenases, a class of enzymes responsible for electron transport, have highlighted the biological importance of flavin-based electron bifurcation (FBEB). FBEB generates biomolecules with very low reduction potential by coupling the oxidation of an electron donor with intermediate potential to the reduction of high and low potential molecules. Bifurcating systems can generate biomolecules with very low reduction potentials, such as reduced ferredoxin (Fd), from species such as NADPH. Metabolic systems that use bifurcation are more efficient and confer a competitive advantage for the organisms that harbor them. Structural models are now available for two NADH-dependent ferredoxin-NADP + oxidoreductase (Nfn) complexes. These models, together with spectroscopic studies, have provided considerable insight into the catalytic process of FBEB. However, much about the mechanism and regulation of these multi-subunit proteins remains unclear. Using hydrogen/deuterium exchange mass spectrometry (HDX-MS) and statistical coupling analysis (SCA), we identified specific pathways of communication within the model FBEB system, Nfn from Pyrococus furiosus, under conditions at each step of the catalytic cycle. HDX-MS revealed evidence for allosteric coupling across protein subunits upon nucleotide and ferredoxin binding. SCA uncovered a network of co-evolving residues that can provide connectivity across the complex. Together, the HDX-MS and SCA data show that protein allostery occurs across the ensemble of iron‑sulfur cofactors and ligand binding sites using specific pathways that connect domains allowing them to function as dynamically coordinated units. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. Genomic insights into a new Citrobacter koseri strain revealed gene exchanges with the virulence-associated Yersinia pestis pPCP1 plasmid

    Directory of Open Access Journals (Sweden)

    Fabrice eArmougom

    2016-03-01

    Full Text Available The history of infectious diseases raised the plague as one of the most devastating for human beings. Far too often considered an ancient disease, the frequent resurgence of the plague has led to consider it as a reemerging disease in Madagascar, Algeria, Libya and Congo. The genetic factors associated with the pathogenicity of Yersinia pestis, the causative agent of the plague, involve the acquisition of the pPCP1 plasmid that promotes host invasion through the expression of the virulence factor Pla. The surveillance of plague foci after the 2003 outbreak in Algeria resulted in a positive detection of the specific pla gene of Y. pestis in rodents. However, the phenotypic characterization of the isolate identified a Citrobacter koseri. The comparative genomics of our sequenced C. koseri URMITE genome revealed a mosaic gene structure resulting from the lifestyle of our isolate and provided evidence for gene exchanges with different enteric bacteria. The most striking was the acquisition of a continuous 2 kb genomic fragment containing the virulence factor Pla of the Y. pestis pPCP1 plasmid; however, the subcutaneous injection of the CKU strain in mice did not produce any pathogenic effect. Our findings demonstrate that fast molecular detection of plague using solely the pla gene is unsuitable and should rather require Y. pestis gene marker combinations. We also suggest that the evolutionary force that might govern the expression of pathogenicity can occur through the acquisition of virulence genes but could also require the loss or the inactivation of resident genes such as antivirulence genes.

  19. Structural Dynamics of the GW182 Silencing Domain Including its RNA Recognition motif (RRM) Revealed by Hydrogen-Deuterium Exchange Mass Spectrometry

    Science.gov (United States)

    Cieplak-Rotowska, Maja K.; Tarnowski, Krzysztof; Rubin, Marcin; Fabian, Marc R.; Sonenberg, Nahum; Dadlez, Michal; Niedzwiecka, Anna

    2018-01-01

    The human GW182 protein plays an essential role in micro(mi)RNA-dependent gene silencing. miRNA silencing is mediated, in part, by a GW182 C-terminal region called the silencing domain, which interacts with the poly(A) binding protein and the CCR4-NOT deadenylase complex to repress protein synthesis. Structural studies of this GW182 fragment are challenging due to its predicted intrinsically disordered character, except for its RRM domain. However, detailed insights into the properties of proteins containing disordered regions can be provided by hydrogen-deuterium exchange mass spectrometry (HDX/MS). In this work, we applied HDX/MS to define the structural state of the GW182 silencing domain. HDX/MS analysis revealed that this domain is clearly divided into a natively unstructured part, including the CCR4-NOT interacting motif 1, and a distinct RRM domain. The GW182 RRM has a very dynamic structure, since water molecules can penetrate the whole domain in 2 h. The finding of this high structural dynamics sheds new light on the RRM structure. Though this domain is one of the most frequently occurring canonical protein domains in eukaryotes, these results are - to our knowledge - the first HDX/MS characteristics of an RRM. The HDX/MS studies show also that the α2 helix of the RRM can display EX1 behavior after a freezing-thawing cycle. This means that the RRM structure is sensitive to environmental conditions and can change its conformation, which suggests that the state of the RRM containing proteins should be checked by HDX/MS in regard of the conformational uniformity. [Figure not available: see fulltext.

  20. Epiphytic invertebrate patterns in coastal lakes along a gradient of salinity and water exchange with the sea

    Science.gov (United States)

    Obolewski, Krystian; Bąkowska, Martyna

    2017-10-01

    The species composition and abundance of epiphytic fauna inhabiting common reed (Phragmites australis (Cav.) Trin. ex Steud.) was performed in five coastal lakes in Słowiński National Park (southern Baltic coast in northern Poland). The lakes represent a salinity gradient (from freshwater to β-oligohaline waters) and four types of coastal lakes: (1) lagoon, L (Lake Łebsko, seawater enters it permanently); (2) coastal lake with periodically brackish water, CLB (Lake Gardno); (3) freshwater costal lake, CLF (Lake Smołdzińskie); and (4) coastal dune lakes, CLD (Dołgie Wielkie and Dołgie Małe). Using statistical ordination techniques, we found that the structure of epiphytic fauna (microinvertebrates and macroinvertebrates) is determined primarily by hydrological connectivity (water exchange) with the sea. Canonical Correspondence Analysis, coupled with variance partitioning, showed that hydrological connectivity accounted for 24% of the variation in the invertebrate community, followed by physico-chemical (19%) and trophic (8%) factors. Our results indicate that the assemblages of Ciliata-libera and Cnidaria are characteristic for L (β-oligohaline), Rotifera, Suctoria, Chaetogaster sp., Gastropoda and Trichoptera are characteristic for CLB (limnetic/β-oligohaline), but no taxonomic groups are characteristic for CLF and CLD (both limnetic). The index of multivariate dispersion showed a decreasing trend with the increasing lake isolation from the open sea, except for CLD. However, in terms of the structure of epiphytic fauna, Multi-Response Permutation Procedures showed that CLD significantly differed only from CLB. Our results suggest that the identified characteristic taxonomic groups of plant-associated macroinvertebrates have a high potential to be used as bioindicators of salinity and water exchange with the sea, due to their sensitivity to environmental stress.

  1. Comparative Analysis of WUSCHEL-Related Homeobox Genes Revealed Their Parent-of-Origin and Cell Type-Specific Expression Pattern During Early Embryogenesis in Tobacco

    Directory of Open Access Journals (Sweden)

    Xuemei Zhou

    2018-03-01

    Full Text Available WUSCHEL-related homeobox (WOX gene is a plant-specific clade of homeobox transcription factors. Increasing evidences reveal that WOXs play critical roles in early embryogenesis, which involves zygote development, initiation of zygote division, and apical or basal cell lineage establishment. However, how WOXs regulate these developmental events remains largely unknown, and even detailed expression pattern in gametes and early proembryos is not yet available. Here, 13 WOX family genes were identified in Nicotiana tabacum genome. Comparative analysis of 13 WOX family genes with their homologs in Arabidopsis thaliana reveals relatively conserved expression pattern of WUS and WOX5 in shoot/root apical meristem. Whereas variations were also found, e.g., lacking homolog of WOX8 (a marker for suspensor cell in tobacco genome and the expression of WOX2/WOX9 in both apical cell and basal cell. Transient transcriptional activity analysis revealed that WOXs in WUS clade have repressive activities for their target's transcription, whereas WOXs in ancient and intermediate clade have activation activities, giving a molecular basis for the phylogenetic classification of tobacco WOXs into three major clades. Expression pattern analysis revealed that some WOXs (e.g., WOX 13a expressed in both male and female gametes and some WOXs (e.g., WOX 11 and WOX 13b displayed the characteristics of parent-of-origin genes. Interestingly, some WOXs (e.g., WOX2 and WOX9, which are essential for early embryo patterning, were de novo transcribed in zygote, indicating relevant mechanism for embryo pattern formation is only established in zygote right after fertilization and not carried in by gametes. We also found that most WOXs displayed a stage-specific and cell type-specific expression pattern. Taken together, this work provides a detailed landscape of WOXs in tobacco during fertilization and early embryogenesis, which will facilitate the understanding of their specific roles

  2. Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends.

    Directory of Open Access Journals (Sweden)

    Julia H Chariker

    Full Text Available G-quadruplex structures (G4 are found throughout the human genome and are known to play a regulatory role in a variety of molecular processes. Structurally, they have many configurations and can form from one or more DNA strands. At the gene level, they regulate gene expression and protein synthesis. In this paper, chromosomal-level patterns of distribution are analyzed on the human genome to identify high-level distribution patterns potentially related to global functional processes. Here we show unique high density banding patterns on individual chromosomes that are highly correlated, appearing in a mirror pattern, across forward and reverse DNA strands. The highest density of G4 sequences occurs within four megabases of one end of most chromosomes and contains G4 motifs that bind with zinc finger proteins. These findings suggest that G4 may play a role in global chromosomal processes such as those found in meiosis.

  3. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

    DEFF Research Database (Denmark)

    Baillie, J. Kenneth; Bretherick, Andrew; Haley, Christopher S.

    2018-01-01

    Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcrip...

  4. Intervessel connectivity and relationship with patterns of lateral water exchange within and between xylem sectors in seven xeric shrubs from the great Sahara desert.

    Science.gov (United States)

    Halis, Youcef; Mayouf, Rabah; Benhaddya, Mohamed Lamine; Belhamra, Mohamed

    2013-03-01

    The main objective of this study was to evaluate the role of intervessel contacts in determining the patterns of hydraulic integration both within and between xylem sectors. The degree of intervessel contacts and the lateral exchange capability within and between sectors were examined and correlated in different xeric shrubs. A dye injection method was used to detect the connections between vessels; an apoplastic dye was sucked through a known number of vessels and its distribution in the xylem network was followed. Hydraulic techniques were used to measure axial and tangential conductivity both within and between xylem sectors. The intra- and inter-sector integration indexes were then determined as the ratio of tangential to axial conductance. Species differed significantly in the degree of intervessel contacts, intra- and inter-sector integration index. In all cases, hydraulic integration was observed to be higher within sector than between sectors. From the correlation analyses, the intervessel contacts showed a very weak relationship with inter-sector integration index and a strong positive relationship with intra-sector integration index. Results suggested that (1) the factors affecting patterns of lateral flow within xylem sectors might be relatively different from those between sectors. (2) The degree of intervessel contacts was a major determinant of hydraulic integration within the same xylem sector. (3) Intervessel connectivity alone was a poor predictor of hydraulic integration between different sectors, implying a significant contribution of other anatomical, physiological and environmental factors in determining the patterns of integrated-sectored transport within woody stems.

  5. Phenotypic plasticity of gas exchange pattern and water loss in Scarabaeus spretus (Coleoptera: Scarabaeidae): deconstructing the basis for metabolic rate variation.

    Science.gov (United States)

    Terblanche, John S; Clusella-Trullas, Susana; Chown, Steven L

    2010-09-01

    Investigation of gas exchange patterns and modulation of metabolism provide insight into metabolic control systems and evolution in diverse terrestrial environments. Variation in metabolic rate in response to environmental conditions has been explained largely in the context of two contrasting hypotheses, namely metabolic depression in response to stressful or resource-(e.g. water) limited conditions, or elevation of metabolism at low temperatures to sustain life in extreme conditions. To deconstruct the basis for metabolic rate changes in response to temperature variation, here we undertake a full factorial study investigating the longer- and short-term effects of temperature exposure on gas exchange patterns. We examined responses of traits of gas exchange [standard metabolic rate (SMR); discontinuous gas exchange (DGE) cycle frequency; cuticular, respiratory and total water loss rate (WLR)] to elucidate the magnitude and form of plastic responses in the dung beetle, Scarabaeus spretus. Results showed that short- and longer-term temperature variation generally have significant effects on SMR and WLR. Overall, acclimation to increased temperature led to a decline in SMR (from 0.071+/-0.004 ml CO(2) h(-1) in 15 degrees C-acclimated beetles to 0.039+/-0.004 ml CO(2) h(-1) in 25 degrees C-acclimated beetles measured at 20 degrees C) modulated by reduced DGE frequency (15 degrees C acclimation: 0.554+/-0.027 mHz, 20 degrees C acclimation: 0.257+/-0.030 mHz, 25 degrees C acclimation: 0.208+/-0.027 mHz recorded at 20 degrees C), reduced cuticular WLRs (from 1.058+/-0.537 mg h(-1) in 15 degrees C-acclimated beetles to 0.900+/-0.400 mg h(-1) in 25 degrees C-acclimated beetles measured at 20 degrees C) and reduced total WLR (from 4.2+/-0.5 mg h(-1) in 15 degrees C-acclimated beetles to 3.1+/-0.5 mg h(-1) in 25 degrees C-acclimated beetles measured at 25 degrees C). Respiratory WLR was reduced from 2.25+/-0.40 mg h(-1) in 15 degrees C-acclimated beetles to 1.60+/-0.40 mg h

  6. Seasonal and Diel Activity Patterns of Eight Sympatric Mammals in Northern Japan Revealed by an Intensive Camera-Trap Survey.

    Directory of Open Access Journals (Sweden)

    Takashi Ikeda

    Full Text Available The activity patterns of mammals are generally categorized as nocturnal, diurnal, crepuscular (active at twilight, and cathemeral (active throughout the day. These patterns are highly variable across regions and seasons even within the same species. However, quantitative data is still lacking, particularly for sympatric species. We monitored the seasonal and diel activity patterns of terrestrial mammals in Hokkaido, Japan. Through an intensive camera-trap survey a total of 13,279 capture events were recorded from eight mammals over 20,344 camera-trap days, i.e., two years. Diel activity patterns were clearly divided into four categories: diurnal (Eurasian red squirrels, nocturnal (raccoon dogs and raccoons, crepuscular (sika deer and mountain hares, and cathemeral (Japanese martens, red foxes, and brown bears. Some crepuscular and cathemeral mammals shifted activity peaks across seasons. Particularly, sika deer changed peaks from twilight during spring-autumn to day-time in winter, possibly because of thermal constraints. Japanese martens were cathemeral during winter-summer, but nocturnal in autumn. We found no clear indication of predator-prey and competitive interactions, suggesting that animal densities are not very high or temporal niche partitioning is absent among the target species. This long-term camera-trap survey was highly cost-effective and provided one of the most detailed seasonal and diel activity patterns in multiple sympatric mammals under natural conditions.

  7. Dynamic expression reveals a two-step patterning of WUS and CLV3 during axillary shoot meristem formation in Arabidopsis.

    Science.gov (United States)

    Xin, Wei; Wang, Zhicai; Liang, Yan; Wang, Yonghong; Hu, Yuxin

    2017-07-01

    Seed plants have a remarkable capability to produce axillary meristems (AM) in the leaf axils, however, the dynamic establishment of a stem cell niche in AM is largely uncharacterized. We comprehensively examined the dynamic patterning of WUSCHEL (WUS) and CLAVATA3 (CLV3), the two key marker genes defining the shoot stem cell niches, during AM formation in Arabidopsis, and we found that a two-step patterning of WUS and CLV3 occurred during AM stem cell niche establishment. Our further work on the wus and clv3 mutants implicates that such two-step patterning is likely critical for the maintenance of AM progenitor cells and the specification of AM stem cell niche. These data provide a cytological frame for how a stem cell niche is established during AM formation. Copyright © 2017 Elsevier GmbH. All rights reserved.

  8. Heat transfer and pressure drop of supercritical carbon dioxide flowing in several printed circuit heat exchanger channel patterns

    International Nuclear Information System (INIS)

    Carlson, M.; Kruizenga, A.; Anderson, M.; Corradini, M.

    2012-01-01

    Closed-loop Brayton cycles using supercritical carbon dioxide (SCO 2 ) show potential for use in high-temperature power generation applications including High Temperature Gas Reactors (HTGR) and Sodium-Cooled Fast Reactors (SFR). Compared to Rankine cycles SCO 2 Brayton cycles offer similar or improved efficiency and the potential for decreased capital costs due to a reduction in equipment size and complexity. Compact printed-circuit heat exchangers (PCHE) are being considered as part of several SCO 2 Brayton designs to further reduce equipment size with increased energy density. Several designs plan to use a gas cooler operating near the pseudo-critical point of carbon dioxide to benefit from large variations in thermophysical properties, but further work is needed to validate correlations for heat transfer and pressure-drop characteristics of SCO 2 flows in candidate PCHE channel designs for a variety of operating conditions. This paper presents work on experimental measurements of the heat transfer and pressure drop behavior of miniature channels using carbon dioxide at supercritical pressure. Results from several plate geometries tested in horizontal cooling-mode flow are presented, including a straight semi-circular channel, zigzag channel with a bend angle of 80 degrees, and a channel with a staggered array of extruded airfoil pillars modeled after a NACA 0020 airfoil with an 8.1 mm chord length facing into the flow. Heat transfer coefficients and bulk temperatures are calculated from measured local wall temperatures and local heat fluxes. The experimental results are compared to several methods for estimating the friction factor and Nusselt number of cooling-mode flows at supercritical pressures in millimeter-scale channels. (authors)

  9. A review of the distribution of Yellowhammer (Emberiza citrinella) dialects in Europe reveals the lack of a clear macrogeographic pattern

    Czech Academy of Sciences Publication Activity Database

    Petrusková, T.; Diblíková, L.; Pipek, P.; Frauendorf, E.; Procházka, Petr; Petrusek, A.

    2015-01-01

    Roč. 156, č. 1 (2015), s. 263-273 ISSN 0021-8375 Institutional support: RVO:68081766 Keywords : Emberiza citrinella * Song variation * Dialect nomenclature * Online sources * Macrogeographic patterns Subject RIV: EG - Zoology Impact factor: 1.419, year: 2015

  10. Brain-based decoding of mentally imagined film clips and sounds reveals experience-based information patterns in film professionals.

    Science.gov (United States)

    de Borst, Aline W; Valente, Giancarlo; Jääskeläinen, Iiro P; Tikka, Pia

    2016-04-01

    In the perceptual domain, it has been shown that the human brain is strongly shaped through experience, leading to expertise in highly-skilled professionals. What has remained unclear is whether specialization also shapes brain networks underlying mental imagery. In our fMRI study, we aimed to uncover modality-specific mental imagery specialization of film experts. Using multi-voxel pattern analysis we decoded from brain activity of professional cinematographers and sound designers whether they were imagining sounds or images of particular film clips. In each expert group distinct multi-voxel patterns, specific for the modality of their expertise, were found during classification of imagery modality. These patterns were mainly localized in the occipito-temporal and parietal cortex for cinematographers and in the auditory cortex for sound designers. We also found generalized patterns across perception and imagery that were distinct for the two expert groups: they involved frontal cortex for the cinematographers and temporal cortex for the sound designers. Notably, the mental representations of film clips and sounds of cinematographers contained information that went beyond modality-specificity. We were able to successfully decode the implicit presence of film genre from brain activity during mental imagery in cinematographers. The results extend existing neuroimaging literature on expertise into the domain of mental imagery and show that experience in visual versus auditory imagery can alter the representation of information in modality-specific association cortices. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. The origins of enhanced activity in factor VIIa analogs and the interplay between key allosteric sites revealed by hydrogen exchange mass spectrometry

    DEFF Research Database (Denmark)

    Rand, Kasper D; Andersen, Mette D; Olsen, Ole H

    2008-01-01

    Factor VIIa (FVIIa) circulates in the blood in a zymogen-like state. Only upon association with membrane-bound tissue factor (TF) at the site of vascular injury does FVIIa become active and able to initiate blood coagulation. Here we used hydrogen exchange monitored by mass spectrometry to invest......Factor VIIa (FVIIa) circulates in the blood in a zymogen-like state. Only upon association with membrane-bound tissue factor (TF) at the site of vascular injury does FVIIa become active and able to initiate blood coagulation. Here we used hydrogen exchange monitored by mass spectrometry...... to investigate the conformational effects of site-directed mutagenesis at key positions in FVIIa and the origins of enhanced intrinsic activity of FVIIa analogs. The differences in hydrogen exchange of two highly active variants, FVIIa(DVQ) and FVIIa(VEAY), imply that enhanced catalytic efficiency was attained...

  12. Wing pattern morphology of three closely related Melitaea (Lepidoptera, Nymphalidae) species reveals highly inaccurate external morphology-based species identification

    OpenAIRE

    Jugovic,Jure; Koren,Toni

    2014-01-01

    Wing morphology of the three closely related species of Melitaea – M. athalia (Rottemburg, 1775), M. aurelia (Nickerl, 1850) and M. britomartis Assmann, 1847 – co-occurring in the Balkans (SE Europe) was investigated in detail through visual inspection, morphometric analysis and multivariate statistical analysis. Results are compared to recent phylogenetic studies, searching for concordant patterns and discrepancies between the two approaches. The morphology of the genitalic structures is als...

  13. Temporal-pattern similarity analysis reveals the beneficial and detrimental effects of context reinstatement on human memory.

    Science.gov (United States)

    Staudigl, Tobias; Vollmar, Christian; Noachtar, Soheyl; Hanslmayr, Simon

    2015-04-01

    A powerful force in human memory is the context in which memories are encoded (Tulving and Thomson, 1973). Several studies suggest that the reinstatement of neural encoding patterns is beneficial for memory retrieval (Manning et al., 2011; Staresina et al., 2012; Jafarpour et al., 2014). However, reinstatement of the original encoding context is not always helpful, for instance, when retrieving a memory in a different contextual situation (Smith and Vela, 2001). It is an open question whether such context-dependent memory effects can be captured by the reinstatement of neural patterns. We investigated this question by applying temporal and spatial pattern similarity analysis in MEG and intracranial EEG in a context-match paradigm. Items (words) were tagged by individual dynamic context stimuli (movies). The results show that beta oscillatory phase in visual regions and the parahippocampal cortex tracks the incidental reinstatement of individual context trajectories on a single-trial level. Crucially, memory benefitted from reinstatement when the encoding and retrieval contexts matched but suffered from reinstatement when the contexts did not match. Copyright © 2015 the authors 0270-6474/15/355373-12$15.00/0.

  14. A Smartphone App Reveals Erratic Diurnal Eating Patterns in Humans that Can Be Modulated for Health Benefits.

    Science.gov (United States)

    Gill, Shubhroz; Panda, Satchidananda

    2015-11-03

    A diurnal rhythm of eating-fasting promotes health, but the eating pattern of humans is rarely assessed. Using a mobile app, we monitored ingestion events in healthy adults with no shift-work for several days. Most subjects ate frequently and erratically throughout wakeful hours, and overnight fasting duration paralleled time in bed. There was a bias toward eating late, with an estimated 35% after 6 p.m. "Metabolic jetlag" resulting from weekday/weekend variation in eating pattern akin to travel across time zones was prevalent. The daily intake duration (95% interval) exceeded 14.75 hr for half of the cohort. When overweight individuals with >14 hr eating duration ate for only 10-11 hr daily for 16 weeks assisted by a data visualization (raster plot of dietary intake pattern, "feedogram") that we developed, they reduced body weight, reported being energetic, and improved sleep. Benefits persisted for a year. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. Mass-Spectrometry-Based Proteomics Reveals Organ-Specific Expression Patterns To Be Used as Forensic Evidence.

    Science.gov (United States)

    Dammeier, Sascha; Nahnsen, Sven; Veit, Johannes; Wehner, Frank; Ueffing, Marius; Kohlbacher, Oliver

    2016-01-04

    Standard forensic procedures to examine bullets after an exchange of fire include a mechanical or ballistic reconstruction of the event. While this is routine to identify which projectile hit a subject by DNA analysis of biological material on the surface of the projectile, it is rather difficult to determine which projectile caused the lethal injury--often the crucial point with regard to legal proceedings. With respect to fundamental law it is the duty of the public authority to make every endeavor to solve every homicide case. To improve forensic examinations, we present a forensic proteomic method to investigate biological material from a projectile's surface and determine the tissues traversed by it. To obtain a range of relevant samples, different major bovine organs were penetrated with projectiles experimentally. After tryptic "on-surface" digestion, mass-spectrometry-based proteome analysis, and statistical data analysis, we were able to achieve a cross-validated organ classification accuracy of >99%. Different types of anticipated external variables exhibited no prominent influence on the findings. In addition, shooting experiments were performed to validate the results. Finally, we show that these concepts could be applied to a real case of murder to substantially improve the forensic reconstruction.

  16. Postnatal mandible growth in wild and laboratory mice: Differences revealed from bone remodeling patterns and geometric morphometrics.

    Science.gov (United States)

    Martínez-Vargas, Jessica; Muñoz-Muñoz, Francesc; Martinez-Maza, Cayetana; Molinero, Amalia; Ventura, Jacint

    2017-08-01

    Comparative information on the variation in the temporospatial patterning of mandible growth in wild and laboratory mice during early postnatal ontogeny is scarce but important to understand variation among wild rodent populations. Here, we compare mandible growth between two ontogenetic series from the second to the eighth week of postnatal life, corresponding to two different groups of mice reared under the same conditions: the classical inbred strain C57BL/6J, and Mus musculus domesticus. We characterize the ontogenetic patterns of bone remodeling of the mandibles belonging to these laboratory and wild mice by analyzing bone surface, as well as examine their ontogenetic form changes and bimodular organization using geometric morphometrics. Through ontogeny, the two mouse groups display similar directions of mandible growth, according to the temporospatial distribution of bone remodeling fields. The allometric shape variation of the mandibles of these mice entails the relative enlargement of the ascending ramus. The organization of the mandible into two modules is confirmed in both groups during the last postnatal weeks. However, especially after weaning, the mandibles of wild and laboratory mice differ in the timing and localization of several remodeling fields, in addition to exhibiting different patterns of shape variation and differences in size. The stimulation of dentary bone growth derived from the harder post-weaning diet might account for some features of postnatal mandible growth common to both groups. Nonetheless, a large component of the postnatal growth of the mouse mandible appears to be driven by the inherent genetic programs, which might explain between-group differences. © 2017 Wiley Periodicals, Inc.

  17. Monitoring Spongospora subterranea Development in Potato Roots Reveals Distinct Infection Patterns and Enables Efficient Assessment of Disease Control Methods.

    Directory of Open Access Journals (Sweden)

    Tamilarasan Thangavel

    Full Text Available Spongospora subterranea is responsible for significant potato root and tuber disease globally. Study of this obligate (non-culturable pathogen that infects below-ground plant parts is technically difficult. The capacity to measure the dynamics and patterns of root infections can greatly assist in determining the efficacy of control treatments on disease progression. This study used qPCR and histological analysis in time-course experiments to measure temporal patterns of pathogen multiplication and disease development in potato (and tomato roots and tubers. Effects of delayed initiation of infection and fungicidal seed tuber and soil treatments were assessed. This study found roots at all plant developmental ages were susceptible to infection but that delaying infection significantly reduced pathogen content and resultant disease at final harvest. The pathogen was first detected in roots 15-20 days after inoculation (DAI and the presence of zoosporangia noted 15-45 DAI. Following initial infection pathogen content in roots increased at a similar rate regardless of plant age at inoculation. All fungicide treatments (except soil-applied mancozeb which had a variable response suppressed pathogen multiplication and root and tuber disease. In contrast to delayed inoculation, the fungicide treatments slowed disease progress (rate rather than delaying onset of infection. Trials under suboptimal temperatures for disease expression provided valuable data on root infection rate, demonstrating the robustness of monitoring root infection. These results provide an early measure of the efficacy of control treatments and indicate two possible patterns of disease suppression by either delayed initiation of infection which then proceeds at a similar rate or diminished epidemic rate.

  18. Monitoring Spongospora subterranea Development in Potato Roots Reveals Distinct Infection Patterns and Enables Efficient Assessment of Disease Control Methods.

    Science.gov (United States)

    Thangavel, Tamilarasan; Tegg, Robert S; Wilson, Calum R

    2015-01-01

    Spongospora subterranea is responsible for significant potato root and tuber disease globally. Study of this obligate (non-culturable) pathogen that infects below-ground plant parts is technically difficult. The capacity to measure the dynamics and patterns of root infections can greatly assist in determining the efficacy of control treatments on disease progression. This study used qPCR and histological analysis in time-course experiments to measure temporal patterns of pathogen multiplication and disease development in potato (and tomato) roots and tubers. Effects of delayed initiation of infection and fungicidal seed tuber and soil treatments were assessed. This study found roots at all plant developmental ages were susceptible to infection but that delaying infection significantly reduced pathogen content and resultant disease at final harvest. The pathogen was first detected in roots 15-20 days after inoculation (DAI) and the presence of zoosporangia noted 15-45 DAI. Following initial infection pathogen content in roots increased at a similar rate regardless of plant age at inoculation. All fungicide treatments (except soil-applied mancozeb which had a variable response) suppressed pathogen multiplication and root and tuber disease. In contrast to delayed inoculation, the fungicide treatments slowed disease progress (rate) rather than delaying onset of infection. Trials under suboptimal temperatures for disease expression provided valuable data on root infection rate, demonstrating the robustness of monitoring root infection. These results provide an early measure of the efficacy of control treatments and indicate two possible patterns of disease suppression by either delayed initiation of infection which then proceeds at a similar rate or diminished epidemic rate.

  19. HYDRA: Revealing heterogeneity of imaging and genetic patterns through a multiple max-margin discriminative analysis framework.

    Science.gov (United States)

    Varol, Erdem; Sotiras, Aristeidis; Davatzikos, Christos

    2017-01-15

    Multivariate pattern analysis techniques have been increasingly used over the past decade to derive highly sensitive and specific biomarkers of diseases on an individual basis. The driving assumption behind the vast majority of the existing methodologies is that a single imaging pattern can distinguish between healthy and diseased populations, or between two subgroups of patients (e.g., progressors vs. non-progressors). This assumption effectively ignores the ample evidence for the heterogeneous nature of brain diseases. Neurodegenerative, neuropsychiatric and neurodevelopmental disorders are largely characterized by high clinical heterogeneity, which likely stems in part from underlying neuroanatomical heterogeneity of various pathologies. Detecting and characterizing heterogeneity may deepen our understanding of disease mechanisms and lead to patient-specific treatments. However, few approaches tackle disease subtype discovery in a principled machine learning framework. To address this challenge, we present a novel non-linear learning algorithm for simultaneous binary classification and subtype identification, termed HYDRA (Heterogeneity through Discriminative Analysis). Neuroanatomical subtypes are effectively captured by multiple linear hyperplanes, which form a convex polytope that separates two groups (e.g., healthy controls from pathologic samples); each face of this polytope effectively defines a disease subtype. We validated HYDRA on simulated and clinical data. In the latter case, we applied the proposed method independently to the imaging and genetic datasets of the Alzheimer's Disease Neuroimaging Initiative (ADNI 1) study. The imaging dataset consisted of T1-weighted volumetric magnetic resonance images of 123 AD patients and 177 controls. The genetic dataset consisted of single nucleotide polymorphism information of 103 AD patients and 139 controls. We identified 3 reproducible subtypes of atrophy in AD relative to controls: (1) diffuse and extensive

  20. Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders

    DEFF Research Database (Denmark)

    Wood, Hannah Marie; Matzke, Nicholas J.; Gillespie, Rosemary G.

    2013-01-01

    Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living...... members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a combined molecular and morphological data set. Dating information is compared with treating...

  1. The Effect of Spectral Quality on Daily Patterns of Gas Exchange, Biomass Gain, and Water-Use-Efficiency in Tomatoes and Lisianthus: An Assessment of Whole Plant Measurements.

    Science.gov (United States)

    Lanoue, Jason; Leonardos, Evangelos D; Ma, Xiao; Grodzinski, Bernard

    2017-01-01

    Advancements in light-emitting diode (LED) technology have made them a viable alternative to current lighting systems for both sole and supplemental lighting requirements. Understanding how wavelength specific LED lighting can affect plants is thus an area of great interest. Much research is available on the wavelength specific responses of leaves from multiple crops when exposed to long-term wavelength specific lighting. However, leaf measurements do not always extrapolate linearly to the complexities which are found within a whole plant canopy, namely mutual shading and leaves of different ages. Taken together, both tomato ( Solanum lycopersicum ) leaves under short-term illumination and lisianthus ( Eustoma grandiflorum ) and tomato whole plant diurnal patterns of plants acclimated to specific lighting indicate wavelength specific responses of both H 2 O and CO 2 gas exchanges involved in the major growth parameters of a plant. Tomato leaves grown under a white light source indicated an increase in transpiration rate and internal CO 2 concentration and a subsequent decrease in water-use-efficiency (WUE) when exposed to a blue LED light source compared to a green LED light source. Interestingly, the maximum photosynthetic rate was observed to be similar. Using plants grown under wavelength specific supplemental lighting in a greenhouse, a decrease in whole plant WUE was seen in both crops under both red-blue (RB) and red-white (RW) LEDs when compared to a high pressure sodium (HPS) light. Whole plant WUE was decreased by 31% under the RB LED treatment for both crops compared to the HPS treatment. Tomato whole plant WUE was decreased by 25% and lisianthus whole plant WUE was decreased by 15% when compared to the HPS treatment when grown under RW LED. The understanding of the effects of wavelength specific lighting on both leaf and whole plant gas exchange has significant implications on basic academic research as well as commercial greenhouse production.

  2. The Effect of Spectral Quality on Daily Patterns of Gas Exchange, Biomass Gain, and Water-Use-Efficiency in Tomatoes and Lisianthus: An Assessment of Whole Plant Measurements

    Directory of Open Access Journals (Sweden)

    Jason Lanoue

    2017-06-01

    Full Text Available Advancements in light-emitting diode (LED technology have made them a viable alternative to current lighting systems for both sole and supplemental lighting requirements. Understanding how wavelength specific LED lighting can affect plants is thus an area of great interest. Much research is available on the wavelength specific responses of leaves from multiple crops when exposed to long-term wavelength specific lighting. However, leaf measurements do not always extrapolate linearly to the complexities which are found within a whole plant canopy, namely mutual shading and leaves of different ages. Taken together, both tomato (Solanum lycopersicum leaves under short-term illumination and lisianthus (Eustoma grandiflorum and tomato whole plant diurnal patterns of plants acclimated to specific lighting indicate wavelength specific responses of both H2O and CO2 gas exchanges involved in the major growth parameters of a plant. Tomato leaves grown under a white light source indicated an increase in transpiration rate and internal CO2 concentration and a subsequent decrease in water-use-efficiency (WUE when exposed to a blue LED light source compared to a green LED light source. Interestingly, the maximum photosynthetic rate was observed to be similar. Using plants grown under wavelength specific supplemental lighting in a greenhouse, a decrease in whole plant WUE was seen in both crops under both red-blue (RB and red-white (RW LEDs when compared to a high pressure sodium (HPS light. Whole plant WUE was decreased by 31% under the RB LED treatment for both crops compared to the HPS treatment. Tomato whole plant WUE was decreased by 25% and lisianthus whole plant WUE was decreased by 15% when compared to the HPS treatment when grown under RW LED. The understanding of the effects of wavelength specific lighting on both leaf and whole plant gas exchange has significant implications on basic academic research as well as commercial greenhouse production.

  3. Spatial patterns of sea surface temperature influences on East African precipitation as revealed by empirical orthogonal teleconnections

    Directory of Open Access Journals (Sweden)

    Tim eAppelhans

    2016-02-01

    Full Text Available East Africa is characterized by a rather dry annual precipitation climatology with two distinct rainy seasons. In order to investigate sea surface temperature driven precipitation anomalies for the region we use the algorithm of empirical orthogonal teleconnection analysis as a data mining tool. We investigate the entire East African domain as well as 5 smaller sub-regions mainly located in areas of mountainous terrain. In searching for influential sea surface temperature patterns we do not focus any particular season or oceanic region. Furthermore, we investigate different time lags from zero to twelve months. The strongest influence is identified for the immediate (i.e. non-lagged influences of the Indian Ocean in close vicinity to the East African coast. None of the most important modes are located in the tropical Pacific Ocean, though the region is sometimes coupled with the Indian Ocean basin. Furthermore, we identify a region in the southern Indian Ocean around the Kerguelen Plateau which has not yet been reported in the literature with regard to precipitation modulation in East Africa. Finally, it is observed that not all regions in East Africa are equally influenced by the identified patterns.

  4. Comparing genomic expression patterns across plant species reveals highly diverged transcriptional dynamics in response to salt stress

    Directory of Open Access Journals (Sweden)

    Close Timothy J

    2009-08-01

    Full Text Available Abstract Background Rice and barley are both members of Poaceae (grass family but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley. Results A hierarchical clustering approach identified several interesting expression trajectories among rice and barley genotypes. There were no major conserved expression patterns between the two species in response to salt stress. A wheat salt-stress dataset was queried for comparison with rice and barley. Roughly one-third of the salt-stress responses of barley were conserved with wheat while overlap between wheat and rice was minimal. These results demonstrate that, at transcriptome level, rice is strikingly different compared to the more closely related barley and wheat. This apparent lack of analogous transcriptional programs in response to salt stress is further highlighted through close examination of genes associated with root growth and development. Conclusion The analysis provides support for the hypothesis that conservation of transcriptional signatures in response to environmental cues depends on the genetic similarity among the genotypes within a species, and on the phylogenetic distance between the species.

  5. Chess players' eye movements reveal rapid recognition of complex visual patterns: Evidence from a chess-related visual search task.

    Science.gov (United States)

    Sheridan, Heather; Reingold, Eyal M

    2017-03-01

    To explore the perceptual component of chess expertise, we monitored the eye movements of expert and novice chess players during a chess-related visual search task that tested anecdotal reports that a key differentiator of chess skill is the ability to visualize the complex moves of the knight piece. Specifically, chess players viewed an array of four minimized chessboards, and they rapidly searched for the target board that allowed a knight piece to reach a target square in three moves. On each trial, there was only one target board (i.e., the "Yes" board), and for the remaining "lure" boards, the knight's path was blocked on either the first move (the "Easy No" board) or the second move (i.e., "the Difficult No" board). As evidence that chess experts can rapidly differentiate complex chess-related visual patterns, the experts (but not the novices) showed longer first-fixation durations on the "Yes" board relative to the "Difficult No" board. Moreover, as hypothesized, the task strongly differentiated chess skill: Reaction times were more than four times faster for the experts relative to novices, and reaction times were correlated with within-group measures of expertise (i.e., official chess ratings, number of hours of practice). These results indicate that a key component of chess expertise is the ability to rapidly recognize complex visual patterns.

  6. Expression profile of the Schistosoma japonicum degradome reveals differential protease expression patterns and potential anti-schistosomal intervention targets.

    Directory of Open Access Journals (Sweden)

    Shuai Liu

    2014-10-01

    Full Text Available Blood fluke proteases play pivotal roles in the processes of invasion, nutrition acquisition, immune evasion, and other host-parasite interactions. Hundreds of genes encoding putative proteases have been identified in the recently published schistosome genomes. However, the expression profiles of these proteases in Schistosoma species have not yet been systematically analyzed. We retrieved and culled the redundant protease sequences of Schistosoma japonicum, Schistosoma mansoni, Echinococcus multilocularis, and Clonorchis sinensis from public databases utilizing bioinformatic approaches. The degradomes of the four parasitic organisms and Homo sapiens were then comparatively analyzed. A total of 262 S. japonicum protease sequences were obtained and the expression profiles generated using whole-genome microarray. Four main clusters of protease genes with different expression patterns were identified: proteases up-regulated in hepatic schistosomula and adult worms, egg-specific or predominantly expressed proteases, cercaria-specific or predominantly expressed proteases, and constantly expressed proteases. A subset of protease genes with different expression patterns were further validated using real-time quantitative PCR. The present study represents the most comprehensive analysis of a degradome in Schistosoma species to date. These results provide a firm foundation for future research on the specific function(s of individual proteases and may help to refine anti-proteolytic strategies in blood flukes.

  7. Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli.

    Directory of Open Access Journals (Sweden)

    Carsten Marr

    Full Text Available The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN. By comparing this network with measured gene expression data, one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with fewer changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: (1 subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation and (2 subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.

  8. Population genomic analysis reveals differential evolutionary histories and patterns of diversity across subgenomes and subpopulations of Brassica napus L.

    Directory of Open Access Journals (Sweden)

    Elodie eGazave

    2016-04-01

    Full Text Available The allotetraploid species Brassica napus L. is a global crop of major economic importance, providing canola oil (seed and vegetables for human consumption and fodder and meal for livestock feed. Characterizing the genetic diversity present in the extant germplasm pool of B. napus is fundamental to better conserve, manage and utilize the genetic resources of this species. We used sequence-based genotyping to identify and genotype 30,881 SNPs in a diversity panel of 782 B. napus accessions, representing samples of winter and spring growth habits originating from 33 countries across Europe, Asia and America. We detected strong population structure broadly concordant with growth habit and geography, and identified three major genetic groups: spring (SP, winter Europe (WE, and winter Asia (WA. Subpopulation-specific polymorphism patterns suggest enriched genetic diversity within the WA group and a smaller effective breeding population for the SP group compared to WE. Interestingly, the two subgenomes of B. napus appear to have different geographic origins, with phylogenetic analysis placing WE and WA as basal clades for the other subpopulations in the C and A subgenomes, respectively. Finally, we identified 16 genomic regions where the patterns of diversity differed markedly from the genome-wide average, several of which are suggestive of genomic inversions. The results obtained in this study constitute a valuable resource for worldwide breeding efforts and the genetic dissection and prediction of complex B. napus traits.

  9. Long-Term Patterns in C-Q Relations in an Adirondack Stream Reveal Decreasing Severity of Episodic Acidification

    Science.gov (United States)

    Burns, D. A.; Lawrence, G. B.; Driscoll, C. T.; Sullivan, T. J.; Shao, S.; McDonnell, T. C.

    2017-12-01

    Episodic acidification occurs when surface water pH and ANC decrease temporarily during rain events and snowmelt. The principal drivers of episodic acidification are increases in sulfuric acid, nitric acid, organic acids, and dilution of base cations. In regions where surface waters are sensitive to acid deposition, ANC values may approach or decline below 0 µeq/L during high flows, which may result in deleterious effects to sensitive aquatic biota. The Adirondack Mountains of New York have abundant streams and lakes, many of which are highly sensitive to the effects of acid deposition. Long-term monitoring data indicate that pH and ANC in regional surface waters are increasing in response to decreases in the acidity of atmospheric deposition that result from decreasing SO2 and NOx emissions as the Clean Air Act and its ancillary rules and amendments have been implemented. Most surface-water monitoring focuses on low-flow and broad seasonal patterns, and less is known about how episodic acidification has responded to emissions decreases. Here, we report on spatial and temporal patterns in episodic acidification through analysis of C-Q relations from surveys that target varying flow conditions as well as data from a few long-term intensively sampled stream monitoring sites. Each stream sample was assigned a Q percentile value based on a resident or nearby gage, and a statistical relation between ANC values and Q percentile was developed. The magnitude of episodic decreases in ANC increases as low-flow ANC increases, a pattern that likely results from an increasing influence of dilution, especially evident when low-flow ANC values exceed 100 µeq/L. Chronically acidic streams with low-flow ANC near 0 µeq/L show little episodic acidification, whereas streams with low-flow ANC values of about 50 µeq/L generally show ANC decreases to less than 0 µeq/L at high flow. Preliminary analysis of a 24-yr data set (1991-2014) at Buck Creek indicates that increases in high

  10. Update heat exchanger designing principles

    International Nuclear Information System (INIS)

    Lipets, A.U.; Yampol'skij, A.E.

    1985-01-01

    Update heat exchanger design principles are analysed. Different coolant pattern in a heat exchanger are considered. It is suggested to rationally organize flow rates irregularity in it. Applying on heat exchanger designing measures on using really existing temperature and flow rate irregularities will permit to improve heat exchanger efficiency. It is expedient in some cases to artificially produce irregularities. In this connection some heat exchanger design principles must be reviewed now

  11. Gaze patterns reveal how texts are remembered: A mental model of what was described is favored over the text itself

    DEFF Research Database (Denmark)

    Traub, Franziska; Johansson, Roger; Holmqvist, Kenneth

    or incongruent with the spatial layout of the text itself. 28 participants read and recalled three texts: (1) a scene description congruent with the spatial layout of the text; (2) a scene description incongruent with the spatial layout of the text; and (3) a control text without any spatial scene content....... Recollection was performed orally while gazing at a blank screen. 
Results demonstrate that participant’s gaze patterns during recall more closely reflect the spatial layout of the scene than the physical locations of the text. We conclude that participants formed a mental model that represents the content...... of what was described, i.e., visuospatial information of the scene, which then guided the retrieval process. During their retellings, they moved the eyes across the blank screen as if they saw the scene in front of them. Whereas previous studies on the involvement of eye movements in mental imagery tasks...

  12. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

    DEFF Research Database (Denmark)

    Baillie, J Kenneth; Bretherick, Andrew; Haley, Christopher S

    2018-01-01

    Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns...... the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes...... in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn's disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely...

  13. Structure predictions of two Bauhinia variegata lectins reveal patterns of C-terminal properties in single chain legume lectins.

    Science.gov (United States)

    Moreira, Gustavo M S G; Conceição, Fabricio R; McBride, Alan J A; Pinto, Luciano da S

    2013-01-01

    Bauhinia variegata lectins (BVL-I and BVL-II) are single chain lectins isolated from the plant Bauhinia variegata. Single chain lectins undergo post-translational processing on its N-terminal and C-terminal regions, which determines their physiological targeting, carbohydrate binding activity and pattern of quaternary association. These two lectins are isoforms, BVL-I being highly glycosylated, and thus far, it has not been possible to determine their structures. The present study used prediction and validation algorithms to elucidate the likely structures of BVL-I and -II. The program Bhageerath-H was chosen from among three different structure prediction programs due to its better overall reliability. In order to predict the C-terminal region cleavage sites, other lectins known to have this modification were analysed and three rules were created: (1) the first amino acid of the excised peptide is small or hydrophobic; (2) the cleavage occurs after an acid, polar, or hydrophobic residue, but not after a basic one; and (3) the cleavage spot is located 5-8 residues after a conserved Leu amino acid. These rules predicted that BVL-I and -II would have fifteen C-terminal residues cleaved, and this was confirmed experimentally by Edman degradation sequencing of BVL-I. Furthermore, the C-terminal analyses predicted that only BVL-II underwent α-helical folding in this region, similar to that seen in SBA and DBL. Conversely, BVL-I and -II contained four conserved regions of a GS-I association, providing evidence of a previously undescribed X4+unusual oligomerisation between the truncated BVL-I and the intact BVL-II. This is the first report on the structural analysis of lectins from Bauhinia spp. and therefore is important for the characterisation C-terminal cleavage and patterns of quaternary association of single chain lectins.

  14. Analysis of plant LTR-retrotransposons at the fine-scale family level reveals individual molecular patterns

    Directory of Open Access Journals (Sweden)

    Domingues Douglas S

    2012-04-01

    Full Text Available Abstract Background Sugarcane is an important crop worldwide for sugar production and increasingly, as a renewable energy source. Modern cultivars have polyploid, large complex genomes, with highly unequal contributions from ancestral genomes. Long Terminal Repeat retrotransposons (LTR-RTs are the single largest components of most plant genomes and can substantially impact the genome in many ways. It is therefore crucial to understand their contribution to the genome and transcriptome, however a detailed study of LTR-RTs in sugarcane has not been previously carried out. Results Sixty complete LTR-RT elements were classified into 35 families within four Copia and three Gypsy lineages. Structurally, within lineages elements were similar, between lineages there were large size differences. FISH analysis resulted in the expected pattern of Gypsy/heterochromatin, Copia/euchromatin, but in two lineages there was localized clustering on some chromosomes. Analysis of related ESTs and RT-PCR showed transcriptional variation between tissues and families. Four distinct patterns were observed in sRNA mapping, the most unusual of which was that of Ale1, with very large numbers of 24nt sRNAs in the coding region. The results presented support the conclusion that distinct small RNA-regulated pathways in sugarcane target the lineages of LTR-RT elements. Conclusions Individual LTR-RT sugarcane families have distinct structures, and transcriptional and regulatory signatures. Our results indicate that in sugarcane individual LTR-RT families have distinct behaviors and can potentially impact the genome in diverse ways. For instance, these transposable elements may affect nearby genes by generating a diverse set of small RNA's that trigger gene silencing mechanisms. There is also some evidence that ancestral genomes contribute significantly different element numbers from particular LTR-RT lineages to the modern sugarcane cultivar genome.

  15. Objective assessment of chromatic and achromatic pattern adaptation reveals the temporal response properties of different visual pathways.

    Science.gov (United States)

    Robson, Anthony G; Kulikowski, Janus J

    2012-11-01

    The aim was to investigate the temporal response properties of magnocellular, parvocellular, and koniocellular visual pathways using increment/decrement changes in contrast to elicit visual evoked potentials (VEPs). Static achromatic and isoluminant chromatic gratings were generated on a monitor. Chromatic gratings were modulated along red/green (R/G) or subject-specific tritanopic confusion axes, established using a minimum distinct border criterion. Isoluminance was determined using minimum flicker photometry. Achromatic and chromatic VEPs were recorded to contrast increments and decrements of 0.1 or 0.2 superimposed on the static gratings (masking contrast 0-0.6). Achromatic increment/decrement changes in contrast evoked a percept of apparent motion when the spatial frequency was low; VEPs to such stimuli were positive in polarity and largely unaffected by high levels of static contrast, consistent with transient response mechanisms. VEPs to finer achromatic gratings showed marked attenuation as static contrast was increased. Chromatic VEPs to R/G or tritan chromatic contrast increments were of negative polarity and showed progressive attenuation as static contrast was increased, in keeping with increasing desensitization of the sustained responses of the color-opponent visual pathways. Chromatic contrast decrement VEPs were of positive polarity and less sensitive to pattern adaptation. The relative contribution of sustained/transient mechanisms to achromatic processing is spatial frequency dependent. Chromatic contrast increment VEPs reflect the sustained temporal response properties of parvocellular and koniocellular pathways. Cortical VEPs can provide an objective measure of pattern adaptation and can be used to probe the temporal response characteristics of different visual pathways.

  16. Historical collections reveal patterns of diffusion of sweet potato in Oceania obscured by modern plant movements and recombination.

    Science.gov (United States)

    Roullier, Caroline; Benoit, Laure; McKey, Doyle B; Lebot, Vincent

    2013-02-05

    The history of sweet potato in the Pacific has long been an enigma. Archaeological, linguistic, and ethnobotanical data suggest that prehistoric human-mediated dispersal events contributed to the distribution in Oceania of this American domesticate. According to the "tripartite hypothesis," sweet potato was introduced into Oceania from South America in pre-Columbian times and was then later newly introduced, and diffused widely across the Pacific, by Europeans via two historically documented routes from Mexico and the Caribbean. Although sweet potato is the most convincing example of putative pre-Columbian connections between human occupants of Polynesia and South America, the search for genetic evidence of pre-Columbian dispersal of sweet potato into Oceania has been inconclusive. Our study attempts to fill this gap. Using complementary sets of markers (chloroplast and nuclear microsatellites) and both modern and herbarium samples, we test the tripartite hypothesis. Our results provide strong support for prehistoric transfer(s) of sweet potato from South America (Peru-Ecuador region) into Polynesia. Our results also document a temporal shift in the pattern of distribution of genetic variation in sweet potato in Oceania. Later reintroductions, accompanied by recombination between distinct sweet potato gene pools, have reshuffled the crop's initial genetic base, obscuring primary patterns of diffusion and, at the same time, giving rise to an impressive number of local variants. Moreover, our study shows that phenotypes, names, and neutral genes do not necessarily share completely parallel evolutionary histories. Multidisciplinary approaches, thus, appear necessary for accurate reconstruction of the intertwined histories of plants and humans.

  17. Dual DNA methylation patterns in the CNS reveal developmentally poised chromatin and monoallelic expression of critical genes.

    Directory of Open Access Journals (Sweden)

    Jinhui Wang

    Full Text Available As a first step towards discovery of genes expressed from only one allele in the CNS, we used a tiling array assay for DNA sequences that are both methylated and unmethylated (the MAUD assay. We analyzed regulatory regions of the entire mouse brain transcriptome, and found that approximately 10% of the genes assayed showed dual DNA methylation patterns. They include a large subset of genes that display marks of both active and silent, i.e., poised, chromatin during development, consistent with a link between differential DNA methylation and lineage-specific differentiation within the CNS. Sixty-five of the MAUD hits and 57 other genes whose function is of relevance to CNS development and/or disorders were tested for allele-specific expression in F(1 hybrid clonal neural stem cell (NSC lines. Eight MAUD hits and one additional gene showed such expression. They include Lgi1, which causes a subtype of inherited epilepsy that displays autosomal dominance with incomplete penetrance; Gfra2, a receptor for glial cell line-derived neurotrophic factor GDNF that has been linked to kindling epilepsy; Unc5a, a netrin-1 receptor important in neurodevelopment; and Cspg4, a membrane chondroitin sulfate proteoglycan associated with malignant melanoma and astrocytoma in human. Three of the genes, Camk2a, Kcnc4, and Unc5a, show preferential expression of the same allele in all clonal NSC lines tested. The other six genes show a stochastic pattern of monoallelic expression in some NSC lines and bi-allelic expression in others. These results support the estimate that 1-2% of genes expressed in the CNS may be subject to allelic exclusion, and demonstrate that the group includes genes implicated in major disorders of the CNS as well as neurodevelopment.

  18. Gene expression in chicken reveals correlation with structural genomic features and conserved patterns of transcription in the terrestrial vertebrates.

    Directory of Open Access Journals (Sweden)

    Haisheng Nie

    Full Text Available BACKGROUND: The chicken is an important agricultural and avian-model species. A survey of gene expression in a range of different tissues will provide a benchmark for understanding expression levels under normal physiological conditions in birds. With expression data for birds being very scant, this benchmark is of particular interest for comparative expression analysis among various terrestrial vertebrates. METHODOLOGY/PRINCIPAL FINDINGS: We carried out a gene expression survey in eight major chicken tissues using whole genome microarrays. A global picture of gene expression is presented for the eight tissues, and tissue specific as well as common gene expression were identified. A Gene Ontology (GO term enrichment analysis showed that tissue-specific genes are enriched with GO terms reflecting the physiological functions of the specific tissue, and housekeeping genes are enriched with GO terms related to essential biological functions. Comparisons of structural genomic features between tissue-specific genes and housekeeping genes show that housekeeping genes are more compact. Specifically, coding sequence and particularly introns are shorter than genes that display more variation in expression between tissues, and in addition intergenic space was also shorter. Meanwhile, housekeeping genes are more likely to co-localize with other abundantly or highly expressed genes on the same chromosomal regions. Furthermore, comparisons of gene expression in a panel of five common tissues between birds, mammals and amphibians showed that the expression patterns across tissues are highly similar for orthologous genes compared to random gene pairs within each pair-wise comparison, indicating a high degree of functional conservation in gene expression among terrestrial vertebrates. CONCLUSIONS: The housekeeping genes identified in this study have shorter gene length, shorter coding sequence length, shorter introns, and shorter intergenic regions, there seems

  19. Navigation strategies as revealed by error patterns on the Magic Carpet test in children with cerebral palsy

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    Vittorio eBelmonti

    2015-07-01

    Full Text Available IntroductionShort-term memory develops differently in navigation vs. manual space. The Magic Carpet (MC is a novel navigation test derived from the Walking Corsi Test and the manual Corsi Block-tapping Task (CBT. The MC requires mental rotations and executive function. In Cerebral Palsy (CP, CBT and MC scores relate differently to clinical and lesional factors. Hypotheses of this study are: that frontal lesions specifically affect navigation in CP; that brain lesions affect MC cognitive strategies.Material and methodsTwenty-two children with spastic CP, aged 5 to 14 years, 14 with a unilateral and 8 with a bilateral form, underwent the CBT and the MC. Errors were classified into 7 patterns by a recently described algorithm. Brain lesions were quantified according to a novel semi-quantitative MRI scale. Control data were partially drawn from a previous study on 91 typically developing children.ResultsChildren with CP performed worse than controls on both tests. Right hemispheric impairment correlated with spatial memory. MC span was reduced less than CBT span and was more selectively related to right middle white-matter and frontal lesions. Error patterns were differently distributed in CP than in typical development and depended on right brain impairment: children with more extensive right lesions made more positional than sequential errors.DiscussionIn CP, navigation is affected only by extensive lesions involving the right frontal lobe. In addition, these are associated with abnormal cognitive strategies. Whereas in typical development positional errors, preserving serial order, increase with age and performance, in CP they are associated with poorer performance and more extensive right-brain lesions. The explanation may lie in lesion side: right brain is crucial for mental rotations, necessary for spatial updating. Left-lateralized spatial memory strategies, relying on serial order, are not efficient if not accompanied by right-brain spatial

  20. Whole-exome sequencing reveals the spectrum of gene mutations and the clonal evolution patterns in paediatric acute myeloid leukaemia.

    Science.gov (United States)

    Shiba, Norio; Yoshida, Kenichi; Shiraishi, Yuichi; Okuno, Yusuke; Yamato, Genki; Hara, Yusuke; Nagata, Yasunobu; Chiba, Kenichi; Tanaka, Hiroko; Terui, Kiminori; Kato, Motohiro; Park, Myoung-Ja; Ohki, Kentaro; Shimada, Akira; Takita, Junko; Tomizawa, Daisuke; Kudo, Kazuko; Arakawa, Hirokazu; Adachi, Souichi; Taga, Takashi; Tawa, Akio; Ito, Etsuro; Horibe, Keizo; Sanada, Masashi; Miyano, Satoru; Ogawa, Seishi; Hayashi, Yasuhide

    2016-11-01

    Acute myeloid leukaemia (AML) is a molecularly and clinically heterogeneous disease. Targeted sequencing efforts have identified several mutations with diagnostic and prognostic values in KIT, NPM1, CEBPA and FLT3 in both adult and paediatric AML. In addition, massively parallel sequencing enabled the discovery of recurrent mutations (i.e. IDH1/2 and DNMT3A) in adult AML. In this study, whole-exome sequencing (WES) of 22 paediatric AML patients revealed mutations in components of the cohesin complex (RAD21 and SMC3), BCORL1 and ASXL2 in addition to previously known gene mutations. We also revealed intratumoural heterogeneities in many patients, implicating multiple clonal evolution events in the development of AML. Furthermore, targeted deep sequencing in 182 paediatric AML patients identified three major categories of recurrently mutated genes: cohesion complex genes [STAG2, RAD21 and SMC3 in 17 patients (8·3%)], epigenetic regulators [ASXL1/ASXL2 in 17 patients (8·3%), BCOR/BCORL1 in 7 patients (3·4%)] and signalling molecules. We also performed WES in four patients with relapsed AML. Relapsed AML evolved from one of the subclones at the initial phase and was accompanied by many additional mutations, including common driver mutations that were absent or existed only with lower allele frequency in the diagnostic samples, indicating a multistep process causing leukaemia recurrence. © 2016 John Wiley & Sons Ltd.

  1. Evaluation of a hierarchy of models reveals importance of substrate limitation for predicting carbon dioxide and methane exchange in restored wetlands

    Science.gov (United States)

    Oikawa, P. Y.; Jenerette, G. D.; Knox, S. H.; Sturtevant, C.; Verfaillie, J.; Dronova, I.; Poindexter, C. M.; Eichelmann, E.; Baldocchi, D. D.

    2017-01-01

    Wetlands and flooded peatlands can sequester large amounts of carbon (C) and have high greenhouse gas mitigation potential. There is growing interest in financing wetland restoration using C markets; however, this requires careful accounting of both CO2 and CH4 exchange at the ecosystem scale. Here we present a new model, the PEPRMT model (Peatland Ecosystem Photosynthesis Respiration and Methane Transport), which consists of a hierarchy of biogeochemical models designed to estimate CO2 and CH4 exchange in restored managed wetlands. Empirical models using temperature and/or photosynthesis to predict respiration and CH4 production were contrasted with a more process-based model that simulated substrate-limited respiration and CH4 production using multiple carbon pools. Models were parameterized by using a model-data fusion approach with multiple years of eddy covariance data collected in a recently restored wetland and a mature restored wetland. A third recently restored wetland site was used for model validation. During model validation, the process-based model explained 70% of the variance in net ecosystem exchange of CO2 (NEE) and 50% of the variance in CH4 exchange. Not accounting for high respiration following restoration led to empirical models overestimating annual NEE by 33-51%. By employing a model-data fusion approach we provide rigorous estimates of uncertainty in model predictions, accounting for uncertainty in data, model parameters, and model structure. The PEPRMT model is a valuable tool for understanding carbon cycling in restored wetlands and for application in carbon market-funded wetland restoration, thereby advancing opportunity to counteract the vast degradation of wetlands and flooded peatlands.

  2. Oligonucleotide array discovery of polymorphisms in cultivated tomato (Solanum lycopersicum L. reveals patterns of SNP variation associated with breeding

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    Zhu Tong

    2009-10-01

    Full Text Available Abstract Background Cultivated tomato (Solanum lycopersicum L. has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. We explored array-based single feature polymorphism (SFP discovery as a high-throughput approach for marker development in cultivated tomato. Results Three varieties, FL7600 (fresh-market, OH9242 (processing, and PI114490 (cherry were used as a source of genomic DNA for hybridization to oligonucleotide arrays. Identification of SFPs was based on outlier detection using regression analysis of normalized hybridization data within a probe set for each gene. A subset of 189 putative SFPs was sequenced for validation. The rate of validation depended on the desired level of significance (α used to define the confidence interval (CI, and ranged from 76% for polymorphisms identified at α ≤ 10-6 to 60% for those identified at α ≤ 10-2. Validation percentage reached a plateau between α ≤ 10-4 and α ≤ 10-7, but failure to identify known SFPs (Type II error increased dramatically at α ≤ 10-6. Trough sequence validation, we identified 279 SNPs and 27 InDels in 111 loci. Sixty loci contained ≥ 2 SNPs per locus. We used a subset of validated SNPs for genetic diversity analysis of 92 tomato varieties and accessions. Pairwise estimation of θ (Fst suggested significant differentiation between collections of fresh-market, processing, vintage, Latin American (landrace, and S. pimpinellifolium accessions. The fresh-market and processing groups displayed high genetic diversity relative to vintage and landrace groups. Furthermore, the patterns of SNP variation indicated that domestication and early breeding practices have led to progressive genetic bottlenecks while modern breeding practices have reintroduced genetic variation into the crop from wild species. Finally, we examined the ratio of non-synonymous (Ka to synonymous substitutions (Ks for 20 loci with multiple SNPs (≥ 4 per

  3. Roles for SH2 and SH3 domains in Lyn kinase association with activated FcepsilonRI in RBL mast cells revealed by patterned surface analysis.

    Science.gov (United States)

    Hammond, Stephanie; Wagenknecht-Wiesner, Alice; Veatch, Sarah L; Holowka, David; Baird, Barbara

    2009-10-01

    In mast cells, antigen-mediated cross-linking of IgE bound to its high-affinity surface receptor, FcepsilonRI, initiates a signaling cascade that culminates in degranulation and release of allergic mediators. Antigen-patterned surfaces, in which the antigen is deposited in micron-sized features on a silicon substrate, were used to examine the spatial relationship between clustered IgE-FcepsilonRI complexes and Lyn, the signal-initiating tyrosine kinase. RBL mast cells expressing wild-type Lyn-EGFP showed co-redistribution of this protein with clustered IgE receptors on antigen-patterned surfaces, whereas Lyn-EGFP containing an inhibitory point mutation in its SH2 domain did not significantly accumulate with the patterned antigen, and Lyn-EGFP with an inhibitory point mutation in its SH3 domain exhibited reduced interactions. Our results using antigen-patterned surfaces and quantitative cross-correlation image analysis reveal that both the SH2 and SH3 domains contribute to interactions between Lyn kinase and cross-linked IgE receptors in stimulated mast cells.

  4. Genome-wide analyses of the Bemisia tabaci species complex reveal contrasting patterns of admixture and complex demographic histories.

    Directory of Open Access Journals (Sweden)

    S Elfekih

    Full Text Available Once considered a single species, the whitefly, Bemisia tabaci, is a complex of numerous morphologically indistinguishable species. Within the last three decades, two of its members (MED and MEAM1 have become some of the world's most damaging agricultural pests invading countries across Europe, Africa, Asia and the Americas and affecting a vast range of agriculturally important food and fiber crops through both feeding-related damage and the transmission of numerous plant viruses. For some time now, researchers have relied on a single mitochondrial gene and/or a handful of nuclear markers to study this species complex. Here, we move beyond this by using 38,041 genome-wide Single Nucleotide Polymorphisms, and show that the two invasive members of the complex are closely related species with signatures of introgression with a third species (IO. Gene flow patterns were traced between contemporary invasive populations within MED and MEAM1 species and these were best explained by recent international trade. These findings have profound implications for delineating the B. tabaci species status and will impact quarantine measures and future management strategies of this global pest.

  5. Differential SPL gene expression patterns reveal candidate genes underlying flowering time and architectural differences in Mimulus and Arabidopsis.

    Science.gov (United States)

    Jorgensen, Stacy A; Preston, Jill C

    2014-04-01

    Evolutionary transitions in growth habit and flowering time responses to variable environmental signals have occurred multiple times independently across angiosperms and have major impacts on plant fitness. Proteins in the SPL family of transcription factors collectively regulate flowering time genes that have been implicated in interspecific shifts in annuality/perenniality. However, their potential importance in the evolution of angiosperm growth habit has not been extensively investigated. Here we identify orthologs representative of the major SPL gene clades in annual Arabidopsis thaliana and Mimulus guttatus IM767, and perennial A. lyrata and M. guttatus PR, and characterize their expression. Spatio-temporal expression patterns are complex across both diverse tissues of the same taxa and comparable tissues of different taxa, consistent with genic sub- or neo-functionalization. However, our data are consistent with a general role for several SPL genes in the promotion of juvenile to adult phase change and/or flowering time in Mimulus and Arabidopsis. Furthermore, several candidate genes were identified for future study whose differential expression correlates with growth habit and architectural variation in annual versus perennial taxa. Copyright © 2014 Elsevier Inc. All rights reserved.

  6. Treating fossils as terminal taxa in divergence time estimation reveals ancient vicariance patterns in the palpimanoid spiders.

    Science.gov (United States)

    Wood, Hannah Marie; Matzke, Nicholas J; Gillespie, Rosemary G; Griswold, Charles E

    2013-03-01

    Incorporation of fossils into biogeographic studies can have a profound effect on the conclusions that result, particularly when fossil ranges are nonoverlapping with extant ranges. This is the case in archaeid spiders, where there are known fossils from the Northern Hemisphere, yet all living members are restricted to the Southern Hemisphere. To better understand the biogeographic patterns of archaeid spiders and their palpimanoid relatives, we estimate a dated phylogeny using a relaxed clock on a combined molecular and morphological data set. Dating information is compared with treating the archaeid fossil taxa as both node calibrations and as noncontemporaneous terminal tips, both with and without additional calibration points. Estimation of ancestral biogeographic ranges is then performed, using likelihood and Bayesian methods to take into account uncertainty in phylogeny and in dating. We find that treating the fossils as terminal tips within a Bayesian framework, as opposed to dating the phylogeny based only on molecular data with the dates coming from node calibrations, removes the subjectivity involved in assigning priors, which has not been possible with previous methods. Our analyses suggest that the diversification of the northern and southern archaeid lineages was congruent with the breakup of Pangaea into Laurasia and Gondwanaland. This analysis provides a rare example, and perhaps the most strongly supported, where a dated phylogeny confirms a biogeographical hypothesis based on vicariance due to the breakup of the ancient continental plates.

  7. Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer

    International Nuclear Information System (INIS)

    Kangaspeska, Sara; Hultsch, Susanne; Jaiswal, Alok; Edgren, Henrik; Mpindi, John-Patrick; Eldfors, Samuli; Brück, Oscar; Aittokallio, Tero; Kallioniemi, Olli

    2016-01-01

    The estrogen receptor (ER) inhibitor tamoxifen reduces breast cancer mortality by 31 % and has served as the standard treatment for ER-positive breast cancers for decades. However, 50 % of advanced ER-positive cancers display de novo resistance to tamoxifen, and acquired resistance evolves in 40 % of patients who initially respond. Mechanisms underlying resistance development remain poorly understood and new therapeutic opportunities are urgently needed. Here, we report the generation and characterization of seven tamoxifen-resistant breast cancer cell lines from four parental strains. Using high throughput drug sensitivity and resistance testing (DSRT) with 279 approved and investigational oncology drugs, exome-sequencing and network analysis, we for the first time, systematically determine the drug response profiles specific to tamoxifen resistance. We discovered emerging vulnerabilities towards specific drugs, such as ERK1/2-, proteasome- and BCL-family inhibitors as the cells became tamoxifen-resistant. Co-resistance to other drugs such as the survivin inhibitor YM155 and the chemotherapeutic agent paclitaxel also occurred. This study indicates that multiple molecular mechanisms dictate endocrine resistance, resulting in unexpected vulnerabilities to initially ineffective drugs, as well as in emerging co-resistances. Thus, combatting drug-resistant tumors will require patient-tailored strategies in order to identify new drug vulnerabilities, and to understand the associated co-resistance patterns. The online version of this article (doi:10.1186/s12885-016-2452-5) contains supplementary material, which is available to authorized users

  8. Systematic drug screening reveals specific vulnerabilities and co-resistance patterns in endocrine-resistant breast cancer.

    Science.gov (United States)

    Kangaspeska, Sara; Hultsch, Susanne; Jaiswal, Alok; Edgren, Henrik; Mpindi, John-Patrick; Eldfors, Samuli; Brück, Oscar; Aittokallio, Tero; Kallioniemi, Olli

    2016-07-04

    The estrogen receptor (ER) inhibitor tamoxifen reduces breast cancer mortality by 31 % and has served as the standard treatment for ER-positive breast cancers for decades. However, 50 % of advanced ER-positive cancers display de novo resistance to tamoxifen, and acquired resistance evolves in 40 % of patients who initially respond. Mechanisms underlying resistance development remain poorly understood and new therapeutic opportunities are urgently needed. Here, we report the generation and characterization of seven tamoxifen-resistant breast cancer cell lines from four parental strains. Using high throughput drug sensitivity and resistance testing (DSRT) with 279 approved and investigational oncology drugs, exome-sequencing and network analysis, we for the first time, systematically determine the drug response profiles specific to tamoxifen resistance. We discovered emerging vulnerabilities towards specific drugs, such as ERK1/2-, proteasome- and BCL-family inhibitors as the cells became tamoxifen-resistant. Co-resistance to other drugs such as the survivin inhibitor YM155 and the chemotherapeutic agent paclitaxel also occurred. This study indicates that multiple molecular mechanisms dictate endocrine resistance, resulting in unexpected vulnerabilities to initially ineffective drugs, as well as in emerging co-resistances. Thus, combatting drug-resistant tumors will require patient-tailored strategies in order to identify new drug vulnerabilities, and to understand the associated co-resistance patterns.

  9. The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota).

    Science.gov (United States)

    Opik, M; Vanatoa, A; Vanatoa, E; Moora, M; Davison, J; Kalwij, J M; Reier, U; Zobel, M

    2010-10-01

    • Here, we describe a new database, MaarjAM, that summarizes publicly available Glomeromycota DNA sequence data and associated metadata. The goal of the database is to facilitate the description of distribution and richness patterns in this group of fungi. • Small subunit (SSU) rRNA gene sequences and available metadata were collated from all suitable taxonomic and ecological publications. These data have been made accessible in an open-access database (http://maarjam.botany.ut.ee). • Two hundred and eighty-two SSU rRNA gene virtual taxa (VT) were described based on a comprehensive phylogenetic analysis of all collated Glomeromycota sequences. Two-thirds of VT showed limited distribution ranges, occurring in single current or historic continents or climatic zones. Those VT that associated with a taxonomically wide range of host plants also tended to have a wide geographical distribution, and vice versa. No relationships were detected between VT richness and latitude, elevation or vascular plant richness. • The collated Glomeromycota molecular diversity data suggest limited distribution ranges in most Glomeromycota taxa and a positive relationship between the width of a taxon's geographical range and its host taxonomic range. Inconsistencies between molecular and traditional taxonomy of Glomeromycota, and shortage of data from major continents and ecosystems, are highlighted.

  10. Wing pattern morphology of three closely related Melitaea (Lepidoptera, Nymphalidae species reveals highly inaccurate external morphology-based species identification

    Directory of Open Access Journals (Sweden)

    Jure Jugovic

    2014-06-01

    Full Text Available Wing morphology of the three closely related species of Melitaea – M. athalia (Rottemburg, 1775, M. aurelia (Nickerl, 1850 and M. britomartis Assmann, 1847 – co-occurring in the Balkans (SE Europe was investigated in detail through visual inspection, morphometric analysis and multivariate statistical analysis. Results are compared to recent phylogenetic studies, searching for concordant patterns and discrepancies between the two approaches. The morphology of the genitalic structures is also compared with the results of the other two approaches. The main conclusions are as follows: (1 small albeit significant differences in wing morphology exist among the three species and (2 while the structure of male genitalia and phylogenetic position of the three species are concordant, they are (3 in discordance with the wing morphology. The present study represents another example where identification based on external morphology would lead to highly unreliable determinations, hence identification based on phylogenetic studies and/or genitalia is strongly recommended not only for the three studied species but also more broadly within the genus. Furthermore, we show that some of the characters generally used in the identification of these three Melitaea species should be avoided in future.

  11. Graph theoretical analysis reveals the reorganization of the brain network pattern in primary open angle glaucoma patients

    International Nuclear Information System (INIS)

    Wang, Jieqiong; Li, Ting; Xian, Junfang; Wang, Ningli; He, Huiguang

    2016-01-01

    Most previous glaucoma studies with resting-state fMRI have focused on the neuronal activity in the individual structure of the brain, yet ignored the functional communication of anatomically separated structures. The purpose of this study is to investigate the efficiency of the functional communication change or not in glaucoma patients. We applied the resting-state fMRI data to construct the connectivity network of 25 normal controls and 25 age-gender-matched primary open angle glaucoma patients. Graph theoretical analysis was performed to assess brain network pattern differences between the two groups. No significant differences of the global network measures were found between the two groups. However, the local measures were radically reorganized in glaucoma patients. Comparing with the hub regions in normal controls' network, we found that six hub regions disappeared and nine hub regions appeared in the network of patients. In addition, the betweenness centralities of two altered hub regions, right fusiform gyrus and right lingual gyrus, were significantly correlated with the visual field mean deviation. Although the efficiency of functional communication is preserved in the brain network of the glaucoma at the global level, the efficiency of functional communication is altered in some specialized regions of the glaucoma. (orig.)

  12. Metabolomic profiling reveals distinct patterns of tricarboxylic acid disorders in blood stasis syndrome associated with coronary heart disease.

    Science.gov (United States)

    Wang, Yong; Li, Chun; Chang, Hong; Lu, Ling-Hui; Qiu, Qi; Ouyang, Yu-Lin; Yu, Jun-da; Guo, Shu-Zhen; Han, Jing; Wang, Wei

    2016-08-01

    To investigate the underlying metabolomic profifiling of coronary heart disease (CHD) with blood stasis syndrome (BSS). CHD model was induced by a nameroid constrictor in Chinese miniature swine. Fifteen miniature swine were randomly divided into a model group (n=9) and a control group (n=6), respectively according to arandom number table. After 4 weeks, plasma hemorheology was detected by automatic hemorheological analyzer, indices including hematocrit, plasma viscosity, blood viscosity, rigidity index and erythrocyte sedimentation rate; cardiac function was assessed by echocardiograph to detect left ventricular end-systolic diameter (LVED), left ventricular end-diastolic diameter (LVEDd), ejection fraction (EF), fractional shortening (FS) and other indicators. Gas chromatography coupled with mass spectrometry (GC-MS) and bioinformatics were applied to analyze spectra of CHD plasma with BSS. The results of hemorheology analysis showed signifificant changes in viscosity, with low shear whole blood viscosity being lower and plasma viscosity higher in the model group compared with the control group. Moreover, whole blood reduction viscosity at high shear rate and whole blood reduction viscosity at low shear rate increased signifificantly (P patterns involved were associated with dysfunction of energy metabolism including glucose and lipid disorders, especially in glycolysis/gluconeogenesis, galactose metabolism and adenosine-triphosphate-binding cassette transporters. Glucose metabolism and lipid metabolism disorders were the major contributors to the syndrome classifification of CHD with BSS.

  13. Graph theoretical analysis reveals the reorganization of the brain network pattern in primary open angle glaucoma patients

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Jieqiong [Chinese Academy of Sciences, State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Beijing (China); Li, Ting; Xian, Junfang [Capital Medical University, Department of Radiology, Beijing Tongren Hospital, Beijing (China); Wang, Ningli [Capital Medical University, Department of Ophthalmology, Beijing Tongren Hospital, Beijing (China); He, Huiguang [Chinese Academy of Sciences, State Key Laboratory of Management and Control for Complex Systems, Institute of Automation, Beijing (China); Chinese Academy of Sciences, Research Center for Brain-Inspired Intelligence, Institute of Automation, Beijing (China)

    2016-11-15

    Most previous glaucoma studies with resting-state fMRI have focused on the neuronal activity in the individual structure of the brain, yet ignored the functional communication of anatomically separated structures. The purpose of this study is to investigate the efficiency of the functional communication change or not in glaucoma patients. We applied the resting-state fMRI data to construct the connectivity network of 25 normal controls and 25 age-gender-matched primary open angle glaucoma patients. Graph theoretical analysis was performed to assess brain network pattern differences between the two groups. No significant differences of the global network measures were found between the two groups. However, the local measures were radically reorganized in glaucoma patients. Comparing with the hub regions in normal controls' network, we found that six hub regions disappeared and nine hub regions appeared in the network of patients. In addition, the betweenness centralities of two altered hub regions, right fusiform gyrus and right lingual gyrus, were significantly correlated with the visual field mean deviation. Although the efficiency of functional communication is preserved in the brain network of the glaucoma at the global level, the efficiency of functional communication is altered in some specialized regions of the glaucoma. (orig.)

  14. Information theoretic measures of network coordination in high-frequency scalp EEG reveal dynamic patterns associated with seizure termination.

    Science.gov (United States)

    Stamoulis, Catherine; Schomer, Donald L; Chang, Bernard S

    2013-08-01

    How a seizure terminates is still under-studied and, despite its clinical importance, remains an obscure phase of seizure evolution. Recent studies of seizure-related scalp EEGs at frequencies >100 Hz suggest that neural activity, in the form of oscillations and/or neuronal network interactions, may play an important role in preictal/ictal seizure evolution (Andrade-Valenca et al., 2011; Stamoulis et al., 2012). However, the role of high-frequency activity in seizure termination, is unknown, if it exists at all. Using information theoretic measures of network coordination, this study investigated ictal and immediate postictal neurodynamic interactions encoded in scalp EEGs from a relatively small sample of 8 patients with focal epilepsy and multiple seizures originating in temporal and/or frontal brain regions, at frequencies ≤ 100 Hz and >100 Hz, respectively. Despite some heterogeneity in the dynamics of these interactions, consistent patterns were also estimated. Specifically, in several seizures, linear or non-linear increase in high-frequency neuronal coordination during ictal intervals, coincided with a corresponding decrease in coordination at frequencies interval, which continues during the postictal interval. This may be one of several possible mechanisms that facilitate seizure termination. In fact, inhibition of pairwise interactions between EEGs by other signals in their spatial neighborhood, quantified by negative interaction information, was estimated at frequencies ≤ 100 Hz, at least in some seizures. Copyright © 2013 Elsevier B.V. All rights reserved.

  15. The effect of channel flow pattern on internal properties distribution of a proton exchange membrane fuel cell for cathode starvation conditions

    International Nuclear Information System (INIS)

    Ko, Dong Soo; Kang, Young Min; Yang, Jang Sik; Jeong, Ji Hwan; Choi, Gyung Min; Kim, Duck Jool

    2010-01-01

    The effect of channel flow pattern on the internal properties distribution of a proton exchange membrane fuel cell (PEMFC) for cathode starvation conditions in a unit cell was investigated through numerical studies and experiments. The polarization curves of a lab-scale mixed serpentine PEMFC were measured with increasing current loads for different cell temperatures (40, 50, and 60 .deg. C) at a relative humidity of 100%. To study the local temperature on the membrane, the water content in the MEA, and the gas velocity in terms of the channel type of the PEMFC with operating characteristics, numerical studies using the es-pemfc module of STAR-CD, which have been matched to the experimental data, were conducted in detail. The water content and velocity at the cathode channel bend of the mixed serpentine channel were relatively higher than those at the single and double channels. Conversely, the local temperature and mean temperature on the membrane of a single serpentine channel were the highest among all channels. These results can be used to design the PEMFC system, the channel flow field, and the cooling device

  16. Eight-Week Remote Monitoring Using a Freely Worn Device Reveals Unstable Gait Patterns in Older Fallers.

    Science.gov (United States)

    Brodie, Matthew A; Lord, Stephen R; Coppens, Milou J; Annegarn, Janneke; Delbaere, Kim

    2015-11-01

    Develop algorithms to detect gait impairments remotely using data from freely worn devices during long-term monitoring. Identify statistical models that describe how gait performances are distributed over several weeks. Determine the data window required to reliably assess an increased propensity for falling. 1085 days of walking data were collected from eighteen independent-living older people (mean age 83 years) using a freely worn pendant sensor (housing a triaxial accelerometer and pressure sensor). Statistical distributions from several accelerometer-derived gait features (encompassing quantity, exposure, intensity, and quality) were compared for those with and without a history of falling. Participants completed more short walks relative to long walks, as approximated by a power law. Walks less than 13.1 s comprised 50% of exposure to walking-related falls. Daily-life cadence was bimodal and step-time variability followed a log-normal distribution. Fallers took significantly fewer steps per walk and had relatively more exposure from short walks and greater mode of step-time variability. Using a freely worn device and wavelet-based analysis tools allowed long-term monitoring of walks greater than or equal to three steps. In older people, short walks constitute a large proportion of exposure to falls. To identify fallers, mode of variability may be a better measure of central tendency than mean of variability. A week's monitoring is sufficient to reliably assess the long-term propensity for falling. Statistical distributions of gait performances provide a reference for future wearable device development and research into the complex relationships between daily-life walking patterns, morbidity, and falls.

  17. Diversification Patterns of Lanternfishes Reveal Multiple Rate Shifts in a Critical Mesopelagic Clade Targeted for Human Exploitation.

    Science.gov (United States)

    Denton, John S S

    2018-03-19

    The mesopelagic (midwater) and deep-sea environments together comprise over 90% of the volume of the world ocean [1] and provide services that are only recently becoming recognized [2]. One of the most significant of these services relates to midwater fish biomass, recently estimated to be two orders of magnitude larger than the current worldwide fisheries catch [3, 4]. Calls to exploit midwater fish biomass have increased despite warnings about the unknown recovery potential of such organisms [2] and despite existing data suggesting that deep-sea fishes could be classified as endangered [5]. Here, to provide a null model for the respondability of midwater fishes, I use lanternfishes-which comprise the majority of worldwide midwater fish biomass [6]-to examine the diversification response of a critical midwater clade to oceanic changes over evolutionary timescales, including several extinction and turnover events. Using a time-calibrated molecular phylogeny based on seven autosomal protein-coding loci, with over 50% species sampling and three ingroup node calibrations, I show that lanternfishes exhibit a continuously increasing diversification rate, consistent with nonequilibrium speciation dynamics, and three major evolutionary rate shift locations with timing that is similar to those of marine clades in more well-known environments. These results suggest that lanternfish diversification patterns overlapped with major events in the physical partitioning of the ocean volume and that the clade has responded positively to a range of pre-Anthropocene extinction drivers [7]. However, lanternfish respondability to modern extinction drivers-habitat loss and overexploitation-is best addressed with populational and ecological data and remains largely unknown. Copyright © 2018 Elsevier Ltd. All rights reserved.

  18. Phylogenetic and population genetic analyses of diploid Leucaena (Leguminosae; Mimosoideae) reveal cryptic species diversity and patterns of divergent allopatric speciation.

    Science.gov (United States)

    Govindarajulu, Rajanikanth; Hughes, Colin E; Bailey, C Donovan

    2011-12-01

    Leucaena comprises 17 diploid species, five tetraploid species, and a complex series of hybrids whose evolutionary histories have been influenced by human seed translocation, cultivation, and subsequent spontaneous hybridization. Here we investigated patterns of evolutionary divergence among diploid Leucaena through comprehensively sampled multilocus phylogenetic and population genetic approaches to address species delimitation, interspecific relationships, hybridization, and the predominant mode of speciation among diploids. Parsimony- and maximum-likelihood-based phylogenetic approaches were applied to 59 accessions sequenced for six SCAR-based nuclear loci, nrDNA ITS, and four cpDNA regions. Population genetic comparisons included 1215 AFLP loci representing 42 populations and 424 individuals. Phylogenetic results provided a well-resolved hypothesis of divergent species relationships, recovering previously recognized clades of diploids as well as newly resolved relationships. Phylogenetic and population genetic assessments identified two cryptic species that are consistent with geography and morphology. Findings from this study highlight the importance and utility of multilocus data in the recovery of complex evolutionary histories. The results are consistent with allopatric divergence representing the predominant mode of speciation among diploid Leucaena. These findings contrast with the potential hybrid origin of several tetraploid species and highlight the importance of human translocation of seed to the origin of these tetraploids. The recognition of one previously unrecognized species (L. cruziana) and the elevation of another taxon (L. collinsii subsp. zacapana) to specific status (L. zacapana) is consistent with a growing number of newly diagnosed species from neotropical seasonally dry forests, suggesting these communities harbor greater species diversity than previously recognized.

  19. RNA-Seq Analysis of Developing Pecan (Carya illinoinensis) Embryos Reveals Parallel Expression Patterns among Allergen and Lipid Metabolism Genes.

    Science.gov (United States)

    Mattison, Christopher P; Rai, Ruhi; Settlage, Robert E; Hinchliffe, Doug J; Madison, Crista; Bland, John M; Brashear, Suzanne; Graham, Charles J; Tarver, Matthew R; Florane, Christopher; Bechtel, Peter J

    2017-02-22

    The pecan nut is a nutrient-rich part of a healthy diet full of beneficial fatty acids and antioxidants, but can also cause allergic reactions in people suffering from food allergy to the nuts. The transcriptome of a developing pecan nut was characterized to identify the gene expression occurring during the process of nut development and to highlight those genes involved in fatty acid metabolism and those that commonly act as food allergens. Pecan samples were collected at several time points during the embryo development process including the water, gel, dough, and mature nut stages. Library preparation and sequencing were performed using Illumina-based mRNA HiSeq with RNA from four time points during the growing season during August and September 2012. Sequence analysis with Trinotate software following the Trinity protocol identified 133,000 unigenes with 52,267 named transcripts and 45,882 annotated genes. A total of 27,312 genes were defined by GO annotation. Gene expression clustering analysis identified 12 different gene expression profiles, each containing a number of genes. Three pecan seed storage proteins that commonly act as allergens, Car i 1, Car i 2, and Car i 4, were significantly up-regulated during the time course. Up-regulated fatty acid metabolism genes that were identified included acyl-[ACP] desaturase and omega-6 desaturase genes involved in oleic and linoleic acid metabolism. Notably, a few of the up-regulated acyl-[ACP] desaturase and omega-6 desaturase genes that were identified have expression patterns similar to the allergen genes based upon gene expression clustering and qPCR analysis. These findings suggest the possibility of coordinated accumulation of lipids and allergens during pecan nut embryogenesis.

  20. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

    Science.gov (United States)

    Baillie, J Kenneth; Bretherick, Andrew; Haley, Christopher S; Clohisey, Sara; Gray, Alan; Neyton, Lucile P A; Barrett, Jeffrey; Stahl, Eli A; Tenesa, Albert; Andersson, Robin; Brown, J Ben; Faulkner, Geoffrey J; Lizio, Marina; Schaefer, Ulf; Daub, Carsten; Itoh, Masayoshi; Kondo, Naoto; Lassmann, Timo; Kawai, Jun; Mole, Damian; Bajic, Vladimir B; Heutink, Peter; Rehli, Michael; Kawaji, Hideya; Sandelin, Albin; Suzuki, Harukazu; Satsangi, Jack; Wells, Christine A; Hacohen, Nir; Freeman, Thomas C; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Hume, David A

    2018-03-01

    Genetic variants underlying complex traits, including disease susceptibility, are enriched within the transcriptional regulatory elements, promoters and enhancers. There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity. Accordingly, shared transcriptional activity (coexpression) may help prioritise loci associated with a given trait, and help to identify underlying biological processes. Using cap analysis of gene expression (CAGE) profiles of promoter- and enhancer-derived RNAs across 1824 human samples, we have analysed coexpression of RNAs originating from trait-associated regulatory regions using a novel quantitative method (network density analysis; NDA). For most traits studied, phenotype-associated variants in regulatory regions were linked to tightly-coexpressed networks that are likely to share important functional characteristics. Coexpression provides a new signal, independent of phenotype association, to enable fine mapping of causative variants. The NDA coexpression approach identifies new genetic variants associated with specific traits, including an association between the regulation of the OCT1 cation transporter and genetic variants underlying circulating cholesterol levels. NDA strongly implicates particular cell types and tissues in disease pathogenesis. For example, distinct groupings of disease-associated regulatory regions implicate two distinct biological processes in the pathogenesis of ulcerative colitis; a further two separate processes are implicated in Crohn's disease. Thus, our functional analysis of genetic predisposition to disease defines new distinct disease endotypes. We predict that patients with a preponderance of susceptibility variants in each group are likely to respond differently to pharmacological therapy. Together, these findings enable a deeper biological understanding of the causal basis of complex traits.

  1. Sonic Hedgehog-signalling patterns the developing chicken comb as revealed by exploration of the pea-comb mutation.

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    Henrik Boije

    Full Text Available The genetic basis and mechanisms behind the morphological variation observed throughout the animal kingdom is still relatively unknown. In the present work we have focused on the establishment of the chicken comb-morphology by exploring the Pea-comb mutant. The wild-type single-comb is reduced in size and distorted in the Pea-comb mutant. Pea-comb is formed by a lateral expansion of the central comb anlage into three ridges and is caused by a mutation in SOX5, which induces ectopic expression of the SOX5 transcription factor in mesenchyme under the developing comb. Analysis of differential gene expression identified decreased Sonic hedgehog (SHH receptor expression in Pea-comb mesenchyme. By experimentally blocking SHH with cyclopamine, the wild-type single-comb was transformed into a Pea-comb-like phenotype. The results show that the patterning of the chicken comb is under the control of SHH and suggest that ectopic SOX5 expression in the Pea-comb change the response of mesenchyme to SHH signalling with altered comb morphogenesis as a result. A role for the mesenchyme during comb morphogenesis is further supported by the recent finding that another comb-mutant (Rose-comb, is caused by ectopic expression of a transcription factor in comb mesenchyme. The present study does not only give knowledge about how the chicken comb is formed, it also adds to our understanding how mutations or genetic polymorphisms may contribute to inherited variations in the human face.

  2. Long-term citizen-collected data reveal geographical patterns and temporal trends in lake water clarity

    Science.gov (United States)

    Lottig, Noah R.; Wagner, Tyler; Henry, Emily N.; Cheruvelil, Kendra Spence; Webster, Katherine E.; Downing, John A.; Stow, Craig A.

    2014-01-01

    We compiled a lake-water clarity database using publically available, citizen volunteer observations made between 1938 and 2012 across eight states in the Upper Midwest, USA. Our objectives were to determine (1) whether temporal trends in lake-water clarity existed across this large geographic area and (2) whether trends were related to the lake-specific characteristics of latitude, lake size, or time period the lake was monitored. Our database consisted of >140,000 individual Secchi observations from 3,251 lakes that we summarized per lake-year, resulting in 21,020 summer averages. Using Bayesian hierarchical modeling, we found approximately a 1% per year increase in water clarity (quantified as Secchi depth) for the entire population of lakes. On an individual lake basis, 7% of lakes showed increased water clarity and 4% showed decreased clarity. Trend direction and strength were related to latitude and median sample date. Lakes in the southern part of our study-region had lower average annual summer water clarity, more negative long-term trends, and greater inter-annual variability in water clarity compared to northern lakes. Increasing trends were strongest for lakes with median sample dates earlier in the period of record (1938–2012). Our ability to identify specific mechanisms for these trends is currently hampered by the lack of a large, multi-thematic database of variables that drive water clarity (e.g., climate, land use/cover). Our results demonstrate, however, that citizen science can provide the critical monitoring data needed to address environmental questions at large spatial and long temporal scales. Collaborations among citizens, research scientists, and government agencies may be important for developing the data sources and analytical tools necessary to move toward an understanding of the factors influencing macro-scale patterns such as those shown here for lake water clarity.

  3. Isolation of a candidate human telomerase catalytic subunit gene, which reveals complex splicing patterns in different cell types.

    Science.gov (United States)

    Kilian, A; Bowtell, D D; Abud, H E; Hime, G R; Venter, D J; Keese, P K; Duncan, E L; Reddel, R R; Jefferson, R A

    1997-11-01

    Telomerase is a multicomponent reverse transcriptase enzyme that adds DNA repeats to the ends of chromosomes using its RNA component as a template for synthesis. Telomerase activity is detected in the germline as well as the majority of tumors and immortal cell lines, and at low levels in several types of normal cells. We have cloned a human gene homologous to a protein from Saccharomyces cerevisiae and Euplotes aediculatus that has reverse transcriptase motifs and is thought to be the catalytic subunit of telomerase in those species. This gene is present in the human genome as a single copy sequence with a dominant transcript of approximately 4 kb in a human colon cancer cell line, LIM1215. The cDNA sequence was determined using clones from a LIM1215 cDNA library and by RT-PCR, cRACE and 3'RACE on mRNA from the same source. We show that the gene is expressed in several normal tissues, telomerase-positive post-crisis (immortal) cell lines and various tumors but is not expressed in the majority of normal tissues analyzed, pre-crisis (non-immortal) cells and telomerase-negative immortal (ALT) cell lines. Multiple products were identified by RT-PCR using primers within the reverse transcriptase domain. Sequencing of these products suggests that they arise by alternative splicing. Strikingly, various tumors, cell lines and even normal tissues (colonic crypt and testis) showed considerable differences in the splicing patterns. Alternative splicing of the telomerase catalytic subunit transcript may be important for the regulation of telomerase activity and may give rise to proteins with different biochemical functions.

  4. Ancient DNA analyses reveal contrasting phylogeographic patterns amongst kiwi (Apteryx spp. and a recently extinct lineage of spotted kiwi.

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    Lara D Shepherd

    Full Text Available The little spotted kiwi (Apteryx owenii is a flightless ratite formerly found throughout New Zealand but now greatly reduced in distribution. Previous phylogeographic studies of the related brown kiwi (A. mantelli, A. rowi and A. australis, with which little spotted kiwi was once sympatric, revealed extremely high levels of genetic structuring, with mitochondrial DNA haplotypes often restricted to populations. We surveyed genetic variation throughout the present and pre-human range of little spotted kiwi by obtaining mitochondrial DNA sequences from contemporary and ancient samples. Little spotted kiwi and great spotted kiwi (A. haastii formed a monophyletic clade sister to brown kiwi. Ancient samples of little spotted kiwi from the northern North Island, where it is now extinct, formed a lineage that was distinct from remaining little spotted kiwi and great spotted kiwi lineages, potentially indicating unrecognized taxonomic diversity. Overall, little spotted kiwi exhibited much lower levels of genetic diversity and structuring than brown kiwi, particularly through the South Island. Our results also indicate that little spotted kiwi (or at least hybrids involving this species survived on the South Island mainland until more recently than previously thought.

  5. Genome-Wide Comparison of Magnaporthe Species Reveals a Host-Specific Pattern of Secretory Proteins and Transposable Elements.

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    Meghana Deepak Shirke

    Full Text Available Blast disease caused by the Magnaporthe species is a major factor affecting the productivity of rice, wheat and millets. This study was aimed at generating genomic information for rice and non-rice Magnaporthe isolates to understand the extent of genetic variation. We have sequenced the whole genome of the Magnaporthe isolates, infecting rice (leaf and neck, finger millet (leaf and neck, foxtail millet (leaf and buffel grass (leaf. Rice and finger millet isolates infecting both leaf and neck tissues were sequenced, since the damage and yield loss caused due to neck blast is much higher as compared to leaf blast. The genome-wide comparison was carried out to study the variability in gene content, candidate effectors, repeat element distribution, genes involved in carbohydrate metabolism and SNPs. The analysis of repeat element footprints revealed some genes such as naringenin, 2-oxoglutarate 3-dioxygenase being targeted by Pot2 and Occan, in isolates from different host species. Some repeat insertions were host-specific while other insertions were randomly shared between isolates. The distributions of repeat elements, secretory proteins, CAZymes and SNPs showed significant variation across host-specific lineages of Magnaporthe indicating an independent genome evolution orchestrated by multiple genomic factors.

  6. Quantitative analysis of diet structure by real-time PCR, reveals different feeding patterns by two dominant grasshopper species

    Science.gov (United States)

    Huang, Xunbing; Wu, Huihui; McNeill, Mark Richard; Qin, Xinghu; Ma, Jingchuan; Tu, Xiongbing; Cao, Guangchun; Wang, Guangjun; Nong, Xiangqun; Zhang, Zehua

    2016-01-01

    Studies on grasshopper diets have historically employed a range of methodologies, each with certain advantages and disadvantages. For example, some methodologies are qualitative instead of quantitative. Others require long experimental periods or examine population-level effects, only. In this study, we used real-time PCR to examine diets of individual grasshoppers. The method has the advantage of being both fast and quantitative. Using two grasshopper species, Oedaleus asiaticus and Dasyhippus barbipes, we designed ITS primer sequences for their three main host plants, Stipa krylovii, Leymus chinensis and Cleistogenes squarrosa and used real-time PCR method to test diet structure both qualitatively and quantitatively. The lowest detection efficiency of the three grass species was ~80% with a strong correlation between actual and PCR-measured food intake. We found that Oedaleus asiaticus maintained an unchanged diet structure across grasslands with different grass communities. By comparison, Dasyhippus barbipes changed its diet structure. These results revealed why O. asiaticus distribution is mainly confined to Stipa-dominated grassland, and D. barbipes is more widely distributed across Inner Mongolia. Overall, real-time PCR was shown to be a useful tool for investigating grasshopper diets, which in turn offers some insight into grasshopper distributions and improved pest management. PMID:27562455

  7. Epitope mapping of the major allergen from Atlantic cod in Spanish population reveals different IgE-binding patterns.

    Science.gov (United States)

    Perez-Gordo, Marina; Pastor-Vargas, Carlos; Lin, Jing; Bardina, Ludmilla; Cases, Barbara; Ibáñez, Maria Dolores; Vivanco, Fernando; Cuesta-Herranz, Javier; Sampson, Hugh A

    2013-07-01

    IgE-epitope mapping of allergens reveal important information about antigen components involved in allergic reactions. The peptide-based microarray immunoassay has been used to map epitopes of some food allergens. We developed a peptide microarray immunoassay to map allergenic epitopes in parvalbumin from Atlantic cod (Gad m 1), the most consumed cod species in Spain. Sera from 13 fish-allergic patients with specific IgE to cod parvalbumin were used. A library of overlapping peptides was synthesized, representing the primary sequence of Gad m 1. Peptides were used to analyze allergen-specific IgE antibodies in patient sera. 100% of the patients recognized one antigenic region of 15 amino acids in length in Gad m 1. This region only partially correlated with one of the three antigenic determinants of Gad c 1 (Allergen M), parvalbumin from Baltic cod (Gadus callarias). In the 3D model of the protein, this region was located on the surface of the protein. We have identified a relevant antigenic region in Gad m 1. This epitope could be considered as a severity marker and provides additional information to improve fish allergy diagnosis and the design of safe immunotherapeutic tools. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals

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    Chen Wei-Chung

    2009-09-01

    Full Text Available Abstract Background Since the drastic reorganisation of the phylogeny of the animal kingdom into three major clades of bilaterians; Ecdysozoa, Lophotrochozoa and Deuterostomia, it became glaringly obvious that the selection of model systems with extensive molecular resources was heavily biased towards only two of these three clades, namely the Ecdysozoa and Deuterostomia. Increasing efforts have been put towards redressing this imbalance in recent years, and one of the principal phyla in the vanguard of this endeavour is the Annelida. Results In the context of this effort we here report our characterisation of an Expressed Sequence Tag (EST screen in the serpulid annelid, Pomatoceros lamarckii. We have sequenced over 5,000 ESTs which consolidate into over 2,000 sequences (clusters and singletons. These sequences are used to build phylogenetic trees to estimate relative branch lengths amongst different taxa and, by comparison to genomic data from other animals, patterns of gene retention and loss are deduced. Conclusion The molecular phylogenetic trees including the P. lamarckii sequences extend early observations that polychaetes tend to have relatively short branches in such trees, and hence are useful taxa with which to reconstruct gene family evolution. Also, with the availability of lophotrochozoan data such as that of P. lamarckii, it is now possible to make much more accurate reconstructions of the gene complement of the ancestor of the bilaterians than was previously possible from comparisons of ecdysozoan and deuterostome genomes to non-bilaterian outgroups. It is clear that the traditional molecular model systems for protostomes (e.g. Drosophila melanogaster and Caenorhabditis elegans, which are restricted to the Ecdysozoa, have undergone extensive gene loss during evolution. These ecdysozoan systems, in terms of gene content, are thus more derived from the bilaterian ancestral condition than lophotrochozoan systems like the polychaetes

  9. Potential of two submontane broadleaved species (Acer opalus, Quercus pubescens) to reveal spatiotemporal patterns of rockfall activity

    Science.gov (United States)

    Favillier, Adrien; Lopez-Saez, Jérôme; Corona, Christophe; Trappmann, Daniel; Toe, David; Stoffel, Markus; Rovéra, Georges; Berger, Frédéric

    2015-10-01

    Long-term records of rockfalls have proven to be scarce and typically incomplete, especially in increasingly urbanized areas where inventories are largely absent and the risk associated with rockfall events rises proportionally with urbanization. On forested slopes, tree-ring analyses may help to fill this gap, as they have been demonstrated to provide annually-resolved data on past rockfall activity over long periods. Yet, the reconstruction of rockfall chronologies has been hampered in the past by the paucity of studies that include broadleaved tree species, which are, in fact, quite common in various rockfall-prone environments. In this study, we test the sensitivity of two common, yet unstudied, broadleaved species - Quercus pubescens Willd. (Qp) and Acer opalus Mill. (Ao) - to record rockfall impacts. The approach is based on a systematic mapping of trees and the counting of visible scars on the stem surface of both species. Data are presented from a site in the Vercors massif (French Alps) where rocks are frequently detached from Valanginian limestone and marl cliffs. We compare recurrence interval maps obtained from both species and from two different sets of tree structures (i.e., single trees vs. coppice stands) based on Cohen's k coefficient and the mean absolute error. A total of 1230 scars were observed on the stem surface of 847 A. opalus and Q. pubescens trees. Both methods yield comparable results on the spatial distribution of relative rockfall activity with similar downslope decreasing recurrence intervals. Yet recurrence intervals vary significantly according to tree species and tree structure. The recurrence interval observed on the stem surface of Q. pubescens exceeds that of A. opalus by > 20 years in the lower part of the studied plot. Similarly, the recurrence interval map derived from A. opalus coppice stands, dominant at the stand scale, does not exhibit a clear spatial pattern. Differences between species may be explained by the bark

  10. Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

    Science.gov (United States)

    Sturgis, James N; Niederman, Robert A

    2008-01-01

    Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

  11. Some ethylene biosynthesis and AP2/ERF genes reveal a specific pattern of expression during somatic embryogenesis in Hevea brasiliensis

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    Piyatrakul Piyanuch

    2012-12-01

    Full Text Available Abstract Background Ethylene production and signalling play an important role in somatic embryogenesis, especially for species that are recalcitrant in in vitro culture. The AP2/ERF superfamily has been identified and classified in Hevea brasiliensis. This superfamily includes the ERFs involved in response to ethylene. The relative transcript abundance of ethylene biosynthesis genes and of AP2/ERF genes was analysed during somatic embryogenesis for callus lines with different regeneration potential, in order to identify genes regulated during that process. Results The analysis of relative transcript abundance was carried out by real-time RT-PCR for 142 genes. The transcripts of ERFs from group I, VII and VIII were abundant at all stages of the somatic embryogenesis process. Forty genetic expression markers for callus regeneration capacity were identified. Fourteen markers were found for proliferating calli and 35 markers for calli at the end of the embryogenesis induction phase. Sixteen markers discriminated between normal and abnormal embryos and, lastly, there were 36 markers of conversion into plantlets. A phylogenetic analysis comparing the sequences of the AP2 domains of Hevea and Arabidopsis genes enabled us to predict the function of 13 expression marker genes. Conclusions This first characterization of the AP2/ERF superfamily in Hevea revealed dramatic regulation of the expression of AP2/ERF genes during the somatic embryogenesis process. The gene expression markers of proliferating callus capacity to regenerate plants by somatic embryogenesis should make it possible to predict callus lines suitable to be used for multiplication. Further functional characterization of these markers opens up prospects for discovering specific AP2/ERF functions in the Hevea species for which somatic embryogenesis is difficult.

  12. Specific patterns of gene space organisation revealed in wheat by using the combination of barley and wheat genomic resources

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    Waugh Robbie

    2010-12-01

    Full Text Available Abstract Background Because of its size, allohexaploid nature and high repeat content, the wheat genome has always been perceived as too complex for efficient molecular studies. We recently constructed the first physical map of a wheat chromosome (3B. However gene mapping is still laborious in wheat because of high redundancy between the three homoeologous genomes. In contrast, in the closely related diploid species, barley, numerous gene-based markers have been developed. This study aims at combining the unique genomic resources developed in wheat and barley to decipher the organisation of gene space on wheat chromosome 3B. Results Three dimensional pools of the minimal tiling path of wheat chromosome 3B physical map were hybridised to a barley Agilent 15K expression microarray. This led to the fine mapping of 738 barley orthologous genes on wheat chromosome 3B. In addition, comparative analyses revealed that 68% of the genes identified were syntenic between the wheat chromosome 3B and barley chromosome 3 H and 59% between wheat chromosome 3B and rice chromosome 1, together with some wheat-specific rearrangements. Finally, it indicated an increasing gradient of gene density from the centromere to the telomeres positively correlated with the number of genes clustered in islands on wheat chromosome 3B. Conclusion Our study shows that novel structural genomics resources now available in wheat and barley can be combined efficiently to overcome specific problems of genetic anchoring of physical contigs in wheat and to perform high-resolution comparative analyses with rice for deciphering the organisation of the wheat gene space.

  13. Revealing polychaetes invasion patterns: Identification, reproduction and potential risks of the Korean ragworm, Perinereis linea (Treadwell), in the Western Mediterranean

    Science.gov (United States)

    Arias, Andrés; Richter, Alexandra; Anadón, Nuria; Glasby, Christopher J.

    2013-10-01

    An established population of the polychaetous annelid Perinereis linea (Treadwell) is reported for the first time outside its native distribution range (NW Pacific). This exotic worm has reached the Western Mediterranean (Mar Menor lagoon) via importing live fishing-bait as it is commonly used by anglers in Mar Menor lagoon, an area largely used for recreational fishing. To avoid confusion with other related species, and because the scientific name has been in synonymy for many years, P. linea is redescribed and illustrated. We focus on the reproductive biology and ecology of P. linea to help to understand its introduction, naturalization and spread along this coastal lagoon. Comparison between the Mediterranean population with a native population from South Korea revealed that the species exhibits a great reproductive plasticity and adaptability, which depends on the environmental conditions. Perinereis linea can reproduce after acquiring the epitokous form or prior to complete epitokal modification. In the Mar Menor lagoon population females release eggs asynchronically without completing epitokal modifications. However, under particular laboratory conditions females produce eggs synchronically and release them after complete epitokal transformations. Fertilization can occur internally in the female coelom, and females release zygotes and larvae through openings in their body walls; they are then incubated in gelatinous masses attached to the female parapodia. The sperm morphology is of the ent-aquasperm type. The eggs and larvae are attacked by symbiotic ciliate protozoa that feed on their yolk reserves. These foreign ciliates may act as carriers of disease in native beachworms and constitute an important risk for the ecosystem health. Finally, we provide recommendations on the prevention of the adverse effects that this exotic ragworm can cause in receiving ecosystems.

  14. Secondary structure of the rRNA ITS2 region reveals key evolutionary patterns in acroporid corals.

    Science.gov (United States)

    Coleman, Annette W; van Oppen, Madeleine J H

    2008-10-01

    This study investigates the ribosomal RNA transcript secondary structure in corals as confirmed by compensatory base changes in Isopora/Acropora species. These species are unique versus all other corals in the absence of a eukaryote-wide conserved structural component, the helix III in internal transcriber spacer (ITS) 2, and their variability in the 5.8S-LSU helix basal to ITS2, a helix with pairings identical among all other scleractinian corals. Furthermore, Isopora/Acropora individuals display at least two, and as many as three, ITS sequence isotypes in their genome which appear to be capable of function. From consideration of the conserved elements in ITS2 and flanking regions, it appears that there are three major groups within the IsoporaAcropora lineage: the Isopora + Acropora "longi" group, the large group including Caribbean Acropora + the Acropora "carib" types plus the bulk of the Indo-Pacific Acropora species, and the remaining enigmatic "pseudo" group found in the Pacific. Interbreeding is possible among Caribbean A. palmata and A. cervicornis and among some species of Indo-Pacific Acropora. Recombinant ITS sequences are obvious among these latter, such that morphology (as represented by species name) does not correlate with common ITS sequence. The combination of characters revealed by RNA secondary structure analyses suggests a recent past/current history of interbreeding among the Indo-Pacific Acropora species and a shared ancestry of some of these with the Caribbean Acropora. The unusual absence of helix III of ITS2 of Isopora/Acropora species may have some causative role in the equally unusual instability in the 5.8S-LSU helix basal to ITS2 of this species complex.

  15. Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences

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    De Marzo Angelo M

    2011-06-01

    Full Text Available Abstract Background DNA methylation has been linked to genome regulation and dysregulation in health and disease respectively, and methods for characterizing genomic DNA methylation patterns are rapidly emerging. We have developed/refined methods for enrichment of methylated genomic fragments using the methyl-binding domain of the human MBD2 protein (MBD2-MBD followed by analysis with high-density tiling microarrays. This MBD-chip approach was used to characterize DNA methylation patterns across all non-repetitive sequences of human chromosomes 21 and 22 at high-resolution in normal and malignant prostate cells. Results Examining this data using computational methods that were designed specifically for DNA methylation tiling array data revealed widespread methylation of both gene promoter and non-promoter regions in cancer and normal cells. In addition to identifying several novel cancer hypermethylated 5' gene upstream regions that mediated epigenetic gene silencing, we also found several hypermethylated 3' gene downstream, intragenic and intergenic regions. The hypermethylated intragenic regions were highly enriched for overlap with intron-exon boundaries, suggesting a possible role in regulation of alternative transcriptional start sites, exon usage and/or splicing. The hypermethylated intergenic regions showed significant enrichment for conservation across vertebrate species. A sampling of these newly identified promoter (ADAMTS1 and SCARF2 genes and non-promoter (downstream or within DSCR9, C21orf57 and HLCS genes hypermethylated regions were effective in distinguishing malignant from normal prostate tissues and/or cell lines. Conclusions Comparison of chromosome-wide DNA methylation patterns in normal and malignant prostate cells revealed significant methylation of gene-proximal and conserved intergenic sequences. Such analyses can be easily extended for genome-wide methylation analysis in health and disease.

  16. Concordant patterns of mtDNA and nuclear phylogeographic structure reveal Pleistocene vicariant event in the green crab Carcinus aestuarii across the Siculo-Tunisian Strait

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    T. DELI

    2016-07-01

    Full Text Available This study focuses on the population genetic structure of the green crab Carcinus aestuarii along part of the African Mediterranean coast, with the main target to confirm genetic subdivision across the well documented genetic boundary of the Siculo-Tunisian Strait. For this purpose, the mitochondrial COI (cytochrome oxidase I gene and five polymorphic microsatellite loci were analysed in 144 and 120 specimens, respectively. Our results show the existence of two distinct haplogroups, separated by 16 mutational steps and revealed a non random distribution of the genetic variation along the African Mediterranean coast. Dating analyses, based on the use of different molecular clock models and rates, placed the divergence among both haplogroups at 1.91 Myr (95% HPD: 1.11–2.68 Myr to 0.69 Myr (95% HPD: 0.44–0.98 Myr. This range of divergence time estimation corresponds to the Early Pleistocene. The particular pattern of genetic divergence among Eastern and Western African Mediterranean populations of C. aestuarii, detected by 2-level AMOVA at the mitochondrial level, was consistent with that inferred from microsatellite analysis and suggests a vicariant event in C. aestuarii. Demographic reconstruction, inferred from mismatch distribution and BSP analyses, yielded different patterns of demographic history between both African Mediterranean groups. The distribution pattern of the two haplogroups across the African Mediterranean coast, along with results of Bayesian analysis of genetic structure revealing an intermediate geographic group between the two divergent groups of the African coast, support the hypothesis of a secondary contact between two historically isolated groups. Although this hypothetical contact zone, thought to be located near the Siculo-Tunisian Strait, still needs to be verified, the asymmetric gene flow from Western to Eastern African Mediterranean, as inferred by the results of a MIGRATE analysis, reinforces the previously

  17. Spatial patterns of atmospheric deposition of nitrogen and sulfur using ion-exchange resin collectors in Rocky Mountain National Park, USA

    Science.gov (United States)

    Clow, David W.; Roop, Heidi; Nanus, Leora; Fenn, Mark; Sexstone, Graham A.

    2015-01-01

    Lakes and streams in Class 1 wilderness areas in the western United States (U.S.) are at risk from atmospheric deposition of nitrogen (N) and sulfur (S), and protection of these resources is mandated under the Federal Clean Air Act and amendments. Assessment of critical loads, which are the maximum exposure to pollution an area can receive without adverse effects on sensitive ecosystems, requires accurate deposition estimates. However, deposition is difficult and expensive to measure in high-elevation wilderness, and spatial patterns in N and S deposition in these areas remain poorly quantified. In this study, ion-exchange resin (IER) collectors were used to measure dissolved inorganic N (DIN) and S deposition during June 2006–September 2007 at approximately 20 alpine/subalpine sites spanning the Continental Divide in Rocky Mountain National Park. Results indicated good agreement between deposition estimated from IER collectors and commonly used wet + dry methods during summer, but poor agreement during winter. Snowpack sampling was found to be a more accurate way of quantifying DIN and S deposition during winter. Summer DIN deposition was significantly greater on the east side of the park than on the west side (25–50%; p ≤ 0.03), consistent with transport of pollutants to the park from urban and agricultural areas to the east. Sources of atmospheric nitrate (NO3−) were examined using N isotopes. The average δ15N of NO3− from IER collectors was 3.5‰ higher during winter than during summer (p model critical loads by filling gaps in geographic coverage of deposition monitoring/modeling programs and thus may enable policy makers to better protect sensitive natural resources in Class 1 Wilderness areas.

  18. A modelling study of hyporheic exchange pattern and the sequence, size, and spacing of stream bedforms in mountain stream networks, Oregon, USA.

    Science.gov (United States)

    Michael N. Gooseff; Justin K. Anderson; Steven M. Wondzell; Justin LaNier; Roy. Haggerty

    2005-01-01

    Studies of hyporheic exchange flows have identified physical features of channels that control exchange flow at the channel unit scale, namely slope breaks in the longitudinal profile of streams that generate subsurface head distributions. We recently completed a field study that suggested channel unit spacing in stream longitudinal profiles can be used to predict the...

  19. Efficient Recombinase-Mediated Cassette Exchange in hPSCs to Study the Hepatocyte Lineage Reveals AAVS1 Locus-Mediated Transgene Inhibition

    Directory of Open Access Journals (Sweden)

    Laura Ordovás

    2015-11-01

    Full Text Available Tools for rapid and efficient transgenesis in “safe harbor” loci in an isogenic context remain important to exploit the possibilities of human pluripotent stem cells (hPSCs. We created hPSC master cell lines suitable for FLPe recombinase-mediated cassette exchange (RMCE in the AAVS1 locus that allow generation of transgenic lines within 15 days with 100% efficiency and without random integrations. Using RMCE, we successfully incorporated several transgenes useful for lineage identification, cell toxicity studies, and gene overexpression to study the hepatocyte lineage. However, we observed unexpected and variable transgene expression inhibition in vitro, due to DNA methylation and other unknown mechanisms, both in undifferentiated hESC and differentiating hepatocytes. Therefore, the AAVS1 locus cannot be considered a universally safe harbor locus for reliable transgene expression in vitro, and using it for transgenesis in hPSC will require careful assessment of the function of individual transgenes.

  20. Complete mitochondrial genome sequences of three bats species and whole genome mitochondrial analyses reveal patterns of codon bias and lend support to a basal split in Chiroptera.

    Science.gov (United States)

    Meganathan, P R; Pagan, Heidi J T; McCulloch, Eve S; Stevens, Richard D; Ray, David A

    2012-01-15

    Order Chiroptera is a unique group of mammals whose members have attained self-powered flight as their main mode of locomotion. Much speculation persists regarding bat evolution; however, lack of sufficient molecular data hampers evolutionary and conservation studies. Of ~1200 species, complete mitochondrial genome sequences are available for only eleven. Additional sequences should be generated if we are to resolve many questions concerning these fascinating mammals. Herein, we describe the complete mitochondrial genomes of three bats: Corynorhinus rafinesquii, Lasiurus borealis and Artibeus lituratus. We also compare the currently available mitochondrial genomes and analyze codon usage in Chiroptera. C. rafinesquii, L. borealis and A. lituratus mitochondrial genomes are 16438 bp, 17048 bp and 16709 bp, respectively. Genome organization and gene arrangements are similar to other bats. Phylogenetic analyses using complete mitochondrial genome sequences support previously established phylogenetic relationships and suggest utility in future studies focusing on the evolutionary aspects of these species. Comprehensive analyses of available bat mitochondrial genomes reveal distinct nucleotide patterns and synonymous codon preferences corresponding to different chiropteran families. These patterns suggest that mutational and selection forces are acting to different extents within Chiroptera and shape their mitochondrial genomes. Copyright © 2011 Elsevier B.V. All rights reserved.

  1. Population Genetics of Two Key Mosquito Vectors of Rift Valley Fever Virus Reveals New Insights into the Changing Disease Outbreak Patterns in Kenya

    Science.gov (United States)

    Tchouassi, David P.; Bastos, Armanda D. S.; Sole, Catherine L.; Diallo, Mawlouth; Lutomiah, Joel; Mutisya, James; Mulwa, Francis; Borgemeister, Christian; Sang, Rosemary; Torto, Baldwyn

    2014-01-01

    Rift Valley fever (RVF) outbreaks in Kenya have increased in frequency and range to include northeastern Kenya where viruses are increasingly being isolated from known (Aedes mcintoshi) and newly-associated (Ae. ochraceus) vectors. The factors contributing to these changing outbreak patterns are unclear and the population genetic structure of key vectors and/or specific virus-vector associations, in particular, are under-studied. By conducting mitochondrial and nuclear DNA analyses on >220 Kenyan specimens of Ae. mcintoshi and Ae. ochraceus, we uncovered high levels of vector complexity which may partly explain the disease outbreak pattern. Results indicate that Ae. mcintoshi consists of a species complex with one of the member species being unique to the newly-established RVF outbreak-prone northeastern region of Kenya, whereas Ae. ochraceus is a homogeneous population that appears to be undergoing expansion. Characterization of specimens from a RVF-prone site in Senegal, where Ae. ochraceus is a primary vector, revealed direct genetic links between the two Ae. ochraceus populations from both countries. Our data strongly suggest that unlike Ae. mcintoshi, Ae. ochraceus appears to be a relatively recent, single 'introduction' into Kenya. These results, together with increasing isolations from this vector, indicate that Ae. ochraceus will likely be of greater epidemiological importance in future RVF outbreaks in Kenya. Furthermore, the overall vector complexity calls into question the feasibility of mosquito population control approaches reliant on genetic modification. PMID:25474018

  2. Age-Related Changes in Locomotor Performance Reveal a Similar Pattern for Caenorhabditis elegans, Mus domesticus, Canis familiaris, Equus caballus, and Homo sapiens.

    Science.gov (United States)

    Marck, Adrien; Berthelot, Geoffroy; Foulonneau, Vincent; Marc, Andy; Antero-Jacquemin, Juliana; Noirez, Philippe; Bronikowski, Anne M; Morgan, Theodore J; Garland, Theodore; Carter, Patrick A; Hersen, Pascal; Di Meglio, Jean-Marc; Toussaint, Jean-François

    2017-04-01

    Locomotion is one of the major physiological functions for most animals. Previous studies have described aging mechanisms linked to locomotor performance among different species. However, the precise dynamics of these age-related changes, and their interactions with development and senescence, are largely unknown. Here, we use the same conceptual framework to describe locomotor performances in Caenorhabditis elegans, Mus domesticus, Canis familiaris, Equus caballus, and Homo sapiens. We show that locomotion is a consistent biomarker of age-related changes, with an asymmetrical pattern throughout life, regardless of the type of effort or its duration. However, there is variation (i) among species for the same mode of locomotion, (ii) within species for different modes of locomotion, and (iii) among individuals of the same species for the same mode of locomotion. Age-related patterns are modulated by genetic (such as selective breeding) as well as environmental conditions (such as temperature). However, in all cases, the intersection of the rising developmental phase and the declining senescent phase reveals neither a sharp transition nor a plateau, but a smooth transition, emphasizing a crucial moment: the age at peak performance. This transition may define a specific target for future investigations on the dynamics of such biological interactions. © The Author 2016. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  3. Population genetics of two key mosquito vectors of Rift Valley Fever virus reveals new insights into the changing disease outbreak patterns in Kenya.

    Directory of Open Access Journals (Sweden)

    David P Tchouassi

    2014-12-01

    Full Text Available Rift Valley fever (RVF outbreaks in Kenya have increased in frequency and range to include northeastern Kenya where viruses are increasingly being isolated from known (Aedes mcintoshi and newly-associated (Ae. ochraceus vectors. The factors contributing to these changing outbreak patterns are unclear and the population genetic structure of key vectors and/or specific virus-vector associations, in particular, are under-studied. By conducting mitochondrial and nuclear DNA analyses on >220 Kenyan specimens of Ae. mcintoshi and Ae. ochraceus, we uncovered high levels of vector complexity which may partly explain the disease outbreak pattern. Results indicate that Ae. mcintoshi consists of a species complex with one of the member species being unique to the newly-established RVF outbreak-prone northeastern region of Kenya, whereas Ae. ochraceus is a homogeneous population that appears to be undergoing expansion. Characterization of specimens from a RVF-prone site in Senegal, where Ae. ochraceus is a primary vector, revealed direct genetic links between the two Ae. ochraceus populations from both countries. Our data strongly suggest that unlike Ae. mcintoshi, Ae. ochraceus appears to be a relatively recent, single 'introduction' into Kenya. These results, together with increasing isolations from this vector, indicate that Ae. ochraceus will likely be of greater epidemiological importance in future RVF outbreaks in Kenya. Furthermore, the overall vector complexity calls into question the feasibility of mosquito population control approaches reliant on genetic modification.

  4. Phylogenetic relationships among Synallaxini spinetails (Aves: Furnariidae) reveal a new biogeographic pattern across the Amazon and Paraná river basins.

    Science.gov (United States)

    Claramunt, Santiago

    2014-09-01

    Relationships among genera in the tribe Synallaxini have proved difficult to resolve. In this study, I investigate relationships among Synallaxis, Certhiaxis and Schoeniophylax using DNA sequences from the mitochondrion and three nuclear regions. I implemented novel primers and protocols for amplifying and sequencing autosomal and sex-linked introns in Furnariidae that resolved basal relationships in the Synallaxini with strong support. Synallaxis propinqua is sister to Schoeniophylax phryganophilus, and together they form a clade with Certhiaxis. The results are robust to analytical approaches when all genomic regions are analyzed jointly (parsimony, maximum likelihood, and species-tree analysis) and the same basal relationships are recovered by most genomic regions when analyzed separately. A sister relationship between S. propinqua, an Amazonian river island specialist, and S. phryganophilus, from the Paraná River basin region, reveals a new biogeographic pattern shared by at least other four pairs of taxa with similar distributions and ecologies. Estimates of divergence times for these five pairs span from the late Miocene to the Pleistocene. Identification of the historical events that produced this pattern is difficult and further advances will require additional studies of the taxa involved and a better understanding of the recent environmental history of South America. A new classification is proposed for the Synallaxini, including the description of a new genus for S. propinqua. Copyright © 2014 Elsevier Inc. All rights reserved.

  5. Magnetic resonance imaging-based cerebral tissue classification reveals distinct spatiotemporal patterns of changes after stroke in non-human primates.

    Science.gov (United States)

    Bouts, Mark J R J; Westmoreland, Susan V; de Crespigny, Alex J; Liu, Yutong; Vangel, Mark; Dijkhuizen, Rick M; Wu, Ona; D'Arceuil, Helen E

    2015-12-15

    Spatial and temporal changes in brain tissue after acute ischemic stroke are still poorly understood. Aims of this study were three-fold: (1) to determine unique temporal magnetic resonance imaging (MRI) patterns at the acute, subacute and chronic stages after stroke in macaques by combining quantitative T2 and diffusion MRI indices into MRI 'tissue signatures', (2) to evaluate temporal differences in these signatures between transient (n = 2) and permanent (n = 2) middle cerebral artery occlusion, and (3) to correlate histopathology findings in the chronic stroke period to the acute and subacute MRI derived tissue signatures. An improved iterative self-organizing data analysis algorithm was used to combine T2, apparent diffusion coefficient (ADC), and fractional anisotropy (FA) maps across seven successive timepoints (1, 2, 3, 24, 72, 144, 240 h) which revealed five temporal MRI signatures, that were different from the normal tissue pattern (P MRI signatures associated with specific tissue fates may further aid in assessing and monitoring the efficacy of novel pharmaceutical treatments for stroke in a pre-clinical and clinical setting.

  6. Genome-wide comparisons reveal a clinal species pattern within a holobenthic octopod-the Australian Southern blue-ringed octopus, Hapalochlaena maculosa (Cephalopoda: Octopodidae).

    Science.gov (United States)

    Morse, Peter; Kjeldsen, Shannon R; Meekan, Mark G; Mccormick, Mark I; Finn, Julian K; Huffard, Christine L; Zenger, Kyall R

    2018-02-01

    The southern blue-ringed octopus, Hapalochlaena maculosa (Hoyle, 1883) lacks a planktonic dispersal phase, yet ranges across Australia's southern coastline. This species' brief and holobenthic life history suggests gene flow might be limited, leaving distant populations prone to strong genetic divergence. This study used 17,523 genome-wide SNP loci to investigate genetic structuring and local adaptation patterns of H. maculosa among eight sampling sites along its reported range. Within sites, interrelatedness was very high, consistent with the limited dispersal of this taxon. However, inbreeding coefficients were proportionally lower among sites where substructuring was not detected, suggesting H. maculosa might possess a mechanism for inbreeding avoidance. Genetic divergence was extremely high among all sites, with the greatest divergence observed between both ends of the distribution, Fremantle, WA, and Stanley, TAS. Genetic distances closely followed an isolation by geographic distance pattern. Outlier analyses revealed distinct selection signatures at all sites, with the strongest divergence reported between Fremantle and the other Western Australian sites. Phylogenetic reconstructions using the described sister taxon H. fasciata (Hoyle, 1886) further supported that the genetic divergence between distal H. maculosa sites in this study was equivalent to that of between established heterospecifics within this genus. However, it is advocated that taxonomic delineations within this species should be made with caution. These data indicate that H. maculosa forms a clinal species pattern across its geographic range, with gene flow present through allele sharing between adjacent populations. Morphological investigations are recommended for a robust resolution of the taxonomic identity and ecotype boundaries of this species.

  7. Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans

    Directory of Open Access Journals (Sweden)

    Valente eAritua

    2015-10-01

    Full Text Available Common bacterial blight is a devastating seed-borne disease of common beans that also occurs on other legume species including lablab and Lima beans. We sequenced and analysed the genomes of 26 isolates of Xanthomonas axonopodis pv. phaseoli and X. fuscans subsp. fuscans, the causative agents of this disease, collected over four decades and six continents. This revealed considerable genetic variation within both taxa, encompassing both single-nucleotide variants and differences in gene content, that could be exploited for tracking pathogen spread. The bacterial isolate from Lima bean fell within the previously described Genetic Lineage 1, along with the pathovar type isolate (NCPPB 3035. The isolates from lablab represent a new, previously unknown genetic lineage closely related to strains of X. axonopodis pv. glycines. Finally, we identified more than 100 genes that appear to have been recently acquired by Xanthomonas axonopodis pv. phaseoli from X. fuscans subsp. fuscans.

  8. Vertical Movements and Patterns in Diving Behavior of Whale Sharks as Revealed by Pop-Up Satellite Tags in the Eastern Gulf of Mexico.

    Directory of Open Access Journals (Sweden)

    John P Tyminski

    Full Text Available The whale shark (Rhincodon typus is a wide-ranging, filter-feeding species typically observed at or near the surface. This shark's sub-surface habits and behaviors have only begun to be revealed in recent years through the use of archival and satellite tagging technology. We attached pop-up satellite archival transmitting tags to 35 whale sharks in the southeastern Gulf of Mexico off the Yucatan Peninsula from 2003-2012 and three tags to whale sharks in the northeastern Gulf off Florida in 2010, to examine these sharks' long-term movement patterns and gain insight into the underlying factors influencing their vertical habitat selection. Archived data were received from 31 tags deployed on sharks of both sexes with total lengths of 5.5-9 m. Nine of these tags were physically recovered facilitating a detailed long-term view into the sharks' vertical movements. Whale sharks feeding inshore on fish eggs off the northeast Yucatan Peninsula demonstrated reverse diel vertical migration, with extended periods of surface swimming beginning at sunrise followed by an abrupt change in the mid-afternoon to regular vertical oscillations, a pattern that continued overnight. When in oceanic waters, sharks spent about 95% of their time within epipelagic depths (500 m that largely occurred during daytime or twilight hours (max. depth recorded 1,928 m, had V-shaped depth-time profiles, and comprised more rapid descents (0.68 m sec-1 than ascents (0.50 m sec-1. Nearly half of these extreme dives had descent profiles with brief but conspicuous changes in vertical direction at a mean depth of 475 m. We hypothesize these stutter steps represent foraging events within the deep scattering layer, however, the extreme dives may have additional functions. Overall, our results demonstrate complex and dynamic patterns of habitat utilization for R. typus that appear to be in response to changing biotic and abiotic conditions influencing the distribution and abundance of their

  9. Vertical Movements and Patterns in Diving Behavior of Whale Sharks as Revealed by Pop-Up Satellite Tags in the Eastern Gulf of Mexico

    Science.gov (United States)

    Tyminski, John P.; de la Parra-Venegas, Rafael; González Cano, Jaime; Hueter, Robert E.

    2015-01-01

    The whale shark (Rhincodon typus) is a wide-ranging, filter-feeding species typically observed at or near the surface. This shark’s sub-surface habits and behaviors have only begun to be revealed in recent years through the use of archival and satellite tagging technology. We attached pop-up satellite archival transmitting tags to 35 whale sharks in the southeastern Gulf of Mexico off the Yucatan Peninsula from 2003–2012 and three tags to whale sharks in the northeastern Gulf off Florida in 2010, to examine these sharks’ long-term movement patterns and gain insight into the underlying factors influencing their vertical habitat selection. Archived data were received from 31 tags deployed on sharks of both sexes with total lengths of 5.5–9 m. Nine of these tags were physically recovered facilitating a detailed long-term view into the sharks’ vertical movements. Whale sharks feeding inshore on fish eggs off the northeast Yucatan Peninsula demonstrated reverse diel vertical migration, with extended periods of surface swimming beginning at sunrise followed by an abrupt change in the mid-afternoon to regular vertical oscillations, a pattern that continued overnight. When in oceanic waters, sharks spent about 95% of their time within epipelagic depths (500 m) that largely occurred during daytime or twilight hours (max. depth recorded 1,928 m), had V-shaped depth-time profiles, and comprised more rapid descents (0.68 m sec-1) than ascents (0.50 m sec-1). Nearly half of these extreme dives had descent profiles with brief but conspicuous changes in vertical direction at a mean depth of 475 m. We hypothesize these stutter steps represent foraging events within the deep scattering layer, however, the extreme dives may have additional functions. Overall, our results demonstrate complex and dynamic patterns of habitat utilization for R. typus that appear to be in response to changing biotic and abiotic conditions influencing the distribution and abundance of their prey

  10. Long-term results of 2 adjuvant trials reveal differences in chemosensitivity and the pattern of metastases between colon cancer and rectal cancer.

    Science.gov (United States)

    Kornmann, Marko; Staib, Ludger; Wiegel, Thomas; Kron, Martina; Henne-Bruns, Doris; Link, Karl-Heinrich; Formentini, Andrea

    2013-03-01

    Two identical randomized controlled trials designed to optimize adjuvant treatment of colon cancer (CC) (n =855) and rectal cancer (RC) (n = 796) were performed. Long-term evaluation confirmed that the addition of folinic acid (FA) to 5-fluorouracil (5-FU) improved 7-year overall survival (OS) in CC but not in RC and revealed different patterns of recurrence in patients with CC and those with RC. Our aim was to compare long-term results of adjuvant treatment of colon cancer (CC) and rectal cancer (RC). Adjuvant chemotherapy of CC improved overall survival (OS), whereas that of RC remained at the level achieved by 5-fluorouracil (5-FU). We separately conducted 2 identically designed adjuvant trials in CC and RC. Patients were assigned to adjuvant chemotherapy with 5-FU alone, 5-FU + folinic acid (FA), or 5-FU + interferon-alfa. The first study enrolled patients with stage IIb/III CC, and the second study enrolled patients with stage II/III RC. All patients with RC received postoperative irradiation. Median follow-up for all patients with CC (n = 855) and RC (n = 796) was 4.9 years. The pattern and frequency of recurrence differed significantly, especially lung metastases, which occurred more frequently in RC (12.7%) than in CC (7.3%; P < .001). Seven-year OS rates for 5-FU, 5-FU + FA, and 5-FU + IFN-alfa were 54.1% (95% confidence interval [CI], 46.5-61.0), 66.8% (95% CI, 59.4-73.1), and 56.7% (95% CI, 49.3-63.4) in CC and 50.6% (95% CI, 43.0-57.7), 56.3% (95% CI, 49.4-62.7), and 54.8% (95% CI, 46.7-62.2) in RC, respectively. A subgroup analysis pointed to a reduced local recurrence (LR) rate and an increased OS by the addition of FA in stage II RC (n = 271) but not in stage III RC (n = 525). FA increased 7-year OS by 12.7 percentage points in CC but was not effective in RC. Based on these results and the pattern of metastases, our results suggest that the chemosensitivity of CC and RC may be different. Strategies different from those used in CC may be successful to

  11. Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.

    Science.gov (United States)

    Kashif, Muhammad; Andersson, Claes; Mansoori, Sharmineh; Larsson, Rolf; Nygren, Peter; Gustafsson, Mats G

    2017-11-28

    We analyzed survival effects for 15 different pairs of clinically relevant anti-cancer drugs in three iso-genic pairs of human colorectal cancer carcinoma cell lines, by applying for the first time our novel software (R package) called COMBIA. In our experiments iso-genic pairs of cell lines were used, differing only with respect to a single clinically important KRAS or BRAF mutation. Frequently, concentration dependent but mutation independent joint Bliss and Loewe synergy/antagonism was found statistically significant. Four combinations were found synergistic/antagonistic specifically to the parental (harboring KRAS or BRAF mutation) cell line of the corresponding iso-genic cell lines pair. COMBIA offers considerable improvements over established software for synergy analysis such as MacSynergy™ II as it includes both Bliss (independence) and Loewe (additivity) analyses, together with a tailored non-parametric statistical analysis employing heteroscedasticity, controlled resampling, and global (omnibus) testing. In many cases Loewe analyses found significant synergistic as well as antagonistic effects in a cell line at different concentrations of a tested drug combination. By contrast, Bliss analysis found only one type of significant effect per cell line. In conclusion, the integrated Bliss and Loewe interaction analysis based on non-parametric statistics may provide more robust interaction analyses and reveal complex patterns of synergy and antagonism.

  12. Phosphorylation- and nucleotide-binding-induced changes to the stability and hydrogen exchange patterns of JNK1ß1 provide insight into its mechanisms of activation

    CSIR Research Space (South Africa)

    Owen, GR

    2014-10-01

    Full Text Available –deuterium exchange (HX) mass spectrometry were used to investigate the changes to the stability and conformation/conformational dynamics of JNK1ß1 induced by phosphorylative activation. Equivalent studies were also employed to determine the effects of nucleotide...

  13. Heat exchanger

    International Nuclear Information System (INIS)

    Dostatni, A.W.; Dostatni, Michel.

    1976-01-01

    In the main patent, a description was given of a heat exchanger with an exchange surface in preformed sheet metal designed for the high pressure and temperature service particularly encountered in nuclear pressurized water reactors and which is characterised by the fact that it is composed of at least one exchanger bundle sealed in a containment, the said bundle or bundles being composed of numerous juxtaposed individual compartments whose exchange faces are built of preformed sheet metal. The present addendun certificate concerns shapes of bundles and their positioning methods in the exchanger containment enabling its compactness to be increased [fr

  14. An Empirical Test of Efficiency of Exchange-Traded Currency Options in India

    OpenAIRE

    Aparna Bhat; Kirti Arekar

    2015-01-01

    The objective of this paper is to examine efficiency of the exchange-traded currency options market in India. Put-call-futures parity for the USD-INR currency options is studied by analyzing daily closing prices of options and futures for thirty two months on the National Stock Exchange. The study reveals frequent violations of the put-call-futures parity creating significant arbitrage opportunities. The pattern of mispricing varies when examined for time to maturity, option moneyness, liquid...

  15. Stakeholder engagement and knowledge exchange in environmental research.

    Science.gov (United States)

    Phillipson, Jeremy; Lowe, Philip; Proctor, Amy; Ruto, Eric

    2012-03-01

    It is commonly put forward that effective uptake of research in policy or practice must be built upon a foundation of active knowledge exchange and stakeholder engagement during the research. However, what is often lacking is a systematic appreciation of the specific practices of knowledge exchange and their relative merits. The paper reports on a 2009 survey of 21 research projects within the UK Research Councils' Rural Economy and Land Use Programme regarding the involvement and perceived impact of over a thousand stakeholders in the research. The survey reveals that most stakeholders were involved as research subjects or as event participants. Large numbers were also engaged in the research process itself, including involvement in shaping the direction of research. Stakeholder engagement is perceived as bringing significant benefits to the process of knowledge production. A close relationship is found between mechanisms and approaches to knowledge exchange and the spread of benefits for researchers and stakeholders. Mutual benefits are gained from exchange of staff or where stakeholders are members of research advisory groups. Different stakeholder sectors are also associated with different patterns of engagement, which lead to contrasting impact patterns. Any efforts to alter knowledge exchange processes and outcomes must overcome these differing engagement tendencies. Overall, much greater attention should be given to early processes of knowledge exchange and stakeholder engagement within the lifetime of research projects. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. Cryptographic Combinatorial Securities Exchanges

    Science.gov (United States)

    Thorpe, Christopher; Parkes, David C.

    We present a useful new mechanism that facilitates the atomic exchange of many large baskets of securities in a combinatorial exchange. Cryptography prevents information about the securities in the baskets from being exploited, enhancing trust. Our exchange offers institutions who wish to trade large positions a new alternative to existing methods of block trading: they can reduce transaction costs by taking advantage of other institutions’ available liquidity, while third party liquidity providers guarantee execution—preserving their desired portfolio composition at all times. In our exchange, institutions submit encrypted orders which are crossed, leaving a “remainder”. The exchange proves facts about the portfolio risk of this remainder to third party liquidity providers without revealing the securities in the remainder, the knowledge of which could also be exploited. The third parties learn either (depending on the setting) the portfolio risk parameters of the remainder itself, or how their own portfolio risk would change if they were to incorporate the remainder into a portfolio they submit. In one setting, these third parties submit bids on the commission, and the winner supplies necessary liquidity for the entire exchange to clear. This guaranteed clearing, coupled with external price discovery from the primary markets for the securities, sidesteps difficult combinatorial optimization problems. This latter method of proving how taking on the remainder would change risk parameters of one’s own portfolio, without revealing the remainder’s contents or its own risk parameters, is a useful protocol of independent interest.

  17. Fuel pattern recognition device

    International Nuclear Information System (INIS)

    Sato, Tomomi.

    1995-01-01

    The device of the present invention monitors normal fuel exchange upon fuel exchanging operation carried out in a reactor of a nuclear power plant. Namely, a fuel exchanger is movably disposed to the upper portion of the reactor and exchanges fuels. An exclusive computer receives operation signals of the fuel exchanger during operation as inputs, and outputs reactor core fuel pattern information signals to a fuel arrangement diagnosis device. An underwater television camera outputs image signals of a fuel pattern in the reactor core to an image processing device. If there is any change in the image signals for the fuel pattern as a result of the fuel exchange operation of the fuel exchanger, the image processing device outputs the change as image signals to the fuel pattern diagnosis device. The fuel pattern diagnosis device compares the pattern information signals from the exclusive computer with the image signals from the image processing device, to diagnose the result of the fuel exchange operation performed by the fuel exchanger and inform the diagnosis by means of an image display. (I.S.)

  18. Course-Taking Patterns of Community College Students Beginning in STEM: Using Data Mining Techniques to Reveal Viable STEM Transfer Pathways

    Science.gov (United States)

    Wang, Xueli

    2016-01-01

    This research focuses on course-taking patterns of beginning community college students enrolled in one or more non-remedial science, technology, engineering, and mathematics (STEM) courses during their first year of college, and how these patterns are mapped against upward transfer in STEM fields of study. Drawing upon postsecondary transcript…

  19. Large regional-scale variation in C3/C4 distribution pattern of Inner Mongolia steppe is revealed by grazer wool carbon isotope composition

    Directory of Open Access Journals (Sweden)

    K. Auerswald

    2009-05-01

    Full Text Available This work explored the spatial variation of C3/C4 distribution in the Inner Mongolia, P. R. China, steppe by geostatistical analysis of carbon isotope data of vegetation and sheep wool. Standing community biomass (n=118 and sheep wool (n=146 were sampled in a ~0.2 Mio km2 area. Samples from ten consecutive years (1998–2007 were obtained. Community biomass samples represented the carbon isotopic composition of standing vegetation on about 1000 m2 ("community-scale", whereas the spatio-temporal scale of wool reflected the isotope composition of the entire area grazed by the herd during a 1-yr period (~5–10 km2, "farm-scale". Pair wise sampling of wool and vegetation revealed a 13C-enrichment of 2.7±0.7‰ (95% confidence interval in wool relative to vegetation, but this shift exhibited no apparent relationships with environmental parameters or stocking rate. The proportion of C4 plants in above-ground biomass (PC4, % was estimated with a two-member mixing model of 13C discrimination by C3 and C4 vegetation (13Δ3 and 13Δ4, respectively, in accounting for the effects of changing 13C in atmospheric CO2 on sample isotope composition, and of altitude and aridity on 13Δ3. PC4 averaged 19%, but the variation was enormous: full-scale (0% to 100% at community-scale, and 0% to 85% at farm-scale. The farm-scale variation of PC4 exhibited a clear regional pattern over a range of ~250 km. Importantly PC4 was significantly higher above the 22°C isotherm of the warmest month, which was obtained from annual high-resolution maps and averaged over the different sampling years. This is consistent with predictions from C3/C4 crossover temperature of quantum yield or light use efficiency in C3 and C4 plants. Still, temperature gradients accounted for only 10% of

  20. Exchange effects in Relativistic Schroedinger Theory

    International Nuclear Information System (INIS)

    Sigg, T.; Sorg, M.

    1998-01-01

    The Relativistic Schroedinger Theory predicts the occurrence of exchange and overlap effects in many-particle systems. For a 2-particle system, the interaction energy of the two particles consists of two contributions: Coulomb energy and exchange energy, where the first one is revealed to be the same as in standard quantum theory. However the exchange energy is mediated by an exchange potential, contrary to the kinematical origin of the exchange term in the standard theory

  1. Comprehensive regional and temporal gene expression profiling of the rat brain during the first 24 h after experimental stroke identifies dynamic ischemia-induced gene expression patterns, and reveals a biphasic activation of genes in surviving tissue

    DEFF Research Database (Denmark)

    Rickhag, Karl Mattias; Wieloch, Tadeusz; Gidö, Gunilla

    2006-01-01

    middle cerebral artery occlusion in the rat. K-means cluster analysis revealed two distinct biphasic gene expression patterns that contained 44 genes (including 18 immediate early genes), involved in cell signaling and plasticity (i.e. MAP2K7, Sprouty2, Irs-2, Homer1, GPRC5B, Grasp). The first gene...

  2. Heat exchanger

    International Nuclear Information System (INIS)

    Leigh, D.G.

    1976-01-01

    The arrangement described relates particularly to heat exchangers for use in fast reactor power plants, in which heat is extracted from the reactor core by primary liquid metal coolant and is then transferred to secondary liquid metal coolant by means of intermediate heat exchangers. One of the main requirements of such a system, if used in a pool type fast reactor, is that the pressure drop on the primary coolant side must be kept to a minimum consistent with the maintenance of a limited dynamic head in the pool vessel. The intermediate heat exchanger must also be compact enough to be accommodated in the reactor vessel, and the heat exchanger tubes must be available for inspection and the detection and plugging of leaks. If, however, the heat exchanger is located outside the reactor vessel, as in the case of a loop system reactor, a higher pressure drop on the primary coolant side is acceptable, and space restriction is less severe. An object of the arrangement described is to provide a method of heat exchange and a heat exchanger to meet these problems. A further object is to provide a method that ensures that excessive temperature variations are not imposed on welded tube joints by sudden changes in the primary coolant flow path. Full constructional details are given. (U.K.)

  3. Study of switching behavior of exchange-coupled nanomagnets by transverse magnetization metrology

    Science.gov (United States)

    Dey, Himadri S.; Csaba, Gyorgy; Bernstein, Gary H.; Porod, Wolfgang

    2017-05-01

    We investigate the static switching modes of nanomagnets patterned from antiferromagnetically exchange-coupled magnetic multilayers, and compare them to nanomagnets having only dipole coupling between the ferromagnetic layers. Vibrating sample magnetometry experiments, supported by micromagnetic simulations, reveal two distinct switching mechanisms between the exchange-coupled and only dipole-coupled nanomagnets. The exchange-coupled nanomagnets exhibit gradual switching of the layers, dictated by the strong antiferromagnetic exchange coupling present between the layers. However, the layers of the only dipole-coupled nanomagnets show abrupt nucleation/growth type switching. A comprehensive understanding of the switching modes of such layered and patterned systems can add new insight into the reversal mechanisms of similar systems employed for spintronic and magneto-logic device applications.

  4. The Phenomenon of Bearish and Bullish in The Indonesian Stock Exchange

    Directory of Open Access Journals (Sweden)

    Berto Usman

    2016-09-01

    Full Text Available The Phenomenon of Bearish and Bullish in The Indonesian Stock ExchangeBearish and bullish pattern commonly exist in any of stock exchanges all over the world. Hereby, the volatility of price on specific stock and index will generally perform a typical co-movement. This study is officially intended to reveal the existence of bearish and bullish phenomenon in Indonesia stock exchange. The technical tool used in this study was known as candlestick analysis. It is utilized to discover the inclination of price movement and the percentage of bearish and bullish shown by the index. Further, it is noted that the object of this study is Indonesia stock exchange, which is surrogated by IDX Composite (IHSG. This research finally proved that there were 61 bearish (38.85% and 96 time bulish (61.15% patterns in IDX Composite (IHSG.DOI: 10.15408/ess.v6i2.3750

  5. A camera-phone based study reveals erratic eating pattern and disrupted daily eating-fasting cycle among adults in India.

    Directory of Open Access Journals (Sweden)

    Neelu Jain Gupta

    Full Text Available The daily rhythm of feeding-fasting and meal-timing are emerging as important determinants of health. Circadian rhythm research in animal models and retrospective analyses of human nutrition data have shown that reduced length of overnight fasting or increased late night eating increases risk for metabolic diseases including obesity and diabetes. However, the daily rhythm in eating pattern in humans is rarely measured. Traditional methods to collect nutrition information through food diary and food log pay little attention to the timing of eating which may also change from day to day. We adopted a novel cell-phone based approach to longitudinally record all events of food and beverage intake in adults. In a feasibility study daily food-eating patterns of 93 healthy individuals were recorded for 21 days using camera phones. Analysis of the daily eating patterns of these individuals indicates deviation from conventional assumption that people eat three meals-a-day within a 12 h interval. We found that eating events are widespread throughout the day, with 30% consumed in evening and late night hours. There was little difference in eating pattern between weekdays and weekends. In this cohort more than 50% of people spread their caloric intake events over 15 h or longer. One decile of the cohort who were spouses of shift-workers or had flexible work schedule spread their caloric intake over 20 h. Although the nutrition quality and diversity of food consumed is different between South-East Asian and Western countries, such overall disruption of daily eating-fasting rhythm is similar. Therefore, in view of hypothesis that disrupted daily eating pattern may contribute to the global increase in metabolic diseases and modification of daily eating pattern is a potential modifiable behavior to contain these diseases, monitoring eating pattern is an important aspect of lifestyle.

  6. A camera-phone based study reveals erratic eating pattern and disrupted daily eating-fasting cycle among adults in India.

    Science.gov (United States)

    Gupta, Neelu Jain; Kumar, Vinod; Panda, Satchidananda

    2017-01-01

    The daily rhythm of feeding-fasting and meal-timing are emerging as important determinants of health. Circadian rhythm research in animal models and retrospective analyses of human nutrition data have shown that reduced length of overnight fasting or increased late night eating increases risk for metabolic diseases including obesity and diabetes. However, the daily rhythm in eating pattern in humans is rarely measured. Traditional methods to collect nutrition information through food diary and food log pay little attention to the timing of eating which may also change from day to day. We adopted a novel cell-phone based approach to longitudinally record all events of food and beverage intake in adults. In a feasibility study daily food-eating patterns of 93 healthy individuals were recorded for 21 days using camera phones. Analysis of the daily eating patterns of these individuals indicates deviation from conventional assumption that people eat three meals-a-day within a 12 h interval. We found that eating events are widespread throughout the day, with 30% consumed in evening and late night hours. There was little difference in eating pattern between weekdays and weekends. In this cohort more than 50% of people spread their caloric intake events over 15 h or longer. One decile of the cohort who were spouses of shift-workers or had flexible work schedule spread their caloric intake over 20 h. Although the nutrition quality and diversity of food consumed is different between South-East Asian and Western countries, such overall disruption of daily eating-fasting rhythm is similar. Therefore, in view of hypothesis that disrupted daily eating pattern may contribute to the global increase in metabolic diseases and modification of daily eating pattern is a potential modifiable behavior to contain these diseases, monitoring eating pattern is an important aspect of lifestyle.

  7. Exchange Network

    Science.gov (United States)

    The Environmental Information Exchange Network (EN) is an Internet-based system used by state, tribal and territorial partners to securely share environmental and health information with one another and EPA.

  8. Online Access Patterns and Students

    Directory of Open Access Journals (Sweden)

    Nasir Butrous

    2011-04-01

    Full Text Available The paper follows accessing patterns of five cohorts of postgraduate students enrolled in a core unit within a master of business administration (MBA program. The unit is designed to provide numerous opportunities for student participation in Discussion Boards using Blackboard technology. Discussion Boards create numerous opportunities for interaction amongst online learners to share and exchange their experiences, creating a sense of a virtual community. Relationships between accessing patterns for each week of the semester for each student are explored in relation to their performance using course statistics generated by the Blackboard technology. Close examination of the significant differences in access patterns to the course window and its components of communication, content, and student areas reveal middle of the semester (week 7 as the common critical point that differentiates high achieving students from low achieving students. Identifying critical points provides the faculty staff member an opportunity to introduce intervention strategies in order to improve the learning experience of all the students.

  9. Intra-individual gait patterns across different time-scales as revealed by means of a supervised learning model using kernel-based discriminant regression.

    Directory of Open Access Journals (Sweden)

    Fabian Horst

    Full Text Available Traditionally, gait analysis has been centered on the idea of average behavior and normality. On one hand, clinical diagnoses and therapeutic interventions typically assume that average gait patterns remain constant over time. On the other hand, it is well known that all our movements are accompanied by a certain amount of variability, which does not allow us to make two identical steps. The purpose of this study was to examine changes in the intra-individual gait patterns across different time-scales (i.e., tens-of-mins, tens-of-hours.Nine healthy subjects performed 15 gait trials at a self-selected speed on 6 sessions within one day (duration between two subsequent sessions from 10 to 90 mins. For each trial, time-continuous ground reaction forces and lower body joint angles were measured. A supervised learning model using a kernel-based discriminant regression was applied for classifying sessions within individual gait patterns.Discernable characteristics of intra-individual gait patterns could be distinguished between repeated sessions by classification rates of 67.8 ± 8.8% and 86.3 ± 7.9% for the six-session-classification of ground reaction forces and lower body joint angles, respectively. Furthermore, the one-on-one-classification showed that increasing classification rates go along with increasing time durations between two sessions and indicate that changes of gait patterns appear at different time-scales.Discernable characteristics between repeated sessions indicate continuous intrinsic changes in intra-individual gait patterns and suggest a predominant role of deterministic processes in human motor control and learning. Natural changes of gait patterns without any externally induced injury or intervention may reflect continuous adaptations of the motor system over several time-scales. Accordingly, the modelling of walking by means of average gait patterns that are assumed to be near constant over time needs to be reconsidered in the

  10. Locked Nucleic Acid-Based In Situ Hybridization Reveals miR-7a as a Hypothalamus-Enriched MicroRNA with a Distinct Expression Pattern

    DEFF Research Database (Denmark)

    Herzer, S; Silahtaroglu, A; Meister, B

    2012-01-01

    , a part of the brain that controls vital bodily functions, we employed locked nucleic acid (LNA) - fluorescent in situ hybridization (FISH). The expression pattern of the mature miRNAs miR-7a, miR-7b, miR-137 and miR-153 in mouse brain tissue sections was investigated. Whereas all studied miRNAs were......R-7a expression was particularly prominent in the subfornical organ, suprachiasmatic, paraventricular, periventricular, supraoptic, dorsomedial and arcuate nuclei. Identical expression patterns for miR-7a was seen in mouse and rat hypothalamus. By combining LNA-FISH with immunohistochemistry...

  11. Intra-individual gait patterns across different time-scales as revealed by means of a supervised learning model using kernel-based discriminant regression.

    Science.gov (United States)

    Horst, Fabian; Eekhoff, Alexander; Newell, Karl M; Schöllhorn, Wolfgang I

    2017-01-01

    Traditionally, gait analysis has been centered on the idea of average behavior and normality. On one hand, clinical diagnoses and therapeutic interventions typically assume that average gait patterns remain constant over time. On the other hand, it is well known that all our movements are accompanied by a certain amount of variability, which does not allow us to make two identical steps. The purpose of this study was to examine changes in the intra-individual gait patterns across different time-scales (i.e., tens-of-mins, tens-of-hours). Nine healthy subjects performed 15 gait trials at a self-selected speed on 6 sessions within one day (duration between two subsequent sessions from 10 to 90 mins). For each trial, time-continuous ground reaction forces and lower body joint angles were measured. A supervised learning model using a kernel-based discriminant regression was applied for classifying sessions within individual gait patterns. Discernable characteristics of intra-individual gait patterns could be distinguished between repeated sessions by classification rates of 67.8 ± 8.8% and 86.3 ± 7.9% for the six-session-classification of ground reaction forces and lower body joint angles, respectively. Furthermore, the one-on-one-classification showed that increasing classification rates go along with increasing time durations between two sessions and indicate that changes of gait patterns appear at different time-scales. Discernable characteristics between repeated sessions indicate continuous intrinsic changes in intra-individual gait patterns and suggest a predominant role of deterministic processes in human motor control and learning. Natural changes of gait patterns without any externally induced injury or intervention may reflect continuous adaptations of the motor system over several time-scales. Accordingly, the modelling of walking by means of average gait patterns that are assumed to be near constant over time needs to be reconsidered in the context of

  12. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-Western cultural environments? Its adaptation and application in urban China

    DEFF Research Database (Denmark)

    Grunert, Klaus; Perrea, Toula; Zhou, Yanfeng

    2011-01-01

    Research related to food-related behaviour in China is still scarce, one reason being the fact that food consumption patterns in East Asia do not appear to be easily analyzed by models originating in Western cultures. The objective of the present work is to examine the ability of the food related...

  13. Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold hardiness in coastal Douglas Fir (Pseudotsuga menziesii var. menziesii).

    Science.gov (United States)

    A. Eckert; J. Wegrzyn; B. Pande; K. Jermstad; J. Lee; J. Liechty; B. Tearse; K. Krutovsky; D. Neale

    2009-01-01

    Forest trees exhibit remarkable adaptations to their environments. The genetic basis for phenotypic adaptation to climatic gradients has been established through a long history of common garden, provenance, and genecological studies. The identities of genes underlying these traits, however, have remained elusive and thus so have the patterns of adaptive molecular...

  14. Response of heat shock protein genes of the oriental fruit moth under diapause and thermal stress reveals multiple patterns dependent on the nature of stress exposure.

    Science.gov (United States)

    Zhang, Bo; Peng, Yu; Zheng, Jincheng; Liang, Lina; Hoffmann, Ary A; Ma, Chun-Sen

    2016-07-01

    Heat shock protein gene (Hsp) families are thought to be important in thermal adaptation, but their expression patterns under various thermal stresses have still been poorly characterized outside of model systems. We have therefore characterized Hsp genes and their stress responses in the oriental fruit moth (OFM), Grapholita molesta, a widespread global orchard pest, and compared patterns of expression in this species to that of other insects. Genes from four Hsp families showed variable expression levels among tissues and developmental stages. Members of the Hsp40, 70, and 90 families were highly expressed under short exposures to heat and cold. Expression of Hsp40, 70, and Hsc70 family members increased in OFM undergoing diapause, while Hsp90 was downregulated. We found that there was strong sequence conservation of members of large Hsp families (Hsp40, Hsp60, Hsp70, Hsc70) across taxa, but this was not always matched by conservation of expression patterns. When the large Hsps as well as small Hsps from OFM were compared under acute and ramping heat stress, two groups of sHsps expression patterns were apparent, depending on whether expression increased or decreased immediately after stress exposure. These results highlight potential differences in conservation of function as opposed to sequence in this gene family and also point to Hsp genes potentially useful as bioindicators of diapause and thermal stress in OFM.

  15. Magnetic resonance imaging-based cerebral tissue classification reveals distinct spatiotemporal patterns of changes after stroke in non-human primates

    NARCIS (Netherlands)

    Bouts, Mark. J. R. J.; Westmoreland, Susan. V.; de Crespigny, Alex J.; Liu, Yutong; Vangel, Mark; Dijkhuizen, Rick M.; Wu, Ona; D'Arceuil, Helen E.

    2015-01-01

    Background: Spatial and temporal changes in brain tissue after acute ischemic stroke are still poorly understood. Aims of this study were three-fold: (1) to determine unique temporal magnetic resonance imaging (MRI) patterns at the acute, subacute and chronic stages after stroke in macaques by

  16. Heat exchanger restart evaluation

    International Nuclear Information System (INIS)

    Morrison, J.M.; Hirst, C.W.; Lentz, T.F.

    1992-01-01

    On December 24, 1991, the K-Reactor was in the shutdown mode with full AC process water flow and full cooling water flow. Safety rod testing was being performed as part of the power ascension testing program. The results of cooling water samples indicated tritium concentrations higher than allowable. Further sampling and testing confirmed a Process Water System to Cooling Water System leak in heat exchanger 4A (HX 4A). The heat exchanger was isolated and the plant shutdown. Heat exchanger 4A was removed from the plant and moved to C-Area prior to performing examinations and diagnostic testing. This included locating and identifying the leaking tube or tubes, eddy current examination of the leaking tube and a number of adjacent tubes, visually inspecting the leaking tube from both the inside as well as the area surrounding the identified tube. The leaking tube was removed and examined metallurgically to determine the failure mechanism. In addition ten other tubes that either exhibited eddy current indications or would represent a baseline condition were removed from heat exchanger 4A for metallurgical examination. Additional analysis and review of heat exchanger leakage history was performed to determine if there are any patterns which can be used for predictive purposes. Compensatory actions have been taken to improve the sensitivity and response time to any future events of this type. The results of these actions are summary herein

  17. Heat exchanger restart evaluation

    International Nuclear Information System (INIS)

    Morrison, J.M.; Hirst, C.W.; Lentz, T.F.

    1992-01-01

    On December 24, 1991, the K-Reactor was in the shutdown mode with full AC process water flow and full cooling water flow. Safety rod testing was being performed as part of the power ascension testing program. The results of cooling water samples indicated tritium concentrations higher than allowable. Further sampling and testing confirmed a Process Water System to Cooling Water System leak in heat exchanger 4A (HX 4A). The heat exchanger was isolated and the plant shutdown. Heat exchanger 4kA was removed from the plant and moved to C-Area prior to performing examinations and diagnostic testing. This included locating and identifying the leaking tube or tubes, eddy current examination of the leaking tube and a number of adjacent tubes, visually inspecting the leaking tube from both the inside as well as the area surrounding the failure mechanism. In addition ten other tubes that either exhibited eddy current indications or would represent a baseline condition were removed from heat exchanger 4A for metallurgical examination. Additional analysis and review of heat exchanger leakage history was performed to determine if there are any patterns which can be used for predictive purposes. Compensatory actions have been taken to improve the sensitivity and response time to any future events of this type. The results of these actions are summarized herein

  18. Heat exchanger restart evaluation

    International Nuclear Information System (INIS)

    Morrison, J.M.; Hirst, C.W.; Lentz, T.F.

    1992-01-01

    On December 24, 1991, the K-Reactor was in the shutdown mode with full AC process water flow and full cooling water flow. Safety rod testing was being performed as part of the power ascension testing program. The results of cooling water samples indicated tritium concentrations higher than allowable. Further sampling and testing confirmed a Process Water System to Cooling Water System leak in heat exchanger 4A (HX 4A). The heat exchanger was isolated and the plant shutdown. Heat exchanger 4A was removed from the plant and moved to C-Area prior to performing examinations and diagnostic testing. This included locating and identifying the leaking tube or tubes, eddy current examination of the leaking tube and a number of adjacent tubes, visually inspecting the leaking tube from both the inside as well as the area surrounding the identified tube. The leaking tube was removed and examined metallurgically to determine the failure mechanism. In addition ten other tubes that either exhibited eddy current indications or would represent a baseline condition were removed from heat exchanger 4A for metallurgical examination. Additional analysis and review of heat exchanger leakage history was performed to determine if there are any patterns which can be used for predictive purposes. Compensatory actions have been taken to improve the sensitivity and response time to any future events of this type. The results of these actions are summarized

  19. Hyporheic Exchange Flows and Biogeochemical Patterns near a Meandering Stream: East Fork of the Jemez River, Valles Caldera National Preserve, New Mexico

    Science.gov (United States)

    Christensen, H.; Wooten, J. P.; Swanson, E.; Senison, J. J.; Myers, K. D.; Befus, K. M.; Warden, J.; Zamora, P. B.; Gomez, J. D.; Wilson, J. L.; Groffman, A.; Rearick, M. S.; Cardenas, M. B.

    2012-12-01

    A study by the 2012 Hydrogeology Field Methods class of the University of Texas at Austin implemented multiple approaches to evaluate and characterize local hyporheic zone flow and biogeochemical trends in a highly meandering reach of the of the East Fork of the Jemez River, a fourth order stream in northwestern New Mexico. This section of the Jemez River is strongly meandering and exhibits distinct riffle-pool morphology. The high stream sinuosity creates inter-meander hyporheic flow that is also largely influenced by local groundwater gradients. In this study, dozens of piezometers were used to map the water table and flow vectors were then calculated. Surface water and ground water samples were collected and preserved for later geochemical analysis by ICPMS and HPLC, and unstable parameters and alkalinity were measured on-site. Additionally, information was collected from thermal monitoring of the streambed, stream gauging, and from a series of electrical resistivity surveys forming a network across the site. Hyporheic flow paths are suggested by alternating gaining and losing sections of the stream as determined by stream gauging at multiple locations along the reach. Water table maps and calculated fluxes across the sediment-water interface also indicate hyporheic flow paths. We find variability in the distribution of biogeochemical constituents (oxidation-reduction potential, nitrate, ammonium, and phosphate) along interpreted flow paths which is partly consistent with hyporheic exchange. The variability and heterogeneity of reducing and oxidizing conditions is interpreted to be a result of groundwater-surface water interaction. Two-dimensional mapping of biogeochemical parameters show redox transitions along interpreted flow paths. Further analysis of various measured unstable chemical parameters results in observable trends strongly delineated along these preferential flow paths that are consistent with the direction of groundwater flow and the assumed

  20. Hydrogen exchange

    DEFF Research Database (Denmark)

    Jensen, Pernille Foged; Rand, Kasper Dyrberg

    2016-01-01

    Hydrogen exchange (HX) monitored by mass spectrometry (MS) is a powerful analytical method for investigation of protein conformation and dynamics. HX-MS monitors isotopic exchange of hydrogen in protein backbone amides and thus serves as a sensitive method for probing protein conformation...... and dynamics along the entire protein backbone. This chapter describes the exchange of backbone amide hydrogen which is highly quenchable as it is strongly dependent on the pH and temperature. The HX rates of backbone amide hydrogen are sensitive and very useful probes of protein conformation......, as they are distributed along the polypeptide backbone and form the fundamental hydrogen-bonding networks of basic secondary structure. The effect of pressure on HX in unstructured polypeptides (poly-dl-lysine and oxidatively unfolded ribonuclease A) and native folded proteins (lysozyme and ribonuclease A) was evaluated...

  1. Differential ontogenetic patterns of levocabastine-sensitive neurotensin NT2 receptors and of NT1 receptors in the rat brain revealed by in situ hybridization.

    Science.gov (United States)

    Lépée-Lorgeoux, I; Betancur, C; Rostène, W; Pélaprat, D

    1999-03-12

    The postnatal ontogeny of the levocabastine-sensitive neurotensin receptor (NT2) mRNA was studied by in situ hybridization in the rat brain and compared with the distribution of the levocabastine-insensitive NT1 receptor. NT2 receptor mRNA was absent at birth from all brain structures except the ependymal cell layer lining the ventricles. The development of NT2 receptor mRNA followed three ontogenetic patterns. The first pattern, involving the majority of the cerebral gray matter, was characterized by a continuous increase from postnatal day 5 (P5) to P30. The second one, involving regions rich in myelinated fibers such as the corpus callosum and lacunosum moleculare layer of the hippocampus, exhibited a pronounced increase between P5 and P10, peaked at P15 and was followed by a plateau or a slight decrease. The third pattern was observed in the ependymal cell layer lining the olfactory and lateral ventricles, where the high labeling already present at birth continued to increase during development. These different developmental patterns could reflect the variety of cells expressing NT2 receptor mRNA, including neurons, protoplasmic astrocytes in gray matter, fibrous astrocytes present in myelinated fibers tracts, and ependymal cells. In contrast, NT1 receptor mRNA, which seems to be associated only with neurons, was highly and transiently expressed during the perinatal period in the cerebral cortex, hippocampus and striatal neuroepithelium. Other regions, notably the ventral tegmental area and substantia nigra compacta, exhibited a gradual increase in NT1 receptor signal, reaching adult levels by P21. Both the differential localization and ontogenetic profiles of NT1 and NT2 receptor mRNAs suggest different involvement of these two receptors in brain functions and development. Copyright 1999 Elsevier Science B.V.

  2. Is food-related lifestyle (FRL) able to reveal food consumption patterns in non-western cultural environments? Its adaptation and application in urban China

    DEFF Research Database (Denmark)

    Grunert, Klaus G.; Perrea, Toula; Zhou, Yanfeng

    Research related to food-related behaviour in China is still scarce, one reason being the fact that food consumption patterns in East Asia do not appear to be easily analyzed by models originating in Western cultures. The objective of the present work is to examine the ability of the Food Related...... for the conceptual meaningfulness and applicability of FRL in non-Western food culture environments, when appropriately adapted....

  3. Heat exchanger

    International Nuclear Information System (INIS)

    Drury, C.R.

    1988-01-01

    A heat exchanger having primary and secondary conduits in heat-exchanging relationship is described comprising: at least one serpentine tube having parallel sections connected by reverse bends, the serpentine tube constituting one of the conduits; a group of open-ended tubes disposed adjacent to the parallel sections, the open-ended tubes constituting the other of the conduits, and forming a continuous mass of contacting tubes extending between and surrounding the serpentine tube sections; and means securing the mass of tubes together to form a predetermined cross-section of the entirety of the mass of open-ended tubes and tube sections

  4. Revealing the Driving Forces of Mid-Cities Urban Growth Patterns Using Spatial Modeling: a Case Study of Los Ángeles, Chile

    Directory of Open Access Journals (Sweden)

    Mauricio I. Aguayo

    2007-06-01

    Full Text Available City growth and changes in land-use patterns cause various important social and environmental impacts. To understand the spatial and temporal dynamics of these processes, the factors that drive urban development must be identified and analyzed, especially those factors that can be used to predict future changes and their potential environmental effects. Our objectives were to quantify the relationship between urban growth and its driving forces and to predict the spatial growth pattern based on historical land-use changes for the city of Los Ángeles in central Chile. This involved the analysis of images from 1978, 1992, and 1998 and characterization of the spatial pattern of land-use change; the construction of digital coverage in GIS; the selection of predictive variables through univariate analysis; the construction of logistic regression models using growth vs. nongrowth for 1978-1992 as the dependent variable; and the prediction of the probability of land-use change by applying the regression model to the 1992-1998 period. To investigate the influence of spatial scale, we constructed several sets of models that contained (1 only distance variables, e.g., distance to highways; (2 only scale-dependent density variables, e.g., density of urban area within a 600-m radius; (3 both distance and density variables; and (4 both distance and density variables at several spatial scales. The environmental variables were included in all models. The combination of distance and density variables at several scales is required to appropriately capture the multiscale urban growth process. The best models correctly predict ~90% of the observed land-use changes for 1992-1998. The distance to access roads, densities of the urban road system and urbanized area at various scales, and soil type were the strongest predictors of the growth pattern. Other variables were less important or not significant in explaining the urban growth process. Our approach, which

  5. The internal auditory clock: what can evoked potentials reveal about the analysis of temporal sound patterns, and abnormal states of consciousness?

    Science.gov (United States)

    Jones, S J

    2002-09-01

    Whereas in vision a large amount of information may in theory be extracted from instantaneous images, sound exists only in its temporal extent, and most of its information is contained in the pattern of changes over time. The "echoic memory" is a pre-attentive auditory sensory store in which sounds are apparently retained in full temporal detail for a period of a few seconds. From the long-latency auditory evoked potentials to spectro-temporal modulation of complex harmonic tones, at least two automatic sound analysis processes can be identified whose time constants suggest participation of the echoic memory. When a steady tone changes its pitch or timbre, "change-type" CP1, CN1 and CP2 potentials are maximally recorded near the vertex. These potentials appear to reflect a process concerned with the distribution of sound energy across the frequency spectrum. When, on the other hand, changes occur in the temporal pattern of tones (in which individual pitch changes are occurring at a rate sufficiently rapid for the C-potentials to be refractory), a large mismatch negativity (or MN1) and following positivity (MP2) are generated. The amplitude of these potentials is influenced by the degree of regularity of the pattern, larger responses being generated to a "deviant" tone when the pitch and time of occurrence of the "standards" are fully specified by the preceding pattern. At the sudden cessation of changes, on resumption of a steady pitch, a mismatch response is generated whose latency is determined with high precision (in the order of a few milliseconds) by the anticipated time of the next change, which did not in fact occur. The mismatch process, therefore, functions as spectro-temporal auditory pattern analyser, whose consequences are manifested each time the pattern changes. Since calibration of the passage of time is essential for all conscious and subconscious behaviour, is it possible that some states of unconsciousness may be directly due to disruption of

  6. Pengaruh Pola MACD Histogram IHSG Terhadap Pola MACD Histogram Perusahaan Dari Daftar Indeks LQ45 (Periode Februari s.d Juli 2015 Bursa Efek Jakarta [Effect of MACD Histogram IHSG Patterns to Patterns of Companies Listed on the Jakarta Stock Exchange LQ-45 (Period February till July 2015

    Directory of Open Access Journals (Sweden)

    Heri Fatkhurrokhim

    2015-09-01

    Full Text Available The purpose of this study is to determine the effect of MACDIHSG pattern to the MACD Company pattern in the L045 index on the period of February until July 2015 at the Indonesia Stock Exchange. This study also aims to facilitate investors to make investment decisions in the stock market. This study provides benefits to capital market investors, especially for stock investors in the Indonesia Stock Exchange as a mean of enhancing their insights in the development of technical analysis on investing. For the general public as well in order to know that investing in the stock market differs from gambling since there are analyzes that easy and can be applied very simply. In addition, this research aims to enhance the reader's desire to invest in the stock market. The samples were the closing data price of IHSG and shares ofLQ45 in the period of February until July 2015 in the Indonesia Stock Exchange. Based on the hypothesis testing, it can be explained that the MACD Histogram IHSG has a significant effect on 38 issuers listed in LQ45. As for the difference between the MACD Histogram effect against one company with another company that is very small. From the 38 stocks that rank on the top 3 company, the Summarecon Agung Tbk is on the top 1, that amounted to 98.3348%, then Alam Sutera Reality Lestari Tbk amounted to 98.2376%, and Adhi Katya (Persero Tbk amounted to 98.1320%. The third of these shares have MACD Histogram movement that approaching the MACD Histogram IHSG.

  7. Exchange Rate and Inflation Dynamics

    OpenAIRE

    Eatzaz Ahmad; Saima Ahmed Ali

    1999-01-01

    This paper studies simultaneous determination of nominal exchange rate and domestic price level in Pakistan. The estimated model contains sufficient built-in dynamics to trace the pattern and speed of adjustment in the two variables in response to temporary or permanent shocks. The two domestic shocks considered in the paper are monetary and real shocks, while the three external shocks considered are import price, export price and foreign exchange reserves shocks. The study finds that the imp...

  8. Heat exchanger

    Science.gov (United States)

    Wolowodiuk, Walter

    1976-01-06

    A heat exchanger of the straight tube type in which different rates of thermal expansion between the straight tubes and the supply pipes furnishing fluid to those tubes do not result in tube failures. The supply pipes each contain a section which is of helical configuration.

  9. Heat exchangers

    International Nuclear Information System (INIS)

    1975-01-01

    The tubes of a heat exchanger tube bank have a portion thereof formed in the shape of a helix, of effective radius equal to the tube radius and the space between two adjacent tubes, to tangentially contact the straight sections of the tubes immediately adjacent thereto and thereby provide support, maintain the spacing and account for differential thermal expansion thereof

  10. Exchange Options

    NARCIS (Netherlands)

    Jamshidian, F.

    2007-01-01

    The contract is described and market examples given. Essential theoretical developments are introduced and cited chronologically. The principles and techniques of hedging and unique pricing are illustrated for the two simplest nontrivial examples: the classical Black-Scholes/Merton/Margrabe exchange

  11. Exchange rates.

    Science.gov (United States)

    Mills, Bev

    2003-09-01

    IN MAY this year, I was lucky enough to go to Larissa in northern Greece as part of Hope Exchange 2003, an annual study tour organised by the European Union's hospital committee and administered by the Institute of Healthcare Management (IHM).

  12. Heat exchanger

    Science.gov (United States)

    Daman, Ernest L.; McCallister, Robert A.

    1979-01-01

    A heat exchanger is provided having first and second fluid chambers for passing primary and secondary fluids. The chambers are spaced apart and have heat pipes extending from inside one chamber to inside the other chamber. A third chamber is provided for passing a purge fluid, and the heat pipe portion between the first and second chambers lies within the third chamber.

  13. Heat exchanger

    International Nuclear Information System (INIS)

    Wolowodiuk, W.

    1976-01-01

    A heat exchanger of the straight tube type is described in which different rates of thermal expansion between the straight tubes and the supply pipes furnishing fluid to those tubes do not result in tube failures. The supply pipes each contain a section which is of helical configuration

  14. Estimation of Global 1km-grid Terrestrial Carbon Exchange Part II: Evaluations and Applications

    Science.gov (United States)

    Murakami, K.; Sasai, T.; Kato, S.; Niwa, Y.; Saito, M.; Takagi, H.; Matsunaga, T.; Hiraki, K.; Maksyutov, S. S.; Yokota, T.

    2015-12-01

    Global terrestrial carbon cycle largely depends on a spatial pattern in land cover type, which is heterogeneously-distributed over regional and global scales. Many studies have been trying to reveal distribution of carbon exchanges between terrestrial ecosystems and atmosphere for understanding global carbon cycle dynamics by using terrestrial biosphere models, satellite data, inventory data, and so on. However, most studies remained within several tens of kilometers grid spatial resolution, and the results have not been enough to understand the detailed pattern of carbon exchanges based on ecological community and to evaluate the carbon stocks by forest ecosystems in each countries. Improving the sophistication of spatial resolution is obviously necessary to enhance the accuracy of carbon exchanges. Moreover, the improvement may contribute to global warming awareness, policy makers and other social activities. We show global terrestrial carbon exchanges (net ecosystem production, net primary production, and gross primary production) with 1km-grid resolution. The methodology for these estimations are shown in the 2015 AGU FM poster "Estimation of Global 1km-grid Terrestrial Carbon Exchange Part I: Developing Inputs and Modelling". In this study, we evaluated the carbon exchanges in various regions with other approaches. We used the satellite-driven biosphere model (BEAMS) as our estimations, GOSAT L4A CO2 flux data, NEP retrieved by NICAM and CarbonTracer2013 flux data, for period from Jun 2001 to Dec 2012. The temporal patterns for this period were indicated similar trends between BEAMS, GOSAT, NICAM, and CT2013 in many sub-continental regions. Then, we estimated the terrestrial carbon exchanges in each countries, and could indicated the temporal patterns of the exchanges in large carbon stock regions.Global terrestrial carbon cycle largely depends on a spatial pattern of land cover type, which is heterogeneously-distributed over regional and global scales. Many

  15. Ancestral regulatory circuits governing ectoderm patterning downstream of Nodal and BMP2/4 revealed by gene regulatory network analysis in an echinoderm.

    Directory of Open Access Journals (Sweden)

    Alexandra Saudemont

    2010-12-01

    Full Text Available Echinoderms, which are phylogenetically related to vertebrates and produce large numbers of transparent embryos that can be experimentally manipulated, offer many advantages for the analysis of the gene regulatory networks (GRN regulating germ layer formation. During development of the sea urchin embryo, the ectoderm is the source of signals that pattern all three germ layers along the dorsal-ventral axis. How this signaling center controls patterning and morphogenesis of the embryo is not understood. Here, we report a large-scale analysis of the GRN deployed in response to the activity of this signaling center in the embryos of the Mediterranean sea urchin Paracentrotus lividus, in which studies with high spatial resolution are possible. By using a combination of in situ hybridization screening, overexpression of mRNA, recombinant ligand treatments, and morpholino-based loss-of-function studies, we identified a cohort of transcription factors and signaling molecules expressed in the ventral ectoderm, dorsal ectoderm, and interposed neurogenic ("ciliary band" region in response to the known key signaling molecules Nodal and BMP2/4 and defined the epistatic relationships between the most important genes. The resultant GRN showed a number of striking features. First, Nodal was found to be essential for the expression of all ventral and dorsal marker genes, and BMP2/4 for all dorsal genes. Second, goosecoid was identified as a central player in a regulatory sub-circuit controlling mouth formation, while tbx2/3 emerged as a critical factor for differentiation of the dorsal ectoderm. Finally, and unexpectedly, a neurogenic ectoderm regulatory circuit characterized by expression of "ciliary band" genes was triggered in the absence of TGF beta signaling. We propose a novel model for ectoderm regionalization, in which neural ectoderm is the default fate in the absence of TGF beta signaling, and suggest that the stomodeal and neural subcircuits that we

  16. Testing the enemy release hypothesis: abundance and distribution patterns of helminth communities in grey mullets (Teleostei: Mugilidae) reveal the success of invasive species.

    Science.gov (United States)

    Sarabeev, Volodimir; Balbuena, Juan Antonio; Morand, Serge

    2017-09-01

    The abundance and aggregation patterns of helminth communities of two grey mullet hosts, Liza haematocheilus and Mugil cephalus, were studied across 14 localities in Atlantic and Pacific marine areas. The analysis matched parasite communities of (i) L. haematocheilus across its native and introduced populations (Sea of Japan and Sea of Azov, respectively) and (ii) the introduced population of L. haematocheilus with native populations of M. cephalus (Mediterranean, Azov-Black and Japan Seas). The total mean abundance (TMA), as a feature of the infection level in helminth communities, and slope b of the Taylor's power law, as a measure of parasite aggregation at the infra and component-community levels, were estimated and compared between host species and localities using ANOVA. The TMA of the whole helminth community in the introduced population of L. haematocheilus was over 15 times lower than that of the native population, but the difference was less pronounced for carried (monogeneans) than for acquired (adult and larval digeneans) parasite communities. Similar to the abundance pattern, the species distribution in communities from the invasive population of L. haematocheilus was less aggregated than from its native population for endoparasitic helminths, including adult and larval digeneans, while monogeneans showed a similar pattern of distribution in the compared populations of L. haematocheilus. The aggregation level of the whole helminth community, endoparasitic helminths, adult and larval digeneans was lower in the invasive host species in comparison with native ones as shown by differences in the slope b. An important theoretical implication from this study is that the pattern of parasite aggregation may explain the success of invasive species in ecosystems. Because the effects of parasites on host mortality are likely dose-dependent, the proportion of susceptible host individuals in invasive species is expected to be lower, as the helminth distribution in

  17. Hydrogen Exchange Mass Spectrometry

    Science.gov (United States)

    Mayne, Leland

    2018-01-01

    Hydrogen exchange (HX) methods can reveal much about the structure, energetics, and dynamics of proteins. The addition of mass spectrometry (MS) to an earlier fragmentation-separation HX analysis now extends HX studies to larger proteins at high structural resolution and can provide information not available before. This chapter discusses experimental aspects of HX labeling, especially with respect to the use of MS and the analysis of MS data. PMID:26791986

  18. Coat of many colours—DNA reveals polymorphism of mantle patterns and colouration in Caribbean Cyphoma Röding, 1798 (Gastropoda, Ovulidae

    Directory of Open Access Journals (Sweden)

    Bastian T. Reijnen

    2017-03-01

    Full Text Available The iconic gastropod genus Cyphoma is commonly observed in the Caribbean, where it lives in association with various octocorallian hosts. Each species in the genus Cyphoma has a unique, characteristic mantle pattern and colouration, which separates the valid taxa. Because of its abundance and recognisability Cyphoma gibbosum has been used as a model organism in several studies concerning allelochemicals, reef degradation, and physical defence mechanisms. Molecular analyses based on four molecular markers (COI, 16S, H3 and 28S for three Cyphoma species (C. gibbosum, C. mcgintyi, C. signatum and an unidentified black morph, collected from three localities in the Caribbean, show that they represent morphological varieties of a single, genetically homogeneous species. This outcome is in agreement with previous anatomical studies. As a result C. mcgintyi and C. signatum are synonymised with C. gibbosum, which is a key result for future work using C. gibbosum as a model organism. The striking morphological differences in mantle pattern and colouration are hypothesised to be the result of one of three possible scenarios: rapid divergence, supergenes (including balanced polymorphism, or incipient speciation.

  19. Patterns of altered neural synchrony in the default mode network in autism spectrum disorder revealed with magnetoencephalography (MEG): Relationship to clinical symptomatology.

    Science.gov (United States)

    Lajiness-O'Neill, Renée; Brennan, Jonathan R; Moran, John E; Richard, Annette E; Flores, Ana-Mercedes; Swick, Casey; Goodcase, Ryan; Andersen, Tiffany; McFarlane, Kaitlyn; Rusiniak, Kenneth; Kovelman, Ioulia; Wagley, Neelima; Ugolini, Maggie; Albright, Jeremy; Bowyer, Susan M

    2018-03-01

    Disrupted neural synchrony may be a primary electrophysiological abnormality in autism spectrum disorders (ASD), altering communication between discrete brain regions and contributing to abnormalities in patterns of connectivity within identified neural networks. Studies exploring brain dynamics to comprehensively characterize and link connectivity to large-scale cortical networks and clinical symptoms are lagging considerably. Patterns of neural coherence within the Default Mode Network (DMN) and Salience Network (SN) during resting state were investigated in 12 children with ASD (M Age  = 9.2) and 13 age and gender-matched neurotypicals (NT) (M Age  = 9.3) with magnetoencephalography. Coherence between 231 brain region pairs within four frequency bands (theta (4-7 Hz), alpha, (8-12 Hz), beta (13-30 Hz), and gamma (30-80 Hz)) was calculated. Relationships between neural coherence and social functioning were examined. ASD was characterized by lower synchronization across all frequencies, reaching clinical significance in the gamma band. Lower gamma synchrony between fronto-temporo-parietal regions was observed, partially consistent with diminished default mode network (DMN) connectivity. Lower gamma coherence in ASD was evident in cross-hemispheric connections between: angular with inferior/middle frontal; middle temporal with middle/inferior frontal; and within right-hemispheric connections between angular, middle temporal, and inferior/middle frontal cortices. Lower gamma coherence between left angular and left superior frontal, right inferior/middle frontal, and right precuneus and between right angular and inferior/middle frontal cortices was related to lower social/social-communication functioning. Results suggest a pattern of lower gamma band coherence in a subset of regions within the DMN in ASD (angular and middle temporal cortical areas) related to lower social/social-communicative functioning. Autism Res 2018, 11: 434-449. © 2017 International

  20. Monoclonal antibodies to murine thrombospondin-1 and thrombospondin-2 reveal differential expression patterns in cancer and low antigen expression in normal tissues

    International Nuclear Information System (INIS)

    Bujak, Emil; Pretto, Francesca; Ritz, Danilo; Gualandi, Laura; Wulhfard, Sarah; Neri, Dario

    2014-01-01

    There is a considerable interest for the discovery and characterization of tumor-associated antigens, which may facilitate antibody-based pharmacodelivery strategies. Thrombospondin-1 and thrombospondin-2 are homologous secreted proteins, which have previously been reported to be overexpressed during remodeling typical for wound healing and tumor progression and to possibly play a functional role in cell proliferation, migration and apoptosis. To our knowledge, a complete immunohistochemical characterization of thrombospondins levels in normal rodent tissues has not been reported so far. Using antibody phage technology, we have generated and characterized monoclonal antibodies specific to murine thrombospondin-1 and thrombospondin-2, two antigens which share 62% aminoacid identity. An immunofluorescence analysis revealed that both antigens are virtually undetectable in normal mouse tissues, except for a weak staining of heart tissue by antibodies specific to thrombospondin-1. The analysis also showed that thrombospondin-1 was strongly expressed in 5/7 human tumors xenografted in nude mice, while it was only barely detectable in 3/8 murine tumors grafted in immunocompetent mice. By contrast, a high-affinity antibody to thrombospondin-2 revealed a much lower level of expression of this antigen in cancer specimens. Our analysis resolves ambiguities related to conflicting reports on thrombosponding expression in health and disease. Based on our findings, thrombospondin-1 (and not thrombospondin-2) may be considered as a target for antibody-based pharmacodelivery strategies, in consideration of its low expression in normal tissues and its upregulation in cancer. - Highlights: • High affinity monoclonal antibodies to murine and human TSP1 and 2 were raised. • Both antigens are virtually undetectable in normal mouse tissues. • Strong positivity of human tumor xenografts for TSP1 was detected. • Study revealed much lower level of TSP2 expression in cancer specimens

  1. Monoclonal antibodies to murine thrombospondin-1 and thrombospondin-2 reveal differential expression patterns in cancer and low antigen expression in normal tissues

    Energy Technology Data Exchange (ETDEWEB)

    Bujak, Emil [Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 2, CH-8093 Zurich (Switzerland); Pretto, Francesca; Ritz, Danilo; Gualandi, Laura; Wulhfard, Sarah [Philochem AG, Libernstrasse 3, CH-8112 Otelfingen (Switzerland); Neri, Dario, E-mail: neri@pharma.ethz.ch [Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 2, CH-8093 Zurich (Switzerland)

    2014-09-10

    There is a considerable interest for the discovery and characterization of tumor-associated antigens, which may facilitate antibody-based pharmacodelivery strategies. Thrombospondin-1 and thrombospondin-2 are homologous secreted proteins, which have previously been reported to be overexpressed during remodeling typical for wound healing and tumor progression and to possibly play a functional role in cell proliferation, migration and apoptosis. To our knowledge, a complete immunohistochemical characterization of thrombospondins levels in normal rodent tissues has not been reported so far. Using antibody phage technology, we have generated and characterized monoclonal antibodies specific to murine thrombospondin-1 and thrombospondin-2, two antigens which share 62% aminoacid identity. An immunofluorescence analysis revealed that both antigens are virtually undetectable in normal mouse tissues, except for a weak staining of heart tissue by antibodies specific to thrombospondin-1. The analysis also showed that thrombospondin-1 was strongly expressed in 5/7 human tumors xenografted in nude mice, while it was only barely detectable in 3/8 murine tumors grafted in immunocompetent mice. By contrast, a high-affinity antibody to thrombospondin-2 revealed a much lower level of expression of this antigen in cancer specimens. Our analysis resolves ambiguities related to conflicting reports on thrombosponding expression in health and disease. Based on our findings, thrombospondin-1 (and not thrombospondin-2) may be considered as a target for antibody-based pharmacodelivery strategies, in consideration of its low expression in normal tissues and its upregulation in cancer. - Highlights: • High affinity monoclonal antibodies to murine and human TSP1 and 2 were raised. • Both antigens are virtually undetectable in normal mouse tissues. • Strong positivity of human tumor xenografts for TSP1 was detected. • Study revealed much lower level of TSP2 expression in cancer specimens

  2. Differences in the diurnal pattern of soil respiration under adjacent Miscanthus x giganteus and barley crops reveal potential flaws in accepted sampling strategies

    Science.gov (United States)

    Keane, James; Ineson, Phil

    2017-04-01

    Soil respiration (Rs) plays an important role in the global carbon cycle and contributes ca. 30% of global ecosystem respiration.However, for convenience, measurements used to compare Rs from different land uses, crops or management practices are often made between 09:00 and 16:00, with an implicit assumption that Rs is largely controlled by temperature. Three months' continuous data presented here show distinctly different diurnal patterns of Rs between barley (Hordeum vulgare) and Miscanthus x giganteus (Miscanthus) grown on adjacent fields. Maximum Rs in barley occurred during the afternoon and correlated with soil temperature, whereas Rs peaked in Miscanthus during the night and was significantly correlated with earlier levels of solar radiation, probably due to delays in translocation of recent photosynthate. Since daily mean Rs in Miscanthus coincided with levels 40% greater than the mean in barley, it is vital to select appropriate times to measure Rs if only single daily measurements are to be made.

  3. Over Expression of a tRNALeu Isoacceptor Changes Charging Pattern of Leucine tRNAs and Reveals New Codon Reading

    DEFF Research Database (Denmark)

    Sørensen, Michael Askvad; Elf, J.; Bouakaz, E.

    2005-01-01

    During mRNA translation, synonymous codons for one amino acid are often read by different isoaccepting tRNAs. The theory of selective tRNA charging predicts greatly varying percentages of aminoacylation among isoacceptors in cells starved for their common amino acid. It also predicts major changes...... in tRNA charging patterns upon concentration changes of single isoacceptors, which suggests a novel type of translational control of gene expression. We therefore tested the theory by measuring with Northern blots the charging of Leu-tRNAs in Escherichia coli under Leu limitation in response to over...... postulated a previously unknown common codon for tRNALeu GAG and tRNALeu UAG. Subsequently, we demonstrated that the tRNALeu GAG codon CUU is, in fact, read also by tRNALeu UAG, due to a uridine-5-oxyacetic acid modification....

  4. A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation

    Directory of Open Access Journals (Sweden)

    Robert G. Moyle

    2017-05-01

    Full Text Available Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient.

  5. Optogenetic stimulation of VTA dopamine neurons reveals that tonic but not phasic patterns of dopamine transmission reduce ethanol self-administration

    Directory of Open Access Journals (Sweden)

    Caroline E Bass

    2013-11-01

    Full Text Available There is compelling evidence that acute ethanol exposure stimulates ventral tegmental area (VTA dopamine cell activity and that VTA-dependent dopamine release in terminal fields within the nucleus accumbens plays an integral role in the regulation of ethanol drinking behaviors. Unfortunately, due to technical limitations, the specific temporal dynamics linking VTA dopamine cell activation and ethanol self-administration are not known. In fact, establishing a causal link between specific patterns of dopamine transmission and ethanol drinking behaviors has proven elusive. Here, we sought to address these gaps in our knowledge using a newly developed viral-mediated gene delivery strategy to selectively express Channelrhodopsin-2 (ChR2 on dopamine cells in the VTA of wild-type rats. We then used this approach to precisely control VTA dopamine transmission during voluntary ethanol drinking sessions. The results confirmed that ChR2 was selectively expressed on VTA dopamine cells and delivery of blue light pulses to the VTA induced dopamine release in accumbal terminal fields with very high temporal and spatial precision. Brief high frequency VTA stimulation induced phasic patterns of dopamine release in the nucleus accumbens. Lower frequency stimulation, applied for longer periods mimicked tonic increases in accumbal dopamine. Notably, using this optogenetic approach in rats engaged in an intermittent ethanol drinking procedure, we found that tonic, but not phasic, stimulation of VTA dopamine cells selectively attenuated ethanol drinking behaviors. Collectively, these data demonstrate the effectiveness of a novel viral targeting strategy that can be used to restrict opsin expression to dopamine cells in standard outbred animals and provide the first causal evidence demonstrating that tonic activation of VTA dopamine neurons selectively decreases ethanol self-administration behaviors.

  6. Long-Term Recordings of Arcuate Nucleus Kisspeptin Neurons Reveal Patterned Activity That Is Modulated by Gonadal Steroids in Male Mice.

    Science.gov (United States)

    Vanacker, Charlotte; Moya, Manuel Ricu; DeFazio, R Anthony; Johnson, Michael L; Moenter, Suzanne M

    2017-10-01

    Pulsatile release of gonadotropin-releasing hormone (GnRH) is key to fertility. Pulse frequency is modulated by gonadal steroids and likely arises subsequent to coordination of GnRH neuron firing activity. The source of rhythm generation and the site of steroid feedback remain critical unanswered questions. Arcuate neurons that synthesize kisspeptin, neurokinin B, and dynorphin (KNDy) may be involved in both of these processes. We tested the hypotheses that action potential firing in KNDy neurons is episodic and that gonadal steroids regulate this pattern. Targeted extracellular recordings were made of green fluorescent protein-identified KNDy neurons in brain slices from adult male mice that were intact, castrated, or castrated and treated with estradiol or dihydrotestosterone (DHT). KNDy neurons exhibited marked peaks and nadirs in action potential firing activity during recordings lasting 1 to 3.5 hours. Peaks, identified by Cluster analysis, occurred more frequently in castrated than intact mice, and either estradiol or DHT in vivo or blocking neurokinin type 3 receptor in vitro restored peak frequency to intact levels. The frequency of peaks in firing rate and estradiol regulation of this frequency is similar to that observed for GnRH neurons, whereas DHT suppressed firing in KNDy but not GnRH neurons. We further examined the patterning of action potentials to identify bursts that may be associated with increased neuromodulator release. Burst frequency and duration are increased in castrated compared with intact and steroid-treated mice. The observation that KNDy neurons fire in an episodic manner that is regulated by steroid feedback is consistent with a role for these neurons in GnRH pulse generation and regulation. Copyright © 2017 Endocrine Society.

  7. Response patterns of phytoplankton growth to variations in resuspension in the German Bight revealed by daily MERIS data in 2003 and 2004

    Directory of Open Access Journals (Sweden)

    Jian Su

    2015-10-01

    Full Text Available Chlorophyll (chl a concentration in coastal seas exhibits variability on various spatial and temporal scales. Resuspension of particulate matter can somewhat limit algal growth, but can also enhance productivity because of the intrusion of nutrient-rich pore water from sediments or bottom water layers into the whole water column. This study investigates whether characteristic changes in net phytoplankton growth can be directly linked to resuspension events within the German Bight. Satellite-derived chl a were used to derive spatial patterns of net rates of chl a increase/decrease (NR in 2003 and 2004. Spatial correlations between NR and mean water column irradiance were analysed. High correlations in space and time were found in most areas of the German Bight (R2 > 0.4, suggesting a tight coupling between light availability and algal growth during spring. These correlations were reduced within a distinct zone in the transition between shallow coastal areas and deeper offshore waters. In summer and autumn, a mismatch was found between phytoplankton blooms (chl a > 6 mg m−3 and spring-tidal induced resuspension events as indicated by bottom velocity, suggesting that there is no phytoplankton resuspension during spring tides. It is instead proposed here that frequent and recurrent spring-tidal resuspension events enhance algal growth by supplying remineralized nutrients. This hypothesis is corroborated by a lag correlation analysis between resuspension events and in-situ measured nutrient concentrations. This study outlines seasonally different patterns in phytoplankton productivity in response to variations in resuspension, which can serve as a reference for modelling coastal ecosystem dynamics.

  8. Spatial genetic analyses reveal cryptic population structure and migration patterns in a continuously harvested grey wolf (Canis lupus population in north-eastern Europe.

    Directory of Open Access Journals (Sweden)

    Maris Hindrikson

    Full Text Available Spatial genetics is a relatively new field in wildlife and conservation biology that is becoming an essential tool for unravelling the complexities of animal population processes, and for designing effective strategies for conservation and management. Conceptual and methodological developments in this field are therefore critical. Here we present two novel methodological approaches that further the analytical possibilities of STRUCTURE and DResD. Using these approaches we analyse structure and migrations in a grey wolf (Canislupus population in north-eastern Europe. We genotyped 16 microsatellite loci in 166 individuals sampled from the wolf population in Estonia and Latvia that has been under strong and continuous hunting pressure for decades. Our analysis demonstrated that this relatively small wolf population is represented by four genetic groups. We also used a novel methodological approach that uses linear interpolation to statistically test the spatial separation of genetic groups. The new method, which is capable of using program STRUCTURE output, can be applied widely in population genetics to reveal both core areas and areas of low significance for genetic groups. We also used a recently developed spatially explicit individual-based method DResD, and applied it for the first time to microsatellite data, revealing a migration corridor and barriers, and several contact zones.

  9. Ion exchange equilibrium constants

    CERN Document Server

    Marcus, Y

    2013-01-01

    Ion Exchange Equilibrium Constants focuses on the test-compilation of equilibrium constants for ion exchange reactions. The book first underscores the scope of the compilation, equilibrium constants, symbols used, and arrangement of the table. The manuscript then presents the table of equilibrium constants, including polystyrene sulfonate cation exchanger, polyacrylate cation exchanger, polymethacrylate cation exchanger, polysterene phosphate cation exchanger, and zirconium phosphate cation exchanger. The text highlights zirconium oxide anion exchanger, zeolite type 13Y cation exchanger, and

  10. Heat exchanger

    International Nuclear Information System (INIS)

    Bennett, J.C.

    1975-01-01

    A heat exchanger such as forms, for example, part of a power steam boiler is made up of a number of tubes that may be arranged in many different ways, and it is necessary that the tubes be properly supported. The means by which the tubes are secured must be as simple as possible so as to facilitate construction and must be able to continue to function effectively under the varying operating conditions to which the heat exchanger is subject. The arrangement described is designed to meet these requirements, in an improved way. The tubes are secured to a member extending past several tubes and abutment means are provided. At least some of the abutment means comprise two abutment pieces and a wedge secured to the supporting member, that acts on these pieces to maintain the engagement. (U.K.)

  11. Heat exchangers

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, E L; Eisenmann, G; Hahne, E [Stuttgart Univ. (TH) (F.R. Germany). Inst. fuer Thermodynamik und Waermetechnik

    1976-04-01

    A survey is presented on publications on design, heat transfer, form factors, free convection, evaporation processes, cooling towers, condensation, annular gap, cross-flowed cylinders, axial flow through a bundle of tubes, roughnesses, convective heat transfer, loss of pressure, radiative heat transfer, finned surfaces, spiral heat exchangers, curved pipes, regeneraters, heat pipes, heat carriers, scaling, heat recovery systems, materials selection, strength calculation, control, instabilities, automation of circuits, operational problems and optimization.

  12. Patterns of traffic polycyclic aromatic hydrocarbon pollution in mountain areas can be revealed by lichen biomonitoring: a case study in the Dolomites (Eastern Italian Alps).

    Science.gov (United States)

    Nascimbene, Juri; Tretiach, Mauro; Corana, Federica; Lo Schiavo, Fiorella; Kodnik, Danijela; Dainese, Matteo; Mannucci, Barbara

    2014-03-15

    In mountain areas of touristic interest the evaluation of the impact of human activities is crucial for ensuring long-term conservation of ecosystem biodiversity, functions and services. This study aimed at verifying the biological impact of polycyclic aromatic hydrocarbon (PAH) emissions due to traffic along the roads leading to seven passes of the Dolomites (SE Alps), which were recently declared a UNESCO World Heritage Site. Thalli of the epiphytic lichen Pseudevernia furfuracea, collected at increasing distances from the roads, were used as biomonitors. Our study revealed a gradient of decreasing PAH pollution within 300 m from the roads. Differences among passes were evident mainly for samples collected nearest to the roads, but PAH concentrations at 300 m were almost always higher than those of undisturbed reference sites, indicating that traffic PAH pollution may impact natural ecosystems and lichen diversity at relatively long distances from the emission source. Copyright © 2014 Elsevier B.V. All rights reserved.

  13. The ventralizing activity of Radar, a maternally expressed bone morphogenetic protein, reveals complex bone morphogenetic protein interactions controlling dorso-ventral patterning in zebrafish.

    Science.gov (United States)

    Goutel, C; Kishimoto, Y; Schulte-Merker, S; Rosa, F

    2000-12-01

    In Xenopus and zebrafish, BMP2, 4 and 7 have been implicated, after the onset of zygotic expression, in inducing and maintaining ventro-lateral cell fate during early development. We provide evidence here that a maternally expressed bone morphogenetic protein (BMP), Radar, may control early ventral specification in zebrafish. We show that Radar ventralizes zebrafish embryos and induces the early expression of bmp2b and bmp4. The analysis of Radar overexpression in both swirl/bmp2b mutants and embryos expressing truncated BMP receptors shows that Radar-induced ventralization is dependent on functional BMP2/4 pathways, and may initially rely on an Alk6-related signaling pathway. Finally, we show that while radar-injected swirl embryos still exhibit a strongly dorsalized phenotype, the overexpression of Radar into swirl/bmp2b mutant embryos restores ventral marker expression, including bmp4 expression. Our results suggest that a complex regulation of different BMP pathways controls dorso-ventral (DV) patterning from early cleavage stages until somitogenesis.

  14. Technical note: Differences in the diurnal pattern of soil respiration under adjacent Miscanthus × giganteus and barley crops reveal potential flaws in accepted sampling strategies

    Science.gov (United States)

    Ben Keane, J.; Ineson, Phil

    2017-03-01

    For convenience, measurements used to compare soil respiration (Rs) from different land uses, crops or management practices are often made between 09:00 and 16:00 UTC, convenience which is justified by an implicit assumption that Rs is largely controlled by temperature. Three months of continuous data presented here show distinctly different diurnal patterns of Rs between barley (Hordeum vulgare) and Miscanthus × giganteus (Miscanthus) grown on adjacent fields. Maximum Rs in barley occurred during the afternoon and correlated with soil temperature, whereas in Miscanthus after an initial early evening decline, Rs increased above the daily average during the night and in July maximum daily rates of Rs were seen at 22:00 and was significantly correlated with earlier levels of solar radiation, probably due to delays in translocation of recent photosynthate. Since the time of the daily mean Rs in Miscanthus occurred when Rs in the barley was 40 % greater than the daily mean, it is vital to select appropriate times to measure Rs especially if only single daily measurements are to be made.

  15. Marriage exchanges, seed exchanges, and the dynamics of manioc diversity.

    Science.gov (United States)

    Delêtre, Marc; McKey, Doyle B; Hodkinson, Trevor R

    2011-11-08

    The conservation of crop genetic resources requires understanding the different variables-cultural, social, and economic-that impinge on crop diversity. In small-scale farming systems, seed exchanges represent a key mechanism in the dynamics of crop genetic diversity, and analyzing the rules that structure social networks of seed exchange between farmer communities can help decipher patterns of crop genetic diversity. Using a combination of ethnobotanical and molecular genetic approaches, we investigated the relationships between regional patterns of manioc genetic diversity in Gabon and local networks of seed exchange. Spatially explicit Bayesian clustering methods showed that geographical discontinuities of manioc genetic diversity mirror major ethnolinguistic boundaries, with a southern matrilineal domain characterized by high levels of varietal diversity and a northern patrilineal domain characterized by low varietal diversity. Borrowing concepts from anthropology--kinship, bridewealth, and filiation--we analyzed the relationships between marriage exchanges and seed exchange networks in patrilineal and matrilineal societies. We demonstrate that, by defining marriage prohibitions, kinship systems structure social networks of exchange between farmer communities and influence the movement of seeds in metapopulations, shaping crop diversity at local and regional levels.

  16. Gendered Pathways: Violent Childhood Maltreatment, Sex Exchange, and Drug Use.

    Science.gov (United States)

    Verona, Edelyn; Murphy, Brett; Javdani, Shabnam

    2015-04-20

    Recent work has emphasized the role of violent victimization, along with risky contexts like sex exchange, in pathways to problems of externalizing and substance use in women. Nonetheless, few studies have empirically tested gender differences involving the roles of adversity factors (e.g., childhood violent maltreatment, sex exchange) in drug use patterns. The present study tested a model of gender differences in relationships between childhood physical and sexual abuse, sex exchange, and two indicators of drug use: engagement and symptoms of disorder. We recruited an ethnically-diverse sample of 304 (130 women) adults with recent histories of violence and/or drug use, who completed a substance use diagnostic interview, the Childhood Trauma Questionnaire, and a sex exchange questionnaire. First, structural equation modeling revealed that childhood sexual and physical abuse were related to increased drug engagement in women and men, respectively, above the influence of early childhood contextual variables (e.g., neighborhood, family) and age. Second, sexual abuse was related to sex exchange, which in turn was related to drug use symptoms in women but not men. These data provide empirical support for distinct trauma-related pathways to drug use problems in men and women, which has implications for gendered explanations and prevention approaches.

  17. 3D CFD fluid flow and thermal analyses of a new design of plate heat exchanger

    Directory of Open Access Journals (Sweden)

    Pianko-Oprych Paulina

    2017-03-01

    Full Text Available The paper presents a Computational Fluid Dynamics (CFD numerical study for a new design of a plate heat exchanger with two different flow patterns. The impact of geometric characteristics of the two studied geometries of exchanger plates on the intensification process of heat transfer was considered. The velocity, temperature and pressure distributions along the heat exchanger were examined. The CFD results were validated against experimental data and a good agreement was achieved. The results revealed that geometrical arrangement of the plates strongly influence the fluid flow. An increase in the Reynolds number led to lowering the friction factor value and increasing the pressure drop. The configuration II of the plate heat exchanger resulted in lower outlet hot fluid temperature in comparison with the configuration I, which means improvement of heat transfer.

  18. Geomorphology, denudation rates, and stream channel profiles reveal patterns of mountain building adjacent to the San Andreas fault in northern California, USA

    Science.gov (United States)

    DeLong, Stephen B.; Hilley, George E.; Prentice, Carol S.; Crosby, Christopher J.; Yokelson, Intan N.

    2017-01-01

    Relative horizontal motion along strike-slip faults can build mountains when motion is oblique to the trend of the strike-slip boundary. The resulting contraction and uplift pose off-fault seismic hazards, which are often difficult to detect because of the poor vertical resolution of satellite geodesy and difficulty of locating offset datable landforms in active mountain ranges. Sparse geomorphic markers, topographic analyses, and measurement of denudation allow us to map spatiotemporal patterns of uplift along the northern San Andreas fault. Between Jenner and Mendocino, California, emergent marine terraces found southwest of the San Andreas fault record late Pleistocene uplift rates between 0.20 and 0.45 mm yr–1 along much of the coast. However, on the northeast side of the San Andreas fault, a zone of rapid uplift (0.6–1.0 mm yr–1) exists adjacent to the San Andreas fault, but rates decay northeastward as the coast becomes more distant from the San Andreas fault. A newly dated 4.5 Ma shallow-marine deposit located at ∼500 m above sea level (masl) adjacent to the San Andreas fault is warped down to just 150 masl 15 km northeast of the San Andreas fault, and it is exposed at just 60–110 masl to the west of the fault. Landscape denudation rates calculated from abundance of cosmogenic radionuclides in fluvial sediment northeast of, and adjacent to, the San Andreas fault are 0.16–0.29 mm yr–1, but they are only 0.03–0.07 mm yr–1 west of the fault. Basin-average channel steepness and the denudation rates can be used to infer the erosive properties of the underlying bedrock. Calibrated erosion rates can then be estimated across the entire landscape using the spatial distribution of channel steepness with these erosive properties. The lower-elevation areas of this landscape that show high channel steepness (and hence calibrated erosion rate) are distinct from higher-elevation areas with systematically lower channel steepness and denudation rates

  19. Model-Based Analysis of Arabidopsis Leaf Epidermal Cells Reveals Distinct Division and Expansion Patterns for Pavement and Guard Cells1[W][OA

    Science.gov (United States)

    Asl, Leila Kheibarshekan; Dhondt, Stijn; Boudolf, Véronique; Beemster, Gerrit T.S.; Beeckman, Tom; Inzé, Dirk; Govaerts, Willy; De Veylder, Lieven

    2011-01-01

    To efficiently capture sunlight for photosynthesis, leaves typically develop into a flat and thin structure. This development is driven by cell division and expansion, but the individual contribution of these processes is currently unknown, mainly because of the experimental difficulties to disentangle them in a developing organ, due to their tight interconnection. To circumvent this problem, we built a mathematic model that describes the possible division patterns and expansion rates for individual epidermal cells. This model was used to fit experimental data on cell numbers and sizes obtained over time intervals of 1 d throughout the development of the first leaf pair of Arabidopsis (Arabidopsis thaliana). The parameters were obtained by a derivative-free optimization method that minimizes the differences between the predicted and experimentally observed cell size distributions. The model allowed us to calculate probabilities for a cell to divide into guard or pavement cells, the maximum size at which it can divide, and its average cell division and expansion rates at each point during the leaf developmental process. Surprisingly, average cell cycle duration remained constant throughout leaf development, whereas no evidence for a maximum cell size threshold for cell division of pavement cells was found. Furthermore, the model predicted that neighboring cells of different sizes within the epidermis expand at distinctly different relative rates, which could be verified by direct observations. We conclude that cell division seems to occur independently from the status of cell expansion, whereas the cell cycle might act as a timer rather than as a size-regulated machinery. PMID:21693673

  20. Deformation patterns, magma supply, and magma storage at Karymsky Volcanic Center, Kamchatka, Russia, 2000-2010, revealed by InSAR

    Science.gov (United States)

    Ji, Lingyun; Izbekov, Pavel; Senyukov, Sergey; Lu, Zhong

    2018-02-01

    Under a complex geological region influenced by the subduction of the Pacific plate, Kamchatka Peninsula is one of the most active volcanic arcs in the Pacific Rim. Due to logistical difficulty in instrumentation, shallow magma plumbing systems beneath some of the Kamchatkan volcanoes are poorly understood. InSAR offers a safe and quick method for monitoring volcanic deformation with a high spatial resolution. In this study, a group of satellite radar interferograms that span the time interval from 2000 to 2010 shows eruptive and non-eruptive deformation at Karymsky Volcanic Center (KVC), Kamchatka, Russia. All the interferograms provide details of the activity around the KVC during 2000-2010, as follows: (1) from 2000 to 2004, the Karymsky-AN (Akademia Nauk) area deflated and the MS (Maly Semyachik) area inflated, (2) from 2004 to 2006, the Karymsky-AN area deflated with ongoing eruption, while the MS area subsided without eruption, (3) from 2006 to 2008, as with 2000-2004, the Karymsky-AN area deflated and the MS area inflated, (4) from 2008 to 2010, the Karymsky-AN area inflated up to 3 cm, and the MS area subsided. Point source models suggest that two magma reservoirs provide a good fit to the observed deformation. One source is located beneath the area between Karymsky and AN at a depth of approximately 7.0 km, and the other one is situated beneath MS at a depth of around 5.8 km. Synchronous deformation patterns suggest that two magma systems are fed from the same deep magma source and connected by a fracture zone. The InSAR results are consistent with GPS ground deformation measurements, seismic data, and petrological constraints.

  1. TRANSCRIPTOME ANALYSES REVEAL DIFFERENTIAL GENE EXPRESSION PATTERNS BETWEEN THE LIFE-CYCLE STAGES OF EMILIANIA HUXLEYI (HAPTOPHYTA) AND REFLECT SPECIALIZATION TO DIFFERENT ECOLOGICAL NICHES(1).

    Science.gov (United States)

    Rokitta, Sebastian D; de Nooijer, Lennart J; Trimborn, Scarlett; de Vargas, Colomban; Rost, Björn; John, Uwe

    2011-08-01

    Coccolithophores, especially the abundant, cosmopolitan species Emiliania huxleyi (Lohmann) W. W. Hay et H. P. Mohler, are one of the main driving forces of the oceanic carbonate pump and contribute significantly to global carbon cycling, due to their ability to calcify. A recent study indicates that termination of diploid blooms by viral infection induces life-cycle transition, and speculation has arisen about the role of the haploid, noncalcifying stage in coccolithophore ecology. To explore gene expression patterns in both life-cycle stages, haploid and diploid cells of E. huxleyi (RCC 1217 and RCC 1216) were acclimated to limiting and saturating photon flux densities. Transcriptome analyses were performed to assess differential genomic expression related to different ploidy levels and acclimation light intensities. Analyses indicated that life-cycle stages exhibit different properties of regulating genome expression (e.g., pronounced gene activation and gene silencing in the diploid stage), proteome maintenance (e.g., increased turnover of proteins in the haploid stage), as well as metabolic processing (e.g., pronounced primary metabolism and motility in the haploid stage and calcification in the diploid stage). Furthermore, higher abundances of transcripts related to endocytotic and digestive machinery were observed in the diploid stage. A qualitative feeding experiment indicated that both life-cycle stages are capable of particle uptake (0.5 μm diameter) in late-stationary growth phase. Results showed that the two life-cycle stages represent functionally distinct entities that are evolutionarily shaped to thrive in the environment they typically inhabit. © 2011 Phycological Society of America.

  2. Analysis of ParB-centromere interactions by multiplex SPR imaging reveals specific patterns for binding ParB in six centromeres of Burkholderiales chromosomes and plasmids.

    Directory of Open Access Journals (Sweden)

    Flavien Pillet

    Full Text Available Bacterial centromeres-also called parS, are cis-acting DNA sequences which, together with the proteins ParA and ParB, are involved in the segregation of chromosomes and plasmids. The specific binding of ParB to parS nucleates the assembly of a large ParB/DNA complex from which ParA-the motor protein, segregates the sister replicons. Closely related families of partition systems, called Bsr, were identified on the chromosomes and large plasmids of the multi-chromosomal bacterium Burkholderia cenocepacia and other species from the order Burkholeriales. The centromeres of the Bsr partition families are 16 bp palindromes, displaying similar base compositions, notably a central CG dinucleotide. Despite centromeres bind the cognate ParB with a narrow specificity, weak ParB-parS non cognate interactions were nevertheless detected between few Bsr partition systems of replicons not belonging to the same genome. These observations suggested that Bsr partition systems could have a common ancestry but that evolution mostly erased the possibilities of cross-reactions between them, in particular to prevent replicon incompatibility. To detect novel similarities between Bsr partition systems, we have analyzed the binding of six Bsr parS sequences and a wide collection of modified derivatives, to their cognate ParB. The study was carried out by Surface Plasmon Resonance imaging (SPRi mulitplex analysis enabling a systematic survey of each nucleotide position within the centromere. We found that in each parS some positions could be changed while maintaining binding to ParB. Each centromere displays its own pattern of changes, but some positions are shared more or less widely. In addition from these changes we could speculate evolutionary links between these centromeres.

  3. A global RNA-seq-driven analysis of CHO host and production cell lines reveals distinct differential expression patterns of genes contributing to recombinant antibody glycosylation.

    Science.gov (United States)

    Könitzer, Jennifer D; Müller, Markus M; Leparc, Germán; Pauers, Martin; Bechmann, Jan; Schulz, Patrick; Schaub, Jochen; Enenkel, Barbara; Hildebrandt, Tobias; Hampel, Martin; Tolstrup, Anne B

    2015-09-01

    Boehringer Ingelheim uses two CHO-DG44 lines for manufacturing biotherapeutics, BI-HEX-1 and BI-HEX-2, which produce distinct cell type-specific antibody glycosylation patterns. A recently established CHO-K1 descended host, BI-HEX-K1, generates antibodies with glycosylation profiles differing from CHO-DG44. Manufacturing process development is significantly influenced by these unique profiles. To investigate the underlying glycosylation related gene expression, we leveraged our CHO host and production cell RNA-seqtranscriptomics and product quality database together with the CHO-K1 genome. We observed that each BI-HEX host and antibody producing cell line has a unique gene expression fingerprint. CHO-DG44 cells only transcribe Fut10, Gfpt2 and ST8Sia6 when expressing antibodies. BI-HEX-K1 cells express ST8Sia6 at host cell level. We detected a link between BI-HEX-1/BI-HEX-2 antibody galactosylation and mannosylation and the gene expression of the B4galt gene family and genes controlling mannose processing. Furthermore, we found major differences between the CHO-DG44 and CHO-K1 lineages in the expression of sialyl transferases and enzymes synthesizing sialic acid precursors, providing a rationale for the lack of immunogenic NeuGc/NGNA synthesis in CHO. Our study highlights the value of systems biotechnology to understand glycoprotein synthesis and product glycoprofiles. Such data improve future production clone selection and process development strategies for better steering of biotherapeutic product quality. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Comparative Analyses of Three Chlorella Species in Response to Light and Sugar Reveal Distinctive Lipid Accumulation Patterns in the Microalga C. sorokiniana

    Science.gov (United States)

    Barnes, Austin; Noel, Eric A.; Betenbaugh, Michael J.; Oyler, George A.

    2014-01-01

    While photosynthetic microalgae, such as Chlorella, serve as feedstocks for nutritional oils and biofuels, heterotrophic cultivation can augment growth rates, support high cell densities, and increase triacylglycerol (TAG) lipid content. However, these species differ significantly in their photoautotrophic and heterotrophic characteristics. In this study, the phylogeny of thirty Chlorella strains was determined in order to inform bioprospecting efforts and detailed physiological assessment of three species. The growth kinetics and lipid biochemistry of C. protothecoides UTEX 411, C. vulgaris UTEX 265, and C. sorokiniana UTEX 1230 were quantified during photoautotrophy in Bold's basal medium (BBM) and heterotrophy in BBM supplemented with glucose (10 g L−1). Heterotrophic growth rates of UTEX 411, 265, and 1230 were found to be 1.5-, 3.7-, and 5-fold higher than their respective autotrophic rates. With a rapid nine-hour heterotrophic doubling time, Chlorella sorokiniana UTEX 1230 maximally accumulated 39% total lipids by dry weight during heterotrophy compared to 18% autotrophically. Furthermore, the discrete fatty acid composition of each strain was examined in order to elucidate lipid accumulation patterns under the two trophic conditions. In both modes of growth, UTEX 411 and 265 produced 18∶1 as the principal fatty acid while UTEX 1230 exhibited a 2.5-fold enrichment in 18∶2 relative to 18∶1. Although the total lipid content was highest in UTEX 411 during heterotrophy, UTEX 1230 demonstrated a two-fold increase in its heterotrophic TAG fraction at a rate of 28.9 mg L−1 d−1 to reach 22% of the biomass, corresponding to as much as 90% of its total lipids. Interestingly, UTEX 1230 growth was restricted during mixotrophy and its TAG production rate was suppressed to 18.2 mg L−1 d−1. This constraint on carbon flow raises intriguing questions about the impact of sugar and light on the metabolic regulation of microalgal lipid biosynthesis. PMID:24699196

  5. Comparative analyses of three Chlorella species in response to light and sugar reveal distinctive lipid accumulation patterns in the Microalga C. sorokiniana.

    Directory of Open Access Journals (Sweden)

    Julian N Rosenberg

    Full Text Available While photosynthetic microalgae, such as Chlorella, serve as feedstocks for nutritional oils and biofuels, heterotrophic cultivation can augment growth rates, support high cell densities, and increase triacylglycerol (TAG lipid content. However, these species differ significantly in their photoautotrophic and heterotrophic characteristics. In this study, the phylogeny of thirty Chlorella strains was determined in order to inform bioprospecting efforts and detailed physiological assessment of three species. The growth kinetics and lipid biochemistry of C. protothecoides UTEX 411, C. vulgaris UTEX 265, and C. sorokiniana UTEX 1230 were quantified during photoautotrophy in Bold's basal medium (BBM and heterotrophy in BBM supplemented with glucose (10 g L-1. Heterotrophic growth rates of UTEX 411, 265, and 1230 were found to be 1.5-, 3.7-, and 5-fold higher than their respective autotrophic rates. With a rapid nine-hour heterotrophic doubling time, Chlorella sorokiniana UTEX 1230 maximally accumulated 39% total lipids by dry weight during heterotrophy compared to 18% autotrophically. Furthermore, the discrete fatty acid composition of each strain was examined in order to elucidate lipid accumulation patterns under the two trophic conditions. In both modes of growth, UTEX 411 and 265 produced 18:1 as the principal fatty acid while UTEX 1230 exhibited a 2.5-fold enrichment in 18:2 relative to 18:1. Although the total lipid content was highest in UTEX 411 during heterotrophy, UTEX 1230 demonstrated a two-fold increase in its heterotrophic TAG fraction at a rate of 28.9 mg L(-1 d(-1 to reach 22% of the biomass, corresponding to as much as 90% of its total lipids. Interestingly, UTEX 1230 growth was restricted during mixotrophy and its TAG production rate was suppressed to 18.2 mg L-1 d-1. This constraint on carbon flow raises intriguing questions about the impact of sugar and light on the metabolic regulation of microalgal lipid biosynthesis.

  6. Analysis of ParB-centromere interactions by multiplex SPR imaging reveals specific patterns for binding ParB in six centromeres of Burkholderiales chromosomes and plasmids.

    Science.gov (United States)

    Pillet, Flavien; Passot, Fanny Marie; Pasta, Franck; Anton Leberre, Véronique; Bouet, Jean-Yves

    2017-01-01

    Bacterial centromeres-also called parS, are cis-acting DNA sequences which, together with the proteins ParA and ParB, are involved in the segregation of chromosomes and plasmids. The specific binding of ParB to parS nucleates the assembly of a large ParB/DNA complex from which ParA-the motor protein, segregates the sister replicons. Closely related families of partition systems, called Bsr, were identified on the chromosomes and large plasmids of the multi-chromosomal bacterium Burkholderia cenocepacia and other species from the order Burkholeriales. The centromeres of the Bsr partition families are 16 bp palindromes, displaying similar base compositions, notably a central CG dinucleotide. Despite centromeres bind the cognate ParB with a narrow specificity, weak ParB-parS non cognate interactions were nevertheless detected between few Bsr partition systems of replicons not belonging to the same genome. These observations suggested that Bsr partition systems could have a common ancestry but that evolution mostly erased the possibilities of cross-reactions between them, in particular to prevent replicon incompatibility. To detect novel similarities between Bsr partition systems, we have analyzed the binding of six Bsr parS sequences and a wide collection of modified derivatives, to their cognate ParB. The study was carried out by Surface Plasmon Resonance imaging (SPRi) mulitplex analysis enabling a systematic survey of each nucleotide position within the centromere. We found that in each parS some positions could be changed while maintaining binding to ParB. Each centromere displays its own pattern of changes, but some positions are shared more or less widely. In addition from these changes we could speculate evolutionary links between these centromeres.

  7. Phylogeography of the sergeants Abudefduf sexfasciatus and A. vaigiensis reveals complex introgression patterns between two widespread and sympatric Indo-West Pacific reef fishes.

    Science.gov (United States)

    Bertrand, Joris A M; Borsa, Philippe; Chen, Wei-Jen

    2017-05-01

    On evolutionary timescales, sea level oscillations lead to recurrent spatio-temporal variation in species distribution and population connectivity. In this situation, applying classical concepts of biogeography is challenging yet necessary to understand the mechanisms underlying biodiversity in highly diverse marine ecosystems such as coral reefs. We aimed at studying the outcomes of such complex biogeographic dynamics on reproductive isolation by sampling populations across a wide spatial range of a species-rich fish genus: the sergeants (Pomacentridae: Abudefduf). We generated a mutlilocus data set that included ten morpho-species from 32 Indo-West Pacific localities. We observed a pattern of mito-nuclear discordance in two common and widely distributed species: Abudefduf sexfasciatus and Abudefduf vaigiensis. The results showed three regional sublineages (Indian Ocean, Coral Triangle region, western Pacific) in A. sexfasciatus (0.6-1.5% divergence at cytb). The other species, A. vaigiensis, is polyphyletic and consists of three distinct genetic lineages (A, B and C) (9% divergence at cytb) whose geographic ranges overlap. Although A. vaigiensis A and A. sexfasciatus were found to be distinct based on nuclear information, A. vaigiensis A was found to be nested within A. sexfasciatus in the mitochondrial gene tree. A. sexfasciatus from the Coral Triangle region and A. vaigiensis A were not differentiated from each other at the mitochondrial locus. We then used coalescent-based simulation to characterize a spatially widespread but weak gene flow between the two species. We showed that these fishes are good candidates to investigate the evolutionary complexity of the discrepancies between phenotypic and genetic similarity in closely related species. © 2017 John Wiley & Sons Ltd.

  8. Epigenome-wide DNA methylation analysis in siblings and monozygotic twins discordant for sporadic Parkinson's disease revealed different epigenetic patterns in peripheral blood mononuclear cells.

    Science.gov (United States)

    Kaut, Oliver; Schmitt, Ina; Tost, Jörg; Busato, Florence; Liu, Yi; Hofmann, Per; Witt, Stephanie H; Rietschel, Marcella; Fröhlich, Holger; Wüllner, Ullrich

    2017-01-01

    Numerous studies have elucidated the genetics of Parkinson's disease; however, the aetiology of the majority of sporadic cases has not yet been resolved. We hypothesized that epigenetic variations could be associated with PD and evaluated the DNA methylation pattern in PD patients compared to brothers or twins without PD. The methylation of DNA from peripheral blood mononuclear cells of 62 discordant siblings including 24 monozygotic twins was characterized with Illumina DNA Methylation 450K bead arrays and subsequently validated in two independent cohorts: 221 PD vs. 227 healthy individuals (cohort 1) applying Illumina's VeraCode and 472 PD patients vs. 487 controls (cohort 2) using pyrosequencing. We choose a delta beta of >15 % and selected 62 differentially methylated CpGs in 51 genes from the discordant siblings. Among them, three displayed multiple CpGs per gene: microRNA 886 (MIR886, 10 CpGs), phosphodiesterase 4D (PDE4D, 2 CpGs) and tripartite motif-containing 34 (TRIM34, 2 CpGs). PDE4D was confirmed in both cohorts (p value 2.44e-05). In addition, for biomarker construction, we used the penalized logistic regression model, resulting in a signature of eight CpGs with an AUC of 0.77. Our findings suggest that a distinct level of PD susceptibility stems from individual, epigenetic modifications of specific genes. We identified a signature of CpGs in blood cells that could separate control from disease with a reasonable discriminatory power, holding promise for future epigenetically based biomarker development.

  9. Contrasting Patterns of Genomic Diversity Reveal Accelerated Genetic Drift but Reduced Directional Selection on X-Chromosome in Wild and Domestic Sheep Species.

    Science.gov (United States)

    Chen, Ze-Hui; Zhang, Min; Lv, Feng-Hua; Ren, Xue; Li, Wen-Rong; Liu, Ming-Jun; Nam, Kiwoong; Bruford, Michael W; Li, Meng-Hua

    2018-04-01

    Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep. Analyzing whole-genome sequences, we observed a substantially reduced X-to-autosome diversity ratio (∼0.6) compared with the value expected under a neutral model (0.75). In particular, one large X-linked segment (43.05-79.25 Mb) was found to show extremely low diversity, most likely due to a high density of coding genes, featuring highly conserved regions. In general, we observed higher nucleotide diversity on the autosomes, but a flat diversity gradient in X-linked segments, as a function of increasing distance from the nearest genes, leading to a decreased X: autosome (X/A) diversity ratio and contrasting to the positive correlation detected in primates and other model animals. Our evidence suggests that accelerated genetic drift but reduced directional selection on X chromosome, as well as sex-biased demographic events, explain low X-chromosome diversity in sheep species. The distinct patterns of X-linked and X/A diversity we observed between Middle Eastern and non-Middle Eastern sheep populations can be explained by multiple migrations, selection, and admixture during the domestic sheep's recent postdomestication demographic expansion, coupled with natural selection for adaptation to new environments. In addition, we identify important novel genes involved in abnormal behavioral phenotypes, metabolism, and immunity, under selection on the sheep X-chromosome.

  10. Microarray analysis of HIV resistant female sex workers reveal a gene expression signature pattern reminiscent of a lowered immune activation state.

    Directory of Open Access Journals (Sweden)

    Elijah M Songok

    Full Text Available To identify novel biomarkers for HIV-1 resistance, including pathways that may be critical in anti-HIV-1 vaccine design, we carried out a gene expression analysis on blood samples obtained from HIV-1 highly exposed seronegatives (HESN from a commercial sex worker cohort in Nairobi and compared their profiles to HIV-1 negative controls. Whole blood samples were collected from 43 HIV-1 resistant sex workers and a similar number of controls. Total RNA was extracted and hybridized to the Affymetrix HUG 133 Plus 2.0 micro arrays (Affymetrix, Santa Clara CA. Output data was analysed through ArrayAssist software (Agilent, San Jose CA. More than 2,274 probe sets were differentially expressed in the HESN as compared to the control group (fold change ≥1.3; p value ≤0.0001, FDR <0.05. Unsupervised hierarchical clustering of the differentially expressed genes readily distinguished HESNs from controls. Pathway analysis through the KEGG signaling database revealed a majority of the impacted pathways (13 of 15, 87% had genes that were significantly down regulated. The most down expressed pathways were glycolysis/gluconeogenesis, pentose phosphate, phosphatidyl inositol, natural killer cell cytotoxicity and T-cell receptor signaling. Ribosomal protein synthesis and tight junction genes were up regulated. We infer that the hallmark of HIV-1 resistance is down regulation of genes in key signaling pathways that HIV-1 depends on for infection.

  11. The pattern and time course of somatosensory changes in the human UVB sunburn model reveal the presence of peripheral and central sensitization.

    Science.gov (United States)

    Gustorff, Burkhard; Sycha, Thomas; Lieba-Samal, Doris; Rolke, Roman; Treede, Rolf-Detlef; Magerl, Walter

    2013-04-01

    The ultraviolet B (UVB) sunburn model was characterized with a comprehensive battery of quantitative sensory testing (QST). Primary hyperalgesia in UVB-irradiated skin and secondary hyperalgesia in adjacent nonirradiated skin were studied in 22 healthy subjects 24h after irradiation with UVB at 3-fold minimal erythema dose of a skin area 5 cm in diameter at the thigh and compared to mirror-image contralateral control areas. The time course of hyperalgesia over 96 h was studied in a subgroup of 12 subjects. Within the sunburn area, cold hyperesthesia (P=.01), profound generalized hyperalgesia to heat (Psunburn was surrounded by large areas of pinprick hyperalgesia (mean±SEM, 218±32 cm(2)) and a small rim of dynamic mechanical allodynia but no other sensory changes. Although of smaller magnitude, secondary hyperalgesia and dynamic mechanical allodynia adjacent to the UVB-irradiated area were statistically highly significant. Primary and secondary hyperalgesia developed in parallel within hours, peaked after 24-32 h, and lasted for more than 96 h. These data reveal that the UVB sunburn model activates a broad spectrum of peripheral and central sensitization mechanisms and hence is a useful human surrogate model to be used as a screening tool for target engagement in phases 1 and 2a of drug development. Copyright © 2013 International Association for the Study of Pain. Published by Elsevier B.V. All rights reserved.

  12. Royal jelly-like protein localization reveals differences in hypopharyngeal glands buildup and conserved expression pattern in brains of bumblebees and honeybees

    Directory of Open Access Journals (Sweden)

    Štefan Albert

    2014-03-01

    Full Text Available Royal jelly proteins (MRJPs of the honeybee bear several open questions. One of them is their expression in tissues other than the hypopharyngeal glands (HGs, the site of royal jelly production. The sole MRJP-like gene of the bumblebee, Bombus terrestris (BtRJPL, represents a pre-diversification stage of the MRJP gene evolution in bees. Here we investigate the expression of BtRJPL in the HGs and the brain of bumblebees. Comparison of the HGs of bumblebees and honeybees revealed striking differences in their morphology with respect to sex- and caste-specific appearance, number of cells per acinus, and filamentous actin (F-actin rings. At the cellular level, we found a temporary F-actin-covered meshwork in the secretory cells, which suggests a role for actin in the biogenesis of the end apparatus in HGs. Using immunohistochemical localization, we show that BtRJPL is expressed in the bumblebee brain, predominantly in the Kenyon cells of the mushroom bodies, the site of sensory integration in insects, and in the optic lobes. Our data suggest that a dual gland-brain function preceded the multiplication of MRJPs in the honeybee lineage. In the course of the honeybee evolution, HGs dramatically changed their morphology in order to serve a food-producing function.

  13. Exchanging information

    International Nuclear Information System (INIS)

    1971-01-01

    The Agency has a statutory mandate to foster 'the exchange of scientific and technical information on the peaceful uses of atomic energy'. The prime responsibility for this work within the Agency lies with the Division of Scientific and Technical Information, a part of the Department of Technical Operations. The Division accomplishes its task by holding conferences and symposia (Scientific Conferences Section), through the Agency Library, by publishing scientific journals, and through the International Nuclear Information System (INIS). The Computer Section of the Division, which offers services to the Agency as a whole, provides resources for the automation of data storage and retrieval. (author)

  14. Phylogeography and Ecological Niche Modeling Reveal Reduced Genetic Diversity and Colonization Patterns of Skunk Cabbage (Symplocarpus foetidus; Araceae From Glacial Refugia in Eastern North America

    Directory of Open Access Journals (Sweden)

    Seon-Hee Kim

    2018-05-01

    Full Text Available Alternating glacial and interglacial periods during the Quaternary have dramatically affected the distribution and population genetic structure of plant and animal species throughout the northern hemisphere. Surprisingly, little is known about the post-glacial recolonization history of wetland herbaceous perennials that are widely distributed in the understory of deciduous or mixed deciduous-evergreen forests in eastern North America. In this study, we investigated infraspecific variation among 32 populations of skunk cabbage, Symplocarpus foetidus, to test the hypothesis that the extant species diversity of skunk cabbage is the result of a post-glacial range expansion from southern refugia during the Quaternary Ice Age. A total of 4041 base pairs (bp of the chloroplast intergenic spacer region (cpDNA was sequenced from 485 individuals sampled from glaciated (18 populations, 275 individuals and unglaciated (14 populations, 210 individuals regions east and west of the Appalachian Mountains. Haplotype number, haplotype diversity, and nucleotide diversity were calculated, and genetic variation within and among populations was assessed by analysis of molecular variance (AMOVA. The geographic pattern of genetic differentiation was further investigated with a spatial analysis of molecular variance (SAMOVA. A total of eight haplotypes and three genetic groups (SAMOVA were recovered and a much higher haplotype number (eight haplotypes and haplotype diversity (0.7425 was observed in unglaciated compared to glaciated populations (five haplotypes, haplotype diversity = 0.6099. All haplotypes found in glaciated regions represented a subset of haplotypes found in unglaciated regions. Haplotypes of S. foetidus likely diverged during the Tertiary (mid-Miocene and late Pliocene, predating the last glacial maximum (LGM. Predictions based on ecological niche modeling (ENM suggested that there was considerably less suitable habitat for skunk cabbage during the LGM

  15. Comprehensive Profiling of the Androgen Receptor in Liquid Biopsies from Castration-resistant Prostate Cancer Reveals Novel Intra-AR Structural Variation and Splice Variant Expression Patterns.

    Science.gov (United States)

    De Laere, Bram; van Dam, Pieter-Jan; Whitington, Tom; Mayrhofer, Markus; Diaz, Emanuela Henao; Van den Eynden, Gert; Vandebroek, Jean; Del-Favero, Jurgen; Van Laere, Steven; Dirix, Luc; Grönberg, Henrik; Lindberg, Johan

    2017-08-01

    Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative. To investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy. Peripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy. We performed profiling of circulating tumour DNA via low-pass whole-genome sequencing and targeted sequencing of the entire AR gene, including introns. Targeted RNA sequencing was performed on enriched circulating tumour cell fractions to assess the expression levels of seven AR splice variants (ARVs). Somatic AR variations, including copy-number alterations, structural variations, and point mutations, were combined with ARV expression patterns and correlated to clinicopathologic parameters. Collectively, any AR perturbation, including ARV, was detected in 25/30 patients. Surprisingly, intra-AR structural variation was present in 15/30 patients, of whom 14 expressed ARVs. The majority of ARV-positive patients expressed multiple ARVs, with AR-V3 the most abundantly expressed. The presence of any ARV was associated with progression-free survival after second-line endocrine treatment (hazard ratio 4.53, 95% confidence interval 1.424-14.41; p=0.0105). Six out of 17 poor responders were AR-V7-negative, but four carried other AR perturbations. Comprehensive AR profiling, which is feasible using liquid biopsies, is necessary to increase our understanding of the mechanisms underpinning resistance to endocrine treatment. Alterations in the androgen receptor are associated with endocrine treatment outcomes. This study demonstrates that it is possible to identify different types of alterations via simple blood draws. Follow-up studies are needed to determine the effect of

  16. Serum reactome induced by Bordetella pertussis infection and Pertussis vaccines: qualitative differences in serum antibody recognition patterns revealed by peptide microarray analysis.

    Science.gov (United States)

    Valentini, Davide; Ferrara, Giovanni; Advani, Reza; Hallander, Hans O; Maeurer, Markus J

    2015-07-01

    Pertussis (whooping cough) remains a public health problem despite extensive vaccination strategies. Better understanding of the host-pathogen interaction and the detailed B. pertussis (Bp) target recognition pattern will help in guided vaccine design. We characterized the specific epitope antigen recognition profiles of serum antibodies ('the reactome') induced by whooping cough and B. pertussis (Bp) vaccines from a case-control study conducted in 1996 in infants enrolled in a Bp vaccine trial in Sweden (Gustafsson, NEJM, 1996, 334, 349-355). Sera from children with whooping cough, vaccinated with Diphtheria Tetanus Pertussis (DTP) whole-cell (wc), acellular 5 (DPTa5), or with the 2 component (a2) vaccines and from infants receiving only DT (n=10 for each group) were tested with high-content peptide microarrays containing 17 Bp proteins displayed as linear (n=3175) peptide stretches. Slides were incubated with serum and peptide-IgG complexes detected with Cy5-labeled goat anti-human IgG and analyzed using a GenePix 4000B microarray scanner, followed by statistical analysis, using PAM (Prediction Analysis for Microarrays) and the identification of uniquely recognized peptide epitopes. 367/3,085 (11.9%) peptides were recognized in 10/10 sera from children with whooping cough, 239 (7.7%) in DTPwc, 259 (8.4%) in DTPa5, 105 (3.4%) DTPa2, 179 (5.8%) in the DT groups. Recognition of strongly recognized peptides was similar between whooping cough and DPTwc, but statistically different between whooping cough vs. DTPa5 (p<0.05), DTPa2 and DT (p<0.001 vs. both) vaccines. 6/3,085 and 2/3,085 peptides were exclusively recognized in (10/10) sera from children with whooping cough and DTPa2 vaccination, respectively. DTPwc resembles more closely the whooping cough reactome as compared to acellular vaccines. We could identify a unique recognition signature common for each vaccination group (10/10 children). Peptide microarray technology allows detection of subtle differences in

  17. Comparative proteome analysis reveals conserved and specific adaptation patterns of Staphylococcus aureus after internalization by different types of human non-professional phagocytic host cells

    Directory of Open Access Journals (Sweden)

    Kristin eSurmann

    2014-08-01

    Full Text Available Staphylococcus aureus is a human pathogen that can cause a wide range of diseases. Although formerly regarded as extracellular pathogen, it has been shown that S. aureus can also be internalized by host cells and persist within these cells. In the present study, we comparatively analyzed survival and physiological adaptation of S. aureus HG001 after internalization by two human lung epithelial cell lines (S9 and A549, and human embryonic kidney cells (HEK 293. Combining enrichment of bacteria from host-pathogen assays by cell sorting and quantitation of the pathogen´s proteome by mass spectrometry we characterized S. aureus adaptation during the initial phase between 2.5 h and 6.5 h post-infection. Starting with about 2x106 bacteria, roughly 1,450 S. aureus proteins, including virulence factors and metabolic enzymes were identified by spectral comparison and classical database searches. Most of the bacterial adaptation reactions, such as decreases in levels of ribosomal proteins and metabolic enzymes or increases in amounts of proteins involved in arginine and lysine biosynthesis, coding for terminal oxidases and stress responsive genes or activation of the sigma factor SigB were observed after internalization into any of the three cell lines studied. However, differences were noted in central carbon metabolism including regulation of fermentation and threonine degradation. Since these differences coincided with different intracellular growth behavior, complementary profiling of the metabolome of the different non-infected host cell types was performed. This revealed similar levels of intracellular glucose but host cell specific differences in the amounts of amino acids such as glycine, threonine or glutamate. With this comparative study we provide an impression of the common and specific features of the adaptation of S. aureus HG001 to specific host cell environments as a starting point for follow-up studies with different strain isolates and

  18. Genomic structure and expression pattern of MHC IIα and IIβ genes reveal an unusual immune trait in lined seahorse Hippocampus erectus.

    Science.gov (United States)

    Luo, Wei; Wang, Xin; Qu, Hongyue; Qin, Geng; Zhang, Huixian; Lin, Qiang

    2016-11-01

    The major histocompatibility complex (MHC) genes are crucial in the adaptive immune system, and the gene duplication of MHC in animals can generally result in immune flexibility. In this study, we found that the lined seahorse (Hippocampus erectus) has only one gene copy number (GCN) of MHC IIα and IIβ, which is different from that in other teleosts. Together with the lack of spleen and gut-associated lymphatic tissue (GALT), the seahorse may be referred to as having a partial but natural "immunodeficiency". Highly variable amino acid residues were found in the IIα and IIβ domains, especially in the α1 and β1 domains with 9.62% and 8.43% allelic variation, respectively. Site models revealed seven and ten positively selected positions in the α1 and β1 domains, respectively. Real-time PCR experiments showed high expression levels of the MHC II genes in intestine (In), gill (Gi) and trunk kidney (TK) and medium in muscle (Mu) and brood pouch (BP), and the expression levels were significantly up-regulated after bacterial infection. Specially, relative higher expression level of both MHC IIα and IIβ was found in Mu and BP when compared with other fish species, in which MHC II is expressed negligibly in Mu. These results indicate that apart from TK, Gi and In, MU and BP play an important role in the immune response against pathogens in the seahorse. In conclusion, high allelic variation and strong positive selection in PBR and relative higher expression in MU and BP are speculated to partly compensate for the immunodeficiency. Copyright © 2016 Elsevier Ltd. All rights reserved.

  19. Clustering patterns of LOD scores for asthma-related phenotypes revealed by a genome-wide screen in 295 French EGEA families.

    Science.gov (United States)

    Bouzigon, Emmanuelle; Dizier, Marie-Hélène; Krähenbühl, Christine; Lemainque, Arnaud; Annesi-Maesano, Isabella; Betard, Christine; Bousquet, Jean; Charpin, Denis; Gormand, Frédéric; Guilloud-Bataille, Michel; Just, Jocelyne; Le Moual, Nicole; Maccario, Jean; Matran, Régis; Neukirch, Françoise; Oryszczyn, Marie-Pierre; Paty, Evelyne; Pin, Isabelle; Rosenberg-Bourgin, Myriam; Vervloet, Daniel; Kauffmann, Francine; Lathrop, Mark; Demenais, Florence

    2004-12-15

    A genome-wide scan for asthma phenotypes was conducted in the whole sample of 295 EGEA families selected through at least one asthmatic subject. In addition to asthma, seven phenotypes involved in the main asthma physiopathological pathways were considered: SPT (positive skin prick test response to at least one of 11 allergens), SPTQ score being the number of positive skin test responses to 11 allergens, Phadiatop (positive specific IgE response to a mixture of allergens), total IgE levels, eosinophils, bronchial responsiveness (BR) to methacholine challenge and %predicted FEV(1). Four regions showed evidence for linkage (Prevealed clustering of LODs for asthma, SPT and Phadiatop on one axis and clustering of LODs for %FEV(1), BR and SPTQ on the other, while LODs for IgE and eosinophils appeared to be independent from all other LODs. These results provide new insights into the potential sharing of genetic determinants by asthma-related phenotypes.

  20. The assessment of daily dietary intake reveals the existence of a different pattern of bioaccumulation of chlorinated pollutants between domestic dogs and cats

    Energy Technology Data Exchange (ETDEWEB)

    Ruiz-Suárez, Norberto; Camacho, María; Boada, Luis D.; Henríquez-Hernández, Luis A.; Rial, Cristian; Valerón, Pilar F.; Zumbado, Manuel; González, Maira Almeida; Luzardo, Octavio P., E-mail: octavio.perez@ulpgc.es

    2015-10-15

    Pet dogs and cats have been proposed as sentinel species to assess environmental contamination and human exposure to a variety of pollutants, including POPs. However, some authors have reported that dogs but not cats exhibit intriguingly low levels of some of the most commonly detected POPs, such as DDT and its metabolites. This research was designed to explore these differences between dogs and cats. Thus, we first determined the concentrations of 53 persistent and semi-persistent pollutants (16 polycyclic aromatic hydrocarbons (PAHs), 18 polychlorinated biphenyls (PCBs) and 19 organochlorine pesticides (OCPs)) in samples of the most consumed brands of commercial feed for dogs and cats, and we calculated the daily dietary intake of these pollutants in both species. Higher levels of pollutants were found in dog food and our results showed that the median values of intake were about twice higher in dogs than in cats for all the three groups of pollutants (ΣPAHs: 274.8 vs. 141.8; ΣOCPs: 233.1 vs. 83; ΣPCBs: 101.8 vs. 43.8 (ng/kg bw/day); respectively). Additionally, we determined the plasma levels of the same pollutants in 42 and 35 pet dogs and cats, respectively. All these animals lived indoors and were fed on the commercial brands of feed analyzed. As expected (considering the intake), the plasma levels of PAHs were higher in dogs than in cats. However, for organochlorines (OCPs and PCBs) the plasma levels were much higher in cats than in dogs (as much as 23 times higher for DDTs), in spite of the higher intake in dogs. This reveals a lower capacity of bioaccumulation of some pollutants in dogs, which is probably related with higher metabolizing capabilities in this species. - Highlights: • First assessment of the dietary intake of POPs in pet animals. • Intake levels of pollutants are more than double in dogs than in cats. • Proportionality between intake of PAHs and their plasma levels in both species. • Lower levels of organochlorines in dog plasma

  1. Comprehensive analysis of differential co-expression patterns reveal transcriptional dysregulation mechanism and identify novel prognostic lncRNAs in esophageal squamous cell carcinoma

    Directory of Open Access Journals (Sweden)

    Li Z

    2017-06-01

    Full Text Available Zhen Li,1 Qianlan Yao,1 Songjian Zhao,1 Yin Wang,2,3 Yixue Li,1,4 Zhen Wang4 1School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 2Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, 3Collaborative Innovation Center for Genetics and Development, Fudan University, 4Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China Abstract: Esophageal squamous cell carcinoma (ESCC is one of the most common malignancies worldwide and occurs at a relatively high frequency in People’s Republic of China. However, the molecular mechanism underlying ESCC is still unclear. In this study, the mRNA and long non-coding RNA (lncRNA expression profiles of ESCC were downloaded from the Gene Expression Omnibus database, and then differential co-expression analysis was used to reveal the altered co-expression relationship of gene pairs in ESCC tumors. A total of 3,709 mRNAs and 923 lncRNAs were differentially co-expressed between normal and tumor tissues, and we found that most of the gene pairs lost associations in the tumor tissues. The differential regulatory networking approach deciphered that transcriptional dysregulation was ubiquitous in ESCC, and most of the differentially regulated links were modulated by 37 TFs. Our study also found that two novel lncRNAs (ADAMTS9-AS1 and AP000696.2 might be essential in the development of ectoderm and epithelial cells, which could significantly stratify ESCC patients into high-risk and low-risk groups, and were much better than traditional clinical tumor markers. Further inspection of two risk groups showed that the changes in TF-target regulation in the high-risk patients were significantly higher than those in the low-risk patients. In addition, four signal transduction-related DCmRNAs (ERBB3, ENSA, KCNK7, MFSD5

  2. The assessment of daily dietary intake reveals the existence of a different pattern of bioaccumulation of chlorinated pollutants between domestic dogs and cats

    International Nuclear Information System (INIS)

    Ruiz-Suárez, Norberto; Camacho, María; Boada, Luis D.; Henríquez-Hernández, Luis A.; Rial, Cristian; Valerón, Pilar F.; Zumbado, Manuel; González, Maira Almeida; Luzardo, Octavio P.

    2015-01-01

    Pet dogs and cats have been proposed as sentinel species to assess environmental contamination and human exposure to a variety of pollutants, including POPs. However, some authors have reported that dogs but not cats exhibit intriguingly low levels of some of the most commonly detected POPs, such as DDT and its metabolites. This research was designed to explore these differences between dogs and cats. Thus, we first determined the concentrations of 53 persistent and semi-persistent pollutants (16 polycyclic aromatic hydrocarbons (PAHs), 18 polychlorinated biphenyls (PCBs) and 19 organochlorine pesticides (OCPs)) in samples of the most consumed brands of commercial feed for dogs and cats, and we calculated the daily dietary intake of these pollutants in both species. Higher levels of pollutants were found in dog food and our results showed that the median values of intake were about twice higher in dogs than in cats for all the three groups of pollutants (ΣPAHs: 274.8 vs. 141.8; ΣOCPs: 233.1 vs. 83; ΣPCBs: 101.8 vs. 43.8 (ng/kg bw/day); respectively). Additionally, we determined the plasma levels of the same pollutants in 42 and 35 pet dogs and cats, respectively. All these animals lived indoors and were fed on the commercial brands of feed analyzed. As expected (considering the intake), the plasma levels of PAHs were higher in dogs than in cats. However, for organochlorines (OCPs and PCBs) the plasma levels were much higher in cats than in dogs (as much as 23 times higher for DDTs), in spite of the higher intake in dogs. This reveals a lower capacity of bioaccumulation of some pollutants in dogs, which is probably related with higher metabolizing capabilities in this species. - Highlights: • First assessment of the dietary intake of POPs in pet animals. • Intake levels of pollutants are more than double in dogs than in cats. • Proportionality between intake of PAHs and their plasma levels in both species. • Lower levels of organochlorines in dog plasma

  3. High-resolution monitoring across the soil-groundwater interface - Revealing small-scale hydrochemical patterns with a novel multi-level well

    Science.gov (United States)

    Gassen, Niklas; Griebler, Christian; Stumpp, Christine

    2016-04-01

    Biogeochemical turnover processes in the subsurface are highly variable both in time and space. In order to capture this variability, high resolution monitoring systems are required. Particular in riparian zones the understanding of small-scale biogeochemical processes is of interest, as they are regarded as important buffer zones for nutrients and contaminants with high turnover rates. To date, riparian research has focused on influences of groundwater-surface water interactions on element cycling, but little is known about processes occurring at the interface between the saturated and the unsaturated zone during dynamic flow conditions. Therefore, we developed a new type of high resolution multi-level well (HR-MLW) that has been installed in the riparian zone of the Selke river. This HR-MLW for the first time enables to derive water samples both from the unsaturated and the saturated zone across one vertical profile with a spatial vertical resolution of 0.05 to 0.5 m to a depth of 4 m b.l.s. Water samples from the unsaturated zone are extracted via suction cup sampling. Samples from the saturated zone are withdrawn through glass filters and steel capillaries. Both, ceramic cups and glass filters, are installed along a 1" HDPE piezometer tube. First high resolution hydrochemical profiles revealed a distinct depth-zonation in the riparian alluvial aquifer. A shallow zone beneath the water table carried a signature isotopically and hydrochemically similar to the nearby river, while layers below 1.5 m were influenced by regional groundwater. This zonation showed temporal dynamics related to groundwater table fluctuations and microbial turnover processes. The HR-MLW delivered new insight into mixing and turnover processes between riverwater and groundwater in riparian zones, both in a temporal and spatial dimension. With these new insights, we are able to improve our understanding of dynamic turnover processes at the soil - groundwater interface and of surface

  4. Deep sequencing of small RNA libraries from human prostate epithelial and stromal cells reveal distinct pattern of microRNAs primarily predicted to target growth factors.

    Science.gov (United States)

    Singh, Savita; Zheng, Yun; Jagadeeswaran, Guru; Ebron, Jey Sabith; Sikand, Kavleen; Gupta, Sanjay; Sunker, Ramanjulu; Shukla, Girish C

    2016-02-28

    Complex epithelial and stromal cell interactions are required during the development and progression of prostate cancer. Regulatory small non-coding microRNAs (miRNAs) participate in the spatiotemporal regulation of messenger RNA (mRNA) and regulation of translation affecting a large number of genes involved in prostate carcinogenesis. In this study, through deep-sequencing of size fractionated small RNA libraries we profiled the miRNAs of prostate epithelial (PrEC) and stromal (PrSC) cells. Over 50 million reads were obtained for PrEC in which 860,468 were unique sequences. Similarly, nearly 76 million reads for PrSC were obtained in which over 1 million were unique reads. Expression of many miRNAs of broadly conserved and poorly conserved miRNA families were identified. Sixteen highly expressed miRNAs with significant change in expression in PrSC than PrEC were further analyzed in silico. ConsensusPathDB showed the target genes of these miRNAs were significantly involved in adherence junction, cell adhesion, EGRF, TGF-β and androgen signaling. Let-7 family of tumor-suppressor miRNAs expression was highly pervasive in both, PrEC and PrSC cells. In addition, we have also identified several miRNAs that are unique to PrEC or PrSC cells and their predicted putative targets are a group of transcription factors. This study provides perspective on the miRNA expression in PrEC and PrSC, and reveals a global trend in miRNA interactome. We conclude that the most abundant miRNAs are potential regulators of development and differentiation of the prostate gland by targeting a set of growth factors. Additionally, high level expression of the most members of let-7 family miRNAs suggests their role in the fine tuning of the growth and proliferation of prostate epithelial and stromal cells. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  5. Matchmaker Exchange.

    Science.gov (United States)

    Sobreira, Nara L M; Arachchi, Harindra; Buske, Orion J; Chong, Jessica X; Hutton, Ben; Foreman, Julia; Schiettecatte, François; Groza, Tudor; Jacobsen, Julius O B; Haendel, Melissa A; Boycott, Kym M; Hamosh, Ada; Rehm, Heidi L

    2017-10-18

    In well over half of the individuals with rare disease who undergo clinical or research next-generation sequencing, the responsible gene cannot be determined. Some reasons for this relatively low yield include unappreciated phenotypic heterogeneity; locus heterogeneity; somatic and germline mosaicism; variants of uncertain functional significance; technically inaccessible areas of the genome; incorrect mode of inheritance investigated; and inadequate communication between clinicians and basic scientists with knowledge of particular genes, proteins, or biological systems. To facilitate such communication and improve the search for patients or model organisms with similar phenotypes and variants in specific candidate genes, we have developed the Matchmaker Exchange (MME). MME was created to establish a federated network connecting databases of genomic and phenotypic data using a common application programming interface (API). To date, seven databases can exchange data using the API (GeneMatcher, PhenomeCentral, DECIPHER, MyGene2, matchbox, Australian Genomics Health Alliance Patient Archive, and Monarch Initiative; the latter included for model organism matching). This article guides usage of the MME for rare disease gene discovery. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley and Sons, Inc.

  6. Heat exchanger

    Energy Technology Data Exchange (ETDEWEB)

    Harada, F; Yanagida, T; Fujie, K; Futawatari, H

    1975-04-30

    The purpose of this construction is the improvement of heat transfer in finned tube heat exchangers, and therefore the improvement of its efficiency or its output per unit volume. This is achieved by preventing the formation of flow boundary layers in gaseous fluid. This effect always occurs on flow of smooth adjacent laminae, and especially if these have pipes carrying liquid passing through them; it worsens the heat transfer of such a boundary layer considerably compared to that in the turbulent range. The fins, which have several rows of heat exchange tubes passing through them, are fixed at a small spacing on theses tubes. The fins have slots cut in them by pressing or punching, where the pressed-out material remains as a web, which runs parallel to the level of the fin and at a small distance from it. These webs and slots are arranged radially around every tube hole, e.g. 6 in number. For a suitable small tube spacing, two adjacent tubes opposite each other have one common slot. Many variants of such slot arrangements are illustrated.

  7. Segmented heat exchanger

    Science.gov (United States)

    Baldwin, Darryl Dean; Willi, Martin Leo; Fiveland, Scott Byron; Timmons, Kristine Ann

    2010-12-14

    A segmented heat exchanger system for transferring heat energy from an exhaust fluid to a working fluid. The heat exchanger system may include a first heat exchanger for receiving incoming working fluid and the exhaust fluid. The working fluid and exhaust fluid may travel through at least a portion of the first heat exchanger in a parallel flow configuration. In addition, the heat exchanger system may include a second heat exchanger for receiving working fluid from the first heat exchanger and exhaust fluid from a third heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the second heat exchanger in a counter flow configuration. Furthermore, the heat exchanger system may include a third heat exchanger for receiving working fluid from the second heat exchanger and exhaust fluid from the first heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the third heat exchanger in a parallel flow configuration.

  8. A novel comparative pattern count analysis reveals a chronic ethanol-induced dynamic shift in immediate early NF-κB genome-wide promoter binding during liver regeneration.

    Science.gov (United States)

    Kuttippurathu, Lakshmi; Patra, Biswanath; Hoek, Jan B; Vadigepalli, Rajanikanth

    2016-03-01

    Liver regeneration after partial hepatectomy is a clinically important process that is impaired by adaptation to chronic alcohol intake. We focused on the initial time points following partial hepatectomy (PHx) to analyze the genome-wide binding activity of NF-κB, a key immediate early regulator. We investigated the effect of chronic alcohol intake on immediate early NF-κB genome-wide localization, in the adapted state as well as in response to partial hepatectomy, using chromatin immunoprecipitation followed by promoter microarray analysis. We found many ethanol-specific NF-κB binding target promoters in the ethanol-adapted state, corresponding to the regulation of biosynthetic processes, oxidation-reduction and apoptosis. Partial hepatectomy induced a diet-independent shift in NF-κB binding loci relative to the transcription start sites. We employed a novel pattern count analysis to exhaustively enumerate and compare the number of promoters corresponding to the temporal binding patterns in ethanol and pair-fed control groups. The highest pattern count corresponded to promoters with NF-κB binding exclusively in the ethanol group at 1 h post PHx. This set was associated with the regulation of cell death, response to oxidative stress, histone modification, mitochondrial function, and metabolic processes. Integration with the global gene expression profiles to identify putative transcriptional consequences of NF-κB binding patterns revealed that several of ethanol-specific 1 h binding targets showed ethanol-specific differential expression through 6 h post PHx. Motif analysis yielded co-incident binding loci for STAT3, AP-1, CREB, C/EBP-β, PPAR-γ and C/EBP-α, likely participating in co-regulatory modules with NF-κB in shaping the immediate early response to PHx. We conclude that adaptation to chronic ethanol intake disrupts the NF-κB promoter binding landscape with consequences for the immediate early gene regulatory response to the acute challenge of PHx.

  9. Expansion of the public sector, the current account and the exchange rate

    OpenAIRE

    Ohr, Renate

    1985-01-01

    Attributing the foreign trade effects of an expansion in the state budget to a single cause cannot do justice to the multitude of macro-economic interrelationships. Both theory and observation can reveal quite differing links between the public sector financial balance, the balance of payments and the exchange rate. The financing and nature of additional budgetary expenditure and the pattern of private investors’ expectations therefore have to be taken into consideration to obtain a clear pic...

  10. Microbial mutualism at a distance: The role of geometry in diffusive exchanges

    Science.gov (United States)

    Peaudecerf, François J.; Bunbury, Freddy; Bhardwaj, Vaibhav; Bees, Martin A.; Smith, Alison G.; Goldstein, Raymond E.; Croze, Ottavio A.

    2018-02-01

    The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.

  11. Diverse phosphorylation patterns of B cell receptor-associated signaling in naïve and memory human B cells revealed by phosphoflow, a powerful technique to study signaling at the single cell level

    Directory of Open Access Journals (Sweden)

    Franklin R Toapanta

    2012-10-01

    Full Text Available Following interaction with cognate antigens, B cells undergo cell activation, proliferation and differentiation. Ligation of the B cell receptor (BCR leads to the phosphorylation of BCR-associated signaling proteins within minutes of antigen binding, a process with profound consequences for the fate of the cells and development of effector immunity. Phosphoflow allows a rapid evaluation of various signaling pathways in complex heterogenous cell subsets. This novel technique was used in combination with multi-chromatic flow cytometry and fluorescent-cell barcoding to study phosphorylation of BCR-associated signaling pathways in naïve and memory human B cell subsets. Proteins of the initiation (Syk, propagation (Btk, Akt and integration (p38MAPK and Erk1/2 signaling units were studied. Switched memory (Sm CD27+ and Sm CD27- phosphorylation patterns were similar when stimulated with anti-IgA or -IgG. In contrast, naïve and unswitched memory (Um cells showed significant differences following IgM stimulation. Enhanced phosphorylation of Syk was observed in Um cells, suggesting a lower activation threshold. This is likely the result of higher amounts of IgM on the cell surface, higher pan-Syk levels and enhanced susceptibility to phosphatase inhibition. All other signaling proteins evaluated also showed some degree of enhanced phosphorylation in Um cells. Furthermore, both the PLC-γ2 and PI3K pathways were activated in Um cells, while only the PI3K pathway was activated on naïve cells. Um cells were the only ones that activated signaling pathways when stimulated with fluorescently-labeled S. Typhi and S. pneumoniae. Finally, simultaneous evaluation of signaling proteins at the single cell level (multi-phosphorylated cells revealed that interaction with gram positive and negative bacteria resulted in complex and diverse signaling patterns. Phosphoflow holds great potential to accelerate vaccine development by identifying signaling profiles in good

  12. Exchange market pressure

    NARCIS (Netherlands)

    Jager, H.; Klaassen, F.; Durlauf, S.N.; Blume, L.E.

    2010-01-01

    Currencies can be under severe pressure in the foreign exchange market, but in a fixed (or managed) exchange rate regime that is not fully visible via the change in the exchange rate. Exchange market pressure (EMP) is a concept developed to nevertheless measure the pressure in such cases. This

  13. Broad-scale sampling of primary freshwater fish populations reveals the role of intrinsic traits, inter-basin connectivity, drainage area and latitude on shaping contemporary patterns of genetic diversity

    Directory of Open Access Journals (Sweden)

    Carla Sousa-Santos

    2016-02-01

    Full Text Available Background. Worldwide predictions suggest that up to 75% of the freshwater fish species occurring in rivers with reduced discharge could be extinct by 2070 due to the combined effect of climate change and water abstraction. The Mediterranean region is considered to be a hotspot of freshwater fish diversity but also one of the regions where the effects of climate change will be more severe. Iberian cyprinids are currently highly endangered, with over 68% of the species raising some level of conservation concern. Methods. During the FISHATLAS project, the Portuguese hydrographical network was extensively covered (all the 34 river basins and 47 sub-basins in order to contribute with valuable data on the genetic diversity distribution patterns of native cyprinid species. A total of 188 populations belonging to 16 cyprinid species of Squalius, Luciobarbus, Achondrostoma, Iberochondrostoma, Anaecypris and Pseudochondrostoma were characterized, for a total of 3,678 cytochrome b gene sequences. Results. When the genetic diversity of these populations was mapped, it highlighted differences among populations from the same species and between species with identical distribution areas. Factors shaping the contemporary patterns of genetic diversity were explored and the results revealed the role of latitude, inter-basin connectivity, migratory behaviour, species maximum size, species range and other species intrinsic traits in determining the genetic diversity of sampled populations. Contrastingly, drainage area and hydrological regime (permanent vs. temporary seem to have no significant effect on genetic diversity. Species intrinsic traits, maximum size attained, inter-basin connectivity and latitude explained over 30% of the haplotype diversity variance and, generally, the levels of diversity were significantly higher for smaller sized species, from connected and southerly river basins. Discussion. Targeting multiple co-distributed species of primary

  14. Mathematics revealed

    CERN Document Server

    Berman, Elizabeth

    1979-01-01

    Mathematics Revealed focuses on the principles, processes, operations, and exercises in mathematics.The book first offers information on whole numbers, fractions, and decimals and percents. Discussions focus on measuring length, percent, decimals, numbers as products, addition and subtraction of fractions, mixed numbers and ratios, division of fractions, addition, subtraction, multiplication, and division. The text then examines positive and negative numbers and powers and computation. Topics include division and averages, multiplication, ratios, and measurements, scientific notation and estim

  15. Synchronization stability and pattern selection in a memristive neuronal network.

    Science.gov (United States)

    Wang, Chunni; Lv, Mi; Alsaedi, Ahmed; Ma, Jun

    2017-11-01

    Spatial pattern formation and selection depend on the intrinsic self-organization and cooperation between nodes in spatiotemporal systems. Based on a memory neuron model, a regular network with electromagnetic induction is proposed to investigate the synchronization and pattern selection. In our model, the memristor is used to bridge the coupling between the magnetic flux and the membrane potential, and the induction current results from the time-varying electromagnetic field contributed by the exchange of ion currents and the distribution of charged ions. The statistical factor of synchronization predicts the transition of synchronization and pattern stability. The bifurcation analysis of the sampled time series for the membrane potential reveals the mode transition in electrical activity and pattern selection. A formation mechanism is outlined to account for the emergence of target waves. Although an external stimulus is imposed on each neuron uniformly, the diversity in the magnetic flux and the induction current leads to emergence of target waves in the studied network.

  16. Synchronization stability and pattern selection in a memristive neuronal network

    Science.gov (United States)

    Wang, Chunni; Lv, Mi; Alsaedi, Ahmed; Ma, Jun

    2017-11-01

    Spatial pattern formation and selection depend on the intrinsic self-organization and cooperation between nodes in spatiotemporal systems. Based on a memory neuron model, a regular network with electromagnetic induction is proposed to investigate the synchronization and pattern selection. In our model, the memristor is used to bridge the coupling between the magnetic flux and the membrane potential, and the induction current results from the time-varying electromagnetic field contributed by the exchange of ion currents and the distribution of charged ions. The statistical factor of synchronization predicts the transition of synchronization and pattern stability. The bifurcation analysis of the sampled time series for the membrane potential reveals the mode transition in electrical activity and pattern selection. A formation mechanism is outlined to account for the emergence of target waves. Although an external stimulus is imposed on each neuron uniformly, the diversity in the magnetic flux and the induction current leads to emergence of target waves in the studied network.

  17. Ion-exchange properties of natural mordenite

    International Nuclear Information System (INIS)

    Chelishchev, N.F.; Volodin, V.F.

    1977-01-01

    Ion exchange properties are studied of natural mordenite Si(Al=4.75) exhibiting adequate mechanical characteristics and sufficient resistance to high temperature acids. Consideration is given to the pattern of exchange ions distribution among mordenite and chloride solutions of K, Cs, Rb, Sr. Mordenite shows sharp selectivity towards large alkali metal cations, particularly Cs + . In these processes the exchange isotherms are characterized by the constant selectivity towards a counterion. For the Sr 2+ -2Na + exchange the isotherm shows a change of selectivity after a definite counterion concentration has been reached in the solution. Correlation between the exchange thermodynamic constants makes it possible to propose the following range of mordenite selectivity towards the cations under study: Cs>Rb>K>Na>Sr

  18. Temporal Dynamics of Social Exchange and the Development of Solidarity: "Testing the Waters" versus "Taking a Leap of Faith"

    Science.gov (United States)

    Kuwabara, Ko; Sheldon, Oliver

    2012-01-01

    In their concerted efforts to unpack the microprocesses that transform repeated exchanges into an exchange relation, exchange theorists have paid little attention to how actors perceive changes and dynamics in exchanges over time. We help fill this gap by studying how temporal patterns of exchange affect the development of cohesion. Some exchange…

  19. Dois padrões de política cambial: América Latina e Sudeste Asiático Patterns of exchange rate policy: East Asia versus Latin America

    Directory of Open Access Journals (Sweden)

    Paulo Gala

    2007-04-01

    Full Text Available Vários trabalhos empíricos têm encontrado uma relação negativa entre desalinhamento cambial e crescimento econômico para uma longa série de países nos últimos trinta anos; quanto mais depreciada a taxa de câmbio, maiores as taxas de crescimento. Nessa literatura, um tema recorrente é a relativa depreciação das moedas asiáticas quando comparadas às moedas latino-americanas e africanas. Nos diversos estudos, surge o resultado de maior depreciação para a Ásia, no que parece constituir um padrão de comportamento dos níveis de taxa de câmbio real para essa região. Com o objetivo de contribuir para a discussão, este trabalho compara a evolução dos níveis de taxas de câmbio reais para países da Ásia e América Latina no período 1970-1999. Discute aspectos do manejo cambial de alguns dos principais países dessas duas regiões e apresenta considerações sobre o papel da política cambial no processo de desenvolvimento destas duas macro-regiões.Some authors argue in favor of a real exchange rate targeting strategy for developing countries in what could be called a development approach to exchange rates. According to the argument, relatively undervalued exchange rates have been a key factor in most East and Southeast Asian successful growth strategies. Following this so-called development approach, the objective of the paper is to compare the path of exchange rate levels in Asia and Latin America from 1970 to 1999. The work reviews some aspects of exchange rate management for some countries in those regions based on several case studies. It also presents an evolution of real exchange rate levels for a set of 20 countries based on World Bank data and on an index of exchange rate distortion.

  20. Exchange rate predictability and state-of-the-art models

    OpenAIRE

    Yeșin, Pınar

    2016-01-01

    This paper empirically evaluates the predictive performance of the International Monetary Fund's (IMF) exchange rate assessments with respect to future exchange rate movements. The assessments of real trade-weighted exchange rates were conducted from 2006 to 2011, and were based on three state-of-the-art exchange rate models with a medium-term focus which were developed by the IMF. The empirical analysis using 26 advanced and emerging market economy currencies reveals that the "diagnosis" of ...

  1. Exchange, x-ray and IR spectral behaviour of lanthanum and praseodymium exchanged zeolite X

    International Nuclear Information System (INIS)

    Das, D.; Upreti, M.C.

    1995-01-01

    Exchange behaviour of lanthanum and praseodymium ions in zeolite X involves three steps: preferential exchange, intrazeolitic exchange and irreversible exchange. At room temperature , higher exchange has been observed with La(III) than with Pr(III) which is attributed to the smaller hydrosphere of lanthanum than praseodymium. IR spectra of these zeolites in KBr pellets show a shift in the major Si-O stretching vibration of 972 cm -1 to higher frequencies. Their x-ray diffraction patterns remain unchanged except a large decrease of the line intensities caused by the absorption of x-rays by heavy La(III) and Pr(III) ions. The present study reports the preparation and physicochemical properties of lanthanum and praseodymium exchanged zeolite X. (author). 12 refs., 3 figs., 3 tabs

  2. The Phosphatidylinositol (3,4,5)-Trisphosphate-dependent Rac Exchanger 1·Ras-related C3 Botulinum Toxin Substrate 1 (P-Rex1·Rac1) Complex Reveals the Basis of Rac1 Activation in Breast Cancer Cells.

    Science.gov (United States)

    Lucato, Christina M; Halls, Michelle L; Ooms, Lisa M; Liu, Heng-Jia; Mitchell, Christina A; Whisstock, James C; Ellisdon, Andrew M

    2015-08-21

    The P-Rex (phosphatidylinositol (3,4,5)-trisphosphate (PIP3)-dependent Rac exchanger) family (P-Rex1 and P-Rex2) of the Rho guanine nucleotide exchange factors (Rho GEFs) activate Rac GTPases to regulate cell migration, invasion, and metastasis in several human cancers. The family is unique among Rho GEFs, as their activity is regulated by the synergistic binding of PIP3 and Gβγ at the plasma membrane. However, the molecular mechanism of this family of multi-domain proteins remains unclear. We report the 1.95 Å crystal structure of the catalytic P-Rex1 DH-PH tandem domain in complex with its cognate GTPase, Rac1 (Ras-related C3 botulinum toxin substrate-1). Mutations in the P-Rex1·Rac1 interface revealed a critical role for this complex in signaling downstream of receptor tyrosine kinases and G protein-coupled receptors. The structural data indicated that the PIP3/Gβγ binding sites are on the opposite surface and markedly removed from the Rac1 interface, supporting a model whereby P-Rex1 binding to PIP3 and/or Gβγ releases inhibitory C-terminal domains to expose the Rac1 binding site. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

  3. Isotopically exchangeable phosphorus

    International Nuclear Information System (INIS)

    Barbaro, N.O.

    1984-01-01

    A critique revision of isotope dilution is presented. The concepts and use of exchangeable phosphorus, the phosphate adsorption, the kinetics of isotopic exchange and the equilibrium time in soils are discussed. (M.A.C.) [pt

  4. NCHRP peer exchange 2008.

    Science.gov (United States)

    2008-09-01

    Peer exchanges for state department of transportation (DOT) research programs originated with : the Intermodal Surface Transportation Efficiency Act of 1991 (ISTEA). That federal legislation : required the states to conduct periodic peer exchanges to...

  5. Indiana Health Information Exchange

    Science.gov (United States)

    The Indiana Health Information Exchange is comprised of various Indiana health care institutions, established to help improve patient safety and is recognized as a best practice for health information exchange.

  6. Fundamentals of ion exchange

    International Nuclear Information System (INIS)

    Townsend, R.P.

    1993-01-01

    In this paper the fundamentals of ion exchange mechanisms and their thermodynamics are described. A range of ion exchange materials is considered and problems of communication and technology transfer between scientists working in the field are discussed. (UK)

  7. Giant exchange interaction in mixed lanthanides

    Science.gov (United States)

    Vieru, Veacheslav; Iwahara, Naoya; Ungur, Liviu; Chibotaru, Liviu F.

    2016-01-01

    Combining strong magnetic anisotropy with strong exchange interaction is a long standing goal in the design of quantum magnets. The lanthanide complexes, while exhibiting a very strong ionic anisotropy, usually display a weak exchange coupling, amounting to only a few wavenumbers. Recently, an isostructural series of mixed (Ln = Gd, Tb, Dy, Ho, Er) have been reported, in which the exchange splitting is estimated to reach hundreds wavenumbers. The microscopic mechanism governing the unusual exchange interaction in these compounds is revealed here by combining detailed modeling with density-functional theory and ab initio calculations. We find it to be basically kinetic and highly complex, involving non-negligible contributions up to seventh power of total angular momentum of each lanthanide site. The performed analysis also elucidates the origin of magnetization blocking in these compounds. Contrary to general expectations the latter is not always favored by strong exchange interaction. PMID:27087470

  8. Exchange networks from close-up: The case of Lipari obsidian

    Directory of Open Access Journals (Sweden)

    Andrea Vianello

    2016-09-01

    Full Text Available A systematic study on obsidian tools in Calabria and Sicily carried out by the authors have revealed the uniqueness in the patterns of production, exchange and consumption of Lipari obsidian. The study has concentrated on the Middle Neolithic primarily, with other Neolithic and Bronze Age contexts recognised at a later stage in the research since many contexts, especially in Sicily, have been excavated by pioneering archaeologists, some over a century ago, or were mislabelled. The chronology is Early Neolithic to Early Bronze Age, with very few materials dating Middle Bronze Age. A review of chronological contexts is in progress, which spans from the 6th millennium BC to the end of the 2nd millennium BC. The typology of obsidian tools is very homogenous, the vast majority of used tools are small blades, bladelets and sharp flakes; there is negligible variance across time; and Lipari obsidian is preferred over other sources. The patterns of the exchanges are also unique, revealing two major types of redistribution of obsidian, one particularly intriguing because it is quite organized with a single source in Lipari, prominent and reminiscent for its stability and reach of Bronze Age redistribution dynamics associated with hierarchical societies. We present here some observations on patterns substantiated by the archaeological record, and consider possible scenarios that can explain them. This work provides an update on progressing research and reveals aspects that will need further investigation, focusing on the patterns identified so far and possible explanations. More work is certainly needed to produce a working model, but the unusual patterns deserve some attention on their own, unencumbered by an overarching explanatory model. In particular, we want to assess the Neolithic redistribution pattern suggestive as typical of hierarchical polities, and contextualize it to the specific situation of Neolithic Lipari.

  9. Revealing Rembrandt

    Directory of Open Access Journals (Sweden)

    Andrew J Parker

    2014-04-01

    Full Text Available The power and significance of artwork in shaping human cognition is self-evident. The starting point for our empirical investigations is the view that the task of neuroscience is to integrate itself with other forms of knowledge, rather than to seek to supplant them. In our recent work, we examined a particular aspect of the appreciation of artwork using present-day functional magnetic resonance imaging (fMRI. Our results emphasised the continuity between viewing artwork and other human cognitive activities. We also showed that appreciation of a particular aspect of artwork, namely authenticity, depends upon the co-ordinated activity between the brain regions involved in multiple decision making and those responsible for processing visual information. The findings about brain function probably have no specific consequences for understanding how people respond to the art of Rembrandt in comparison with their response to other artworks. However, the use of images of Rembrandt’s portraits, his most intimate and personal works, clearly had a significant impact upon our viewers, even though they have been spatially confined to the interior of an MRI scanner at the time of viewing. Neuroscientific studies of humans viewing artwork have the capacity to reveal the diversity of human cognitive responses that may be induced by external advice or context as people view artwork in a variety of frameworks and settings.

  10. Environmental variation, vegetation distribution, carbon dynamics and water/energy exchange at high latitudes

    Science.gov (United States)

    McGuire, A.D.; Wirth, C.; Apps, M.; Beringer, J.; Clein, J.; Epstein, H.; Kicklighter, D.W.; Bhatti, J.; Chapin, F. S.; De Groot, B.; Efremov, D.; Eugster, W.; Fukuda, M.; Gower, T.; Hinzman, L.; Huntley, B.; Jia, G.J.; Kasischke, E.; Melillo, J.; Romanovsky, V.; Shvidenko, A.; Vaganov, E.; Walker, D.

    2002-01-01

    The responses of high latitude ecosystems to global change involve complex interactions among environmental variables, vegetation distribution, carbon dynamics, and water and energy exchange. These responses may have important consequences for the earth system. In this study, we evaluated how vegetation distribution, carbon stocks and turnover, and water and energy exchange are related to environmental variation spanned by the network of the IGBP high latitude transects. While the most notable feature of the high latitude transects is that they generally span temperature gradients from southern to northern latitudes, there are substantial differences in temperature among the transects. Also, along each transect temperature co-varies with precipitation and photosynthetically active radiation, which are also variable among the transects. Both climate and disturbance interact to influence latitudinal patterns of vegetation and soil carbon storage among the transects, and vegetation distribution appears to interact with climate to determine exchanges of heat and moisture in high latitudes. Despite limitations imposed by the data we assembled, the analyses in this study have taken an important step toward clarifying the complexity of interactions among environmental variables, vegetation distribution, carbon stocks and turnover, and water and energy exchange in high latitude regions. This study reveals the need to conduct coordinated global change studies in high latitudes to further elucidate how interactions among climate, disturbance, and vegetation distribution influence carbon dynamics and water and energy exchange in high latitudes.

  11. The study of RMB exchange rate complex networks based on fluctuation mode

    Science.gov (United States)

    Yao, Can-Zhong; Lin, Ji-Nan; Zheng, Xu-Zhou; Liu, Xiao-Feng

    2015-10-01

    In the paper, we research on the characteristics of RMB exchange rate time series fluctuation with methods of symbolization and coarse gaining. First, based on fluctuation features of RMB exchange rate, we define the first type of fluctuation mode as one specific foreign currency against RMB in four days' fluctuating situations, and the second type as four different foreign currencies against RMB in one day's fluctuating situation. With the transforming method, we construct the unique-currency and multi-currency complex networks. Further, through analyzing the topological features including out-degree, betweenness centrality and clustering coefficient of fluctuation-mode complex networks, we find that the out-degree distribution of both types of fluctuation mode basically follows power-law distributions with exponents between 1 and 2. The further analysis reveals that the out-degree and the clustering coefficient generally obey the approximated negative correlation. With this result, we confirm previous observations showing that the RMB exchange rate exhibits a characteristic of long-range memory. Finally, we analyze the most probable transmission route of fluctuation modes, and provide probability prediction matrix. The transmission route for RMB exchange rate fluctuation modes exhibits the characteristics of partially closed loop, repeat and reversibility, which lays a solid foundation for predicting RMB exchange rate fluctuation patterns with large volume of data.

  12. Exchange rate policy

    Directory of Open Access Journals (Sweden)

    Plačkov Slađana

    2013-01-01

    Full Text Available Small oscillations of exchange rate certainly affect the loss of confidence in the currency (Serbian dinar, CSD and because of the shallow market even the smallest change in the supply and demand leads to a shift in exchange rate and brings uncertainty. Some economists suggest that the course should be linked to inflation and thus ensure predictable and stable exchange rates. Real exchange rate or slightly depressed exchange rate will encourage the competitiveness of exporters and perhaps ensure the development of new production lines which, in terms of overvalued exchange rate, had no economic justification. Fixed exchange rate will bring lower interest rates, lower risk and lower business uncertainty (uncertainty avoidance, but Serbia will also reduce foreign exchange reserves by following this trend. On the other hand, a completely free exchange rate, would lead to a (real fall of Serbian currency, which in a certain period would lead to a significant increase in exports, but the consequences for businessmen and citizens with loans pegged to the euro exchange rate, would be disastrous. We will pay special attention to the depreciation of the exchange rate, as it is generally favorable to the export competitiveness of Serbia and, on the other hand, it leads to an increase in debt servicing costs of the government as well as of the private sector. Oscillations of the dinar exchange rate, appreciation and depreciation, sometimes have disastrous consequences on the economy, investors, imports and exports. In subsequent work, we will observe the movement of the dinar exchange rate in Serbia, in the time interval 2009-2012, in order to strike a balance and maintain economic equilibrium. A movement of foreign currencies against the local currency is controlled in the foreign exchange market, so in case economic interests require, The National Bank of Serbia (NBS, on the basis of arbitrary criteria, can intervene in the market.

  13. Charge exchange in galaxy clusters

    Science.gov (United States)

    Gu, Liyi; Mao, Junjie; de Plaa, Jelle; Raassen, A. J. J.; Shah, Chintan; Kaastra, Jelle S.

    2018-03-01

    Context. Though theoretically expected, the charge exchange emission from galaxy clusters has never been confidently detected. Accumulating hints were reported recently, including a rather marginal detection with the Hitomi data of the Perseus cluster. As previously suggested, a detection of charge exchange line emission from galaxy clusters would not only impact the interpretation of the newly discovered 3.5 keV line, but also open up a new research topic on the interaction between hot and cold matter in clusters. Aim. We aim to perform the most systematic search for the O VIII charge exchange line in cluster spectra using the RGS on board XMM-Newton. Methods: We introduce a sample of 21 clusters observed with the RGS. In order to search for O VIII charge exchange, the sample selection criterion is a >35σ detection of the O VIII Lyα line in the archival RGS spectra. The dominating thermal plasma emission is modeled and subtracted with a two-temperature thermal component, and the residuals are stacked for the line search. The systematic uncertainties in the fits are quantified by refitting the spectra with a varying continuum and line broadening. Results: By the residual stacking, we do find a hint of a line-like feature at 14.82 Å, the characteristic wavelength expected for oxygen charge exchange. This feature has a marginal significance of 2.8σ, and the average equivalent width is 2.5 × 10-4 keV. We further demonstrate that the putative feature can be barely affected by the systematic errors from continuum modeling and instrumental effects, or the atomic uncertainties of the neighboring thermal lines. Conclusions: Assuming a realistic temperature and abundance pattern, the physical model implied by the possible oxygen line agrees well with the theoretical model proposed previously to explain the reported 3.5 keV line. If the charge exchange source indeed exists, we expect that the oxygen abundance could have been overestimated by 8-22% in previous X

  14. Automated exchange transfusion and exchange rate.

    Science.gov (United States)

    Funato, M; Shimada, S; Tamai, H; Taki, H; Yoshioka, Y

    1989-10-01

    An automated blood exchange transfusion (BET) with a two-site technique has been devised by Goldmann et al and by us, using an infusion pump. With this method, we successfully performed exchange transfusions 189 times in the past four years on 110 infants with birth weights ranging from 530 g to 4,000 g. The exchange rate by the automated method was compared with the rate by Diamond's method. Serum bilirubin (SB) levels before and after BET and the maximal SB rebound within 24 hours after BET were: 21.6 +/- 2.4, 11.5 +/- 2.2, and 15.0 +/- 1.5 mg/dl in the automated method, and 22.0 +/- 2.9, 11.2 +/- 2.5, and 17.7 +/- 3.2 mg/dl in Diamond's method, respectively. The result showed that the maximal rebound of the SB level within 24 hours after BET was significantly lower in the automated method than in Diamond's method (p less than 0.01), though SB levels before and after BET were not significantly different between the two methods. The exchange rate was also measured by means of staining the fetal red cells (F cells) both in the automated method and in Diamond's method, and comparing them. The exchange rate of F cells in Diamond's method went down along the theoretical exchange curve proposed by Diamond, while the rate in the automated method was significantly better than in Diamond's, especially in the early stage of BET (p less than 0.01). We believe that the use of this automated method may give better results than Diamond's method in the rate of exchange, because this method is performed with a two-site technique using a peripheral artery and vein.

  15. Fluctuation Dynamics of Exchange Rates on Indian Financial Market

    Science.gov (United States)

    Sarkar, A.; Barat, P.

    Here we investigate the scaling behavior and the complexity of the average daily exchange rate returns of the Indian Rupee against four foreign currencies namely US Dollar, Euro, Great Britain Pound and Japanese Yen. Our analysis revealed that the average daily exchange rate return of the Indian Rupee against the US Dollar exhibits a persistent scaling behavior and follow Levy stable distribution. On the contrary the average daily exchange rate returns of the other three foreign currencies show randomness and follow Gaussian distribution. Moreover, it is seen that the complexity of the average daily exchange rate return of the Indian Rupee against US Dollar is less than the other three exchange rate returns.

  16. Expert system for aiding fuel exchange planning

    International Nuclear Information System (INIS)

    Shiratori, Yoshitake.

    1992-01-01

    A fuel exchange plan is prepared based on intelligence bases such as a method of zoning a reactor core, a fuel arrangement rule and a procedure for fuel exchange, as well as initial data. Then, the fuel exchange plans are patterned to several groups based on the intelligence bases such as patterning of fuel arrangement. A typical pattern is analyzed by a reactor core analyzing code and allowance or rejection for the analyzed patterns is judged based on intelligence bases regarding life time of the reactor core, thermal limit value of fuels, burning of fuel for irradiation test. The result of the judgement is fed-back as an estimation information and the initial data and the intelligence data are added to prepare a plan again. A similar analysis is also conducted for the plan of the rejected group. The allowance or rejection is judged for all of the plans in the same manner. The intelligence bases are used and the result of the judgement is fed-back as a condition for estimation, thereby enabling to remarkably save labors and time and prepare non-typical exchange plans. (N.H.)

  17. The coordination value of monetary exchange: Experimental evidence

    OpenAIRE

    Camera, Gabriele; Casari, Marco

    2011-01-01

    A new behavioral foundation is uncovered for why money promotes impersonal exchange. In an experiment, subjects could cooperate by intertemporally exchanging goods with anonymous opponents met at random. Indefinite repetition supported multiple equilibria, from full defection to the efficient outcome. Introducing the possibility to hold and exchange intrinsically worthless tickets affected outcomes and cooperation patterns. Tickets resembled fiat money, which emerged as a tool for equilibrium...

  18. Outlook for ion exchange

    International Nuclear Information System (INIS)

    Kunin, R.

    1977-01-01

    This paper presents the history and theory of ion exchange technology and discusses the usefulness of ion exchange resins which found broad applications in chemical operations. It is demonstrated that the theory of ion exchange technology seems to be moving away from the physical chemist back to the polymer chemist where it started originally. This but confronted the polymer chemists with some knotty problems. It is pointed out that one has still to learn how to use ion exchange materials as efficiently as possible in terms of the waste load that is being pumped into the environment. It is interesting to note that, whereas ion exchange is used for abating pollution, it is also a polluter. One must learn how to use ion exchange as an antipollution device, and at the same time minimize its polluting properties

  19. Structural Implications of Reciprocal Exchange: A Power-Dependence Approach

    Science.gov (United States)

    Bonacich, Phillip; Bienenstock, Elisa Jayne

    2009-01-01

    This paper presents and tests a general model to predict emergent exchange patterns and power differences in reciprocal exchange networks when individual actors follow the norm of reciprocity. With an interesting qualification, the experimental results reported here support the power-dependence approach (Emerson 1972a, b): those who acquire the…

  20. Microsoft Exchange 2013 cookbook

    CERN Document Server

    Van Horenbeeck, Michael

    2013-01-01

    This book is a practical, hands-on guide that provides the