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Sample records for convergently evolved enzymes

  1. Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function

    PubMed Central

    Almonacid, Daniel E.; Yera, Emmanuel R.; Mitchell, John B. O.; Babbitt, Patricia C.

    2010-01-01

    Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine

  2. Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.

    PubMed

    Almonacid, Daniel E; Yera, Emmanuel R; Mitchell, John B O; Babbitt, Patricia C

    2010-03-12

    Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry, providing a window on the different structural strategies nature has used to evolve required catalysts. Identification and use of this information to improve reaction classification and computational annotation of enzymes newly discovered in the genome projects would benefit from systematic determination of reaction similarities. Here, we quantified similarity in bond changes for overall reactions and catalytic mechanisms for 95 pairs of functionally analogous enzymes (non-homologous enzymes with identical first three numbers of their EC codes) from the MACiE database. Similarity of overall reactions was computed by comparing the sets of bond changes in the transformations from substrates to products. For similarity of mechanisms, sets of bond changes occurring in each mechanistic step were compared; these similarities were then used to guide global and local alignments of mechanistic steps. Using this metric, only 44% of pairs of functionally analogous enzymes in the dataset had significantly similar overall reactions. For these enzymes, convergence to the same mechanism occurred in 33% of cases, with most pairs having at least one identical mechanistic step. Using our metric, overall reaction similarity serves as an upper bound for mechanistic similarity in functional analogs. For example, the four carbon-oxygen lyases acting on phosphates (EC 4.2.3) show neither significant overall reaction similarity nor significant mechanistic similarity. By contrast, the three carboxylic-ester hydrolases (EC 3.1.1) catalyze overall reactions with identical bond changes and have converged to almost identical mechanisms. The large proportion of enzyme pairs that do not show significant overall reaction similarity (56%) suggests that at least for the functionally analogous enzymes studied here, more stringent criteria could be used to refine

  3. Divergence and Convergence in Enzyme Evolution*

    PubMed Central

    Galperin, Michael Y.; Koonin, Eugene V.

    2012-01-01

    Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes. PMID:22069324

  4. Convergently Evolved Toxic Secondary Metabolites in Plants Drive the Parallel Molecular Evolution of Insect Resistance.

    PubMed

    Petschenka, Georg; Wagschal, Vera; von Tschirnhaus, Michael; Donath, Alexander; Dobler, Susanne

    2017-08-01

    Natural selection imposed by natural toxins has led to striking levels of convergent evolution at the molecular level. Cardiac glycosides represent a group of plant toxins that block the Na,K-ATPase, a vital membrane protein in animals. Several herbivorous insects have convergently evolved resistant Na,K-ATPases, and in some species, convergent gene duplications have also arisen, likely to cope with pleiotropic costs of resistance. To understand the genetic basis and predictability of these adaptations, we studied five independent lineages of leaf-mining flies (Diptera: Agromyzidae). These flies have colonized host plants in four botanical families that convergently evolved cardiac glycosides of two structural types: cardenolides and bufadienolides. We compared each of six fly species feeding on such plants to a phylogenetically related but nonadapted species. Irrespective of the type of cardiac glycoside in the host plant, five out of six exposed species displayed substitutions in the cardiac glycoside-binding site of the Na,K-ATPase that were previously described in other insect orders; in only one species was the gene duplicated. In vitro assays of nervous tissue extractions confirmed that the substitutions lead to increased resistance of the Na,K-ATPase. Our results demonstrate that target site insensitivity of Na,K-ATPase is a common response to dietary cardiac glycosides leading to highly predictable amino acid changes; nonetheless, convergent evolution of gene duplication for this multifunctional enzyme appears more constrained.

  5. Svecofennian orogeny in an evolving convergent margin setting

    NASA Astrophysics Data System (ADS)

    Korja, Annakaisa

    2015-04-01

    The dominant tectonic mode changes from extension to convergence at around 1.9 Ga in Fennoscandian. The lithological record suggests short lived subduction-related magmatic events followed by deformation and low-pressure high temperature metamorphism. At around 1.8 Ga the subduction systems seem to have stabilized implying continuous supply of oceanic lithosphere. The evolution of the convergent margin is recorded in the rock record and crustal architecture of the long lived Svecofennian orogeny (1.9-1.7 Ga). A closer look at the internal structure of the Svecofennian orogen reveals distinct regional differences. The northern and central parts of the Svecofennian orogen that have been formed during the initial accretionary phase - or compilation of the nucleus - have a thick three-layer crust and with thick mafic lower crust (10-30 km) and block-like internal architecture. Reflection profiles (FIRE1-3) image listric structures flattening on crustal scale décollement zones at the upper-middle crust and middle-upper crust boundaries. The crustal architecture together with large volumes of exposed granitoid rocks suggests spreading of the orogen and the development of an orogenic plateau west of the continental convergence boundary. The architecture is reminiscent of a large hot orogen. Within the western and southwestern part of the Svecofennian orogen (BABEL B, 1, 2, 3&4), which have been envisioned to have formed during continuous subduction phase, the crust is thinner (45-50 km) and it is hosting crustal blocks having one to two crustal layers. Layering is poorly developed in crustal blocks that are found S-SW of NE-dipping mantle reflections previously interpreted as paleo-subduction zones. Within these blocks, the crustal scale reflective structures dip NE (prowedge) or form pop-up wedges (uplifted plug) above the paleo-subduction zones. Crustal blocks with well-developed two-layer crust are located NE of the paleo-subduction zone. The architecture can be

  6. Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes.

    PubMed

    Huang, Ruiqi; O'Donnell, Andrew J; Barboline, Jessica J; Barkman, Todd J

    2016-09-20

    Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study.

  7. Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes

    PubMed Central

    Huang, Ruiqi; O’Donnell, Andrew J.; Barboline, Jessica J.; Barkman, Todd J.

    2016-01-01

    Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study. PMID:27638206

  8. An analysis of why highly similar enzymes evolve differently.

    PubMed Central

    Majiduddin, Fahd K; Palzkill, Timothy

    2003-01-01

    The TEM-1 and SHV-1 beta-lactamases are important contributors to resistance to beta-lactam antibiotics in gram-negative bacteria. These enzymes share 68% amino acid sequence identity and their atomic structures are nearly superimposable. Extended-spectrum cephalosporins were introduced to avoid the action of these beta-lactamases. The widespread use of antibiotics has led to the evolution of variant TEM and SHV enzymes that can hydrolyze extended-spectrum antibiotics. Despite being highly similar in structure, the TEM and SHV enzymes have evolved differently in response to the selective pressure of antibiotic therapy. Examples of this are at residues Arg164 and Asp179. Among TEM variants, substitutions are found only at position 164, while among SHV variants, substitutions are found only at position 179. To explain this observation, the effects of substitutions at position 164 in both TEM-1 and SHV-1 on antibiotic resistance and on enzyme catalytic efficiency were examined. Competition experiments were performed between mutants to understand why certain substitutions preferentially evolve in response to the selective pressure of antibiotic therapy. The data presented here indicate that substitutions at position Asp179 in SHV-1 and Arg164 in TEM-1 are more beneficial to bacteria because they provide increased fitness relative to either wild type or other mutants. PMID:12618385

  9. Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks.

    PubMed

    Ellis, Nicholas A; Glazer, Andrew M; Donde, Nikunj N; Cleves, Phillip A; Agoglia, Rachel M; Miller, Craig T

    2015-07-15

    Teeth are a classic model system of organogenesis, as repeated and reciprocal epithelial and mesenchymal interactions pattern placode formation and outgrowth. Less is known about the developmental and genetic bases of tooth formation and replacement in polyphyodonts, which are vertebrates with continual tooth replacement. Here, we leverage natural variation in the threespine stickleback fish Gasterosteus aculeatus to investigate the genetic basis of tooth development and replacement. We find that two derived freshwater stickleback populations have both convergently evolved more ventral pharyngeal teeth through heritable genetic changes. In both populations, evolved tooth gain manifests late in development. Using pulse-chase vital dye labeling to mark newly forming teeth in adult fish, we find that both high-toothed freshwater populations have accelerated tooth replacement rates relative to low-toothed ancestral marine fish. Despite the similar evolved phenotype of more teeth and an accelerated adult replacement rate, the timing of tooth number divergence and the spatial patterns of newly formed adult teeth are different in the two populations, suggesting distinct developmental mechanisms. Using genome-wide linkage mapping in marine-freshwater F2 genetic crosses, we find that the genetic basis of evolved tooth gain in the two freshwater populations is largely distinct. Together, our results support a model whereby increased tooth number and an accelerated tooth replacement rate have evolved convergently in two independently derived freshwater stickleback populations using largely distinct developmental and genetic mechanisms.

  10. Distinct developmental genetic mechanisms underlie convergently evolved tooth gain in sticklebacks

    PubMed Central

    Ellis, Nicholas A.; Glazer, Andrew M.; Donde, Nikunj N.; Cleves, Phillip A.; Agoglia, Rachel M.; Miller, Craig T.

    2015-01-01

    Teeth are a classic model system of organogenesis, as repeated and reciprocal epithelial and mesenchymal interactions pattern placode formation and outgrowth. Less is known about the developmental and genetic bases of tooth formation and replacement in polyphyodonts, which are vertebrates with continual tooth replacement. Here, we leverage natural variation in the threespine stickleback fish Gasterosteus aculeatus to investigate the genetic basis of tooth development and replacement. We find that two derived freshwater stickleback populations have both convergently evolved more ventral pharyngeal teeth through heritable genetic changes. In both populations, evolved tooth gain manifests late in development. Using pulse-chase vital dye labeling to mark newly forming teeth in adult fish, we find that both high-toothed freshwater populations have accelerated tooth replacement rates relative to low-toothed ancestral marine fish. Despite the similar evolved phenotype of more teeth and an accelerated adult replacement rate, the timing of tooth number divergence and the spatial patterns of newly formed adult teeth are different in the two populations, suggesting distinct developmental mechanisms. Using genome-wide linkage mapping in marine-freshwater F2 genetic crosses, we find that the genetic basis of evolved tooth gain in the two freshwater populations is largely distinct. Together, our results support a model whereby increased tooth number and an accelerated tooth replacement rate have evolved convergently in two independently derived freshwater stickleback populations using largely distinct developmental and genetic mechanisms. PMID:26062935

  11. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-09-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  12. Rapid divergence and convergence of life-history in experimentally evolved Drosophila melanogaster.

    PubMed

    Burke, Molly K; Barter, Thomas T; Cabral, Larry G; Kezos, James N; Phillips, Mark A; Rutledge, Grant A; Phung, Kevin H; Chen, Richard H; Nguyen, Huy D; Mueller, Laurence D; Rose, Michael R

    2016-09-01

    Laboratory selection experiments are alluring in their simplicity, power, and ability to inform us about how evolution works. A longstanding challenge facing evolution experiments with metazoans is that significant generational turnover takes a long time. In this work, we present data from a unique system of experimentally evolved laboratory populations of Drosophila melanogaster that have experienced three distinct life-history selection regimes. The goal of our study was to determine how quickly populations of a certain selection regime diverge phenotypically from their ancestors, and how quickly they converge with independently derived populations that share a selection regime. Our results indicate that phenotypic divergence from an ancestral population occurs rapidly, within dozens of generations, regardless of that population's evolutionary history. Similarly, populations sharing a selection treatment converge on common phenotypes in this same time frame, regardless of selection pressures those populations may have experienced in the past. These patterns of convergence and divergence emerged much faster than expected, suggesting that intermediate evolutionary history has transient effects in this system. The results we draw from this system are applicable to other experimental evolution projects, and suggest that many relevant questions can be sufficiently tested on shorter timescales than previously thought. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  13. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2004-12-01

    Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and long-haul services. These

  14. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-08-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  15. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-04-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  16. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-06-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  17. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-05-01

    Call for Papers: Convergence The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and

  18. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-02-01

    Call for Papers: Convergence Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and

  19. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-03-01

    Call for Papers: Convergence Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly within an evolved but backward-compatible SDH/SONET (synchronous digital hierarchy and synchronous optical network) multiplexing hierarchy. From this common underlying theme follow many specific instantiations. Examples include the convergence at the physical, logical, and operational levels of voice and data, video and data, private-line and virtual private-line, fixed and mobile, and local and

  20. Genome Assembly Improvement and Mapping Convergently Evolved Skeletal Traits in Sticklebacks with Genotyping-by-Sequencing.

    PubMed

    Glazer, Andrew M; Killingbeck, Emily E; Mitros, Therese; Rokhsar, Daniel S; Miller, Craig T

    2015-06-03

    Marine populations of the threespine stickleback (Gasterosteus aculeatus) have repeatedly colonized and rapidly adapted to freshwater habitats, providing a powerful system to map the genetic architecture of evolved traits. Here, we developed and applied a binned genotyping-by-sequencing (GBS) method to build dense genome-wide linkage maps of sticklebacks using two large marine by freshwater F2 crosses of more than 350 fish each. The resulting linkage maps significantly improve the genome assembly by anchoring 78 new scaffolds to chromosomes, reorienting 40 scaffolds, and rearranging scaffolds in 4 locations. In the revised genome assembly, 94.6% of the assembly was anchored to a chromosome. To assess linkage map quality, we mapped quantitative trait loci (QTL) controlling lateral plate number, which mapped as expected to a 200-kb genomic region containing Ectodysplasin, as well as a chromosome 7 QTL overlapping a previously identified modifier QTL. Finally, we mapped eight QTL controlling convergently evolved reductions in gill raker length in the two crosses, which revealed that this classic adaptive trait has a surprisingly modular and nonparallel genetic basis. Copyright © 2015 Glazer et al.

  1. Convergence

    NASA Astrophysics Data System (ADS)

    Darcie, Thomas E.; Doverspike, Robert; Zirngibl, Martin; Korotky, Steven K.

    2005-01-01

    Call for Papers: Convergence

    Guest Editors: Thomas E. Darcie, University of Victoria Robert Doverspike, AT&T Martin Zirngibl, Lucent Technologies

    Coordinating Associate Editor: Steven K. Korotky, Lucent Technologies

    The Journal of Optical Networking (JON) invites submissions to a special issue on Convergence. Convergence has become a popular theme in telecommunications, one that has broad implications across all segments of the industry. Continual evolution of technology and applications continues to erase lines between traditionally separate lines of business, with dramatic consequences for vendors, service providers, and consumers. Spectacular advances in all layers of optical networking-leading to abundant, dynamic, cost-effective, and reliable wide-area and local-area connections-have been essential drivers of this evolution. As services and networks continue to evolve towards some notion of convergence, the continued role of optical networks must be explored. One vision of convergence renders all information in a common packet (especially IP) format. This vision is driven by the proliferation of data services. For example, time-division multiplexed (TDM) voice becomes VoIP. Analog cable-television signals become MPEG bits streamed to digital set-top boxes. T1 or OC-N private lines migrate to Ethernet virtual private networks (VPNs). All these packets coexist peacefully within a single packet-routing methodology built on an optical transport layer that combines the flexibility and cost of data networks with telecom-grade reliability. While this vision is appealing in its simplicity and shared widely, specifics of implementation raise many challenges and differences of opinion. For example, many seek to expand the role of Ethernet in these transport networks, while massive efforts are underway to make traditional TDM networks more data friendly

  2. Arginine Deiminase Enzyme Evolving As A Potential Antitumor Agent.

    PubMed

    Somani, Rakesh; Chaskar, Pratip K

    2016-08-17

    Some melanomas and hepatocellular carcinomas have been shown to be auxotrophic for arginine. Arginine deiminase (ADI), an arginine degrading enzyme isolated from Mycoplasma, can inhibit the growth of these tumors. It is a catabolizing enzyme which catabolizes arginine to citrulline. Tumor cells do not express an enzyme called arginosuccinate synthetase (ASS) and hence, these cells becomes auxotrophic for arginine. It is found that ADI is specific for arginine and did not degrade other amino acid. This review covers various aspects of ADIs like origin, properties and chemical modifications for better antitumor activity.

  3. Adenosylcobalamin enzymes: theory and experiment begin to converge.

    PubMed

    Marsh, E Neil G; Meléndez, Gabriel D Román

    2012-11-01

    Adenosylcobalamin (coenzyme B(12)) serves as the cofactor for a group of enzymes that catalyze unusual rearrangement or elimination reactions. The role of the cofactor as the initiator of reactive free radicals needed for these reactions is well established. Less clear is how these enzymes activate the coenzyme towards homolysis and control the radicals once generated. The availability of high resolution X-ray structures combined with detailed kinetic and spectroscopic analyses have allowed several adenosylcobalamin enzymes to be computationally modeled in some detail. Computer simulations have generally obtained good agreement with experimental data and provided valuable insight into the mechanisms of these unusual reactions. Importantly, atomistic modeling of the enzymes has allowed the role of specific interactions between protein, substrate and coenzyme to be explored, leading to mechanistic predictions that can now be tested experimentally. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology. Copyright © 2012 Elsevier B.V. All rights reserved.

  4. Effect of time-evolving age and convergence rate of the subducting plate on the Cenozoic adakites and boninites

    NASA Astrophysics Data System (ADS)

    Kim, Yoon-Mi; Lee, Changyeol

    2014-12-01

    Partial melting of subducting oceanic crust expressed as high-Mg volcanic rocks such as adakites and boninites has been actively studied for decades, and Lee and King (2010) reported that time-evolving subduction parameters such as the age and the subduction rate of the converging oceanic plate play important roles in transient partial melting of the subducting oceanic crust (e.g., Aleutians). However, few subduction model experiments have considered time-evolving subduction parameters, posing problems for studies of transient partial melting of subducting oceanic crust in many subduction zones. Therefore, we constructed two-dimensional kinematic-dynamic subduction models for the Izu-Bonin, Mariana, Northeast Japan, Kuril, Tonga, Java-Sunda, and Aleutian subduction zones that account for the last 50 Myr of their evolution. The models include the time-evolving age and convergence rate of the incoming oceanic plate, so the effect of time-evolving subduction parameters on transient partial melting of oceanic crust can be evaluated. Our model calculations revealed that adakites and boninites in the Izu-Bonin and Aleutian subduction zones resulted from transient partial melting of oceanic crust. However, the steady-state subduction model using current subduction parameters did not produce any partial melting of oceanic crust in the aforementioned subduction zones, indicating that time-evolving subduction parameters are crucial for modeling transient eruption of adakites and boninites. Our model calculations confirm that other geological processes such as forearc extension, back-arc opening, mantle plumes and ridge subduction are required for partial melting of the oceanic crust in the Mariana, Northeast Japan, Tonga, and southeastern Java-Sunda subduction zones.

  5. Evolving minimally invasive spine surgery: a surgeon's perspective on technological convergence and digital or control system.

    PubMed

    Chiu, John C; Maziad, Ali M; Rappard, George; Thacker, James T; Liu, Brent; Documet, Jorge

    2010-04-01

    Degenerated spinal disc and spinal stenosis are common problems requiring decompressive spinal surgery. Traditional open spinal discectomy is associated with significant tissue trauma, greater morbidity/complications, scarring, often longer term of convalescence, and even destabilization of the spine. Therefore, the pursuit of less traumatic minimally invasive spine surgery (MISS) began. The trend of spinal surgery is rapidly moving toward MISS. MISS is a technologically dependent surgery, and requires increased utilization of advanced endoscopic surgical instruments, imaging-video technology, and tissue modulation technology for performing spinal surgery in a digital operating room (DOR). It requires seamless connectivity and control to perform the surgical procedures in a precise and orchestrated manner. A new integrated DOR, the technological convergence and control system SurgMatix(R), was created in response to the need and to facilitate MISS with "organized control instead of organized chaos" in the endoscopic OR suite. It facilitates the performance, training, and further development of MISS.

  6. Convergence in feeding posture occurs through different genetic loci in independently evolved cave populations of Astyanax mexicanus

    PubMed Central

    Kowalko, Johanna E.; Rohner, Nicolas; Linden, Tess A.; Rompani, Santiago B.; Warren, Wesley C.; Borowsky, Richard; Tabin, Clifford J.; Jeffery, William R.; Yoshizawa, Masato

    2013-01-01

    When an organism colonizes a new environment, it needs to adapt both morphologically and behaviorally to survive and thrive. Although recent progress has been made in understanding the genetic architecture underlying morphological evolution, behavioral evolution is poorly understood. Here, we use the Mexican cavefish, Astyanax mexicanus, to study the genetic basis for convergent evolution of feeding posture. When river-dwelling surface fish became entrapped in the caves, they were confronted with dramatic changes in the availability and type of food source and in their ability to perceive it. In this setting, multiple independent populations of cavefish exhibit an altered feeding posture compared with their ancestral surface forms. We determined that this behavioral change in feeding posture is not due to changes in cranial facial morphology, body depth, or to take advantage of the expansion in the number of taste buds. Quantitative genetic analysis demonstrates that two different cave populations have evolved similar feeding postures through a small number of genetic changes, some of which appear to be distinct. This work indicates that independently evolved populations of cavefish can evolve the same behavioral traits to adapt to similar environmental challenges by modifying different sets of genes. PMID:24085851

  7. Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity.

    PubMed

    Koenen, Erik J M; Clarkson, James J; Pennington, Terence D; Chatrou, Lars W

    2015-07-01

    Tropical rainforest hyperdiversity is often suggested to have evolved over a long time-span (the 'museum' model), but there is also evidence for recent rainforest radiations. The mahoganies (Meliaceae) are a prominent plant group in lowland tropical rainforests world-wide but also occur in all other tropical ecosystems. We investigated whether rainforest diversity in Meliaceae has accumulated over a long time or has more recently evolved. We inferred the largest time-calibrated phylogeny for the family to date, reconstructed ancestral states for habitat and deciduousness, estimated diversification rates and modeled potential shifts in macro-evolutionary processes using a recently developed Bayesian method. The ancestral Meliaceae is reconstructed as a deciduous species that inhabited seasonal habitats. Rainforest clades have diversified from the Late Oligocene or Early Miocene onwards. Two contemporaneous Amazonian clades have converged on similar ecologies and high speciation rates. Most species-level diversity of Meliaceae in rainforest is recent. Other studies have found steady accumulation of lineages, but the large majority of plant species diversity in rainforests is recent, suggesting (episodic) species turnover. Rainforest hyperdiversity may best be explained by recent radiations from a large stock of higher level taxa. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  8. Antibiotic resistance evolved via inactivation of a ribosomal RNA methylating enzyme

    PubMed Central

    Stojković, Vanja; Noda-Garcia, Lianet; Tawfik, Dan S.; Fujimori, Danica Galonić

    2016-01-01

    Modifications of the bacterial ribosome regulate the function of the ribosome and modulate its susceptibility to antibiotics. By modifying a highly conserved adenosine A2503 in 23S rRNA, methylating enzyme Cfr confers resistance to a range of ribosome-targeting antibiotics. The same adenosine is also methylated by RlmN, an enzyme widely distributed among bacteria. While RlmN modifies C2, Cfr modifies the C8 position of A2503. Shared nucleotide substrate and phylogenetic relationship between RlmN and Cfr prompted us to investigate evolutionary origin of antibiotic resistance in this enzyme family. Using directed evolution of RlmN under antibiotic selection, we obtained RlmN variants that mediate low-level resistance. Surprisingly, these variants confer resistance not through the Cfr-like C8 methylation, but via inhibition of the endogenous RlmN C2 methylation of A2503. Detection of RlmN inactivating mutations in clinical resistance isolates suggests that the mechanism used by the in vitro evolved variants is also relevant in a clinical setting. Additionally, as indicated by a phylogenetic analysis, it appears that Cfr did not diverge from the RlmN family but from another distinct family of predicted radical SAM methylating enzymes whose function remains unknown. PMID:27496281

  9. Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long-chain 2-hydroxy acid oxidases.

    PubMed

    Esser, Christian; Kuhn, Anke; Groth, Georg; Lercher, Martin J; Maurino, Veronica G

    2014-05-01

    Glycolate oxidase (GOX) is a crucial enzyme of plant photorespiration. The encoding gene is thought to have originated from endosymbiotic gene transfer between the eukaryotic host and the cyanobacterial endosymbiont at the base of plantae. However, animals also possess GOX activities. Plant and animal GOX belong to the gene family of (L)-2-hydroxyacid-oxidases ((L)-2-HAOX). We find that all (L)-2-HAOX proteins in animals and archaeplastida go back to one ancestral eukaryotic sequence; the sole exceptions are green algae of the chlorophyta lineage. Chlorophyta replaced the ancestral eukaryotic (L)-2-HAOX with a bacterial ortholog, a lactate oxidase that may have been obtained through the primary endosymbiosis at the base of plantae; independent losses of this gene may explain its absence in other algal lineages (glaucophyta, rhodophyta, and charophyta). We also show that in addition to GOX, plants possess (L)-2-HAOX proteins with different specificities for medium- and long-chain hydroxyacids (lHAOX), likely involved in fatty acid and protein catabolism. Vertebrates possess lHAOX proteins acting on similar substrates as plant lHAOX; however, the existence of GOX and lHAOX subfamilies in both plants and animals is not due to shared ancestry but is the result of convergent evolution in the two most complex eukaryotic lineages. On the basis of targeting sequences and predicted substrate specificities, we conclude that the biological role of plantae (L)-2-HAOX in photorespiration evolved by co-opting an existing peroxisomal protein.

  10. Molecular dynamics explorations of active site structure in designed and evolved enzymes.

    PubMed

    Osuna, Sílvia; Jiménez-Osés, Gonzalo; Noey, Elizabeth L; Houk, K N

    2015-04-21

    This Account describes the use of molecular dynamics (MD) simulations to reveal how mutations alter the structure and organization of enzyme active sites. As proposed by Pauling about 70 years ago and elaborated by many others since then, biocatalysis is efficient when functional groups in the active site of an enzyme are in optimal positions for transition state stabilization. Changes in mechanism and covalent interactions are often critical parts of enzyme catalysis. We describe our explorations of the dynamical preorganization of active sites using MD, studying the fluctuations between active and inactive conformations normally concealed to static crystallography. MD shows how the various arrangements of active site residues influence the free energy of the transition state and relates the populations of the catalytic conformational ensemble to the enzyme activity. This Account is organized around three case studies from our laboratory. We first describe the importance of dynamics in evaluating a series of computationally designed and experimentally evolved enzymes for the Kemp elimination, a popular subject in the enzyme design field. We find that the dynamics of the active site is influenced not only by the original sequence design and subsequent mutations but also by the nature of the ligand present in the active site. In the second example, we show how microsecond MD has been used to uncover the role of remote mutations in the active site dynamics and catalysis of a transesterase, LovD. This enzyme was evolved by Tang at UCLA and Codexis, Inc., and is a useful commercial catalyst for the production of the drug simvastatin. X-ray analysis of inactive and active mutants did not reveal differences in the active sites, but relatively long time scale MD in solution showed that the active site of the wild-type enzyme preorganizes only upon binding of the acyl carrier protein (ACP) that delivers the natural acyl group to the active site. In the absence of bound ACP

  11. Directed evolution to re-adapt a co-evolved network within an enzyme.

    PubMed

    Strafford, John; Payongsri, Panwajee; Hibbert, Edward G; Morris, Phattaraporn; Batth, Sukhjeet S; Steadman, David; Smith, Mark E B; Ward, John M; Hailes, Helen C; Dalby, Paul A

    2012-01-01

    We have previously used targeted active-site saturation mutagenesis to identify a number of transketolase single mutants that improved activity towards either glycolaldehyde (GA), or the non-natural substrate propionaldehyde (PA). Here, all attempts to recombine the singles into double mutants led to unexpected losses of specific activity towards both substrates. A typical trade-off occurred between soluble expression levels and specific activity for all single mutants, but many double mutants decreased both properties more severely suggesting a critical loss of protein stability or native folding. Statistical coupling analysis (SCA) of a large multiple sequence alignment revealed a network of nine co-evolved residues that affected all but one double mutant. Such networks maintain important functional properties such as activity, specificity, folding, stability, and solubility and may be rapidly disrupted by introducing one or more non-naturally occurring mutations. To identify variants of this network that would accept and improve upon our best D469 mutants for activity towards PA, we created a library of random single, double and triple mutants across seven of the co-evolved residues, combining our D469 variants with only naturally occurring mutations at the remaining sites. A triple mutant cluster at D469, E498 and R520 was found to behave synergistically for the specific activity towards PA. Protein expression was severely reduced by E498D and improved by R520Q, yet variants containing both mutations led to improved specific activity and enzyme expression, but with loss of solubility and the formation of inclusion bodies. D469S and R520Q combined synergistically to improve k(cat) 20-fold for PA, more than for any previous transketolase mutant. R520Q also doubled the specific activity of the previously identified D469T to create our most active transketolase mutant to date. Our results show that recombining active-site mutants obtained by saturation mutagenesis

  12. Chemiluminescence-based pesticide biosensor utilizing the intelligent evolved properties of the enzyme alkaline phosphatase

    SciTech Connect

    Ayyagari, M.; Kamtekar, S.; Pande, R.; Marx, K.; Kumar, J.

    1994-12-31

    A methodology is described for immobilizing the enzyme alkaline phosphatase onto a glass surface using a novel biotinylated copolymer, poly(3-undecylthiophene-co-3- methanoithiophene). A streptavidin conjugate of alkaline phosphatase is used in this study. The biotinylated polymer is attached to the silanized glass surface via hydrophobic interactions and the enzyme is interfaced with the polymer through the classical biotin- streptavidin interaction. Alkaline phosphatase catalyzes the dephosphorylation of a macrocyclic compound, chloro-3-(4-methoxy spiro) (1,2 dioxetane-3-2`-tricyclo-) (3.3.1.1 )-(decani-4-yl) phenyl phosphate, to a species which emits energy by chemiluminescence. This chemiluminescence signal can be detected with a photomultiplier tube for enzymatic catalysis with the biocatalyst both in solution and immobilized on a glass surface. The signal generation is inhibited by the organophosphorus based insecticides such as paraoxon as well as nerve agents. We demonstrate in this study that a number of organophosphorus based insecticides inhibit the enzyme-mediated generation of chemiluminescence signal. This is true for the enzyme conjugate both free in solution and immobilized on a glass surface. In solution, the inhibition resembles the case of a partially uncompetitive system. By this type of inhibition we are able to detect pesticides down to about 50 ppb for the enzyme in solution. The pesticide detection limit of immobilized enzyme is currently being investigated. The enzyme is capable of a number of measurement cycles without significant loss of signal level.

  13. Biosynthetic Ca2+/Sr2+ exchange in the photosystem II oxygen-evolving enzyme of Thermosynechococcus elongatus.

    PubMed

    Boussac, Alain; Rappaport, Fabrice; Carrier, Patrick; Verbavatz, Jean-Marc; Gobin, Renée; Kirilovsky, Diana; Rutherford, A William; Sugiura, Miwa

    2004-05-28

    The thermophilic cyanobacterium, Thermosynechococcus elongatus, has been grown in the presence of Sr2+ instead of Ca2+ with the aim of biosynthetically replacing the Ca2+ of the oxygen-evolving enzyme with Sr2+. Not only were the cells able to grow normally with Sr2+, they actively accumulated the ion to levels higher than those of Ca2+ in the normal cultures. A protocol was developed to purify a fully active Sr(2+)-containing photosystem II (PSII). The modified enzyme contained a normal polypeptide profile and 1 strontium/4 manganese, indicating that the normal enzyme contains 1 calcium/4 manganese. The Sr(2+)- and Ca(2+)-containing enzymes were compared using EPR spectroscopy, UV-visible absorption spectroscopy, and O2 polarography. The Ca2+/Sr2+ exchange resulted in the modification of the EPR spectrum of the manganese cluster and a slower turnover of the redox cycle (the so-called S-state cycle), resulting in diminished O2 evolution activity under continuous saturating light: all features reported previously by biochemical Ca2+/Sr2+ exchange in plant PSII. This allays doubts that these changes could be because of secondary effects induced by the biochemical treatments themselves. In addition, the Sr(2+)-containing PSII has other kinetics modifications: 1) it has an increased stability of the S3 redox state; 2) it shows an increase in the rate of electron donation from TyrD, the redox-active tyrosine of the D2 protein, to the oxygen-evolving complex in the S3-state forming S2; 3) the rate of oxidation of the S0-state to the S1-state by TyrD* is increased; and 4) the release of O2 is slowed down to an extent similar to that seen for the slowdown of the S3TyrZ* to S0TyrZ transition, consistent with the latter constituting the limiting step of the water oxidation mechanism in Sr(2+)-substituted enzyme as well as in the normal enzyme. The replacement of Ca2+ by Sr2+ appears to have multiple effects on kinetics properties of the enzyme that may be explained by S

  14. Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae.

    PubMed

    Lee, Sun-Mi; Jellison, Taylor; Alper, Hal S

    2016-03-01

    Bioprospecting is an effective way to find novel enzymes from strains with desirable phenotypes. Such bioprospecting has enabled organisms such as Saccharomyces cerevisiae to utilize nonnative pentose sugars. Yet, the efficiency of this pentose catabolism (especially for the case of arabinose) remains suboptimal. Thus, further pathway optimization or identification of novel, optimal pathways is needed. Previously, we identified a novel set of xylan catabolic pathway enzymes from a superior pentose-utilizing strain of Ustilago bevomyces. These enzymes were used to successfully engineer a xylan-utilizing S. cerevisiae through a blended approach of bioprospecting and evolutionary engineering. Here, we expanded this approach to xylose and arabinose catabolic pathway engineering and demonstrated that bioprospected xylose and arabinose catabolic pathways from U. bevomyces offer alternative choices for enabling efficient pentose catabolism in S. cerevisiae. By introducing a novel set of xylose catabolic genes from U. bevomyces, growth rates were improved up to 85 % over a set of traditional Scheffersomyces stipitis pathway genes. In addition, we suggested an alternative arabinose catabolic pathway which, after directed evolution and pathway engineering, enabled S. cerevisiae to grow on arabinose as a sole carbon source in minimal medium with growth rates upwards of 0.05 h(-1). This pathway represents the most efficient growth of yeast on pure arabinose minimal medium. These pathways provide great starting points for further strain development and demonstrate the utility of bioprospecting from U. bevomyces.

  15. Lipid peroxidation and antioxidant enzymes activity in Plasmodium vivax malaria patients evolving with cholestatic jaundice

    PubMed Central

    2013-01-01

    Background Plasmodium vivax infection has been considered a benign and self-limiting disease, however, recent studies highlight the association between vivax malaria and life-threatening manifestations. Increase in reactive oxygen species has already been described in vivax malaria, as a result of the increased metabolic rate triggered by the multiplying parasite, and large quantities of toxic redox-active byproducts generated. The present study aimed to study the oxidative stress responses in patients infected with P. vivax, who developed jaundice (hyperbilirubinaemia) in the course of the disease, a common clinical complication related to this species. Methods An evaluation of the lipid peroxidation and antioxidant enzymes profile was performed in 28 healthy individuals and compared with P. vivax infected patients with jaundice, i.e., bilirubin < 51.3 μmol/L (8 patients) or without jaundice (34 patients), on day 1 (D1) and day 14 (D14) after anti-malarial therapy. Results Hyperbilirubinaemia was more frequent among women and patients experiencing their first malarial infection, and lower haemoglobin and higher lactate dehydrogenase levels were observed in this group. Malondialdehyde levels and activity of celuroplasmin and glutathione reductase were increased in the plasma from patients with P. vivax with jaundice compared to the control group on D1. However, the activity of thioredoxin reductase was decreased. The enzymes glutathione reductase, thioredoxin reductase, thiols and malondialdehyde also differed between jaundiced versus non-jaundiced patients. On D14 jaundice and parasitaemia had resolved and oxidative stress biomarkers were very similar to the control group. Conclusion Cholestatic hyperbilirubinaemia in vivax malaria cannot be totally disassociated from malaria-related haemolysis. However, significant increase of lipid peroxidation markers and changes in antioxidant enzymes in patients with P. vivax-related jaundice was observed. These results

  16. Biosynthetic exchange of bromide for chloride and strontium for calcium in the photosystem II oxygen-evolving enzymes.

    PubMed

    Ishida, Naoko; Sugiura, Miwa; Rappaport, Fabrice; Lai, Thanh-Lan; Rutherford, A William; Boussac, Alain

    2008-05-09

    The active site for water oxidation in photosystem II goes through five sequential oxidation states (S(0) to S(4)) before O(2) is evolved. It consists of a Mn(4)Ca cluster close to a redox-active tyrosine residue (Tyr(Z)). Cl(-) is also required for enzyme activity. To study the role of Ca(2+) and Cl(-) in PSII, these ions were biosynthetically substituted by Sr(2+) and Br(-), respectively, in the thermophilic cyanobacterium Thermosynechococcus elongatus. Irrespective of the combination of the non-native ions used (Ca/Br, Sr/Cl, Sr/Br), the enzyme could be isolated in a state that was fully intact but kinetically limited. The electron transfer steps affected by the exchanges were identified and then investigated by using time-resolved UV-visible absorption spectroscopy, time-resolved O(2) polarography, and thermoluminescence spectroscopy. The effect of the Ca(2+)/Sr(2+) and Cl(-)/Br(-) exchanges was additive, and the magnitude of the effect varied in the following order: Ca/Cl < Ca/Br < Sr/Cl < Sr/Br. In all cases, the rate of O(2) release was similar to that of the S(3)Tyr(Z)(.) to S(0)Tyr(Z) transition, with the slowest kinetics (i.e. the Sr/Br enzyme) being approximately 6-7 slower than in the native Ca/Cl enzyme. This slowdown in the kinetics was reflected in a decrease in the free energy level of the S(3) state as manifest by thermoluminescence. These observations indicate that Cl(-) is involved in the water oxidation mechanism. The possibility that Cl(-) is close to the active site is discussed in terms of recent structural models.

  17. Enzyme

    MedlinePlus

    Enzymes are complex proteins that cause a specific chemical change in all parts of the body. For ... use them. Blood clotting is another example of enzymes at work. Enzymes are needed for all body ...

  18. Toward mechanistic classification of enzyme functions.

    PubMed

    Almonacid, Daniel E; Babbitt, Patricia C

    2011-06-01

    Classification of enzyme function should be quantitative, computationally accessible, and informed by sequences and structures to enable use of genomic information for functional inference and other applications. Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often converge to similar mechanisms too, suggesting that reaction mechanisms could be used to develop finer-grained functional descriptions than provided by the Enzyme Commission (EC) system currently in use. Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic similarities. Together, these provide a foundation for new classifications of enzyme function.

  19. C(4) photosynthesis: convergence upon convergence upon...

    PubMed

    Roalson, Eric H

    2007-09-04

    C(4) photosynthesis has evolved independently numerous times in plants. New work suggests that these multiple origins are the result of recurring selection on a few amino acid positions in the key enzyme phosphoenolpyruvate carboxylase.

  20. Convergent evidences from human and animal studies implicate angiotensin I-converting enzyme activity in cognitive performance in schizophrenia

    PubMed Central

    Gadelha, A; Vendramini, A M; Yonamine, C M; Nering, M; Berberian, A; Suiama, M A; Oliveira, V; Lima-Landman, M T; Breen, G; Bressan, R A; Abílio, V; Hayashi, M A F

    2015-01-01

    In schizophrenia (SCZ), higher angiotensin I-converting enzyme (ACE) levels have been reported in patient's blood and cerebrospinal fluid (CSF). Hereby, we propose to explore whether the ACE activity levels are associated to cognitive performance in SCZ. Seventy-two patients with SCZ or schizoaffective disorder diagnosis, and 69 healthy controls (HCs) underwent a cognitive battery with parallel collection of peripheral blood samples to measure ACE activity. Significant higher ACE activity levels were confirmed in the plasma of SCZ patients compared with HCs (Student's t=−5.216; P<0.001). ACE activity significantly correlated to Hopkins delayed recall measures (r=−0.247; P=0.004) and Hopkins total (r=−0.214; P=0.012). Subjects grouped as high ACE activity (above average) had worse performance compared with low ACE activity level group for Hopkins delayed recall measure, even after correction for clinical condition, age, gender and years of education (P=0.029). The adjusted R squared for this final model was 0.343. This result was evident only comparing extreme groups for ACE activity, when splitting the sample in three groups with similar number of subjects. To clarify this finding, we performed an evaluation of the cognitive performance of transgenic mice with three copies of ACE gene in novel object recognition (NOR) test, which showed that such animals presented impairment in NOR (P<0.05) compared with two copies of wild-type animals. The results observed in SCZ patients and animal model suggest both the association of ACE to cognitive deficits in SCZ. This finding may support the evaluation of novel treatment protocols and/or of innovative drugs for specific intervention of cognitive deficits in SCZ envisioning concomitant ACE activity and behavior evaluations. PMID:26645626

  1. Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

    PubMed Central

    2016-01-01

    Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the kcat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates. PMID:28026940

  2. Convergent evolution in plant specialized metabolism.

    PubMed

    Pichersky, Eran; Lewinsohn, Efraim

    2011-01-01

    Plants synthesize a multitude of compounds that contribute to adaptation to their ecological niches. Such compounds serve as attractants of other living organisms beneficial to the plants or as defense against other biotic as well as abiotic agents. Selection for increased fitness, a never-ending process, has resulted in each plant lineage synthesizing a distinct set of specialized metabolites appropriate for its environment. The total number of specialized metabolites found in the plant kingdom far exceeds the capacity of any one plant genome to encode the necessary enzymes, and just as a plant lineage acquires the ability to make new specialized compounds during evolution, it also loses the ability to make others. Although the ability of plants to make novel, specialized metabolites continues to evolve, there are also many examples in which different plants have independently evolved the ability to make compounds already present in other plant lineages or to make different compounds that fulfill the same role-both are examples of convergent evolution. Here, we discuss many examples of convergent evolution in specialized metabolism. There are many genetic and biochemical mechanisms that can give rise to convergent evolution, and we conclude that, overall, convergent evolution in plant specialized metabolism is surprisingly common.

  3. Convergence Insufficiency

    MedlinePlus

    ... report of improvement in symptoms. What is the method of treatment for convergence insufficiency? Convergence insufficiency can ... be brought in to the office visit. Which method of treatment will be used for an individual ...

  4. Convergence, adaptation, and constraint.

    PubMed

    Losos, Jonathan B

    2011-07-01

    Convergent evolution of similar phenotypic features in similar environmental contexts has long been taken as evidence of adaptation. Nonetheless, recent conceptual and empirical developments in many fields have led to a proliferation of ideas about the relationship between convergence and adaptation. Despite criticism from some systematically minded biologists, I reaffirm that convergence in taxa occupying similar selective environments often is the result of natural selection. However, convergent evolution of a trait in a particular environment can occur for reasons other than selection on that trait in that environment, and species can respond to similar selective pressures by evolving nonconvergent adaptations. For these reasons, studies of convergence should be coupled with other methods-such as direct measurements of selection or investigations of the functional correlates of trait evolution-to test hypotheses of adaptation. The independent acquisition of similar phenotypes by the same genetic or developmental pathway has been suggested as evidence of constraints on adaptation, a view widely repeated as genomic studies have documented phenotypic convergence resulting from change in the same genes, sometimes even by the same mutation. Contrary to some claims, convergence by changes in the same genes is not necessarily evidence of constraint, but rather suggests hypotheses that can test the relative roles of constraint and selection in directing phenotypic evolution. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

  5. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products1[OPEN

    PubMed Central

    Yuen, Macaire M.S.; Bohlmann, Jörg

    2016-01-01

    Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I–IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes. PMID:26936895

  6. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products.

    PubMed

    Geisler, Katrin; Jensen, Niels Berg; Yuen, Macaire M S; Madilao, Lina; Bohlmann, Jörg

    2016-05-01

    Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I-IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes. © 2016 American Society of Plant Biologists. All Rights Reserved.

  7. Giant lobelias exemplify convergent evolution.

    PubMed

    Givnish, Thomas J

    2010-01-14

    Giant lobeliads on tropical mountains in East Africa and Hawaii have highly unusual, giant-rosette growth forms that appear to be convergent on each other and on those of several independently evolved groups of Asteraceae and other families. A recent phylogenetic analysis by Antonelli, based on sequencing the widest selection of lobeliads to date, raises doubts about this paradigmatic example of convergent evolution. Here I address the kinds of evidence needed to test for convergent evolution and argue that the analysis by Antonelli fails on four points. Antonelli's analysis makes several important contributions to our understanding of lobeliad evolution and geographic spread, but his claim regarding convergence appears to be invalid. Giant lobeliads in Hawaii and Africa represent paradigmatic examples of convergent evolution.

  8. Convergence and the multidimensional niche.

    PubMed

    Harmon, Luke J; Kolbe, Jason J; Cheverud, James M; Losos, Jonathan B

    2005-02-01

    Convergent evolution has played an important role in the development of the ecological niche concept. We investigated patterns of convergent and divergent evolution of Caribbean Anolis lizards. These lizards diversified independently on each of the islands of the Greater Antilles, producing the same set of habitat specialists on each island. Using a phylogenetic comparative framework, we examined patterns of morphological convergence in five functionally distinct sets of morphological characters: body size, body shape, head shape, lamella number, and sexual size dimorphism. We find evidence for convergence among members of the habitat specialist types for each of these five datasets. Furthermore, the patterns of convergence differ among at least four of the five datasets; habitat specialists that are similar for one set of characters are often greatly different for another. This suggests that the habitat specialist niches into which these anoles have evolved are multidimensional, involving several distinct and independent aspects of morphology.

  9. Giant lobelias exemplify convergent evolution

    PubMed Central

    2010-01-01

    Giant lobeliads on tropical mountains in East Africa and Hawaii have highly unusual, giant-rosette growth forms that appear to be convergent on each other and on those of several independently evolved groups of Asteraceae and other families. A recent phylogenetic analysis by Antonelli, based on sequencing the widest selection of lobeliads to date, raises doubts about this paradigmatic example of convergent evolution. Here I address the kinds of evidence needed to test for convergent evolution and argue that the analysis by Antonelli fails on four points. Antonelli's analysis makes several important contributions to our understanding of lobeliad evolution and geographic spread, but his claim regarding convergence appears to be invalid. Giant lobeliads in Hawaii and Africa represent paradigmatic examples of convergent evolution. PMID:20074322

  10. Adenine phosphoribosyltransferase from Sulfolobus solfataricus is an enzyme with unusual kinetic properties and a crystal structure that suggests it evolved from a 6-oxopurine phosphoribosyltransferase.

    PubMed

    Jensen, Kaj Frank; Hansen, Michael Riis; Jensen, Kristine Steen; Christoffersen, Stig; Poulsen, Jens-Christian Navarro; Mølgaard, Anne; Kadziola, Anders

    2015-04-14

    The adenine phosphoribosyltransferase (APRTase) encoded by the open reading frame SSO2342 of Sulfolobus solfataricus P2 was subjected to crystallographic, kinetic, and ligand binding analyses. The enzyme forms dimers in solution and in the crystals, and binds one molecule of the reactants 5-phosphoribosyl-α-1-pyrophosphate (PRPP) and adenine or the product adenosine monophosphate (AMP) or the inhibitor adenosine diphosphate (ADP) in each active site. The individual subunit adopts an overall structure that resembles a 6-oxopurine phosphoribosyltransferase (PRTase) more than known APRTases implying that APRT functionality in Crenarchaeotae has its evolutionary origin in this family of PRTases. Only the N-terminal two-thirds of the polypeptide chain folds as a traditional type I PRTase with a five-stranded β-sheet surrounded by helices. The C-terminal third adopts an unusual three-helix bundle structure that together with the nucleobase-binding loop undergoes a conformational change upon binding of adenine and phosphate resulting in a slight contraction of the active site. The inhibitor ADP binds like the product AMP with both the α- and β-phosphates occupying the 5'-phosphoribosyl binding site. The enzyme shows activity over a wide pH range, and the kinetic and ligand binding properties depend on both pH and the presence/absence of phosphate in the buffers. A slow hydrolysis of PRPP to ribose 5-phosphate and pyrophosphate, catalyzed by the enzyme, may be facilitated by elements in the C-terminal three-helix bundle part of the protein.

  11. Natural Variants of the KPC-2 Carbapenemase have Evolved Increased Catalytic Efficiency for Ceftazidime Hydrolysis at the Cost of Enzyme Stability

    PubMed Central

    Mehta, Shrenik C.; Rice, Kacie; Palzkill, Timothy

    2015-01-01

    The spread of β-lactamases that hydrolyze penicillins, cephalosporins and carbapenems among Gram-negative bacteria has limited options for treating bacterial infections. Initially, Klebsiella pneumoniae carbapenemase-2 (KPC-2) emerged as a widespread carbapenem hydrolyzing β-lactamase that also hydrolyzes penicillins and cephalosporins but not cephamycins and ceftazidime. In recent years, single and double amino acid substitution variants of KPC-2 have emerged among clinical isolates that show increased resistance to ceftazidime. Because it confers multi-drug resistance, KPC β-lactamase is a threat to public health. In this study, the evolution of KPC-2 function was determined in nine clinically isolated variants by examining the effects of the substitutions on enzyme kinetic parameters, protein stability and antibiotic resistance profile. The results indicate that the amino acid substitutions associated with KPC-2 natural variants lead to increased catalytic efficiency for ceftazidime hydrolysis and a consequent increase in ceftazidime resistance. Single substitutions lead to modest increases in catalytic activity while the double mutants exhibit significantly increased ceftazidime hydrolysis and resistance levels. The P104R, V240G and H274Y substitutions in single and double mutant combinations lead to the largest increases in ceftazidime hydrolysis and resistance. Molecular modeling suggests that the P104R and H274Y mutations could facilitate ceftazidime hydrolysis through increased hydrogen bonding interactions with the substrate while the V240G substitution may enhance backbone flexibility so that larger substrates might be accommodated in the active site. Additionally, we observed a strong correlation between gain of catalytic function for ceftazidime hydrolysis and loss of enzyme stability, which is in agreement with the ‘stability-function tradeoff’ phenomenon. The high Tm of KPC-2 (66.5°C) provides an evolutionary advantage as compared to other

  12. [Analysis of the Cochrane Review: Angiotensin Converging Enzyme Inhibitors Versus Angiotensin Receptor Blockers for Primary Hypertension. Cochrane Database Syst Rev. 2014,8: CD009096].

    PubMed

    Nogueira-Silva, Luís; Fonseca, João A

    2015-01-01

    Angiotensin converting enzyme inhibitors and angiotensin receptor blockers are first line drugs in the treatment of hypertension. The aim of this review was to assess if there are differences between these drug classes regarding the prevention of total mortality, occurrence of cardiovascular events and of adverse effects. A systematic review and metanalysis was performed, searching for studies that compare angiotensin converting enzyme inhibitors and angiotensin receptor blockers face-to-face, in several databases until July 2014. The study selection and data extraction were performed by 2 independent researchers. Nine studies were included, with a total of 10 963 participants, 9 398 of which participated in the same study and had high cardiovascular risk. No differences were observed regarding total mortality, cardiovascular mortality or total cardiovascular events. A slightly smaller risk was observed with angiotensin receptor blockers regarding withdrawal due to adverse effects (55 people were needed to be treated with angiotensin receptor blockers for 4.1 years to avoid one withdrawal due to adverse effect), mainly due to the occurrence of dry cough with angiotensin converting enzyme inhibitors. Thus, no differences were observed between angiotensin converting enzyme inhibitors and angiotensin receptor blockers in the prevention of total mortality and cardiovascular events, and angiotensin receptor blockers were better tolerated. Given the large proportion of participants with a high cardiovascular risk, the generalization of these results to other populations is limited.

  13. Convergent evolution of chromatin modification by structurally distinct enzymes: comparative enzymology of histone H3 Lys²⁷ methylation by human polycomb repressive complex 2 and vSET.

    PubMed

    Swalm, Brooke M; Hallenbeck, Kenneth K; Majer, Christina R; Jin, Lei; Scott, Margaret Porter; Moyer, Mikel P; Copeland, Robert A; Wigle, Tim J

    2013-07-15

    H3K27 (histone H3 Lys27) methylation is an important epigenetic modification that regulates gene transcription. In humans, EZH (enhancer of zeste homologue) 1 and EZH2 are the only enzymes capable of catalysing methylation of H3K27. There is great interest in understanding structure-function relationships for EZH2, as genetic alterations in this enzyme are thought to play a causal role in a number of human cancers. EZH2 is challenging to study because it is only active in the context of the multi-subunit PRC2 (polycomb repressive complex 2). vSET is a viral lysine methyltransferase that represents the smallest protein unit capable of catalysing H3K27 methylation. The crystal structure of this minimal catalytic protein has been solved and researchers have suggested that vSET might prove useful as an EZH2 surrogate for the development of active site-directed inhibitors. To test this proposition, we conducted comparative enzymatic analysis of human EZH2 and vSET and report that, although both enzymes share similar preferences for methylation of H3K27, they diverge in terms of their permissiveness for catalysing methylation of alternative histone lysine sites, their relative preferences for utilization of multimeric macromolecular substrates, their active site primary sequences and, most importantly, their sensitivity to inhibition by drug-like small molecules. The cumulative data led us to suggest that EZH2 and vSET have very distinct active site structures, despite the commonality of the reaction catalysed by the two enzymes. Hence, the EZH2 and vSET pair of enzymes represent an example of convergent evolution in which distinct structural solutions have developed to solve a common catalytic need.

  14. Convergent chaos

    NASA Astrophysics Data System (ADS)

    Pradas, Marc; Pumir, Alain; Huber, Greg; Wilkinson, Michael

    2017-07-01

    Chaos is widely understood as being a consequence of sensitive dependence upon initial conditions. This is the result of an instability in phase space, which separates trajectories exponentially. Here, we demonstrate that this criterion should be refined. Despite their overall intrinsic instability, trajectories may be very strongly convergent in phase space over extremely long periods, as revealed by our investigation of a simple chaotic system (a realistic model for small bodies in a turbulent flow). We establish that this strong convergence is a multi-facetted phenomenon, in which the clustering is intense, widespread and balanced by lacunarity of other regions. Power laws, indicative of scale-free features, characterize the distribution of particles in the system. We use large-deviation and extreme-value statistics to explain the effect. Our results show that the interpretation of the ‘butterfly effect’ needs to be carefully qualified. We argue that the combination of mixing and clustering processes makes our specific model relevant to understanding the evolution of simple organisms. Lastly, this notion of convergent chaos, which implies the existence of conditions for which uncertainties are unexpectedly small, may also be relevant to the valuation of insurance and futures contracts.

  15. Establishing the role of detoxifying enzymes in field-evolved resistance to various insecticides in the brown planthopper (Nilaparvata lugens) in South India.

    PubMed

    Malathi, Vijayakumar Maheshwari; Jalali, Sushil K; Gowda, Dandinashivara K Sidde; Mohan, Muthugounder; Venkatesan, Thiruvengadam

    2017-02-01

    The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the major pests of rice throughout Asia. Extensive use of insecticides for suppressing N. lugens has resulted in the development of insecticide resistance leading to frequent control failures in the field. The aim of the present study was to evaluate resistance in the field populations of N. lugens from major rice growing states of South India to various insecticides. We also determined the activity of detoxifying enzymes (esterases [ESTs], glutathione S-transferases [GSTs], and mixed-function oxidases [MFOs]). Moderate levels of resistance were detected in the field populations to acephate, thiamethoxam and buprofezin (resistance factors 1.05-20.92 fold, 4.52-14.99 fold, and 1.00-18.09 fold, respectively) as compared with susceptible strain while there were low levels of resistance to imidacloprid (resistance factor 1.23-6.70 fold) and complete sensitivity to etofenoprox (resistance factor 1.05-1.66 fold). EST activities in the field populations were 1.06 to 3.09 times higher than the susceptible strain while for GST and MFO the ratios varied from 1.29 to 3.41 and 1.03 to 1.76, respectively. The EST activity was found to be correlated to acephate resistance (r = 0.999, P ≥ 0.001). The high selection pressure of organophosphate, neonicotinoid, and insect growth regulator (IGR) in the field is likely to be contributing for resistance in BPH to multiple insecticides, leading to control failures. The results obtained will be beneficial to IPM recommendations for the use of effective insecticides against BPH. © 2015 Institute of Zoology, Chinese Academy of Sciences.

  16. Convergent Evolution of Polysaccharide Debranching Defines a Common Mechanism for Starch Accumulation in Cyanobacteria and Plants[W

    PubMed Central

    Cenci, Ugo; Chabi, Malika; Ducatez, Mathieu; Tirtiaux, Catherine; Nirmal-Raj, Jennifer; Utsumi, Yoshinori; Kobayashi, Daiki; Sasaki, Satoshi; Suzuki, Eiji; Nakamura, Yasunori; Putaux, Jean-Luc; Roussel, Xavier; Durand-Terrasson, Amandine; Bhattacharya, Debashish; Vercoutter-Edouart, Anne-Sophie; Maes, Emmanuel; Arias, Maria Cecilia; Palcic, Monica; Sim, Lyann; Ball, Steven G.; Colleoni, Christophe

    2013-01-01

    Starch, unlike hydrosoluble glycogen particles, aggregates into insoluble, semicrystalline granules. In photosynthetic eukaryotes, the transition to starch accumulation occurred after plastid endosymbiosis from a preexisting cytosolic host glycogen metabolism network. This involved the recruitment of a debranching enzyme of chlamydial pathogen origin. The latter is thought to be responsible for removing misplaced branches that would otherwise yield a water-soluble polysaccharide. We now report the implication of starch debranching enzyme in the aggregation of semicrystalline granules of single-cell cyanobacteria that accumulate both glycogen and starch-like polymers. We show that an enzyme of analogous nature to the plant debranching enzyme but of a different bacterial origin was recruited for the same purpose in these organisms. Remarkably, both the plant and cyanobacterial enzymes have evolved through convergent evolution, showing novel yet identical substrate specificities from a preexisting enzyme that originally displayed the much narrower substrate preferences required for glycogen catabolism. PMID:24163312

  17. Do convergent developmental mechanisms underlie convergent phenotypes?

    NASA Technical Reports Server (NTRS)

    Wray, Gregory A.

    2002-01-01

    Convergence is a pervasive evolutionary process, affecting many aspects of phenotype and even genotype. Relatively little is known about convergence in developmental processes, however, nor about the degree to which convergence in development underlies convergence in anatomy. A switch in the ecology of sea urchins from feeding to nonfeeding larvae illustrates how convergence in development can be associated with convergence in anatomy. Comparisons to more distantly related taxa, however, suggest that this association may be limited to relatively close phylogenetic comparisons. Similarities in gene expression during development provide another window into the association between convergence in developmental processes and convergence in anatomy. Several well-studied transcription factors exhibit likely cases of convergent gene expression in distantly related animal phyla. Convergence in regulatory gene expression domains is probably more common than generally acknowledged, and can arise for several different reasons. Copyright 2002 S. Karger AG, Basel.

  18. Do convergent developmental mechanisms underlie convergent phenotypes?

    NASA Technical Reports Server (NTRS)

    Wray, Gregory A.

    2002-01-01

    Convergence is a pervasive evolutionary process, affecting many aspects of phenotype and even genotype. Relatively little is known about convergence in developmental processes, however, nor about the degree to which convergence in development underlies convergence in anatomy. A switch in the ecology of sea urchins from feeding to nonfeeding larvae illustrates how convergence in development can be associated with convergence in anatomy. Comparisons to more distantly related taxa, however, suggest that this association may be limited to relatively close phylogenetic comparisons. Similarities in gene expression during development provide another window into the association between convergence in developmental processes and convergence in anatomy. Several well-studied transcription factors exhibit likely cases of convergent gene expression in distantly related animal phyla. Convergence in regulatory gene expression domains is probably more common than generally acknowledged, and can arise for several different reasons. Copyright 2002 S. Karger AG, Basel.

  19. Enzyme Informatics

    PubMed Central

    Alderson, Rosanna G.; Ferrari, Luna De; Mavridis, Lazaros; McDonagh, James L.; Mitchell, John B. O.; Nath, Neetika

    2012-01-01

    Over the last 50 years, sequencing, structural biology and bioinformatics have completely revolutionised biomolecular science, with millions of sequences and tens of thousands of three dimensional structures becoming available. The bioinformatics of enzymes is well served by, mostly free, online databases. BRENDA describes the chemistry, substrate specificity, kinetics, preparation and biological sources of enzymes, while KEGG is valuable for understanding enzymes and metabolic pathways. EzCatDB, SFLD and MACiE are key repositories for data on the chemical mechanisms by which enzymes operate. At the current rate of genome sequencing and manual annotation, human curation will never finish the functional annotation of the ever-expanding list of known enzymes. Hence there is an increasing need for automated annotation, though it is not yet widespread for enzyme data. In contrast, functional ontologies such as the Gene Ontology already profit from automation. Despite our growing understanding of enzyme structure and dynamics, we are only beginning to be able to design novel enzymes. One can now begin to trace the functional evolution of enzymes using phylogenetics. The ability of enzymes to perform secondary functions, albeit relatively inefficiently, gives clues as to how enzyme function evolves. Substrate promiscuity in enzymes is one example of imperfect specificity in protein-ligand interactions. Similarly, most drugs bind to more than one protein target. This may sometimes result in helpful polypharmacology as a drug modulates plural targets, but also often leads to adverse side-effects. Many cheminformatics approaches can be used to model the interactions between druglike molecules and proteins in silico. We can even use quantum chemical techniques like DFT and QM/MM to compute the structural and energetic course of enzyme catalysed chemical reaction mechanisms, including a full description of bond making and breaking. PMID:23116471

  20. Convergent evolution of the genomes of marine mammals

    PubMed Central

    Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret E.; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

    2015-01-01

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and are therefore a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and de novo assembled the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome, and that a subset were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that while convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare. PMID:25621460

  1. Convergent evolution of the genomes of marine mammals

    USGS Publications Warehouse

    Foote, Andrew D.; Liu, Yue; Thomas, Gregg W.C.; Vinař, Tomáš; Alföldi, Jessica; Deng, Jixin; Dugan, Shannon; van Elk, Cornelis E.; Hunter, Margaret; Joshi, Vandita; Khan, Ziad; Kovar, Christie; Lee, Sandra L.; Lindblad-Toh, Kerstin; Mancia, Annalaura; Nielsen, Rasmus; Qin, Xiang; Qu, Jiaxin; Raney, Brian J.; Vijay, Nagarjun; Wolf, Jochen B. W.; Hahn, Matthew W.; Muzny, Donna M.; Worley, Kim C.; Gilbert, M. Thomas P.; Gibbs, Richard A.

    2015-01-01

    Marine mammals from different mammalian orders share several phenotypic traits adapted to the aquatic environment and therefore represent a classic example of convergent evolution. To investigate convergent evolution at the genomic level, we sequenced and performed de novo assembly of the genomes of three species of marine mammals (the killer whale, walrus and manatee) from three mammalian orders that share independently evolved phenotypic adaptations to a marine existence. Our comparative genomic analyses found that convergent amino acid substitutions were widespread throughout the genome and that a subset of these substitutions were in genes evolving under positive selection and putatively associated with a marine phenotype. However, we found higher levels of convergent amino acid substitutions in a control set of terrestrial sister taxa to the marine mammals. Our results suggest that, whereas convergent molecular evolution is relatively common, adaptive molecular convergence linked to phenotypic convergence is comparatively rare.

  2. Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis.

    PubMed

    Xiang, Heng; Zhang, Ruizhi; Li, Nengzhang; Vossbrinck, Charles R

    2014-06-01

    There are numerous examples of convergent evolution in nature. Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? Manganese Superoxide Dismutase (MnSOD) is a manganesedependant metallo-enzyme which plays a crucial role in protecting cells from anti-oxidative stress by eliminating reactive (superoxide) oxygen species. It is a ubiquitous housekeeping enzyme found in nearly all organisms. In this study we compare phylogenies based on MnSOD protein sequences to those based on scores from Hydrophobic Cluster Analysis (HCA). We calculated HCA similarity values for each pair of taxa to obtain a pair-wise distance matrix. A UPGMA tree based on the HCA distance matrix and a common tree based on the primary protein sequence for MnSOD was constructed. Differences between these two trees within animals, enterobacteriaceae, planctomycetes and cyanobacteria are presented and cited as possible examples of convergence. We note that several residue changes result in changes in hydrophobicity at positions which apparently are under the effect of positive selection.

  3. Searching for convergent evolution in manganese superoxidase dismutase using hydrophobic cluster analysis

    PubMed Central

    Xiang, Heng; Zhang, Ruizhi; Li, Nengzhang; Vossbrinck, Charles R.

    2014-01-01

    There are numerous examples of convergent evolution in nature. Major ecological adaptations such as flight, loss of limbs in vertebrates, pesticide resistance, adaptation to a parasitic way of life, etc., have all evolved more than once, as seen by their analogous functions in separate taxa. But what about protein evolution? Does the environment have a strong enough influence on intracellular processes that enzymes and other functional proteins play, to evolve similar functional roles separately in different organisms? Manganese Superoxide Dismutase (MnSOD) is a manganesedependant metallo-enzyme which plays a crucial role in protecting cells from anti-oxidative stress by eliminating reactive (superoxide) oxygen species. It is a ubiquitous housekeeping enzyme found in nearly all organisms. In this study we compare phylogenies based on MnSOD protein sequences to those based on scores from Hydrophobic Cluster Analysis (HCA). We calculated HCA similarity values for each pair of taxa to obtain a pair-wise distance matrix. A UPGMA tree based on the HCA distance matrix and a common tree based on the primary protein sequence for MnSOD was constructed. Differences between these two trees within animals, enterobacteriaceae, planctomycetes and cyanobacteria are presented and cited as possible examples of convergence. We note that several residue changes result in changes in hydrophobicity at positions which apparently are under the effect of positive selection. PMID:25071412

  4. Compartments, Customers, or Convergence?: Evolving Challenges to IT Progress

    ERIC Educational Resources Information Center

    Jackson, Gregory A.

    2007-01-01

    For most of the past decade, IT leaders in higher education felt on top of things. Challenges were usually comprehensible and addressable, doing reasonable things yielded reasonable results, and for the most part, IT was a substantial contributor to institutional progress. But these days, IT leaders rarely feel on top of things. Instead, some days…

  5. Evolvable synthetic neural system

    NASA Technical Reports Server (NTRS)

    Curtis, Steven A. (Inventor)

    2009-01-01

    An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

  6. The Convergence of Intelligences

    NASA Astrophysics Data System (ADS)

    Diederich, Joachim

    Minsky (1985) argued an extraterrestrial intelligence may be similar to ours despite very different origins. ``Problem- solving'' offers evolutionary advantages and individuals who are part of a technical civilisation should have this capacity. On earth, the principles of problem-solving are the same for humans, some primates and machines based on Artificial Intelligence (AI) techniques. Intelligent systems use ``goals'' and ``sub-goals'' for problem-solving, with memories and representations of ``objects'' and ``sub-objects'' as well as knowledge of relations such as ``cause'' or ``difference.'' Some of these objects are generic and cannot easily be divided into parts. We must, therefore, assume that these objects and relations are universal, and a general property of intelligence. Minsky's arguments from 1985 are extended here. The last decade has seen the development of a general learning theory (``computational learning theory'' (CLT) or ``statistical learning theory'') which equally applies to humans, animals and machines. It is argued that basic learning laws will also apply to an evolved alien intelligence, and this includes limitations of what can be learned efficiently. An example from CLT is that the general learning problem for neural networks is intractable, i.e. it cannot be solved efficiently for all instances (it is ``NP-complete''). It is the objective of this paper to show that evolved intelligences will be constrained by general learning laws and will use task-decomposition for problem-solving. Since learning and problem-solving are core features of intelligence, it can be said that intelligences converge despite very different origins.

  7. The genes and enzymes for the catabolism of galactitol, D-tagatose, and related carbohydrates in Klebsiella oxytoca M5a1 and other enteric bacteria display convergent evolution.

    PubMed

    Shakeri-Garakani, A; Brinkkötter, A; Schmid, K; Turgut, S; Lengeler, J W

    2004-07-01

    Enteric bacteria (Enteriobacteriaceae) carry on their single chromosome about 4000 genes that all strains have in common (referred to here as "obligatory genes"), and up to 1300 "facultative" genes that vary from strain to strain and from species to species. In closely related species, obligatory and facultative genes are orthologous genes that are found at similar loci. We have analyzed a set of facultative genes involved in the degradation of the carbohydrates galactitol, D-tagatose, D-galactosamine and N-acetyl-galactosamine in various pathogenic and non-pathogenic strains of these bacteria. The four carbohydrates are transported into the cell by phosphotransferase (PTS) uptake systems, and are metabolized by closely related or even identical catabolic enzymes via pathways that share several intermediates. In about 60% of Escherichia coli strains the genes for galactitol degradation map to a gat operon at 46.8 min. In strains of Salmonella enterica, Klebsiella pneumoniae and K. oxytoca, the corresponding gat genes, although orthologous to their E. coli counterparts, are found at 70.7 min, clustered in a regulon together with three tag genes for the degradation of D-tagatose, an isomer of D-fructose. In contrast, in all the E. coli strains tested, this chromosomal site was found to be occupied by an aga/kba gene cluster for the degradation of D-galactosamine and N-acetyl-galactosamine. The aga/kba and the tag genes were paralogous either to the gat cluster or to the fru genes for degradation of D-fructose. Finally, in more then 90% of strains of both Klebsiella species, and in about 5% of the E. coli strains, two operons were found at 46.8 min that comprise paralogous genes for catabolism of the isomers D-arabinitol (genes atl or dal) and ribitol (genes rtl or rbt). In these strains gat genes were invariably absent from this location, and they were totally absent in S. enterica. These results strongly indicate that these various gene clusters and metabolic

  8. Lack of convergence in aquatic Anolis lizards.

    PubMed

    Leal, Manuel; Knox, Alison K; Losos, Jonathan B

    2002-04-01

    Why convergent evolution occurs among some species occupying similar habitats but not among others is a question that has received surprisingly little attention. Caribbean Anolis lizards, known for their extensive convergent evolution among islands in the Greater Antilles, are an appropriate group with which to address this question. Despite the well-documented pattern of between-island convergence, some Greater Antillean anoles are not obviously part of the convergence syndrome. One example involves aquatic anoles--species that are found near to and readily enter streams-which have evolved independently twice in the Caribbean and also twice on mainland Central America. Despite being found in similar habitats, no previous study has investigated whether aquatic anoles represent yet another case of morphological convergence. We tested this hypothesis by collecting morphological data for seven aquatic anole species and 29 species from the six convergent types of Greater Antillean habitat specialists. We failed to find evidence for morphological convergence: the two Caribbean aquatic species are greatly dissimilar to each other and to the Central American species, which, however, may be convergent upon each other. We suggest two possible reasons for this lack of convergence in an otherwise highly convergent system: either there is more than one habitat type occupied by anoles in the proximity of water, or there is more than one way to adapt to a single aquatic habitat. We estimate that almost all of the 113 species of Greater Antillean anoles occupy habitats that are also used by distantly related species, but only 15% of these species are not morphologically similar to their distantly related ecological counterparts. Comparative data from other taxa would help enlighten the question of why the extent of convergence is so great in some lineages and not in others.

  9. The definition, recognition, and interpretation of convergent evolution, and two new measures for quantifying and assessing the significance of convergence.

    PubMed

    Stayton, C Tristan

    2015-08-01

    Convergent evolution is an important phenomenon in the history of life. Despite this, there is no common definition of convergence used by biologists. Instead, several conceptually different definitions are employed. The primary dichotomy is between pattern-based definitions, where independently evolved similarity is sufficient for convergence, and process-based definitions, where convergence requires a certain process to produce this similarity. The unacknowledged diversity of definitions can lead to problems in evolutionary research. Process-based definitions may bias researchers away from studying or recognizing other sources of independently evolved similarity, or lead researchers to interpret convergent patterns as necessarily caused by a given process. Thus, pattern-based definitions are recommended. Existing measures of convergence are reviewed, and two new measures are developed. Both are pattern based and conceptually minimal, quantifying nothing but independently evolved similarity. One quantifies the amount of phenotypic distance between two lineages that is closed by subsequent evolution; the other simply counts the number of lineages entering a region of phenotypic space. The behavior of these measures is explored in simulations; both show acceptable Type I and Type II error. The study of convergent evolution will be facilitated if researchers are explicit about working definitions of convergence and adopt a standard toolbox of convergence measures.

  10. Gradual neofunctionalization in the convergent evolution of trichomonad lactate and malate dehydrogenases

    PubMed Central

    Steindel, Phillip A.; Chen, Emily H.; Wirth, Jacob D.

    2016-01-01

    Abstract Lactate and malate dehydrogenases (LDH and MDH) are homologous, core metabolic enzymes common to nearly all living organisms. LDHs have evolved convergently from MDHs at least four times, achieving altered substrate specificity by a different mechanism each time. For instance, the LDH of anaerobic trichomonad parasites recently evolved independently from an ancestral trichomonad MDH by gene duplication. LDH plays a central role in trichomonad metabolism by catalyzing the reduction of pyruvate to lactate, thereby regenerating the NAD+ required for glycolysis. Using ancestral reconstruction methods, we identified the biochemical and evolutionary mechanisms responsible for this convergent event. The last common ancestor of these enzymes was a highly specific MDH, similar to modern trichomonad MDHs. In contrast, the LDH lineage evolved promiscuous activity by relaxing specificity in a gradual process of neofunctionalization involving one highly detrimental substitution at the “specificity residue” (R91L) and many additional mutations of small effect. L91 has different functional consequences in LDHs and in MDHs, indicating a prominent role for epistasis. Crystal structures of modern‐day and ancestral enzymes show that the evolution of substrate specificity paralleled structural changes in dimerization and α‐helix orientation. The relatively small “specificity residue” of the trichomonad LDHs can accommodate a range of substrate sizes and may permit solvent to access the active site, both of which promote substrate promiscuity. The trichomonad LDHs present a multi‐faceted counterpoint to the independent evolution of LDHs in other organisms and illustrate the diverse mechanisms by which protein function, structure, and stability coevolve. PMID:26889885

  11. Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases.

    PubMed

    Michener, Joshua K; Nielsen, Jens; Smolke, Christina D

    2012-11-20

    Recent advances in metabolic engineering have demonstrated that microbial biosynthesis can provide a viable alternative to chemical synthesis for the production of bulk and fine chemicals. Introduction of a new biosynthetic pathway typically requires the expression of multiple heterologous enzymes in the production host, which can impose stress on the host cell and, thereby, limit performance of the pathway. Unfortunately, analysis and treatment of the host stress response can be difficult, because there are many sources of stress that may interact in complex ways. We use a systems biological approach to analyze the stress imposed by expressing different enzyme variants from a lineage of soluble P450 monooxygenases, previously evolved for heterologous activity in Saccharomyces cerevisiae. Our analysis identifies patterns of stress imposed on the host by heterologous enzyme overexpression that are consistent across the evolutionary lineage, ultimately implicating heme depletion as the major stress. We show that the monooxygenase evolution, starting from conditions of either high or low stress, caused the cellular stress to converge to a common level. Overexpression of rate-limiting enzymes in the endogenous heme biosynthetic pathway alleviates the stress imposed by expression of the P450 monooxygenases and increases the enzymatic activity of the final evolved P450 by an additional 2.3-fold. Heme overexpression also increases the total activity of an endogenous cytosolic heme-containing catalase but not a heterologous P450 that is membrane-associated. This work demonstrates the utility of combining systems and synthetic biology to analyze and optimize heterologous enzyme expression.

  12. Transport on randomly evolving trees

    NASA Astrophysics Data System (ADS)

    Pál, L.

    2005-11-01

    The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes, a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to nodes. It is assumed that at t=0 the tree consists of a single living node (root), from which the evolution may begin. At a certain time instant τ⩾0 , the root produces ν⩾0 living nodes connected by lines to the root which becomes dead at the moment of the offspring production. In the evolution process each of the new living nodes evolves further like a root independently of the others. By using the methods of the age-dependent branching processes we derive the joint distribution function of the numbers of living and dead nodes, and determine the correlation between these node numbers as a function of time. It is proved that the correlation function converges to 3/2 independently of the distributions of ν and τ when q1→1 and t→∞ . Also analyzed are the stochastic properties of the end nodes; and the correlation between the numbers of living and dead end nodes is shown to change its character suddenly at the very beginning of the evolution process. The survival probability of random trees is investigated and expressions are derived for this probability.

  13. Transport on randomly evolving trees.

    PubMed

    Pál, L

    2005-11-01

    The time process of transport on randomly evolving trees is investigated. By introducing the notions of living and dead nodes, a model of random tree evolution is constructed which describes the spreading in time of objects corresponding to nodes. It is assumed that at t=0 the tree consists of a single living node (root), from which the evolution may begin. At a certain time instant tau> or =0, the root produces v> or =0 living nodes connected by lines to the root which becomes dead at the moment of the offspring production. In the evolution process each of the new living nodes evolves further like a root independently of the others. By using the methods of the age-dependent branching processes we derive the joint distribution function of the numbers of living and dead nodes, and determine the correlation between these node numbers as a function of time. It is proved that the correlation function converges to square root of 3/2 independently of the distributions of v and tau when q1-->1 and t-->infinity. Also analyzed are the stochastic properties of the end nodes; and the correlation between the numbers of living and dead end nodes is shown to change its character suddenly at the very beginning of the evolution process. The survival probability of random trees is investigated and expressions are derived for this probability.

  14. Convergent designs for electrogenesis and electroreception.

    PubMed

    Hopkins, C D

    1995-12-01

    New- and old-world tropical electric fish lack a common electrical ancestor, suggesting that the mechanisms of signal generation and recognition evolved independently in the two groups. Recent research on convergent designs for electrogenesis and electroreception has focused on the structure of electric organs, the neural circuitry controlling the pacemaker driving the electric organ, and the neural circuitry underlying time coding of electric waveforms.

  15. Genomic medicine: evolving science, evolving ethics

    PubMed Central

    Soden, Sarah E; Farrow, Emily G; Saunders, Carol J; Lantos, John D

    2012-01-01

    Genomic medicine is rapidly evolving. Next-generation sequencing is changing the diagnostic paradigm by allowing genetic testing to be carried out more quickly, less expensively and with much higher resolution; pushing the envelope on existing moral norms and legal regulations. Early experience with implementation of next-generation sequencing to diagnose rare genetic conditions in symptomatic children suggests ways that genomic medicine might come to be used and some of the ethical issues that arise, impacting test design, patient selection, consent, sequencing analysis and communication of results. The ethical issues that arise from use of new technologies cannot be satisfactorily analyzed until they are understood and they cannot be understood until the technologies are deployed in the real world. PMID:23173007

  16. Nonaccommodative convergence excess.

    PubMed

    von Noorden, G K; Avilla, C W

    1986-01-15

    Nonaccommodative convergence excess is a condition in which a patient has orthotropia or a small-angle esophoria or esotropia at distance and a large-angle esotropia at near, not significantly reduced by the addition of spherical plus lenses. The AC/A ratio, determined with the gradient method, is normal or subnormal. Tonic convergence is suspected of causing the convergence excess in these patients. Nonaccommodative convergence excess must be distinguished from esotropia with a high AC/A ratio and from hypoaccommodative esotropia. In 24 patients treated with recession of both medial recti muscles with and without posterior fixation or by posterior fixation alone, the mean correction of esotropia was 7.4 prism diopters at distance and 17 prism diopters at near.

  17. Convergence of estuarine channels

    NASA Astrophysics Data System (ADS)

    Dronkers, Job

    2017-07-01

    Tide-dominated coastal plain estuaries have typically up-estuary convergent tidal channels. Analysis of estuarine characteristics indicates a dependence of the convergence length on relative tidal amplitude, relative intertidal area and river flow velocity. In order to explain these relationships we investigate a condition for continuity of net sediment transport throughout the estuary, corresponding to morphodynamic equilibrium. We show, by using an analytical solution of the tidal equations, that this condition is equivalent to a condition on the convergence length. This condition is evaluated for 21 estuaries in different regions of the world. It appears that the convergence length determined in this way can explain observed convergence lengths for the considered set of estuaries. The dependence of the convergence length on different estuarine characteristics is analysed by solving the fully coupled hydro-morphodynamic equations. We show that this dependence limits the range of variation of the tidal velocity amplitude. The analysis provides insight in the morphological response of estuaries to human interventions. The condition can easily be evaluated to yield an estimate of this response.

  18. Genome-wide signatures of convergent evolution in echolocating mammals.

    PubMed

    Parker, Joe; Tsagkogeorga, Georgia; Cotton, James A; Liu, Yuan; Provero, Paolo; Stupka, Elia; Rossiter, Stephen J

    2013-10-10

    Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes. However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures. Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution, although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized.

  19. Genome-wide signatures of convergent evolution in echolocating mammals

    PubMed Central

    Parker, Joe; Tsagkogeorga, Georgia; Cotton, James A.; Liu, Yuan; Provero, Paolo; Stupka, Elia; Rossiter, Stephen J.

    2013-01-01

    Evolution is typically thought to proceed through divergence of genes, proteins, and ultimately phenotypes1-3. However, similar traits might also evolve convergently in unrelated taxa due to similar selection pressures4,5. Adaptive phenotypic convergence is widespread in nature, and recent results from a handful of genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level6-9. Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution9,10 although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show for the first time that convergence is not a rare process restricted to a handful of loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four new bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Surprisingly we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognised. PMID:24005325

  20. Transhydrogenase Promotes the Robustness and Evolvability of E. coli Deficient in NADPH Production

    PubMed Central

    Chou, Hsin-Hung; Marx, Christopher J.; Sauer, Uwe

    2015-01-01

    Metabolic networks revolve around few metabolites recognized by diverse enzymes and involved in myriad reactions. Though hub metabolites are considered as stepping stones to facilitate the evolutionary expansion of biochemical pathways, changes in their production or consumption often impair cellular physiology through their system-wide connections. How does metabolism endure perturbations brought immediately by pathway modification and restore hub homeostasis in the long run? To address this question we studied laboratory evolution of pathway-engineered Escherichia coli that underproduces the redox cofactor NADPH on glucose. Literature suggests multiple possibilities to restore NADPH homeostasis. Surprisingly, genetic dissection of isolates from our twelve evolved populations revealed merely two solutions: (1) modulating the expression of membrane-bound transhydrogenase (mTH) in every population; (2) simultaneously consuming glucose with acetate, an unfavored byproduct normally excreted during glucose catabolism, in two subpopulations. Notably, mTH displays broad phylogenetic distribution and has also played a predominant role in laboratory evolution of Methylobacterium extorquens deficient in NADPH production. Convergent evolution of two phylogenetically and metabolically distinct species suggests mTH as a conserved buffering mechanism that promotes the robustness and evolvability of metabolism. Moreover, adaptive diversification via evolving dual substrate consumption highlights the flexibility of physiological systems to exploit ecological opportunities. PMID:25715029

  1. Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections.

    PubMed

    Traverse, Charles C; Mayo-Smith, Leslie M; Poltak, Steffen R; Cooper, Vaughn S

    2013-01-15

    How diversity evolves and persists in biofilms is essential for understanding much of microbial life, including the uncertain dynamics of chronic infections. We developed a biofilm model enabling long-term selection for daily adherence to and dispersal from a plastic bead in a test tube. Focusing on a pathogen of the cystic fibrosis lung, Burkholderia cenocepacia, we sequenced clones and metagenomes to unravel the mutations and evolutionary forces responsible for adaptation and diversification of a single biofilm community during 1,050 generations of selection. The mutational patterns revealed recurrent evolution of biofilm specialists from generalist types and multiple adaptive alleles at relatively few loci. Fitness assays also demonstrated strong interference competition among contending mutants that preserved genetic diversity. Metagenomes from five other independently evolved biofilm lineages revealed extraordinary mutational parallelism that outlined common routes of adaptation, a subset of which was found, surprisingly, in a planktonic population. These mutations in turn were surprisingly well represented among mutations that evolved in cystic fibrosis isolates of both Burkholderia and Pseudomonas. These convergent pathways included altered metabolism of cyclic diguanosine monophosphate, polysaccharide production, tricarboxylic acid cycle enzymes, global transcription, and iron scavenging. Evolution in chronic infections therefore may be driven by mutations in relatively few pathways also favored during laboratory selection, creating hope that experimental evolution may illuminate the ecology and selective dynamics of chronic infections and improve treatment strategies.

  2. An Evolving Astrobiology Glossary

    NASA Astrophysics Data System (ADS)

    Meech, K. J.; Dolci, W. W.

    2009-12-01

    One of the resources that evolved from the Bioastronomy 2007 meeting was an online interdisciplinary glossary of terms that might not be universally familiar to researchers in all sub-disciplines feeding into astrobiology. In order to facilitate comprehension of the presentations during the meeting, a database driven web tool for online glossary definitions was developed and participants were invited to contribute prior to the meeting. The glossary was downloaded and included in the conference registration materials for use at the meeting. The glossary web tool is has now been delivered to the NASA Astrobiology Institute so that it can continue to grow as an evolving resource for the astrobiology community.

  3. Multiscale modelling of evolving foams

    NASA Astrophysics Data System (ADS)

    Saye, R. I.; Sethian, J. A.

    2016-06-01

    We present a set of multi-scale interlinked algorithms to model the dynamics of evolving foams. These algorithms couple the key effects of macroscopic bubble rearrangement, thin film drainage, and membrane rupture. For each of the mechanisms, we construct consistent and accurate algorithms, and couple them together to work across the wide range of space and time scales that occur in foam dynamics. These algorithms include second order finite difference projection methods for computing incompressible fluid flow on the macroscale, second order finite element methods to solve thin film drainage equations in the lamellae and Plateau borders, multiphase Voronoi Implicit Interface Methods to track interconnected membrane boundaries and capture topological changes, and Lagrangian particle methods for conservative liquid redistribution during rearrangement and rupture. We derive a full set of numerical approximations that are coupled via interface jump conditions and flux boundary conditions, and show convergence for the individual mechanisms. We demonstrate our approach by computing a variety of foam dynamics, including coupled evolution of three-dimensional bubble clusters attached to an anchored membrane and collapse of a foam cluster.

  4. Contrasting patterns of adaptive sequence convergence among echolocating mammals.

    PubMed

    Lambert, Matthew J; Nevue, Alexander A; Portfors, Christine V

    2017-03-20

    Several recent studies have described genes demonstrating adaptive sequence convergence between echolocating bats and dolphin, suggesting that common selective pressures can induce common molecular changes, even in distantly related species. However, in the case of the auditory genes Otoferlin (Otof), Cadherin 23 (Cdh23) and Protocadherin 15 (Pcdh15), the reported sequence convergence was supported only by incongruent gene and species trees and counts of convergent substitutions. Therefore, it remains unclear whether echolocating bats and dolphin really do demonstrate evidence of adaptive sequence convergence, or whether there is simply a high level of random background convergence in these genes. To address this question, we estimated the number of convergent and divergent amino acid substitutions along all independent branches of a sufficiently deep phylogeny containing between 22 and 32 mammals for each gene, and compared convergence between the two proposed suborders of bat, Yangochiroptera and Yinpterochiroptera, and dolphin. We find no support for convergence between bats and dolphin in the gene Pcdh15. For the gene Otof we report minimal evidence for convergent evolution only between the Yinpterochiroptera and dolphin. Cdh23 displayed a high level of convergence between dolphin and the Yinpterochiroptera. In addition, dolphin and certain members of the Yangochiroptera that emit high frequency echolocation calls shared several unique convergent substitutions. These results indicate that the convergent evolution of Cdh23 was likely driven by selection for hearing above a certain frequency threshold. Moreover, the contrasting patterns of convergence between the two bat suborders and dolphin in all auditory genes studied thus far suggest echolocation may have evolved independently in the Yinpterochiroptera and Yangochiroptera.

  5. Evolution of Enzyme Kinetic Mechanisms.

    PubMed

    Ulusu, Nuriye Nuray

    2015-06-01

    This review paper discusses the reciprocal kinetic behaviours of enzymes and the evolution of structure-function dichotomy. Kinetic mechanisms have evolved in response to alterations in ecological and metabolic conditions. The kinetic mechanisms of single-substrate mono-substrate enzyme reactions are easier to understand and much simpler than those of bi-bi substrate enzyme reactions. The increasing complexities of kinetic mechanisms, as well as the increasing number of enzyme subunits, can be used to shed light on the evolution of kinetic mechanisms. Enzymes with heterogeneous kinetic mechanisms attempt to achieve specific products to subsist. In many organisms, kinetic mechanisms have evolved to aid survival in response to changing environmental factors. Enzyme promiscuity is defined as adaptation to changing environmental conditions, such as the introduction of a toxin or a new carbon source. Enzyme promiscuity is defined as adaptation to changing environmental conditions, such as the introduction of a toxin or a new carbon source. Enzymes with broad substrate specificity and promiscuous properties are believed to be more evolved than single-substrate enzymes. This group of enzymes can adapt to changing environmental substrate conditions and adjust catalysing mechanisms according to the substrate's properties, and their kinetic mechanisms have evolved in response to substrate variability.

  6. Multicopy Suppression Underpins Metabolic Evolvability

    PubMed Central

    Patrick, Wayne M.; Quandt, Erik M.; Swartzlander, Dan B.; Matsumura, Ichiro

    2009-01-01

    Our understanding of the origins of new metabolic functions is based upon anecdotal genetic and biochemical evidence. Some auxotrophies can be suppressed by overexpressing substrate-ambiguous enzymes (i.e., those that catalyze the same chemical transformation on different substrates). Other enzymes exhibit weak but detectable catalytic promiscuity in vitro (i.e., they catalyze different transformations on similar substrates). Cells adapt to novel environments through the evolution of these secondary activities, but neither their chemical natures nor their frequencies of occurrence have been characterized en bloc. Here, we systematically identified multifunctional genes within the Escherichia coli genome. We screened 104 single-gene knockout strains and discovered that many (20%) of these auxotrophs were rescued by the overexpression of at least one noncognate E. coli gene. The deleted gene and its suppressor were generally unrelated, suggesting that promiscuity is a product of contingency. This genome-wide survey demonstrates that multifunctional genes are common and illustrates the mechanistic diversity by which their products enhance metabolic robustness and evolvability. PMID:17884825

  7. Methods Evolved by Observation

    ERIC Educational Resources Information Center

    Montessori, Maria

    2016-01-01

    Montessori's idea of the child's nature and the teacher's perceptiveness begins with amazing simplicity, and when she speaks of "methods evolved," she is unveiling a methodological system for observation. She begins with the early childhood explosion into writing, which is a familiar child phenomenon that Montessori has written about…

  8. IS THERE CONVERGENCE ACROSS COUNTRIES? A SPATIAL APPROACH

    PubMed Central

    Berry, Heather; Guillen, Mauro F.; Hendi, Arun S.

    2014-01-01

    We analyze convergence across countries over the last half century as a result of globalizing forces. Drawing on theories of modernization, dependency, the world-system, political trade blocs, and the world-society, we consider economic, demographic, knowledge, financial, and political dimensions of convergence. Using a new methodology, we calculate the minimum volume ellipsoid encompassing different groupings of countries, finding that during the 1960–2009 period, countries have not evolved significantly closer or similar to one another, although groups of countries based on their core-periphery status or membership in trade blocs exhibit increasing internal convergence and divergence between one another. PMID:25580035

  9. Convergent evolution within an adaptive radiation of cichlid fishes.

    PubMed

    Muschick, Moritz; Indermaur, Adrian; Salzburger, Walter

    2012-12-18

    The recurrent evolution of convergent forms is a widespread phenomenon in adaptive radiations (e.g., [1-9]). For example, similar ecotypes of anoles lizards have evolved on different islands of the Caribbean, benthic-limnetic species pairs of stickleback fish emerged repeatedly in postglacial lakes, equivalent sets of spider ecomorphs have arisen on Hawaiian islands, and a whole set of convergent species pairs of cichlid fishes evolved in East African Lakes Malawi and Tanganyika. In all these cases, convergent phenotypes originated in geographic isolation from each other. Recent theoretical models, however, predict that convergence should be common within species-rich communities, such as species assemblages resulting from adaptive radiations. Here, we present the most extensive quantitative analysis to date of an adaptive radiation of cichlid fishes, discovering multiple instances of convergence in body and trophic morphology. Moreover, we show that convergent morphologies are associated with adaptations to specific habitats and resources and that Lake Tanganyika's cichlid communities are characterized by the sympatric occurrence of convergent forms. This prevalent coexistence of distantly related yet ecomorphologically similar species offers an explanation for the greatly elevated species numbers in cichlid species flocks. Copyright © 2012 Elsevier Ltd. All rights reserved.

  10. Self-regulating and self-evolving particle swarm optimizer

    NASA Astrophysics Data System (ADS)

    Wang, Hui-Min; Qiao, Zhao-Wei; Xia, Chang-Liang; Li, Liang-Yu

    2015-01-01

    In this article, a novel self-regulating and self-evolving particle swarm optimizer (SSPSO) is proposed. Learning from the idea of direction reversal, self-regulating behaviour is a modified position update rule for particles, according to which the algorithm improves the best position to accelerate convergence in situations where the traditional update rule does not work. Borrowing the idea of mutation from evolutionary computation, self-evolving behaviour acts on the current best particle in the swarm to prevent the algorithm from prematurely converging. The performance of SSPSO and four other improved particle swarm optimizers is numerically evaluated by unimodal, multimodal and rotated multimodal benchmark functions. The effectiveness of SSPSO in solving real-world problems is shown by the magnetic optimization of a Halbach-based permanent magnet machine. The results show that SSPSO has good convergence performance and high reliability, and is well matched to actual problems.

  11. Formation of polarity convergences underlying shoot outgrowths

    PubMed Central

    Abley, Katie; Sauret-Güeto, Susanna; Marée, Athanasius FM; Coen, Enrico

    2016-01-01

    The development of outgrowths from plant shoots depends on formation of epidermal sites of cell polarity convergence with high intracellular auxin at their centre. A parsimonious model for generation of convergence sites is that cell polarity for the auxin transporter PIN1 orients up auxin gradients, as this spontaneously generates convergent alignments. Here we test predictions of this and other models for the patterns of auxin biosynthesis and import. Live imaging of outgrowths from kanadi1 kanadi2 Arabidopsis mutant leaves shows that they arise by formation of PIN1 convergence sites within a proximodistal polarity field. PIN1 polarities are oriented away from regions of high auxin biosynthesis enzyme expression, and towards regions of high auxin importer expression. Both expression patterns are required for normal outgrowth emergence, and may form part of a common module underlying shoot outgrowths. These findings are more consistent with models that spontaneously generate tandem rather than convergent alignments. DOI: http://dx.doi.org/10.7554/eLife.18165.001 PMID:27478985

  12. Convergent evolution in biosynthesis of cyanogenic defence compounds in plants and insects.

    PubMed

    Jensen, Niels Bjerg; Zagrobelny, Mika; Hjernø, Karin; Olsen, Carl Erik; Houghton-Larsen, Jens; Borch, Jonas; Møller, Birger Lindberg; Bak, Søren

    2011-01-01

    For more than 420 million years, plants, insects and their predators have co-evolved based on a chemical arms race including deployment of refined chemical defence systems by each player. Cyanogenic glucosides are produced by numerous plants and by some specialized insects and serve an important role as defence compounds in these intimate interactions. Burnet moth larvae are able to sequester cyanogenic glucosides from their food plant as well as to carry out de novo biosynthesis. Here we show that three genes (CYP405A2, CYP332A3 and UGT33A1) encode the entire biosynthetic pathway of cyanogenic glucosides in the Burnet moth Zygaena filipendulae. In both plants and insects, convergent evolution has led to two multifunctional P450 enzymes each catalysing unusual reactions and a glucosyl-transferase acting in sequence to catalyse cyanogenic glucoside formation. Thus, plants and insects have independently found a way to package a cyanide time bomb to fend off herbivores and predators.

  13. Self Evolving Modular Network

    NASA Astrophysics Data System (ADS)

    Tokunaga, Kazuhiro; Kawabata, Nobuyuki; Furukawa, Tetsuo

    We propose a novel modular network called the Self-Evolving Modular Network (SEEM). The SEEM has a modular network architecture with a graph structure and these following advantages: (1) new modules are added incrementally to allow the network to adapt in a self-organizing manner, and (2) graph's paths are formed based on the relationships between the models represented by modules. The SEEM is expected to be applicable to evolving functions of an autonomous robot in a self-organizing manner through interaction with the robot's environment and categorizing large-scale information. This paper presents the architecture and an algorithm for the SEEM. Moreover, performance characteristic and effectiveness of the network are shown by simulations using cubic functions and a set of 3D-objects.

  14. Evolvable Neural Software System

    NASA Technical Reports Server (NTRS)

    Curtis, Steven A.

    2009-01-01

    The Evolvable Neural Software System (ENSS) is composed of sets of Neural Basis Functions (NBFs), which can be totally autonomously created and removed according to the changing needs and requirements of the software system. The resulting structure is both hierarchical and self-similar in that a given set of NBFs may have a ruler NBF, which in turn communicates with other sets of NBFs. These sets of NBFs may function as nodes to a ruler node, which are also NBF constructs. In this manner, the synthetic neural system can exhibit the complexity, three-dimensional connectivity, and adaptability of biological neural systems. An added advantage of ENSS over a natural neural system is its ability to modify its core genetic code in response to environmental changes as reflected in needs and requirements. The neural system is fully adaptive and evolvable and is trainable before release. It continues to rewire itself while on the job. The NBF is a unique, bilevel intelligence neural system composed of a higher-level heuristic neural system (HNS) and a lower-level, autonomic neural system (ANS). Taken together, the HNS and the ANS give each NBF the complete capabilities of a biological neural system to match sensory inputs to actions. Another feature of the NBF is the Evolvable Neural Interface (ENI), which links the HNS and ANS. The ENI solves the interface problem between these two systems by actively adapting and evolving from a primitive initial state (a Neural Thread) to a complicated, operational ENI and successfully adapting to a training sequence of sensory input. This simulates the adaptation of a biological neural system in a developmental phase. Within the greater multi-NBF and multi-node ENSS, self-similar ENI s provide the basis for inter-NBF and inter-node connectivity.

  15. The Convergence Years

    ERIC Educational Resources Information Center

    Kolodzy, Janet; Grant, August E.; DeMars, Tony R.; Wilkinson, Jeffrey S.

    2014-01-01

    The emergence of the Internet, social media, and digital technologies in the twenty-first century accelerated an evolution in journalism and communication that fit under the broad term of convergence. That evolution changed the relationship between news producers and consumers. It broke down the geographical boundaries in defining our communities,…

  16. Convergence of Arnoldi method

    SciTech Connect

    Nevanlinna, O.

    1994-12-31

    This note summarizes some results on (a monitored version of) the Arnoldi method in Hilbert spaces. The interest in working in infinite dimensional spaces comes partly from the fact that only then can one have meaningful asymptotical statements (which hopefully give some light to the convergence of Arnoldi in large dimensional problems with iteration indices far less than the dimension).

  17. The Convergence Years

    ERIC Educational Resources Information Center

    Kolodzy, Janet; Grant, August E.; DeMars, Tony R.; Wilkinson, Jeffrey S.

    2014-01-01

    The emergence of the Internet, social media, and digital technologies in the twenty-first century accelerated an evolution in journalism and communication that fit under the broad term of convergence. That evolution changed the relationship between news producers and consumers. It broke down the geographical boundaries in defining our communities,…

  18. Converging or Diverging Lens?

    ERIC Educational Resources Information Center

    Branca, Mario

    2013-01-01

    Why does a lens magnify? Why does it shrink objects? Why does this happen? The activities that we propose here are useful in helping us to understand how lenses work, and they show that the same lens can have different magnification capabilities. A converging lens can also act as a diverging lens. (Contains 4 figures.)

  19. Converging or Diverging Lens?

    ERIC Educational Resources Information Center

    Branca, Mario

    2013-01-01

    Why does a lens magnify? Why does it shrink objects? Why does this happen? The activities that we propose here are useful in helping us to understand how lenses work, and they show that the same lens can have different magnification capabilities. A converging lens can also act as a diverging lens. (Contains 4 figures.)

  20. Twin Convergence Zones

    NASA Technical Reports Server (NTRS)

    2002-01-01

    NASA's QuikSCAT satellite has confirmed a 30-year old largely unproven theory that there are two areas near the equator where the winds converge year after year and drive ocean circulation south of the equator. By analyzing winds, QuikSCAT has found a year-round southern and northern Intertropical Convergence Zone. This find is important to climate modelers and weather forecasters because it provides more detail on how the oceans and atmosphere interact near the equator. The Intertropical Convergence Zone (ITCZ) is the region that circles the Earth near the equator, where the trade winds of both the Northern and Southern Hemispheres come together. North of the equator, strong sun and warm water of the equator heats the air in the ITCZ, drawing air in from north and south and causing the air to rise. As the air rises it cools, releasing the accumulated moisture in an almost perpetual series of thunderstorms. Satellite data, however, has confirmed that there is an ITCZ north of the equator and a parallel ITCZ south of the equator. Variation in the location of the ITCZ is important to people around the world because it affects the north-south atmospheric circulation, which redistributes energy. It drastically affects rainfall in many equatorial nations, resulting in the wet and dry seasons of the tropics rather than the cold and warm seasons of higher latitudes. Longer term changes in the ITCZ can result in severe droughts or flooding in nearby areas. 'The double ITCZ is usually only identified in the Pacific and Atlantic Oceans on a limited and seasonal basis,' said Timothy Liu, of NASA's Jet Propulsion Laboratory and California Institute of Technology, Pasadena, Calif., and lead researcher on the project. In the eastern Pacific Ocean, the southern ITCZ is usually seen springtime. In the western Atlantic Ocean, the southern ITCZ was recently clearly identified only in the summertime. However, QuikSCAT's wind data has seen the southern ITCZ in all seasons across the

  1. Twin Convergence Zones

    NASA Technical Reports Server (NTRS)

    2002-01-01

    NASA's QuikSCAT satellite has confirmed a 30-year old largely unproven theory that there are two areas near the equator where the winds converge year after year and drive ocean circulation south of the equator. By analyzing winds, QuikSCAT has found a year-round southern and northern Intertropical Convergence Zone. This find is important to climate modelers and weather forecasters because it provides more detail on how the oceans and atmosphere interact near the equator. The Intertropical Convergence Zone (ITCZ) is the region that circles the Earth near the equator, where the trade winds of both the Northern and Southern Hemispheres come together. North of the equator, strong sun and warm water of the equator heats the air in the ITCZ, drawing air in from north and south and causing the air to rise. As the air rises it cools, releasing the accumulated moisture in an almost perpetual series of thunderstorms. Satellite data, however, has confirmed that there is an ITCZ north of the equator and a parallel ITCZ south of the equator. Variation in the location of the ITCZ is important to people around the world because it affects the north-south atmospheric circulation, which redistributes energy. It drastically affects rainfall in many equatorial nations, resulting in the wet and dry seasons of the tropics rather than the cold and warm seasons of higher latitudes. Longer term changes in the ITCZ can result in severe droughts or flooding in nearby areas. 'The double ITCZ is usually only identified in the Pacific and Atlantic Oceans on a limited and seasonal basis,' said Timothy Liu, of NASA's Jet Propulsion Laboratory and California Institute of Technology, Pasadena, Calif., and lead researcher on the project. In the eastern Pacific Ocean, the southern ITCZ is usually seen springtime. In the western Atlantic Ocean, the southern ITCZ was recently clearly identified only in the summertime. However, QuikSCAT's wind data has seen the southern ITCZ in all seasons across the

  2. Converged Librarian/Academic Roles in the 'Wired' University.

    ERIC Educational Resources Information Center

    Dugdale, Christine

    New technologies allow universities to extend pedagogical practices, enhance learning experiences and develop self-managed lifelong learners. To take full advantage of evolving technologies, multi-skilled teaching and development teams are required with a merging and converging of academic and librarian roles. Conclusions are reported from the…

  3. Highly-evolved stars

    NASA Technical Reports Server (NTRS)

    Heap, S. R.

    1981-01-01

    The ways in which the IUE has proved useful in studying highly evolved stars are reviewed. The importance of high dispersion spectra for abundance analyses of the sd0 stars and for studies of the wind from the central star of NGC 6543 and the wind from the 0 type component of Vela X-1 is shown. Low dispersion spectra are used for absolute spectrophotometry of the dwarf nova, Ex Hya. Angular resolution is important for detecting and locating UV sources in globular clusters.

  4. Regolith Evolved Gas Analyzer

    NASA Technical Reports Server (NTRS)

    Hoffman, John H.; Hedgecock, Jud; Nienaber, Terry; Cooper, Bonnie; Allen, Carlton; Ming, Doug

    2000-01-01

    The Regolith Evolved Gas Analyzer (REGA) is a high-temperature furnace and mass spectrometer instrument for determining the mineralogical composition and reactivity of soil samples. REGA provides key mineralogical and reactivity data that is needed to understand the soil chemistry of an asteroid, which then aids in determining in-situ which materials should be selected for return to earth. REGA is capable of conducting a number of direct soil measurements that are unique to this instrument. These experimental measurements include: (1) Mass spectrum analysis of evolved gases from soil samples as they are heated from ambient temperature to 900 C; and (2) Identification of liberated chemicals, e.g., water, oxygen, sulfur, chlorine, and fluorine. REGA would be placed on the surface of a near earth asteroid. It is an autonomous instrument that is controlled from earth but does the analysis of regolith materials automatically. The REGA instrument consists of four primary components: (1) a flight-proven mass spectrometer, (2) a high-temperature furnace, (3) a soil handling system, and (4) a microcontroller. An external arm containing a scoop or drill gathers regolith samples. A sample is placed in the inlet orifice where the finest-grained particles are sifted into a metering volume and subsequently moved into a crucible. A movable arm then places the crucible in the furnace. The furnace is closed, thereby sealing the inner volume to collect the evolved gases for analysis. Owing to the very low g forces on an asteroid compared to Mars or the moon, the sample must be moved from inlet to crucible by mechanical means rather than by gravity. As the soil sample is heated through a programmed pattern, the gases evolved at each temperature are passed through a transfer tube to the mass spectrometer for analysis and identification. Return data from the instrument will lead to new insights and discoveries including: (1) Identification of the molecular masses of all of the gases

  5. Thoughts on the diversity of convergent evolution of bioluminescence on earth

    NASA Astrophysics Data System (ADS)

    Waldenmaier, Hans E.; Oliveira, Anderson G.; Stevani, Cassius V.

    2012-10-01

    The widespread independent evolution of analogous bioluminescent systems is one of the most impressive and diverse examples of convergent evolution on earth. There are roughly 30 extant bioluminescent systems that have evolved independently on Earth, with each system likely having unique enzymes responsible for catalysing the bioluminescent reaction. Bioluminescence is a chemical reaction involving a luciferin molecule and a luciferase or photoprotein that results in the emission of light. Some independent systems utilize the same luciferin, such as the use of tetrapyrrolic compounds by krill and dinoflagellates, and the wide use of coelenterazine by marine organisms, while the enzymes involved are unique. One common thread among all the different bioluminescent systems is the requirement of molecular oxygen. Bioluminescence is found in most forms of life, especially marine organisms. Bioluminescence in known to benefit the organism by: attraction, repulsion, communication, camouflage, and illumination. The marine ecosystem is significantly affected by bioluminescence, the only light found in the pelagic zone and below is from bioluminescent organisms. Transgenic bioluminescent organisms have revolutionized molecular research, medicine and the biotechnology industry. The use of bioluminescence in studying molecular pathways and disease allows for non-invasive and real-time analysis. Bioluminescence-based assays have been developed for several analytes by coupling luminescence to many enzyme-catalysed reactions.

  6. From Coexistence to Convergence: Studying Partnerships and Collaboration among Libraries, Archives and Museums

    ERIC Educational Resources Information Center

    Duff, Wendy M.; Carter, Jennifer; Cherry, Joan M.; MacNeil, Heather; Howarth, Lynne C.

    2013-01-01

    Introduction: The convergence of libraries, archives and museums is an evolving phenomenon that has garnered increased attention in the literature and professional practice over the past decade. To date, little research exists documenting the experiences of these institutions as they engage in different forms of collaboration and convergence.…

  7. Transistor Level Circuit Experiments using Evolvable Hardware

    NASA Technical Reports Server (NTRS)

    Stoica, A.; Zebulum, R. S.; Keymeulen, D.; Ferguson, M. I.; Daud, Taher; Thakoor, A.

    2005-01-01

    The Jet Propulsion Laboratory (JPL) performs research in fault tolerant, long life, and space survivable electronics for the National Aeronautics and Space Administration (NASA). With that focus, JPL has been involved in Evolvable Hardware (EHW) technology research for the past several years. We have advanced the technology not only by simulation and evolution experiments, but also by designing, fabricating, and evolving a variety of transistor-based analog and digital circuits at the chip level. EHW refers to self-configuration of electronic hardware by evolutionary/genetic search mechanisms, thereby maintaining existing functionality in the presence of degradations due to aging, temperature, and radiation. In addition, EHW has the capability to reconfigure itself for new functionality when required for mission changes or encountered opportunities. Evolution experiments are performed using a genetic algorithm running on a DSP as the reconfiguration mechanism and controlling the evolvable hardware mounted on a self-contained circuit board. Rapid reconfiguration allows convergence to circuit solutions in the order of seconds. The paper illustrates hardware evolution results of electronic circuits and their ability to perform under 230 C temperature as well as radiations of up to 250 kRad.

  8. Knowledge Convergence and Collaborative Learning

    ERIC Educational Resources Information Center

    Jeong, Heisawn; Chi, Michelene T. H.

    2007-01-01

    This paper operationalized the notion of knowledge convergence and assessed quantitatively how much knowledge convergence occurred during collaborative learning. Knowledge convergence was defined as an increase in common knowledge where common knowledge referred to the knowledge that all collaborating partners had. Twenty pairs of college students…

  9. Knowledge Convergence and Collaborative Learning

    ERIC Educational Resources Information Center

    Jeong, Heisawn; Chi, Michelene T. H.

    2007-01-01

    This paper operationalized the notion of knowledge convergence and assessed quantitatively how much knowledge convergence occurred during collaborative learning. Knowledge convergence was defined as an increase in common knowledge where common knowledge referred to the knowledge that all collaborating partners had. Twenty pairs of college students…

  10. Convergent sequence evolution between echolocating bats and dolphins.

    PubMed

    Liu, Yang; Cotton, James A; Shen, Bin; Han, Xiuqun; Rossiter, Stephen J; Zhang, Shuyi

    2010-01-26

    Cases of convergent evolution - where different lineages have evolved similar traits independently - are common and have proven central to our understanding of selection. Yet convincing examples of adaptive convergence at the sequence level are exceptionally rare [1]. The motor protein Prestin is expressed in mammalian outer hair cells (OHCs) and is thought to confer high frequency sensitivity and selectivity in the mammalian auditory system [2]. We previously reported that the Prestin gene has undergone sequence convergence among unrelated lineages of echolocating bat [3]. Here we report that this gene has also undergone convergent amino acid substitutions in echolocating dolphins, which group with echolocating bats in a phylogenetic tree of Prestin. Furthermore, we find evidence that these changes were driven by natural selection.

  11. Our evolving universe

    NASA Astrophysics Data System (ADS)

    Longair, Malcolm S.

    Our Evolving Universe is a lucid, non-technical and infectiously enthusiastic introduction to current astronomy and cosmology. Highly illustrated throughout with the latest colour images from the world's most advanced telescopes, it also provides a colourful view of our Universe. Malcolm Longair takes us on a breathtaking tour of the most dramatic recent results astronomers have on the birth of stars, the hunt for black holes and dark matter, on gravitational lensing and the latest tests of the Big Bang. He leads the reader right up to understand the key questions that future research in astronomy and cosmology must answer. A clear and comprehensive glossary of technical terms is also provided. For the general reader, student or professional wishing to understand the key questions today's astronomers and cosmologists are trying to answer, this is an invaluable and inspiring read.

  12. Activity-induced convergence of APP and BACE-1 in acidic microdomains via an endocytosis-dependent pathway.

    PubMed

    Das, Utpal; Scott, David A; Ganguly, Archan; Koo, Edward H; Tang, Yong; Roy, Subhojit

    2013-08-07

    The convergence of APP (substrate) and BACE-1 (enzyme) is a rate-limiting, obligatory event triggering the amyloidogenic pathway-a key step in Alzheimer's disease (AD) pathology. However, as both APP/BACE-1 are highly expressed in brain, mechanisms precluding their unabated convergence are unclear. Exploring dynamic localization of APP/BACE-1 in cultured hippocampal neurons, we found that after synthesis via the secretory pathway, dendritic APP/BACE-1-containing vesicles are largely segregated in physiologic states. While BACE-1 is sorted into acidic recycling endosomes, APP is conveyed in Golgi-derived vesicles. However, upon activity induction-a known trigger of the amyloidogenic pathway-APP is routed into BACE-1-positive recycling endosomes via a clathrin-dependent mechanism. A partitioning/convergence of APP/BACE-1 vesicles is also apparent in control/AD brains, respectively. Considering BACE-1 is optimally active in an acidic environment, our experiments suggest that neurons have evolved trafficking strategies that normally limit APP/BACE-1 proximity and also uncover a pathway routing APP into BACE-1-containing organelles, triggering amyloidogenesis.

  13. Activity-induced convergence of APP and BACE-1 in acidic microdomains via an endocytosis-dependent pathway

    PubMed Central

    Das, Utpal; Scott, David; Ganguly, Archan; Koo, Edward H.; Tang, Yong; Roy, Subhojit

    2013-01-01

    The convergence of APP (substrate) and BACE-1 (enzyme) is a rate-limiting, obligatory event triggering the amyloidogenic pathway – a key step in Alzheimer’s disease (AD) pathology. However, as both APP/BACE-1 are highly expressed in brain, mechanisms precluding their unabated convergence are unclear. Exploring dynamic localization of APP/BACE-1 in cultured hippocampal neurons, we found that after synthesis via the secretory-pathway, dendritic APP/BACE-1-containing vesicles are largely segregated in physiologic states. While BACE-1 is largely sorted into acidic recycling endosomes, APP is conveyed in Golgi-derived vesicles. However upon activity-induction – a known trigger of the amyloidogenic pathway – APP is routed into BACE-1-positive recycling endosomes via a clathrin-dependent mechanism. A partitioning/convergence of APP/BACE-1 vesicles is also apparent in control/AD brains respectively. Considering BACE-1 is optimally active in an acidic environment, our experiments suggest that neurons have evolved trafficking strategies that normally limit APP/BACE-1 proximity; and also uncover a pathway routing APP into BACE-1-containing organelles – triggering amyloidogenesis. PMID:23931995

  14. Disparity and convergence in bipedal archosaur locomotion

    PubMed Central

    Bates, K. T.; Schachner, E. R.

    2012-01-01

    This study aims to investigate functional disparity in the locomotor apparatus of bipedal archosaurs. We use reconstructions of hindlimb myology of extant and extinct archosaurs to generate musculoskeletal biomechanical models to test hypothesized convergence between bipedal crocodile-line archosaurs and dinosaurs. Quantitative comparison of muscle leverage supports the inference that bipedal crocodile-line archosaurs and non-avian theropods had highly convergent hindlimb myology, suggesting similar muscular mechanics and neuromuscular control of locomotion. While these groups independently evolved similar musculoskeletal solutions to the challenges of parasagittally erect bipedalism, differences also clearly exist, particularly the distinct hip and crurotarsal ankle morphology characteristic of many pseudosuchian archosaurs. Furthermore, comparative analyses of muscle design in extant archosaurs reveal that muscular parameters such as size and architecture are more highly adapted or optimized for habitual locomotion than moment arms. The importance of these aspects of muscle design, which are not directly retrievable from fossils, warns against over-extrapolating the functional significance of anatomical convergences. Nevertheless, links identified between posture, muscle moments and neural control in archosaur locomotion suggest that functional interpretations of osteological changes in limb anatomy traditionally linked to postural evolution in Late Triassic archosaurs could be constrained through musculoskeletal modelling. PMID:22112652

  15. Design Space Issues for Intrinsic Evolvable Hardware

    NASA Technical Reports Server (NTRS)

    Hereford, James; Gwaltney, David

    2004-01-01

    This paper discusses the problem of increased programming time for intrinsic evolvable hardware (EM) as the complexity of the circuit grows. As the circuit becomes more complex, then more components will be required and a longer programming string, L, is required. We develop equations for the size of the population, n, and the number of generations required for the population to converge, based on L. Our analytical results show that even though the design search space grows as 2L (assuming a binary programming string), the number of circuit evaluations, n*ngen, only grows as O(Lg3), or slightly less than O(L). This makes evolvable techniques a good tool for exploring large design spaces. The major hurdle for intrinsic EHW is evaluation time for each possible circuit. The evaluation time involves downloading the bit string to the device, updating the device configuration, measuring the output and then transferring the output data to the control processor. Each of these steps must be done for each member of the population. The processing time of the computer becomes negligible since the selection/crossover/mutation steps are only done once per generation. Evaluation time presently limits intrinsic evolvable hardware techniques to designing only small or medium-sized circuits. To evolve large or complicated circuits, several researchers have proposed using hierarchical design or reuse techniques where submodules are combined together to form complex circuits. However, these practical approaches limit the search space of available designs and preclude utilizing parasitic coupling or other effects within the programmable device. The practical approaches also raise the issue of why intrinsic EHW techniques do not easily apply to large design spaces, since the analytical results show only an O(L) complexity growth.

  16. Enzyme assays.

    PubMed

    Reymond, Jean-Louis; Fluxà, Viviana S; Maillard, Noélie

    2009-01-07

    Enzyme assays are analytical tools to visualize enzyme activities. In recent years a large variety of enzyme assays have been developed to assist the discovery and optimization of industrial enzymes, in particular for "white biotechnology" where selective enzymes are used with great success for economically viable, mild and environmentally benign production processes. The present article highlights the aspects of fluorogenic and chromogenic substrates, sensors, and enzyme fingerprinting, which are our particular areas of interest.

  17. Why did heterospory evolve?

    PubMed

    Petersen, Kurt B; Burd, Martin

    2016-10-11

    The primitive land plant life cycle featured the production of spores of unimodal size, a condition called homospory. The evolution of bimodal size distributions with small male spores and large female spores, known as heterospory, was an innovation that occurred repeatedly in the history of land plants. The importance of desiccation-resistant spores for colonization of the land is well known, but the adaptive value of heterospory has never been well established. It was an addition to a sexual life cycle that already involved male and female gametes. Its role as a precursor to the evolution of seeds has received much attention, but this is an evolutionary consequence of heterospory that cannot explain the transition from homospory to heterospory (and the lack of evolutionary reversal from heterospory to homospory). Enforced outcrossing of gametophytes has often been mentioned in connection to heterospory, but we review the shortcomings of this argument as an explanation of the selective advantage of heterospory. Few alternative arguments concerning the selective forces favouring heterospory have been proposed, a paucity of attention that is surprising given the importance of this innovation in land plant evolution. In this review we highlight two ideas that may lead us to a better understanding of why heterospory evolved. First, models of optimal resource allocation - an approach that has been used for decades in evolutionary ecology to help understand parental investment and other life-history patterns - suggest that an evolutionary increase in spore size could reach a threshold at which small spores yielding small, sperm-producing gametophytes would return greater fitness per unit of resource investment than would large spores and bisexual gametophytes. With the advent of such microspores, megaspores would evolve under frequency-dependent selection. This argument can account for the appearance of heterospory in the Devonian, when increasingly tall and complex

  18. Kaiser Permanente's Convergent Medical Terminology.

    PubMed

    Dolin, Robert H; Mattison, John E; Cohn, Simon; Campbell, Keith E; Wiesenthal, Andrew M; Hochhalter, Brad; LaBerge, Diane; Barsoum, Rita; Shalaby, James; Abilla, Alan; Clements, Robert J; Correia, Carol M; Esteva, Diane; Fedack, John M; Goldberg, Bruce J; Gopalarao, Sridhar; Hafeza, Eza; Hendler, Peter; Hernandez, Enrique; Kamangar, Ron; Kahn, Rafique A; Kurtovich, Georgina; Lazzareschi, Gerry; Lee, Moon H; Lee, Tracy; Levy, David; Lukoff, Jonathan Y; Lundberg, Cyndie; Madden, Michael P; Ngo, Trongtu L; Nguyen, Ben T; Patel, Nikhilkumar P; Resneck, Jim; Ross, David E; Schwarz, Kathleen M; Selhorst, Charles C; Snyder, Aaron; Umarji, Mohamed I; Vilner, Max; Zer-Chen, Roy; Zingo, Chris

    2004-01-01

    This paper describes Kaiser Permanente's (KP) enterprise-wide medical terminology solution, referred to as our Convergent Medical Terminology (CMT). Initially developed to serve the needs of a regional electronic health record, CMT has evolved into a core KP asset, serving as the common terminology across all applications. CMT serves as the definitive source of concept definitions for the organization, provides a consistent structure and access method to all codes used by the organization, and is KP's language of interoperability, with cross-mappings to regional ancillary systems and administrative billing codes. The core of CMT is comprised of SNOMED CT, laboratory LOINC, and First DataBank drug terminology. These are integrated into a single poly-hierarchically structured knowledge base. Cross map sets provide bi-directional translations between CMT and ancillary applications and administrative billing codes. Context sets provide subsets of CMT for use in specific contexts. Our experience with CMT has lead us to conclude that a successful terminology solution requires that: (1) usability considerations are an organizational priority; (2) "interface" terminology is differentiated from "reference" terminology; (3) it be easy for clinicians to find the concepts they need; (4) the immediate value of coded data be apparent to clinician user; (5) there be a well defined approach to terminology extensions. Over the past several years, there has been substantial progress made in the domain coverage and standardization of medical terminology. KP has learned to exploit that terminology in ways that are clinician-acceptable and that provide powerful options for data analysis and reporting.

  19. Evolving a photosynthetic organelle.

    PubMed

    Nakayama, Takuro; Archibald, John M

    2012-04-24

    The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles.The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis--the conversion of solar energy into chemical energy--and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

  20. Communicability across evolving networks.

    PubMed

    Grindrod, Peter; Parsons, Mark C; Higham, Desmond J; Estrada, Ernesto

    2011-04-01

    Many natural and technological applications generate time-ordered sequences of networks, defined over a fixed set of nodes; for example, time-stamped information about "who phoned who" or "who came into contact with who" arise naturally in studies of communication and the spread of disease. Concepts and algorithms for static networks do not immediately carry through to this dynamic setting. For example, suppose A and B interact in the morning, and then B and C interact in the afternoon. Information, or disease, may then pass from A to C, but not vice versa. This subtlety is lost if we simply summarize using the daily aggregate network given by the chain A-B-C. However, using a natural definition of a walk on an evolving network, we show that classic centrality measures from the static setting can be extended in a computationally convenient manner. In particular, communicability indices can be computed to summarize the ability of each node to broadcast and receive information. The computations involve basic operations in linear algebra, and the asymmetry caused by time's arrow is captured naturally through the noncommutativity of matrix-matrix multiplication. Illustrative examples are given for both synthetic and real-world communication data sets. We also discuss the use of the new centrality measures for real-time monitoring and prediction.

  1. Evolving Concepts of Asthma

    PubMed Central

    Ray, Anuradha; Wenzel, Sally E.

    2015-01-01

    Our understanding of asthma has evolved over time from a singular disease to a complex of various phenotypes, with varied natural histories, physiologies, and responses to treatment. Early therapies treated most patients with asthma similarly, with bronchodilators and corticosteroids, but these therapies had varying degrees of success. Similarly, despite initial studies that identified an underlying type 2 inflammation in the airways of patients with asthma, biologic therapies targeted toward these type 2 pathways were unsuccessful in all patients. These observations led to increased interest in phenotyping asthma. Clinical approaches, both biased and later unbiased/statistical approaches to large asthma patient cohorts, identified a variety of patient characteristics, but they also consistently identified the importance of age of onset of disease and the presence of eosinophils in determining clinically relevant phenotypes. These paralleled molecular approaches to phenotyping that developed an understanding that not all patients share a type 2 inflammatory pattern. Using biomarkers to select patients with type 2 inflammation, repeated trials of biologics directed toward type 2 cytokine pathways saw newfound success, confirming the importance of phenotyping in asthma. Further research is needed to clarify additional clinical and molecular phenotypes, validate predictive biomarkers, and identify new areas for possible interventions. PMID:26161792

  2. Evolving synergetic interactions

    PubMed Central

    Wu, Bin; Arranz, Jordi; Du, Jinming; Zhou, Da; Traulsen, Arne

    2016-01-01

    Cooperators forgo their own interests to benefit others. This reduces their fitness and thus cooperators are not likely to spread based on natural selection. Nonetheless, cooperation is widespread on every level of biological organization ranging from bacterial communities to human society. Mathematical models can help to explain under which circumstances cooperation evolves. Evolutionary game theory is a powerful mathematical tool to depict the interactions between cooperators and defectors. Classical models typically involve either pairwise interactions between individuals or a linear superposition of these interactions. For interactions within groups, however, synergetic effects may arise: their outcome is not just the sum of its parts. This is because the payoffs via a single group interaction can be different from the sum of any collection of two-player interactions. Assuming that all interactions start from pairs, how can such synergetic multiplayer games emerge from simpler pairwise interactions? Here, we present a mathematical model that captures the transition from pairwise interactions to synergetic multiplayer ones. We assume that different social groups have different breaking rates. We show that non-uniform breaking rates do foster the emergence of synergy, even though individuals always interact in pairs. Our work sheds new light on the mechanisms underlying such synergetic interactions. PMID:27466437

  3. Synchronization in evolving snowdrift game model

    NASA Astrophysics Data System (ADS)

    Huang, Y.; Wu, L.; Zhu, S. Q.

    2009-06-01

    The interaction between the evolution of the game and the underlying network structure with evolving snowdrift game model is investigated. The constructed network follows a power-law degree distribution typically showing scale-free feature. The topological features of average path length, clustering coefficient, degree-degree correlations and the dynamical feature of synchronizability are studied. The synchronizability of the constructed networks changes by the interaction. It will converge to a certain value when sufficient new nodes are added. It is found that initial payoffs of nodes greatly affect the synchronizability. When initial payoffs for players are equal, low common initial payoffs may lead to more heterogeneity of the network and good synchronizability. When initial payoffs follow certain distributions, better synchronizability is obtained compared to equal initial payoff. The result is also true for phase synchronization of nonidentical oscillators.

  4. Design Space Issues for Intrinsic Evolvable Hardware

    NASA Technical Reports Server (NTRS)

    Hereford, James; Gwaltney, David

    2004-01-01

    This paper discuss the problem of increased programming time for intrinsic evolvable hardware (EHW) as the complexity of the circuit grows. We develop equations for the size of the population, n, and the number of generations required for the population to converge, ngen, based on L, the length of the programming string. We show that the processing time of the computer becomes negligible for intrinsic EHW since the selection/crossover/mutation steps are only done once per generation, suggesting there is room for use of more complex evolutionary algorithms m intrinsic EHW. F i y , we review the state of the practice and discuss the notion of a system design approach for intrinsic EHW.

  5. Evolution of enzyme superfamilies.

    PubMed

    Glasner, Margaret E; Gerlt, John A; Babbitt, Patricia C

    2006-10-01

    Enzyme evolution is often constrained by aspects of catalysis. Sets of homologous proteins that catalyze different overall reactions but share an aspect of catalysis, such as a common partial reaction, are called mechanistically diverse superfamilies. The common mechanistic steps and structural characteristics of several of these superfamilies, including the enolase, Nudix, amidohydrolase, and haloacid dehalogenase superfamilies have been characterized. In addition, studies of mechanistically diverse superfamilies are helping to elucidate mechanisms of functional diversification, such as catalytic promiscuity. Understanding how enzyme superfamilies evolve is vital for accurate genome annotation, predicting protein functions, and protein engineering.

  6. ONMCGP: Orthogonal Neighbourhood Mutation Cartesian Genetic Programming for Evolvable Hardware

    NASA Astrophysics Data System (ADS)

    I, Fuchuan N.; I, Yuanxiang L.; E, Peng K.

    2014-03-01

    Evolvable Hardware is facing the problems of scalability and stalling effect. This paper proposed a novel Orthogonal Neighbourhood Mutation (ONM) operator in Cartesian genetic programming (CGP), to reduce the stalling effect in CGP and improve the efficiency of the algorithms.The method incorporates with Differential Evolution strategy. Demonstrated by experiments on benchmark, the proposed Orthogonal Neighbourhood Search can jump out of Local optima, reduce the stalling effect in CGP and the algorithm convergence faster.

  7. Consensus in evolving networks of mobile agents

    NASA Astrophysics Data System (ADS)

    Baronchelli, Andrea; Díaz-Guilera, Albert

    2012-02-01

    Populations of mobile and communicating agents describe a vast array of technological and natural systems, ranging from sensor networks to animal groups. Here, we investigate how a group-level agreement may emerge in the continuously evolving networks defined by the local interactions of the moving individuals. We adopt a general scheme of motion in two dimensions and we let the individuals interact through the minimal naming game, a prototypical scheme to investigate social consensus. We distinguish different regimes of convergence determined by the emission range of the agents and by their mobility, and we identify the corresponding scaling behaviors of the consensus time. In the same way, we rationalize also the behavior of the maximum memory used during the convergence process, which determines the minimum cognitive/storage capacity needed by the individuals. Overall, we believe that the simple and general model presented in this talk can represent a helpful reference for a better understanding of the behavior of populations of mobile agents.

  8. Homology, convergence and parallelism.

    PubMed

    Ghiselin, Michael T

    2016-01-05

    Homology is a relation of correspondence between parts of parts of larger wholes. It is used when tracking objects of interest through space and time and in the context of explanatory historical narratives. Homologues can be traced through a genealogical nexus back to a common ancestral precursor. Homology being a transitive relation, homologues remain homologous however much they may come to differ. Analogy is a relationship of correspondence between parts of members of classes having no relationship of common ancestry. Although homology is often treated as an alternative to convergence, the latter is not a kind of correspondence: rather, it is one of a class of processes that also includes divergence and parallelism. These often give rise to misleading appearances (homoplasies). Parallelism can be particularly hard to detect, especially when not accompanied by divergences in some parts of the body. © 2015 The Author(s).

  9. Grand network convergence.

    PubMed

    Bader, Joel S

    2011-06-17

    A report of the Systems Biology: Networks meeting, Cold Spring Harbor, USA, 22-26 March 2011.The success of the human genome project has provided a model for an analogous interactome project to map how proteins, genes, metabolites and other regulatory components interact to transform a biochemical soup into a living system. These maps promise to serve as a framework for models that predict how a biological system responds to a perturbation or an input, which is relevant to gene mutations and therapeutic treatment in human disease, and as a framework for designing new systems in synthetic biology.Three major themes arose during the 2011 meeting: technological drivers and data generation, algorithmic advances, and convergence on biological applications with context-sensitive networks.

  10. Homology, convergence and parallelism

    PubMed Central

    Ghiselin, Michael T.

    2016-01-01

    Homology is a relation of correspondence between parts of parts of larger wholes. It is used when tracking objects of interest through space and time and in the context of explanatory historical narratives. Homologues can be traced through a genealogical nexus back to a common ancestral precursor. Homology being a transitive relation, homologues remain homologous however much they may come to differ. Analogy is a relationship of correspondence between parts of members of classes having no relationship of common ancestry. Although homology is often treated as an alternative to convergence, the latter is not a kind of correspondence: rather, it is one of a class of processes that also includes divergence and parallelism. These often give rise to misleading appearances (homoplasies). Parallelism can be particularly hard to detect, especially when not accompanied by divergences in some parts of the body. PMID:26598721

  11. The emotion system promotes diversity and evolvability

    PubMed Central

    Giske, Jarl; Eliassen, Sigrunn; Fiksen, Øyvind; Jakobsen, Per J.; Aksnes, Dag L.; Mangel, Marc; Jørgensen, Christian

    2014-01-01

    Studies on the relationship between the optimal phenotype and its environment have had limited focus on genotype-to-phenotype pathways and their evolutionary consequences. Here, we study how multi-layered trait architecture and its associated constraints prescribe diversity. Using an idealized model of the emotion system in fish, we find that trait architecture yields genetic and phenotypic diversity even in absence of frequency-dependent selection or environmental variation. That is, for a given environment, phenotype frequency distributions are predictable while gene pools are not. The conservation of phenotypic traits among these genetically different populations is due to the multi-layered trait architecture, in which one adaptation at a higher architectural level can be achieved by several different adaptations at a lower level. Our results emphasize the role of convergent evolution and the organismal level of selection. While trait architecture makes individuals more constrained than what has been assumed in optimization theory, the resulting populations are genetically more diverse and adaptable. The emotion system in animals may thus have evolved by natural selection because it simultaneously enhances three important functions, the behavioural robustness of individuals, the evolvability of gene pools and the rate of evolutionary innovation at several architectural levels. PMID:25100697

  12. Evolution of substrate specificity in a retained enzyme driven by gene loss.

    PubMed

    Juárez-Vázquez, Ana Lilia; Edirisinghe, Janaka E; Verduzco-Castro, Ernesto A; Michalska, Karolina; Wu, Chenggang; Noda-García, Lianet; Babnigg, Gyorgy; Endres, Michael; Medina-Ruíz, Sofía; Santoyo-Flores, Julián; Carrillo-Tripp, Mauricio; Ton-That, Hung; Joachimiak, Andrzej; Henry, Christopher S; Barona-Gómez, Francisco

    2017-03-31

    The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.

  13. Series that Converge Absolutely but Don't Converge

    ERIC Educational Resources Information Center

    Kantrowitz, Robert; Schramm, Michael

    2012-01-01

    If a series of real numbers converges absolutely, then it converges. The usual proof requires completeness in the form of the Cauchy criterion. Failing completeness, the result is false. We provide examples of rational series that illustrate this point. The Cantor set appears in connection with one of the examples.

  14. Series that Converge Absolutely but Don't Converge

    ERIC Educational Resources Information Center

    Kantrowitz, Robert; Schramm, Michael

    2012-01-01

    If a series of real numbers converges absolutely, then it converges. The usual proof requires completeness in the form of the Cauchy criterion. Failing completeness, the result is false. We provide examples of rational series that illustrate this point. The Cantor set appears in connection with one of the examples.

  15. Disgust: Evolved Function and Structure

    ERIC Educational Resources Information Center

    Tybur, Joshua M.; Lieberman, Debra; Kurzban, Robert; DeScioli, Peter

    2013-01-01

    Interest in and research on disgust has surged over the past few decades. The field, however, still lacks a coherent theoretical framework for understanding the evolved function or functions of disgust. Here we present such a framework, emphasizing 2 levels of analysis: that of evolved function and that of information processing. Although there is…

  16. Mechanical basis of morphogenesis and convergent evolution of spiny seashells.

    PubMed

    Chirat, Régis; Moulton, Derek E; Goriely, Alain

    2013-04-09

    Convergent evolution is a phenomenon whereby similar traits evolved independently in not closely related species, and is often interpreted in functional terms. Spines in mollusk seashells are classically interpreted as having repeatedly evolved as a defense in response to shell-crushing predators. Here we consider the morphogenetic process that shapes these structures and underlies their repeated emergence. We develop a mathematical model for spine morphogenesis based on the mechanical interaction between the secreting mantle edge and the calcified shell edge to which the mantle adheres during shell growth. It is demonstrated that a large diversity of spine structures can be accounted for through small variations in control parameters of this natural mechanical process. This physical mechanism suggests that convergent evolution of spines can be understood through a generic morphogenetic process, and provides unique perspectives in understanding the phenotypic evolution of this second largest phylum in the animal kingdom.

  17. Genomic basis for the convergent evolution of electric organs

    PubMed Central

    Gallant, Jason R.; Traeger, Lindsay L.; Volkening, Jeremy D.; Moffett, Howell; Chen, Po-Hao; Novina, Carl D.; Phillips, George N.; Anand, Rene; Wells, Gregg B.; Pinch, Matthew; Güth, Robert; Unguez, Graciela A.; Albert, James S.; Zakon, Harold H.; Samanta, Manoj P.; Sussman, Michael R.

    2017-01-01

    Little is known about the genetic basis of convergent traits that originate repeatedly over broad taxonomic scales. The myogenic electric organ has evolved six times in fishes to produce electric fields used in communication, navigation, predation, or defense. We have examined the genomic basis of the convergent anatomical and physiological origins of these organs by assembling the genome of the electric eel (Electrophorus electricus) and sequencing electric organ and skeletal muscle transcriptomes from three lineages that have independently evolved electric organs. Our results indicate that, despite millions of years of evolution and large differences in the morphology of electric organ cells, independent lineages have leveraged similar transcription factors and developmental and cellular pathways in the evolution of electric organs. PMID:24970089

  18. Evolutionary basins of attraction and convergence in plants and animals.

    PubMed

    Gardiner, John

    2013-11-01

    Living organisms evolve, in part, according to the underlying properties of the amino acids and other compounds of which they are composed. Thus there are evolutionary basins of attraction that living organisms will tend to evolve toward. These processes are complex and probably beyond our current capabilities to fully envisage. But progress is being made toward an understanding of such principles by efforts to catalog protein folds and protein-protein interactions. Even plants and animals show convergent evolution, possibly driven by underlying evolutionary basins of attraction. Physical and chemical parameters and the properties of proteins present in the last common ancestor of these 2 taxa, including a putative connexin ancestor, may have played key roles here. Thus evolution is perhaps not as random as is sometimes depicted, but will follow predefined pathways. Here I address convergent evolution in plants and animals beginning at the molecular level and progressing to the organismic one.

  19. Evolutionary basins of attraction and convergence in plants and animals

    PubMed Central

    Gardiner, John

    2013-01-01

    Living organisms evolve, in part, according to the underlying properties of the amino acids and other compounds of which they are composed. Thus there are evolutionary basins of attraction that living organisms will tend to evolve toward. These processes are complex and probably beyond our current capabilities to fully envisage. But progress is being made toward an understanding of such principles by efforts to catalog protein folds and protein–protein interactions. Even plants and animals show convergent evolution, possibly driven by underlying evolutionary basins of attraction. Physical and chemical parameters and the properties of proteins present in the last common ancestor of these 2 taxa, including a putative connexin ancestor, may have played key roles here. Thus evolution is perhaps not as random as is sometimes depicted, but will follow predefined pathways. Here I address convergent evolution in plants and animals beginning at the molecular level and progressing to the organismic one. PMID:24505506

  20. Evolving virtual creatures and catapults.

    PubMed

    Chaumont, Nicolas; Egli, Richard; Adami, Christoph

    2007-01-01

    We present a system that can evolve the morphology and the controller of virtual walking and block-throwing creatures (catapults) using a genetic algorithm. The system is based on Sims' work, implemented as a flexible platform with an off-the-shelf dynamics engine. Experiments aimed at evolving Sims-type walkers resulted in the emergence of various realistic gaits while using fairly simple objective functions. Due to the flexibility of the system, drastically different morphologies and functions evolved with only minor modifications to the system and objective function. For example, various throwing techniques evolved when selecting for catapults that propel a block as far as possible. Among the strategies and morphologies evolved, we find the drop-kick strategy, as well as the systematic invention of the principle behind the wheel, when allowing mutations to the projectile.

  1. Convergent ablator performance measurements

    SciTech Connect

    Hicks, D. G.; Spears, B. K.; Braun, D. G.; Sorce, C. M.; Celliers, P. M.; Collins, G. W.; Landen, O. L.; Olson, R. E.

    2010-10-15

    The velocity and remaining ablator mass of an imploding capsule are critical metrics for assessing the progress toward ignition of an inertially confined fusion experiment. These and other convergent ablator performance parameters have been measured using a single streaked x-ray radiograph. Traditional Abel inversion of such a radiograph is ill-posed since backlighter intensity profiles and x-ray attenuation by the ablated plasma are unknown. To address this we have developed a regularization technique which allows the ablator density profile {rho}(r) and effective backlighter profile I{sub 0}(y) at each time step to be uniquely determined subject to the constraints that {rho}(r) is localized in radius space and I{sub 0}(y) is delocalized in object space. Moments of {rho}(r) then provide the time-resolved areal density, mass, and average radius (and thus velocity) of the remaining ablator material. These results are combined in the spherical rocket model to determine the ablation pressure and mass ablation rate during the implosion. The technique has been validated on simulated radiographs of implosions at the National Ignition Facility [Miller et al., Nucl. Fusion 44, 228 (2004)] and implemented on experiments at the OMEGA laser facility [Boehly et al., Opt. Commun. 133, 495 (1997)].

  2. The Intertropical Convergence Zone

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Intertropical Convergence Zone, or ITCZ, is the region that circles the Earth, near the equator, where the trade winds of the Northern and Southern Hemispheres come together. The intense sun and warm water of the equator heats the air in the ITCZ, raising its humidity and causing it to rise. As the air rises it cools, releasing the accumulated moisture in an almost perpetual series of thunderstorms. Variation in the location of the ITCZ drastically affects rainfall in many equatorial nations, resulting in the wet and dry seasons of the tropics rather than the cold and warm seasons of higher latitudes. Longer term changes in the ITCZ can result in severe droughts or flooding in nearby areas. This image is a combination of cloud data from NOAA's newest Geostationary Operational Environmental Satellite (GOES-11) and color land cover classification data. The ITCZ is the band of bright white clouds that cuts across the center of the image. For more GOES images, visit the GOES Project Science site. Image Courtesy GOES Project Science Office

  3. The Intertropical Convergence Zone

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Intertropical Convergence Zone, or ITCZ, is the region that circles the Earth, near the equator, where the trade winds of the Northern and Southern Hemispheres come together. The intense sun and warm water of the equator heats the air in the ITCZ, raising its humidity and causing it to rise. As the air rises it cools, releasing the accumulated moisture in an almost perpetual series of thunderstorms. Variation in the location of the ITCZ drastically affects rainfall in many equatorial nations, resulting in the wet and dry seasons of the tropics rather than the cold and warm seasons of higher latitudes. Longer term changes in the ITCZ can result in severe droughts or flooding in nearby areas. This image is a combination of cloud data from NOAA's newest Geostationary Operational Environmental Satellite (GOES-11) and color land cover classification data. The ITCZ is the band of bright white clouds that cuts across the center of the image. For more GOES images, visit the GOES Project Science site. Image Courtesy GOES Project Science Office

  4. Some Observations on Grid Convergence

    NASA Technical Reports Server (NTRS)

    Salas, manuel D.

    2006-01-01

    It is claimed that current practices in grid convergence studies, particularly in the field of external aerodynamics, are flawed. The necessary conditions to properly establish grid convergence are presented. A theoretical model and a numerical example are used to demonstrate these ideas.

  5. Enzyme Kinetics.

    ERIC Educational Resources Information Center

    Moe, Owen; Cornelius, Richard

    1988-01-01

    Conveys an appreciation of enzyme kinetic analysis by using a practical and intuitive approach. Discusses enzyme assays, kinetic models and rate laws, the kinetic constants (V, velocity, and Km, Michaels constant), evaluation of V and Km from experimental data, and enzyme inhibition. (CW)

  6. Enzyme Kinetics.

    ERIC Educational Resources Information Center

    Moe, Owen; Cornelius, Richard

    1988-01-01

    Conveys an appreciation of enzyme kinetic analysis by using a practical and intuitive approach. Discusses enzyme assays, kinetic models and rate laws, the kinetic constants (V, velocity, and Km, Michaels constant), evaluation of V and Km from experimental data, and enzyme inhibition. (CW)

  7. Exceptional Convergent Evolution in a Virus

    PubMed Central

    Bull, J. J.; Badgett, M. R.; Wichman, H. A.; Huelsenbeck, J. P.; Hillis, D. M.; Gulati, A.; Ho, C.; Molineux, I. J.

    1997-01-01

    Replicate lineages of the bacteriophage φX 174 adapted to growth at high temperature on either of two hosts exhibited high rates of identical, independent substitutions. Typically, a dozen or more substitutions accumulated in the 5.4-kilobase genome during propagation. Across the entire data set of nine lineages, 119 independent substitutions occurred at 68 nucleotide sites. Over half of these substitutions, accounting for one third of the sites, were identical with substitutions in other lineages. Some convergent substitutions were specific to the host used for phage propagation, but others occurred across both hosts. Continued adaptation of an evolved phage at high temperature, but on the other host, led to additional changes that included reversions of previous substitutions. Phylogenetic reconstruction using the complete genome sequence not only failed to recover the correct evolutionary history because of these convergent changes, but the true history was rejected as being a significantly inferior fit to the data. Replicate lineages subjected to similar environmental challenges showed similar rates of substitution and similar rates of fitness improvement across corresponding times of adaptation. Substitution rates and fitness improvements were higher during the initial period of adaptation than during a later period, except when the host was changed. PMID:9409816

  8. Why does continental convergence stop

    SciTech Connect

    Hynes, A.

    1985-01-01

    Convergence between India and Asia slowed at 45 Ma when they collided, but continues today. This requires that substantial proportions of the Indian and/or Asian lithospheric mantle are still being subducted. The resulting slab-pull is probably comparable with that from complete lithospheric slabs and may promote continued continental convergence even after collision. Since descending lithospheric slabs are present at all collision zones at the time of collision such continued convergence may be general after continental collisions. It may cease only when there is a major (global) plate reorganization which results in new forces on the convergent continents that may counteract the slab-pull. These inferences may be tested on the late Paleozoic collision between Gondwanaland and Laurasia. This is generally considered to have been complete by mid-Permian time (250 Ma). However, this may be only the time of docking of Gondwanaland with North America, not that of the cessation of convergence. Paleomagnetic polar-wander paths for the Gondwanide continents exhibit consistently greater latitudinal shifts from 250 Ma to 200 Ma than those of Laurasia when corrected for post-Triassic drift, suggesting that convergence continued through late Permian well into the Triassic. It may have been accommodated by crustal thickening under what is now the US Coastal Plain, or by strike-slip faulting. Convergence may have ceased only when Pangea began to fragment again, in which case the cause for its cessation may be related to the cause of continental fragmentation.

  9. Convergence insufficiency and vision therapy.

    PubMed

    McGregor, Mary Lou

    2014-06-01

    There is no standard meaning of the term "vision therapy", and for this reason it is often a controversial topic between some members of the ophthalmic and optometric community. Most pediatric ophthalmologists avoid using the term because it is nonspecific. Convergence Insufficiency (CI) is a binocular visual problem that causes problems and symptoms with near fixation. There is consensus among eye care professionals that convergence therapy is effective in treating CI. Convergence therapy is not effective in treating learning disabilities, but can sometimes relieve symptoms that might be a barrier to reading. Copyright © 2014 Elsevier Inc. All rights reserved.

  10. How did the cilium evolve?

    PubMed

    Satir, Peter; Mitchell, David R; Jékely, Gáspár

    2008-01-01

    The cilium is a characteristic organelle of eukaryotes constructed from over 600 proteins. Bacterial flagella are entirely different. 9 + 2 motile cilia evolved before the divergence of the last eukaryotic common ancestor (LECA). This chapter explores, compares, and contrasts two potential pathways of evolution: (1) via invasion of a centriolar-like virus and (2) via autogenous formation from a pre-existing microtubule-organizing center (MTOC). In either case, the intraflagellar transport (IFT) machinery that is nearly universally required for the assembly and maintenance of cilia derived from the evolving intracellular vesicular transport system. The sensory function of cilia evolved first and the ciliary axoneme evolved gradually with ciliary motility, an important selection mechanism, as one of the driving forces.

  11. Natural selection promotes antigenic evolvability.

    PubMed

    Graves, Christopher J; Ros, Vera I D; Stevenson, Brian; Sniegowski, Paul D; Brisson, Dustin

    2013-01-01

    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.

  12. Spacetimes containing slowly evolving horizons

    SciTech Connect

    Kavanagh, William; Booth, Ivan

    2006-08-15

    Slowly evolving horizons are trapping horizons that are ''almost'' isolated horizons. This paper reviews their definition and discusses several spacetimes containing such structures. These include certain Vaidya and Tolman-Bondi solutions as well as (perturbatively) tidally distorted black holes. Taking into account the mass scales and orders of magnitude that arise in these calculations, we conjecture that slowly evolving horizons are the norm rather than the exception in astrophysical processes that involve stellar-scale black holes.

  13. Convergent evolution of anti-bat sounds.

    PubMed

    Corcoran, Aaron J; Hristov, Nickolay I

    2014-09-01

    Bats and their insect prey rely on acoustic sensing in predator prey encounters--echolocation in bats, tympanic hearing in moths. Some insects also emit sounds for bat defense. Here, we describe a previously unknown sound-producing organ in Geometrid moths--a prothoracic tymbal in the orange beggar moth (Eubaphe unicolor) that generates bursts of ultrasonic clicks in response to tactile stimulation and playback of a bat echolocation attack sequence. Using scanning electron microscopy and high-speed videography, we demonstrate that E. unicolor and phylogenetically distant tiger moths have evolved serially homologous thoracic tymbal organs with fundamentally similar functional morphology, a striking example of convergent evolution. We compared E. unicolor clicks to that of five sympatric tiger moths and found that 9 of 13 E. unicolor clicking parameters were within the range of sympatric tiger moths. Remaining differences may result from the small size of the E. unicolor tymbal. Four of the five sympatric clicking tiger moth species were unpalatable to bats (0-20% eaten), whereas E. unicolor was palatable to bats (86% eaten). Based on these results, we hypothesize that E. unicolor evolved tymbal organs that mimic the sounds produced by toxic tiger moths when attacked by echolocating bats.

  14. Convergence, Consilience, and the Evolution of Temperate Deciduous Forests.

    PubMed

    Edwards, Erika J; Chatelet, David S; Chen, Bo-Chang; Ong, Jin Yao; Tagane, Shuichiro; Kanemitsu, Hironobu; Tagawa, Kazuki; Teramoto, Kentaro; Park, Brian; Chung, Kuo-Fang; Hu, Jer-Ming; Yahara, Tetsukazu; Donoghue, Michael J

    2017-08-01

    The deciduous habit of northern temperate trees and shrubs provides one of the most obvious examples of convergent evolution, but how did it evolve? Hypotheses based on the fossil record posit that deciduousness evolved first in response to drought or darkness and preadapted certain lineages as cold climates spread. An alternative is that evergreens first established in freezing environments and later evolved the deciduous habit. We monitored phenological patterns of 20 species of Viburnum spanning tropical, lucidophyllous (subtropical montane and warm temperate), and cool temperate Asian forests. In lucidophyllous forests, all viburnums were evergreen plants that exhibited coordinated leaf flushes with the onset of the rainy season but varied greatly in the timing of leaf senescence. In contrast, deciduous species exhibited tight coordination of both flushing and senescence, and we found a perfect correlation between the deciduous habit and prolonged annual freezing. In contrast to previous stepwise hypotheses, a consilience of independent lines of evidence supports a lockstep model in which deciduousness evolved in situ, in parallel, and concurrent with a gradual cooling climate. A pervasive selective force combined with the elevated evolutionary accessibility of a particular response may explain the massive convergence of adaptive strategies that characterizes the world's biomes.

  15. Optimality Functions and Lopsided Convergence

    DTIC Science & Technology

    2015-03-16

    Royset and E.Y. Pee . Rate of convergence analysis of discretization and smoothing algorithms for semi-infinite minimax problems. Journal of Optimization Theory and Applications, 155(3):855– 882, 2012. 17

  16. Spaces of Ideal Convergent Sequences

    PubMed Central

    Mursaleen, M.; Sharma, Sunil K.

    2014-01-01

    In the present paper, we introduce some sequence spaces using ideal convergence and Musielak-Orlicz function ℳ = (Mk). We also examine some topological properties of the resulting sequence spaces. PMID:24592143

  17. Convergence palsy secondary to amoxicillin.

    PubMed

    Pérez-Roca, F; Alfaro Juárez, A; Sánchez Merino, C; Navarro Mingorance, A

    2016-12-01

    We present the case of an 11-year-old boy with acute diplopia in near vision secondary to transient convergence palsy, possibly in relation to amoxicillin. Convergence palsy is an uncommon eye disorder. The causes are reviewed, and amoxicilin is identified as presumptive etiologic agent. This is the first case reported. Copyright © 2016 Sociedad Española de Oftalmología. Publicado por Elsevier España, S.L.U. All rights reserved.

  18. Robustness to Faults Promotes Evolvability: Insights from Evolving Digital Circuits

    PubMed Central

    Nolfi, Stefano

    2016-01-01

    We demonstrate how the need to cope with operational faults enables evolving circuits to find more fit solutions. The analysis of the results obtained in different experimental conditions indicates that, in absence of faults, evolution tends to select circuits that are small and have low phenotypic variability and evolvability. The need to face operation faults, instead, drives evolution toward the selection of larger circuits that are truly robust with respect to genetic variations and that have a greater level of phenotypic variability and evolvability. Overall our results indicate that the need to cope with operation faults leads to the selection of circuits that have a greater probability to generate better circuits as a result of genetic variation with respect to a control condition in which circuits are not subjected to faults. PMID:27409589

  19. Robustness to Faults Promotes Evolvability: Insights from Evolving Digital Circuits.

    PubMed

    Milano, Nicola; Nolfi, Stefano

    2016-01-01

    We demonstrate how the need to cope with operational faults enables evolving circuits to find more fit solutions. The analysis of the results obtained in different experimental conditions indicates that, in absence of faults, evolution tends to select circuits that are small and have low phenotypic variability and evolvability. The need to face operation faults, instead, drives evolution toward the selection of larger circuits that are truly robust with respect to genetic variations and that have a greater level of phenotypic variability and evolvability. Overall our results indicate that the need to cope with operation faults leads to the selection of circuits that have a greater probability to generate better circuits as a result of genetic variation with respect to a control condition in which circuits are not subjected to faults.

  20. Marine enzymes.

    PubMed

    Debashish, Ghosh; Malay, Saha; Barindra, Sana; Joydeep, Mukherjee

    2005-01-01

    Marine enzyme biotechnology can offer novel biocatalysts with properties like high salt tolerance, hyperthermostability, barophilicity, cold adaptivity, and ease in large-scale cultivation. This review deals with the research and development work done on the occurrence, molecular biology, and bioprocessing of marine enzymes during the last decade. Exotic locations have been accessed for the search of novel enzymes. Scientists have isolated proteases and carbohydrases from deep sea hydrothermal vents. Cold active metabolic enzymes from psychrophilic marine microorganisms have received considerable research attention. Marine symbiont microorganisms growing in association with animals and plants were shown to produce enzymes of commercial interest. Microorganisms isolated from sediment and seawater have been the most widely studied, proteases, carbohydrases, and peroxidases being noteworthy. Enzymes from marine animals and plants were primarily studied for their metabolic roles, though proteases and peroxidases have found industrial applications. Novel techniques in molecular biology applied to assess the diversity of chitinases, nitrate, nitrite, ammonia-metabolizing, and pollutant-degrading enzymes are discussed. Genes encoding chitinases, proteases, and carbohydrases from microbial and animal sources have been cloned and characterized. Research on the bioprocessing of marine-derived enzymes, however, has been scanty, focusing mainly on the application of solid-state fermentation to the production of enzymes from microbial sources.

  1. Behavioral convergence and adaptive radiation: effects of habitat use on territorial behavior in Anolis lizards.

    PubMed

    Johnson, Michele A; Revell, Liam J; Losos, Jonathan B

    2010-04-01

    Most studies of adaptive radiations focus on morphological aspects of differentiation, yet behavior is also an important component of evolutionary diversification, often mediating the relationship between animal ecology and morphology. In species within radiations that are convergent in ecology and morphology, we then also expect convergence in behavior. Here, we examined 13 Anolis lizard species to determine whether territorial strategies have evolved convergently with morphology and habitat use. We evaluated two aspects of territoriality: behavioral defense of space via territorial displays, and territory overlap within and between sexes. Controlling for the phylogenetic relationships of the taxa in our study, we found that species similar in perch height and diameter convergently evolved patterns of territory overlap, whereas species similar in habitat visibility (the proportion of space that can be seen from a perch) convergently evolved display behavior. We also found that species with greater display time have more extensive male-male territory overlap. This study provides strong evidence for the role of habitat in the evolution of territoriality and suggests that the social structure of a species ultimately evolves in concert with habitat use and morphology.

  2. Convergent Evolution of Tetrodotoxin-Resistant Sodium Channels in Predators and Prey.

    PubMed

    Toledo, G; Hanifin, C; Geffeney, S; Brodie, E D

    2016-01-01

    Convergent evolution of similar adaptive traits may arise from either common or disparate molecular and physiological mechanisms. The forces that determine the degree of underlying mechanistic similarities across convergent phenotypes are highly debated and poorly understood. Some garter snakes are able to consume newts that possess the channel blocking compound tetrodotoxin (TTX). Despite belonging to unrelated lineages, both the predators and prey have independently evolved remarkably similar physiological mechanisms of resistance to TTX that involve chemical and structural changes in voltage-gated sodium channels (NaV). The evolution of TTX resistance in this predator-prey pair constitutes a natural experiment that allows us to explore the causes of molecular convergence. Here, we review broad patterns of convergence at the level of amino acid changes in NaV channels of animals that evolved TTX resistance and make comparisons to known TTX-resistant channels that did not evolve under the selective pressures imposed by TTX. We conclude that convergence likely stems from the interplay of the target specificity of TTX and functional constraints of NaV that are shared among taxa. These and other factors can limit channel evolution to favor a few functionally permissible paths of adaptation, which can explain the observed predictability of changes to channel structure. By studying the functional causes of convergence in NaV channels, we can further our understanding of the role of these important channel proteins at the center of the evolution of the nervous system.

  3. Understanding Enzymes.

    ERIC Educational Resources Information Center

    Sinnott, M. L.

    1979-01-01

    Describes the way enzymes operate through reaction energetics, and explains that most of the catalytic power of enzymes lies in the strong noncovalent forces responsible for initial binding of substrate, which are only manifested at the transition state of the reaction. (Author/GA)

  4. Enzymes, Industrial

    USDA-ARS?s Scientific Manuscript database

    Enzymes serve key roles in numerous biotechnology processes and products that are commonly encountered in the forms of food and beverages, cleaning supplies, clothing, paper products, transportation fuels, pharmaceuticals, and monitoring devices. Enzymes can display regio- and stereo-specificity, p...

  5. Characterization of Function of the GlgA2 Glycogen/Starch Synthase in Cyanobacterium sp. Clg1 Highlights Convergent Evolution of Glycogen Metabolism into Starch Granule Aggregation.

    PubMed

    Kadouche, Derifa; Ducatez, Mathieu; Cenci, Ugo; Tirtiaux, Catherine; Suzuki, Eiji; Nakamura, Yasunori; Putaux, Jean-Luc; Terrasson, Amandine Durand; Diaz-Troya, Sandra; Florencio, Francisco Javier; Arias, Maria Cecilia; Striebeck, Alexander; Palcic, Monica; Ball, Steven G; Colleoni, Christophe

    2016-07-01

    At variance with the starch-accumulating plants and most of the glycogen-accumulating cyanobacteria, Cyanobacterium sp. CLg1 synthesizes both glycogen and starch. We now report the selection of a starchless mutant of this cyanobacterium that retains wild-type amounts of glycogen. Unlike other mutants of this type found in plants and cyanobacteria, this mutant proved to be selectively defective for one of the two types of glycogen/starch synthase: GlgA2. This enzyme is phylogenetically related to the previously reported SSIII/SSIV starch synthase that is thought to be involved in starch granule seeding in plants. This suggests that, in addition to the selective polysaccharide debranching demonstrated to be responsible for starch rather than glycogen synthesis, the nature and properties of the elongation enzyme define a novel determinant of starch versus glycogen accumulation. We show that the phylogenies of GlgA2 and of 16S ribosomal RNA display significant congruence. This suggests that this enzyme evolved together with cyanobacteria when they diversified over 2 billion years ago. However, cyanobacteria can be ruled out as direct progenitors of the SSIII/SSIV ancestral gene found in Archaeplastida. Hence, both cyanobacteria and plants recruited similar enzymes independently to perform analogous tasks, further emphasizing the importance of convergent evolution in the appearance of starch from a preexisting glycogen metabolism network.

  6. On the Discovery of Evolving Truth

    PubMed Central

    Li, Yaliang; Li, Qi; Gao, Jing; Su, Lu; Zhao, Bo; Fan, Wei; Han, Jiawei

    2015-01-01

    In the era of big data, information regarding the same objects can be collected from increasingly more sources. Unfortunately, there usually exist conflicts among the information coming from different sources. To tackle this challenge, truth discovery, i.e., to integrate multi-source noisy information by estimating the reliability of each source, has emerged as a hot topic. In many real world applications, however, the information may come sequentially, and as a consequence, the truth of objects as well as the reliability of sources may be dynamically evolving. Existing truth discovery methods, unfortunately, cannot handle such scenarios. To address this problem, we investigate the temporal relations among both object truths and source reliability, and propose an incremental truth discovery framework that can dynamically update object truths and source weights upon the arrival of new data. Theoretical analysis is provided to show that the proposed method is guaranteed to converge at a fast rate. The experiments on three real world applications and a set of synthetic data demonstrate the advantages of the proposed method over state-of-the-art truth discovery methods. PMID:26705502

  7. On the Discovery of Evolving Truth.

    PubMed

    Li, Yaliang; Li, Qi; Gao, Jing; Su, Lu; Zhao, Bo; Fan, Wei; Han, Jiawei

    2015-08-01

    In the era of big data, information regarding the same objects can be collected from increasingly more sources. Unfortunately, there usually exist conflicts among the information coming from different sources. To tackle this challenge, truth discovery, i.e., to integrate multi-source noisy information by estimating the reliability of each source, has emerged as a hot topic. In many real world applications, however, the information may come sequentially, and as a consequence, the truth of objects as well as the reliability of sources may be dynamically evolving. Existing truth discovery methods, unfortunately, cannot handle such scenarios. To address this problem, we investigate the temporal relations among both object truths and source reliability, and propose an incremental truth discovery framework that can dynamically update object truths and source weights upon the arrival of new data. Theoretical analysis is provided to show that the proposed method is guaranteed to converge at a fast rate. The experiments on three real world applications and a set of synthetic data demonstrate the advantages of the proposed method over state-of-the-art truth discovery methods.

  8. The camera convergence problem revisited

    NASA Astrophysics Data System (ADS)

    Allison, Robert S.

    2004-05-01

    Convergence of the real or virtual stereoscopic cameras is an important operation in stereoscopic display systems. For example, convergence can shift the range of portrayed depth to improve visual comfort; can adjust the disparity of targets to bring them nearer to the screen and reduce accommodation-vergence conflict; or can bring objects of interest into the binocular field-of-view. Although camera convergence is acknowledged as a useful function, there has been considerable debate over the transformation required. It is well known that rotational camera convergence or 'toe-in' distorts the images in the two cameras producing patterns of horizontal and vertical disparities that can cause problems with fusion of the stereoscopic imagery. Behaviorally, similar retinal vertical disparity patterns are known to correlate with viewing distance and strongly affect perception of stereoscopic shape and depth. There has been little analysis of the implications of recent findings on vertical disparity processing for the design of stereoscopic camera and display systems. We ask how such distortions caused by camera convergence affect the ability to fuse and perceive stereoscopic images.

  9. NONSURGICAL TREATMENT OF CONVERGENT STRABISMUS

    PubMed Central

    Tour, Robert L.

    1959-01-01

    It is generally agreed that surgical treatment of convergent strabismus should be withheld until all other less traumatic approaches have proved ineffectual. There are four categories of nonsurgical treatment. One is psychiatric. Too often psychiatric problems in the causation of convergent strabismus are either overlooked or unrecognized. Another is the proper employment of optical devices. For example, spectacle lenses to eliminate the need for excessive accommodation with its associated convergence excess, and the employment of prisms in the lenses to permit the two eyes to see as a unit even though they may not be properly anatomically oriented. Another kind of treatment is orthoptics, the use of exercises and rather complex optical equipment in a laboratory to train the patient in coordination between the two eyes. Treatment with drugs is based on the fact that certain drugs reduce the effort necessary for accommodation (much as eye-glasses do) and therefore lessen the stimulus toward convergence which may possibly tend toward the development of convergent strabismus. PMID:13662849

  10. Probing dark energy using convergence power spectrum and bi-spectrum

    NASA Astrophysics Data System (ADS)

    Dinda, Bikash R.

    2017-09-01

    Weak lensing convergence statistics is a powerful tool to probe dark energy. Dark energy plays an important role to the structure formation and the effects can be detected through the convergence power spectrum, bi-spectrum etc. One of the most promising and simplest dark energy model is the ΛCDM . However, it is worth investigating different dark energy models with evolving equation of state of the dark energy. In this work, detectability of different dark energy models from ΛCDM model has been explored through convergence power spectrum and bi-spectrum.

  11. More than one way to be an herbivore: convergent evolution of herbivory using different digestive strategies in prickleback fishes (Stichaeidae).

    PubMed

    German, Donovan P; Sung, Aaron; Jhaveri, Parth; Agnihotri, Ritika

    2015-06-01

    In fishes, the evolution of herbivory has occured within a spectrum of digestive strategies, with two extremes on opposite ends: (i) a rate-maximization strategy characterized by high intake, rapid throughput of food through the gut, and little reliance on microbial digestion or (ii) a yield-maximization strategy characterized by measured intake, slower transit of food through the gut, and more of a reliance on microbial digestion in the hindgut. One of these strategies tends to be favored within a given clade of fishes. Here, we tested the hypothesis that rate or yield digestive strategies can arise in convergently evolved herbivores within a given lineage. In the family Stichaeidae, convergent evolution of herbivory occured in Cebidichthys violaceus and Xiphister mucosus, and despite nearly identical diets, these two species have different digestive physiologies. We found that C. violaceus has more digesta in its distal intestine than other gut regions, has comparatively high concentrations (>11 mM) of short-chain fatty acids (SCFA, the endpoints of microbial fermentation) in its distal intestine, and a spike in β-glucosidase activity in this gut region, findings that, when coupled to long retention times (>20 h) of food in the guts of C. violaceus, suggest a yield-maximizing strategy in this species. X. mucosus showed none of these features and was more similar to its sister taxon, the omnivorous Xiphister atropurpureus, in terms of digestive enzyme activities, gut content partitioning, and concentrations of SCFA in their distal intestines. We also contrasted these herbivores and omnivores with other sympatric stichaeid fishes, Phytichthys chirus (omnivore) and Anoplarchus purpurescens (carnivore), each of which had digestive physiologies consistent with the consumption of animal material. This study shows that rate- and yield-maximizing strategies can evolve in closely related fishes and suggests that resource partitioning can play out on the level of

  12. Phylogenomics of C(4) photosynthesis in sedges (Cyperaceae): multiple appearances and genetic convergence.

    PubMed

    Besnard, Guillaume; Muasya, A Muthama; Russier, Flavien; Roalson, Eric H; Salamin, Nicolas; Christin, Pascal-Antoine

    2009-08-01

    C(4) photosynthesis is an adaptive trait conferring an advantage in warm and open habitats. It originated multiple times and is currently reported in 18 plant families. It has been recently shown that phosphoenolpyruvate carboxylase (PEPC), a key enzyme of the C(4) pathway, evolved through numerous independent but convergent genetic changes in grasses (Poaceae). To compare the genetics of multiple C(4) origins on a broader scale, we reconstructed the evolutionary history of the C(4) pathway in sedges (Cyperaceae), the second most species-rich C(4) family. A sedge phylogeny based on two plastome genes (rbcL and ndhF) has previously identified six fully C(4) clades. Here, a relaxed molecular clock was used to calibrate this tree and showed that the first C(4) acquisition occurred in this family between 19.6 and 10.1 Ma. According to analyses of PEPC-encoding genes (ppc), at least five distinct C(4) origins are present in sedges. Two C(4) Eleocharis species, which were unrelated in the plastid phylogeny, acquired their C(4)-specific PEPC genes from a single source, probably through reticulate evolution or a horizontal transfer event. Acquisitions of C(4) PEPC in sedges have been driven by positive selection on at least 16 codons (3.5% of the studied gene segment). These sites underwent parallel genetic changes across the five sedge C(4) origins. Five of these sites underwent identical changes also in grass and eudicot C(4) lineages, indicating that genetic convergence is most important within families but that identical genetic changes occurred even among distantly related taxa. These lines of evidence give new insights into the constraints that govern molecular evolution.

  13. Convergent Evolution of Health Information Management and Health Informatics

    PubMed Central

    Gibson, C. J.; Abrams, K.

    2015-01-01

    Summary Clearly defined boundaries are disappearing among the activities, sources, and uses of health care data and information managed by health information management (HIM) and health informatics (HI) professionals. Definitions of the professional domains and scopes of practice for HIM and HI are converging with the proliferation of information and communication technologies in health care settings. Convergence is changing both the roles that HIM and HI professionals serve in their organizations as well as the competencies necessary for training future professionals. Many of these changes suggest a blurring of roles and responsibilities with increasingly overlapping curricula, job descriptions, and research agendas. Blurred lines in a highly competitive market create confusion for students and employers. In this essay, we provide some perspective on the changing landscape and suggest a course for the future. First we review the evolving definitions of HIM and HI. We next compare the current domains and competencies, review the characteristics as well as the education and credentialing of both disciplines, and examine areas of convergence. Given the current state, we suggest a path forward to strengthen the contributions HIM and HI professionals and educators make to the evolving health care environment. PMID:25848421

  14. Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas.

    PubMed

    Hu, Yibo; Wu, Qi; Ma, Shuai; Ma, Tianxiao; Shan, Lei; Wang, Xiao; Nie, Yonggang; Ning, Zemin; Yan, Li; Xiu, Yunfang; Wei, Fuwen

    2017-01-31

    Phenotypic convergence between distantly related taxa often mirrors adaptation to similar selective pressures and may be driven by genetic convergence. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to different families in the order Carnivora, but both have evolved a specialized bamboo diet and adaptive pseudothumb, representing a classic model of convergent evolution. However, the genetic bases of these morphological and physiological convergences remain unknown. Through de novo sequencing the red panda genome and improving the giant panda genome assembly with added data, we identified genomic signatures of convergent evolution. Limb development genes DYNC2H1 and PCNT have undergone adaptive convergence and may be important candidate genes for pseudothumb development. As evolutionary responses to a bamboo diet, adaptive convergence has occurred in genes involved in the digestion and utilization of bamboo nutrients such as essential amino acids, fatty acids, and vitamins. Similarly, the umami taste receptor gene TAS1R1 has been pseudogenized in both pandas. These findings offer insights into genetic convergence mechanisms underlying phenotypic convergence and adaptation to a specialized bamboo diet.

  15. Comparative genomics reveals convergent evolution between the bamboo-eating giant and red pandas

    PubMed Central

    Hu, Yibo; Wu, Qi; Ma, Shuai; Ma, Tianxiao; Shan, Lei; Wang, Xiao; Nie, Yonggang; Ning, Zemin; Yan, Li; Xiu, Yunfang; Wei, Fuwen

    2017-01-01

    Phenotypic convergence between distantly related taxa often mirrors adaptation to similar selective pressures and may be driven by genetic convergence. The giant panda (Ailuropoda melanoleuca) and red panda (Ailurus fulgens) belong to different families in the order Carnivora, but both have evolved a specialized bamboo diet and adaptive pseudothumb, representing a classic model of convergent evolution. However, the genetic bases of these morphological and physiological convergences remain unknown. Through de novo sequencing the red panda genome and improving the giant panda genome assembly with added data, we identified genomic signatures of convergent evolution. Limb development genes DYNC2H1 and PCNT have undergone adaptive convergence and may be important candidate genes for pseudothumb development. As evolutionary responses to a bamboo diet, adaptive convergence has occurred in genes involved in the digestion and utilization of bamboo nutrients such as essential amino acids, fatty acids, and vitamins. Similarly, the umami taste receptor gene TAS1R1 has been pseudogenized in both pandas. These findings offer insights into genetic convergence mechanisms underlying phenotypic convergence and adaptation to a specialized bamboo diet. PMID:28096377

  16. Origins of stereoselectivity in evolved ketoreductases.

    PubMed

    Noey, Elizabeth L; Tibrewal, Nidhi; Jiménez-Osés, Gonzalo; Osuna, Sílvia; Park, Jiyong; Bond, Carly M; Cascio, Duilio; Liang, Jack; Zhang, Xiyun; Huisman, Gjalt W; Tang, Yi; Houk, Kendall N

    2015-12-22

    Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP(+)-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation.

  17. Origins of stereoselectivity in evolved ketoreductases

    PubMed Central

    Noey, Elizabeth L.; Tibrewal, Nidhi; Jiménez-Osés, Gonzalo; Osuna, Sílvia; Park, Jiyong; Bond, Carly M.; Cascio, Duilio; Liang, Jack; Zhang, Xiyun; Huisman, Gjalt W.; Tang, Yi; Houk, Kendall N.

    2015-01-01

    Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP+-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation. PMID:26644568

  18. Structural Organization of Enzymes of the Phenylacetate Catabolic Hybrid Pathway.

    PubMed

    Grishin, Andrey M; Cygler, Miroslaw

    2015-06-12

    Aromatic compounds are the second most abundant class of molecules on the earth and frequent environmental pollutants. They are difficult to metabolize due to an inert chemical structure, and of all living organisms, only microbes have evolved biochemical pathways that can open an aromatic ring and catabolize thus formed organic molecules. In bacterial genomes, the phenylacetate (PA) utilization pathway is abundant and represents the central route for degradation of a variety of organic compounds, whose degradation reactions converge at this pathway. The PA pathway is a hybrid pathway and combines the dual features of aerobic metabolism, i.e., usage of both oxygen to open the aromatic ring and of anaerobic metabolism-coenzyme A derivatization of PA. This allows the degradation process to be adapted to fluctuating oxygen conditions. In this review we focus on the structural and functional aspects of enzymes and their complexes involved in the PA degradation by the catabolic hybrid pathway. We discuss the ability of the central PaaABCE monooxygenase to reversibly oxygenate PA, the controlling mechanisms of epoxide concentration by the pathway enzymes, and the similarity of the PA utilization pathway to the benzoate utilization Box pathway and β-oxidation of fatty acids.

  19. Phage lytic enzymes: a history.

    PubMed

    Trudil, David

    2015-02-01

    There are many recent studies regarding the efficacy of bacteriophage-related lytic enzymes: the enzymes of 'bacteria-eaters' or viruses that infect bacteria. By degrading the cell wall of the targeted bacteria, these lytic enzymes have been shown to efficiently lyse Gram-positive bacteria without affecting normal flora and non-related bacteria. Recent studies have suggested approaches for lysing Gram-negative bacteria as well (Briersa Y, et al., 2014). These enzymes include: phage-lysozyme, endolysin, lysozyme, lysin, phage lysin, phage lytic enzymes, phageassociated enzymes, enzybiotics, muralysin, muramidase, virolysin and designations such as Ply, PAE and others. Bacteriophages are viruses that kill bacteria, do not contribute to antimicrobial resistance, are easy to develop, inexpensive to manufacture and safe for humans, animals and the environment. The current focus on lytic enzymes has been on their use as anti-infectives in humans and more recently in agricultural research models. The initial translational application of lytic enzymes, however, was not associated with treating or preventing a specific disease but rather as an extraction method to be incorporated in a rapid bacterial detection assay (Bernstein D, 1997).The current review traces the translational history of phage lytic enzymes-from their initial discovery in 1986 for the rapid detection of group A streptococcus in clinical specimens to evolving applications in the detection and prevention of disease in humans and in agriculture.

  20. Evolving Sensitivity Balances Boolean Networks

    PubMed Central

    Luo, Jamie X.; Turner, Matthew S.

    2012-01-01

    We investigate the sensitivity of Boolean Networks (BNs) to mutations. We are interested in Boolean Networks as a model of Gene Regulatory Networks (GRNs). We adopt Ribeiro and Kauffman’s Ergodic Set and use it to study the long term dynamics of a BN. We define the sensitivity of a BN to be the mean change in its Ergodic Set structure under all possible loss of interaction mutations. Insilico experiments were used to selectively evolve BNs for sensitivity to losing interactions. We find that maximum sensitivity was often achievable and resulted in the BNs becoming topologically balanced, i.e. they evolve towards network structures in which they have a similar number of inhibitory and excitatory interactions. In terms of the dynamics, the dominant sensitivity strategy that evolved was to build BNs with Ergodic Sets dominated by a single long limit cycle which is easily destabilised by mutations. We discuss the relevance of our findings in the context of Stem Cell Differentiation and propose a relationship between pluripotent stem cells and our evolved sensitive networks. PMID:22586459

  1. How evolvable are polarization machines?

    NASA Astrophysics Data System (ADS)

    Laan, Liedewij; Murray, Andrew

    2012-02-01

    In many different cell types proper polarization is essential for cell function. Polarization mechanisms however, differ between cell types and even closely related species use a variety of polarization machines. Budding yeast, for example, depends on several parallel mechanisms to establish polarity. One mechanism (i) depends on reaction and diffusion of proteins in the membrane. Another one (ii) depends on reorganization of the actin cytoskeleton. So why does yeast use several mechanisms simultaneously? Can yeast also polarize robustly in the absence of one of them? We addressed these questions by evolving budding yeast in the absence of mechanism (i) or (ii). We deleted a mechanism by deleting one or two genes that are essential for its function. After the deletion of either mechanism the growth rate of cells was highly decreased (2-5 fold) and their cell shape was highly perturbed. Subsequently, we evolved these cells for 10 days. Surprisingly, the evolved cells rapidly overcame most of their polarity defects. They grow at 0.9x wildtype growth rate and their cell shape is signifigantly less perturbed. Now we will study how these cells rescued polarization. Did they fix the deleted mechanism, strengthen other mechanisms or evolve a completely new one?

  2. Slippery Texts and Evolving Literacies

    ERIC Educational Resources Information Center

    Mackey, Margaret

    2007-01-01

    The idea of "slippery texts" provides a useful descriptor for materials that mutate and evolve across different media. Eight adult gamers, encountering the slippery text "American McGee's Alice," demonstrate a variety of ways in which players attempt to manage their attention as they encounter a new text with many resonances. The range of their…

  3. Thermal and evolved gas analyzer

    NASA Technical Reports Server (NTRS)

    Williams, M. S.; Boynton, W. V.; James, R. L.; Verts, W. T.; Bailey, S. H.; Hamara, D. K.

    1998-01-01

    The Thermal and Evolved Gas Analyzer (TEGA) instrument will perform calorimetry and evolved gas analysis on soil samples collected from the Martian surface. TEGA is one of three instruments, along with a robotic arm, that form the Mars Volatile and Climate Survey (MVACS) payload. The other instruments are a stereo surface imager, built by Peter Smith of the University of Arizona and a meteorological station, built by JPL. The MVACS lander will investigate a Martian landing site at approximately 70 deg south latitude. Launch will take place from Kennedy Space Center in January, 1999. The TEGA project started in February, 1996. In the intervening 24 months, a flight instrument concept has been designed, prototyped, built as an engineering model and flight model, and tested. The instrument performs laboratory-quality differential-scanning calorimetry (DSC) over the temperature range of Mars ambient to 1400K. Low-temperature volatiles (water and carbon dioxide ices) and the carbonates will be analyzed in this temperature range. Carbonates melt and evolve carbon dioxide at temperatures above 600 C. Evolved oxygen (down to a concentration of 1 ppm) is detected, and C02 and water vapor and the isotopic variations of C02 and water vapor are detected and their concentrations measured. The isotopic composition provides important tests of the theory of solar system formation.

  4. The Evolving Demand for Skills.

    ERIC Educational Resources Information Center

    Greenspan, Alan

    From a macroeconomic perspective, the evolving demand for skills in the United States has been triggered by the accelerated expansion of computer and information technology, which has, in turn, brought significant changes to the workplace. Technological advances have made some wholly manual jobs obsolete. But even for many other workers, a rapidly…

  5. Signing Apes and Evolving Linguistics.

    ERIC Educational Resources Information Center

    Stokoe, William C.

    Linguistics retains from its antecedents, philology and the study of sacred writings, some of their apologetic and theological bias. Thus it has not been able to face squarely the question how linguistic function may have evolved from animal communication. Chimpanzees' use of signs from American Sign Language forces re-examination of language…

  6. Evolving enhanced topologies for the synchronization of dynamical complex networks.

    PubMed

    Gorochowski, Thomas E; di Bernardo, Mario; Grierson, Claire S

    2010-05-01

    Enhancing the synchronization of dynamical networks is of great interest to those designing and analyzing many man-made and natural systems. In this work, we investigate how network topology can be evolved to improve this property through the rewiring of edges. A computational tool called NETEVO performs this task using a simulated annealing metaheuristic. In contrast to other work which considers topological attributes when assessing current performance, we instead take a dynamical approach using simulated output from the system to direct the evolution of the network. Resultant topologies are analyzed using standard network measures, B matrices, and motif distributions. These uncover the convergence of many similar features for all our networks, highlighting also significant differences between those evolved using topological rather than dynamical performance measures.

  7. [Advances on enzymes and enzyme inhibitors research based on microfluidic devices].

    PubMed

    Hou, Feng-Hua; Ye, Jian-Qing; Chen, Zuan-Guang; Cheng, Zhi-Yi

    2010-06-01

    With the continuous development in microfluidic fabrication technology, microfluidic analysis has evolved from a concept to one of research frontiers in last twenty years. The research of enzymes and enzyme inhibitors based on microfluidic devices has also made great progress. Microfluidic technology improved greatly the analytical performance of the research of enzymes and enzyme inhibitors by reducing the consumption of reagents, decreasing the analysis time, and developing automation. This review focuses on the development and classification of enzymes and enzyme inhibitors research based on microfluidic devices.

  8. The evolving placenta: convergent evolution of variations in the endotheliochorial relationship.

    PubMed

    Enders, A C; Carter, A M

    2012-05-01

    Endotheliochorial placentas occur in orders from all four major clades of eutherian mammal. Species with this type of placenta include one of the smallest (pygmy shrew) and largest (African elephant) land mammals. The endotheliochorial placenta as a definitive form has an interhemal area consisting of maternal endothelium, interstitial lamina, trophoblast, individual or conjoint basal laminas, and fetal endothelium. We commonly think of such placentas as having hypertrophied maternal endothelium with abundant rough endoplasmic reticulum (rER), and as having hemophagous regions. Considering them as a whole, the trophoblast may be syncytial or cellular, fenestrated or nonfenestrated, and there may or may not be hemophagous regions. Variations also appear in the extent of hypertrophy of the maternal endothelium and in the abundance of rER in these cells. This combination of traits and a few other features produces many morphological variants. In addition to endotheliochorial as a definitive condition, a transitory endotheliochorial condition may appear in the course of forming a hemochorial placenta. In some emballonurid bats the early endotheliochorial placenta has two layers of trophoblast, but the definitive placenta lacks an outer syncytial trophoblast layer. In mollosid bats a well developed endotheliochorial placenta is present for a short time even after a definitive hemochorial placenta has developed in a different region. It is concluded that the endotheliochorial placenta is more widespread and diversified than originally thought, with the variant with cellular trophoblast in particular appearing in several species studied recently. Copyright © 2012. Published by Elsevier Ltd.

  9. Provoking Points of Convergence: Museum and University Collaborating and Co-Evolving

    ERIC Educational Resources Information Center

    Kalin, Nadine; Grauer, Kit; Baird, Jill; Meszaros, Cheryl

    2007-01-01

    This article outlines art education courses undertaken in museum and gallery contexts as a component of the Certificate Programme in Visual and Material Culture within the University of British Columbia's Department of Curriculum Studies. With the creation of this programme and through the forging of relationships with area museums, unique ways…

  10. Gene duplications circumvent trade-offs in enzyme function: Insect adaptation to toxic host plants.

    PubMed

    Dalla, Safaa; Dobler, Susanne

    2016-12-01

    Herbivorous insects and their adaptations against plant toxins provide striking opportunities to investigate the genetic basis of traits involved in coevolutionary interactions. Target site insensitivity to cardenolides has evolved convergently across six orders of insects, involving identical substitutions in the Na,K-ATPase gene and repeated convergent gene duplications. The large milkweed bug, Oncopeltus fasciatus, has three copies of the Na,K-ATPase α-subunit gene that bear differing numbers of amino acid substitutions in the binding pocket for cardenolides. To analyze the effect of these substitutions on cardenolide resistance and to infer possible trade-offs in gene function, we expressed the cardenolide-sensitive Na,K-ATPase of Drosophila melanogaster in vitro and introduced four distinct combinations of substitutions observed in the three gene copies of O. fasciatus. With an increasing number of substitutions, the sensitivity of the Na,K-ATPase to a standard cardenolide decreased in a stepwise manner. At the same time, the enzyme's overall activity decreased significantly with increasing cardenolide resistance and only the least substituted mimic of the Na,K-ATPase α1C copy maintained activity similar to the wild-type enzyme. Our results suggest that the Na,K-ATPase copies in O. fasciatus have diverged in function, enabling specific adaptations to dietary cardenolides while maintaining the functionality of this critical ion carrier. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  11. Non-uniform Evolving Hypergraphs and Weighted Evolving Hypergraphs

    PubMed Central

    Guo, Jin-Li; Zhu, Xin-Yun; Suo, Qi; Forrest, Jeffrey

    2016-01-01

    Firstly, this paper proposes a non-uniform evolving hypergraph model with nonlinear preferential attachment and an attractiveness. This model allows nodes to arrive in batches according to a Poisson process and to form hyperedges with existing batches of nodes. Both the number of arriving nodes and that of chosen existing nodes are random variables so that the size of each hyperedge is non-uniform. This paper establishes the characteristic equation of hyperdegrees, calculates changes in the hyperdegree of each node, and obtains the stationary average hyperdegree distribution of the model by employing the Poisson process theory and the characteristic equation. Secondly, this paper constructs a model for weighted evolving hypergraphs that couples the establishment of new hyperedges, nodes and the dynamical evolution of the weights. Furthermore, what is obtained are respectively the stationary average hyperdegree and hyperstrength distributions by using the hyperdegree distribution of the established unweighted model above so that the weighted evolving hypergraph exhibits a scale-free behavior for both hyperdegree and hyperstrength distributions. PMID:27845334

  12. Genome-level and biochemical diversity of the acyl-activating enzyme superfamily in plants.

    PubMed

    Shockey, Jay; Browse, John

    2011-04-01

    In higher plants, the superfamily of carboxyl-CoA ligases and related proteins, collectively called acyl activating enzymes (AAEs), has evolved to provide enzymes for many pathways of primary and secondary metabolism and for the conjugation of hormones to amino acids. Across the superfamily there is only limited sequence similarity, but a series of highly conserved motifs, including the AMP-binding domain, make it easy to identify members. These conserved motifs are best understood in terms of the unique domain-rotation architecture that allows AAE enzymes to catalyze the two distinct steps of the CoA ligase reaction. Arabidopsis AAE sequences were used to identify the AAE gene families in the sequenced genomes of green algae, mosses, and trees; the size of the respective families increased with increasing degree of organismal cellular complexity, size, and generation time. Large-scale genome duplications and small-scale tandem gene duplications have contributed to AAE gene family complexity to differing extents in each of the multicellular species analyzed. Gene duplication and evolution of novel functions in Arabidopsis appears to have occurred rapidly, because acquisition of new substrate specificity is relatively easy in this class of proteins. Convergent evolution has also occurred between members of distantly related clades. These features of the AAE superfamily make it difficult to use homology searches and other genomics tools to predict enzyme function. The Plant Journal © 2011 Blackwell Publishing Ltd. No claim to original US government works.

  13. Monotonically convergent optimization in quantum control using Krotov's method.

    PubMed

    Reich, Daniel M; Ndong, Mamadou; Koch, Christiane P

    2012-03-14

    The non-linear optimization method developed by A. Konnov and V. Krotov [Autom. Remote Cont. (Engl. Transl.) 60, 1427 (1999)] has been used previously to extend the capabilities of optimal control theory from the linear to the non-linear Schrödinger equation [S. E. Sklarz and D. J. Tannor, Phys. Rev. A 66, 053619 (2002)]. Here we show that based on the Konnov-Krotov method, monotonically convergent algorithms are obtained for a large class of quantum control problems. It includes, in addition to nonlinear equations of motion, control problems that are characterized by non-unitary time evolution, nonlinear dependencies of the Hamiltonian on the control, time-dependent targets, and optimization functionals that depend to higher than second order on the time-evolving states. We furthermore show that the nonlinear (second order) contribution can be estimated either analytically or numerically, yielding readily applicable optimization algorithms. We demonstrate monotonic convergence for an optimization functional that is an eighth-degree polynomial in the states. For the "standard" quantum control problem of a convex final-time functional, linear equations of motion and linear dependency of the Hamiltonian on the field, the second-order contribution is not required for monotonic convergence but can be used to speed up convergence. We demonstrate this by comparing the performance of first- and second-order algorithms for two examples.

  14. Monotonically convergent optimization in quantum control using Krotov's method

    SciTech Connect

    Reich, Daniel M.; Koch, Christiane P.; Ndong, Mamadou

    2012-03-14

    The non-linear optimization method developed by A. Konnov and V. Krotov [Autom. Remote Cont. (Engl. Transl.) 60, 1427 (1999)] has been used previously to extend the capabilities of optimal control theory from the linear to the non-linear Schroedinger equation [S. E. Sklarz and D. J. Tannor, Phys. Rev. A 66, 053619 (2002)]. Here we show that based on the Konnov-Krotov method, monotonically convergent algorithms are obtained for a large class of quantum control problems. It includes, in addition to nonlinear equations of motion, control problems that are characterized by non-unitary time evolution, nonlinear dependencies of the Hamiltonian on the control, time-dependent targets, and optimization functionals that depend to higher than second order on the time-evolving states. We furthermore show that the nonlinear (second order) contribution can be estimated either analytically or numerically, yielding readily applicable optimization algorithms. We demonstrate monotonic convergence for an optimization functional that is an eighth-degree polynomial in the states. For the ''standard'' quantum control problem of a convex final-time functional, linear equations of motion and linear dependency of the Hamiltonian on the field, the second-order contribution is not required for monotonic convergence but can be used to speed up convergence. We demonstrate this by comparing the performance of first- and second-order algorithms for two examples.

  15. Identical skin toxins by convergent molecular adaptation in frogs.

    PubMed

    Roelants, Kim; Fry, Bryan G; Norman, Janette A; Clynen, Elke; Schoofs, Liliane; Bossuyt, Franky

    2010-01-26

    The Tree of Life is rife with adaptive convergences at all scales and biological levels of complexity. However, natural selection is not likely to result in the independent evolution of identical gene products. Here we report such a striking example of evolutionary convergence in the toxic skin secretions of two distantly related frog lineages. Caeruleins are important decapeptides in pharmacological and clinical research [1] and are commonly believed to represent a single evolutionary class of peptides [2-4]. Instead, our phylogenetic analyses combining transcriptome and genome data reveal that independently evolved precursor genes encode identical caeruleins in Xenopus and Litoria frogs. The former arose by duplication from the cholecystokinin (cck) gene, whereas the latter was derived from the gastrin gene. These hormone genes that are involved in many physiological processes diverged early in vertebrate evolution, after a segmental duplication during the Cambrian period. Besides implicating convergent mutations of the peptide-encoding sequence, recurrent caerulein origins entail parallel shifts of expression from the gut-brain axis to skin secretory glands. These results highlight extreme structural convergence in anciently diverged genes as an evolutionary mechanism through which recurrent adaptation is attained across large phylogenetic distances. Copyright 2010 Elsevier Ltd. All rights reserved.

  16. Convergence methods on time scales

    NASA Astrophysics Data System (ADS)

    Turan, Ceylan; Duman, Oktay

    2013-10-01

    In this paper, we introduce the concepts of lacunary statistical convergence and strongly lacunary Cesàro summability of delta measurable functions on time scales and obtain some inclusion results between them. We also display some examples containing discrete and continuous cases.

  17. Convergence of a Catalan Series

    ERIC Educational Resources Information Center

    Koshy, Thomas; Gao, Zhenguang

    2012-01-01

    This article studies the convergence of the infinite series of the reciprocals of the Catalan numbers. We extract the sum of the series as well as some related ones, illustrating the power of the calculus in the study of the Catalan numbers.

  18. Convergent genetic architecture underlies social organization in ants.

    PubMed

    Purcell, Jessica; Brelsford, Alan; Wurm, Yannick; Perrin, Nicolas; Chapuisat, Michel

    2014-11-17

    Complex adaptive polymorphisms are common in nature, but what mechanisms maintain the underlying favorable allelic combinations? The convergent evolution of polymorphic social organization in two independent ant species provides a great opportunity to investigate how genomes evolved under parallel selection. Here, we demonstrate that a large, nonrecombining "social chromosome" is associated with social organization in the Alpine silver ant, Formica selysi. This social chromosome shares architectural characteristics with that of the fire ant Solenopsis invicta, but the two show no detectable similarity in gene content. The discovery of convergence at two levels--the phenotype and the genetic architecture associated with alternative social forms--points at general genetic mechanisms underlying transitions in social organization. More broadly, our findings are consistent with recent theoretical studies suggesting that suppression of recombination plays a key role in facilitating coordinated shifts in coadapted traits.

  19. Convergent local adaptation to climate in distantly related conifers.

    PubMed

    Yeaman, Sam; Hodgins, Kathryn A; Lotterhos, Katie E; Suren, Haktan; Nadeau, Simon; Degner, Jon C; Nurkowski, Kristin A; Smets, Pia; Wang, Tongli; Gray, Laura K; Liepe, Katharina J; Hamann, Andreas; Holliday, Jason A; Whitlock, Michael C; Rieseberg, Loren H; Aitken, Sally N

    2016-09-23

    When confronted with an adaptive challenge, such as extreme temperature, closely related species frequently evolve similar phenotypes using the same genes. Although such repeated evolution is thought to be less likely in highly polygenic traits and distantly related species, this has not been tested at the genome scale. We performed a population genomic study of convergent local adaptation among two distantly related species, lodgepole pine and interior spruce. We identified a suite of 47 genes, enriched for duplicated genes, with variants associated with spatial variation in temperature or cold hardiness in both species, providing evidence of convergent local adaptation despite 140 million years of separate evolution. These results show that adaptation to climate can be genetically constrained, with certain key genes playing nonredundant roles.

  20. Convergent evolution in locomotory patterns of flying and swimming animals.

    PubMed

    Gleiss, Adrian C; Jorgensen, Salvador J; Liebsch, Nikolai; Sala, Juan E; Norman, Brad; Hays, Graeme C; Quintana, Flavio; Grundy, Edward; Campagna, Claudio; Trites, Andrew W; Block, Barbara A; Wilson, Rory P

    2011-06-14

    Locomotion is one of the major energetic costs faced by animals and various strategies have evolved to reduce its cost. Birds use interspersed periods of flapping and gliding to reduce the mechanical requirements of level flight while undergoing cyclical changes in flight altitude, known as undulating flight. Here we equipped free-ranging marine vertebrates with accelerometers and demonstrate that gait patterns resembling undulating flight occur in four marine vertebrate species comprising sharks and pinnipeds. Both sharks and pinnipeds display intermittent gliding interspersed with powered locomotion. We suggest, that the convergent use of similar gait patterns by distinct groups of animals points to universal physical and physiological principles that operate beyond taxonomic limits and shape common solutions to increase energetic efficiency. Energetically expensive large-scale migrations performed by many vertebrates provide common selection pressure for efficient locomotion, with potential for the convergence of locomotory strategies by a wide variety of species.

  1. Coupled oscillators on evolving networks

    NASA Astrophysics Data System (ADS)

    Singh, R. K.; Bagarti, Trilochan

    2016-12-01

    In this work we study coupled oscillators on evolving networks. We find that the steady state behavior of the system is governed by the relative values of the spread in natural frequencies and the global coupling strength. For coupling strong in comparison to the spread in frequencies, the system of oscillators synchronize and when coupling strength and spread in frequencies are large, a phenomenon similar to amplitude death is observed. The network evolution provides a mechanism to build inter-oscillator connections and once a dynamic equilibrium is achieved, oscillators evolve according to their local interactions. We also find that the steady state properties change by the presence of additional time scales. We demonstrate these results based on numerical calculations studying dynamical evolution of limit-cycle and van der Pol oscillators.

  2. Evolvable Hardware for Space Applications

    NASA Technical Reports Server (NTRS)

    Lohn, Jason; Globus, Al; Hornby, Gregory; Larchev, Gregory; Kraus, William

    2004-01-01

    This article surveys the research of the Evolvable Systems Group at NASA Ames Research Center. Over the past few years, our group has developed the ability to use evolutionary algorithms in a variety of NASA applications ranging from spacecraft antenna design, fault tolerance for programmable logic chips, atomic force field parameter fitting, analog circuit design, and earth observing satellite scheduling. In some of these applications, evolutionary algorithms match or improve on human performance.

  3. Ranking in evolving complex networks

    NASA Astrophysics Data System (ADS)

    Liao, Hao; Mariani, Manuel Sebastian; Medo, Matúš; Zhang, Yi-Cheng; Zhou, Ming-Yang

    2017-05-01

    Complex networks have emerged as a simple yet powerful framework to represent and analyze a wide range of complex systems. The problem of ranking the nodes and the edges in complex networks is critical for a broad range of real-world problems because it affects how we access online information and products, how success and talent are evaluated in human activities, and how scarce resources are allocated by companies and policymakers, among others. This calls for a deep understanding of how existing ranking algorithms perform, and which are their possible biases that may impair their effectiveness. Many popular ranking algorithms (such as Google's PageRank) are static in nature and, as a consequence, they exhibit important shortcomings when applied to real networks that rapidly evolve in time. At the same time, recent advances in the understanding and modeling of evolving networks have enabled the development of a wide and diverse range of ranking algorithms that take the temporal dimension into account. The aim of this review is to survey the existing ranking algorithms, both static and time-aware, and their applications to evolving networks. We emphasize both the impact of network evolution on well-established static algorithms and the benefits from including the temporal dimension for tasks such as prediction of network traffic, prediction of future links, and identification of significant nodes.

  4. Evolving Systems and Adaptive Key Component Control

    NASA Technical Reports Server (NTRS)

    Frost, Susan A.; Balas, Mark J.

    2009-01-01

    We propose a new framework called Evolving Systems to describe the self-assembly, or autonomous assembly, of actively controlled dynamical subsystems into an Evolved System with a higher purpose. An introduction to Evolving Systems and exploration of the essential topics of the control and stability properties of Evolving Systems is provided. This chapter defines a framework for Evolving Systems, develops theory and control solutions for fundamental characteristics of Evolving Systems, and provides illustrative examples of Evolving Systems and their control with adaptive key component controllers.

  5. Two developmentally temporal quantitative trait loci underlie convergent evolution of increased branchial bone length in sticklebacks.

    PubMed

    Erickson, Priscilla A; Glazer, Andrew M; Cleves, Phillip A; Smith, Alyson S; Miller, Craig T

    2014-08-07

    In convergent evolution, similar phenotypes evolve repeatedly in independent populations, often reflecting adaptation to similar environments. Understanding whether convergent evolution proceeds via similar or different genetic and developmental mechanisms offers insight towards the repeatability and predictability of evolution. Oceanic populations of threespine stickleback fish, Gasterosteus aculeatus, have repeatedly colonized countless freshwater lakes and streams, where new diets lead to morphological adaptations related to feeding. Here, we show that heritable increases in branchial bone length have convergently evolved in two independently derived freshwater stickleback populations. In both populations, an increased bone growth rate in juveniles underlies the convergent adult phenotype, and one population also has a longer cartilage template. Using F2 crosses from these two freshwater populations, we show that two quantitative trait loci (QTL) control branchial bone length at distinct points in development. In both populations, a QTL on chromosome 21 controls bone length throughout juvenile development, and a QTL on chromosome 4 controls bone length only in adults. In addition to these similar developmental profiles, these QTL show similar chromosomal locations in both populations. Our results suggest that sticklebacks have convergently evolved longer branchial bones using similar genetic and developmental programmes in two independently derived populations. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  6. A Dome-Headed Stem Archosaur Exemplifies Convergence among Dinosaurs and Their Distant Relatives.

    PubMed

    Stocker, Michelle R; Nesbitt, Sterling J; Criswell, Katharine E; Parker, William G; Witmer, Lawrence M; Rowe, Timothy B; Ridgely, Ryan; Brown, Matthew A

    2016-10-10

    Similarities in body plan evolution, such as wings in pterosaurs, birds, and bats or limblessness in snakes and amphisbaenians, can be recognized as classical examples of convergence among animals [1-3]. We introduce a new Triassic stem archosaur that is unexpectedly and remarkably convergent with the "dome-headed" pachycephalosaur dinosaurs that lived over 100 million years later. Surprisingly, numerous additional taxa in the same assemblage (the Otis Chalk assemblage from the Dockum Group of Texas) demonstrate the early acquisition of morphological novelties that were later convergently evolved by post-Triassic dinosaurs. As one of the most successful clades of terrestrial vertebrates, dinosaurs came to occupy an extensive morphospace throughout their diversification in the Mesozoic Era [4, 5], but their distant relatives were first to evolve many of those "dinosaurian" body plans in the Triassic Period [6-8]. Our analysis of convergence between archosauromorphs from the Triassic Period and post-Triassic archosaurs demonstrates the early and extensive exploration of morphospace captured in a single Late Triassic assemblage, and we hypothesize that many of the "novel" morphotypes interpreted to occur among archosaurs later in the Mesozoic already were in place during the initial Triassic archosauromorph, largely non-dinosaurian, radiation and only later convergently evolved in diverse dinosaurian lineages.

  7. Converging Higher Education Systems in a Global Setting: The Example of France and India

    ERIC Educational Resources Information Center

    Pilkington, Marc

    2014-01-01

    We present a comparative survey between the French and Indian higher education systems. In spite of their respective idiosyncratic features, we show that the two countries have both evolved comprehensively toward a knowledge-based society, in order to ensure the prosperity of their citizens. Secondly, we single out a threefold convergence between…

  8. Convergent evolution of modularity in metabolic networks through different community structures.

    PubMed

    Zhou, Wanding; Nakhleh, Luay

    2012-09-14

    It has been reported that the modularity of metabolic networks of bacteria is closely related to the variability of their living habitats. However, given the dependency of the modularity score on the community structure, it remains unknown whether organisms achieve certain modularity via similar or different community structures. In this work, we studied the relationship between similarities in modularity scores and similarities in community structures of the metabolic networks of 1021 species. Both similarities are then compared against the genetic distances. We revisited the association between modularity and variability of the microbial living environments and extended the analysis to other aspects of their life style such as temperature and oxygen requirements. We also tested both topological and biological intuition of the community structures identified and investigated the extent of their conservation with respect to the taxonomy. We find that similar modularities are realized by different community structures. We find that such convergent evolution of modularity is closely associated with the number of (distinct) enzymes in the organism's metabolome, a consequence of different life styles of the species. We find that the order of modularity is the same as the order of the number of the enzymes under the classification based on the temperature preference but not on the oxygen requirement. Besides, inspection of modularity-based communities reveals that these communities are graph-theoretically meaningful yet not reflective of specific biological functions. From an evolutionary perspective, we find that the community structures are conserved only at the level of kingdoms. Our results call for more investigation into the interplay between evolution and modularity: how evolution shapes modularity, and how modularity affects evolution (mainly in terms of fitness and evolvability). Further, our results call for exploring new measures of modularity and network

  9. 5G: The Convergence of Wireless Communications.

    PubMed

    Chávez-Santiago, Raúl; Szydełko, Michał; Kliks, Adrian; Foukalas, Fotis; Haddad, Yoram; Nolan, Keith E; Kelly, Mark Y; Masonta, Moshe T; Balasingham, Ilangko

    As the rollout of 4G mobile communication networks takes place, representatives of industry and academia have started to look into the technological developments toward the next generation (5G). Several research projects involving key international mobile network operators, infrastructure manufacturers, and academic institutions, have been launched recently to set the technological foundations of 5G. However, the architecture of future 5G systems, their performance, and mobile services to be provided have not been clearly defined. In this paper, we put forth the vision for 5G as the convergence of evolved versions of current cellular networks with other complementary radio access technologies. Therefore, 5G may not be a single radio access interface but rather a "network of networks". Evidently, the seamless integration of a variety of air interfaces, protocols, and frequency bands, requires paradigm shifts in the way networks cooperate and complement each other to deliver data rates of several Gigabits per second with end-to-end latency of a few milliseconds. We provide an overview of the key radio technologies that will play a key role in the realization of this vision for the next generation of mobile communication networks. We also introduce some of the research challenges that need to be addressed.

  10. Bat echolocation calls: adaptation and convergent evolution

    PubMed Central

    Jones, Gareth; Holderied, Marc W

    2007-01-01

    Bat echolocation calls provide remarkable examples of ‘good design’ through evolution by natural selection. Theory developed from acoustics and sonar engineering permits a strong predictive basis for understanding echolocation performance. Call features, such as frequency, bandwidth, duration and pulse interval are all related to ecological niche. Recent technological breakthroughs have aided our understanding of adaptive aspects of call design in free-living bats. Stereo videogrammetry, laser scanning of habitat features and acoustic flight path tracking permit reconstruction of the flight paths of echolocating bats relative to obstacles and prey in nature. These methods show that echolocation calls are among the most intense airborne vocalizations produced by animals. Acoustic tracking has clarified how and why bats vary call structure in relation to flight speed. Bats using broadband echolocation calls adjust call design in a range-dependent manner so that nearby obstacles are localized accurately. Recent phylogenetic analyses based on gene sequences show that particular types of echolocation signals have evolved independently in several lineages of bats. Call design is often influenced more by perceptual challenges imposed by the environment than by phylogeny, and provides excellent examples of convergent evolution. Now that whole genome sequences of bats are imminent, understanding the functional genomics of echolocation will become a major challenge. PMID:17251105

  11. Evolutionary Aspects of Enzyme Dynamics*

    PubMed Central

    Klinman, Judith P.; Kohen, Amnon

    2014-01-01

    The role of evolutionary pressure on the chemical step catalyzed by enzymes is somewhat enigmatic, in part because chemistry is not rate-limiting for many optimized systems. Herein, we present studies that examine various aspects of the evolutionary relationship between protein dynamics and the chemical step in two paradigmatic enzyme families, dihydrofolate reductases and alcohol dehydrogenases. Molecular details of both convergent and divergent evolution are beginning to emerge. The findings suggest that protein dynamics across an entire enzyme can play a role in adaptation to differing physiological conditions. The growing tool kit of kinetics, kinetic isotope effects, molecular biology, biophysics, and bioinformatics provides means to link evolutionary changes in structure-dynamics function to the vibrational and conformational states of each protein. PMID:25210031

  12. Convergence.

    ERIC Educational Resources Information Center

    Hancock, Alan

    1984-01-01

    Characterizes the development over the past 30 years of the communication technologies employed in education by examining technological developments, structure of individual media, objectives and audiences of media systems, access to communications technologies, appropriateness of technology in new environments, social impact, and policy…

  13. Convergence.

    ERIC Educational Resources Information Center

    Hancock, Alan

    1984-01-01

    Characterizes the development over the past 30 years of the communication technologies employed in education by examining technological developments, structure of individual media, objectives and audiences of media systems, access to communications technologies, appropriateness of technology in new environments, social impact, and policy…

  14. Evolving Dynamics of the Supergranular Flow Field

    NASA Astrophysics Data System (ADS)

    De Rosa, M. L.; Lisle, J. P.; Toomre, J.

    2000-05-01

    We study several large (45-degree square) fields of supergranules for as long as they remain visible on the solar disk (about 6 days) to characterize the dynamics of the supergranular flow field and its interaction with surrounding photospheric magnetic field elements. These flow fields are determined by applying correlation tracking methods to time series of mesogranules seen in full-disk SOI-MDI velocity images. We have shown previously that mesogranules observed in this way are systematically advected by the larger scale supergranular flow field in which they are embedded. Applying correlation tracking methods to such time series yields the positions of the supergranular outflows quite well, even for locations close to disk center. These long-duration datasets contain several instances where individual supergranules are recognizable for time scales as long as 50 hours, though most cells persist for about 25 hours that is often quoted as a supergranular lifetime. Many supergranule merging and splitting events are observed, as well as other evolving flow patterns such as lanes of converging and diverging fluid. By comparing the flow fields with the corresponding images of magnetic fields, we confirm the result that small-scale photospheric magnetic field elements are quickly advected to the intercellular lanes to form a network between the supergranular outflows. In addition, we characterize the influence of larger-scale regions of magnetic flux, such as active regions, on the flow fields. Furthermore, we have measured even larger-scale flows by following the motions of the supergranules, but these flow fields contain a high noise component and are somewhat difficult to interpret. This research was supported by NASA through grants NAG 5-8133 and NAG 5-7996, and by NSF through grant ATM-9731676.

  15. Phylogenetic origins of biological cognition: convergent patterns in the early evolution of learning.

    PubMed

    van Duijn, Marc

    2017-06-06

    Various forms of elementary learning have recently been discovered in organisms lacking a nervous system, such as protists, fungi and plants. This finding has fundamental implications for how we view the role of convergent evolution in biological cognition. In this article, I first review the evidence for basic forms of learning in aneural organisms, focusing particularly on habituation and classical conditioning and considering the plausibility for convergent evolution of these capacities. Next, I examine the possible role of convergent evolution regarding these basic learning abilities during the early evolution of nervous systems. The evolution of nervous systems set the stage for at least two major events relevant to convergent evolution that are central to biological cognition: (i) nervous systems evolved, perhaps more than once, because of strong selection pressures for sustaining sensorimotor strategies in increasingly larger multicellular organisms and (ii) associative learning was a subsequent adaptation that evolved multiple times within the neuralia. Although convergent evolution of basic forms of learning among distantly related organisms such as protists, plants and neuralia is highly plausible, more research is needed to verify whether these forms of learning within the neuralia arose through convergent or parallel evolution.

  16. The evolvability of programmable hardware

    PubMed Central

    Raman, Karthik; Wagner, Andreas

    2011-01-01

    In biological systems, individual phenotypes are typically adopted by multiple genotypes. Examples include protein structure phenotypes, where each structure can be adopted by a myriad individual amino acid sequence genotypes. These genotypes form vast connected ‘neutral networks’ in genotype space. The size of such neutral networks endows biological systems not only with robustness to genetic change, but also with the ability to evolve a vast number of novel phenotypes that occur near any one neutral network. Whether technological systems can be designed to have similar properties is poorly understood. Here we ask this question for a class of programmable electronic circuits that compute digital logic functions. The functional flexibility of such circuits is important in many applications, including applications of evolutionary principles to circuit design. The functions they compute are at the heart of all digital computation. We explore a vast space of 1045 logic circuits (‘genotypes’) and 1019 logic functions (‘phenotypes’). We demonstrate that circuits that compute the same logic function are connected in large neutral networks that span circuit space. Their robustness or fault-tolerance varies very widely. The vicinity of each neutral network contains circuits with a broad range of novel functions. Two circuits computing different functions can usually be converted into one another via few changes in their architecture. These observations show that properties important for the evolvability of biological systems exist in a commercially important class of electronic circuitry. They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry. PMID:20534598

  17. Converging beam optical Fourier transforms

    NASA Astrophysics Data System (ADS)

    Puang-ngern, Srisuda; Almeida, Silverio P.

    1985-08-01

    The classical, most often used, system for performing the optical Fourier transform is by using parallel coherent beam illumination. Lenses used in this method can become quite costly. In this paper we present results obtained using converging beam illumination which is suitable for many applications and is less expensive than the parallel beam method. The input objects for which the Fourier transforms were made are transparencies of snowflakes.

  18. Adaptive sampling in convergent beams.

    PubMed

    Espinosa, Julián; Mas, David; Pérez, Jorge; Illueca, Carlos

    2008-09-01

    Numerical calculation of convergent Fresnel patterns through fast Fourier transform usually requires a large number of samples to fulfill the Nyquist sampling condition around the focus. From polynomial decomposition of the wavefront it is possible to determine which polynomial orders are the main contributors to the number of samples. This information can be used to properly modify the initial wavefront and relax the Nyquist condition thus giving a more efficient numerical algorithm.

  19. Regolith Evolved Gas Analyzer (REGA)

    NASA Technical Reports Server (NTRS)

    Allen, Carlton C.; McKay, David S.

    1997-01-01

    The instrument consists of five subsystems: (1) a programmable furnace which can be loaded with samples of regolith, (2) a mass spectrometer which detects and measures atmospheric gases or gases evolved during heating, (3) a tank of pressurized gas which can be introduced to the regolith material while detecting and measuring volatile reaction products, (4) a mechanism for dumping the regolith sample and repeating the experiment on a fresh sample, and (5) a data system which controls and monitors the furnace, gas system, and mass spectrometer.

  20. The 'E' factor -- evolving endodontics.

    PubMed

    Hunter, M J

    2013-03-01

    Endodontics is a constantly developing field, with new instruments, preparation techniques and sealants competing with trusted and traditional approaches to tooth restoration. Thus general dental practitioners must question and understand the significance of these developments before adopting new practices. In view of this, the aim of this article, and the associated presentation at the 2013 British Dental Conference & Exhibition, is to provide an overview of endodontic methods and constantly evolving best practice. The presentation will review current preparation techniques, comparing rotary versus reciprocation, and question current trends in restoration of the endodontically treated tooth.

  1. Regolith Evolved Gas Analyzer (REGA)

    NASA Technical Reports Server (NTRS)

    Allen, Carlton C.; McKay, David S.

    1997-01-01

    The instrument consists of five subsystems: (1) a programmable furnace which can be loaded with samples of regolith, (2) a mass spectrometer which detects and measures atmospheric gases or gases evolved during heating, (3) a tank of pressurized gas which can be introduced to the regolith material while detecting and measuring volatile reaction products, (4) a mechanism for dumping the regolith sample and repeating the experiment on a fresh sample, and (5) a data system which controls and monitors the furnace, gas system, and mass spectrometer.

  2. Improving Evolvability through Generative Representations

    NASA Technical Reports Server (NTRS)

    Hornby, Gregory S.

    2004-01-01

    One of the main limitations of computer automated design systems is the representation used for encoding designs. Using computer programs as an analogy, representations can be thought of as having the properties of combination, control-flow and abstraction. Generative representations are those which have the ability to reuse elements in an encoding through either iteration, a form of control-flow, or abstraction. Here we argue that generative representations improve the evolvability of designs by capturing design dependencies in a way that makes them easier to change, and we support this with examples from two design substrates.

  3. Languages evolve in punctuational bursts.

    PubMed

    Atkinson, Quentin D; Meade, Andrew; Venditti, Chris; Greenhill, Simon J; Pagel, Mark

    2008-02-01

    Linguists speculate that human languages often evolve in rapid or punctuational bursts, sometimes associated with their emergence from other languages, but this phenomenon has never been demonstrated. We used vocabulary data from three of the world's major language groups-Bantu, Indo-European, and Austronesian-to show that 10 to 33% of the overall vocabulary differences among these languages arose from rapid bursts of change associated with language-splitting events. Our findings identify a general tendency for increased rates of linguistic evolution in fledgling languages, perhaps arising from a linguistic founder effect or a desire to establish a distinct social identity.

  4. Zinc Enzymes.

    ERIC Educational Resources Information Center

    Bertini, I.; And Others

    1985-01-01

    Discusses the role of zinc in various enzymes concerned with hydration, hydrolysis, and redox reactions. The binding of zinc to protein residues, properties of noncatalytic zinc(II) and catalytic zinc, and the reactions catalyzed by zinc are among the topics considered. (JN)

  5. Food Enzymes

    ERIC Educational Resources Information Center

    McBroom, Rachel; Oliver-Hoyo, Maria T.

    2007-01-01

    Many students view biology and chemistry as two unrelated, separate sciences; how these courses are generally taught in high schools may do little to change that impression. The study of enzymes provide a great opportunity for both biology and chemistry teachers to share with students the interdisciplinary nature of science. This article describes…

  6. Zinc Enzymes.

    ERIC Educational Resources Information Center

    Bertini, I.; And Others

    1985-01-01

    Discusses the role of zinc in various enzymes concerned with hydration, hydrolysis, and redox reactions. The binding of zinc to protein residues, properties of noncatalytic zinc(II) and catalytic zinc, and the reactions catalyzed by zinc are among the topics considered. (JN)

  7. Engineering enzymes.

    PubMed

    Dutton, P Leslie; Moser, Christopher C

    2011-01-01

    Fundamental research into bioinorganic catalysis of the kind presented at this Faraday Discussion has the potential to turn inspiration drawn from impressive natural energy and chemical transformations into artificial catalyst constructions useful to mankind. Creating bio-inspired artificial constructions requires a level of understanding well beyond simple description of structures and mechanisms of natural enzymes. To be useful, such description must be augmented by a practical sense of structural and energetic engineering tolerances of the mechanism. Significant barriers to achieving an engineering understanding of enzyme mechanisms arise from natural protein complexity. In certain cases we can surmount these barriers to understanding, such as natural electron tunneling, coupling of electron tunneling to light capture and proton exchange as well as simpler bond breaking redox catalysis. Hope for similar solutions of more complex bioinorganic enzymes is indicated in several papers presented in this Discussion. Armed with an engineering understanding of mechanism, the current serious frustrations to successful creation of functional artificial proteins that are rooted in protein complexity can fall away. Here we discuss the genetic and biological roots of protein complexity and show how to dodge and minimize the effects of complexity. In the best-understood cases, artificial enzymes can be designed from scratch using the simplest of protein scaffolds.

  8. Food Enzymes

    ERIC Educational Resources Information Center

    McBroom, Rachel; Oliver-Hoyo, Maria T.

    2007-01-01

    Many students view biology and chemistry as two unrelated, separate sciences; how these courses are generally taught in high schools may do little to change that impression. The study of enzymes provide a great opportunity for both biology and chemistry teachers to share with students the interdisciplinary nature of science. This article describes…

  9. Widespread convergence in toxin resistance by predictable molecular evolution

    PubMed Central

    Ujvari, Beata; Casewell, Nicholas R.; Sunagar, Kartik; Arbuckle, Kevin; Wüster, Wolfgang; Lo, Nathan; O’Meally, Denis; Beckmann, Christa; King, Glenn F.; Deplazes, Evelyne; Madsen, Thomas

    2015-01-01

    The question about whether evolution is unpredictable and stochastic or intermittently constrained along predictable pathways is the subject of a fundamental debate in biology, in which understanding convergent evolution plays a central role. At the molecular level, documented examples of convergence are rare and limited to occurring within specific taxonomic groups. Here we provide evidence of constrained convergent molecular evolution across the metazoan tree of life. We show that resistance to toxic cardiac glycosides produced by plants and bufonid toads is mediated by similar molecular changes to the sodium-potassium-pump (Na+/K+-ATPase) in insects, amphibians, reptiles, and mammals. In toad-feeding reptiles, resistance is conferred by two point mutations that have evolved convergently on four occasions, whereas evidence of a molecular reversal back to the susceptible state in varanid lizards migrating to toad-free areas suggests that toxin resistance is maladaptive in the absence of selection. Importantly, resistance in all taxa is mediated by replacements of 2 of the 12 amino acids comprising the Na+/K+-ATPase H1–H2 extracellular domain that constitutes a core part of the cardiac glycoside binding site. We provide mechanistic insight into the basis of resistance by showing that these alterations perturb the interaction between the cardiac glycoside bufalin and the Na+/K+-ATPase. Thus, similar selection pressures have resulted in convergent evolution of the same molecular solution across the breadth of the animal kingdom, demonstrating how a scarcity of possible solutions to a selective challenge can lead to highly predictable evolutionary responses. PMID:26372961

  10. Widespread convergence in toxin resistance by predictable molecular evolution.

    PubMed

    Ujvari, Beata; Casewell, Nicholas R; Sunagar, Kartik; Arbuckle, Kevin; Wüster, Wolfgang; Lo, Nathan; O'Meally, Denis; Beckmann, Christa; King, Glenn F; Deplazes, Evelyne; Madsen, Thomas

    2015-09-22

    The question about whether evolution is unpredictable and stochastic or intermittently constrained along predictable pathways is the subject of a fundamental debate in biology, in which understanding convergent evolution plays a central role. At the molecular level, documented examples of convergence are rare and limited to occurring within specific taxonomic groups. Here we provide evidence of constrained convergent molecular evolution across the metazoan tree of life. We show that resistance to toxic cardiac glycosides produced by plants and bufonid toads is mediated by similar molecular changes to the sodium-potassium-pump (Na(+)/K(+)-ATPase) in insects, amphibians, reptiles, and mammals. In toad-feeding reptiles, resistance is conferred by two point mutations that have evolved convergently on four occasions, whereas evidence of a molecular reversal back to the susceptible state in varanid lizards migrating to toad-free areas suggests that toxin resistance is maladaptive in the absence of selection. Importantly, resistance in all taxa is mediated by replacements of 2 of the 12 amino acids comprising the Na(+)/K(+)-ATPase H1-H2 extracellular domain that constitutes a core part of the cardiac glycoside binding site. We provide mechanistic insight into the basis of resistance by showing that these alterations perturb the interaction between the cardiac glycoside bufalin and the Na(+)/K(+)-ATPase. Thus, similar selection pressures have resulted in convergent evolution of the same molecular solution across the breadth of the animal kingdom, demonstrating how a scarcity of possible solutions to a selective challenge can lead to highly predictable evolutionary responses.

  11. Open questions in the ethics of convergence.

    PubMed

    Khushf, George

    2007-01-01

    After historically situating NBIC Convergence in the context of earlier bioethical debate on genetics, ten questions are raised in areas related to the ethics of Convergence, indicating where future research is needed.

  12. Virulence-Associated Enzymes of Cryptococcus neoformans

    PubMed Central

    Almeida, Fausto; Wolf, Julie M.

    2015-01-01

    Enzymes play key roles in fungal pathogenesis. Manipulation of enzyme expression or activity can significantly alter the infection process, and enzyme expression profiles can be a hallmark of disease. Hence, enzymes are worthy targets for better understanding pathogenesis and identifying new options for combatting fungal infections. Advances in genomics, proteomics, transcriptomics, and mass spectrometry have enabled the identification and characterization of new fungal enzymes. This review focuses on recent developments in the virulence-associated enzymes from Cryptococcus neoformans. The enzymatic suite of C. neoformans has evolved for environmental survival, but several of these enzymes play a dual role in colonizing the mammalian host. We also discuss new therapeutic and diagnostic strategies that could be based on the underlying enzymology. PMID:26453651

  13. Converging shocks for DSD modelling

    NASA Astrophysics Data System (ADS)

    Matignon, Christophe

    2013-06-01

    Modelling of pyrotechnic systems requires both, a good understanding and precise prediction capabilities of the dynamics of detonation. When using insensitive high explosives IHE (such as TATB-based explosives) the interaction of the detonation front with the confinement can lead to very different detonation velocities. One of the most popular engineering tools used to model this behaviour is the Detonation Shock Dynamics (DSD). In the DSD assumption, the detonation front propagates at a normal shock velocity (Dn) which depends only on its local curvature (κ). For divergent detonations, the DSD limit is very well established both experimentally and theoretically and one can easily propose a model (which obeys the 1D quasi-steady weakly curved detonation theory) to reproduce this behavior. We propose to extend the DSD theory to slightly convergent detonation fronts and to validate it against experimental data. Two series of experiments were carried out. The first series was designed to collect precise information regarding converging detonation. Usually, in such configurations, the detonation is non steady, making precise and simultaneous measurements of velocity and curvature difficult to achieve. The originality of the proposed setup is to drive a self similar convergent detonation at constant speed in an IHE rod by an external explosive tube of greater detonation velocity (allowing an accurate recording of both velocity and curvature). A wide range EOS/reaction rate model (inspired from previous works of Wescott et al.) was then calibrated to reproduce both the strong shock initiation and the newly extended (Dn- κ) law. This model can be used to perform either direct numerical simulation (DNS) on fine resolved mesh grid, or its reduced PZR model (DSD based) on a much coarser grid. This model was then successfully validated against the second series of experiments involving a detonation propagating around an obstacle and exhibiting a non steady converging front

  14. Stability of Evolving Multiagent Systems.

    PubMed

    De Wilde, P; Briscoe, G

    2011-08-01

    A multiagent system is a distributed system where the agents or nodes perform complex functions that cannot be written down in analytic form. Multiagent systems are highly connected, and the information they contain is mostly stored in the connections. When agents update their state, they take into account the state of the other agents, and they have access to those states via the connections. There is also external user-generated input into the multiagent system. As so much information is stored in the connections, agents are often memory less. This memory-less property, together with the randomness of the external input, has allowed us to model multiagent systems using Markov chains. In this paper, we look at multiagent systems that evolve, i.e., the number of agents varies according to the fitness of the individual agents. We extend our Markov chain model and define stability. This is the start of a methodology to control multiagent systems. We then build upon this to construct an entropy-based definition for the degree of instability (entropy of the limit probabilities), which we used to perform a stability analysis. We then investigated the stability of evolving agent populations through simulation and show that the results are consistent with the original definition of stability in nonevolving multiagent systems, proposed by Chli and De Wilde. This paper forms the theoretical basis for the construction of digital business ecosystems, and applications have been reported elsewhere.

  15. Evolving Robust Gene Regulatory Networks

    PubMed Central

    Noman, Nasimul; Monjo, Taku; Moscato, Pablo; Iba, Hitoshi

    2015-01-01

    Design and implementation of robust network modules is essential for construction of complex biological systems through hierarchical assembly of ‘parts’ and ‘devices’. The robustness of gene regulatory networks (GRNs) is ascribed chiefly to the underlying topology. The automatic designing capability of GRN topology that can exhibit robust behavior can dramatically change the current practice in synthetic biology. A recent study shows that Darwinian evolution can gradually develop higher topological robustness. Subsequently, this work presents an evolutionary algorithm that simulates natural evolution in silico, for identifying network topologies that are robust to perturbations. We present a Monte Carlo based method for quantifying topological robustness and designed a fitness approximation approach for efficient calculation of topological robustness which is computationally very intensive. The proposed framework was verified using two classic GRN behaviors: oscillation and bistability, although the framework is generalized for evolving other types of responses. The algorithm identified robust GRN architectures which were verified using different analysis and comparison. Analysis of the results also shed light on the relationship among robustness, cooperativity and complexity. This study also shows that nature has already evolved very robust architectures for its crucial systems; hence simulation of this natural process can be very valuable for designing robust biological systems. PMID:25616055

  16. Convergent evolution across the Australian continent: ecotype diversification drives morphological convergence in two distantly related clades of Australian frogs.

    PubMed

    Vidal-García, M; Keogh, J S

    2015-12-01

    Animals from different clades but subject to similar environments often evolve similar body shapes and physiological adaptations due to convergent evolution, but this has been rarely tested at the transcontinental level and across entire classes of animal. Australia's biome diversity, isolation and aridification history provide excellent opportunities for comparative analyses on broad-scale macroevolutionary patterns. We collected morphological and environmental data on eighty-four (98%) Australian hylid frog species and categorized them into ecotypes. Using a phylogenetic framework, we tested the hypothesis that frogs from the same ecotype display similar body shape patterns: (i) across all the Australian hylids, and (ii) through comparison with a similar previous study on 127 (97%) Australian myobatrachid species. Body size and shape variation did not follow a strong phylogenetic pattern and was not tightly correlated with environment, but there was a stronger association between morphotype and ecotype. Both arboreal and aquatic frogs had long limbs, whereas limbs of fossorial species were shorter. Other terrestrial species were convergent on the more typical frog body shape. We quantified the strength of morphological convergence at two levels: (i) between fossorial myobatrachid and hylid frogs, and (ii) in each ecomorph within the hylids. We found strong convergence within ecotypes, especially in fossorial species. Ecotypes were also reflected in physiological adaptations: both arboreal and cocooned fossorial frogs tend to have higher rates of evaporative water loss. Our results illustrate how adaptation to different ecological niches plays a crucial role in morphological evolution, boosting phenotypic diversity within a clade. Despite phylogenetic conservatism, morphological adaptation to repeatedly emerging new environments can erase the signature of ancestral morphotypes, resulting in phenotypic diversification and convergence both within and between diverse

  17. Convergence of m-bonacci 'golden ratios'

    NASA Astrophysics Data System (ADS)

    Ahrens, K.; Brown, D. A.; Kramer, A.

    2014-05-01

    This paper proves that the ratios of consecutive terms of the m-bonacci sequence converge to a limit φm < 2 and, as m → ∞, these φm converge to 2. Further, it is shown that the generating functions for the m-bonacci sequences converge pointwise to the geometric series.

  18. Convergence analysis of combinations of different methods

    SciTech Connect

    Kang, Y.

    1994-12-31

    This paper provides a convergence analysis for combinations of different numerical methods for solving systems of differential equations. The author proves that combinations of two convergent linear multistep methods or Runge-Kutta methods produce a new convergent method of which the order is equal to the smaller order of the two original methods.

  19. "Nanoselves": NBIC and the Culture of Convergence

    ERIC Educational Resources Information Center

    Venkatesan, Priya

    2010-01-01

    The subject of this essay is NBIC convergence (nanotechnology, biotechnology, information technology and cognitive science convergence). NBIC convergence is a recurring trope that is dominated by the paradigm of integration of the sciences. It is largely influenced by the considerations of social and economic impact, and it assumes positivism in…

  20. "Nanoselves": NBIC and the Culture of Convergence

    ERIC Educational Resources Information Center

    Venkatesan, Priya

    2010-01-01

    The subject of this essay is NBIC convergence (nanotechnology, biotechnology, information technology and cognitive science convergence). NBIC convergence is a recurring trope that is dominated by the paradigm of integration of the sciences. It is largely influenced by the considerations of social and economic impact, and it assumes positivism in…

  1. Genetic architecture underlying convergent evolution of egg-laying behavior in a seed-feeding beetle.

    PubMed

    Fox, Charles W; Wagner, James D; Cline, Sara; Thomas, Frances Ann; Messina, Frank J

    2009-05-01

    Independent populations subjected to similar environments often exhibit convergent evolution. An unresolved question is the frequency with which such convergence reflects parallel genetic mechanisms. We examined the convergent evolution of egg-laying behavior in the seed-feeding beetle Callosobruchus maculatus. Females avoid ovipositing on seeds bearing conspecific eggs, but the degree of host discrimination varies among geographic populations. In a previous experiment, replicate lines switched from a small host to a large one evolved reduced discrimination after 40 generations. We used line crosses to determine the genetic architecture underlying this rapid response. The most parsimonious genetic models included dominance and/or epistasis for all crosses. The genetic architecture underlying reduced discrimination in two lines was not significantly different from the architecture underlying differences between geographic populations, but the architecture underlying the divergence of a third line differed from all others. We conclude that convergence of this complex trait may in some cases involve parallel genetic mechanisms.

  2. Convergent evolution as a generator of phenotypic diversity in threespine stickleback.

    PubMed

    McGee, Matthew D; Wainwright, Peter C

    2013-04-01

    Convergent evolution, in which populations produce similar phenotypes in response to similar selection pressure, is strong evidence for the role of natural selection in shaping biological diversity. In some cases, closely related populations can produce functionally similar but phenotypically divergence forms in response to selection. Functional convergence with morphological divergence has been observed in laboratory selection experiments and computer simulations, but while potentially common, is rarely recognized in nature. Here, we present data from the North Pacific threespine stickleback radiation showing that ecologically and functionally similar, but morphologically divergent phenotypes rapidly evolved when an ancestral population colonized freshwater benthic habitats in parallel. In addition, we show that in this system, functional convergence substantially increases morphospace occupation relative to ancestral phenotypes, which suggests that convergent evolution may, paradoxically, be an important and previously underappreciated source of morphological diversity. © 2013 The Author(s). Evolution© 2013 The Society for the Study of Evolution.

  3. optix drives the repeated convergent evolution of butterfly wing pattern mimicry.

    PubMed

    Reed, Robert D; Papa, Riccardo; Martin, Arnaud; Hines, Heather M; Counterman, Brian A; Pardo-Diaz, Carolina; Jiggins, Chris D; Chamberlain, Nicola L; Kronforst, Marcus R; Chen, Rui; Halder, Georg; Nijhout, H Frederik; McMillan, W Owen

    2011-08-26

    Mimicry--whereby warning signals in different species evolve to look similar--has long served as a paradigm of convergent evolution. Little is known, however, about the genes that underlie the evolution of mimetic phenotypes or to what extent the same or different genes drive such convergence. Here, we characterize one of the major genes responsible for mimetic wing pattern evolution in Heliconius butterflies. Mapping, gene expression, and population genetic work all identify a single gene, optix, that controls extreme red wing pattern variation across multiple species of Heliconius. Our results show that the cis-regulatory evolution of a single transcription factor can repeatedly drive the convergent evolution of complex color patterns in distantly related species, thus blurring the distinction between convergence and homology.

  4. Mapping convergence points in the initial emergency response to 9/11.

    PubMed

    Bevc, Christine A; Barlau, Ashly N; Passanante, Nick A

    2009-10-01

    In response to extreme events, researchers have recognised the convergence of volunteers, emergency responders, and other individuals and organisations. In 2000, geographer Paul Routledge presented the concept of convergence spaces as a theoretical means to explain social movements. In applying this concept, this paper explores the geographic space in which organisations and individuals converged immediately following the 11 September 2001 attacks on the World Trade Center. The paper begins to answer the question of whether there were in fact any patterns of convergence among the locations utilised by organisations responding to the attacks. Using data collected from field documents, these geographic locations are mapped over 12 days to help identify possible patterns of clustering. Results of this analysis will begin to provide researchers, policy makers and practitioners with a better understanding of how emergency response evolves geographically following an event.

  5. Biomimetic molecular design tools that learn, evolve, and adapt

    PubMed Central

    2017-01-01

    A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine. PMID:28694872

  6. Primordial evolvability: Impasses and challenges.

    PubMed

    Vasas, Vera; Fernando, Chrisantha; Szilágyi, András; Zachár, István; Santos, Mauro; Szathmáry, Eörs

    2015-09-21

    While it is generally agreed that some kind of replicating non-living compounds were the precursors of life, there is much debate over their possible chemical nature. Metabolism-first approaches propose that mutually catalytic sets of simple organic molecules could be capable of self-replication and rudimentary chemical evolution. In particular, the graded autocatalysis replication domain (GARD) model, depicting assemblies of amphiphilic molecules, has received considerable interest. The system propagates compositional information across generations and is suggested to be a target of natural selection. However, evolutionary simulations indicate that the system lacks selectability (i.e. selection has negligible effect on the equilibrium concentrations). We elaborate on the lessons learnt from the example of the GARD model and, more widely, on the issue of evolvability, and discuss the implications for similar metabolism-first scenarios. We found that simple incorporation-type chemistry based on non-covalent bonds, as assumed in GARD, is unlikely to result in alternative autocatalytic cycles when catalytic interactions are randomly distributed. An even more serious problem stems from the lognormal distribution of catalytic factors, causing inherent kinetic instability of such loops, due to the dominance of efficiently catalyzed components that fail to return catalytic aid. Accordingly, the dynamics of the GARD model is dominated by strongly catalytic, but not auto-catalytic, molecules. Without effective autocatalysis, stable hereditary propagation is not possible. Many repetitions and different scaling of the model come to no rescue. Despite all attempts to show the contrary, the GARD model is not evolvable, in contrast to reflexively autocatalytic networks, complemented by rare uncatalyzed reactions and compartmentation. The latter networks, resting on the creation and breakage of chemical bonds, can generate novel ('mutant') autocatalytic loops from a given set of

  7. Imaging enzymes at work: metabolic mapping by enzyme histochemistry.

    PubMed

    Van Noorden, Cornelis J F

    2010-06-01

    For the understanding of functions of proteins in biological and pathological processes, reporter molecules such as fluorescent proteins have become indispensable tools for visualizing the location of these proteins in intact animals, tissues, and cells. For enzymes, imaging their activity also provides information on their function or functions, which does not necessarily correlate with their location. Metabolic mapping enables imaging of activity of enzymes. The enzyme under study forms a reaction product that is fluorescent or colored by conversion of either a fluorogenic or chromogenic substrate or a fluorescent substrate with different spectral characteristics. Most chromogenic staining methods were developed in the latter half of the twentieth century but still find new applications in modern cell biology and pathology. Fluorescence methods have rapidly evolved during the last decade. This review critically evaluates the methods that are available at present for metabolic mapping in living animals, unfixed cryostat sections of tissues, and living cells, and refers to protocols of the methods of choice.

  8. Evolving phenotype of Marfan's syndrome

    PubMed Central

    Lipscomb, K.; Clayton-Smith, J.; Harris, R.

    1997-01-01

    Accepted 20 August 1996
 AIM—To examine evolution of the physical characteristics of Marfan's syndrome throughout childhood.
METHODS—40 children were ascertained during the development of a regional register for Marfan's syndrome. Evolution of the clinical characteristics was determined by repeat evaluation of 10 patients with sporadic Marfan's syndrome and 30 with a family history of the condition. DNA marker studies were used to facilitate diagnosis in those with the familial condition.
RESULTS—Musculoskeletal features predominated and evolved throughout childhood. Gene tracking enabled early diagnosis in children with familial Marfan's syndrome.
CONCLUSIONS—These observations may aid the clinical diagnosis of Marfan's syndrome in childhood, especially in those with the sporadic condition. Gene tracking has a role in the early diagnosis of familial Marfan's syndrome, allowing appropriate follow up and preventive care.

 PMID:9059160

  9. Isotopic Analysis and Evolved Gases

    NASA Technical Reports Server (NTRS)

    Swindle, Timothy D.; Boynton, William V.; Chutjian, Ara; Hoffman, John H.; Jordan, Jim L.; Kargel, Jeffrey S.; McEntire, Richard W.; Nyquist, Larry

    1996-01-01

    Precise measurements of the chemical, elemental, and isotopic composition of planetary surface material and gases, and observed variations in these compositions, can contribute significantly to our knowledge of the source(s), ages, and evolution of solar system materials. The analyses discussed in this paper are mostly made by mass spectrometers or some other type of mass analyzer, and address three broad areas of interest: (1) atmospheric composition - isotopic, elemental, and molecular, (2) gases evolved from solids, and (3) solids. Current isotopic data on nine elements, mostly from in situ analysis, but also from meteorites and telescopic observations are summarized. Potential instruments for isotopic analysis of lunar, Martian, Venusian, Mercury, and Pluto surfaces, along with asteroid, cometary and icy satellites, surfaces are discussed.

  10. [The evolving of cardiac interventions].

    PubMed

    Billinger, Michael

    2014-12-01

    Treatment modalities for heart diseases have considerable evolved during the last 20 years. Coronary and valvular heart disease are treated increasingly by less invasive percutaneous catheter based procedures instead of open-heart surgery. In addition, new cutting-edge interventions allow to cure heart disease for which until recently only medical treatment options were available. Whilst many patients benefit from these innovative therapies, rapidly developing technologies potentially carry the risk of overtreatment. In order to select patients for the most appropriate treatment, an intensive interdisciplinary teamwork between cardiologists and cardiac surgeons is a mandatory requirement. Additionally, knowledge transfer between cardiologists, their growing subspecialties and practitioners should be encouraged. Finally, timely scientific evaluation of new therapies and subsequent incorporation in guidelines remains crucial.

  11. Rapidly evolving homing CRISPR barcodes.

    PubMed

    Kalhor, Reza; Mali, Prashant; Church, George M

    2017-02-01

    We present an approach for engineering evolving DNA barcodes in living cells. A homing guide RNA (hgRNA) scaffold directs the Cas9-hgRNA complex to the DNA locus of the hgRNA itself. We show that this homing CRISPR-Cas9 system acts as an expressed genetic barcode that diversifies its sequence and that the rate of diversification can be controlled in cultured cells. We further evaluate these barcodes in cell populations and show that they can be used to record lineage history and that the barcode RNA can be amplified in situ, a prerequisite for in situ sequencing. This integrated approach will have wide-ranging applications, such as in deep lineage tracing, cellular barcoding, molecular recording, dissecting cancer biology, and connectome mapping.

  12. The evolving Gleason grading system.

    PubMed

    Chen, Ni; Zhou, Qiao

    2016-02-01

    The Gleason grading system for prostate adenocarcinoma has evolved from its original scheme established in the 1960s-1970s, to a significantly modified system after two major consensus meetings conducted by the International Society of Urologic Pathology (ISUP) in 2005 and 2014, respectively. The Gleason grading system has been incorporated into the WHO classification of prostate cancer, the AJCC/UICC staging system, and the NCCN guidelines as one of the key factors in treatment decision. Both pathologists and clinicians need to fully understand the principles and practice of this grading system. We here briefly review the historical aspects of the original scheme and the recent developments of Gleason grading system, focusing on major changes over the years that resulted in the modern Gleason grading system, which has led to a new "Grade Group" system proposed by the 2014 ISUP consensus, and adopted by the 2016 WHO classification of tumours of the prostate.

  13. The evolving Gleason grading system

    PubMed Central

    Chen, Ni

    2016-01-01

    The Gleason grading system for prostate adenocarcinoma has evolved from its original scheme established in the 1960s–1970s, to a significantly modified system after two major consensus meetings conducted by the International Society of Urologic Pathology (ISUP) in 2005 and 2014, respectively. The Gleason grading system has been incorporated into the WHO classification of prostate cancer, the AJCC/UICC staging system, and the NCCN guidelines as one of the key factors in treatment decision. Both pathologists and clinicians need to fully understand the principles and practice of this grading system. We here briefly review the historical aspects of the original scheme and the recent developments of Gleason grading system, focusing on major changes over the years that resulted in the modern Gleason grading system, which has led to a new “Grade Group” system proposed by the 2014 ISUP consensus, and adopted by the 2016 WHO classification of tumours of the prostate. PMID:27041927

  14. Evolving networks by merging cliques

    NASA Astrophysics Data System (ADS)

    Takemoto, Kazuhiro; Oosawa, Chikoo

    2005-10-01

    We propose a model for evolving networks by merging building blocks represented as complete graphs, reminiscent of modules in biological system or communities in sociology. The model shows power-law degree distributions, power-law clustering spectra, and high average clustering coefficients independent of network size. The analytical solutions indicate that a degree exponent is determined by the ratio of the number of merging nodes to that of all nodes in the blocks, demonstrating that the exponent is tunable, and are also applicable when the blocks are classical networks such as Erdös-Rényi or regular graphs. Our model becomes the same model as the Barabási-Albert model under a specific condition.

  15. Behavioural plasticity in evolving robots.

    PubMed

    Carvalho, Jônata Tyska; Nolfi, Stefano

    2016-12-01

    In this paper, we show how the development of plastic behaviours, i.e., behaviour displaying a modular organisation characterised by behavioural subunits that are alternated in a context-dependent manner, can enable evolving robots to solve their adaptive task more efficiently also when it does not require the accomplishment of multiple conflicting functions. The comparison of the results obtained in different experimental conditions indicates that the most important prerequisites for the evolution of behavioural plasticity are: the possibility to generate and perceive affordances (i.e., opportunities for behaviour execution), the possibility to rely on flexible regulatory processes that exploit both external and internal cues, and the possibility to realise smooth and effective transitions between behaviours.

  16. Speech processing: An evolving technology

    SciTech Connect

    Crochiere, R.E.; Flanagan, J.L.

    1986-09-01

    As we enter the information age, speech processing is emerging as an important technology for making machines easier and more convenient for humans to use. It is both an old and a new technology - dating back to the invention of the telephone and forward, at least in aspirations, to the capabilities of HAL in 2001. Explosive advances in microelectronics now make it possible to implement economical real-time hardware for sophisticated speech processing - processing that formerly could be demonstrated only in simulations on main-frame computers. As a result, fundamentally new product concepts - as well as new features and functions in existing products - are becoming possible and are being explored in the marketplace. As the introductory piece to this issue, the authors draw a brief perspective on the evolving field of speech processing and assess the technology in the the three constituent sectors: speech coding, synthesis, and recognition.

  17. Widespread flower color convergence in Solanaceae via alternate biochemical pathways.

    PubMed

    Ng, Julienne; Smith, Stacey D

    2016-01-01

    Phenotypic convergence is rampant throughout the tree of life. While recent studies have made significant progress in ascertaining the proximate mechanisms underlying convergent phenotypes, less is known about the frequency and predictability with which convergent phenotypes arise via the same or multiple pathways at the macroevolutionary scale. We investigated the proximate causes and evolutionary patterns of red flower color in the tomato family, Solanaceae, using large-scale data mining and new sequence data to reconstruct a megaphylogeny of 1341 species. We then combined spectral and anatomical data to assess how many times red flowers have evolved, the relative contribution of different pathways to independent origins of red, and whether the underlying pathway is predicted by phylogenetic relatedness. We estimated at least 30 relatively recent origins of red flowers using anthocyanins, carotenoids, or a dual production of both pigments, with significant phylogenetic signal in the use of anthocyanins and dual production, indicating that closely related red-flowered species tend to employ the same mechanism for coloration. Our study is the first to test whether developmental pathways exhibit phylogenetic signal and implies that historical contingency strongly influences the evolution of new phenotypes.

  18. Genome-Wide Convergence during Evolution of Mangroves from Woody Plants.

    PubMed

    Xu, Shaohua; He, Ziwen; Guo, Zixiao; Zhang, Zhang; Wyckoff, Gerald J; Greenberg, Anthony; Wu, Chung-I; Shi, Suhua

    2017-04-01

    When living organisms independently invade a new environment, the evolution of similar phenotypic traits is often observed. An interesting but contentious issue is whether the underlying molecular biology also converges in the new habitat. Independent invasions of tropical intertidal zones by woody plants, collectively referred to as mangrove trees, represent some dramatic examples. The high salinity, hypoxia, and other stressors in the new habitat might have affected both genomic features and protein structures. Here, we developed a new method for detecting convergence at conservative Sites (CCS) and applied it to the genomic sequences of mangroves. In simulations, the CCS method drastically reduces random convergence at rapidly evolving sites as well as falsely inferred convergence caused by the misinferences of the ancestral character. In mangrove genomes, we estimated ∼400 genes that have experienced convergence over the background level of convergence in the nonmangrove relatives. The convergent genes are enriched in pathways related to stress response and embryo development, which could be important for mangroves' adaptation to the new habitat.

  19. Nucleosome signalling; an evolving concept.

    PubMed

    Turner, Bryan M

    2014-08-01

    The nucleosome core particle is the first stage of DNA packaging in virtually all eukaryotes. It both organises nuclear DNA and protects it from adventitious binding of transcription factors and the consequent deregulation of gene expression. Both properties are essential to allow the genome expansion characteristic of complex eukaryotes. The nucleosome is a flexible structure in vivo, allowing selective relaxation of its intrinsically inhibitory effects in response to external signals. Structural changes are brought about by dedicated remodelling enzymes and by posttranslational modifications of the core histones. Histone modifications occasionally alter nucleosome structure directly, but their more usual roles are to act as receptors on the nucleosome surface that are recognised by specific protein domains. The bound proteins, in turn, affect nucleosome structure and function. This strategy enormously expands the signalling capacity of the nucleosome and its ability to influence both the initiation and elongation stages of transcription. The enzymes responsible for placing and removing histone modifications, and the modification-binding proteins themselves, are ubiquitous, numerous and conserved amongst eukaryotes. Like the nucleosome, they date back to the earliest eukaryotes and may have played integral and essential roles in eukaryotic evolution. The present properties and epigenetic functions of the nucleosome reflect its evolutionary past and the selective pressures to which it has responded and can be better understood in this context. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.

  20. Convergent evolution of defense mechanisms in oribatid mites (Acari, Oribatida) shows no "ghosts of predation past".

    PubMed

    Pachl, Patrick; Domes, Katja; Schulz, Garvin; Norton, Roy A; Scheu, Stefan; Schaefer, Ina; Maraun, Mark

    2012-11-01

    Oribatid mites are diverse and abundant terrestrial soil arthropods that are involved in decomposition of organic matter and nutrient cycling. As indicated by fossils starting from the Devonian, they evolved varied mechanisms and structures for defense from predators. We investigated four of these defensive structures (ptychoid body, hologastry, mineralization and opisthonotal glands) and used ancestral character state reconstruction to determine whether they evolved convergently and how many times this may have happened. Phylogenetic trees based on 18S rDNA were constructed for 42 oribatid mite species and two outgroup taxa using likelihood and Bayesian algorithms. The results suggest that at least three of the four defensive structures evolved convergently several times; for opisthonotal glands convergent evolution remains equivocal. This high level of convergence indicates that predation has been an important factor throughout the evolution of oribatid mites, contributing to morphological diversity and potentially also to species richness, as there are indications that some taxa radiated after the evolution of defense structures. Despite the ancientness of oribatid mites, defense structures seems to have been rarely lost, suggesting that they still are functional and necessary to reduce predation, rather than being 'ghosts of predation past'. Copyright © 2012 Elsevier Inc. All rights reserved.

  1. Ocular Convergence Deficits in Schizophrenia

    PubMed Central

    Bolding, Mark S.; Lahti, Adrienne C.; Gawne, Timothy J.; Hopkins, Kristine B.; Gurler, Demet; Gamlin, Paul D.

    2012-01-01

    Individuals with schizophrenia (SZ) have been reported to exhibit a higher prevalence of convergence insufficiency (CI) than the “normal” adult population. The purpose of this study was to determine if individuals with SZ exhibit clinical signs of CI and to determine if the Convergence Insufficiency Symptom Survey (CISS) is an effective instrument for identifying CI in this population. Twenty participants with SZ and 20 healthy controls (HC) completed the study. The prevalence of CI (15%) in the SZ group was slightly higher than reported norms, but the difference was not significant. The SZ group had significantly higher scores on the CISS than the HC group, but the CISS scores did not correlate with clinical measures of CI in individuals with SZ. The only exception was that SZ patients had a significantly reduced fusional reserve as determined by Sheard’s criteria. Further study is needed to determine why individuals with SZ reported symptoms associated with CI even though clinical measures did not support this diagnosis. PMID:23087652

  2. A Quantitative Approach to Assessing System Evolvability

    NASA Technical Reports Server (NTRS)

    Christian, John A., III

    2004-01-01

    When selecting a system from multiple candidates, the customer seeks the one that best meets his or her needs. Recently the desire for evolvable systems has become more important and engineers are striving to develop systems that accommodate this need. In response to this search for evolvability, we present a historical perspective on evolvability, propose a refined definition of evolvability, and develop a quantitative method for measuring this property. We address this quantitative methodology from both a theoretical and practical perspective. This quantitative model is then applied to the problem of evolving a lunar mission to a Mars mission as a case study.

  3. Divergent and Convergent Evolution of Fungal Pathogenicity.

    PubMed

    Shang, Yanfang; Xiao, Guohua; Zheng, Peng; Cen, Kai; Zhan, Shuai; Wang, Chengshu

    2016-05-12

    Fungal pathogens of plants and animals have multifarious effects; they cause devastating damages to agricultures, lead to life-threatening diseases in humans, or induce beneficial effects by reducing insect pest populations. Many virulence factors have been determined in different fungal pathogens; however, the molecular determinants contributing to fungal host selection and adaptation are largely unknown. In this study, we sequenced the genomes of seven ascomycete insect pathogens and performed the genome-wide analyses of 33 species of filamentous ascomycete pathogenic fungi that infect insects (12 species), plants (12), and humans (9). Our results revealed that the genomes of plant pathogens encode more proteins and protein families than the insect and human pathogens. Unexpectedly, more common orthologous protein groups are shared between the insect and plant pathogens than between the two animal group pathogens. We also found that the pathogenicity of host-adapted fungi evolved multiple times, and that both divergent and convergent evolutions occurred during pathogen-host cospeciation thus resulting in protein families with similar features in each fungal group. However, the role of phylogenetic relatedness on the evolution of protein families and therefore pathotype formation could not be ruled out due to the effect of common ancestry. The evolutionary correlation analyses led to the identification of different protein families that correlated with alternate pathotypes. Particularly, the effector-like proteins identified in plant and animal pathogens were strongly linked to fungal host adaptation, suggesting the existence of similar gene-for-gene relationships in fungus-animal interactions that has not been established before. These results well advance our understanding of the evolution of fungal pathogenicity and the factors that contribute to fungal pathotype formation. © The Author 2016. Published by Oxford University Press on behalf of the Society for

  4. Divergent and Convergent Evolution of Fungal Pathogenicity

    PubMed Central

    Shang, Yanfang; Xiao, Guohua; Zheng, Peng; Cen, Kai; Zhan, Shuai; Wang, Chengshu

    2016-01-01

    Fungal pathogens of plants and animals have multifarious effects; they cause devastating damages to agricultures, lead to life-threatening diseases in humans, or induce beneficial effects by reducing insect pest populations. Many virulence factors have been determined in different fungal pathogens; however, the molecular determinants contributing to fungal host selection and adaptation are largely unknown. In this study, we sequenced the genomes of seven ascomycete insect pathogens and performed the genome-wide analyses of 33 species of filamentous ascomycete pathogenic fungi that infect insects (12 species), plants (12), and humans (9). Our results revealed that the genomes of plant pathogens encode more proteins and protein families than the insect and human pathogens. Unexpectedly, more common orthologous protein groups are shared between the insect and plant pathogens than between the two animal group pathogens. We also found that the pathogenicity of host-adapted fungi evolved multiple times, and that both divergent and convergent evolutions occurred during pathogen–host cospeciation thus resulting in protein families with similar features in each fungal group. However, the role of phylogenetic relatedness on the evolution of protein families and therefore pathotype formation could not be ruled out due to the effect of common ancestry. The evolutionary correlation analyses led to the identification of different protein families that correlated with alternate pathotypes. Particularly, the effector-like proteins identified in plant and animal pathogens were strongly linked to fungal host adaptation, suggesting the existence of similar gene-for-gene relationships in fungus–animal interactions that has not been established before. These results well advance our understanding of the evolution of fungal pathogenicity and the factors that contribute to fungal pathotype formation. PMID:27071652

  5. Many Paths to a Common Destination: Morphological Differentiation of a Functionally Convergent Visual Signal.

    PubMed

    Hagman, Mattias; Ord, Terry J

    2016-09-01

    Understanding the interacting outcomes of selection and historical contingency in shaping adaptive evolution remains a challenge in evolutionary biology. While selection can produce convergent outcomes when species occupy similar environments, the unique history of each species can also influence evolutionary trajectories and result in different phenotypic end points. The question is to what extent historical contingency places species on different adaptive pathways and, in turn, the extent to which we can predict evolutionary outcomes. Among lizards there are several distantly related genera that have independently evolved an elaborate extendible dewlap for territorial communication. We conducted a detailed morphological study and employed new phylogenetic comparative methods to investigate the evolution of the underlying hyoid that powers the extension of the dewlap. This analysis showed that there appear to have been multiple phenotypic pathways for evolving a functionally convergent dewlap. The biomechanical complexity that underlies this morphological structure implies that adaptation should have been constrained to a narrow phenotypic pathway. However, multiple adaptive solutions have been possible in apparent response to a common selection pressure. Thus, the phenotypic outcome that subsequently evolved in different genera seems to have been contingent on the history of the group in question. This blurs the distinction between convergent and historically contingent adaptation and suggests that adaptive phenotypic diversity can evolve without the need for divergent natural selection.

  6. Increased longevity evolves from grandmothering.

    PubMed

    Kim, Peter S; Coxworth, James E; Hawkes, Kristen

    2012-12-22

    Postmenopausal longevity may have evolved in our lineage when ancestral grandmothers subsidized their daughters' fertility by provisioning grandchildren, but the verbal hypothesis has lacked mathematical support until now. Here, we present a formal simulation in which life spans similar to those of modern chimpanzees lengthen into the modern human range as a consequence of grandmother effects. Greater longevity raises the chance of living through the fertile years but is opposed by costs that differ for the sexes. Our grandmother assumptions are restrictive. Only females who are no longer fertile themselves are eligible, and female fertility extends to age 45 years. Initially, there are very few eligible grandmothers and effects are small. Grandmothers can support only one dependent at a time and do not care selectively for their daughters' offspring. They must take the oldest juveniles still relying on mothers; and infants under the age of 2 years are never eligible for subsidy. Our model includes no assumptions about brains, learning or pair bonds. Grandmother effects alone are sufficient to propel the doubling of life spans in less than sixty thousand years.

  7. Circumstellar Crystalline Silicates: Evolved Stars

    NASA Astrophysics Data System (ADS)

    Tartar, Josh; Speck, A. K.

    2008-05-01

    One of the most exciting developments in astronomy in the last 15 years was the discovery of crystalline silicate stardust by the Short Wavelength Spectrometer (SWS) on board of ISO; discovery of the crystalline grains was indeed one of the biggest surprises of the ISO mission. Initially discovered around AGB stars (evolved stars in the range of 0.8 > M/M¤>8) at far-infrared (IR) wavelengths, crystalline silicates have since been seen in many astrophysical environments including young stellar objects (T Tauri and Herbig Ae/Be), comets and Ultra Luminous Infrared Galaxies. Low and intermediate mass stars (LIMS) comprise 95% of the contributors to the ISM, so study of the formation of crystalline silicates is critical to our understanding of the ISM, which is thought to be primarily amorphous (one would expect an almost exact match between the composition of AGB dust shells and the dust in the ISM). Whether the crystalline dust is merely undetectable or amorphized remains a mystery. The FORCAST instrument on SOFIA as well as the PACS instrument on Herschel will provide exciting observing opportunities for the further study of crystalline silicates.

  8. Magnetic fields around evolved stars

    NASA Astrophysics Data System (ADS)

    Leal-Ferreira, M.; Vlemmings, W.; Kemball, A.; Amiri, N.; Maercker, M.; Ramstedt, S.; Olofsson, G.

    2014-04-01

    A number of mechanisms, such as magnetic fields, (binary) companions and circumstellar disks have been suggested to be the cause of non-spherical PNe and in particular collimated outflows. This work investigates one of these mechanisms: the magnetic fields. While MHD simulations show that the fields can indeed be important, few observations of magnetic fields have been done so far. We used the VLBA to observe five evolved stars, with the goal of detecting the magnetic field by means of water maser polarization. The sample consists in four AGB stars (IK Tau, RT Vir, IRC+60370 and AP Lyn) and one pPN (OH231.8+4.2). In four of the five sources, several strong maser features were detected allowing us to measure the linear and/or circular polarization. Based on the circular polarization detections, we infer the strength of the component of the field along the line of sight to be between ~30 mG and ~330 mG in the water maser regions of these four sources. When extrapolated to the surface of the stars, the magnetic field strength would be between a few hundred mG and a few Gauss when assuming a toroidal field geometry and higher when assuming more complex magnetic fields. We conclude that the magnetic energy we derived in the water maser regions is higher than the thermal and kinetic energy, leading to the conclusion that, indeed, magnetic fields probably play an important role in shaping Planetary Nebulae.

  9. How do drumlin patterns evolve?

    NASA Astrophysics Data System (ADS)

    Ely, Jeremy; Clark, Chris; Spagnolo, Matteo; Hughes, Anna

    2016-04-01

    The flow of a geomorphic agent over a sediment bed creates patterns in the substrate composed of bedforms. Ice is no exception to this, organising soft sedimentary substrates into subglacial bedforms. As we are yet to fully observe their initiation and evolution beneath a contemporary ice mass, little is known about how patterns in subglacial bedforms develop. Here we study 36,222 drumlins, divided into 72 flowsets, left behind by the former British-Irish Ice sheet. These flowsets provide us with 'snapshots' of drumlin pattern development. The probability distribution functions of the size and shape metrics of drumlins within these flowsets were analysed to determine whether behaviour that is common of other patterned phenomena has occurred. Specifically, we ask whether drumlins i) are printed at a specific scale; ii) grow or shrink after they initiate; iii) stabilise at a specific size and shape; and iv) migrate. Our results indicate that drumlins initiate at a minimum size and spacing. After initiation, the log-normal distribution of drumlin size and shape metrics suggests that drumlins grow, or possibly shrink, as they develop. We find no evidence for stabilisation in drumlin length, supporting the idea of a subglacial bedform continuum. Drumlin migration is difficult to determine from the palaeo-record. However, there are some indications that a mixture of static and mobile drumlins occurs, which could potentially lead to collisions, cannibalisation and coarsening. Further images of modern drumlin fields evolving beneath ice are required to capture stages of drumlin pattern evolution.

  10. Increased longevity evolves from grandmothering

    PubMed Central

    Kim, Peter S.; Coxworth, James E.; Hawkes, Kristen

    2012-01-01

    Postmenopausal longevity may have evolved in our lineage when ancestral grandmothers subsidized their daughters' fertility by provisioning grandchildren, but the verbal hypothesis has lacked mathematical support until now. Here, we present a formal simulation in which life spans similar to those of modern chimpanzees lengthen into the modern human range as a consequence of grandmother effects. Greater longevity raises the chance of living through the fertile years but is opposed by costs that differ for the sexes. Our grandmother assumptions are restrictive. Only females who are no longer fertile themselves are eligible, and female fertility extends to age 45 years. Initially, there are very few eligible grandmothers and effects are small. Grandmothers can support only one dependent at a time and do not care selectively for their daughters' offspring. They must take the oldest juveniles still relying on mothers; and infants under the age of 2 years are never eligible for subsidy. Our model includes no assumptions about brains, learning or pair bonds. Grandmother effects alone are sufficient to propel the doubling of life spans in less than sixty thousand years. PMID:23097518

  11. Recommendation in evolving online networks

    NASA Astrophysics Data System (ADS)

    Hu, Xiao; Zeng, An; Shang, Ming-Sheng

    2016-02-01

    Recommender system is an effective tool to find the most relevant information for online users. By analyzing the historical selection records of users, recommender system predicts the most likely future links in the user-item network and accordingly constructs a personalized recommendation list for each user. So far, the recommendation process is mostly investigated in static user-item networks. In this paper, we propose a model which allows us to examine the performance of the state-of-the-art recommendation algorithms in evolving networks. We find that the recommendation accuracy in general decreases with time if the evolution of the online network fully depends on the recommendation. Interestingly, some randomness in users' choice can significantly improve the long-term accuracy of the recommendation algorithm. When a hybrid recommendation algorithm is applied, we find that the optimal parameter gradually shifts towards the diversity-favoring recommendation algorithm, indicating that recommendation diversity is essential to keep a high long-term recommendation accuracy. Finally, we confirm our conclusions by studying the recommendation on networks with the real evolution data.

  12. The evolving defense communications system

    NASA Astrophysics Data System (ADS)

    Testa, Ann M.; Jones, Walter I.

    1992-05-01

    Command, control, and communications (C3) systems 'help lift the fog of war that adds uncertainty to any military operation.' They multiply the effectiveness of weapon systems and are critical components of our nation's warfighting capability. One of these critical systems is the Defense Communications System (DCS) which evolved over the past 30 years. Several factors drove this evolution, including constrained budgets, the need to improve the effectiveness and efficiency of the service provided, compatibility and interoperability, and technological advances. Based on lessons learned from Desert Shield/Desert Storm and the changing environment, force structure, and strategy, it is time to advance the DCS to its next stage. The future DCS must be flexible enough to adapt to any situation anywhere in the world. Mobile, modular building block packages of communications equipment must be available to provide effective communications capability to deployed units immediately upon arrival. Total integration and interoperability among military, commercial, and other government agencies' communication systems is a must if survivable, robust connectivity is going to be available when needed. Integration planning must begin now.

  13. Convergent Validity of the PUTS

    PubMed Central

    Brandt, Valerie Cathérine; Beck, Christian; Sajin, Valeria; Anders, Silke; Münchau, Alexander

    2016-01-01

    Premonitory urges are a cardinal feature in Gilles de la Tourette syndrome. Severity of premonitory urges can be assessed with the “Premonitory Urge for Tic Disorders Scale” (PUTS). However, convergent validity of the measure has been difficult to assess due to the lack of other urge measures. We investigated the relationship between average real-time urge intensity assessed by an in-house developed real-time urge monitor (RUM), measuring urge intensity continuously for 5 min on a visual analog scale, and general urge intensity assessed by the PUTS in 22 adult Tourette patients (mean age 29.8 ± 10.3 SD, 19 males). Additionally, underlying factors of premonitory urges assessed by the PUTS were investigated in the adult sample using factor analysis and were replicated in 40 children and adolescents diagnosed with Tourette syndrome (mean age 12.05 ± 2.83 SD, 31 males). Cronbach’s α for the PUTS 10 was acceptable (α = 0.79) in the adult sample. Convergent validity between average real-time urge intensity scores (as assessed with the RUM) and the 10-item version of the PUTS (r = 0.64) and the 9-item version of the PUTS (r = 0.66) was good. A factor analysis including the 10 items of the PUTS and average real-time urge intensity scores revealed three factors. One factor included the average real-time urge intensity score and appeared to measure urge intensity, whereas the other two factors can be assumed to reflect the (sensory) quality of urges and subjective control, respectively. The factor structure of the 10 PUTS items alone was replicated in a sample of children and adolescents. The results indicate that convergent validity between the PUTS and the real-time urge assessment monitor is good. Furthermore, the results suggest that the PUTS might assess more than one dimension of urges, and it may be worthwhile developing different subscales of the PUTS assessing premonitory urges in terms of intensity and quality, as well as

  14. Primary enzyme quantitation

    DOEpatents

    Saunders, G.C.

    1982-03-04

    The disclosure relates to the quantitation of a primary enzyme concentration by utilizing a substrate for the primary enzyme labeled with a second enzyme which is an indicator enzyme. Enzyme catalysis of the substrate occurs and results in release of the indicator enzyme in an amount directly proportional to the amount of primary enzyme present. By quantifying the free indicator enzyme one determines the amount of primary enzyme present.

  15. Convergence in Thunniform Anatomy in Lamnid Sharks and Jurassic Ichthyosaurs.

    PubMed

    Lingham-Soliar, Theagarten

    2016-12-01

    Among extinct ichthyosaurs the Jurassic forms Ichthyosaurus and Stenopterygius share a number of anatomical specializations with lamnid sharks, characterized in the white shark, Carcharodon carcharias These features allow their inclusion within the mode of high-speed thunniform swimming to which only two other equally distinctive phylogenetic groups belong, tuna and dolphins-a striking testaments to evolutionary convergence. Jurassic ichthyosaurs evolved from reptiles that had returned to the sea (secondarily adapted) about 250 million years ago (MYA) while lamnid sharks evolved about 50 MYA from early cartilaginous fishes (originating ca. 400 MYA). Their shared independently evolved anatomical characteristics are discussed. These include a deep tear-drop body shape that helped initially define members as thunniform swimmers. Later, other critical structural characteristics were discovered such as the crossed-fiber architecture of the skin, high-speed adapted dorsal and caudal fins, a caudal peduncle and series of ligaments to enable transmission of power from the musculature located anteriorly to the caudal fin. Both groups also share a similar chemistry of the dermal fibers, i.e., the scleroprotein collagen.

  16. Particles Acceleration in Converged Shocks

    NASA Astrophysics Data System (ADS)

    Wang, Xin

    2016-07-01

    Observations show that there is a proton spectral ``break" with E_{break} at 1-10MeV in some large CME-driven shocks. However, the understanding of this energy spectral ``break" from the diffusive shock acceleration theory still remains uncertain. Although previous numerical methods can hardly predict this ``break" from current theoretical models due to high computational expense, the present paper focuses on simulating this energy spectrum in converged two shocks by Monte Carlo numerical method. Considering the Dec 13 2006 CME-driven shock interaction with an Earth bow shock, we examine whether the energy spectral ``break" could occur on an interaction between two shocks. As result, we indeed obtain the maximum proton energy up to 10MeV, and we further find a proton spectral ``break" appears distinctly at the energy ˜5MeV.

  17. Cosmic Convergence: Art and Science

    NASA Astrophysics Data System (ADS)

    Mayo, Elizabeth A.; Zisholtz, E.; Hilton, H.

    2010-01-01

    The I.P. Stanback Museum and Planetarium is a major educational and teaching resource for South Carolina State University, K-12 schools, other universities and the community of Orangeburg and well beyond. The concept of creating a museum with a planetarium on the campus of SC State was ahead of its time. Today scholars are writing about the unity of creative disciplines. Through its integration of the arts, humanities and sciences, the Stanback, the only art museum with a planetarium at any of the Historically Black Colleges and Universities and one of the few in the nation, stands in the forefront of modern thinking. Cosmic Convergence: Art and Science, opening at the I.P. Stanback Museum and Planetarium in February 2010, will feature the works of Mildred Thompson (1936-2003), a prominent African American artist who worked in the media of painting, drawing, print making, sculpture, and photography. Thompson’s artwork shows the strong influences of her interest in physics, astronomy, and metaphysics as well as music and spiritualism. “My work in the visual arts is, and has always been, a continuous search for understanding. It is an expression of purpose and reflects a personal interpretation of the Universe.” Cosmic Convergence will explore the meeting of Art and Science through Mildred Thompson's work and the scientific basis of that work. The paintings and sculptures of the exhibit will be combined with astronomical images showing both the reality and interpretation of the surrounding Universe. Support for this work was provided by the NSF PAARE program to South Carolina State University under award AST-0750814.

  18. Convergent biosynthetic pathways to β-lactam antibiotics

    PubMed Central

    Townsend, Craig A.

    2016-01-01

    Five naturally-occurring β-lactams have inspired a class of drugs that constitute >60% of the antimicrobials used in human medicine. Their biosynthetic pathways reveal highly individualized synthetic strategies that yet converge on a common azetidinone ring assembled in structural contexts that confer selective binding and inhibition of D,D-transpeptidases that play essential roles in bacterial cell wall (peptidoglycan) biosynthesis. These enzymes belong to a single “clan” of evolutionarily distinct serine hydrolases whose active site geometry and mechanism of action is specifically matched by these antibiotics for inactivation that is kinetically competitive with their native function. Unusual enzyme-mediated reactions and catalytic multitasking in these pathways are discussed with particular attention to the diverse ways the β-lactam itself is generated, and more broadly how the intrinsic reactivity of this core structural element is modulated in natural systems through the introduction of ring strain and electronic effects. PMID:27693891

  19. Estimator reduction and convergence of adaptive BEM.

    PubMed

    Aurada, Markus; Ferraz-Leite, Samuel; Praetorius, Dirk

    2012-06-01

    A posteriori error estimation and related adaptive mesh-refining algorithms have themselves proven to be powerful tools in nowadays scientific computing. Contrary to adaptive finite element methods, convergence of adaptive boundary element schemes is, however, widely open. We propose a relaxed notion of convergence of adaptive boundary element schemes. Instead of asking for convergence of the error to zero, we only aim to prove estimator convergence in the sense that the adaptive algorithm drives the underlying error estimator to zero. We observe that certain error estimators satisfy an estimator reduction property which is sufficient for estimator convergence. The elementary analysis is only based on Dörfler marking and inverse estimates, but not on reliability and efficiency of the error estimator at hand. In particular, our approach gives a first mathematical justification for the proposed steering of anisotropic mesh-refinements, which is mandatory for optimal convergence behavior in 3D boundary element computations.

  20. Optimizing convergence rates of alternating minimization reconstruction algorithms for real-time explosive detection applications

    NASA Astrophysics Data System (ADS)

    Bosch, Carl; Degirmenci, Soysal; Barlow, Jason; Mesika, Assaf; Politte, David G.; O'Sullivan, Joseph A.

    2016-05-01

    X-ray computed tomography reconstruction for medical, security and industrial applications has evolved through 40 years of experience with rotating gantry scanners using analytic reconstruction techniques such as filtered back projection (FBP). In parallel, research into statistical iterative reconstruction algorithms has evolved to apply to sparse view scanners in nuclear medicine, low data rate scanners in Positron Emission Tomography (PET) [5, 7, 10] and more recently to reduce exposure to ionizing radiation in conventional X-ray CT scanners. Multiple approaches to statistical iterative reconstruction have been developed based primarily on variations of expectation maximization (EM) algorithms. The primary benefit of EM algorithms is the guarantee of convergence that is maintained when iterative corrections are made within the limits of convergent algorithms. The primary disadvantage, however is that strict adherence to correction limits of convergent algorithms extends the number of iterations and ultimate timeline to complete a 3D volumetric reconstruction. Researchers have studied methods to accelerate convergence through more aggressive corrections [1], ordered subsets [1, 3, 4, 9] and spatially variant image updates. In this paper we describe the development of an AM reconstruction algorithm with accelerated convergence for use in a real-time explosive detection application for aviation security. By judiciously applying multiple acceleration techniques and advanced GPU processing architectures, we are able to perform 3D reconstruction of scanned passenger baggage at a rate of 75 slices per second. Analysis of the results on stream of commerce passenger bags demonstrates accelerated convergence by factors of 8 to 15, when comparing images from accelerated and strictly convergent algorithms.

  1. Submillimeter observations of evolved stars

    SciTech Connect

    Sopka, R.J.; Hildebrand, R.; Jaffe, D.T.; Gatley, I.; Roellig, T.; Werner, M.; Jura, M.; Zuckerman, B.

    1985-07-01

    Broad-band submillimeter observations of the thermal emission from evolved stars have been obtained with the United Kingdom Infrared Telescope on Mauna Kea, Hawaii. These observations, at an effective wavelength of 400 ..mu..m, provide the most direct method for estimating the mass loss rate in dust from these stars and also help to define the long-wavelength thermal spectrum of the dust envelopes. The mass loss rates in dust that we derive range from 10/sup -9/ to 10/sup -6/ M/sub sun/ yr/sup -1/ and are compared with mass loss rates derived from molecular line observations to estimate gas-to-dust ratios in outflowing envelopes. These values are found to be generally compatible with the interstellar gas-to-dust ratio of approx.100 if submillimeter emissivities appropriate to amorphous grain structures are assumed. Our analysis of the spectrum of IRC+10216 confirms previous suggestions that the grain emissivity varies as lambda/sup -1.2/ rather than as lambda/sup -2/ for 10

  2. Idiopathic pulmonary fibrosis: evolving concepts.

    PubMed

    Ryu, Jay H; Moua, Teng; Daniels, Craig E; Hartman, Thomas E; Yi, Eunhee S; Utz, James P; Limper, Andrew H

    2014-08-01

    Idiopathic pulmonary fibrosis (IPF) occurs predominantly in middle-aged and older adults and accounts for 20% to 30% of interstitial lung diseases. It is usually progressive, resulting in respiratory failure and death. Diagnostic criteria for IPF have evolved over the years, and IPF is currently defined as a disease characterized by the histopathologic pattern of usual interstitial pneumonia occurring in the absence of an identifiable cause of lung injury. Understanding of the pathogenesis of IPF has shifted away from chronic inflammation and toward dysregulated fibroproliferative repair in response to alveolar epithelial injury. Idiopathic pulmonary fibrosis is likely a heterogeneous disorder caused by various interactions between genetic components and environmental exposures. High-resolution computed tomography can be diagnostic in the presence of typical findings such as bilateral reticular opacities associated with traction bronchiectasis/bronchiolectasis in a predominantly basal and subpleural distribution, along with subpleural honeycombing. In other circumstances, a surgical lung biopsy may be needed. The clinical course of IPF can be unpredictable and may be punctuated by acute deteriorations (acute exacerbation). Although progress continues in unraveling the mechanisms of IPF, effective therapy has remained elusive. Thus, clinicians and patients need to reach informed decisions regarding management options including lung transplant. The findings in this review were based on a literature search of PubMed using the search terms idiopathic pulmonary fibrosis and usual interstitial pneumonia, limited to human studies in the English language published from January 1, 2000, through December 31, 2013, and supplemented by key references published before the year 2000. Copyright © 2014 Mayo Foundation for Medical Education and Research. Published by Elsevier Inc. All rights reserved.

  3. Voyages Through Time: Everything Evolves

    NASA Astrophysics Data System (ADS)

    Pendleton, Y. J.; Tarter, J. C.; DeVore, E. K.; O'Sullivan, K. A.; Taylor, S. M.

    2001-12-01

    Evolutionary change is a powerful framework for studying our world and our place therein. It is a recurring theme in every realm of science: over time, the universe, the planet Earth, life, and human technologies all change, albeit on vastly different scales. Evolution offers scientific explanations for the age-old question, "Where did we come from?" In addition, historical perspectives of science show how our understanding has evolved over time. The complexities of all of these systems will never reveal a "finished" story. But it is a story of epic size, capable of inspiring awe and of expanding our sense of time and place, and eminently worthy of investigating. This story is the basis of Voyages Through Time. Voyages Through Time (VTT), provides teachers with not only background science content and pedagogy, but also with materials and resources for the teaching of evolution. The six modules, Cosmic Evolution, Planetary Evolution, Origin of Life, Evolution of Life, Hominid Evolution, and Evolution of Technology, emphasize student inquiry, and promote the nature of science, as recommended in the NSES and BSL. The modules are unified by the overarching theme of evolution and the meta questions: "What is changing?" "What is the rate of change?" and "What is the mechanism of change?" Determination of student outcomes for the project required effective collaboration of scientists, teachers, students and media specialists. The broadest curricula students outcomes are 1) an enjoyment of science, 2) an understanding of the nature of science, especially the understanding of evidence and re-evaluation, and 3) key science content. The curriculum is being developed by the SETI Institute, NASA Ames Research Center, California Academy of Sciences, and San Francisco State University, and is funded by the NSF (IMD 9730693), with support form Hewlett-Packard Company, The Foundation for Microbiology, Combined Federated Charities, NASA Astrobiology Institute, and NASA Fundamental

  4. Convergence Analysis of LMS based Adaptive filter

    NASA Astrophysics Data System (ADS)

    Rai, Amrita; Kohli, Amit Kumar

    2010-11-01

    A standard algorithm for LMS-filter simulation, tested with several convergence criteria is presented in this paper. We analyze the steady-state mean square error (MSE) convergence of the LMS algorithm when random functions are used as reference inputs. In this paper, we make a more precise analysis using the deterministic nature of the reference inputs and their time-variant correlation matrix. Simulations performed under MATLAB show remarkable differences between convergence criteria with various value of the step size.

  5. Systematically Accelerated Convergence of Path Integrals

    SciTech Connect

    Bogojevic, A.; Balaz, A.; Belic, A.

    2005-05-13

    We present a new analytical method that systematically improves the convergence of path integrals of a generic N-fold discretized theory. Using it we calculate the effective actions S{sup (p)} for p{<=}9, which lead to the same continuum amplitudes as the starting action, but that converge to that continuum limit as 1/N{sup p}. We checked this derived speedup in convergence by performing Monte Carlo simulations on several different models.

  6. Evolving evolutionary algorithms using linear genetic programming.

    PubMed

    Oltean, Mihai

    2005-01-01

    A new model for evolving Evolutionary Algorithms is proposed in this paper. The model is based on the Linear Genetic Programming (LGP) technique. Every LGP chromosome encodes an EA which is used for solving a particular problem. Several Evolutionary Algorithms for function optimization, the Traveling Salesman Problem and the Quadratic Assignment Problem are evolved by using the considered model. Numerical experiments show that the evolved Evolutionary Algorithms perform similarly and sometimes even better than standard approaches for several well-known benchmarking problems.

  7. Acquiring Evolving Technologies: Web Services Standards

    DTIC Science & Technology

    2016-06-30

    2006 Carnegie Mellon University Acquiring Evolving Technologies : Web Services Standards Harry L. Levinson Software Engineering Institute Carnegie...Acquiring Evolving Technologies : Web Services Standards 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d. PROJECT...298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 2 Acquiring Evolving Technologies : Web Services Standards © 2006 Carnegie Mellon University Acquiring

  8. Testing hypotheses of convergence with multivariate data: morphological and functional convergence among herbivorous lizards.

    PubMed

    Stayton, C Tristan

    2006-04-01

    Despite its importance to evolutionary theory, convergence remains an understudied phenomenon and is usually investigated using qualitative data. This paper advances a new, multidimensional view of convergence. Three patterns indicative of convergence are discussed, and techniques to discover and test convergent patterns in a quantitative framework are developed. These concepts and methods are applied to a dataset of digitized coordinates on 1554 lizard skulls and 1292 lower jaws to test hypotheses of convergence among herbivorous lizards. Encompassing seven independent acquisitions of herbivory, this lizard sample provides an ideal natural experiment for exploring ideas of convergence among different systems (here, morphological and functional). Three related questions are addressed: (1) Do herbivorous lizards show evidence of convergence in skull and lower jaw morphology? (2) What, if any, is the morphospace pattern associated with this convergence? (3) Is it possible to predict the direction of convergence using functional models? Relative warp analysis and permutation tests reveal that the skulls and lower jaws of herbivorous lizards do show evidence of convergence. Herbivore skulls deviate from their carnivorous or omnivorous sister groups toward the same area of morphospace. Without a phylogenetic perspective, this pattern would not be recognizable. Lower jaws of herbivores are not convergent in morphology but are convergent in function: herbivores deviate away from their carnivorous sister groups toward higher values of mechanical advantage. These results illustrate the desirability of quantitative methods, informed by phylogenetic information, in the study of convergence.

  9. Water in evolved lunar rocks

    NASA Astrophysics Data System (ADS)

    Robinson, Katharine Lynn

    The Moon was thought to be completely anhydrous until indigenous water was found in lunar samples in 2008. This discovery raised two fundamental questions about the Moon: how much water is present in the bulk Moon and is water uniformly distributed in the lunar interior? To address these questions, I studied a suite of lunar samples rich in a chemical component called KREEP (K, Rare Earth Elements, P), all of which are incompatible elements. Water behaves as an incompatible element in magmas, so KREEP-rich lunar samples are potentially water rich. In this dissertation, I present the results of a petrologic study of KREEP-rich lunar rocks, measurements of their water contents and deuterium (D) to hydrogen (H) ratios (D/H), and examined where these rocks fit into our understanding of water in the Moon as a whole. We performed a study of highly evolved, KREEP-rich lunar rocks called felsites and determined that they contain quartz. Using cooling rates derived from quartz-Ti thermometry, we show the felsites originated at a minimum pressure of ˜1 kbar, corresponding to a minimum depth of 20-25 km in the lunar crust. We calculate that at that pressure water would have been soluble in the melt, indicating that degassing of H2O from the felsite parental melts was likely minimal and hydrogen isotopes in intrusive rocks are likely unfractionated. We then measured D/H in apatite in KREEP-rich intrusive rocks to clarify the solar system source of the Moon's water. When viewed in the context of other lunar D/H studies, our results indicate there are at least three distinctive reservoirs in the lunar interior, including an ultra-low D reservoir that could represent a primitive component in the Moon's interior. Furthermore, our measurements of residual glass in a KREEP basalt show that the KREEP basaltic magmas contained 10 times less water than the source of the Apollo 17 pyroclastic glass beads, indicating that, though wetter than previously thought, the concentration of

  10. Trophic divergence despite morphological convergence in a continental radiation of snakes

    PubMed Central

    Grundler, Michael C.; Rabosky, Daniel L.

    2014-01-01

    Ecological and phenotypic convergence is a potential outcome of adaptive radiation in response to ecological opportunity. However, a number of factors may limit convergence during evolutionary radiations, including interregional differences in biogeographic history and clade-specific constraints on form and function. Here, we demonstrate that a single clade of terrestrial snakes from Australia—the oxyuranine elapids—exhibits widespread morphological convergence with a phylogenetically diverse and distantly related assemblage of snakes from North America. Australian elapids have evolved nearly the full spectrum of phenotypic modalities that occurs among North American snakes. Much of the convergence appears to involve the recurrent evolution of stereotyped morphologies associated with foraging mode, locomotion and habitat use. By contrast, analysis of snake diets indicates striking divergence in feeding ecology between these faunas, partially reflecting regional differences in ecological allometry between Australia and North America. Widespread phenotypic convergence with the North American snake fauna coupled with divergence in feeding ecology are clear examples of how independent continental radiations may converge along some ecological axes yet differ profoundly along others. PMID:24920479

  11. Trophic divergence despite morphological convergence in a continental radiation of snakes.

    PubMed

    Grundler, Michael C; Rabosky, Daniel L

    2014-07-22

    Ecological and phenotypic convergence is a potential outcome of adaptive radiation in response to ecological opportunity. However, a number of factors may limit convergence during evolutionary radiations, including interregional differences in biogeographic history and clade-specific constraints on form and function. Here, we demonstrate that a single clade of terrestrial snakes from Australia--the oxyuranine elapids--exhibits widespread morphological convergence with a phylogenetically diverse and distantly related assemblage of snakes from North America. Australian elapids have evolved nearly the full spectrum of phenotypic modalities that occurs among North American snakes. Much of the convergence appears to involve the recurrent evolution of stereotyped morphologies associated with foraging mode, locomotion and habitat use. By contrast, analysis of snake diets indicates striking divergence in feeding ecology between these faunas, partially reflecting regional differences in ecological allometry between Australia and North America. Widespread phenotypic convergence with the North American snake fauna coupled with divergence in feeding ecology are clear examples of how independent continental radiations may converge along some ecological axes yet differ profoundly along others. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  12. Image sharing: evolving solutions in the age of interoperability.

    PubMed

    Mendelson, David S; Erickson, Bradley J; Choy, Garry

    2014-12-01

    Interoperability is a major focus of the quickly evolving world of Health IT. Easy, yet secure and confidential exchange of imaging exams and the associated reports must be a part of the solutions that are implemented. The availability of historical exams is essential in providing a quality interpretation and reducing inappropriate utilization of imaging services. Today, the exchange of imaging exams is most often achieved via a compact disc. We describe the virtues of this solution as well as challenges that have surfaced. Internet- and cloud-based technologies employed for many consumer services can provide a better solution. Vendors are making these solutions available. Standards for Internet-based exchange are emerging. Just as radiology converged on DICOM as a standard to store and view images, we need a common exchange standard. We will review the existing standards and how they are organized into useful workflows through Integrating the Healthcare Enterprise profiles. Integrating the Healthcare Enterprise and standards development processes are discussed. Health care and the domain of radiology must stay current with quickly evolving Internet standards. The successful use of the "cloud" will depend on both the technologies and the policies put into place around them, both of which we discuss. The radiology community must lead the way and provide a solution that works for radiologists and clinicians with use of the electronic medical record. We describe features we believe radiologists should consider when adding Internet-based exchange solutions to their practice.

  13. Integrating the Human Sciences to Evolve Effective Policies

    PubMed Central

    Biglan, Anthony; Cody, Christine

    2012-01-01

    This paper describes an evolutionary perspective on human development and wellbeing and contrasts it with the model of self-interest that is prominent in economics. The two approaches have considerably different implications for how human wellbeing might be improved. Research in psychology, prevention science, and neuroscience is converging on an evolutionary account of the importance of two contrasting suites of social behavior—prosociality vs. antisocial behaviors (crime, drug abuse, risky sexual behavior) and related problems such as depression. Prosociality of individuals and groups evolves in environments that minimize toxic biological and social conditions, promote and richly reinforce prosocial behavior and attitudes, limit opportunities for antisocial behavior, and nurture the pursuit of prosocial values. Conversely, antisocial behavior and related problems emerge in environments that are high in threat and conflict. Over the past 30 years, randomized trials have shown numerous family, school, and community interventions to prevent most problem behaviors and promote prosociality. Research has also shown that poverty and economic inequality are major risk factors for the development of problem behaviors. The paper describes policies that can reduce poverty and benefit youth development. Although it is clear that the canonical economic model of rational self-interest has made a significant contribution to the science of economics, the evidence reviewed here shows that it must be reconciled with an evolutionary perspective on human development and wellbeing if society is going to evolve public policies that advance the health and wellbeing of the entire population. PMID:23833332

  14. Nonhuman genetics. Genomic basis for the convergent evolution of electric organs.

    PubMed

    Gallant, Jason R; Traeger, Lindsay L; Volkening, Jeremy D; Moffett, Howell; Chen, Po-Hao; Novina, Carl D; Phillips, George N; Anand, Rene; Wells, Gregg B; Pinch, Matthew; Güth, Robert; Unguez, Graciela A; Albert, James S; Zakon, Harold H; Samanta, Manoj P; Sussman, Michael R

    2014-06-27

    Little is known about the genetic basis of convergent traits that originate repeatedly over broad taxonomic scales. The myogenic electric organ has evolved six times in fishes to produce electric fields used in communication, navigation, predation, or defense. We have examined the genomic basis of the convergent anatomical and physiological origins of these organs by assembling the genome of the electric eel (Electrophorus electricus) and sequencing electric organ and skeletal muscle transcriptomes from three lineages that have independently evolved electric organs. Our results indicate that, despite millions of years of evolution and large differences in the morphology of electric organ cells, independent lineages have leveraged similar transcription factors and developmental and cellular pathways in the evolution of electric organs. Copyright © 2014, American Association for the Advancement of Science.

  15. Ecomorphological convergence of cave communities.

    PubMed

    Trontelj, Peter; Blejec, Andrej; Fišer, Cene

    2012-12-01

    Extreme selective environments are commonly believed to funnel evolution toward a few predictable outcomes. Caves are well-known extreme environments with characteristically adapted faunas that are similar in appearance, physiology, and behavior all over the world, even if not closely related. Morphological diversity between closely related cave species has been explained by difference in time since colonization and different ecological influence from the surface. Here, we tested a more classical hypothesis: morphological diversity is niche-based, and different morphologies reflect properties of microhabitats within caves. We analyzed seven communities with altogether 30 species of the subterranean amphipod (crustacean) genus Niphargus using multivariate morphometrics, multinomial logit models cross-validation, and phylogenetic reconstruction. Species clustered into four distinct ecomorph classes-small pore, cave stream, cave lake, and lake giants-associated with specific cave microhabitats and of multiple independent phylogenetic origins. Traits commonly regarded as adaptations to caves, such as antenna length, were shown to be related to microhabitat parameters, such as flow velocity. These results demonstrate that under the selection pressure of extreme environment, the ecomorphological structure of communities can converge. Thus, morphological diversity does not result from adaptive response to temporal and ecological gradients, but from fine-level niche partitioning. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

  16. Hepatitis C Virus Antigenic Convergence

    PubMed Central

    Campo, David S.; Dimitrova, Zoya; Yokosawa, Jonny; Hoang, Duc; Perez, Nestor O.; Ramachandran, Sumathi; Khudyakov, Yury

    2012-01-01

    Vaccine development against hepatitis C virus (HCV) is hindered by poor understanding of factors defining cross-immunoreactivity among heterogeneous epitopes. Using synthetic peptides and mouse immunization as a model, we conducted a quantitative analysis of cross-immunoreactivity among variants of the HCV hypervariable region 1 (HVR1). Analysis of 26,883 immunological reactions among pairs of peptides showed that the distribution of cross-immunoreactivity among HVR1 variants was skewed, with antibodies against a few variants reacting with all tested peptides. The HVR1 cross-immunoreactivity was accurately modeled based on amino acid sequence alone. The tested peptides were mapped in the HVR1 sequence space, which was visualized as a network of 11,319 sequences. The HVR1 variants with a greater network centrality showed a broader cross-immunoreactivity. The entire sequence space is explored by each HCV genotype and subtype. These findings indicate that HVR1 antigenic diversity is extensively convergent and effectively limited, suggesting significant implications for vaccine development. PMID:22355779

  17. Convergence of a Linear Recursive Sequence

    ERIC Educational Resources Information Center

    Tay, E. G.; Toh, T. L.; Dong, F. M.; Lee, T. Y.

    2004-01-01

    A necessary and sufficient condition is found for a linear recursive sequence to be convergent, no matter what initial values are given. Its limit is also obtained when the sequence is convergent. Methods from various areas of mathematics are used to obtain the results.

  18. New concurrent iterative methods with monotonic convergence

    SciTech Connect

    Yao, Qingchuan

    1996-12-31

    This paper proposes the new concurrent iterative methods without using any derivatives for finding all zeros of polynomials simultaneously. The new methods are of monotonic convergence for both simple and multiple real-zeros of polynomials and are quadratically convergent. The corresponding accelerated concurrent iterative methods are obtained too. The new methods are good candidates for the application in solving symmetric eigenproblems.

  19. Selective Grammatical Convergence: Learning from Desirable Speakers

    ERIC Educational Resources Information Center

    Lev-Ari, Shiri

    2016-01-01

    Models of language learning often assume that we learn from all the input we receive. This assumption is particularly strong in the domain of short-term and long-term grammatical convergence, where researchers argue that grammatical convergence is mostly an automatic process insulated from social factors. This article shows that the degree to…

  20. Numerical simulation of converging shock waves

    NASA Astrophysics Data System (ADS)

    Yee, Seokjune; Abe, Kanji

    We can achieve the high pressure and high temperature state of gas if the shock wave converges stably. In order to check the stability of the converging shock wave, we introduce two kinds of perturbed initial conditions. The Euler equations of conservation form are integrated by using explicit Non-Muscl TVD finite difference scheme.

  1. Selective Grammatical Convergence: Learning from Desirable Speakers

    ERIC Educational Resources Information Center

    Lev-Ari, Shiri

    2016-01-01

    Models of language learning often assume that we learn from all the input we receive. This assumption is particularly strong in the domain of short-term and long-term grammatical convergence, where researchers argue that grammatical convergence is mostly an automatic process insulated from social factors. This article shows that the degree to…

  2. Convergence of a Linear Recursive Sequence

    ERIC Educational Resources Information Center

    Tay, E. G.; Toh, T. L.; Dong, F. M.; Lee, T. Y.

    2004-01-01

    A necessary and sufficient condition is found for a linear recursive sequence to be convergent, no matter what initial values are given. Its limit is also obtained when the sequence is convergent. Methods from various areas of mathematics are used to obtain the results.

  3. The Problem of Evolving a Genetic Code

    ERIC Educational Resources Information Center

    Woese, Carl R.

    1970-01-01

    Proposes models for the evolution of the genetic code and translation mechanisms. Suggests that the translation process is so complex and precise that it must have evolved in many stages, and that the evolution of the code was influenced by the constraints imposed by the evolving translation mechanism. (EB)

  4. Evolving Technologies: A View to Tomorrow

    ERIC Educational Resources Information Center

    Tamarkin, Molly; Rodrigo, Shelley

    2011-01-01

    Technology leaders must participate in strategy creation as well as operational delivery within higher education institutions. The future of higher education--the view to tomorrow--is irrevocably integrated and intertwined with evolving technologies. This article focuses on two specific evolving technologies: (1) alternative IT sourcing; and (2)…

  5. Evolving Technologies: A View to Tomorrow

    ERIC Educational Resources Information Center

    Tamarkin, Molly; Rodrigo, Shelley

    2011-01-01

    Technology leaders must participate in strategy creation as well as operational delivery within higher education institutions. The future of higher education--the view to tomorrow--is irrevocably integrated and intertwined with evolving technologies. This article focuses on two specific evolving technologies: (1) alternative IT sourcing; and (2)…

  6. What Technology? Reflections on Evolving Services

    ERIC Educational Resources Information Center

    Collins, Sharon

    2009-01-01

    Each year, the members of the EDUCAUSE Evolving Technologies Committee identify and research the evolving technologies that are having--or are predicted to have--the most direct impact on higher education institutions. The committee members choose the relevant topics, write white papers, and present their findings at the EDUCAUSE annual…

  7. Genetic Program Based Data Mining of Fuzzy Decision Trees and Methods of Improving Convergence and Reducing Bloat

    DTIC Science & Technology

    2007-04-01

    A data mining procedure for automatic determination of fuzzy decision tree structure using a genetic program (GP) is discussed. A GP is an algorithm...that evolves other algorithms or mathematical expressions. Innovative methods for accelerating convergence of the data mining procedure and reducing...Finally, additional methods that have been used to validate the data mining algorithm are referenced.

  8. Measuring phonetic convergence in speech production

    PubMed Central

    Pardo, Jennifer S.

    2013-01-01

    Phonetic convergence is defined as an increase in the similarity of acoustic-phonetic form between talkers. Previous research has demonstrated phonetic convergence both when a talker listens passively to speech and while talkers engage in social interaction. Much of this research has focused on a diverse array of acoustic-phonetic attributes, with fewer studies incorporating perceptual measures of phonetic convergence. The current paper reviews research on phonetic convergence in both non-interactive and conversational settings, and attempts to consolidate the diverse array of findings by proposing a paradigm that models perceptual and acoustic measures together. By modeling acoustic measures as predictors of perceived phonetic convergence, this paradigm has the potential to reconcile some of the diverse and inconsistent findings currently reported in the literature. PMID:23986738

  9. Did Convergent Protein Evolution Enable Phytoplasmas to Generate 'Zombie Plants'?

    PubMed

    Rümpler, Florian; Gramzow, Lydia; Theißen, Günter; Melzer, Rainer

    2015-12-01

    Phytoplasmas are pathogenic bacteria that reprogram plant development such that leaf-like structures instead of floral organs develop. Infected plants are sterile and mainly serve to propagate phytoplasmas and thus have been termed 'zombie plants'. The developmental reprogramming relies on specific interactions of the phytoplasma protein SAP54 with a small subset of MADS-domain transcription factors. Here, we propose that SAP54 folds into a structure that is similar to that of the K-domain, a protein-protein interaction domain of MADS-domain proteins. We suggest that undergoing convergent structural and sequence evolution, SAP54 evolved to mimic the K-domain. Given the high specificity of resulting developmental alterations, phytoplasmas might be used to study flower development in genetically intractable plants.

  10. Convergent and divergent mechanisms of sugar recognition across kingdoms

    PubMed Central

    Taylor, Maureen E; Drickamer, Kurt

    2014-01-01

    Protein modules that bind specific oligosaccharides are found across all kingdoms of life from single-celled organisms to man. Different, overlapping and evolving designations for sugar-binding domains in proteins can sometimes obscure common features that often reflect convergent solutions to the problem of distinguishing sugars with closely similar structures and binding them with sufficient affinity to achieve biologically meaningful results. Structural and functional analysis has revealed striking parallels between protein domains with widely different structures and evolutionary histories that employ common solutions to the sugar recognition problem. Recent studies also demonstrate that domains descended from common ancestors through divergent evolution appear more widely across the kingdoms of life than had previously been recognized. PMID:25102772

  11. Convergence and divergence in the evolution of aquatic birds.

    PubMed

    Van Tuinen, M; Butvill, D B; Kirsch, J A; Hedges, S B

    2001-07-07

    Aquatic birds exceed other terrestrial vertebrates in the diversity of their adaptations to aquatic niches. For many species this has created difficulty in understanding their evolutionary origin and, in particular, for the flamingos, hamerkop, shoebill and pelecaniforms. Here, new evidence from nuclear and mitochondrial DNA sequences and DNA-DNA hybridization data indicates extensive morphological convergence and divergence in aquatic birds. Among the unexpected findings is a grouping of flamingos and grebes, species which otherwise show no resemblance. These results suggest that the traditional characters used to unite certain aquatic groups, such as totipalmate feet, foot-propelled diving and long legs, evolved more than once and that organismal change in aquatic birds has proceeded at a faster pace than previously recognized.

  12. Convergence and divergence in the evolution of aquatic birds.

    PubMed Central

    Van Tuinen, M.; Butvill, D. B.; Kirsch, J. A.; Hedges, S. B.

    2001-01-01

    Aquatic birds exceed other terrestrial vertebrates in the diversity of their adaptations to aquatic niches. For many species this has created difficulty in understanding their evolutionary origin and, in particular, for the flamingos, hamerkop, shoebill and pelecaniforms. Here, new evidence from nuclear and mitochondrial DNA sequences and DNA-DNA hybridization data indicates extensive morphological convergence and divergence in aquatic birds. Among the unexpected findings is a grouping of flamingos and grebes, species which otherwise show no resemblance. These results suggest that the traditional characters used to unite certain aquatic groups, such as totipalmate feet, foot-propelled diving and long legs, evolved more than once and that organismal change in aquatic birds has proceeded at a faster pace than previously recognized. PMID:11429133

  13. Convergent transcriptional specializations in the brains of humans and song-learning birds

    PubMed Central

    Pfenning, Andreas R.; Hara, Erina; Whitney, Osceola; Rivas, Miriam V.; Wang, Rui; Roulhac, Petra L.; Howard, Jason T.; Wirthlin, Morgan; Lovell, Peter V.; Ganapathy, Ganeshkumar; Mouncastle, Jacquelyn; Moseley, M. Arthur; Thompson, J. Will; Soderblom, Erik J.; Iriki, Atsushi; Kato, Masaki; Gilbert, M. Thomas P.; Zhang, Guojie; Bakken, Trygve; Bongaarts, Angie; Bernard, Amy; Lein, Ed; Mello, Claudio V.; Hartemink, Alexander J.; Jarvis, Erich D.

    2015-01-01

    Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes. PMID:25504733

  14. Convergent transcriptional specializations in the brains of humans and song-learning birds.

    PubMed

    Pfenning, Andreas R; Hara, Erina; Whitney, Osceola; Rivas, Miriam V; Wang, Rui; Roulhac, Petra L; Howard, Jason T; Wirthlin, Morgan; Lovell, Peter V; Ganapathy, Ganeshkumar; Mouncastle, Jacquelyn; Moseley, M Arthur; Thompson, J Will; Soderblom, Erik J; Iriki, Atsushi; Kato, Masaki; Gilbert, M Thomas P; Zhang, Guojie; Bakken, Trygve; Bongaarts, Angie; Bernard, Amy; Lein, Ed; Mello, Claudio V; Hartemink, Alexander J; Jarvis, Erich D

    2014-12-12

    Song-learning birds and humans share independently evolved similarities in brain pathways for vocal learning that are essential for song and speech and are not found in most other species. Comparisons of brain transcriptomes of song-learning birds and humans relative to vocal nonlearners identified convergent gene expression specializations in specific song and speech brain regions of avian vocal learners and humans. The strongest shared profiles relate bird motor and striatal song-learning nuclei, respectively, with human laryngeal motor cortex and parts of the striatum that control speech production and learning. Most of the associated genes function in motor control and brain connectivity. Thus, convergent behavior and neural connectivity for a complex trait are associated with convergent specialized expression of multiple genes.

  15. The Formation of Cores of Giant Planets at Convergence Zones of Planetary Migration

    NASA Astrophysics Data System (ADS)

    Sirono, Sin-iti; Katayama, Masahumi

    2016-10-01

    The formation of solid cores in giant planets of mass ∼ 10 {M}\\oplus is numerically simulated following the scenario of Sándor et al. In this scenario, there are two convergence zones, corresponding to the outer and inner edges of the dead zone, where the torque exerted on planetary embryos by the gas nebula is zero. At the outer edge of the dead zone, anticyclonic vortices accumulate infalling dust aggregates, and planetary embryos are continuously formed in this scenario. We performed N-body simulations and show that massive objects of ≃ 10 {M}\\oplus are formed in ∼2.5 Myr, starting from the embryos. The largest object is formed at the inner convergence zone, although planetary embryos are placed at the outer convergence zone. This is due to the scattering of embryos from the outer to the inner convergence zone, and the shorter damping timescale of eccentricity at the inner convergence zone compared to the outer one. We varied the migration timescale due to the torque from gas by changing the gas surface density around the convergence zones. We found that there is a critical migration timescale below which 10 {M}\\oplus -sized objects are formed. Furthermore, we conducted simulations in which the gas surface density evolves according to viscous accretion. The largest object is also formed at the inner convergence zone irrespective of the strength of turbulence. Throughout the simulations, the location of the largest mass is the inner convergence zone. We confirmed that the formation timescale of a core of a Jovian planet can be explained in this scenario.

  16. New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships*

    PubMed Central

    Brown, Shoshana D.; Babbitt, Patricia C.

    2014-01-01

    Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes. PMID:25210038

  17. New insights about enzyme evolution from large scale studies of sequence and structure relationships.

    PubMed

    Brown, Shoshana D; Babbitt, Patricia C

    2014-10-31

    Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes.

  18. Multiple convergent evolution of arboreal life in oribatid mites indicates the primacy of ecology.

    PubMed

    Maraun, Mark; Erdmann, Georgia; Schulz, Garvin; Norton, Roy A; Scheu, Stefan; Domes, Katja

    2009-09-22

    Frequent convergent evolution in phylogenetically unrelated taxa points to the importance of ecological factors during evolution, whereas convergent evolution in closely related taxa indicates the importance of favourable pre-existing characters (pre-adaptations). We investigated the transitions to arboreal life in oribatid mites (Oribatida, Acari), a group of mostly soil-living arthropods. We evaluated which general force-ecological factors, historical constraints or chance-was dominant in the evolution of arboreal life in oribatid mites. A phylogenetic study of 51 oribatid mite species and four outgroup taxa, using the ribosomal 18S rDNA region, indicates that arboreal life evolved at least 15 times independently. Arboreal oribatid mite species are not randomly distributed in the phylogenetic tree, but are concentrated among strongly sclerotized, sexual and evolutionary younger taxa. They convergently evolved a capitate sensillus, an anemoreceptor that either precludes overstimulation in the exposed bark habitat or functions as a gravity receptor. Sexual reproduction and strong sclerotization were important pre-adaptations for colonizing the bark of trees that facilitated the exploitation of living resources (e.g. lichens) and served as predator defence, respectively. Overall, our results indicate that ecological factors are most important for the observed pattern of convergent evolution of arboreal life in oribatid mites, supporting an adaptationist view of evolution.

  19. Multiple convergent evolution of arboreal life in oribatid mites indicates the primacy of ecology

    PubMed Central

    Maraun, Mark; Erdmann, Georgia; Schulz, Garvin; Norton, Roy A.; Scheu, Stefan; Domes, Katja

    2009-01-01

    Frequent convergent evolution in phylogenetically unrelated taxa points to the importance of ecological factors during evolution, whereas convergent evolution in closely related taxa indicates the importance of favourable pre-existing characters (pre-adaptations). We investigated the transitions to arboreal life in oribatid mites (Oribatida, Acari), a group of mostly soil-living arthropods. We evaluated which general force—ecological factors, historical constraints or chance—was dominant in the evolution of arboreal life in oribatid mites. A phylogenetic study of 51 oribatid mite species and four outgroup taxa, using the ribosomal 18S rDNA region, indicates that arboreal life evolved at least 15 times independently. Arboreal oribatid mite species are not randomly distributed in the phylogenetic tree, but are concentrated among strongly sclerotized, sexual and evolutionary younger taxa. They convergently evolved a capitate sensillus, an anemoreceptor that either precludes overstimulation in the exposed bark habitat or functions as a gravity receptor. Sexual reproduction and strong sclerotization were important pre-adaptations for colonizing the bark of trees that facilitated the exploitation of living resources (e.g. lichens) and served as predator defence, respectively. Overall, our results indicate that ecological factors are most important for the observed pattern of convergent evolution of arboreal life in oribatid mites, supporting an adaptationist view of evolution. PMID:19535377

  20. Data Convergence - An Australian Perspective

    NASA Astrophysics Data System (ADS)

    Allen, S. S.; Howell, B.

    2012-12-01

    Coupled numerical physical, biogeochemical and sediment models are increasingly being used as integrators to help understand the cumulative or far field effects of change in the coastal environment. This reliance on modeling has forced observations to be delivered as data streams ingestible by modeling frameworks. This has made it easier to create near real-time or forecasting models than to try to recreate the past, and has lead in turn to the conversion of historical data into data streams to allow them to be ingested by the same frameworks. The model and observation frameworks under development within Australia's Commonwealth and Industrial Research Organisation (CSIRO) are now feeding into the Australian Ocean Data Network's (AODN's) MARine Virtual Laboratory (MARVL) . The sensor, or data stream, brokering solution is centred around the "message" and all data flowing through the gateway is wrapped as a message. Messages consist of a topic and a data object and their routing through the gateway to pre-processors and listeners is determined by the topic. The Sensor Message Gateway (SMG) method is allowing data from different sensors measuring the same thing but with different temporal resolutions, units or spatial coverage to be ingested or visualized seamlessly. At the same time the model output as a virtual sensor is being explored, this again being enabled by the SMG. It is only for two way communications with sensor that rigorous adherence to standards is needed, by accepting existing data in less than ideal formats, but exposing them though the SMG we can move a step closer to the Internet Of Things by creating an Internet of Industries where each vested interest can continue with business as usual, contribute to data convergence and adopt more open standards when investment seems appropriate to that sector or business.Architecture Overview

  1. Evolution of enzymes in metabolism: a network perspective.

    PubMed

    Alves, Rui; Chaleil, Raphael A G; Sternberg, Michael J E

    2002-07-19

    Several models have been proposed to explain the origin and evolution of enzymes in metabolic pathways. Initially, the retro-evolution model proposed that, as enzymes at the end of pathways depleted their substrates in the primordial soup, there was a pressure for earlier enzymes in pathways to be created, using the later ones as initial template, in order to replenish the pools of depleted metabolites. Later, the recruitment model proposed that initial templates from other pathways could be used as long as those enzymes were similar in chemistry or substrate specificity. These two models have dominated recent studies of enzyme evolution. These studies are constrained by either the small scale of the study or the artificial restrictions imposed by pathway definitions. Here, a network approach is used to study enzyme evolution in fully sequenced genomes, thus removing both constraints. We find that homologous pairs of enzymes are roughly twice as likely to have evolved from enzymes that are less than three steps away from each other in the reaction network than pairs of non-homologous enzymes. These results, together with the conservation of the type of chemical reaction catalyzed by evolutionarily related enzymes, suggest that functional blocks of similar chemistry have evolved within metabolic networks. One possible explanation for these observations is that this local evolution phenomenon is likely to cause less global physiological disruptions in metabolism than evolution of enzymes from other enzymes that are distant from them in the metabolic network.

  2. Evolution of substrate specificity in a retained enzyme driven by gene loss

    DOE PAGES

    Juárez-Vázquez, Ana Lilia; Edirisinghe, Janaka N.; Verduzco-Castro, Ernesto A.; ...

    2017-03-31

    The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional,more » yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes.« less

  3. Evolution of Substrate Specificity in A Retained Enzyme Driven by Gene Loss

    DOE PAGES

    Juarez-Vazquez, Ana L.; Edirisinghe, Janaka N.; Verduzco-Castro, Ernesto A.; ...

    2017-03-31

    The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. Here, we apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We also observe that the dual-substrate phosphoribosyl isomerase A or priA gene, at which these pathways converge, appears to coevolve with the occurrence of trp and his genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to amore » monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. These results show how gene loss can drive the evolution of substrate specificity from retained enzymes.« less

  4. Genes involved in convergent evolution of eusociality in bees.

    PubMed

    Woodard, S Hollis; Fischman, Brielle J; Venkat, Aarti; Hudson, Matt E; Varala, Kranthi; Cameron, Sydney A; Clark, Andrew G; Robinson, Gene E

    2011-05-03

    Eusociality has arisen independently at least 11 times in insects. Despite this convergence, there are striking differences among eusocial lifestyles, ranging from species living in small colonies with overt conflict over reproduction to species in which colonies contain hundreds of thousands of highly specialized sterile workers produced by one or a few queens. Although the evolution of eusociality has been intensively studied, the genetic changes involved in the evolution of eusociality are relatively unknown. We examined patterns of molecular evolution across three independent origins of eusociality by sequencing transcriptomes of nine socially diverse bee species and combining these data with genome sequence from the honey bee Apis mellifera to generate orthologous sequence alignments for 3,647 genes. We found a shared set of 212 genes with a molecular signature of accelerated evolution across all eusocial lineages studied, as well as unique sets of 173 and 218 genes with a signature of accelerated evolution specific to either highly or primitively eusocial lineages, respectively. These results demonstrate that convergent evolution can involve a mosaic pattern of molecular changes in both shared and lineage-specific sets of genes. Genes involved in signal transduction, gland development, and carbohydrate metabolism are among the most prominent rapidly evolving genes in eusocial lineages. These findings provide a starting point for linking specific genetic changes to the evolution of eusociality.

  5. Genes involved in convergent evolution of eusociality in bees

    PubMed Central

    Woodard, S. Hollis; Fischman, Brielle J.; Venkat, Aarti; Hudson, Matt E.; Varala, Kranthi; Cameron, Sydney A.; Clark, Andrew G.; Robinson, Gene E.

    2011-01-01

    Eusociality has arisen independently at least 11 times in insects. Despite this convergence, there are striking differences among eusocial lifestyles, ranging from species living in small colonies with overt conflict over reproduction to species in which colonies contain hundreds of thousands of highly specialized sterile workers produced by one or a few queens. Although the evolution of eusociality has been intensively studied, the genetic changes involved in the evolution of eusociality are relatively unknown. We examined patterns of molecular evolution across three independent origins of eusociality by sequencing transcriptomes of nine socially diverse bee species and combining these data with genome sequence from the honey bee Apis mellifera to generate orthologous sequence alignments for 3,647 genes. We found a shared set of 212 genes with a molecular signature of accelerated evolution across all eusocial lineages studied, as well as unique sets of 173 and 218 genes with a signature of accelerated evolution specific to either highly or primitively eusocial lineages, respectively. These results demonstrate that convergent evolution can involve a mosaic pattern of molecular changes in both shared and lineage-specific sets of genes. Genes involved in signal transduction, gland development, and carbohydrate metabolism are among the most prominent rapidly evolving genes in eusocial lineages. These findings provide a starting point for linking specific genetic changes to the evolution of eusociality. PMID:21482769

  6. Convergent bacterial microbiotas in the fungal agricultural systems of insects

    SciTech Connect

    Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; Klepzig, Kier D.; Currie, Cameron R.

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.

  7. Convergent bacterial microbiotas in the fungal agricultural systems of insects

    DOE PAGES

    Aylward, Frank O.; Suen, Garret; Biedermann, Peter H. W.; ...

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associatedmore » with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes.« less

  8. Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects

    PubMed Central

    Suen, Garret; Biedermann, Peter H. W.; Adams, Aaron S.; Scott, Jarrod J.; Malfatti, Stephanie A.; Glavina del Rio, Tijana; Tringe, Susannah G.; Poulsen, Michael; Raffa, Kenneth F.; Klepzig, Kier D.

    2014-01-01

    ABSTRACT The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes. PMID:25406380

  9. Convergent Evolution During Local Adaptation to Patchy Landscapes

    PubMed Central

    2015-01-01

    Species often encounter, and adapt to, many patches of similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species. The tension between the two reflects the constraint imposed on evolution by the underlying genetic architecture versus how effectively selection and geographic isolation act to inhibit the geographic spread of locally adapted alleles. This paper studies the balance between these two routes to adaptation in a model of continuous environments with patchy selection pressures. We address the following questions: How long does it take for a novel allele to appear in a patch where it is locally adapted through mutation? Or, through migration from another, already adapted patch? Which is more likely to occur, as a function of distance between the patches? What population genetic signal is left by the spread of migrant alleles? To answer these questions we examine the family structure underlying migration–selection equilibrium surrounding an already adapted patch, treating those rare families that reach new patches as spatial branching processes. A main result is that patches further apart than a critical distance will likely evolve independent locally adapted alleles; this distance is proportional to the spatial scale of selection (σ/sm, where σ is the dispersal distance and s m is the selective disadvantage of these alleles between patches), and depends linearly on log(s m/μ), where μ is the mutation rate. This provides a way to understand the role of geographic separation between patches in promoting convergent adaptation and the genomic signals it leaves behind. We illustrate these ideas using the convergent evolution of cryptic coloration in the rock pocket mouse, Chaetodipus intermedius, as an empirical example. PMID:26571125

  10. Warning signals evolve to disengage Batesian mimics.

    PubMed

    Franks, Daniel W; Ruxton, Graeme D; Sherratt, Thomas N

    2009-01-01

    Prey that are unprofitable to attack are typically conspicuous in appearance. Conventional theory assumes that these warning signals have evolved in response to predator receiver biases. However, such biases might be a symptom rather than a cause of warning signals. We therefore examine an alternative theory: that conspicuousness evolves in unprofitable prey to avoid confusion with profitable prey. One might wonder why unprofitable prey do not find a cryptic means to be distinct from profitable prey, reducing both their risk of confusion with profitable prey and their rate of detection by predators. Here we present the first coevolutionary model to allow for Batesian mimicry and signals with different levels of detectability. We find that unprofitable prey do indeed evolve ways of distinguishing themselves using cryptic signals, particularly when appearance traits can evolve in multiple dimensions. However, conspicuous warning signals readily evolve in unprofitable prey when there are more ways to look different from the background than to match it. Moreover, the more unprofitable the prey species, the higher its evolved conspicuousness. Our results provide strong support for the argument that unprofitable species evolve conspicuous signals to avoid confusion with profitable prey and indicate that peak shift in conspicuousness-linked traits is a major factor in its establishment.

  11. Early evolution of efficient enzymes and genome organization

    PubMed Central

    2012-01-01

    Background Cellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specificities: they were generalist. When and under what conditions could primordial metabolism run by generalist enzymes evolve to contemporary-type metabolism run by specific enzymes? Results Here we show by numerical simulation of an enzyme-catalyzed reaction chain that specialist enzymes spread after the invention of the chromosome because protocells harbouring unlinked genes maintain largely non-specific enzymes to reduce their assortment load. When genes are linked on chromosomes, high enzyme specificity evolves because it increases biomass production, also by reducing taxation by side reactions. Conclusion The constitution of the genetic system has a profound influence on the limits of metabolic efficiency. The major evolutionary transition to chromosomes is thus proven to be a prerequisite for a complex metabolism. Furthermore, the appearance of specific enzymes opens the door for the evolution of their regulation. Reviewers This article was reviewed by Sándor Pongor, Gáspár Jékely, and Rob Knight. PMID:23114029

  12. Canonical forms of unconditionally convergent multipliers☆

    PubMed Central

    Stoeva, D.T.; Balazs, P.

    2013-01-01

    Multipliers are operators that combine (frame-like) analysis, a multiplication with a fixed sequence, called the symbol, and synthesis. They are very interesting mathematical objects that also have a lot of applications for example in acoustical signal processing. It is known that bounded symbols and Bessel sequences guarantee unconditional convergence. In this paper we investigate necessary and equivalent conditions for the unconditional convergence of multipliers. In particular, we show that, under mild conditions, unconditionally convergent multipliers can be transformed by shifting weights between symbol and sequence, into multipliers with symbol (1) and Bessel sequences (called multipliers in canonical form). PMID:23564973

  13. Canonical forms of unconditionally convergent multipliers.

    PubMed

    Stoeva, D T; Balazs, P

    2013-03-01

    Multipliers are operators that combine (frame-like) analysis, a multiplication with a fixed sequence, called the symbol, and synthesis. They are very interesting mathematical objects that also have a lot of applications for example in acoustical signal processing. It is known that bounded symbols and Bessel sequences guarantee unconditional convergence. In this paper we investigate necessary and equivalent conditions for the unconditional convergence of multipliers. In particular, we show that, under mild conditions, unconditionally convergent multipliers can be transformed by shifting weights between symbol and sequence, into multipliers with symbol (1) and Bessel sequences (called multipliers in canonical form).

  14. On the Local Convergence of Pattern Search

    NASA Technical Reports Server (NTRS)

    Dolan, Elizabeth D.; Lewis, Robert Michael; Torczon, Virginia; Bushnell, Dennis M. (Technical Monitor)

    2000-01-01

    We examine the local convergence properties of pattern search methods, complementing the previously established global convergence properties for this class of algorithms. We show that the step-length control parameter which appears in the definition of pattern search algorithms provides a reliable asymptotic measure of first-order stationarity. This gives an analytical justification for a traditional stopping criterion for pattern search methods. Using this measure of first-order stationarity, we analyze the behavior of pattern search in the neighborhood of an isolated local minimizer. We show that a recognizable subsequence converges r-linearly to the minimizer.

  15. Sex chromosomes evolved from independent ancestral linkage groups in winged insects.

    PubMed

    Pease, James B; Hahn, Matthew W

    2012-06-01

    The evolution of a pair of chromosomes that differ in appearance between males and females (heteromorphic sex chromosomes) has occurred repeatedly across plants and animals. Recent work has shown that the male heterogametic (XY) and female heterogametic (ZW) sex chromosomes evolved independently from different pairs of homomorphic autosomes in the common ancestor of birds and mammals but also that X and Z chromosomes share many convergent molecular features. However, little is known about how often heteromorphic sex chromosomes have either evolved convergently from different autosomes or in parallel from the same pair of autosomes and how universal patterns of molecular evolution on sex chromosomes really are. Among winged insects with sequenced genomes, there are male heterogametic species in both the Diptera (e.g., Drosophila melanogaster) and the Coleoptera (Tribolium castaneum), female heterogametic species in the Lepidoptera (Bombyx mori), and haplodiploid species in the Hymenoptera (e.g., Nasonia vitripennis). By determining orthologous relationships among genes on the X and Z chromosomes of insects with sequenced genomes, we are able to show that these chromosomes are not homologous to one another but are homologous to autosomes in each of the other species. These results strongly imply that heteromorphic sex chromosomes have evolved independently from different pairs of ancestral chromosomes in each of the insect orders studied. We also find that the convergently evolved X chromosomes of Diptera and Coleoptera share genomic features with each other and with vertebrate X chromosomes, including excess gene movement from the X to the autosomes. However, other patterns of molecular evolution--such as increased codon bias, decreased gene density, and the paucity of male-biased genes on the X--differ among the insect X and Z chromosomes. Our results provide evidence for both differences and nearly universal similarities in patterns of evolution among

  16. Convergent evolution of hemoglobin switching in jawed and jawless vertebrates.

    PubMed

    Rohlfing, Kim; Stuhlmann, Friederike; Docker, Margaret F; Burmester, Thorsten

    2016-02-01

    During development, humans and other jawed vertebrates (Gnathostomata) express distinct hemoglobin genes, resulting in different hemoglobin tetramers. Embryonic and fetal hemoglobin have higher oxygen affinities than the adult hemoglobin, sustaining the oxygen demand of the developing organism. Little is known about the expression of hemoglobins during development of jawless vertebrates (Agnatha). We identified three hemoglobin switches in the life cycle of the sea lamprey. Three hemoglobin genes are specifically expressed in the embryo, four genes in the filter feeding larva (ammocoete), and nine genes correspond to the adult hemoglobin chains. During the development from the parasitic to the reproductive adult, the composition of hemoglobin changes again, with a massive increase of chain aHb1. A single hemoglobin chain is expressed constitutively in all stages. We further showed the differential expression of other globin genes: Myoglobin 1 is most highly expressed in the reproductive adult, myoglobin 2 expression peaks in the larva. Globin X1 is restricted to the embryo; globin X2 was only found in the reproductive adult. Cytoglobin is expressed at low levels throughout the life cycle. Because the hemoglobins of jawed and jawless vertebrates evolved independently from a common globin ancestor, hemoglobin switching must also have evolved convergently in these taxa. Notably, the ontogeny of sea lamprey hemoglobins essentially recapitulates their phylogeny, with the embryonic hemoglobins emerging first, followed by the evolution of larval and adult hemoglobins.

  17. Convergent evolution of vascular optimization in kelp (Laminariales).

    PubMed

    Drobnitch, Sarah Tepler; Jensen, Kaare H; Prentice, Paige; Pittermann, Jarmila

    2015-10-07

    Terrestrial plants and mammals, although separated by a great evolutionary distance, have each arrived at a highly conserved body plan in which universal allometric scaling relationships govern the anatomy of vascular networks and key functional metabolic traits. The universality of allometric scaling suggests that these phyla have each evolved an 'optimal' transport strategy that has been overwhelmingly adopted by extant species. To truly evaluate the dominance and universality of vascular optimization, however, it is critical to examine other, lesser-known, vascularized phyla. The brown algae (Phaeophyceae) are one such group--as distantly related to plants as mammals, they have convergently evolved a plant-like body plan and a specialized phloem-like transport network. To evaluate possible scaling and optimization in the kelp vascular system, we developed a model of optimized transport anatomy and tested it with measurements of the giant kelp, Macrocystis pyrifera, which is among the largest and most successful of macroalgae. We also evaluated three classical allometric relationships pertaining to plant vascular tissues with a diverse sampling of kelp species. Macrocystis pyrifera displays strong scaling relationships between all tested vascular parameters and agrees with our model; other species within the Laminariales display weak or inconsistent vascular allometries. The lack of universal scaling in the kelps and the presence of optimized transport anatomy in M. pyrifera raises important questions about the evolution of optimization and the possible competitive advantage conferred by optimized vascular systems to multicellular phyla. © 2015 The Author(s).

  18. Photonanomedicine: a convergence of photodynamic therapy and nanotechnology

    NASA Astrophysics Data System (ADS)

    Obaid, Girgis; Broekgaarden, Mans; Bulin, Anne-Laure; Huang, Huang-Chiao; Kuriakose, Jerrin; Liu, Joyce; Hasan, Tayyaba

    2016-06-01

    As clinical nanomedicine has emerged over the past two decades, phototherapeutic advancements using nanotechnology have also evolved and impacted disease management. Because of unique features attributable to the light activation process of molecules, photonanomedicine (PNM) holds significant promise as a personalized, image-guided therapeutic approach for cancer and non-cancer pathologies. The convergence of advanced photochemical therapies such as photodynamic therapy (PDT) and imaging modalities with sophisticated nanotechnologies is enabling the ongoing evolution of fundamental PNM formulations, such as Visudyne®, into progressive forward-looking platforms that integrate theranostics (therapeutics and diagnostics), molecular selectivity, the spatiotemporally controlled release of synergistic therapeutics, along with regulated, sustained drug dosing. Considering that the envisioned goal of these integrated platforms is proving to be realistic, this review will discuss how PNM has evolved over the years as a preclinical and clinical amalgamation of nanotechnology with PDT. The encouraging investigations that emphasize the potent synergy between photochemistry and nanotherapeutics, in addition to the growing realization of the value of these multi-faceted theranostic nanoplatforms, will assist in driving PNM formulations into mainstream oncological clinical practice as a necessary tool in the medical armamentarium.

  19. Convergent bacterial microbiotas in the fungal agricultural systems of insects.

    PubMed

    Aylward, Frank O; Suen, Garret; Biedermann, Peter H W; Adams, Aaron S; Scott, Jarrod J; Malfatti, Stephanie A; Glavina del Rio, Tijana; Tringe, Susannah G; Poulsen, Michael; Raffa, Kenneth F; Klepzig, Kier D; Currie, Cameron R

    2014-11-18

    The ability to cultivate food is an innovation that has produced some of the most successful ecological strategies on the planet. Although most well recognized in humans, where agriculture represents a defining feature of civilization, species of ants, beetles, and termites have also independently evolved symbioses with fungi that they cultivate for food. Despite occurring across divergent insect and fungal lineages, the fungivorous niches of these insects are remarkably similar, indicating convergent evolution toward this successful ecological strategy. Here, we characterize the microbiota of ants, beetles, and termites engaged in nutritional symbioses with fungi to define the bacterial groups associated with these prominent herbivores and forest pests. Using culture-independent techniques and the in silico reconstruction of 37 composite genomes of dominant community members, we demonstrate that different insect-fungal symbioses that collectively shape ecosystems worldwide have highly similar bacterial microbiotas comprised primarily of the genera Enterobacter, Rahnella, and Pseudomonas. Although these symbioses span three orders of insects and two phyla of fungi, we show that they are associated with bacteria sharing high whole-genome nucleotide identity. Due to the fine-scale correspondence of the bacterial microbiotas of insects engaged in fungal symbioses, our findings indicate that this represents an example of convergence of entire host-microbe complexes. The cultivation of fungi for food is a behavior that has evolved independently in ants, beetles, and termites and has enabled many species of these insects to become ecologically important and widely distributed herbivores and forest pests. Although the primary fungal cultivars of these insects have been studied for decades, comparatively little is known of their bacterial microbiota. In this study, we show that diverse fungus-growing insects are associated with a common bacterial community composed of the

  20. Neural mechanisms underlying the evolvability of behaviour

    PubMed Central

    Katz, Paul S.

    2011-01-01

    The complexity of nervous systems alters the evolvability of behaviour. Complex nervous systems are phylogenetically constrained; nevertheless particular species-specific behaviours have repeatedly evolved, suggesting a predisposition towards those behaviours. Independently evolved behaviours in animals that share a common neural architecture are generally produced by homologous neural structures, homologous neural pathways and even in the case of some invertebrates, homologous identified neurons. Such parallel evolution has been documented in the chromatic sensitivity of visual systems, motor behaviours and complex social behaviours such as pair-bonding. The appearance of homoplasious behaviours produced by homologous neural substrates suggests that there might be features of these nervous systems that favoured the repeated evolution of particular behaviours. Neuromodulation may be one such feature because it allows anatomically defined neural circuitry to be re-purposed. The developmental, genetic and physiological mechanisms that contribute to nervous system complexity may also bias the evolution of behaviour, thereby affecting the evolvability of species-specific behaviour. PMID:21690127

  1. Evolvability Characterization in the Context of SOA

    NASA Astrophysics Data System (ADS)

    Arciniegas H., Jose L.; Dueñas L., Juan C.

    Service-Oriented Architecture (SOA) is an architectural style which promotes reuse of self-contained services. These self-contained services allow a better consideration of software quality characteristics as they can be independently analyzed. In our work, the evolvability quality characteristic has been considered, due to its impact in the stages of Maintenance and Evolution (M&E) for the software enterprises. Three goals are underlined in this paper: first, the relationship between SOA and quality characteristics focusing on a precise definition of evolvability of a software product from the SOA perspective, second a M&E model for SOA, and finally, some experiences are presented in order to assess evolvability in real software products. Two case studies have been executed: the first one analyzing the evolvability of the OSGi framework. And in the second case, the model is used in local Small and Medium Enterprises (SMEs), where an improvement process has been executed.

  2. Neural mechanisms underlying the evolvability of behaviour.

    PubMed

    Katz, Paul S

    2011-07-27

    The complexity of nervous systems alters the evolvability of behaviour. Complex nervous systems are phylogenetically constrained; nevertheless particular species-specific behaviours have repeatedly evolved, suggesting a predisposition towards those behaviours. Independently evolved behaviours in animals that share a common neural architecture are generally produced by homologous neural structures, homologous neural pathways and even in the case of some invertebrates, homologous identified neurons. Such parallel evolution has been documented in the chromatic sensitivity of visual systems, motor behaviours and complex social behaviours such as pair-bonding. The appearance of homoplasious behaviours produced by homologous neural substrates suggests that there might be features of these nervous systems that favoured the repeated evolution of particular behaviours. Neuromodulation may be one such feature because it allows anatomically defined neural circuitry to be re-purposed. The developmental, genetic and physiological mechanisms that contribute to nervous system complexity may also bias the evolution of behaviour, thereby affecting the evolvability of species-specific behaviour.

  3. Elevated Liver Enzymes

    MedlinePlus

    Symptoms Elevated liver enzymes By Mayo Clinic Staff Elevated liver enzymes may indicate inflammation or damage to cells in the liver. Inflamed or ... than normal amounts of certain chemicals, including liver enzymes, into the bloodstream, which can result in elevated ...

  4. New convergence estimates for multigrid algorithms

    SciTech Connect

    Bramble, J.H.; Pasciak, J.E.

    1987-10-01

    In this paper, new convergence estimates are proved for both symmetric and nonsymmetric multigrid algorithms applied to symmetric positive definite problems. Our theory relates the convergence of multigrid algorithms to a ''regularity and approximation'' parameter ..cap alpha.. epsilon (0, 1) and the number of relaxations m. We show that for the symmetric and nonsymmetric ..nu.. cycles, the multigrid iteration converges for any positive m at a rate which deteriorates no worse than 1-cj/sup -(1-//sup ..cap alpha..//sup )///sup ..cap alpha../, where j is the number of grid levels. We then define a generalized ..nu.. cycle algorithm which involves exponentially increasing (for example, doubling) the number of smoothings on successively coarser grids. We show that the resulting symmetric and nonsymmetric multigrid iterations converge for any ..cap alpha.. with rates that are independent of the mesh size. The theory is presented in an abstract setting which can be applied to finite element multigrid and finite difference multigrid methods.

  5. Morphological and molecular convergences in mammalian phylogenetics.

    PubMed

    Zou, Zhengting; Zhang, Jianzhi

    2016-09-02

    Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference.

  6. On Convergent Probability of a Random Walk

    ERIC Educational Resources Information Center

    Lee, Y.-F.; Ching, W.-K.

    2006-01-01

    This note introduces an interesting random walk on a straight path with cards of random numbers. The method of recurrent relations is used to obtain the convergent probability of the random walk with different initial positions.

  7. Topics in global convergence of density estimates

    NASA Technical Reports Server (NTRS)

    Devroye, L.

    1982-01-01

    The problem of estimating a density f on R sup d from a sample Xz(1),...,X(n) of independent identically distributed random vectors is critically examined, and some recent results in the field are reviewed. The following statements are qualified: (1) For any sequence of density estimates f(n), any arbitrary slow rate of convergence to 0 is possible for E(integral/f(n)-fl); (2) In theoretical comparisons of density estimates, integral/f(n)-f/ should be used and not integral/f(n)-f/sup p, p 1; and (3) For most reasonable nonparametric density estimates, either there is convergence of integral/f(n)-f/ (and then the convergence is in the strongest possible sense for all f), or there is no convergence (even in the weakest possible sense for a single f). There is no intermediate situation.

  8. Cultivate technology convergence for product innovation.

    PubMed

    Wilkinson, J Malcolm

    2006-04-01

    Technologies from diverse scientific disciplines are being combined to drive innovation in medical devices. How technology convergence and innovation could be further stimulated is explored here using developments in imaging and point-of-care devices as examples.

  9. Convergence results for elliptic quasivariational inequalities

    NASA Astrophysics Data System (ADS)

    Sofonea, Mircea; Benraouda, Ahlem

    2017-02-01

    In this paper, we state and prove various convergence results for a general class of elliptic quasivariational inequalities with constraints. Thus, we prove the convergence of the solution of a class of penalized problems to the solution of the original inequality, as the penalty parameter converges to zero. We also prove a continuous dependence result of the solution with respect the convex set of constraints. Then, we consider a mathematical model which describes the equilibrium of an elastic rod attached to a nonlinear spring. We derive the variational formulation of the model which is in a form of an elliptic quasivariational inequality for the displacement field. We prove the unique weak solvability of the model, and then we state and prove two convergence results and provide their corresponding mechanical interpretation.

  10. Convergence of Attitudes among College Students

    ERIC Educational Resources Information Center

    Whatley, Alice E.; Appel, Victor H.

    1973-01-01

    Attempts to determine whether the intersex convergence phenomenon could be applicable to the measured attitudes of collegiate samples. Both sexes seemed to be moving toward a more liberal view on issues related to marriage and the family. (Author)

  11. Morphological and molecular convergences in mammalian phylogenetics

    PubMed Central

    Zou, Zhengting; Zhang, Jianzhi

    2016-01-01

    Phylogenetic trees reconstructed from molecular sequences are often considered more reliable than those reconstructed from morphological characters, in part because convergent evolution, which confounds phylogenetic reconstruction, is believed to be rarer for molecular sequences than for morphologies. However, neither the validity of this belief nor its underlying cause is known. Here comparing thousands of characters of each type that have been used for inferring the phylogeny of mammals, we find that on average morphological characters indeed experience much more convergences than amino acid sites, but this disparity is explained by fewer states per character rather than an intrinsically higher susceptibility to convergence for morphologies than sequences. We show by computer simulation and actual data analysis that a simple method for identifying and removing convergence-prone characters improves phylogenetic accuracy, potentially enabling, when necessary, the inclusion of morphologies and hence fossils for reliable tree inference. PMID:27585543

  12. On Convergent Probability of a Random Walk

    ERIC Educational Resources Information Center

    Lee, Y.-F.; Ching, W.-K.

    2006-01-01

    This note introduces an interesting random walk on a straight path with cards of random numbers. The method of recurrent relations is used to obtain the convergent probability of the random walk with different initial positions.

  13. Testing Adaptive Hypotheses of Convergence with Functional Landscapes: A Case Study of Bone-Cracking Hypercarnivores

    PubMed Central

    Tseng, Zhijie Jack

    2013-01-01

    Morphological convergence is a well documented phenomenon in mammals, and adaptive explanations are commonly employed to infer similar functions for convergent characteristics. I present a study that adopts aspects of theoretical morphology and engineering optimization to test hypotheses about adaptive convergent evolution. Bone-cracking ecomorphologies in Carnivora were used as a case study. Previous research has shown that skull deepening and widening are major evolutionary patterns in convergent bone-cracking canids and hyaenids. A simple two-dimensional design space, with skull width-to-length and depth-to-length ratios as variables, was used to examine optimized shapes for two functional properties: mechanical advantage (MA) and strain energy (SE). Functionality of theoretical skull shapes was studied using finite element analysis (FEA) and visualized as functional landscapes. The distribution of actual skull shapes in the landscape showed a convergent trend of plesiomorphically low-MA and moderate-SE skulls evolving towards higher-MA and moderate-SE skulls; this is corroborated by FEA of 13 actual specimens. Nevertheless, regions exist in the landscape where high-MA and lower-SE shapes are not represented by existing species; their vacancy is observed even at higher taxonomic levels. Results highlight the interaction of biomechanical and non-biomechanical factors in constraining general skull dimensions to localized functional optima through evolution. PMID:23734244

  14. Convergent evolution of phenotypic integration and its alignment with morphological diversification in Caribbean Anolis ecomorphs.

    PubMed

    Kolbe, Jason J; Revell, Liam J; Szekely, Brian; Brodie, Edmund D; Losos, Jonathan B

    2011-12-01

    The adaptive landscape and the G-matrix are keys concepts for understanding how quantitative characters evolve during adaptive radiation. In particular, whether the adaptive landscape can drive convergence of phenotypic integration (i.e., the pattern of phenotypic variation and covariation summarized in the P-matrix) is not well studied. We estimated and compared P for 19 morphological traits in eight species of Caribbean Anolis lizards, finding that similarity in P among species was not correlated with phylogenetic distance. However, greater similarity in P among ecologically similar Anolis species (i.e., the trunk-ground ecomorph) suggests the role of convergent natural selection. Despite this convergence and relatively deep phylogenetic divergence, a large portion of eigenstructure of P is retained among our eight focal species. We also analyzed P as an approximation of G to test for correspondence with the pattern of phenotypic divergence in 21 Caribbean Anolis species. These patterns of covariation were coincident, suggesting that either genetic constraint has influenced the pattern of among-species divergence or, alternatively, that the adaptive landscape has influenced both G and the pattern of phenotypic divergence among species. We provide evidence for convergent evolution of phenotypic integration for one class of Anolis ecomorph, revealing yet another important dimension of evolutionary convergence in this group. No Claim to original U.S. government works.

  15. International Convergence on Geoscience Cyberinfrastructure

    NASA Astrophysics Data System (ADS)

    Allison, M. L.; Atkinson, R.; Arctur, D. K.; Cox, S.; Jackson, I.; Nativi, S.; Wyborn, L. A.

    2012-04-01

    There is growing international consensus on addressing the challenges to cyber(e)-infrastructure for the geosciences. These challenges include: Creating common standards and protocols; Engaging the vast number of distributed data resources; Establishing practices for recognition of and respect for intellectual property; Developing simple data and resource discovery and access systems; Building mechanisms to encourage development of web service tools and workflows for data analysis; Brokering the diverse disciplinary service buses; Creating sustainable business models for maintenance and evolution of information resources; Integrating the data management life-cycle into the practice of science. Efforts around the world are converging towards de facto creation of an integrated global digital data network for the geosciences based on common standards and protocols for data discovery and access, and a shared vision of distributed, web-based, open source interoperable data access and integration. Commonalities include use of Open Geospatial Consortium (OGC) and ISO specifications and standardized data interchange mechanisms. For multidisciplinarity, mediation, adaptation, and profiling services have been successfully introduced to leverage the geosciences standards which are commonly used by the different geoscience communities -introducing a brokering approach which extends the basic SOA archetype. Principal challenges are less technical than cultural, social, and organizational. Before we can make data interoperable, we must make people interoperable. These challenges are being met by increased coordination of development activities (technical, organizational, social) among leaders and practitioners in national and international efforts across the geosciences to foster commonalities across disparate networks. In doing so, we will 1) leverage and share resources, and developments, 2) facilitate and enhance emerging technical and structural advances, 3) promote

  16. Vulnerabilities—bibliometric analysis and literature review of evolving concepts

    NASA Astrophysics Data System (ADS)

    Giupponi, Carlo; Biscaro, Claudio

    2015-12-01

    In this work we analyse the evolution of the vulnerability concept in the research streams of climate change adaptation (CCA) and disaster risk reduction (DRR). We combine a traditional literature review with data mining procedures applied to bibliographic databases to reconstruct the history of the concept within various research topics, showing its evolution and convergences over time. To do that, we integrate different methods combining machine learning algorithms with network and cluster analyses to examine a set of 3757 articles, analysing their distinctive features and similarities on the basis of their contents as well as co-authorships. Bibliometric analyses enable the identification of different communities of articles, pinpointing key papers and authors, while literature review makes it possible to assess the concept of vulnerability evolved within and beyond research communities and scientific networks. Moreover, this work examines the role played by documents published by UN institutions (UNDRO, UNISDR, IPCC) in contributing to the evolution of vulnerability and related concepts. Results show that signs of convergence are evident between the two research streams, and that the IPCC reports have played a major role in proposing solutions for unifying definitions of vulnerability. We observe that the phases of preparation of the IPCC reports are very rich in methodological and terminological developments, while after publication, the literature shows evident signs of propagation of the proposed concepts. The DRR research stream developed before the research stream on CCA, but the latter flourished rapidly and became much larger in terms of number of publications. Nevertheless, in terms of contents, adaptation studies and the IPCC have shown increasing adoption of the concepts developed within the disaster research stream, in particular with regard to the interpretation of vulnerability as one of the dimensions of risk.

  17. Evolving efficiency of restraining bends within wet kaolin analog experiments

    NASA Astrophysics Data System (ADS)

    Hatem, Alexandra E.; Cooke, Michele L.; Madden, Elizabeth H.

    2015-03-01

    Restraining bends along strike-slip fault systems evolve by both propagation of new faults and abandonment of fault segments. Scaled analog modeling using wet kaolin allows for qualitative and quantitative observations of this evolution. To explore how bend geometry affects evolution, we model bends with a variety of initial angles, θ, from θ = 0° for a straight fault to θ = 30°. High-angle restraining bends (θ ≥ 20°) overcome initial inefficiencies by abandoning unfavorably oriented restraining segments and propagating multiple new, inwardly dipping, oblique-slip faults that are well oriented to accommodate convergence within the bend. Restraining bends with 0° < θ ≤ 15° maintain activity along the restraining bend segment and grow a single new oblique slip fault on one side of the bend. In all restraining bends, the first new fault propagates at ~5 mm of accumulated convergence. Particle Image Velocimetry analysis provides a complete velocity field throughout the experiments. From these data, we quantify the strike-slip efficiency of the system as the percentage of applied plate-parallel velocity accommodated as slip in the direction of plate motion along faults within the restraining bend. Bends with small θ initially have higher strike-slip efficiency compared to bends with large θ. Although they have different fault geometries, all systems with a 5 cm bend width reach a steady strike-slip efficiency of 80% after 50 mm of applied plate displacement. These experimental restraining bends resemble crustal faults in their asymmetric fault growth, asymmetric topographic gradient, and strike-slip efficiency.

  18. Post-production modification of industrial enzymes.

    PubMed

    Minten, Inge J; Abello, Nicolas; Schooneveld-Bergmans, Margot E F; van den Berg, Marco A

    2014-01-01

    Industry has an increasing interest in the use of enzymes as environmentally friendly, highly efficient, and specific bio-catalysts. Enzymes have primarily evolved to function in aqueous environments at ambient temperature and pressure. These conditions however do not always correspond with industrial processes or applications, and only a small portion of all known enzymes are therefore suitable for industrial use. Protein engineering can sometimes be applied to convey more desirable properties to enzymes, such as increased stability, but is limited to the 20 naturally occurring amino acids or homologs thereof. Using post-production modification, which has the potential to combine desirable properties from the enzyme and the conjugated compounds, enzymes can be modified with both natural and synthetic molecules. This offers access to a myriad of possibilities for tuning the properties of enzymes. At this moment, however, the effects of post-production modification cannot yet be reliably predicted. The increasing number of applications will improve this so that the potential of this technology can be fully exploited. This review will focus on post-production modification of enzymes and its use and opportunities in industry.

  19. The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters.

    PubMed

    Bar-Even, Arren; Noor, Elad; Savir, Yonatan; Liebermeister, Wolfram; Davidi, Dan; Tawfik, Dan S; Milo, Ron

    2011-05-31

    The kinetic parameters of enzymes are key to understanding the rate and specificity of most biological processes. Although specific trends are frequently studied for individual enzymes, global trends are rarely addressed. We performed an analysis of k(cat) and K(M) values of several thousand enzymes collected from the literature. We found that the "average enzyme" exhibits a k(cat) of ~0 s(-1) and a k(cat)/K(M) of ~10(5) s(-1) M(-1), much below the diffusion limit and the characteristic textbook portrayal of kinetically superior enzymes. Why do most enzymes exhibit moderate catalytic efficiencies? Maximal rates may not evolve in cases where weaker selection pressures are expected. We find, for example, that enzymes operating in secondary metabolism are, on average, ~30-fold slower than those of central metabolism. We also find indications that the physicochemical properties of substrates affect the kinetic parameters. Specifically, low molecular mass and hydrophobicity appear to limit K(M) optimization. In accordance, substitution with phosphate, CoA, or other large modifiers considerably lowers the K(M) values of enzymes utilizing the substituted substrates. It therefore appears that both evolutionary selection pressures and physicochemical constraints shape the kinetic parameters of enzymes. It also seems likely that the catalytic efficiency of some enzymes toward their natural substrates could be increased in many cases by natural or laboratory evolution.

  20. [Convergence in health: dream or reality?].

    PubMed

    Comín Novella, D

    1997-01-01

    In the last fifty years the distance between the poorest and the richest countries, measured in income per capita, has augmented. Keeping in mind the absence of economic convergence, this paper use the life expectancy data compiled by the World Bank for 125 countries to examine whether their health levels have converged in the period 1960-1992. In order to answer this question we apply the concepts of beta and sigma convergence and the evolution of the distribution developed in the economic literature. The most relevant results that arise from the analysis are that 1) there is convergence in the health levels in the world during the period 1960-89, 2) the existence of convergence is not sensible to the measure used but it is to the variable used to proxy the health level, 3) the speed of convergence fell down from the eighties, and 4) the African countries reduced the distance from their health level to the levels of the rest of the world but, within Africa, the differences increased along 1960-92. These evidences suggest a nonlinear relation between health and income per capita.

  1. Auto convergence for stereoscopic 3D cameras

    NASA Astrophysics Data System (ADS)

    Zhang, Buyue; Kothandaraman, Sreenivas; Batur, Aziz Umit

    2012-03-01

    Viewing comfort is an important concern for 3-D capable consumer electronics such as 3-D cameras and TVs. Consumer generated content is typically viewed at a close distance which makes the vergence-accommodation conflict particularly pronounced, causing discomfort and eye fatigue. In this paper, we present a Stereo Auto Convergence (SAC) algorithm for consumer 3-D cameras that reduces the vergence-accommodation conflict on the 3-D display by adjusting the depth of the scene automatically. Our algorithm processes stereo video in realtime and shifts each stereo frame horizontally by an appropriate amount to converge on the chosen object in that frame. The algorithm starts by estimating disparities between the left and right image pairs using correlations of the vertical projections of the image data. The estimated disparities are then analyzed by the algorithm to select a point of convergence. The current and target disparities of the chosen convergence point determines how much horizontal shift is needed. A disparity safety check is then performed to determine whether or not the maximum and minimum disparity limits would be exceeded after auto convergence. If the limits would be exceeded, further adjustments are made to satisfy the safety limits. Finally, desired convergence is achieved by shifting the left and the right frames accordingly. Our algorithm runs real-time at 30 fps on a TI OMAP4 processor. It is tested using an OMAP4 embedded prototype stereo 3-D camera. It significantly improves 3-D viewing comfort.

  2. Effect of genetic convergence on phylogenetic inference.

    PubMed

    Christin, Pascal-Antoine; Besnard, Guillaume; Edwards, Erika J; Salamin, Nicolas

    2012-03-01

    Phylogenetic reconstructions are a major component of many studies in evolutionary biology, but their accuracy can be reduced under certain conditions. Recent studies showed that the convergent evolution of some phenotypes resulted from recurrent amino acid substitutions in genes belonging to distant lineages. It has been suggested that these convergent substitutions could bias phylogenetic reconstruction toward grouping convergent phenotypes together, but such an effect has never been appropriately tested. We used computer simulations to determine the effect of convergent substitutions on the accuracy of phylogenetic inference. We show that, in some realistic conditions, even a relatively small proportion of convergent codons can strongly bias phylogenetic reconstruction, especially when amino acid sequences are used as characters. The strength of this bias does not depend on the reconstruction method but varies as a function of how much divergence had occurred among the lineages prior to any episodes of convergent substitutions. While the occurrence of this bias is difficult to predict, the risk of spurious groupings is strongly decreased by considering only 3rd codon positions, which are less subject to selection, as long as saturation problems are not present. Therefore, we recommend that, whenever possible, topologies obtained with amino acid sequences and 3rd codon positions be compared to identify potential phylogenetic biases and avoid evolutionarily misleading conclusions. Copyright © 2011 Elsevier Inc. All rights reserved.

  3. Convergence of a discretized self-adaptive evolutionary algorithm on multi-dimensional problems.

    SciTech Connect

    Hart, William Eugene; DeLaurentis, John Morse

    2003-08-01

    We consider the convergence properties of a non-elitist self-adaptive evolutionary strategy (ES) on multi-dimensional problems. In particular, we apply our recent convergence theory for a discretized (1,{lambda})-ES to design a related (1,{lambda})-ES that converges on a class of seperable, unimodal multi-dimensional problems. The distinguishing feature of self-adaptive evolutionary algorithms (EAs) is that the control parameters (like mutation step lengths) are evolved by the evolutionary algorithm. Thus the control parameters are adapted in an implicit manner that relies on the evolutionary dynamics to ensure that more effective control parameters are propagated during the search. Self-adaptation is a central feature of EAs like evolutionary stategies (ES) and evolutionary programming (EP), which are applied to continuous design spaces. Rudolph summarizes theoretical results concerning self-adaptive EAs and notes that the theoretical underpinnings for these methods are essentially unexplored. In particular, convergence theories that ensure convergence to a limit point on continuous spaces have only been developed by Rudolph, Hart, DeLaurentis and Ferguson, and Auger et al. In this paper, we illustrate how our analysis of a (1,{lambda})-ES for one-dimensional unimodal functions can be used to ensure convergence of a related ES on multidimensional functions. This (1,{lambda})-ES randomly selects a search dimension in each iteration, along which points generated. For a general class of separable functions, our analysis shows that the ES searches along each dimension independently, and thus this ES converges to the (global) minimum.

  4. The Evolving Challenges of Black Urban Administration

    ERIC Educational Resources Information Center

    Herbert, Adam W.

    1975-01-01

    Analyzes some of the major administrative forces, personalities, problems and issues which will converge, it is stated, as urban governments seek to address the "urban crisis" from the perspective of black urban dwellers: the "urban crises" includes resource demands (i.e. for energy) and growing requests for expanded social services, unemployment…

  5. OUTWARD MIGRATION OF JUPITER AND SATURN IN EVOLVED GASEOUS DISKS

    SciTech Connect

    D'Angelo, Gennaro; Marzari, Francesco E-mail: francesco.marzari@pd.infn.it

    2012-09-20

    The outward migration of a pair of resonant-orbit planets, driven by tidal interactions with a gas-dominated disk, is studied in the context of evolved solar nebula models. The planets' masses, M{sub 1} and M{sub 2}, correspond to those of Jupiter and Saturn. Hydrodynamical calculations in two and three dimensions are used to quantify the migration rates and analyze the conditions under which the outward migration mechanism may operate. The planets are taken to be fully formed after 10{sup 6} and before 3 Multiplication-Sign 10{sup 6} years. The orbital evolution of the planets in an evolving disk is then calculated until the disk's gas is completely dissipated. Orbital locking in the 3:2 mean motion resonance may lead to outward migration under appropriate conditions of disk viscosity and temperature. However, resonance locking does not necessarily result in outward migration. This is the case, for example, if convergent migration leads to locking in the 2:1 mean motion resonance, as post-formation disk conditions seem to suggest. Accretion of gas on the planets may deactivate the outward migration mechanism by raising the mass ratio M{sub 2}/M{sub 1} and/or by reducing the accretion rate toward the star, and hence depleting the inner disk. For migrating planets locked in the 3:2 mean motion resonance, there are stalling radii that depend on disk viscosity and on stellar irradiation, when it determines the disk's thermal balance. Planets locked in the 3:2 orbital resonance that start moving outward from within 1-2 AU may reach beyond Almost-Equal-To 5 AU only under favorable conditions. However, within the explored space of disk parameters, only a small fraction-less than a few percent-of the models predict that the interior planet reaches beyond Almost-Equal-To 4 AU.

  6. Comparative transcriptomics of convergent evolution: different genes but conserved pathways underlie caste phenotypes across lineages of eusocial insects.

    PubMed

    Berens, Ali J; Hunt, James H; Toth, Amy L

    2015-03-01

    An area of great interest in evolutionary genomics is whether convergently evolved traits are the result of convergent molecular mechanisms. The presence of queen and worker castes in insect societies is a spectacular example of convergent evolution and phenotypic plasticity. Multiple insect lineages have evolved environmentally induced alternative castes. Given multiple origins of eusociality in Hymenoptera (bees, ants, and wasps), it has been proposed that insect castes evolved from common genetic "toolkits" consisting of deeply conserved genes. Here, we combine data from previously published studies on fire ants and honey bees with new data for Polistes metricus paper wasps to assess the toolkit idea by presenting the first comparative transcriptome-wide analysis of caste determination among three major hymenopteran social lineages. Overall, we found few shared caste differentially expressed transcripts across the three social lineages. However, there is substantially more overlap at the levels of pathways and biological functions. Thus, there are shared elements but not on the level of specific genes. Instead, the toolkit appears to be relatively "loose," that is, different lineages show convergent molecular evolution involving similar metabolic pathways and molecular functions but not the exact same genes. Additionally, our paper wasp data do not support a complementary hypothesis that "novel" taxonomically restricted genes are related to caste differences. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  7. Possibilities for global governance of converging technologies

    NASA Astrophysics Data System (ADS)

    Roco, Mihail C.

    2008-01-01

    The convergence of nanotechnology, modern biology, the digital revolution and cognitive sciences will bring about tremendous improvements in transformative tools, generate new products and services, enable opportunities to meet and enhance human potential and social achievements, and in time reshape societal relationships. This paper focuses on the progress made in governance of such converging, emerging technologies and suggests possibilities for a global approach. Specifically, this paper suggests creating a multidisciplinary forum or a consultative coordinating group with members from various countries to address globally governance of converging, emerging technologies. The proposed framework for governance of converging technologies calls for four key functions: supporting the transformative impact of the new technologies; advancing responsible development that includes health, safety and ethical concerns; encouraging national and global partnerships; and establishing commitments to long-term planning and investments centered on human development. Principles of good governance guiding these functions include participation of all those who are forging or affected by the new technologies, transparency of governance strategies, responsibility of each participating stakeholder, and effective strategic planning. Introduction and management of converging technologies must be done with respect for immediate concerns, such as privacy, access to medical advancements, and potential human health effects. At the same time, introduction and management should also be done with respect for longer-term concerns, such as preserving human integrity, dignity and welfare. The suggested governance functions apply to four levels of governance: (a) adapting existing regulations and organizations; (b) establishing new programs, regulations and organizations specifically to handle converging technologies; (c) building capacity for addressing these issues into national policies and

  8. Convergence of gut microbiomes in myrmecophagous mammals.

    PubMed

    Delsuc, Frédéric; Metcalf, Jessica L; Wegener Parfrey, Laura; Song, Se Jin; González, Antonio; Knight, Rob

    2014-03-01

    Mammals have diversified into many dietary niches. Specialized myrmecophagous (ant- and termite-eating) placental mammals represent a textbook example of evolutionary convergence driven by extreme diet specialization. Armadillos, anteaters, aardvarks, pangolins and aardwolves thus provide a model system for understanding the potential role of gut microbiota in the convergent adaptation to myrmecophagy. Here, we expand upon previous mammalian gut microbiome studies by using high-throughput barcoded Illumina sequencing of the 16S rRNA gene to characterize the composition of gut microbiota in 15 species representing all placental myrmecophagous lineages and their close relatives from zoo- and field-collected samples. We confirm that both diet and phylogeny drive the evolution of mammalian gut microbiota, with cases of convergence in global composition, but also examples of phylogenetic inertia. Our results reveal specialized placental myrmecophages as a spectacular case of large-scale convergence in gut microbiome composition. Indeed, neighbour-net networks and beta-diversity plots based on UniFrac distances show significant clustering of myrmecophagous species (anteaters, aardvarks and aardwolves), even though they belong to phylogenetically distant lineages representing different orders. The aardwolf, which diverged from carnivorous hyenas only in the last 10 million years, experienced a convergent shift in the composition of its gut microbiome to become more similar to other myrmecophages. These results confirm diet adaptation to be a major driving factor of convergence in gut microbiome composition over evolutionary timescales. This study sets the scene for future metagenomic studies aiming at evaluating potential convergence in functional gene content in the microbiomes of specialized mammalian myrmecophages. © 2013 John Wiley & Sons Ltd.

  9. Recent advances in evolvable systems--ICES 96 (International Conference on Evolvable Systems).

    PubMed

    Frank, I; Manderick, B; Higuchi, T

    1997-01-01

    This paper reviews the developments in evolvable hardware systems presented at the First International Conference on Evolvable Systems (ICES 96). The main body of the review gives an overview of the 34 papers presented orally, splitting them into three broad groups according to whether they involve (1) evolving a fit solution to a problem as a member of a population of competing candidates, (2) evolving solutions that can individually learn from and adapt to their environments, or (3) the embryonic growth of solutions. We also review the discussion sessions of the conference and give pointers to related upcoming events.

  10. Partitioning the Fitness Components of RNA Populations Evolving In Vitro

    PubMed Central

    Díaz Arenas, Carolina; Lehman, Niles

    2013-01-01

    All individuals in an evolving population compete for resources, and their performance is measured by a fitness metric. The performance of the individuals is relative to their abilities and to the biotic surroundings – the conditions under which they are competing – and involves many components. Molecules evolving in a test tube can also face complex environments and dynamics, and their fitness measurements should reflect the complexity of various contributing factors as well. Here, the fitnesses of a set of ligase ribozymes evolved by the continuous in vitro evolution system were measured. During these evolution cycles there are three different catalytic steps, ligation, reverse transcription, and forward transcription, each with a potential differential influence on the total fitness of each ligase. For six distinct ligase ribozyme genotypes that resulted from continuous evolution experiments, the rates of reaction were measured for each catalytic step by tracking the kinetics of enzymes reacting with their substrates. The reaction products were analyzed for the amount of product formed per time. Each catalytic step of the evolution cycle was found to have a differential incidence in the total fitness of the ligases, and therefore the total fitness of any ligase cannot be inferred from only one catalytic step of the evolution cycle. Generally, the ribozyme-directed ligation step tends to impart the largest effect on overall fitness. Yet it was found that the ligase genotypes have different absolute fitness values, and that they exploit different stages of the overall cycle to gain a net advantage. This is a new example of molecular niche partitioning that may allow for coexistence of more than one species in a population. The dissection of molecular events into multiple components of fitness provides new insights into molecular evolutionary studies in the laboratory, and has the potential to explain heretofore counterintuitive findings. PMID:24391957

  11. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes.

    PubMed

    Affaticati, Pierre E; Dai, Shao-Bo; Payongsri, Panwajee; Hailes, Helen C; Tittmann, Kai; Dalby, Paul A

    2016-10-21

    The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies.

  12. Structural Analysis of an Evolved Transketolase Reveals Divergent Binding Modes

    PubMed Central

    Affaticati, Pierre E.; Dai, Shao-Bo; Payongsri, Panwajee; Hailes, Helen C.; Tittmann, Kai; Dalby, Paul A.

    2016-01-01

    The S385Y/D469T/R520Q variant of E. coli transketolase was evolved previously with three successive smart libraries, each guided by different structural, bioinformatical or computational methods. Substrate-walking progressively shifted the target acceptor substrate from phosphorylated aldehydes, towards a non-phosphorylated polar aldehyde, a non-polar aliphatic aldehyde, and finally a non-polar aromatic aldehyde. Kinetic evaluations on three benzaldehyde derivatives, suggested that their active-site binding was differentially sensitive to the S385Y mutation. Docking into mutants generated in silico from the wild-type crystal structure was not wholly satisfactory, as errors accumulated with successive mutations, and hampered further smart-library designs. Here we report the crystal structure of the S385Y/D469T/R520Q variant, and molecular docking of three substrates. This now supports our original hypothesis that directed-evolution had generated an evolutionary intermediate with divergent binding modes for the three aromatic aldehydes tested. The new active site contained two binding pockets supporting π-π stacking interactions, sterically separated by the D469T mutation. While 3-formylbenzoic acid (3-FBA) preferred one pocket, and 4-FBA the other, the less well-accepted substrate 3-hydroxybenzaldehyde (3-HBA) was caught in limbo with equal preference for the two pockets. This work highlights the value of obtaining crystal structures of evolved enzyme variants, for continued and reliable use of smart library strategies. PMID:27767080

  13. The correspondence between X-ray bright points and evolving magnetic features in the quiet sun

    NASA Technical Reports Server (NTRS)

    Webb, D. F.; Martin, S. F.; Moses, D.; Harvey, J. W.

    1993-01-01

    The results of a study of X-ray bright points (XBPs) and small-scale evolving magnetic structures are presented. X-ray images obtained during rocket flights, full-disk magnetograms, and time-lapse magnetograms of multiple fields make up the coordinated data set. XBPs were found to be more frequently associated with pre-existing magnetic features of opposite polarity which appeared to be cancelling than with new or emerging flux regions. Most of the XBPs appeared to correspond to opposite polarity magnetic features which were converging towards each other, and some of which had not yet begun cancelling. It is suggested that most XBPs are created when converging flow brings together oppositely directed field lines. This leads to reconnection and heating in the low corona of the newly-formed loops.

  14. The correspondence between X-ray bright points and evolving magnetic features in the quiet sun

    NASA Technical Reports Server (NTRS)

    Webb, D. F.; Martin, S. F.; Moses, D.; Harvey, J. W.

    1993-01-01

    The results of a study of X-ray bright points (XBPs) and small-scale evolving magnetic structures are presented. X-ray images obtained during rocket flights, full-disk magnetograms, and time-lapse magnetograms of multiple fields make up the coordinated data set. XBPs were found to be more frequently associated with pre-existing magnetic features of opposite polarity which appeared to be cancelling than with new or emerging flux regions. Most of the XBPs appeared to correspond to opposite polarity magnetic features which were converging towards each other, and some of which had not yet begun cancelling. It is suggested that most XBPs are created when converging flow brings together oppositely directed field lines. This leads to reconnection and heating in the low corona of the newly-formed loops.

  15. A single molecule perspective on the functional diversity of in vitro evolved β-glucuronidase.

    PubMed

    Liebherr, Raphaela B; Renner, Max; Gorris, Hans H

    2014-04-23

    The mechanisms that drive the evolution of new enzyme activity have been investigated by comparing the kinetics of wild-type and in vitro evolved β-glucuronidase (GUS) at the single molecule level. Several hundred single GUS molecules were separated in large arrays of 62,500 ultrasmall reaction chambers etched into the surface of a fused silica slide to observe their individual substrate turnover rates in parallel by fluorescence microscopy. Individual GUS molecules feature long-lived but divergent activity states, and their mean activity is consistent with classic Michaelis-Menten kinetics. The large number of single molecule substrate turnover rates is representative of the activity distribution within an entire enzyme population. Partially evolved GUS displays a much broader activity distribution among individual enzyme molecules than wild-type GUS. The broader activity distribution indicates a functional division of work between individual molecules in a population of partially evolved enzymes that-as so-called generalists-are characterized by their promiscuous activity with many different substrates.

  16. Evolving networks in the human epileptic brain

    NASA Astrophysics Data System (ADS)

    Lehnertz, Klaus; Ansmann, Gerrit; Bialonski, Stephan; Dickten, Henning; Geier, Christian; Porz, Stephan

    2014-01-01

    Network theory provides novel concepts that promise an improved characterization of interacting dynamical systems. Within this framework, evolving networks can be considered as being composed of nodes, representing systems, and of time-varying edges, representing interactions between these systems. This approach is highly attractive to further our understanding of the physiological and pathophysiological dynamics in human brain networks. Indeed, there is growing evidence that the epileptic process can be regarded as a large-scale network phenomenon. We here review methodologies for inferring networks from empirical time series and for a characterization of these evolving networks. We summarize recent findings derived from studies that investigate human epileptic brain networks evolving on timescales ranging from few seconds to weeks. We point to possible pitfalls and open issues, and discuss future perspectives.

  17. Quantifying evolvability in small biological networks

    SciTech Connect

    Nemenman, Ilya; Mugler, Andrew; Ziv, Etay; Wiggins, Chris H

    2008-01-01

    The authors introduce a quantitative measure of the capacity of a small biological network to evolve. The measure is applied to a stochastic description of the experimental setup of Guet et al. (Science 2002, 296, pp. 1466), treating chemical inducers as functional inputs to biochemical networks and the expression of a reporter gene as the functional output. The authors take an information-theoretic approach, allowing the system to set parameters that optimise signal processing ability, thus enumerating each network's highest-fidelity functions. All networks studied are highly evolvable by the measure, meaning that change in function has little dependence on change in parameters. Moreover, each network's functions are connected by paths in the parameter space along which information is not significantly lowered, meaning a network may continuously change its functionality without completely losing it along the way. This property further underscores the evolvability of the networks.

  18. Metanetworks of artificially evolved regulatory networks

    NASA Astrophysics Data System (ADS)

    Danacı, Burçin; Erzan, Ayşe

    2016-04-01

    We study metanetworks arising in genotype and phenotype spaces, in the context of a model population of Boolean graphs evolved under selection for short dynamical attractors. We define the adjacency matrix of a graph as its genotype, which gets mutated in the course of evolution, while its phenotype is its set of dynamical attractors. Metanetworks in the genotype and phenotype spaces are formed, respectively, by genetic proximity and by phenotypic similarity, the latter weighted by the sizes of the basins of attraction of the shared attractors. We find that evolved populations of Boolean graphs form tree-like giant clusters in genotype space, while random populations of Boolean graphs are typically so far removed from each other genetically that they cannot form a metanetwork. In phenotype space, the metanetworks of evolved populations are super robust both under the elimination of weak connections and random removal of nodes.

  19. Grid Convergence for Turbulent Flows(Invited)

    NASA Technical Reports Server (NTRS)

    Diskin, Boris; Thomas, James L.; Rumsey, Christopher L.; Schwoppe, Axel

    2015-01-01

    A detailed grid convergence study has been conducted to establish accurate reference solutions corresponding to the one-equation linear eddy-viscosity Spalart-Allmaras turbulence model for two dimensional turbulent flows around the NACA 0012 airfoil and a flat plate. The study involved three widely used codes, CFL3D (NASA), FUN3D (NASA), and TAU (DLR), and families of uniformly refined structured grids that differ in the grid density patterns. Solutions computed by different codes on different grid families appear to converge to the same continuous limit, but exhibit different convergence characteristics. The grid resolution in the vicinity of geometric singularities, such as a sharp trailing edge, is found to be the major factor affecting accuracy and convergence of discrete solutions, more prominent than differences in discretization schemes and/or grid elements. The results reported for these relatively simple turbulent flows demonstrate that CFL3D, FUN3D, and TAU solutions are very accurate on the finest grids used in the study, but even those grids are not sufficient to conclusively establish an asymptotic convergence order.

  20. Experimental and numerical analysis of convergent nozzlex

    NASA Astrophysics Data System (ADS)

    Srinivas, G.; Rakham, Bhupal

    2017-05-01

    In this paper the main focus was given to convergent nozzle where both the experimental and numerical calculations were carried out with the support of standardized literature. In the recent years the field of air breathing and non-air breathing engine developments significantly increase its performance. To enhance the performance of both the type of engines the nozzle is the one of the component which will play a vital role, especially selecting the type of nozzle depends upon the vehicle speed requirement and aerodynamic behavior at most important in the field of propulsion. The convergent nozzle flow experimental analysis done using scaled apparatus and the similar setup was arranged artificially in the ANSYS software for doing the flow analysis across the convergent nozzle. The consistent calculation analysis are done based on the public literature survey to validate the experimental and numerical simulation results of convergent nozzle. Using these two experimental and numerical simulation approaches the best fit results will bring up to meet the design requirements. However the comparison also made to meet the reliability of the work on design criteria of convergent nozzle which can entrench in the field of propulsion applications.

  1. Numerical Convergence In Smoothed Particle Hydrodynamics

    NASA Astrophysics Data System (ADS)

    Zhu, Qirong; Hernquist, Lars; Li, Yuexing

    2015-02-01

    We study the convergence properties of smoothed particle hydrodynamics (SPH) using numerical tests and simple analytic considerations. Our analysis shows that formal numerical convergence is possible in SPH only in the joint limit N → ∞, h → 0, and Nnb → ∞, where N is the total number of particles, h is the smoothing length, and Nnb is the number of neighbor particles within the smoothing volume used to compute smoothed estimates. Previous work has generally assumed that the conditions N → ∞ and h → 0 are sufficient to achieve convergence, while holding Nnb fixed. We demonstrate that if Nnb is held fixed as the resolution is increased, there will be a residual source of error that does not vanish as N → ∞ and h → 0. Formal numerical convergence in SPH is possible only if Nnb is increased systematically as the resolution is improved. Using analytic arguments, we derive an optimal compromise scaling for Nnb by requiring that this source of error balance that present in the smoothing procedure. For typical choices of the smoothing kernel, we find Nnb vpropN 0.5. This means that if SPH is to be used as a numerically convergent method, the required computational cost does not scale with particle number as O(N), but rather as O(N 1 + δ), where δ ≈ 0.5, with a weak dependence on the form of the smoothing kernel.

  2. Uplift of Zagros Mountains slows plate convergence

    NASA Astrophysics Data System (ADS)

    Balcerak, Ernie

    2013-05-01

    Research has indicated that mountain ranges can slow down the convergence between two tectonic plates on timescales as short as a few million years, as the growing mountains provide enough tectonic force to impact plate motions. Focusing on the convergence of the Arabian and Eurasian plates at the Zagros mountain range, which runs across Iran and Iraq, Austermann and Iaffaldano reconstructed the relative motion of the plates using published paleomagnetic data covering the past 13 million years, as well as current geodetic measurements. They show that the convergence of the two plates has decreased by about 30% over the past 5 million years. Looking at the geological record to infer past topography and using a computer model of the mantle-lithosphere system, the authors examined whether the recent uplift across the Zagros Mountains could have caused the observed slowdown. They also considered several other geological events that might have influenced the convergence rate, but the authors were able to rule those out as dominant controls. The authors conclude that the uplift across the Zagros Mountains in the past 5 million years did indeed play a key role in slowing down the convergence between the Eurasian and Arabian plates. (Tectonics, doi:10.1002/tect.20027, 2013)

  3. JavaGenes: Evolving Graphs with Crossover

    NASA Technical Reports Server (NTRS)

    Globus, Al; Atsatt, Sean; Lawton, John; Wipke, Todd

    2000-01-01

    Genetic algorithms usually use string or tree representations. We have developed a novel crossover operator for a directed and undirected graph representation, and used this operator to evolve molecules and circuits. Unlike strings or trees, a single point in the representation cannot divide every possible graph into two parts, because graphs may contain cycles. Thus, the crossover operator is non-trivial. A steady-state, tournament selection genetic algorithm code (JavaGenes) was written to implement and test the graph crossover operator. All runs were executed by cycle-scavagging on networked workstations using the Condor batch processing system. The JavaGenes code has evolved pharmaceutical drug molecules and simple digital circuits. Results to date suggest that JavaGenes can evolve moderate sized drug molecules and very small circuits in reasonable time. The algorithm has greater difficulty with somewhat larger circuits, suggesting that directed graphs (circuits) are more difficult to evolve than undirected graphs (molecules), although necessary differences in the crossover operator may also explain the results. In principle, JavaGenes should be able to evolve other graph-representable systems, such as transportation networks, metabolic pathways, and computer networks. However, large graphs evolve significantly slower than smaller graphs, presumably because the space-of-all-graphs explodes combinatorially with graph size. Since the representation strongly affects genetic algorithm performance, adding graphs to the evolutionary programmer's bag-of-tricks should be beneficial. Also, since graph evolution operates directly on the phenotype, the genotype-phenotype translation step, common in genetic algorithm work, is eliminated.

  4. Fundamentals of enzyme kinetics.

    PubMed

    Seibert, Eleanore; Tracy, Timothy S

    2014-01-01

    This chapter provides a general introduction to the kinetics of enzyme-catalyzed reactions, with a focus on drug-metabolizing enzymes. A prerequisite to understanding enzyme kinetics is having a clear grasp of the meanings of "enzyme" and "catalysis." Catalysts are reagents that can increase the rate of a chemical reaction without being consumed in the reaction. Enzymes are proteins that form a subset of catalysts. These concepts are further explored below.

  5. A Stefan problem on an evolving surface

    PubMed Central

    Alphonse, Amal; Elliott, Charles M.

    2015-01-01

    We formulate a Stefan problem on an evolving hypersurface and study the well posedness of weak solutions given L1 data. To do this, we first develop function spaces and results to handle equations on evolving surfaces in order to give a natural treatment of the problem. Then, we consider the existence of solutions for data; this is done by regularization of the nonlinearity. The regularized problem is solved by a fixed point theorem and then uniform estimates are obtained in order to pass to the limit. By using a duality method, we show continuous dependence, which allows us to extend the results to L1 data. PMID:26261364

  6. How the first biopolymers could have evolved.

    PubMed Central

    Abkevich, V I; Gutin, A M; Shakhnovich, E I

    1996-01-01

    In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution. PMID:8570645

  7. The Evolving Diagnostic and Genetic Landscapes of Autism Spectrum Disorder

    PubMed Central

    Ziats, Mark N.; Rennert, Owen M.

    2016-01-01

    The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome. PMID:27200076

  8. The Evolving Diagnostic and Genetic Landscapes of Autism Spectrum Disorder.

    PubMed

    Ziats, Mark N; Rennert, Owen M

    2016-01-01

    The autism spectrum disorders (ASD) are a heterogeneous set of neurodevelopmental syndromes defined by impairments in verbal and non-verbal communication, restricted social interaction, and the presence of stereotyped patterns of behavior. The prevalence of ASD is rising, and the diagnostic criteria and clinical perspectives on the disorder continue to evolve in parallel. Although the majority of individuals with ASD will not have an identifiable genetic cause, almost 25% of cases have identifiable causative DNA variants. The rapidly improving ability to identify genetic mutations because of advances in next generation sequencing, coupled with previous epidemiological studies demonstrating high heritability of ASD, have led to many recent attempts to identify causative genetic mutations underlying the ASD phenotype. However, although hundreds of mutations have been identified to date, they are either rare variants affecting only a handful of ASD patients, or are common variants in the general population conferring only a small risk for ASD. Furthermore, the genes implicated thus far are heterogeneous in their structure and function, hampering attempts to understand shared molecular mechanisms among all ASD patients; an understanding that is crucial for the development of targeted diagnostics and therapies. However, new work is beginning to suggest that the heterogeneous set of genes implicated in ASD may ultimately converge on a few common pathways. In this review, we discuss the parallel evolution of our diagnostic and genetic understanding of autism spectrum disorders, and highlight recent attempts to infer common biology underlying this complicated syndrome.

  9. Evolving Improvements to TRMM Ground Validation Rainfall Estimates

    NASA Technical Reports Server (NTRS)

    Robinson, M.; Kulie, M. S.; Marks, D. A.; Wolff, D. B.; Ferrier, B. S.; Amitai, E.; Silberstein, D. S.; Fisher, B. L.; Wang, J.; Einaudi, Franco (Technical Monitor)

    2000-01-01

    The primary function of the TRMM Ground Validation (GV) Program is to create GV rainfall products that provide basic validation of satellite-derived precipitation measurements for select primary sites. Since the successful 1997 launch of the TRMM satellite, GV rainfall estimates have demonstrated systematic improvements directly related to improved radar and rain gauge data, modified science techniques, and software revisions. Improved rainfall estimates have resulted in higher quality GV rainfall products and subsequently, much improved evaluation products for the satellite-based precipitation estimates from TRMM. This presentation will demonstrate how TRMM GV rainfall products created in a semi-automated, operational environment have evolved and improved through successive generations. Monthly rainfall maps and rainfall accumulation statistics for each primary site will be presented for each stage of GV product development. Contributions from individual product modifications involving radar reflectivity (Ze)-rain rate (R) relationship refinements, improvements in rain gauge bulk-adjustment and data quality control processes, and improved radar and gauge data will be discussed. Finally, it will be demonstrated that as GV rainfall products have improved, rainfall estimation comparisons between GV and satellite have converged, lending confidence to the satellite-derived precipitation measurements from TRMM.

  10. Convergent Evolution of Unique Morphological Adaptations to a Subterranean Environment in Cave Millipedes (Diplopoda)

    PubMed Central

    Golovatch, Sergei; Wesener, Thomas; Tian, Mingyi

    2017-01-01

    Animal life in caves has fascinated researchers and the public alike because of the unusual and sometimes bizarre morphological adaptations observed in numerous troglobitic species. Despite their worldwide diversity, the adaptations of cave millipedes (Diplopoda) to a troglobitic lifestyle have rarely been examined. In this study, morphological characters were analyzed in species belonging to four different orders (Glomerida, Polydesmida, Chordeumatida, and Spirostreptida) and six different families (Glomeridae, Paradoxosomatidae, Polydesmidae, Haplodesmidae, Megalotylidae, and Cambalopsidae) that represent the taxonomic diversity of class Diplopoda. We focused on the recently discovered millipede fauna of caves in southern China. Thirty different characters were used to compare cave troglobites and epigean species within the same genera. A character matrix was created to analyze convergent evolution of cave adaptations. Males and females were analyzed independently to examine sex differences in cave adaptations. While 10 characters only occurred in a few phylogenetic groups, 20 characters were scored for in all families. Of these, four characters were discovered to have evolved convergently in all troglobitic millipedes. The characters that represented potential morphological cave adaptations in troglobitic species were: (1) a longer body; (2) a lighter body color; (3) elongation of the femora; and (4) elongation of the tarsi of walking legs. Surprisingly, female, but not male, antennae were more elongated in troglobites than in epigean species. Our study clearly shows that morphological adaptations have evolved convergently in different, unrelated millipede orders and families, most likely as a direct adaptation to cave life. PMID:28178274

  11. Convergent Evolution of Unique Morphological Adaptations to a Subterranean Environment in Cave Millipedes (Diplopoda).

    PubMed

    Liu, Weixin; Golovatch, Sergei; Wesener, Thomas; Tian, Mingyi

    2017-01-01

    Animal life in caves has fascinated researchers and the public alike because of the unusual and sometimes bizarre morphological adaptations observed in numerous troglobitic species. Despite their worldwide diversity, the adaptations of cave millipedes (Diplopoda) to a troglobitic lifestyle have rarely been examined. In this study, morphological characters were analyzed in species belonging to four different orders (Glomerida, Polydesmida, Chordeumatida, and Spirostreptida) and six different families (Glomeridae, Paradoxosomatidae, Polydesmidae, Haplodesmidae, Megalotylidae, and Cambalopsidae) that represent the taxonomic diversity of class Diplopoda. We focused on the recently discovered millipede fauna of caves in southern China. Thirty different characters were used to compare cave troglobites and epigean species within the same genera. A character matrix was created to analyze convergent evolution of cave adaptations. Males and females were analyzed independently to examine sex differences in cave adaptations. While 10 characters only occurred in a few phylogenetic groups, 20 characters were scored for in all families. Of these, four characters were discovered to have evolved convergently in all troglobitic millipedes. The characters that represented potential morphological cave adaptations in troglobitic species were: (1) a longer body; (2) a lighter body color; (3) elongation of the femora; and (4) elongation of the tarsi of walking legs. Surprisingly, female, but not male, antennae were more elongated in troglobites than in epigean species. Our study clearly shows that morphological adaptations have evolved convergently in different, unrelated millipede orders and families, most likely as a direct adaptation to cave life.

  12. Convergence Estimates for Multidisciplinary Analysis and Optimization

    NASA Technical Reports Server (NTRS)

    Arian, Eyal

    1997-01-01

    A quantitative analysis of coupling between systems of equations is introduced. This analysis is then applied to problems in multidisciplinary analysis, sensitivity, and optimization. For the sensitivity and optimization problems both multidisciplinary and single discipline feasibility schemes are considered. In all these cases a "convergence factor" is estimated in terms of the Jacobians and Hessians of the system, thus it can also be approximated by existing disciplinary analysis and optimization codes. The convergence factor is identified with the measure for the "coupling" between the disciplines in the system. Applications to algorithm development are discussed. Demonstration of the convergence estimates and numerical results are given for a system composed of two non-linear algebraic equations, and for a system composed of two PDEs modeling aeroelasticity.

  13. Convergence studies in meshfree peridynamic simulations

    SciTech Connect

    Seleson, Pablo; Littlewood, David J.

    2016-04-15

    Meshfree methods are commonly applied to discretize peridynamic models, particularly in numerical simulations of engineering problems. Such methods discretize peridynamic bodies using a set of nodes with characteristic volume, leading to particle-based descriptions of systems. In this article, we perform convergence studies of static peridynamic problems. We show that commonly used meshfree methods in peridynamics suffer from accuracy and convergence issues, due to a rough approximation of the contribution to the internal force density of nodes near the boundary of the neighborhood of a given node. We propose two methods to improve meshfree peridynamic simulations. The first method uses accurate computations of volumes of intersections between neighbor cells and the neighborhood of a given node, referred to as partial volumes. The second method employs smooth influence functions with a finite support within peridynamic kernels. Numerical results demonstrate great improvements in accuracy and convergence of peridynamic numerical solutions, when using the proposed methods.

  14. Convergence Properties of KKR Green Function Methods

    NASA Astrophysics Data System (ADS)

    Moghadam, N. Y.; Stocks, G. M.; Zhang, X.-G.; Nicholson, D. M. C.; Shelton, W. A.; Wang, Yang; Faulkner, J. S.

    1998-03-01

    Most multiple scattering theory (MST) electronic structure methods (e.g. KKR, KKR-CPA, impurity Greens function, O[N] LSMS method(Yang Wang et al. Phys. Rev. Letters 75), 2867,(1995)) make use of a expression for the single particle Green function that is based on a single center expansion(J. S. Faulkner and G. M. Stocks, Phys. Rev. B 21),3222, (1980). Because the electronic structure is rapidly convergent in angular momentum, l, the multiple scattering equations are typically truncated at l_max <= 4. Using the LSMS method as illustrative we show that the Green function and, therefore, the cell densities of states and charge density converge more slowly requiring l_max ~ 8 arrow 12 even for muffin-tin potentails. We discuss the consequences of this for previous MST based work, and show that this slow convergence can be trivially accommodated within the LSMS method.

  15. Convergence studies in meshfree peridynamic simulations

    SciTech Connect

    Seleson, Pablo; Littlewood, David J.

    2016-04-15

    Meshfree methods are commonly applied to discretize peridynamic models, particularly in numerical simulations of engineering problems. Such methods discretize peridynamic bodies using a set of nodes with characteristic volume, leading to particle-based descriptions of systems. In this article, we perform convergence studies of static peridynamic problems. We show that commonly used meshfree methods in peridynamics suffer from accuracy and convergence issues, due to a rough approximation of the contribution to the internal force density of nodes near the boundary of the neighborhood of a given node. We propose two methods to improve meshfree peridynamic simulations. The first method uses accurate computations of volumes of intersections between neighbor cells and the neighborhood of a given node, referred to as partial volumes. The second method employs smooth influence functions with a finite support within peridynamic kernels. Numerical results demonstrate great improvements in accuracy and convergence of peridynamic numerical solutions, when using the proposed methods.

  16. Theoretical convergence guarantees for cooperative coevolutionary algorithms.

    PubMed

    Panait, Liviu

    2010-01-01

    Cooperative coevolutionary algorithms have the potential to significantly speed up the search process by dividing the space into parts that can each be conquered separately. However, recent research presented theoretical and empirical arguments that these algorithms tend to converge to suboptimal solutions in the search space, and are thus not fit for optimization tasks. This paper details an extended formal model for cooperative coevolutionary algorithms, and uses it to explore possible reasons these algorithms converge to optimal or suboptimal solutions. We demonstrate that, under specific conditions, this theoretical model will converge to the globally optimal solution. The proofs provide the underlying theoretical foundation for a better application of cooperative coevolutionary algorithms. We demonstrate the practical advantages of applying ideas from this theoretical work to a simple problem domain.

  17. On phonetic convergence during conversational interaction.

    PubMed

    Pardo, Jennifer S

    2006-04-01

    Following research that found imitation in single-word shadowing, this study examines the degree to which interacting talkers increase similarity in phonetic repertoire during conversational interaction. Between-talker repetitions of the same lexical items produced in a conversational task were examined for phonetic convergence by asking a separate set of listeners to detect similarity in pronunciation across items in a perceptual task. In general, a listener judged a repeated item spoken by one talker in the task to be more similar to a sample production spoken by the talker's partner than corresponding pre- and postinteraction utterances. Both the role of a participant in the task and the sex of the pair of talkers affected the degree of convergence. These results suggest that talkers in conversational settings are susceptible to phonetic convergence, which can mark nonlinguistic functions in social discourse and can form the basis for phenomena such as accent change and dialect formation.

  18. Convergence studies in meshfree peridynamic simulations

    DOE PAGES

    Seleson, Pablo; Littlewood, David J.

    2016-04-15

    Meshfree methods are commonly applied to discretize peridynamic models, particularly in numerical simulations of engineering problems. Such methods discretize peridynamic bodies using a set of nodes with characteristic volume, leading to particle-based descriptions of systems. In this article, we perform convergence studies of static peridynamic problems. We show that commonly used meshfree methods in peridynamics suffer from accuracy and convergence issues, due to a rough approximation of the contribution to the internal force density of nodes near the boundary of the neighborhood of a given node. We propose two methods to improve meshfree peridynamic simulations. The first method uses accuratemore » computations of volumes of intersections between neighbor cells and the neighborhood of a given node, referred to as partial volumes. The second method employs smooth influence functions with a finite support within peridynamic kernels. Numerical results demonstrate great improvements in accuracy and convergence of peridynamic numerical solutions, when using the proposed methods.« less

  19. Mnemonic convergence in the human hippocampus

    PubMed Central

    Backus, Alexander R.; Bosch, Sander E.; Ekman, Matthias; Grabovetsky, Alejandro Vicente; Doeller, Christian F.

    2016-01-01

    The ability to form associations between a multitude of events is the hallmark of episodic memory. Computational models have espoused the importance of the hippocampus as convergence zone, binding different aspects of an episode into a coherent representation, by integrating information from multiple brain regions. However, evidence for this long-held hypothesis is limited, since previous work has largely focused on representational and network properties of the hippocampus in isolation. Here we identify the hippocampus as mnemonic convergence zone, using a combination of multivariate pattern and graph-theoretical network analyses of functional magnetic resonance imaging data from humans performing an associative memory task. We observe overlap of conjunctive coding and hub-like network attributes in the hippocampus. These results provide evidence for mnemonic convergence in the hippocampus, underlying the integration of distributed information into episodic memory representations. PMID:27325442

  20. Science and technology convergence: with emphasis for nanotechnology-inspired convergence

    NASA Astrophysics Data System (ADS)

    Bainbridge, William S.; Roco, Mihail C.

    2016-07-01

    Convergence offers a new universe of discovery, innovation, and application opportunities through specific theories, principles, and methods to be implemented in research, education, production, and other societal activities. Using a holistic approach with shared goals, convergence seeks to transcend existing human limitations to achieve improved conditions for work, learning, aging, physical, and cognitive wellness. This paper outlines ten key theories that offer complementary perspectives on this complex dynamic. Principles and methods are proposed to facilitate and enhance science and technology convergence. Several convergence success stories in the first part of the 21st century—including nanotechnology and other emerging technologies—are discussed in parallel with case studies focused on the future. The formulation of relevant theories, principles, and methods aims at establishing the convergence science.

  1. Surveying The Digital Landscape: Evolving Technologies 2004. The EDUCAUSE Evolving Technologies Committee

    ERIC Educational Resources Information Center

    EDUCAUSE Review, 2004

    2004-01-01

    Each year, the members of the EDUCAUSE Evolving Technologies Committee identify and research the evolving technologies that are having the most direct impact on higher education institutions. The committee members choose the relevant topics, write white papers, and present their findings at the EDUCAUSE annual conference. This year, under the…

  2. Surveying The Digital Landscape: Evolving Technologies 2004. The EDUCAUSE Evolving Technologies Committee

    ERIC Educational Resources Information Center

    EDUCAUSE Review, 2004

    2004-01-01

    Each year, the members of the EDUCAUSE Evolving Technologies Committee identify and research the evolving technologies that are having the most direct impact on higher education institutions. The committee members choose the relevant topics, write white papers, and present their findings at the EDUCAUSE annual conference. This year, under the…

  3. Convergent evolutionary reduction of atrial septation in lungless salamanders.

    PubMed

    Lewis, Zachary R; Hanken, James

    2017-01-01

    Nearly two thirds of the approximately 700 species of living salamanders are lungless. These species respire entirely through the skin and buccopharyngeal mucosa. Lung loss dramatically impacts the configuration of the circulatory system but the effects of evolutionary lung loss on cardiac morphology have long been controversial. For example, there is presumably little need for an atrial septum in lungless salamanders due to the absence of pulmonary veins and the presence of a single source of mixed blood flowing into the heart, but whether lungless salamanders possess an atrial septum and whether the sinoatrial aperture is located in the left or right atrium are unresolved; authors have stated opposing claims since the late 1800s. Here, we use micro-computed tomography (μ-CT) imaging, gross dissection and histological reconstruction to compare cardiac morphology among lungless plethodontid salamanders (Plethodontidae), salamanders with lungs, and the convergently lungless species Onychodactylus japonicus (Hynobiidae). Plethodontid salamanders have partial atrial septa and incomplete separation of the atrium into left and right halves. Partial septation is also seen in O. japonicus. Hence, lungless salamanders from two lineages convergently evolved similar morphology of the atrial septum. The partial septum in lungless salamanders can make it appear that the sinoatrial aperture is in the left atrium, but this interpretation is incorrect. Outgroup comparisons demonstrate that the aperture is located in a posterodorsal extension of the right atrium into the left side of the heart. Independent evolutionary losses of the atrial septum may have a similar developmental basis. In mammals, the lungs induce formation of the atrial septum by secreting morphogens to neighboring mesenchyme. We hypothesize that the lungs induce atrial septum development in amphibians in a similar fashion to mammals, and that atrial septum reduction in lungless salamanders is a direct result

  4. Deterministic convergence in iterative phase shifting

    SciTech Connect

    Luna, Esteban; Salas, Luis; Sohn, Erika; Ruiz, Elfego; Nunez, Juan M.; Herrera, Joel

    2009-03-10

    Previous implementations of the iterative phase shifting method, in which the phase of a test object is computed from measurements using a phase shifting interferometer with unknown positions of the reference, do not provide an accurate way of knowing when convergence has been attained. We present a new approach to this method that allows us to deterministically identify convergence. The method is tested with a home-built Fizeau interferometer that measures optical surfaces polished to {lambda}/100 using the Hydra tool. The intrinsic quality of the measurements is better than 0.5 nm. Other possible applications for this technique include fringe projection or any problem where phase shifting is involved.

  5. Experience and convergence in spiritual direction.

    PubMed

    Evans, Jean

    2015-02-01

    The practice of spiritual direction concerns the human experience of God. As praxis, spiritual direction has a long tradition in Western Christianity. It is a process rooted in spirituality with theology as its foundation. This paper explores the convergences between aspects of philosophy (contemplative awareness), psychology (Rogerian client-centered approach) and phenomenology. There are significant points of convergence between phenomenology and spiritual direction: first, in Ignatius of Loyola's phenomenological approach to his religious experience; second, in the appropriation by spiritual directors of concepts of epochē and empathy; third, in the process of "unpacking" religious experience within a spiritual direction interview.

  6. Antibiotics from microbes: converging to kill.

    PubMed

    Fischbach, Michael A

    2009-10-01

    As genetically encoded small molecules, antibiotics are phenotypes that have resulted from mutation and natural selection. Advances in genetics, biochemistry, and bioinformatics have connected hundreds of antibiotics to the gene clusters that encode them, allowing these molecules to be analyzed using the tools of evolutionary biology. This review surveys examples of convergent evolution from microbially produced antibiotics, including the convergence of distinct gene clusters on similar phenotypes and the merger of distinct gene clusters into a single functional unit. Examining antibiotics through an evolutionary lens highlights the versatility of biosynthetic pathways, reveals lessons for combating antibiotic resistance, and provides an entry point for studying the natural roles of these natural products.

  7. On Iλ -statistical convergence of weight g

    NASA Astrophysics Data System (ADS)

    Savas, Ekrem

    2016-08-01

    In this paper, following a very recent and new approach of [M. Balcerzak, P. Das, M. Filipczak, and J. Swaczyna, Acta Math. Hungar. 147, 97-115 (2015)], we further generalize the recently introduced summability method of [E. Savas, and P. Das, Appl. Math. Lett. 24, 826-830 (2011)] and introduce the new notion namely, Iλ -statistical convergence of weight g, where g : ℕ → [0, ∞) is a function satisfying g(n) → ∞ and g(n) ↛ 0 as n → ∞. We mainly investigate certain properties of this convergence.

  8. Toward an Evolved Concept of Landrace

    PubMed Central

    Casañas, Francesc; Simó, Joan; Casals, Joan; Prohens, Jaime

    2017-01-01

    The term “landrace” has generally been defined as a cultivated, genetically heterogeneous variety that has evolved in a certain ecogeographical area and is therefore adapted to the edaphic and climatic conditions and to its traditional management and uses. Despite being considered by many to be inalterable, landraces have been and are in a constant state of evolution as a result of natural and artificial selection. Many landraces have disappeared from cultivation but are preserved in gene banks. Using modern selection and breeding technology tools to shape these preserved landraces together with the ones that are still cultivated is a further step in their evolution in order to preserve their agricultural significance. Adapting historical landraces to present agricultural conditions using cutting-edge breeding technology represents a challenging opportunity to use them in a modern sustainable agriculture, as an immediate return on the investment is highly unlikely. Consequently, we propose a more inclusive definition of landraces, namely that they consist of cultivated varieties that have evolved and may continue evolving, using conventional or modern breeding techniques, in traditional or new agricultural environments within a defined ecogeographical area and under the influence of the local human culture. This includes adaptation of landraces to new management systems and the unconscious or conscious selection made by farmers or breeders using available technology. In this respect, a mixed selection system might be established in which farmers and other social agents develop evolved landraces from the variability generated by public entities. PMID:28228769

  9. Apollo 16 Evolved Lithology Sodic Ferrogabbro

    NASA Technical Reports Server (NTRS)

    Zeigler, Ryan; Jolliff, B. L.; Korotev, R. L.

    2014-01-01

    Evolved lunar igneous lithologies, often referred to as the alkali suite, are a minor but important component of the lunar crust. These evolved samples are incompatible-element rich samples, and are, not surprisingly, most common in the Apollo sites in (or near) the incompatible-element rich region of the Moon known as the Procellarum KREEP Terrane (PKT). The most commonly occurring lithologies are granites (A12, A14, A15, A17), monzogabbro (A14, A15), alkali anorthosites (A12, A14), and KREEP basalts (A15, A17). The Feldspathic Highlands Terrane is not entirely devoid of evolved lithologies, and rare clasts of alkali gabbronorite and sodic ferrogabbro (SFG) have been identified in Apollo 16 station 11 breccias 67915 and 67016. Curiously, nearly all pristine evolved lithologies have been found as small clasts or soil particles, exceptions being KREEP basalts 15382/6 and granitic sample 12013 (which is itself a breccia). Here we reexamine the petrography and geochemistry of two SFG-like particles found in a survey of Apollo 16 2-4 mm particles from the Cayley Plains 62283,7-15 and 62243,10-3 (hereafter 7-15 and 10-3 respectively). We will compare these to previously reported SFG samples, including recent analyses on the type specimen of SFG from lunar breccia 67915.

  10. Did Language Evolve Like the Vertebrate Eye?

    ERIC Educational Resources Information Center

    Botha, Rudolf P.

    2002-01-01

    Offers a critical appraisal of the way in which the idea that human language or some of its features evolved like the vertebrate eye by natural selection is articulated in Pinker and Bloom's (1990) selectionist account of language evolution. Argues that this account is less than insightful because it fails to draw some of the conceptual…

  11. The Evolving Leadership Path of Visual Analytics

    SciTech Connect

    Kluse, Michael; Peurrung, Anthony J.; Gracio, Deborah K.

    2012-01-02

    This is a requested book chapter for an internationally authored book on visual analytics and related fields, coordianted by a UK university and to be published by Springer in 2012. This chapter is an overview of the leadship strategies that PNNL's Jim Thomas and other stakeholders used to establish visual analytics as a field, and how those strategies may evolve in the future.

  12. Evolving Neural Networks for Nonlinear Control.

    DTIC Science & Technology

    1996-09-30

    An approach to creating Amorphous Recurrent Neural Networks (ARNN) using Genetic Algorithms (GA) called 2pGA has been developed and shown to be...effective in evolving neural networks for the control and stabilization of both linear and nonlinear plants, the optimal control for a nonlinear regulator

  13. Toward an Evolved Concept of Landrace.

    PubMed

    Casañas, Francesc; Simó, Joan; Casals, Joan; Prohens, Jaime

    2017-01-01

    The term "landrace" has generally been defined as a cultivated, genetically heterogeneous variety that has evolved in a certain ecogeographical area and is therefore adapted to the edaphic and climatic conditions and to its traditional management and uses. Despite being considered by many to be inalterable, landraces have been and are in a constant state of evolution as a result of natural and artificial selection. Many landraces have disappeared from cultivation but are preserved in gene banks. Using modern selection and breeding technology tools to shape these preserved landraces together with the ones that are still cultivated is a further step in their evolution in order to preserve their agricultural significance. Adapting historical landraces to present agricultural conditions using cutting-edge breeding technology represents a challenging opportunity to use them in a modern sustainable agriculture, as an immediate return on the investment is highly unlikely. Consequently, we propose a more inclusive definition of landraces, namely that they consist of cultivated varieties that have evolved and may continue evolving, using conventional or modern breeding techniques, in traditional or new agricultural environments within a defined ecogeographical area and under the influence of the local human culture. This includes adaptation of landraces to new management systems and the unconscious or conscious selection made by farmers or breeders using available technology. In this respect, a mixed selection system might be established in which farmers and other social agents develop evolved landraces from the variability generated by public entities.

  14. Did Language Evolve Like the Vertebrate Eye?

    ERIC Educational Resources Information Center

    Botha, Rudolf P.

    2002-01-01

    Offers a critical appraisal of the way in which the idea that human language or some of its features evolved like the vertebrate eye by natural selection is articulated in Pinker and Bloom's (1990) selectionist account of language evolution. Argues that this account is less than insightful because it fails to draw some of the conceptual…

  15. Thermal and Evolved-Gas Analyzer Illustration

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This is a computer-aided drawing of the Thermal and Evolved-Gas Analyzer, or TEGA, on NASA's Phoenix Mars Lander.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  16. The Evolving Office of the Registrar

    ERIC Educational Resources Information Center

    Pace, Harold L.

    2011-01-01

    A healthy registrar's office will continue to evolve as it considers student, faculty, and institutional needs; staff talents and expectations; technological opportunities; economic realities; space issues; work environments; and where the strategic plan is taking the institution in support of the mission. Several recognized leaders in the field…

  17. A Course Evolves-Physical Anthropology.

    ERIC Educational Resources Information Center

    O'Neil, Dennis

    2001-01-01

    Describes the development of an online physical anthropology course at Palomar College (California) that evolved from online tutorials. Discusses the ability to update materials on the Web more quickly than in traditional textbooks; creating Web pages that are readable by most Web browsers; test security issues; and clarifying ownership of online…

  18. Septa and processes: convergent evolution of the orbit in haplorhine primates and strigiform birds.

    PubMed

    Menegaz, Rachel A; Kirk, E Christopher

    2009-12-01

    According to the "nocturnal visual predation hypothesis" (NVPH), the convergent eyes and orbits of primates result from selection for improved stereoscopic depth perception to facilitate manual capture of prey at night. Within primates, haplorhines share additional derived orbital morphologies, including a postorbital septum and greater orbital convergence than any other mammalian clade. While the homology and function of the haplorhine septum remain controversial, experimental data suggest that septa evolved to inhibit mechanical disturbance of the orbital contents by the anterior temporalis muscle during mastication. According to this "insulation hypothesis," haplorhines are particularly susceptible to disruption of the orbital contents because they have large and highly convergent eyes and orbits. However, comparative tests of the insulation hypothesis have been hindered by the morphological uniqueness of the haplorhine septum among mammals. Among birds, owls (Strigiformes) exhibit an expanded postorbital process that may be functionally analogous to the haplorhine septum. Here we present a comparative analysis of orbital morphology in 103 avian species that tests two hypotheses: (1) large, convergent orbits are associated with nocturnal visual predation, and (2) the strigiform postorbital process and haplorhine postorbital septum similarly function to insulate the eyes from contractions of mandibular adductors. Strigiforms, as nocturnal visual predators, possess relatively large orbits and exhibit the highest degree of orbital convergence in our sample. Notably, orbital convergence does not scale with orbit size in birds as in mammals. Owls are also unique among the birds examined in possessing extensive, plate-like postorbital processes that largely isolate the orbits from the temporal fossae. Furthermore, dissections of four owl species demonstrate that the expanded strigiform postorbital process deflects the path of mandibular adductors around the eye

  19. Convergent evolution of sexual dimorphism in skull shape using distinct developmental strategies.

    PubMed

    Sanger, Thomas J; Sherratt, Emma; McGlothlin, Joel W; Brodie, Edmund D; Losos, Jonathan B; Abzhanov, Arhat

    2013-08-01

    Studies integrating evolutionary and developmental analyses of morphological variation are of growing interest to biologists as they promise to shed fresh light on the mechanisms of morphological diversification. Sexually dimorphic traits tend to be incredibly divergent across taxa. Such diversification must arise through evolutionary modifications to sex differences during development. Nevertheless, few studies of dimorphism have attempted to synthesize evolutionary and developmental perspectives. Using geometric morphometric analysis of head shape for 50 Anolis species, we show that two clades have converged on extreme levels of sexual dimorphism through similar, male-specific changes in facial morphology. In both clades, males have evolved highly elongate faces whereas females retain faces of more moderate proportion. This convergence is accomplished using distinct developmental mechanisms; one clade evolved extreme dimorphism through the exaggeration of a widely shared, potentially ancestral, developmental strategy whereas the other clade evolved a novel developmental strategy not observed elsewhere in the genus. Together, our analyses indicate that both shared and derived features of development contribute to macroevolutionary patterns of morphological diversity among Anolis lizards. © 2013 The Author(s). Evolution © 2013 The Society for the Study of Evolution.

  20. Convergent and correlated evolution of major life-history traits in the angiosperm genus Leucadendron (Proteaceae).

    PubMed

    Tonnabel, Jeanne; Mignot, Agnès; Douzery, Emmanuel J P; Rebelo, Anthony G; Schurr, Frank M; Midgley, Jeremy; Illing, Nicola; Justy, Fabienne; Orcel, Denis; Olivieri, Isabelle

    2014-10-01

    Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life-history traits. Here, we quantify the extent of convergence of five key life-history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed-dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire-prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse genus that involves more taxa and molecular markers than previously. This reconstruction identifies new clades that were not detected by previous molecular study and morphological classifications. Using this new phylogeny and robust methods that account for phylogenetic uncertainty, we show that the five life-history traits studied were labile during the evolutionary history of the genus. This diversity allowed us to tackle major questions about the correlated evolution of life-history strategies. We found that species with longer seed-dispersal distances tended to evolve lower pollen-dispersal distance, that insect-pollinated species evolved decreased sexual dimorphism, and that species with a persistent soil seed-bank evolved toward reduced fire-survival ability of adults.

  1. Endemism and functional convergence across the North American soil mycobiome.

    PubMed

    Talbot, Jennifer M; Bruns, Thomas D; Taylor, John W; Smith, Dylan P; Branco, Sara; Glassman, Sydney I; Erlandson, Sonya; Vilgalys, Rytas; Liao, Hui-Ling; Smith, Matthew E; Peay, Kabir G

    2014-04-29

    Identifying the ecological processes that structure communities and the consequences for ecosystem function is a central goal of ecology. The recognition that fungi, bacteria, and viruses control key ecosystem functions has made microbial communities a major focus of this field. Because many ecological processes are apparent only at particular spatial or temporal scales, a complete understanding of the linkages between microbial community, environment, and function requires analysis across a wide range of scales. Here, we map the biological and functional geography of soil fungi from local to continental scales and show that the principal ecological processes controlling community structure and function operate at different scales. Similar to plants or animals, most soil fungi are endemic to particular bioregions, suggesting that factors operating at large spatial scales, like dispersal limitation or climate, are the first-order determinants of fungal community structure in nature. By contrast, soil extracellular enzyme activity is highly convergent across bioregions and widely differing fungal communities. Instead, soil enzyme activity is correlated with local soil environment and distribution of fungal traits within the community. The lack of structure-function relationships for soil fungal communities at continental scales indicates a high degree of functional redundancy among fungal communities in global biogeochemical cycles.

  2. Ethanologenic Enzymes of Zymomonas mobilis

    SciTech Connect

    Ingram, Lonnie O'Neal

    1999-03-01

    Zymomonas mobilis is a unique microorganism in being both obligately fermentative and utilizing a Entner-Doudoroff pathway for glycolysis. Glycolytic flux in this organism is readily measured as evolved carbon dioxide, ethanol, or glucose consumed and exceeds 1 {micro}mole glucose/min per mg cell protein. To support this rapid glycolysis, approximately 50% of cytoplasmic protein is devoted to the 13 glycolytic and fermentative enzymes which constitute this central catabolic pathway. Only 1 ATP (net) is produced from each glucose metabolized. During the past grant period, we have completed the characterization of 11 of the 13 glycolytic genes from Z. mobilis together with complementary but separate DOE-fimded research by a former post-dot and collaborator, Dr. Tyrrell Conway. Research funded in my lab by DOE, Division of Energy Biosciences can be divided into three sections: A. Fundamental studies; B. Applied studies and utility; and C. Miscellaneous investigations.

  3. Insolubilization process increases enzyme stability

    NASA Technical Reports Server (NTRS)

    Billingham, J.; Lyn, J.

    1971-01-01

    Enzymes complexed with polymeric matrices contain properties suggesting application to enzyme-controlled reactions. Stability of insolubilized enzyme derivatives is markedly greater than that of soluble enzymes and physical form of insolubilized enzymes is useful in column and batch processes.

  4. Grasping convergent evolution in syngnathids: a unique tale of tails.

    PubMed

    Neutens, C; Adriaens, D; Christiaens, J; De Kegel, B; Dierick, M; Boistel, R; Van Hoorebeke, L

    2014-06-01

    Seahorses and pipehorses both possess a prehensile tail, a unique characteristic among teleost fishes, allowing them to grasp and hold onto substrates such as sea grasses. Although studies have focused on tail grasping, the pattern of evolutionary transformations that made this possible is poorly understood. Recent phylogenetic studies show that the prehensile tail evolved independently in different syngnathid lineages, including seahorses, Haliichthys taeniophorus and several types of so-called pipehorses. This study explores the pattern that characterizes this convergent evolution towards a prehensile tail, by comparing the caudal musculoskeletal organization, as well as passive bending capacities in pipefish (representing the ancestral state), pipehorse, seahorse and H. taeniophorus. To study the complex musculoskeletal morphology, histological sectioning, μCT-scanning and phase contrast synchrotron scanning were combined with virtual 3D-reconstructions. Results suggest that the independent evolution towards tail grasping in syngnathids reflects at least two quite different strategies in which the ancestral condition of a heavy plated and rigid system became modified into a highly flexible one. Intermediate skeletal morphologies (between the ancestral condition and seahorses) could be found in the pygmy pipehorses and H. taeniophorus, which are phylogenetically closely affiliated with seahorses. This study suggests that the characteristic parallel myoseptal organization as already described in seahorse (compared with a conical organization in pipefish and pipehorse) may not be a necessity for grasping, but represents an apomorphy for seahorses, as this pattern is not found in other syngnathid species possessing a prehensile tail. One could suggest that the functionality of grasping evolved before the specialized, parallel myoseptal organization seen in seahorses. However, as the grasping system in pipehorses is a totally different one, this cannot be

  5. Convergent evolution of escape from hepaciviral antagonism in primates.

    PubMed

    Patel, Maulik R; Loo, Yueh-Ming; Horner, Stacy M; Gale, Michael; Malik, Harmit S

    2012-01-01

    The ability to mount an interferon response on sensing viral infection is a critical component of mammalian innate immunity. Several viruses directly antagonize viral sensing pathways to block activation of the host immune response. Here, we show that recurrent viral antagonism has shaped the evolution of the host protein MAVS--a crucial component of the viral-sensing pathway in primates. From sequencing and phylogenetic analyses of MAVS from 21 simian primates, we found that MAVS has evolved under strong positive selection. We focused on how this positive selection has shaped MAVS' susceptibility to Hepatitis C virus (HCV). We functionally tested MAVS proteins from diverse primate species for their ability to resist antagonism by HCV, which uses its protease NS3/4A to cleave human MAVS. We found that MAVS from multiple primates are resistant to inhibition by the HCV protease. This resistance maps to single changes within the protease cleavage site in MAVS, which protect MAVS from getting cleaved by the HCV protease. Remarkably, most of these changes have been independently acquired at a single residue 506 that evolved under positive selection. We show that "escape" mutations lower affinity of the NS3 protease for MAVS and allow it to better restrict HCV replication. We further show that NS3 proteases from all other primate hepaciviruses, including the highly divergent GBV-A and GBV-C viruses, are functionally similar to HCV. We conclude that convergent evolution at residue 506 in multiple primates has resulted in escape from antagonism by hepaciviruses. Our study provides a model whereby insights into the ancient history of viral infections in primates can be gained using extant host and virus genes. Our analyses also provide a means by which primates might clear infections by extant hepaciviruses like HCV.

  6. Grasping convergent evolution in syngnathids: a unique tale of tails

    PubMed Central

    Neutens, C; Adriaens, D; Christiaens, J; De Kegel, B; Dierick, M; Boistel, R; Van Hoorebeke, L

    2014-01-01

    Seahorses and pipehorses both possess a prehensile tail, a unique characteristic among teleost fishes, allowing them to grasp and hold onto substrates such as sea grasses. Although studies have focused on tail grasping, the pattern of evolutionary transformations that made this possible is poorly understood. Recent phylogenetic studies show that the prehensile tail evolved independently in different syngnathid lineages, including seahorses, Haliichthys taeniophorus and several types of so-called pipehorses. This study explores the pattern that characterizes this convergent evolution towards a prehensile tail, by comparing the caudal musculoskeletal organization, as well as passive bending capacities in pipefish (representing the ancestral state), pipehorse, seahorse and H. taeniophorus. To study the complex musculoskeletal morphology, histological sectioning, μCT-scanning and phase contrast synchrotron scanning were combined with virtual 3D-reconstructions. Results suggest that the independent evolution towards tail grasping in syngnathids reflects at least two quite different strategies in which the ancestral condition of a heavy plated and rigid system became modified into a highly flexible one. Intermediate skeletal morphologies (between the ancestral condition and seahorses) could be found in the pygmy pipehorses and H. taeniophorus, which are phylogenetically closely affiliated with seahorses. This study suggests that the characteristic parallel myoseptal organization as already described in seahorse (compared with a conical organization in pipefish and pipehorse) may not be a necessity for grasping, but represents an apomorphy for seahorses, as this pattern is not found in other syngnathid species possessing a prehensile tail. One could suggest that the functionality of grasping evolved before the specialized, parallel myoseptal organization seen in seahorses. However, as the grasping system in pipehorses is a totally different one, this cannot be

  7. Another Perspective: A Response to "Toward Convergence"

    ERIC Educational Resources Information Center

    Regelski, Thomas A.

    2013-01-01

    This response by Thomas A. Regelski was solicited to complement the lead article in this issue, "Toward Convergence: Adapting Music Education to Contemporary Society and Participatory Culture" by Evan S. Tobias. The author notes that many interesting and vital questions and alternatives that are often studiously ignored, overlooked, or taken for…

  8. Sweet! Generation "D" Takes on Media Convergence.

    ERIC Educational Resources Information Center

    Tarpenning, David; Schaub, Laura

    2002-01-01

    Notes that professional journalists continually emphasize the need for developing skills for all delivery systems. Proposes that students interested in journalism should learn about technology and develop projects without the guidance of a teacher or advisor. Describes students' experience with media convergence in a summer journalism workshop.…

  9. [Conservative and surgical treatment of convergence excess].

    PubMed

    Ehrt, O

    2016-07-01

    Convergence excess is a common finding especially in pediatric strabismus. A detailed diagnostic approach has to start after full correction of any hyperopia measured in cycloplegia. It includes measurements of manifest and latent deviation at near and distance fixation, near deviation after relaxation of accommodation with addition of +3 dpt, assessment of binocular function with and without +3 dpt as well as the accommodation range. This diagnostic approach is important for the classification into three types of convergence excess, which require different therapeutic approaches: 1) hypo-accommodative convergence excess is treated with permanent bifocal glasses, 2) norm-accommodative patients should be treated with bifocals which can be weaned over years, especially in patients with good stereopsis and 3) non-accommodative convergence excess and patients with large distance deviations need a surgical approach. The most effective operations include those which reduce the muscle torque, e. g. bimedial Faden operations or Y‑splitting of the medial rectus muscles.

  10. Convergence of some asynchronous nonlinear multisplitting methods

    NASA Astrophysics Data System (ADS)

    Szyld, Daniel B.; Xu, Jian-Jun

    2000-09-01

    Frommer's nonlinear multisplitting methods for solving nonlinear systems of equations are extended to the asynchronous setting. Block methods are extended to include overlap as well. Several specific cases are discussed. Sufficient conditions to guarantee their local convergence are given. A numerical example is presented illustrating the performance of the new approach.

  11. Convergence of coupled cluster perturbation theory

    NASA Astrophysics Data System (ADS)

    Eriksen, Janus J.; Kristensen, Kasper; Matthews, Devin A.; Jørgensen, Poul; Olsen, Jeppe

    2016-12-01

    The convergence of a recently proposed coupled cluster (CC) family of perturbation series [J. J. Eriksen et al., J. Chem. Phys. 140, 064108 (2014)], in which the energetic difference between two CC models—a low-level parent and a high-level target model—is expanded in orders of the Møller-Plesset (MP) fluctuation potential, is investigated for four prototypical closed-shell systems (Ne, singlet CH2, distorted HF, and F-) in standard and augmented basis sets. In these investigations, energy corrections of the various series have been calculated to high orders and their convergence radii have been determined by probing for possible front- and back-door intruder states, the existence of which would make the series divergent. In summary, we conclude how it is primarily the choice of the target state, and not the choice of the parent state, which ultimately governs the convergence behavior of a given series. For example, restricting the target state to, say, triple or quadruple excitations might remove intruders present in series which target the full configuration interaction limit, such as the standard MP series. Furthermore, we find that whereas a CC perturbation series might converge within standard correlation consistent basis sets, it may start to diverge whenever these become augmented by diffuse functions, similar to the MP case. However, unlike for the MP case, such potential divergences are not found to invalidate the practical use of the low-order corrections of the CC perturbation series.

  12. The Convergence Coefficient across Political Systems

    PubMed Central

    Schofield, Norman

    2013-01-01

    Formal work on the electoral model often suggests that parties or candidates should locate themselves at the electoral mean. Recent research has found no evidence of such convergence. In order to explain nonconvergence, the stochastic electoral model is extended by including estimates of electoral valence. We introduce the notion of a convergence coefficient, c. It has been shown that high values of c imply that there is a significant centrifugal tendency acting on parties. We used electoral surveys to construct a stochastic valence model of the the elections in various countries. We find that the convergence coefficient varies across elections in a country, across countries with similar regimes, and across political regimes. In some countries, the centripetal tendency leads parties to converge to the electoral mean. In others the centrifugal tendency dominates and some parties locate far from the electoral mean. In particular, for countries with proportional electoral systems, namely, Israel, Turkey, and Poland, the centrifugal tendency is very high. In the majoritarian polities of the United States and Great Britain, the centrifugal tendency is very low. In anocracies, the autocrat imposes limitations on how far from the origin the opposition parties can move. PMID:24385886

  13. Professionalization in Universities and European Convergence

    ERIC Educational Resources Information Center

    Vivas, Amparo Jimenez; Hevia, David Menendez Alvarez

    2009-01-01

    The constant assessment of the quality of higher education within the framework of European convergence is a challenge for all those universities that wish their degrees and diplomas to reflect a unified Europe. As is the case in any assessment, change and review process, the quest to improve quality implies measuring achievement of the objectives…

  14. Professionalization in Universities and European Convergence

    ERIC Educational Resources Information Center

    Vivas, Amparo Jimenez; Hevia, David Menendez Alvarez

    2009-01-01

    The constant assessment of the quality of higher education within the framework of European convergence is a challenge for all those universities that wish their degrees and diplomas to reflect a unified Europe. As is the case in any assessment, change and review process, the quest to improve quality implies measuring achievement of the objectives…

  15. Culture and Social Psychology: Converging Perspectives

    ERIC Educational Resources Information Center

    Dimaggio, Paul; Markus, Hazel Rose

    2010-01-01

    Views of culture in psychology and sociology have converged markedly in the past two decades. Both have rejected what Adams and Markus (2004) refer to as the "entity" conception of culture--the view that culture is coherent, stable, and located in the heads of collectivities' members--in favor of more supple and dynamic constructs. Culture, in…

  16. Collaborative Instructional Strategies to Enhance Knowledge Convergence

    ERIC Educational Resources Information Center

    Draper, Darryl C.

    2015-01-01

    To promote knowledge convergence through collaborative learning activities in groups, this qualitative case study involved a layered approach for the design and delivery of a highly collaborative learning environment incorporating various instructional technologies grounded in learning theory. In a graduate-level instructional technology course,…

  17. Bandlimited image extrapolation with faster convergence.

    PubMed

    Cahana, D; Stark, H

    1981-08-15

    The Gerchberg-Papoulis (GP) algorithm has been widely discussed in the literature in connection with band-limited or space-limited image extrapolation. Despite its seemingly superior noise-resistant properties over earlier superresolution schemes, the GP algorithm generally exhibits very slow convergence thereby making the choice of starting point critical. We discuss how additional a priori information, such as the low-pass projection of the image (LPI), can be incorporated in the algorithm to decrease the initial error between the starting point of the recursion and the true signal. We also investigate how convergence rates might be improved by (1) using the LPI in each iteration to achieve a double per cycle correction, and (2) applying adaptive thresholding. Somewhat surprisingly, it was found that using the LPI had only a minor effect on the rate of convergence. On the other hand, when combined with adaptive thresholding the use of the LPI both significantly reduced the starting point error and improved the rate of convergence.

  18. Phonological Convergence in a Contracting Language Variety

    ERIC Educational Resources Information Center

    Bullock, Barbara E.; Gerfen, Chip

    2004-01-01

    Most work investigating the role of convergence in situations of language attrition has focused on the morpho-syntactic restructuring of the dying language variety. A central concern of such research has been untangling the factors driving the restructuring with an eye towards establishing whether the changes observed are best viewed as externally…

  19. Collaborative Instructional Strategies to Enhance Knowledge Convergence

    ERIC Educational Resources Information Center

    Draper, Darryl C.

    2015-01-01

    To promote knowledge convergence through collaborative learning activities in groups, this qualitative case study involved a layered approach for the design and delivery of a highly collaborative learning environment incorporating various instructional technologies grounded in learning theory. In a graduate-level instructional technology course,…

  20. Culture and Social Psychology: Converging Perspectives

    ERIC Educational Resources Information Center

    Dimaggio, Paul; Markus, Hazel Rose

    2010-01-01

    Views of culture in psychology and sociology have converged markedly in the past two decades. Both have rejected what Adams and Markus (2004) refer to as the "entity" conception of culture--the view that culture is coherent, stable, and located in the heads of collectivities' members--in favor of more supple and dynamic constructs. Culture, in…

  1. Converging Oceaniac Internal Waves, Somalia, Africa

    NASA Image and Video Library

    1988-10-03

    The arculate fronts of these apparently converging internal waves off the northeast coast of Somalia (11.5N, 51.5E) probably were produced by interaction with two parallel submarine canyons off the Horn of Africa. Internal waves are packets of tidally generated waves traveling within the ocean at varying depths and are not detectable by any surface disturbance.

  2. The convergence coefficient across political systems.

    PubMed

    Gallego, Maria; Schofield, Norman

    2013-01-01

    Formal work on the electoral model often suggests that parties or candidates should locate themselves at the electoral mean. Recent research has found no evidence of such convergence. In order to explain nonconvergence, the stochastic electoral model is extended by including estimates of electoral valence. We introduce the notion of a convergence coefficient, c. It has been shown that high values of c imply that there is a significant centrifugal tendency acting on parties. We used electoral surveys to construct a stochastic valence model of the the elections in various countries. We find that the convergence coefficient varies across elections in a country, across countries with similar regimes, and across political regimes. In some countries, the centripetal tendency leads parties to converge to the electoral mean. In others the centrifugal tendency dominates and some parties locate far from the electoral mean. In particular, for countries with proportional electoral systems, namely, Israel, Turkey, and Poland, the centrifugal tendency is very high. In the majoritarian polities of the United States and Great Britain, the centrifugal tendency is very low. In anocracies, the autocrat imposes limitations on how far from the origin the opposition parties can move.

  3. Governance Challenges of Technological Systems Convergence

    ERIC Educational Resources Information Center

    Whitman, Jim

    2006-01-01

    The convergence of several technological systems (especially nanotechnology, biotechnology, information technology, and robotics) has now been adopted as a strategic goal by several countries, most notably the United States and those of the European Union. The anticipated benefits and related fears of competitive disadvantage have brought together…

  4. World health inequality: convergence, divergence, and development.

    PubMed

    Clark, Rob

    2011-02-01

    Recent studies characterize the last half of the twentieth century as an era of cross-national health convergence, with some attributing welfare gains in the developing world to economic growth. In this study, I examine the extent to which welfare outcomes have actually converged and the extent to which economic development is responsible for the observed trends. Drawing from estimates covering 195 nations during the 1955-2005 period, I find that life expectancy averages converged during this time, but that infant mortality rates continuously diverged. I develop a narrative that implicates economic development in these contrasting trends, suggesting that health outcomes follow a "welfare Kuznets curve." Among poor countries, economic development improves life expectancy more than it reduces infant mortality, whereas the situation is reversed among wealthier nations. In this way, development has contributed to both convergence in life expectancy and divergence in infant mortality. Drawing from 674 observations across 163 countries during the 1980-2005 period, I find that the positive effect of GDP PC on life expectancy attenuates at higher levels of development, while the negative effect of GDP PC on infant mortality grows stronger. Copyright © 2010 Elsevier Ltd. All rights reserved.

  5. Convergence behavior of a new DSMC algorithm.

    SciTech Connect

    Gallis, Michail A.; Rader, Daniel John; Torczynski, John Robert; Bird, Graeme A.

    2008-10-01

    The convergence rate of a new direct simulation Monte Carlo (DSMC) method, termed 'sophisticated DSMC', is investigated for one-dimensional Fourier flow. An argon-like hard-sphere gas at 273.15K and 266.644Pa is confined between two parallel, fully accommodating walls 1mm apart that have unequal temperatures. The simulations are performed using a one-dimensional implementation of the sophisticated DSMC algorithm. In harmony with previous work, the primary convergence metric studied is the ratio of the DSMC-calculated thermal conductivity to its corresponding infinite-approximation Chapman-Enskog theoretical value. As discretization errors are reduced, the sophisticated DSMC algorithm is shown to approach the theoretical values to high precision. The convergence behavior of sophisticated DSMC is compared to that of original DSMC. The convergence of the new algorithm in a three-dimensional implementation is also characterized. Implementations using transient adaptive sub-cells and virtual sub-cells are compared. The new algorithm is shown to significantly reduce the computational resources required for a DSMC simulation to achieve a particular level of accuracy, thus improving the efficiency of the method by a factor of 2.

  6. Converging Oceaniac Internal Waves, Somalia, Africa

    NASA Technical Reports Server (NTRS)

    1988-01-01

    The arculate fronts of these apparently converging internal waves off the northeast coast of Somalia (11.5N, 51.5E) probably were produced by interaction with two parallel submarine canyons off the Horn of Africa. Internal waves are packets of tidally generated waves traveling within the ocean at varying depths and are not detectable by any surface disturbance.

  7. Convergent evolution to an aptamer observed in small populations on DNA microarrays

    NASA Astrophysics Data System (ADS)

    Rowe, W.; Platt, M.; Wedge, D. C.; Day, P. J. R.; Kell, D. B.; Knowles, J. D.

    2010-09-01

    The development of aptamers on custom synthesized DNA microarrays, which has been demonstrated in recent publications, can facilitate detailed analyses of sequence and fitness relationships. Here we use the technique to observe the paths taken through sequence-fitness space by three different evolutionary regimes: asexual reproduction, recombination and model-based evolution. The different evolutionary runs are made on the same array chip in triplicate, each one starting from a small population initialized independently at random. When evolving to a common target protein, glucose-6-phosphate dehydrogenase (G6PD), these nine distinct evolutionary runs are observed to develop aptamers with high affinity and to converge on the same motif not present in any of the starting populations. Regime specific differences in the evolutions, such as speed of convergence, could also be observed.

  8. Network analysis of metabolic enzyme evolution in Escherichia coli

    PubMed Central

    Light, Sara; Kraulis, Per

    2004-01-01

    Background The two most common models for the evolution of metabolism are the patchwork evolution model, where enzymes are thought to diverge from broad to narrow substrate specificity, and the retrograde evolution model, according to which enzymes evolve in response to substrate depletion. Analysis of the distribution of homologous enzyme pairs in the metabolic network can shed light on the respective importance of the two models. We here investigate the evolution of the metabolism in E. coli viewed as a single network using EcoCyc. Results Sequence comparison between all enzyme pairs was performed and the minimal path length (MPL) between all enzyme pairs was determined. We find a strong over-representation of homologous enzymes at MPL 1. We show that the functionally similar and functionally undetermined enzyme pairs are responsible for most of the over-representation of homologous enzyme pairs at MPL 1. Conclusions The retrograde evolution model predicts that homologous enzymes pairs are at short metabolic distances from each other. In general agreement with previous studies we find that homologous enzymes occur close to each other in the network more often than expected by chance, which lends some support to the retrograde evolution model. However, we show that the homologous enzyme pairs which may have evolved through retrograde evolution, namely the pairs that are functionally dissimilar, show a weaker over-representation at MPL 1 than the functionally similar enzyme pairs. Our study indicates that, while the retrograde evolution model may have played a small part, the patchwork evolution model is the predominant process of metabolic enzyme evolution. PMID:15113413

  9. NUMERICAL CONVERGENCE IN SMOOTHED PARTICLE HYDRODYNAMICS

    SciTech Connect

    Zhu, Qirong; Li, Yuexing; Hernquist, Lars

    2015-02-10

    We study the convergence properties of smoothed particle hydrodynamics (SPH) using numerical tests and simple analytic considerations. Our analysis shows that formal numerical convergence is possible in SPH only in the joint limit N → ∞, h → 0, and N{sub nb} → ∞, where N is the total number of particles, h is the smoothing length, and N{sub nb} is the number of neighbor particles within the smoothing volume used to compute smoothed estimates. Previous work has generally assumed that the conditions N → ∞ and h → 0 are sufficient to achieve convergence, while holding N{sub nb} fixed. We demonstrate that if N{sub nb} is held fixed as the resolution is increased, there will be a residual source of error that does not vanish as N → ∞ and h → 0. Formal numerical convergence in SPH is possible only if N{sub nb} is increased systematically as the resolution is improved. Using analytic arguments, we derive an optimal compromise scaling for N{sub nb} by requiring that this source of error balance that present in the smoothing procedure. For typical choices of the smoothing kernel, we find N{sub nb} ∝N {sup 0.5}. This means that if SPH is to be used as a numerically convergent method, the required computational cost does not scale with particle number as O(N), but rather as O(N {sup 1} {sup +} {sup δ}), where δ ≈ 0.5, with a weak dependence on the form of the smoothing kernel.

  10. Multidimensional Convergence in Future 5G Networks

    NASA Astrophysics Data System (ADS)

    Ruffini, Marco

    2017-02-01

    Future 5G services are characterised by unprecedented need for high rate, ubiquitous availability, ultra-low latency and high reliability. The fragmented network view that is widespread in current networks will not stand the challenge posed by next generations of users. A new vision is required, and this paper provides an insight on how network convergence and application-centric approaches will play a leading role towards enabling the 5G vision. The paper, after expressing the view on the need for an end-to-end approach to network design, brings the reader into a journey on the expected 5G network requirements and outlines some of the work currently carried out by main standardisation bodies. It then proposes the use of the concept of network convergence for providing the overall architectural framework to bring together all the different technologies within a unifying and coherent network ecosystem. The novel interpretation of multi-dimensional convergence we introduce leads us to the exploration of aspects of node consolidation and converged network architectures, delving into details of optical-wireless integration and future convergence of optical data centre and access-metro networks. We then discuss how ownership models enabling network sharing will be instrumental in realising the 5G vision. The paper concludes with final remarks on the role SDN will play in 5G and on the need for new business models that reflect the application-centric view of the network. Finally, we provide some insight on growing research areas in 5G networking.

  11. Synthetic metabolism: metabolic engineering meets enzyme design.

    PubMed

    Erb, Tobias J; Jones, Patrik R; Bar-Even, Arren

    2017-04-01

    Metabolic engineering aims at modifying the endogenous metabolic network of an organism to harness it for a useful biotechnological task, for example, production of a value-added compound. Several levels of metabolic engineering can be defined and are the topic of this review. Basic 'copy, paste and fine-tuning' approaches are limited to the structure of naturally existing pathways. 'Mix and match' approaches freely recombine the repertoire of existing enzymes to create synthetic metabolic networks that are able to outcompete naturally evolved pathways or redirect flux toward non-natural products. The space of possible metabolic solution can be further increased through approaches including 'new enzyme reactions', which are engineered on the basis of known enzyme mechanisms. Finally, by considering completely 'novel enzyme chemistries' with de novo enzyme design, the limits of nature can be breached to derive the most advanced form of synthetic pathways. We discuss the challenges and promises associated with these different metabolic engineering approaches and illuminate how enzyme engineering is expected to take a prime role in synthetic metabolic engineering for biotechnology, chemical industry and agriculture of the future. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  12. A phylogenetic test for adaptive convergence in rock-dwelling lizards.

    PubMed

    Revell, Liam J; Johnson, Michele A; Schulte, James A; Kolbe, Jason J; Losos, Jonathan B

    2007-12-01

    Phenotypic similarity of species occupying similar habitats has long been taken as strong evidence of adaptation, but this approach implicitly assumes that similarity is evolutionarily derived. However, even derived similarities may not represent convergent adaptation if the similarities did not evolve as a result of the same selection pressures; an alternative possibility is that the similar features evolved for different reasons, but subsequently allowed the species to occupy the same habitat, in which case the convergent evolution of the same feature by species occupying similar habitats would be the result of exaptation. Many lizard lineages have evolved to occupy vertical rock surfaces, a habitat that places strong functional and ecological demands on lizards. We examined four clades in which species that use vertical rock surfaces exhibit long hindlimbs and flattened bodies. Morphological change on the phylogenetic branches leading to the rock-dwelling species in the four clades differed from change on other branches of the phylogeny; evolutionary transitions to rock-dwelling generally were associated with increases in limb length and decreases in head depth. Examination of particular characters revealed several different patterns of evolutionary change. Rock-dwelling lizards exhibited similarities in head depth as a result of both adaptation and exaptation. Moreover, even though rock-dwelling species generally had longer limbs than their close relatives, clade-level differences in limb length led to an overall lack of difference between rock- and non-rock-dwelling lizards. These results indicate that evolutionary change in the same direction in independent lineages does not necessarily produce convergence, and that the existence of similar advantageous structures among species independently occupying the same environment may not indicate adaptation.

  13. Are there ergodic limits to evolution? Ergodic exploration of genome space and convergence.

    PubMed

    McLeish, Tom C B

    2015-12-06

    We examine the analogy between evolutionary dynamics and statistical mechanics to include the fundamental question of ergodicity-the representative exploration of the space of possible states (in the case of evolution this is genome space). Several properties of evolutionary dynamics are identified that allow a generalization of the ergodic dynamics, familiar in dynamical systems theory, to evolution. Two classes of evolved biological structure then arise, differentiated by the qualitative duration of their evolutionary time scales. The first class has an ergodicity time scale (the time required for representative genome exploration) longer than available evolutionary time, and has incompletely explored the genotypic and phenotypic space of its possibilities. This case generates no expectation of convergence to an optimal phenotype or possibility of its prediction. The second, more interesting, class exhibits an evolutionary form of ergodicity-essentially all of the structural space within the constraints of slower evolutionary variables have been sampled; the ergodicity time scale for the system evolution is less than the evolutionary time. In this case, some convergence towards similar optima may be expected for equivalent systems in different species where both possess ergodic evolutionary dynamics. When the fitness maximum is set by physical, rather than co-evolved, constraints, it is additionally possible to make predictions of some properties of the evolved structures and systems. We propose four structures that emerge from evolution within genotypes whose fitness is induced from their phenotypes. Together, these result in an exponential speeding up of evolution, when compared with complete exploration of genomic space. We illustrate a possible case of application and a prediction of convergence together with attaining a physical fitness optimum in the case of invertebrate compound eye resolution.

  14. Formation and Initiation of Erupting Flux Rope and Embedded Filament Driven by Photospheric Converging Motion

    NASA Astrophysics Data System (ADS)

    Zhao, Xiaozhou; Xia, Chun; Keppens, Rony; Gan, Weiqun

    2017-06-01

    In this paper, we study how a flux rope (FR) is formed and evolves into the corresponding structure of a coronal mass ejection (CME) numerically driven by photospheric converging motion. A two-and-a-half-dimensional magnetohydrodynamics simulation is conducted in a chromosphere-transition-corona setup. The initial arcade-like linear force-free magnetic field is driven by an imposed slow motion converging toward the magnetic inversion line at the bottom boundary. The convergence brings opposite-polarity magnetic flux to the polarity inversion, giving rise to the formation of an FR by magnetic reconnection and eventually to the eruption of a CME. During the FR formation, an embedded prominence gets formed by the levitation of chromospheric material. We confirm that the converging flow is a potential mechanism for the formation of FRs and a possible triggering mechanism for CMEs. We investigate the thermal, dynamical, and magnetic properties of the FR and its embedded prominence by tracking their thermal evolution, analyzing their force balance, and measuring their kinematic quantities. The phase transition from the initiation phase to the acceleration phase of the kinematic evolution of the FR was observed in our simulation. The FR undergoes a series of quasi-static equilibrium states in the initiation phase; while in the acceleration phase the FR is driven by Lorentz force and the impulsive acceleration occurs. The underlying physical reason for the phase transition is the change of the reconnection mechanism from the Sweet-Parker to the unsteady bursty regime of reconnection in the evolving current sheet underneath the FR.

  15. Developments in Enzyme Technology.

    ERIC Educational Resources Information Center

    Chaplin, M. F.

    1984-01-01

    Enzyme technology has a well-established industrial base, with applications that have survived competition. The most prominent applications of enzymes in biotechnology are examined with an explanation of some theoretical background. Topics include extending an enzyme's useful life, partition and diffusion, industrial uses, and therapeutic uses.…

  16. Developments in Enzyme Technology.

    ERIC Educational Resources Information Center

    Chaplin, M. F.

    1984-01-01

    Enzyme technology has a well-established industrial base, with applications that have survived competition. The most prominent applications of enzymes in biotechnology are examined with an explanation of some theoretical background. Topics include extending an enzyme's useful life, partition and diffusion, industrial uses, and therapeutic uses.…

  17. Dust obscuration by an evolving galaxy population

    NASA Technical Reports Server (NTRS)

    Najita, Joan; Silk, Joseph; Wachter, Kenneth W.

    1990-01-01

    The effect of an evolving luminosity function (LF) on the ability of foreground galaxies to obscure background sources is discussed, using the Press-Schechter/CDM standard evolving LF model. Galaxies are modeled as simplified versions of local spirals and Poisson statistics are used to estimate the fraction of sky covered by intervening dusty galaxies and the mean optical depths due to these galaxies. The results are compared to those obtained in the case of nonevolving luminosity function in a low-density universe. It is found that evolution of the galaxy LF does not allow the quasar dust obscuration hypothesis to be sustained for dust disks with plausible sizes. Even in a low-density universe, where evolution at z = less than 10 is unimportant, large disk radii are needed to achieve the desired obscuring effect. The mean fraction of sky covered is presented as a function of the redshift z along with adequate diagram illustrations.

  18. The management of evolving bronchopulmonary dysplasia.

    PubMed

    Schulzke, Sven M; Pillow, J Jane

    2010-09-01

    Bronchopulmonary dysplasia (BPD) is associated with increased mortality and significant long-term cardiorespiratory and neurodevelopmental sequelae. Treatment of evolving BPD in the neonatal intensive care unit (NICU) is challenging due to the complex interplay of contributing risk factors which include preterm birth per se, supplemental oxygen, positive pressure ventilation, patent ductus arterious, and pre- and postnatal infection. Management of evolving BPD requires a multimodal approach including adequate nutrition, careful fluid management, effective and safe pharmacotherapy, and respiratory support aiming at minimal lung injury. Among pharmacological interventions, caffeine has the best risk-benefit profile. Systemic postnatal corticosteroids should be reserved to ventilated infants at highest risk of BPD who cannot be weaned from the ventilator. Several ongoing randomised trials are evaluating optimal oxygen saturation targets in preterm infants. The most beneficial respiratory support strategy to minimise lung injury remains unclear and requires further investigation. Copyright 2009 Elsevier Ltd. All rights reserved.

  19. Evolved gas analysis of secondary organic aerosols

    SciTech Connect

    Grosjean, D.; Williams, E.L. II; Grosjean, E. ); Novakov, T. )

    1994-11-01

    Secondary organic aerosols have been characterized by evolved gas analysis (EGA). Hydrocarbons selected as aerosol precursors were representative of anthropogenic emissions (cyclohexene, cyclopentene, 1-decene and 1-dodecene, n-dodecane, o-xylene, and 1,3,5-trimethylbenzene) and of biogenic emissions (the terpenes [alpha]-pinene, [beta]-pinene and d-limonene and the sesquiterpene trans-caryophyllene). Also analyzed by EGA were samples of secondary, primary (highway tunnel), and ambient (urban) aerosols before and after exposure to ozone and other photochemical oxidants. The major features of the EGA thermograms (amount of CO[sub 2] evolved as a function of temperature) are described. The usefulness and limitations of EGA data for source apportionment of atmospheric particulate carbon are briefly discussed. 28 refs., 7 figs., 4 tabs.

  20. [Families and psychiatry: models and evolving links].

    PubMed

    Frankhauser, Adeline

    2016-01-01

    The role of the families of persons with severe psychiatric disorders (schizophrenia in particular) in the care of their relatives has recently evolved: once seen as pathogenic to be kept at a distance, the family is now recognised by professionals as a partner in the care process. The links between families and psychiatric institutions remain complex and marked by ambivalence and paradoxes. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  1. The evolving definition of systemic arterial hypertension.

    PubMed

    Ram, C Venkata S; Giles, Thomas D

    2010-05-01

    Systemic hypertension is an important risk factor for premature cardiovascular disease. Hypertension also contributes to excessive morbidity and mortality. Whereas excellent therapeutic options are available to treat hypertension, there is an unsettled issue about the very definition of hypertension. At what level of blood pressure should we treat hypertension? Does the definition of hypertension change in the presence of co-morbid conditions? This article covers in detail the evolving concepts in the diagnosis and management of hypertension.

  2. Quantum games on evolving random networks

    NASA Astrophysics Data System (ADS)

    Pawela, Łukasz

    2016-09-01

    We study the advantages of quantum strategies in evolutionary social dilemmas on evolving random networks. We focus our study on the two-player games: prisoner's dilemma, snowdrift and stag-hunt games. The obtained result show the benefits of quantum strategies for the prisoner's dilemma game. For the other two games, we obtain regions of parameters where the quantum strategies dominate, as well as regions where the classical strategies coexist.

  3. Nursing administration research: an evolving science.

    PubMed

    Murphy, Lyn Stankiewicz; Scott, Elaine S; Warshawsky, Nora E

    2014-12-01

    The nature and focus of nursing administrative research have evolved over time. Recently, the research agenda has primarily reflected the national health policy agenda. Although nursing research has traditionally been dominated by clinical interests, nursing administrative research has historically addressed the interface of reimbursement, quality, and care delivery systems. This article traces the evolution of nursing administrative research to answer questions relevant to scope, practice, and policy and suggests future directions.

  4. Evolving nanomaterials using enzyme-driven dynamic peptide libraries (eDPL).

    PubMed

    Das, Apurba K; Hirsth, Andrew R; Ulijn, Rein V

    2009-01-01

    This paper describes the application of dynamic combinatorial libraries (DCL) towards the discovery of self-assembling nanostructures based on aromatic peptide derivatives and the continuous enzymatic exchange of amino acid sequences. Ultimately, the most thermodynamically stable self-assembling structures will dominate the system. In this respect, a library of precursor components, based on N-fluorenyl-9-methoxycarbonyl (Fmoc)-amino acids (serine, S and threonine, T) and nucleophiles (leucine, L-; phenylalanine, F-; tyrosine, Y-; valine, V-; glycine, G-; alanine, A-OMe amino-acid esters) were investigated to produce Fmoc-dipeptide esters, denoted Fmoc-XY-OMe. Upon exposure to a protease (thermolysin), which catalyses peptide bond formation and hydrolysis under aqueous conditions at pH 8, dynamic libraries of self-assembling gelator species were generated. Depending on the molecular composition of the precursors present in the library different behaviours were observed. Single components, Fmoc-SF-OMe and Fmoc-TF-OMe, dominated over time in Fmoc-S/(L+F+Y+V+G+A)-OMe and Fmoc-T/ (L+F+Y+V+G+A)-OMe libraries. This represented > 80% of all peptide formed suggesting that a single component molecular structure dominates in these systems. In a competition experiment between Fmoc-(S+T)/F-OMe, conversions to each peptide corresponded directly with ratios of starting materials, implying that a bi-component nanostructure, where Fmoc-TF-OMe and Fmoc-SF-OMe are incorporated equally favourably, was formed. Several techniques including HPLC, LCMS and fluorescence spectroscopy were used to characterize library composition and molecular interactions within the self-selecting libraries. Fluorescence spectroscopy analysis suggests that the most stable peptide nanostructures show significant pi-pi intermolecular electronic communication. Overall, the paper demonstrates a novel evolution-based approach with self-selection and amplification of supramolecular peptide nanostructures from a complex mixture of amino acid precursors.

  5. Dysregulation of Acetylation Enzymes in Animal Models of Psychostimulant use Disorders: Evolving Stories

    PubMed Central

    Cadet, Jean Lud

    2016-01-01

    Substance use disorders are neuropsychiatric illnesses that have substantial negative biopsychosocial impact. These diseases are defined as compulsive abuse of licit or illicit substances despite adverse medicolegal consequences. Although much research has been conducted to elucidate the pathobiological bases of these disorders, much remains to be done to develop an overarching neurobiological understanding that might be translatable to beneficial pharmacological therapies. Recent advances in epigenetics promise to lead to such an elucidation. Here I provide a brief overview of observations obtained using some models of psychostimulant administration in rodents. The review identifies CREB binding protein (CBP), HDAC1, HDAC2, HADC3, HDAC4, and HDAC5 as important players in the acetylation and deacetylation processes that occur after contingent or non-contingent administration of psychostimulants. These observations are discussed within a framework that suggests a need for better animal models of addiction in order to bring these epigenetic advances to bear on the pharmacological treatment of human addicts. PMID:26813118

  6. Continuous Evaluation of Evolving Behavioral Intervention Technologies

    PubMed Central

    Mohr, David C.; Cheung, Ken; Schueller, Stephen M.; Brown, C. Hendricks; Duan, Naihua

    2013-01-01

    Behavioral intervention technologies (BITs) are web-based and mobile interventions intended to support patients and consumers in changing behaviors related to health, mental health, and well-being. BITs are provided to patients and consumers in clinical care settings and commercial marketplaces, frequently with little or no evaluation. Current evaluation methods, including RCTs and implementation studies, can require years to validate an intervention. This timeline is fundamentally incompatible with the BIT environment, where technology advancement and changes in consumer expectations occur quickly, necessitating rapidly evolving interventions. However, BITs can routinely and iteratively collect data in a planned and strategic manner and generate evidence through systematic prospective analyses, thereby creating a system that can “learn.” A methodologic framework, Continuous Evaluation of Evolving Behavioral Intervention Technologies (CEEBIT), is proposed that can support the evaluation of multiple BITs or evolving versions, eliminating those that demonstrate poorer outcomes, while allowing new BITs to be entered at any time. CEEBIT could be used to ensure the effectiveness of BITs provided through deployment platforms in clinical care organizations or BIT marketplaces. The features of CEEBIT are described, including criteria for the determination of inferiority, determination of BIT inclusion, methods of assigning consumers to BITs, definition of outcomes, and evaluation of the usefulness of the system. CEEBIT offers the potential to collapse initial evaluation and postmarketing surveillance, providing ongoing assurance of safety and efficacy to patients and consumers, payers, and policymakers. PMID:24050429

  7. Continuous evaluation of evolving behavioral intervention technologies.

    PubMed

    Mohr, David C; Cheung, Ken; Schueller, Stephen M; Hendricks Brown, C; Duan, Naihua

    2013-10-01

    Behavioral intervention technologies (BITs) are web-based and mobile interventions intended to support patients and consumers in changing behaviors related to health, mental health, and well-being. BITs are provided to patients and consumers in clinical care settings and commercial marketplaces, frequently with little or no evaluation. Current evaluation methods, including RCTs and implementation studies, can require years to validate an intervention. This timeline is fundamentally incompatible with the BIT environment, where technology advancement and changes in consumer expectations occur quickly, necessitating rapidly evolving interventions. However, BITs can routinely and iteratively collect data in a planned and strategic manner and generate evidence through systematic prospective analyses, thereby creating a system that can "learn." A methodologic framework, Continuous Evaluation of Evolving Behavioral Intervention Technologies (CEEBIT), is proposed that can support the evaluation of multiple BITs or evolving versions, eliminating those that demonstrate poorer outcomes, while allowing new BITs to be entered at any time. CEEBIT could be used to ensure the effectiveness of BITs provided through deployment platforms in clinical care organizations or BIT marketplaces. The features of CEEBIT are described, including criteria for the determination of inferiority, determination of BIT inclusion, methods of assigning consumers to BITs, definition of outcomes, and evaluation of the usefulness of the system. CEEBIT offers the potential to collapse initial evaluation and postmarketing surveillance, providing ongoing assurance of safety and efficacy to patients and consumers, payers, and policymakers.

  8. Evolving specialization of the arthropod nervous system.

    PubMed

    Jarvis, Erin; Bruce, Heather S; Patel, Nipam H

    2012-06-26

    The diverse array of body plans possessed by arthropods is created by generating variations upon a design of repeated segments formed during development, using a relatively small "toolbox" of conserved patterning genes. These attributes make the arthropod body plan a valuable model for elucidating how changes in development create diversity of form. As increasingly specialized segments and appendages evolved in arthropods, the nervous systems of these animals also evolved to control the function of these structures. Although there is a remarkable degree of conservation in neural development both between individual segments in any given species and between the nervous systems of different arthropod groups, the differences that do exist are informative for inferring general principles about the holistic evolution of body plans. This review describes developmental processes controlling neural segmentation and regionalization, highlighting segmentation mechanisms that create both ectodermal and neural segments, as well as recent studies of the role of Hox genes in generating regional specification within the central nervous system. We argue that this system generates a modular design that allows the nervous system to evolve in concert with the body segments and their associated appendages. This information will be useful in future studies of macroevolutionary changes in arthropod body plans, especially in understanding how these transformations can be made in a way that retains the function of appendages during evolutionary transitions in morphology.

  9. Weak Convergence of a Mass-Structured Individual-Based Model

    SciTech Connect

    Campillo, Fabien; Fritsch, Coralie

    2015-08-15

    We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional ordinary differential equation. These two components are coupled with the bacterial consumption. Mechanisms acting on the bacteria are explicitly described (growth, division and washout). Bacteria interact via consumption. We set the exact Monte Carlo simulation algorithm of this model and its mathematical representation as a stochastic process. We prove the convergence of this process to the solution of an integro-differential equation when the population size tends to infinity. Finally, we propose several numerical simulations.

  10. Convergent evolution led ribosome inactivating proteins to interact with ribosomal stalk.

    PubMed

    Lapadula, Walter J; Sanchez-Puerta, M Virginia; Ayub, Maximiliano Juri

    2012-03-01

    Ribosome-inactivating proteins (RIPs) inhibit protein synthesis by depurinating an adenine on the sarcin-ricin loop (SRL) of the large subunit ribosomal RNA. Several RIPs interact with the C-terminal end of ribosomal stalk P proteins, and this interaction is required for their full activity. In contrast, the activity of Pokeweed Antiviral Protein is not affected by blocking this stalk component. Here, we provide evidence from phylogenetic analyses and sequence alignments suggesting that the interaction with the C-terminal end of P proteins evolved independently in different RIPs by convergent evolution.

  11. The Convergent Cancer Evolution toward a Single Cellular Destination.

    PubMed

    Chen, Han; He, Xionglei

    2016-01-01

    The essence of Darwin's theory is that evolution is driven by purposeless mutations that are subsequently selected by natural environments, so there is often no predefined destination in organismal evolution. Using gene expressions of 107 cell types, we built a functional space of human cells to trace the evolutionary trajectory of 18 types of solid tumor cancers. We detected a dominant evolving trend toward the functional status of embryonic stem cells (ESC) for approximately 3,000 tumors growing in distinct tissue environments. This pattern remained the same after excluding known cancer/ESC signature genes (∼ 3,000 genes) or excluding all oncogenic gene sets (∼ 12,000 genes) annotated in MSigDB, suggesting a convergent evolution of the overall functional status in cancers. In support of this, the functional distance to ESC served as a common prognostic indicator for cancers of various types, with shorter distance corresponding to poor prognosis, which was true even when randomly selected gene sets were considered. Thus, regardless of the external environments, cancer evolution is a directional process toward a defined cellular destination, a finding reconciling development and evolution, the two seemingly incompatible philosophies both adopted by the cancer research community, and also raising new questions to evolutionary biology. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. The average enzyme principle

    PubMed Central

    Reznik, Ed; Chaudhary, Osman; Segrè, Daniel

    2013-01-01

    The Michaelis-Menten equation for an irreversible enzymatic reaction depends linearly on the enzyme concentration. Even if the enzyme concentration changes in time, this linearity implies that the amount of substrate depleted during a given time interval depends only on the average enzyme concentration. Here, we use a time re-scaling approach to generalize this result to a broad category of multi-reaction systems, whose constituent enzymes have the same dependence on time, e.g. they belong to the same regulon. This “average enzyme principle” provides a natural methodology for jointly studying metabolism and its regulation. PMID:23892076

  13. On domains of convergence in optimization problems

    NASA Technical Reports Server (NTRS)

    Diaz, Alejandro R.; Shaw, Steven S.; Pan, Jian

    1990-01-01

    Numerical optimization algorithms require the knowledge of an initial set of design variables. Starting from an initial design x(sup 0), improved solutions are obtained by updating the design iteratively in a way prescribed by the particular algorithm used. If the algorithm is successful, convergence is achieved to a local optimal solution. Let A denote the iterative procedure that characterizes a typical optimization algorithm, applied to the problem: Find x belonging to R(sup n) that maximizes f(x) subject to x belonging to Omega contained in R(sup n). We are interested in problems with several local maxima (x(sub j))(sup *), j=1, ..., m, in the feasible design space Omega. In general, convergence of the algorithm A to a specific solution (x(sub j))(sup *) is determined by the choice of initial design x(sup 0). The domain of convergence D(sub j) of A associated with a local maximum (x(sub j))(sup *) is a subset of initial designs x(sup 0) in Omega such that the sequence (x(sup k)), k=0,1,2,... defined by x(sup k+1) = A(x(sup k)), k=0,1,... converges to (x(sub j))(sup *). The set D(sub j) is also called the basin of attraction of (x(sub j))(sup *). Cayley first proposed the problem of finding the basin of attraction for Newton's method in 1897. It has been shown that the basin of attraction for Newton's method exhibits chaotic behavior in problems with polynomial objective. This implies that there may be regions in the feasible design space where arbitrarily close starting points will converge to different local optimal solutions. Furthermore, the boundaries of the domains of convergence may have a very complex, even fractal structure. In this paper we show that even simple structural optimization problems solved using standard gradient based (first order) algorithms exhibit similar features.

  14. Convergence characteristics of the multiple input, multiple output LMS algorithm

    NASA Technical Reports Server (NTRS)

    Snyder, Scott D.; Hansen, Colin H.; Clark, Robert L.

    1992-01-01

    The convergence characteristics of the multiple input, multiple output LMS algorithm, as applied to active noise and vibration control systems, are examined. The mean square error during the convergence process, as well as the final converged value, are examined analytically and in computer simulation. It is shown that the ratio of number of error sensors to number of control sources has a significant influence upon both the converging and converged value of the mean square error. Other active control system variables, such as the inherent time delays and structural/acoustic transfer functions, are also shown to have a significant influence upon the convergence process.

  15. Convergence characteristics of the multiple input, multiple output LMS algorithm

    NASA Technical Reports Server (NTRS)

    Snyder, Scott D.; Hansen, Colin H.; Clark, Robert L.

    1992-01-01

    The convergence characteristics of the multiple input, multiple output LMS algorithm, as applied to active noise and vibration control systems, are examined. The mean square error during the convergence process, as well as the final converged value, are examined analytically and in computer simulation. It is shown that the ratio of number of error sensors to number of control sources has a significant influence upon both the converging and converged value of the mean square error. Other active control system variables, such as the inherent time delays and structural/acoustic transfer functions, are also shown to have a significant influence upon the convergence process.

  16. eVolver: an optimization engine for evolving protein sequences to stabilize the respective structures.

    PubMed

    Brylinski, Michal

    2013-07-31

    Many structural bioinformatics approaches employ sequence profile-based threading techniques. To improve fold recognition rates, homology searching may include artificially evolved amino acid sequences, which were demonstrated to enhance the sensitivity of protein threading in targeting midnight zone templates. We describe implementation details of eVolver, an optimization algorithm that evolves protein sequences to stabilize the respective structures by a variety of potentials, which are compatible with those commonly used in protein threading. In a case study focusing on LARG PDZ domain, we show that artificially evolved sequences have quite high capabilities to recognize the correct protein structures using standard sequence profile-based fold recognition. Computationally design protein sequences can be incorporated in existing sequence profile-based threading approaches to increase their sensitivity. They also provide a desired linkage between protein structure and function in in silico experiments that relate to e.g. the completeness of protein structure space, the origin of folds and protein universe. eVolver is freely available as a user-friendly webserver and a well-documented stand-alone software distribution at http://www.brylinski.org/evolver.

  17. Convergent adaptive radiations in Madagascan and Asian ranid frogs reveal covariation between larval and adult traits

    PubMed Central

    Bossuyt, Franky; Milinkovitch, Michel C.

    2000-01-01

    Recent studies have reported that independent adaptive radiations can lead to identical ecomorphs. Our phylogenetic analyses of nuclear and mitochondrial DNA sequences here indicate that a major radiation of ranid frogs on Madagascar produced morphological, physiological, and developmental characters that are remarkably similar to those that independently evolved on the Indian subcontinent. We demonstrate further that, in several cases, adult and larval stages each evolved sets of characters which are not only convergent between independent lineages, but also allowed both developmental stages to invade the same adaptive zone. It is likely that such covariations are produced by similar selective pressures on independent larval and adult characters rather than by genetic or functional linkage. We briefly discuss why larval/adult covariations might constitute an important evolutionary phenomenon in species for which more than one developmental stage potentially has access to multiple environmental conditions. PMID:10841558

  18. A comparative mechanical analysis of plant and animal cells reveals convergence across kingdoms.

    PubMed

    Durand-Smet, Pauline; Chastrette, Nicolas; Guiroy, Axel; Richert, Alain; Berne-Dedieu, Annick; Szecsi, Judit; Boudaoud, Arezki; Frachisse, Jean-Marie; Bendahmane, Mohammed; Bendhamane, Mohammed; Hamant, Oliver; Asnacios, Atef

    2014-11-18

    Plant and animals have evolved different strategies for their development. Whether this is linked to major differences in their cell mechanics remains unclear, mainly because measurements on plant and animal cells relied on independent experiments and setups, thus hindering any direct comparison. In this study we used the same micro-rheometer to compare animal and plant single cell rheology. We found that wall-less plant cells exhibit the same weak power law rheology as animal cells, with comparable values of elastic and loss moduli. Remarkably, microtubules primarily contributed to the rheological behavior of wall-less plant cells whereas rheology of animal cells was mainly dependent on the actin network. Thus, plant and animal cells evolved different molecular strategies to reach a comparable cytoplasmic mechanical core, suggesting that evolutionary convergence could include the internal biophysical properties of cells.

  19. Profiling the orphan enzymes.

    PubMed

    Sorokina, Maria; Stam, Mark; Médigue, Claudine; Lespinet, Olivier; Vallenet, David

    2014-06-06

    The emergence of Next Generation Sequencing generates an incredible amount of sequence and great potential for new enzyme discovery. Despite this huge amount of data and the profusion of bioinformatic methods for function prediction, a large part of known enzyme activities is still lacking an associated protein sequence. These particular activities are called "orphan enzymes". The present review proposes an update of previous surveys on orphan enzymes by mining the current content of public databases. While the percentage of orphan enzyme activities has decreased from 38% to 22% in ten years, there are still more than 1,000 orphans among the 5,000 entries of the Enzyme Commission (EC) classification. Taking into account all the reactions present in metabolic databases, this proportion dramatically increases to reach nearly 50% of orphans and many of them are not associated to a known pathway. We extended our survey to "local orphan enzymes" that are activities which have no representative sequence in a given clade, but have at least one in organisms belonging to other clades. We observe an important bias in Archaea and find that in general more than 30% of the EC activities have incomplete sequence information in at least one superkingdom. To estimate if candidate proteins for local orphans could be retrieved by homology search, we applied a simple strategy based on the PRIAM software and noticed that candidates may be proposed for an important fraction of local orphan enzymes. Finally, by studying relation between protein domains and catalyzed activities, it appears that newly discovered enzymes are mostly associated with already known enzyme domains. Thus, the exploration of the promiscuity and the multifunctional aspect of known enzyme families may solve part of the orphan enzyme issue. We conclude this review with a presentation of recent initiatives in finding proteins for orphan enzymes and in extending the enzyme world by the discovery of new activities.

  20. Requirements for Instrument Approaches to Converging Runways,

    DTIC Science & Technology

    1981-09-01

    PERSPECTIVE 2-1 2.1 Definition 2-1 2.2 Types of Converging Runways 2-1 2.2.1 Intersecting Approach Streams 2-3 2.2.2 Intersecting Runways 2-3 2.2.3...Therefore, a methodology to define and characterize ’e converging approaches is presented in this chapter. 2.1 Definition If two runways are not parallel...c nter of ARC, the positive X-direction is paralel to IA, and the positive Y-direction is parallel to TC,i C-1 *z / ,i// \\2D 2B0 C-2 FIUE w 4Z a!w wV

  1. Stability of spherical converging shock wave

    SciTech Connect

    Murakami, M.; Sanz, J.; Iwamoto, Y.

    2015-07-15

    Based on Guderley's self-similar solution, stability of spherical converging shock wave is studied. A rigorous linear perturbation theory is developed, in which the growth rate of perturbation is given as a function of the spherical harmonic number ℓ and the specific heats ratio γ. Numerical calculation reveals the existence of a γ-dependent cut-off mode number ℓ{sub c}, such that all the eigenmode perturbations for ℓ > ℓ{sub c} are smeared out as the shock wave converges at the center. The analysis is applied to partially spherical geometries to give significant implication for different ignition schemes of inertial confinement fusion. Two-dimensional hydrodynamic simulations are performed to verify the theory.

  2. The genetic causes of convergent evolution.

    PubMed

    Stern, David L

    2013-11-01

    The evolution of phenotypic similarities between species, known as convergence, illustrates that populations can respond predictably to ecological challenges. Convergence often results from similar genetic changes, which can emerge in two ways: the evolution of similar or identical mutations in independent lineages, which is termed parallel evolution; and the evolution in independent lineages of alleles that are shared among populations, which I call collateral genetic evolution. Evidence for parallel and collateral evolution has been found in many taxa, and an emerging hypothesis is that they result from the fact that mutations in some genetic targets minimize pleiotropic effects while simultaneously maximizing adaptation. If this proves correct, then the molecular changes underlying adaptation might be more predictable than has been appreciated previously.

  3. Antibiotics From Microbes: Converging To Kill

    PubMed Central

    Fischbach, Michael A.

    2011-01-01

    Summary As genetically encoded small molecules, antibiotics are phenotypes that have resulted from mutation and natural selection. Advances in genetics, biochemistry, and bioinformatics have connected hundreds of antibiotics to the gene clusters that encode them, allowing these molecules to be analyzed using the tools of evolutionary biology. This review surveys examples of convergent evolution from microbially produced antibiotics, including the convergence of distinct gene clusters on similar phenotypes and the merger of distinct gene clusters into a single functional unit. Examining antibiotics through an evolutionary lens highlights the versatility of biosynthetic pathways, reveals lessons for combating antibiotic resistance, and provides an entry point for studying the natural roles of these natural products. PMID:19695947

  4. A Numerical, Literal, and Converged Perturbation Algorithm

    NASA Astrophysics Data System (ADS)

    Wiesel, William E.

    2017-09-01

    The KAM theorem and von Ziepel's method are applied to a perturbed harmonic oscillator, and it is noted that the KAM methodology does not allow for necessary frequency or angle corrections, while von Ziepel does. The KAM methodology can be carried out with purely numerical methods, since its generating function does not contain momentum dependence. The KAM iteration is extended to allow for frequency and angle changes, and in the process apparently can be successfully applied to degenerate systems normally ruled out by the classical KAM theorem. Convergence is observed to be geometric, not exponential, but it does proceed smoothly to machine precision. The algorithm produces a converged perturbation solution by numerical methods, while still retaining literal variable dependence, at least in the vicinity of a given trajectory.

  5. Non-surgical interventions for convergence insufficiency

    PubMed Central

    Scheiman, Mitchell; Gwiazda, Jane; Li, Tianjing

    2014-01-01

    Background Convergence insufficiency is a common eye muscle co-ordination problem in which the eyes have a strong tendency to drift outward (exophoria) when reading or doing close work. Symptoms may include eye strain, headaches, double vision, print moving on the page, frequent loss of place when reading, inability to concentrate, and short attention span. Objectives To systematically assess and synthesize evidence from randomized controlled trials (RCTs) on the effectiveness of non-surgical interventions for convergence insufficiency. Search strategy We searched The Cochrane Library, MEDLINE, EMBASE, Science Citation Index, the metaRegister of Controlled Trials (mRCT) (www.controlled-trials.com) and ClinicalTrials.gov (www.clinicaltrials.gov) on 7 October 2010. We manually searched reference lists and optometric journals. Selection criteria We included RCTs examining any form of non-surgical intervention against placebo, no treatment, sham treatment, or each other. Data collection and analysis Two authors independently assessed eligibility, risk of bias, and extracted data. We performed meta-analyses when appropriate. Main results We included six trials (three in children, three in adults) with a total of 475 participants. We graded four trials at low risk of bias. Evidence from one trial (graded at low risk of bias) suggests that base-in prism reading glasses was no more effective than placebo reading glasses in improving clinical signs or symptoms in children. Evidence from one trial (graded at high risk of bias) suggests that base-in prism glasses using a progressive addition lens design was more effective than progressive addition lens alone in decreasing symptoms in adults. At three weeks of therapy, the mean difference in Convergence Insufficiency Symptoms Survey (CISS) score was −10.24 points (95% confidence interval (CI) −15.45 to −5.03). Evidence from two trials (graded at low risk of bias) suggests that outpatient (or office-based as used in the

  6. [Orthoptic treatment efficiency in convergence insufficiency treatment].

    PubMed

    Dragomir, M; Truş, L; Chirilă, D; Stîngu, C

    2001-01-01

    We studied a group of 162 patients(89 females, 73 males), with ages between 15-30 years, who complained of blurred vision at near work. 98 patients(60.4%) were diagnosed with convergence insufficiency (C.I.), the rest of 64 patients(39.6%) had: low refractive errors, heterophoria and intermittent heterotropia. Patients with convergence insufficiency were divided in 3 groups: group 1(34 patients--34.6%) were treated with orthoptic exercises and near point exercises at home, group 2 (34 patients--34.6%) were treated with only near point exercises at home and control group 3 (30 patients--30.8%) without treatment. The result of the treatment of C.I. was good at 25 patients(73.5%) of group 1, at 8 patients(23.5%) of group 2 while in group 3 at only one patient the symptoms disappeared.

  7. On the convergence of validity interval analysis.

    PubMed

    Maire, F

    2000-01-01

    Validity interval analysis (VIA) is a generic tool for analyzing the input-output behavior of feedforward neural networks. VIA is a rule extraction technique that relies on a rule refinement algorithm. The rules are of the form R(i)-->R(0) which reads if the input of the neural network is in the region R(i), then its output is in the region R(0), where regions are axis parallel hypercubes. VIA conjectures, then refines and checks rules for inconsistency. This process can be computationally expensive, and the rule refinement phase becomes critical. Hence, the importance of knowing the complexity of these rule refinement algorithms. In this paper, we show that the rule refinement part of VIA always converges in one run for single-weight-layer networks, and has an exponential average rate of convergence for multilayer networks. We also discuss some variations of the standard VIA formulae.

  8. What contribution can international relations make to the evolving global health agenda?

    PubMed

    Davies, Sara E

    2010-01-01

    This article presents two approaches that have dominated International Relations in their approach to the international politics of health. The statist approach, which is primarily security-focused, seeks to link health initiatives to a foreign or defence policy remit. The globalist approach, in contrast, seeks to advance health not because of its intrinsic security value but because it advances the well-being and rights of individuals. This article charts the evolution of these approaches and demonstrates why both have the potential to shape our understanding of the evolving global health agenda. It examines how the statist and globalist perspectives have helped shape contemporary initiatives in global health governance and suggests that there is evidence of an emerging convergence between the two perspectives. This convergence is particularly clear in the articulation of a number of UN initiatives in this area - especially the One World, One Health Strategic Framework and the Oslo Ministerial Declaration (2007) which inspired the first UN General Assembly resolution on global health and foreign policy in 2009 and the UN Secretary-General's note "Global health and foreign policy: strategic opportunities and challenges". What remains to be seen is whether this convergence will deliver on securing states' interest long enough to promote the interests of the individuals who require global efforts to deliver local health improvements.

  9. Broadband converging plano-concave lens.

    PubMed

    Yang, Rui; Lei, Zhenya; Chen, Lei; Zhang, Jiawei; Wang, Zhaoxu; Xie, Yongjun

    2013-07-01

    A plano-concave lens with source-tailored geometric profile and transformational gradient index is proposed for broadband illumination. Such a design, capable of focusing and collimating the electromagnetic fields, fulfils the functionality of a converging lens and can also achieve a steerable beam and multiple beams efficiently. Nonresonant synthesis with a perforated dielectric plate and dielectric rod arrays is demonstrated for the lensing realization, promising a wide operating frequency band in the practical implementation.

  10. Convergence Creates Opportunities Across Health Care System

    PubMed Central

    Fox, Brent I.; Felkey, Bill G.

    2014-01-01

    Industrial design students at Auburn do a creativity exercise where they are asked to combine a common household appliance with an animal. Have you seen a snake light? In health technology, we have a similar opportunity. In the connection between jewelry and vital sign monitoring technology or household security and health status monitoring, we are witnessing active convergence that will benefit patients, providers, and health systems. PMID:24958948

  11. A Practical, Convergent Method for Glycopeptide Synthesis

    DTIC Science & Technology

    1993-07-23

    deprotection, the overall yield from oligosaccharide to glycopeptide is low. This may be acceptable for monosaccharides or for oligosaccharides which...in Figure 3. GIcNAcNH2 (1) is commercially available. Chitobiose constitutes the disaccharide core of N-linked sugars; the peracetylated compound (2...glycopeptides containing this sugar cannot be easily prepared by non- convergent methods. 43 The peracetylated disaccharide (5) was synthesized from L

  12. Convergence of the Naval Information Infrastructure

    DTIC Science & Technology

    2004-06-01

    REPORT TYPE AND DATES COVERED Master’s Thesis 4. TITLE AND SUBTITLE: Convergence of the Naval Information Infrastructure 6. AUTHOR( S ) James A...Knoll 5. FUNDING NUMBERS 7. PERFORMING ORGANIZATION NAME( S ) AND ADDRESS(ES) Naval Postgraduate School Monterey, CA 93943-5000 8. PERFORMING...ORGANIZATION REPORT NUMBER 9. SPONSORING /MONITORING AGENCY NAME( S ) AND ADDRESS(ES) N/A 10. SPONSORING/MONITORING AGENCY REPORT NUMBER 11

  13. The cumulative effect of convergent seismic waves

    NASA Astrophysics Data System (ADS)

    Guglielmi, A. V.

    2015-11-01

    This methodical note is devoted to the nonlinear impact of convergent seismic waves on a medium. Special attention is paid to the similarity and distinctions of the phenomena occurring in the Earth, on one hand, and on the Moon and Mercury, on the other hand. The importance of the experimental and theoretical study of the round-the-world seismic echo which induces repeated shocks in the epicentral zones of the earthquakes is noted.

  14. Sequences of Rational Numbers Converging to Surds

    ERIC Educational Resources Information Center

    Fletcher, Rodney

    2010-01-01

    In this sequence 1/1, 7/5, 41/29, 239/169 and so on, Thomas notes that the sequence converges to square root of 2. By observation, the sequence of numbers in the numerator of the above sequence, have a pattern of generation which is the same as that in the denominator. That is, the next term is found by multiplying the previous term by six and…

  15. Design Calculations For NIF Convergent Ablator Experiments

    SciTech Connect

    Olson, R E; Hicks, D G; Meezan, N B; Callahan, D A; Landen, O L; Jones, O S; Langer, S H; Kline, J L; Wilson, D C; Rinderknecht, H; Zylstra, A; Petrasso, R D

    2011-10-25

    The NIF convergent ablation tuning effort is underway. In the early experiments, we have discovered that the design code simulations over-predict the capsule implosion velocity and shock flash rhor, but under-predict the hohlraum x-ray flux measurements. The apparent inconsistency between the x-ray flux and radiography data implies that there are important unexplained aspects of the hohlraum and/or capsule behavior.

  16. Uniform Convergence to Equilibrium for Granular Media

    NASA Astrophysics Data System (ADS)

    Bolley, François; Gentil, Ivan; Guillin, Arnaud

    2013-05-01

    We study the long time asymptotics of a nonlinear, nonlocal equation used in the modelling of granular media. We prove a uniform exponential convergence to equilibrium for degenerately convex and nonconvex interaction or confinement potentials, improving in particular results by J. A. Carrillo, R. J. McCann and C. Villani. The method is based on studying the dissipation of the Wasserstein distance between a solution and the steady state.

  17. New Type Continuities via Abel Convergence

    PubMed Central

    Albayrak, Mehmet

    2014-01-01

    We investigate the concept of Abel continuity. A function f defined on a subset of ℝ, the set of real numbers, is Abel continuous if it preserves Abel convergent sequences. Some other types of continuities are also studied and interesting result is obtained. It turned out that uniform limit of a sequence of Abel continuous functions is Abel continuous and the set of Abel continuous functions is a closed subset of continuous functions. PMID:24883393

  18. Variational Convergence Of Bifunctions: Motivating Applications

    DTIC Science & Technology

    2011-01-01

    Research Office (ARO) W911NS1010246 and Fondap- Matematicas Aplicadas, Universidad de Chile 1 Variational convergence of bifunctions The analysis of...The public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing...problems. 1 . REPORT DATE (DD-MM-YYYY) 4. TITLE AND SUBTITLE 13. SUPPLEMENTARY NOTES The views, opinions and/or findings contained in this report are those

  19. Fabric stability in oblique convergence and divergence

    NASA Astrophysics Data System (ADS)

    Teyssier, Christian; Tikoff, Basil

    1999-08-01

    Forward modeling of transpression-transtension, assuming homogeneous strain and a direct relationship between finite strain axes and foliation-lineation in tectonites, investigates fields of stability of foliation and lineation orientations in oblique convergence and divergence. Vertical foliation-horizontal lineation (VF-HL) develop for angles of convergence-divergence between 0 and 20°. With increasing finite strain, this narrow window of stability is further reduced; lineation switches to vertical in transpression and foliation switches to horizontal in transtension. If a shear zone contains VF-HL, it either developed as a zone very close to pure wrenching, or recorded low finite strain. The stability of VF-HL at high strain and higher angles of convergence is enhanced by lateral extrusion of material along transpression zones. VF-HL may be stabilized in magmatic bodies that progressively intrude transtension zones, if the wrench component of deformation partitions within them. Alternatively, if these bodies are dike-like, cool fast, and do not record large deformation, they take up the extension component of transtension through anisotropic volume addition, leaving a larger component of wrench deformation in the country rocks; this effect stabilizes VF-HL effectively at low strain, but only marginally so at high strain.

  20. Crenulative Turbulence in a Converging Nonhomogeneous Material

    SciTech Connect

    Romero, Casildo A.

    1999-01-01

    Crenulative turbulence is a nonlinear extension of the Bell-Plesset instability, usually observed in a converging system in which there is a nonhomogeneous response of stress to strain and/or strain rate. In general, crenelation occurs in any circumstance in which the mean flow streamlines converge the material more strongly than the compressibility can accommodate. Elements of the material slip past each other, resulting in local fluctuations in velocity from that of the mean flow, producing a type of turbulence that is more kinematic than inertial. For a homogeneous material, crenelation occurs at the atomic or molecular scale. With nonhomogeneous stress response at larger scales, the crenulative process can also occur at those larger scales. The results are manifested by a decrease in the rate of dissipation to heat, and by the configurationally-irreversible mixing of nonhomogeneities across any mean-flow-transported interface. We obtain a mathematical description of the crenulative process by means of Reynolds decomposition of the appropriate variables, and the derivation of transport equations for the second-order moments that arise in the mean-flow momentum and energy equations. The theory is illustrated by application to the spherical convergence of an incompressible fluid with nonhomogeneous distribution of kinematic viscosity.