Crystal structure of 4-hydroxybutyryl-CoA dehydratase: radical catalysis involving a [4Fe-4S] cluster and flavin.

PubMed

Martins, Berta M; Dobbek, Holger; Cinkaya, Irfan; Buckel, Wolfgang; Messerschmidt, Albrecht

2004-11-02

Dehydratases catalyze the breakage of a carbon-oxygen bond leading to unsaturated products via the elimination of water. The 1.6-A resolution crystal structure of 4-hydroxybutyryl-CoA dehydratase from the gamma-aminobutyrate-fermenting Clostridium aminobutyricum represents a new class of dehydratases with an unprecedented active site architecture. A [4Fe-4S](2+) cluster, coordinated by three cysteine and one histidine residues, is located 7 A from the Re-side of a flavin adenine dinucleotide (FAD) moiety. The structure provides insight into the function of these ubiquitous prosthetic groups in the chemically nonfacile, radical-mediated dehydration of 4-hydroxybutyryl-CoA. The substrate can be bound between the [4Fe-4S](2+) cluster and the FAD with both cofactors contributing to its radical activation and catalytic conversion. Our results raise interesting questions regarding the mechanism of acyl-CoA dehydrogenases, which are involved in fatty acid oxidation, and address the divergent evolution of the ancestral common gene.

Merging C-H activation and alkene difunctionalization at room temperature: a palladium-catalyzed divergent synthesis of indoles and indolines.

PubMed

Manna, Manash Kumar; Hossian, Asik; Jana, Ranjan

2015-02-06

A palladium-catalyzed 1,2-carboamination through C-H activation at room temperature is reported for the synthesis of 2-arylindoles, and indolines from readily available, inexpensive aryl ureas and vinyl arenes. The reaction initiates with a urea-directed electrophilic ortho palladation, alkene insertion, and β-hydride elimination sequences to provide the Fujiwara-Moritani arylation product. Subsequently, aza-Wacker cyclization, and β-hydride elimination provide the 2-arylindoles in high yields. Intercepting the common σ-alkyl-Pd intermediate, corresponding indolines are also achieved. The indoline formation is attributed to the generation of stabilized, cationic π-benzyl-Pd species to suppress β-hydride elimination.

Time-asymptotic solutions of the Navier-Stokes equation for free shear flows using an alternating-direction implicit method

NASA Technical Reports Server (NTRS)

Rudy, D. H.; Morris, D. J.

1976-01-01

An uncoupled time asymptotic alternating direction implicit method for solving the Navier-Stokes equations was tested on two laminar parallel mixing flows. A constant total temperature was assumed in order to eliminate the need to solve the full energy equation; consequently, static temperature was evaluated by using algebraic relationship. For the mixing of two supersonic streams at a Reynolds number of 1,000, convergent solutions were obtained for a time step 5 times the maximum allowable size for an explicit method. The solution diverged for a time step 10 times the explicit limit. Improved convergence was obtained when upwind differencing was used for convective terms. Larger time steps were not possible with either upwind differencing or the diagonally dominant scheme. Artificial viscosity was added to the continuity equation in order to eliminate divergence for the mixing of a subsonic stream with a supersonic stream at a Reynolds number of 1,000.

Three Types of Flower Structures in a Divergent-Wrench Fault Zone

NASA Astrophysics Data System (ADS)

Huang, Lei; Liu, Chi-yang

2017-12-01

Flower structures are typical features of wrench fault zones. In conventional studies, two distinct kinds of flower structures have been identified based on differences in their internal structural architecture: (1) negative flower structures characterized by synforms and normal separations and (2) positive flower structures characterized by antiforms and reverse separations. In addition to negative and positive flower structures, in this study, a third kind of flower structure was identified in a divergent-wrench fault zone, a hybrid characterized by both antiforms and normal separations. Negative flower structures widely occur in divergent-wrench fault zones, and their presence indicates the combined effects of extensional and strike-slip motion. In contrast, positive and hybrid flower structures occur only in fault restraining bends and step overs. A hybrid flower structure can be considered as product of a kind of structural deformation typical of divergent-wrench zones; it is the result of the combined effects of extensional, compressional, and strike-slip strains under a locally appropriate compressional environment. The strain situation in it represents the transition stage that in between positive and negative flower structures. Kinematic and dynamic characteristics of the hybrid flower structures indicate the salient features of structural deformation in restraining bends and step overs along divergent-wrench faults, including the coexistence of three kinds of strains (i.e., compression, extension, and strike-slip) and synchronous presence of compressional (i.e., typical fault-bend fold) and extensional (normal faults) deformation in the same place. Hybrid flower structures are also favorable for the accumulation of hydrocarbons because of their special structural configuration in divergent-wrench fault zones.

Eliminating Racism: Profiles in Controversy.

ERIC Educational Resources Information Center

Katz, Phyllis A., Ed.; Taylor, Dalmas A., Ed.

Dialogue and research on racism since the mid-1970s have yielded increased controversy over the theories, foundation, and continued existence of racism. The chapters presented in this book provide various divergent views of what constitutes racism and frameworks for reducing it. The following chapters (and their authors) are included: (1)…

Transonic aerodynamic characteristics of the 10-percent-thick NASA supercritical airfoil 31

NASA Technical Reports Server (NTRS)

Harris, C. D.

1975-01-01

Refinements in a 10 percent thick supercritical airfoil (airfoil 31) have produced significant improvements in the drag characteristics compared with those for an earlier supercritical airfoil (airfoil 12) designed for the same normal force coefficient of 0.7. Drag creep was practically eliminated at normal force coefficients between about 0.4 and 0.7 and was greatly reduced at other normal force coefficients. Substantial reductions in the drag levels preceding drag divergence were also achieved at all normal force coefficients. The Mach numbers at which drag diverges were delayed for airfoil 31 at normal force coefficients up to about 0.6 (by approximately 0.01 and 0.02 at normal force coefficients of 0.4 and 0.6, respectively) but drag divergence occurred at slightly lower Mach numbers at higher normal force coefficients.

Nonperturbative study of the four gluon vertex

NASA Astrophysics Data System (ADS)

Binosi, D.; Ibañez, D.; Papavassiliou, J.

2014-09-01

In this paper we study the nonperturbative structure of the SU(3) four-gluon vertex in the Landau gauge, concentrating on contributions quadratic in the metric. We employ an approximation scheme where "one-loop" diagrams are computed using fully dressed gluon and ghost propagators, and tree-level vertices. When a suitable kinematical configuration depending on a single momentum scale p is chosen, only two structures emerge: the tree-level four-gluon vertex, and a tensor orthogonal to it. A detailed numerical analysis reveals that the form factor associated with this latter tensor displays a change of sign (zero-crossing) in the deep infrared, and finally diverges logarithmically. The origin of this characteristic behavior is proven to be entirely due to the masslessness of the ghost propagators forming the corresponding ghost-loop diagram, in close analogy to a similar effect established for the three-gluon vertex. However, in the case at hand, and under the approximations employed, this particular divergence does not affect the form factor proportional to the tree-level tensor, which remains finite in the entire range of momenta, and deviates moderately from its naive tree-level value. It turns out that the kinematic configuration chosen is ideal for carrying out lattice simulations, because it eliminates from the connected Green's function all one-particle reducible contributions, projecting out the genuine one-particle irreducible vertex. Motivated by this possibility, we discuss in detail how a hypothetical lattice measurement of this quantity would compare to the results presented here, and the potential interference from an additional tensorial structure, allowed by Bose symmetry, but not encountered within our scheme.

Bifurcations, chaos and adaptive backstepping sliding mode control of a power system with excitation limitation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Min, Fuhong, E-mail: minfuhong@njnu.edu.cn; Wang, Yaoda; Peng, Guangya

2016-08-15

The bifurcation and Lyapunov exponent for a single-machine-infinite bus system with excitation model are carried out by varying the mechanical power, generator damping factor and the exciter gain, from which periodic motions, chaos and the divergence of system are observed respectively. From given parameters and different initial conditions, the coexisting motions are developed in power system. The dynamic behaviors in power system may switch freely between the coexisting motions, which will bring huge security menace to protection operation. Especially, the angle divergences due to the break of stable chaotic oscillation are found which causes the instability of power system. Finally,more » a new adaptive backstepping sliding mode controller is designed which aims to eliminate the angle divergences and make the power system run in stable orbits. Numerical simulations are illustrated to verify the effectivity of the proposed method.« less

Image registration based on subpixel localization and Cauchy-Schwarz divergence

NASA Astrophysics Data System (ADS)

Ge, Yongxin; Yang, Dan; Zhang, Xiaohong; Lu, Jiwen

2010-07-01

We define a new matching metric-corner Cauchy-Schwarz divergence (CCSD) and present a new approach based on the proposed CCSD and subpixel localization for image registration. First, we detect the corners in an image by a multiscale Harris operator and take them as initial interest points. And then, a subpixel localization technique is applied to determine the locations of the corners and eliminate the false and unstable corners. After that, CCSD is defined to obtain the initial matching corners. Finally, we use random sample consensus to robustly estimate the parameters based on the initial matching. The experimental results demonstrate that the proposed algorithm has a good performance in terms of both accuracy and efficiency.

Investigation of the Low-Speed Stability and Control Characteristics of a 1/10-Scale Model of the Douglas XF4D-1 Airplane in the Langley Free-Flight Tunnel TED No. NACA DE 349

NASA Technical Reports Server (NTRS)

Johnson, Joseph L.

1951-01-01

An investigation of the low-speed, power-off stability and control characteristics of a 1/10-scale model of the Douglas XF4D-1 airplane has been made in the Langley free-flight tunnel. The model was flown with leading-edge slats retracted and extended over a lift-coefficient range from 0.5 to the stall. Only relatively low-altitude conditions were simulated and no attempt was made to determine the effect on the stability characteristics of freeing the controls. The longitudinal stability and control characteristics of the model were satisfactory for all conditions investigated except near the stall with slats extended, where the model had a slight nosing-up tendency. The lateral stability and control characteristics of the model were considered satisfactory for all conditions investigated except near the stall with slats retracted, where a change in sign of the static- directional-stability parameter Cn(sub beta) caused the model to be directionally divergent. The addition of an extension to the top of the vertical tail did not increase Cn(sub beta) enough to eliminate the directional divergence of the model, but a large increase in Cn(sub beta) that was obtainable by artificial means appeared to eliminate the divergence and flights near the stall could be made. Artificially increasing the stability derivative-Cn(sub r) (yawing moment due to yawing) and Cn(sub p) (yawing moment due to rolling) had little effect on the divergence for the range of these parameters investigated. Calculations indicate that the damping of the lateral oscillation of the airplane with slats retracted or extended will be satisfactory at sea level but will be only marginally satisfactory at 40,000 feet.

Lineage diversification in a widespread species: roles for niche divergence and conservatism in the common kingsnake, Lampropeltis getula.

PubMed

Alexander Pyron, R; Burbrink, Frank T

2009-08-01

Niche conservatism and niche divergence are both important ecological mechanisms associated with promoting allopatric speciation across geographical barriers. However, the potential for variable responses in widely distributed organisms has not been fully investigated. For allopatric sister lineages, three patterns for the interaction of ecological niche preference and geographical barriers are possible: (i) niche conservatism at a physical barrier; (ii) niche divergence at a physical barrier; and (iii) niche divergence in the absence of a physical barrier. We test for the presence of these patterns in a transcontinentally distributed snake species, the common kingsnake (Lampropeltis getula), to determine the relative frequency of niche conservatism or divergence in a single species complex inhabiting multiple distinct ecoregions. We infer the phylogeographic structure of the kingsnake using a range-wide data set sampled for the mitochondrial gene cytochrome b. We use coalescent simulation methods to test for the presence of structured lineage formation vs. fragmentation of a widespread ancestor. Finally, we use statistical techniques for creating and evaluating ecological niche models to test for conservatism of ecological niche preferences. Significant geographical structure is present in the kingsnake, for which coalescent tests indicate structured population division. Surprisingly, we find evidence for all three patterns of conservatism and divergence. This suggests that ecological niche preferences may be labile on recent phylogenetic timescales, and that lineage formation in widespread species can result from an interaction between inertial tendencies of niche conservatism and natural selection on populations in ecologically divergent habitats.

Synthesizing epidemiological and economic optima for control of immunizing infections.

PubMed

Klepac, Petra; Laxminarayan, Ramanan; Grenfell, Bryan T

2011-08-23

Epidemic theory predicts that the vaccination threshold required to interrupt local transmission of an immunizing infection like measles depends only on the basic reproductive number and hence transmission rates. When the search for optimal strategies is expanded to incorporate economic constraints, the optimum for disease control in a single population is determined by relative costs of infection and control, rather than transmission rates. Adding a spatial dimension, which precludes local elimination unless it can be achieved globally, can reduce or increase optimal vaccination levels depending on the balance of costs and benefits. For weakly coupled populations, local optimal strategies agree with the global cost-effective strategy; however, asymmetries in costs can lead to divergent control optima in more strongly coupled systems--in particular, strong regional differences in costs of vaccination can preclude local elimination even when elimination is locally optimal. Under certain conditions, it is locally optimal to share vaccination resources with other populations.

Ice tracking techniques, implementation, performance, and applications

NASA Technical Reports Server (NTRS)

Rothrock, D. A.; Carsey, F. D.; Curlander, J. C.; Holt, B.; Kwok, R.; Weeks, W. F.

1992-01-01

Present techniques of ice tracking make use both of cross-correlation and of edge tracking, the former being more successful in heavy pack ice, the latter being critical for the broken ice of the pack margins. Algorithms must assume some constraints on the spatial variations of displacements to eliminate fliers, but must avoid introducing any errors into the spatial statistics of the measured displacement field. We draw our illustrations from the implementation of an automated tracking system for kinematic analyses of ERS-1 and JERS-1 SAR imagery at the University of Alaska - the Alaska SAR Facility's Geophysical Processor System. Analyses of the ice kinematic data that might have some general interest to analysts of cloud-derived wind fields are the spatial structure of the fields, and the evaluation and variability of average deformation and its invariants: divergence, vorticity and shear. Many problems in sea ice dynamics and mechanics can be addressed with the kinematic data from SAR.

Immersogeometric cardiovascular fluid–structure interaction analysis with divergence-conforming B-splines

PubMed Central

Kamensky, David; Hsu, Ming-Chen; Yu, Yue; Evans, John A.; Sacks, Michael S.; Hughes, Thomas J. R.

2016-01-01

This paper uses a divergence-conforming B-spline fluid discretization to address the long-standing issue of poor mass conservation in immersed methods for computational fluid–structure interaction (FSI) that represent the influence of the structure as a forcing term in the fluid subproblem. We focus, in particular, on the immersogeometric method developed in our earlier work, analyze its convergence for linear model problems, then apply it to FSI analysis of heart valves, using divergence-conforming B-splines to discretize the fluid subproblem. Poor mass conservation can manifest as effective leakage of fluid through thin solid barriers. This leakage disrupts the qualitative behavior of FSI systems such as heart valves, which exist specifically to block flow. Divergence-conforming discretizations can enforce mass conservation exactly, avoiding this problem. To demonstrate the practical utility of immersogeometric FSI analysis with divergence-conforming B-splines, we use the methods described in this paper to construct and evaluate a computational model of an in vitro experiment that pumps water through an artificial valve. PMID:28239201

Phylogenetic and Functional Structure of Wintering Waterbird Communities Associated with Ecological Differences.

PubMed

Che, Xianli; Zhang, Min; Zhao, Yanyan; Zhang, Qiang; Quan, Qing; Møller, Anders; Zou, Fasheng

2018-01-19

Ecological differences may be related to community component divisions between Oriental (west) and Sino-Japanese (east) realms, and such differences may result in weak geographical breaks in migratory species that are highly mobile. Here, we conducted comparative phylogenetic and functional structure analyses of wintering waterbird communities in southern China across two realms and subsequently examined possible climate drivers of the observed patterns. An analysis based on such highly migratory species is particularly telling because migration is bound to reduce or completely eliminate any divergence between communities. Phylogenetic and functional structure of eastern communities showed over-dispersion while western communities were clustered. Basal phylogenetic and functional turnover of western communities was significant lower than that of eastern communities. The break between eastern and western communities was masked by these two realms. Geographic patterns were related to mean temperature changes and temperature fluctuations, suggesting that temperature may filter waterbird lineages and traits, thus underlying geographical community divisions. These results suggest phylogenetic and functional divisions in southern China, coinciding with biogeography. This study shows that temperature fluctuations constitute an essential mechanism shaping geographical divisions that have largely gone undetected previously, even under climate change.

Performance of the high speed anechoic wind tunnel at Lyon University

NASA Technical Reports Server (NTRS)

Sunyach, M.; Brunel, B.; Comte-Bellot, G.

1986-01-01

The characteristics of the feed duct, the wind tunnel, and the experiments run in the convergent-divergent anechoic wind tunnel at Lyon University are described. The wind tunnel was designed to eliminate noise from the entrance of air or from flow interactions with the tunnel walls so that noise caused by the flow-test structure interactions can be studied. The channel contains 1 x 1 x 0.2 m glass and metal foil baffles spaced 0.2 m apart. The flow is forced by a 350 kW fan in the primary circuit, and a 110 kW blower in the secondary circuit. The primary circuit features a factor of four throat reductions, followed by a 1.6 reduction before the test section. Upstream and downstream sensors permit monitoring of the anechoic effectiveness of the channel. Other sensors allow modeling of the flow structures in the tunnel. The tunnel was used to examine turbulent boundary layers in flows up to 140 m/sec, tubulence-excited vibrations in walls, and the effects of laminar and turbulent flows on the appearance and locations of noise sources.

Auxiliary basis expansions for large-scale electronic structure calculations.

PubMed

Jung, Yousung; Sodt, Alex; Gill, Peter M W; Head-Gordon, Martin

2005-05-10

One way to reduce the computational cost of electronic structure calculations is to use auxiliary basis expansions to approximate four-center integrals in terms of two- and three-center integrals, usually by using the variationally optimum Coulomb metric to determine the expansion coefficients. However, the long-range decay behavior of the auxiliary basis expansion coefficients has not been characterized. We find that this decay can be surprisingly slow. Numerical experiments on linear alkanes and a toy model both show that the decay can be as slow as 1/r in the distance between the auxiliary function and the fitted charge distribution. The Coulomb metric fitting equations also involve divergent matrix elements for extended systems treated with periodic boundary conditions. An attenuated Coulomb metric that is short-range can eliminate these oddities without substantially degrading calculated relative energies. The sparsity of the fit coefficients is assessed on simple hydrocarbon molecules and shows quite early onset of linear growth in the number of significant coefficients with system size using the attenuated Coulomb metric. Hence it is possible to design linear scaling auxiliary basis methods without additional approximations to treat large systems.

Strong genetic structure corresponds to small-scale geographic breaks in the Australian alpine grasshopper Kosciuscola tristis.

PubMed

Slatyer, Rachel A; Nash, Michael A; Miller, Adam D; Endo, Yoshinori; Umbers, Kate D L; Hoffmann, Ary A

2014-10-02

Mountain landscapes are topographically complex, creating discontinuous 'islands' of alpine and sub-alpine habitat with a dynamic history. Changing climatic conditions drive their expansion and contraction, leaving signatures on the genetic structure of their flora and fauna. Australia's high country covers a small, highly fragmented area. Although the area is thought to have experienced periods of relative continuity during Pleistocene glacial periods, small-scale studies suggest deep lineage divergence across low-elevation gaps. Using both DNA sequence data and microsatellite markers, we tested the hypothesis that genetic partitioning reflects observable geographic structuring across Australia's mainland high country, in the widespread alpine grasshopper Kosciuscola tristis (Sjösted). We found broadly congruent patterns of regional structure between the DNA sequence and microsatellite datasets, corresponding to strong divergence among isolated mountain regions. Small and isolated mountains in the south of the range were particularly distinct, with well-supported divergence corresponding to climate cycles during the late Pliocene and Pleistocene. We found mixed support, however, for divergence among other mountain regions. Interestingly, within areas of largely contiguous alpine and sub-alpine habitat around Mt Kosciuszko, microsatellite data suggested significant population structure, accompanied by a strong signature of isolation-by-distance. Consistent patterns of strong lineage divergence among different molecular datasets indicate genetic breaks between populations inhabiting geographically distinct mountain regions. Three primary phylogeographic groups were evident in the highly fragmented Victorian high country, while within-region structure detected with microsatellites may reflect more recent population isolation. Despite the small area of Australia's alpine and sub-alpine habitats, their low topographic relief and lack of extensive glaciation, divergence among populations was on the same scale as that detected in much more extensive Northern hemisphere mountain systems. The processes driving divergence in the Australian mountains might therefore differ from their Northern hemisphere counterparts.

Defining the limits of flowers: the challenge of distinguishing between the evolutionary products of simple versus compound strobili

PubMed Central

Rudall, Paula J.; Bateman, Richard M.

2010-01-01

Recent phylogenetic reconstructions suggest that axially condensed flower-like structures evolved iteratively in seed plants from either simple or compound strobili. The simple-strobilus model of flower evolution, widely applied to the angiosperm flower, interprets the inflorescence as a compound strobilus. The conifer cone and the gnetalean ‘flower’ are commonly interpreted as having evolved from a compound strobilus by extreme condensation and (at least in the case of male conifer cones) elimination of some structures present in the presumed ancestral compound strobilus. These two hypotheses have profoundly different implications for reconstructing the evolution of developmental genetic mechanisms in seed plants. If different flower-like structures evolved independently, there should intuitively be little commonality of patterning genes. However, reproductive units of some early-divergent angiosperms, including the extant genus Trithuria (Hydatellaceae) and the extinct genus Archaefructus (Archaefructaceae), apparently combine features considered typical of flowers and inflorescences. We re-evaluate several disparate strands of comparative data to explore whether flower-like structures could have arisen by co-option of flower-expressed patterning genes into independently evolved condensed inflorescences, or vice versa. We discuss the evolution of the inflorescence in both gymnosperms and angiosperms, emphasising the roles of heterotopy in dictating gender expression and heterochrony in permitting internodal compression. PMID:20047867

Defining the limits of flowers: the challenge of distinguishing between the evolutionary products of simple versus compound strobili.

PubMed

Rudall, Paula J; Bateman, Richard M

2010-02-12

Recent phylogenetic reconstructions suggest that axially condensed flower-like structures evolved iteratively in seed plants from either simple or compound strobili. The simple-strobilus model of flower evolution, widely applied to the angiosperm flower, interprets the inflorescence as a compound strobilus. The conifer cone and the gnetalean 'flower' are commonly interpreted as having evolved from a compound strobilus by extreme condensation and (at least in the case of male conifer cones) elimination of some structures present in the presumed ancestral compound strobilus. These two hypotheses have profoundly different implications for reconstructing the evolution of developmental genetic mechanisms in seed plants. If different flower-like structures evolved independently, there should intuitively be little commonality of patterning genes. However, reproductive units of some early-divergent angiosperms, including the extant genus Trithuria (Hydatellaceae) and the extinct genus Archaefructus (Archaefructaceae), apparently combine features considered typical of flowers and inflorescences. We re-evaluate several disparate strands of comparative data to explore whether flower-like structures could have arisen by co-option of flower-expressed patterning genes into independently evolved condensed inflorescences, or vice versa. We discuss the evolution of the inflorescence in both gymnosperms and angiosperms, emphasising the roles of heterotopy in dictating gender expression and heterochrony in permitting internodal compression.

Structural Insight into How Bacteria Prevent Interference between Multiple Divergent Type IV Secretion Systems

PubMed Central

Phan, Isabelle Q. H.; Scheib, Holger; Subramanian, Sandhya; Edwards, Thomas E.; Lehman, Stephanie S.; Piitulainen, Hanna; Sayeedur Rahman, M.; Rennoll-Bankert, Kristen E.; Staker, Bart L.; Taira, Suvi; Stacy, Robin; Myler, Peter J.; Azad, Abdu F.

2015-01-01

ABSTRACT Prokaryotes use type IV secretion systems (T4SSs) to translocate substrates (e.g., nucleoprotein, DNA, and protein) and/or elaborate surface structures (i.e., pili or adhesins). Bacterial genomes may encode multiple T4SSs, e.g., there are three functionally divergent T4SSs in some Bartonella species (vir, vbh, and trw). In a unique case, most rickettsial species encode a T4SS (rvh) enriched with gene duplication. Within single genomes, the evolutionary and functional implications of cross-system interchangeability of analogous T4SS protein components remains poorly understood. To lend insight into cross-system interchangeability, we analyzed the VirB8 family of T4SS channel proteins. Crystal structures of three VirB8 and two TrwG Bartonella proteins revealed highly conserved C-terminal periplasmic domain folds and dimerization interfaces, despite tremendous sequence divergence. This implies remarkable structural constraints for VirB8 components in the assembly of a functional T4SS. VirB8/TrwG heterodimers, determined via bacterial two-hybrid assays and molecular modeling, indicate that differential expression of trw and vir systems is the likely barrier to VirB8-TrwG interchangeability. We also determined the crystal structure of Rickettsia typhi RvhB8-II and modeled its coexpressed divergent paralog RvhB8-I. Remarkably, while RvhB8-I dimerizes and is structurally similar to other VirB8 proteins, the RvhB8-II dimer interface deviates substantially from other VirB8 structures, potentially preventing RvhB8-I/RvhB8-II heterodimerization. For the rvh T4SS, the evolution of divergent VirB8 paralogs implies a functional diversification that is unknown in other T4SSs. Collectively, our data identify two different constraints (spatiotemporal for Bartonella trw and vir T4SSs and structural for rvh T4SSs) that mediate the functionality of multiple divergent T4SSs within a single bacterium. PMID:26646013

Many behavioral tendencies associated with right-leaning (conservative) political ideologies are malleable and unrelated to negativity.

PubMed

Olivola, Christopher Y; Sussman, Abigail B

2014-06-01

Recent research has identified several judgment and decision making tendencies associated with right-leaning political ideologies that are difficult (if not impossible) to explain in terms of stable, negative affective appraisals because they (1) are uncorrelated with the negativity of the stimuli being considered, (2) do not reflect divergent affective evaluations, and (3) can be eliminated by superficial manipulations and interventions.

Static investigation of a two-dimensional convergent-divergent exhaust nozzle with multiaxis thrust-vectoring capability

NASA Technical Reports Server (NTRS)

Taylor, John G.

1990-01-01

An investigation was conducted in the Static Test Facility of the NASA Langley 16-Foot Transonic Tunnel to determine the internal performance of two-dimensional convergent-divergent nozzles designed to have simultaneous pitch and yaw thrust vectoring capability. This concept utilized divergent flap rotation of thrust vectoring in the pitch plane and deflection of flat yaw flaps hinged at the end of the sidewalls for yaw thrust vectoring. The hinge location of the yaw flaps was varied at four positions from the nozzle exit plane to the throat plane. The yaw flaps were designed to contain the flow laterally independent of power setting. In order to eliminate any physical interference between the yaw flap deflected into the exhaust stream and the divergent flaps, the downstream corners of both upper and lower divergent flaps were cut off to allow for up to 30 deg of yaw flap deflection. The impact of varying the nozzle pitch vector angle, throat area, yaw flap hinge location, yaw flap length, and yaw flap deflection angle on nozzle internal performance characteristics, was studied. High-pressure air was used to simulate jet exhaust at nozzle pressure ratios up to 7.0. Static results indicate that configurations with the yaw flap hinge located upstream of the exit plane provide relatively high levels of thrust vectoring efficiency without causing large losses in resultant thrust ratio. Therefore, these configurations represent a viable concept for providing simultaneous pitch and yaw thrust vectoring.

Evolutionary dynamics of emblematic Araucaria species (Araucariaceae) in New Caledonia: nuclear and chloroplast markers suggest recent diversification, introgression, and a tight link between genetics and geography within species.

PubMed

Gaudeul, Myriam; Gardner, Martin F; Thomas, Philip; Ennos, Richard A; Hollingsworth, Pete M

2014-09-05

New Caledonia harbours a highly diverse and endemic flora, and 13 (out of the 19 worldwide) species of Araucaria are endemic to this territory. Their phylogenetic relationships remain largely unresolved. Using nuclear microsatellites and chloroplast DNA sequencing, we focused on five closely related Araucaria species to investigate among-species relationships and the distribution of within-species genetic diversity across New Caledonia. The species could be clearly distinguished here, except A. montana and A. laubenfelsii that were not differentiated and, at most, form a genetic cline. Given their apparent morphological and ecological similarity, we suggested that these two species may be considered as a single evolutionary unit. We observed cases of nuclear admixture and incongruence between nuclear and chloroplast data, probably explained by introgression and shared ancestral polymorphism. Ancient hybridization was evidenced between A. biramulata and A. laubenfelsii in Mt Do, and is strongly suspected between A. biramulata and A. rulei in Mt Tonta. In both cases, extensive asymmetrical backcrossing eliminated the influence of one parent in the nuclear DNA composition. Shared ancestral polymorphism was also observed for cpDNA, suggesting that species diverged recently, have large effective sizes and/or that cpDNA experienced slow rates of molecular evolution. Within-species genetic structure was pronounced, probably because of low gene flow and significant inbreeding, and appeared clearly influenced by geography. This may be due to survival in distinct refugia during Quaternary climatic oscillations. The study species probably diverged recently and/or are characterized by a slow rate of cpDNA sequence evolution, and introgression is strongly suspected. Within-species genetic structure is tightly linked with geography. We underline the conservation implications of our results, and highlight several perspectives.

Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation.

PubMed

Cosentino, Bradley J; Phillips, Christopher A; Schooley, Robert L; Lowe, Winsor H; Douglas, Marlis R

2012-04-22

Theory predicts that founder effects have a primary role in determining metapopulation genetic structure. However, ecological factors that affect extinction-colonization dynamics may also create spatial variation in the strength of genetic drift and migration. We tested the hypothesis that ecological factors underlying extinction-colonization dynamics influenced the genetic structure of a tiger salamander (Ambystoma tigrinum) metapopulation. We used empirical data on metapopulation dynamics to make a priori predictions about the effects of population age and ecological factors on genetic diversity and divergence among 41 populations. Metapopulation dynamics of A. tigrinum depended on wetland area, connectivity and presence of predatory fish. We found that newly colonized populations were more genetically differentiated than established populations, suggesting that founder effects influenced genetic structure. However, ecological drivers of metapopulation dynamics were more important than age in predicting genetic structure. Consistent with demographic predictions from metapopulation theory, genetic diversity and divergence depended on wetland area and connectivity. Divergence was greatest in small, isolated wetlands where genetic diversity was low. Our results show that ecological factors underlying metapopulation dynamics can be key determinants of spatial genetic structure, and that habitat area and isolation may mediate the contributions of drift and migration to divergence and evolution in local populations.

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae)

PubMed Central

Zhang, Yong-Hua; Wang, Ian J.; Comes, Hans Peter; Peng, Hua; Qiu, Ying-Xiong

2016-01-01

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels – phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important – climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors. PMID:27137438

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae).

PubMed

Zhang, Yong-Hua; Wang, Ian J; Comes, Hans Peter; Peng, Hua; Qiu, Ying-Xiong

2016-05-03

Examining how historical and contemporary geographic and environmental factors contribute to genetic divergence at different evolutionary scales is a central yet largely unexplored question in ecology and evolution. Here, we examine this key question by investigating how environmental and geographic factors across different epochs have driven genetic divergence at deeper (phylogeographic) and shallower (landscape genetic) evolutionary scales in the Chinese Tertiary relict tree Emmenopterys henryi. We found that geography played a predominant role at all levels - phylogeographic clades are broadly geographically structured, the deepest levels of divergence are associated with major geological or pre-Quaternary climatic events, and isolation by distance (IBD) primarily explained population genetic structure. However, environmental factors are clearly also important - climatic fluctuations since the Last Interglacial (LIG) have likely contributed to phylogeographic structure, and the population genetic structure (in our AFLP dataset) was partly explained by isolation by environment (IBE), which may have resulted from natural selection in environments with divergent climates. Thus, historical and contemporary geography and historical and contemporary environments have all shaped patterns of genetic structure in E. henryi, and, in fact, changes in the landscape through time have also been critical factors.

Spatial phenotypic and genetic structure of threespine stickleback (Gasterosteus aculeatus) in a heterogeneous natural system, Lake Mývatn, Iceland.

PubMed

Millet, Antoine; Kristjánsson, Bjarni K; Einarsson, Arni; Räsänen, Katja

2013-09-01

Eco-evolutionary responses of natural populations to spatial environmental variation strongly depend on the relative strength of environmental differences/natural selection and dispersal/gene flow. In absence of geographic barriers, as often is the case in lake ecosystems, gene flow is expected to constrain adaptive divergence between environments - favoring phenotypic plasticity or high trait variability. However, if divergent natural selection is sufficiently strong, adaptive divergence can occur in face of gene flow. The extent of divergence is most often studied between two contrasting environments, whereas potential for multimodal divergence is little explored. We investigated phenotypic (body size, defensive structures, and feeding morphology) and genetic (microsatellites) structure in threespine stickleback (Gasterosteus aculeatus) across five habitat types and two basins (North and South) within the geologically young and highly heterogeneous Lake Mývatn, North East Iceland. We found that (1) North basin stickleback were, on average, larger and had relatively longer spines than South basin stickleback, whereas (2) feeding morphology (gill raker number and gill raker gap width) differed among three of five habitat types, and (3) there was only subtle genetic differentiation across the lake. Overall, our results indicate predator and prey mediated phenotypic divergence across multiple habitats in the lake, in face of gene flow.

Spatial phenotypic and genetic structure of threespine stickleback (Gasterosteus aculeatus) in a heterogeneous natural system, Lake Mývatn, Iceland

PubMed Central

Millet, Antoine; Kristjánsson, Bjarni K; Einarsson, Árni; Räsänen, Katja

2013-01-01

Eco-evolutionary responses of natural populations to spatial environmental variation strongly depend on the relative strength of environmental differences/natural selection and dispersal/gene flow. In absence of geographic barriers, as often is the case in lake ecosystems, gene flow is expected to constrain adaptive divergence between environments – favoring phenotypic plasticity or high trait variability. However, if divergent natural selection is sufficiently strong, adaptive divergence can occur in face of gene flow. The extent of divergence is most often studied between two contrasting environments, whereas potential for multimodal divergence is little explored. We investigated phenotypic (body size, defensive structures, and feeding morphology) and genetic (microsatellites) structure in threespine stickleback (Gasterosteus aculeatus) across five habitat types and two basins (North and South) within the geologically young and highly heterogeneous Lake Mývatn, North East Iceland. We found that (1) North basin stickleback were, on average, larger and had relatively longer spines than South basin stickleback, whereas (2) feeding morphology (gill raker number and gill raker gap width) differed among three of five habitat types, and (3) there was only subtle genetic differentiation across the lake. Overall, our results indicate predator and prey mediated phenotypic divergence across multiple habitats in the lake, in face of gene flow. PMID:24223263

Passive wick fluxmeters: Design considerations and field applications

NASA Astrophysics Data System (ADS)

Gee, G. W.; Newman, B. D.; Green, S. R.; Meissner, R.; Rupp, H.; Zhang, Z. F.; Keller, J. M.; Waugh, W. J.; van der Velde, M.; Salazar, J.

2009-04-01

Optimization of water use in agriculture and quantification of percolation from landfills and watersheds require reliable estimates of vadose zone water fluxes. Current technology is limited primarily to lysimeters, which directly measure water flux but are expensive and may in some way disrupt flow, causing errors in the measured drainage. We report on design considerations and field tests of an alternative approach, passive wick fluxmeters, which use a control tube to minimize convergent or divergent flow. Design calculations with a quasi-three-dimensional model illustrate how convergence and divergence can be minimized for a range of soil and climatic conditions under steady state and transient fluxes using control tubes of varying heights. There exists a critical recharge rate for a given wick length, where the fluxmeter collection efficiency is 100% regardless of the height of the control tube. Otherwise, convergent or divergent flow will occur, especially when the control tube height is small. While divergence is eliminated in coarse soils using control tubes, it is reduced but not eliminated in finer soils, particularly for fluxes <100 mm/a. Passive wick fluxmeters were tested in soils ranging from nonvegetated semiarid settings in the United States to grasslands in Germany and rain-fed crops in New Zealand and the South Pacific. Where side-by-side comparisons of drainage were made between passive wick fluxmeters and conventional lysimeters in the United States and Germany, agreement was very good. In semiarid settings, drainage was found to depend upon precipitation distribution, surface soil, topographic relief, and the type and amount of vegetation. In Washington State, United States, soil texture dominated all factors controlling drainage from test landfill covers. As expected, drainage was greatest (>60% annual precipitation) from gravel surfaces and least (no drainage) from silt loam soils. In Oregon and New Mexico, United States, and in New Zealand, drainage showed substantial spatial variability. The New Mexico tests were located in semiarid canyon bottom terraces, with flash flood prone locations having extremely high drainage/precipitation ratios. In the wettest environments, drainage was found to be closely linked to the rate and duration of precipitation events.

Divergences in holographic complexity

NASA Astrophysics Data System (ADS)

Reynolds, Alan; Ross, Simon F.

2017-05-01

We study the UV divergences in the action of the ‘Wheeler-de Witt patch’ in asymptotically AdS spacetimes, which has been conjectured to be dual to the computational complexity of the state of the dual field theory on a spatial slice of the boundary. We show that including a surface term in the action on the null boundaries which ensures invariance under coordinate transformations has the additional virtue of removing a stronger than expected divergence, making the leading divergence proportional to the proper volume of the boundary spatial slice. We compare the divergences in the action to divergences in the volume of a maximal spatial slice in the bulk, finding that the qualitative structure is the same, but subleading divergences have different relative coefficients in the two cases.

Natural selection and neutral evolution jointly drive population divergence between alpine and lowland ecotypes of the allopolyploid plant Anemone multifida (Ranunculaceae).

PubMed

McEwen, Jamie R; Vamosi, Jana C; Rogers, Sean M

2013-01-01

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074-0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041-0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence.

Nonlinear sigma model in the loop expansion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Appelquist, T.; Bernard, C.

1981-01-15

The nonlinear sigma model in four dimensions is discussed in the context of the loop expansion. Since the model is perturbatively nonrenormalizable, divergences not of the form of the Lagrangian are of course expected; what is perhaps surprising is that there are divergences which appear not to be invariant under the original nonlinear symmetry. We demonstrate, however, that these apparently noninvariant terms do not contribute to on-mass-shell quantities and may be eliminated order by order by a field redefinition involving space-time derivatives. The linear sigma model is then examined in detail; it is shown how the nonlinear model, including themore » apparently noninvariant terms, emerges as the limit of the linear model as the sigma mass goes to infinity. Finally, we compare our approach with other treatments of the ''noninvariant'' terms in the nonlinear model.« less

Application of dynamical systems theory to the high angle of attack dynamics of the F-14

NASA Technical Reports Server (NTRS)

Jahnke, Craig C.; Culick, Fred E. C.

1990-01-01

Dynamical systems theory has been used to study the nonlinear dynamics of the F-14. An eight degree of freedom model that does not include the control system present in operational F-14s has been analyzed. The aerodynamic model, supplied by NASA, includes nonlinearities as functions of the angles of attack and sideslip, the rotation rate, and the elevator deflection. A continuation method has been used to calculate the steady states of the F-14 as continuous functions of the control surface deflections. Bifurcations of these steady states have been used to predict the onset of wing rock, spiral divergence, and jump phenomena which cause the aircraft to enter a spin. A simple feedback control system was designed to eliminate the wing rock and spiral divergence instabilities. The predictions were verified with numerical simulations.

The interplay between local ecology, divergent selection, and genetic drift in population divergence of a sexually antagonistic female trait.

PubMed

Green, Kristina Karlsson; Svensson, Erik I; Bergsten, Johannes; Härdling, Roger; Hansson, Bengt

2014-07-01

Genetically polymorphic species offer the possibility to study maintenance of genetic variation and the potential role for genetic drift in population divergence. Indirect inference of the selection regimes operating on polymorphic traits can be achieved by comparing population divergence in neutral genetic markers with population divergence in trait frequencies. Such an approach could further be combined with ecological data to better understand agents of selection. Here, we infer the selective regimes acting on a polymorphic mating trait in an insect group; the dorsal structures (either rough or smooth) of female diving beetles. Our recent work suggests that the rough structures have a sexually antagonistic function in reducing male mating attempts. For two species (Dytiscus lapponicus and Graphoderus zonatus), we could not reject genetic drift as an explanation for population divergence in morph frequencies, whereas for the third (Hygrotus impressopunctatus) we found that divergent selection pulls morph frequencies apart across populations. Furthermore, population morph frequencies in H. impressopunctatus were significantly related to local bioclimatic factors, providing an additional line of evidence for local adaptation in this species. These data, therefore, suggest that local ecological factors and sexual conflict interact over larger spatial scales to shape population divergence in the polymorphism. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Population genetic structure and social kin associations of franciscana dolphin, Pontoporia blainvillei.

PubMed

Costa-Urrutia, Paula; Abud, Carolina; Secchi, Eduardo R; Lessa, Enrique P

2012-01-01

We investigated population and social structure of the franciscana dolphin, Pontoporia blainvillei, an endemic and the most endangered cetacean of the southwestern Atlantic Ocean. We analyzed samples from the Rio de la Plata estuary obtained in Uruguayan waters and from the Atlantic Ocean obtained in both Uruguayan and Brazilian waters. Mitochondrial and microsatellite DNA markers were used to study differentiation between the estuary and the ocean and the association between kinship and social group structure. Although multilocus analyses suggested that franciscanas are structured into 2 subpopulations (K = 2, divergence among clusters: F(ST) = 0.06, P = 0.002; R(ST) = 0.3, P = 0.001), mitochondrial markers did not support such divergence (F(ST) = 0.02, P = 0.12; Ф(ST) = 0.06, P =0.06). However, these units are not entirely segregated geographically. Regarding social structure, some groups are composed by first-order related individuals (R ≥ 0.5, P < 0.5). Overall, the data suggest that matrilines could be the social unit in this species. We argue that the divergence found could be associated to local adaptation and social structure, resulting from either feature leading to a recent divergence or reflecting equilibrium between local differentiation and gene flow. This evidence supports considering franciscanas from the Rio de la Plata estuary a discrete management unit.

Relative information content of polymorphic microsatellites and mitochondrial DNA for inferring dispersal and population genetic structure in the olive sea snake, Aipysurus laevis.

PubMed

Lukoschek, V; Waycott, M; Keogh, J S

2008-07-01

Polymorphic microsatellites are widely considered more powerful for resolving population structure than mitochondrial DNA (mtDNA) markers, particularly for recently diverged lineages or geographically proximate populations. Weaker population subdivision for biparentally inherited nuclear markers than maternally inherited mtDNA may signal male-biased dispersal but can also be attributed to marker-specific evolutionary characteristics and sampling properties. We discriminated between these competing explanations with a population genetic study on olive sea snakes, Aipysurus laevis. A previous mtDNA study revealed strong regional population structure for A. laevis around northern Australia, where Pleistocene sea-level fluctuations have influenced the genetic signatures of shallow-water marine species. Divergences among phylogroups dated to the Late Pleistocene, suggesting recent range expansions by previously isolated matrilines. Fine-scale population structure within regions was, however, poorly resolved for mtDNA. In order to improve estimates of fine-scale genetic divergence and to compare population structure between nuclear and mtDNA, 354 olive sea snakes (previously sequenced for mtDNA) were genotyped for five microsatellite loci. F statistics and Bayesian multilocus genotype clustering analyses found similar regional population structure as mtDNA and, after standardizing microsatellite F statistics for high heterozygosities, regional divergence estimates were quantitatively congruent between marker classes. Over small spatial scales, however, microsatellites recovered almost no genetic structure and standardized F statistics were orders of magnitude smaller than for mtDNA. Three tests for male-biased dispersal were not significant, suggesting that recent demographic expansions to the typically large population sizes of A. laevis have prevented microsatellites from reaching mutation-drift equilibrium and local populations may still be diverging.

Scale-dependent genetic structure of the Idaho giant salamander (Dicamptodon aterrimus) in stream networks.

PubMed

Mullen, Lindy B; Arthur Woods, H; Schwartz, Michael K; Sepulveda, Adam J; Lowe, Winsor H

2010-03-01

The network architecture of streams and rivers constrains evolutionary, demographic and ecological processes of freshwater organisms. This consistent architecture also makes stream networks useful for testing general models of population genetic structure and the scaling of gene flow. We examined genetic structure and gene flow in the facultatively paedomorphic Idaho giant salamander, Dicamptodon aterrimus, in stream networks of Idaho and Montana, USA. We used microsatellite data to test population structure models by (i) examining hierarchical partitioning of genetic variation in stream networks; and (ii) testing for genetic isolation by distance along stream corridors vs. overland pathways. Replicated sampling of streams within catchments within three river basins revealed that hierarchical scale had strong effects on genetic structure and gene flow. amova identified significant structure at all hierarchical scales (among streams, among catchments, among basins), but divergence among catchments had the greatest structural influence. Isolation by distance was detected within catchments, and in-stream distance was a strong predictor of genetic divergence. Patterns of genetic divergence suggest that differentiation among streams within catchments was driven by limited migration, consistent with a stream hierarchy model of population structure. However, there was no evidence of migration among catchments within basins, or among basins, indicating that gene flow only counters the effects of genetic drift at smaller scales (within rather than among catchments). These results show the strong influence of stream networks on population structure and genetic divergence of a salamander, with contrasting effects at different hierarchical scales.

Typing Speed as a Confounding Variable and the Measurement of Quality in Divergent Thinking

ERIC Educational Resources Information Center

Forthmann, Boris; Holling, Heinz; Çelik, Pinar; Storme, Martin; Lubart, Todd

2017-01-01

The need to control for writing or typing speed when assessing divergent-thinking performance has been recognized since the early '90s. An even longer tradition in divergent-thinking research has the issue of scoring the responses for quality. This research addressed both issues within structural equation modeling. Three dimensions of…

Cryptic genetic diversity, population structure, and gene flow in the Mojave rattlesnake (Crotalus scutulatus).

PubMed

Schield, Drew R; Adams, Richard H; Card, Daren C; Corbin, Andrew B; Jezkova, Tereza; Hales, Nicole R; Meik, Jesse M; Perry, Blair W; Spencer, Carol L; Smith, Lydia L; García, Gustavo Campillo; Bouzid, Nassima M; Strickland, Jason L; Parkinson, Christopher L; Borja, Miguel; Castañeda-Gaytán, Gamaliel; Bryson, Robert W; Flores-Villela, Oscar A; Mackessy, Stephen P; Castoe, Todd A

2018-06-15

The Mojave rattlesnake (Crotalus scutulatus) inhabits deserts and arid grasslands of the western United States and Mexico. Despite considerable interest in its highly toxic venom and the recognition of two subspecies, no molecular studies have characterized range-wide genetic diversity and population structure or tested species limits within C. scutulatus. We used mitochondrial DNA and thousands of nuclear loci from double-digest restriction site associated DNA sequencing to infer population genetic structure throughout the range of C. scutulatus, and to evaluate divergence times and gene flow between populations. We find strong support for several divergent mitochondrial and nuclear clades of C. scutulatus, including splits coincident with two major phylogeographic barriers: the Continental Divide and the elevational increase associated with the Central Mexican Plateau. We apply Bayesian clustering, phylogenetic inference, and coalescent-based species delimitation to our nuclear genetic data to test hypotheses of population structure. We also performed demographic analyses to test hypotheses relating to population divergence and gene flow. Collectively, our results support the existence of four distinct lineages within C. scutulatus, and genetically defined populations do not correspond with currently recognized subspecies ranges. Finally, we use approximate Bayesian computation to test hypotheses of divergence among multiple rattlesnake species groups distributed across the Continental Divide, and find evidence for co-divergence at this boundary during the mid-Pleistocene. Copyright © 2018 Elsevier Inc. All rights reserved.

Divergent host-plant use promotes reproductive isolation among cynipid gall wasp populations

PubMed Central

Egan, Scott P.; Hood, Glen R.; Feder, Jeff L.; Ott, James R.

2012-01-01

Ecological speciation occurs when reproductive isolation evolves as a consequence of divergent natural selection among environments. A direct prediction of this process is that ecologically divergent pairs of populations will exhibit greater reproductive isolation than ecologically similar pairs of populations. By comparing allopatric populations of the cynipid gall wasp Belonocnema treatae infesting Quercus virginiana and Quercus geminata, we tested the role that divergent host use plays in generating ecological divergence and sexual isolation. We found differences in body size and gall structure associated with divergent host use, but no difference in neutral genetic divergence between populations on the same or different host plant. We observed significant assortative mating between populations from alternative host plants but not between allopatric populations on the same host plant. Thus, we provide evidence that divergent host use promotes speciation among gall wasp populations. PMID:22337505

Evolution of rDNA in Nicotiana Allopolyploids: A Potential Link between rDNA Homogenization and Epigenetics

PubMed Central

Kovarik, Ales; Dadejova, Martina; Lim, Yoong K.; Chase, Mark W.; Clarkson, James J.; Knapp, Sandra; Leitch, Andrew R.

2008-01-01

Background The evolution and biology of rDNA have interested biologists for many years, in part, because of two intriguing processes: (1) nucleolar dominance and (2) sequence homogenization. We review patterns of evolution in rDNA in the angiosperm genus Nicotiana to determine consequences of allopolyploidy on these processes. Scope Allopolyploid species of Nicotiana are ideal for studying rDNA evolution because phylogenetic reconstruction of DNA sequences has revealed patterns of species divergence and their parents. From these studies we also know that polyploids formed over widely different timeframes (thousands to millions of years), enabling comparative and temporal studies of rDNA structure, activity and chromosomal distribution. In addition studies on synthetic polyploids enable the consequences of de novo polyploidy on rDNA activity to be determined. Conclusions We propose that rDNA epigenetic expression patterns established even in F1 hybrids have a material influence on the likely patterns of divergence of rDNA. It is the active rDNA units that are vulnerable to homogenization, which probably acts to reduce mutational load across the active array. Those rDNA units that are epigenetically silenced may be less vulnerable to sequence homogenization. Selection cannot act on these silenced genes, and they are likely to accumulate mutations and eventually be eliminated from the genome. It is likely that whole silenced arrays will be deleted in polyploids of 1 million years of age and older. PMID:18310159

Poincaré resonances and the limits of trajectory dynamics.

PubMed Central

Petrosky, T; Prigogine, I

1993-01-01

In previous papers we have shown that the elimination of the resonance divergences in large Poincare systems leads to complex irreducible spectral representations for the Liouville-von Neumann operator. Complex means that time symmetry is broken and irreducibility means that this representation is implementable only by statistical ensembles and not by trajectories. We consider in this paper classical potential scattering. Our theory applies to persistent scattering. Numerical simulations show quantitative agreement with our predictions. PMID:11607428

Natural Selection and Neutral Evolution Jointly Drive Population Divergence between Alpine and Lowland Ecotypes of the Allopolyploid Plant Anemone multifida (Ranunculaceae)

PubMed Central

McEwen, Jamie R.; Vamosi, Jana C.; Rogers, Sean M.

2013-01-01

Population differentiation can be driven in large part by natural selection, but selectively neutral evolution can play a prominent role in shaping patters of population divergence. The decomposition of the evolutionary history of populations into the relative effects of natural selection and selectively neutral evolution enables an understanding of the causes of population divergence and adaptation. In this study, we examined heterogeneous genomic divergence between alpine and lowland ecotypes of the allopolyploid plant, Anemone multifida. Using peak height and dominant AFLP data, we quantified population differentiation at non-outlier (neutral) and outlier loci to determine the potential contribution of natural selection and selectively neutral evolution to population divergence. We found 13 candidate loci, corresponding to 2.7% of loci, with signatures of divergent natural selection between alpine and lowland populations and between alpine populations (Fst  = 0.074–0.445 at outlier loci), but neutral population differentiation was also evident between alpine populations (FST  = 0.041–0.095 at neutral loci). By examining population structure at both neutral and outlier loci, we determined that the combined effects of selection and neutral evolution are associated with the divergence of alpine populations, which may be linked to extreme abiotic conditions and isolation between alpine sites. The presence of outlier levels of genetic variation in structured populations underscores the importance of separately analyzing neutral and outlier loci to infer the relative role of divergent natural selection and neutral evolution in population divergence. PMID:23874801

Auxiliary basis expansions for large-scale electronic structure calculations

PubMed Central

Jung, Yousung; Sodt, Alex; Gill, Peter M. W.; Head-Gordon, Martin

2005-01-01

One way to reduce the computational cost of electronic structure calculations is to use auxiliary basis expansions to approximate four-center integrals in terms of two- and three-center integrals, usually by using the variationally optimum Coulomb metric to determine the expansion coefficients. However, the long-range decay behavior of the auxiliary basis expansion coefficients has not been characterized. We find that this decay can be surprisingly slow. Numerical experiments on linear alkanes and a toy model both show that the decay can be as slow as 1/r in the distance between the auxiliary function and the fitted charge distribution. The Coulomb metric fitting equations also involve divergent matrix elements for extended systems treated with periodic boundary conditions. An attenuated Coulomb metric that is short-range can eliminate these oddities without substantially degrading calculated relative energies. The sparsity of the fit coefficients is assessed on simple hydrocarbon molecules and shows quite early onset of linear growth in the number of significant coefficients with system size using the attenuated Coulomb metric. Hence it is possible to design linear scaling auxiliary basis methods without additional approximations to treat large systems. PMID:15845767

Multiple-channel, total-reflection optic with controllable divergence

DOEpatents

Gibson, David M.; Downing, Robert G.

1997-01-01

An apparatus and method for providing focused x-ray, gamma-ray, charged particle and neutral particle, including neutron, radiation beams with a controllable amount of divergence are disclosed. The apparatus features a novel use of a radiation blocking structure, which, when combined with multiple-channel total reflection optics, increases the versatility of the optics by providing user-controlled output-beam divergence.

Multiple-channel, total-reflection optic with controllable divergence

DOEpatents

Gibson, D.M.; Downing, R.G.

1997-02-18

An apparatus and method for providing focused x-ray, gamma-ray, charged particle and neutral particle, including neutron, radiation beams with a controllable amount of divergence are disclosed. The apparatus features a novel use of a radiation blocking structure, which, when combined with multiple-channel total reflection optics, increases the versatility of the optics by providing user-controlled output-beam divergence. 11 figs.

Measuring graph similarity through continuous-time quantum walks and the quantum Jensen-Shannon divergence.

PubMed

Rossi, Luca; Torsello, Andrea; Hancock, Edwin R

2015-02-01

In this paper we propose a quantum algorithm to measure the similarity between a pair of unattributed graphs. We design an experiment where the two graphs are merged by establishing a complete set of connections between their nodes and the resulting structure is probed through the evolution of continuous-time quantum walks. In order to analyze the behavior of the walks without causing wave function collapse, we base our analysis on the recently introduced quantum Jensen-Shannon divergence. In particular, we show that the divergence between the evolution of two suitably initialized quantum walks over this structure is maximum when the original pair of graphs is isomorphic. We also prove that under special conditions the divergence is minimum when the sets of eigenvalues of the Hamiltonians associated with the two original graphs have an empty intersection.

Explosive radiation and spatial expansion across the cold environments of the Old World in an avian family.

PubMed

Liu, Baoyan; Alström, Per; Olsson, Urban; Fjeldså, Jon; Quan, Qing; Roselaar, Kees C S; Saitoh, Takema; Yao, Cheng-Te; Hao, Yan; Wang, Wenjuan; Qu, Yanhua; Lei, Fumin

2017-08-01

Our objective was to elucidate the biogeography and speciation patterns in an entire avian family, which shows a complex pattern of overlapping and nonoverlapping geographical distributions, and much variation in plumage, but less in size and structure. We estimated the phylogeny and divergence times for all of the world's species of Prunella based on multiple genetic loci, and analyzed morphometric divergence and biogeographical history. The common ancestor of Prunella was present in the Sino-Himalayan Mountains or these mountains and Central Asia-Mongolia more than 9 million years ago (mya), but a burst of speciations took place during the mid-Pliocene to early Pleistocene. The relationships among the six primary lineages resulting from that differentiation are unresolved, probably because of the rapid radiation. A general increase in sympatry with increasing time since divergence is evident. With one exception, species in clades younger than c. 3.7 my are allopatric. Species that are widely sympatric, including the most recently diverged (2.4 mya) sympatric sisters, are generally more divergent in size/structure than allo-/parapatric close relatives. The distributional pattern and inferred ages suggest divergence in allopatry and substantial waiting time until secondary contact, likely due to competitive exclusion. All sympatrically breeding species are ecologically segregated, as suggested by differences in size/structure and habitat. Colonizations of new areas were facilitated during glacial periods, followed by fragmentation during interglacials-contrary to the usual view that glacial periods resulted mainly in fragmentations.

Cryptic speciation reversal in the Etheostoma zonale (Teleostei: Percidae) species group, with an examination of the effect of recombination and introgression on species tree inference.

PubMed

Halas, Dominik; Simons, Andrew M

2014-01-01

Mitochondrial and nuclear introgression among closely related taxa can greatly complicate the process of determining their phylogenetic relationships. In the Central Highlands of North America, many fish taxa have undergone introgression; in this study, we demonstrate the existence of an unusual introgression event in the Etheostoma zonale species group. We used one mitochondrial and seven nuclear loci to determine the relationships of the taxa within the E. zonale group, and their degree of differentiation. We found evidence of multiple divergent populations within each species; much of the divergence within species has taken place during the Pleistocene. We also found evidence of a previously unknown cryptic species in the Upper Tennessee River which diverged from the remainder of the group during the Pliocene, and has undergone mitochondrial and nuclear introgression with E. zonale, in an apparent process of speciation reversal. We examined the effects that using varying types of recombination tests to eliminate the signal of recombination from nuclear loci would have on the phylogenetic placement of this introgressed lineage in our species tree analyses. Copyright © 2013 Elsevier Inc. All rights reserved.

Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides

PubMed Central

Hopwood, Paul E.; Head, Megan L.; Jordan, Eleanor J.; Carter, Mauricio J.; Davey, Emma; Moore, Allen J.; Royle, Nick J.

2016-01-01

Male and female genital morphology varies widely across many taxa, and even among populations. Disentangling potential sources of selection on genital morphology is problematic because each sex is predicted to respond to adaptations in the other due to reproductive conflicts of interest. To test how variation in this sexual conflict trait relates to variation in genital morphology we used our previously developed artificial selection lines for high and low repeated mating rates. We selected for high and low repeated mating rates using monogamous pairings to eliminate contemporaneous female choice and male–male competition. Male and female genital shape responded rapidly to selection on repeated mating rate. High and low mating rate lines diverged from control lines after only 10 generations of selection. We also detected significant patterns of male and female genital shape coevolution among selection regimes. We argue that because our selection lines differ in sexual conflict, these results support the hypothesis that sexually antagonistic coevolution can drive the rapid divergence of genital morphology. The greatest divergence in morphology corresponded with lines in which the resolution of sexual conflict over mating rate was biased in favor of male interests. PMID:27144373

Sexual selection and the evolution of genital shape and complexity in water striders.

PubMed

Rowe, Locke; Arnqvist, Göran

2012-01-01

Animal genitalia show two striking but incompletely understood evolutionary trends: a great evolutionary divergence in the shape of genitalic structures, and characteristic structural complexity. Both features are thought to result from sexual selection, but explicit comparative tests are hampered by the fact that it is difficult to quantify both morphological complexity and divergence in shape. We undertake a comparative study of multiple nongenitalic and male genital traits in a clade of 15 water strider species to quantify complexity and shape divergence. We show that genital structures are more complex and their shape more divergent among species than nongenital traits. Further, intromittent genital traits are more complex and have evolved more divergently than nonintromittent genital traits. More importantly, shape and complexity of nonintromittent genital traits show correlated evolution with indices of premating sexual selection and intromittent genital traits with postmating sexual selection, suggesting that the evolution of different components of genital morphology are shaped independently by distinct forms of sexual selection. Our quantitative results provide direct comparative support for the hypothesis that sexual selection is associated with morphological complexity in genitalic traits and highlight the importance of quantifying morphological shape and complexity, rather than size in studies of genital evolution. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

Parametric study of solar thermal rocket nozzle performance

NASA Technical Reports Server (NTRS)

Pearson, J. Boise; Landrum, D. Brian; Hawk, Clark W.

1995-01-01

This paper details a numerical investigation of performance losses in low-thrust solar thermal rocket nozzles. The effects of nozzle geometry on three types of losses were studied; finite rate dissociation-recombination kinetic losses, two dimensional axisymmetric divergence losses, and compressible viscous boundary layer losses. Short nozzle lengths and supersonic flow produce short residence times in the nozzle and a nearly frozen flow, resulting in large kinetic losses. Variations in geometry have a minimal effect on kinetic losses. Divergence losses are relatively small, and careful shaping of the nozzle can nearly eliminate them. The boundary layer in these small nozzles can grow to a major fraction of nozzle radius, and cause large losses. These losses are attributed to viscous drag on the nozzle walls and flow blockage by the boundary layer, especially in the throat region. Careful shaping of the nozzle can produce a significant reduction in viscous losses.

Bubble Divergences: Sorting out Topology from Cell Structure

NASA Astrophysics Data System (ADS)

Bonzom, Valentin; Smerlak, Matteo

2012-02-01

We conclude our analysis of bubble divergences in the flat spinfoam model. In [arXiv:1008.1476] we showed that the divergence degree of an arbitrary two-complex Gamma can be evaluated exactly by means of twisted cohomology. Here, we specialize this result to the case where Gamma is the two-skeleton of the cell decomposition of a pseudomanifold, and sharpen it with a careful analysis of the cellular and topological structures involved. Moreover, we explain in detail how this approach reproduces all the previous powercounting results for the Boulatov-Ooguri (colored) tensor models, and sheds light on algebraic-topological aspects of Gurau's 1/N expansion.

Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA

PubMed Central

de Jésus, Karine Pereira; Serre, Laurence; Zelwer, Charles; Castaing, Bertrand

2005-01-01

Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site at the 3′ and 5′ sides by βδ-elimination. Here, we present the high-resolution crystal structures of the wild-type and the P1G defective mutant of Fpg from Lactococcus lactis bound to 14mer DNA duplexes containing either a tetrahydrofuran (THF) or 1,3-propanediol (Pr) AP site analogues. Structures show that THF is less extrahelical than Pr and its backbone C5′–C4′–C3′ diverges significantly from those of Pr, rAP, 8-oxodG and FapydG. Clearly, the heterocyclic oxygen of THF is pushed back by the carboxylate of the strictly conserved E2 residue. We can propose that the ring-opened form of the damaged deoxyribose is the structure active form of the sugar for Fpg catalysis process. Both structural and functional data suggest that the first step of catalysis mediated by Fpg involves the expulsion of the O4′ leaving group facilitated by general acid catalysis (involving E2), rather than the immediate cleavage of the N-glycosic bond of the damaged nucleoside. PMID:16243784

Flame balls dynamics in divergent channel

NASA Astrophysics Data System (ADS)

Fursenko, R.; Minaev, S.

2011-12-01

A three-dimensional reaction-diffusion model for lean low-Lewis-number premixed flames with radiative heat losses propagating in divergent channel is studied numerically. Effects of inlet gas velocity and heat-loss intensity on flame structure at low Lewis numbers are investigated. It is found that continuous flame front exists at small heat losses and the separate flame balls settled within restricted domain inside the divergent channel at large heat losses. It is shown that the time averaged flame balls coordinate may be considered as important characteristic analogous to coordinate of continuous flame stabilized in divergent channel.

Loop-corrected Virasoro symmetry of 4D quantum gravity

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, T.; Kapec, D.; Raclariu, A.

Recently a boundary energy-momentum tensor T zz has been constructed from the soft graviton operator for any 4D quantum theory of gravity in asymptotically flat space. Up to an “anomaly” which is one-loop exact, T zz generates a Virasoro action on the 2D celestial sphere at null infinity. Here we show by explicit construction that the effects of the IR divergent part of the anomaly can be eliminated by a one-loop renormalization that shifts T zz .

Research methodology in recurrent pregnancy loss.

PubMed

Christiansen, Ole B

2014-03-01

The aim of this article is to highlight pitfalls in research methodology that may explain why studies in recurrent pregnancy loss (RPL) often provide very divergent results. It is hoped that insight into this issue may help clinicians decide which published studies are the most valid. It may help researchers to eliminate methodological flaws in future studies, which may hopefully come to some kind of agreement about the usefulness of diagnostic tests and treatments in RPL. Copyright © 2014 Elsevier Inc. All rights reserved.

Loop-corrected Virasoro symmetry of 4D quantum gravity

DOE PAGES

He, T.; Kapec, D.; Raclariu, A.; ...

2017-08-16

Recently a boundary energy-momentum tensor T zz has been constructed from the soft graviton operator for any 4D quantum theory of gravity in asymptotically flat space. Up to an “anomaly” which is one-loop exact, T zz generates a Virasoro action on the 2D celestial sphere at null infinity. Here we show by explicit construction that the effects of the IR divergent part of the anomaly can be eliminated by a one-loop renormalization that shifts T zz .

Balanced-Rotating-Spray Tank-And-Pipe-Cleaning System

NASA Technical Reports Server (NTRS)

Thaxton, Eric A.; Caimi, Raoul E. B.

1995-01-01

Spray head translates and rotates to clean entire inner surface of tank or pipe. Cleansing effected by three laterally balanced gas/liquid jets from spray head that rotates about longitudinal axis. Uses much less liquid. Cleaning process in system relies on mechanical action of jets instead of contaminant dissolution. Eliminates very difficult machining needed to make multiple converging/diverging nozzles within one spray head. Makes nozzle much smaller. Basic two-phase-flow, supersonic-nozzle design applied to other spray systems for interior or exterior cleaning.

Casimir effect due to a single boundary as a manifestation of the Weyl problem

NASA Astrophysics Data System (ADS)

Kolomeisky, Eugene B.; Straley, Joseph P.; Langsjoen, Luke S.; Zaidi, Hussain

2010-09-01

The Casimir self-energy of a boundary is ultraviolet-divergent. In many cases, the divergences can be eliminated by methods such as zeta-function regularization or through physical arguments (ultraviolet transparency of the boundary would provide a cutoff). Using the example of a massless scalar field theory with a single Dirichlet boundary, we explore the relationship between such approaches, with the goal of better understanding of the origin of the divergences. We are guided by the insight due to Dowker and Kennedy (1978 J. Phys. A: Math. Gen. 11 895) and Deutsch and Candelas (1979 Phys. Rev. D 20 3063) that the divergences represent measurable effects that can be interpreted with the aid of the theory of the asymptotic distribution of eigenvalues of the Laplacian discussed by Weyl. In many cases, the Casimir self-energy is the sum of cutoff-dependent (Weyl) terms having a geometrical origin, and an 'intrinsic' term that is independent of the cutoff. The Weyl terms make a measurable contribution to the physical situation even when regularization methods succeed in isolating the intrinsic part. Regularization methods fail when the Weyl terms and intrinsic parts of the Casimir effect cannot be clearly separated. Specifically, we demonstrate that the Casimir self-energy of a smooth boundary in two dimensions is a sum of two Weyl terms (exhibiting quadratic and logarithmic cutoff dependence), a geometrical term that is independent of cutoff and a non-geometrical intrinsic term. As by-products, we resolve the puzzle of the divergent Casimir force on a ring and correct the sign of the coefficient of linear tension of the Dirichlet line predicted in earlier treatments.

The potential influence of morphology on the evolutionary divergence of an acoustic signal

PubMed Central

Pitchers, W. R.; Klingenberg, C.P.; Tregenza, Tom; Hunt, J.; Dworkin, I.

2014-01-01

The evolution of acoustic behaviour and that of the morphological traits mediating its production are often coupled. Lack of variation in the underlying morphology of signalling traits has the potential to constrain signal evolution. This relationship is particularly likely in field crickets, where males produce acoustic advertisement signals to attract females by stridulating with specialized structures on their forewings. In this study, we characterise the size and geometric shape of the forewings of males from six allopatric populations of the black field cricket (Teleogryllus commodus) known to have divergent advertisement calls. We sample from each of these populations using both wild-caught and common-garden reared cohorts, allowing us to test for multivariate relationships between wing morphology and call structure. We show that the allometry of shape has diverged across populations. However, there was a surprisingly small amount of covariation between wing shape and call structure within populations. Given the importance of male size for sexual selection in crickets, the divergence we observe among populations has the potential to influence the evolution of advertisement calls in this species. PMID:25223712

Validation of the Social Appearance Anxiety Scale: factor, convergent, and divergent validity.

PubMed

Levinson, Cheri A; Rodebaugh, Thomas L

2011-09-01

The Social Appearance Anxiety Scale (SAAS) was created to assess fear of overall appearance evaluation. Initial psychometric work indicated that the measure had a single-factor structure and exhibited excellent internal consistency, test-retest reliability, and convergent validity. In the current study, the authors further examined the factor, convergent, and divergent validity of the SAAS in two samples of undergraduates. In Study 1 (N = 323), the authors tested the factor structure, convergent, and divergent validity of the SAAS with measures of the Big Five personality traits, negative affect, fear of negative evaluation, and social interaction anxiety. In Study 2 (N = 118), participants completed a body evaluation that included measurements of height, weight, and body fat content. The SAAS exhibited excellent convergent and divergent validity with self-report measures (i.e., self-esteem, trait anxiety, ethnic identity, and sympathy), predicted state anxiety experienced during the body evaluation, and predicted body fat content. In both studies, results confirmed a single-factor structure as the best fit to the data. These results lend additional support for the use of the SAAS as a valid measure of social appearance anxiety.

Creative Cognition in Secondary Science: An exploration of divergent thinking in science among adolescents

NASA Astrophysics Data System (ADS)

Antink-Meyer, Allison; Lederman, Norman G.

2015-07-01

The divergent thinking skills in science of 282 US high school students were investigated across 16 weeks of instruction in order to determine whether typical academic time periods can significantly influence changes in thinking skills. Students' from 6 high school science classrooms completed the Scientific Structures Creativity Measure (SSCM) before and after a semester of instruction. Even the short time frame of a typical academic term was found to be sufficient to promote both improvements in divergent thinking skills as well as declining divergent thinking. Declining divergent thinking skills were more common in this time frame than were improvements. The nature of student performance on the SSCM and implications are discussed.

Structure of UV divergences in maximally supersymmetric gauge theories

NASA Astrophysics Data System (ADS)

Kazakov, D. I.; Borlakov, A. T.; Tolkachev, D. M.; Vlasenko, D. E.

2018-06-01

We consider the UV divergences up to sub-subleading order for the four-point on-shell scattering amplitudes in D =8 supersymmetric Yang-Mills theory in the planar limit. We trace how the leading, subleading, etc divergences appear in all orders of perturbation theory. The structure of these divergences is typical for any local quantum field theory independently on renormalizability. We show how the generalized renormalization group equations allow one to evaluate the leading, subleading, etc. contributions in all orders of perturbation theory starting from one-, two-, etc. loop diagrams respectively. We focus then on subtraction scheme dependence of the results and show that in full analogy with renormalizable theories the scheme dependence can be absorbed into the redefinition of the couplings. The only difference is that the role of the couplings play dimensionless combinations like g2s2 or g2t2, where s and t are the Mandelstam variables.

The Rényi divergence enables accurate and precise cluster analysis for localisation microscopy.

PubMed

Staszowska, Adela D; Fox-Roberts, Patrick; Hirvonen, Liisa M; Peddie, Christopher J; Collinson, Lucy M; Jones, Gareth E; Cox, Susan

2018-06-01

Clustering analysis is a key technique for quantitatively characterising structures in localisation microscopy images. To build up accurate information about biological structures, it is critical that the quantification is both accurate (close to the ground truth) and precise (has small scatter and is reproducible). Here we describe how the Rényi divergence can be used for cluster radius measurements in localisation microscopy data. We demonstrate that the Rényi divergence can operate with high levels of background and provides results which are more accurate than Ripley's functions, Voronoi tesselation or DBSCAN. Data supporting this research will be made accessible via a web link. Software codes developed for this work can be accessed via http://coxphysics.com/Renyi_divergence_software.zip. Implemented in C ++. Correspondence and requests for materials can be also addressed to the corresponding author. adela.staszowska@gmail.com or susan.cox@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

Adjustable liquid aperture to eliminate undesirable light in holographic projection.

PubMed

Wang, Di; Liu, Chao; Li, Lei; Zhou, Xin; Wang, Qiong-Hua

2016-02-08

In this paper, we propose an adjustable liquid aperture to eliminate the undesirable light in a holographic projection. The aperture is based on hydrodynamic actuation. A chamber is formed with a cylindrical tube. A black droplet is filled in the sidewall of the cylinder tube and the outside space is the transparent oil which is immiscible with the black droplet. An ultrathin glass sheet is attached on the bottom substrate of the device and a black shading film is secured to the central area of the glass sheet. By changing the volume of the black droplet, the black droplet will move to the middle or sidewall due to hydrodynamic actuation, so the device can be used as an adjustable aperture. A divergent spherical wave and a solid lens are used to separate the focus planes of the reconstructed image and diffraction beams induced by the liquid crystal on silicon in the holographic projection. Then the aperture is used to eliminate the diffraction beams by adjusting the size of the liquid aperture and the holographic projection does not have undesirable light.

Shape - but Not Size - Codivergence between Male and Female Copulatory Structures in Onthophagus Beetles

PubMed Central

Macagno, Anna L. M.; Pizzo, Astrid; Parzer, Harald F.; Palestrini, Claudia; Rolando, Antonio; Moczek, Armin P.

2011-01-01

Genitalia are among the fastest evolving morphological traits in arthropods. Among the many hypotheses aimed at explaining this observation, some explicitly or implicitly predict concomitant male and female changes of genital traits that interact during copulation (i.e., lock and key, sexual conflict, cryptic female choice and pleiotropy). Testing these hypotheses requires insights into whether male and female copulatory structures that physically interact during mating also affect each other's evolution and patterns of diversification. Here we compare and contrast size and shape evolution of male and female structures that are known to interact tightly during copulation using two model systems: (a) the sister species O. taurus (1 native, 3 recently established populations) and O. illyricus, and (b) the species-complex O. fracticornis-similis-opacicollis. Partial Least Squares analyses indicated very little to no correlation between size and shape of copulatory structures, both in males and females. Accordingly, comparing shape and size diversification patterns of genitalia within each sex showed that the two components diversify readily - though largely independently of each other - within and between species. Similarly, comparing patterns of divergence across sexes showed that relative sizes of male and female copulatory organs diversify largely independent of each other. However, performing this analysis for genital shape revealed a signature of parallel divergence. Our results therefore suggest that male and female copulatory structures that are linked mechanically during copulation may diverge in concert with respect to their shapes. Furthermore, our results suggest that genital divergence in general, and co-divergence of male and female genital shape in particular, can evolve over an extraordinarily short time frame. Results are discussed in the framework of the hypotheses that assume or predict concomitant evolutionary changes in male and female copulatory organs. PMID:22194942

Homologous and Homeologous Intermolecular Gene Conversion Are Not Differentially Affected by Mutations in the DNA Damage or the Mismatch Repair Genes Rad1, Rad50, Rad51, Rad52, Rad54, Pms1 and Msh2

PubMed Central

Porter, G.; Westmoreland, J.; Priebe, S.; Resnick, M. A.

1996-01-01

Mismatch repair (MMR) genes or genes involved in both DNA damage repair and homologous recombination might affect homeologous vs. homologous recombination differentially. Spontaneous mitotic gene conversion between a chromosome and a homologous or homeologous donor sequence (14% diverged) on a single copy plasmid was examined in wild-type Saccharomyces cerevisiae strains and in MMR or DNA damage repair mutants. Homologous recombination in rad51, rad52 and rad54 mutants was considerably reduced, while there was little effect of rad1, rad50, pms1 and msh2 null mutations. DNA divergence resulted in no differential effect on recombination rates in the wild type or the mutants; there was only a five- to 10-fold reduction in homeologous relative to homologous recombination regardless of background. Since DNA divergence is known to affect recombination in some systems, we propose that differences in the role of MMR depends on the mode of recombination and/or the level of divergence. Based on analysis of the recombination breakpoints, there is a minimum of three homologous bases required at a recombination junction. A comparison of Rad(+) vs. rad52 strains revealed that while all conversion tracts are continuous, elimination of RAD52 leads to the appearance of a novel class of very short conversion tracts. PMID:8725224

The influence of gene flow and drift on genetic and phenotypic divergence in two species of Zosterops in Vanuatu

PubMed Central

Clegg, Sonya M.; Phillimore, Albert B.

2010-01-01

Colonization of an archipelago sets the stage for adaptive radiation. However, some archipelagos are home to spectacular radiations, while others have much lower levels of diversification. The amount of gene flow among allopatric populations is one factor proposed to contribute to this variation. In island colonizing birds, selection for reduced dispersal ability is predicted to produce changing patterns of regional population genetic structure as gene flow-dominated systems give way to drift-mediated divergence. If this transition is important in facilitating phenotypic divergence, levels of genetic and phenotypic divergence should be associated. We consider population genetic structure and phenotypic divergence among two co-distributed, congeneric (Genus: Zosterops) bird species inhabiting the Vanuatu archipelago. The more recent colonist, Z. lateralis, exhibits genetic patterns consistent with a strong influence of distance-mediated gene flow. However, complex patterns of asymmetrical gene flow indicate variation in dispersal ability or inclination among populations. The endemic species, Z. flavifrons, shows only a partial transition towards a drift-mediated system, despite a long evolutionary history on the archipelago. We find no strong evidence that gene flow constrains phenotypic divergence in either species, suggesting that levels of inter-island gene flow do not explain the absence of a radiation across this archipelago. PMID:20194170

Theoretical Study of Gilbert Damping and Spin Dynamics in Spintronic Devices

NASA Astrophysics Data System (ADS)

Qu, Tao

The determination of damping mechanisms is one of the most fundamental problems of magnetism. It represents the elimination of the magnetic energy and thus has broad impact in both science and technology. The dynamic time scale in spintronic devices is controlled by the damping and the consumed power depends on the damping constant squared. In recent years, the interest in high perpendicular anisotropy materials and thin film structures have increased considerably, owing to their stability over a wide temperature range when scaling devices to nanometer length scales. However, the conventional measurement method-Ferromagnetic resonance (FMR) can not produce accurate damping results in the high magnetic crystalline anisotropy materials/structures, and the intrinsic damping reported experimentally diverges among investigators, probably due to the varying fabrication techniques. This thesis describes the application of the Kambersky torque correlation technique, within the tight binding method, to multiple materials with high perpendicular magnetic anisotropy ( 10 7 erg/cm3), in both bulk and thin film structures. The impact of the inevitable experimental defects on the energy dissipation is identified and the experimental damping divergence among investigators due to the material degree of order is explained. It is demonstrated that this corresponds to an enhanced DOS at the Fermi level, owing to the rounding of the DOS with loss of long-range order. The consistency of the predicted damping constant with experimental measurement is demonstrated and the interface contribution to the energy damping constant in potential superlattices and heterostructures for spintronic devices is explored. An optimized structure will be a tradeoff involving both anisotropy and damping. The damping related spin dynamics in spintronic devices for different applications is investigated. One device is current perpendicular to planes(CPP) spin valve. Incoherent scattering matrices are applied to calculate the angle dependent magnetoresistantce and obtain analytic expressions for the spin valve. The non-linearity of magnetoresistance can be quantitatively explained by reflected electrons using only experimental spin polarization as input. The other device is a spin-transfer-torque nano-oscillator. The Landau-Lifshitz-Gilbert equation is applied and the synchronization requirement for experimentally fabricated non-identical multi spintronic oscillators is explored. Power enhancement and noise decrease for the synchronized state is demonstrated in a temperature range. Through introducing combined electric and magnetic coupling effect, a design for an optimized feasible nanopillar structure suitable for thin-film deposition is developed.

The roles of host evolutionary relationships (genus: Nasonia) and development in structuring microbial communities.

PubMed

Brucker, Robert M; Bordenstein, Seth R

2012-02-01

The comparative structure of bacterial communities among closely related host species remains relatively unexplored. For instance, as speciation events progress from incipient to complete stages, does divergence in the composition of the species' microbial communities parallel the divergence of host nuclear genes? To address this question, we used the recently diverged species of the parasitoid wasp genus Nasonia to test whether the evolutionary relationships of their bacterial microbiotas recapitulate the Nasonia phylogenetic history. We also assessed microbial diversity in Nasonia at different stages of development to determine the role that host age plays in microbiota structure. The results indicate that all three species of Nasonia share simple larval microbiotas dominated by the γ-proteobacteria class; however, bacterial species diversity increases as Nasonia develop into pupae and adults. Finally, under identical environmental conditions, the relationships of the microbial communities reflect the phylogeny of the Nasonia host species at multiple developmental stages, which suggests that the structure of an animal's microbial community is closely allied with divergence of host genes. These findings highlight the importance of host evolutionary relationships on microbiota composition and have broad implications for future studies of microbial symbiosis and animal speciation. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

USGS Publications Warehouse

Ramstad, K.M.; Woody, C.A.; Sage, G.K.; Allendorf, F.W.

2004-01-01

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sock-eye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.

A Handbook of Sound and Vibration Parameters

DTIC Science & Technology

1978-09-18

fixed in space. (Reference 1.) no motion atay node Static Divergence: (See Divergence.) Statistical Energy Analysis (SEA): Statistical energy analysis is...parameters of the circuits come from statistics of the vibrational characteristics of the structure. Statistical energy analysis is uniquely successful

The evolutionary history of Plasmodium vivax as inferred from mitochondrial genomes: parasite genetic diversity in the Americas.

PubMed

Taylor, Jesse E; Pacheco, M Andreína; Bacon, David J; Beg, Mohammad A; Machado, Ricardo Luiz; Fairhurst, Rick M; Herrera, Socrates; Kim, Jung-Yeon; Menard, Didier; Póvoa, Marinete Marins; Villegas, Leopoldo; Mulyanto; Snounou, Georges; Cui, Liwang; Zeyrek, Fadile Yildiz; Escalante, Ananias A

2013-09-01

Plasmodium vivax is the most prevalent human malaria parasite in the Americas. Previous studies have contrasted the genetic diversity of parasite populations in the Americas with those in Asia and Oceania, concluding that New World populations exhibit low genetic diversity consistent with a recent introduction. Here we used an expanded sample of complete mitochondrial genome sequences to investigate the diversity of P. vivax in the Americas as well as in other continental populations. We show that the diversity of P. vivax in the Americas is comparable to that in Asia and Oceania, and we identify several divergent clades circulating in South America that may have resulted from independent introductions. In particular, we show that several haplotypes sampled in Venezuela and northeastern Brazil belong to a clade that diverged from the other P. vivax lineages at least 30,000 years ago, albeit not necessarily in the Americas. We propose that, unlike in Asia where human migration increases local genetic diversity, the combined effects of the geographical structure and the low incidence of vivax malaria in the Americas has resulted in patterns of low local but high regional genetic diversity. This could explain previous views that P. vivax in the Americas has low genetic diversity because these were based on studies carried out in limited areas. Further elucidation of the complex geographical pattern of P. vivax variation will be important both for diversity assessments of genes encoding candidate vaccine antigens and in the formulation of control and surveillance measures aimed at malaria elimination.

The Evolutionary History of Plasmodium vivax as Inferred from Mitochondrial Genomes: Parasite Genetic Diversity in the Americas

PubMed Central

Taylor, Jesse E.; Pacheco, M. Andreína; Bacon, David J.; Beg, Mohammad A.; Machado, Ricardo Luiz; Fairhurst, Rick M.; Herrera, Socrates; Kim, Jung-Yeon; Menard, Didier; Póvoa, Marinete Marins; Villegas, Leopoldo; Mulyanto; Snounou, Georges; Cui, Liwang; Zeyrek, Fadile Yildiz; Escalante, Ananias A.

2013-01-01

Plasmodium vivax is the most prevalent human malaria parasite in the Americas. Previous studies have contrasted the genetic diversity of parasite populations in the Americas with those in Asia and Oceania, concluding that New World populations exhibit low genetic diversity consistent with a recent introduction. Here we used an expanded sample of complete mitochondrial genome sequences to investigate the diversity of P. vivax in the Americas as well as in other continental populations. We show that the diversity of P. vivax in the Americas is comparable to that in Asia and Oceania, and we identify several divergent clades circulating in South America that may have resulted from independent introductions. In particular, we show that several haplotypes sampled in Venezuela and northeastern Brazil belong to a clade that diverged from the other P. vivax lineages at least 30,000 years ago, albeit not necessarily in the Americas. We propose that, unlike in Asia where human migration increases local genetic diversity, the combined effects of the geographical structure and the low incidence of vivax malaria in the Americas has resulted in patterns of low local but high regional genetic diversity. This could explain previous views that P. vivax in the Americas has low genetic diversity because these were based on studies carried out in limited areas. Further elucidation of the complex geographical pattern of P. vivax variation will be important both for diversity assessments of genes encoding candidate vaccine antigens and in the formulation of control and surveillance measures aimed at malaria elimination. PMID:23733143

Phylogenetics and evolution of Trx SET genes in fully sequenced land plants.

PubMed

Zhu, Xinyu; Chen, Caoyi; Wang, Baohua

2012-04-01

Plant Trx SET proteins are involved in H3K4 methylation and play a key role in plant floral development. Genes encoding Trx SET proteins constitute a multigene family in which the copy number varies among plant species and functional divergence appears to have occurred repeatedly. To investigate the evolutionary history of the Trx SET gene family, we made a comprehensive evolutionary analysis on this gene family from 13 major representatives of green plants. A novel clustering (here named as cpTrx clade), which included the III-1, III-2, and III-4 orthologous groups, previously resolved was identified. Our analysis showed that plant Trx proteins possessed a variety of domain organizations and gene structures among paralogs. Additional domains such as PHD, PWWP, and FYR were early integrated into primordial SET-PostSET domain organization of cpTrx clade. We suggested that the PostSET domain was lost in some members of III-4 orthologous group during the evolution of land plants. At least four classes of gene structures had been formed at the early evolutionary stage of land plants. Three intronless orphan Trx SET genes from the Physcomitrella patens (moss) were identified, and supposedly, their parental genes have been eliminated from the genome. The structural differences among evolutionary groups of plant Trx SET genes with different functions were described, contributing to the design of further experimental studies.

Further Evidence of Increasing Diversity of Plasmodium vivax in the Republic of Korea in Recent Years.

PubMed

Kim, Jung-Yeon; Goo, Youn-Kyoung; Zo, Young-Gun; Ji, So-Young; Trimarsanto, Hidayat; To, Sheren; Clark, Taane G; Price, Ric N; Auburn, Sarah

2016-01-01

Vivax malaria was successfully eliminated from the Republic of Korea (ROK) in the late 1970s but re-emerged in 1993. Two decades later as the ROK enters the final stages of malaria elimination, dedicated surveillance of the local P. vivax population is critical. We apply a population genetic approach to gauge P. vivax transmission dynamics in the ROK between 2010 and 2012. P. vivax positive blood samples from 98 autochthonous cases were collected from patients attending health centers in the ROK in 2010 (n = 27), 2011 (n = 48) and 2012 (n = 23). Parasite genotyping was undertaken at 9 tandem repeat markers. Although not reaching significance, a trend of increasing population diversity was observed from 2010 (HE = 0.50 ± 0.11) to 2011 (HE = 0.56 ± 0.08) and 2012 (HE = 0.60 ± 0.06). Conversely, linkage disequilibrium declined during the same period: IAS = 0.15 in 2010 (P = 0.010), 0.09 in 2011 (P = 0.010) and 0.05 in 2012 (P = 0.010). In combination with data from other ROK studies undertaken between 1994 and 2007, our results are consistent with increasing parasite divergence since re-emergence. Polyclonal infections were rare (3% infections) suggesting that local out-crossing alone was unlikely to explain the increased divergence. Cases introduced from an external reservoir may therefore have contributed to the increased diversity. Aside from one isolate, all infections carried a short MS20 allele (142 or 149 bp), not observed in other studies in tropical endemic countries despite high diversity, inferring that these regions are unlikely reservoirs. Whilst a number of factors may explain the observed population genetic trends, the available evidence suggests that an external geographic reservoir with moderate diversity sustains the majority of P. vivax infection in the ROK, with important implications for malaria elimination.

Three Divergent Subpopulations of the Malaria Parasite Plasmodium knowlesi

PubMed Central

Lin, Lee C.; Rovie-Ryan, Jeffrine J.; Kadir, Khamisah A.; Anderios, Fread; Hisam, Shamilah; Sharma, Reuben S.K.; Singh, Balbir; Conway, David J.

2017-01-01

Multilocus microsatellite genotyping of Plasmodium knowlesi isolates previously indicated 2 divergent parasite subpopulations in humans on the island of Borneo, each associated with a different macaque reservoir host species. Geographic divergence was also apparent, and independent sequence data have indicated particularly deep divergence between parasites from mainland Southeast Asia and Borneo. To resolve the overall population structure, multilocus microsatellite genotyping was conducted on a new sample of 182 P. knowlesi infections (obtained from 134 humans and 48 wild macaques) from diverse areas of Malaysia, first analyzed separately and then in combination with previous data. All analyses confirmed 2 divergent clusters of human cases in Malaysian Borneo, associated with long-tailed macaques and pig-tailed macaques, and a third cluster in humans and most macaques in peninsular Malaysia. High levels of pairwise divergence between each of these sympatric and allopatric subpopulations have implications for the epidemiology and control of this zoonotic species. PMID:28322705

Improvement of Mishchenko's T-matrix code for absorbing particles.

PubMed

Moroz, Alexander

2005-06-10

The use of Gaussian elimination with backsubstitution for matrix inversion in scattering theories is discussed. Within the framework of the T-matrix method (the state-of-the-art code by Mishchenko is freely available at http://www.giss.nasa.gov/-crmim), it is shown that the domain of applicability of Mishchenko's FORTRAN 77 (F77) code can be substantially expanded in the direction of strongly absorbing particles where the current code fails to converge. Such an extension is especially important if the code is to be used in nanoplasmonic or nanophotonic applications involving metallic particles. At the same time, convergence can also be achieved for large nonabsorbing particles, in which case the non-Numerical Algorithms Group option of Mishchenko's code diverges. Computer F77 implementation of Mishchenko's code supplemented with Gaussian elimination with backsubstitution is freely available at http://www.wave-scattering.com.

Selection on an antagonistic behavioral trait can drive rapid genital coevolution in the burying beetle, Nicrophorus vespilloides.

PubMed

Hopwood, Paul E; Head, Megan L; Jordan, Eleanor J; Carter, Mauricio J; Davey, Emma; Moore, Allen J; Royle, Nick J

2016-06-01

Male and female genital morphology varies widely across many taxa, and even among populations. Disentangling potential sources of selection on genital morphology is problematic because each sex is predicted to respond to adaptations in the other due to reproductive conflicts of interest. To test how variation in this sexual conflict trait relates to variation in genital morphology we used our previously developed artificial selection lines for high and low repeated mating rates. We selected for high and low repeated mating rates using monogamous pairings to eliminate contemporaneous female choice and male-male competition. Male and female genital shape responded rapidly to selection on repeated mating rate. High and low mating rate lines diverged from control lines after only 10 generations of selection. We also detected significant patterns of male and female genital shape coevolution among selection regimes. We argue that because our selection lines differ in sexual conflict, these results support the hypothesis that sexually antagonistic coevolution can drive the rapid divergence of genital morphology. The greatest divergence in morphology corresponded with lines in which the resolution of sexual conflict over mating rate was biased in favor of male interests. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes.

PubMed

Long, Yunming; Zhao, Lifeng; Niu, Baixiao; Su, Jing; Wu, Hao; Chen, Yuanling; Zhang, Qunyu; Guo, Jingxin; Zhuang, Chuxiong; Mei, Mantong; Xia, Jixing; Wang, Lan; Wu, Haibin; Liu, Yao-Guang

2008-12-02

Sterility is common in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa). Although multiple loci for plant hybrid sterility have been identified, it remains unknown how alleles of the loci interact at the molecular level. Here we show that a locus for indica-japonica hybrid male sterility, Sa, comprises two adjacent genes, SaM and SaF, encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein, respectively. Most indica cultivars contain a haplotype SaM(+)SaF(+), whereas all japonica cultivars have SaM(-)SaF(-) that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM(-). This allele-specific gamete elimination results from a selective interaction of SaF(+) with SaM(-), a truncated protein, but not with SaM(+) because of the presence of an inhibitory domain, although SaM(+) is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility. We propose a two-gene/three-component interaction model for this hybrid male sterility system. The findings have implications for overcoming male sterility in inter-subspecific hybrid rice breeding.

Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes

PubMed Central

Long, Yunming; Zhao, Lifeng; Niu, Baixiao; Su, Jing; Wu, Hao; Chen, Yuanling; Zhang, Qunyu; Guo, Jingxin; Zhuang, Chuxiong; Mei, Mantong; Xia, Jixing; Wang, Lan; Wu, Haibin; Liu, Yao-Guang

2008-01-01

Sterility is common in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa). Although multiple loci for plant hybrid sterility have been identified, it remains unknown how alleles of the loci interact at the molecular level. Here we show that a locus for indica-japonica hybrid male sterility, Sa, comprises two adjacent genes, SaM and SaF, encoding a small ubiquitin-like modifier E3 ligase-like protein and an F-box protein, respectively. Most indica cultivars contain a haplotype SaM+SaF+, whereas all japonica cultivars have SaM−SaF− that diverged by nucleotide variations in wild rice. Male semi-sterility in this heterozygous complex locus is caused by abortion of pollen carrying SaM−. This allele-specific gamete elimination results from a selective interaction of SaF+ with SaM−, a truncated protein, but not with SaM+ because of the presence of an inhibitory domain, although SaM+ is required for this male sterility. Lack of any one of the three alleles in recombinant plants does not produce male sterility. We propose a two-gene/three-component interaction model for this hybrid male sterility system. The findings have implications for overcoming male sterility in inter-subspecific hybrid rice breeding. PMID:19033192

On the two-loop divergences of the 2-point hypermultiplet supergraphs for 6D, N = (1 , 1) SYM theory

NASA Astrophysics Data System (ADS)

Buchbinder, I. L.; Ivanov, E. A.; Merzlikin, B. S.; Stepanyantz, K. V.

2018-03-01

We consider 6D, N = (1 , 1) supersymmetric Yang-Mills theory formulated in N = (1 , 0) harmonic superspace and analyze the structure of the two-loop divergences in the hypermultiplet sector. Using the N = (1 , 0) superfield background field method we study the two-point supergraphs with the hypermultiplet legs and prove that their total contribution to the divergent part of effective action vanishes off shell.

An integrated view of the 1987 Australian monsoon and its mesoscale convective systems. II - Vertical structure

NASA Technical Reports Server (NTRS)

Mapes, Brian; Houze, Robert A., Jr.

1993-01-01

The vertical structure of monsoon thermal forcing by precipitating convection is diagnosed in terms of horizontal divergence. Airborne Doppler-radar divergence profiles from nine diverse mesoscale convective systems (MCSs) are presented. The MCSs consisted of multicellular convective elements which in time gave rise to areas of stratiform precipitation. Each of the three basic building blocks of the MCSs - convective, intermediary, and stratiform precipitation areas - has a consistent, characteristic divergence profile. Convective areas have low-level convergence, with its peak at 2-4 km altitude, and divergence above 6 km. Intermediary areas have convergence aloft, peaked near 10 km, feeding into mean ascent high in the upper troposphere. Stratiform areas have mid-level convergence, indicating a mesoscale downdraught below the melting level, and a mesoscale updraught aloft. Rawinsonde composite divergence profiles agree with the Doppler data in at least one important respect: the lower-tropospheric convergence into the MCSs peaks 2-4-km above the surface. Rawinsonde vorticity profiles show that monsoonal tropical cyclones spin-up at these elevated levels first, then later descend to the surface. Rawinsonde observations on a larger, continental scale demonstrate that at large horizontal scales only the 'gravest vertical mode' of MCS heating is felt, while the effects of shallower components of the heating (or divergence) profiles are trapped near the heating, as predicted by geostrophic adjustment theory.

Genetic structure and divergence in populations of Lutzomyia cruciata, a phlebotomine sand fly (Diptera: Psychodidae) vector of Leishmania mexicana in southeastern Mexico.

PubMed

Pech-May, Angélica; Marina, Carlos F; Vázquez-Domínguez, Ella; Berzunza-Cruz, Miriam; Rebollar-Téllez, Eduardo A; Narváez-Zapata, José A; Moo-Llanes, David; Ibáñez-Bernal, Sergio; Ramsey, Janine M; Becker, Ingeborg

2013-06-01

The low dispersal capacity of sand flies could lead to population isolation due to geographic barriers, climate variation, or to population fragmentation associated with specific local habitats due to landscape modification. The phlebotomine sand fly Lutzomyia cruciata has a wide distribution throughout Mexico and is a vector of Leishmania mexicana in the southeast. The aim of this study was to evaluate the genetic diversity, structure, and divergence within and among populations of Lu. cruciata in the state of Chiapas, and to infer the intra-specific phylogeny using the 3' end of the mitochondrial cytochrome b gene. We analyzed 62 sequences from four Lu. cruciata populations and found 26 haplotypes, high genetic differentiation and restricted gene flow among populations (Fst=0.416, Nm=0.701, p<0.001). The highest diversity values were recorded in populations from Loma Bonita and Guadalupe Miramar. Three lineages (100% bootstrap and 7% overall divergence) were identified using a maximum likelihood phylogenetic analysis which showed high genetic divergence (17.2-22.7%). A minimum spanning haplotype network also supported separation into three lineages. Genetic structure and divergence within and among Lu. cruciata populations are hence affected by geographic heterogeneity and evolutionary background. Data obtained in the present study suggest that Lu. cruciata in the state of Chiapas consists of at least three lineages. Such findings may have implications for vector capacity and hence for vector control strategies. Copyright © 2013 Elsevier B.V. All rights reserved.

Vortical structures and development of laminar flow over convergent-divergent riblets

NASA Astrophysics Data System (ADS)

Xu, Fang; Zhong, Shan; Zhang, Shanying

2018-05-01

In this work, the development of a laminar boundary layer over a rectangular convergent-divergent riblet section with a finite streamwise length is studied experimentally using dye visualization and particle image velocimetry in a water flume. The flow topology over this highly directional spanwise roughness is established from this study. It is shown that convergent-divergent riblets generate a spanwise flow above the riblets from the diverging line toward the adjacent converging line. This consequently leads to the formation of a weak recirculating secondary flow in cross-stream planes across the boundary layer that creates a downwash motion over the diverging line and an upwash motion over the converging line. It is found that the fluid inside the riblet valley follows a helicoidal path and it also interacts with the crossflow boundary layer hence playing a key role in determining the structure of the secondary flow across the boundary layer. The impact of riblet wavelength on vortical structures is also revealed for the first time. A larger riblet wavelength is seen to produce a stronger upwash/downwash and hence a more intense secondary flow as well as a stronger deceleration effect on the crossflow. Furthermore, the streamwise development of the flow over the riblet section can be divided into a developing stage followed by a developed stage. In the developing stage, the magnitude of induced streamwise velocity and vorticity over the converging line continues to increase, whereas in the developed stage the values of these parameters remain essentially unchanged.

Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl.

PubMed

Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F

2012-01-01

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.

Environmental Heterogeneity Explains the Genetic Structure of Continental and Mediterranean Populations of Fraxinus angustifolia Vahl

PubMed Central

Temunović, Martina; Franjić, Jozo; Satovic, Zlatko; Grgurev, Marin; Frascaria-Lacoste, Nathalie; Fernández-Manjarrés, Juan F.

2012-01-01

Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations. PMID:22905171

Computational aspects of helicopter trim analysis and damping levels from Floquet theory

NASA Technical Reports Server (NTRS)

Gaonkar, Gopal H.; Achar, N. S.

1992-01-01

Helicopter trim settings of periodic initial state and control inputs are investigated for convergence of Newton iteration in computing the settings sequentially and in parallel. The trim analysis uses a shooting method and a weak version of two temporal finite element methods with displacement formulation and with mixed formulation of displacements and momenta. These three methods broadly represent two main approaches of trim analysis: adaptation of initial-value and finite element boundary-value codes to periodic boundary conditions, particularly for unstable and marginally stable systems. In each method, both the sequential and in-parallel schemes are used and the resulting nonlinear algebraic equations are solved by damped Newton iteration with an optimally selected damping parameter. The impact of damped Newton iteration, including earlier-observed divergence problems in trim analysis, is demonstrated by the maximum condition number of the Jacobian matrices of the iterative scheme and by virtual elimination of divergence. The advantages of the in-parallel scheme over the conventional sequential scheme are also demonstrated.

Reduced Dirac equation and Lamb shift as off-mass-shell effect in quantum electrodynamics

NASA Astrophysics Data System (ADS)

Ni, Guang-Jiong; Xu, Jian-Jun; Lou, Sen-Yue

2011-02-01

Based on the accurate experimental data of energy-level differences in hydrogen-like atoms, especially the 1S—2S transitions of hydrogen and deuterium, the necessity of introducing a reduced Dirac equation with reduced mass as the substitution of original electron mass is stressed. Based on new cognition about the essence of special relativity, we provide a reasonable argument for the reduced Dirac equation to have two symmetries, the invariance under the (newly defined) space-time inversion and that under the pure space inversion, in a noninertial frame. By using the reduced Dirac equation and within the framework of quantum electrodynamics in covariant form, the Lamb shift can be evaluated (at one-loop level) as the radiative correction on a bound electron staying in an off-mass-shell state—-a new approach eliminating the infrared divergence. Hence the whole calculation, though with limited accuracy, is simplified, getting rid of all divergences and free of ambiguity.

The role of lipids in host microbe interactions.

PubMed

Lang, Roland; Mattner, Jochen

2017-06-01

Lipids are one of the major subcellular constituents and serve as signal molecules, energy sources, metabolic precursors and structural membrane components in various organisms. The function of lipids can be modified by multiple biochemical processes such as (de-)phosphorylation or (de-)glycosylation, and the organization of fatty acids into distinct cellular pools and subcellular compartments plays a pivotal role for the morphology and function of various cell populations. Thus, lipids regulate, for example, phagosome formation and maturation within host cells and thus, are critical for the elimination of microbial pathogens. Vice versa, microbial pathogens can manipulate the lipid composition of phagosomal membranes in host cells, and thus avoid their delivery to phagolysosomes. Lipids of microbial origin belong also to the strongest and most versatile inducers of mammalian immune responses upon engagement of distinct receptors on myeloid and lymphoid cells. Furthermore, microbial lipid toxins can induce membrane injuries and cell death. Thus, we will review here selected examples for mutual host-microbe interactions within the broad and divergent universe of lipids in microbial defense, tissue injury and immune evasion.

Development of a 2-micron Pulsed Direct Detection IPDA Lidar for CO2 Measurement

NASA Astrophysics Data System (ADS)

Yu, J.; Petros, M.; Singh, U. N.

2013-12-01

NASA Langley is developing a 2-micron pulsed Integrated Path Differential Absorption (IPDA) lidar for atmospheric CO2 measurements. The high pulse energy, direct detection lidar operating at CO2 2-micron absorption band provides an alternate approach to measure CO2 concentrations with significant advantages. The objective of this development is to integrate an existing high energy double-pulsed 2-micron laser transmitter with a direct detection receiver and telescope to enable a first proof of principle demonstration of airborne direct detection CO2 measurements at 2-micron wavelength. It is expected to provide high-precision measurement capability by unambiguously eliminating contamination from aerosols and clouds that can bias the IPDA measurement. The system is scheduled to fly on NASA UC12 or B200 research aircrafts before the end of 2013. This paper will describe the design of the airborne 2-micron pulsed IPDA lidar system; the lidar operation parameters; the wavelength pair selection; laser transmitter energy, pulse rate, beam divergence, double pulse generation and accurate frequency control; detector characterization; telescope design; lidar structure design; and lidar signal to noise ratio estimation.

Toxic hydrogen sulfide and dark caves: phenotypic and genetic divergence across two abiotic environmental gradients in Poecilia mexicana.

PubMed

Tobler, Michael; Dewitt, Thomas J; Schlupp, Ingo; García de León, Francisco J; Herrmann, Roger; Feulner, Philine G D; Tiedemann, Ralph; Plath, Martin

2008-10-01

Divergent natural selection drives evolutionary diversification. It creates phenotypic diversity by favoring developmental plasticity within populations or genetic differentiation and local adaptation among populations. We investigated phenotypic and genetic divergence in the livebearing fish Poecilia mexicana along two abiotic environmental gradients. These fish typically inhabit nonsulfidic surface rivers, but also colonized sulfidic and cave habitats. We assessed phenotypic variation among a factorial combination of habitat types using geometric and traditional morphometrics, and genetic divergence using quantitative and molecular genetic analyses. Fish in caves (sulfidic or not) exhibited reduced eyes and slender bodies. Fish from sulfidic habitats (surface or cave) exhibited larger heads and longer gill filaments. Common-garden rearing suggested that these morphological differences are partly heritable. Population genetic analyses using microsatellites as well as cytochrome b gene sequences indicate high population differentiation over small spatial scale and very low rates of gene flow, especially among different habitat types. This suggests that divergent environmental conditions constitute barriers to gene flow. Strong molecular divergence over short distances as well as phenotypic and quantitative genetic divergence across habitats in directions classic to fish ecomorphology suggest that divergent selection is structuring phenotypic variation in this system.

The Evolution of Ribosomal DNA: Divergent Paralogues and Phylogenetic Implications

PubMed Central

Buckler-IV, E. S.; Ippolito, A.; Holtsford, T. P.

1997-01-01

Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies. PMID:9055091

A Contigency Model for Predicting Institutionalization of Innovation Across Divergent Organizations.

ERIC Educational Resources Information Center

Howes, Nancy J.

This study was undertaken to compare the variables related to the successful institutionalization of changes across divergent organizations, and to design, through cross-validation, an interorganization model of change. Descriptive survey questionnaires and structured interviews were the instruments used. The respondent sample consisted of 1,500…

A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments.

PubMed

Rajan, Vaibhav

2013-03-01

Inaccurate inference of positional homologies in multiple sequence alignments and systematic errors introduced by alignment heuristics obfuscate phylogenetic inference. Alignment masking, the elimination of phylogenetically uninformative or misleading sites from an alignment before phylogenetic analysis, is a common practice in phylogenetic analysis. Although masking is often done manually, automated methods are necessary to handle the much larger data sets being prepared today. In this study, we introduce the concept of subsplits and demonstrate their use in extracting phylogenetic signal from alignments. We design a clustering approach for alignment masking where each cluster contains similar columns-similarity being defined on the basis of compatible subsplits; our approach then identifies noisy clusters and eliminates them. Trees inferred from the columns in the retained clusters are found to be topologically closer to the reference trees. We test our method on numerous standard benchmarks (both synthetic and biological data sets) and compare its performance with other methods of alignment masking. We find that our method can eliminate sites more accurately than other methods, particularly on divergent data, and can improve the topologies of the inferred trees in likelihood-based analyses. Software available upon request from the author.

Ending versus controlling versus employing addiction in the tobacco-caused disease endgame: moral psychological perspectives.

PubMed

Kozlowski, Lynn T

2013-05-01

Even though interest in reducing or eliminating tobacco-caused diseases is a common goal in tobacco control, many experts hold different views on addiction as a target of intervention. Some consider tobacco-caused addiction as a tobacco-caused disease to be eliminated alongside the other diseases. Some consider tobacco-caused addiction as a much lower priority disease to be eliminated, and a subset of this group is prepared to employ addiction to tobacco (nicotine) as a tool to reduce other tobacco-caused disease. These varying attitudes towards ending, controlling or employing tobacco addiction to reduce damage from tobacco use constitute quite different approaches to tobacco control and cause conflict among those in tobacco control. Moral psychological analyses argue that there is more than scientific evidence involved in supporting this continuum of approaches. Divergent values also influence positions in tobacco control. Attention to these values as well as the scientific evidence should be included in policy and practice in tobacco control. It is not that one constellation of values is necessarily superior, but debates need to be informed by and engage discussions of these values as well as the scientific evidence.

HMMerThread: detecting remote, functional conserved domains in entire genomes by combining relaxed sequence-database searches with fold recognition.

PubMed

Bradshaw, Charles Richard; Surendranath, Vineeth; Henschel, Robert; Mueller, Matthias Stefan; Habermann, Bianca Hermine

2011-03-10

Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10), a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in proteins based on weak sequence similarity. Our predictions open up new avenues for biological and medical studies. Genome-wide HMMerThread domains are available at http://vm1-hmmerthread.age.mpg.de.

HMMerThread: Detecting Remote, Functional Conserved Domains in Entire Genomes by Combining Relaxed Sequence-Database Searches with Fold Recognition

PubMed Central

Bradshaw, Charles Richard; Surendranath, Vineeth; Henschel, Robert; Mueller, Matthias Stefan; Habermann, Bianca Hermine

2011-01-01

Conserved domains in proteins are one of the major sources of functional information for experimental design and genome-level annotation. Though search tools for conserved domain databases such as Hidden Markov Models (HMMs) are sensitive in detecting conserved domains in proteins when they share sufficient sequence similarity, they tend to miss more divergent family members, as they lack a reliable statistical framework for the detection of low sequence similarity. We have developed a greatly improved HMMerThread algorithm that can detect remotely conserved domains in highly divergent sequences. HMMerThread combines relaxed conserved domain searches with fold recognition to eliminate false positive, sequence-based identifications. With an accuracy of 90%, our software is able to automatically predict highly divergent members of conserved domain families with an associated 3-dimensional structure. We give additional confidence to our predictions by validation across species. We have run HMMerThread searches on eight proteomes including human and present a rich resource of remotely conserved domains, which adds significantly to the functional annotation of entire proteomes. We find ∼4500 cross-species validated, remotely conserved domain predictions in the human proteome alone. As an example, we find a DNA-binding domain in the C-terminal part of the A-kinase anchor protein 10 (AKAP10), a PKA adaptor that has been implicated in cardiac arrhythmias and premature cardiac death, which upon stress likely translocates from mitochondria to the nucleus/nucleolus. Based on our prediction, we propose that with this HLH-domain, AKAP10 is involved in the transcriptional control of stress response. Further remotely conserved domains we discuss are examples from areas such as sporulation, chromosome segregation and signalling during immune response. The HMMerThread algorithm is able to automatically detect the presence of remotely conserved domains in proteins based on weak sequence similarity. Our predictions open up new avenues for biological and medical studies. Genome-wide HMMerThread domains are available at http://vm1-hmmerthread.age.mpg.de. PMID:21423752

Waking the undead: Implications of a soft explosive model for the timing of placental mammal diversification.

PubMed

Springer, Mark S; Emerling, Christopher A; Meredith, Robert W; Janečka, Jan E; Eizirik, Eduardo; Murphy, William J

2017-01-01

The explosive, long fuse, and short fuse models represent competing hypotheses for the timing of placental mammal diversification. Support for the explosive model, which posits both interordinal and intraordinal diversification after the KPg mass extinction, derives from morphological cladistic studies that place Cretaceous eutherians outside of crown Placentalia. By contrast, most molecular studies favor the long fuse model wherein interordinal cladogenesis occurred in the Cretaceous followed by intraordinal cladogenesis after the KPg boundary. Phillips (2016) proposed a soft explosive model that allows for the emergence of a few lineages (Xenarthra, Afrotheria, Euarchontoglires, Laurasiatheria) in the Cretaceous, but otherwise agrees with the explosive model in positing the majority of interordinal diversification after the KPg mass extinction. Phillips (2016) argues that rate transference errors associated with large body size and long lifespan have inflated previous estimates of interordinal divergence times, and further suggests that most interordinal divergences are positioned after the KPg boundary when rate transference errors are avoided through the elimination of calibrations in large-bodied and/or long lifespan clades. Here, we show that rate transference errors can also occur in the opposite direction and drag forward estimated divergence dates when calibrations in large-bodied/long lifespan clades are omitted. This dragging forward effect results in the occurrence of more than half a billion years of 'zombie lineages' on Phillips' preferred timetree. By contrast with ghost lineages, which are a logical byproduct of an incomplete fossil record, zombie lineages occur when estimated divergence dates are younger than the minimum age of the oldest crown fossils. We also present the results of new timetree analyses that address the rate transference problem highlighted by Phillips (2016) by deleting taxa that exceed thresholds for body size and lifespan. These analyses recover all interordinal divergence times in the Cretaceous and are consistent with the long fuse model of placental diversification. Finally, we outline potential problems with morphological cladistic analyses of higher-level relationships among placental mammals that may account for the perceived discrepancies between molecular and paleontological estimates of placental divergence times. Copyright © 2016 Elsevier Inc. All rights reserved.

Structural differences in the bacterial flagellar motor among bacterial species.

PubMed

Terashima, Hiroyuki; Kawamoto, Akihiro; Morimoto, Yusuke V; Imada, Katsumi; Minamino, Tohru

2017-01-01

The bacterial flagellum is a supramolecular motility machine consisting of the basal body as a rotary motor, the hook as a universal joint, and the filament as a helical propeller. Intact structures of the bacterial flagella have been observed for different bacterial species by electron cryotomography and subtomogram averaging. The core structures of the basal body consisting of the C ring, the MS ring, the rod and the protein export apparatus, and their organization are well conserved, but novel and divergent structures have also been visualized to surround the conserved structure of the basal body. This suggests that the flagellar motors have adapted to function in various environments where bacteria live and survive. In this review, we will summarize our current findings on the divergent structures of the bacterial flagellar motor.

Intercontinental divergence in the Populus-associated ectomycorrhizal fungus, Tricholoma populinum.

PubMed

Grubisha, Lisa C; Levsen, Nicholas; Olson, Matthew S; Taylor, D Lee

2012-04-01

The ectomycorrhizal fungus Tricholoma populinum is host-specific with Populus species. T. populinum has wind-dispersed progagules and may be capable of long-distance dispersal. In this study, we tested the hypothesis of a panmictic population between Scandinavia and North America. DNA sequences from five nuclear loci were used to assess phylogeographic structure and nucleotide divergence between continents. Tricholoma populinum was composed of Scandinavian and North American lineages with complete absence of shared haplotypes and only one shared nucleotide mutation. Divergence of these lineages was estimated at approx. 1.7-1.0 million yr ago (Ma), which occurred after the estimated divergence of host species Populus tremula and Populus balsamifera/Populus trichocarpa at 5 Ma. Phylogeographic structure was not observed within Scandinavian or North American lineages of T. populinum. Intercontinental divergence appears to have resulted from either allopatric isolation; a recent, rare long-distance dispersal founding event followed by genetic drift; or the response in an obligate mycorrhizal fungus with a narrow host range to contractions and expansion of host distribution during glacial and interglacial episodes within continents. Understanding present genetic variation in populations is important for predicting how obligate symbiotic fungi will adapt to present and future changing climatic conditions. © 2012 The Authors. New Phytologist © 2012 New Phytologist Trust.

First comparative insight into the architecture of COI mitochondrial minicircle molecules of dicyemids reveals marked inter-species variation.

PubMed

Catalano, Sarah R; Whittington, Ian D; Donnellan, Stephen C; Bertozzi, Terry; Gillanders, Bronwyn M

2015-07-01

Dicyemids, poorly known parasites of benthic cephalopods, are one of the few phyla in which mitochondrial (mt) genome architecture departs from the typical ~16 kb circular metazoan genome. In addition to a putative circular genome, a series of mt minicircles that each comprises the mt encoded units (I-III) of the cytochrome c oxidase complex have been reported. Whether the structure of the mt minicircles is a consistent feature among dicyemid species is unknown. Here we analyse the complete cytochrome c oxidase subunit I (COI) minicircle molecule, containing the COI gene and an associated non-coding region (NCR), for ten dicyemid species, allowing for first time comparisons between species of minicircle architecture, NCR function and inferences of minicircle replication. Divergence in COI nucleotide sequences between dicyemid species was high (average net divergence = 31.6%) while within species diversity was lower (average net divergence = 0.2%). The NCR and putative 5' section of the COI gene were highly divergent between dicyemid species (average net nucleotide divergence of putative 5' COI section = 61.1%). No tRNA genes were found in the NCR, although palindrome sequences with the potential to form stem-loop structures were identified in some species, which may play a role in transcription or other biological processes.

Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

PubMed Central

Miner, Brooks E.; Kerr, Benjamin

2011-01-01

Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system. PMID:20943691

History, geography and host use shape genomewide patterns of genetic variation in the redheaded pine sawfly (Neodiprion lecontei).

PubMed

Bagley, Robin K; Sousa, Vitor C; Niemiller, Matthew L; Linnen, Catherine R

2017-02-01

Divergent host use has long been suspected to drive population differentiation and speciation in plant-feeding insects. Evaluating the contribution of divergent host use to genetic differentiation can be difficult, however, as dispersal limitation and population structure may also influence patterns of genetic variation. In this study, we use double-digest restriction-associated DNA (ddRAD) sequencing to test the hypothesis that divergent host use contributes to genetic differentiation among populations of the redheaded pine sawfly (Neodiprion lecontei), a widespread pest that uses multiple Pinus hosts throughout its range in eastern North America. Because this species has a broad range and specializes on host plants known to have migrated extensively during the Pleistocene, we first assess overall genetic structure using model-based and model-free clustering methods and identify three geographically distinct genetic clusters. Next, using a composite-likelihood approach based on the site frequency spectrum and a novel strategy for maximizing the utility of linked RAD markers, we infer the population topology and date divergence to the Pleistocene. Based on existing knowledge of Pinus refugia, estimated demographic parameters and patterns of diversity among sawfly populations, we propose a Pleistocene divergence scenario for N. lecontei. Finally, using Mantel and partial Mantel tests, we identify a significant relationship between genetic distance and geography in all clusters, and between genetic distance and host use in two of three clusters. Overall, our results indicate that Pleistocene isolation, dispersal limitation and ecological divergence all contribute to genomewide differentiation in this species and support the hypothesis that host use is a common driver of population divergence in host-specialized insects. © 2016 John Wiley & Sons Ltd.

Multifactorial genetic divergence processes drive the onset of speciation in an Amazonian fish

PubMed Central

Torrente-Vilara, Gislene; Quilodran, Claudio; Rodrigues da Costa Doria, Carolina; Montoya-Burgos, Juan I.

2017-01-01

Understanding the processes that drive population genetic divergence in the Amazon is challenging because of the vast scale, the environmental richness and the outstanding biodiversity of the region. We addressed this issue by determining the genetic structure of the widespread Amazonian common sardine fish Triportheus albus (Characidae). We then examined the influence, on this species, of all previously proposed population-structuring factors, including isolation-by-distance, isolation-by-barrier (the Teotônio Falls) and isolation-by-environment using variables that describe floodplain and water characteristics. The population genetics analyses revealed an unusually strong structure with three geographical groups: Negro/Tapajós rivers, Lower Madeira/Central Amazon, and Upper Madeira. Distance-based redundancy analyses showed that the optimal model for explaining the extreme genetic structure contains all proposed structuring factors and accounts for up to 70% of the genetic structure. We further quantified the contribution of each factor via a variance-partitioning analysis. Our results demonstrate that multiple factors, often proposed as individual drivers of population divergence, have acted in conjunction to divide T. albus into three genetic lineages. Because the conjunction of multiple long-standing population-structuring processes may lead to population reproductive isolation, that is, the onset of speciation, we suggest that the multifactorial population-structuring processes highlighted in this study could account for the high speciation rate characterising the Amazon Basin. PMID:29261722

980 nm tapered lasers with photonic crystal structure for low vertical divergence

NASA Astrophysics Data System (ADS)

Ma, Xiaolong; Qu, Hongwei; Zhao, Pengchao; Liu, Yun; Zheng, Wanhua

2016-10-01

High power tapered lasers with nearly diffraction-limited beam quality have attracted much attention in numerous applications such as nonlinear frequency conversion, optical pumping of solid-state and fiber lasers, medical treatment and others. However, the large vertical divergence of conventional tapered lasers is a disadvantage, which makes beam shaping difficult and expensive in applications. Diode lasers with photonic crystal structure can achieve a large mode size and a narrow vertical divergence. In this paper, we present tapered lasers with photonic crystal structure emitting at 980 nm. The epitaxial layer is grown using metal organic chemical vapor deposition. The device has a total cavity length of 2 mm, which consists of a 400-um long ridge-waveguide section and a 1600-um long tapered section. The taper angle is 4°. An output power of 3.3 W is achieved with a peak conversion efficiency of 35% in pulsed mode. The threshold current is 240 mA and the slope efficiency is 0.78 W/A. In continuous wave mode, the output power is 2.87 W, which is limited by a suddenly failure resulting from catastrophic optical mirror damage. The far field divergences with full width at half maximum are 12.3° in the vertical direction and 2.9° in the lateral direction at 0.5 A. At high injection level the vertical divergence doesn't exceed 16°. Beam quality factor M2 is measured based on second moment definition in CW mode. High beam quality is demonstrated by M2 value of less than 2 in both vertical and lateral directions.

Mesoscale kinematics derived from X-band Doppler radar observations of convective versus stratiform precipitation and comparison with GPS radiosonde profiles

NASA Astrophysics Data System (ADS)

Deshpande, Sachin M.; Dhangar, N.; Das, S. K.; Kalapureddy, M. C. R.; Chakravarty, K.; Sonbawne, S.; Konwar, M.

2015-11-01

Single Doppler analysis techniques known as velocity azimuth display (VAD) and volume velocity processing (VVP) are used to analyze kinematics of mesoscale flow such as horizontal wind and divergence using X-band Doppler weather radar observations, for selected cases of convective, stratiform, and shallow cloud systems near tropical Indian sites Pune (18.58°N, 73.92°E, above sea level (asl) 560 m) and Mandhardev (18.51°N, 73.85°E, asl 1297 m). The vertical profiles of horizontal wind estimated from radar VVP/VAD methods agree well with GPS radiosonde profiles, with the low-level jet at about 1.5 km during monsoon season well depicted in both. The vertical structure and temporal variability of divergence and reflectivity profiles are indicative of the dynamical and microphysical characteristics of shallow convective, deep convective, and stratiform cloud systems. In shallow convective systems, vertical development of reflectivity profiles is limited below 5 km. In deep convective systems, reflectivity values as large as 55 dBZ were observed above freezing level. The stratiform system shows the presence of a reflectivity bright band (~35 dBZ) near the melting level. The diagnosed vertical profiles of divergence in convective and stratiform systems are distinct. In shallow convective conditions, convergence was seen below 4 km with divergence above. Low-level convergence and upper level divergence are observed in deep convective profiles, while stratiform precipitation has midlevel convergence present between lower level and upper level divergence. The divergence profiles in stratiform precipitation exhibit intense shallow layers of "melting convergence" at 0°C level, near 4.5 km altitude, with a steep gradient on the both sides of the peak. The level of nondivergence in stratiform situations is lower than that in convective situations. These observed vertical structures of divergence are largely indicative of latent heating profiles in the atmosphere, an important ingredient of monsoon dynamics.

Evidence of host-associated divergence from coral-eating snails (genus Coralliophila) in the Coral Triangle

NASA Astrophysics Data System (ADS)

Simmonds, Sara E.; Chou, Vincent; Cheng, Samantha H.; Rachmawati, Rita; Calumpong, Hilconida P.; Ngurah Mahardika, G.; Barber, Paul H.

2018-06-01

We studied how host-associations and geography shape the genetic structure of sister species of marine snails Coralliophila radula (A. Adams, 1853) and C. violacea (Kiener, 1836). These obligate ectoparasites prey upon corals and are sympatric throughout much of their ranges in coral reefs of the tropical and subtropical Indo-Pacific. We tested for population genetic structure of snails in relation to geography and their host corals using mtDNA (COI) sequences in minimum spanning trees and AMOVAs. We also examined the evolutionary relationships of their Porites host coral species using maximum likelihood trees of RAD-seq (restriction site-associated DNA sequencing) loci mapped to a reference transcriptome. A maximum likelihood tree of host corals revealed three distinct clades. Coralliophila radula showed a pronounced genetic break across the Sunda Shelf ( Φ CT = 0.735) but exhibited no genetic structure with respect to host. C. violacea exhibited significant geographic structure ( Φ CT = 0.427), with divergence among Hawaiian populations, the Coral Triangle and the Indian Ocean. Notably, C. violacea showed evidence of ecological divergence; two lineages were associated with different groups of host coral species, one widespread found at all sites, and the other restricted to the Coral Triangle. Sympatric populations of C. violacea found on different suites of coral species were highly divergent ( Φ CT = 0.561, d = 5.13%), suggesting that symbiotic relationships may contribute to lineage diversification in the Coral Triangle.

Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of Chthamalus montagui (Crustacea, Cirripedia).

PubMed

Pannacciulli, Federica G; Maltagliati, Ferruccio; de Guttry, Christian; Achituv, Yair

2017-01-01

The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0.750 and 0.967. Parameters of genetic divergence, haplotype network and Bayesian assignment analysis were consistent in rejecting the hypothesis of panmixia. C. montagui is genetically structured in three geographically discrete populations, which corresponded to north-eastern Atlantic Ocean, western-central Mediterranean Sea, and Aegean Sea-Black Sea. These populations are separated by two main effective barriers to gene flow located at the Almeria-Oran Front and in correspondence of the Cyclades Islands. According to the 'isolation with migration' model, adjacent population pairs diverged during the early to middle Pleistocene transition, a period in which geological events provoked significant changes in the structure and composition of palaeocommunities. Mismatch distributions, neutrality tests and Bayesian skyline plots showed past population expansions, which started approximately in the Mindel-Riss interglacial, in which ecological conditions were favourable for temperate species and calcium-uptaking marine organisms.

Phylogeography on the rocks: The contribution of current and historical factors in shaping the genetic structure of Chthamalus montagui (Crustacea, Cirripedia)

PubMed Central

Pannacciulli, Federica G.; de Guttry, Christian; Achituv, Yair

2017-01-01

The model marine broadcast-spawner barnacle Chthamalus montagui was investigated to understand its genetic structure and quantify levels of population divergence, and to make inference on historical demography in terms of time of divergence and changes in population size. We collected specimens from rocky shores of the north-east Atlantic Ocean (4 locations), Mediterranean Sea (8) and Black Sea (1). The 312 sequences 537 bp) of the mitochondrial cytochrome c oxidase I allowed to detect 130 haplotypes. High within-location genetic variability was recorded, with haplotype diversity ranging between h = 0.750 and 0.967. Parameters of genetic divergence, haplotype network and Bayesian assignment analysis were consistent in rejecting the hypothesis of panmixia. C. montagui is genetically structured in three geographically discrete populations, which corresponded to north-eastern Atlantic Ocean, western-central Mediterranean Sea, and Aegean Sea-Black Sea. These populations are separated by two main effective barriers to gene flow located at the Almeria-Oran Front and in correspondence of the Cyclades Islands. According to the ‘isolation with migration’ model, adjacent population pairs diverged during the early to middle Pleistocene transition, a period in which geological events provoked significant changes in the structure and composition of palaeocommunities. Mismatch distributions, neutrality tests and Bayesian skyline plots showed past population expansions, which started approximately in the Mindel-Riss interglacial, in which ecological conditions were favourable for temperate species and calcium-uptaking marine organisms. PMID:28594840

High Order Filter Methods for the Non-ideal Compressible MHD Equations

NASA Technical Reports Server (NTRS)

Yee, H. C.; Sjoegreen, Bjoern

2003-01-01

The generalization of a class of low-dissipative high order filter finite difference methods for long time wave propagation of shock/turbulence/combustion compressible viscous gas dynamic flows to compressible MHD equations for structured curvilinear grids has been achieved. The new scheme is shown to provide a natural and efficient way for the minimization of the divergence of the magnetic field numerical error. Standard divergence cleaning is not required by the present filter approach. For certain non-ideal MHD test cases, divergence free preservation of the magnetic fields has been achieved.

Divergence Free High Order Filter Methods for the Compressible MHD Equations

NASA Technical Reports Server (NTRS)

Yea, H. C.; Sjoegreen, Bjoern

2003-01-01

The generalization of a class of low-dissipative high order filter finite difference methods for long time wave propagation of shock/turbulence/combustion compressible viscous gas dynamic flows to compressible MHD equations for structured curvilinear grids has been achieved. The new scheme is shown to provide a natural and efficient way for the minimization of the divergence of the magnetic field numerical error. Standard diver- gence cleaning is not required by the present filter approach. For certain MHD test cases, divergence free preservation of the magnetic fields has been achieved.

The mitochondrial genomes of Campodea fragilis and C. lubbocki(Hexapoda: Diplura): high genetic divergence in a morphologically uniformtaxon

DOE Office of Scientific and Technical Information (OSTI.GOV)

Podsiadlowski, L.; Carapelli, A.; Nardi, F.

2005-12-01

Mitochondrial genomes from two dipluran hexapods of the genus Campodea have been sequenced. Gene order is the same as in most other hexapods and crustaceans. Secondary structures of tRNAs reveal specific structural changes in tRNA-C, tRNA-R, tRNA-S1 and tRNA-S2. Comparative analyses of nucleotide and amino acid composition, as well as structural features of both ribosomal RNA subunits, reveal substantial differences among the analyzed taxa. Although the two Campodea species are morphologically highly uniform, genetic divergence is larger than expected, suggesting a long evolutionary history under stable ecological conditions.

High-Temperature Magnetism as a Probe for Structural and Compositional Uniformity in Ligand-Capped Magnetite Nanoparticles

PubMed Central

2015-01-01

To investigate magnetostructural relationships in colloidal magnetite (Fe3O4) nanoparticles (NPs) at high temperature (300–900 K), we measured the temperature dependence of magnetization (M) of oleate-capped magnetite NPs ca. 20 nm in size. Magnetometry revealed an unusual irreversible high-temperature dependence of M for these NPs, with dip and loop features observed during heating–cooling cycles. Detailed characterizations of as-synthesized and annealed Fe3O4 NPs as well as reference ligand-free Fe3O4 NPs indicate that both types of features in M(T) are related to thermal decomposition of the capping ligands. The ligand decomposition upon the initial heating induces a reduction of Fe3+ to Fe2+ and the associated dip in M, leading to more structurally and compositionally uniform magnetite NPs. Having lost the protective ligands, the NPs continually sinter during subsequent heating cycles, resulting in divergent M curves featuring loops. The increase in M with sintering proceeds not only through elimination of a magnetically dead layer on the particle surface, as a result of a decrease in specific surface area with increasing size, but also through an uncommonly invoked effect resulting from a significant change in Fe3+/Fe2+ ratio with heat treatment. The interpretation of irreversible features in M(T) indicates that reversible M(T) behavior, conversely, can be expected only for ligand-free, structurally and compositionally uniform magnetite NPs, suggesting a general applicability of high-temperature M(T) measurements as an analytical method for probing the structure and composition of magnetic nanomaterials. PMID:25506407

3-D Magnetotelluric Forward Modeling And Inversion Incorporating Topography By Using Vector Finite-Element Method Combined With Divergence Corrections Based On The Magnetic Field (VFEH++)

NASA Astrophysics Data System (ADS)

Shi, X.; Utada, H.; Jiaying, W.

2009-12-01

The vector finite-element method combined with divergence corrections based on the magnetic field H, referred to as VFEH++ method, is developed to simulate the magnetotelluric (MT) responses of 3-D conductivity models. The advantages of the new VFEH++ method are the use of edge-elements to eliminate the vector parasites and the divergence corrections to explicitly guarantee the divergence-free conditions in the whole modeling domain. 3-D MT topographic responses are modeling using the new VFEH++ method, and are compared with those calculated by other numerical methods. The results show that MT responses can be modeled highly accurate using the VFEH+ +method. The VFEH++ algorithm is also employed for the 3-D MT data inversion incorporating topography. The 3-D MT inverse problem is formulated as a minimization problem of the regularized misfit function. In order to avoid the huge memory requirement and very long time for computing the Jacobian sensitivity matrix for Gauss-Newton method, we employ the conjugate gradient (CG) approach to solve the inversion equation. In each iteration of CG algorithm, the cost computation is the product of the Jacobian sensitivity matrix with a model vector x or its transpose with a data vector y, which can be transformed into two pseudo-forwarding modeling. This avoids the full explicitly Jacobian matrix calculation and storage which leads to considerable savings in the memory required by the inversion program in PC computer. The performance of CG algorithm will be illustrated by several typical 3-D models with horizontal earth surface and topographic surfaces. The results show that the VFEH++ and CG algorithms can be effectively employed to 3-D MT field data inversion.

α-Oxo-Ketenimines from Isocyanides and α-Haloketones: Synthesis and Divergent Reactivity.

PubMed

Mamboury, Mathias; Wang, Qian; Zhu, Jieping

2017-09-18

The palladium-catalyzed reaction of α-haloketones with isocyanides afforded α-oxo-ketenimines through β-hydride elimination of the β-oxo-imidoyl palladium intermediates. Reaction of these relatively stable α-oxo-ketenimines with nucleophiles such as hydrazines, hydrazoic acid, amines, and Grignard reagent afforded pyrazoles, tetrazole, β-keto amidines, and enaminone, respectively, with high chemoselectivity. Whereas amines attack exclusively on the ketenimine functions, the formal [3+2] cycloaddition between N-monosubstituted hydrazines and α-oxo-ketenimines was initiated by nucleophilic addition to the carbonyl group. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Domain decomposition for a mixed finite element method in three dimensions

USGS Publications Warehouse

Cai, Z.; Parashkevov, R.R.; Russell, T.F.; Wilson, J.D.; Ye, X.

2003-01-01

We consider the solution of the discrete linear system resulting from a mixed finite element discretization applied to a second-order elliptic boundary value problem in three dimensions. Based on a decomposition of the velocity space, these equations can be reduced to a discrete elliptic problem by eliminating the pressure through the use of substructures of the domain. The practicality of the reduction relies on a local basis, presented here, for the divergence-free subspace of the velocity space. We consider additive and multiplicative domain decomposition methods for solving the reduced elliptic problem, and their uniform convergence is established.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Scarlatescu, Ioana, E-mail: scarlatescuioana@gmail.com; Avram, Calin N.; Virag, Vasile

In this paper we present one treatment plan for irradiation cases which involve a complex technique with multiple beams, using the 3D conformational technique. As the main purpose of radiotherapy is to administrate a precise dose into the tumor volume and protect as much as possible all the healthy tissues around it, for a case diagnosed with a primitive neuro ectoderm tumor, we have developed a new treatment plan, by controlling one of the two adjacent fields used at spinal field, in a way that avoids the fields superposition. Therefore, the risk of overdose is reduced by eliminating the fieldmore » divergence.« less

Psychometric Properties of the Beck Depression Inventory-II in a Clinically-Identified Sample of Mexican American Adolescents

ERIC Educational Resources Information Center

VanVoorhis, Carmen R. Wilson; Blumentritt, Tracie L.

2007-01-01

We examined the internal consistency reliability, convergent and divergent validity, and factor structure of the Beck Depression Inventory-II (BDI-II) in a sample of 131 Mexican American youth. The BDI-II demonstrated excellent internal consistency reliability (alpha = 0.90) and solid convergent and divergent validity with various clinical scales…

Creative Cognition in Secondary Science: An Exploration of Divergent Thinking in Science among Adolescents

ERIC Educational Resources Information Center

Antink-Meyer, Allison; Lederman, Norman G.

2015-01-01

The divergent thinking skills in science of 282 US high school students were investigated across 16 weeks of instruction in order to determine whether typical academic time periods can significantly influence changes in thinking skills. Students' from 6 high school science classrooms completed the Scientific Structures Creativity Measure (SSCM)…

Creative Self-Efficacy: The Influence of Affective States and Social Persuasion as Antecedents and Imagination and Divergent Thinking as Consequences

ERIC Educational Resources Information Center

Puente-Díaz, Rogelio; Cavazos-Arroyo, Judith

2017-01-01

Two studies examined the influence of encouragement for creativity, curiosity, harmonious passion, and autonomy support as antecedents of creative self-efficacy and imagination and divergent thinking as consequences. College students completed a battery of questionnaires. Structural equation modeling treating the variables as latent and not…

Genetic structure and hierarchical population divergence history of Acer mono var. mono in South and Northeast China.

PubMed

Liu, Chunping; Tsuda, Yoshiaki; Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species' evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST  = 0.073; G'ST  = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species' more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study.

Genetic Structure and Hierarchical Population Divergence History of Acer mono var. mono in South and Northeast China

PubMed Central

Shen, Hailong; Hu, Lijiang; Saito, Yoko; Ide, Yuji

2014-01-01

Knowledge of the genetic structure and evolutionary history of tree species across their ranges is essential for the development of effective conservation and forest management strategies. Acer mono var. mono, an economically and ecologically important maple species, is extensively distributed in Northeast China (NE), whereas it has a scattered and patchy distribution in South China (SC). In this study, the genetic structure and demographic history of 56 natural populations of A. mono var. mono were evaluated using seven nuclear microsatellite markers. Neighbor-joining tree and STRUCTURE analysis clearly separated populations into NE and SC groups with two admixed-like populations. Allelic richness significantly decreased with increasing latitude within the NE group while both allelic richness and expected heterozygosity showed significant positive correlation with latitude within the SC group. Especially in the NE region, previous studies in Quercus mongolica and Fraxinus mandshurica have also detected reductions in genetic diversity with increases in latitude, suggesting this pattern may be common for tree species in this region, probably due to expansion from single refugium following the last glacial maximum (LGM). Approximate Bayesian Computation-based analysis revealed two major features of hierarchical population divergence in the species’ evolutionary history. Recent divergence between the NE group and the admixed-like group corresponded to the LGM period and ancient divergence of SC groups took place during mid-late Pleistocene period. The level of genetic differentiation was moderate (FST = 0.073; G′ST = 0.278) among all populations, but significantly higher in the SC group than the NE group, mirroring the species’ more scattered distribution in SC. Conservation measures for this species are proposed, taking into account the genetic structure and past demographic history identified in this study. PMID:24498039

Improved power and efficiency for tapered lasers with optimized photonic crystal structures

NASA Astrophysics Data System (ADS)

Ma, Xiaolong; Qu, Hongwei; Zhao, Shaoyu; Zhou, Xuyan; Lin, Yuzhe; Zheng, Wanhua

2017-10-01

High power and high beam quality laser sources are required in numerous applications such as nonlinear frequency conversion, optical pumping of solid-state and fiber lasers, material processing and others. Tapered lasers can provide a high output power while keeping a high beam quality. However, the conventional tapered lasers suffer from a large vertical beam divergence. We have demonstrated 2-mm long tapered lasers with photonic crystal structures. A high beam quality and a narrow vertical divergence are achieved. In this paper, we optimized the photonic crystal structure and fabricated a 4-mm long tapered laser to further increase the output power and the wall-plug efficiency. Compared with our precious wafer, the optimized structure has a lower doping level to reduce the internal loss. The period of the photonic crystal structure and the thickness of the upper cladding are also reduced. The device has a 1-mm long ridge-waveguide section and a 3-mm long tapered section. The taper angle is 4°. An output power of 7.3 W is achieved with a peak wall-plug efficiency of 46% in continuous-wave mode. The threshold current is around 500 mA and the slope efficiency is 0.93 W/A. In pulsed mode, the output power is 15.6 W and the maximum wall-plug efficiency is 48.1%. The far-field divergence with full width at half maximum is 6.3° for the lateral direction at 3 A. The vertical far-field beam divergence is around 11° at different injection levels. High beam qualities are demonstrated by beam quality factor M2 of 1.52 for the lateral direction and 1.54 for the vertical direction.

Evidence for cryptic northern refugia in the last glacial period in Cryptomeria japonica

PubMed Central

Kimura, Megumi K.; Uchiyama, Kentaro; Nakao, Katsuhiro; Moriguchi, Yoshinari; San Jose-Maldia, Lerma; Tsumura, Yoshihiko

2014-01-01

Background and Aims Distribution shifts and natural selection during past climatic changes are important factors in determining the genetic structure of forest species. In particular, climatic fluctuations during the Quaternary appear to have caused changes in the distribution ranges of plants, and thus strongly affected their genetic structure. This study was undertaken to identify the responses of the conifer Cryptomeria japonica, endemic to the Japanese Archipelago, to past climatic changes using a combination of phylogeography and species distribution modelling (SDM) methods. Specifically, this study focused on the locations of refugia during the last glacial maximum (LGM). Methods Genetic diversity and structure were examined using 20 microsatellite markers in 37 populations of C. japonica. The locations of glacial refugia were assessed using STRUCTURE analysis, and potential habitats under current and past climate conditions were predicted using SDM. The process of genetic divergence was also examined using the approximate Bayesian computation procedure (ABC) in DIY ABC to test the divergence time between the gene pools detected by the STRUCTURE analysis. Key Results STRUCTURE analysis identified four gene pools: northern Tohoku district; from Chubu to Chugoku district; from Tohoku to Shikoku district on the Pacific Ocean side of the Archipelago; and Yakushima Island. DIY ABC analysis indicated that the four gene pools diverged at the same time before the LGM. SDM also indicated potential northern cryptic refugia. Conclusions The combined evidence from microsatellites and SDM clearly indicates that climatic changes have shaped the genetic structure of C. japonica. The gene pool detected in northern Tohoku district is likely to have been established by cryptic northern refugia on the coast of the Japan Sea to the west of the Archipelago. The gene pool in Yakushima Island can probably be explained simply by long-term isolation from the other gene pools since the LGM. These results are supported by those of SDM and the predicted divergence time determined using ABC analysis. PMID:25355521

Comments on the Parameters and Processes that Affect the Preservation Potential and Style of Oblique-Divergent Plate Boundaries

NASA Astrophysics Data System (ADS)

Umhoefer, P. J.

2014-12-01

Oblique-divergent or transtensional zones present particular challenges in ancient belts because of the poor preservation potential of the thinned continental crust and young oceanic crust. Many oblique belts will preferentially preserve their boundary zones that lie within continents rather than the main plate boundary zone, which will be at a much lower elevation and composed of denser crust. Zones of tectonic escape or strike-slip overprinting of arcs or plateaus deform continental crust and may be better preserved. Here I highlight parameters and processes that have major effects on oblique divergent belts. Strain partitioning is common, but not ubiquitous, along and across oblique boundaries; the causes of partitioning are not always clear and make this especially vexing for work in ancient belts. Partitioning causes complexity in the patterns of structures at all scales. Inherited structures commonly determine the orientation and style of structures along oblique boundaries and can control the pattern of faults across transtensional belts. Regionally, inherited trends of arcs or other 1000-km-scale features can control boundary structures. Experiments and natural examples suggest that oblique boundary zones contain less of a record of strike-slip faulting and more extensional structures. The obliquity of divergence produces predictable families of structures that typify (i) strike-slip dominated zones (obliquity <~20°), (ii) mixed zones (~20° - ~35°), and (iii) extension dominated zones (>~35°). The combination of partitioning and mixed structures in oblique zones means that the boundaries of belts with large-magnitude strike-slip faulting will commonly preserve little of no record of that faulting history. Plate boundaries localize strain onto the main plate boundary structures from the broader plate boundary and therefore the boundary zones commonly preserve the earlier structures more than later structures, a major problem in interpreting ancient belts. Sediment input is critical in some oblique plate boundaries because these belts become more pronounced sediment sinks over time. The evolving topography of oblique boundaries means that they have great variability of sediment flux into differing parts of the system; large rivers enter these belts only in special circumstances.

Divergence within and among 3 varieties of the endemic tree, 'Ohi'a Lehua (Metrosideros polymorpha) on the eastern slope of Hawai'i Island.

PubMed

DeBoer, Nicholas; Stacy, Elizabeth A

2013-01-01

Examination of neutral genetic structure within young, hypervariable tree species over heterogeneous landscapes can yield insight into the causes of divergence within trees. Three varieties of the Hawaiian-forest-dominant, Metrosideros polymorpha, occur across the main islands and partition 2 striking environmental gradients on young Hawai'i Island. In an examination of 6 nuclear microsatellite loci across 10 populations on east Hawai'i, we found differentiation among varieties (mean F ST = 0.065; max = 0.081) that exceeded that observed among populations of some continental tree species over much broader spatial scales. High-elevation var. polymorpha exhibited the strongest average differentiation (F ST = 0.071). Weaker differentiation between the early- and late-successional varieties was consistent with previous records of high hybridization between these varieties coupled with differential selection favoring var. incana in early-successional or dry environments, and var. glaberrima in late-successional environments. A comparison of within-variety F ST values suggests that active volcanoes shape the genetic structure of early- and late-successional varieties differently. Examination of genetic structure of these same varieties on older islands is required to assess the degree to which the differentiation observed on Hawai'i Island is attributable to multiple colonizations of this young island by partially diverged forms versus divergence in situ.

Determinants of echolocation call frequency variation in the Formosan lesser horseshoe bat (Rhinolophus monoceros)

PubMed Central

Chen, Shiang-Fan; Jones, Gareth; Rossiter, Stephen J.

2009-01-01

The origin and maintenance of intraspecific variation in vocal signals is important for population divergence and speciation. Where vocalizations are transmitted by vertical cultural inheritance, similarity will reflect co-ancestry, and thus vocal divergence should reflect genetic structure. Horseshoe bats are characterized by echolocation calls dominated by a constant frequency component that is partly determined by maternal imprinting. Although previous studies showed that constant frequency calls are also influenced by some non-genetic factors, it is not known how frequency relates to genetic structure. To test this, we related constant frequency variation to genetic and non-genetic variables in the Formosan lesser horseshoe bat (Rhinolophus monoceros). Recordings of bats from across Taiwan revealed that females called at higher frequencies than males; however, we found no effect of environmental or morphological factors on call frequency. By comparison, variation showed clear population structure, with frequencies lower in the centre and east, and higher in the north and south. Within these regions, frequency divergence was directional and correlated with geographical distance, suggesting that call frequencies are subject to cultural drift. However, microsatellite clustering analysis showed that broad differences in constant frequency among populations corresponded to discontinuities in allele frequencies resulting from vicariant events. Our results provide evidence that the processes shaping genetic subdivision have concomitant consequences for divergence in echolocation call frequency. PMID:19692399

Contemporary and historical evolutionary processes interact to shape patterns of within-lake phenotypic divergences in polyphenic pumpkinseed sunfish, Lepomis gibbosus.

PubMed

Weese, Dylan J; Ferguson, Moira M; Robinson, Beren W

2012-03-01

Historical and contemporary evolutionary processes can both contribute to patterns of phenotypic variation among populations of a species. Recent studies are revealing how interactions between historical and contemporary processes better explain observed patterns of phenotypic divergence than either process alone. Here, we investigate the roles of evolutionary history and adaptation to current environmental conditions in structuring phenotypic variation among polyphenic populations of sunfish inhabiting 12 postglacial lakes in eastern North America. The pumpkinseed sunfish polyphenism includes sympatric ecomorphs specialized for littoral or pelagic lake habitats. First, we use population genetic methods to test the evolutionary independence of within-lake phenotypic divergences of ecomorphs and to describe patterns of genetic structure among lake populations that clustered into three geographical groupings. We then used multivariate analysis of covariance (MANCOVA) to partition body shape variation (quantified with geometric morphometrics) among the effects of evolutionary history (reflecting phenotypic variation among genetic clusters), the shared phenotypic response of all populations to alternate habitats within lakes (reflecting adaptation to contemporary conditions), and unique phenotypic responses to habitats within lakes nested within genetic clusters. All effects had a significant influence on body form, but the effects of history and the interaction between history and contemporary habitat were larger than contemporary processes in structuring phenotypic variation. This highlights how divergence can be better understood against a known backdrop of evolutionary history.

Genetic divergence is decoupled from ecological diversification in the Hawaiian Nesosydne planthoppers.

PubMed

Roesch Goodman, Kari; Welter, Stephen C; Roderick, George K

2012-09-01

Adaptive radiation involves ecological shifts coupled with isolation of gene pools. However, we know little about what drives the initial stages of divergence. We study a system in which ecological diversification is found within a chronologically well-defined geological matrix to provide insight into this enigmatic phase of radiation. We tested the hypothesis that a period of geographic isolation precedes ecological specialization in an adaptive radiation of host-specialized Hawaiian planthoppers. We examined population structure and history using mitochondrial and multiple independent microsatellite loci in a species whose geographic distribution on the island of Hawaii enabled us to observe the chronology of divergence in its very earliest stages. We found that genetic divergence is associated with geographic features but not different plant hosts and that divergence times are very recent and on the same timescales as the dynamic geology of the island. Our results suggest an important role for geography in the dynamics of the early stages of divergence. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Divergence in genital morphology may contribute to mechanical reproductive isolation in a millipede

PubMed Central

Wojcieszek, Janine M; Simmons, Leigh W

2013-01-01

Genitalia appear to evolve rapidly and divergently in taxa with internal fertilization. The current consensus is that intense directional sexual selection drives the rapid evolution of genitalia. Recent research on the millipede Antichiropus variabilis suggests that the male genitalia are currently experiencing stabilizing selection – a pattern of selection expected for lock-and-key structures that enforce mate recognition and reproductive isolation. Here, we investigate how divergence in genital morphology affects reproductive compatibility among isolated populations of A. variabilis. Females from a focal population were mated first to a male from their own population and, second, to a male from one of two populations with divergent genital morphology. We observed variation in mating behavior that might indicate the emergence of precopulatory reproductive barriers: males from one divergent population took significantly longer to recognize females and exhibited mechanical difficulty in genital insertion. Moreover, we observed very low paternity success for extra-population males who were successful in copulating. Our data suggest that divergence in genital shape may be contributing to reproductive isolation, and incipient speciation among isolated populations of A. variabilis. PMID:23467632

Semantic search during divergent thinking.

PubMed

Hass, Richard W

2017-09-01

Divergent thinking, as a method of examining creative cognition, has not been adequately analyzed in the context of modern cognitive theories. This article casts divergent thinking responding in the context of theories of memory search. First, it was argued that divergent thinking tasks are similar to semantic fluency tasks, but are more constrained, and less well structured. Next, response time distributions from 54 participants were analyzed for temporal and semantic clustering. Participants responded to two prompts from the alternative uses test: uses for a brick and uses for a bottle, for two minutes each. Participants' cumulative response curves were negatively accelerating, in line with theories of search of associative memory. However, results of analyses of semantic and temporal clustering suggested that clustering is less evident in alternative uses responding compared to semantic fluency tasks. This suggests either that divergent thinking responding does not involve an exhaustive search through a clustered memory trace, but rather that the process is more exploratory, yielding fewer overall responses that tend to drift away from close associates of the divergent thinking prompt. Copyright © 2017 Elsevier B.V. All rights reserved.

Silencing urease: a key evolutionary step that facilitated the adaptation of Yersinia pestis to the flea-borne transmission route.

PubMed

Chouikha, Iman; Hinnebusch, B Joseph

2014-12-30

The arthropod-borne transmission route of Yersinia pestis, the bacterial agent of plague, is a recent evolutionary adaptation. Yersinia pseudotuberculosis, the closely related food-and water-borne enteric species from which Y. pestis diverged less than 6,400 y ago, exhibits significant oral toxicity to the flea vectors of plague, whereas Y. pestis does not. In this study, we identify the Yersinia urease enzyme as the responsible oral toxin. All Y. pestis strains, including those phylogenetically closest to the Y. pseudotuberculosis progenitor, contain a mutated ureD allele that eliminated urease activity. Restoration of a functional ureD was sufficient to make Y. pestis orally toxic to fleas. Conversely, deletion of the urease operon in Y. pseudotuberculosis rendered it nontoxic. Enzymatic activity was required for toxicity. Because urease-related mortality eliminates 30-40% of infective flea vectors, ureD mutation early in the evolution of Y. pestis was likely subject to strong positive selection because it significantly increased transmission potential.

Silencing urease: A key evolutionary step that facilitated the adaptation of Yersinia pestis to the flea-borne transmission route

PubMed Central

Chouikha, Iman; Hinnebusch, B. Joseph

2014-01-01

The arthropod-borne transmission route of Yersinia pestis, the bacterial agent of plague, is a recent evolutionary adaptation. Yersinia pseudotuberculosis, the closely related food-and water-borne enteric species from which Y. pestis diverged less than 6,400 y ago, exhibits significant oral toxicity to the flea vectors of plague, whereas Y. pestis does not. In this study, we identify the Yersinia urease enzyme as the responsible oral toxin. All Y. pestis strains, including those phylogenetically closest to the Y. pseudotuberculosis progenitor, contain a mutated ureD allele that eliminated urease activity. Restoration of a functional ureD was sufficient to make Y. pestis orally toxic to fleas. Conversely, deletion of the urease operon in Y. pseudotuberculosis rendered it nontoxic. Enzymatic activity was required for toxicity. Because urease-related mortality eliminates 30–40% of infective flea vectors, ureD mutation early in the evolution of Y. pestis was likely subject to strong positive selection because it significantly increased transmission potential. PMID:25453069

Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution.

PubMed

Medina-Carmona, Encarnación; Fuchs, Julian E; Gavira, Jose A; Mesa-Torres, Noel; Neira, Jose L; Salido, Eduardo; Palomino-Morales, Rogelio; Burgos, Miguel; Timson, David J; Pey, Angel L

2017-09-15

Human proteins are vulnerable towards disease-associated single amino acid replacements affecting protein stability and function. Interestingly, a few studies have shown that consensus amino acids from mammals or vertebrates can enhance protein stability when incorporated into human proteins. Here, we investigate yet unexplored relationships between the high vulnerability of human proteins towards disease-associated inactivation and recent evolutionary site-specific divergence of stabilizing amino acids. Using phylogenetic, structural and experimental analyses, we show that divergence from the consensus amino acids at several sites during mammalian evolution has caused local protein destabilization in two human proteins linked to disease: cancer-associated NQO1 and alanine:glyoxylate aminotransferase, mutated in primary hyperoxaluria type I. We demonstrate that a single consensus mutation (H80R) acts as a disease suppressor on the most common cancer-associated polymorphism in NQO1 (P187S). The H80R mutation reactivates P187S by enhancing FAD binding affinity through local and dynamic stabilization of its binding site. Furthermore, we show how a second suppressor mutation (E247Q) cooperates with H80R in protecting the P187S polymorphism towards inactivation through long-range allosteric communication within the structural ensemble of the protein. Our results support that recent divergence of consensus amino acids may have occurred with neutral effects on many functional and regulatory traits of wild-type human proteins. However, divergence at certain sites may have increased the propensity of some human proteins towards inactivation due to disease-associated mutations and polymorphisms. Consensus mutations also emerge as a potential strategy to identify structural hot-spots in proteins as targets for pharmacological rescue in loss-of-function genetic diseases. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

High power tapered lasers with optimized photonic crystal structure for low divergence and high efficiency

NASA Astrophysics Data System (ADS)

Ma, Xiaolong; Qu, Hongwei; Qi, Aiyi; Zhou, Xuyan; Ma, Pijie; Liu, Anjin; Zheng, Wanhua

2018-04-01

High power tapered lasers are designed and fabricated. A one-dimensional photonic crystal structure in the vertical direction is adopted to narrow the far field divergence. The thickness of the defect layer and the photonic crystal layers are optimized by analyzing the optical field theoretically. For tapered lasers, the continuous-wave power is 7.3 W and the pulsed power is 17 W. A maximum wall-plug efficiency of 46% under continuous-wave operation and 49.3% in pulsed mode are obtained. The beam divergences are around 11° and 6° for the vertical and lateral directions, respectively. High beam qualities are also obtained with a vertical M2 value of 1.78 and a lateral M2 value of 1.62. As the current increases, the lateral M2 value increases gradually while the vertical M2 value remains around 2.

Divergence of perturbation theory in large scale structures

NASA Astrophysics Data System (ADS)

Pajer, Enrico; van der Woude, Drian

2018-05-01

We make progress towards an analytical understanding of the regime of validity of perturbation theory for large scale structures and the nature of some non-perturbative corrections. We restrict ourselves to 1D gravitational collapse, for which exact solutions before shell crossing are known. We review the convergence of perturbation theory for the power spectrum, recently proven by McQuinn and White [1], and extend it to non-Gaussian initial conditions and the bispectrum. In contrast, we prove that perturbation theory diverges for the real space two-point correlation function and for the probability density function (PDF) of the density averaged in cells and all the cumulants derived from it. We attribute these divergences to the statistical averaging intrinsic to cosmological observables, which, even on very large and "perturbative" scales, gives non-vanishing weight to all extreme fluctuations. Finally, we discuss some general properties of non-perturbative effects in real space and Fourier space.

Genetic structuring of European anchovy (Engraulis encrasicolus) populations through mitochondrial DNA sequences.

PubMed

Keskin, Emre; Atar, Hasan Huseyin

2012-04-01

Mitochondrial DNA sequence variation in 655 bpfragments of the cytochrome oxidase c subunit I gene, known as the DNA barcode, of European anchovy (Engraulis encrasicolus) was evaluated by analyzing 1529 individuals representing 16 populations from the Black Sea, through the Marmara Sea and the Aegean Sea to the Mediterranean Sea. A total of 19 (2.9%) variable sites were found among individuals, and these defined 10 genetically diverged populations with an overall mean distance of 1.2%. The highest nucleotide divergence was found between samples of eastern Mediterranean and northern Aegean (2.2%). Evolutionary history analysis among 16 populations clustered the Mediterranean Sea clades in one main branch and the other clades in another branch. Diverging pattern of the European anchovy populations correlated with geographic dispersion supports the genetic structuring through the Black Sea-Marmara Sea-Aegean Sea-Mediterranean Sea quad.

Waveguide and active region structure optimization for low-divergence InAs/InGaAs quantum dot comb lasers

NASA Astrophysics Data System (ADS)

Korenev, Vladimir V.; Savelyev, Artem V.; Zhukov, Alexey E.; Maximov, Mikhail V.; Omelchenko, Alexander V.

2015-05-01

Ways to improve beam divergence and energy consumption of quantum dot lasers emitting via the ground-state optical transitions by optimization of the key parameters of laser active region are discussed. It is shown that there exist an optimal cavity length, dispersion of inhomogeneous broadening and number of QD layers in active region allowing to obtain lasing spectrum of a given width at minimum injection current. The planar dielectric waveguide of the laser is optimized by analytical means for a better trade-off between high Γ-factor and low beam divergence.

Optimization of structures to satisfy aeroelastic requirements

NASA Technical Reports Server (NTRS)

Rudisill, C. S.

1975-01-01

A method for the optimization of structures to satisfy flutter velocity constraints is presented along with a method for determining the flutter velocity. A method for the optimization of structures to satisfy divergence velocity constraints is included.

Resilience of biochemical activity in protein domains in the face of structural divergence.

PubMed

Zhang, Dapeng; Iyer, Lakshminarayan M; Burroughs, A Maxwell; Aravind, L

2014-06-01

Recent studies point to the prevalence of the evolutionary phenomenon of drastic structural transformation of protein domains while continuing to preserve their basic biochemical function. These transformations span a wide spectrum, including simple domains incorporated into larger structural scaffolds, changes in the structural core, major active site shifts, topological rewiring and extensive structural transmogrifications. Proteins from biological conflict systems, such as toxin-antitoxin, restriction-modification, CRISPR/Cas, polymorphic toxin and secondary metabolism systems commonly display such transformations. These include endoDNases, metal-independent RNases, deaminases, ADP ribosyltransferases, immunity proteins, kinases and E1-like enzymes. In eukaryotes such transformations are seen in domains involved in chromatin-related peptide recognition and protein/DNA-modification. Intense selective pressures from 'arms-race'-like situations in conflict and macromolecular modification systems could favor drastic structural divergence while preserving function. Published by Elsevier Ltd.

Functional and evolutionary relationships between bacteriorhodopsin and halorhodopsin in the archaebacterium, halobacterium halobium

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1986-01-01

The archaebacteria occupy a unique place in phylogenetic trees constructed from analyses of sequences from key informational macromolecules, and their study continues to yield interesting ideas on the early evolution and divergence of biological forms. It is now known that the halobacteria among these species contain various retinal-proteins, resembling eukaryotic rhodopsins, but with different functions. Two of these pigments, located in the cytoplasmic membranes of the bacteria, are bacteriorhodopsin (a light-driven proton pump) and halorhodopsin (a light-driven chloride pump). Comparison of these systems is expected to reveal structure/function relationships in these simple (primitive?) energy transducing membrane components and evolutionary relationships which had produced the structural features which allow the divergent functions. Findings indicate that very different primary structures are needed for these proteins to accomplish their different functions. Indeed, analysis of partial amino acid sequences from halo-opsin shows already that few if any long segments exist which are homologous to bacterio-opsin. Either these proteins diverged a very long time ago to allow for the observed differences, or the evolutionary clock in the halobacteria runs faster than usual.

Critical analysis of the discrepancy between V(beta) and V(ss) for drugs exhibiting different two-compartment disposition profiles.

PubMed

Sobol, Eyal; Bialer, Meir

2005-03-01

It is well known that in the two-compartment open body model the values of apparent volume of distribution (V(beta)) and volume of distribution at steady state (V(ss)) are never identical. There are at least two conditions when V(beta) significantly overestimates V(ss). The first is when most of a drug is eliminated relatively rapidly but a small fraction of the dose persists and gives rise to an extremely long half-life. The second is when a drug is rapidly cleared from the central compartment with a short half-life. The primary purpose of the current paper was to investigate how different two-compartment disposition profiles affect the magnitude of difference between V(beta) and V(ss). Novel equations have been developed that relate the V(beta)/V(ss) ratio to f1 (fraction of drug elimination associated with the distributive phase) and to beta/alpha (ratio of the exponential coefficients). This paper demonstrates mathematically that an increasing value of f1 is associated with a greater divergence between V(beta) and V(ss). A similar relationship was also found for the divergence between the terminal half-life (t(1/2beta)) and the mean residence time (MRT). An increase in the beta/alpha ratio results in a substantial decrease of this discrepancy and provides a maximal possible value, or an upper limit to the V(beta)/V(ss) ratio. The newly derived equations along with their graphical presentation may serve as an excellent predictive tool for checking the accuracy of the experimentally obtained values of V(beta) and V(ss). Copyright 2004 John Wiley & Sons, Ltd.

Problems of allometric scaling analysis: examples from mammalian reproductive biology.

PubMed

Martin, Robert D; Genoud, Michel; Hemelrijk, Charlotte K

2005-05-01

Biological scaling analyses employing the widely used bivariate allometric model are beset by at least four interacting problems: (1) choice of an appropriate best-fit line with due attention to the influence of outliers; (2) objective recognition of divergent subsets in the data (allometric grades); (3) potential restrictions on statistical independence resulting from phylogenetic inertia; and (4) the need for extreme caution in inferring causation from correlation. A new non-parametric line-fitting technique has been developed that eliminates requirements for normality of distribution, greatly reduces the influence of outliers and permits objective recognition of grade shifts in substantial datasets. This technique is applied in scaling analyses of mammalian gestation periods and of neonatal body mass in primates. These analyses feed into a re-examination, conducted with partial correlation analysis, of the maternal energy hypothesis relating to mammalian brain evolution, which suggests links between body size and brain size in neonates and adults, gestation period and basal metabolic rate. Much has been made of the potential problem of phylogenetic inertia as a confounding factor in scaling analyses. However, this problem may be less severe than suspected earlier because nested analyses of variance conducted on residual variation (rather than on raw values) reveals that there is considerable variance at low taxonomic levels. In fact, limited divergence in body size between closely related species is one of the prime examples of phylogenetic inertia. One common approach to eliminating perceived problems of phylogenetic inertia in allometric analyses has been calculation of 'independent contrast values'. It is demonstrated that the reasoning behind this approach is flawed in several ways. Calculation of contrast values for closely related species of similar body size is, in fact, highly questionable, particularly when there are major deviations from the best-fit line for the scaling relationship under scrutiny.

A novel mitochondrial genome of Arborophila and new insight into Arborophila evolutionary history.

PubMed

Yan, Chaochao; Mou, Biqin; Meng, Yang; Tu, Feiyun; Fan, Zhenxin; Price, Megan; Yue, Bisong; Zhang, Xiuyue

2017-01-01

The lineage of the Bar-backed Partridge (Arborophila brunneopectus) was investigated to determine the phylogenetic relationships within Arborophila as the species is centrally distributed within an area covered by the distributions of 22 South-east Asian hill partridge species. The complete mitochondrial genome (mitogenome) of A. brunneopectus was determined and compared with four other hill partridge species mitogenomes. NADH subunit genes are radical in hill partridge mitogenomes and contain the most potential positive selective sites around where variable sites are abundant. Together with 44 other mitogenomes of closely related species, we reconstructed highly resolved phylogenetic trees using maximum likelihood (ML) and Bayesian inference (BI) analyses and calculated the divergence and dispersal history of Arborophila using combined datasets composed of their 13-protein coding sequences. Arborophila is reportedly be the oldest group in Phasianidae whose ancestors probably originated in Asia. A. rufipectus shares a closer relationship with A. ardens and A. brunneopectus compared to A. gingica and A. rufogularis, and such relationships were supported and profiled by NADH dehydrogenase subunit 5 (ND5). The intragenus divergence of all five Arborophila species occurred in the Miocene (16.84~5.69 Mya) when there were periods of climate cooling. We propose that these cooling events in the Miocene forced hill partridges from higher to lower altitudes, which led to geographic isolation and speciation. We demonstrated that the apparently deleterious +1 frameshift mutation in NADH dehydrogenase subunit 3 (ND3) found in all Arborophila is an ancient trait that has been eliminated in some younger lineages, such as Passeriformes. It is unclear of the biological advantages of this elimination for the relevant taxa and this requires further investigation.

Comparative evolution of flower and fruit morphology

PubMed Central

Whitney, Kenneth D.

2009-01-01

Angiosperm diversification has resulted in a vast array of plant morphologies. Only recently has it been appreciated that diversification might have proceeded quite differently for the two key diagnostic structures of this clade, flowers and fruits. These structures are hypothesized to have experienced different selective pressures via their interactions with animals in dispersal mutualisms, resulting in a greater amount of morphological diversification in animal-pollinated flowers than in animal-dispersed fruits. I tested this idea using size and colour traits for the flowers and fruits of 472 species occurring in three floras (St John, Hawaii and the Great Plains). Phylogenetically controlled analyses of nearest-neighbour distances in multidimensional trait space matched the predicted pattern: in each of the three floras, flowers were more divergent from one another than were fruits. In addition, the spacing of species clusters differed for flowers versus fruits in the flora of St John, with clusters in flower space more divergent than those in fruit space. The results are consistent with the idea that a major driver of angiosperm diversification has been stronger selection for divergent floral morphology than for divergent fruit morphology, although genetic, physiological and ecological constraints may also play a role. PMID:19474045

Facile construction of structurally diverse thiazolidinedione-derived compounds via divergent stereoselective cascade organocatalysis and their biological exploratory studies.

PubMed

Zhang, Yongqiang; Wang, Shengzheng; Wu, Shanchao; Zhu, Shiping; Dong, Guoqiang; Miao, Zhenyuan; Yao, Jianzhong; Zhang, Wannian; Sheng, Chunquan; Wang, Wei

2013-06-10

In this article, we present a new approach by merging two powerful synthetic tactics, divergent synthesis and cascade organocatalysis, to create a divergent cascade organocatalysis strategy for the facile construction of new "privileged" substructure-based DOS (pDOS) library. As demonstrated, notably 5 distinct molecular architectures are produced facilely from readily available simple synthons thiazolidinedione and its analogues and α,β-unsaturated aldehydes in 1-3 steps with the powerful strategy. The beauty of the chemistry is highlighted by the efficient formation of structurally new and diverse products from structurally close reactants under the similar reaction conditions. Notably, structurally diverse spiro-thiazolidinediones and -rhodanines are produced from organocatalytic enantioselective 3-component Michael-Michael-aldol cascade reactions of respective thiazolidinediones and rhodanines with enals. Nevertheless, under the similar reaction conditions, reactions of isorhodanine via a Michael-cyclization cascade lead to structurally different fused thiopyranoid scaffolds. This strategy significantly minimizes time- and cost-consuming synthetic works. Furthermore, these molecules possess high structural complexity and functional, stereochemical, and skeletal diversity with similarity to natural scaffolds. In the preliminary biological studies of these molecules, compounds 4f, 8a, and 10a exhibit inhibitory activity against the human breast cancer cells, while compounds 8a, 9a, and 9b display good antifungal activities against Candida albicans and Cryptococcus neoformans. Notably, their structures are different from clinically used triazole antifungal drugs. Therefore, they could serve as good lead compounds for the development of new generation of antifungal agents.

Phenotypic and Genetic Divergence among Poison Frog Populations in a Mimetic Radiation

PubMed Central

Twomey, Evan; Yeager, Justin; Brown, Jason Lee; Morales, Victor; Cummings, Molly; Summers, Kyle

2013-01-01

The evolution of Müllerian mimicry is, paradoxically, associated with high levels of diversity in color and pattern. In a mimetic radiation, different populations of a species evolve to resemble different models, which can lead to speciation. Yet there are circumstances under which initial selection for divergence under mimicry may be reversed. Here we provide evidence for the evolution of extensive phenotypic divergence in a mimetic radiation in Ranitomeya imitator, the mimic poison frog, in Peru. Analyses of color hue (spectral reflectance) and pattern reveal substantial divergence between morphs. However, we also report that there is a “transition-zone” with mixed phenotypes. Analyses of genetic structure using microsatellite variation reveals some differentiation between populations, but this does not strictly correspond to color pattern divergence. Analyses of gene flow between populations suggest that, while historical levels of gene flow were low, recent levels are high in some cases, including substantial gene flow between some color pattern morphs. We discuss possible explanations for these observations. PMID:23405150

Climatic drivers of leaf traits and genetic divergence in the tree Annona crassiflora: a broad spatial survey in the Brazilian savannas.

PubMed

Ribeiro, Priciane C; Souza, Matheus L; Muller, Larissa A C; Ellis, Vincenzo A; Heuertz, Myriam; Lemos-Filho, José P; Lovato, Maria Bernadete

2016-11-01

The Cerrado is the largest South American savanna and encompasses substantial species diversity and environmental variation. Nevertheless, little is known regarding the influence of the environment on population divergence of Cerrado species. Here, we searched for climatic drivers of genetic (nuclear microsatellites) and leaf trait divergence in Annona crassiflora, a widespread tree in the Cerrado. The sampling encompassed all phytogeographic provinces of the continuous area of the Cerrado and included 397 individuals belonging to 21 populations. Populations showed substantial genetic and leaf trait divergence across the species' range. Our data revealed three spatially defined genetic groups (eastern, western and southern) and two morphologically distinct groups (eastern and western only). The east-west split in both the morphological and genetic data closely mirrors previously described phylogeographic patterns of Cerrado species. Generalized linear mixed effects models and multiple regression analyses revealed several climatic factors associated with both genetic and leaf trait divergence among populations of A. crassiflora. Isolation by environment (IBE) was mainly due to temperature seasonality and precipitation of the warmest quarter. Populations that experienced lower precipitation summers and hotter winters had heavier leaves and lower specific leaf area. The southwestern area of the Cerrado had the highest genetic diversity of A. crassiflora, suggesting that this region may have been climatically stable. Overall, we demonstrate that a combination of current climate and past climatic changes have shaped the population divergence and spatial structure of A. crassiflora. However, the genetic structure of A. crassiflora reflects the biogeographic history of the species more strongly than leaf traits, which are more related to current climate. © 2016 John Wiley & Sons Ltd.

Tracing early stages of species differentiation: Ecological, morphological and genetic divergence of Galápagos sea lion populations

PubMed Central

2008-01-01

Background Oceans are high gene flow environments that are traditionally believed to hamper the build-up of genetic divergence. Despite this, divergence appears to occur occasionally at surprisingly small scales. The Galápagos archipelago provides an ideal opportunity to examine the evolutionary processes of local divergence in an isolated marine environment. Galápagos sea lions (Zalophus wollebaeki) are top predators in this unique setting and have an essentially unlimited dispersal capacity across the entire species range. In theory, this should oppose any genetic differentiation. Results We find significant ecological, morphological and genetic divergence between the western colonies and colonies from the central region of the archipelago that are exposed to different ecological conditions. Stable isotope analyses indicate that western animals use different food sources than those from the central area. This is likely due to niche partitioning with the second Galápagos eared seal species, the Galápagos fur seal (Arctocephalus galapagoensis) that exclusively dwells in the west. Stable isotope patterns correlate with significant differences in foraging-related skull morphology. Analyses of mitochondrial sequences as well as microsatellites reveal signs of initial genetic differentiation. Conclusion Our results suggest a key role of intra- as well as inter-specific niche segregation in the evolution of genetic structure among populations of a highly mobile species under conditions of free movement. Given the monophyletic arrival of the sea lions on the archipelago, our study challenges the view that geographical barriers are strictly needed for the build-up of genetic divergence. The study further raises the interesting prospect that in social, colonially breeding mammals additional forces, such as social structure or feeding traditions, might bear on the genetic partitioning of populations. PMID:18485220

Nearly complete rRNA genes assembled from across the metazoan animals: effects of more taxa, a structure-based alignment, and paired-sites evolutionary models on phylogeny reconstruction.

PubMed

Mallatt, Jon; Craig, Catherine Waggoner; Yoder, Matthew J

2010-04-01

This study (1) uses nearly complete rRNA-gene sequences from across Metazoa (197 taxa) to reconstruct animal phylogeny; (2) presents a highly annotated, manual alignment of these sequences with special reference to rRNA features including paired sites (http://purl.oclc.org/NET/rRNA/Metazoan_alignment) and (3) tests, after eliminating as few disruptive, rogue sequences as possible, if a likelihood framework can recover the main metazoan clades. We found that systematic elimination of approximately 6% of the sequences, including the divergent or unstably placed sequences of cephalopods, arrowworm, symphylan and pauropod myriapods, and of myzostomid and nemertodermatid worms, led to a tree that supported Ecdysozoa, Lophotrochozoa, Protostomia, and Bilateria. Deuterostomia, however, was never recovered, because the rRNA of urochordates goes (nonsignificantly) near the base of the Bilateria. Counterintuitively, when we modeled the evolution of the paired sites, phylogenetic resolution was not increased over traditional tree-building models that assume all sites in rRNA evolve independently. The rRNA genes of non-bilaterians contain a higher % AT than do those of most bilaterians. The rRNA genes of Acoela and Myzostomida were found to be secondarily shortened, AT-enriched, and highly modified, throwing some doubt on the location of these worms at the base of Bilateria in the rRNA tree--especially myzostomids, which other evidence suggests are annelids instead. Other findings are marsupial-with-placental mammals, arrowworms in Ecdysozoa (well supported here but contradicted by morphology), and Placozoa as sister to Cnidaria. Finally, despite the difficulties, the rRNA-gene trees are in strong concordance with trees derived from multiple protein-coding genes in supporting the new animal phylogeny. (c) 2009 Elsevier Inc. All rights reserved.

Sexual selection and the evolution of secondary sexual traits: sex comb evolution in Drosophila.

PubMed

Snook, Rhonda R; Gidaszewski, Nelly A; Chapman, Tracey; Simmons, Leigh W

2013-04-01

Sexual selection can drive rapid evolutionary change in reproductive behaviour, morphology and physiology. This often leads to the evolution of sexual dimorphism, and continued exaggerated expression of dimorphic sexual characteristics, although a variety of other alternative selection scenarios exist. Here, we examined the evolutionary significance of a rapidly evolving, sexually dimorphic trait, sex comb tooth number, in two Drosophila species. The presence of the sex comb in both D. melanogaster and D. pseudoobscura is known to be positively related to mating success, although little is yet known about the sexually selected benefits of sex comb structure. In this study, we used experimental evolution to test the idea that enhancing or eliminating sexual selection would lead to variation in sex comb tooth number. However, the results showed no effect of either enforced monogamy or elevated promiscuity on this trait. We discuss several hypotheses to explain the lack of divergence, focussing on sexually antagonistic coevolution, stabilizing selection via species recognition and nonlinear selection. We discuss how these are important, but relatively ignored, alternatives in understanding the evolution of rapidly evolving sexually dimorphic traits. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Dissecting the relationship between protein structure and sequence variation

NASA Astrophysics Data System (ADS)

Shahmoradi, Amir; Wilke, Claus; Wilke Lab Team

2015-03-01

Over the past decade several independent works have shown that some structural properties of proteins are capable of predicting protein evolution. The strength and significance of these structure-sequence relations, however, appear to vary widely among different proteins, with absolute correlation strengths ranging from 0 . 1 to 0 . 8 . Here we present the results from a comprehensive search for the potential biophysical and structural determinants of protein evolution by studying more than 200 structural and evolutionary properties in a dataset of 209 monomeric enzymes. We discuss the main protein characteristics responsible for the general patterns of protein evolution, and identify sequence divergence as the main determinant of the strengths of virtually all structure-evolution relationships, explaining ~ 10 - 30 % of observed variation in sequence-structure relations. In addition to sequence divergence, we identify several protein structural properties that are moderately but significantly coupled with the strength of sequence-structure relations. In particular, proteins with more homogeneous back-bone hydrogen bond energies, large fractions of helical secondary structures and low fraction of beta sheets tend to have the strongest sequence-structure relation. BEACON-NSF center for the study of evolution in action.

Isolation driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae)

PubMed Central

Manthey, Joseph D.; Klicka, John; Spellman, Garth M.

2011-01-01

Lineage, or true “species,” trees may differ from gene trees because of stochastic processes in molecular evolution leading to gene-tree heterogeneity. Problems with inferring species trees due to excessive incomplete lineage sorting may be exacerbated in lineages with rapid diversification or recent divergences necessitating the use of multiple loci and individuals. Many recent multilocus studies that investigate divergence times identify lineage splitting to be more recent than single locus studies, forcing the revision of biogeographic scenarios driving divergence. Here we use 21 nuclear loci from regional populations to reevaluate hypotheses identified in an mtDNA phylogeographic study of the Brown Creeper (Certhia americana), as well as identify processes driving divergence. Nuclear phylogeographic analyses identified hierarchical genetic structure, supporting a basal split at roughly 32°N latitude, splitting northern and southern populations, with mixed patterns of genealogical concordance and discordance between datasets within the major lineages. Coalescent-based analyses identify isolation, with little to no gene flow, as the primary driver of divergence between lineages. Recent isolation appears to have caused genetic bottlenecks in populations in the Sierra Madre Oriental and coastal mountain ranges of California, which may be targets for conservation concerns. PMID:21933295

Divergent morphological and acoustic traits in sympatric communities of Asian barbets

PubMed Central

Tamma, Krishnapriya

2016-01-01

The opposing effects of environmental filtering and competitive interactions may influence community assembly and coexistence of related species. Competition, both in the domain of ecological resources, and in the sensory domain (for example, acoustic interference) may also result in sympatric species evolving divergent traits and niches. Delineating these scenarios within communities requires understanding trait distributions and phylogenetic structure within the community, as well as patterns of trait evolution. We report that sympatric assemblages of Asian barbets (frugivorous canopy birds) consist of a random phylogenetic sample of species, but are divergent in both morphological and acoustic traits. Additionally, we find that morphology is more divergent than expected under Brownian evolution, whereas vocal frequency evolution is close to the pattern expected under Brownian motion (i.e. a random walk). Together, these patterns are consistent with a role for competition or competitive exclusion in driving community assembly. Phylogenetic patterns of morphological divergence between related species suggest that these traits are key in species coexistence. Because vocal frequency and size are correlated in barbets, we therefore hypothesize that frequency differences between sympatric barbets are a by-product of their divergent morphologies. PMID:27853589

The Influence of Building Block Play on Mathematics Achievement and Logical and Divergent Thinking in Italian Primary School Mathematics Classes

ERIC Educational Resources Information Center

Pirrone, Concetta; Tienken, Christopher H.; Pagano, Tatiana; Di Nuovo, Santo

2018-01-01

In an experimental study to explain the effect of structured Building Block Play with LEGO™ bricks on 6-year-old student mathematics achievement and in the areas of logical thinking, divergent thinking, nonverbal reasoning, and mental imagery, students in the experimental group scored significantly higher (p = 0.05) in mathematics achievement and…

Numerical simulation of current-free double layers created in a helicon plasma device

NASA Astrophysics Data System (ADS)

Rao, Sathyanarayan; Singh, Nagendra

2012-09-01

Two-dimensional simulations reveal that when radially confined source plasma with magnetized electrons and unmagnetized ions expands into diverging magnetic field B, a current-free double layer (CFDL) embedded in a conical density structure forms, as experimentally measured in the Australian helicon plasma device (HPD). The magnetized electrons follow the diverging B while the unmagnetized ions tend to flow directly downstream of the source, resulting in a radial electric field (E⊥) structure, which couples the ion and electron flows. Ions are transversely (radially) accelerated by E⊥ on the high potential side of the double layer in the CFDL. The accelerated ions are trapped near the conical surface, where E⊥ reverses direction. The potential structure of the CFDL is U-shaped and the plasma density is enhanced on the conical surface. The plasma density is severely depleted downstream of the parallel potential drop (φ||o) in the CFDL; the density depletion and the potential drop are related by quasi-neutrality condition, including the divergence in the magnetic field and in the plasma flow in the conical structure. The potential and density structures, the CFDL spatial size, its electric field strengths and the electron and ion velocities and energy distributions in the CFDL are found to be in good agreements with those measured in the Australian experiment. The applicability of our results to measured axial potential profiles in magnetic nozzle experiments in HPDs is discussed.

Genetic divergence of common bean cultivars.

PubMed

Veloso, J S; Silva, W; Pinheiro, L R; Dos Santos, J B; Fonseca, N S; Euzebio, M P

2015-09-22

The aim of this study was to evaluate genetic divergence in the 'Carioca' (beige with brown stripes) common bean cultivar used by different institutions and in 16 other common bean cultivars used in the Rede Cooperativa de Pesquisa de Feijão (Cooperative Network of Common Bean Research), by using simple sequence repeats associated with agronomic traits that are highly distributed in the common bean genome. We evaluated 22 polymorphic loci using bulks containing DNA from 30 plants. There was genetic divergence among the Carioca cultivar provided by the institutions. Nevertheless, there was lower divergence among them than among the other cultivars. The cultivar used by Instituto Agronômico do Paraná was the most divergent in relation to the Carioca samples. The least divergence was observed among the samples used by Universidade Federal de Lavras and by Embrapa Arroz e Feijão. Of all the cultivars, 'CNFP 10104' and 'BRSMG Realce' showed the greatest dissimilarity. The cultivars were separated in two groups of greatest similarity using the Structure software. Genetic variation among cultivars was greater than the variation within or between the groups formed. This fact, together with the high estimate of heterozygosity observed and the genetic divergence of the samples of the Carioca cultivar in relation to the original provided by Instituto Agronômico de Campinas, indicates a mixture of cultivars. The high divergence among cultivars provides potential for the utilization of this genetic variability in plant breeding.

Genetic structure and demographic history of the endangered and endemic schizothoracine fish Gymnodiptychus pachycheilus in Qinghai-Tibetan Plateau.

PubMed

Su, Junhu; Ji, Weihong; Wei, Yanming; Zhang, Yanping; Gleeson, Dianne M; Lou, Zhongyu; Ren, Jing

2014-08-01

The endangered schizothoracine fish Gymnodiptychus pachycheilus is endemic to the Qinghai-Tibetan Plateau (QTP), but very little genetic information is available for this species. Here, we accessed the current genetic divergence of G. pachycheilus population to evaluate their distributions modulated by contemporary and historical processes. Population structure and demographic history were assessed by analyzing 1811-base pairs of mitochondrial DNA from 61 individuals across a large proportion of its geographic range. Our results revealed low nucleotide diversity, suggesting severe historical bottleneck events. Analyses of molecular variance and the conventional population statistic FST (0.0435, P = 0.0215) confirmed weak genetic structure. The monophyly of G. pachycheilus was statistically well-supported, while two divergent evolutionary clusters were identified by phylogenetic analyses, suggesting a microgeographic population structure. The consistent scenario of recent population expansion of two clusters was identified based on several complementary analyses of demographic history (0.096 Ma and 0.15 Ma). This genetic divergence and evolutionary process are likely to have resulted from a series of drainage arrangements triggered by the historical tectonic events of the region. The results obtained here provide the first insights into the evolutionary history and genetic status of this little-known fish.

Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation.

PubMed

Ochoa, Luz Eneida; Pereira, Luiz Henrique G; Costa-Silva, Guilherme Jose; Roxo, Fábio F; Batista, Jacqueline S; Formiga, Kyara; Foresti, Fausto; Oliveira, Claudio

2015-05-01

Brachyplatystoma platynemum is a catfish species widely distributed in the Amazon basin. Despite being considered of little commercial interest, the decline in other fish populations has contributed to the increase in the catches of this species. The structure, population genetic variability, and evolutionary process that have driven the diversification of this species are presently unknown. Considering that, in order to better understand the genetic structure of this species, we analyzed individuals from seven locations of the Amazon basin using eight molecular markers: control region and cytochrome b mtDNA sequences, and a set of six nuclear microsatellite loci. The results show high levels of haplotype diversity and point to the occurrence of two structured populations (Amazon River and the Madeira River) with high values for F ST. Divergence time estimates based on mtDNA indicated that these populations diverged about 1.0 Mya (0.2-2.5 Mya 95% HPD) using cytochrome b and 1.4 Mya (0.2-2.7 Mya 95% HPD) using control region. During that time, the influence of climate changes and hydrological events such as sea level oscillations and drainage isolation as a result of geological processes in the Pleistocene may have contributed to the current structure of B. platynemum populations, as well as of differences in water chemistry in Madeira River. The strong genetic structure and the time of genetic divergence estimated for the groups may indicate the existence of strong structure populations of B. platynemum in the Amazon basin.

Genetic structure and historical diversification of catfish Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with implications for its conservation

PubMed Central

Ochoa, Luz Eneida; Pereira, Luiz Henrique G; Costa-Silva, Guilherme Jose; Roxo, Fábio F; Batista, Jacqueline S; Formiga, Kyara; Foresti, Fausto; Oliveira, Claudio

2015-01-01

Brachyplatystoma platynemum is a catfish species widely distributed in the Amazon basin. Despite being considered of little commercial interest, the decline in other fish populations has contributed to the increase in the catches of this species. The structure, population genetic variability, and evolutionary process that have driven the diversification of this species are presently unknown. Considering that, in order to better understand the genetic structure of this species, we analyzed individuals from seven locations of the Amazon basin using eight molecular markers: control region and cytochrome b mtDNA sequences, and a set of six nuclear microsatellite loci. The results show high levels of haplotype diversity and point to the occurrence of two structured populations (Amazon River and the Madeira River) with high values for FST. Divergence time estimates based on mtDNA indicated that these populations diverged about 1.0 Mya (0.2–2.5 Mya 95% HPD) using cytochrome b and 1.4 Mya (0.2–2.7 Mya 95% HPD) using control region. During that time, the influence of climate changes and hydrological events such as sea level oscillations and drainage isolation as a result of geological processes in the Pleistocene may have contributed to the current structure of B. platynemum populations, as well as of differences in water chemistry in Madeira River. The strong genetic structure and the time of genetic divergence estimated for the groups may indicate the existence of strong structure populations of B. platynemum in the Amazon basin. PMID:26045952

Interaction between central volcanoes and regional tectonics along divergent plate boundaries: Askja, Iceland

NASA Astrophysics Data System (ADS)

Trippanera, Daniele; Ruch, Joël; Acocella, Valerio; Thordarson, Thor; Urbani, Stefano

2018-01-01

Activity within magmatic divergent plate boundaries (MDPB) focuses along both regional fissure swarms and central volcanoes. An ideal place to investigate their mutual relationship is the Askja central volcano in Iceland. Askja consists of three nested calderas (namely Kollur, Askja and Öskjuvatn) located within a hyaloclastite massif along the NNE-SSW trending Icelandic MDPB. We performed an extensive field-based structural analysis supported by a remote sensing study of tectonic and volcanic features of Askja's calderas and of the eastern flank of the hyaloclastite massif. In the massif, volcano-tectonic structures trend N 10° E to N 40° E, but they vary around the Askja caldera being both parallel to the caldera rim and cross-cutting on the Western side. Structural trends around the Öskjuvatn caldera are typically rim parallel. Volcanic vents and dikes are preferentially distributed along the caldera ring faults; however, they follow the NNE-SSW regional structures when located outside the calderas. Our results highlight that the Askja volcano displays a balanced amount of regional (fissure-swarm related) and local (shallow-magma-chamber related) tectonic structures along with a mutual interaction among these. This is different from Krafla volcano (to the north of Askja) dominated by regional structures and Grímsvötn (to the South) dominated by local structures. Therefore, Askja represents an intermediate tectono-magmatic setting for volcanoes located in a slow divergent plate boundary. This is also likely in accordance with a northward increase in the spreading rate along the Icelandic MDPB.

Epigenetic differentiation and relationship to adaptive genetic divergence in discrete populations of the violet Viola cazorlensis.

PubMed

Herrera, Carlos M; Bazaga, Pilar

2010-08-01

*In plants, epigenetic variations based on DNA methylation are often heritable and could influence the course of evolution. Before this hypothesis can be assessed, fundamental questions about epigenetic variation remain to be addressed in a real-world context, including its magnitude, structuring within and among natural populations, and autonomy in relation to the genetic context. *Extent and patterns of cytosine methylation, and the relationship to adaptive genetic divergence between populations, were investigated for wild populations of the southern Spanish violet Viola cazorlensis (Violaceae) using the methylation-sensitive amplified polymorphism (MSAP) technique, a modification of the amplified fragment length polymorphism method (AFLP) based on the differential sensitivity of isoschizomeric restriction enzymes to site-specific cytosine methylation. *The genome of V. cazorlensis plants exhibited extensive levels of methylation, and methylation-based epigenetic variation was structured into distinct between- and within- population components. Epigenetic differentiation of populations was correlated with adaptive genetic divergence revealed by a Bayesian population-genomic analysis of AFLP data. Significant associations existed at the individual genome level between adaptive AFLP loci and the methylation state of methylation-susceptible MSAP loci. *Population-specific, divergent patterns of correlated selection on epigenetic and genetic individual variation could account for the coordinated epigenetic-genetic adaptive population differentiation revealed by this study.

More reliable estimates of divergence times in Pan using complete mtDNA sequences and accounting for population structure.

PubMed

Stone, Anne C; Battistuzzi, Fabia U; Kubatko, Laura S; Perry, George H; Trudeau, Evan; Lin, Hsiuman; Kumar, Sudhir

2010-10-27

Here, we report the sequencing and analysis of eight complete mitochondrial genomes of chimpanzees (Pan troglodytes) from each of the three established subspecies (P. t. troglodytes, P. t. schweinfurthii and P. t. verus) and the proposed fourth subspecies (P. t. ellioti). Our population genetic analyses are consistent with neutral patterns of evolution that have been shaped by demography. The high levels of mtDNA diversity in western chimpanzees are unlike those seen at nuclear loci, which may reflect a demographic history of greater female to male effective population sizes possibly owing to the characteristics of the founding population. By using relaxed-clock methods, we have inferred a timetree of chimpanzee species and subspecies. The absolute divergence times vary based on the methods and calibration used, but relative divergence times show extensive uniformity. Overall, mtDNA produces consistently older times than those known from nuclear markers, a discrepancy that is reduced significantly by explicitly accounting for chimpanzee population structures in time estimation. Assuming the human-chimpanzee split to be between 7 and 5 Ma, chimpanzee time estimates are 2.1-1.5, 1.1-0.76 and 0.25-0.18 Ma for the chimpanzee/bonobo, western/(eastern + central) and eastern/central chimpanzee divergences, respectively.

mRNA export in the apicomplexan parasite Toxoplasma gondii: emerging divergent components of a crucial pathway.

PubMed

Ávila, Andréa Rodrigues; Cabezas-Cruz, Alexjandro; Gissot, Mathieu

2018-01-25

Control of gene expression is crucial for parasite survival and is the result of a series of processes that are regulated to permit fine-tuning of gene expression in response to biological changes during the life-cycle of apicomplexan parasites. Control of mRNA nuclear export is a key process in eukaryotic cells but is poorly understood in apicomplexan parasites. Here, we review recent knowledge regarding this process with an emphasis on T. gondii. We describe the presence of divergent orthologs and discuss structural and functional differences in export factors between apicomplexans and other eukaryotic lineages. Undoubtedly, the use of the CRISPR/Cas9 system in high throughput screenings associated with the discovery of mRNA nuclear export complexes by proteomic analysis will contribute to identify these divergent factors. Ligand-based or structure-based strategies may be applied to investigate the potential use of these proteins as targets for new antiprotozoal agents.

Archimedean Voronoi spiral tilings

NASA Astrophysics Data System (ADS)

Yamagishi, Yoshikazu; Sushida, Takamichi

2018-01-01

We study the transition of the number of spirals (called parastichy in the theory of phyllotaxis) within a Voronoi tiling for Archimedean spiral lattices. The transition of local parastichy numbers within a tiling is regarded as a transition at the base site point in a continuous family of tilings. This gives a natural description of the quasiperiodic structure of the grain boundaries. It is proved that the number of tiles in the grain boundaries are denominators of rational approximations of the argument (called the divergence angle) of the generator. The local parastichy numbers are non-decreasing functions of the plastochron parameter. The bifurcation diagram of local parastichy numbers has a Farey tree structure. We also prove Richards’ formula of spiral phyllotaxis in the case of Archimedean Voronoi spiral tilings, and show that, if the divergence angle is a quadratic irrational number, then the shapes of tiles in the grain boundaries are close to rectangles. If the divergence angle is linearly equivalent to the golden section, then the shape of tiles in the grain boundaries is close to square.

Inter- and intra-specific genetic divergence of Asian tiger frogs (genus Hoplobatrachus), with special reference to the population structure of H. tigerinus in Bangladesh.

PubMed

Sultana, Nasrin; Igawa, Takeshi; Islam, Mohammed Mafizul; Hasan, Mahmudul; Alam, Mohammad Shafiqul; Komaki, Shohei; Kawamura, Kensuke; Khan, Md Mukhlesur Rahman; Sumida, Masayuki

2017-03-17

The five frog species of the genus Hoplobatrachus are widely distributed in Asia and Africa, with Asia being considered the genus' origin. However, the evolutionary relationships of Asian Hoplobatrachus species remain ambiguous. Additionally, genetic diversity and fundamental differentiation processes within species have not been studied. We conducted molecular phylogenetic analysis on Asian Hoplobatrachus frogs and population genetic analysis on H. tigerinus in Bangladesh using the mitochondrial CYTB gene and 21 microsatellite markers. The resultant phylogenetic tree revealed monophyly in each species, notwithstanding the involvement of cryptic species in H. chinensis and H. tigerinus, which are evident from the higher genetic divergence between populations. Bayesian inference of population structure revealed genetic divergence between western and eastern H. tigerinus populations in Bangladesh, suggesting restricted gene flow caused by barriers posed by major rivers. However, genetic distances among populations were generally low. A discrete population is located in the low riverine delta region, which likely reflects long-distance dispersal. These results strongly suggest that the environment specific to this river system has maintained the population structure of H. tigerinus in this region.

Imprints from genetic drift and mutation imply relative divergence times across marine transition zones in a pan-European small pelagic fish (Sprattus sprattus).

PubMed

Limborg, M T; Hanel, R; Debes, P V; Ring, A K; André, C; Tsigenopoulos, C S; Bekkevold, D

2012-08-01

Geographic distributions of most temperate marine fishes are affected by postglacial recolonisation events, which have left complex genetic imprints on populations of marine species. This study investigated population structure and demographic history of European sprat (Sprattus sprattus L.) by combining inference from both mtDNA and microsatellite genetic markers throughout the species' distribution. We compared effects from genetic drift and mutation for both genetic markers in shaping genetic differentiation across four transition zones. Microsatellite markers revealed significant isolation by distance and a complex population structure across the species' distribution (overall θ(ST)=0.038, P<0.01). Across transition zones markers indicated larger effects of genetic drift over mutations in the northern distribution of sprat contrasting a stronger relative impact of mutation in the species' southern distribution in the Mediterranean region. These results were interpreted to reflect more recent divergence times between northern populations in accordance with previous findings. This study demonstrates the usefulness of comparing inference from different markers and estimators of divergence for phylogeographic and population genetic studies in species with weak genetic structure, as is the case in many marine species.

The genetic basis of developmental abnormalities in interpopulation hybrids of the moss Ceratodon purpureus.

PubMed

McDaniel, Stuart F; Willis, John H; Shaw, A Jonathan

2008-07-01

Divergent populations are intrinsically reproductively isolated when hybrids between them either fail to develop properly or do not produce viable offspring. Intrinsic isolation may result from Dobzhansky-Muller (DM) incompatibilities, in which deleterious interactions among genes or gene products lead to developmental problems or underdominant chromosome structure differences between the parents. These mechanisms can be tested by studying marker segregation patterns in a hybrid mapping population. Here we examine the genetic basis of abnormal development in hybrids between two geographically distant populations of the moss Ceratodon purpureus. Approximately half of the hybrid progeny exhibited a severely reduced growth rate in early gametophyte development. We identified four unlinked quantitative trait loci (QTL) that interacted asymmetrically to cause the abnormal development phenotype. This pattern is consistent with DM interactions. We also found an excess of recombination between three marker pairs in the abnormally developing progeny, relative to that estimated in the normal progeny. This suggests that structural differences in these regions contribute to hybrid breakdown. Two QTL coincided with inferred structural differences, consistent with recent theory suggesting that rearrangements may harbor population divergence alleles. These observations suggest that multiple complex genetic factors contribute to divergence among populations of C. purpureus.

Structural Plasticity of Helical Nanotubes Based on Coiled-Coil Assemblies

DOE PAGES

Egelman, Edward H.; Xu, C.; DiMaio, F.; ...

2015-01-22

Numerous instances can be seen in evolution in which protein quaternary structures have diverged while the sequences of the building blocks have remained fairly conserved. However, the path through which such divergence has taken place is usually not known. We have designed two synthetic 29-residue α-helical peptides, based on the coiled-coil structural motif, that spontaneously self-assemble into helical nanotubes in vitro. Using electron cryomicroscopy with a newly available direct electron detection capability, we can achieve near-atomic resolution of these thin structures. We show how conservative changes of only one or two amino acids result in dramatic changes in quaternary structure,more » in which the assemblies can be switched between two very different forms. This system provides a framework for understanding how small sequence changes in evolution can translate into very large changes in supramolecular structure, a phenomenon that may have significant implications for the de novo design of synthetic peptide assemblies.« less

Neopolyploidy and diversification in Heuchera grossulariifolia

PubMed Central

Oswald, Benjamin P.; Nuismer, Scott L.

2013-01-01

Newly formed polyploid lineages must contend with several obstacles to avoid extinction, including minority cytotype exclusion, competition, and inbreeding depression. If polyploidization results in immediate divergence of phenotypic characters these hurdles may be reduced and establishment made more likely. In addition, if polyploidization alters the phenotypic and genotypic associations between traits, i.e. the P and G matrices, polyploids may be able to explore novel evolutionary paths, facilitating their divergence and successful establishment. Here we report results from a study of the perennial plant Heuchera grossulariifolia in which the phenotypic divergence and changes in phenotypic and genotypic covariance matrices caused by neopolyploidization have been estimated. Our results reveal that polyploidization causes immediate divergence for traits relevant to establishment and results in significant changes in the structure of the phenotypic covariance matrix. In contrast, our results do not provide evidence that polyploidization results in immediate and substantial shifts in the genetic covariance matrix. PMID:21143472

Distinguishing molecular features and clinical characteristics of a putative new rhinovirus species, human rhinovirus C (HRV C).

PubMed

McErlean, Peter; Shackelton, Laura A; Andrews, Emily; Webster, Dale R; Lambert, Stephen B; Nissen, Michael D; Sloots, Theo P; Mackay, Ian M

2008-04-02

Human rhinoviruses (HRVs) are the most frequently detected pathogens in acute respiratory tract infections (ARTIs) and yet little is known about the prevalence, recurrence, structure and clinical impact of individual members. During 2007, the complete coding sequences of six previously unknown and highly divergent HRV strains were reported. To catalogue the molecular and clinical features distinguishing the divergent HRV strains, we undertook, for the first time, in silico analyses of all available polyprotein sequences and performed retrospective reviews of the medical records of cases in which variants of the prototype strain, HRV-QPM, had been detected. Genomic analyses revealed that the six divergent strains, residing within a clade we previously called HRV A2, had the shortest polyprotein of all picornaviruses investigated. Structure-based amino acid alignments identified conserved motifs shared among members of the genus Rhinovirus as well as substantive deletions and insertions unique to the divergent strains. Deletions mostly affected regions encoding proteins traditionally involved in antigenicity and serving as HRV and HEV receptor footprints. Because the HRV A2 strains cannot yet be cultured, we created homology models of predicted HRV-QPM structural proteins. In silico comparisons confirmed that HRV-QPM was most closely related to the major group HRVs. HRV-QPM was most frequently detected in infants with expiratory wheezing or persistent cough who had been admitted to hospital and required supplemental oxygen. It was the only virus detected in 65% of positive individuals. These observations contributed to an objective clinical impact ranging from mild to severe. The divergent strains did not meet classification requirements for any existing species of the genus Rhinovirus or Enterovirus. HRV A2 strains should be partitioned into at least one new species, putatively called Human rhinovirus C, populated by members detected with high frequency, from individuals with respiratory symptoms requiring hospital admission.

Modelling of Continental Lithosphere Breakup and Rifted Margin Formation in Response to an Upwelling Divergent Flow Field Incorporating a Temperature Dependent Rheology

NASA Astrophysics Data System (ADS)

Tymms, V. J.; Kusznir, N. J.

2005-05-01

We numerically model continental lithosphere deformation leading to breakup and sea floor spreading initiation in response to an imposed upwelling and divergent flow field applied to continental lithosphere and asthenosphere. The model is used to predict rifted continental margin lithosphere thinning and temperature structure. Model predictions are compared with observed rifted margin structure for four diverse case studies. Prior to application of the upwelling divergent flow field the continental lithosphere is undeformed with a uniform temperature gradient. The upwelling divergent flow field is defined kinematically using boundary conditions consisting of the upwelling velocity Vz at the divergence axis and the half divergence rate Vx . The resultant velocity field throughout the continuum is computed using finite element (FE) code incorporating a Newtonian temperature dependent rheology. The flow field is used to advect the continental lithosphere material and lithospheric and asthenospheric temperatures. Viscosity structure is hence modified and the velocities change correspondingly in a feedback loop. We find the kinematic boundary conditions Vz and Vx to be of first order importance. A high Vz/Vx (greater than10), corresponding to buoyancy assisted flow, leads to minimal mantle exhumation and a well defined continent ocean transition consistent with observations at volcanic margins. For Vz/Vx near unity, corresponding to plate boundary driven divergence, mantle exhumation over widths of up to 100 km is predicted which is consistent with observations at non-volcanic margins. The FE method allows the upwelling velocity Vz to be propagated upwards from the top of the asthenosphere to the Earth's surface without the requirement of imposing Vx. When continental breakup is achieved the half divergence velocity Vx can be applied at the lithosphere surface and the upwelling velocity Vz left free. We find this time and space dependent set of boundary conditions is more plausible than a constant corner flow type solution and predicts levels of depth dependent stretching and continent ocean transitions consistent with observation. Depth dependent lithosphere stretching, which is observed at rifted continental margins, is predicted to occur before continental breakup and sea-floor spreading initiation. The model may be used to predict surface heat flow and bathymetry, and to provide estimates of melt production rates and cumulative thickness. We compare model predictions with observed margin structure for four diverse rifted margins: the Lofoten Margin (a mature volcanic margin), Goban Spur (a mature non-volcanic margin), the Woodlark Basin (a neotectonic young ocean basin) and the Faroe-Shetland Basin (a failed attempt at continental breakup). This work forms part of the NERC Margins iSIMM project. iSIMM investigators are from Liverpool and Cambridge Universities, Badley Geoscience & Schlumberger Cambridge Research supported by the NERC, the DTI, Agip UK, BP, Amerada Hess Ltd, Anadarko, Conoco¬Phillips, Shell, Statoil and WesternGeco. The iSIMM team comprises NJ Kusznir, RS White, AM Roberts, PAF Christie, A Chappell, J Eccles, R Fletcher, D Healy, N Hurst, ZC Lunnon, CJ Parkin, AW Roberts, LK Smith, V Tymms & R Spitzer.

77 FR 34927 - National Pollutant Discharge Elimination System-Proposed Regulations To Establish Requirements...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-12

...-5] RIN 2040-AE95 National Pollutant Discharge Elimination System--Proposed Regulations To Establish Requirements for Cooling Water Intake Structures at Existing Facilities; Notice of Data Availability Related to... availability. SUMMARY: On April 20, 2011, EPA published proposed standards for cooling water intake structures...

The Relation between Gray Matter Morphology and Divergent Thinking in Adolescents and Young Adults

PubMed Central

Zanolie, Kiki; Kleibeuker, Sietske W.; Crone, Eveline A.

2014-01-01

Adolescence and early adulthood are developmental time periods during which creative cognition is highly important for adapting to environmental changes. Divergent thinking, which refers to generating novel and useful solutions to open-ended problems, has often been used as a measure of creative cognition. The first goal of this structural neuroimaging study was to elucidate the relationship between gray matter morphology and performance in the verbal (AUT; alternative uses task) and visuo-spatial (CAT; creative ability test) domain of divergent thinking in adolescents and young adults. The second goal was to test if gray matter morphology is related to brain activity during AUT performance. Neural and behavioral data were combined from a cross-sectional study including 25 adolescents aged 15–17 and 20 young adults aged 25–30. Brain-behavior relationships were assessed without a priori location assumptions and within areas that were activated during an AUT-scanner task. Gray matter volume and cortical thickness were not significantly associated with verbal divergent thinking. However, visuo-spatial divergent thinking (CAT originality and fluency) was positively associated with cortical thickness of the right middle temporal gyrus and left brain areas including the superior frontal gyrus and various occipital, parietal, and temporal areas, independently of age. AUT brain activity was not associated with cortical thickness. The results support an important role of a widespread brain network involved in flexible visuo-spatial divergent thinking, providing evidence for a relation between cortical thickness and visuo-spatial divergent thinking in adolescents and young adults. However, studies including visuo-spatial divergent thinking tasks in the scanner are warranted. PMID:25514366

Convergent and divergent validity of the Mullen Scales of Early Learning in young children with and without autism spectrum disorder.

PubMed

Swineford, Lauren B; Guthrie, Whitney; Thurm, Audrey

2015-12-01

The purpose of this study was to report on the construct, convergent, and divergent validity of the Mullen Scales of Early Learning (MSEL), a widely used test of development for young children. The sample consisted of 399 children with a mean age of 3.38 years (SD = 1.14) divided into a group of children with autism spectrum disorder (ASD) and a group of children not on the autism spectrum, with and without developmental delays. The study used the MSEL and several other measures assessing constructs relevant to the age range--including developmental skills, autism symptoms, and psychopathology symptoms--across multiple methods of assessment. Multiple-group confirmatory factor analyses revealed good overall fit and equal form of the MSEL 1-factor model across the ASD and nonspectrum groups, supporting the construct validity of the MSEL. However, neither full nor partial invariance of factor loadings was established because of the lower loadings in the ASD group compared with the nonspectrum group. Exploratory structural equation modeling revealed that other measures of developmental skills loaded together with the MSEL domain scores on a Developmental Functioning factor, supporting convergent validity of the MSEL. Divergent validity was supported by the lack of loading of MSEL domain scores on Autism Symptoms or Emotion/Behavior Problems factors. Although factor structure and loadings varied across groups, convergent and divergent validity findings were similar in the ASD and nonspectrum samples. Together, these results demonstrate evidence for the construct, convergent, and divergent validity of the MSEL using powerful data-analytic techniques. (c) 2015 APA, all rights reserved).

Divergent population structure and climate associations of a chromosomal inversion polymorphism across the Mimulus guttatus species complex

PubMed Central

Oneal, Elen; Lowry, David B.; Wright, Kevin M.; Zhu, Zhirui; Willis, John H.

2014-01-01

Chromosomal rearrangement polymorphisms are common and increasingly found to be associated with adaptive ecological divergence and speciation. Rearrangements, such as inversions, reduce recombination in heterozygous individuals and thus can protect favourable allelic combinations at linked loci, facilitating their spread in the presence of gene flow. Recently, we identified a chromosomal inversion polymorphism that contributes to ecological adaptation and reproductive isolation between annual and perennial ecotypes of the yellow monkeyflower, Mimulus guttatus. Here we evaluate the population genetic structure of this inverted region in comparison with the collinear regions of the genome across the M. guttatus species complex. We tested whether annual and perennial M. guttatus exhibit different patterns of divergence for loci in the inverted and noninverted regions of the genome. We then evaluated whether there are contrasting climate associations with these genomic regions through redundancy analysis. We found that the inversion exhibits broadly different patterns of divergence among annual and perennial M. guttatus and is associated with environmental variation across population accessions. This study is the first widespread population genetic survey of the diversity of the M. guttatus species complex. Our findings contribute to a greater understanding of morphological, ecological, and genetic evolutionary divergence across this highly diverse group of closely related ecotypes and species. Finally, understanding species relationships among M. guttatus sp. has hitherto been stymied by accumulated evidence of substantial gene flow among populations as well as designated species. Nevertheless, our results shed light on these relationships and provide insight into adaptation in life history traits within the complex. PMID:24796267

Late-time structure of the Bunch-Davies FRW wavefunction

NASA Astrophysics Data System (ADS)

Konstantinidis, George; Mahajan, Raghu; Shaghoulian, Edgar

2016-10-01

In this short note we organize a perturbation theory for the Bunch-Davies wavefunction in flat, accelerating cosmologies. The calculational technique avoids the in-in formalism and instead uses an analytic continuation from Euclidean signature. We will consider both massless and conformally coupled self-interacting scalars. These calculations explicitly illustrate two facts. The first is that IR divergences get sharper as the acceleration slows. The second is that UV-divergent contact terms in the Euclidean computation can contribute to the absolute value of the wavefunction in Lorentzian signature. Here UV divergent refers to terms involving inverse powers of the radial cutoff in the Euclidean computation. In Lorentzian signature such terms encode physical time dependence of the wavefunction.

Correlation of fitness landscapes from three orthologous TIM barrels originates from sequence and structure constraints

PubMed Central

Chan, Yvonne H.; Venev, Sergey V.; Zeldovich, Konstantin B.; Matthews, C. Robert

2017-01-01

Sequence divergence of orthologous proteins enables adaptation to environmental stresses and promotes evolution of novel functions. Limits on evolution imposed by constraints on sequence and structure were explored using a model TIM barrel protein, indole-3-glycerol phosphate synthase (IGPS). Fitness effects of point mutations in three phylogenetically divergent IGPS proteins during adaptation to temperature stress were probed by auxotrophic complementation of yeast with prokaryotic, thermophilic IGPS. Analysis of beneficial mutations pointed to an unexpected, long-range allosteric pathway towards the active site of the protein. Significant correlations between the fitness landscapes of distant orthologues implicate both sequence and structure as primary forces in defining the TIM barrel fitness landscape and suggest that fitness landscapes can be translocated in sequence space. Exploration of fitness landscapes in the context of a protein fold provides a strategy for elucidating the sequence-structure-fitness relationships in other common motifs. PMID:28262665

Sequence space and the ongoing expansion of the protein universe.

PubMed

Povolotskaya, Inna S; Kondrashov, Fyodor A

2010-06-17

The need to maintain the structural and functional integrity of an evolving protein severely restricts the repertoire of acceptable amino-acid substitutions. However, it is not known whether these restrictions impose a global limit on how far homologous protein sequences can diverge from each other. Here we explore the limits of protein evolution using sequence divergence data. We formulate a computational approach to study the rate of divergence of distant protein sequences and measure this rate for ancient proteins, those that were present in the last universal common ancestor. We show that ancient proteins are still diverging from each other, indicating an ongoing expansion of the protein sequence universe. The slow rate of this divergence is imposed by the sparseness of functional protein sequences in sequence space and the ruggedness of the protein fitness landscape: approximately 98 per cent of sites cannot accept an amino-acid substitution at any given moment but a vast majority of all sites may eventually be permitted to evolve when other, compensatory, changes occur. Thus, approximately 3.5 x 10(9) yr has not been enough to reach the limit of divergent evolution of proteins, and for most proteins the limit of sequence similarity imposed by common function may not exceed that of random sequences.

Melanopsin Signaling in Mammalian Iris and Retina

PubMed Central

Xue, T.; Do, M. T. H.; Riccio, A.; Jiang, Z.; Hsieh, J.; Wang, H. C.; Merbs, S. L.; Welsbie, D. S.; Yoshioka, T.; Weissgerber, P.; Stolz, S.; Flockerzi, V.; Freichel, M.; Simon, M. I.; Clapham, D. E.; Yau, K.-W.

2011-01-01

Lower vertebrates have an intrinsically-photosensitive iris and thus a local pupillary light reflex (PLR). In contrast, it has been a dogma that the PLR in mammals generally requires neuronal circuitry connecting the eye and the brain. We report here that an intrinsic component of the PLR is actually widespread in nocturnal and crepuscular mammals. In mouse, this intrinsic PLR requires the visual pigment, melanopsin. It also requires PLCβ4, the vertebrate homolog of the Drosophila NorpA phospholipase C mediating rhabdomeric phototransduction. The Plcβ4−/− genotype, besides removing the intrinsic PLR, also essentially eliminates the intrinsic light response of the M1-subtype of melanopsin-expressing, intrinsically-photosensitive retinal ganglion cells (M1-ipRGCs), by far the most photosensitive ipRGCs and with the largest responses. Ablating in mouse the expression of both TRPC6 and TRPC7, members of the TRP channel superfamily, likewise essentially eliminated the M1-ipRGC light response, but spared the intrinsic PLR. Thus, melanopsin signaling exists in both iris and retina, involving a PLCβ4-mediated pathway that nonetheless diverges in the two locations. PMID:22051675

The contribution of alu elements to mutagenic DNA double-strand break repair.

PubMed

Morales, Maria E; White, Travis B; Streva, Vincent A; DeFreece, Cecily B; Hedges, Dale J; Deininger, Prescott L

2015-03-01

Alu elements make up the largest family of human mobile elements, numbering 1.1 million copies and comprising 11% of the human genome. As a consequence of evolution and genetic drift, Alu elements of various sequence divergence exist throughout the human genome. Alu/Alu recombination has been shown to cause approximately 0.5% of new human genetic diseases and contribute to extensive genomic structural variation. To begin understanding the molecular mechanisms leading to these rearrangements in mammalian cells, we constructed Alu/Alu recombination reporter cell lines containing Alu elements ranging in sequence divergence from 0%-30% that allow detection of both Alu/Alu recombination and large non-homologous end joining (NHEJ) deletions that range from 1.0 to 1.9 kb in size. Introduction of as little as 0.7% sequence divergence between Alu elements resulted in a significant reduction in recombination, which indicates even small degrees of sequence divergence reduce the efficiency of homology-directed DNA double-strand break (DSB) repair. Further reduction in recombination was observed in a sequence divergence-dependent manner for diverged Alu/Alu recombination constructs with up to 10% sequence divergence. With greater levels of sequence divergence (15%-30%), we observed a significant increase in DSB repair due to a shift from Alu/Alu recombination to variable-length NHEJ which removes sequence between the two Alu elements. This increase in NHEJ deletions depends on the presence of Alu sequence homeology (similar but not identical sequences). Analysis of recombination products revealed that Alu/Alu recombination junctions occur more frequently in the first 100 bp of the Alu element within our reporter assay, just as they do in genomic Alu/Alu recombination events. This is the first extensive study characterizing the influence of Alu element sequence divergence on DNA repair, which will inform predictions regarding the effect of Alu element sequence divergence on both the rate and nature of DNA repair events.

The roles of calving migration and climate change in the formation of the weak genetic structure in the Tibetan antelope (Pantholops hodgsonii).

PubMed

Chen, Jiarui; Lin, Gonghua; Qin, Wen; Yan, Jingyan; Zhang, Tongzuo; Su, Jianping

2018-05-31

Geographical barriers and distance can reduce gene exchange among animals, resulting in genetic divergence of geographically isolated populations. The habitats of Tibetan antelope (Pantholops hodgsonii) has a geographical range of approximately 1,600 km across the Qinghai-Tibet Plateau (QTP) with a series tall mountains and big rivers. However, previously studies indicated that there was little genetic differentiation among their geographically delineated populations. To better understand the genetic structure of P. hodgsonii populations, we collected 145 samples from the three major calving regions considering their various calving grounds and migration routes. We used a combination of mitochondrial sequences (Cyt b, ATPase, D-loop and COX I) to investigate the genetic structure and the evolutionary divergence of the populations. Significant, albeit weak, genetic differentiation was detected among the three geographical populations. Analysis of the genetic divergence process revealed that the animals gradually entered into a period of rapid genetic differentiation since approximately 60,000 years ago. The calving migration of P. hodgsonii cannot be the main cause of their weak genetic structure since such cannot fully homogenize the genetic pool. Instead, the geological and climatic events as well as the coupling vegetation succession process during this period have been suggested to greatly contribute to the genetic structure and the expansion of genetic diversity. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

β-Functionalization of Indolin-2-one-Derived Aliphatic Acids for the Divergent Synthesis of Spirooxindole γ-Butyrolactones.

PubMed

Cao, Jing; Dong, Shuding; Jiang, Delu; Zhu, Peiyu; Zhang, Han; Li, Rui; Li, Zhanyi; Wang, Xuanyu; Tang, Weifang; Du, Ding

2017-04-21

β-Functionalization of indolin-2-one-derived aliphatic acids has been applied in formal [3 + 2] annualtions for catalyst-free and divergent synthesis of two series of structurally interesting 3,3'-spirooxindole γ-butyrolactones that may be attractive for potential drug discovery. These findings also pave the way for further diversity-oriented synthesis of spirooxindoles starting from indolin-2-one-derived aliphatic acids or their derivatives.

Islands within an island: Population genetic structure of the endemic Sardinian newt, Euproctus platycephalus.

PubMed

Ball, Sarah E; Bovero, Stefano; Sotgiu, Giuseppe; Tessa, Giulia; Angelini, Claudio; Bielby, Jon; Durrant, Christopher; Favelli, Marco; Gazzaniga, Enrico; Garner, Trenton W J

2017-02-01

The identification of historic and contemporary barriers to dispersal is central to the conservation of endangered amphibians, but may be hindered by their complex life history and elusive nature. The complementary information generated by mitochondrial (mtDNA) and microsatellite markers generates a valuable tool in elucidating population structure and the impact of habitat fragmentation. We applied this approach to the study of an endangered montane newt, Euproctus platycephalus . Endemic to the Mediterranean island of Sardinia, it is threatened by anthropogenic activity, disease, and climate change. We have demonstrated a clear hierarchy of structure across genetically divergent and spatially distinct subpopulations. Divergence between three main mountain regions dominated genetic partitioning with both markers. Mitochondrial phylogeography revealed a deep division dating to ca. 1 million years ago (Mya), isolating the northern region, and further differentiation between the central and southern regions ca. 0.5 Mya, suggesting an association with Pleistocene severe glacial oscillations. Our findings are consistent with a model of southward range expansion during glacial periods, with postglacial range retraction to montane habitat and subsequent genetic isolation. Microsatellite markers revealed further strong population structure, demonstrating significant divergence within the central region, and partial differentiation within the south. The northern population showed reduced genetic diversity. Discordance between mitochondrial and microsatellite markers at this scale indicated a further complexity of population structure, in keeping with male-biased dispersal and female philopatry. Our study underscores the need to elucidate cryptic population structure in the ecology and conservation strategies for endangered island-restricted amphibians, especially in the context of disease and climate change.

Noise elimination algorithm for modal analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bao, X. X., E-mail: baoxingxian@upc.edu.cn; Li, C. L.; Xiong, C. B.

2015-07-27

Modal analysis is an ongoing interdisciplinary physical issue. Modal parameters estimation is applied to determine the dynamic characteristics of structures under vibration excitation. Modal analysis is more challenging for the measured vibration response signals are contaminated with noise. This study develops a mathematical algorithm of structured low rank approximation combined with the complex exponential method to estimate the modal parameters. Physical experiments using a steel cantilever beam with ten accelerometers mounted, excited by an impulse load, demonstrate that this method can significantly eliminate noise from measured signals and accurately identify the modal frequencies and damping ratios. This study provides amore » fundamental mechanism of noise elimination using structured low rank approximation in physical fields.« less

Legislating Change? Responses to Criminalizing Female Genital Cutting in Senegal

PubMed Central

Shell-Duncan, Bettina; Hernlund, Ylva; Wander, Katherine; Moreau, Amadou

2014-01-01

Although the international community has recently promoted legislation as an important reform strategy for ending female genital cutting (FGC), there exist divergent views on its potential effects. Supporters argue that legal prohibition of FGC has a general deterrent effect, while others argue legislation can be perceived as coercive, and derail local efforts to end the practice. This study examines the range of responses observed in rural Senegal, where a 1999 anti-FGC law was imposed on communities in which the practice was being actively contested and targeted for elimination. Drawing on data from a mixed-methods study, we analyze responses in relation to two leading theories on social regulation, the law and economics and law and society paradigms, which make divergent predictions on the interplay between social norms and legal norms. Among supporters of FGC, legal norms ran counter to social norms, and did little to deter the practice, and in some instances incited reactance or drove the practice underground. Conversely, where FGC was being contested, legislation served to strengthen the stance of those contemplating or favoring abandonment. We conclude that legislation can complement other reform strategies by creating an “enabling environment” that supports those who have or wish to abandon FGC. PMID:24771947

Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted, independent, or multiple evolutionary responses?

PubMed Central

Bagley, Justin C; Johnson, Jerald B

2014-01-01

A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns (“concerted-response hypothesis”); (2) independent responses, indicated by spatial incongruence (“independent-response hypothesis”); or (3) multiple responses (“multiple-response hypothesis”), indicated by spatial congruence but temporal incongruence (“pseudocongruence”) or spatial and temporal incongruence (“pseudoincongruence”). We tested these competing hypotheses using DNA sequence data from three livebearing fish species codistributed in the Nicaraguan depression of Central America (Alfaro cultratus, Poecilia gillii, and Xenophallus umbratilis) that we predicted might display congruent responses due to co-occurrence in identical freshwater drainages. Spatial analyses recovered different subdivisions of genetic structure for each species, despite shared finer-scale breaks in northwestern Costa Rica (also supported by phylogenetic results). Isolation-with-migration models estimated incongruent timelines of among-region divergences, with A. cultratus and Xenophallus populations diverging over Miocene–mid-Pleistocene while P. gillii populations diverged over mid-late Pleistocene. Approximate Bayesian computation also lent substantial support to multiple discrete divergences over a model of simultaneous divergence across shared spatial breaks (e.g., Bayes factor [B10] = 4.303 for Ψ [no. of divergences] > 1 vs. Ψ = 1). Thus, the data support phylogeographic pseudoincongruence consistent with the multiple-response hypothesis. Model comparisons also indicated incongruence in historical demography, for example, support for intraspecific late Pleistocene population growth was unique to P. gillii, despite evidence for finer-scale population expansions in the other taxa. Empirical tests for phylogeographic congruence indicate that multiple evolutionary responses to historical events have shaped the population structure of freshwater species codistributed within the complex landscapes in/around the Nicaraguan depression. Recent community assembly through different routes (i.e., different past distributions or colonization routes), and intrinsic ecological differences among species, has likely contributed to the unique phylogeographical patterns displayed by these Neotropical fishes. PMID:24967085

77 FR 32155 - Self-Regulatory Organizations; NYSE Arca, Inc.; Notice of Filing of Proposed Rule Change Amending...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-05-31

... Company, Into and With NYSE Group, Inc. (``NYSE Group''), Thereby Eliminating Archipelago Holdings From...''), an intermediate holding company, into and with NYSE Group, Inc. (``NYSE Group''), thereby eliminating... company, into and with NYSE Group, thereby eliminating Archipelago Holdings from the ownership structure...

An Immersed Boundary method with divergence-free velocity interpolation and force spreading

NASA Astrophysics Data System (ADS)

Bao, Yuanxun; Donev, Aleksandar; Griffith, Boyce E.; McQueen, David M.; Peskin, Charles S.

2017-10-01

The Immersed Boundary (IB) method is a mathematical framework for constructing robust numerical methods to study fluid-structure interaction in problems involving an elastic structure immersed in a viscous fluid. The IB formulation uses an Eulerian representation of the fluid and a Lagrangian representation of the structure. The Lagrangian and Eulerian frames are coupled by integral transforms with delta function kernels. The discretized IB equations use approximations to these transforms with regularized delta function kernels to interpolate the fluid velocity to the structure, and to spread structural forces to the fluid. It is well-known that the conventional IB method can suffer from poor volume conservation since the interpolated Lagrangian velocity field is not generally divergence-free, and so this can cause spurious volume changes. In practice, the lack of volume conservation is especially pronounced for cases where there are large pressure differences across thin structural boundaries. The aim of this paper is to greatly reduce the volume error of the IB method by introducing velocity-interpolation and force-spreading schemes with the properties that the interpolated velocity field in which the structure moves is at least C1 and satisfies a continuous divergence-free condition, and that the force-spreading operator is the adjoint of the velocity-interpolation operator. We confirm through numerical experiments in two and three spatial dimensions that this new IB method is able to achieve substantial improvement in volume conservation compared to other existing IB methods, at the expense of a modest increase in the computational cost. Further, the new method provides smoother Lagrangian forces (tractions) than traditional IB methods. The method presented here is restricted to periodic computational domains. Its generalization to non-periodic domains is important future work.

Measurement of the Specific Heat Using a Gravity Cancellation Approach

NASA Technical Reports Server (NTRS)

Zhong, Fang

2003-01-01

The specific heat at constant volume C(sob V) of a simple fluid diverges near its liquid-vapor critical point. However, gravity-induced density stratification due to the divergence of isothermal susceptibility hinders the direct comparison of the experimental data with the predictions of renormalization group theory. In the past, a microgravity environment has been considered essential to eliminate the density stratification. We propose to perform specific heat measurements of He-3 on the ground using a method to cancel the density stratification. A He-3 fluid layer will be heated from below, using the thermal expansion of the fluid to cancel the hydrostatic compression. A 6% density stratification at a reduced temperature of 10(exp -5) can be cancelled to better than 0.1% with a steady 1.7 micro K temperature difference across a 0.05 cm thick fluid layer. A conventional AC calorimetry technique will be used to determine the heat capacity. The minimized bulk density stratification with a relaxation time 6500 sec at a reduced temperature of 10(exp -5) will stay unchanged during 1 Hz AC heating. The smear of the specific heat divergence due to the temperature difference across the cell is about 0.1% at a reduced temperature of 10(exp -6). The combination of using High Resolution Thermometry with a 0.5 n K temperature resolution in the AC technique and the cancellation of the density stratification will enable C(sub V) to be measured down to a reduced temperature of 10(exp -6) with less than a 1% systematic error.

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence

PubMed Central

2017-01-01

During cell division, spindle fibers attach to chromosomes at centromeres. The DNA sequence at regional centromeres is fast evolving with no conserved genetic signature for centromere identity. Instead CENH3, a centromere-specific histone H3 variant, is the epigenetic signature that specifies centromere location across both plant and animal kingdoms. Paradoxically, CENH3 is also adaptively evolving. An ongoing question is whether CENH3 evolution is driven by a functional relationship with the underlying DNA sequence. Here, we demonstrate that despite extensive protein sequence divergence, CENH3 histones from distant species assemble centromeres on the same underlying DNA sequence. We first characterized the organization and diversity of centromere repeats in wild-type Arabidopsis thaliana. We show that A. thaliana CENH3-containing nucleosomes exhibit a strong preference for a unique subset of centromeric repeats. These sequences are largely missing from the genome assemblies and represent the youngest and most homogeneous class of repeats. Next, we tested the evolutionary specificity of this interaction in a background in which the native A. thaliana CENH3 is replaced with CENH3s from distant species. Strikingly, we find that CENH3 from Lepidium oleraceum and Zea mays, although specifying epigenetically weaker centromeres that result in genome elimination upon outcrossing, show a binding pattern on A. thaliana centromere repeats that is indistinguishable from the native CENH3. Our results demonstrate positional stability of a highly diverged CENH3 on independently evolved repeats, suggesting that the sequence specificity of centromeres is determined by a mechanism independent of CENH3. PMID:28223399

Can superhorizon cosmological perturbations explain the acceleration of the universe?

NASA Astrophysics Data System (ADS)

Hirata, Christopher M.; Seljak, Uroš

2005-10-01

We investigate the recent suggestions by Barausse et al. and Kolb et al. that the acceleration of the universe could be explained by large superhorizon fluctuations generated by inflation. We show that no acceleration can be produced by this mechanism. We begin by showing how the application of Raychaudhuri equation to inhomogeneous cosmologies results in several “no go” theorems for accelerated expansion. Next we derive an exact solution for a specific case of initial perturbations, for which application of the Kolb et al. expressions leads to an acceleration, while the exact solution reveals that no acceleration is present. We show that the discrepancy can be traced to higher-order terms that were dropped in the Kolb et al. analysis. We proceed with the analysis of initial value formulation of general relativity to argue that causality severely limits what observable effects can be derived from superhorizon perturbations. By constructing a Riemann normal coordinate system on initial slice we show that no infrared divergence terms arise in this coordinate system. Thus any divergences found previously can be eliminated by a local rescaling of coordinates and are unobservable. We perform an explicit analysis of the variance of the deceleration parameter for the case of single-field inflation using usual coordinates and show that the infrared-divergent terms found by Barausse et al. and Kolb et al. cancel against several additional terms not considered in their analysis. Finally, we argue that introducing isocurvature perturbations does not alter our conclusion that the accelerating expansion of the universe cannot be explained by superhorizon modes.

ADP-ribosyl-N₃: A Versatile Precursor for Divergent Syntheses of ADP-ribosylated Compounds.

PubMed

Li, Lingjun; Li, Qianqian; Ding, Shengqiang; Xin, Pengyang; Zhang, Yuqin; Huang, Shenlong; Zhang, Guisheng

2017-08-14

Adenosine diphosphate-ribose (ADP-ribose) and its derivatives play important roles in a series of complex physiological procedures. The design and synthesis of artificial ADP-ribosylated compounds is an efficient way to develop valuable chemical biology tools and discover new drug candidates. However, the synthesis of ADP-ribosylated compounds is currently difficult due to structural complexity, easily broken pyrophosphate bond and high hydrophilicity. In this paper, ADP-ribosyl-N₃ was designed and synthesized for the first time. With ADP-ribosyl-N₃ as the key precursor, a divergent post-modification strategy was developed to prepare structurally diverse ADP-ribosylated compounds including novel nucleotides and peptides bearing ADP-ribosyl moieties.

Trichomes: different regulatory networks lead to convergent structures.

PubMed

Serna, Laura; Martin, Cathie

2006-06-01

Sometimes, proteins, biological structures or even organisms have similar functions and appearances but have evolved through widely divergent pathways. There is experimental evidence to suggest that different developmental pathways have converged to produce similar outgrowths of the aerial plant epidermis, referred to as trichomes. The emerging picture suggests that trichomes in Arabidopsis thaliana and, perhaps, in cotton develop through a transcriptional regulatory network that differs from those regulating trichome formation in Antirrhinum and Solanaceous species. Several lines of evidence suggest that the duplication of a gene controlling anthocyanin production and subsequent divergence might be the major force driving trichome formation in Arabidopsis, whereas the multicellular trichomes of Antirrhinum and Solanaceous species appear to have a different regulatory origin.

Ion Beam Deflection (AKA Push-Me/Pull-You)

NASA Technical Reports Server (NTRS)

Brophy, John

2013-01-01

The Ion Beam Deflection provides the following potential advantages over other asteroid deflection systems. Like the gravity tractor, it doesn't require despinning of the asteroid. Unlike the gravity tractor, it provides a significantly higher coupling force that is independent of the asteroid size. The concept could be tested as part of the baseline Asteroid Redirect Robotic Mission. The thrust and total impulse are entirely within the design of the SEP vehicle. The total impulse is potentially competitive with kinetic impactors and eliminates the need for a second rendezvous spacecraft.?Gridded ion thrusters provide beam divergence angles of a few degrees enabling long stand-off distances from the asteroid. Mitigating control issues. Minimizing back-sputter contamination risks

Spreading of multiple epidemics with cross immunization.

PubMed

Uekermann, Florian; Sneppen, Kim

2012-09-01

Pathogen-host relationships are the result of an ongoing coevolutionary race where the immune system of the host attempts to eliminate the pathogen, while the successful pathogen mutates to become invisible for the host's immune system. We here propose a minimal pathogen-host evolution model that takes into account cross immunization and allows for evolution of a spatially heterogeneous immune status of a population of hosts. With only the mutation rate as a determining parameter, the model allows us to produce an evolutionary tree of diseases which is highly branched, but hardly ever splits into separate long-lived trunks. Side branches remain short lived and seldom diverge to the extent of losing all cross immunizations.

Numerical-assisted design of a wind tunnel used in the estimation of volatilization from water, waste or soil.

PubMed

Baléo, J N; Le Cloirec, P

2006-04-01

Numerical simulations of the flow inside two wind tunnel geometries used for determining emission volatilization have been conducted. The flow pattern was examined in a plane close to the emitting surface. A reduced surface, characterizing the low velocity zones in this plane, has been defined. The proposed geometry modification, consisting of a convergent/divergent system, decreases the low velocity regions by a factor ranging between 2 and 3.5. Large vortices present in the conventional configuration are almost eliminated. The new velocity distribution, close to the emitting surface, is more uniform and should therefore generate a more efficient mass transfer to the flowing air.

Development of an integrated aeroservoelastic analysis program and correlation with test data

NASA Technical Reports Server (NTRS)

Gupta, K. K.; Brenner, M. J.; Voelker, L. S.

1991-01-01

The details and results are presented of the general-purpose finite element STructural Analysis RoutineS (STARS) to perform a complete linear aeroelastic and aeroservoelastic analysis. The earlier version of the STARS computer program enabled effective finite element modeling as well as static, vibration, buckling, and dynamic response of damped and undamped systems, including those with pre-stressed and spinning structures. Additions to the STARS program include aeroelastic modeling for flutter and divergence solutions, and hybrid control system augmentation for aeroservoelastic analysis. Numerical results of the X-29A aircraft pertaining to vibration, flutter-divergence, and open- and closed-loop aeroservoelastic controls analysis are compared to ground vibration, wind-tunnel, and flight-test results. The open- and closed-loop aeroservoelastic control analyses are based on a hybrid formulation representing the interaction of structural, aerodynamic, and flight-control dynamics.

Fourier imaging of non-linear structure formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brandbyge, Jacob; Hannestad, Steen, E-mail: jacobb@phys.au.dk, E-mail: sth@phys.au.dk

We perform a Fourier space decomposition of the dynamics of non-linear cosmological structure formation in ΛCDM models. From N -body simulations involving only cold dark matter we calculate 3-dimensional non-linear density, velocity divergence and vorticity Fourier realizations, and use these to calculate the fully non-linear mode coupling integrals in the corresponding fluid equations. Our approach allows for a reconstruction of the amount of mode coupling between any two wavenumbers as a function of redshift. With our Fourier decomposition method we identify the transfer of power from larger to smaller scales, the stable clustering regime, the scale where vorticity becomes important,more » and the suppression of the non-linear divergence power spectrum as compared to linear theory. Our results can be used to improve and calibrate semi-analytical structure formation models.« less

Evolution of the arginase fold and functional diversity

PubMed Central

Dowling, Daniel P.; Costanzo, Luigi Di; Gennadios, Heather A.; Christianson, David W.

2009-01-01

The large number of protein structures deposited in the Protein Data Bank allows for the identification of novel structural superfamilies based on conservation of fold in addition to conservation of amino acid sequence. Since sequence diverges more rapidly than fold in protein evolution, proteins with little or no significant sequence identity are occasionally observed to adopt similar folds, thereby reflecting unanticipated evolutionary relationships. Here, we review the unique α/β fold first observed in the manganese metalloenzyme rat liver arginase, consisting of a parallel 8 stranded β-sheet surrounded by several helices, and its evolutionary relationship with the zinc-requiring and/or iron-requiring histone deacetylases and acetylpolyamine amidohydrolases. Structural comparisons reveal key features of the core α/β fold that contribute to the divergent metal ion specificity and stoichiometry required for the chemical and biological functions of these enzymes. PMID:18360740

Sympatric speciation revealed by genome-wide divergence in the blind mole rat Spalax.

PubMed

Li, Kexin; Hong, Wei; Jiao, Hengwu; Wang, Guo-Dong; Rodriguez, Karl A; Buffenstein, Rochelle; Zhao, Yang; Nevo, Eviatar; Zhao, Huabin

2015-09-22

Sympatric speciation (SS), i.e., speciation within a freely breeding population or in contiguous populations, was first proposed by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection] and is still controversial despite theoretical support [Gavrilets S (2004) Fitness Landscapes and the Origin of Species (MPB-41)] and mounting empirical evidence. Speciation of subterranean mammals generally, including the genus Spalax, was considered hitherto allopatric, whereby new species arise primarily through geographic isolation. Here we show in Spalax a case of genome-wide divergence analysis in mammals, demonstrating that SS in continuous populations, with gene flow, encompasses multiple widespread genomic adaptive complexes, associated with the sharply divergent ecologies. The two abutting soil populations of S. galili in northern Israel habituate the ancestral Senonian chalk population and abutting derivative Plio-Pleistocene basalt population. Population divergence originated ∼0.2-0.4 Mya based on both nuclear and mitochondrial genome analyses. Population structure analysis displayed two distinctly divergent clusters of chalk and basalt populations. Natural selection has acted on 300+ genes across the genome, diverging Spalax chalk and basalt soil populations. Gene ontology enrichment analysis highlights strong but differential soil population adaptive complexes: in basalt, sensory perception, musculature, metabolism, and energetics, and in chalk, nutrition and neurogenetics are outstanding. Population differentiation of chemoreceptor genes suggests intersoil population's mate and habitat choice substantiating SS. Importantly, distinctions in protein degradation may also contribute to SS. Natural selection and natural genetic engineering [Shapiro JA (2011) Evolution: A View From the 21st Century] overrule gene flow, evolving divergent ecological adaptive complexes. Sharp ecological divergences abound in nature; therefore, SS appears to be an important mode of speciation as first envisaged by Darwin [Darwin C (1859) On the Origins of Species by Means of Natural Selection].

Shaping species with ephemeral boundaries: The distribution and genetic structure of desert tortoise (Gopherus morafkai) in the Sonoran Desert region

USGS Publications Warehouse

Edwards, Taylor; Vaughn, Mercy; Rosen, Philip C.; Torres, Ma. Cristina Melendez; Karl, Alice E.; Culver, Melanie; Murphy, Robert W.

2015-01-01

The historically shifting ecotone between tropical deciduous forest and Sonoran desertscrub appears to be a boundary that fostered divergence between parapatric lineages of tortoises. The sharp genetic cline between the two lineages suggests that periods of isolation in temporary refugia due to Pleistocene climatic cycling influenced divergence. Despite incomplete reproductive isolation, the Sonoran and Sinaloan lineages of G. morafkai are on separate evolutionary trajectories.

Divergent modes of enzyme inhibition in a homologous structure-activity series.

PubMed

Ferreira, Rafaela S; Bryant, Clifford; Ang, Kenny K H; McKerrow, James H; Shoichet, Brian K; Renslo, Adam R

2009-08-27

A docking screen identified reversible, noncovalent inhibitors (e.g., 1) of the parasite cysteine protease cruzain. Chemical optimization of 1 led to a series of oxadiazoles possessing interpretable SAR and potencies as much as 500-fold greater than 1. Detailed investigation of the SAR series subsequently revealed that many members of the oxadiazole class (and surprisingly also 1) act via divergent modes of inhibition (competitive or via colloidal aggregation) depending on the assay conditions employed.

Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population.

PubMed

Aykanat, Tutku; Johnston, Susan E; Orell, Panu; Niemelä, Eero; Erkinaro, Jaakko; Primmer, Craig R

2015-10-01

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high-resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined single nucleotide polymorphism (SNP)-based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine-scale subpopulation differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring subpopulations had low but significant genetic differentiation (FST  = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late-maturing individuals were virtually absent from one of the two subpopulations, and there were significant differences in juvenile growth rates and size at age after oceanic migration between individuals in the respective subpopulations. Our findings suggest that different evolutionary processes affect each subpopulation and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence. © 2015 John Wiley & Sons Ltd.

Two divergent endo-beta-1,4-glucanase genes exhibit overlapping expression in ripening fruit and abscising flowers.

PubMed Central

Lashbrook, C C; Gonzalez-Bosch, C; Bennett, A B

1994-01-01

Two structurally divergent endo-beta-1,4-glucanase (EGase) cDNAs were cloned from tomato. Although both cDNAs (Cel1 and Cel2) encode potentially glycosylated, basic proteins of 51 to 53 kD and possess multiple amino acid domains conserved in both plant and microbial EGases, Cel1 and Cel2 exhibit only 50% amino acid identity at the overall sequence level. Amino acid sequence comparisons to other plant EGases indicate that tomato Cel1 is most similar to bean abscission zone EGase (68%), whereas Cel2 exhibits greatest sequence identity to avocado fruit EGase (57%). Sequence comparisons suggest the presence of at least two structurally divergent EGase families in plants. Unlike ripening avocado fruit and bean abscission zones in which a single EGase mRNA predominates, EGase expression in tomato reflects the overlapping accumulation of both Cel1 and Cel2 transcripts in ripening fruit and in plant organs undergoing cell separation. Cel1 mRNA contributes significantly to total EGase mRNA accumulation within plant organs undergoing cell separation (abscission zones and mature anthers), whereas Cel2 mRNA is most abundant in ripening fruit. The overlapping expression of divergent EGase genes within a single species may suggest that multiple activities are required for the cooperative disassembly of cell wall components during fruit ripening, floral abscission, and anther dehiscence. PMID:7994180

Renormalization of the one-loop theory of fluctuations in polymer blends and diblock copolymer melts.

PubMed

Grzywacz, Piotr; Qin, Jian; Morse, David C

2007-12-01

Attempts to use coarse-grained molecular theories to calculate corrections to the random-phase approximation (RPA) for correlations in polymer mixtures have been plagued by an unwanted sensitivity to the value of an arbitrary cutoff length, i.e., by an ultraviolet (UV) divergence. We analyze the UV divergence of the inverse structure factor S(-1)(k) predicted by a "one-loop" approximation similar to that used in several previous studies. We consider both miscible homopolymer blends and disordered diblock copolymer melts. We show, in both cases, that all UV divergent contributions can be absorbed into a renormalization of the values of the phenomenological parameters of a generalized self-consistent field theory (SCFT). This observation allows the construction of an UV convergent theory of corrections to SCFT phenomenology. The UV-divergent one-loop contribution to S(-1)(k) is shown to be the sum of (i) a k -independent contribution that arises from a renormalization of the effective chi parameter, (ii) a k-dependent contribution that arises from a renormalization of monomer statistical segment lengths, (iii) a contribution proportional to k(2) that arises from a square-gradient contribution to the one-loop fluctuation free energy, and (iv) a k-dependent contribution that is inversely proportional to the degree of polymerization, which arises from local perturbations in fluid structure near chain ends and near junctions between blocks in block copolymers.

Expansion of divergent SEA domains in cell surface proteins and nucleoporin 54.

PubMed

Pei, Jimin; Grishin, Nick V

2017-03-01

SEA (sea urchin sperm protein, enterokinase, agrin) domains, many of which possess autoproteolysis activity, have been found in a number of cell surface and secreted proteins. Despite high sequence divergence, SEA domains were also proposed to be present in dystroglycan based on a conserved autoproteolysis motif and receptor-type protein phosphatase IA-2 based on structural similarity. The presence of a SEA domain adjacent to the transmembrane segment appears to be a recurring theme in quite a number of type I transmembrane proteins on the cell surface, such as MUC1, dystroglycan, IA-2, and Notch receptors. By comparative sequence and structural analyses, we identified dystroglycan-like proteins with SEA domains in Capsaspora owczarzaki of the Filasterea group, one of the closest single-cell relatives of metazoans. We also detected novel and divergent SEA domains in a variety of cell surface proteins such as EpCAM, α/ε-sarcoglycan, PTPRR, collectrin/Tmem27, amnionless, CD34, KIAA0319, fibrocystin-like protein, and a number of cadherins. While these proteins are mostly from metazoans or their single cell relatives such as choanoflagellates and Filasterea, fibrocystin-like proteins with SEA domains were found in several other eukaryotic lineages including green algae, Alveolata, Euglenozoa, and Haptophyta, suggesting an ancient evolutionary origin. In addition, the intracellular protein Nucleoporin 54 (Nup54) acquired a divergent SEA domain in choanoflagellates and metazoans. © 2016 The Protein Society.

Bathymetric and geographic population structure in the pan-Atlantic deep-sea bivalve Deminucula atacellana (Schenck, 1939).

PubMed

Zardus, John D; Etter, Ron J; Chase, Michael R; Rex, Michael A; Boyle, Elizabeth E

2006-03-01

The deep-sea soft-sediment environment hosts a diverse and highly endemic fauna of uncertain origin. We know little about how this fauna evolved because geographic patterns of genetic variation, the essential information for inferring patterns of population differentiation and speciation are poorly understood. Using formalin-fixed specimens from archival collections, we quantify patterns of genetic variation in the protobranch bivalve Deminucula atacellana, a species widespread throughout the Atlantic Ocean at bathyal and abyssal depths. Samples were taken from 18 localities in the North American, West European and Argentine basins. A hypervariable region of mitochondrial 16S rDNA was amplified by polymerase chain reaction (PCR) and sequenced from 130 individuals revealing 21 haplotypes. Except for several important exceptions, haplotypes are unique to each basin. Overall gene diversity is high (h = 0.73) with pronounced population structure (Phi(ST) = 0.877) and highly significant geographic associations (P < 0.0001). Sequences cluster into four major clades corresponding to differences in geography and depth. Genetic divergence was much greater among populations at different depths within the same basin, than among those at similar depths but separated by thousands of kilometres. Isolation by distance probably explains much of the interbasin variation. Depth-related divergence may reflect historical patterns of colonization or strong environmental selective gradients. Broadly distributed deep-sea organisms can possess highly genetically divergent populations, despite the lack of any morphological divergence.

A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice

PubMed Central

White, Michael A.; Ikeda, Akihiro; Payseur, Bret A.

2012-01-01

The pseudoautosomal region (PAR) is essential for the accurate pairing and segregation of the X and Y chromosomes during meiosis. Despite its functional significance, the PAR shows substantial evolutionary divergence in structure and sequence between mammalian species. An instructive example of PAR evolution is the house mouse Mus musculus domesticus (represented by the C57BL/6J strain), which has the smallest PAR among those that have been mapped. In C57BL/6J, the PAR boundary is located just ~700 kb from the distal end of the X chromosome, whereas the boundary is found at a more proximal position in Mus spretus, a species that diverged from house mice 2–4 million years ago. Here, we use a combination of genetic and physical mapping to document a pronounced shift in the PAR boundary in a second house mouse subspecies, Mus musculus castaneus (represented by the CAST/EiJ strain), ~430 kb proximal of the M. m. domesticus boundary. We demonstrate molecular evolutionary consequences of this shift, including a marked lineage-specific increase in sequence divergence within Mid1, a gene that resides entirely within the M. m. castaneus PAR but straddles the boundary in other subspecies. Our results extend observations of structural divergence in the PAR to closely related subspecies, pointing to major evolutionary changes in this functionally important genomic region over a short time period. PMID:22763584

A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice.

PubMed

White, Michael A; Ikeda, Akihiro; Payseur, Bret A

2012-08-01

The pseudoautosomal region (PAR) is essential for the accurate pairing and segregation of the X and Y chromosomes during meiosis. Despite its functional significance, the PAR shows substantial evolutionary divergence in structure and sequence between mammalian species. An instructive example of PAR evolution is the house mouse Mus musculus domesticus (represented by the C57BL/6J strain), which has the smallest PAR among those that have been mapped. In C57BL/6J, the PAR boundary is located just ~700 kb from the distal end of the X chromosome, whereas the boundary is found at a more proximal position in Mus spretus, a species that diverged from house mice 2-4 million years ago. In this study we used a combination of genetic and physical mapping to document a pronounced shift in the PAR boundary in a second house mouse subspecies, Mus musculus castaneus (represented by the CAST/EiJ strain), ~430 kb proximal of the M. m. domesticus boundary. We demonstrate molecular evolutionary consequences of this shift, including a marked lineage-specific increase in sequence divergence within Mid1, a gene that resides entirely within the M. m. castaneus PAR but straddles the boundary in other subspecies. Our results extend observations of structural divergence in the PAR to closely related subspecies, pointing to major evolutionary changes in this functionally important genomic region over a short time period.

Distinguishing Between Convergent Evolution and Violation of the Molecular Clock for Three Taxa.

PubMed

Mitchell, Jonathan D; Sumner, Jeremy G; Holland, Barbara R

2018-05-18

We give a non-technical introduction to convergence-divergence models, a new modeling approach for phylogenetic data that allows for the usual divergence of lineages after lineage-splitting but also allows for taxa to converge, i.e. become more similar over time. By examining the 3-taxon case in some detail we illustrate that phylogeneticists have been "spoiled" in the sense of not having to think about the structural parameters in their models by virtue of the strong assumption that evolution is tree-like. We show that there are not always good statistical reasons to prefer the usual class of tree-like models over more general convergence-divergence models. Specifically we show many 3-taxon data sets can be equally well explained by supposing violation of the molecular clock due to change in the rate of evolution along different edges, or by keeping the assumption of a constant rate of evolution but instead assuming that evolution is not a purely divergent process. Given the abundance of evidence that evolution is not strictly tree-like, our discussion is an illustration that as phylogeneticists we need to think clearly about the structural form of the models we use. For cases with four taxa we show that there will be far greater ability to distinguish models with convergence from non-clock-like tree models.

Divergent estimation error in portfolio optimization and in linear regression

NASA Astrophysics Data System (ADS)

Kondor, I.; Varga-Haszonits, I.

2008-08-01

The problem of estimation error in portfolio optimization is discussed, in the limit where the portfolio size N and the sample size T go to infinity such that their ratio is fixed. The estimation error strongly depends on the ratio N/T and diverges for a critical value of this parameter. This divergence is the manifestation of an algorithmic phase transition, it is accompanied by a number of critical phenomena, and displays universality. As the structure of a large number of multidimensional regression and modelling problems is very similar to portfolio optimization, the scope of the above observations extends far beyond finance, and covers a large number of problems in operations research, machine learning, bioinformatics, medical science, economics, and technology.

Divergent evapotranspiration partition dynamics between shrubs and grasses in a shrub-encroached steppe ecosystem.

PubMed

Wang, Pei; Li, Xiao-Yan; Wang, Lixin; Wu, Xiuchen; Hu, Xia; Fan, Ying; Tong, Yaqin

2018-06-04

Previous evapotranspiration (ET) partitioning studies have usually neglected competitions and interactions between antagonistic plant functional types. This study investigated whether shrubs and grasses have divergent ET partition dynamics impacted by different water-use patterns, canopy structures, and physiological properties in a shrub-encroached steppe ecosystem in Inner Mongolia, China. The soil water-use patterns of shrubs and grasses have been quantified by an isotopic tracing approach and coupled into an improved multisource energy balance model to partition ET fluxes into soil evaporation, grass transpiration, and shrub transpiration. The mean fractional contributions to total ET were 24 ± 13%, 20 ± 4%, and 56 ± 16% for shrub transpiration, grass transpiration, and soil evaporation respectively during the growing season. Difference in ecohydrological connectivity and leaf development both contributed to divergent transpiration partitioning between shrubs and grasses. Shrub-encroachment processes result in larger changes in the ET components than in total ET flux, which could be well explained by changes in canopy resistance, an ecosystem function dominated by the interaction of soil water-use patterns and ecosystem structure. The analyses presented here highlight the crucial effects of vegetation structural changes on the processes of land-atmosphere interaction and climate feedback. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Structures of pyruvate kinases display evolutionarily divergent allosteric strategies

PubMed Central

Morgan, Hugh P.; Zhong, Wenhe; McNae, Iain W.; Michels, Paul A. M.; Fothergill-Gilmore, Linda A.; Walkinshaw, Malcolm D.

2014-01-01

The transition between the inactive T-state (apoenzyme) and active R-state (effector bound enzyme) of Trypanosoma cruzi pyruvate kinase (PYK) is accompanied by a symmetrical 8° rigid body rocking motion of the A- and C-domain cores in each of the four subunits, coupled with the formation of additional salt bridges across two of the four subunit interfaces. These salt bridges provide increased tetramer stability correlated with an enhanced specificity constant (kcat/S0.5). A detailed kinetic and structural comparison between the potential drug target PYKs from the pathogenic protists T. cruzi, T. brucei and Leishmania mexicana shows that their allosteric mechanism is conserved. By contrast, a structural comparison of trypanosomatid PYKs with the evolutionarily divergent PYKs of humans and of bacteria shows that they have adopted different allosteric strategies. The underlying principle in each case is to maximize (kcat/S0.5) by stabilizing and rigidifying the tetramer in an active R-state conformation. However, bacterial and mammalian PYKs have evolved alternative ways of locking the tetramers together. In contrast to the divergent allosteric mechanisms, the PYK active sites are highly conserved across species. Selective disruption of the varied allosteric mechanisms may therefore provide a useful approach for the design of species-specific inhibitors. PMID:26064527

The effect of climate on acoustic signals: does atmospheric sound absorption matter for bird song and bat echolocation?

PubMed

Snell-Rood, Emilie C

2012-02-01

The divergence of signals along ecological gradients may lead to speciation. The current research tests the hypothesis that variation in sound absorption selects for divergence in acoustic signals along climatic gradients, which has implications for understanding not only diversification, but also how organisms may respond to climate change. Because sound absorption varies with temperature, humidity, and the frequency of sound, individuals or species may vary signal structure with changes in climate over space or time. In particular, signals of lower frequency, narrower bandwidth, and longer duration should be more detectable in environments with high sound absorption. Using both North American wood warblers (Parulidae) and bats of the American Southwest, this work found evidence of associations between signal structure and sound absorption. Warbler species with higher mean absorption across their range were more likely to have narrow bandwidth songs. Bat species found in higher absorption habitats were more likely to have lower frequency echolocation calls. In addition, bat species changed echolocation call structure across seasons, using longer duration, lower frequency calls in the higher absorption rainy season. These results suggest that signals may diverge along climatic gradients due to variation in sound absorption, although the effects of absorption are modest. © 2012 Acoustical Society of America

Biochemical Regulatory Features of Activation-Induced Cytidine Deaminase Remain Conserved from Lampreys to Humans

PubMed Central

King, Justin J.; Amemiya, Chris T.; Hsu, Ellen

2017-01-01

ABSTRACT Activation-induced cytidine deaminase (AID) is a genome-mutating enzyme that initiates class switch recombination and somatic hypermutation of antibodies in jawed vertebrates. We previously described the biochemical properties of human AID and found that it is an unusual enzyme in that it exhibits binding affinities for its substrate DNA and catalytic rates several orders of magnitude higher and lower, respectively, than a typical enzyme. Recently, we solved the functional structure of AID and demonstrated that these properties are due to nonspecific DNA binding on its surface, along with a catalytic pocket that predominantly assumes a closed conformation. Here we investigated the biochemical properties of AID from a sea lamprey, nurse shark, tetraodon, and coelacanth: representative species chosen because their lineages diverged at the earliest critical junctures in evolution of adaptive immunity. We found that these earliest-diverged AID orthologs are active cytidine deaminases that exhibit unique substrate specificities and thermosensitivities. Significant amino acid sequence divergence among these AID orthologs is predicted to manifest as notable structural differences. However, despite major differences in sequence specificities, thermosensitivities, and structural features, all orthologs share the unusually high DNA binding affinities and low catalytic rates. This absolute conservation is evidence for biological significance of these unique biochemical properties. PMID:28716949

A meta-analysis of neuroimaging studies on divergent thinking using activation likelihood estimation.

PubMed

Wu, Xin; Yang, Wenjing; Tong, Dandan; Sun, Jiangzhou; Chen, Qunlin; Wei, Dongtao; Zhang, Qinglin; Zhang, Meng; Qiu, Jiang

2015-07-01

In this study, an activation likelihood estimation (ALE) meta-analysis was used to conduct a quantitative investigation of neuroimaging studies on divergent thinking. Based on the ALE results, the functional magnetic resonance imaging (fMRI) studies showed that distributed brain regions were more active under divergent thinking tasks (DTTs) than those under control tasks, but a large portion of the brain regions were deactivated. The ALE results indicated that the brain networks of the creative idea generation in DTTs may be composed of the lateral prefrontal cortex, posterior parietal cortex [such as the inferior parietal lobule (BA 40) and precuneus (BA 7)], anterior cingulate cortex (ACC) (BA 32), and several regions in the temporal cortex [such as the left middle temporal gyrus (BA 39), and left fusiform gyrus (BA 37)]. The left dorsolateral prefrontal cortex (BA 46) was related to selecting the loosely and remotely associated concepts and organizing them into creative ideas, whereas the ACC (BA 32) was related to observing and forming distant semantic associations in performing DTTs. The posterior parietal cortex may be involved in the semantic information related to the retrieval and buffering of the formed creative ideas, and several regions in the temporal cortex may be related to the stored long-term memory. In addition, the ALE results of the structural studies showed that divergent thinking was related to the dopaminergic system (e.g., left caudate and claustrum). Based on the ALE results, both fMRI and structural MRI studies could uncover the neural basis of divergent thinking from different aspects (e.g., specific cognitive processing and stable individual difference of cognitive capability). © 2015 Wiley Periodicals, Inc.

An experimental investigation of velocity fields in divergent glottal models of the human vocal tract

NASA Astrophysics Data System (ADS)

Erath, Byron D.; Plesniak, Michael W.

2005-09-01

In speech, sound production arises from fluid-structure interactions within the larynx as well as viscous flow phenomena that is most likely to occur during the divergent orientation of the vocal folds. Of particular interest are the flow mechanisms that influence the location of flow separation points on the vocal folds walls. Physiologically scaled pulsatile flow fields in 7.5 times real size static divergent glottal models were investigated. Three divergence angles were investigated using phase-averaged particle image velocimetry (PIV). The pulsatile glottal jet exhibited a bi-modal stability toward both glottal walls, although there was a significant amount of variance in the angle the jet deflected from the midline. The attachment of the Coanda effect to the glottal model walls occurred when the pulsatile velocity was a maximum, and the acceleration of the waveform was zero. The location of the separation and reattachment points of the flow from the glottal models was a function of the velocity waveform and divergence angle. Acoustic analogies show that a dipole sound source contribution arising from the fluid interaction (Coanda jet) with the vocal fold walls is expected. [Work funded by NIH Grant RO1 DC03577.

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Structural Basis for Specific Inhibition of tRNA Synthetase by an ATP Competitive Inhibitor.

PubMed

Fang, Pengfei; Han, Hongyan; Wang, Jing; Chen, Kaige; Chen, Xin; Guo, Min

2015-06-18

Pharmaceutical inhibitors of aminoacyl-tRNA synthetases demand high species and family specificity. The antimalarial ATP-mimetic cladosporin selectively inhibits Plasmodium falciparum LysRS (PfLysRS). How the binding to a universal ATP site achieves the specificity is unknown. Here we report three crystal structures of cladosporin with human LysRS, PfLysRS, and a Pf-like human LysRS mutant. In all three structures, cladosporin occupies the class defining ATP-binding pocket, replacing the adenosine portion of ATP. Three residues holding the methyltetrahydropyran moiety of cladosporin are critical for the specificity of cladosporin against LysRS over other class II tRNA synthetase families. The species-exclusive inhibition of PfLysRS is linked to a structural divergence beyond the active site that mounts a lysine-specific stabilizing response to binding cladosporin. These analyses reveal that inherent divergence of tRNA synthetase structural assembly may allow for highly specific inhibition even through the otherwise universal substrate binding pocket and highlight the potential for structure-driven drug development. Copyright © 2015 Elsevier Ltd. All rights reserved.

Multivariate sequence analysis reveals additional function impacting residues in the SDR superfamily.

PubMed

Tiwari, Pratibha; Singh, Noopur; Dixit, Aparna; Choudhury, Devapriya

2014-10-01

The "extended" type of short chain dehydrogenases/reductases (SDR), share a remarkable similarity in their tertiary structures inspite of being highly divergent in their functions and sequences. We have carried out principal component analysis (PCA) on structurally equivalent residue positions of 10 SDR families using information theoretic measures like Jensen-Shannon divergence and average shannon entropy as variables. The results classify residue positions in the SDR fold into six groups, one of which is characterized by low Shannon entropies but high Jensen-Shannon divergence against the reference family SDR1E, suggesting that these positions are responsible for the specific functional identities of individual SDR families, distinguishing them from the reference family SDR1E. Site directed mutagenesis of three residues from this group in the enzyme UDP-Galactose 4-epimerase belonging to SDR1E shows that the mutants promote the formation of NADH containing abortive complexes. Finally, molecular dynamics simulations have been used to suggest a mechanism by which the mutants interfere with the re-oxidation of NADH leading to the formation of abortive complexes. © 2014 Wiley Periodicals, Inc.

Genetic divergence between freshwater and marine morphs of alewife (Alosa pseudoharengus): a 'next-generation' sequencing analysis.

PubMed

Czesny, Sergiusz; Epifanio, John; Michalak, Pawel

2012-01-01

Alewife Alosa pseudoharengus, a small clupeid fish native to Atlantic Ocean, has recently (∼150 years ago) invaded the North American Great Lakes and despite challenges of freshwater environment its populations exploded and disrupted local food web structures. This range expansion has been accompanied by dramatic changes at all levels of organization. Growth rates, size at maturation, or fecundity are only a few of the most distinct morphological and life history traits that contrast the two alewife morphs. A question arises to what extent these rapidly evolving differences between marine and freshwater varieties result from regulatory (including phenotypic plasticity) or structural mutations. To gain insights into expression changes and sequence divergence between marine and freshwater alewives, we sequenced transcriptomes of individuals from Lake Michigan and Atlantic Ocean. Population specific single nucleotide polymorphisms were rare but interestingly occurred in sequences of genes that also tended to show large differences in expression. Our results show that the striking phenotypic divergence between anadromous and lake alewives can be attributed to massive regulatory modifications rather than coding changes.

Genetic Divergence between Freshwater and Marine Morphs of Alewife (Alosa pseudoharengus): A ‘Next-Generation’ Sequencing Analysis

PubMed Central

Czesny, Sergiusz; Epifanio, John; Michalak, Pawel

2012-01-01

Alewife Alosa pseudoharengus, a small clupeid fish native to Atlantic Ocean, has recently (∼150 years ago) invaded the North American Great Lakes and despite challenges of freshwater environment its populations exploded and disrupted local food web structures. This range expansion has been accompanied by dramatic changes at all levels of organization. Growth rates, size at maturation, or fecundity are only a few of the most distinct morphological and life history traits that contrast the two alewife morphs. A question arises to what extent these rapidly evolving differences between marine and freshwater varieties result from regulatory (including phenotypic plasticity) or structural mutations. To gain insights into expression changes and sequence divergence between marine and freshwater alewives, we sequenced transcriptomes of individuals from Lake Michigan and Atlantic Ocean. Population specific single nucleotide polymorphisms were rare but interestingly occurred in sequences of genes that also tended to show large differences in expression. Our results show that the striking phenotypic divergence between anadromous and lake alewives can be attributed to massive regulatory modifications rather than coding changes. PMID:22438868

The role of habitat shift in the evolution of lizard morphology: evidence from tropical Tropidurus

PubMed Central

Vitt, Laurie J.; Caldwell, Janalee P.; Zani, Peter A.; Titus, Tom A.

1997-01-01

We compared morphology of two geographically close populations of the tropical lizard Tropidurus hispidus to test the hypothesis that habitat structure influences the evolution of morphology and ecology at the population level. T. hispidus isolated on a rock outcrop surrounded by tropical forest use rock crevices for refuge and appear dorsoventrally compressed compared with those in open savanna. A principal components analysis revealed that the populations were differentially distributed along an axis representing primarily three components of shape: body width, body height, and hind-leg length. Morphological divergence was supported by a principal components analysis of size-free morphological variables. Mitochondrial DNA sequences of ATPase 6 indicate that these populations are closely related relative to other T. hispidus, the rock outcrop morphology and ecology are derived within T. hispidus, and morphological and ecological divergence has occurred more rapidly than genetic divergence. This suggests that natural selection can rapidly adjust morphology and ecology in response to a recent history of exposure to habitats differing in structure, a result heretofore implied from comparative studies among lizard species. PMID:9108063

The role of habitat shift in the evolution of lizard morphology: evidence from tropical Tropidurus.

PubMed

Vitt, L J; Caldwell, J P; Zani, P A; Titus, T A

1997-04-15

We compared morphology of two geographically close populations of the tropical lizard Tropidurus hispidus to test the hypothesis that habitat structure influences the evolution of morphology and ecology at the population level. T. hispidus isolated on a rock outcrop surrounded by tropical forest use rock crevices for refuge and appear dorsoventrally compressed compared with those in open savanna. A principal components analysis revealed that the populations were differentially distributed along an axis representing primarily three components of shape: body width, body height, and hind-leg length. Morphological divergence was supported by a principal components analysis of size-free morphological variables. Mitochondrial DNA sequences of ATPase 6 indicate that these populations are closely related relative to other T. hispidus, the rock outcrop morphology and ecology are derived within T. hispidus, and morphological and ecological divergence has occurred more rapidly than genetic divergence. This suggests that natural selection can rapidly adjust morphology and ecology in response to a recent history of exposure to habitats differing in structure, a result heretofore implied from comparative studies among lizard species.

Molecular basis of the evolution of alternative tyrosine biosynthetic routes in plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schenck, Craig A.; Holland, Cynthia K.; Schneider, Matthew R.

L-Tyrosine (Tyr) is essential for protein synthesis and is a precursor of numerous specialized metabolites crucial for plant and human health. Tyr can be synthesized via two alternative routes by different key regulatory TyrA family enzymes, prephenate dehydrogenase (PDH, also known as TyrAp) or arogenate dehydrogenase (ADH, also known as TyrAa), representing a unique divergence of primary metabolic pathways. The molecular foundation underlying the evolution of these alternative Tyr pathways is currently unknown. Here we characterized recently diverged plant PDH and ADH enzymes, obtained the X-ray crystal structure of soybean PDH, and identified a single amino acid residue that definesmore » TyrA substrate specificity and regulation. Structures of mutated PDHs co-crystallized with Tyr indicate that substitutions of Asn222 confer ADH activity and Tyr sensitivity. Reciprocal mutagenesis of the corresponding residue in divergent plant ADHs further introduced PDH activity and relaxed Tyr sensitivity, highlighting the critical role of this residue in TyrA substrate specificity that underlies the evolution of alternative Tyr biosynthetic pathways in plants.« less

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae).

PubMed

da Silva, Marjorie; Noll, Fernando Barbosa; E Castro, Adriana C Morales-Corrêa

2018-01-01

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks.

Phylogeographic analysis reveals high genetic structure with uniform phenotypes in the paper wasp Protonectarina sylveirae (Hymenoptera: Vespidae)

PubMed Central

2018-01-01

Swarm-founding wasps are endemic and common representatives of neotropical fauna and compose an interesting social tribe of vespids, presenting both complex social characteristics and uncommon traits for a eusocial group, such as the absence of castes with distinct morphology. The paper wasp Protonectarina sylveirae (Saussure) presents a broad distribution from Brazil, Argentina and Paraguay, occurring widespread in the Atlantic rainforest and arboreal Caatinga, being absent in the Amazon region. Given the peculiar distribution among swarm-founding wasps, an integrative approach to reconstruct the evolutionary history of P. sylveirae in a spatial-temporal framework was performed to investigate: the presence of genetic structure and its relationship with the geography, the evolution of distinct morphologic lineages and the possible historical event(s) in Neotropical region, which could explain the observed phylogeographic pattern. Individuals of P. sylveirae were obtained from populations of 16 areas throughout its distribution for DNA extraction and amplification of mitochondrial genes 12S, 16S and COI. Analysis of genetic diversity, construction of haplotype net, analysis of population structure and dating analysis of divergence time were performed. A morphometric analysis was also performed using 8 measures of the body of the adult (workers) to test if there are morphological distinction among populations. Thirty-five haplotypes were identified, most of them exclusively of a group and a high population structure was found. The possibility of genetic divergence because of isolation by distance was rejected. Morphological analysis pointed to a great uniformity in phenotypes, with only a small degree of differentiation between populations of south and the remaining. Divergence time analysis showed a Middle/Late Miocene origin, a period where an extensive marine ingression occurred in South America. Divergence of haplogroups began from the Plio/Pleistocene boundary and the last glacial maximum most likely modeled the current distribution of species, even though it was not the cause of genetic breaks. PMID:29538451

Disturbance by an endemic rodent in an arid shrubland is a habitat filter: effects on plant invasion and taxonomical, functional and phylogenetic community structure

PubMed Central

Escobedo, Víctor M.; Rios, Rodrigo S.; Salgado-Luarte, Cristian; Stotz, Gisela C.

2017-01-01

Abstract Background and Aims Disturbance often drives plant invasion and may modify community assembly. However, little is known about how these modifications of community patterns occur in terms of taxonomic, functional and phylogenetic structure. This study evaluated in an arid shrubland the influence of disturbance by an endemic rodent on community functional divergence and phylogenetic structure as well as on plant invasion. It was expected that disturbance would operate as a habitat filter favouring exotic species with short life cycles. Methods Sixteen plots were sampled along a disturbance gradient caused by the endemic fossorial rodent Spalacopus cyanus, measuring community parameters and estimating functional divergence for life history traits (functional dispersion index) and the relative contribution to functional divergence of exotic and native species. The phylogenetic signal (Pagel’s lambda) and phylogenetic community structure (mean phylogenetic distance and mean nearest taxon phylogenetic distance) were also estimated. The use of a continuous approach to the disturbance gradient allowed the identification of non-linear relationships between disturbance and community parameters. Key Results The relationship between disturbance and both species richness and abundance was positive for exotic species and negative for native species. Disturbance modified community composition, and exotic species were associated with more disturbed sites. Disturbance increased trait convergence, which resulted in phylogenetic clustering because traits showed a significant phylogenetic signal. The relative contribution of exotic species to functional divergence increased, while that of natives decreased, with disturbance. Exotic and native species were not phylogenetically distinct. Conclusions Disturbance by rodents in this arid shrubland constitutes a habitat filter over phylogeny-dependent life history traits, leading to phylogenetic clustering, and drives invasion by favouring species with short life cycles. Results can be explained by high phenotypic and phylogenetic resemblance between exotic and native species. The use of continuous gradients when studying the effects of disturbance on community assembly is advocated. PMID:28087661

Novel Concordance Between Geographic, Environmental, and Genetic Structure in the Ecological Generalist Prickly Sculpin (Cottus asper) in California.

PubMed

Baumsteiger, Jason; Kinziger, Andrew P; Aguilar, Andres

2016-11-01

Ecological generalists may contain a wealth of information concerning diversity, ecology, and geographic connectivity throughout their range. We explored these ideas in prickly sculpin (Cottus asper), a small generalist freshwater fish species where coastal forms have potentially undergone radiations into inland lacustrine and riverine environments. Using a 962bp cytochrome b mtDNA marker and 11 microsatellites, we estimated diversity, divergence times, gene flow, and structure among populations at 43 locations throughout California. We then incorporated genetic and GIS data into ecological niche models to assess ecological conditions within identified groups. Though not reciprocally monophyletic, unique mtDNA haplotypes, microsatellite clustering, and measures of isolation by distance (Coastal: r = 0.960, P < 0.001; Inland: r = 0.277, P = 0.148) suggest 2 novel taxonomic groups, Coastal and Inland (constrained to Great Central Valley). Divergence estimates of 41-191 kya combined with the regional biogeographic history suggest geographic barriers are absent between groups since divergence, but ecological niche modeling revealed significant environmental differences (t = 10.84, P < 0.001). Introgressed individuals were also discovered between groups in an ecologically and geographically intermediate region. Population structure was limited, predominately found in tributaries of the San Joaquin basin in the Inland group. Overall, C. asper exhibited substantial genetic diversity, despite its ecological generality, reflecting California's historically unique and complex hydrology. More broadly, this study illustrates variable environments within the range of a generalist species may mask genetic divergences and should not be overlooked in biodiversity assessments. © The American Genetic Association 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Neopolyploidy and diversification in Heuchera grossulariifolia.

PubMed

Oswald, Benjamin P; Nuismer, Scott L

2011-06-01

Newly formed polyploid lineages must contend with several obstacles to avoid extinction, including minority cytotype exclusion, competition, and inbreeding depression. If polyploidization results in immediate divergence of phenotypic characters these hurdles may be reduced and establishment made more likely. In addition, if polyploidization alters the phenotypic and genotypic associations between traits, that is, the P and G matrices, polyploids may be able to explore novel evolutionary paths, facilitating their divergence and successful establishment. Here, we report results from a study of the perennial plant Heuchera grossulariifolia in which the phenotypic divergence and changes in phenotypic and genotypic covariance matrices caused by neopolyploidization have been estimated. Our results reveal that polyploidization causes immediate divergence for traits relevant to establishment and results in significant changes in the structure of the phenotypic covariance matrix. In contrast, our results do not provide evidence that polyploidization results in immediate and substantial shifts in the genetic covariance matrix. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Long range surface plasmon resonance with ultra-high penetration depth for self-referenced sensing and ultra-low detection limit using diverging beam approach

DOE Office of Scientific and Technical Information (OSTI.GOV)

Isaacs, Sivan, E-mail: sivan.isaacs@gmail.com; Abdulhalim, Ibrahim; NEW CREATE Programme, School of Materials Science and Engineering, 1 CREATE Way, Research Wing, #02-06/08, Singapore 138602

2015-05-11

Using an insulator-metal-insulator structure with dielectric having refractive index (RI) larger than the analyte, long range surface plasmon (SP) resonance exhibiting ultra-high penetration depth is demonstrated for sensing applications of large bioentities at wavelengths in the visible range. Based on the diverging beam approach in Kretschmann-Raether configuration, one of the SP resonances is shown to shift in response to changes in the analyte RI while the other is fixed; thus, it can be used as a built in reference. The combination of the high sensitivity, high penetration depth and self-reference using the diverging beam approach in which a dark linemore » is detected of the high sensitivity, high penetration depth, self-reference, and the diverging beam approach in which a dark line is detected using large number of camera pixels with a smart algorithm for sub-pixel resolution, a sensor with ultra-low detection limit is demonstrated suitable for large bioentities.« less

Phylogeny and evolution of ferns (monilophytes) with a focus on the early leptosporangiate divergences.

PubMed

Pryer, Kathleen M; Schuettpelz, Eric; Wolf, Paul G; Schneider, Harald; Smith, Alan R; Cranfill, Raymond

2004-10-01

The phylogenetic structure of ferns (= monilophytes) is explored here, with a special focus on the early divergences among leptosporangiate lineages. Despite considerable progress in our understanding of fern relationships, a rigorous and comprehensive analysis of the early leptosporangiate divergences was lacking. Therefore, a data set was designed here to include critical taxa that were not included in earlier studies. More than 5000 bp from the plastid (rbcL, atpB, rps4) and the nuclear (18S rDNA) genomes were sequenced for 62 taxa. Phylogenetic analyses of these data (1) confirm that Osmundaceae are sister to the rest of the leptosporangiates, (2) resolve a diverse set of ferns formerly thought to be a subsequent grade as possibly monophyletic (((Dipteridaceae, Matoniaceae), Gleicheniaceae), Hymenophyllaceae), and (3) place schizaeoid ferns as sister to a large clade of "core leptosporangiates" that includes heterosporous ferns, tree ferns, and polypods. Divergence time estimates for ferns are reported from penalized likelihood analyses of our molecular data, with constraints from a reassessment of the fossil record.

Genome-Wide Survey on Genomic Variation, Expression Divergence, and Evolution in Two Contrasting Rice Genotypes under High Salinity Stress

PubMed Central

Jiang, Shu-Ye; Ma, Ali; Ramamoorthy, Rengasamy; Ramachandran, Srinivasan

2013-01-01

Expression profiling is one of the most important tools for dissecting biological functions of genes and the upregulation or downregulation of gene expression is sufficient for recreating phenotypic differences. Expression divergence of genes significantly contributes to phenotypic variations. However, little is known on the molecular basis of expression divergence and evolution among rice genotypes with contrasting phenotypes. In this study, we have implemented an integrative approach using bioinformatics and experimental analyses to provide insights into genomic variation, expression divergence, and evolution between salinity-sensitive rice variety Nipponbare and tolerant rice line Pokkali under normal and high salinity stress conditions. We have detected thousands of differentially expressed genes between these two genotypes and thousands of up- or downregulated genes under high salinity stress. Many genes were first detected with expression evidence using custom microarray analysis. Some gene families were preferentially regulated by high salinity stress and might play key roles in stress-responsive biological processes. Genomic variations in promoter regions resulted from single nucleotide polymorphisms, indels (1–10 bp of insertion/deletion), and structural variations significantly contributed to the expression divergence and regulation. Our data also showed that tandem and segmental duplication, CACTA and hAT elements played roles in the evolution of gene expression divergence and regulation between these two contrasting genotypes under normal or high salinity stress conditions. PMID:24121498

Patterns of Positive Selection of the Myogenic Regulatory Factor Gene Family in Vertebrates

PubMed Central

Zhao, Xiao; Yu, Qi; Huang, Ling; Liu, Qing-Xin

2014-01-01

The functional divergence of transcriptional factors is critical in the evolution of transcriptional regulation. However, the mechanism of functional divergence among these factors remains unclear. Here, we performed an evolutionary analysis for positive selection in members of the myogenic regulatory factor (MRF) gene family of vertebrates. We selected 153 complete vertebrate MRF nucleotide sequences from our analyses, which revealed substantial evidence of positive selection. Here, we show that sites under positive selection were more frequently detected and identified from the genes encoding the myogenic differentiation factors (MyoG and Myf6) than the genes encoding myogenic determination factors (Myf5 and MyoD). Additionally, the functional divergence within the myogenic determination factors or differentiation factors was also under positive selection pressure. The positive selection sites were more frequently detected from MyoG and MyoD than Myf6 and Myf5, respectively. Amino acid residues under positive selection were identified mainly in their transcription activation domains and on the surface of protein three-dimensional structures. These data suggest that the functional gain and divergence of myogenic regulatory factors were driven by distinct positive selection of their transcription activation domains, whereas the function of the DNA binding domains was conserved in evolution. Our study evaluated the mechanism of functional divergence of the transcriptional regulation factors within a family, whereby the functions of their transcription activation domains diverged under positive selection during evolution. PMID:24651579

Juvenile skeletogenesis in anciently diverged sea urchin clades.

PubMed

Gao, Feng; Thompson, Jeffrey R; Petsios, Elizabeth; Erkenbrack, Eric; Moats, Rex A; Bottjer, David J; Davidson, Eric H

2015-04-01

Mechanistic understanding of evolutionary divergence in animal body plans devolves from analysis of those developmental processes that, in forms descendant from a common ancestor, are responsible for their morphological differences. The last common ancestor of the two extant subclasses of sea urchins, i.e., euechinoids and cidaroids, existed well before the Permian/Triassic extinction (252 mya). Subsequent evolutionary divergence of these clades offers in principle a rare opportunity to solve the developmental regulatory events underlying a defined evolutionary divergence process. Thus (i) there is an excellent and fairly dense (if yet incompletely analyzed) fossil record; (ii) cladistically confined features of the skeletal structures of modern euechinoid and cidaroid sea urchins are preserved in fossils of ancestral forms; (iii) euechinoids and cidaroids are among current laboratory model systems in molecular developmental biology (here Strongylocentrotus purpuratus [Sp] and Eucidaris tribuloides [Et]); (iv) skeletogenic specification in sea urchins is uncommonly well understood at the causal level of interactions of regulatory genes with one another, and with known skeletogenic effector genes, providing a ready arsenal of available molecular tools. Here we focus on differences in test and perignathic girdle skeletal morphology that distinguish all modern euechinoid from all modern cidaroid sea urchins. We demonstrate distinct canonical test and girdle morphologies in juveniles of both species by use of SEM and X-ray microtomography. Among the sharply distinct morphological features of these clades are the internal skeletal structures of the perignathic girdle to which attach homologous muscles utilized for retraction and protraction of Aristotles׳ lantern and its teeth. We demonstrate that these structures develop de novo between one and four weeks after metamorphosis. In order to study the underlying developmental processes, a method of section whole mount in situ hybridization was adapted. This method displays current gene expression in the developing test and perignathic girdle skeletal elements of both Sp and Et juveniles. Active, specific expression of the sm37 biomineralization gene in these muscle attachment structures accompanies morphogenetic development of these clade-specific features in juveniles of both species. Skeletogenesis at these clade-specific muscle attachment structures displays molecular earmarks of the well understood embryonic skeletogenic GRN: thus the upstream regulatory gene alx1 and the gene encoding the vegfR signaling receptor are both expressed at the sites where they are formed. This work opens the way to analysis of the alternative spatial specification processes that were installed at the evolutionary divergence of the two extant subclasses of sea urchins. Copyright © 2015 Elsevier Inc. All rights reserved.

Radiofrequency catheter ablation of ventricular tachycardia in patients without structural heart disease.

PubMed

Klein, L S; Shih, H T; Hackett, F K; Zipes, D P; Miles, W M

1992-05-01

Radiofrequency energy has been used safely and successfully to eliminate accessory pathways in patients with the Wolff-Parkinson-White syndrome and the substrate for atrioventricular nodal reentrant tachycardia. However, this form of ablation has had only limited success in eliminating ventricular tachycardia in patients with structural heart disease. In contrast, direct-current catheter ablation has been used successfully to eliminate ventricular tachycardia in patients with and without structural heart disease. The purpose of this study was to test whether radiofrequency energy can safely and effectively ablate ventricular tachycardia in patients without structural heart disease. Sixteen patients (nine women and seven men; mean age, 38 years; range, 18-55 years) without structural heart disease who had ventricular tachycardia underwent radiofrequency catheter ablation to eliminate the ventricular tachycardia. Two patients presented with syncope, nine with presyncope, and five with palpitations only. Mean duration of symptoms was 6.7 years (range, 0.5-20 years). Radiofrequency catheter ablation successfully eliminated ventricular tachycardia in 15 of 16 patients (94%). Sites of ventricular tachycardia origin included the high right ventricular outflow tract (12 patients), the right ventricular septum near the tricuspid valve (three patients), and the left ventricular septum (one patient). The only ablation failure was in a patient whose ventricular tachycardia arose from a region near the His bundle. An accurate pace map, early local endocardial activation, and firm catheter contact with endocardium were associated with successful ablation. Radiofrequency ablation did not cause arrhythmias, produced minimal cardiac enzyme rise, and resulted in no detectable change in cardiac function by Doppler echocardiography. Radiofrequency catheter ablation of ventricular tachycardia in patients without structural heart disease is effective and safe and may be considered as early therapy in these patients.

Short-range phenotypic divergence among genetically distinct parapatric populations of an Australian funnel-web spider.

PubMed

Wong, Mark K L; Woodman, James D; Rowell, David M

2017-07-01

Speciation involves divergence at genetic and phenotypic levels. Where substantial genetic differentiation exists among populations, examining variation in multiple phenotypic characters may elucidate the mechanisms by which divergence and speciation unfold. Previous work on the Australian funnel-web spider Atrax sutherlandi Gray (2010; Records of the Australian Museum 62 , 285-392; Mygalomorphae: Hexathelidae: Atracinae) has revealed a marked genetic structure along a 110-kilometer transect, with six genetically distinct, parapatric populations attributable to past glacial cycles. In the present study, we explore variation in three classes of phenotypic characters (metabolic rate, water loss, and morphological traits) within the context of this phylogeographic structuring. Variation in metabolic and water loss rates shows no detectable association with genetic structure; the little variation observed in these rates may be due to the spiders' behavioral adaptations (i.e., burrowing), which buffer the effects of climatic gradients across the landscape. However, of 17 morphological traits measured, 10 show significant variation among genetic populations, in a disjunct manner that is clearly not latitudinal. Moreover, patterns of variation observed for morphological traits serving different organismic functions (e.g., prey capture, burrowing, and locomotion) are dissimilar. In contrast, a previous study of an ecologically similar sympatric spider with little genetic structure indicated a strong latitudinal response in 10 traits over the same range. The congruence of morphological variation with deep phylogeographic structure in Tallaganda's A. sutherlandi populations, as well as the inconsistent patterns of variation across separate functional traits, suggest that the spiders are likely in early stages of speciation, with parapatric populations independently responding to local selective forces.

Numerical simulation of current-free double layers created in a helicon plasma device

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Sathyanarayan; Singh, Nagendra

2012-09-15

Two-dimensional simulations reveal that when radially confined source plasma with magnetized electrons and unmagnetized ions expands into diverging magnetic field B, a current-free double layer (CFDL) embedded in a conical density structure forms, as experimentally measured in the Australian helicon plasma device (HPD). The magnetized electrons follow the diverging B while the unmagnetized ions tend to flow directly downstream of the source, resulting in a radial electric field (E{sub Up-Tack }) structure, which couples the ion and electron flows. Ions are transversely (radially) accelerated by E{sub Up-Tack} on the high potential side of the double layer in the CFDL. Themore » accelerated ions are trapped near the conical surface, where E{sub Up-Tack} reverses direction. The potential structure of the CFDL is U-shaped and the plasma density is enhanced on the conical surface. The plasma density is severely depleted downstream of the parallel potential drop ({phi}{sub Double-Vertical-Line Double-Vertical-Line o}) in the CFDL; the density depletion and the potential drop are related by quasi-neutrality condition, including the divergence in the magnetic field and in the plasma flow in the conical structure. The potential and density structures, the CFDL spatial size, its electric field strengths and the electron and ion velocities and energy distributions in the CFDL are found to be in good agreements with those measured in the Australian experiment. The applicability of our results to measured axial potential profiles in magnetic nozzle experiments in HPDs is discussed.« less

Structural and Functional Divergence of the Aldolase Fold in Toxoplasma gondii

DOE PAGES

Tonkin, Michelle L.; Halavaty, Andrei S.; Ramaswamy, Raghavendran; ...

2014-10-02

Parasites of the phylum Apicomplexa are highly successful pathogens of humans and animals worldwide. As obligate intracellular parasites, they have significant energy requirements for invasion and gliding motility that are supplied by various metabolic pathways. Aldolases have emerged as key enzymes involved in these pathways, and all apicomplexans express one or both of fructose 1,6-bisphosphate (F16BP) aldolase and 2-deoxyribose 5-phosphate (dR5P) aldolase (DERA). Intriguingly, Toxoplasma gondii, a highly successful apicomplexan parasite, expresses F16BP aldolase (TgALD1), d5RP aldolase (TgDERA), and a divergent dR5P aldolase-like protein (TgDPA) exclusively in the latent bradyzoite stage. While the importance of TgALD1 in glycolysis is wellmore » established and TgDERA is also likely to be involved in parasite metabolism, the detailed function of TgDPA remains elusive. Here, to gain mechanistic insight into the function of different T. gondii aldolases, we first determined the crystal structures of TgALD1 and TgDPA. Structural analysis revealed that both aldolases adopt a TIM barrel fold accessorized with divergent secondary structure elements. Structural comparison of TgALD1 and TgDPA with members of their respective enzyme families revealed that, while the active-site residues are conserved in TgALD1, key catalytic residues are absent in TgDPA. Consistent with this observation, biochemical assays showed that, while TgALD1 was active on F16BP, TgDPA was inactive on dR5P. In conclusion, intriguingly, both aldolases are competent to bind polymerized actin in vitro. Altogether, structural and biochemical analyses of T. gondii aldolase and aldolase-like proteins reveal diverse functionalization of the classic TIM barrel aldolase fold.« less

Structural and functional divergence of the aldolase fold in Toxoplasma gondii.

PubMed

Tonkin, Michelle L; Halavaty, Andrei S; Ramaswamy, Raghavendran; Ruan, Jiapeng; Igarashi, Makoto; Ngô, Huân M; Boulanger, Martin J

2015-02-27

Parasites of the phylum Apicomplexa are highly successful pathogens of humans and animals worldwide. As obligate intracellular parasites, they have significant energy requirements for invasion and gliding motility that are supplied by various metabolic pathways. Aldolases have emerged as key enzymes involved in these pathways, and all apicomplexans express one or both of fructose 1,6-bisphosphate (F16BP) aldolase and 2-deoxyribose 5-phosphate (dR5P) aldolase (DERA). Intriguingly, Toxoplasma gondii, a highly successful apicomplexan parasite, expresses F16BP aldolase (TgALD1), d5RP aldolase (TgDERA), and a divergent dR5P aldolase-like protein (TgDPA) exclusively in the latent bradyzoite stage. While the importance of TgALD1 in glycolysis is well established and TgDERA is also likely to be involved in parasite metabolism, the detailed function of TgDPA remains elusive. To gain mechanistic insight into the function of different T. gondii aldolases, we first determined the crystal structures of TgALD1 and TgDPA. Structural analysis revealed that both aldolases adopt a TIM barrel fold accessorized with divergent secondary structure elements. Structural comparison of TgALD1 and TgDPA with members of their respective enzyme families revealed that, while the active-site residues are conserved in TgALD1, key catalytic residues are absent in TgDPA. Consistent with this observation, biochemical assays showed that, while TgALD1 was active on F16BP, TgDPA was inactive on dR5P. Intriguingly, both aldolases are competent to bind polymerized actin in vitro. Altogether, structural and biochemical analyses of T. gondii aldolase and aldolase-like proteins reveal diverse functionalization of the classic TIM barrel aldolase fold. Copyright © 2014 Elsevier Ltd. All rights reserved.

Measles virus genotypes circulating in India, 2011-2015.

PubMed

Vaidya, Sunil R; Chowdhury, Deepika T

2017-05-01

The Government of India is accepted to participate in the measles elimination and rubella control goal 2020, hence genetic characterization of measles viruses (MeV) becomes essential. At National Reference Laboratory (National Institute of Virology, Pune), the throat swabs/urine specimens (n = 380) or PCR products (n = 219) obtained from the suspected measles cases were referred for the molecular testing and subsequently, MeV nucleoprotein (N) gene sequencing/genotyping. In addition, 2,449 suspected measles cases, mainly from the Maharashtra state were referred for the laboratory diagnosis. A detailed study was performed on N gene sequences obtained during last two decades. Indian MeV sequences obtained during 2011-2015 were compared with 1996-2010 sequences and genetic divergence was studied. Circulation of measles genotypes B3 (n = 3), D4 (n = 49), and D8 (n = 351) strains were observed in 19 States and three Union Territories of India. In addition, 64 measles viruses were isolated from 253 throat swab or urine specimens obtained from the suspected measles cases. During 2011-2015, 67.9% (1,663/2,449) suspected measles cases were laboratory confirmed. Molecular studies showed circulation of measles genotype B3 in India along with prominently circulating genotypes D4 and D8 except D7 strains. The genetic diversion within Indian B3, D4, and D8 genotypes was 0.3%, 1.1%, and 2.1%, respectively. The genetic divergence of Indian B3, D4, and D8 measles strains with the WHO reference sequences was 2.5%, 2.6%, and 1.8%, respectively. It is crucial data for national immunization program. More measles/rubella genotyping studies are necessary to track transmission and to support measles elimination and rubella control. J. Med. Virol. 89:753-758, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development.

PubMed

Sun, Cheng; Wyngaard, Grace; Walton, D Brian; Wichman, Holly A; Mueller, Rachel Lockridge

2014-03-11

Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution--some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 - 75 Gb, 12-74 Gb of which are lost from pre-somatic cell lineages at germline--soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown. Here, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1) verifiable transposable elements (TEs), or 2) non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger (i.e. less divergent) elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome. Our results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms.

Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development

PubMed Central

2014-01-01

Background Chromatin diminution is the programmed deletion of DNA from presomatic cell or nuclear lineages during development, producing single organisms that contain two different nuclear genomes. Phylogenetically diverse taxa undergo chromatin diminution — some ciliates, nematodes, copepods, and vertebrates. In cyclopoid copepods, chromatin diminution occurs in taxa with massively expanded germline genomes; depending on species, germline genome sizes range from 15 – 75 Gb, 12–74 Gb of which are lost from pre-somatic cell lineages at germline – soma differentiation. This is more than an order of magnitude more sequence than is lost from other taxa. To date, the sequences excised from copepods have not been analyzed using large-scale genomic datasets, and the processes underlying germline genomic gigantism in this clade, as well as the functional significance of chromatin diminution, have remained unknown. Results Here, we used high-throughput genomic sequencing and qPCR to characterize the germline and somatic genomes of Mesocyclops edax, a freshwater cyclopoid copepod with a germline genome of ~15 Gb and a somatic genome of ~3 Gb. We show that most of the excised DNA consists of repetitive sequences that are either 1) verifiable transposable elements (TEs), or 2) non-simple repeats of likely TE origin. Repeat elements in both genomes are skewed towards younger (i.e. less divergent) elements. Excised DNA is a non-random sample of the germline repeat element landscape; younger elements, and high frequency DNA transposons and LINEs, are disproportionately eliminated from the somatic genome. Conclusions Our results suggest that germline genome expansion in M. edax reflects explosive repeat element proliferation, and that billions of base pairs of such repeats are deleted from the somatic genome every generation. Thus, we hypothesize that chromatin diminution is a mechanism that controls repeat element load, and that this load can evolve to be divergent between tissue types within single organisms. PMID:24618421

Cloning and structural analysis of two highly divergent IgA isotypes, IgA1 and IgA2 from the duck billed platypus, Ornithorhynchus anatinus.

PubMed

Vernersson, M; Belov, K; Aveskogh, M; Hellman, L

2010-01-01

To trace the emergence of modern IgA isotypes during vertebrate evolution we have studied the immunoglobulin repertoire of a model monotreme, the platypus. Two highly divergent IgA-like isotypes (IgA1 and IgA2) were identified and their primary structures were determined from full-length cDNAs. A comparative analysis of the amino acid sequences for IgA from various animal species showed that the two platypus IgA isotypes form a branch clearly separated from their eutherian (placental) counterparts. However, they still conform to the general structure of eutherian IgA, with a hinge region and three constant domains. This indicates that the deletion of the second domain and the formation of a hinge region in IgA did occur very early during mammalian evolution, more than 166 million years ago. The two IgA isotypes in platypus differ in primary structure and appear to have arisen from a very early gene duplication, possibly preceding the metatherian eutherian split. Interestingly, one of these isotypes, IgA1, appears to be expressed in only the platypus, but is present in the echidna based on Southern blot analysis. The platypus may require a more effective mucosal immunity, with two highly divergent IgA forms, than the terrestrial echidna, due to its lifestyle, where it is exposed to pathogens both on land and in the water. Copyright 2010 Elsevier Ltd. All rights reserved.

A Divergent SAR Study Allows Optimization of a Potent 5-HT2c Inhibitor to a Promising Antimalarial Scaffold.

PubMed

Calderón, Félix; Vidal-Mas, Jaume; Burrows, Jeremy; de la Rosa, Juan Carlos; Jiménez-Díaz, María Belén; Mulet, Teresa; Prats, Sara; Solana, Jorge; Witty, Michael; Gamo, Francisco Javier; Fernández, Esther

2012-05-10

From the 13 533 chemical structures published by GlaxoSmithKline in 2010, we identified 47 quality starting points for lead optimization. One of the most promising hits was the TCMDC-139046, a molecule presenting an indoline core, which is well-known for its anxiolytic properties by interacting with serotonin antagonist receptors 5-HT2. The inhibition of this target will complicate the clinical development of these compounds as antimalarials. Herein, we present the antimalarial profile of this series and our efforts to avoid interaction with this receptor, while maintaining a good antiparasitic potency. By using a double-divergent structure-activity relationship analysis, we have obtained a novel lead compound harboring an indoline core.

Eco-evo-devo in the Study of Adaptive Divergence: Examples from Threespine Stickleback (Gasterosteus aculeatus).

PubMed

Jamniczky, Heather A; Barry, Tegan N; Rogers, Sean M

2015-07-01

The tight fit between form and function in organisms suggests the influence of adaptive evolution in biomechanics; however, the prevalence of adaptive traits, the mechanisms by which they arise and the corresponding responses to selection are subjects of extensive debate. We used three-dimensional microcomputed tomography and geometric morphometrics to characterize the structure of phenotypic covariance within the G. aculeatus trophic apparatus and its supporting structures in wild and controlled crosses of fish from two different localities. Our results reveal that while the structure of phenotypic covariance is conserved in marine and freshwater forms, it may be disrupted in the progeny of artificial crosses or during rapid adaptive divergence events. We discuss these results within the context of integrating covariance structure with quantitative genetics, toward establishing predictive links between genes, development, biomechanics, and the environment. © The Author 2015. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Elimination sequence optimization for SPAR

NASA Technical Reports Server (NTRS)

Hogan, Harry A.

1986-01-01

SPAR is a large-scale computer program for finite element structural analysis. The program allows user specification of the order in which the joints of a structure are to be eliminated since this order can have significant influence over solution performance, in terms of both storage requirements and computer time. An efficient elimination sequence can improve performance by over 50% for some problems. Obtaining such sequences, however, requires the expertise of an experienced user and can take hours of tedious effort to affect. Thus, an automatic elimination sequence optimizer would enhance productivity by reducing the analysts' problem definition time and by lowering computer costs. Two possible methods for automating the elimination sequence specifications were examined. Several algorithms based on the graph theory representations of sparse matrices were studied with mixed results. Significant improvement in the program performance was achieved, but sequencing by an experienced user still yields substantially better results. The initial results provide encouraging evidence that the potential benefits of such an automatic sequencer would be well worth the effort.

The biogeodynamics of microbial landscapes

NASA Astrophysics Data System (ADS)

Battin, T. J.; Hödl, I.; Bertuzzo, E.; Mari, L.; Suweis, S. S.; Rinaldo, A.

2011-12-01

Spatial configuration is fundamental in defining the structural and functional properties of biological systems. Biofilms, surface-attached and matrix-enclosed microorganisms, are a striking example of spatial organisation. Coupled biotic and abiotic processes shape the spatial organisation across scales of the landscapes formed by these benthic biofilms in streams and rivers. Experimenting with such biofilms in streams, we found that, depending on the streambed topography and the related hydrodynamic microenvironment, biofilm landscapes form increasingly diverging spatial patterns as they grow. Strikingly, however, cluster size distributions tend to converge even in contrasting hydrodynamic microenvironments. To reproduce the observed cluster size distributions we used a continuous, size-structured population model. The model accounts for the formation, growth, erosion and merging of biofilm clusters. Our results suggest not only that hydrodynamic forcing induce the diverging patterning of the microbial landscape, but also that microorganisms have developed strategies to equally exploit spatial resources independently of the physical structure of the microenvironment where they live.

Entropy measure of credit risk in highly correlated markets

NASA Astrophysics Data System (ADS)

Gottschalk, Sylvia

2017-07-01

We compare the single and multi-factor structural models of corporate default by calculating the Jeffreys-Kullback-Leibler divergence between their predicted default probabilities when asset correlations are either high or low. Single-factor structural models assume that the stochastic process driving the value of a firm is independent of that of other companies. A multi-factor structural model, on the contrary, is built on the assumption that a single firm's value follows a stochastic process correlated with that of other companies. Our main results show that the divergence between the two models increases in highly correlated, volatile, and large markets, but that it is closer to zero in small markets, when asset correlations are low and firms are highly leveraged. These findings suggest that during periods of financial instability, when asset volatility and correlations increase, one of the models misreports actual default risk.

Theoretical study of the ionospheric plasma cave in the equatorial ionization anomaly region

NASA Astrophysics Data System (ADS)

Chen, Yu-Tsung; Lin, C. H.; Chen, C. H.; Liu, J. Y.; Huba, J. D.; Chang, L. C.; Liu, H.-L.; Lin, J. T.; Rajesh, P. K.

2014-12-01

This paper investigates the physical mechanism of an unusual equatorial electron density structure, plasma cave, located underneath the equatorial ionization anomaly by using theoretical simulations. The simulation results provide important new understanding of the dynamics of the equatorial ionosphere. It has been suggested previously that unusual E>⇀×B>⇀ drifts might be responsible for the observed plasma cave structure, but model simulations in this paper suggest that the more likely cause is latitudinal meridional neutral wind variations. The neutral winds are featured by two divergent wind regions at off-equator latitudes and a convergent wind region around the magnetic equator, resulting in plasma divergences and convergence, respectively, to form the plasma caves structure. The tidal-decomposition analysis further suggests that the cave related meridional neutral winds and the intensity of plasma cave are highly associated with the migrating terdiurnal tidal component of the neutral winds.

Robust boundary treatment for open-channel flows in divergence-free incompressible SPH

NASA Astrophysics Data System (ADS)

Pahar, Gourabananda; Dhar, Anirban

2017-03-01

A robust Incompressible Smoothed Particle Hydrodynamics (ISPH) framework is developed to simulate specified inflow and outflow boundary conditions for open-channel flow. Being purely divergence-free, the framework offers smoothed and structured pressure distribution. An implicit treatment of Pressure Poison Equation and Dirichlet boundary condition is applied on free-surface to minimize error in velocity-divergence. Beyond inflow and outflow threshold, multiple layers of dummy particles are created according to specified boundary condition. Inflow boundary acts as a soluble wave-maker. Fluid particles beyond outflow threshold are removed and replaced with dummy particles with specified boundary velocity. The framework is validated against different cases of open channel flow with different boundary conditions. The model can efficiently capture flow evolution and vortex generation for random geometry and variable boundary conditions.

A Prescriptive, Intergenerational-Tension Ageism Scale: Succession, Identity, and Consumption (SIC)

PubMed Central

North, Michael S.; Fiske, Susan T.

2014-01-01

We introduce a novel ageism scale, focusing on prescriptive beliefs concerning potential intergenerational tensions: active, envied resource Succession, symbolic Identity avoidance, and passive, shared-resource Consumption (SIC). Four studies (2,010 total participants) developed the scale. EFA formed an initial 20-item, three-factor solution (Study 1). The scale converges appropriately with other prejudice measures and diverges from other social control measures (Study 2). It diverges from anti-youth ageism (Study 3). Study 4’s experiment yielded both predictive and divergent validity apropos another ageism measure. Structural equation modeling confirmed model fit across all studies. Per an intergenerational-tension focus, younger people consistently scored the highest. As generational equity issues intensify, the scale provides a contemporary tool for current and future ageism research. PMID:23544391

Quantifying predictability variations in a low-order ocean-atmosphere model - A dynamical systems approach

NASA Technical Reports Server (NTRS)

Nese, Jon M.; Dutton, John A.

1993-01-01

The predictability of the weather and climatic states of a low-order moist general circulation model is quantified using a dynamic systems approach, and the effect of incorporating a simple oceanic circulation on predictability is evaluated. The predictability and the structure of the model attractors are compared using Liapunov exponents, local divergence rates, and the correlation and Liapunov dimensions. It was found that the activation of oceanic circulation increases the average error doubling time of the atmosphere and the coupled ocean-atmosphere system by 10 percent and decreases the variance of the largest local divergence rate by 20 percent. When an oceanic circulation develops, the average predictability of annually averaged states is improved by 25 percent and the variance of the largest local divergence rate decreases by 25 percent.

A SEM Model in Assessing the Effect of Convergent, Divergent and Logical Thinking on Students' Understanding of Chemical Phenomena

ERIC Educational Resources Information Center

Stamovlasis, D.; Kypraios, N.; Papageorgiou, G.

2015-01-01

In this study, structural equation modeling (SEM) is applied to an instrument assessing students' understanding of chemical change. The instrument comprised items on understanding the structure of substances, chemical changes and their interpretation. The structural relationships among particular groups of items are investigated and analyzed using…

Technology as an Occasion for Structuring: Evidence from Observations of CT Scanners and the Social Order of Radiology Departments.

ERIC Educational Resources Information Center

Barley, Stephen R.

1986-01-01

New technologies such as the CT scanner are challenging traditional role relations among radiology workers and may be altering the organizational and occupational structure of radiological work. This paper expands recent sociological thought by showing how identical CT scanners occasion similar structuring processes and created divergent forms of…

Anisotropy in Gravity and Holography

NASA Astrophysics Data System (ADS)

Melby-Thompson, Charles Milton

In this thesis, we examine the dynamical structure of Hořava-Lifshitz gravity, and investigate its relationship with holography for anisotropic systems. Hořava-Lifshitz gravity refers to a broad class of gravitational models that incorporate anisotropy at a fundamental level. The idea behind Hořava-Lifshitz gravity is to utilize ideas from the theory of dynamical critical phenomena into gravity to produce a theory of dynamical spacetime that is power-counting renormalizable, and is thus a candidate renormalizable quantum field theory of gravity. One of the most distinctive features of Hořava-Lifshitz gravity is that its group of symmetries consists not of the diffeomorphisms of spacetime, but instead of the group of diffeomorphisms that preserve a given foliation by spatial slices. As a result of having a smaller group of symmetries, HL gravity naturally has one more propagating degree of freedom than general relativity. The extra mode presents two possible difficulties with the theory, one relating to consistency, and the second to its viability as a phenomenological model. (1) It may destabilize the theory. (2) Phenomenologically, there are severe constraints on the existence of an extra propagating graviton polarization, as well as strong experimental constraints on the value of a parameter appearing in the dispersion relation of the extra mode. In the first part of this dissertation we show that the extra mode can be eliminated by introducing a new local symmetry which steps in and takes the place of general covariance in the anisotropic context. While the identification of the appropriate symmetry is quite subtle in the full non-linear theory, once the dust settles, the resulting theory has a spectrum which matches that of general relativity in the infrared. This goes a good way toward answering the question of how close Hořava-Lifshitz gravity can come to reproducing general relativity in the infrared regime. In the second part of the thesis we pursue the relationship between Hořava-Lifshitz gravity and holographic duals for anisotropic systems. A holographic correspondence is one that posits an equivalence between a theory of gravity on a given spacetime background and a field theory living on the "boundary" of that spacetime, which resides at infinite spatial separation from the interior. It is a non-trivial problem how to define this boundary, but in the case of relativistic boundary field theories, there is a well-known definition due to Penrose of the boundary which produces the geometric structure required to make sense of the correspondence. However, the proposed dual geometries to anisotropic quantum field theories have a Penrose boundary that is incompatible with the assumed correspondence. We generalize Penrose's approach, using concepts from Hořava-Lifshitz gravity, to spacetimes with anisotropic boundary conditions, thereby arriving at the concept of anisotropic conformal infinity that is compatible with the holographic correspondence in these spacetimes. We then apply this work to understanding the structure of holography for anisotropic systems in more detail. In particular, we examine the structure of divergences of a certain theory of gravity on Lifshitz space. We find, using our construction of anisotropic conformal infinity, that the appropriate geometric structure of the boundary is that of a foliated spacetime with an anisotropic metric complex. We then perform holographic renormalization in these spacetimes, yielding a computation of the divergent part of the effective action, and find that it exhibits precisely the structure of a Hořava-Lifshitz action. Moreover, we find that, for dynamical exponent z = 2, the logarithmic divergence gives rise to a conformal anomaly in 2+1 dimensions, whose general form is precisely that of conformal Hořava-Lifshitz gravity with detailed balance.

The Effect of Structured Divergent Prompts on Knowledge Construction

ERIC Educational Resources Information Center

Howell, Ginger S.; Akpanudo, Usenime; Chen, Mengyi; Sutherlin, Autumn L.; James, Laura E.

2014-01-01

Discussion forums are a widely used activity in online courses. However, knowledge construction within online discussion rarely reaches higher levels. Therefore, it is important to understand which aspects of online discussion encourage learning and increase knowledge construction. This paper investigates the effect three Structured Divergent…

The Structure of Intellect, Its Interpretations and Uses.

ERIC Educational Resources Information Center

Meeker, Mary Nacol

Using Guilford's model, the text reviews the structure of the intellect (SOI) and its operations, contents, and products. Those operations and components are further described, including the factors of cognition, memory, evaluation, convergent-production, and divergent-production. For each factor, the figural, symbolic, and semantic dimensions are…

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand

PubMed Central

2011-01-01

Background The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. Results A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. Conclusions The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. PMID:21672265

Connecting Amazonian, Cerrado, and Atlantic Forest histories: Paraphyly, old divergences, and modern population dynamics in tyrant-manakins (Neopelma/Tyranneutes, Aves: Pipridae).

PubMed

Capurucho, João Marcos Guimarães; Ashley, Mary V; Ribas, Camila C; Bates, John M

2018-06-11

Several biogeographic hypotheses have been proposed to explain connections between Amazonian and Atlantic forest biotas. These hypotheses are related to the timing of the connections and their geographic patterns. We performed a phylogeographic investigation of Tyrant-manakins (Aves: Pipridae, Neopelma/Tyranneutes) which include species inhabiting the Amazon and Atlantic forests, as well as gallery forests of the Cerrado. Using DNA sequence data, we determined phylogenetic relationships, temporal and geographic patterns of diversification, and recent intraspecific population genetic patterns, relative to the history of these biomes. We found Neopelma to be a paraphyletic genus, as N. chrysolophum is sister to Neopelma + Tyranneutes, with an estimated divergence of approximately 18 Myrs BP, within the oldest estimated divergence times of other Amazonian and Atlantic forest avian taxa. Subsequent divergences in the group occurred from Mid Miocene to Early Pliocene and involved mainly the Amazonian species, with an expansion into and subsequent speciation in the Cerrado gallery forests by N. pallescens. We found additional structure within N. chrysocephalum and N. sulphureiventer. Analysis of recent population dynamics in N. chrysocephalum, N. sulphureiventer, and N. pallescens revealed recent demographic fluctuations and restrictions to gene flow related to environmental changes since the last glacial cycle. No genetic structure was detected across the Amazon River in N. pallescens. The tyrant-manakins represent an old historical connection between the Amazon and Atlantic Forest. Copyright © 2018. Published by Elsevier Inc.

Genetic structure of the Mon-Khmer speaking groups and their affinity to the neighbouring Tai populations in Northern Thailand.

PubMed

Kutanan, Wibhu; Kampuansai, Jatupol; Fuselli, Silvia; Nakbunlung, Supaporn; Seielstad, Mark; Bertorelle, Giorgio; Kangwanpong, Daoroong

2011-06-15

The Mon-Khmer speaking peoples inhabited northern Thailand before the arrival of the Tai speaking people from southern China in the thirteenth century A.D. Historical and anthropological evidence suggests a close relationship between the Mon-Khmer groups and the present day majority northern Thai groups. In this study, mitochondrial and Y-chromosomal DNA polymorphisms in more than 800 volunteers from eight Mon-Khmer and ten Tai speaking populations were investigated to estimate the degree of genetic divergence between these major linguistic groups and their internal structure. A large fraction of genetic variation is observed within populations (about 80% and 90% for mtDNA and the Y-chromosome, respectively). The genetic divergence between populations is much higher in Mon-Khmer than in Tai speaking groups, especially at the paternally inherited markers. The two major linguistic groups are genetically distinct, but only for a marginal fraction (1 to 2%) of the total genetic variation. Genetic distances between populations correlate with their linguistic differences, whereas the geographic distance does not explain the genetic divergence pattern. The Mon-Khmer speaking populations in northern Thailand exhibited the genetic divergence among each other and also when compared to Tai speaking peoples. The different drift effects and the post-marital residence patterns between the two linguistic groups are the explanation for a small but significant fraction of the genetic variation pattern within and between them. © 2011 Kutanan et al; licensee BioMed Central Ltd.

The roles of associative and executive processes in creative cognition.

PubMed

Beaty, Roger E; Silvia, Paul J; Nusbaum, Emily C; Jauk, Emanuel; Benedek, Mathias

2014-10-01

How does the mind produce creative ideas? Past research has pointed to important roles of both executive and associative processes in creative cognition. But such work has largely focused on the influence of one ability or the other-executive or associative-so the extent to which both abilities may jointly affect creative thought remains unclear. Using multivariate structural equation modeling, we conducted two studies to determine the relative influences of executive and associative processes in domain-general creative cognition (i.e., divergent thinking). Participants completed a series of verbal fluency tasks, and their responses were analyzed by means of latent semantic analysis (LSA) and scored for semantic distance as a measure of associative ability. Participants also completed several measures of executive function-including broad retrieval ability (Gr) and fluid intelligence (Gf). Across both studies, we found substantial effects of both associative and executive abilities: As the average semantic distance between verbal fluency responses and cues increased, so did the creative quality of divergent-thinking responses (Study 1 and Study 2). Moreover, the creative quality of divergent-thinking responses was predicted by the executive variables-Gr (Study 1) and Gf (Study 2). Importantly, the effects of semantic distance and the executive function variables remained robust in the same structural equation model predicting divergent thinking, suggesting unique contributions of both constructs. The present research extends recent applications of LSA in creativity research and provides support for the notion that both associative and executive processes underlie the production of novel ideas.

Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence.

PubMed

Maheshwari, Shamoni; Ishii, Takayoshi; Brown, C Titus; Houben, Andreas; Comai, Luca

2017-03-01

During cell division, spindle fibers attach to chromosomes at centromeres. The DNA sequence at regional centromeres is fast evolving with no conserved genetic signature for centromere identity. Instead CENH3, a centromere-specific histone H3 variant, is the epigenetic signature that specifies centromere location across both plant and animal kingdoms. Paradoxically, CENH3 is also adaptively evolving. An ongoing question is whether CENH3 evolution is driven by a functional relationship with the underlying DNA sequence. Here, we demonstrate that despite extensive protein sequence divergence, CENH3 histones from distant species assemble centromeres on the same underlying DNA sequence. We first characterized the organization and diversity of centromere repeats in wild-type Arabidopsis thaliana We show that A. thaliana CENH3-containing nucleosomes exhibit a strong preference for a unique subset of centromeric repeats. These sequences are largely missing from the genome assemblies and represent the youngest and most homogeneous class of repeats. Next, we tested the evolutionary specificity of this interaction in a background in which the native A. thaliana CENH3 is replaced with CENH3s from distant species. Strikingly, we find that CENH3 from Lepidium oleraceum and Zea mays , although specifying epigenetically weaker centromeres that result in genome elimination upon outcrossing, show a binding pattern on A. thaliana centromere repeats that is indistinguishable from the native CENH3. Our results demonstrate positional stability of a highly diverged CENH3 on independently evolved repeats, suggesting that the sequence specificity of centromeres is determined by a mechanism independent of CENH3. © 2017 Maheshwari et al.; Published by Cold Spring Harbor Laboratory Press.

Validation of the XDP-MDSP rating scale for the evaluation of patients with X-linked dystonia-parkinsonism.

PubMed

Pasco, Paul Matthew D; Jamora, Roland Dominic G; Rosales, Raymond L; Diesta, Cid Czarina E; Ng, Arlene R; Teleg, Rosalia A; Go, Criscely L; Lee, Lillian; Fernandez, Hubert H

2017-01-01

X-linked dystonia-parkinsonism(XDP) is a neurodegenerative disorder endemic to the Philippines. A rating scale was developed by the authors under the guidance of the Movement Disorder Society of the Philippines (MDSP) to assess XDP severity and progression, functional impact, and response to treatment in future clinical trials. Our main objective was to validate our new scale, the XDP-MDSP scale. The initial validation process included pragmatic testing to XDP patients followed by a modified Delphi procedure with an international advisory panel of dystonia, parkinsonism and scale development experts. Pearson correlation was used to assess construct validity of our new scale versus the assess construct validity of our new scale versus standard dystonia, parkinsonism, non-motor and functional scales; and also to assess divergent validity against behavioral and cognitive scales. The 37-item XDP-MDSP scale has five parts: I-dystonia, II-parkinsonism, III-non-motor features, IV-ADL, and V-global impression. After initial validation, the scale was administered to 204 XDP patients. Inter-domain correlation for the first four parts was acceptable. The correlation between these domains and the global rating was slightly lower. Correlations between Parts I, II, III, and IV versus standard dystonia, parkinsonism, non-motor and functional scales were acceptable with values ranging from 0.323 to 0.428. For divergent validity, a significant correlation was seen with behavioral scales. No significant correlation was noted with the cognitive scale. The proposed XDP-MDSP scale is internally valid but the global rating subscale may need to be modified or eliminated. While there is convergent validity, divergent validation was successful only on cognitive and not behavioral scales. The frequent co-occurrence of anxiety and depression, and its effect on the motor and functional state, may explain this finding.

Numerical integration of KPZ equation with restrictions

NASA Astrophysics Data System (ADS)

Torres, M. F.; Buceta, R. C.

2018-03-01

In this paper, we introduce a novel integration method of Kardar–Parisi–Zhang (KPZ) equation. It is known that if during the discrete integration of the KPZ equation the nearest-neighbor height-difference exceeds a critical value, instabilities appear and the integration diverges. One way to avoid these instabilities is to replace the KPZ nonlinear-term by a function of the same term that depends on a single adjustable parameter which is able to control pillars or grooves growing on the interface. Here, we propose a different integration method which consists of directly limiting the value taken by the KPZ nonlinearity, thereby imposing a restriction rule that is applied in each integration time-step, as if it were the growth rule of a restricted discrete model, e.g. restricted-solid-on-solid (RSOS). Taking the discrete KPZ equation with restrictions to its dimensionless version, the integration depends on three parameters: the coupling constant g, the inverse of the time-step k, and the restriction constant ε which is chosen to eliminate divergences while keeping all the properties of the continuous KPZ equation. We study in detail the conditions in the parameters’ space that avoid divergences in the 1-dimensional integration and reproduce the scaling properties of the continuous KPZ with a particular parameter set. We apply the tested methodology to the d-dimensional case (d = 3, 4 ) with the purpose of obtaining the growth exponent β, by establishing the conditions of the coupling constant g under which we recover known values reached by other authors, particularly for the RSOS model. This method allows us to infer that d  =  4 is not the critical dimension of the KPZ universality class, where the strong-coupling phase disappears.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Austin, Dane R.; Witting, Tobias; Walmsley, Ian A.

We describe the elimination of the astigmatism of a Czerny-Turner imaging spectrometer, built using spherical optics and a plane grating, over a broad spectral region. Starting with the principle of divergent illumination of the grating, which removes astigmatism at one chosen wavelength, we obtain design equations for the distance from the grating to the focusing mirror and the detector angle that remove the astigmatism to first order in wavelength. Experimentally, we demonstrate near diffraction-limited performance from 740 to 860 nm and over a 5 mm transverse spatial extent, while ray-tracing calculations show that barring finite-aperture and detector size limitations, thismore » range extends from 640 to 900 nm and over 10 mm transversely. Our technique requires no additional optics and uses standard off-the-shelf components.« less

Electronic transport coefficients in plasmas using an effective energy-dependent electron-ion collision-frequency

NASA Astrophysics Data System (ADS)

Faussurier, G.; Blancard, C.; Combis, P.; Decoster, A.; Videau, L.

2017-10-01

We present a model to calculate the electrical and thermal electronic conductivities in plasmas using the Chester-Thellung-Kubo-Greenwood approach coupled with the Kramers approximation. The divergence in photon energy at low values is eliminated using a regularization scheme with an effective energy-dependent electron-ion collision-frequency. Doing so, we interpolate smoothly between the Drude-like and the Spitzer-like regularizations. The model still satisfies the well-known sum rule over the electrical conductivity. Such kind of approximation is also naturally extended to the average-atom model. A particular attention is paid to the Lorenz number. Its nondegenerate and degenerate limits are given and the transition towards the Drude-like limit is proved in the Kramers approximation.

Non-cross talk multi-channel photomultiplier using guided electron multipliers

DOEpatents

Gomez, J.; Majewski, S.; Weisenberger, A.G.

1995-09-26

An improved multi-channel electron multiplier is provided that exhibits zero cross-talk and high rate operation. Resistive material input and output masks are employed to control divergence of electrons. Electron multiplication takes place in closed channels. Several embodiments are provided for these channels including a continuous resistive emissive multiplier and a discrete resistive multiplier with discrete dynode chains interspaced with resistive layers-masks. Both basic embodiments provide high gain multiplication of electrons without accumulating surface charges while containing electrons to their proper channels to eliminate cross-talk. The invention can be for example applied to improve the performance of ion mass spectrometers, positron emission tomography devices, in DNA sequencing and other beta radiography applications and in many applications in particle physics. 28 figs.

Non cross talk multi-channel photomultiplier using guided electron multipliers

DOEpatents

Gomez, Javier; Majewski, Stanislaw; Weisenberger, Andrew G.

1995-01-01

An improved multi-channel electron multiplier is provided that exhibits zero cross-talk and high rate operation. Resistive material input and output masks are employed to control divergence of electrons. Electron multiplication takes place in closed channels. Several embodiments are provided for these channels including a continuous resistive emissive multiplier and a discrete resistive multiplier with discrete dynode chains interspaced with resistive layers-masks. Both basic embodiments provide high gain multiplication of electrons without accumulating surface charges while containing electrons to their proper channels to eliminate cross-talk. The invention can be for example applied to improve the performance of ion mass spectrometers, positron emission tomography devices, in DNA sequencing and other beta radiography applications and in many applications in particle physics.

Gut microbiota may predict host divergence time during Glires evolution.

PubMed

Li, Huan; Qu, Jiapeng; Li, Tongtong; Yao, Minjie; Li, Jiaying; Li, Xiangzhen

2017-03-01

The gut microbial communities of animals play key roles in host evolution. However, the possible relationship between gut microbiota and host divergence time remains unknown. Here, we investigated the gut microbiota of eight Glires species (four lagomorph species and four rodent species) distributed throughout the Qinghai-Tibet plateau and Inner Mongolia grassland. Lagomorphs and rodents had distinct gut microbial compositions. Three out of four lagomorph species were dominated by Firmicutes, while rodents were dominated by Bacteroidetes in general. The alpha diversity values (Shannon diversity and evenness) exhibited significant differences between any two species within the lagomorphs, whereas there were no significant differences among rodents. The structure of the gut microbiota showed significant differences between lagomorphs and rodents. In addition, we calculated host phylogeny and divergence times, and used a phylogenetic approach to reconstruct how the animal gut microbiota has diverged from their ancestral species. Some core bacterial genera (e.g. Prevotella and Clostridium) shared by more than nine-tenths of all the Glires individuals associated with plant polysaccharide degradation showed marked changes within lagomorphs. Differences in Glires gut microbiota (based on weighted UniFrac and Bray-Curtis dissimilarity metrics) were positively correlated with host divergence time. Our results thus suggest the gut microbial composition is associated with host phylogeny, and further suggest that dissimilarity of animal gut microbiota may predict host divergence time. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Positive selection and propeptide repeats promote rapid interspecific divergence of a gastropod sperm protein.

PubMed

Hellberg, M E; Moy, G W; Vacquier, V D

2000-03-01

Male-specific proteins have increasingly been reported as targets of positive selection and are of special interest because of the role they may play in the evolution of reproductive isolation. We report the rapid interspecific divergence of cDNA encoding a major acrosomal protein of unknown function (TMAP) of sperm from five species of teguline gastropods. A mitochondrial DNA clock (calibrated by congeneric species divided by the Isthmus of Panama) estimates that these five species diverged 2-10 MYA. Inferred amino acid sequences reveal a propeptide that has diverged rapidly between species. The mature protein has diverged faster still due to high nonsynonymous substitution rates (> 25 nonsynonymous substitutions per site per 10(9) years). cDNA encoding the mature protein (89-100 residues) shows evidence of positive selection (Dn/Ds > 1) for 4 of 10 pairwise species comparisons. cDNA and predicted secondary-structure comparisons suggest that TMAP is neither orthologous nor paralogous to abalone lysin, and thus marks a second, phylogenetically independent, protein subject to strong positive selection in free-spawning marine gastropods. In addition, an internal repeat in one species (Tegula aureotincta) produces a duplicated cleavage site which results in two alternatively processed mature proteins differing by nine amino acid residues. Such alternative processing may provide a mechanism for introducing novel amino acid sequence variation at the amino-termini of proteins. Highly divergent TMAP N-termini from two other tegulines (Tegula regina and Norrisia norrisii) may have originated by such a mechanism.

Estimation of population divergence times from non-overlapping genomic sequences: examples from dogs and wolves.

PubMed

Skoglund, Pontus; Götherström, Anders; Jakobsson, Mattias

2011-04-01

Despite recent technological advances in DNA sequencing, incomplete coverage remains to be an issue in population genomics, in particular for studies that include ancient samples. Here, we describe an approach to estimate population divergence times for non-overlapping sequence data that is based on probabilities of different genealogical topologies under a structured coalescent model. We show that the approach can be adapted to accommodate common problems such as sequencing errors and postmortem nucleotide misincorporations, and we use simulations to investigate biases involved with estimating genealogical topologies from empirical data. The approach relies on three reference genomes and should be particularly useful for future analysis of genomic data that comprise of nonoverlapping sets of sequences, potentially from different points in time. We applied the method to shotgun sequence data from an ancient wolf together with extant dogs and wolves and found striking resemblance to previously described fine-scale population structure among dog breeds. When comparing modern dogs to four geographically distinct wolves, we find that the divergence time between dogs and an Indian wolf is smallest, followed by the divergence times to a Chinese wolf and a Spanish wolf, and a relatively long divergence time to an Alaskan wolf, suggesting that the origin of modern dogs is somewhere in Eurasia, potentially southern Asia. We find that less than two-thirds of all loci in the boxer and poodle genomes are more similar to each other than to a modern gray wolf and that--assuming complete isolation without gene flow--the divergence time between gray wolves and modern European dogs extends to 3,500 generations before the present, corresponding to approximately 10,000 years ago (95% confidence interval [CI]: 9,000-13,000). We explicitly study the effect of gene flow between dogs and wolves on our estimates and show that a low rate of gene flow is compatible with an even earlier domestication date ∼30,000 years ago (95% CI: 15,000-90,000). This observation is in agreement with recent archaeological findings and indicates that human behavior necessary for domestication of wild animals could have appeared much earlier than the development of agriculture.

Phase transition and thermodynamic geometry of f (R ) AdS black holes in the grand canonical ensemble

NASA Astrophysics Data System (ADS)

Li, Gu-Qiang; Mo, Jie-Xiong

2016-06-01

The phase transition of a four-dimensional charged AdS black hole solution in the R +f (R ) gravity with constant curvature is investigated in the grand canonical ensemble, where we find novel characteristics quite different from that in the canonical ensemble. There exists no critical point for T -S curve while in former research critical point was found for both the T -S curve and T -r+ curve when the electric charge of f (R ) black holes is kept fixed. Moreover, we derive the explicit expression for the specific heat, the analog of volume expansion coefficient and isothermal compressibility coefficient when the electric potential of f (R ) AdS black hole is fixed. The specific heat CΦ encounters a divergence when 0 <Φ b . This finding also differs from the result in the canonical ensemble, where there may be two, one or no divergence points for the specific heat CQ . To examine the phase structure newly found in the grand canonical ensemble, we appeal to the well-known thermodynamic geometry tools and derive the analytic expressions for both the Weinhold scalar curvature and Ruppeiner scalar curvature. It is shown that they diverge exactly where the specific heat CΦ diverges.