bluuebunny/crossref_metadata_2025 huggingface dataset:
Archaeal eukaryote-like Orc1/Cdc6 initiators physically interact with DNA polymerase B1 and regulate its functions
Authors: Zhang Lu , Zhang Lei , Liu Yi , Yang Shifan , Gao Chunhui , Gong Hongchao , Feng Ying , He Zheng-Guo
Published: April 2009

Archaeal DNA replication machinery represents a core version of that found in eukaryotes. However, the proteins essential for the coordination of origin selection and the functioning of DNA polymerase have not yet been characterized in archaea, and they are still being investigated in eukaryotes. In the current study, the Orc1/Cdc6 (SsoCdc6) proteins from the crenarchaeon
Sulfolobus solfataricus
were found to physically interact with its DNA polymerase B1 (SsoPolB1). These SsoCdc6 proteins stimulated the DNA-binding ability of SsoPolB1 and differentially regulated both its polymerase and nuclease activities. Furthermore, the proteins also mutually regulated their interactions with SsoPolB1. In addition, SsoPolB1c467, a nuclease domain-deleted mutant of SsoPolB1 defective in DNA binding, retains the ability to physically interact with SsoCdc6 proteins. Its DNA polymerase activity could be stimulated by these proteins. We report on a linkage between the initiator protein Orc1/Cdc6 and DNA polymerase in the archaeon. Our present and previous findings indicate that archaeal Orc1/Cdc6 proteins could potentially play critical roles in the coordination of origin selection and cell-cycle control of replication.
Grain boundaries exhibit the dynamics of glass-forming liquids
Authors: Zhang Hao , Srolovitz David J. , Douglas Jack F. , Warren James A.
Published: April 2009

Polycrystalline materials are composites of crystalline particles or “grains” separated by thin “amorphous” grain boundaries (GBs). Although GBs have been exhaustively investigated at low temperatures, at which these regions are relatively ordered, much less is known about them at higher temperatures, where they exhibit significant mobility and structural disorder and characterization methods are limited. The time and spatial scales accessible to molecular dynamics (MD) simulation are appropriate for investigating the dynamical and structural properties of GBs at elevated temperatures, and we exploit MD to explore basic aspects of GB dynamics as a function of temperature. It has long been hypothesized that GBs have features in common with glass-forming liquids based on the processing characteristics of polycrystalline materials. We find remarkable support for this suggestion, as evidenced by string-like collective atomic motion and transient caging of atomic motion, and a non-Arrhenius GB mobility describing the average rate of large-scale GB displacement.
The organic cation transporter-3 is a pivotal modulator of neurodegeneration in the nigrostriatal dopaminergic pathway
Authors: Cui Mei , Aras Radha , Christian Whitney V. , Rappold Phillip M. , Hatwar Mamata , Panza Joseph , Jackson-Lewis Vernice , Javitch Jonathan A. , Ballatori Nazzareno , Przedborski Serge , Tieu Kim
Published: April 2009

Toxic organic cations can damage nigrostriatal dopaminergic pathways as seen in most parkinsonian syndromes and in some cases of illicit drug exposure. Here, we show that the organic cation transporter 3 (Oct3) is expressed in nondopaminergic cells adjacent to both the soma and terminals of midbrain dopaminergic neurons. We hypothesized that Oct3 contributes to the dopaminergic damage by bidirectionally regulating the local bioavailability of toxic species. Consistent with this view, Oct3 deletion and pharmacological inhibition hampers the release of the toxic organic cation 1-methyl-4-phenylpyridinium from astrocytes and protects against 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced dopaminergic neurodegeneration in mice. Furthermore, Oct3 deletion impairs the removal of the excess extracellular dopamine induced by methamphetamine and enhances striatal dopaminergic terminal damage caused by this psychostimulant. These results may have far-reaching implications for our understanding of the mechanism of cell death in a wide range of neurodegenerative diseases and may open new avenues for neuroprotective intervention.
Niche partitioning in the coevolution of 2 distinct RNA enzymes
Authors: Voytek Sarah B. , Joyce Gerald F.
Published: April 2009

Organisms that compete for limited resources within a common environment may evolve traits that allow them to exploit distinct ecological niches, thus enabling multiple species to coexist within the same habitat. The process of niche partitioning now has been captured at the molecular level, employing the method of continuous in vitro evolution. Mixed populations of 2 different “species” of RNA enzymes were made to compete for limited amounts of one or more substrates, with utilization of the substrate being necessary for amplification of the RNA. Evolution in the presence of a single substrate led to the extinction of one or the other enzyme, whereas evolution in the presence of 5 alternative substrates led to the accumulation of mutations that allowed each enzyme to exploit a different preferred resource. The evolved enzymes were capable of sustained coevolution within a common environment, exemplifying the emergence of stable ecological niche behavior in a model system. Biochemical characterization of the 2 evolved enzymes revealed marked differences in their kinetic properties and adaptive strategies. One enzyme reacted with its preferred substrate ≈100-fold faster than the other, but the slower-reacting species produced 2- to 3-fold more progeny per reacted parent molecule. The in vitro coevolution of 2 or more species of RNA enzymes will make possible further studies in molecular ecology, including the exploration of more complex behaviors, such as predation or cooperation, under controlled laboratory conditions.
THE ‘EUROPEANISATION’ OF REFERENCE GROUPS
Authors: Whelan Christopher T. , Maître Bertrand
Published: April 2009

In this paper we address the question of the relative importance of within and between country differences in income and material deprivation in the European Union in the context of recent suggestions that insufficient attention has been paid to the latter. In particular, we respond to the argument that the ‘state bounded’ relative income approach obscures the significance of EU-wide reference groups. Making use of EU-SILC 2004, we have sought to quantify the magnitude of relevant within and between country differences and their relative impact. Overall, our analysis supports the view that the predominant frame of reference is a national one. The limited impact of European reference groups observed in our analysis does not require explanation in terms of the emergence of a European social stratification system. Furthermore, the significance of such comparisons depends not only on the expectations of those affected by European inequalities but on the degree of legitimacy afforded to ensuing demands. While an EU-wide income-threshold can provide information regarding progress of the Union towards greater social cohesion, its usage for this purpose does not require a strong sense of European identity. Given the current status of the European Social Model, it would seem unwise to attribute an undue degree of policy relevance to the relatively modest impact of EU-wide reference groups revealed in our analysis.
WHO WANTS WHAT FROM THE WELFARE STATE?
Authors: Bonoli Giuliano , Häusermann Silja
Published: April 2009

This article investigates socio-structural cleavages in relation to social policies in Switzerland. It examines the extent to which vertical stratification, age and gender explain variation in individual social policy preferences. We use survey data on reported voting behaviour in 22 direct democratic referendums on distributional issues between 1981 and 2004. Our two main findings are the following: (1) age seems to be the most relevant line of conflict in most distributional issues and (2) vertical stratification (income and education) and gender are less important in explaining individual voting decisions. Our data also suggest that material interests based on socio-structural characteristics account for only part of the variation in social policy preferences, and that value cleavages are also important.
ADULT LEARNING ACTIVITIES, SOCIAL NETWORKS AND DIFFERENT NEIGHBOURHOODS
Authors: Krašovec Sabina Jelenc , Kump Sonja
Published: April 2009

This is a paper on adult education and learning activities within the neighbourhood that pays special attention to the social networks of the individual. It starts off with the thesis that life circumstances and social networks (especially family and neighbourhood) have a greater influence upon the understanding of the role and importance of education then age. We have analysed the quantitative and qualitative data from the research on social networks of the elderly in Slovenia and focused on two generations (parents and grandparents) at two different points in time (1987 and 2005). We have established that regardless of the various external encouragements, the most important factors for further learning are family values and the individual's attitude towards learning that is formed throughout life and is influenced by social networks.
Capture and release of partially zipped trans-SNARE complexes on intact organelles
Authors: Schwartz Matthew L. , Merz Alexey J.
Published: May 2009

Soluble N-ethyl-maleimide sensitive fusion protein attachment protein receptors (SNAREs) are hypothesized to trigger membrane fusion by complexing in trans through their membrane-distal N termini and zippering toward their membrane-embedded C termini, which in turn drives the two membranes together. In this study, we use a set of truncated SNAREs to trap kinetically stable, partially zipped trans-SNARE complexes on intact organelles in the absence of hemifusion and content mixing. We show that the C-terminal zippering of SNARE cytoplasmic domains controls the onset of lipid mixing but not the subsequent transition from hemifusion to full fusion. Moreover, we find that a partially zipped nonfusogenic trans-complex is rescued by Sec17, a universal SNARE cochaperone. Rescue occurs independently of the Sec17-binding partner Sec18, and it exhibits steep cooperativity, indicating that Sec17 engages multiple stalled trans-complexes to drive fusion. These experiments delineate distinct functions within the trans-complex, provide a straightforward method to trap and study prefusion complexes on native membranes, and reveal that Sec17 can rescue a stalled, partially zipped trans-complex.
Non-inductive current drive and transport in high βN plasmas in JET
Authors: Voitsekhovitch I. , Alper B. , Brix M. , Budny R.V. , Buratti P. , Challis C.D. , Ferron J. , Giroud C. , Joffrin E. , Laborde L. , Luce T.C. , McCune D. , Menard J. , Murakami M. , Park J.M.
Published: April 2009

A route to stationary MHD stable operation at high βN has been explored at the Joint European Torus (JET) by optimizing the current ramp-up, heating start time and the waveform of neutral beam injection (NBI) power. In these scenarios the current ramp-up has been accompanied by plasma pre-heat (or the NBI has been started before the current flat-top) and NBI power up to 22 MW has been applied during the current flat-top. In the discharges considered transient total βN ≈ 3.3 and stationary (during high power phase) βN ≈ 3 have been achieved by applying the feedback control of βN with the NBI power in configurations with monotonic or flat core safety factor profile and without an internal transport barrier (ITB). The transport and current drive in this scenario is analysed here by using the TRANSP and ASTRA codes. The interpretative analysis performed with TRANSP shows that 50–70% of current is driven non-inductively; half of this current is due to the bootstrap current which has a broad profile since an ITB was deliberately avoided. The GLF23 transport model predicts the temperature profiles within a ±22% discrepancy with the measurements over the explored parameter space. Predictive simulations with this model show that the E × B rotational shear plays an important role for thermal ion transport in this scenario, producing up to a 40% increase of the ion temperature. By applying transport and current drive models validated in self-consistent simulations of given reference scenarios in a wider parameter space, the requirements for fully non-inductive stationary operation at JET are estimated. It is shown that the strong stiffness of the temperature profiles predicted by the GLF23 model restricts the bootstrap current at larger heating power. In this situation full non-inductive operation without an ITB can be rather expensive strongly relying on the external non-inductive current drive sources.
High resolution numerical studies of separatrix splitting due to non-axisymmetric perturbation in DIII-D
Authors: Wingen A. , Evans T.E. , Spatschek K.H.
Published: April 2009

In DIII-D the splitting and deformation of the separatrix due to externally applied resonant magnetic perturbations is calculated using a vacuum field line integration code (TRIP3D–MAFOT). The resulting footprint pattern on the divertor target plates is shown in high resolution by contour plots of the connection lengths and penetration depths of the magnetic field lines. Substructures inside the divertor footprint stripes are discovered. Regions of deep penetrating long connecting field lines, which are related to the internal resonances by their manifolds, alternate with regions of regular short connecting field lines. The latter are identified as compact laminar flux tubes, which perforate the perturbed plasma region close to the x-point. The properties and consequences of such flux tubes are investigated in detail. The interaction of different resonant magnetic perturbations is analysed considering the separatrix manifolds. Constructive and destructive interference of the manifolds is discovered and studied.
Unbiased and non-supervised learning methods for disruption prediction at JET
Authors: Murari A. , Vega J. , Rattá G.A. , Vagliasindi G. , Johnson M.F. , Hong S.H.
Published: April 2009

The importance of predicting the occurrence of disruptions is going to increase significantly in the next generation of tokamak devices. The expected energy content of ITER plasmas, for example, is such that disruptions could have a significant detrimental impact on various parts of the device, ranging from erosion of plasma facing components to structural damage. Early detection of disruptions is therefore needed with evermore increasing urgency. In this paper, the results of a series of methods to predict disruptions at JET are reported. The main objective of the investigation consists of trying to determine how early before a disruption it is possible to perform acceptable predictions on the basis of the raw data, keeping to a minimum the number of ‘ad hoc’ hypotheses. Therefore, the chosen learning techniques have the common characteristic of requiring a minimum number of assumptions. Classification and Regression Trees (CART) is a supervised but, on the other hand, a completely unbiased and nonlinear method, since it simply constructs the best classification tree by working directly on the input data. A series of unsupervised techniques, mainly K-means and hierarchical, have also been tested, to investigate to what extent they can autonomously distinguish between disruptive and non-disruptive groups of discharges. All these independent methods indicate that, in general, prediction with a success rate above 80% can be achieved not earlier than 180 ms before the disruption. The agreement between various completely independent methods increases the confidence in the results, which are also confirmed by a visual inspection of the data performed with pseudo Grand Tour algorithms.
Anterograde Microtubule Transport Drives Microtubule Bending in LLC-PK1 Epithelial Cells
Authors: Bicek Andrew D. , Tüzel Erkan , Demtchouk Aleksey , Uppalapati Maruti , Hancock William O. , Kroll Daniel M. , Odde David J.
Published: April 2009

Microtubules (MTs) have been proposed to act mechanically as compressive struts that resist both actomyosin contractile forces and their own polymerization forces to mechanically stabilize cell shape. To identify the origin of MT bending, we directly observed MT bending and F-actin transport dynamics in the periphery of LLC-PK1 epithelial cells. We found that F-actin is nearly stationary in these cells even as MTs are deformed, demonstrating that MT bending is not driven by actomyosin contractility. Furthermore, the inhibition of myosin II activity through the use of blebbistatin results in microtubules that are still dynamically bending. In addition, as determined by fluorescent speckle microscopy, MT polymerization rarely results, if ever, in bending. We suppressed dynamic instability using nocodazole, and we observed no qualitative change in the MT bending dynamics. Bending most often results from anterograde transport of proximal portions of the MT toward a nearly stationary distal tip. Interestingly, we found that in an in vitro kinesin-MT gliding assay, MTs buckle in a similar manner. To make quantitative comparisons, we measured curvature distributions of observed MTs and found that the in vivo and in vitro curvature distributions agree quantitatively. In addition, the measured MT curvature distribution is not Gaussian, as expected for a thermally driven semiflexible polymer, indicating that thermal forces play a minor role in MT bending. We conclude that many of the known mechanisms of MT deformation, such as polymerization and acto-myosin contractility, play an inconsequential role in mediating MT bending in LLC-PK1 cells and that MT-based molecular motors likely generate most of the strain energy stored in the MT lattice. The results argue against models in which MTs play a major mechanical role in LLC-PK1 cells and instead favor a model in which mechanical forces control the spatial distribution of the MT array.
Normal Formation of a Subset of Intestinal Granules inCaenorhabditis elegansRequires ATP-binding Cassette Transporters HAF-4 and HAF-9, Which Are Highly Homologous to Human Lysosomal Peptide Transporter TAP-Like
Authors: Kawai Hiromi , Tanji Takahiro , Shiraishi Hirohisa , Yamada Mitsuo , Iijima Ryoko , Inoue Takao , Kezuka Yasuko , Ohashi Kazuaki , Yoshida Yasuo , Tohyama Koujiro , Gengyo-Ando Keiko , Mitani Shohei , Arai Hiroyuki , Ohashi-Kobayashi Ayako , Maeda Masatomo
Published: April 2009

TAP-like (TAPL; ABCB9) is a half-type ATP-binding cassette (ABC) transporter that localizes in lysosome and putatively conveys peptides from cytosol to lysosome. However, the physiological role of this transporter remains to be elucidated. Comparison of genome databases reveals that TAPL is conserved in various species from a simple model organism, Caenorhabditis elegans, to mammals. C. elegans possesses homologous TAPL genes: haf-4 and haf-9. In this study, we examined the tissue-specific expression of these two genes and analyzed the phenotypes of the loss-of-function mutants for haf-4 and haf-9 to elucidate the in vivo function of these genes. Both HAF-4 and HAF-9 tagged with green fluorescent protein (GFP) were mainly localized on the membrane of nonacidic but lysosome-associated membrane protein homologue (LMP-1)-positive intestinal granules from larval to adult stage. The mutants for haf-4 and haf-9 exhibited granular defects in late larval and young adult intestinal cells, associated with decreased brood size, prolonged defecation cycle, and slow growth. The intestinal granular phenotype was rescued by the overexpression of the GFP-tagged wild-type protein, but not by the ATP-unbound form of HAF-4. These results demonstrate that two ABC transporters, HAF-4 and HAF-9, are related to intestinal granular formation and some other physiological aspects.
Control of Protein and Sterol Trafficking by Antagonistic Activities of a Type IV P-type ATPase and Oxysterol Binding Protein Homologue
Authors: Muthusamy Baby-Periyanayaki , Raychaudhuri Sumana , Natarajan Paramasivam , Abe Fumiyoshi , Liu Ke , Prinz William A. , Graham Todd R.
Published: April 2009

The oxysterol binding protein homologue Kes1p has been implicated in nonvesicular sterol transport in Saccharomyces cerevisiae. Kes1p also represses formation of protein transport vesicles from the trans-Golgi network (TGN) through an unknown mechanism. Here, we show that potential phospholipid translocases in the Drs2/Dnf family (type IV P-type ATPases [P4-ATPases]) are downstream targets of Kes1p repression. Disruption of KES1 suppresses the cold-sensitive (cs) growth defect of drs2Δ, which correlates with an enhanced ability of Dnf P4-ATPases to functionally substitute for Drs2p. Loss of Kes1p also suppresses a drs2-ts allele in a strain deficient for Dnf P4-ATPases, suggesting that Kes1p antagonizes Drs2p activity in vivo. Indeed, Drs2-dependent phosphatidylserine translocase (flippase) activity is hyperactive in TGN membranes from kes1Δ cells and is potently attenuated by addition of recombinant Kes1p. Surprisingly, Drs2p also antagonizes Kes1p activity in vivo. Drs2p deficiency causes a markedly increased rate of cholesterol transport from the plasma membrane to the endoplasmic reticulum (ER) and redistribution of endogenous ergosterol to intracellular membranes, phenotypes that are Kes1p dependent. These data suggest a homeostatic feedback mechanism in which appropriately regulated flippase activity in the Golgi complex helps establish a plasma membrane phospholipid organization that resists sterol extraction by a sterol binding protein.
Dual Roles for RHOA/RHO-Kinase In the Regulated Trafficking of a Voltage-sensitive Potassium Channel
Authors: Stirling Lee , Williams Michael R. , Morielli Anthony D.
Published: April 2009

Kv1.2 is a member of the Shaker family of voltage-sensitive potassium channels and contributes to regulation of membrane excitability. The electrophysiological activity of Kv1.2 undergoes tyrosine kinase-dependent suppression in a process involving RhoA. We report that RhoA elicits suppression of Kv1.2 ionic current by modulating channel endocytosis. This occurs through two distinct pathways, one clathrin-dependent and the other cholesterol-dependent. Activation of Rho kinase (ROCK) via the lysophosphatidic acid (LPA) receptor elicits clathrin-dependent Kv1.2 endocytosis and consequent attenuation of its ionic current. LPA-induced channel endocytosis is blocked by the ROCK inhibitor Y27632 or by clathrin RNA interference. In contrast, steady-state endocytosis of Kv1.2 in unstimulated cells is cholesterol dependent. Inhibition of basal ROCK signaling with Y27632 increased surface Kv1.2, an effect that persists in the presence of clathrin small interfering RNA and that is not additive to the increase in surface channel levels elicited by the cholesterol sequestering drug filipin. Temperature block experiments show that ROCK affects cholesterol-dependent trafficking by modulating the recycling of endocytosed channel back to the plasma membrane. Both receptor-stimulated and steady-state Kv1.2 trafficking modulated by RhoA/ROCK required the activation of dynamin as well as the ROCK effector Lim-kinase, indicating a key role for actin remodeling in RhoA-dependent Kv1.2 regulation.
Varp Is a Novel Rab32/38-binding Protein That Regulates Tyrp1 Trafficking in Melanocytes
Authors: Tamura Kanako , Ohbayashi Norihiko , Maruta Yuto , Kanno Eiko , Itoh Takashi , Fukuda Mitsunori
Published: April 2009

Two small GTPase Rabs, Rab32 and Rab38, have recently been proposed to regulate trafficking of melanogenic enzymes to melanosomes in mammalian epidermal melanocytes; however, the exact molecular mechanism of Rab32/38-mediated transport of melanogenic enzymes has never been clarified, because no Rab32/38-specific effector has ever been identified. In this study, we screened for a Rab32/38-specific effector by a yeast two-hybrid assay using a guanosine triphosphate (GTP)-locked Rab32/38 as bait and found that VPS9-ankyrin-repeat protein (Varp)/Ankrd27, characterized previously as a guanine nucleotide exchange factor (GEF) for Rab21, functions as a specific Rab32/38-binding protein in mouse melanocyte cell line melan-a. Deletion analysis showed that the first ankyrin-repeat (ANKR1) domain functions as a GTP-dependent Rab32/38-binding domain, but that the N-terminal VPS9 domain (i.e., Rab21-GEF domain) does not. Small interfering RNA-mediated knockdown of endogenous Varp in melan-a cells caused a dramatic reduction in Tyrp1 (tyrosinase-related protein 1) signals from melanosomes but did not cause any reduction in Pmel17 signals. Furthermore, expression of the ANKR1 domain in melan-a cells also caused a dramatic reduction of Tyrp1 signals, whereas the VPS9 domain had no effect. Based on these findings, we propose that Varp functions as the Rab32/38 effector that controls trafficking of Tyrp1 in melanocytes.
Dynein-Driven Mitotic Spindle Positioning Restricted to Anaphase by She1p Inhibition of Dynactin Recruitment
Authors: Woodruff Jeffrey B. , Drubin David G. , Barnes Georjana
Published: April 2009

Dynein is a minus-end–directed microtubule motor important for mitotic spindle positioning. In budding yeast, dynein activity is restricted to anaphase when the nucleus enters the bud neck, yet the nature of the underlying regulatory mechanism is not known. Here, the microtubule-associated protein She1p is identified as a novel regulator of dynein activity. In she1Δ cells, dynein is activated throughout the cell cycle, resulting in aberrant spindle movements that misposition the spindle. We also found that dynactin, a cofactor essential for dynein motor function, is a dynamic complex whose recruitment to astral microtubules (aMTs) increases dramatically during anaphase. Interestingly, loss of She1p eliminates the cell-cycle regulation of dynactin recruitment and permits enhanced dynactin accumulation on aMTs throughout the cell cycle. Furthermore, localization of the dynactin complex to aMTs requires dynein, suggesting that dynactin is recruited to aMTs via interaction with dynein and not the microtubule itself. Lastly, we present evidence supporting the existence of an incomplete dynactin subcomplex localized at the SPB, and a complete complex that is loaded onto aMTs from the cytoplasm. We propose that She1p restricts dynein-dependent spindle positioning to anaphase by inhibiting the association of dynein with the complete dynactin complex.
Epidermal Growth Factor–induced Contraction Regulates Paxillin Phosphorylation to Temporally Separate Traction Generation from De-adhesion
Authors: Schneider Ian C. , Hays Cristen K. , Waterman Clare M.
Published: April 2009

Directed cell migration is mediated by cycles of protrusion, adhesion, traction generation on the extracellular matrix and retraction. However, how the events after protrusion are timed, and what dictates their temporal order is completely unknown. We used acute epidermal growth factor (EGF) stimulation of epidermal keratinocytes to initiate the cell migration cycle to study the mechanism of the timing of adhesion, traction generation, and de-adhesion. Using microscopic and biochemical assays, we surprisingly found that at ∼2 min after EGF stimulation protrusion, activation of myosin-II, traction generation, adhesion assembly, and paxillin phosphorylation occurred nearly simultaneously, followed by a 10-min delay during which paxillin became dephosphorylated before cell retraction. Inhibition of myosin-II blocked both the EGF-stimulated paxillin phosphorylation and cell retraction, and a paxillin phosphomimic blocked retraction. These results suggest that EGF-mediated activation of myosin-II acts as a mechanical signal to promote a cycle of paxillin phosphorylation/dephosphorylation that mediates a cycle of adhesion strengthening and weakening that delays cell retraction. Thus, we reveal for the first time a mechanism by which cells may temporally segregate protrusion, adhesion, and traction generation from retraction during EGF-stimulated cell migration.
Optimizing the design of acoustic surveys of Peruvian anchoveta
Authors: Simmonds E. John , Gutiérrez Mariano , Chipollini Andres , Gerlotto Francois , Woillez Mathieu , Bertrand Arnaud
Published: April 2009

Simmonds, E.J., Gutiérrez, M., Chipollini, A., Gerlotto, F., Woillez, M., and Bertrand, A. 2009. Optimizing the design of acoustic surveys of Peruvian anchoveta. – ICES Journal of Marine Science, 66: 1341–1348. Acoustic surveys of stocks of small pelagic fish, in particular the Peruvian anchovy or anchoveta (Engraulis ringens), have been carried out off the coast of Peru since the late 1970s. In all, 51 of these have been carefully archived since 1983. The surveys provide a wealth of data on the distribution and abundance of pelagic fish in the most productive of the world's upwelling ecosystems. The data comprise integrated acoustic data at a resolution of 1 or 2 nautical miles along the cruise tracks, and trawl data, which include catch-by-species and catch-by-length information for anchoveta. Data since 1992 are sufficiently complete to allow a full re-evaluation of the surveys to determine their precision, taking account of the spatial variability of the catch and acoustic data. The methods used include bootstrap by trawl sample and transect segment, geostatistical simulation, and simulated surveys. The results reveal consistent spatial patterns of abundance with a more variable distribution of variance and a strong relationship between the local mean abundance and the variance. The temporal and spatial variabilities are considered in an evaluation of alternative survey designs, including pre-stratified and adaptive designs.
“Linking Herring”: do we really understand plasticity?
Authors: Dickey-Collas Mark , Clarke Maurice , Slotte Aril
Published: April 2009

Dickey-Collas, M., Clarke, M., and Slotte, A. 2009. “Linking Herring”: do we really understand plasticity? – ICES Journal of Marine Science, 66: 1649–1651.
Giving Order to Districts: Estimating Voter Distributions with National Election Returns
Authors: Kernell Georgia
Published: April 2009

Correctly measuring district preferences is crucial for empirical research on legislative responsiveness and voting behavior. This article argues that the common practice of using presidential vote shares to measure congressional district ideology systematically produces incorrect estimates. I propose an alternative method that employs multiple election returns to estimate voters' ideological distributions within districts. I develop two estimation procedures—a least squared error model and a Bayesian model—and test each with simulations and empirical applications. The models are shown to outperform vote shares, and they are validated with direct measures of voter ideology and out-of-sample election predictions. Beyond estimating district ideology, these models provide valuable information on constituency heterogeneity—an important, but often immeasurable, quantity for research on representatives— strategic behavior.
Secondary structures in a one-dimensional complex Ginzburg–Landau equation with homogeneous boundary conditions
Authors: Nana Laurent , Ezersky Alexander B. , Mutabazi Innocent
Published: April 2009

Experiments in extended systems, such as the counter-rotating Couette–Taylor flow or the Taylor–Dean flow system, have shown that patterns with vanishing amplitude may exhibit periodic spatio-temporal defects for some range of control parameters. These observations could not be interpreted by the complex Ginzburg–Landau equation (CGLE) with periodic boundary conditions. We have investigated the one-dimensional CGLE with homogeneous boundary conditions. We found that, in the ‘Benjamin–Feir stable’ region, the basic wave train bifurcates to state with periodic spatio-temporal defects. The numerical results match the observations quite well. We have built a new state diagram in the parameter plane spanned by the criticality (or equivalently the linear group velocity) and the nonlinear frequency detuning.
Evolutional trends and palaeobiogeography of the Ordovician trilobiteOvalocephalusKoroleva 1959
Authors: Zhiyi Zhou , Wenwei Yuan , Zhiqiang Zhou
Published: April 2009

Ovalocephalushas a long stratigraphic range and wide geographical distribution in Ordovician peri-Gondwana. Based largely on the well-preserved specimens recently collected from China, all known forms are revised and listed. Phylogenetic analysis was conducted on the genus, involving 10 species. As suggested by the strict consensus tree, evolutional trends of the genus include mainly the isolation of the anterior glabellar portion anterior to S1, the forward shifting of eyes and the related lengthening (exsag.) of the posterior fixigena, the reduction of the number of pygidial axial segments and pleural abaxial rounded free tips, the shortening of the pygidial postaxial region, and the development of cranidial genal spines.Ovalocephalusmay have originated in shallow-water sites of the South China Plate in the Early Floian, but migrated into the deep-water regions from the Darriwilian onwards. All the records of the genus from the Early Floian to Early Katian were confined to eastern peri-Gondwanan plates and terranes in low-latitude zones. It was only restricted to the South China, Tarim and North China plates until the Middle Darriwilian, but the Late Darriwilian eustatic sea-level rise and especially the Sandbian–Early Katian immense transgression may have brought about its dispersal to Alborz, Sibumasu and central Asian terranes. Following the closure of the Tornquist Sea, the genus was even able to spread to Baltica during the latest Katian, and the pre-Hirnantian warming (the Boda event) may have promoted a wider distribution ofOvalocephalusto western peri-Gondwana (the Taurides and Armorica terranes) in the then-high latitudes.
Group differences in the heritability of items and test scores
Authors: Wicherts Jelte M. , Johnson Wendy
Published: April 2009

It is important to understand potential sources of group differences in the heritability of intelligence test scores. On the basis of a basic item response model we argue that heritabilities which are based on dichotomous item scores normally do not generalize from one sample to the next. If groups differ in mean ability, the functioning of items at different ability levels may result in group differences in the heritability of items, even when these items function equivalently across groups and the heritability of the underlying ability is equal across groups. We illustrate this graphically, by computer simulation, and by focusing on several problems associated with a recent study by Rushton
et al
. who argued that the heritability estimates of items of Raven's Progressive Matrices test in North-American twin samples generalized to other population groups, and hence that the population group differences on this test of general mental ability (or intelligence) had a substantial genetic component. Our results show that item heritabilities are strongly dependent on the group on which the heritabilities were based. Rushton
et al
.'s results were artefactual and do not speak to the nature of population group differences in intelligence test performance.
Dinosaur diversity and the rock record
Authors: Barrett Paul M. , McGowan Alistair J. , Page Victoria
Published: April 2009

Palaeobiodiversity analysis underpins macroevolutionary investigations, allowing identification of mass extinctions and adaptive radiations. However, recent large-scale studies on marine invertebrates indicate that geological factors play a central role in moulding the shape of diversity curves and imply that many features of such curves represent sampling artefacts, rather than genuine evolutionary events. In order to test whether similar biases affect diversity estimates for terrestrial taxa, we compiled genus-richness estimates for three Mesozoic dinosaur clades (Ornithischia, Sauropodomorpha and Theropoda). Linear models of expected genus richness were constructed for each clade, using the number of dinosaur-bearing formations available through time as a proxy for the amount of fossiliferous rock outcrop. Modelled diversity estimates were then compared with observed patterns. Strong statistically robust correlations demonstrate that almost all aspects of ornithischian and theropod diversity curves can be explained by geological megabiases, whereas the sauropodomorph record diverges from modelled predictions and may be a stronger contender for identifying evolutionary signals. In contrast to other recent studies, we identify a marked decline in dinosaur genus richness during the closing stages of the Cretaceous Period, indicating that the clade decreased in diversity for several million years prior to the final extinction of non-avian dinosaurs at the Cretaceous–Palaeocene boundary.
Growing with siblings: a common ground for cooperation or for fiercer competition among plants?
Authors: Milla Rubén , Forero Diana M. , Escudero Adrián , Iriondo Jose M.
Published: April 2009

Recent work has shown that certain plants can identify their kin in competitive settings through root recognition, and react by decreasing root growth when competing with relatives. Although this may be a necessary step in kin selection, no clear associated improvement in individual or group fitness has been reported to qualify as such. We designed an experiment to address whether genetic relatedness between neighbouring plants affects individual or group fitness in artificial populations. Seeds ofLupinus angustifoliuswere sown in groups of siblings, groups of different genotypes from the same population and groups of genotypes from different populations. Both plants surrounded by siblings and by genotypes from the same population had lower individual fitness and produced fewer flowers and less vegetative biomass as a group. We conclude that genetic relatedness entails decreased individual and group fitness inL. angustifolius. This, together with earlier work, precludes the generalization that kin recognition may act as a widespread, major microevolutionary mechanism in plants.
Tonically immobilized selfish prey can survive by sacrificing others
Authors: Miyatake Takahisa , Nakayama Satoshi , Nishi Yusuke , Nakajima Shuhei
Published: April 2009

Death-feigning, also called tonic immobility, is found in a number of animal species across vertebrate and invertebrate taxa. To date, five hypotheses have been proposed for the adaptive significance of tonic immobility. These are that tonic immobility is effective for prey because (i) avoiding dead prey is safer for predators, (ii) immobility plays a role in physical defence, (iii) immobility plays a role in concealment and/or background matching, (iv) predators lose interest in unmoving prey, and (v) the characteristic immobilization posture signals a bad taste to predators. The fourth and fifth hypotheses have been considered suitable explanations for tonic immobility of the red flour beetle against its predator, the jumping spider. In the present study, we used chemical analyses of secretions by the red flour beetles under attack by the jumping spider to reject the fifth hypothesis for this system. More importantly, we tested a selfish-prey hypothesis for the adaptive significance of death-feigning as an anti-predator strategy, in which individuals adopting tonic immobility survive by sacrificing neighbours. Findings showed that survival rates of feigners were higher when in the presence of non-feigners or prey of a different species, compared to when alone, thus confirming our selfish-prey hypothesis. In summary, our results suggest that immobility following a spider attack is selfish; death-feigning prey increase their probability of survival at the expense of more mobile neighbours.
The polyadenylation site of Mimivirus transcripts obeys a stringent ‘hairpin rule’
Authors: Byrne Deborah , Grzela Renata , Lartigue Audrey , Audic Stéphane , Chenivesse Sabine , Encinas Stéphanie , Claverie Jean-Michel , Abergel Chantal
Published: April 2009

Mimivirus, a giant DNA virus infecting Acanthamoeba, is revealing an increasing list of unique features such as a 1.2-Mb genome with numerous genes not found in other viruses, a uniquely conserved promoter signal, and a particle of unmatched complexity using two distinct portals for genome delivery and packaging. Herein, we contribute a further Mimivirus distinctive feature discovered by sequencing a panel of viral cDNAs produced for probing the structure of Mimivirus transcripts. All Mimivirus mRNAs are polyadenylated at a site coinciding exactly with unrelated, but strongly palindromic, genomic sequences. The analysis of 454 Life Sciences (Roche) FLX cDNA tags (150,651) confirmed this finding for all Mimivirus genes independent of their transcription timings and expression levels. The absence of a suitable palindromic signal between adjacent genes results in transcripts encompassing multiple ORFs in the same or even in opposite orientations. Surprisingly, Mimivirus tRNAs are expressed as polyadenylated messengers, including an ORF/tRNA composite mRNA. To our knowledge, both the nature and the stringency of the “hairpin rule” defining the location of polyadenylation sites are unique, raising once more the question of Mimivirus's evolutionary origin. The precise molecular mechanisms implementing the hairpin rule into the 3′-end processing of Mimivirus pre-mRNAs remain to be elucidated.
Fatty acid amide hydrolase (FAAH) inhibition enhances memory acquisition through activation of PPAR-α nuclear receptors
Authors: Mazzola Carmen , Medalie Julie , Scherma Maria , Panlilio Leigh V. , Solinas Marcello , Tanda Gianluigi , Drago Filippo , Cadet Jean Lud , Goldberg Steven R. , Yasar Sevil
Published: April 2009

Inhibitors of fatty acid amide hydrolase (FAAH) increase endogenous levels of anandamide (a cannabinoid CB1-receptor ligand) and oleoylethanolamide and palmitoylethanolamide (OEA and PEA, ligands for α-type peroxisome proliferator-activated nuclear receptors, PPAR-α) when and where they are naturally released in the brain. Using a passive-avoidance task in rats, we found that memory acquisition was enhanced by the FAAH inhibitor URB597 or by the PPAR-α agonist WY14643, and these enhancements were blocked by the PPAR-α antagonist MK886. These findings demonstrate novel mechanisms for memory enhancement by activation of PPAR-α, either directly by administering a PPAR-α agonist or indirectly by administering a FAAH inhibitor.
Stimulus–outcome learnability differentially activates anterior cingulate and hippocampus at feedback processing
Authors: Rodriguez Paul F.
Published: April 2009

Memory systems are known to be influenced by feedback and error processing, but it is not well known what aspects of outcome contingencies are related to different memory systems. Here we use the Rescorla–Wagner model to estimate prediction errors in an fMRI study of stimulus–outcome association learning. The conditional probabilities of outcomes for a given stimulus are manipulated so that associations are either learnable or unlearnable (pseudorandom). The delay between stimulus and outcome is jittered so that we can separately compare activity for either stimulus processing or feedback processing. We find that hippocampus and anterior cingulate are differentially active primarily at feedback processing: Learnable associations are correlated with significantly more hippocampal activity and significantly less anterior cingulate activity than unlearnable associations. We also find that positive prediction errors modulate feedback processing in the midbrain for both types of associations. We suggest that learnable associations use more declarative memory, unlearnable associations involve more uncertainty monitoring, and, in both kinds of associations, positive prediction errors provide a reinforcement signal.
Model-based reinforcement learning under concurrent schedules of reinforcement in rodents
Authors: Huh Namjung , Jo Suhyun , Kim Hoseok , Sul Jung Hoon , Jung Min Whan
Published: April 2009

Reinforcement learning theories postulate that actions are chosen to maximize a long-term sum of positive outcomes based on value functions, which are subjective estimates of future rewards. In simple reinforcement learning algorithms, value functions are updated only by trial-and-error, whereas they are updated according to the decision-maker's knowledge or model of the environment in model-based reinforcement learning algorithms. To investigate how animals update value functions, we trained rats under two different free-choice tasks. The reward probability of the unchosen target remained unchanged in one task, whereas it increased over time since the target was last chosen in the other task. The results show that goal choice probability increased as a function of the number of consecutive alternative choices in the latter, but not the former task, indicating that the animals were aware of time-dependent increases in arming probability and used this information in choosing goals. In addition, the choice behavior in the latter task was better accounted for by a model-based reinforcement learning algorithm. Our results show that rats adopt a decision-making process that cannot be accounted for by simple reinforcement learning models even in a relatively simple binary choice task, suggesting that rats can readily improve their decision-making strategy through the knowledge of their environments.
Visual object pattern separation deficits in nondemented older adults
Authors: Toner Chelsea K. , Pirogovsky Eva , Kirwan C. Brock , Gilbert Paul E.
Published: April 2009

Young and nondemented older adults were tested on a continuous recognition memory task requiring visual pattern separation. During the task, some objects were repeated across trials and some objects, referred to as lures, were presented that were similar to previously presented objects. The lures resulted in increased interference and an increased need for pattern separation. For each object, the participant was asked to indicate whether (1) this was the first time the object was seen (new), (2) the object was seen previously (old), or (3) the object was similar to a previous object (similar). Older adults were able to correctly identify objects as old or new as well as young adults; however, older adults were impaired when identifying lures as similar. Therefore, pattern separation may be less efficient in older adults resulting in poorer recognition memory performance when interference is increased.
Intrahippocampal infusions of anisomycin produce amnesia: Contribution of increased release of norepinephrine, dopamine, and acetylcholine
Authors: Qi Zhenghan , Gold Paul E.
Published: April 2009

Intra-amygdala injections of anisomycin produce large increases in the release of norepinephrine (NE), dopamine (DA), and serotonin in the amygdala. Pretreatment with intra-amygdala injections of the β-adrenergic receptor antagonist propranolol attenuates anisomycin-induced amnesia without reversing the inhibition of protein synthesis, and injections of NE alone produce amnesia. These findings suggest that abnormal neurotransmitter responses may be the basis for amnesia produced by inhibition of protein synthesis. The present experiment extends these findings to the hippocampus and adds acetylcholine (ACh) to the list of neurotransmitters affected by anisomycin. Using in vivo microdialysis at the site of injection, release of NE, DA, and ACh was measured before and after injections of anisomycin into the hippocampus. Anisomycin impaired inhibitory avoidance memory when rats were tested 48 h after training and also produced substantial increases in local release of NE, DA, and ACh. In an additional experiment, pretreatment with intrahippocampal injections of propranolol prior to anisomycin and training significantly attenuated anisomycin-induced amnesia. The disruption of neurotransmitter release patterns at the site of injection appears to contribute significantly to the mechanisms underlying amnesia produced by protein synthesis inhibitors, calling into question the dominant interpretation that the amnesia reflects loss of training-initiated protein synthesis necessary for memory formation. Instead, the findings suggest that proteins needed for memory formation are available prior to an experience, and that post-translational modifications of these proteins may be sufficient to enable the formation of new memories.