N-Terminal Disordered Domain of Saccharomyces cerevisiae Hop1 Protein Is Dispensable for DNA Binding, Bridging, and Synapsis of Double-Stranded DNA Molecules But Is Necessary for Spore Formation

The cytological architecture of the synaptonemal complex (SC), a meiosis-specific proteinaceous structure, is evolutionarily conserved among eukaryotes. However, little is known about the biochemical properties of SC components or the mechanisms underlying their roles in meiotic chromosome synapsis and recombination. Functional analysis of Saccharomyces cerevisiae Hop1, a key structural component of SC, has begun to reveal important insights into its function in interhomolog recombination. Previously, we showed that Hop1 is a structure-specific DNA-binding protein, exhibits higher binding affinity for the Holliday junction, and induces structural distortion at the core of the junction. Furthermore, Hop1 promotes DNA condensation and intra- and intermolecular synapsis between duplex DNA molecules. Here, we show that Hop1 possesses a modular domain organization, consisting of an intrinsically disordered N-terminal domain and a protease-resistant C-terminal domain (Hop1CTD). Furthermore, we found that Hop1CTD exhibits strong homotypic as well as heterotypic protein protein interactions, and its biochemical activities were similar to those of the full-length Hop1 protein. However, Hop1CTD failed to complement the meiotic recombination defects of the Delta hop1 strain, indicating that both N- and C-terminal domains of Hop1 are essential for meiosis and spore formation. Altogether, our findings reveal novel insights into the structure-function relationships of Hop1 and help to further our understanding of its role in meiotic chromosome synapsis and recombination.

Differences in host species relationships and biogeographic influences produce contrasting patterns of prevalence, community composition and genetic structure in two genera of avian malaria parasites in southern Melanesia

1. Host-parasite interactions have the potential to influence broadscale ecological and evolutionary processes, levels of endemism, divergence patterns and distributions in host populations. Understanding the mechanisms involved requires identification of the factors that shape parasite distribution and prevalence. 2. A lack of comparative information on community-level host-parasite associations limits our understanding of the role of parasites in host population divergence processes. Avian malaria (haemosporidian) parasites in bird communities offer a tractable model system to examine the potential for pathogens to influence evolutionary processes in natural host populations. 3. Using cytochrome b variation, we characterized phylogenetic diversity and prevalence of two genera of avian haemosporidian parasites, Plasmodium and Haemoproteus, and analysed biogeographic patterns of lineages across islands and avian hosts, in southern Melanesian bird communities to identify factors that explain patterns of infection. 4. Plasmodium spp. displayed isolation-by-distance effects, a significant amount of genetic variation distributed among islands but insignificant amounts among host species and families, and strong local island effects with respect to prevalence. Haemoproteus spp. did not display isolation-by-distance patterns, showed marked structuring of genetic variation among avian host species and families, and significant host species prevalence patterns. 5. These differences suggest that Plasmodium spp. infection patterns were shaped by geography and the abiotic environment, whereas Haemoproteus spp. infection patterns were shaped predominantly by host associations. Heterogeneity in the complement and prevalence of parasite lineages infecting local bird communities likely exposes host species to a mosaic of spatially divergent disease selection pressures across their naturally fragmented distributions in southern Melanesia. Host associations for Haemoproteus spp. indicate a capacity for the formation of locally co-adapted host-parasite relationships, a feature that may limit intraspecific gene flow or range expansions of closely related host species.

The Structure of the Holo-Acyl Carrier Protein of Leishmania major Displays a Remarkably Different Phosphopantetheinyl Transferase Binding Interface

The genome of Leishmania major encodes a type II fatty acid biosynthesis pathway for which no structural or biochemical information exists. Here, for the first time, we have characterized the central player of the pathway, the acyl carrier protein (LmACP), using nuclear magnetic resonance (NMR). Structurally, the LmACP molecule is similar to other type II ACPs, comprising a four-helix bundle, enclosing a hydrophobic core. Dissimilarities in sequence, however, exist in helix II (recognition helix) of the protein. The enzymatic conversion of apo-LmACP into the holo form using type I (Escherichia coli AcpS) and type II (Sfp type) phosphopantetheinyl transferases (PPTs) is relatively slow. Mutagenesis studies underscore the importance of the residues present at the protein protein interaction interface of LmACP in modulating the activity of PPTs. Interestingly, the cognate PPT for this ACP, the L. major 4'-phosphopantetheinyl transferase (LmPPT), does not show any enzymatic activity toward it, though it readily converts other type I and type II ACPs into their holo forms. NMR chemical shift perturbation studies suggest a moderately tight complex between LmACP and its cognate PPT, suggesting inhibition. We surmise that the unique surface of LmACP might have evolved to complement its cognate enzyme (LmPPT), possibly for the purpose of regulation.

Mutations in the nucleotide binding and hydrolysis domains of Helicobacter pylori MutS2 lead to altered biochemical activities and inactivation of its in vivo function

Background: Helicobacter pylori MutS2 (HpMutS2), an inhibitor of recombination during transformation is a non-specific nuclease with two catalytic sites, both of which are essential for its anti-recombinase activity. Although HpMutS2 belongs to a highly conserved family of ABC transporter ATPases, the role of its ATP binding and hydrolysis activities remains elusive. Results: To explore the putative role of ATP binding and hydrolysis activities of HpMutS2 we specifically generated point mutations in the nucleotide-binding Walker-A (HpMutS2-G338R) and hydrolysis Walker-B (HpMutS2-E413A) domains of the protein. Compared to wild-type protein, HpMutS2-G338R exhibited similar to 2.5-fold lower affinity for both ATP and ADP while ATP hydrolysis was reduced by similar to 3-fold. Nucleotide binding efficiencies of HpMutS2-E413A were not significantly altered; however the ATP hydrolysis was reduced by similar to 10-fold. Although mutations in the Walker-A and Walker-B motifs of HpMutS2 only partially reduced its ability to bind and hydrolyze ATP, we demonstrate that these mutants not only exhibited alterations in the conformation, DNA binding and nuclease activities of the protein but failed to complement the hyper-recombinant phenotype displayed by mutS2-disrupted strain of H. pylori. In addition, we show that the nucleotide cofactor modulates the conformation, DNA binding and nuclease activities of HpMutS2. Conclusions: These data describe a strong crosstalk between the ATPase, DNA binding, and nuclease activities of HpMutS2. Furthermore these data show that both, ATP binding and hydrolysis activities of HpMutS2 are essential for the in vivo anti-recombinase function of the protein.

White light emissive molecular siblings

The design and synthesis of two structurally close and complementarily fluorescent boron based molecular siblings 2 and 3 are reported. The luminescence properties of individual triads are modulated to complement each other by controlling the intramolecular energy transfer in 2 and 3. The binary mixture of 2 and 3 emits white-light.

El debate “nacionalismo sano” versus “patriotismo republicano”

Teniendo en cuenta la grave crisis política, económica y social que persiste en gran parte de los países de Latinoamérica, la discusión acerca de qué proyecto de Nación queremos continúa vigente y debería seguir discutiéndose. El artículo se propone contribuir a profundizar y enriquecer esta discusión a partir de una recuperación y abordaje crítico del debate iniciado por un grupo de intelectuales argentinos entre la perspectiva del “patriotismo republicano” y los defensores del “nacionalismo sano”. Según se sostiene, ambos enfoques no son necesariamente incompatibles, pudiendo complementarse entre sí a partir de un orden prioritario.

Observar el movimiento : construcción del formato de campo “el salto en psicomotricidad durante el tercer año de vida”

[Es]Este artículo repasa los hitos más significativos de la elaboración del instrumento de observación del formato de campo “el salto en psicomotricidad durante el tercer año de vida”. La aplicación de la Metodología Observacional a la Práctica Psicomotriz Aucouturier (PPA)es posible ya que existe una doble complementariedad entre ambas: la metodología observacional es la única que puede evaluar y explicar, y no sólo describir, el complejo flujo de actividad psicomotriz infantil o expresividad psicomotriz y la práctica psicomotriz aucouturier, a su vez, cumple el perfil óptimo de la metodología observacional. El proceso metodológico observacional impone entre sus condiciones la sistematización del instrumento de observación; lo que comienza siendo un sistema de categorías en base a la propuesta observacional de la propia PPA, termina siendo un formato de campo al servicio del objetivo inicial de la investigación, que es la evaluación del comportamiento psicomotor infantil.

PICES-GLOBEC International Program on Climate Change and Carrying Capacity: Report of the PICES 2002 Volunteer Observing Ship Workshop.

On April 4-5, 2002, the PICES MONITOR Task Team, the PICES Continuous Plankton Recorder (CPR) Advisory Panel, and the Exxon Valdez Oil Spill Trustee Council’s Gulf Ecosystem Monitoring (GEM) program convened a workshop in Seattle, U.S.A., to consider enhanced instrumentation for volunteer observing ships (VOS), particularly instruments to complement CPR data. (PDF contains 44 pages)

Invariant-free deduction systems for temporal logic

In this thesis we propose a new approach to deduction methods for temporal logic. Our proposal is based on an inductive definition of eventualities that is different from the usual one. On the basis of this non-customary inductive definition for eventualities, we first provide dual systems of tableaux and sequents for Propositional Linear-time Temporal Logic (PLTL). Then, we adapt the deductive approach introduced by means of these dual tableau and sequent systems to the resolution framework and we present a clausal temporal resolution method for PLTL. Finally, we make use of this new clausal temporal resolution method for establishing logical foundations for declarative temporal logic programming languages. The key element in the deduction systems for temporal logic is to deal with eventualities and hidden invariants that may prevent the fulfillment of eventualities. Different ways of addressing this issue can be found in the works on deduction systems for temporal logic. Traditional tableau systems for temporal logic generate an auxiliary graph in a first pass.Then, in a second pass, unsatisfiable nodes are pruned. In particular, the second pass must check whether the eventualities are fulfilled. The one-pass tableau calculus introduced by S. Schwendimann requires an additional handling of information in order to detect cyclic branches that contain unfulfilled eventualities. Regarding traditional sequent calculi for temporal logic, the issue of eventualities and hidden invariants is tackled by making use of a kind of inference rules (mainly, invariant-based rules or infinitary rules) that complicates their automation. A remarkable consequence of using either a two-pass approach based on auxiliary graphs or aone-pass approach that requires an additional handling of information in the tableau framework, and either invariant-based rules or infinitary rules in the sequent framework, is that temporal logic fails to carry out the classical correspondence between tableaux and sequents. In this thesis, we first provide a one-pass tableau method TTM that instead of a graph obtains a cyclic tree to decide whether a set of PLTL-formulas is satisfiable. In TTM tableaux are classical-like. For unsatisfiable sets of formulas, TTM produces tableaux whose leaves contain a formula and its negation. In the case of satisfiable sets of formulas, TTM builds tableaux where each fully expanded open branch characterizes a collection of models for the set of formulas in the root. The tableau method TTM is complete and yields a decision procedure for PLTL. This tableau method is directly associated to a one-sided sequent calculus called TTC. Since TTM is free from all the structural rules that hinder the mechanization of deduction, e.g. weakening and contraction, then the resulting sequent calculus TTC is also free from this kind of structural rules. In particular, TTC is free of any kind of cut, including invariant-based cut. From the deduction system TTC, we obtain a two-sided sequent calculus GTC that preserves all these good freeness properties and is finitary, sound and complete for PLTL. Therefore, we show that the classical correspondence between tableaux and sequent calculi can be extended to temporal logic. The most fruitful approach in the literature on resolution methods for temporal logic, which was started with the seminal paper of M. Fisher, deals with PLTL and requires to generate invariants for performing resolution on eventualities. In this thesis, we present a new approach to resolution for PLTL. The main novelty of our approach is that we do not generate invariants for performing resolution on eventualities. Our method is based on the dual methods of tableaux and sequents for PLTL mentioned above. Our resolution method involves translation into a clausal normal form that is a direct extension of classical CNF. We first show that any PLTL-formula can be transformed into this clausal normal form. Then, we present our temporal resolution method, called TRS-resolution, that extends classical propositional resolution. Finally, we prove that TRS-resolution is sound and complete. In fact, it finishes for any input formula deciding its satisfiability, hence it gives rise to a new decision procedure for PLTL. In the field of temporal logic programming, the declarative proposals that provide a completeness result do not allow eventualities, whereas the proposals that follow the imperative future approach either restrict the use of eventualities or deal with them by calculating an upper bound based on the small model property for PLTL. In the latter, when the length of a derivation reaches the upper bound, the derivation is given up and backtracking is used to try another possible derivation. In this thesis we present a declarative propositional temporal logic programming language, called TeDiLog, that is a combination of the temporal and disjunctive paradigms in Logic Programming. We establish the logical foundations of our proposal by formally defining operational and logical semantics for TeDiLog and by proving their equivalence. Since TeDiLog is, syntactically, a sublanguage of PLTL, the logical semantics of TeDiLog is supported by PLTL logical consequence. The operational semantics of TeDiLog is based on TRS-resolution. TeDiLog allows both eventualities and always-formulas to occur in clause heads and also in clause bodies. To the best of our knowledge, TeDiLog is the first declarative temporal logic programming language that achieves this high degree of expressiveness. Since the tableau method presented in this thesis is able to detect that the fulfillment of an eventuality is prevented by a hidden invariant without checking for it by means of an extra process, since our finitary sequent calculi do not include invariant-based rules and since our resolution method dispenses with invariant generation, we say that our deduction methods are invariant-free.

Biogeographic analysis of the Tortugas Ecological Reserve: Examining the refuge effect following reserve establishment

Almost 120 days at sea aboard three NOAA research vessels and one fishing vessel over the past three years have supported biogeographic characterization of Tortugas Ecological Reserve (TER). This work initiated measurement of post-implementation effects of TER as a refuge for exploited species. In Tortugas South, seafloor transect surveys were conducted using divers, towed operated vehicles (TOV), remotely operated vehicles (ROV), various sonar platforms, and the Deepworker manned submersible. ARGOS drifter releases, satellite imagery, ichthyoplankton surveys, sea surface temperature, and diver census were combined to elucidate potential dispersal of fish spawning in this environment. Surveys are being compiled into a GIS to allow resource managers to gauge benthic resource status and distribution. Drifter studies have determined that within the ~ 30 days of larval life stage for fishes spawning at Tortugas South, larvae could reach as far downstream as Tampa Bay on the west Florida coast and Cape Canaveral on the east coast. Together with actual fish surveys and water mass delineation, this work demonstrates that the refuge status of this area endows it with tremendous downstream spillover and larval export potential for Florida reef habitats and promotes the maintenance of their fish communities. In Tortugas North, 30 randomly selected, permanent stations were established. Five stations were assigned to each of the following six areas: within Dry Tortugas National Park, falling north of the prevailing currents (Park North); within Dry Tortugas National Park, falling south of the prevailing currents (Park South); within the Ecological Reserve falling north of the prevailing currents (Reserve North); within the Ecological Reserve falling south of the prevailing currents (Reserve South); within areas immediately adjacent to these two strata, falling north of the prevailing currents (Out North); and within areas immediately adjacent to these two strata, falling south of the prevailing currents (Out South). Intensive characterization of these sites was conducted using multiple sonar techniques, TOV, ROV, diver-based digital video collection, diver-based fish census, towed fish capture, sediment particle-size, benthic chlorophyll analyses, and stable isotope analyses of primary producers, fish, and, shellfish. In order to complement and extend information from studies focused on the coral reef, we have targeted the ecotone between the reef and adjacent, non-reef habitats as these areas are well-known in ecology for indicating changes in trophic relationships at the ecosystem scale. Such trophic changes are hypothesized to occur as top-down control of the system grows with protection of piscivorous fishes. Preliminary isotope data, in conjunction with our prior results from the west Florida shelf, suggest that the shallow water benthic habitats surrounding the coral reefs of TER will prove to be the source of a significant amount of the primary production ultimately fueling fish production throughout TER and downstream throughout the range of larval fish dispersal. Therefore, the status and influence of the previously neglected, non-reef habitat within the refuge (comprising ~70% of TER) appears to be intimately tied to the health of the coral reef community proper. These data, collected in a biogeographic context, employing an integrated Before-After Control Impact design at multiple spatial scales, leave us poised to document and quantify the postimplementation effects of TER. Combined with the work at Tortugas South, this project represents a multi-disciplinary effort of sometimes disparate disciplines (fishery oceanography, benthic ecology, food web analysis, remote sensing/geography/landscape ecology, and resource management) and approaches (physical, biological, ecological). We expect the continuation of this effort to yield critical information for the management of TER and the evaluation of protected areas as a refuge for exploited species. (PDF contains 32 pages.)

Rol semantikoen etiketatze automatikoa : rol multzoak eta hautapen murriztapenak

158 p. : graf.

Basque nominalizations and the role of structural Case in the licensing of null arguments

[EN] This article investigates the question of the licensing of null arguments in the so-called pro-drop languages. By focusing on the licensing of null subjects in the different types of -T(Z)E nominalizations in Basque, it aims at defining in a precise way the crucial feature that makes pro-drop possible in a clause. The central claim is that what licenses subject-drop is the assignment of structural Case. That is, it is argued that a subject can be null if and only if it is assigned structural Case. Different aspects of T(Z)E nominalizations are also explored, which show that even if these clauses are similar in the surface, they can be syntactically very different and furthermore, that infinitive clauses marked with the same nominalizing morpheme can also have diverging structures.

Investment in the training of technologists for commercial aquaculture

The protein shortage in Nigeria is noted and the role of aquaculture (=fish farming) as a complement in increasing the dwindling food supply is registered. In addition, the manpower shortage especially in the technology cadre is noted and attributed to the lack of co-ordination and standard curricula especially in aquaculture. An inventory of tasks performed in the aquaculture industry was taken and these were classified and validated, then their final priority level was used to assess which ones were critical, important or desirable and which ones would result in disaster or not with inadequate mastery. Based on the above, recommendations are made that all critical and important tasks be included in the teaching curriculum for aquaculture in both theory and practicals: while it is advocated that all tasks listed be undertaken in fish farm operations. This will raise the competence of technologists to run the commercial aquaculture projects

Asymptotic analysis of thin plates under normal load and horizontal edge thrust

We consider the radially symmetric nonlinear von Kármán plate equations for circular or annular plates in the limit of small thickness. The loads on the plate consist of a radially symmetric pressure load and a uniform edge load. The dependence of the steady states on the edge load and thickness is studied using asymptotics as well as numerical calculations. The von Kármán plate equations are a singular perturbation of the Fӧppl membrane equation in the asymptotic limit of small thickness. We study the role of compressive membrane solutions in the small thickness asymptotic behavior of the plate solutions.

We give evidence for the existence of a singular compressive solution for the circular membrane and show by a singular perturbation expansion that the nonsingular compressive solution approach this singular solution as the radial stress at the center of the plate vanishes. In this limit, an infinite number of folds occur with respect to the edge load. Similar behavior is observed for the annular membrane with zero edge load at the inner radius in the limit as the circumferential stress vanishes.

We develop multiscale expansions, which are asymptotic to members of this family for plates with edges that are elastically supported against rotation. At some thicknesses this approximation breaks down and a boundary layer appears at the center of the plate. In the limit of small normal load, the points of breakdown approach the bifurcation points corresponding to buckling of the nondeflected state. A uniform asymptotic expansion for small thickness combining the boundary layer with a multiscale approximation of the outer solution is developed for this case. These approximations complement the well known boundary layer expansions based on tensile membrane solutions in describing the bending and stretching of thin plates. The approximation becomes inconsistent as the clamped state is approached by increasing the resistance against rotation at the edge. We prove that such an expansion for the clamped circular plate cannot exist unless the pressure load is self-equilibrating.

Syntactic change

[ES] En este trabajo se define el cambio sintáctico, se analizan los factores que lo causan o facilitan y se estudian sus tipos principales en griego antiguo.