Chromatin structure mapping in Saccharomyces cerevisiae in vivo with DNase I

Most methods for assessment of chromatin structure involve chemical or nuclease damage to DNA followed by analysis of distribution and susceptibility of cutting sites. The agents used generally do not permeate cells, making nuclear isolation mandatory. In vivo mapping strategies might allow detection of labile constituents and/or structures that are lost when chromatin is swollen in isolated nuclei at low ionic strengths. DNase I has been the most widely used enzyme to detect chromatin sites where DNA is active in transcription, replication or recombination. We have introduced the bovine DNase I gene into yeast under control of a galactose-responsive promoter. Expression of the nuclease leads to DNA degradation and cell death. Shorter exposure to the active enzyme allows mapping of chromatin structure in whole cells without isolation of nuclei. The validity and efficacy of the strategy are demonstrated by footprinting a labile repressor bound to its operator. Investigation of the inter-nucleosome linker regions in several types of repressed domains has revealed different degrees of protection in cells, relative to isolated nuclei.

Analogical Reasoning Techniques in Intelligent Counterterrorism Systems

The paper develops a set of ideas and techniques supporting analogical reasoning throughout the life-cycle of terrorist acts. Implementation of these ideas and techniques can enhance the intellectual level of computer-based systems for a wide range of personnel dealing with various aspects of the problem of terrorism and its effects. The method combines techniques of structure-sensitive distributed representations in the framework of Associative-Projective Neural Networks, and knowledge obtained through the progress in analogical reasoning, in particular the Structure Mapping Theory. The impact of these analogical reasoning tools on the efforts to minimize the effects of terrorist acts on civilian population is expected by facilitating knowledge acquisition and formation of terrorism-related knowledge bases, as well as supporting the processes of analysis, decision making, and reasoning with those knowledge bases for users at various levels of expertise before, during, and after terrorist acts.

Global properties of the mapping between local amino acid sequence and local structure in proteins.

Local protein structure prediction efforts have consistently failed to exceed approximately 70% accuracy. We characterize the degeneracy of the mapping from local sequence to local structure responsible for this failure by investigating the extent to which similar sequence segments found in different proteins adopt similar three-dimensional structures. Sequence segments 3-15 residues in length from 154 different protein families are partitioned into neighborhoods containing segments with similar sequences using cluster analysis. The consistency of the sequence-to-structure mapping is assessed by comparing the local structures adopted by sequence segments in the same neighborhood in proteins of known structure. In the 154 families, 45% and 28% of the positions occur in neighborhoods in which one and two local structures predominate, respectively. The sequence patterns that characterize the neighborhoods in the first class probably include virtually all of the short sequence motifs in proteins that consistently occur in a particular local structure. These patterns, many of which occur in transitions between secondary structural elements, are an interesting combination of previously studied and novel motifs. The identification of sequence patterns that consistently occur in one or a small number of local structures in proteins should contribute to the prediction of protein structure from sequence.

Learning organizations: Empirically investigating metaphors

Learning organizations are a special form of organization where enhancing learning is a strategy to increase intellectual capital. Developing learning organizations has become an imperative for many managers, since an organization's learning methods and rate may be the only source of sustainable competitive advantage. However, learning organization theory tends to be prescriptive and rhetorical, with empirical research still relatively new. This paper contributes to the literature by reporting case-study research in progress based on four Australian organizations. In the organizations studied, use of the learning organization metaphor was coupled with an emergent metaphor: organization as `family". By employing structure mapping of metaphor within analytical induction, both established methods but not combined before, this paper shows how theory might be developed from metaphor.

La structure de Jordan des matrices de transfert des modèles de boucles et la relation avec les hamiltoniens XXZ

Les modèles sur réseau comme ceux de la percolation, d’Ising et de Potts servent à décrire les transitions de phase en deux dimensions. La recherche de leur solution analytique passe par le calcul de la fonction de partition et la diagonalisation de matrices de transfert. Au point critique, ces modèles statistiques bidimensionnels sont invariants sous les transformations conformes et la construction de théories des champs conformes rationnelles, limites continues des modèles statistiques, permet un calcul de la fonction de partition au point critique. Plusieurs chercheurs pensent cependant que le paradigme des théories des champs conformes rationnelles peut être élargi pour inclure les modèles statistiques avec des matrices de transfert non diagonalisables. Ces modèles seraient alors décrits, dans la limite d’échelle, par des théories des champs logarithmiques et les représentations de l’algèbre de Virasoro intervenant dans la description des observables physiques seraient indécomposables. La matrice de transfert de boucles D_N(λ, u), un élément de l’algèbre de Temperley- Lieb, se manifeste dans les théories physiques à l’aide des représentations de connectivités ρ (link modules). L’espace vectoriel sur lequel agit cette représentation se décompose en secteurs étiquetés par un paramètre physique, le nombre d de défauts. L’action de cette représentation ne peut que diminuer ce nombre ou le laisser constant. La thèse est consacrée à l’identification de la structure de Jordan de D_N(λ, u) dans ces représentations. Le paramètre β = 2 cos λ = −(q + 1/q) fixe la théorie : β = 1 pour la percolation et √2 pour le modèle d’Ising, par exemple. Sur la géométrie du ruban, nous montrons que D_N(λ, u) possède les mêmes blocs de Jordan que F_N, son plus haut coefficient de Fourier. Nous étudions la non diagonalisabilité de F_N à l’aide des divergences de certaines composantes de ses vecteurs propres, qui apparaissent aux valeurs critiques de λ. Nous prouvons dans ρ(D_N(λ, u)) l’existence de cellules de Jordan intersectorielles, de rang 2 et couplant des secteurs d, d′ lorsque certaines contraintes sur λ, d, d′ et N sont satisfaites. Pour le modèle de polymères denses critique (β = 0) sur le ruban, les valeurs propres de ρ(D_N(λ, u)) étaient connues, mais les dégénérescences conjecturées. En construisant un isomorphisme entre les modules de connectivités et un sous-espace des modules de spins du modèle XXZ en q = i, nous prouvons cette conjecture. Nous montrons aussi que la restriction de l’hamiltonien de boucles à un secteur donné est diagonalisable et trouvons la forme de Jordan exacte de l’hamiltonien XX, non triviale pour N pair seulement. Enfin nous étudions la structure de Jordan de la matrice de transfert T_N(λ, ν) pour des conditions aux frontières périodiques. La matrice T_N(λ, ν) a des blocs de Jordan intrasectoriels et intersectoriels lorsque λ = πa/b, et a, b ∈ Z×. L’approche par F_N admet une généralisation qui permet de diagnostiquer des cellules intersectorielles dont le rang excède 2 dans certains cas et peut croître indéfiniment avec N. Pour les blocs de Jordan intrasectoriels, nous montrons que les représentations de connectivités sur le cylindre et celles du modèle XXZ sont isomorphes sauf pour certaines valeurs précises de q et du paramètre de torsion v. En utilisant le comportement de la transformation i_N^d dans un voisinage des valeurs critiques (q_c, v_c), nous construisons explicitement des vecteurs généralisés de Jordan de rang 2 et discutons l’existence de blocs de Jordan intrasectoriels de plus haut rang.

Uma Fundamentação Intervalar Aplicada à Morfologia Matemática

This work present a interval approach to deal with images with that contain uncertainties, as well, as treating these uncertainties through morphologic operations. Had been presented two intervals models. For the first, is introduced an algebraic space with three values, that was constructed based in the tri-valorada logic of Lukasiewiecz. With this algebraic structure, the theory of the interval binary images, that extends the classic binary model with the inclusion of the uncertainty information, was introduced. The same one can be applied to represent certain binary images with uncertainty in pixels, that it was originated, for example, during the process of the acquisition of the image. The lattice structure of these images, allow the definition of the morphologic operators, where the uncertainties are treated locally. The second model, extend the classic model to the images in gray levels, where the functions that represent these images are mapping in a finite set of interval values. The algebraic structure belong the complete lattices class, what also it allow the definition of the elementary operators of the mathematical morphology, dilation and erosion for this images. Thus, it is established a interval theory applied to the mathematical morphology to deal with problems of uncertainties in images

Cosmic microwave background theory

A long-standing goal of theorists has been to constrain cosmological parameters that define the structure formation theory from cosmic microwave background (CMB) anisotropy experiments and large-scale structure (LSS) observations. The status and future promise of this enterprise is described. Current band-powers in ℓ-space are consistent with a ΔT flat in frequency and broadly follow inflation-based expectations. That the levels are ∼(10−5)2 provides strong support for the gravitational instability theory, while the Far Infrared Absolute Spectrophotometer (FIRAS) constraints on energy injection rule out cosmic explosions as a dominant source of LSS. Band-powers at ℓ ≳ 100 suggest that the universe could not have re-ionized too early. To get the LSS of Cosmic Background Explorer (COBE)-normalized fluctuations right provides encouraging support that the initial fluctuation spectrum was not far off the scale invariant form that inflation models prefer: e.g., for tilted Λ cold dark matter sequences of fixed 13-Gyr age (with the Hubble constant H0 marginalized), ns = 1.17 ± 0.3 for Differential Microwave Radiometer (DMR) only; 1.15 ± 0.08 for DMR plus the SK95 experiment; 1.00 ± 0.04 for DMR plus all smaller angle experiments; 1.00 ± 0.05 when LSS constraints are included as well. The CMB alone currently gives weak constraints on Λ and moderate constraints on Ωtot, but theoretical forecasts of future long duration balloon and satellite experiments are shown which predict percent-level accuracy among a large fraction of the 10+ parameters characterizing the cosmic structure formation theory, at least if it is an inflation variant.

The French fifth Republic as an opportunity structure:a neo-institutional and cultural approach to the study of leadership politics

The Gaullist settlement of 1958 reconfigured the political institutions of France, introducing into the republican mainstream a new form of leadership politics. Adapting the literature on political opportunity structure (POS) theory, and using the French left as a case study, can help us understand how political parties, ideology and leadership adapt to political institutions and norms. It also illuminates what the consequences are of such adaptation in the contemporary period, particularly as regards the institutionally bound roles of political 'character', protocol and discourse. The paper appraises the relevance and appropriateness of POS theory to leadership politics in France.

La enseñanza de las construcciones pasivas e impersonales con "se" en español como L2. ¿Cuántas distinciones son necesarias?

Este artículo sugiere un enfoque nuevo a la enseñanza de las dos estructuras gramaticales la pasiva refleja y el “se” impersonal para las clases universitarias de E/LE. Concretamente, se argumenta que las dos se deberían tratar como construcciones pasivas, basada en un análisis léxico-funcional de ellas que enfoca la lingüística contrastiva. Incluso para la instrucción de E/LE, se recomienda una aproximación contrastiva en la que se enfocan tanto la reflexión metalingüística como la competencia del estudiante en el L2. Específicamente, el uso de córpora lingüísticos en la clase forma una parte integral de la instrucción. El uso de un corpus estimula la curiosidad del estudiante, le expone a material de lengua auténtica, y promulga la reflexión inductiva independiente.

Linking Agentive Objects in Mandarin Chinese

This paper is concerned with the problem of argument-function mismatch observed in the apparent subject-object inversion in Chinese consumption verbs, e.g., chi 'eat' and he 'drink', and accommodation verbs, e.g., zhu 'live' and shui 'sleep'. These verbs seem to allow the linking of [agent-SUBJ theme-OBJ] as well as [agent-OBJ theme-SUBJ], but only when the agent is also the semantic role denoting the measure or extent of the action. The account offered is formulated within LFG's lexical mapping theory. Under the simplest and also the strictest interpretation of the one-to-one argument-function mapping principle (or the theta-criterion), a composite role such as ag-ext receives syntactic assignment via one composing role only. One-to-one linking thus entails the suppression of the other composing role. Apparent subject-object inversion occurs when the more prominent agent role is suppressed and thus allows the less prominent extent role to dictate the linking of the entire ag-ext composite role. This LMT account also potentially facilitates a natural explanation of markedness among the competing syntactic structures.

Sporadic and familial pheochromocytomas are associated with loss of at least two discrete intervals on chromosome 1p

Pheochromocytomas are tumors of the adrenal medulla originating in the chromaffin cells derived from the neural crest. Ten % of these tumors are associated with the familial cancer syndromes multiple endocrine neoplasia type 2, von Hippel-Lindau disease (VHL), and rarely, neurofibromatosis type 1, in which germ-line mutations have been identified in RET, VHL, and NF1, respectively. In both the sporadic and familial forms of pheochromocytoma, allelic loss at 1p, 3p, 17p, and 22q has been reported, yet the molecular pathogenesis of these tumors is largely unknown. Allelic loss at chromosome 1p has also been reported in other endocrine tumors, such as medullary thyroid cancer and tumors of the parathyroid gland, as well as in tumors of neural crest origin including neuroblastoma and malignant melanoma, In this study, we performed fine structure mapping of deletions at chromosome 1p in familial and sporadic pheochromocytomas to identify discrete regions likely housing tumor suppressor genes involved in the development of these tumors. Ten microsatellite markers spanning a region of similar to 70 cM (Ipter to 1p34.3) were used to screen 20 pheochromocytomas from 19 unrelated patients for loss of heterozygosity (LOH). LOH was detected at five or more loci in 8 of 13 (61%)sporadic samples and at five or more loci in four of five (80%) tumor samples from patients with multiple endocrine neoplasia type 2. No LOH at 1p was detected in pheochromocytomas from two VHL patients, Analysis of the combined sporadic and familial tumor data suggested three possible regions of common somatic loss, designated as PCI (D1S243 to D1S244), PC2 (D1S228 to D1S507), and PC3 (D1S507 toward the centromere). We propose that chromosome Ip may be the site of at least three putative tumor suppressor loci involved in the tumorigenesis of pheochromocytomas. At least one of these loci, PC2 spanning an interval of <3.8 cM, is Likely to have a broader role in the development of endocrine malignancies.