Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.

Cellular stresses activate the tumor suppressor p53 protein leading to selective binding to DNA response elements (REs) and gene transactivation from a large pool of potential p53 REs (p53REs). To elucidate how p53RE sequences and local chromatin context interact to affect p53 binding and gene transactivation, we mapped genome-wide binding localizations of p53 and H3K4me3 in untreated and doxorubicin (DXR)-treated human lymphoblastoid cells. We examined the relationships among p53 occupancy, gene expression, H3K4me3, chromatin accessibility (DNase 1 hypersensitivity, DHS), ENCODE chromatin states, p53RE sequence, and evolutionary conservation. We observed that the inducible expression of p53-regulated genes was associated with the steady-state chromatin status of the cell. Most highly inducible p53-regulated genes were suppressed at baseline and marked by repressive histone modifications or displayed CTCF binding. Comparison of p53RE sequences residing in different chromatin contexts demonstrated that weaker p53REs resided in open promoters, while stronger p53REs were located within enhancers and repressed chromatin. p53 occupancy was strongly correlated with similarity of the target DNA sequences to the p53RE consensus, but surprisingly, inversely correlated with pre-existing nucleosome accessibility (DHS) and evolutionary conservation at the p53RE. Occupancy by p53 of REs that overlapped transposable element (TE) repeats was significantly higher (p<10-7) and correlated with stronger p53RE sequences (p<10-110) relative to nonTE-associated p53REs, particularly for MLT1H, LTR10B, and Mer61 TEs. However, binding at these elements was generally not associated with transactivation of adjacent genes. Occupied p53REs located in L2-like TEs were unique in displaying highly negative PhyloP scores (predicted fast-evolving) and being associated with altered H3K4me3 and DHS levels. These results underscore the systematic interaction between chromatin status and p53RE context in the induced transactivation response. This p53 regulated response appears to have been tuned via evolutionary processes that may have led to repression and/or utilization of p53REs originating from primate-specific transposon elements.

Universality and self-similarity of an energy-constrained sandpile model with random neighbors

We study an energy-constrained sandpile model with random neighbors. The critical behavior of the model is in the same universality class as the mean-field self-organized criticality sandpile. The critical energy E-c depends on the number of neighbors n for each site, but the various exponents are independent of n. A self-similar structure with n-1 major peaks is developed for the energy distribution p(E) when the system approaches its stationary state. The avalanche dynamics contributes to the major peaks appearing at E-Pk = 2k/(2n - 1) with k = 1,2,...,n-1, while the fine self-similar structure is a natural result of the way the system is disturbed. [S1063-651X(99)10307-6].

Le site CjEd-8 : l'Archaïque supérieur au Témiscouata

Occupé depuis près de 10 000 ans, le Témiscouata est un lieu clé pour mieux comprendre la préhistoire du Québec, en raison de son emplacement stratégique entre l’Atlantique et la vallée du Saint-Laurent et de la cinquantaine de sites archéologiques connus dans la région. Le site CjEd-8 est le seul site associé à l’Archaïque supérieur (6 000 à 4 000 ans avant aujourd’hui) connu dans la région. Cette recherche palethnographique porte sur l’analyse de la collection lithique du site archéologique CjEd-8. Nos questions de recherche sont les suivantes : quel était le mode de vie et les activités des occupants du site CjEd-8? Quel était leur environnement et comment s’y sont-ils adapté? Comment l’espace était-il utilisé sur le site? Comment ce site se compare-t-il aux autres sites de l’Archaïque supérieur au Québec et dans le nord-est américain? Est-il possible de relier l’occupation du site CjEd-8 à un plus vaste cadre régional ou culturel, comme un réseau d’interaction, par exemple? Nous avons effectué une analyse techno-morphologique individuelle de tous les outils et du débitage de la collection. Nous avons pu constater que tous les stades de réduction lithique (initial, intermédiaire et final) sont présents sur le site CjEd-8. Les matières premières locales sont représentées dans tous ces stades de réduction, bien que les matières premières exotiques soient surtout présentes au sein du stade initial de réduction, davantage que les matières premières locales. Ceci laisse croire que le dégrossissement initial des blocs et galets de matière première locale se faisait ailleurs que sur le site, fort probablement sur les carrières de chert de la région, et que des matières exotiques ont aussi été travaillées sur le site. Des activités de taille ont eu lieu sur les deux zones du site, probablement autour de deux foyers distincts. Les quelques individus présents y sont demeurés très brièvement, semblent avoir effectué un nombre limité d’activités et sont peut-être repassés quelques temps après. L’Archaïque supérieur est caractérisé par une augmentation de la population et par l’intensification des interactions et de l’appartenance régionale. Or, il semblerait que ce soit l’inverse que l’on observe archéologiquement au Témiscouata. L’assemblage de CjEd-8 ne présente aucune ressemblance particulière avec les sites associés à l’Archaïque supérieur au Québec, bien que pour presque tous ces sites, on constate une exploitation importante des matières premières locales (même si ces dernières sont de qualité moyenne), combinée à l’exploitation de matières premières exotiques de sources très éloignées. L’industrie du quartz, importante dans la plupart des sites de l’Archaïque supérieur, se reflète très peu sur CjEd-8. Bien qu’il nous soit impossible d’associer l’occupation du site CjEd-8 à une tradition culturelle précise, cela ne signifie pas que ses occupants n’étaient pas en interaction avec l’une ou l’autre des entités culturelles de la fin de l’Archaïque, que ce soit avec les groupes de la région de Quoddy, de la Gaspésie, de la Vallée du Saint-Laurent, de l’Outaouais, de la Haute Côte nord, du Vermont, de l’État de New York et de l’intérieur du Maine. La question des modes de subsistance des occupants de CjEd-8 n’a pas été soulevée lors de nos analyses. Nous savons toutefois que les occupants du Témiscouata avaient alors accès à une faune riche et diversifiée.

Caractérisation moléculaire du rôle de facteurs accessoires ArgR et PepA au niveau de la recombinaison spécifique sur le site cer

Mon projet de recherche avait pour but de caractériser le rôle de deux protéines, ArgR et PepA, qui agissent en tant que facteurs accessoires de la recombinaison au niveau de deux sites cer du plasmide ColE1 présent dans la bactérie Escherichia coli. Ces deux protéines, couplées aux deux recombinases à tyrosine XerC et XerD, permettent la catalyse de la recombinaison site spécifique au niveau de la séquence cer, convertissant les multimères instables de ColE1 en monomères stables. Cette étude a principalement porté sur la région C-terminale de la protéine ArgR. Cette région de la protéine ArgR possède une séquence en acides-aminés et une structure similaire à celle de la protéine AhrC de Bacillus subtilis. De plus, AhrC, le répresseur de l’arginine de cette bactérie, est capable de complémenter des Escherichia coli mutantes déficientes en ArgR. Les régions C-terminales de ces protéines, montrent une forte similarité. De précédents travaux dans notre laboratoire ont démontré que des mutants d’ArgR comprenant des mutations dans cette région, en particulier les mutants ArgR149, une version tronquée d’ArgR de 149 acides-aminés, et ArgR5aa, une version comprenant une insertion de cinq acides-aminés dans la partie C-terminale, perdaient la capacité de permettre la recombinaison au niveau de deux sites cer présents dans le plasmide pCS210. Malgré cette incapacité à promouvoir la réaction de recombinaison en cer, ces deux mutants étaient toujours capables de se lier spécifiquement à l’ADN et de réprimer une fusion argA :: lacZ. Dans ce travail, les versions mutantes et sauvages d’ArgR furent surexprimées en tant que protéines de fusion 6-histidine. Des analyses crosslinking ont montré que la version sauvage et ArgR5aa pouvaient former des hexamères in-vitro de manière efficace, alors qu’ArgR149 formait des multimères de plus faible poids moléculaire. Des formes tronquées d’ArgR qui comportaient 150 acides-aminés ou plus, étaient encore capables de permettre la recombinaison en cer. Les mutants par substitution ArgRL149A et ArgRL151A ont tous montré que les substitutions d’un seul acide-aminé au sein de cette région avaient peu d’effets sur la recombinaison en cer. Les expériences de crosslinking protéine-à-protéine ont montré que le type sauvage et les formes mutantes d’ArgR étaient capables d’interagir avec la protéine accessoire PepA, également impliquée dans la recombinaison en cer. Les expériences de recombinaison in-vitro utilisant la forme sauvage et les formes mutantes d’ArgR combinées avec les protéines PepA, XerC et XerD purifiées, ont montré que le mutant ArgR149 ne soutenait pas la recombinaison, mais que le mutant ArgR5aa permettait la formation d’une jonction d’Holliday. Des expériences de topologie ont montré que PepA était capable de protéger l’ADN de la topoisomérase 1, et d’empêcher ArgRWt de se lier à l’ADN. Les deux mutants ArgR149 et ArgR5aa protègent aussi l’ADN avec plus de surenroulements. Quand on ajoute PepA, les profils de migration montrent un problème de liaison des deux mutants avec PepA. D’autres expériences impliquant le triplet LEL (leucine-acide glutamique-leucine) et les acides-aminés alentour devraient être réalisés dans le but de connaitre l’existence d’un site de liaison potentiel pour PepA.

Bioethics’ Lack in Relation to Person-Centred User-Driven Health Systems Planning: A Call for Change

La tribune de l'éditeur / Editor's Soapbox

Dilemmas in Military Medical Ethics: A Call for Conceptual Clarity

Article

Estrategias de tercerización en Colombia como centro de operaciones enfocado a los Call Centers en Barranquilla

El sector BPO&O es un sector con alto potencial en Colombia que aún se encuentra Incipiente. Dentro de este sector, los Call Centers juegan un papel importante para su desarrollo y Barranquilla posee grandes cualidades para permitir este crecimiento si se plantean las estrategias adecuadas.

Modeling based on the structure of vicilins predicts a histidine cluster in the active site of oxalate oxidase

It is known that germin, which is a marker of the onset of growth in germinating wheat, is an oxalate oxidase, and also that germins possess sequence similarity with legumin and vicilin seed storage proteins. These two pieces of information have been combined in order to generate a 3D model of germin based on the structure of vicilin and to examine the model with regard to a potential oxalate oxidase active site. A cluster of three histidine residues has been located within the conserved beta-barrel structure. While there is a relatively low level of overall sequence similarity between the model and the vicilin structures, the conservation of amino acids important in maintaining the scaffold of the beta-barrel lends confidence to the juxtaposition of the histidine residues. The cluster is similar structurally to those found in copper amine oxidase and other proteins, leading to the suggestion that it defines a metal-binding location within the oxalate oxidase active site. It is also proposed that the structural elements involved in intermolecular interactions in vicilins may play a role in oligomer formation in germin/oxalate oxidase.

The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria

The rulAB operon of Pseudomonas spp. confers fitness traits on the host and has been suggested to be a hotspot for insertion of mobile elements that carry avirulence genes. Here, for the first time, we show that rulB on plasmid pWW0 is a hotspot for the active site-specific integration of related integron-like elements (ILEs) found in six environmental pseudomonads (strains FH1–FH6). Integration into rulB on pWW0 occurred at position 6488 generating a 3 bp direct repeat. ILEs from FH1 and FH5 were 9403 bp in length and contained eight open reading frames (ORFs), while the ILE from FH4 was 16 233 bp in length and contained 16 ORFs. In all three ILEs, the first 5.1 kb (containing ORFs 1–4) were structurally conserved and contained three predicted site-specific recombinases/integrases and a tetR homologue. Downstream of these resided ORFs of the ‘variable side’ with structural and sequence similarity to those encoding survival traits on the fitness enhancing plasmid pGRT1 (ILEFH1 and ILEFH5) and the NR-II virulence region of genomic island PAGI-5 (ILEFH4). Collectively, these ILEs share features with the previously described type III protein secretion system effector ILEs and are considered important to host survival and transfer of fitness enhancing and (a)virulence genes between bacteria.

Novel Application of 2D and 3D-Similarity Searches To Identify Substrates among Cytochrome P450 2C9, 2D6, and 3A4

Cytochrome P450 (CYP450) is a class of enzymes where the substrate identification is particularly important to know. It would help medicinal chemists to design drugs with lower side effects due to drug-drug interactions and to extensive genetic polymorphism. Herein, we discuss the application of the 2D and 3D-similarity searches in identifying reference Structures with higher capacity to retrieve Substrates of three important CYP enzymes (CYP2C9, CYP2D6, and CYP3A4). On the basis of the complementarities of multiple reference structures selected by different similarity search methods, we proposed the fusion of their individual Tanimoto scores into a consensus Tanimoto score (T(consensus)). Using this new score, true positive rates of 63% (CYP2C9) and 81% (CYP2D6) were achieved with false positive rates of 4% for the CYP2C9-CYP2D6 data Set. Extended similarity searches were carried out oil a validation data set, and the results showed that by using the T(consensus) score, not only the area of a ROC graph increased, but also more substrates were recovered at the beginning of a ranked list.

Embodying a mine site : enacting cyborg curriculum

This paper focuses on the construction of my post-operatively scarred body as a mine site, my experiences with reconstructively normalizing its appearance as a cyborg, and the implications for my work as an environmental educator  interested in how the body of a theorist is presented within theoretical spaces. The paper is not a victim's story as such, but rather a response to the  hypothesis that illness is a call for stories, that the body needs a voice that disease and illness take away. It relates Donna Haraway's notions of the cyborg and other feminist poststructuralist work to both my living body and the body of my curriculum work in environmental education.

Ploughzone archaeology on an Australian historic site

Archaeologists are often confronted with sites featuring post-occupation disturbance. At rural sites, this disturbance often comes in the form of agricultural activity, such as ploughing and grazing. These disturbances can call into question the value of site spatial relationships and broader data integrity. Between 2006 and 2007, archaeologists from La Trobe University and New Zealand-based consultancy firm Geometria carried out a programme of fieldwork at an 18411861 cottage in Gippsland, Victoria. The site is now an open grazing paddock that has been ploughed on several occasions in the past. The survey techniques used by the archaeological team, which included geomagnetic survey and artefact surface scatter mapping, allowed for testing the integrity of the ploughed archaeological deposits prior to excavation, and provide a case study for the applicability of ploughzone archaeology techniques to Australian historic sites.

Why has the rising economic tide failed to float the disability employment boat? A call to action : business,community, government and people power

It is well established that people with disabilities are under-represented in the workforce. Disability labour market scholars agree that there is a significant gap between labour market participation of people with disabilities and people without disabilities, with on-going labour market disadvantage widely reported. All indicate that notwithstanding the recent economic growth of Western economies, the employment rate for people with disabilities has not improved. This paper draws on the findings of three recent research projects on disability employment in Australia and on data from contemporary literature on workplace discrimination and proposes that a combination of more robust social inclusion policies and legislation, revitalised supported employment models, intensive social marketing, and radical disability advocacy is required.

Karyotypic similarity among Barycholos temetzi and five species of the genus Eleutherodactylus from southeastern Brazil (Anura, Brachycephalidae)

Comparative cytogenetic analyses were carried out in six species of Brachycephalidae from southeastern Brazil. Barycholos ternetzi, Eleutherodactylus binotatus, Eleutherodactylus guentheri, Eleutherodactylus juipoca, Eleutherodactylus parvus and Eleutherodactylus sp. have 2n = 22 karyotypes with a marked variation in the morphology of chromosome pairs 8, 10 and 11, which are of telocentric or metacentric types, resulting in FN = 38, 40 and 44. Eleutherodactylus have a single chromosome pair bearing Ag-NOR, i.e. pair 1 in E. binotatus, pair 6 in E. guentheri and E. parvus, and pair 11 in E. juipoca and Eleutherodactylus sp. In contrast, B. ternetzi showed Ag-positive sites in the chromosome pairs 1, 4, 5, 9 and 11, and only one to three labelings per metdphase in each individual. Nevertheless, the main chromosome pair with Ag-NOR in the species seems to be the 11th, like in E. juipoca and Eleutherodactylus sp. The NOR site was confirmed by fluorescence in situ hybridization (FISH) technique in E. binotatus and in B. ternetzi, bearing 1p1p and 9p11p11p Ag-NOR pattern, respectively. All the species exhibited predominantly centromeric C-banding pattern, but interstitial bands have also been observed in some cases. In E. binotatus, there is an indication of geographical difference in the distribution of the interstitial C-bands. The fluorochromes GC-specific chromomycin A(3) (CMA(3)) and AT-specific 4',6-diamidino-2-phenylindole (DAPI), with distamycin A (DA) counterstaining, provided the molecular content of some repetitive regions in the karyotypes of the species. One male of E. binotatus presented an extensive heteromorphism, involving at least five different pairs, probably as a consequence of multiple reciprocal translocations. Such rearrangements might be responsible for the multivalent chain seen in the meiosis of this specimen, as well as in another male, although not exhibiting chromosome heteromorphism. The remaining males and those belonging to the other species have always shown 11 bivalents in diplotene and metaphase I cells. In all male specimens, metaphases II presented 11 chromosomes. Despite the observed discrepancies, the five species of Eleutherodactylus have a great uniformity in the 2n = 22 karyotypes, suggesting an assemblage of species from southeastern and southern Brazil, in contrast to northern and northeastern assemblage which is characterized by higher diploid numbers. Undoubtedly, B. ternetzi could be included in that proposed assemblage, due to its karyotypic similarity with the Eleutherodactylus species, as evidenced in the present study. This fact strongly supports the close relationships of both genera, previously inferred on the basis of several characters shared by their species. (C) 2006 Elsevier Ltd. All rights reserved.