DOUBLE-STRAND BREAK REPAIR PATHWAYS IN DNA STRUCTURE-INDUCED GENETIC INSTABILITY

Genetic instability in mammalian cells can occur by many different mechanisms. In the absence of exogenous sources of DNA damage, the DNA structure itself has been implicated in genetic instability. When the canonical B-DNA helix is naturally altered to form a non-canonical DNA structure such as a Z-DNA or H-DNA, this can lead to genetic instability in the form of DNA double-strand breaks (DSBs) (1, 2). Our laboratory found that the stability of these non-B DNA structures was different in mammals versus Escherichia coli (E.coli) bacteria (1, 2). One explanation for the difference between these species may be a result of how DSBs are repaired within each species. Non-homologous end-joining (NHEJ) is primed to repair DSBs in mammalian cells, while bacteria that lack NHEJ (such as E.coli), utilize homologous recombination (HR) to repair DSBs. To investigate the role of the error-prone NHEJ repair pathway in DNA structure-induced genetic instability, E.coli cells were modified to express genes to allow for a functional NHEJ system under different HR backgrounds. The Mycobacterium tuberculosis NHEJ sufficient system is composed of Ku and Ligase D (LigD) (3). These inducible NHEJ components were expressed individually and together in E.coli cells, with or without functional HR (RecA/RecB), and the Z-DNA and H-DNA-induced mutations were characterized. The Z-DNA structure gave rise to higher mutation frequencies compared to the controls, regardless of the DSB repair pathway(s) available; however, the type of mutants produced after repair was greatly dictated on the available DSB repair system, indicated by the shift from 2% large-scale deletions in the total mutant population to 24% large-scale deletions when NHEJ was present (4). This suggests that NHEJ has a role in the large deletions induced by Z-DNA-forming sequences. H-DNA structure, however, did not exhibit an increase in mutagenesis in the newly engineered E.coli environment, suggesting the involvement of other factors in regulating H-DNA formation/stability in bacterial cells. Accurate repair by established DNA DSB repair pathways is essential to maintain the stability of eukaryotic and prokaryotic genomes and our results suggest that an error-prone NHEJ pathway was involved in non-B DNA structure-induced mutagenesis in both prokaryotes and eukaryotes.

Energy harvesting through arterial wall deformation: A FEM approach to fluid–structure interactions and magneto-hydrodynamics

Engineers are confronted with the energy demand of active medical implants in patients with increasing life expectancy. Scavenging energy from the patient’s body is envisioned as an alternative to conventional power sources. Joining in this effort towards human-powered implants, we propose an innovative concept that combines the deformation of an artery resulting from the arterial pressure pulse with a transduction mechanism based on magneto-hydrodynamics. To overcome certain limitations of a preliminary analytical study on this topic, we demonstrate here a more accurate model of our generator by implementing a three-dimensional multiphysics finite element method (FEM) simulation combining solid mechanics, fluid mechanics, electric and magnetic fields as well as the corresponding couplings. This simulation is used to optimize the generator with respect to several design parameters. A first validation is obtained by comparing the results of the FEM simulation with those of the analytical approach adopted in our previous study. With an expected overall conversion efficiency of 20% and an average output power of 30 μW, our generator outperforms previous devices based on arterial wall deformation by more than two orders of magnitude. Most importantly, our generator provides sufficient power to supply a cardiac pacemaker.

THEORETICAL STUDIES ON THE METHODS OF RECONSTRUCTING PHYLOGENETIC TREES FROM DNA SEQUENCE DATA (MOLECULAR EVOLUTION, HOMINOID EVOLUTION, COMPUTER SIMULATION)

(1) A mathematical theory for computing the probabilities of various nucleotide configurations is developed, and the probability of obtaining the correct phylogenetic tree (model tree) from sequence data is evaluated for six phylogenetic tree-making methods (UPGMA, distance Wagner method, transformed distance method, Fitch-Margoliash's method, maximum parsimony method, and compatibility method). The number of nucleotides (m*) necessary to obtain the correct tree with a probability of 95% is estimated with special reference to the human, chimpanzee, and gorilla divergence. m* is at least 4,200, but the availability of outgroup species greatly reduces m* for all methods except UPGMA. m* increases if transitions occur more frequently than transversions as in the case of mitochondrial DNA. (2) A new tree-making method called the neighbor-joining method is proposed. This method is applicable either for distance data or character state data. Computer simulation has shown that the neighbor-joining method is generally better than UPGMA, Farris' method, Li's method, and modified Farris method on recovering the true topology when distance data are used. A related method, the simultaneous partitioning method, is also discussed. (3) The maximum likelihood (ML) method for phylogeny reconstruction under the assumption of both constant and varying evolutionary rates is studied, and a new algorithm for obtaining the ML tree is presented. This method gives a tree similar to that obtained by UPGMA when constant evolutionary rate is assumed, whereas it gives a tree similar to that obtained by the maximum parsimony tree and the neighbor-joining method when varying evolutionary rate is assumed. ^

Conjugal Transfer of the Tn916-like Transposon TnFO1 from Enterococcus faecalis Isolated from Cheese to Other Gram-positive Bacteria

A Tn916-like transposon (TnFO1) was found in the multiple antibiotic resistant Enterococcus faecalis strain FO1 isolated from a raw milk cheese. In this strain, the tetracycline determinant was localized by DNA-DNA hybridization with a tetM nucleotide probe on the chromosome and on a 30-kb plasmid. The transposon TnFO1 was identified and characterized by DNA-DNA hybridization experiments with the five internal HincII fragments of Tn916. The tetracycline resistance determinant was identified by its complete nucleotide sequence as TetM. Transposon TnFO1 was also detected in its circular form by DNA-DNA hybridization and PCR amplification. Both ends including the joining region of the closed circular transposon TnFO1 were sequenced. TnFO1 could be transferred by conjugation from Enterococcus faecalis into Enterococcus faecalis, Lactococcus lactis subsp. lactis biovar. diacetylactis, Listeria innocua, Leuconostoc mesenteroides and Staphylococcus aureus, and from Lactococcus lactis subsp. lactis biovar. diacetylactis into Listeria innocua. Pulsed-field electrophoresis of genomic DNA from E. faecalis FO1 transconjugants showed that transposon TnFO1 integrated at different sites.

Phylogenetic Relationships of Clawed Lobster Genera (Decapoda : Nephropidae) Based on Mitochondrial 16S rRNA Gene Sequences

Approximately 350 base pairs (bp) of the mitochondrial 16S rRNA gene were used to study the phylogenetic relationships among 5 genera of the clawed lobster family Nephropidae (infraorder Astacidea), including Homarus, Homarinus, Metanephrops, Nephrops, and Nephropsis. Maximum-parsimony analysis, using a hermit crab, Pagurus pollicaris (infraorder Anomura), as an outgroup. produced a tree topology in which Homarus and Nephrops formed a well-supported clade that excluded Homarinus. The same tree topology was obtained from both neighbor-joining and maximum-likelihood analyses, Some morphological characters that appear synapomorphic for Nephrops and Metanephrops may be due to convergence rather than symplesiomorphy. The current taxonomy, therefore, does not reflect the phylogeny of this group as suggested by the molecular data. More molecular data and studies using homologous morphological characters me needed to reach a better understanding of the phylogenetic history of clawed lobsters.

Capitalisation of Experiences of the Swiss Support to Sustainable Management of Natural Resources (SMNR) in Bulgaria

Following the collapse of the communist regime in 1989, Bulgaria has undergone dramatic political, economic and social transformations. The transition process of the past two decades was characterized by several reforms to support democratisation of the political system and the functioning of a free-market economy. Since 1992, Switzerland has been active in Bulgaria providing assistance to the transition process, with support to Sustainable Management of Natural Resources (SMNR) starting in 1995. The SMNR Capitalisation of Experiences (CapEx) took place between March and September 2007, in the context of SDC phasing out its programmes in Bulgaria by the end of 2007 due to the country’s accession to the European Union. The CapEx exercise has culminated in the identification of 17 lessons learned. In the view of the CapEx team, many of these lessons are relevant for countries that are in the process of joining the EU, facing similar democratisation challenges as Bulgaria. Overall, the Swiss SMNR projects have been effective entry points to support areas that are crucial to democratic transitions, namely participation in public goods management, decentralisation, human capacity development in research and management, and preparation for EU membership. The specificity of the Swiss support stems from an approach that combines a long-term commitment with a clear thematic focus (forestry, biodiversity conservation and organic agriculture). The multistakeholder approach and diversification of support between local, regional and national levels are also important elements that contributed to make a difference in relation to other donors supporting the Bulgarian transition. At the institutional level, there are a number of challenges where the contribution of SMNR activities was only modest, namely improving the legal framework and creating more transparency and accountability, both of which are time and resource-consuming processes. In addition, the emergence of competent and sustainable non-government organisations (NGOs) is a complex process that requires support to membership based organisations, a challenge that was hardly met in the case of SMNR. Finally, reform of government institutions involved in management of natural resources is difficult to achieve via project support only, as it requires leverage and commitment at the level of policy dialogue. At the programme management level, the CapEx team notes that corruption was not systematically addressed in SMNR projects, indicating that more attention should be given to this issue at the outset of any new project.

REV7 counteracts DNA double-strand break resection and affects PARP inhibition

Error-free repair of DNA double-strand breaks (DSBs) is achieved by homologous recombination (HR), and BRCA1 is an important factor for this repair pathway. In the absence of BRCA1-mediated HR, the administration of PARP inhibitors induces synthetic lethality of tumour cells of patients with breast or ovarian cancers. Despite the benefit of this tailored therapy, drug resistance can occur by HR restoration. Genetic reversion of BRCA1-inactivating mutations can be the underlying mechanism of drug resistance, but this does not explain resistance in all cases. In particular, little is known about BRCA1-independent restoration of HR. Here we show that loss of REV7 (also known as MAD2L2) in mouse and human cell lines re-establishes CTIP-dependent end resection of DSBs in BRCA1-deficient cells, leading to HR restoration and PARP inhibitor resistance, which is reversed by ATM kinase inhibition. REV7 is recruited to DSBs in a manner dependent on the H2AX-MDC1-RNF8-RNF168-53BP1 chromatin pathway, and seems to block HR and promote end joining in addition to its regulatory role in DNA damage tolerance. Finally, we establish that REV7 blocks DSB resection to promote non-homologous end-joining during immunoglobulin class switch recombination. Our results reveal an unexpected crucial function of REV7 downstream of 53BP1 in coordinating pathological DSB repair pathway choices in BRCA1-deficient cells.

Deletion of exon 8 from the EXT1 gene causes multiple osteochondromas (MO) in a family with three affected members.

Multiple osteochondromas (also called hereditary multiple exostoses) is an autosomal dominant disorder characterized by multiple cartilaginous tumors, which are caused by mutations in the genes for exostosin-1 (EXT1) and exostosin-2 (EXT2). The goal of this study was to elucidate the genetic alterations in a family with three affected members. Isolation of RNA from the patients' blood followed by reverse transcription and PCR amplification of selected fragments showed that the three patients lack a specific region of 90 bp from their EXT1 mRNA. This region corresponds to the sequence of exon 8 from the EXT1 gene. No splice site mutation was found around exon 8. However, long-range PCR amplification of the region from intron 7 to intron 8 indicated that the three patients contain a deletion of 4318 bp, which includes exon 8 and part of the flanking introns. There is evidence that the deletion was caused by non-homologous end joining because the breakpoints are not located within a repetitive element, but contain multiple copies of the deletion hotspot sequence TGRRKM. Exon 8 encodes part of the active site of the EXT1 enzyme, including the DXD signature of all UDP-sugar glycosyltransferases. It is conceivable that the mutant protein exerts a dominant negative effect on the activity of the EXT glycosyltransferase since it might interact with normal copies of the enzyme to form an inactive hetero-oligomeric complex. We suggest that sequencing of RNA might be superior to exome sequencing to detect short deletions of a single exon.

The mechanism of action of a novel benzo[c]phenanthridine alkaloid, NK314 and the cellular responses

NK314 is a novel synthetic benzo[c]phenanthridine alkaloid that is currently in clinical trials as an antitumor compound, based on impressive activities in preclinical models. However, its mechanism of action is unknown. The present investigations were directed at determining the mechanism of action of this agent and cellular responses to NK314. My studies demonstrated that NK314 intercalated into DNA, trapped topoisomerase IIα in its cleavage complex intermediate, and inhibited the ability of topoisomerase IIα to relax super-coiled DNA. CEM/VM1 cells, which are resistant to etoposide due to mutations in topoisomerase IIα, were cross-resistant to NK314. However, CEM/C2 cells, which are resistant to camptothecin due to mutations in topoisomerase I, retained sensitivity. This indicates topoisomerase IIα is the target of NK314 in the cells. NK314 caused phosphorylation of the histone variant, H2AX, which is considered a marker of DNA double-strand breaks. DNA double-strand breaks were also evidenced by pulsed-field gel electrophoresis and visualized as chromosomal aberrations after cells were treated with NK314 and arrested in mitosis. Cell cycle checkpoints are activated following DNA damage. NK314 induced significant G2 cell cycle arrest in several cell lines, independent of p53 status, suggesting the existence of a common mechanism of checkpoint activation. The Chk1-Cdc25C-Cdk1 G2 checkpoint pathway was activated in response to NK314, which can be abrogated by the Chk1 inhibitor UCN-01. Cell cycle checkpoint activation may be a defensive mechanism that provides time for DNA repair. DNA double-strand breaks are repaired either through ATM-mediated homologous recombination or DNA-PK-mediated non-homologous end-joining repair pathways. Clonogenic assays demonstrated a significant decrease of colony formation in both ATM deficient and DNA-PK deficient cells compared to ATM repleted and DNA-PK wild type cells respectively, indicating that both ATM and DNA-PK play important roles in the survival of the cells in response to NK314. The DNA-PK specific inhibitor NU7441 also significantly sensitized cells to NK314. In conclusion, the major mechanism of NK314 is to intercalate into DNA, trap and inhibit topoisomerase IIα, an action that leads to the generation of double-strand DNA breaks, which activate ATM and DNA-PK mediated DNA repair pathways and Chk1 mediated G2 checkpoint pathway. ^

The role of ATM in the cell cycle control of V(D)J recombination

Lymphocyte development requires the assembly of diversified antigen receptor complexes generated by the genetically programmed V(D)J recombination event. Because germline DNA is cut, introducing potentially dangerous double-stranded breaks (DSBs) and rearranged prior to repair, its activity is limited to the non-cycling stages of the cell cycle, G0/G1. The potential involvement of a key mediator, Ataxia Telangiectasia Mutated or ATM, in the DNA damage response (DDR) and cell cycle checkpoints has been implicated in recombination, but its role is not fully understood. Thymic lymphomas from ATM deficient mice contain clonal chromosomal translocations involving the T-cell antigen receptor (TCR). A previous report found ATM and its downstream target p53 associated with V(D)J intermediates, suggesting the DDR senses recombination. In this study, we sought to understand the role of ATM in V(D)J recombination. Developing thymocytes from ATM deficient mice were analyzed according to the cell cycle to detect V(D)J intermediates. Examination of all TCR loci in the non-cycling (G0/G1) and cycling (S/G2/M) fractions revealed the persistence of intermediates in ATM deficient thymocytes, contrary to the wild-type in which intermediates are found only during G0/G1. Further analysis found no defect in end-joining of intermediates, nor were they detected in developed T-cells. Based upon the presence of persisting intermediates, the recombination initiating nuclease Rag-2 was examined; strict regulation limits it to G 0/G1. Rag-2 regulation was not affected by an ATM deficiency as Rag-2 expression remained contained within G0/G 1, indicating recombination is not continuous. To determine if an ATM deficiency affects recognition of V(D)J breaks, sites of recombination identified by a TCR locus or Rag expression were analyzed according to co-localization with a DDR factor phosphorylated immediately after DNA damage, phosphorylated H2AX (γH2AX). No differences in co-localization were found between the wild-type and ATM deficiency, demonstrating ATM deficient lymphocytes retain the ability to recognize DSBs. Together, these results suggest ATM is necessary in the cell cycle regulation of recombination but not essential for the identification of V(D)J breaks. ATM ensures the containment of intermediates within G0/G1 and maintains genomic stability of developing lymphocytes, emphasizing its fundamental role in preventing tumorigenesis.^

Laberintos verbales de autoficción y metaficción en Borges y Cortázar

Este artículo investiga las relaciones que existen entre autoficción y metaficción en la literatura contemporánea, sobre todo en el marco de la posmodernidad. Si bien la bibliografía refiere estos conceptos, en general, al campo de la novela, aquí se analizan en dos cuentos de escritores argentinos paradigmáticos: Borges y Cortázar. Se intenta demostrar que estos procedimientos se generan en tramas complejas, que contienen una fábula fantástica y permiten inferir, además, algunos aspectos de las poéticas implícitas de sus autores. Esta propuesta, netamente híbrida, produce en el lector el extrañamiento de la reunión de pactos antitéticos y su actitud es compleja en relación con la verosimilitud. Su contrato de lectura oscila desde la certeza de lo autobiográfico hasta la ficción más descarnada. El lector decidirá acompañar o no a los autores en estos laberintos verbales aunque estará avisado de los procedimientos más evidentes: ficcionalidad, intertextualidad, autoconciencia, autorreflexividad, mise en abyme, entre otros.

Sociología, Economía e Historia : de la división del trabajo de producción del conocimiento a la fragmentación del objeto : efectos en la carrera de Sociología

Este artículo forma parte de un trabajo de investigación más amplio cuyo objeto es analizar los problemas de la inserción social de los jóvenes desde una perspectiva sociológica y plantea que frente al abandono de líneas de investigación que abordenlos fenómenos sociales en sus múltiples realciones engarzando armónicamente trabajo de campo y producción teórica, resulta imperioso preguntarse en qué consiste la especificidad de una perspectiva de este tipo. Para responder a este interrogante se desarrolla una posición teórica y se tratan las dificultades para encontrar , en nuestra casa de estudios, los insumos teóricos que esta posición transforma en imprescindibles.

La Economía Solidaria y la Gestión Compartida, en el marco de las Políticas Sociales de la Provincia de Buenos Aires : Análisis del caso del Consorcio de Gestión Compartida de la Provincia de Buenos Aires

La debacle estructural del modelo económico implementado en los años 90 y desatada a partir de la crisis de 2001, generó el surgimiento de nuevas prácticas de acción colectiva y diferentes formas de intervención del Estado en la cuestión social. Una de las propuestas más novedosas en este sentido, es el enfoque en las políticas públicas de la denominada "Economía Social" que engloba diversas maneras de organización alternativas en torno a la producción, la reproducción del trabajo y de la vida y la gestión de recursos. En este marco se plantea el análisis de un caso de una herramienta de política pública provincial: el Consorcio de Gestión Compartida para el Desarrollo Local de la Provincia de Buenos Aires, creado en el 2007 a partir de la adhesión a la Ley Nacional de Microcrédito. Proyecto que tuvo alcance provincial y que será estudiado en su fase inicial comprendida entre el mes de noviembre de 2007 y finales del 2009. Se planteará como objetivo mostrar, a través del análisis de este caso de cierta proporción, el posible surgimiento de nuevas lógicas de intervención en políticas sociales: un cambio de rumbo que habría tomado el Estado junto con las organizaciones frente a la realidad social en la segunda mitad de esta década. Esta tesina abordará la investigación desde dos ejes de análisis a través de los cuales se busca interpretar el caso. Estos son: la gestión compartida del Estado junto con las organizaciones sociales y la Economía Social como práctica económica alternativa. Intentando dilucidar el proceso donde la acción del Estado y las políticas públicas son permeadas por nuevas prácticas y saberes provenientes de la sociedad civil. Se utilizará una metodología de investigación cualitativa. Se realizarán entrevistas en profundidad y semiestructuradas a integrantes de las organizaciones que forman parte del Consorcio de Gestión Compartida, así como también a los técnicos del Estado provincial que trabajaron en la implementación del proyecto. A su vez, ésta estará complementada con registros obtenidos y fuentes propias del Consorcio de Gestión Compartida, sumado a observaciones participantes en diversas reuniones de dicha organización, además de documentos y material recolectado en diferentes instancias de la investigación

L'aspect linguistique des fusions-acquisitions d'entreprises

In the business world, mergers can also be seen as the joining of two or more "company-speaks". Contrasts between different "speaks" are brought out when the communities are together and this can be observed in the spoken and written language. This situation can be compared to that of languages in contact from the sociolinguistic and dialectological points of view. Terminology offers an adapted perspective on descriptive, historical and cultural levels.

Tal es la su auze : El héroe afortunado del Cantar de Mio Cid

El protagonista del Cantar de mio Cid es un héore mesurado, pero también afortunado, agraciado con auze o buenaventura y "en buen hora nado". Su fortuna es innata, pero también cultivada a través de la prudencia. La suma de templanza y osadía sirva para mantener el auze del Campeador, lo que, unido al optimismo del héroe afortunado, impregna el poema épico de un fuerte dinamismo.