Conditionally replicating mycobacteriophages: A system for transposon delivery to Mycobacterium tuberculosis

Transposon mutagenesis provides a direct selection for mutants and is an extremely powerful technique to analyze genetic functions in a variety of prokaryotes. Transposon mutagenesis of Mycobacterium tuberculosis has been limited in part because of the inefficiency of the delivery systems. This report describes the development of conditionally replicating shuttle phasmids from the mycobacteriophages D29 and TM4 that enable efficient delivery of transposons into both fast- and slow-growing mycobacteria. These shuttle phasmids consist of an Escherichia coli cosmid vector containing either a mini-Tn10(kan) or Tn5367 inserted into a nonessential region of the phage genome. Thermosensitive mutations were created in the mycobacteriophage genome that allow replication at 30°C but not at 37°C (TM4) or 38.5°C (D29). Infection of mycobacteria at the nonpermissive temperature results in highly efficient transposon delivery to the entire population of mycobacterial cells. Transposition of mini-Tn10(kan) occurred in a site-specific fashion in M. smegmatis whereas Tn5367 transposed apparently randomly in M. phlei, Bacille Calmette–Guérin (BCG), and M. tuberculosis. Sequence analysis of the M. tuberculosis and BCG chromosomal regions adjacent to Tn5367 insertions, in combination with M. tuberculosis genomic sequence and physical map data, indicates that the transpositions have occurred randomly in diverse genes in every quadrant of the genome. Using this system, it has been readily possible to generate libraries containing thousands of independent mutants of M. phlei, BCG, and M. tuberculosis.

Uracil-DNA glycosylase–DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects

Enzymatic transformations of macromolecular substrates such as DNA repair enzyme/DNA transformations are commonly interpreted primarily by active-site functional-group chemistry that ignores their extensive interfaces. Yet human uracil–DNA glycosylase (UDG), an archetypical enzyme that initiates DNA base-excision repair, efficiently excises the damaged base uracil resulting from cytosine deamination even when active-site functional groups are deleted by mutagenesis. The 1.8-Å resolution substrate analogue and 2.0-Å resolution cleaved product cocrystal structures of UDG bound to double-stranded DNA suggest enzyme–DNA substrate-binding energy from the macromolecular interface is funneled into catalytic power at the active site. The architecturally stabilized closing of UDG enforces distortions of the uracil and deoxyribose in the flipped-out nucleotide substrate that are relieved by glycosylic bond cleavage in the product complex. This experimentally defined substrate stereochemistry implies the enzyme alters the orientation of three orthogonal electron orbitals to favor electron transpositions for glycosylic bond cleavage. By revealing the coupling of this anomeric effect to a delocalization of the glycosylic bond electrons into the uracil aromatic system, this structurally implicated mechanism resolves apparent paradoxes concerning the transpositions of electrons among orthogonal orbitals and the retention of catalytic efficiency despite mutational removal of active-site functional groups. These UDG/DNA structures and their implied dissociative excision chemistry suggest biology favors a chemistry for base-excision repair initiation that optimizes pathway coordination by product binding to avoid the release of cytotoxic and mutagenic intermediates. Similar excision chemistry may apply to other biological reaction pathways requiring the coordination of complex multistep chemical transformations.

Dynamics of mobile element activity in chalcone synthase loci in the common morning glory (Ipomoea purpurea)

Mobile element dynamics in seven alleles of the chalcone synthase D locus (CHS-D) of the common morning glory (Ipomoea purpurea) are analyzed in the context of synonymous nucleotide sequence distances for CHS-D exons. By using a nucleotide sequence of CHS-D from the sister species Ipomoea nil (Japanese morning glory [Johzuka-Hisatomi, Y., Hoshino, A., Mori, T., Habu, Y. & Iida, S. (1999) Genes Genet. Syst. 74, 141–147], it is also possible to determine the relative frequency of insertion and loss of elements within the CHS-D locus between these two species. At least four different types of transposable elements exist upstream of the coding region, or within the single intron of the CHS-D locus in I. purpurea. There are three distinct families of miniature inverted-repeat transposable elements (MITES), and some recent transpositions of Activator/Dissociation (Ac/Ds)-like elements (Tip100), of some short interspersed repetitive elements (SINEs), and of an insertion sequence (InsIpCHSD) found in the neighborhood of this locus. The data provide no compelling evidence of the transposition of the mites since the separation of I. nil and I. purpurea roughly 8 million years ago. Finally, it is shown that the number and frequency of mobile elements are highly heterogeneous among different duplicate CHS loci, suggesting that the dynamics observed at CHS-D are locus-specific.

Highly plastic chromosomal organization in Salmonella typhi.

Gene order in the chromosomes of Escherichia coli K-12 and Salmonella typhimurium LT2, and in many other species of Salmonella, is strongly conserved, even though the genera diverged about 160 million years ago. However, partial digestion of chromosomal DNA of Salmonella typhi, the causal organism of typhoid fever, with the endonuclease I-CeuI followed by separation of the DNA fragments by pulsed-field gel electrophoresis showed that the chromosomes of independent wild-type isolates of S. typhi are rearranged due to homologous recombination between the seven rrn genes that code for ribosomal RNA. The order of genes within the I-CeuI fragments is largely conserved, but the order of the fragments on the chromosome is rearranged. Twenty-one different orders of the I-CeuI fragments were detected among the 127 wild-type strains we examined. Duplications and deletions were not found, but transpositions and inversions were common. Transpositions of I-CeuI fragments into sites that do not change their distance from the origin of replication (oriC) are frequently detected among the wild-type strains, but transpositions that move the fragments much further from oriC were rare. This supports the gene dosage hypothesis that genes at different distances from oriC have different gene dosages and, hence, different gene expression, and that during evolution genes become adapted to their specific location; thus, cells with changes in gene location due to transpositions may be less fit. Therefore, gene dosage may be one of the forces that conserves gene order, although its effects seem less strong in S. typhi than in other enteric bacteria. However, both the gene dosage and the genomic balance hypotheses, the latter of which states that the origin (oriC) and terminus (TER) of replication must be separated by 180 degrees C, need further investigation.

CemaT1 is an active transposon within the Caenorhabditis elegans genome

The maT clade of transposons is a group of transposable elements intermediate in sequence and predicted protein structure to mariner and T-C transposons, with a distribution thus far limited to a few invertebrate species. In the nematode Caenorhabditis elegans, there are eight copies of CemaT1 that are predicted to encode a functional transposase, with five copies being >99% identical. We present evidence, based on searches of publicly available databases and on PCR-based mobility assays, that the CemaT1 transposase is expressed in C. elegans and that the CemaT transposons are capable of excising in both somatic and germline tissues. We also show that the frequency of CemaT1 excisions within the genome of the N2 strain of C. elegans is comparable to that of the Tc1 transposon. However, unlike T-C transposons in mutator strains of C elegans, maT transposons do not exhibit increased frequencies of mobility, suggesting that maT is not regulated by the same factors that control T-C activity in these strains. Finally, we show that CemaT1 transposons are capable of precise transpositions as well as orientation inversions at some loci, and thereby become members of an increasing number of identified active transposons within the C. elegans genome. (C) 2004 Elsevier B.V. All rights reserved.

Le football rwanda : un simulacre guerrier dans la créolisation d'une société 1900-50

L'histoire du football Rwanda commence avec la colonisation du pays. En une cinquantaine d'années, ce jeu sport d'origine anglaise, en intégrant une société agro-pastorale et guerrière, est devenu une pratique culturelle locale. Comprendre ce phénomène nécessite d'articuler l'ancrage colonial d'une activité cosmopolite aux [ré]inventions culturelles locales suscitées par son implantation. Ce texte vise à montrer comment un jeu de balle, en traversant une société en cours d'occidentalisation, a marqué l'édification d'une modernité guerrière reçue et façonnée par les joueurs de l'époque. En traversant les transpositions ludiques d'enjeux sociaux et politiques plus larges, on observe que cette pratique, tout en participant du procès de "civilisation" que s'administra l'institution coloniale, constitua l'un des fers de lance de la lutte pour l'émancipation.

Guiding Monte Carlo tree searches with neural networks in the game of go

A dissertation submitted in fulfillment of the requirements to the degree of Master in Computer Science and Computer Engineering

A study of culture specific items and translation strategies in Bahram Beyza'i’s play “Marionettes”

L'objectif de cette recherche est de fournir une analyse de la pièce de théâtre perse ''Marionettes'' de Bahrām Beyzā'ī (1963) ainsi que de sa traduction anglaise (1989) afin de comparer et de mettre en contraste les traits propres à la culture «Culture-specific items» (CSI) et des stratégies de traduction. Les formes problématiques pertinentes des différences culturelles seront étudiées et les procédés suggérés par Newmark (1988) seront examinés afin de déterminer dans quelle mesure ils sont pertinents dans la traduction des différences culturelles du perse à l'anglais. La pièce a été traduite par une équipe de traducteurs: Sujata G.Bhatt, Jacquelin Hoats, Imran A. Nyazee et Kamiar K. Oskouee. (Parvin Loloi et Glyn Pursglove 2002:66). Les oeuvres théâtrales de Beyzā'ī sont basées sur les traditions ainsi que sur le folklore iranien. L'auteur aborde la réalité sous une perspective philosophique. « (Un point de vue) enveloppé dans une cape de comparaisons complexes à tel point que nombre des personnages de son oeuvre errent entre des symboles de la mythologie et de l’histoire, ou sociaux» (M.R. Ghanoonparvar, John Green 1989, p.xxii notre traduction). La classification des éléments culturels de Newmark (1988) va comme suit: «Écologie, culture matérielle, culture sociale, organisations, coutumes / moeurs, gestes et habitudes» (Newmark 1988:95). La recherche mettra l’accent sur les procédés suggérés pour traduire les CSI ainsi que sur les stratégies de traduction selon Newmark. Ces procédés comprennent : «traduction littérale, transfert, équivalent culturel, neutralisation, équivalent fonctionnel, équivalent descriptif, synonymie, par le biais de la traduction, transposition, modulation, traduction reconnue, étiquette de traduction, compensation, analyse componentielle, réduction et expansion, paraphraser, distique, notes, additions, gloses» (Newmark 1988:81-93). L'objectif ici est de déterminer si les procédés suggérés sont applicables à la traduction des CSIs du perse à l'anglais, et quels sont les procédés les plus fréquemment utilisés par les traducteurs.

A study of culture specific items and translation strategies in Bahram Beyza'i’s play “Marionettes”

L'objectif de cette recherche est de fournir une analyse de la pièce de théâtre perse ''Marionettes'' de Bahrām Beyzā'ī (1963) ainsi que de sa traduction anglaise (1989) afin de comparer et de mettre en contraste les traits propres à la culture «Culture-specific items» (CSI) et des stratégies de traduction. Les formes problématiques pertinentes des différences culturelles seront étudiées et les procédés suggérés par Newmark (1988) seront examinés afin de déterminer dans quelle mesure ils sont pertinents dans la traduction des différences culturelles du perse à l'anglais. La pièce a été traduite par une équipe de traducteurs: Sujata G.Bhatt, Jacquelin Hoats, Imran A. Nyazee et Kamiar K. Oskouee. (Parvin Loloi et Glyn Pursglove 2002:66). Les oeuvres théâtrales de Beyzā'ī sont basées sur les traditions ainsi que sur le folklore iranien. L'auteur aborde la réalité sous une perspective philosophique. « (Un point de vue) enveloppé dans une cape de comparaisons complexes à tel point que nombre des personnages de son oeuvre errent entre des symboles de la mythologie et de l’histoire, ou sociaux» (M.R. Ghanoonparvar, John Green 1989, p.xxii notre traduction). La classification des éléments culturels de Newmark (1988) va comme suit: «Écologie, culture matérielle, culture sociale, organisations, coutumes / moeurs, gestes et habitudes» (Newmark 1988:95). La recherche mettra l’accent sur les procédés suggérés pour traduire les CSI ainsi que sur les stratégies de traduction selon Newmark. Ces procédés comprennent : «traduction littérale, transfert, équivalent culturel, neutralisation, équivalent fonctionnel, équivalent descriptif, synonymie, par le biais de la traduction, transposition, modulation, traduction reconnue, étiquette de traduction, compensation, analyse componentielle, réduction et expansion, paraphraser, distique, notes, additions, gloses» (Newmark 1988:81-93). L'objectif ici est de déterminer si les procédés suggérés sont applicables à la traduction des CSIs du perse à l'anglais, et quels sont les procédés les plus fréquemment utilisés par les traducteurs.