Cluster K Mycobacteriophages: Insights into the Evolutionary Origins of Mycobacteriophage TM4

Five newly isolated mycobacteriophages –Angelica, CrimD, Adephagia, Anaya, and Pixie – have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them – with the exception of TM4 – form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species

Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists

Développement à l'ombre de la violence : un programme de connaissances pour l'action; l'orientation future des investissements en recherche sur les questions de fragilité, conflit, et sécurité, Genève, le 22 Septembre, 2011

Version anglaise disponible dans la Bibliothèque numérique du CRDIVersion espagnole disponible dans la Bibliothèque numérique du CRDILes États fragiles sont sujets à des cycles de violence récurrents. La violence alimente leur sous-développement chronique. Les taux de pauvreté dans les pays pauvres et violents sont, en moyenne, de 20 points supérieurs à ceux des pays pauvres et pacifiques. Par le passé, les travaux consacrés aux conflits cherchaient souvent à les expliquer par une seule cause (l’ethnicité, la « cupidité », etc.). Il s’agissait de trouver l’arme secrète correspondante pour remédier au problème de la fragilité. Nous savons désormais avec certitude que des causes multiples et complexes, en général conjuguées, sont à l’origine d’un conflit. Nous savons qu’il est difficile, mais pas impossible, de sortir durablement d’un conflit, que des règlements politiques inclusifs sont importants pour la paix, et qu’il est vital pour y parvenir d’instaurer la confiance dans le règlement politique et dans des institutions réformées. Nous savons également que cela prend du temps, souvent des décennies. Mais quelle que soit la complexité des causes, la logique de base, sous-jacente à ces conflits, reste simple : les violences se produisent dans des contextes où les alternatives institutionnelles à la violence sont faibles ou inexistantes ; des institutions faibles conjuguées à un ensemble de motivations politiques, sécuritaires et économiques (et à des pressions extérieures) créent les conditions du conflit et de la violence..

Desarrollo en la sombra de la violencia : agenda de conocimiento para políticas; informe sobre la dirección a futuro de la inversión en evidencia en problemas de fragilidad, seguridad y conflicto, Ginebra, 22 de septiembre de 2011

The table of contents for this item can be shared with the requester. The requester may then choose one chapter, up to 10% of the item, as per the Fair Dealing provision of the Canadian Copyright ActVersión en inglés disponible en la Biblioteca Digital del IDRC: Development in the shadow of violence : a knowledge agenda for policy; report on the Future Direction of Investment in Evidence on Issues of Fragility, Security and Conflict Geneva, September 22, 2011Versión en francés disponible en la Biblioteca Digital del IDRC: Développement à l'ombre de la violence : un programme de connaissances pour l'action; l'orientation future des investissements en recherche sur les questions de fragilité, conflit, et sécurité, Genève, le 22 Septembre, 2011Ciclos recurrentes de violencia acosan y definen a los estados frágiles y la violencia alimenta su subdesarrollo crónico. Las tasas de pobreza en los países empobrecidos que sufren de violencia son, en promedio, 20 puntos más altas que las de sus contrapartes pobres donde prevalece la paz. El trabajo realizado en el tema de conflictos en el pasado a menudo buscaba una explicación simple, una causa única (etnia, “avaricia”, etc.), con su respectiva bala mágica para resolver el problema de la fragilidad. Ahora sabemos con certeza que las causas de los conflictos son múltiples y complejas y que generalmente ocurren en combinación. Sabemos que es difícil, pero no imposible sostener una salida del conflicto; que los arreglos políticos incluyentes son importantes para la paz; que es vital para el éxito la confianza que se logre en los arreglos políticos y en instituciones reformadas. También sabemos que esto toma tiempo, con frecuencia medido en décadas. A pesar de la complejidad de las causas, el razonamiento general que subyace a los conflictos es sencillo: para decirlo de un modo simple, la violencia ocurre en contextos donde no existen alternativas institucionales a la violencia o si las hay son débiles. Instituciones débiles combinadas con una gama de motivaciones políticas, económicas y de seguridad (y presiones externas) crean las condiciones para el conflicto y la violencia..

Development in the shadow of violence : a knowledge agenda for policy; report on the Future Direction of Investment in Evidence on Issues of Fragility, Security and Conflict Geneva, September 22, 2011

French version available in IDRC Digital LibrarySpanish version available in IDRC Digital LibraryThe table of contents for this item can be shared with the requester. The requester may then choose one chapter, up to 10% of the item, as per the Fair Dealing provision of the Canadian Copyright ActFragile states are beset and defined by recurring cycles of violence, and violence feeds their chronic underdevelopment. Violent and impoverished countries have poverty rates that are, on average, 20 points higher than their impoverished but peaceful counterparts. However, much of what is “known” by the research community is not “known” by policy and practice communities. Three pieces, in particular are key to understanding this gap: academic research tends not to focus on policy tools, limiting its relevance to decision-makers; donor funded evidence is rarely rigorous enough to translate into implementation; and we have lacked (until now) a baseline framework against which knowledge can accumulate

Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays

Localized accessibility of critical DNA sequences to the regulatory machinery is a key requirement for regulation of human genes. Here we describe a high-resolution, genome-scale approach for quantifying chromatin accessibility by measuring DNase I sensitivity as a continuous function of genome position using tiling DNA microarrays (DNase-array). We demonstrate this approach across 1% ( approximately 30 Mb) of the human genome, wherein we localized 2,690 classical DNase I hypersensitive sites with high sensitivity and specificity, and also mapped larger-scale patterns of chromatin architecture. DNase I hypersensitive sites exhibit marked aggregation around transcriptional start sites (TSSs), though the majority mark nonpromoter functional elements. We also developed a computational approach for visualizing higher-order features of chromatin structure. This revealed that human chromatin organization is dominated by large (100-500 kb) 'superclusters' of DNase I hypersensitive sites, which encompass both gene-rich and gene-poor regions. DNase-array is a powerful and straightforward approach for systematic exposition of the cis-regulatory architecture of complex genomes

Cluster k mycobacteriophages: Insights into the evolutionary origins of mycobacteriophage tm4

Five newly isolated mycobacteriophages -Angelica, CrimD, Adephagia, Anaya, and Pixie - have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them - with the exception of TM4 - form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species. © 2011 Pope et al.Fil: Pope, Welkin H.. University of Pittsburgh; Estados UnidosFil: Ferreira, Christina M.. University of Pittsburgh; Estados UnidosFil: Jacobs Sera, Deborah. University of Pittsburgh; Estados UnidosFil: Benjamin, Robert C.. University of North Texas; Estados UnidosFil: Davis, Ariangela J.. Calvin College; Estados UnidosFil: DeJong, Randall J.. Calvin College; Estados UnidosFil: Elgin, Sarah C. R.. Washington University in St. Louis; Estados UnidosFil: Guilfoile, Forrest R.. University of Pittsburgh; Estados UnidosFil: Forsyth, Mark H.. The College Of William And Mary; Estados UnidosFil: Harris, Alexander D.. Calvin College; Estados UnidosFil: Harvey, Samuel E.. The College Of William And Mary; Estados UnidosFil: Hughes, Lee E.. University of North Texas; Estados UnidosFil: Hynes, Peter M.. Washington University in St. Louis; Estados UnidosFil: Jackson, Arrykka S.. The College Of William And Mary; Estados UnidosFil: Jalal, Marilyn D.. University of North Texas; Estados UnidosFil: MacMurray, Elizabeth A.. The College Of William And Mary; Estados UnidosFil: Manley, Coreen M.. University of North Texas; Estados UnidosFil: McDonough, Molly J.. The College Of William And Mary; Estados UnidosFil: Mosier, Jordan L.. University of North Texas; Estados UnidosFil: Osterbann, Larissa J.. Calvin College; Estados UnidosFil: Rabinowitz, Hannah S.. Washington University in St. Louis; Estados UnidosFil: Rhyan, Corwin N.. Washington University in St. Louis; Estados UnidosFil: Russell, Daniel A.. University of Pittsburgh; Estados UnidosFil: Saha, Margaret S.. The College Of William And Mary; Estados UnidosFil: Shaffer, Christopher D.. Washington University in St. Louis; Estados UnidosFil: Simon, Stephanie E.. University of North Texas; Estados UnidosFil: Sims, Erika F.. Washington University in St. Louis; Estados UnidosFil: Tovar, Isabel G.. University of North Texas; Estados UnidosFil: Weisser, Emilie G.. Washington University in St. Louis; Estados UnidosFil: Wertz, John T.. Calvin College; Estados UnidosFil: Weston-Hafer, Kathleen A.. Washington University in St. Louis; Estados UnidosFil: Williamson, Kurt E.. The College Of William And Mary; Estados UnidosFil: Zhang, Bo. Washington University in St. Louis; Estados UnidosFil: Cresawn, Steven G.. James Madison University; Estados UnidosFil: Jain, Paras. Albert Einstein College Of Medicine Of Yeshiva University; Estados UnidosFil: Piuri, Mariana. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. University of Pittsburgh; Estados UnidosFil: Jacobs, William R.. Albert Einstein College Of Medicine Of Yeshiva University; Estados UnidosFil: Hendrix, Roger W.. University of Pittsburgh; Estados UnidosFil: Hatfull, Graham F.. University of Pittsburgh; Estados Unido