1,787 research outputs found
Virophages or satellite viruses?
No full textInternational audienceIt has been argued that the smaller viruses associated with giant DNA viruses are a new biological entity. However, Mart Krupovic and Virginija Cvirkaite-Krupovic argue here that these smaller viruses should be classified with the satellite viruses
What Do Quarterly Workforce Dynamics Tell Us About Wal-Mart? Evidence from New Stores in Pennsylvania
Full text linkIn this paper I seek to better inform debate regarding Wal-Mart’s local impact on wages, and employment dynamics by combining data on Wal-Mart stores with the recently release Quarterly Workforce Indicators provided by the US Census. Use a panel of Pennsylvania counties, who saw entrance of a Wal-Mart in 2002, I find a new store has no effect on existing employee wages in the retail sector. However, new retail sector hires experience a roughly 1,500 purchases of diapers annual since 1999 I have no financial relationship with Wal-Mart or any affiliate that I am aware of.Wal-Mart, Pennsylvania, Quarterly Workforce Indicators
A Critical Overview of Epistemology of Tanzimat Literature: Duality and Teacher-Author / Student-Reader Relationship
No full textGüngör, Bilgin, (Çanakkale Onsekiz Mart Üniversitesi Fen Edebiyat Fakültesi Türk Dili ve Edebiyatı Bölümü)Tanzimat döneminin düşünsel yapısı ve edebi estetiği üzerine Ziya Gökalp’ten Ahmet Hamdi Tanpınar’a; Hilmi Ziya Ülken›den Mehmet Kaplan’a kadar pek çok aydın çeşitli yorumlar getirmişlerdir. Bu yorumlar, barındırdıkları çeşitli tezlerle birlikte, çoğunlukla “düalite” ekseninde yürür. Tanzimat dönemi -ve sonraki dönem- aydınlarının kaleme aldığı edebi ve edebiyat-dışı eserler göz önünde bulundurulduğunda bu “postula”nın somut bir temeli olduğunu söyleyebilmek mümkündür. Bununla birlikte Jale Parla, Babalar ve Oğullar (Tanzimat Romanının Epistemolojik Temelleri) adlı eserinde, Tanzimat döneminin düşünsel evreni üzerine farklı yorumlar getirmiş ve böyle bir evren için “düalite” kavramının yersiz olduğunu; bu dönemin aydınlarının ve romancılarının eserlerinde Doğulu değerlere evcilleştirilmiş Batılı değerlerin -en azından Beşir Fuad’a kadar- sorunsuzca eklemlendiğini ileri sürer. Ayrıca bu dönem romancıları ve roman kahramanları ile okur kitlesi arasında “baba-oğul” ilişkisine benzer bir ilişkinin somutlaştığını; Tanzimat Fermanı ile yetkileri kısıtlanan padişahın toplum karşısındaki “baba”lığını bu dönemde romancıların -ve genel Tanzimat aydınlarının- üstlendiğini belirtir. Şüphesiz Parla’nın söz konusu tezleri, kısmen somut bir zemine otursa da, çalışmamız sırasında da görüleceği gibi, bu dönem romancılarının -ve genel olarak Tanzimat aydınlarının- eserleri göz önünde bulundurulduğunda, oldukça “yanlışlanabilir” bir konumda belirir.Many intellectuals from Ziya Gökalp to Ahmet Hamdi Tanpınar and Hilmi Ziya Ülken to Mehmet Kaplan brought various interpretations on the intellectual structure and literary aesthetics of the Tanzimat period. These comments, along with the various theses they hold, often walk on the axis of “duality”. It is possible to say that this “postulat” is a concrete foundation when the literary and non-literary works received by the intellectuals of the Tanzimat period - and later periods - are taken into consideration. Jale Parla, in Babalar ve Oğullar (Tanzimat Romanının Epistemolojik Temelleri), however, brought different interpretations of the intellectual universe of the Tanzimat period and concluded that the concept of “duality” is unfounded for such a universe; argued that in the works of the intellectuals and novelists of this period, the domesticated Western values of Oriental values - at least to Beşir Fuad - were articulated without problems. In addition, this period embodies a similar relationship between the heroes of novels and novels and the readership of the “father-son” relationship, and indicates that the sultan, who was restricted by Tanzimat Fermanı and the authority of the sultan, assumed the “father” of the society in this period and the romans and generally Tanzimat intellectuals. Undoubtedly, even if Parla’s theses are partially tangible, this period can be seen as a “falsifiable” position when the works of the novelists - and generally Tanzimat intellectuals - are taken into consideration. In this review, we will focus on the disproportionate aspects of the theses, and some determinations will be made on the author-reader relationship of the period
Networks of evolutionary interactions underlying the polyphyletic origin of ssDNA viruses
No full textThis review comes from a themed issue on Virus evolutionEdited by Valerian V Dolja and Mart KrupovicFor a complete overview see the Issue and the EditorialInternational audienceViruses with single-stranded (ss) DNA genomes infect hosts from all three domains of life and are present in all imaginable environments. Many new ssDNA viruses have been recently isolated, including those infecting algae, fungi, insects and even archaea. In parallel, culture-independent metagenomic approaches have illuminated the tremendous genetic diversity of these viruses, yielding valuable insights into their evolution. Here, I integrate this knowledge to propose a scenario in which certain groups of ssDNA viruses (including Geminiviridae, Circoviridae, Parvoviridae and Microviridae) have originated from plasmids via acquisition of jelly-roll capsid protein genes from ssRNA viruses. This scenario places structurally related viruses with DNA and RNA genomes into an evolutionary continuum and highlights general evolutionary trends in the virosphere
Transportation and Infrastructure, Retail Clustering, and Local Public Finance: Evidence from Wal-Mart's Expansion
Full text linkThe author examines the role highway infrastructure and local property tax rate variability play in retail agglomeration in Indiana from 1988 through 2003. To account for data errors and the potential endogeneity of taxes and infrastructure on retail agglomeration, he introduces a unique identification strategy that exploits the entrance timing and location of Wal-Mart stores in Indiana. Using a time-series cross-sectional model of Indiana’s 92 counties from 1988 through 2003, he estimates the impact highway infrastructure, property taxes, and big-box competition have in creating regional agglomerations. Among two separate specifications and a full and rural-only set of the data, the author finds considerable agreement in the results. In the full sample, he finds no relationship between property tax rates or highway infrastructure and retail agglomeration. Within the non-metropolitan statistical area (MSA) counties, this relationship is very modest, though it possesses considerable statistical certainty. Highway impacts within the non-MSA counties are significant and positively related to retail agglomeration, with the presence of highways explaining about 10 percent of total agglomeration variability. (JEL R11, R53)Infrastructure; endogeneity; taxation; Wal-Mart
Les archées thermoacidophiles du genre Saccharolobus : programmés comme un eucaryote, manipulés par un virus, vieillisant comme une tortue
No full textLe cycle cellulaire est une séquence d'événements où la cellule grandit, réplique son génome et se divise. Chez les eucaryotes, ce cycle est régi par divers points de contrôle, tandis que chez les bactéries, les processus de réplication de l'ADN, de ségrégation du génome et de cytokinèse se produisent simultanément. Les archées thermoacidophiles du genre Saccharolobus suivent un programme de cycle semblable à celui des eucaryotes. Les cellules passent par une phase G1 de croissance pré-réplicative ; la phase S de réplication chromosomique; la phase G2, une deuxième période de croissance, puis les phases M et D, correspondant respectivement à la ségrégation du génome et à la cytokinèse. Certains virus eucaryotes perturbent le cycle cellulaire de l'hôte, conduisant à une prolifération accrue qui, dans les organismes multicellulaires, peut provoquer des maladies comme le cancer. Chez les archées, le Saccharolobus islandicus virus STSV2 peut également bloquer le cycle cellulaire de son hôte en phase S. Les cellules infectées passent alors à une division cellulaire asymétrique, suggérant l'existence d'un schéma de vieillissement/rajeunissement. Cette thèse vise à comprendre les changements durant le cycle cellulaire dans les cellules de Saccharolobus et à analyser l'impact de l'infection virale. Parallèlement, j'ai étudié si les paradigmes du vieillissement biologique, généralement appliqués aux organismes multicellulaires, s'appliquent également à cet archéen unicellulaire. Dans le chapitre 1, nous avons analysé les changements transcriptionnels tout au long du cycle cellulaire. Nous avons synchronisé les cultures de S. islandicus et réalisé une analyse transcriptomique d'échantillons enrichis en cellules en phase M-G1, S ou G2. Les analyses d'expression génique et de réseaux de coexpression génique ont permis d'identifier des traits spécifiques à chaque phase, incluant des voies métaboliques, l'appareil de motilité cellulaire et des systèmes de défense antiviraux. Grâce à le machine learning nous avons défini un ensemble robuste de gènes signatures pour chaque phase du cycle. Ces résultats ont fourni une image raffinée du cycle cellulaire de S. islandicus et montrent qu'il ressemble plus à celui des eucaryotes que présumé. Dans le chapitre 2, nous avons étudié l'impact du virus non lytique P2V sur le cycle cellulaire de son hôte, S. solfataricus, un parent de S. islandicus. L'analyse transcriptomique montre que le virus affecte le métabolisme de l'hôte et la division cellulaire, provoquant un arrêt de la croissance. Le croisement du profil transcriptionnel des cellules infectées par P2V avec les ensembles de gènes spécifiques au cycle cellulaire définis dans le chapitre 1 suggère que P2V redirige le cycle cellulaire vers un état de type M-G1. Comme l'infection par le P2V inhibe la division cellulaire, les changements observés sont cohérents avec une inversion de la progression du cycle vers une phase optimale pour la reproduction virale. Au chapitre 3, nous avons examiné si les cellules de S. islandicus présentaient des signes de vieillissement et de rajeunissement. Une analyse des réseaux de coexpression génique à différentes phases du cycle a révélé des caractéristiques du vieillissement biologique. Nous avons observé un pic de mortalité après la division cellulaire, ce qui pourrait signifier une baisse de la mortalité préreproductrice. Pour concilier ces observations, un modèle de vieillissement et de rajeunissement a été proposé, offrant un aperçu des origines évolutives du vieillissement et un nouveau paradigme pour explorer les racines procaryotes du rajeunissement cellulaire eucaryote. Ces études affinent la compréhension du cycle cellulaire chez Saccharolobus, révélant des changements dans l'expression de fonctions cellulaires dépendantes du cycle cellulaire et la capacité d'un virus à manipuler ce cycle. Elles fournissent également des indices sur le vieillissement de cet organisme unicellulaire.The cell cycle is a sequence of events happening as the cell grows, replicates its genome and divides. The eukaryotic cell cycle is controlled by various checkpoints, while bacteria generally lack strong oversight allowing DNA replication, genome segregation and cytokinesis to occur concurrently. Thermoacidophilic archaea of the genus Saccharolobus follow a defined cell cycle program resembling that of eukaryotes: the cells go through (i) G1 phase of pre-replicative growth; (ii) the chromosome replication S phase; (iii) G2 phase, a second period of cellular growth, (iv) genome segregation M phase, and (v) cell division D phase. Some eukaryotic viruses affect the progression of the host cell cycle, leading to enhanced proliferation that, in multicellular organisms, may cause various pathologies, such as cancer. It has been recently demonstrated that Saccharolobus islandicus virus STSV2 blocks the host cell cycle in the S phase, when the genome replication is most active. Moreover, STSV2-infected cells switch to an asymmetric cell division, suggesting the existence of a pattern of aging/rejuvenation. Thus, the main objective of this PhD thesis was to gain a better understanding of the changes taking place throughout the cell cycle in Saccharolobus cells and analyze how virus infection impacts the cell cycle. In parallel, I investigated if paradigms of biological aging and rejuvenation, typically considered in the framework of multicellular organisms, also apply to Saccharolobus cells. In Chapter 1, we analyzed the transcriptional changes occurring during different cell cycle phases. To this end, we synchronized the cultures of S. islandicus and performed an in-depth transcriptomic analysis of samples enriched in cells undergoing the M-G1, S and G2 phases. Differential gene expression and gene co-expression network analyses allowed us to identify many phase-specific traits, which included many metabolic pathways, the cell motility apparatus and certain antiviral defense systems. Using machine learning, we denoted a robust set of signature genes defining each of the cell cycle phases. These results provide a refined picture of the S. islandicus cell cycle and show that it more closely resembles that of eukaryotes than previously appreciated. In Chapter 2, we studied the impact of the virus P2V on the progression of the cell cycle of its host, S. solfataricus, a close relative of S. islandicus. Transcriptomic analysis of the infection time course showed that P2V significantly affects host metabolism and cell division, leading to cell growth arrest. Moreover, cross-referencing the transcriptional profile of P2V-infected cells against the cell cycle phase specific gene sets defined in Chapter 1 indicated that P2V redirects the cell cycle towards M-G1-like state. As P2V infection leads to inhibition of cell division, the observed changes are consistent with a virus-mediated reversal of cell cycle progression towards a phase most optimal for virus reproduction. In Chapter 3, we explored if S. islandicus cells display patterns of aging and rejuvenation. Analysis of gene co-expression networks during different cell cycle phases revealed features of biological aging in S. islandicus. Notably, at the population level, we observed a peak of mortality shortly after cell division, which may signify pre-reproductive mortality decline. To reconcile these observations, we proposed a model of S. islandicus aging and rejuvenation, offering insights into the evolutionary origins of aging and a new paradigm to explore whether cellular senescence and rejuvenation in eukaryotes may have prokaryotic roots. Collectively, the three studies refine the understanding on the cell cycle in Saccharolobus, revealing changes in cell cycle-dependent expression of diverse cellular functions and the ability of a virus to manipulate the cell cycle. We also provide the first clues into aging in this unicellular organism
LUCA, ses contemporains et leurs virus, 20 ans après / LUCA, its contemporaries and their viruses: 20 years after
No full textSéminaire organisé par Patrick Forterre, David Prangishvili et Mart Krupovic (Institut Pasteur, Paris, France) du 9 au 14 mai 2016 Participants Tamara Basta-Le Berre, Ryan Catchpole, Violette Da Cunha, Matthias Fischer, Patrick Forterre, Georges E. Fox, Morgan Gaia, Manolo Gouy, Matti Jalasvuori, Eugene V. Koonin, Mart Krupovic, Carlos Mariscal, Armen Y. Mulkidjanian, Jacques Oberto, Anthony M. Poole, David Prangishvili Et François-Xavier Vives et Arnaud Mansir pour Transparences Production R..
Primer-independent DNA polymerases and their use for DNA synthesis
No full textThe present invention provides an isolated peptide of SEQ ID NO: 1 needed for primase active as well as new replicative DNA polymerase enzymes, preferably that of SEQ ID NO: 2, comprising said peptide. Thus, these DNA polymerases are endowed with priming activity and do not require externally provided primers for initiating and performing DNA amplification. These polymerases are able to carry out a faithful and processive de novo DNA synthesis of DNA templates in the absence of pre-synthetized primers. Therefore, these enzymes of the invention act both as primases and DNA polymerases. Furthermore, they show translesion synthesis capacity, so that they may be useful not only for whole-genome amplification but also for the amplification of damaged DNAs. The invention further refers to methods for amplifying templates DNAs using these enzymesPeer reviewedConsejo Superior de Investigaciones Científicas (España), Institut PasteurA1 Solicitud de patente con informe sobre el estado de la técnic
Evolution of replicative DNA polymerases in archaea and their contributions to the eukaryotic replication machinery
No full textThe elaborate eukaryotic DNA replication machinery evolved from the archaeal ancestors that themselves show considerable complexity. Here we discuss the comparative genomic and phylogenetic analysis of the core replication enzymes, the DNA polymerases, in archaea and their relationships with the eukaryotic polymerases. In archaea, there are three groups of family B DNA polymerases, historically known as PolB1, PolB2 and PolB3. All three groups appear to descend from the last common ancestors of the extant archaea but their subsequent evolutionary trajectories seem to have been widely different. Although PolB3 is present in all archaea, with the exception of Thaumarchaeota, and appears to be directly involved in lagging strand replication, the evolution of this gene does not follow the archaeal phylogeny, conceivably due to multiple horizontal transfers and/or dramatic differences in evolutionary rates. In contrast, PolB1 is missing in Euryarchaeota but otherwise seems to have evolved vertically. The third archaeal group of family B polymerases, PolB2, includes primarily proteins in which the catalytic centers of the polymerase and exonuclease domains are disrupted and accordingly the enzymes appear to be inactivated. The members of the PolB2 group are scattered across archaea and might be involved in repair or regulation of replication along with inactivated members of the RadA family ATPases and an additional, uncharacterized protein that are encoded within the same predicted operon. In addition to the family B polymerases, all archaea, with the exception of the Crenarchaeota, encode enzymes of a distinct family D the origin of which is unclear. We examine multiple considerations that appear compatible with the possibility that family D polymerases are highly derived homologs of family B. The eukaryotic DNA polymerases show a highly complex relationship with their archaeal ancestors including contributions of proteins and domains from both the family B and the fa
Plant Satellite Viruses (Albetovirus, Aumaivirus, Papanivirus, Virtovirus)
No full textInternational audienceSatellite viruses are a polyphyletic group of viruses encoding structural components of their virions, but incapable of completing the infection cycle without the assistance of a helper virus. Satellite viruses have been described in animals, protists and plants. Satellite viruses replicating in plants have small icosahedral virions and encapsidate positive-sense RNA genomes typically carrying a single gene for the capsid protein. Thus, for genome replication these viruses necessarily depend on helper viruses which can belong to different families. Plant satellite viruses are classified into genera Albetovirus, Aumaivirus, Papanivirus and Virtovirus. This article describes the diversity and properties of these viruses
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