Influence of different functional elements of plasmid pGT232 on maintenance of recombinant plasmids in Lactobacillus reuteri populations in vitro and in vivo

Plasmid pGT232 (5.1 kb), an indigenous plasmid of Lactobacillus reuteri 100-23, was determined, on the basis of nucleotide and deduced protein sequence data, to belong to the pC194-pUB110 family of plasmids that replicate via the rolling-circle mechanism. The minimal replicon of pGT232 was located on a 1.7-kb sequence consisting of a double-strand origin of replication and a gene encoding the replication initiation protein, repA. An erythromycin-selectable recombinant plasmid containing this minimal replicon was stably maintained (>97% erythromycin-resistant cells) without antibiotic selection in an L. reuteri population under laboratory growth conditions but was poorly maintained (90% resistant cells) of pGT232-derived plasmids in the lactobacillus population in vivo required an additional 1.0-kb sequence which contained a putative single-strand replication origin (SSO). The SSO of pGT232 is believed to be novel and functions in an orientation-specific manner

Charge Lattices and Consistency of 6D Supergravity

We extend the known consistency conditions on the low-energy theory of six-dimensional N = 1 supergravity. We review some facts about the theory of two-form gauge fields and conclude that the charge lattice Gamma for such a theory has to be self-dual. The Green-Schwarz anomaly cancellation conditions in the supergravity theory determine a sublattice of Gamma. The condition that this sublattice can be extended to a self-dual lattice Gamma leads to a strong constraint on theories that otherwise appear to be self-consistent.Comment: 15 pages. v2: minor changes; references, additional example added; v3: minor corrections and clarifications added, JHEP versio

Wall-Crossing in Coupled 2d-4d Systems

We introduce a new wall-crossing formula which combines and generalizes the Cecotti-Vafa and Kontsevich-Soibelman formulas for supersymmetric 2d and 4d systems respectively. This 2d-4d wall-crossing formula governs the wall-crossing of BPS states in an N=2 supersymmetric 4d gauge theory coupled to a supersymmetric surface defect. When the theory and defect are compactified on a circle, we get a 3d theory with a supersymmetric line operator, corresponding to a hyperholomorphic connection on a vector bundle over a hyperkahler space. The 2d-4d wall-crossing formula can be interpreted as a smoothness condition for this hyperholomorphic connection. We explain how the 2d-4d BPS spectrum can be determined for 4d theories of class S, that is, for those theories obtained by compactifying the six-dimensional (0,2) theory with a partial topological twist on a punctured Riemann surface C. For such theories there are canonical surface defects. We illustrate with several examples in the case of A_1 theories of class S. Finally, we indicate how our results can be used to produce solutions to the A_1 Hitchin equations on the Riemann surface C.Comment: 170 pages, 45 figure

GLSMs for non-Kahler Geometries

We identify a simple mechanism by which H-flux satisfying the modified Bianchi identity arises in garden-variety (0,2) gauged linear sigma models. Taking suitable limits leads to effective gauged linear sigma models with Green-Schwarz anomaly cancellation. We test the quantum-consistency of a class of such effective theories by constructing an off-shell superconformal algebra, providing evidence that these models run to good CFTs in the deep IR.Comment: 37 pages, Minor updates for v

Finite-Temperature Fractional D2-Branes and the Deconfinement Transition in 2+1 Dimensions

The supergravity dual to N regular and M fractional D2-branes on the cone over \mathbb{CP}^3 has a naked singularity in the infrared. One can resolve this singularity and obtain a regular fractional D2-brane solution dual to a confining 2+1 dimensional N = 1 supersymmetric field theory. The confining vacuum of this theory is described by the solution of Cvetic, Gibbons, Lu and Pope. In this paper, we explore the alternative possibility for resolving the singularity - the creation of a regular horizon. The black-hole solution we find corresponds to the deconfined phase of this dual gauge theory in three dimensions. This solution is derived in perturbation theory in the number of fractional branes. We argue that there is a first-order deconfinement transition. Connections to Chern--Simons matter theories, the ABJM proposal and fractional M2-branes are presented.Comment: v3: analytic solutions are expose

5-dim Superconformal Index with Enhanced En Global Symmetry

The five-dimensional $\mathcal{N}=1$ supersymmetric gauge theory with Sp(N) gauge group and SO(2N_f) flavor symmetry describes the physics on N D4-branes with $N_f$ D8-branes on top of a single O8 orientifold plane in Type I' theory. This theory is known to be superconformal at the strong coupling limit with the enhanced global symmetry $E_{N_f+1}$ for $N_f\le 7$. In this work we calculate the superconformal index on $S^1\times S^4$ for the Sp(1) gauge theory by the localization method and confirm such enhancement of the global symmetry at the superconformal limit for $N_f\le 5$ to a few leading orders in the chemical potential. Both perturbative and (anti)instanton contributions are present in this calculation. For $N_f=6,7$ cases some issues related the pole structure of the instanton calculation could not be resolved and here we could provide only some suggestive answer for the leading contributions to the index. For the Sp(N) case, similar issues related to the pole structure appear.Comment: 70 pages, references added, published versio

Hypotensive Hemostasis in Patients Presenting with Ruptured Aortic Aneurysm

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Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict

Horizontal DNA transfer (HDT) is a pervasive mechanism of diversification in many microbial species, but its primary evolutionary role remains controversial. Much recent research has emphasised the adaptive benefit of acquiring novel DNA, but here we argue instead that intragenomic conflict provides a coherent framework for understanding the evolutionary origins of HDT. To test this hypothesis, we developed a mathematical model of a clonally descended bacterial population undergoing HDT through transmission of mobile genetic elements (MGEs) and genetic transformation. Including the known bias of transformation toward the acquisition of shorter alleles into the model suggested it could be an effective means of counteracting the spread of MGEs. Both constitutive and transient competence for transformation were found to provide an effective defence against parasitic MGEs; transient competence could also be effective at permitting the selective spread of MGEs conferring a benefit on their host bacterium. The coordination of transient competence with cell-cell killing, observed in multiple species, was found to result in synergistic blocking of MGE transmission through releasing genomic DNA for homologous recombination while simultaneously reducing horizontal MGE spread by lowering the local cell density. To evaluate the feasibility of the functions suggested by the modelling analysis, we analysed genomic data from longitudinal sampling of individuals carrying Streptococcus pneumoniae. This revealed the frequent within-host coexistence of clonally descended cells that differed in their MGE infection status, a necessary condition for the proposed mechanism to operate. Additionally, we found multiple examples of MGEs inhibiting transformation through integrative disruption of genes encoding the competence machinery across many species, providing evidence of an ongoing "arms race." Reduced rates of transformation have also been observed in cells infected by MGEs that reduce the concentration of extracellular DNA through secretion of DNases. Simulations predicted that either mechanism of limiting transformation would benefit individual MGEs, but also that this tactic's effectiveness was limited by competition with other MGEs coinfecting the same cell. A further observed behaviour we hypothesised to reduce elimination by transformation was MGE activation when cells become competent. Our model predicted that this response was effective at counteracting transformation independently of competing MGEs. Therefore, this framework is able to explain both common properties of MGEs, and the seemingly paradoxical bacterial behaviours of transformation and cell-cell killing within clonally related populations, as the consequences of intragenomic conflict between self-replicating chromosomes and parasitic MGEs. The antagonistic nature of the different mechanisms of HDT over short timescales means their contribution to bacterial evolution is likely to be substantially greater than previously appreciated

Exact Results in D=2 Supersymmetric Gauge Theories

We compute exactly the partition function of two dimensional N=(2,2) gauge theories on S^2 and show that it admits two dual descriptions: either as an integral over the Coulomb branch or as a sum over vortex and anti-vortex excitations on the Higgs branches of the theory. We further demonstrate that correlation functions in two dimensional Liouville/Toda CFT compute the S^2 partition function for a class of N=(2,2) gauge theories, thereby uncovering novel modular properties in two dimensional gauge theories. Some of these gauge theories flow in the infrared to Calabi-Yau sigma models - such as the conifold - and the topology changing flop transition is realized as crossing symmetry in Liouville/Toda CFT. Evidence for Seiberg duality in two dimensions is exhibited by demonstrating that the partition function of conjectured Seiberg dual pairs are the same.Comment: 78 pages, LaTeX; v2: small corrections and references added; v3: JHEP version, discussing factorization further in new appendix F; v4: sign corrected for non simply-connected gauge grou

The stellar halo of the Galaxy

Stellar halos may hold some of the best preserved fossils of the formation history of galaxies. They are a natural product of the merging processes that probably take place during the assembly of a galaxy, and hence may well be the most ubiquitous component of galaxies, independently of their Hubble type. This review focuses on our current understanding of the spatial structure, the kinematics and chemistry of halo stars in the Milky Way. In recent years, we have experienced a change in paradigm thanks to the discovery of large amounts of substructure, especially in the outer halo. I discuss the implications of the currently available observational constraints and fold them into several possible formation scenarios. Unraveling the formation of the Galactic halo will be possible in the near future through a combination of large wide field photometric and spectroscopic surveys, and especially in the era of Gaia.Comment: 46 pages, 16 figures. References updated and some minor changes. Full-resolution version available at http://www.astro.rug.nl/~ahelmi/stellar-halo-review.pd