Open G2 Strings

We consider an open string version of the topological twist previously proposed for sigma-models with G2 target spaces. We determine the cohomology of open strings states and relate these to geometric deformations of calibrated submanifolds and to flat or anti-self-dual connections on such submanifolds. On associative three-cycles we show that the worldvolume theory is a gauge-fixed Chern-Simons theory coupled to normal deformations of the cycle. For coassociative four-cycles we find a functional that extremizes on anti-self-dual gauge fields. A brane wrapping the whole G2 induces a seven-dimensional associative Chern-Simons theory on the manifold. This theory has already been proposed by Donaldson and Thomas as the higher-dimensional generalization of real Chern-Simons theory. When the G2 manifold has the structure of a Calabi-Yau times a circle, these theories reduce to a combination of the open A-model on special Lagrangians and the open B+\bar{B}-model on holomorphic submanifolds. We also comment on possible applications of our results.Comment: 55 pages, no figure

Black Hole Bound States in AdS(3) x S**2

We systematically construct the geometries dual to the 1+1 dimensional (0, 4) conformal field theories that arise in the low-energy description of wrapped M5-branes in S1 × CY3 compactifications of M-theory. This includes a large number of multicentered black hole bound states asymptotic to AdS3 × S2. In addition, we find many geometries that develop multiple, mutually decoupled AdS3 × S2 throats. We argue there is a useful one to one correspondence between the connected components of the space of solutions and particular limits of type IIA attractor flow trees. We point out that there is a thermodynamic instability of small supersymmetric BTZ black holes to localization on the S2, a supersymmetric and exactly solvable analog of the well known AdS-Schwarzschild localization instability, and identify this with the "Entropy Enigma" in four dimensions. We discuss the phase transition this suggests, and initiate the CFT interpretation of these results.Physic

Kerr/CFT, dipole theories and nonrelativistic CFTs

We study solutions of type IIB supergravity which are SL(2,R) x SU(2) x U(1)^2 invariant deformations of AdS_3 x S^3 x K3 and take the form of products of self-dual spacelike warped AdS_3 and a deformed three-sphere. One of these backgrounds has been recently argued to be relevant for a derivation of Kerr/CFT from string theory, whereas the remaining ones are holographic duals of two-dimensional dipole theories and their S-duals. We show that each of these backgrounds is holographically dual to a deformation of the DLCQ of the D1-D5 CFT by a specific supersymmetric (1,2) operator, which we write down explicitly in terms of twist operators at the free orbifold point. The deforming operator is argued to be exactly marginal with respect to the zero-dimensional nonrelativistic conformal (or Schroedinger) group - which is simply SL(2,R)_L x U(1)_R. Moreover, in the supergravity limit of large N and strong coupling, no other single-trace operators are turned on. We thus propose that the field theory duals to the backgrounds of interest are nonrelativistic CFTs defined by adding the single Schroedinger-invariant (1,2) operator mentioned above to the original CFT action. Our analysis indicates that the rotating extremal black holes we study are best thought of as finite right-moving temperature (non-supersymmetric) states in the above-defined supersymmetric nonrelativistic CFT and hints towards a more general connection between Kerr/CFT and two-dimensional non-relativistic CFTs.Comment: 48+8 pages, 4 figures; minor corrections and references adde

A bound on the entropy of supergravity?

We determine, in two independent ways, the number of BPS quantum states arising from supergravity degrees of freedom in a system with fixed total D4D0 charge. First, we count states generated by quantizing the spacetime degrees of freedom of 'entropyless' multicentered solutions consisting of anti-D0-branes bound to a D6-anti-D6 pair. Second, we determine the number of free supergravity excitations of the corresponding AdS_3 geometry with the same total charge. We find that, although these two approaches yield a priori different sets of states, the leading degeneracies in a large charge expansion are equal to each other and that, furthermore, the number of such states is parametrically smaller than that arising from the D4D0 black hole's entropy. This strongly suggests that supergravity alone is not sufficient to capture all degrees of freedom of large supersymmetric black holes. Comparing the free supergravity calculation to that of the D6-anti-D6-D0 system we find that the bound on the free spectrum imposed by the stringy exclusion principle (a unitarity bound in the dual CFT) seems to be captured in the dynamics of the fully interacting but classcial supergravity equations of motion.Comment: 33 pages, 5 figure

Black Holes as Effective Geometries

Gravitational entropy arises in string theory via coarse graining over an underlying space of microstates. In this review we would like to address the question of how the classical black hole geometry itself arises as an effective or approximate description of a pure state, in a closed string theory, which semiclassical observers are unable to distinguish from the "naive" geometry. In cases with enough supersymmetry it has been possible to explicitly construct these microstates in spacetime, and understand how coarse-graining of non-singular, horizon-free objects can lead to an effective description as an extremal black hole. We discuss how these results arise for examples in Type II string theory on AdS_5 x S^5 and on AdS_3 x S^3 x T^4 that preserve 16 and 8 supercharges respectively. For such a picture of black holes as effective geometries to extend to cases with finite horizon area the scale of quantum effects in gravity would have to extend well beyond the vicinity of the singularities in the effective theory. By studying examples in M-theory on AdS_3 x S^2 x CY that preserve 4 supersymmetries we show how this can happen.Comment: Review based on lectures of JdB at CERN RTN Winter School and of VB at PIMS Summer School. 68 pages. Added reference

CTCF binds to sites in the major histocompatibility complex that are rapidly reconfigured in response to interferon-gamma

Activation of the major histocompatibility complex (MHC) by interferon-gamma (IFN−γ) is a fundamental step in the adaptive immune response to pathogens. Here, we show that reorganization of chromatin loop domains in the MHC is evident within the first 30 min of IFN−γ treatment of fibroblasts, and that further dynamic alterations occur up to 6 h. These very rapid changes occur at genomic sites which are occupied by CTCF and are close to IFN−γ-inducible MHC genes. Early responses to IFN−γ are thus initiated independently of CIITA, the master regulator of MHC class II genes and prepare the MHC for subsequent induction of transcription

Quantizing N=2 Multicenter Solutions

N=2 supergravity in four dimensions, or equivalently N=1 supergravity in five dimensions, has an interesting set of BPS solutions that each correspond to a number of charged centers. This set contains black holes, black rings and their bound states, as well as many smooth solutions. Moduli spaces of such solutions carry a natural symplectic form which we determine, and which allows us to study their quantization. By counting the resulting wavefunctions we come to an independent derivation of some of the wall-crossing formulae. Knowledge of the explicit form of these wavefunctions allows us to find quantum resolutions to some apparent classical paradoxes such as solutions with barely bound centers and those with an infinitely deep throat. We show that quantum effects seem to cap off the throat at a finite depth and we give an estimate for the corresponding mass gap in the dual CFT. This is an interesting example of a system where quantum effects cannot be neglected at macroscopic scales even though the curvature is everywhere small.Comment: 49 pages + appendice

Widespread Expression of BORIS/CTCFL in Normal and Cancer Cells

BORIS (CTCFL) is the paralog of CTCF (CCCTC-binding factor; NM_006565), a ubiquitously expressed DNA-binding protein with diverse roles in gene expression and chromatin organisation. BORIS and CTCF have virtually identical zinc finger domains, yet display major differences in their respective C- and N-terminal regions. Unlike CTCF, BORIS expression has been reported only in the testis and certain malignancies, leading to its classification as a “cancer-testis” antigen. However, the expression pattern of BORIS is both a significant and unresolved question in the field of DNA binding proteins. Here, we identify BORIS in the cytoplasm and nucleus of a wide range of normal and cancer cells. We compare the localization of CTCF and BORIS in the nucleus and demonstrate enrichment of BORIS within the nucleolus, inside the nucleolin core structure and adjacent to fibrillarin in the dense fibrillar component. In contrast, CTCF is not enriched in the nucleolus. Live imaging of cells transiently transfected with GFP tagged BORIS confirmed the nucleolar accumulation of BORIS. While BORIS transcript levels are low compared to CTCF, its protein levels are readily detectable. These findings show that BORIS expression is more widespread than previously believed, and suggest a role for BORIS in nucleolar function

Generation of a genomic tiling array of the human Major Histocompatibility Complex (MHC) and its application for DNA methylation analysis

Background: The major histocompatibility complex (MHC) is essential for human immunity and is highly associated with common diseases, including cancer. While the genetics of the MHC has been studied intensively for many decades, very little is known about the epigenetics of this most polymorphic and disease-associated region of the genome.Methods: To facilitate comprehensive epigenetic analyses of this region, we have generated a genomic tiling array of 2 Kb resolution covering the entire 4 Mb MHC region. The array has been designed to be compatible with chromatin immunoprecipitation (ChIP), methylated DNA immunoprecipitation (MeDIP), array comparative genomic hybridization (aCGH) and expression profiling, including of non-coding RNAs. The array comprises 7832 features, consisting of two replicates of both forward and reverse strands of MHC amplicons and appropriate controls.Results: Using MeDIP, we demonstrate the application of the MHC array for DNA methylation profiling and the identification of tissue-specific differentially methylated regions (tDMRs). Based on the analysis of two tissues and two cell types, we identified 90 tDMRs within the MHC and describe their characterisation.Conclusion: A tiling array covering the MHC region was developed and validated. Its successful application for DNA methylation profiling indicates that this array represents a useful tool for molecular analyses of the MHC in the context of medical genomics

Binding binding: Departure points for a different version of the perceptual retouch theory

In the perceptual retouch theory, masking and related microgenetic phenomena were explained as a result of interaction between specific cortical representational systems and the non-specific sub-cortical modulation system. Masking appears as deprivation of sufficient modulation of the consciousness mechanism suffered by the target-specific signals because of the temporal delay of non-specific modulation (necessary for conscious representation), which explicates the later-coming mask information instead of the already decayed target information. The core of the model envisaged relative magnitudes of EPSPs of single cortical cells driven by target and mask signals at the moment when the nonspecific, presynaptic, excitatory input arrives from the thalamus. In the light of the current evidence about the importance of synchronised activity of specific and non-specific systems in generating consciousness, the retouch theory requires perhaps a different view. This article presents some premises for modification of the retouch theory, where instead of the cumulative presynaptic spike activities and EPSPs of single cells, the oscillatory activity in the gamma range of the participating systems is considered and shown to be consistent with the basic ideas of the retouch theory. In this conceptualisation, O-binding refers to specific encoding which is based on gamma-band synchronised oscillations in the activity of specific cortical sensory modules that represent features and objects; C-binding refers to the gamma-band oscillations in the activity of the non-specific thalamic systems, which is necessary for the O-binding based data to become consciously experienced