Sequencing-independent delocalization in a DNA-Like double chain with base pairing

The question of whether or not DNA is intrinsically conducting is still a challenge. The ongoing debate on DNA molecules as an electronic material has so far underestimated a key distinction of the system: the role of base pairing in opposition to correlations along each chain. We show that a disordered base paired double chain presents truly or, at least, effectively delocalized states. This effect is irrespective to the sequencing along each chain.951

On holographic three point functions for GKP strings from integrability

Adapting the powerful integrability-based formalism invented previously for the calculation of gluon scattering amplitudes at strong coupling, we develop a method for computing the holographic three point functions for the large spin limit of Gubser-Klebanov- Polyakov (GKP) strings. Although many of the ideas from the gluon scattering problem can be transplanted with minor modifications, the fact that the information of the external states is now encoded in the singularities at the vertex insertion points necessitates several new techniques. Notably, we develop a new generalized Riemann bilinear identity, which allows one to express the area integral in terms of appropriate contour integrals in the presence of such singularities. We also give some general discussions on how semiclassical vertex operators for heavy string states should be constructed systematically from the solutions of the Hamilton-Jacobi equation.Comment: 62 pages;v2 Typos and equation (3.7) corrected. Clarifying remarks added in Section 4.1. Published version;v3 Minor errors found in version 2 are corrected. For explanation of the revision, see Erratum published in http://www.springerlink.com/content/m67055235407vx67/?MUD=M

Wave functions and correlation functions for GKP strings from integrability

We develop a general method of computing the contribution of the vertex operators to the semi-classical correlation functions of heavy string states, based on the state-operator correspondence and the integrable structure of the system. Our method requires only the knowledge of the local behavior of the saddle point configuration around each vertex insertion point and can be applied to cases where the precise forms of the vertex operators are not known. As an important application, we compute the contributions of the vertex operators to the three-point functions of the large spin limit of the Gubser-Klebanov-Polyakov (GKP) strings in $AdS_3$ spacetime, left unevaluated in our previous work [arXiv:1110.3949] which initiated such a study. Combining with the finite part of the action already computed previously and with the newly evaluated divergent part of the action, we obtain finite three-point functions with the expected dependence of the target space boundary coordinates on the dilatation charge and the spin.Comment: 80 pages, 7 figures, v2: typos and minor errors corrected, a reference added, v3: typos and a reference corrected, published versio

Holographic three-point functions for short operators

We consider holographic three-point functions for operators dual to short string states at strong coupling in N=4 super Yang-Mills. We treat the states as point-like as they come in from the boundary but as strings in the interaction region in the bulk. The interaction position is determined by saddle point, which is equivalent to conservation of the canonical momentum for the interacting particles, and leads to conservation of their conformal charges. We further show that for large dimensions the rms size of the interaction region is small compared to the radius of curvature of the AdS space, but still large compared to the string Compton wave-length. Hence, one can approximate the string vertex operators as flat-space vertex operators with a definite momentum, which depends on the conformal and R-charges of the operator. We then argue that the string vertex operator dual to a primary operator is chosen by satisfying a twisted version of Q^L=Q^R, up to spurious terms. This leads to a unique choice for a scalar vertex operator with the appropriate charges at the first massive level. We then comment on some features of the corresponding three-point functions, including the application of these results to Konishi operators.Comment: 24 pages; v2: References added, typos fixed, minor change

Phylostratigraphic tracking of cancer genes suggests a link to the emergence of multicellularity in metazoa

Background: Phylostratigraphy is a method used to correlate the evolutionary origin of founder genes (that is, functional founder protein domains) of gene families with particular macroevolutionary transitions. It is based on a model of genome evolution that suggests that the origin of complex phenotypic innovations will be accompanied by the emergence of such founder genes, the descendants of which can still be traced in extant organisms. The origin of multicellularity can be considered to be a macroevolutionary transition, for which new gene functions would have been required. Cancer should be tightly connected to multicellular life since it can be viewed as a malfunction of interaction between cells in a multicellular organism. A phylostratigraphic tracking of the origin of cancer genes should, therefore, also provide insights into the origin of multicellularity. Results: We find two strong peaks of the emergence of cancer related protein domains, one at the time of the origin of the first cell and the other around the time of the evolution of the multicellular metazoan organisms. These peaks correlate with two major classes of cancer genes, the 'caretakers', which are involved in general functions that support genome stability and the 'gatekeepers', which are involved in cellular signalling and growth processes. Interestingly, this phylogenetic succession mirrors the ontogenetic succession of tumour progression, where mutations in caretakers are thought to precede mutations in gatekeepers. Conclusions: A link between multicellularity and formation of cancer has often been predicted. However, this has not so far been explicitly tested. Although we find that a significant number of protein domains involved in cancer predate the origin of multicellularity, the second peak of cancer protein domain emergence is, indeed, connected to a phylogenetic level where multicellular animals have emerged. The fact that we can find a strong and consistent signal for this second peak in the phylostratigraphic map implies that a complex multi-level selection process has driven the transition to multicellularity

The Role of the Yap5 Transcription Factor in Remodeling Gene Expression in Response to Fe Bioavailability

The budding yeast Saccharomyces cerevisiae has developed several mechanisms to avoid either the drastic consequences of iron deprivation or the toxic effects of iron excess. In this work, we analysed the global gene expression changes occurring in yeast cells undergoing iron overload. Several genes directly or indirectly involved in iron homeostasis showed altered expression and the relevance of these changes are discussed. Microarray analyses were also performed to identify new targets of the iron responsive factor Yap5. Besides the iron vacuolar transporter CCC1, Yap5 also controls the expression of glutaredoxin GRX4, previously known to be involved in the regulation of Aft1 nuclear localization. Consistently, we show that in the absence of Yap5 Aft1 nuclear exclusion is slightly impaired. These studies provide further evidence that cells control iron homeostasis by using multiple pathways