An Unusual Distribution of 6-nt Sequences Near The Transcription Start Site

SummaryA new look at the transcription start is presented in which we can see transcription factors binding to both sides of the TSS as an essential requirement. Naturally the factor binding to the downstream region must be removed so that transcription process can continue. The presence of a number of distinct transcription factors also can be used to explain selective activation of various genes. The transcription start site by itself plays only a minor role in the whole process. We also suggest that mutations close to the TSS on the coding side can be fatal even if preserves the codon table

Quantum geometry and gravitational entropy

Most quantum states have wavefunctions that are widely spread over the accessible Hilbert space and hence do not have a good description in terms of a single classical geometry. In order to understand when geometric descriptions are possible, we exploit the AdS/CFT correspondence in the half-BPS sector of asymptotically AdS_5 x S^5 universes. In this sector we devise a "coarse-grained metric operator" whose eigenstates are well described by a single spacetime topology and geometry. We show that such half-BPS universes have a non-vanishing entropy if and only if the metric is singular, and that the entropy arises from coarse-graining the geometry. Finally, we use our entropy formula to find the most entropic spacetimes with fixed asymptotic moments beyond the global charges.Comment: 29 pages, 2 figures; references adde

Bacterial Community Structure of an IFAS-MBRs Wastewater Treatment Plant

In this work, the bacterial community putatively involved in BNR events of a UCT-MBMBR pilot plant was elucidated by both culture-dependent and metagenomics DNA analyses. The presence of bacterial isolates belonging to Bacillus (in the anoxic compartment) and to Acinetobacter, Stenotrophomonas, Rhodococcus, Escherichia and Aeromonas (in the aerobic compartment) is in agreement with the nitrification/denitrification processes observed in the plant. Moreover, the study of bacterial community structure by NGS revealed a microbial diversity suggesting a biochemical complexity which can be further explored and exploited to improve UCT-MBMBR plant performance

Bacterial Community Structure of an IFAS-MBRs Wastewater Treatment Plant

In this work, the bacterial community putatively involved in BNR events of a UCT-MBMBR pilot plant was elucidated by both culture-dependent and metagenomics DNA analyses. The presence of bacterial isolates belonging to Bacillus (in the anoxic compartment) and to Acinetobacter, Stenotrophomonas, Rhodococcus, Escherichia and Aeromonas (in the aerobic compartment) is in agreement with the nitrification/denitrification processes observed in the plant. Moreover, the study of bacterial community structure by NGS revealed a microbial diversity suggesting a biochemical complexity which can be further explored and exploited to improve UCT-MBMBR plant performance

BPS R-balls in N=4 SYM on R X S^3, Quantum Hall Analogy and AdS/CFT Holography

In this paper, we propose a new approach to study the BPS dynamics in N=4 supersymmetric U(N) Yang-Mills theory on R X S^3, in order to better understand the emergence of gravity in the gauge theory. Our approach is based on supersymmetric, space-filling Q-balls with R-charge, which we call R-balls. The usual collective coordinate method for non-topological scalar solitons is applied to quantize the half and quarter BPS R-balls. In each case, a different quantization method is also applied to confirm the results from the collective coordinate quantization. For finite N, the half BPS R-balls with a U(1) R-charge have a moduli space which, upon quantization, results in the states of a quantum Hall droplet with filling factor one. These states are known to correspond to the ``sources'' in the Lin-Lunin-Maldacena geometries in IIB supergravity. For large N, we find a new class of quarter BPS R-balls with a non-commutativity parameter. Quantization on the moduli space of such R-balls gives rise to a non-commutative Chern-Simons matrix mechanics, which is known to describe a fractional quantum Hall system. In view of AdS/CFT holography, this demonstrates a profound connection of emergent quantum gravity with non-commutative geometry, of which the quantum Hall effect is a special case.Comment: 42 pages, 2 figures; v3: a new paragraph on counting unbroken susy of NC R-balls and references adde

On dynamic network entropy in cancer

The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level insights into disease mechanisms and ultimately for developing improved therapies. By integrating gene expression data with a protein interaction network to induce a stochastic dynamics on the network, we here demonstrate that cancer cells are characterised by an increase in the dynamic network entropy, compared to cells of normal physiology. Using a fundamental relation between the macroscopic resilience of a dynamical system and the uncertainty (entropy) in the underlying microscopic processes, we argue that cancer cells will be more robust to random gene perturbations. In addition, we formally demonstrate that gene expression differences between normal and cancer tissue are anticorrelated with local dynamic entropy changes, thus providing a systemic link between gene expression changes at the nodes and their local network dynamics. In particular, we also find that genes which drive cell-proliferation in cancer cells and which often encode oncogenes are associated with reductions in the dynamic network entropy. In summary, our results support the view that the observed increased robustness of cancer cells to perturbation and therapy may be due to an increase in the dynamic network entropy that allows cells to adapt to the new cellular stresses. Conversely, genes that exhibit local flux entropy decreases in cancer may render cancer cells more susceptible to targeted intervention and may therefore represent promising drug targets.Comment: 10 pages, 3 figures, 4 tables. Submitte

Mesonic Chiral Rings in Calabi-Yau Cones from Field Theory

We study the half-BPS mesonic chiral ring of the N=1 superconformal quiver theories arising from N D3-branes stacked at Y^pq and L^abc Calabi-Yau conical singularities. We map each gauge invariant operator represented on the quiver as an irreducible loop adjoint at some node, to an invariant monomial, modulo relations, in the gauged linear sigma model describing the corresponding bulk geometry. This map enables us to write a partition function at finite N over mesonic half-BPS states. It agrees with the bulk gravity interpretation of chiral ring states as cohomologically trivial giant gravitons. The quiver theories for L^aba, which have singular base geometries, contain extra operators not counted by the naive bulk partition function. These extra operators have a natural interpretation in terms of twisted states localized at the orbifold-like singularities in the bulk.Comment: Latex, 25pgs, 12 figs, v2: minor clarification

The Library of Babel: On the origin of gravitational thermodynamics

We show that heavy pure states of gravity can appear to be mixed states to almost all probes. For AdS_5 Schwarzschild black holes, our arguments are made using the field theory dual to string theory in such spacetimes. Our results follow from applying information theoretic notions to field theory operators capable of describing very heavy states in gravity. For half-BPS states of the theory which are incipient black holes, our account is exact: typical microstates are described in gravity by a spacetime ``foam'', the precise details of which are almost invisible to almost all probes. We show that universal low-energy effective description of a foam of given global charges is via certain singular spacetime geometries. When one of the specified charges is the number of D-branes, the effective singular geometry is the half-BPS ``superstar''. We propose this as the general mechanism by which the effective thermodynamic character of gravity emerges.Comment: LaTeX, 6 eps figures, uses young.sty and wick.sty; Version 2: typos corrected, minor rewordings and clarifications, references adde