DNA polymerase α (swi7) and the flap endonuclease fen1 (rad2) act together in the s-phase alkylation damage response in S. pombe

Polymerase α is an essential enzyme mainly mediating Okazaki fragment synthesis during lagging strand replication. A specific point mutation in Schizosaccharomyces pombe polymerase α named swi7-1, abolishes imprinting required for mating-type switching. Here we investigate whether this mutation confers any genome-wide defects. We show that the swi7-1 mutation renders cells hypersensitive to the DNA damaging agents methyl methansulfonate (MMS), hydroxyurea (HU) and UV and incapacitates activation of the intra-S checkpoint in response to DNA damage. In addition we show that, in the swi7-1 background, cells are characterized by an elevated level of repair foci and recombination, indicative of increased genetic instability. Furthermore, we detect novel Swi1-, -Swi3- and Pol α- dependent alkylation damage repair intermediates with mobility on 2D-gel that suggests presence of single-stranded regions. Genetic interaction studies showed that the flap endonuclease Fen1 works in the same pathway as Pol α in terms of alkylation damage response. Fen1 was also required for formation of alkylation- damage specific repair intermediates. We propose a model to explain how Pol α, Swi1, Swi3 and Fen1 might act together to detect and repair alkylation damage during S-phase

Defining Textual Entailment

Textual entailment is a relationship that obtains between fragments of text when one fragment in some sense implies the other fragment. The automation of textual entailment recognition supports a wide variety of text-based tasks, including information retrieval, information extraction, question answering, text summarization, and machine translation. Much ingenuity has been devoted to developing algorithms for identifying textual entailments, but relatively little to saying what textual entailment actually is. This article is a review of the logical and philosophical issues involved in providing an adequate definition of textual entailment. We show that many natural definitions of textual entailment are refuted by counterexamples, including the most widely cited definition of Dagan et al. We then articulate and defend the following revised definition: T textually entails H = df typically, a human reading T would be justified in inferring the proposition expressed by H from the proposition expressed by T. We also show that textual entailment is context-sensitive, nontransitive, and nonmonotonic

Mud of a Mud Bank in Kerala, South-West Coast of India

Fine particles of mud measuring < 1 to 300 p.m constitute the mud of the AUeppey mud bank. These particles, with some variations in their size, occur throughout the year in the region of the mud bank. Total phosphorus content of the mud is high and its carbon content is related to the texture of the mud. Mud, largely composed of very fine particles, has a rela. tively high organic carbon content Plant pigments and carbohydrate occur in very low coucen• trations and the caloric value of the mud is also low indicating that the mud is of poor nutritional value. Fish and prawns caught froOl the region of the mud bank contain large quantities of mud in their guts suggesting that mud is ingested when probably other food organisms are not readily available

Topological Transitions in Metamaterials

The ideas of mathematical topology play an important role in many aspects of modern physics - from phase transitions to field theory to nonlinear dynamics (Nakahara M (2003) in Geometry, Topology and Physics, ed Brewer DF (IOP Publishing Ltd, Bristol and Philadelphia), Monastryskiy M (1987) in Riemann Topology and Physics, (Birkhauser Verlag AG)). An important example of this is the Lifshitz transition (Lifshitz IM (1960) Anomalies of electron characteristics of a metal in the high-pressure region, Sov Phys JETP 11: 1130-1135), where the transformation of the Fermi surface of a metal from a closed to an open geometry (due to e.g. external pressure) leads to a dramatic effect on the electron magneto-transport (Kosevich AM (2004) Topology and solid-state physics. Low Temp Phys 30: 97-118). Here, we present the optical equivalent of the Lifshitz transition in strongly anisotropic metamaterials. When one of the components of the dielectric permittivity tensor of such a composite changes sign, the corresponding iso-frequency surface transforms from an ellipsoid to a hyperboloid. Since the photonic density of states can be related to the volume enclosed by the iso-frequency surface, such a topological transition in a metamaterial leads to a dramatic change in the photonic density of states, with a resulting effect on every single physical parameter related to the metamaterial - from thermodynamic quantities such as its equilibrium electromagnetic energy to the nonlinear optical response to quantum-electrodynamic effects such as spontaneous emission. In the present paper, we demonstrate the modification of spontaneous light emission from quantum dots placed near the surface of the metamaterial undergoing the topological Lifshitz transition, and present the theoretical description of the effect

Broadband super-Planckian thermal emission from hyperbolic metamaterials

We develop the fluctuational electrodynamics of metamaterials with hyperbolic dispersion and show the existence of broadband thermal emission beyond the black body limit in the near field. This arises due to the thermal excitation of unique bulk metamaterial modes, which do not occur in conventional media. We consider a practical realization of the hyperbolic metamaterial and estimate that the effect will be observable using the characteristic dispersion (topological transitions) of the metamaterial states. Our work paves the way for engineering the near-field thermal emission using metamaterials

Novel type of phase transition in a system of self-driven particles

A simple model with a novel type of dynamics is introduced in order to investigate the emergence of self-ordered motion in systems of particles with biologically motivated interaction. In our model particles are driven with a constant absolute velocity and at each time step assume the average direction of motion of the particles in their neighborhood with some random perturbation ($\eta$) added. We present numerical evidence that this model results in a kinetic phase transition from no transport (zero average velocity, $| {\bf v}_a | =0$) to finite net transport through spontaneous symmetry breaking of the rotational symmetry. The transition is continuous since $| {\bf v}_a |$ is found to scale as $(\eta_c-\eta)^\beta$ with $\beta\simeq 0.45$

Charge Solitons in 1-D Arrays of Serially Coupled Josephson Junctions

We study a 1-D array of Josephson coupled superconducting grains with kinetic inductance which dominates over the Josephson inductance. In this limit the dynamics of excess Cooper pairs in the array is described in terms of charge solitons, created by polarization of the grains. We analyze the dynamics of these topological excitations, which are dual to the fluxons in a long Josephson junction, using the continuum sine-Gordon model. We find that their classical relativistic motion leads to saturation branches in the I-V characteristic of the array. We then discuss the semi-classical quantization of the charge soliton, and show that it is consistent with the large kinetic inductance of the array. We study the dynamics of a quantum charge soliton in a ring-shaped array biased by an external flux through its center. If the dephasing length of the quantum charge soliton is larger than the circumference of the array, quantum phenomena like persistent current and coherent current oscillations are expected. As the characteristic width of the charge soliton is of the order of 100 microns, it is a macroscopic quantum object. We discuss the dephasing mechanisms which can suppress the quantum behaviour of the charge soliton.Comment: 26 pages, LaTex, 7 Postscript figure

Color modeling of protein optical probes

We present a strategy for modeling optical probes within heterogeneous environments of restricted dimension. The method is based on a multiphysics approach comprising sequential structure modeling by means of hybrid Car-Parrinello molecular dynamics and property modeling by means of quantum mechanics/molecular mechanics response theory. For demonstration we address the structural and optical properties of nile red within the beta-lacto globulin protein. We consider the cases with the probe situated on the surface or within the cavity of the protein, or embedded in a water solvent. We find the absorption properties of the probe to be highly dependent on its position relative to the protein. Structural rearrangements of the optical probe are found to contribute significantly to these environmental effects.</p