986 research outputs found

    Investigation of Novel Functions for DNA Damage Response and Repair Proteins in Escherichia coli and Humans

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    Endogenous and exogenous agents that can damage DNA are a constant threat to genome stability in all living cells. In response, cells have evolved an array of mechanisms to repair DNA damage or to eliminate the cells damaged beyond repair. One of these mechanisms is nucleotide excision repair (NER) which is the major repair pathway responsible for removing a wide variety of bulky DNA lesions. Deficiency, or mutation, in one or several of the NER repair proteins is responsible for many diseases, including cancer. Prokaryotic NER involves only three proteins to recognize and incise a damaged site, while eukaryotic NER requires more than 25 proteins to efficiently recognize and incise a damaged site. XPC-RAD23B (XPC) is the damage recognition factor in eukaryotic global genome NER. The association rate of XPC to damaged DNA has been extensively studied; however, our data suggests that the dissociation of the XPC-DNA complex is the rate-limiting step in NER. The factor that verifies DNA-damage downstream of XPC is XPA. XPA also has been implicated in binding of ds-ssDNA junctions and has been found to bind at or near double-strand break sites in the premature aging syndrome Hutchinson-Gilford progeria (HGPS). This role for XPA is outside of its known function in NER and suggests that XPA may bind at collapsed replication forks in HGPS that are unprotected due to a lack of binding by replication proteins. Along with XPC and XPA, ataxia telangiectasia and Rad3-related (ATR) is activated in response to DNA damage and initiates the cell cycle checkpoint pathway to rescue cells from genomic instability. We found that ATR functions outside of its known role in the checkpoint signaling cascade. Our data demonstrate that ATR can rescue cells from apoptosis by inhibiting cytochrome c release at the mitochondria though direct interaction with the outer mitochondrial membrane and the proapoptotic protein tBid. The role of ATR in apoptosis is regulated by Pin1, which can change the structure of ATR at the backbone level. All of the results presented here suggest novel roles for DNA repair proteins in the maintenance of genome stability

    Microwave detection of buried mines using non-contact, synthetic near-field focusing

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    Existing ground penetrating radars (GPR) are limited in their 3-D resolution. For the detection of buried land-mines, their performance is also seriously restricted by `clutter'. Previous work by the authors has concentrated on removing these limitations by employing multi-static synthetic focusing from a 2-D real aperture. This contribution presents this novel concept, describes the proposed implementation, examines the influence of clutter and of various ground features on the system's performance, and discusses such practicalities as digitisation and time-sharing of a single transmitter and receiver. Experimental results from a variety of scenarios are presented

    Oscillatory chiral flows in confined active fluids with obstacles

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    An active colloidal fluid comprised of self-propelled spinning particles injecting energy and angular momentum at the microscale demonstrates spontaneous collective states that range from flocks to coherent vortices. Despite their seeming simplicity, the emergent far-from-equilibrium behavior of these fluids remains poorly understood, presenting a challenge to the design and control of next-generation active materials. When confined in a ring, such so-called polar active fluids acquire chirality once the spontaneous flow chooses a direction. In a perfect ring, this chirality is indefinitely long-lived. Here, we combine experiments on self-propelled colloidal Quincke rollers and mesoscopic simulations of continuum Toner-Tu equations to explore how such chiral states can be controlled and manipulated by obstacles. For different obstacle geometries three dynamic steady states have been realized: long-lived chiral flow, an apolar state in which the flow breaks up into counter-rotating vortices and an unconventional collective state with flow having an oscillating chirality. The chirality reversal proceeds through the formation of intermittent vortex chains in the vicinity of an obstacle. We demonstrate that the frequency of collective states with oscillating chirality can be tuned by obstacle parameters. We vary obstacle shapes to design chiral states that are independent of initial conditions. Building on our findings, we realize a system with two triangular obstacles that force the active fluid towards a state with a density imbalance of active particles across the ring. Our results demonstrate how spontaneous polar active flows in combination with size and geometry of scatterers can be used to control dynamic patterns of polar active liquids for materials design.Comment: 13 pages, 5 figure

    Spanning Forests and the Golden Ratio

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    For a graph G, let f_{ij} be the number of spanning rooted forests in which vertex j belongs to a tree rooted at i. In this paper, we show that for a path, the f_{ij}'s can be expressed as the products of Fibonacci numbers; for a cycle, they are products of Fibonacci and Lucas numbers. The {\em doubly stochastic graph matrix} is the matrix F=(f_{ij})/f, where f is the total number of spanning rooted forests of G and n is the number of vertices in G. F provides a proximity measure for graph vertices. By the matrix forest theorem, F^{-1}=I+L, where L is the Laplacian matrix of G. We show that for the paths and the so-called T-caterpillars, some diagonal entries of F (which provides a measure of the self-connectivity of vertices) converge to \phi^{-1} or to 1-\phi^{-1}, where \phi is the golden ratio, as the number of vertices goes to infinity. Thereby, in the asymptotic, the corresponding vertices can be metaphorically considered as "golden introverts" and "golden extroverts," respectively. This metaphor is reinforced by a Markov chain interpretation of the doubly stochastic graph matrix, according to which F equals the overall transition matrix of a random walk with a random number of steps on G.Comment: 12 pages, 2 figures, 25 references. As accepted by Disc. Appl. Math. (2007
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