Interactions between N- and C-terminal domains of the Saccharomyces cerevisiae high-mobility group protein HMO1 are required for DNA bending

The Saccharomyces cerevisiae high-mobility group protein HMO1 is composed of two DNA-binding domains termed box A and box B, of which only box B is predicted to adopt a HMG fold, and a lysine-rich C-terminal extension. To assess the interaction between individual domains and their contribution to DNA binding, several HMO1 variants were analyzed. Using circular dichroism spectroscopy, thermal stability was measured. While the melting temperatures of HMO1-boxA and HMO1-boxB are 57.2 and 47.2 °C, respectively, HMO1-boxBC, containing box B and the entire C-terminal tail, melts at 46.1 °C, suggesting little interaction between box B and the tail. In contrast, full-length HMO1 exhibits a single melting transition at 47.9 °C, indicating that interaction between box A and either box B or the tail destabilizes this domain. As HMO1-boxAB, lacking only the lysine-rich C-terminal segment, exhibits two melting transitions at 46.0 and 63.3 °C, we conclude that the destabilization of the box A domain seen in full-length HMO1 is due primarily to its interaction with the lysine-rich tail. Determination of DNA substrate specificity using electrophoretic mobility shift assays shows unexpectedly that the lysine-rich tail does not increase DNA binding affinity but instead is required for DNA bending by full-length HMO1; HMO1-boxBC, lacking the box A domain, also fails to bend DNA. In contrast, both HMO1 and HMO1-boxAB, but not the individual HMG domains, exhibit preferred binding to constrained DNA minicircles. Taken together, our data suggest that interactions between box A and the C-terminal tail induce a conformation that is required for DNA bending. © 2006 American Chemical Society

The Saccharomyces cerevisiae high mobility group box protein HMO1 contains two functional DNA binding domains

High mobility group box (HMGB) proteins are architectural proteins whose HMG DNA binding domains confer significant preference for distorted DNA, such as 4-way junctions. HMO1 is one of 10 Saccharomyces cerevisiae HMGB proteins, and it is required for normal growth and plasmid maintenance and for regulating the susceptibility of yeast chromatin to nuclease. Using electrophoretic mobility shift assays, we have shown here that HMO1 binds 26-bp duplex DNA with K d = 39.6 ± 5.0 nM and that its divergent box A domain participates in DNA interactions, albeit with low affinity. HMO1 has only modest preference for DNA with altered conformations, including DNA with nicks, gaps, overhangs, or loops, as well as for 4-way junction structures and supercoiled DNA. HMO1 binds 4-way junctions with half-maximal saturation of 19.6 ± 2.2 nM, with only a modest increase in affinity in the absence of magnesium ions (half-maximal saturation 6.1 ± 1.1 nM). Whereas the box A domain contributes modest structure-specific binding, the box B domain is required for high affinity binding. HMO1 bends DNA, as measured by DNA cyclization assays, facilitating cyclization of 136-, 105-, and 87-bp DNA, but not 75-bp DNA, and it has a significantly longer residence time on DNA minicircles compared with linear duplex DNA. The unique DNA binding properties of HMO1 are consistent with global roles in the maintenance of chromatin structure

Inhibition of nuclear factor-kappa B differentially affects thyroid cancer cell growth, apoptosis, and invasion

<p>Abstract</p> <p>Background</p> <p>Nuclear factor-κB (NF-κB) is constitutively activated in many cancers and plays a key role in promoting cell proliferation, survival, and invasion. Our understanding of NF-κB signaling in thyroid cancer, however, is limited. In this study, we have investigated the role of NF-κB signaling in thyroid cancer cell proliferation, invasion, and apoptosis using selective genetic inhibition of NF-κB in advanced thyroid cancer cell lines.</p> <p>Results</p> <p>Three pharmacologic inhibitors of NF-κB differentially inhibited growth in a panel of advanced thyroid cancer cell lines, suggesting that these NF-κB inhibitors may have off-target effects. We therefore used a selective genetic approach to inhibit NF-κB signaling by overexpression of a dominant-negative IκBα (mIκBα). These studies revealed decreased cell growth in only one of five thyroid cancer cell lines (8505C), which occurred through a block in the S-G2/M transition. Resistance to TNFα-induced apoptosis was observed in all cell lines, likely through an NF-κB-dependent mechanism. Inhibition of NF-κB by mIκBα sensitized a subset of cell lines to TNFα-induced apoptosis. Sensitive cell lines displayed sustained activation of the stress-activated protein kinase/c-Jun NH2-terminal kinase (SAPK/JNK) pathway, defining a potential mechanism of response. Finally, NF-κB inhibition by mIκBα expression differentially reduced thyroid cancer cell invasion in these thyroid cancer cell lines. Sensitive cell lines demonstrated approximately a two-fold decrease in invasion, which was associated with differential expression of MMP-13. MMP-9 was reduced by mIκBα expression in all cell lines tested.</p> <p>Conclusions</p> <p>These data indicate that selective inhibition of NF-κB represents an attractive therapeutic target for the treatment of advanced thyroid. However, it is apparent that global regulation of thyroid cancer cell growth and invasion is not achieved by NF-κB signaling alone. Instead, our findings suggest that other important molecular processes play a critical role in defining the extent of NF-κB function within cancer cells.</p

Kondo decoherence: finding the right spin model for iron impurities in gold and silver

We exploit the decoherence of electrons due to magnetic impurities, studied via weak localization, to resolve a longstanding question concerning the classic Kondo systems of Fe impurities in the noble metals gold and silver: which Kondo-type model yields a realistic description of the relevant multiple bands, spin and orbital degrees of freedom? Previous studies suggest a fully screened spin $S$ Kondo model, but the value of $S$ remained ambiguous. We perform density functional theory calculations that suggest $S = 3/2$. We also compare previous and new measurements of both the resistivity and decoherence rate in quasi 1-dimensional wires to numerical renormalization group predictions for $S=1/2,1$ and 3/2, finding excellent agreement for $S=3/2$.Comment: 4 pages, 4 figures, shortened for PR

Slow 4He^{4}He Quenches Produce Fuzzy, Transient Vortices

We examine the Zurek scenario for the production of vortices in quenches of liquid $^{4}He$ in the light of recent experiments. Extending our previous results to later times, we argue that short wavelength thermal fluctuations make vortices poorly defined until after the transition has occurred. Further, if and when vortices appear, it is plausible that that they will decay faster than anticipated from turbulence experiments, irrespective of quench rates.Comment: 4 pages, Revtex file, no figures Apart from a more appropriate title, this paper differs from its predecessor by including temperature, as well as pressure, quenche

Zurek-Kibble domain structures: The Dynamics of Spontaneous Vortex formation in Annular Josephson Tunnel Junctions

Phase transitions executed in a finite time show a domain structure with defects, that has been argued by Zurek and Kibble to depend in a characteristic way on the quench rate. In this letter we present an experiment to measure the Zurek-Kibble scaling exponent sigma. Using symmetric and long Josephson Tunnel Junctions, for which the predicted index is sigma = 0.25, we find sigma = 0.27 +/- 0.05. Further, there is agreement with the ZK prediction for the overall normalisation.Comment: To be published in Phys. Rev. Lett

Spontaneous symmetry breaking in a quenched ferromagnetic spinor Bose condensate

A central goal in condensed matter and modern atomic physics is the exploration of many-body quantum phases and the universal characteristics of quantum phase transitions in so far as they differ from those established for thermal phase transitions. Compared with condensed-matter systems, atomic gases are more precisely constructed and also provide the unique opportunity to explore quantum dynamics far from equilibrium. Here we identify a second-order quantum phase transition in a gaseous spinor Bose-Einstein condensate, a quantum fluid in which superfluidity and magnetism, both associated with symmetry breaking, are simultaneously realized. $^{87}$Rb spinor condensates were rapidly quenched across this transition to a ferromagnetic state and probed using in-situ magnetization imaging to observe spontaneous symmetry breaking through the formation of spin textures, ferromagnetic domains and domain walls. The observation of topological defects produced by this symmetry breaking, identified as polar-core spin-vortices containing non-zero spin current but no net mass current, represents the first phase-sensitive in-situ detection of vortices in a gaseous superfluid.Comment: 6 pages, 4 figure

Testing the Kibble-Zurek Scenario with Annular Josephson Tunnel Junctions

In parallel with Kibble's description of the onset of phase transitions in the early universe, Zurek has provided a simple picture for the onset of phase transitions in condensed matter systems, strongly supported by agreement with experiments in He3. In this letter we show how experiments with annular Josephson tunnel Junctions can and do provide further support for this scenario.Comment: Revised version with correct formula for the Swihart velocity. The results are qualitatively the same as with the previous version but differ quantitatively. 4 pages, RevTe

Dynamics of Quantum Phase Transition in an Array of Josephson Junctions

We study the dynamics of the Mott insulator-superfluid quantum phase transition in a periodic 1D array of Josephson junctions. We show that crossing the critical point diabatically i.e. at a finite rate with a quench time $\tau_Q$ induces finite quantum fluctuations of the current around the loop proportional to $\tau_Q^{-1/6}$. This scaling could be experimentally verified with in array of weakly coupled Bose-Einstein condensates or superconducting grains.Comment: 4 pages in RevTex, 3 .eps figures; 2 references added; accepted for publication in Phys.Rev.Let

Unraveling critical dynamics: The formation and evolution of topological textures

We study the formation of topological textures in a nonequilibrium phase transition of an overdamped classical O(3) model in 2+1 dimensions. The phase transition is triggered through an external, time-dependent effective mass, parameterized by quench timescale \tau. When measured near the end of the transition the texture separation and the texture width scale respectively as \tau^(0.39 \pm 0.02) and \tau^(0.46 \pm 0.04), significantly larger than \tau^(0.25) predicted from the Kibble-Zurek mechanism. We show that Kibble-Zurek scaling is recovered at very early times but that by the end of the transition the power-laws result instead from a competition between the length scale determined at freeze-out and the ordering dynamics of a textured system. In the context of phase ordering these results suggest that the multiple length scales characteristic of the late-time ordering of a textured system derive from the critical dynamics of a single nonequilibrium correlation length. In the context of defect formation these results imply that significant evolution of the defect network can occur before the end of the phase transition. Therefore a quantitative understanding of the defect network at the end of the phase transition generally requires an understanding of both critical dynamics and the interactions among topological defects.Comment: 12 pages, revtex, 9 figures in eps forma