Elastic properties of (N(CH3)3H) (I) (TCNQ)

Journal ArticleWe present the results of a study of the temperature dependence of the Young's modulus and internal friction of (N(CH3 )3H)(I)(TCNQ). The Young's modulus was measured in a direction parallel to the TCNQ (tetracyanoquinodimethane) stacking axis using a vibrating reed technique. The results confirmed a transition observed via transport measurements at 150 K and predicted a transition (later observed) at 89 K. The data support the model that this system is a semiconductor at temperatures above 150 K despite the "metal-like" dc conductivity

Purification of the yeast Slx5–Slx8 protein complex and characterization of its DNA-binding activity

SLX5 and SLX8 encode RING-finger proteins that were previously identified based on their requirement for viability in yeast cells lacking Sgs1 DNA helicase. Slx5 and Slx8 proteins are known to be required for genome stability and to physically interact in yeast extracts; however, their biochemical functions are unknown. To address this question we purified and characterized recombinant Slx5 and Slx8 proteins. Here we show that Slx5 and Slx8 form a heterodimeric complex with double-stranded DNA (dsDNA)-binding activity. Individually, only the Slx8 subunit displays this activity. Structure–function studies indicate that the DNA-binding activity requires only the N-terminal 160 amino acids of Slx8, but not its C-terminal RING-finger domain. Alleles of SLX8 that express the RING-finger domain alone show almost complete complementation in yeast indicating that this DNA-binding domain is not essential for this in vivo function. Consistent with these findings we show that Slx5 immunolocalizes to the nucleus and that a portion of the Slx8 protein co-fractionates with chromatin. These results suggest that Slx5–Slx8 may act directly on DNA to promote genome stability

Themed Issue Article: Conservation Physiology of Marine Fishes Fisheries conservation on the high seas: linking conservation physiology and fisheries ecology for the management of large pelagic fishes

Populations of tunas, billfishes and pelagic sharks are fished at or over capacity in many regions of the world. They are captured by directed commercial and recreational fisheries (the latter of which often promote catch and release) or as incidental catch or bycatch in commercial fisheries. Population assessments of pelagic fishes typically incorporate catch-per-unit-effort time-series data from commercial and recreational fisheries; however, there have been notable changes in target species, areas fished and depth-specific gear deployments over the years that may have affected catchability. Some regional fisheries management organizations take into account the effects of time-and area-specific changes in the behaviours of fish and fishers, as well as fishing gear, to standardize catch-per-unit-effort indices and refine population estimates. However, estimates of changes in stock size over time may be very sensitive to underlying assumptions of the effects of oceanographic conditions and prey distribution on the horizontal and vertical movement patterns and distribution of pelagic fishes. Effective management and successful conservation of pelagic fishes requires a mechanistic understanding of their physiological and behavioural responses to environmental variability, potential for interaction with commercial and recreational fishing gear, and the capture process. The interdisciplinary field of conservation physiology can provide insights into pelagic fish demography and ecology (including environmental relationships and interspecific interactions) by uniting the complementary expertise and skills of fish physiologists and fisheries scientists. The iterative testing by one discipline of hypotheses generated by the other can span the fundamental-applied science continuum, leading to the development of robust insights supporting informed management. The resulting species-specific understanding of physiological abilities and tolerances can help to improve stock assessments, develop effective bycatch-reduction strategies, predict rates of post-release mortality, and forecast the population effects of environmental change. In this synthesis, we review several examples of these interdisciplinary collaborations that currently benefit pelagic fisheries management

Resolution by Unassisted Top3 Points to Template Switch Recombination Intermediates during DNA Replication

The evolutionarily conserved Sgs1/Top3/Rmi1 (STR) complex plays vital roles in DNA replication and repair. One crucial activity of the complex is dissolution of toxic X-shaped recombination intermediates that accumulate during replication of damaged DNA. However, despite several years of study the nature of these X-shaped molecules remains debated. Here we use genetic approaches and two-dimensional gel electrophoresis of genomic DNA to show that Top3, unassisted by Sgs1 and Rmi1, has modest capacities to provide resistance to MMS and to resolve recombination-dependent X-shaped molecules. The X-shaped molecules have structural properties consistent with hemicatenane-related template switch recombination intermediates (Rec-Xs) but not Holliday junction (HJ) intermediates. Consistent with these findings, we demonstrate that purified Top3 can resolve a synthetic Rec-X but not a synthetic double HJ in vitro. We also find that unassisted Top3 does not affect crossing over during double strand break repair, which is known to involve double HJ intermediates, confirming that unassisted Top3 activities are restricted to substrates that are distinct from HJs. These data help illuminate the nature of the X-shaped molecules that accumulate during replication of damaged DNA templates, and also clarify the roles played by Top3 and the STR complex as a whole during the resolution of replication-associated recombination intermediates

1949 Ruby Yearbook

A digitized copy of the 1949 Ruby, the Ursinus College yearbook.https://digitalcommons.ursinus.edu/ruby/1051/thumbnail.jp

Srs2 promotes Mus81-Mms4-mediated resolution of recombination intermediates

A variety of DNA lesions, secondary DNA structures or topological stress within the DNA template may lead to stalling of the replication fork. Recovery of such forks is essential for the maintenance of genomic stability. The structure-specific endonuclease Mus81–Mms4 has been implicated in processing DNA intermediates that arise from collapsed forks and homologous recombination. According to previous genetic studies, the Srs2 helicase may play a role in the repair of double-strand breaks and ssDNA gaps together with Mus81–Mms4. In this study, we show that the Srs2 and Mus81–Mms4 proteins physically interact in vitro and in vivo and we map the interaction domains within the Srs2 and Mus81 proteins. Further, we show that Srs2 plays a dual role in the stimulation of the Mus81–Mms4 nuclease activity on a variety of DNA substrates. First, Srs2 directly stimulates Mus81–Mms4 nuclease activity independent of its helicase activity. Second, Srs2 removes Rad51 from DNA to allow access of Mus81–Mms4 to cleave DNA. Concomitantly, Mus81–Mms4 inhibits the helicase activity of Srs2. Taken together, our data point to a coordinated role of Mus81–Mms4 and Srs2 in processing of recombination as well as replication intermediates

Radiation recoil from highly distorted black holes

We present results from numerical evolutions of single black holes distorted by axisymmetric, but equatorially asymmetric, gravitational (Brill) waves. Net radiated energies, apparent horizon embeddings, and recoil velocities are shown for a range of Brill wave parameters, including both even and odd parity distortions of Schwarzschild black holes. We find that a wave packet initially concentrated on the black hole throat, a likely model also for highly asymmetric stellar collapse and late stage binary mergers, can generate a maximum recoil velocity of about 150 (23) km/sec for even (odd) parity perturbations, significantly less than that required to eject black holes from galactic cores.Comment: 15 pages, 8 figure

Three Dimensional Distorted Black Holes

We present three-dimensional, {\it non-axisymmetric} distorted black hole initial data which generalizes the axisymmetric, distorted, non-rotating [Bernstein93a] and rotating [Brandt94a] single black hole data developed by Bernstein, Brandt, and Seidel. These initial data should be useful for studying the dynamics of fully 3D, distorted black holes, such as those created by the spiraling coalescence of two black holes. We describe the mathematical construction of several families of such data sets, and show how to construct numerical solutions. We survey quantities associated with the numerically constructed solutions, such as ADM masses, apparent horizons, measurements of the horizon distortion, and the maximum possible radiation loss ($MRL$).Comment: 23 pages, 12 figures, accepted for publication in Classical and Quantum Gravit

Entropy in Black Hole Pair Production

Pair production of Reissner-Nordstrom black holes in a magnetic field can be described by a euclidean instanton. It is shown that the instanton amplitude contains an explicit factor of $e^{A/4}$, where $A$ is the area of the event horizon. This is consistent with the hypothesis that $e^{A/4}$ measures the number of black hole states.Comment: 24 pages (harvmac l mode