A role for chromatin remodellers in replication of damaged DNA

In eukaryotic cells, replication past damaged sites in DNA is regulated by the ubiquitination of proliferating cell nuclear antigen (PCNA). Little is known about how this process is affected by chromatin structure. There are two isoforms of the Remodels the Structure of Chromatin (RSC) remodelling complex in yeast. We show that deletion of RSC2 results in a dramatic reduction in the level of PCNA ubiquitination after DNA-damaging treatments, whereas no such effect was observed after deletion of RSC1. Similarly, depletion of the BAF180 component of the corresponding PBAF (Polybromo BRG1 (Brahma-Related Gene 1) Associated Factor) complex in human cells led to a similar reduction in PCNA ubiquitination. Remarkably, we found that depletion of BAF180 resulted after UV-irradiation, in a reduction not only of ubiquitinated PCNA but also of chromatin-associated unmodified PCNA and Rad18 (the E3 ligase that ubiquitinates PCNA). This was accompanied by a modest decrease in fork progression. We propose a model to account for these findings that postulates an involvement of PBAF in repriming of replication downstream from replication forks blocked at sites of DNA damage. In support of this model, chromatin immunoprecipitation data show that the RSC complex in yeast is present in the vicinity of the replication forks, and by extrapolation, this is also likely to be the case for the PBAF complex in human cells

Optimal Moments for the Analysis of Peculiar Velocity Surveys II: Testing

Analyses of peculiar velocity surveys face several challenges, including low signal--to--noise in individual velocity measurements and the presence of small--scale, nonlinear flows. This is the second in a series of papers in which we describe a new method of overcoming these problems by using data compression as a filter with which to separate large--scale, linear flows from small--scale noise that can bias results. We demonstrate the effectiveness of our method using realistic catalogs of galaxy velocities drawn from N--body simulations. Our tests show that a likelihood analysis of simulated catalogs that uses all of the information contained in the peculiar velocities results in a bias in the estimation of the power spectrum shape parameter $\Gamma$ and amplitude $\beta$, and that our method of analysis effectively removes this bias. We expect that this new method will cause peculiar velocity surveys to re--emerge as a useful tool to determine cosmological parameters.Comment: 28 pages, 9 figure

Fork rotation and DNA precatenation are restricted during DNA replication to prevent chromosomal instability

Faithful genome duplication and inheritance require the complete resolution of all intertwines within the parental DNA duplex. This is achieved by topoisomerase action ahead of the replication fork or by fork rotation and subsequent resolution of the DNA precatenation formed. Although fork rotation predominates at replication termination, in vitro studies have suggested that it also occurs frequently during elongation. However, the factors that influence fork rotation and how rotation and precatenation may influence other replication-associated processes are unknown. Here we analyze the causes and consequences of fork rotation in budding yeast. We find that fork rotation and precatenation preferentially occur in contexts that inhibit topoisomerase action ahead of the fork, including stable protein–DNA fragile sites and termination. However, generally, fork rotation and precatenation are actively inhibited by Timeless/Tof1 and Tipin/Csm3. In the absence of Tof1/Timeless, excessive fork rotation and precatenation cause extensive DNA damage following DNA replication. With Tof1, damage related to precatenation is focused on the fragile protein–DNA sites where fork rotation is induced. We conclude that although fork rotation and precatenation facilitate unwinding in hard-to-replicate contexts, they intrinsically disrupt normal chromosome duplication and are therefore restricted by Timeless/Tipin

Summary of information on low-speed lateral-directional derivatives due to rate of change of sideslip beta prime

The results presented show that the magnitudes of the aerodynamic stability derivatives due to rate of change of sideslip become quite large at high angles of attack for swept- and delta-wing configurations, and that such derivatives have large effects on the calculated dynamic stability of these configurations at high angles of attack. The wind-tunnel test techniques used to measure the beta prime derivatives and various approaches used to predict them are discussed. Both the conventional oscillating-airfoil theory and the lag-of-the-sidewash theory are shown to be inadequate for predicting the vertical-tail contribution to the acceleration-in-sideslip derivative; a flow-field-lag theory, which is discussed, appears to give qualitative agreement with experimental data for a current twin-jet fighter configuration

Camera Trap Success Among Carnivores and Prey Animals in Tazewell County, Virginia

Obtaining basic ecological information on occurrence and activity levels in cryptic and elusive species is often difficult. Camera trapping provides a relatively inexpensive opportunity to acquire such data. We used infrared-triggered cameras to assess trap success and activity levels of several species across four consecutive seasons, including: Ursus americanus (black bear), Lynx rufus (bobcat), Canis latrans (coyote), Vulpes vulpes (red fox), Urocyon cinereoargenteus (gray fox), Procyon lotor (raccoon), Odocoileus virginianus (white-tailed deer), Didelphis virginiana (opossum), Sciurus carolinensis (gray squirrel), and Meleagris gallopavo (wild turkey). With a total of 396 trap nights (TN) at one station over the span of four consecutive seasons, overall trap success rate was 86.87 captures per 100 TN. Trap success was highest in wild turkeys (31.57/100 TN), followed by raccoons (15.66/100 TN), gray squirrels (10.86/100 TN), gray foxes (8.59/100 TN), white-tailed deer (8.08/100 TN), opossums (5.56/100 TN), coyotes (1.52/100 TN), red foxes (1.26/100 TN), and bobcats (0.76/100 TN). Overall trap success significantly varied across all target species combined (Kruskal Wallis Chi-Square = 349, d.f. = 10, p \u3c 0.0001). However, trap success did not vary across all seasons for all target species combined (Kruskal Wallis Chi-Square = 0.99, d.f. = 3, p = 0.78). This study is the first to use camera trapping to examine species presence and activity levels in a longitudinal manner for cryptic and elusive species of southwest Virginia

Crystallization of the oligopeptide-binding protein AppA from Bacillus subtilis

AppA is the membrane-anchored extracellular receptor component of an ABC transporter responsible for the uptake of oligopeptides into Bacillus subtilis. AppA has been overexpressed as a cleavable maltose-binding protein fusion in Escherichia coli. Following removal of the fusion portion, AppA has been crystallized from morpholino-ethanesulfonic acid-buffered solutions at pH 6.5 containing polyethylene glycol and zinc acetate. A complete X-ray diffraction data set extending to 2.3 Angstrom spacing has been collected

Optimal Moments for the Analysis of Peculiar Velocity Surveys

We present a new method for the analysis of peculiar velocity surveys which removes contributions to velocities from small scale, nonlinear velocity modes while retaining information about large scale motions. Our method utilizes Karhunen--Lo\`eve methods of data compression to construct a set of moments out of the velocities which are minimally sensitive to small scale power. The set of moments are then used in a likelihood analysis. We develop criteria for the selection of moments, as well as a statistic to quantify the overall sensitivity of a set of moments to small scale power. Although we discuss our method in the context of peculiar velocity surveys, it may also prove useful in other situations where data filtering is required.Comment: 25 Pages, 3 figures. Submitted to Ap

Much Ado About Nothing Much: Protestant Episcopal Church in the Diocese of Virginia v. Truro Church

This essay reviews the issues the Supreme Court of Virginia resolved in Truro and notes important issues it did not resolve. Part II supplies the factual background and procedural history ofthe dispute. Part III summarizes the court\u27s opinion and the reasoning underlying its determination that Virginia Code section57-9(A) is not applicable to this particular action. Part IV critiques the opinion, noting the issues the court resolved and how it resolved them. Part V briefly addresses issues that remain unresolved by the court\u27s decision and discusses the implications of leaving those issues unresolved. Part VI presents the authors\u27 conclusions

Exposure to liquid sweetness in early childhood:artificially-sweetened and sugar-sweetened beverage consumption at 4–5 years and risk of overweight and obesity at 7–8 years

Background: A significant gap exists in longitudinal evidence on early exposure to artificially sweetened beverages (ASBs) and weight outcomes for paediatric populations. Objective: The objective of this study is to examine the relationship between ASB/sugar‐sweetened beverage (SSB) consumption at 4–5 years and risk of overweight and obesity at 7–8 years. Methods: Data from a nationally representative cohort (n = 2986) in Scotland were analysed using logistic regression to evaluate the association between exposure to ASBs/SSBs at 4–5 years and risk of overweight and obesity at 7–8 years. Results: There were positive unadjusted associations between ASB consumption and risk of obesity, and following adjustment for confounders, ASB associations attenuated, and only the middle consumption category (1 to 6 times per week) remained significant (odds ratio 1.57, 95% confidence interval {CI} 1.05–2.36). For SSB consumption, there were no significant unadjusted associations, and following adjustment for confounders, only the middle consumption category was significant (odds ratio 1.65, 95% CI 1.12–2.44). There were no significant associations for risk of overweight. Conclusions: Longitudinal analysis from 4–5 to 7–8 years demonstrated some evidence of associations between ASBs/SSB consumption and risk of obesity. However, non‐linear patterns and wide CIs suggest cautious interpretation and need for future studies with long‐term follow‐up