Nucleon resonances in the constituent quark model with chiral symmetry

The mass spectra of nucleon resonances with spin 1/2, 3/2, and 5/2 are systematically studied in the constituent quark model with meson-quark coupling, which is inspired by the spontaneous breaking of chiral symmetry of QCD. The meson-quark coupling gives rise not only to the one-meson-exchange potential between quarks but also to the self-energy of baryon resonances due to the existence of meson-baryon decay channels. The two contributions are consistently taken into account in the calculation. The gross properties of the nucleon resonance spectra are reproduced fairly well although the predicted mass of N(1440) is too high.Comment: 14 pages, 6 figures, Late

A model of methane concentration profiles in the open ocean

Methane-bearing particulate matter formed in the upper ocean layer is allowed to settle and degrade, releasing methane into the water column as a source in one-dimensional advection-diffusion equations. Predicted carbon and methane particulate fluxes are in good agreement with sediment trap data, using parameters of expected magnitude and particulate methane production well within the mixed layer. This suggests a rapid pathway to the atmosphere and reduced effects on methane concentrations below. Vertical advection rates yielding a good fit between methane concentration calculations and data are larger than expected unless methane oxidation is included. This confirms the significance of methane oxidation in shaping open-ocean methane concentration profiles in spite of turnover times of decades. Predictions of the isotopic composition of dissolved methane δ13 C with the one-dimensional model are more difficult, although trends in measured vertical profiles can be reproduced. While this work does not shed light on the purported mechanism of methane generation in the upper ocean, it shows that methane of particulate origin is sufficient to explain observed open-ocean methane concentrations

Notes on the modeling of methane in aging hydrothermal plumes

Marine hydrothermal vent fields represent a unique environment for the study of aerobic microbial methane oxidation because of high methane concentrations and limited spatial and temporal scales. Earlier data collected in lateral plumes at the Endeavour Segment of the Juan de Fuca Ridge, including methane concentration, methane oxidation rate and stable carbon isotopic composition (δ13C), are carefully interpreted with a suite of simple analytical models. Methane oxidation is defined with a rate constant k as a first order process with respect to both substrate and methanotroph concentration. This elementary formalism coupled with simplified representations of advection and diffusion through the lateral plume is sufficient to reproduce salient features of the data: maximum methane turnover times of about a week 2 km from the vent field location and stable carbon isotopic enrichment from -47‰ to values exceeding -5‰ over a distance of 15 km. Results suggest that k is of order 10-8 (nM-s)-1 at local conditions and that methane oxidizing bacteria hold about 12 fg of carbon per cell

LABORATORY EXPERIMENTS TO SIMULATE CO2 OCEAN DISPOSAL

This Final Technical Report summarizes the technical accomplishments of an investigation entitled ''Laboratory Experiments to Simulate CO{sub 2} Ocean Disposal'', funded by the U.S. Department of Energy's University Coal Research Program. This investigation responds to the possibility that restrictions on greenhouse gas emissions may be imposed in the future to comply with the Framework Convention on Climate Change. The primary objective of the investigation was to obtain experimental data that can be applied to assess the technical feasibility and environmental impacts of oceanic containment strategies to limit release of carbon dioxide (CO{sub 2}) from coal and other fossil fuel combustion systems into the atmosphere. A number of critical technical uncertainties of ocean disposal of CO{sub 2} were addressed by performing laboratory experiments on liquid CO{sub 2} jet break-up into a dispersed droplet phase, and hydrate formation, under deep ocean conditions. Major accomplishments of this study included: (1) five jet instability regimes were identified that occur in sequence as liquid CO{sub 2} jet disintegration progresses from laminar instability to turbulent atomization; (2) linear regression to the data yielded relationships for the boundaries between the five instability regimes in dimensionless Ohnesorge Number, Oh, and jet Reynolds Number, Re, space; (3) droplet size spectra was measured over the full range of instabilities; (4) characteristic droplet diameters decrease steadily with increasing jet velocity (and increasing Weber Number), attaining an asymptotic value in instability regime 5 (full atomization); and (5) pre-breakup hydrate formation appears to affect the size distribution of the droplet phase primary by changing the effective geometry of the jet

ATR-mediated phosphorylation of DNA polymerase η is needed for efficient recovery from UV damage

DNA polymerase η (polη) belongs to the Y-family of DNA polymerases and facilitates translesion synthesis past UV damage. We show that, after UV irradiation, polη becomes phosphorylated at Ser601 by the ataxia-telangiectasia mutated and Rad3-related (ATR) kinase. DNA damage–induced phosphorylation of polη depends on its physical interaction with Rad18 but is independent of PCNA monoubiquitination. It requires the ubiquitin-binding domain of polη but not its PCNA-interacting motif. ATR-dependent phosphorylation of polη is necessary to restore normal survival and postreplication repair after ultraviolet irradiation in xeroderma pigmentosum variant fibroblasts, and is involved in the checkpoint response to UV damage. Taken together, our results provide evidence for a link between DNA damage–induced checkpoint activation and translesion synthesis in mammalian cells

A Study of Degenerate Four-quark states in SU(2) Lattice Monte Carlo

The energies of four-quark states are calculated for geometries in which the quarks are situated on the corners of a series of tetrahedra and also for geometries that correspond to gradually distorting these tetrahedra into a plane. The interest in tetrahedra arises because they are composed of {\bf three } degenerate partitions of the four quarks into two two-quark colour singlets. This is an extension of earlier work showing that geometries with {\bf two} degenerate partitions (e.g.\ squares) experience a large binding energy. It is now found that even larger binding energies do not result, but that for the tetrahedra the ground and first excited states become degenerate in energy. The calculation is carried out using SU(2) for static quarks in the quenched approximation with $\beta=2.4$ on a $16^3\times 32$ lattice. The results are analysed using the correlation matrix between different euclidean times and the implications of these results are discussed for a model based on two-quark potentials.Comment: Original Raw PS file replace by a tarred, compressed and uuencoded PS fil

Quarterly Technical Progress Report for the Period Ending 30 September 2002 (Quarterly Report #8)

Most of the anthropogenic emissions of carbon dioxide result from the combustion of fossil fuels for energy production. Photosynthesis has long been recognized as a means, at least in theory, to sequester anthropogenic carbon dioxide. Aquatic microalgae have been identified as fast growing species whose carbon fixing rates are higher than those of land-based plants by one order of magnitude. Physical Sciences Inc. (PSI), Aquasearch, and the Hawaii Natural Energy Institute at the University of Hawaii are jointly developing technologies for recovery and sequestration of CO{sub 2} from stationary combustion systems by photosynthesis of microalgae. The research is aimed primarily at demonstrating the ability of selected species of microalgae to effectively fix carbon from typical power plant exhaust gases. This report covers the reporting period 1 July to 30 September 2002 in which PSI, Aquasearch and University of Hawaii conducted their tasks. Based on the work conducted during the previous reporting period, PSI initiated work on feasibility demonstration of direct feeding of coal combustion gas to microalgae. Aquasearch continued their effort on selection and characterization of microalgae suitable for CO{sub 2} sequestration. University of Hawaii continued effort on system optimization of the CO{sub 2} sequestration system

Simultaneous disruption of two DNA polymerases, Polη and Polζ, in Avian DT40 cells unmasks the role of Polη in cellular response to various DNA lesions

Replicative DNA polymerases are frequently stalled by DNA lesions. The resulting replication blockage is released by homologous recombination (HR) and translesion DNA synthesis (TLS). TLS employs specialized TLS polymerases to bypass DNA lesions. We provide striking in vivo evidence of the cooperation between DNA polymerase η, which is mutated in the variant form of the cancer predisposition disorder xeroderma pigmentosum (XP-V), and DNA polymerase ζ by generating POLη−/−/POLζ−/− cells from the chicken DT40 cell line. POLζ−/− cells are hypersensitive to a very wide range of DNA damaging agents, whereas XP-V cells exhibit moderate sensitivity to ultraviolet light (UV) only in the presence of caffeine treatment and exhibit no significant sensitivity to any other damaging agents. It is therefore widely believed that Polη plays a very specific role in cellular tolerance to UV-induced DNA damage. The evidence we present challenges this assumption. The phenotypic analysis of POLη−/−/POLζ−/− cells shows that, unexpectedly, the loss of Polη significantly rescued all mutant phenotypes of POLζ−/− cells and results in the restoration of the DNA damage tolerance by a backup pathway including HR. Taken together, Polη contributes to a much wide range of TLS events than had been predicted by the phenotype of XP-V cells

Interaction of hHR23 with S5a. The ubiquitin-like domain of hHR23 mediates interaction with S5a subunit of 26 S proteasome

hHR23B is one of two human homologs of the Saccharomyces cerevisiae nucleotide excision repair (NER) gene product RAD23 and a component of a protein complex that specifically complements the NER defect of xeroderma pigmentosum group C (XP-C) cell extracts in vitro. Although a small proportion of hHR23B is tightly complexed with the XP-C responsible gene product, XPC protein, a vast majority exists as an XPC-free form, indicating that hHR23B has additional functions other than NER in vivo. Here we demonstrate that the human NER factor hHR23B as well as another human homolog of RAD23, hHR23A, interact specifically with S5a, a subunit of the human 26 S proteasome using the yeast two-hybrid system. Furthermore, hHR23 proteins were detected with S5a at the position where 26 S proteasome sediments in glycerol gradient centrifugation of HeLa S100 extracts. Intriguingly, hHR23B showed the inhibitory effect on the degradation of (125)I-lysozyme in the rabbit reticulocyte lysate. hHR23 proteins thus appear to associate with 26 S proteasome in vivo. From co-precipitation experiments using several series of deletion mutants, we defined the domains in hHR23B and S5a that mediate this interaction. From these results, we propose that part of hHR23 proteins are involved in the proteolytic pathway in cells

The influence of droplet size and biodegradation on the transport of subsurface oil droplets during the Deepwater Horizon: a model sensitivity study

A better understanding of oil droplet formation, degradation, and dispersal in deep waters is needed to enhance prediction of the fate and transport of subsurface oil spills. This research evaluates the influence of initial droplet size and rates of biodegradation on the subsurface transport of oil droplets, specifically those from the Deepwater Horizon oil spill. A three-dimensional coupled model was employed with components that included analytical multiphase plume, hydrodynamic and Lagrangian models. Oil droplet biodegradation was simulated based on first order decay rates of alkanes. The initial diameter of droplets (10–300 μm) spanned a range of sizes expected from dispersant-treated oil. Results indicate that model predictions are sensitive to biodegradation processes, with depth distributions deepening by hundreds of meters, horizontal distributions decreasing by hundreds to thousands of kilometers, and mass decreasing by 92–99% when biodegradation is applied compared to simulations without biodegradation. In addition, there are two- to four-fold changes in the area of the seafloor contacted by oil droplets among scenarios with different biodegradation rates. The spatial distributions of hydrocarbons predicted by the model with biodegradation are similar to those observed in the sediment and water column, although the model predicts hydrocarbons to the northeast and east of the well where no observations were made. This study indicates that improvement in knowledge of droplet sizes and biodegradation processes is important for accurate prediction of subsurface oil spills.National Science Foundation (U.S.) (RAPID: Deepwater Horizon Grant OCE-1048630)National Science Foundation (U.S.) (RAPID: Deepwater Horizon Grant OCE-1044573)National Science Foundation (U.S.) (RAPID: Deepwater Horizon Grant CBET-1045831)Gulf of Mexico Research Initiativ