DNA repair nucleases

Stability of DNA largely depends on accuracy of repair mechanisms, which remove structural anomalies induced by exogenous and endogenous agents or introduced by DNA metabolism, such as replication. Most repair mechanisms include nucleolytic processing of DNA, where nucleases cleave a phosphodiester bond between a deoxyribose and a phosphate residue, thereby producing 5′-terminal phosphate and 3′-terminal hydroxyl groups. Exonucleases hydrolyse nucleotides from either the 5′ or 3′ end of DNA, while endonucleases incise internal sites of DNA. Flap endonucleases cleave DNA flap structures at or near the junction between single-stranded and double-stranded regions. DNA nucleases play a crucial role in mismatch repair, nucleotide excision repair, base excision repair and double-strand break repair. In addition, nucleolytic repair functions are required during replication to remove misincorporated nucleotides, Okazaki fragments and 3′ tails that may be formed after repair of stalled replication fork

RAM: A Relativistic Adaptive Mesh Refinement Hydrodynamics Code

We have developed a new computer code, RAM, to solve the conservative equations of special relativistic hydrodynamics (SRHD) using adaptive mesh refinement (AMR) on parallel computers. We have implemented a characteristic-wise, finite difference, weighted essentially non-oscillatory (WENO) scheme using the full characteristic decomposition of the SRHD equations to achieve fifth-order accuracy in space. For time integration we use the method of lines with a third-order total variation diminishing (TVD) Runge-Kutta scheme. We have also implemented fourth and fifth order Runge-Kutta time integration schemes for comparison. The implementation of AMR and parallelization is based on the FLASH code. RAM is modular and includes the capability to easily swap hydrodynamics solvers, reconstruction methods and physics modules. In addition to WENO we have implemented a finite volume module with the piecewise parabolic method (PPM) for reconstruction and the modified Marquina approximate Riemann solver to work with TVD Runge-Kutta time integration. We examine the difficulty of accurately simulating shear flows in numerical relativistic hydrodynamics codes. We show that under-resolved simulations of simple test problems with transverse velocity components produce incorrect results and demonstrate the ability of RAM to correctly solve these problems. RAM has been tested in one, two and three dimensions and in Cartesian, cylindrical and spherical coordinates. We have demonstrated fifth-order accuracy for WENO in one and two dimensions and performed detailed comparison with other schemes for which we show significantly lower convergence rates. Extensive testing is presented demonstrating the ability of RAM to address challenging open questions in relativistic astrophysics.Comment: ApJS in press, 21 pages including 18 figures (6 color figures

Genetic mapping, synteny, and physical location of two loci for Fusarium oxysporum f. sp. tracheiphilum race 4 resistance in cowpea [Vignaunguiculata (L.) Walp].

Fusarium wilt is a vascular disease caused by the fungus Fusariumoxysporum f.sp. tracheiphilum (Fot) in cowpea [Vignaunguiculata (L.) Walp]. In this study, we mapped loci conferring resistance to Fot race 4 in three cowpea RIL populations: IT93K-503-1 × CB46, CB27 × 24-125B-1, and CB27 × IT82E-18/Big Buff. Two independent loci which confer resistance to Fot race 4 were identified, Fot4-1 and Fot4-2. Fot4-1 was identified in the IT93K-503-1 (resistant) × CB46 (susceptible) population and was positioned on the cowpea consensus genetic map, spanning 21.57-29.40 cM on linkage group 5. The Fot4-2 locus was validated by identifying it in both the CB27 (resistant) × 24-125B-1 (susceptible) and CB27 (resistant) × IT82E-18/Big Buff (susceptible) populations. Fot4-2 was positioned on the cowpea consensus genetic map on linkage group 3; the minimum distance spanned 71.52-71.75 cM whereas the maximum distance spanned 64.44-80.23 cM. These genomic locations of Fot4-1 and Fot4-2 on the cowpea consensus genetic map, relative to Fot3-1 which was previously identified as the locus conferring resistance to Fot race 3, established that all three loci were independent. The Fot4-1 and Fot4-2 syntenic loci were examined in Glycine max, where several disease-resistance candidate genes were identified for both loci. In addition, Fot4-1 and Fot4-2 were coarsely positioned on the cowpea physical map. Fot4-1 and Fot4-2 will contribute to molecular marker development for future use in marker-assisted selection, thereby expediting introgression of Fot race 4 resistance into future cowpea cultivars

Flaring Activity of Sgr A* at 43 and 22 GHz: Evidence for Expanding Hot Plasma

We have carried out Very Large Array (VLA) continuum observations to study the variability of Sgr A* at 43 GHz ($\lambda$=7mm) and 22 GHz ($\lambda$=13mm). A low level of flare activity has been detected with a duration of $\sim$ 2 hours at these frequencies, showing the peak flare emission at 43 GHz leading the 22 GHz peak flare by $\sim20$ to 40 minutes. The overall characteristics of the flare emission are interpreted in terms of the plasmon model of Van der Laan (1966) by considering the ejection and adiabatically expansion of a uniform, spherical plasma blob due to flare activity. The observed peak of the flare emission with a spectral index $\nu^{-\alpha}$ of $\alpha$=1.6 is consistent with the prediction that the peak emission shifts toward lower frequencies in an adiabatically-expanding self-absorbed source. We present the expected synchrotron light curves for an expanding blob as well as the peak frequency emission as a function of the energy spectral index constrained by the available flaring measurements in near-IR, sub-millimeter, millimeter and radio wavelengths. We note that the blob model is consistent with the available measurements, however, we can not rule out the jet of Sgr A*. If expanding material leaves the gravitational potential of Sgr A*, the total mass-loss rate of nonthermal and thermal particles is estimated to be $\le 2\times10^{-8}$ M$_\odot$ yr$^{-1}$. We discuss the implication of the mass-loss rate since this value matches closely with the estimated accretion rate based on polarization measurements.Comment: Revised with new Figures 1 and 2, 17 pages, 4 figures, ApJ (in press

Contribution to the fungus flora of the Natíonal Park of Ordesa and Monte Perdido (Central Pyrenean range, NE Spain).

[EN]This work is a floristic catalogue of the fungi collected during an exploration of the National Park of Ordesa and Monte Perdido, in the fall of 1989. Commentaries and iconography are provided in the case of interesting species, such as Lentinus adhaerens (A. et S. : Fr.) FR., Naucoria permixta P. D. Orton, Tephrocybe baeosperma (Romagn.) Moser and Xcromphalina cornui (Quél.) Favre.[CAT] Presentem un catàleg florístic de les espècies recol.lectades en el curs d´una exploració del Parc Nacional d´Ordesa i Monte Perdido (Pirineus centrals) a la tardor de 1989, en el qual comentem i il.lustrem les que considerem més interessants, com són Lentinus adhacrens (A. et S. : Fr.) Fr., Naucoria permixta P. D. Orton, Tephrocybe baeosperma (Romagn) Moser i Xeromphalina cornui (Quél) Favre.Peer reviewe

Obesity and immunocompetence

The increasing worldwide prevalence of obesity is a major health problem since excessive body weight constitutes a risk factor in a number of chronic diseases. It has been reported that obese individuals are more susceptible to infection than lean subjects; however, the underlying factors are not fully understood. Limited and often controversial information exists comparing immunocompetence in obese and nonobese subjects as well as the cellular and molecular mechanisms involved, although much evidence supports a link between adipose tissue metabolism and immunocompetent cell functions. The complexity and heterogeneity of nutritional status and immune system interactions require an integral study of the immunocompetent cells, their subsets and products, as well as specific and non-specific inducer/regulatory systems in situations of human obesity. Additional research is needed to determine the clinical implications of these alterations on immunity and whether various interventions such as weight loss, exercise or nutrient supplementation could help to ameliorate them

The Lotic Intersite Nitrogen Experiments: an example of successful ecological research collaboration

Collaboration is an essential skill for modern ecologists because it brings together diverse expertise, viewpoints, and study systems. The Lotic Intersite Nitrogen eXperiments (LINX I and II), a 17-y research endeavor involving scores of early- to late-career stream ecologists, is an example of the benefits, challenges, and approaches of successful collaborative research in ecology. The scientific success of LINX reflected tangible attributes including clear scientific goals (hypothesis-driven research), coordinated research methods, a team of cooperative scientists, excellent leadership, extensive communication, and a philosophy of respect for input from all collaborators. Intangible aspects of the collaboration included camaraderie and strong team chemistry. LINX further benefited from being part of a discipline in which collaboration is a tradition, clear data-sharing and authorship guidelines, an approach that melded field experiments and modeling, and a shared collaborative goal in the form of a universal commitment to see the project and resulting data products through to completion