Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses

Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three computationally inexpensive simulation methods-normal mode analysis using the elastic network model, rigidity analysis using the pebble game algorithm, and geometric simulation of protein motion-to explore conformational change along normal mode eigenvectors. Using a combination of ELNEMO and FIRST/FRODA software, large-amplitude motions in proteins with hundreds or thousands of residues can be rapidly explored within minutes using desktop computing resources. We apply the method to a representative set of six proteins covering a range of sizes and structural characteristics and show that the method identifies specific types of motion in each case and determines their amplitude limits.Comment: 34 pages, 22 Figures, Phys. Biol. 9 (2012

Regional and seasonal patterns of litterfall in tropical South America

The production of aboveground soft tissue represents an important share of total net primary production in tropical rain forests. Here we draw from a large number of published and unpublished datasets (n=81 sites) to assess the determinants of litterfall variation across South American tropical forests. We show that across old-growth tropical rainforests, litterfall averages 8.61±1.91 Mg ha−1 yr−1 (mean ± standard deviation, in dry mass units). Secondary forests have a lower annual litterfall than old-growth tropical forests with a mean of 8.01±3.41 Mg ha−1 yr−1. Annual litterfall shows no significant variation with total annual rainfall, either globally or within forest types. It does not vary consistently with soil type, except in the poorest soils (white sand soils), where litterfall is significantly lower than in other soil types (5.42±1.91 Mg ha−1 yr−1). We also study the determinants of litterfall seasonality, and find that it does not depend on annual rainfall or on soil type. However, litterfall seasonality is significantly positively correlated with rainfall seasonality. Finally, we assess how much carbon is stored in reproductive organs relative to photosynthetic organs. Mean leaf fall is 5.74±1.83 Mg ha−1 yr−1 (71% of total litterfall). Mean allocation into reproductive organs is 0.69±0.40 Mg ha−1 yr−1 (9% of total litterfall). The investment into reproductive organs divided by leaf litterfall increases with soil fertility, suggesting that on poor soils, the allocation to photosynthetic organs is prioritized over that to reproduction. Finally, we discuss the ecological and biogeochemical implications of these result

Atomic X-ray Spectroscopy of Accreting Black Holes

Current astrophysical research suggests that the most persistently luminous objects in the Universe are powered by the flow of matter through accretion disks onto black holes. Accretion disk systems are observed to emit copious radiation across the electromagnetic spectrum, each energy band providing access to rather distinct regimes of physical conditions and geometric scale. X-ray emission probes the innermost regions of the accretion disk, where relativistic effects prevail. While this has been known for decades, it also has been acknowledged that inferring physical conditions in the relativistic regime from the behavior of the X-ray continuum is problematic and not satisfactorily constraining. With the discovery in the 1990s of iron X-ray lines bearing signatures of relativistic distortion came the hope that such emission would more firmly constrain models of disk accretion near black holes, as well as provide observational criteria by which to test general relativity in the strong field limit. Here we provide an introduction to this phenomenon. While the presentation is intended to be primarily tutorial in nature, we aim also to acquaint the reader with trends in current research. To achieve these ends, we present the basic applications of general relativity that pertain to X-ray spectroscopic observations of black hole accretion disk systems, focusing on the Schwarzschild and Kerr solutions to the Einstein field equations. To this we add treatments of the fundamental concepts associated with the theoretical and modeling aspects of accretion disks, as well as relevant topics from observational and theoretical X-ray spectroscopy.Comment: 63 pages, 21 figures, Einstein Centennial Review Article, Canadian Journal of Physics, in pres

Tratamiento quirúrgico de linfedema peneano secundario a hidrosadenitis supurativa

Penoscrotal lymphedema is a rare disease in the developed countries, although it is relatively frequent in tropical countries. The most common cause is filariasis, although in our practice usually is associate to neoplasic and inflammatory processes, surgery, radiotherapy, hidroelectrolitic disbalances and idiopathic. We present a 22 years old patient with penoscrotal lymphedema due to hidradenitis suppurativa. After unsuccessful medical treatment, was performed a total excision of the penile skin and subcutaneous tissue to Buck's fascia. Split thickness skin grafts were used to cover the defect. Even medical management of penoscrotal lymphedema is not effective for most patients, surgery is a safe and effective procedure that gives excellent functional and cosmetic results

HPM Approximations for Trajectories: From a Golf Ball Path to Mercury’s Orbit

In this work, we propose the approximated analytical solutions for two highly nonlinear problems using the homotopy perturbation method (HPM). We obtained approximations for a golf ball trajectory model and a Mercury orbit’s model. In addition, to enlarge the domain of convergence of the first case study, we apply the Laplace-Padé resummation method to the HPM series solution. For both case studies, we were able to obtain approximations in good agreement with numerical methods, depicting the basic nature of the trajectories of the phenomena

Investigation on the Behavior of Austenite and Ferrite Phases at Stagnation Region in the Turning of Duplex Stainless Steel Alloys

This paper investigates the deformation mechanisms and plastic behavior of austenite and ferrite phases in duplex stainless steel alloys 2205 and 2507 under chip formation from a machine turning operation. SEM images and EBSD phase mapping of frozen chip root samples detected a build-up of ferrite bands in the stagnation region, and between 65 and 85 pct, more ferrite was identified in the stagnation region compared to austenite. SEM images detected micro-cracks developing in the ferrite phase, indicating ferritic build-up in the stagnation region as a potential triggering mechanism to the formation of built-up edge, as transgranular micro-cracks found in the stagnation region are similar to micro-cracks initiating built-up edge formation. Higher plasticity of austenite due to softening under high strain is seen responsible for the ferrite build-up. Flow lines indicate that austenite is plastically deforming at a greater rate into the chip, while ferrite shows to partition most of the strain during deformation. The loss of annealing twins and activation of multiple slip planes triggered at high strain may explain the highly plastic behavior shown by austenite

Measurement of (anti)deuteron and (anti)proton production in DIS at HERA

The first observation of (anti)deuterons in deep inelastic scattering at HERA has been made with the ZEUS detector at a centre-of-mass energy of 300--318 GeV using an integrated luminosity of 120 pb-1. The measurement was performed in the central rapidity region for transverse momentum per unit of mass in the range 0.3<p_T/M<0.7. The particle rates have been extracted and interpreted in terms of the coalescence model. The (anti)deuteron production yield is smaller than the (anti)proton yield by approximately three orders of magnitude, consistent with the world measurements.Comment: 26 pages, 9 figures, 5 tables, submitted to Nucl. Phys.

Interinstrument comparison of remote-sensing devices and a new method for calculating on-road nitrogen oxides emissions and validation of vehicle-specific power

Emissions of nitrogen oxides (NOx) by vehicles in real driving environments are only partially understood. This has been brought to the attention of the world with recent revelations of the cheating of the type of approval tests exposed in the dieselgate scandal. Remote-sensing devices offer investigators an opportunity to directly measure in situ real driving emissions of tens of thousands of vehicles. Remote-sensing NO₂ measurements are not as widely available as would be desirable. The aim of this study is to improve the ability of investigators to estimate the NO₂ emissions and to improve the confidence of the total NOx results calculated from standard remote-sensing device (RSD) measurements. The accuracy of the RSD speed and acceleration module was also validated using state-of-the-art onboard global positioning system (GPS) tracking. Two RSDs used in roadside vehicle emissions surveys were tested side by side under off-carriageway conditions away from transient pollution sources to ascertain the consistency of their measurements. The speed correlation was consistent across the range of measurements at 95% confidence and the acceleration correlation was consistent at 95% confidence intervals for all but the most extreme acceleration cases. VSP was consistent at 95% confidence across all measurements except for those at VSP ≥ 15 kW t−¹, which show a small underestimate. The controlled distribution gas nitric oxide measurements follow a normal distribution with 2σ equal to 18.9% of the mean, compared to 15% observed during factory calibration indicative of additional error introduced into the system. Systematic errors of +84 ppm were observed but within the tolerance of the control gas. Interinstrument correlation was performed, with the relationship between the FEAT and the RSD4600 being linear with a gradient of 0.93 and an R² of 0.85, indicating good correlation. A new method to calculate NOx emissions using fractional NO₂ combined with NO measurements made by the RSD4600 was constructed, validated, and shown to be more accurate than previous methods. Implications: Synchronized remote-sensing measurements of NO were taken using two different remote-sensing devices in an off-road study. It was found that the measurements taken by both instruments were well correlated. Fractional NO₂ measurements from a prior study, measurable on only one device, were used to create new NOₓ emission factors for the device that could not be measured by the second device. These estimates were validated against direct measurement of total NOₓ emission factors and shown to be an improvement on previous methodologies. Validation of vehicle-specific power was performed with good correlation observed

Forward jet production in deep inelastic ep scattering and low-x parton dynamics at HERA

Differential inclusive jet cross sections in neutral current deep inelastic ep scattering have been measured with the ZEUS detector. Three phase-space regions have been selected in order to study parton dynamics where the effects of BFKL evolution might be present. The measurements have been compared to the predictions of leading-logarithm parton shower Monte Carlo models and fixed-order perturbative QCD calculations. In the forward region, QCD calculations at order alpha_s^1 underestimate the data up to an order of magnitude at low x. An improved description of the data in this region is obtained by including QCD corrections at order alpha_s^2, which account for the lowest-order t-channel gluon-exchange diagrams, highlighting the importance of such terms in parton dynamics at low x.Comment: 25 pages, 4 figure

A novel 65 kDa RNA-binding protein in squid presynaptic terminals

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Neuroscience 166 (2010): 73-83, doi:10.1016/j.neuroscience.2009.12.005.A polyclonal antibody (C4), raised against the head domain of chicken myosin Va, reacted strongly towards a 65 kDa polypeptide (p65) on western blots of extracts from squid optic lobes but did not recognize the heavy chain of squid myosin V. This peptide was not recognized by other myosin Va antibodies, nor by an antibody specific for squid myosin V. In an attempt to identify it, p65 was purified from optic lobes of Loligo plei by cationic exchange and reverse phase chromatography. Several peptide sequences were obtained by mass spectroscopy from p65 cut from SDS-PAGE gels. BLAST analysis and partial matching with ESTs from a Loligo pealei data bank indicated that p65 contains consensus signatures for the hnRNP A/B family of RNA-binding proteins. Centrifugation of post mitochondrial extracts from optic lobes on sucrose gradients after treatment with RNase gave biochemical evidence that p65 associates with cytoplasmic RNP complexes in an RNA-dependent manner. Immunohistochemistry and immunofluorescence studies using the C4 antibody showed partial co-labeling with an antibody against squid synaptotagmin in bands within the outer plexiform layer of the optic lobes and at the presynaptic zone of the stellate ganglion. Also, punctate labeling by the C4 antibody was observed within isolated optic lobe synaptosomes. The data indicate that p65 is a novel RNA-binding protein located to the presynaptic terminal within squid neurons and may have a role in synaptic localization of RNA and its translation or processing.REL, JCR and JEM received financial support from the Fundação de Amparo à Pesquisa do Estado de Sao Paulo (FAPESP), the Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) and the Fundação de Apoio ao Ensino, Pesquisa e Assistência do Hospital das Clínicas da FMRP-USP (FAEPA). JAD received financial support from the RI-INBRE Program Grant #P20RR016457 from the Nation Center for Research Resources, NIH, Bethesda, MD. DTPL, LC, SBFT, EJRV and MMAB were recipients of research fellowships from FAPESP and CNPq. REL and JEM received Productivityin- Research fellowships from CNPq