Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin in the multiphoton regime and biological relevance

How does chemistry scale in complexity to unerringly direct biological functions? Nass Kovacs et al. have shown that bacteriorhodopsin undergoes structural changes tantalizingly similar to the expected pathway even under excessive excitation. Is the protein structure so highly evolved that it directs all deposited energy into the designed function

Toward detailed prominence seismology - I. Computing accurate 2.5D magnetohydrodynamic equilibria

Context. Prominence seismology exploits our knowledge of the linear eigenoscillations for representative magnetohydro- dynamic models of filaments. To date, highly idealized models for prominences have been used, especially with respect to the overall magnetic configurations. Aims. We initiate a more systematic survey of filament wave modes, where we consider full multi-dimensional models with twisted magnetic fields representative of the surrounding magnetic flux rope. This requires the ability to compute accurate 2.5 dimensional magnetohydrodynamic equilibria that balance Lorentz forces, gravity, and pressure gradients, while containing density enhancements (static or in motion). Methods. The governing extended Grad-Shafranov equation is discussed, along with an analytic prediction for circular flux ropes for the Shafranov shift of the central magnetic axis due to gravity. Numerical equilibria are computed with a finite element-based code, demonstrating fourth order accuracy on an explicitly known, non-trivial test case. Results. The code is then used to construct more realistic prominence equilibria, for all three possible choices of a free flux-function. We quantify the influence of gravity, and generate cool condensations in hot cavities, as well as multi- layered prominences. Conclusions. The internal flux rope equilibria computed here have the prerequisite numerical accuracy to allow a yet more advanced analysis of the complete spectrum of linear magnetohydrodynamic perturbations, as will be demonstrated in the companion paper.Comment: Accepted by Astronomy & Astrophysics, 15 pages, 15 figure

Lack of phenotypic and evolutionary cross-resistance against parasitoids and pathogens in Drosophila melanogaster

BackgroundWhen organisms are attacked by multiple natural enemies, the evolution of a resistance mechanism to one natural enemy will be influenced by the degree of cross-resistance to another natural enemy. Cross-resistance can be positive, when a resistance mechanism against one natural enemy also offers resistance to another; or negative, in the form of a trade-off, when an increase in resistance against one natural enemy results in a decrease in resistance against another. Using Drosophila melanogaster, an important model system for the evolution of invertebrate immunity, we test for the existence of cross-resistance against parasites and pathogens, at both a phenotypic and evolutionary level.MethodsWe used a field strain of D. melanogaster to test whether surviving parasitism by the parasitoid Asobara tabida has an effect on the resistance against Beauveria bassiana, an entomopathogenic fungus; and whether infection with the microsporidian Tubulinosema kingi has an effect on the resistance against A. tabida. We used lines selected for increased resistance to A. tabida to test whether increased parasitoid resistance has an effect on resistance against B. bassiana and T. kingi. We used lines selected for increased tolerance against B. bassiana to test whether increased fungal resistance has an effect on resistance against A. tabida.Results/ConclusionsWe found no positive cross-resistance or trade-offs in the resistance to parasites and pathogens. This is an important finding, given the use of D. melanogaster as a model system for the evolution of invertebrate immunity. The lack of any cross-resistance to parasites and pathogens, at both the phenotypic and the evolutionary level, suggests that evolution of resistance against one class of natural enemies is largely independent of evolution of resistance against the other

Toward detailed prominence seismology - II. Charting the continuous magnetohydrodynamic spectrum

Starting from accurate MHD flux rope equilibria containing prominence condensations, we initiate a systematic survey of their linear eigenoscillations. To quantify the full spectrum of linear MHD eigenmodes, we require knowledge of all flux-surface localized modes, charting out the continuous parts of the MHD spectrum. We combine analytical and numerical findings for the continuous spectrum for realistic prominence configurations. The equations governing all eigenmodes for translationally symmetric, gravitating equilibria containing an axial shear flow, are analyzed, along with their flux-surface localized limit. The analysis is valid for general 2.5D equilibria, where either density, entropy, or temperature vary from one flux surface to another. We analyze the mode couplings caused by the poloidal variation in the flux rope equilibria, by performing a small gravity parameter expansion. We contrast the analytical results with continuous spectra obtained numerically. For equilibria where the density is a flux function, we show that continuum modes can be overstable, and we present the stability criterion for these convective continuum instabilities. Furthermore, for all equilibria, a four-mode coupling scheme between an Alfvenic mode of poloidal mode number m and three neighboring (m-1, m, m+1) slow modes is identified, occurring in the vicinity of rational flux surfaces. For realistically prominence equilibria, this coupling is shown to play an important role, from weak to stronger gravity parameter g values. The analytic predictions for small g are compared with numerical spectra, and progressive deviations for larger g are identified. The unstable continuum modes could be relevant for short-lived prominence configurations. The gaps created by poloidal mode coupling in the continuous spectrum need further analysis, as they form preferred frequency ranges for global eigenoscillations.Comment: Accepted by Astronmy & Astrophysics, 21 pages, 15 figure

Estimation of solar prominence magnetic fields based on the reconstructed 3D trajectories of prominence knots

We present an estimation of the lower limits of local magnetic fields in quiescent, activated, and active (surges) promineces, based on reconstructed 3-dimensional (3D) trajectories of individual prominence knots. The 3D trajectories, velocities, tangential and centripetal accelerations of the knots were reconstructed using observational data collected with a single ground-based telescope equipped with a Multi-channel Subtractive Double Pass imaging spectrograph. Lower limits of magnetic fields channeling observed plasma flows were estimated under assumption of the equipartition principle. Assuming approximate electron densities of the plasma n_e = 5*10^{11} cm^{-3} in surges and n_e = 5*10^{10} cm^{-3} in quiescent/activated prominences, we found that the magnetic fields channeling two observed surges range from 16 to 40 Gauss, while in quiescent and activated prominences they were less than 10 Gauss. Our results are consistent with previous detections of weak local magnetic fields in the solar prominences.Comment: 14 pages, 12 figures, 1 tabl

Solar science with the Atacama Large Millimeter/submillimeter Array - A new view of our Sun

The Atacama Large Millimeter/submillimeter Array (ALMA) is a new powerful tool for observing the Sun at high spatial, temporal, and spectral resolution. These capabilities can address a broad range of fundamental scientific questions in solar physics. The radiation observed by ALMA originates mostly from the chromosphere - a complex and dynamic region between the photosphere and corona, which plays a crucial role in the transport of energy and matter and, ultimately, the heating of the outer layers of the solar atmosphere. Based on first solar test observations, strategies for regular solar campaigns are currently being developed. State-of-the-art numerical simulations of the solar atmosphere and modeling of instrumental effects can help constrain and optimize future observing modes for ALMA. Here we present a short technical description of ALMA and an overview of past efforts and future possibilities for solar observations at submillimeter and millimeter wavelengths. In addition, selected numerical simulations and observations at other wavelengths demonstrate ALMA's scientific potential for studying the Sun for a large range of science cases.Comment: 73 pages, 21 figures ; Space Science Reviews (accepted December 10th, 2015); accepted versio

The Rho-Family GTPase Rac1 Regulates Integrin Localization in Drosophila Immunosurveillance Cells

BACKGROUND: When the parasitoid wasp Leptopilina boulardi lays an egg in a Drosophila larva, phagocytic cells called plasmatocytes and specialized cells known as lamellocytes encapsulate the egg. The Drosophila β-integrin Myospheroid (Mys) is necessary for lamellocytes to adhere to the cellular capsule surrounding L. boulardi eggs. Integrins are heterodimeric adhesion receptors consisting of α and β subunits, and similar to other plasma membrane receptors undergo ligand-dependent endocytosis. In mammalian cells it is known that integrin binding to the extracellular matrix induces the activation of Rac GTPases, and we have previously shown that Rac1 and Rac2 are necessary for a proper encapsulation response in Drosophila larvae. We wanted to test the possibility that Myospheroid and Rac GTPases interact during the Drosophila anti-parasitoid immune response. RESULTS: In the current study we demonstrate that Rac1 is required for the proper localization of Myospheroid to the cell periphery of haemocytes after parasitization. Interestingly, the mislocalization of Myospheroid in Rac1 mutants is rescued by hyperthermia, involving the heat shock protein Hsp83. From these results we conclude that Rac1 and Hsp83 are required for the proper localization of Mys after parasitization. SIGNIFICANCE: We show for the first time that the small GTPase Rac1 is required for Mysopheroid localization. Interestingly, the necessity of Rac1 in Mys localization was negated by hyperthermia. This presents a problem, in Drosophila we quite often raise larvae at 29°C when using the GAL4/UAS misexpression system. If hyperthermia rescues receptor endosomal recycling defects, raising larvae in hyperthermic conditions may mask potentially interesting phenotypes

An improved parameter estimation and comparison for soft tissue constitutive models containing an exponential function

Motivated by the well-known result that stiffness of soft tissue is proportional to the stress, many of the constitutive laws for soft tissues contain an exponential function. In this work, we analyze properties of the exponential function and how it affects the estimation and comparison of elastic parameters for soft tissues. In particular, we find that as a consequence of the exponential function there are lines of high covariance in the elastic parameter space. As a result, one can have widely varying mechanical parameters defining the tissue stiffness but similar effective stress–strain responses. Drawing from elementary algebra, we propose simple changes in the norm and the parameter space, which significantly improve the convergence of parameter estimation and robustness in the presence of noise. More importantly, we demonstrate that these changes improve the conditioning of the problem and provide a more robust solution in the case of heterogeneous material by reducing the chances of getting trapped in a local minima. Based upon the new insight, we also propose a transformed parameter space which will allow for rational parameter comparison and avoid misleading conclusions regarding soft tissue mechanics