The physics of twisted magnetic tubes rising in a stratified medium: two dimensional results

The physics of a twisted magnetic flux tube rising in a stratified medium is studied using a numerical MHD code. The problem considered is fully compressible (no Boussinesq approximation), includes ohmic resistivity, and is two dimensional, i.e., there is no variation of the variables in the direction of the tube axis. We study a high plasma beta case with small ratio of radius to external pressure scaleheight. The results obtained can therefore be of relevance to understand the transport of magnetic flux across the solar convection zone.Comment: To be published in ApJ, Vol. 492, Jan 10th, 1998; 25 pages, 16 figures. NEW VERSION: THE PREVIOUS ONE DIDN'T PRINT CORRECTLY. The style file overrulehere.sty is include

The importance of strigolactone transport regulation for symbiotic signaling and shoot branching.

This review presents the role of strigolactone transport in regulating plant root and shoot architecture, plant-fungal symbiosis and the crosstalk with several phytohormone pathways. The authors, based on their data and recently published results, suggest that long-distance, as well local strigolactone transport might occur in a cell-to-cell manner rather than via the xylem stream. Strigolactones (SLs) are recently characterized carotenoid-derived phytohormones. They play multiple roles in plant architecture and, once exuded from roots to soil, in plant-rhizosphere interactions. Above ground SLs regulate plant developmental processes, such as lateral bud outgrowth, internode elongation and stem secondary growth. Below ground, SLs are involved in lateral root initiation, main root elongation and the establishment of the plant-fungal symbiosis known as mycorrhiza. Much has been discovered on players and patterns of SL biosynthesis and signaling and shown to be largely conserved among different plant species, however little is known about SL distribution in plants and its transport from the root to the soil. At present, the only characterized SL transporters are the ABCG protein PLEIOTROPIC DRUG RESISTANCE 1 from Petunia axillaris (PDR1) and, in less detail, its close homologue from Nicotiana tabacum PLEIOTROPIC DRUG RESISTANCE 6 (PDR6). PDR1 is a plasma membrane-localized SL cellular exporter, expressed in root cortex and shoot axils. Its expression level is regulated by its own substrate, but also by the phytohormone auxin, soil nutrient conditions (mainly phosphate availability) and mycorrhization levels. Hence, PDR1 integrates information from nutrient availability and hormonal signaling, thus synchronizing plant growth with nutrient uptake. In this review we discuss the effects of PDR1 de-regulation on plant development and mycorrhization, the possible cross-talk between SLs and other phytohormone transporters and finally the need for SL transporters in different plant species

Numerical Experiments on the Two-step Emergence of Twisted Magnetic Flux Tubes in the Sun

We present the new results of the two-dimensional numerical experiments on the cross-sectional evolution of a twisted magnetic flux tube rising from the deeper solar convection zone (-20,000 km) to the corona through the surface. The initial depth is ten times deeper than most of previous calculations focusing on the flux emergence from the uppermost convection zone. We find that the evolution is illustrated by the two-step process described below: the initial tube rises due to its buoyancy, subject to aerodynamic drag due to the external flow. Because of the azimuthal component of the magnetic field, the tube maintains its coherency and does not deform to become a vortex roll pair. When the flux tube approaches the photosphere and expands sufficiently, the plasma on the rising tube accumulates to suppress the tube's emergence. Therefore, the flux decelerates and extends horizontally beneath the surface. This new finding owes to our large scale simulation calculating simultaneously the dynamics within the interior as well as above the surface. As the magnetic pressure gradient increases around the surface, magnetic buoyancy instability is triggered locally and, as a result, the flux rises further into the solar corona. We also find that the deceleration occurs at a higher altitude than in our previous experiment using magnetic flux sheets (Toriumi and Yokoyama). By conducting parametric studies, we investigate the conditions for the two-step emergence of the rising flux tube: field strength > 1.5x10^4 G and the twist > 5.0x10^-4 km^-1 at -20,000 km depth.Comment: 42 pages, 13 figures, 2 tables, accepted for publication in ApJ. High-resolution figures will appear in the published versio

Relationship between cellular response and behavioral variability in bacterial chemotaxis

Bacterial chemotaxis in Escherichia coli is a canonical system for the study of signal transduction. A remarkable feature of this system is the coexistence of precise adaptation in population with large fluctuating cellular behavior in single cells (Korobkova et al. 2004, Nature, 428, 574). Using a stochastic model, we found that the large behavioral variability experimentally observed in non-stimulated cells is a direct consequence of the architecture of this adaptive system. Reversible covalent modification cycles, in which methylation and demethylation reactions antagonistically regulate the activity of receptor-kinase complexes, operate outside the region of first-order kinetics. As a result, the receptor-kinase that governs cellular behavior exhibits a sigmoidal activation curve. This curve simultaneously amplifies the inherent stochastic fluctuations in the system and lengthens the relaxation time in response to stimulus. Because stochastic fluctuations cause large behavioral variability and the relaxation time governs the average duration of runs in response to small stimuli, cells with the greatest fluctuating behavior also display the largest chemotactic response. Finally, Large-scale simulations of digital bacteria suggest that the chemotaxis network is tuned to simultaneously optimize the random spread of cells in absence of nutrients and the cellular response to gradients of attractant.Comment: 15 pages, 4 figures, Supporting information available here http://cluzel.uchicago.edu/data/emonet/arxiv_070531_supp.pd

Increased Immune Response Variability during Simultaneous Viral Coinfection Leads to Unpredictability in CD8 T Cell Immunity and Pathogenesis

T cell memory is usually studied in the context of infection with a single pathogen in naive mice, but how memory develops during a coinfection with two pathogens, as frequently occurs in nature or after vaccination, is far less studied. Here, we questioned how the competition between immune responses to two viruses in the same naive host would influence the development of CD8 T cell memory and subsequent disease outcome upon challenge. Using two different models of coinfection, including the well-studied lymphocytic choriomeningitis (LCMV) and Pichinde (PICV) viruses, several differences were observed within the CD8 T cell responses to either virus. Compared to single-virus infection, coinfection resulted in substantial variation among mice in the size of epitope-specific T cell responses to each virus. Some mice had an overall reduced number of virus-specific cells to either one of the viruses, and other mice developed an immunodominant response to a normally subdominant, cross-reactive epitope (nucleoprotein residues 205 to 212, or NP205). These changes led to decreased protective immunity and enhanced pathology in some mice upon challenge with either of the original coinfecting viruses. In mice with PICV-dominant responses, during a high-dose challenge with LCMV clone 13, increased immunopathology was associated with a reduced number of LCMV-specific effector memory CD8 T cells. In mice with dominant cross-reactive memory responses, during challenge with PICV increased immunopathology was directly associated with these cross-reactive NP205-specific CD8 memory cells. In conclusion, the inherent competition between two simultaneous immune responses results in significant alterations in T cell immunity and subsequent disease outcome upon reexposure. IMPORTANCE: Combination vaccines and simultaneous administration of vaccines are necessary to accommodate required immunizations and maintain vaccination rates. Antibody responses generally correlate with protection and vaccine efficacy. However, live attenuated vaccines also induce strong CD8 T cell responses, and the impact of these cells on subsequent immunity, whether beneficial or detrimental, has seldom been studied, in part due to the lack of known T cell epitopes to vaccine viruses. We questioned if the inherent increased competition and stochasticity between two immune responses during a simultaneous coinfection would significantly alter CD8 T cell memory in a mouse model where CD8 T cell epitopes are clearly defined. We show that some of the coinfected mice have sufficiently altered memory T cell responses that they have decreased protection and enhanced immunopathology when reexposed to one of the two viruses. These data suggest that a better understanding of human T cell responses to vaccines is needed to optimize immunization strategies

Use of Treponema pallidum PCR in Testing of Ulcers for Diagnosis of Primary Syphilis(1.).

Treponema pallidum PCR (Tp-PCR) has been noted as a valid method for diagnosing syphilis. We compared Tp-PCR to a combination of darkfield microscopy (DFM), the reference method, and serologic testing in a cohort of 273 patients from France and Switzerland and found the diagnostic accuracy of Tp-PCR was higher than that for DFM

Approche méthodologique de la modélisation du transport des HAP dans les sols et les eaux

Afin de préciser le cadre d'utilisation de codes de transport de polluants dans les sols et les eaux, un programme d'intercomparaison de méthodes et de codes a été mis en oeuvre avec la collaboration de huit équipes appartenant à des instituts de recherche ou des bureaux d'études. Parmi les types de polluants étudiés, les hydrocarbures aromatiques polycycliques (HAP) ont fait l'objet de simulations par deux groupes de travail. Le premier groupe, composé de cinq équipes, s'est intéressé à leur comportement en phase dissoute à partir d'un cas réel de pollution. Disposant des mêmes données d'étude, chaque équipe avait pour mission de concevoir un modèle conceptuel (description géologique, définition de la source, paramètres d'écoulement et de transport) et de simuler la pollution de la nappe avec le code de son choix. Les résultats obtenus montrent des différences significatives qui trouvent leur explication dans les paramètres des modèles conceptuels adoptés plus que dans les simulateurs choisis. Cet exercice a confirmé l'importance des paramètres suivants qui sont souvent incertains mais justifieraient d'être mieux appréciés lors de diagnostics : paramètres hydrodynamiques (détermination du champ de vitesse), coefficient de partition (pour chaque horizon géologique), temps de demi-vie du ou des polluants, extension de la source de pollution. Le second groupe a étudié les écoulements en phase libre (phase liquide non aqueuse) sur un cas théorique inspiré d'un cas réel de déversement massif de naphtalène. La modélisation a été conduite par trois équipes avec trois codes polyphasiques différents (SIMUSCOPP, TOUGH/T2VOC, UTCHEM). Cet exercice comprend le suivi du déversement et de la migration du naphtalène sous formes liquide et dissoute sur une distance de 300 m et une durée de 10 ans. Le naphtalène révèle un comportement d'hydrocarbure " lourd " avec une phase huile (partiellement miscible) qui tend à descendre à travers la nappe. Ce comportement a été reproduit par chacune des équipes, de manière plus ou moins complète en fonction des possibilités de modélisation offertes par les codes. Les résultats obtenus permettent de vérifier la cohérence des différentes approches polyphasiques entre elles. Bien que plus complexe (paramètres plus nombreux, difficulté numérique accrue), l'approche polyphasique se justifie pour mieux comprendre et déterminer la répartition spatiale de HAP en profondeur dans une nappe

Feedback control architecture and the bacterial chemotaxis network.

PMCID: PMC3088647This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to 'reset' (adapt) the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a 'cascade control' feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance

3D MHD Flux Emergence Experiments: Idealized models and coronal interactions

This paper reviews some of the many 3D numerical experiments of the emergence of magnetic fields from the solar interior and the subsequent interaction with the pre-existing coronal magnetic field. The models described here are idealized, in the sense that the internal energy equation only involves the adiabatic, Ohmic and viscous shock heating terms. However, provided the main aim is to investigate the dynamical evolution, this is adequate. Many interesting observational phenomena are explained by these models in a self-consistent manner.Comment: Review article, accepted for publication in Solar Physic

Toward a comprehensive language for biological systems

Rule-based modeling has become a powerful approach for modeling intracellular networks, which are characterized by rich molecular diversity. Truly comprehensive models of cell behavior, however, must address spatial complexity at both the intracellular level and at the level of interacting populations of cells, and will require richer modeling languages and tools. A recent paper in BMC Systems Biology represents a signifcant step toward the development of a unified modeling language and software platform for the development of multi-level, multiscale biological models