Writ large: Genomic dissection of the effect of cellular environment on immune response

Cells of the immune system routinely respond to cues from their local environment and feed back to their surroundings through transient responses, choice of differentiation trajectories, plastic changes in cell state, and malleable adaptation to their tissue of residence. Genomic approaches have opened the way for comprehensive interrogation of such orchestrated responses. Focusing on genomic profiling of transcriptional and epigenetic cell states, we discuss how they are applied to investigate immune cells faced with various environmental cues. We highlight some of the emerging principles on the role of dense regulatory circuitry, epigenetic memory, cell type fluidity, and reuse of regulatory modules in achieving and maintaining appropriate responses to a changing environment.These provide a first step toward a systematic understanding of molecular circuits in complex tissues

Trunk Refugia : A Simple, Inexpensive Method for Sampling Tree Trunk Arthropods

Trees host a large share of the global arthropod diversity. Several methodologies have been described to sample arthropods from trees, ranging from active sampling techniques (e.g., visual searching, beating, or shaking the branches) to passive sampling devices. The majority of these collection techniques are destructive, and do not specifically target the tree trunk arthropod fauna. Here, we describe an alternative sampling method called trunk refugia (TR). TR are cylindrical shelters made of corrugated cardboard that can be secured to trees using string, and can remain exposed for varying time periods. These refugia are inexpensive, easy to use, and suitable to monitor a diverse array of insects and arachnids. Moreover, TR are nonlethal sampling tools, and allow collecting live individuals for behavioral studies or for rearing.RESUMEN: Los árboles albergan una gran parte de la diversidad global de artrópodos. Varias metodologías han sido descritas para muestrear artrópodos de árboles, desde técnicas activas (e.g., búsqueda visual, red de golpeo) hasta dispositivos de muestreo pasivo. La mayoría de estas técnicas son letales, y no están dirigidas específicamente a los artrópodos de troncos de árboles. Describimos aquí un método alternativo llamado trampas refugio (TR). Las TR son refugios hechos de cartón corrugado que se colocan en los troncos usando cuerda, y pueden permanecer expuestos por períodos variables. Estas trampas son económicas, fáciles de usar, y apropiadas para monitorear una gran variedad de insectos y arácnidos. Además, las TR son no-letales, por lo que permiten la colección de individuos vivos para estudios de comportamiento o crianza.Jacob Blaustein Center for Scientific Cooperation; Israel Nature and Parks Authorities (INPA); Israel's National Nature Assessment Program (HAMAARAG); Israel Ministry of Agriculture (131-1793-14)info:eu-repo/semantics/publishedVersio

Herpesviruses shape tumour microenvironment through exosomal transfer of viral microRNAs

Metabolic changes within the cell and its niche affect cell fate and are involved in many diseases and disorders including cancer and viral infections. Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi's sarcoma (KS). KSHV latently infected cells express only a subset of viral genes, mainly located within the latency-associated region, among them 12 microRNAs. Notably, these miRNAs are responsible for inducing the Warburg effect in infected cells. Here we identify a novel mechanism enabling KSHV to manipulate the metabolic nature of the tumour microenvironment. We demonstrate that KSHV infected cells specifically transfer the virus-encoded microRNAs to surrounding cells via exosomes. This flow of genetic information results in a metabolic shift toward aerobic glycolysis in the surrounding non-infected cells. Importantly, this exosome-mediated metabolic reprogramming of neighbouring cells supports the growth of infected cells, thereby contributing to viral fitness. Finally, our data show that this miRNA transfer-based regulation of cell metabolism is a general mechanism used by other herpesviruses, such as EBV, as well as for the transfer of non-viral onco-miRs. This exosome-based crosstalk provides viruses with a mechanism for non-infectious transfer of genetic material without production of new viral particles, which might expose them to the immune system. We suggest that viruses and cancer cells use this mechanism to shape a specific metabolic niche that will contribute to their fitness

Impact assessment of the biological control of the cassava mealybug, Phenacoccus manihoti Matile-Ferrero (Hemiptera: Pseudococcidae), by the introduced parasitoid Epidinocarsis lopezi (De Santis) (Hymenoptera: Encyrtidae)

The impact of Phenacoccus manihoti Matile-Ferrero on growth and tuber yield of cassava, and the results of its biological control by the exotic parasitoid Epidinocarsis lopezi (De Santis) were investigated in a survey of 60 farmers' fields in Ghana and Ivory Coast over an area of 180 000 km2 of the savana and forest ecosystems. Twenty-nine variables associated with plant growth, agronomic and environmental factors, and insect populations were recorded. Densities of P. manihoti were closely correlated with stunting of the cassava shoot tips and, less so, with the rate of stunting early in the growing season. With increasing mealybug infestations, average harvest indices declined and populations of E. lopezi and of indigenous coccinellids increased, but parasitoids were found at lower host levels than were predators. The length of time E. lopezi had been present in an area was the most important factor influencing mealybug densities. Thus, P. manihoti populations were significantly lower where E. lopezi had been present for more than half the planting season than in areas where E. lopezi was lacking or had been only recently introduced. A significant proportion of the farmers in the savanna zone, where P. manihoti populations were much higher than in the forest zone, had observed this decline due to E. lopezi. Tuber yield losses due to P. manihoti in the absence of E. lopezi were tentatively estimated at 463 g/plant in the savanna zone. No significant effect was found in the forest region. When E. lopezi was present, average P. manihoti damage scores were reduced significantly, both in the savanna and forest regions. The increase in yields was 228g/plant or about 2.48 t/ha in the savanna regio

Magnetically Torqued Thin Accretion Disks

We compute the properties of a geometrically thin, steady accretion disk surrounding a central rotating, magnetized star. The magnetosphere is assumed to entrain the disk over a wide range of radii. The model is simplified in that we adopt two (alternate) ad hoc, but plausible, expressions for the azimuthal component of the magnetic field as a function of radial distance. We find a solution for the angular velocity profile tending to corotation close to the central star, and smoothly matching a Keplerian curve at a radius where the viscous stress vanishes. The value of this ''transition'' radius is nearly the same for both of our adopted B-field models. We then solve analytically for the torques on the central star and for the disk luminosity due to gravity and magnetic torques. When expressed in a dimensionless form, the resulting quantities depend on one parameter alone, the ratio of the transition radius to the corotation radius. For rapid rotators, the accretion disk may be powered mostly by spin-down of the central star. These results are independent of the viscosity prescription in the disk. We also solve for the disk structure for the special case of an optically thick alpha disk. Our results are applicable to a range of astrophysical systems including accreting neutron stars, intermediate polar cataclysmic variables, and T Tauri systems.Comment: 9 sharper figs, updated reference

Biochemical Reaction Rules with Constraints

International audienceWe propose React(C), an expressive programming language for stochastic modeling and simulation in systems biology, that is based on biochemical reactions with constraints. We prove that React(C) can express the stochastic pi-calculus, in contrast to previous rule-based programming languages, and further illustrate the high expressiveness of React(C). We present a stochastic simulator for React(C) independently of the choice of the constraint language C. Our simulator must decide for a given reaction rule whether it can be applied to the current biochemical solution. We show that this decision problem is NP-complete for arbitrary constraint systems C, and that it can be solved in polynomial time for rules of bounded arity. In practice, we propose to solve this problem by constraint programming

Process algebra modelling styles for biomolecular processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed

Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway.

BACKGROUND: Appropriately formulated quantitative computational models can support researchers in understanding the dynamic behaviour of biological pathways and support hypothesis formulation and selection by "in silico" experimentation. An obstacle to widespread adoption of this approach is the requirement to formulate a biological pathway as machine executable computer code. We have recently proposed a novel, biologically intuitive, narrative-style modelling language for biologists to formulate the pathway which is then automatically translated into an executable format and is, thus, usable for analysis via existing simulation techniques. RESULTS: Here we use a high-level narrative language in designing a computational model of the gp130/JAK/STAT signalling pathway and show that the model reproduces the dynamic behaviour of the pathway derived by biological observation. We then "experiment" on the model by simulation and sensitivity analysis to define those parameters which dominate the dynamic behaviour of the pathway. The model predicts that nuclear compartmentalisation and phosphorylation status of STAT are key determinants of the pathway and that alternative mechanisms of signal attenuation exert their influence on different timescales. CONCLUSION: The described narrative model of the gp130/JAK/STAT pathway represents an interesting case study showing how, by using this approach, researchers can model biological systems without explicitly dealing with formal notations and mathematical expressions (typically used for biochemical modelling), nevertheless being able to obtain simulation and analysis results. We present the model and the sensitivity analysis results we have obtained, that allow us to identify the parameters which are most sensitive to perturbations. The results, which are shown to be in agreement with existing mathematical models of the gp130/JAK/STAT pathway, serve us as a form of validation of the model and of the approach itself

Survey on nonlocal games and operator space theory

This review article is concerned with a recently uncovered connection between operator spaces, a noncommutative extension of Banach spaces, and quantum nonlocality, a striking phenomenon which underlies many of the applications of quantum mechanics to information theory, cryptography, and algorithms. Using the framework of nonlocal games, we relate measures of the nonlocality of quantum mechanics to certain norms in the Banach and operator space categories. We survey recent results that exploit this connection to derive large violations of Bell inequalities, study the complexity of the classical and quantum values of games and their relation to Grothendieck inequalities, and quantify the nonlocality of different classes of entangled states