Silencing of ATP Synthase ß Impairs Egg Development in the Leafhopper Scaphoideus titanus, Vector of the Phytoplasma Associated with Grapevine Flavescence Dorée.

Scaphoideus titanus (Hemiptera: Cicadellidae) is the natural vector of Flavescence dorée phytoplasma, a quarantine pest of grapevine with severe impact on European viticulture. RNA interference (RNAi) machinery components are present in S. titanus transcriptome and injection of ATP synthase ß dsRNAs into adults caused gene silencing, starting three days post injection (dpi) up to 20 dpi, leading to decrease cognate protein. Silencing of this gene in the closely related leafhopper Euscelidiusvariegatus previously showed female sterility and lack of mature eggs in ovaries. Here, alteration of developing egg morphology in S. titanus ovaries as well as overexpression of hexamerin transcript (amino acid storage protein) and cathepsin L protein (lysosome proteinase) were observed in dsATP-injected females. To evaluate RNAi-specificity, E.variegatus was used as dsRNA-receiving model-species. Different doses of two sets of dsRNA-constructs targeting distinct portions of ATP synthase ß gene of both species induced silencing, lack of egg development, and female sterility in E. variegatus, indicating that off-target effects must be evaluated case by case. The effectiveness of RNAi in S. titanus provides a powerful tool for functional genomics of this non-model species and paves the way toward RNAi-based strategies to limit vector population, despite several technical and regulatory constraints that still need to be overcome to allow open field application.

Pollination features and floral volatiles of Gymnospermium scipetarum (Berberidaceae).

The discovery of few isolated populations of Gymnospermium scipetarum (since now considered as an amphi-Adriatic endemic) in the S-Apennines prompted to investigate, also for conservation purposes, some aspects of its reproductive biology. We aim: (1) to determine if insects play an important role in pollination; (2) to describe the pollinator community; (3) to detect floral scent composition. Experiments of insect exclusion were carried out in the field using 24 flowering individuals: one raceme was capped whereas the nearest one was used as control to ascertain differences in seed set. Pollinator community was detected during the blooming phase of two consecutive flowering seasons by visual observation; insect identification was made at the highest possible taxonomic resolution with the help of digital photographs. In order to determine the chemical composition of the volatiles, we used SPME sampling of cultivated plants. Mann-Whitney U test reveals significant differences for treatment in mean seed set with very low values for capped flowers, thus clearly indicating as insects are crucial for successful pollination. During the 42 h of observations we detected 326 visitors belonging to only three guilds: 79% were Diptera, 20% Hymenoptera and 1% Coleoptera. We identified overall 36 floral organic compounds with only two compounds common to the other studied Berberidaceae. Ambrox was never identified before in the floral scents of any angiosperm. The presence in the scent of several aldehydes and one ketone (benzophenone) could be related to the detected dominance of muscoid flies as pollinators. Floral morphology and composition of the pollinators community indicate a generalist pollination behaviour probably related to its phenology and habitat preference. The possibility of being pollinated also by muscoid flies can be considered an advantage for the reproductive fitness of the species, since these Diptera are abundant in the mountain pastures surrounding the forest habitat of Gymnospermium.

Bimodal behaviour of interfollicular epidermal progenitors regulated by hair follicle position and cycling.

Interfollicular epidermal (IFE) homeostasis is a major physiological process allowing maintenance of the skin barrier function. Despite progress in our understanding of stem cell populations in different hair follicle compartments, cellular mechanisms of IFE maintenance, in particular, whether a hierarchy of progenitors exists within this compartment, have remained controversial. We here used multicolour lineage tracing with Brainbow transgenic labels activated in the epidermis to track individual keratinocyte clones. Two modes of clonal progression could be observed in the adult murine dorsal skin. Clones attached to hair follicles showed rapid increase in size during the growth phase of the hair cycle. On the other hand, clones distant from hair follicles were slow cycling, but could be mobilized by a proliferative stimulus. Reinforced by mathematical modelling, these data support a model where progenitor cycling characteristics are differentially regulated in areas surrounding or away from growing hair follicles. Thus, while IFE progenitors follow a non-hierarchical mode of development, spatiotemporal control by their environment can change their potentialities, with far-reaching implications for epidermal homeostasis, wound repair and cancer development.

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.

BACKGROUND: A rapidly growing amount of knowledge about signaling and gene regulatory networks is available in databases such as KEGG, Reactome, or RegulonDB. There is an increasing need to relate this knowledge to high-throughput data in order to (in)validate network topologies or to decide which interactions are present or inactive in a given cell type under a particular environmental condition. Interaction graphs provide a suitable representation of cellular networks with information flows and methods based on sign consistency approaches have been shown to be valuable tools to (i) predict qualitative responses, (ii) to test the consistency of network topologies and experimental data, and (iii) to apply repair operations to the network model suggesting missing or wrong interactions. RESULTS: We present a framework to unify different notions of sign consistency and propose a refined method for data discretization that considers uncertainties in experimental profiles. We furthermore introduce a new constraint to filter undesired model behaviors induced by positive feedback loops. Finally, we generalize the way predictions can be made by the sign consistency approach. In particular, we distinguish strong predictions (e.g. increase of a node level) and weak predictions (e.g., node level increases or remains unchanged) enlarging the overall predictive power of the approach. We then demonstrate the applicability of our framework by confronting a large-scale gene regulatory network model of Escherichia coli with high-throughput transcriptomic measurements. CONCLUSION: Overall, our work enhances the flexibility and power of the sign consistency approach for the prediction of the behavior of signaling and gene regulatory networks and, more generally, for the validation and inference of these networks.

Tactile interactions lead to coherent motion and enhanced chemotaxis of migrating cells.

When motile cells come into contact with one another their motion is often considerably altered. In a process termed contact inhibition of locomotion (CIL) cells reshape and redirect their movement as a result of cell-cell contact. Here we describe a mathematical model that demonstrates that CIL alone is sufficient to produce coherent, collective cell migration. Our model illustrates a possible mechanism behind collective cell migration that is observed, for example, in neural crest cells during development, and in metastasizing cancer cells. We analyse the effects of varying cell density and shape on the alignment patterns produced and the transition to coherent motion. Finally, we demonstrate that this process may have important functional consequences by enhancing the accuracy and robustness of the chemotactic response, and factors such as cell shape and cell density are more significant determinants of migration accuracy than the individual capacity to detect environmental gradients.

Mathematical model for growth regulation of fission yeast Schizosaccharomyces pombe.

Regulation of polarised cell growth is essential for many cellular processes including spatial coordination of cell morphology changes during the division cycle. We present a mathematical model of the core mechanism responsible for the regulation of polarised growth dynamics during the fission yeast cell cycle. The model is based on the competition of growth zones localised at the cell tips for a common substrate distributed uniformly in the cytosol. We analyse the bifurcations in this model as the cell length increases, and show that the growth activation dynamics provides an explanation for the new-end take-off (NETO) as a saddle-node bifurcation at which the cell sharply switches from monopolar to bipolar growth. We study the parameter sensitivity of the bifurcation diagram and relate qualitative changes of the growth pattern, e.g. delayed or absent NETO, to previously observed mutant phenotypes. We investigate the effects of imperfect asymmetric cell division, and show that this leads to distinct growth patterns that provide experimentally testable predictions for validating the presented competitive growth zone activation model. Finally we discuss extension of the model for describing mutant cells with more than two growth zones.

Differential gene expression regulated by oscillatory transcription factors.

Cells respond to changes in the internal and external environment by a complex regulatory system whose end-point is the activation of transcription factors controlling the expression of a pool of ad-hoc genes. Recent experiments have shown that certain stimuli may trigger oscillations in the concentration of transcription factors such as NF-κB and p53 influencing the final outcome of the genetic response. In this study we investigate the role of oscillations in the case of three different well known gene regulatory mechanisms using mathematical models based on ordinary differential equations and numerical simulations. We considered the cases of direct regulation, two-step regulation and feed-forward loops, and characterized their response to oscillatory input signals both analytically and numerically. We show that in the case of indirect two-step regulation the expression of genes can be turned on or off in a frequency dependent manner, and that feed-forward loops are also able to selectively respond to the temporal profile of oscillating transcription factors.

Integrating multiple signals into cell decisions by networks of protein modification cycles.

Posttranslational protein modifications play a key role in regulating cellular processes. We present a general model of reversible protein modification networks and demonstrate that a single protein modified by several enzymes is capable of integrating multiple signals into robust digital decisions by switching between multiple forms that can activate distinct cellular processes. First we consider two competing protein modification cycles and show that in the saturated regime, the protein is concentrated into a single form determined by the enzyme activities. We generalize this to protein modification networks with tree structure controlled by multiple enzymes that can be characterized by their phase diagram, which is a partition of the space of enzyme activities into regions corresponding to different dominant forms. We show that the phase diagram can be obtained analytically from the wiring diagram of the modification network by recursively solving a set of balance equations for the steady-state distributions and then applying a positivity condition to determine the regions corresponding to different responses. We also implement this method in a computer algebra system that automatically generates the phase diagram as a set of inequalities. Based on this theoretical framework, we determine some general properties of protein modification systems.

MicroRNA-155 promotes resolution of hypoxia-inducible factor 1alpha activity during prolonged hypoxia.

The hypoxia-inducible factor (HIF) is a key regulator of the transcriptional response to hypoxia. While the mechanism underpinning HIF activation is well understood, little is known about its resolution. Both the protein and the mRNA levels of HIF-1α (but not HIF-2α) were decreased in intestinal epithelial cells exposed to prolonged hypoxia. Coincident with this, microRNA (miRNA) array analysis revealed multiple hypoxia-inducible miRNAs. Among these was miRNA-155 (miR-155), which is predicted to target HIF-1α mRNA. We confirmed the hypoxic upregulation of miR-155 in cultured cells and intestinal tissue from mice exposed to hypoxia. Furthermore, a role for HIF-1α in the induction of miR-155 in hypoxia was suggested by the identification of hypoxia response elements in the miR-155 promoter and confirmed experimentally. Application of miR-155 decreased the HIF-1α mRNA, protein, and transcriptional activity in hypoxia, and neutralization of endogenous miR-155 reversed the resolution of HIF-1α stabilization and activity. Based on these data and a mathematical model of HIF-1α suppression by miR-155, we propose that miR-155 induction contributes to an isoform-specific negative-feedback loop for the resolution of HIF-1α activity in cells exposed to prolonged hypoxia, leading to oscillatory behavior of HIF-1α-dependent transcription.