Analysis of IL6 Signal Transduction Model using Reduced Rank Regression

This work presents the application of reduced rank regression to the field of systems biology. A computational approach is used to investigate the mechanisms of the janus-associated kinases/signal transducers and transcription factors (JAK/STAT) and mitogen activated protein kinases (MAPK) signal transduction pathways in hepatic cells stimulated by interleukin-6. The results obtained identify the contribution of individual reactions to the dynamics of the model. These findings are compared to previously available results from sensitivity analysis of the model which focused on the parameters involved and their effect. This application of reduced rank regression allows for an understanding of the individual reaction terms involved in the modelled signal transduction pathways and has the benefit of being computationally inexpensive. The obtained results complement existing findings and also confirm the importance of several protein complexes in the MAPK pathway which hints at benefits that can be achieved by further refining the model.

A co-operative formation-based collision avoidance approach for a group of autonomous vehicles (Special Issue on Adaptive Control and Signal Processing in Marine System)

This paper employs a unique decentralised cooperative control method to realise a formation-based collision avoidance strategy for a group of autonomous vehicles. In this approach, the vehicles' role in the formation and their alert and danger areas are first defined, and the formation-based intra-group and external collision avoidance methods are then proposed to translate the collision avoidance problem into the formation stability problem. The extension–decomposition–aggregation formation control method is next employed to stabilise the original and modified formations, whilst manoeuvring, and subsequently solve their collision avoidance problem indirectly. Simulation study verifies the feasibility and effectiveness of the intra-group and external collision avoidance strategy. It is demonstrated that both formation control and collision avoidance problems can be simultaneously solved if the stability of the expanded formation including external obstacles can be satisfied.

Binding of Lassa virus perturbs extracellular matrix-induced signal transduction via dystroglycan.

The arenavirus Lassa virus (LASV) causes a severe haemorrhagic fever with high mortality in man. The cellular receptor for LASV is dystroglycan (DG). DG is a ubiquitous receptor for extracellular matrix (ECM) proteins, which cooperates with β1 integrins to control cell-matrix interactions. Here, we investigated whether LASV binding to DG triggers signal transduction, mimicking the natural ligands. Engagement of DG by LASV resulted in the recruitment of the adaptor protein Grb2 and the protein kinase MEK1 by the cytoplasmic domain of DG without activating the MEK/ERK pathway, indicating assembly of an inactive signalling complex. LASV binding to cells however affected the activation of the MEK/ERK pathway via α6β1 integrins. The virus-induced perturbation of α6β1 integrin signalling critically depended on high-affinity LASV binding to DG and DG's cytoplasmic domain, indicating that LASV-receptor binding perturbed signalling cross-talk between DG and β1 integrins.

Molekularbiologische Funktionsanalysen von Thioredoxinen aus Dictyostelium discoideum und Identifizierung neuer Interaktionspartner durch das Two-Hybrid-System

Thioredoxins are small, regulatory proteins with a mass of approximately 12 kDa and a characteristic conserved active center, which is represented in the pentapeptide trp-cys-gly-pro-cys. Up to now it is not possible to present a complete list of thioredoxin interaction partners because there is no predictable sequence in the target enzymes where thioredoxins can interact with. To get closer information about the functions and possible interaction partners of the three thioredoxins from the social soil amoeba Dictyostelium discoideum (DdTrx1 - 3) we have chosen two different strategies. In the first one the thioredoxin levels in the cell should changed by different mutants. But both the antisense technique as well as the creation of knock out mutants were not appropiate strategies in this case. Just an thioredoxin overexpressing mutant results in a developmental phenotype which allows some conclusions for possible functions of the thioredoxin in Dictyostelium discoideum. The second strategie was the two hybrid system where thioredoxin interactions partners can identified systematically. After a screening with a cDNA library from Dictyostelium 13 potential interaction partners could be detected, among them a ribonucleotid reductase, TRFA, two different cytochrome c oxidase subunits, filopodin, three ribosomal proteins, the elongationfactor 1a and the alcohol dehydrogenase from yeast. The verification of the interaction between thioredoxin and these two hybrid clones happened indirectly by a dobble mutant of thioredoxin 1, where the cysteines in the active center were replaced by redox-inactive serins. Further examinations of two choosen candidates resulted that the alcohol dehydrogenase from yeast is a thioredoxin-modululated enzym and that there is an interaction between the elongationfactor 1a and the thioredoxin 1 from Dictyostelium discoideum.

Electrophysiological analysis of the olfactory signal transduction cascade in the hawkmoth Manduca sexta

Neben der Verbreitung von gefährlichen Krankheiten sind Insekten für enorme agrarwirtschaftliche Schäden verantwortlich. Ein Großteil der Verhaltensweisen bei Insekten wird über den Geruchssinn gesteuert, der somit einen möglichen Angriffspunkt zur Bekämpfung von Schadinsekten darstellt. Hierzu ist es allerdings nötig, die Mechanismen der olfaktorischen Signalübertragung im Detail zu verstehen. Neben den duftstoffbindenden olfaktorischen Rezeptoren spielt hier auch ein konservierter Korezeptor (Orco) eine entscheidende Rolle. Inwieweit bei diesen Proteinen ionotrope bzw. metabotrope Prozesse involviert sind ist bislang nicht vollständig aufgeklärt. Um weitere Einzelheiten aufzuklären wurden daher Einzelsensillenableitungen am Tabakschwärmer Manduca sexta durchgeführt. Orco-Agonisten und Antagonisten wurden eingesetzt, um die Funktion des Korezeptors besser zu verstehen. Bei dem Einsatz des Orco-Agonisten VUAA1 konnte keine Verstärkung der Pheromonantworten bzw. eine Sensitivierung beobachtet werden, wie im Falle einer ionotropen Signalweiterleitung zu erwarten gewesen wäre. Ein ionotroper Signalweg über den OR/Orco-Komplex in M. sexta ist daher unwahrscheinlich. Der Orco-Antagonist OLC15 beeinflusste die gleichen Parameter wie VUAA1 und konnte die von VUAA1 generierte Spontanaktivität blocken. Daher ist es wahrscheinlich, dass dieser einen spezifischen Orco-Blocker darstellt. Sowohl VUAA1 als auch OLC15 hatten großen Effekt auf die langanhaltende Pheromonantwort, welches die Vermutung nahelegt, dass Orco modulierend auf die Sensitivität der Nervenzelle einwirkt. Von OLC15 abweichende Effekte durch die getesteten Amiloride HMA und MIA auf die Pheromonantwort lassen nicht auf eine spezifische Wirkung dieser Agenzien auf Orco schließen und zusätzliche Wirkorte sind anzunehmen. Um die These eines metabotropen Signalwegs zu überprüfen wurde ebenfalls der G-Protein-Blocker GDP-β-S eingesetzt. Alle Parameter der Pheromonantwort die innerhalb der ersten Millisekunden analysiert wurden wiesen eine Reduktion der Sensitivität auf. Im Gegensatz dazu hatte GDP-β-S keinen Effekt auf die langanhaltende Pheromonantwort. Somit scheint ausschließlich die schnelle Pheromonantwort über einen Ligand-bindenden G-Protein-gesteuerten Rezeptor gesteuert zu werden.

Functional significance of the signal transduction pathways Akt and Erk in ovarian follicles: in vitro and in vivo studies in cattle and sheep

BACKGROUND: The intracellular signalling mechanisms that regulate ovarian follicle development are unclear; however, we have recently shown differences in the Akt and Erk signalling pathways in dominant compared to subordinate follicles. The aim of this study was to investigate the effects of inhibiting Akt and Erk phosphorylation on IGF- and gonadotropin- stimulated granulosa and theca cell function in vitro, and on follicle development in vivo. METHODS: Bovine granulosa and theca cells were cultured for six days and stimulated with FSH and/or IGF, or LH in combination with PD98059 (Erk inhibitor) and/or LY294002 (Akt inhibitor) and their effect on cell number and hormone secretion (estradiol, activin-A, inhibin-A, follistatin, progesterone and androstenedione) determined. In addition, ovarian follicles were treated in vivo with PD98059 and/or LY294002 in ewes on Day 3 of the cycle and follicles were recovered 48 hours later. RESULTS: We have shown that gonadotropin- and IGF-stimulated hormone production by granulosa and theca cells is reduced by treatment with PD98059 and LY294002 in vitro. Furthermore, treatment with PD98059 and LY294002 reduced follicle growth and oestradiol production in vivo. CONCLUSION: These results demonstrate an important functional role for the Akt and Erk signalling pathways in follicle function, growth and development.

Self-assembly of two-component gels: stoichiometric control and component selection

Two-component systems capable of self-assembling into soft gel-phase materials are of considerable interest due to their tunability and versatility. This paper investigates two-component gels based on a combination of a L-lysine-based dendron and a rigid diamine spacer (1,4-diaminobenzene or 1,4-diaminocyclohexane). The networked gelator was investigated using thermal measurements, circular dichroism, NMR spectroscopy and small angle neutron scattering (SANS) giving insight into the macroscopic properties, nanostructure and molecular-scale organisation. Surprisingly, all of these techniques confirmed that irrespective of the molar ratio of the components employed, the "solid-like" gel network always consisted of a 1:1 mixture of dendron/diamine. Additionally, the gel network was able to tolerate a significant excess of diamine in the "liquid-like" phase before being disrupted. In the light of this observation, we investigated the ability of the gel network structure to evolve from mixtures of different aromatic diamines present in excess. We found that these two-component gels assembled in a component-selective manner, with the dendron preferentially recognising 1,4-diaminobenzene (>70%). when similar competitor diamines (1,2- and 1,3-diaminobenzene) are present. Furthermore, NMR relaxation measurements demonstrated that the gel based oil 1,4-diaminobenzene was better able to form a selective ternary complex with pyrene than the gel based oil 1,4-diaminocyclohexane, indicative of controlled and selective pi-pi interactions within a three-component assembly. As such, the results ill this paper demonstrate how component selection processes in two-component gel systems call control hierarchical self-assembly.

The role of phase separation and feed cycle length in leach beds coupled to methanogenic reactors for digestion of a solid substrate (Part 2): Hydrolysis, acidification and methanogenesis in a two-phase system

The effect of phase separation and batch duration on the trophic stages of anaerobic digestion was assessed for the first time in leach beds coupled to methanogenic reactors digesting maize (Zea mays). The system was operated for consecutive batches of 7, 14 and 28 days for ~120 days. Hydrolysis rate was higher the shorter the batch, reaching 8.5 gTSdestroyed d-1 in the 7-day system. Phase separation did not affect acidification but methanogenesis was enhanced in the short feed cycle leach beds. Phase separation was inefficient on the 7-day system, where ~89% of methane was produced in the leach bed. Methane production rate increased with shortening the feed cycle, reaching 3.523 l d-1 average in the 7-day system. Low strength leachate from the leach beds decreased methanogenic activity of methanogenic reactors’ sludges. Enumeration of cellulolytic and methanogenic microorganisms indicated a constant inoculation of leach beds and methanogenic reactors through leachate recirculation.

Regulation of early steps of GPVI signal transduction by phosphatases: a systems biology approach

We present a data-driven mathematical model of a key initiating step in platelet activation, a central process in the prevention of bleeding following Injury. In vascular disease, this process is activated inappropriately and causes thrombosis, heart attacks and stroke. The collagen receptor GPVI is the primary trigger for platelet activation at sites of injury. Understanding the complex molecular mechanisms initiated by this receptor is important for development of more effective antithrombotic medicines. In this work we developed a series of nonlinear ordinary differential equation models that are direct representations of biological hypotheses surrounding the initial steps in GPVI-stimulated signal transduction. At each stage model simulations were compared to our own quantitative, high-temporal experimental data that guides further experimental design, data collection and model refinement. Much is known about the linear forward reactions within platelet signalling pathways but knowledge of the roles of putative reverse reactions are poorly understood. An initial model, that includes a simple constitutively active phosphatase, was unable to explain experimental data. Model revisions, incorporating a complex pathway of interactions (and specifically the phosphatase TULA-2), provided a good description of the experimental data both based on observations of phosphorylation in samples from one donor and in those of a wider population. Our model was used to investigate the levels of proteins involved in regulating the pathway and the effect of low GPVI levels that have been associated with disease. Results indicate a clear separation in healthy and GPVI deficient states in respect of the signalling cascade dynamics associated with Syk tyrosine phosphorylation and activation. Our approach reveals the central importance of this negative feedback pathway that results in the temporal regulation of a specific class of protein tyrosine phosphatases in controlling the rate, and therefore extent, of GPVI-stimulated platelet activation.

Light modulates the melanophore response to alpha-MSH in Xenopus laevis: An analysis of the signal transduction crosstalk mechanisms involved

Melanin granule (melanosome) dispersion within Xenopus laevis melanophores is evoked either by light or alpha-MSH. We have previously demonstrated that the initial biochemical steps of light and alpha-MSH signaling are distinct, since the increase in cAMP observed in response to alpha-MSH was not seen after light exposure. cAMP concentrations in response to alpha-MSH were significantly lower in cells pre-exposed to light as compared to the levels in dark-adapted melanophores. Here we demonstrate the presence of an adenylyl cyclase (AC) in the Xenopus melanophore, similar to the mammalian type IX which is inhibited by Ca(2+)-calmodulin-activated phosphatase. This finding supports the hypothesis that the cyclase could be negatively modulated by a light-promoted Ca(2+) increase. In fact, the activity of calcineurin PP2B phosphatase was increased by light, which could result in AC IX inhibition, thus decreasing the response to alpha-MSH. St-Ht31, a disrupting agent of protein kinase A (PKA)-anchoring kinase A protein (AKAP) complex totally blocked the melanosome dispersing response to alpha-MSH, but did not impair the photo-response in Xenopus melanophores. Sequence comparison of a melanophore AKAP partial clone with GenBank sequences showed that the anchoring protein was a gravin-like adaptor previously sequenced from Xenopus non-pigmentary tissues. Co-immunoprecipitation of Xenopus AKAP and the catalytic subunit of PKA demonstrated that PKA is associated with AKAP and it is released in the presence of alpha-MSH. We conclude that in X laevis melanophores, AKAP12 (gravin-like) contains a site for binding the inactive PKA thus compartmentalizing PKA signaling and also possesses binding sites for PKC. Light diminishes alpha-MSH-induced increase of cAMP by increasing calcineurin (PP2B) activity, which in turn inhibits adenylyl cyclase type IX, and/or by activating PKC, which phosphorylates the gravin-like molecule, thus destabilizing its binding to the cell membrane. (C) 2009 Elsevier Inc. All rights reserved.

Solitons of two-component Bose-Einstein condensates modulated in space and time

In this Letter we present soliton solutions of two coupled nonlinear Schrodinger equations modulated in space and time. The approach allows us to obtain solitons for a large variety of solutions depending on the nonlinearity and potential profiles. As examples we show three cases with soliton solutions: a solution for the case of a potential changing from repulsive to attractive behavior, and the other two solutions corresponding to localized and delocalized nonlinearity terms, respectively. (C) 2010 Elsevier B.V. All rights reserved.

The calcineurin signal transduction pathway is essential for successful muscle regeneration in mdx dystrophic mice

Although mdx mice share the same genetic defect and lack dystrophin expression as in Duchenne muscular dystrophy (DMD), their limb muscles have a high regenerative capacity that ensures a more benign phenotype and essentially normal function. The cellular pathways responsible for this enhanced regenerative capacity are unknown. We tested the hypothesis that the calcineurin signal transduction pathway is essential for the successful regeneration following severe degeneration observed in the limb muscles of young mdx mice (2–4 weeks old) and that inhibition of this pathway using cyclosporine A (CsA) would exacerbate the dystrophic pathology. Eighteen-day-old mdx and C57BL/10 mice were treated with CsA for 16 days. CsA administration severely disrupted muscle regeneration in mdx mice, but had minimal effect in C57BL/10 mice. Muscles from CsA-treated mdx mice had fewer centrally nucleated fibers and extensive collagen, connective tissue, and mononuclear cell infiltration than muscles from vehicle-treated littermates. The deleterious effects of CsA on muscle morphology were accompanied by a 30–35% decrease in maximal force producing capacity. Taken together, these observations indicate that the calcineurin signal transduction pathway is a significant determinant of successful skeletal muscle regeneration in young mdx mice. Up-regulating this pathway may have clinical significance for DMD.

A syntactic two-component encoding model for the trajectories of human actions

Human actions have been widely studied for their potential application in various areas such as sports, pervasive patient monitoring, and rehabilitation. However, challenges still persist pertaining to determining the most useful ways to describe human actions at the sensor, then limb and complete action levels of representation and deriving important relations between these levels each involving their own atomic components. In this paper, we report on a motion encoder developed for the sensor level based on the need to distinguish between the shape of the sensor's trajectory and its temporal characteristics during execution. This distinction is critical as it provides a different encoding scheme than the usual velocity and acceleration measures which confound these two attributes of any motion. At the same time, we eliminate noise from sensors by comparing temporal and spatial indexing schemes and a number of optimal filtering models for robust encoding. Results demonstrate the benefits of spatial indexing and separating the shape and dynamics of a motion, as well as its ability to decompose complex motions into several atomic ones. Finally, we discuss how this specific type of sensor encoder bears on the derivation of limb and complete action descriptions.