Stochastic models for regulatory networks of the genetic toggle switch

Bistability arises within a wide range of biological systems from the λ phage switch in bacteria to cellular signal transduction pathways in mammalian cells. Changes in regulatory mechanisms may result in genetic switching in a bistable system. Recently, more and more experimental evidence in the form of bimodal population distributions indicates that noise plays a very important role in the switching of bistable systems. Although deterministic models have been used for studying the existence of bistability properties under various system conditions, these models cannot realize cell-to-cell fluctuations in genetic switching. However, there is a lag in the development of stochastic models for studying the impact of noise in bistable systems because of the lack of detailed knowledge of biochemical reactions, kinetic rates, and molecular numbers. In this work, we develop a previously undescribed general technique for developing quantitative stochastic models for large-scale genetic regulatory networks by introducing Poisson random variables into deterministic models described by ordinary differential equations. Two stochastic models have been proposed for the genetic toggle switch interfaced with either the SOS signaling pathway or a quorum-sensing signaling pathway, and we have successfully realized experimental results showing bimodal population distributions. Because the introduced stochastic models are based on widely used ordinary differential equation models, the success of this work suggests that this approach is a very promising one for studying noise in large-scale genetic regulatory networks.

A crystallographic snapshot of tyrosine trans-phosphorylation in action

Tyrosine trans-phosphorylation is a key event in receptor tyrosine kinase signaling, yet, the structural basis for this process has eluded definition. Here, we present the crystal structure of the FGF receptor 2 kinases caught in the act of trans-phosphorylation of Y769, the major C-terminal phosphorylation site. The structure reveals that enzyme- and substrate-acting kinases engage each other through elaborate and specific interactions not only in the immediate vicinity of Y769 and the enzyme active site, but also in regions that are as much of 18 A away from D626, the catalytic base in the enzyme active site. These interactions lead to an unprecedented level of specificity and precision during the trans-phosphorylation on Y769. Time-resolved mass spectrometry analysis supports the observed mechanism of trans-phosphorylation. Our data provide a molecular framework for understanding the mechanism of action of Kallmann syndrome mutations and the order of trans-phosphorylation reactions in FGFRs. We propose that the salient mechanistic features of Y769 trans-phosphorylation are applicable to trans-phosphorylation of the equivalent major phosphorylation sites in many other RTKs.

Learning from episodes of degradation and recovery in variable Australian rangelands

Land-change science emphasizes the intimate linkages between the human and environmental components of land management systems. Recent theoretical developments in drylands identify a small set of key principles that can guide the understanding of these linkages. Using these principles, a detailed study of seven major degradation episodes over the past century in Australian grazed rangelands was reanalyzed to show a common set of events: (i) good climatic and economic conditions for a period, leading to local and regional social responses of increasing stocking rates, setting the preconditions for rapid environmental collapse, followed by (ii) a major drought coupled with a fall in the market making destocking financially unattractive, further exacerbating the pressure on the environment; then (iii) permanent or temporary declines in grazing productivity, depending on follow-up seasons coupled again with market and social conditions. The analysis supports recent theoretical developments but shows that the establishment of environmental knowledge that is strictly local may be insufficient on its own for sustainable management. Learning systems based in a wider community are needed that combine local knowledge, formal research, and institutional support. It also illustrates how natural variability in the state of both ecological and social systems can interact to precipitate nonequilibrial change in each other, so that planning cannot be based only on average conditions. Indeed, it is this variability in both environment and social subsystems that hinders the local learning required to prevent collapse.

Refining animal models in fracture research: Seeking consensus in optimising both animal welfare and scientific validity for appropriate biomedical use

Background In an attempt to establish some consensus on the proper use and design of experimental animal models in musculoskeletal research, AOVET (the veterinary specialty group of the AO Foundation) in concert with the AO Research Institute (ARI), and the European Academy for the Study of Scientific and Technological Advance, convened a group of musculoskeletal researchers, veterinarians, legal experts, and ethicists to discuss, in a frank and open forum, the use of animals in musculoskeletal research. Methods The group narrowed the field to fracture research. The consensus opinion resulting from this workshop can be summarized as follows: Results & Conclusion Anaesthesia and pain management protocols for research animals should follow standard protocols applied in clinical work for the species involved. This will improve morbidity and mortality outcomes. A database should be established to facilitate selection of anaesthesia and pain management protocols for specific experimental surgical procedures and adopted as an International Standard (IS) according to animal species selected. A list of 10 golden rules and requirements for conduction of animal experiments in musculoskeletal research was drawn up comprising 1) Intelligent study designs to receive appropriate answers; 2) Minimal complication rates (5 to max. 10%); 3) Defined end-points for both welfare and scientific outputs analogous to quality assessment (QA) audit of protocols in GLP studies; 4) Sufficient details for materials and methods applied; 5) Potentially confounding variables (genetic background, seasonal, hormonal, size, histological, and biomechanical differences); 6) Post-operative management with emphasis on analgesia and follow-up examinations; 7) Study protocols to satisfy criteria established for a "justified animal study"; 8) Surgical expertise to conduct surgery on animals; 9) Pilot studies as a critical part of model validation and powering of the definitive study design; 10) Criteria for funding agencies to include requirements related to animal experiments as part of the overall scientific proposal review protocols. Such agencies are also encouraged to seriously consider and adopt the recommendations described here when awarding funds for specific projects. Specific new requirements and mandates related both to improving the welfare and scientific rigour of animal-based research models are urgently needed as part of international harmonization of standards.

Dopamine responsiveness is regulated by targeted sorting of D2 receptors

Abstract Aberrant dopaminergic signaling is a critical determinant in multiple psychiatric disorders, and in many disease states, dopamine receptor number is altered. Here we identify a molecular mechanism that selectively targets D2 receptors for degradation after their activation by dopamine. The degradative fate of D2 receptors is determined by an interaction with G protein coupled receptor-associated sorting protein (GASP). As a consequence of this GASP interaction, D2 responses in rat brain fail to resensitize after agonist treatment. Disruption of the D2-GASP interaction facilitates recovery of D2 responses, suggesting that modulation of the D2-GASP interaction is important for the functional down-regulation of D2 receptors.

Estrogen receptor-Beta activated apoptosis in benign hyperplasia and cancer of the prostate is androgen independent and TNF-alpha mediated

Prostate cancer (PCa) and benign prostatic hyperplasia (BPH) are androgen-dependent diseases commonly treated by inhibiting androgen action. However, androgen ablation or castration fail to target androgen-independent cells implicated in disease etiology and recurrence. Mechanistically different to castration, this study shows beneficial proapoptotic actions of estrogen receptor–β (ERβ) in BPH and PCa. ERβ agonist induces apoptosis in prostatic stromal, luminal and castrate-resistant basal epithelial cells of estrogen-deficient aromatase knock-out mice. This occurs via extrinsic (caspase-8) pathways, without reducing serum hormones, and perturbs the regenerative capacity of the epithelium. TNFα knock-out mice fail to respond to ERβ agonist, demonstrating the requirement for TNFα signaling. In human tissues, ERβ agonist induces apoptosis in stroma and epithelium of xenografted BPH specimens, including in the CD133+ enriched putative stem/progenitor cells isolated from BPH-1 cells in vitro. In PCa, ERβ causes apoptosis in Gleason Grade 7 xenografted tissues and androgen-independent cells lines (PC3 and DU145) via caspase-8. These data provide evidence of the beneficial effects of ERβ agonist on epithelium and stroma of BPH, as well as androgen-independent tumor cells implicated in recurrent disease. Our data are indicative of the therapeutic potential of ERβ agonist for treatment of PCa and/or BPH with or without androgen withdrawal.

A Bayesian model predicts the response of axons to molecular gradients

Axon guidance by molecular gradients plays a crucial role in wiring up the nervous system. However, the mechanisms axons use to detect gradients are largely unknown. We first develop a Bayesian “ideal observer” analysis of gradient detection by axons, based on the hypothesis that a principal constraint on gradient detection is intrinsic receptor binding noise. Second, from this model, we derive an equation predicting how the degree of response of an axon to a gradient should vary with gradient steepness and absolute concentration. Third, we confirm this prediction quantitatively by performing the first systematic experimental analysis of how axonal response varies with both these quantities. These experiments demonstrate a degree of sensitivity much higher than previously reported for any chemotacting system. Together, these results reveal both the quantitative constraints that must be satisfied for effective axonal guidance and the computational principles that may be used by the underlying signal transduction pathways, and allow predictions for the degree of response of axons to gradients in a wide variety of in vivo and in vitro settings.

Varenicline, an alpha-4 beta-2 nicotinic acetylcholine receptor partial agonist, selectively decreases ethanol consumption and seeking

Abstract Alcohol dependence is a disease that impacts millions of individuals worldwide. There has been some progress with pharmacotherapy for alcohol-dependent individuals; however, there remains a critical need for the development of novel and additional therapeutic approaches. Alcohol and nicotine are commonly abused together, and there is evidence that neuronal nicotinic acetylcholine receptors (nAChRs) play a role in both alcohol and nicotine dependence. Varenicline, a partial agonist at the alpha4beta2 nAChRs, reduces nicotine intake and was recently approved as a smoking cessation aid. We have investigated the role of varenicline in the modulation of ethanol consumption and seeking using three different animal models of drinking. We show that acute administration of varenicline, in doses reported to reduce nicotine reward, selectively reduced ethanol but not sucrose seeking using an operant self-administration drinking paradigm and also decreased voluntary ethanol but not water consumption in animals chronically exposed to ethanol for 2 months before varenicline treatment. Furthermore, chronic varenicline administration decreased ethanol consumption, which did not result in a rebound increase in ethanol intake when the varenicline was no longer administered. The data suggest that the alpha4beta2 nAChRs may play a role in ethanol-seeking behaviors in animals chronically exposed to ethanol. The selectivity of varenicline in decreasing ethanol consumption combined with its reported safety profile and mild side effects in humans suggest that varenicline may prove to be a treatment for alcohol dependence.

Bricolage as a path to innovation for resource constrained new firms

Evidence suggests that both start-up and young firms (henceforth: new firms) – despite typically being resource-constrained – are sometimes able to innovate (Katila & Shane 2005). Such firms are seldom able to invest in expensive innovation processes, which suggests that they may rely on other pathways to innovation. In this paper, we test arguments that “bricolage,” defined as making do by applying combinations of the resources at hand to new problems and opportunities, provides a pathway to innovation for new firms. Our results suggest that variations in bricolage behaviors can provide an explanation of innovation under resource constraints by new firms.

An analysis of schema change intervention

Successful organizational transformation relies on being able to achieve paradigm or collective schema change, and more particularly, the ability to manage the interplay between pre-existing schemas and alternative schemas required for new environments. This conceptual paper presents an analysis and critique of collective schema change dynamics. Two schema change pathways are reflected in the literature: frame-juxtapose-transition and frame-disengage-learning. Research findings in each pathway are limited and/or contradictory. Moreover, research on schema change focuses primarily on social dynamics and less on the relationship between social schema change dynamics and individual schema change dynamics. One implication of this lack of focus on individual schema change dynamics is the masking of the high level of cognitive processing and cognitive effort required by individuals to effect schema change. The capacity to achieve organizational transformation requires that more attention is given to managing these dynamics, which, in turn, requires significant investment in developing the change leadership capabilities of managers and the organizations they manage.

Enlightening, balancing and transcending entrepreneurial orientation : the 4th annual EO3 research PDW

Entrepreneurial Orientation (EO) has a 30 year history as one of the most used concepts in entrepreneurship research. “Recent attention in formal sessions at the Academy of Management conference programs confirm Entrepreneurial Orientation as a primary construct with a majority of Entrepreneurship Division sponsored sessions devoted to studies using EO related measures”, as reported by the 2010 division program chair, Per Davidson (Roberts, 2010: 9). However, questions continue to be raised concerning over-dependence on parts of one strategic scale, possible inappropriate or under-theorized adaptations, and the lack of theoretical development on application and performance variance in emergent, organizational, and socioeconomic settings. One recent area of investigation in analysis, methods, theory and application concerns an “EO gestalt”, focusing on the family of EO-related measures and theory, rather than on one or more dimensions, in order to explore the theory and process of the Entrepreneurial Orientation phenomenon. The goals of the 4th Annual EO3 PDW are to enlighten researchers on the development of Entrepreneurial Orientation theory and related scales, balance the use of Entrepreneurial Orientation current knowledge with new research frontiers suggested by EO3 scholars’ questions, and transcend boundaries in the discoveries undertaken in the shared interdisciplinary and cross-cultural research agenda currently developing for Entrepreneurial Orientation concepts. Going into its forth year, the EO3 PDW has been pivotal in formalizing discussion, pushing research forward, and gaining insights from experienced and cutting edge scholars, as it provides a point of reference for coalescing research questions and findings surrounding this important concept.