Targeting mutant fibroblast growth factor receptors in cancer

Fibroblast growth factor receptors (FGFRs) play diverse roles in the control of cell proliferation, cell differentiation, angiogenesis and development. Activating the mutations of FGFRs in the germline has long been known to cause a variety of skeletal developmental disorders, but it is only recently that a similar spectrum of somatic FGFR mutations has been associated with human cancers. Many of these somatic mutations are gain-of-function and oncogenic and create dependencies in tumor cell lines harboring such mutations. A combination of knockdown studies and pharmaceutical inhibition in preclinical models has further substantiated genomically altered FGFR as a therapeutic target in cancer, and the oncology community is responding with clinical trials evaluating multikinase inhibitors with anti-FGFR activity and a new generation of specific pan-FGFR inhibitors.

Computational approaches for modelling intrinsic noise and delays in genetic regulatory networks

This chapter focuses on the interactions and roles between delays and intrinsic noise effects within cellular pathways and regulatory networks. We address these aspects by focusing on genetic regulatory networks that share a common network motif, namely the negative feedback loop, leading to oscillatory gene expression and protein levels. In this context, we discuss computational simulation algorithms for addressing the interplay of delays and noise within the signaling pathways based on biological data. We address implementational issues associated with efficiency and robustness. In a molecular biology setting we present two case studies of temporal models for the Hes1 gene (Monk, 2003; Hirata et al., 2002), known to act as a molecular clock, and the Her1/Her7 regulatory system controlling the periodic somite segmentation in vertebrate embryos (Giudicelli and Lewis, 2004; Horikawa et al., 2006).

Stochastic simulation for spatial modelling of dynamic process in a living cell

One of the fundamental motivations underlying computational cell biology is to gain insight into the complicated dynamical processes taking place, for example, on the plasma membrane or in the cytosol of a cell. These processes are often so complicated that purely temporal mathematical models cannot adequately capture the complex chemical kinetics and transport processes of, for example, proteins or vesicles. On the other hand, spatial models such as Monte Carlo approaches can have very large computational overheads. This chapter gives an overview of the state of the art in the development of stochastic simulation techniques for the spatial modelling of dynamic processes in a living cell.

Modeling intrinsic noise and delays in chemical kinetics of coupled autoregulated oscillating cells

Delays are an important feature in temporal models of genetic regulation due to slow biochemical processes, such as transcription and translation. In this paper, we show how to model intrinsic noise effects in a delayed setting by either using a delay stochastic simulation algorithm (DSSA) or, for larger and more complex systems, a generalized Binomial τ-leap method (Bτ-DSSA). As a particular application, we apply these ideas to modeling somite segmentation in zebra fish across a number of cells in which two linked oscillatory genes (her1 and her7) are synchronized via Notch signaling between the cells.

Computer-intensive simulations for cellular models

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Peer partnership to enhance scholarship of teaching : a case study

This paper reports on the outcomes of a peer partnership program trialled at the Queensland University of Technology (QUT), Australia. The program was designed based on a community of practice methodology to bring together academic staff for the purpose of advancing teaching practice. The program encouraged professional and supportive environments for the purpose of critical reflection and personal development. The belief was that quality teaching is core business and vital to university organisational goals. Peer partnership programs support improvement in teaching and learning. Participants in the program reported the program enhanced their commitment and insight into teaching and that there is willingness to be involved if supported by colleagues and an organisation. Feedback from participants in the program was positive and outcomes arising from the QUT Peer Partnership Project were the development of an online peer partner tool-kit, staff development training, an instructional DVD and integration of the project goals within QUT staff development programs.

Regulating greenhouse gas emissions from coal mining activities in the context of climate change

Current approaches to the regulation of coal mining activities in Australia have facilitated the extraction of substantial amounts of coal and coal seam gas. The regulation of coal mining activities must now achieve the reduction or mitigation of greenhouse gas emissions in order to address the challenge of climate change and achieve ecologically sustainable development. Several legislative mechanisms currently exist which appear to offer the means to bring about the reduction or mitigation of greenhouse gas emissions from coal mining activities, yet Australia’s emissions from coal mining continue to rise. This article critiques these existing legislative mechanisms and presents recommendations for reform.

A formative evaluation of the Stronger Smarter Learning Communities Project. 2011 report.

This report is a formative evaluation of the operations of the DEEWR funded Stronger Smarter Learning Community (SSLC) project from September 2009 to July 2011. It is undertaken by an independent team of researchers from Queensland University of Technology, the University of Newcastle and Harvard University. It reports on findings from: documentary analysis; qualitative case studies of SSLC Hub schools; descriptive, multivariate and multilevel analysis of survey data from school leaders and teachers from SSLC Hub and Affiliate schools and from a control group of non-SSLC schools; and multilevel analysis of school-level data on SSLC Hubs, Affiliates and ACARA like-schools. Key findings from this work are that: • SSLC school leaders and teachers are reporting progress in changing school ethos around issues of: recognition of Indigenous identity, Indigenous leadership, innovative approaches to staffing and school models, Indigenous community engagement and high expectations leadership; • Many Stronger Smarter messages are reportedly having better uptake in schools with high percentages of Indigenous students; • There are no major or consistent patterns of differences between SSLC and non-SSLC schools in teacher and school leader self-reports of curriculum and pedagogy practices; and • There is no evidence to date that SSLC Hubs and Affiliates have increased attendance or increased achievement gains compared to ACARA like-schools. Twenty-one months is relatively early in this school reform project. Hence the major focus of subsequent reports will be on the documentation of comparative longitudinal gains in achievement tests and improved attendance. The 2011 and 2012 research also will model the relationships between change in school ethos/climate, changed Indigenous community relations, improved curriculum/pedagogy, and gains in Indigenous student achievement, attendance and outcomes. The key challenge for SSLC and the Stronger Smarter approach will be whether it can systematically generate change and reform in curriculum and pedagogy practices that can be empirically linked to improved student outcomes.

Editorial : Decolonising action research (Electronic Version)

This edition of the ALAR Action learning action research journal aims to capture some of the current dilemmas, solutions and actions researchers experience in the decolonising space. This collection of papers demonstrates that researchers are not only undertaking action research with and within Indigenous and non-Indigenous contexts, but that they are doing so in exciting and dynamic ways across a diversity of situations. First we will address some of the literature on decolonisation. Then we will explain how this specific edition of the Journal came to fruition and aspects of action research.

Low rank Runge-Kutta methods, symplecticity and stochastic Hamiltonian problems with additive noise

In this paper we extend the ideas of Brugnano, Iavernaro and Trigiante in their development of HBVM($s,r$) methods to construct symplectic Runge-Kutta methods for all values of $s$ and $r$ with $s\geq r$. However, these methods do not see the dramatic performance improvement that HBVMs can attain. Nevertheless, in the case of additive stochastic Hamiltonian problems an extension of these ideas, which requires the simulation of an independent Wiener process at each stage of a Runge-Kutta method, leads to methods that have very favourable properties. These ideas are illustrated by some simple numerical tests for the modified midpoint rule.

FGFR2 point mutations in 466 Endometrioid Endometrial Tumors : relationship with MSI, KRAS, PIK3CA, CTNNB1 mutations and Clinicopathological features

Mutations in multiple oncogenes including KRAS, CTNNB1, PIK3CA and FGFR2 have been identified in endometrial cancer. The aim of this study was to provide insight into the clinicopathological features associated with patterns of mutation in these genes, a necessary step in planning targeted therapies for endometrial cancer. 466 endometrioid endometrial tumors were tested for mutations in FGFR2, KRAS, CTNNB1, and PIK3CA. The relationships between mutation status, tumor microsatellite instability (MSI) and clinicopathological features including overall survival (OS) and disease-free survival (DFS) were evaluated using Kaplan-Meier survival analysis and Cox proportional hazard models. Mutations were identified in FGFR2 (48/466); KRAS (87/464); CTNNB1 (88/454) and PIK3CA (104/464). KRAS and FGFR2 mutations were significantly more common, and CTNNB1 mutations less common, in MSI positive tumors. KRAS and FGFR2 occurred in a near mutually exclusive pattern (p = 0.05) and, surprisingly, mutations in KRAS and CTNNB1 also occurred in a near mutually exclusive pattern (p = 0.0002). Multivariate analysis revealed that mutation in KRAS and FGFR2 showed a trend (p = 0.06) towards longer and shorter DFS, respectively. In the 386 patients with early stage disease (stage I and II), FGFR2 mutation was significantly associated with shorter DFS (HR = 3.24; 95% confidence interval, CI, 1.35-7.77; p = 0.008) and OS (HR = 2.00; 95% CI 1.09-3.65; p = 0.025) and KRAS was associated with longer DFS (HR = 0.23; 95% CI 0.05-0.97; p = 0.045). In conclusion, although KRAS and FGFR2 mutations share similar activation of the MAPK pathway, our data suggest very different roles in tumor biology. This has implications for the implementation of anti-FGFR or anti-MEK biologic therapies.

Cellular settings mediating Src Substrate switching between Focal Adhesion Kinase Tyrosine 861 and CUB-domain-containing protein 1 (CDCP1) Tyrosine 734

Reciprocal interactions between Src family kinases (SFKs) and focal adhesion kinase (FAK) are critical during changes in cell attachment. Recently it has been recognized that another SFK substrate, CUB-domain-containing protein 1 (CDCP1), is differentially phosphorylated during these events. However, the molecular processes underlying SFK-mediated phosphorylation of CDCP1 are poorly understood. Here we identify a novel mechanism in which FAK tyrosine 861 and CDCP1-Tyr-734 compete as SFK substrates and demonstrate cellular settings in which SFKs switch between these sites. Our results show that stable CDCP1 expression induces robust SFK-mediated phosphorylation of CDCP1-Tyr-734 with concomitant loss of p-FAK-Tyr-861 in adherent HeLa cells. SFK substrate switching in these cells is dependent on the level of expression of CDCP1 and is also dependent on CDCP1-Tyr-734 but is independent of CDCP1-Tyr-743 and -Tyr-762. In HeLa CDCP1 cells, engagement of SFKs with CDCP1 is accompanied by an increase in phosphorylation of Src-Tyr-416 and a change in cell morphology to a fibroblastic appearance dependent on CDCP1-Tyr-734. SFK switching between FAK-Tyr-861 and CDCP1-Tyr-734 also occurs during changes in adhesion of colorectal cancer cell lines endogenously expressing these two proteins. Consistently, increased p-FAK-Tyr-861 levels and a more epithelial morphology are seen in colon cancer SW480 cells silenced for CDCP1. Unlike protein kinase Cδ, FAK does not appear to form a trimeric complex with Src and CDCP1. These data demonstrate novel aspects of the dynamics of SFK-mediated cell signaling that may be relevant during cancer progression.