Evidence for u.v. induction of CDKN2 mutations in melanoma cell lines

The CDKN2 gene, encoding the cyclin dependent kinase inhibitor p16, is a tumour suppressor gene involved in melanoma and maps to chromosome band 9p22. Mutations or interstitial deletions of this gene have been found both in the germline of familial melanoma cases and somatically in melanoma cell lines. Previous mutation analyses of melanoma cell lines have indicated a high frequency of C:G to T:A transitions, with all of these mutations occurring at dipyrimidine sites. Including three melanoma cell lines carrying tandem CC to TT mutations, the spectrum of mutations so far reported indicates a possible role for u.v. radiation in the mutagenesis of this gene in some tumours. To further examine this hypothesis we have characterised mutations of the CDKN2 gene in 30 melanoma cell lines. Nineteen lines carried complete or partial homozygous deletions of the gene. Of the remaining cell lines, eight were shown by direct sequencing of PCR products from exon 1 and exon 2 to carry a total of nine different mutations of CDKN2. Two cell lines carried tandem CC to TT mutations and a high rate of C:G to T:A transitions was observed. This study provides further evidence for the role of u.v. light in the genesis of melanoma, with one target being the CDKN2 tumour suppressor gene.

Analysis of the CDKN2A, CDKN2B and CDK4 genes in 48 Australian melanoma kindreds

Germline mutations within the cyclin-dependent kinase inhibitor 2A (CDKN2A) gene and one of its targets, the cyclin dependent kinase 4 (CDK4) gene, have been identified in a proportion of melanoma kindreds. In the case of CDK4, only one specific mutation, resulting in the substitution of a cysteine for an arginine at codon 24 (R24C), has been found to be associated with melanoma. We have previously reported the identification of germline CDKN2A mutations in 7/18 Australian melanoma kindreds and the absence of the R24C CDK4 mutation in 21 families lacking evidence of a CDKN2A mutation. The current study represents an expansion of these efforts and includes a total of 48 melanoma families from Australia. All of these families have now been screened for mutations within CDKN2A and CDK4, as well as for mutations within the CDKN2A homolog and 9p21 neighbor, the CDKN2B gene, and the alternative exon 1 (E1beta) of CDKN2A. Families lacking CDKN2A mutations, but positive for a polymorphism(s) within this gene, were further evaluated to determine if their disease was associated with transcriptional silencing of one CDKN2A allele. Overall, CDKN2A mutations were detected in 3/30 (10%) of the new kindreds. Two of these mutations have been observed previously: a 24 bp duplication at the 5' end of the gene and a G to C transversion in exon 2 resulting in an M531 substitution. A novel G to A transition in exon 2, resulting in a D108N substitution was also detected. Combined with our previous findings, we have now detected germline CDKN2A mutations in 10/48 (21%) of our melanoma kindreds. In none of the 'CDKN2A-negative' families was melanoma found to segregate with either an untranscribed CDKN2A allele, an R24C CDK4 mutation, a CDKN2B mutation, or an E1beta mutation. The last three observations suggest that these other cell cycle control genes (or alternative gene products) are either not involved at all, or to any great extent, in melanoma predisposition.

Evidence for three tumor suppressor loci on chromosome 9p involved in melanoma development

Cytogenetic and loss of heterozygosity (LOH) studies have long indicated the presence of a tumor suppressor gene (TSG) on 9p involved in the development of melanoma. Although LOH at 9p has been reported in approximately 60% of melanoma tumors, only 5-10% of these tumors have been shown to carry CDKN2A mutations, raising the possibility that another TSG involved in melanoma maps to chromosome 9p. To investigate this possibility, a panel of 37 melanomas derived from 35 individuals was analyzed for CDKN2A mutations by single-strand conformation polymorphism analysis and sequencing. The melanoma samples were then typed for 15 markers that map to 9p13-24 to investigate LOH trends in this region. In those tumors demonstrating retention of heterozygosity at markers flanking CDKN2A and LOH on one or both sides of the gene, multiplex microsatellite PCR was performed to rule out homozygous deletion of the region encompassing CDKN2A. CDKN2A mutations were found in tumors from 5 patients [5 (14%) of 35], 4 of which demonstrated LOH across the entire region examined. The remaining tumor with no observed LOH carried two point mutations, one on each allele. Although LOH was identified at one or more markers in 22 (59%) of 37 melanoma tumors corresponding to 20 (57%) of 35 individuals, only 11 tumors from 9 individuals [9 (26%) of 35] demonstrated LOH at D9S942 and D9S1748 the markers closest to CDKN2A. Of the remaining 11 tumors with LOH 9 demonstrated LOH at two or more contiguous markers either centromeric and/or telomeric to CDKN2A while retaining heterozygosity at several markers adjacent to CDKN2A. Multiplex PCR revealed one tumor carried a homozygous deletion extending from D9S1748 to the IFN-alpha locus. In the remaining eight tumors, multiplex PCR demonstrated that the observed heterozygosity was not attributable to homozygous deletion and stromal contamination at D9S1748, D9S942, or D9S974, as measured by comparative amplification strengths, which indicates that retention of heterozygosity with flanking LOH does not always indicate a homozygous deletion. This report supports the conclusions of previous studies that a least two TSGs involved in melanoma development in addition to CDKN2A may reside on chromosome 9p.

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).

Evolving noisy oscillatory dynamics in genetic regulatory networks

We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.

External auditors' reliance on internal auditing : further evidence.

Purpose – The purpose of this paper is to explore whether internal audit’s reporting relationship with the audit committee and the client’s business risk environment impact external auditors’ reliance on the work of internal audit. Design/methodology/approach – An experiment is conducted using a 2 £ 2 between-subjects design where we manipulate the above two factors at strong and weak levels. Participants are 66 audit partners, managers and seniors, all experienced with clients having internal audit functions. Findings – The results indicate that both factors affect external auditors’ reliance on work already undertaken by internal audit and their use of internal auditors (IA) as assistants. The results also indicate that external auditors are more likely to use internal audit for control evaluation tasks than for substantive tests of balances. The study does not find any significant interaction effects between the two factors. Originality/value – No prior studies have examined the influence of reporting relationship and client business risk on external auditors’ reliance decisions in the current governance environment. Further, the paper examines the impact of these factors on reliance on work already undertaken by internal audit and on using IA as assistants, with respect to both control evaluation work and substantive testing of balances.

Functional fixation : experimental evidence on the presentation of financial information through different digital formats

This study examines whether, in the presentation of financial information, digital formats address the concern over users’ functional fixation. The accounting literature indicates that the presentation of financial information either within the financial statements or in the notes to the financial statements often creates functional fixation where users of financial statements fail to adjust for differences in accounting policy. This leads users to judge what would otherwise be identical financial situations as being different due to the different accounting policies and methods adopted. It has been suggested that the use of digital formats in presenting financial reports may overcome functional fixation. Using an experimental design involving accountants in public practice, the results indicate that the use of digital formats to present financial reports does not fully overcome the issue of functional fixation in the processing of financial information. Although the participants were able to identify and extract relevant information, irrespective of whether or not the information was presented within the financial statements or in the notes to the accounts, the evidence indicates that functional fixation remained when the participants made final decisions based on available information. This suggests that functional fixation may not be caused by access to or extraction of information but by the level of perceived significance based on where the information is reported in the financial statements. In general, the results indicate that current technology may not be able to fully reduce functional fixation in the evaluation of financial information prepared in accordance with different accounting policies and methods.

Surrogacy and IVF

While in the past surrogacy was illegal in Queensland, since June 2010 the Surrogacy Act 2010 (Qld) (“the Act”) has made altruistic surrogacy arrangements lawful in Queensland. In addition, it provides a mechanism for transfer of legal parentage from the surrogate to the person(s) wishing to have a child (the intended parent(s)). Commercial surrogacy – where a payment, reward or other material benefit of advantage (other than the reimbursement of the “birth mother’s surrogacy costs” (s11 of the Act) is made for entering into a surrogacy arrangement – remains unlawful. The paramount guiding principle underpinning the Act is that of the wellbeing and best interests of a child born as a result of surrogacy. The Surrogacy Act 2010 (Qld) allows a single person or a couple (heterosexual or same sex couples) to enter into an agreement with a woman, and her partner (if she has one), to become pregnant with the intention that the child will be relinquished to the intended parent(s). The Act also provides a mechanism for the intended parent(s) to be legally recognised as the parent(s) of the child. In order for the intended parent(s) to be legally recognised (via a parentage order, discussed below) it must be shown that the surrogacy arrangement was entered into when all the parties were over 25 years of age and the intended parent(s) are male or, in a heterosexual or lesbian couple the female(s) are not likely to conceive or give birth to a healthy child due to medical reasons. The arrangement must be entered into before the surrogate becomes pregnant and all parties must have obtained independent legal advice and counselling about the proposed arrangement, and evidence of this is required at the time a parentage order is applied for. For the purposes of the Act it does not matter how the surrogate conceives the child or if the child is genetically related to the parties. During the period of the pregnancy, the surrogate has the right to manage her pregnancy in the way she wishes. Although she cannot profit from acting as a surrogate, section 11 states that she is entitled to surrogacy costs. These include, for example, reasonable medical costs related to pregnancy and the birth of the child; counselling and legal costs associated with the surrogacy arrangement; actual lost earnings because of leave taken during pregnancy or following birth and any reasonable travel expenses incurred. The surrogacy arrangement itself is not legally enforceable; however, obligations to pay a surrogate’s surrogacy costs are enforceable unless she chooses not to relinquish the child to the intending parents. While the Act does not specifically deal with the situation where the surrogate decides she is unprepared to relinquish the child to the intended parents, there have been examples where parties have entered into these kinds of arrangements, and the arrangements have become difficult. For example, the Family Court case of Re Evelyn (1998) FLC 92–807 involved a child born to a surrogate mother who decided not to surrender her. The child was the genetic child of the surrogate mother and the husband of the couple who had contracted with the surrogate mother. Both sets of parents brought proceedings in the court, seeking that the child live with them. In hearing the application, the court applied the paramount principle of the ‘best interests of the child’. The court made clear that there is no presumption in favour of the birth mother, although in this case the court found that the child may be better placed with the surrogate mother’s family.

The nature and prevalence of inter-organizational project ventures : evidence from a large scale field study in the Netherlands 2006-2009

There has recently been noted a rapid increase in research attention to projects that involve outside partners. Our knowledge of such inter-organizational projects, however, is limited. This paper reports large scale data from a repeated trend survey amongst 2000 SMEs in 2006 and 2009 that focused on inter-organizational project ventures. Our major findings indicate that the overall prevalence of inter-organizational project ventures remained significant and stable over time, even despite the economic crisis. Moreover, we find that these ventures predominantly solve repetitive rather than unique tasks and are embedded in prior relations between the partnering organizations. These findings provide empirical support for the recent claims that project management should pay more attention to inter-organizational forms of project organization, and suggest that the archetypical view of projects as being unique in every respect should be reconsidered. Both have important implications for project management, especially in the area of project-based learning.

Operational performance of low-cost carriers and international airlines : New evidence using a bootstrap truncated regression

Between 2001 and 2005, the US airline industry faced financial turmoil. At the same time, the European airline industry entered a period of substantive deregulation. This period witnessed opportunities for low-cost carriers to become more competitive in the market as a result of these combined events. To help assess airline performance in the aftermath of these events, this paper provides new evidence of technical efficiency for 42 national and international airlines in 2006 using the data envelopment analysis (DEA) bootstrap approach first proposed by Simar and Wilson (J Econ, 136:31-64, 2007). In the first stage, technical efficiency scores are estimated using a bootstrap DEA model. In the second stage, a truncated regression is employed to quantify the economic drivers underlying measured technical efficiency. The results highlight the key role played by non-discretionary inputs in measures of airline technical efficiency.

Population genetic structure and patterns of dispersal in the Giant Long-Armed Prawn, Macrobrachium lar (Fabricius, 1798) (Decapoda : Palaemonidae)

The Giant Long-Armed Prawn, Macrobrachium lar is a freshwater species native to the Indo-Pacific. M. lar has a long-lived, passive, pelagic marine larval stage where larvae need to colonise freshwater within three months to complete their development. Dispersal is likely to be influenced by the extensive distances larvae must transit between small oceanic islands to find suitable freshwater habitat, and by prevailing east to west wind and ocean currents in the southern Pacific Ocean. Thus, both intrinsic and extrinsic factors are likely to influence wild population structure in this species. The present study sought to define the contemporary broad and fine-scale population genetic structure of Macrobrachium lar in the south-western Pacific Ocean. Three polymorphic microsatellite loci were used to assess patterns of genetic variation within and among 19 wild adult sample sites. Statistical procedures that partition variation implied that at both spatial scales, essentially all variation was present within sample sites and differentiation among sites was low. Any differentiation observed also was not correlated with geographical distance. Statistical approaches that measure genetic distance, at the broad-scale, showed that all south-western Pacific Islands were essentially homogeneous, with the exception of a well supported divergent Cook Islands group. These findings are likely the result of some combination of factors that may include the potential for allelic homoplasy, through to the effects of sampling regime. Based on the findings, there is most likely a divergent M. lar Cook Islands clade in the south-western Pacific Ocean, resulting from prevailing ocean currents. Confirmation of this pattern will require a more detailed analysis of nDNA variation using a larger number of loci and, where possible, use of larger population sizes.

A mathematical model for genetic regulation of the lactose operon

In this paper we construct a mathematical model for the genetic regulatory network of the lactose operon. This mathematical model contains transcription and translation of the lactose permease (LacY) and a reporter gene GFP. The probability of transcription of LacY is determined by 14 binding states out of all 50 possible binding states of the lactose operon based on the quasi-steady-state assumption for the binding reactions, while we calculate the probability of transcription for the reporter gene GFP based on 5 binding states out of 19 possible binding states because the binding site O2 is missing for this reporter gene. We have tested different mechanisms for the transport of thio-methylgalactoside (TMG) and the effect of different Hill coefficients on the simulated LacY expression levels. Using this mathematical model we have realized one of the experimental results with different LacY concentrations, which are induced by different concentrations of TMG.

Evolving genetic regulatory networks performing as stochastic switches

Recent studies have shown that small genetic regulatory networks (GRNs) can be evolved in silico displaying certain dynamics in the underlying mathematical model. It is expected that evolutionary approaches can help to gain a better understanding of biological design principles and assist in the engineering of genetic networks. To take the stochastic nature of GRNs into account, our evolutionary approach models GRNs as biochemical reaction networks based on simple enzyme kinetics and simulates them by using Gillespie’s stochastic simulation algorithm (SSA). We have already demonstrated the relevance of considering intrinsic stochasticity by evolving GRNs that show oscillatory dynamics in the SSA but not in the ODE regime. Here, we present and discuss first results in the evolution of GRNs performing as stochastic switches.

Intensive Case Management: A Critical Re-Appraisal of the Scientific Evidence for Effectiveness

Intensive Case Management (ICM) is widely claimed to be an evidence-based and cost effective program for people with high levels of disability as a result of mental illness. However, the findings of recent randomized controlled trials comparing ICM with ‘usual services’ suggest that both clinical and cost effectiveness of ICM may be weakening. Possible reasons for this, including fidelity of implementation, researcher allegiance effects and changes in the wider service environment within which ICM is provided, are considered. The implications for service delivery and research are discussed.

Strategic dalliances as an enabler for discontinuous innovation in slow clockspeed industries: evidence from the oil and gas industry

The concept of ‘strategic dalliances’– defined as non-committal relationships that companies can ‘dip in and out of,’ or dally with, while simultaneously maintaining longer-term strategic partnerships with other firms and suppliers – has emerged as a promising strategy by which organizations can create discontinuous innovations. But does this approach work equally well for every sector? Moreover, how can these links be effectively used to foster the process of discontinuous innovation? Toward assessing the role that industry clockspeed plays in the success or failure of strategic dalliances, we provide case study evidence from Twister BV, an upstream oil and gas technology provider, and show that strategic dalliances can be an enabler for the discontinuous innovation process in slow clockspeed industries. Implications for research and practice are discussed, and conclusions from our findings are drawn.