Senataxin plays an essential role with DNA damage response proteins in meiotic recombination and gene silencing

Senataxin, mutated in the human genetic disorder ataxia with oculomotor apraxia type 2 (AOA2), plays an important role in maintaining genome integrity by coordination of transcription, DNA replication, and the DNA damage response. We demonstrate that senataxin is essential for spermatogenesis and that it functions at two stages in meiosis during crossing-over in homologous recombination and in meiotic sex chromosome inactivation (MSCI). Disruption of the Setx gene caused persistence of DNA double-strand breaks, a defect in disassembly of Rad51 filaments, accumulation of DNA:RNA hybrids (R-loops), and ultimately a failure of crossing-over. Senataxin localised to the XY body in a Brca1-dependent manner, and in its absence there was incomplete localisation of DNA damage response proteins to the XY chromosomes and ATR was retained on the axial elements of these chromosomes, failing to diffuse out into chromatin. Furthermore persistence of RNA polymerase II activity, altered ubH2A distribution, and abnormal XY-linked gene expression in Setx⁻/⁻ revealed an essential role for senataxin in MSCI. These data support key roles for senataxin in coordinating meiotic crossing-over with transcription and in gene silencing to protect the integrity of the genome.

Using enterprise information architecture methods to model wicked problems in information systems design research

Design Science is the process of solving ‘wicked problems’ through designing, developing, instantiating, and evaluating novel solutions (Hevner, March, Park and Ram, 2004). Wicked problems are described as agent finitude in combination with problem complexity and normative constraint (Farrell and Hooker, 2013). In Information Systems Design Science, determining that problems are ‘wicked’ differentiates Design Science research from Solutions Engineering (Winter, 2008) and is a necessary part of proving the relevance to Information Systems Design Science research (Hevner, 2007; Iivari, 2007). Problem complexity is characterised as many problem components with nested, dependent and co-dependent relationships interacting through multiple feedback and feed-forward loops. Farrell and Hooker (2013) specifically state for wicked problems “it will often be impossible to disentangle the consequences of specific actions from those of other co-occurring interactions”. This paper discusses the application of an Enterprise Information Architecture modelling technique to disentangle the wicked problem complexity for one case. It proposes that such a modelling technique can be applied to other wicked problems and can lay the foundations for proving relevancy to DSR, provide solution pathways for artefact development, and aid to substantiate those elements required to produce Design Theory.

Yhh1p/Cft1p directly links poly(A) site recognition and RNA polymerase II transcription termination

RNA polymerase II (pol II) transcription termination requires co‐transcriptional recognition of a functional polyadenylation signal, but the molecular mechanisms that transduce this signal to pol II remain unclear. We show that Yhh1p/Cft1p, the yeast homologue of the mammalian AAUAAA interacting protein CPSF 160, is an RNA‐binding protein and provide evidence that it participates in poly(A) site recognition. Interestingly, RNA binding is mediated by a central domain composed of predicted β‐propeller‐forming repeats, which occurs in proteins of diverse cellular functions. We also found that Yhh1p/Cft1p bound specifically to the phosphorylated C‐terminal domain (CTD) of pol II in vitro and in a two‐hybrid test in vivo. Furthermore, transcriptional run‐on analysis demonstrated that yhh1 mutants were defective in transcription termination, suggesting that Yhh1p/Cft1p functions in the coupling of transcription and 3′‐end formation. We propose that direct interactions of Yhh1p/Cft1p with both the RNA transcript and the CTD are required to communicate poly(A) site recognition to elongating pol II to initiate transcription termination.

Independent functions of yeast Pcf11p in pre-mRNA 3' end processing and in transcription termination

Pcf11p, an essential subunit of the yeast cleavage factor IA, is required for pre‐mRNA 3′ end processing, binds to the C‐terminal domain (CTD) of the largest subunit of RNA polymerase II (RNAP II) and is involved in transcription termination. We show that the conserved CTD interaction domain (CID) of Pcf11p is essential for cell viability. Interestingly, the CTD binding and 3′ end processing activities of Pcf11p can be functionally uncoupled from each other and provided by distinct Pcf11p fragments in trans. Impaired CTD binding did not affect the 3′ end processing activity of Pcf11p and a deficiency of Pcf11p in 3′ end processing did not prevent CTD binding. Transcriptional run‐on analysis with the CYC1 gene revealed that loss of cleavage activity did not correlate with a defect in transcription termination, whereas loss of CTD binding did. We conclude that Pcf11p is a bifunctional protein and that transcript cleavage is not an obligatory step prior to RNAP II termination.

The role of radiotherapy patients in provision of student interpersonal skills feedback

Background At Queensland University of Technology, student radiation therapists receive regular feedback from clinical staff relating to clinical interpersonal skills. Although this is of great value, there is anecdotal evidence that students communicate differently with patients when under observation. Purpose The aim of this pilot was to counter this perceived observer effect by allowing patients to provide students with additional feedback. Materials and methods Radiotherapy patients from two departments were provided with anonymous feedback forms relating to aspects of student interpersonal skills. Clinical assessors, mentors and students were also provided with feedback forms, including questions about the role of patient feedback. Patient perceptions of student performance were correlated with staff feedback and assessment scores. Results Results indicated that the feedback was valued by both students and patients. Students reported that the additional dimension focused them on communication, set goals for development and increased motivation. These changes derived from both feedback and study participation, suggesting that the questionnaires could be a useful teaching tool. Patients scored more generously than mentors, although there was agreement in relative grading. Conclusions The anonymous questionnaire is a convenient and valuable method of gathering patient feedback on students. Future iterations will determine the optimum timing for this method of feedback.

Activation of forkhead box O transcription factors by oncogenic BRAF promotes p21cip1-dependent senescence

Oncogene-induced senescence (OIS) is a potent tumor-suppressive mechanism that is thought to come at the cost of aging. The Forkhead box O (FOXO) transcription factors are regulators of life span and tumor suppression. However, whether and how FOXOs function in OIS have been unclear. Here, we show a role for FOXO4 in mediating senescence by the human BRAFV600E oncogene, which arises commonly in melanoma. BRAFV600E signaling through mitogen-activated protein kinase/extracellular signal-regulated kinase kinase resulted in increased reactive oxygen species levels and c-Jun NH 2 terminal kinase-mediated activation of FOXO4 via its phosphorylation on Thr223, Ser226, Thr447, and Thr451. BRAFV600E-induced FOXO4 phosphorylation resulted in p21cip1-mediated cell senescence independent of p16 ink4a or p27kip1. Importantly, melanocyte-specific activation of BRAFV600E in vivo resulted in the formation of skin nevi expressing Thr223/Ser226-phosphorylated FOXO4 and elevated p21cip1. Together, these findings support a model in which FOXOs mediate a trade-off between cancer and aging.

Identification of direct transcriptional targets of V600EBRAF/MEK signalling in melanoma

Oncogenic mutations in BRAF are common in melanoma and drive constitutive activation of the MEK/ERK pathway. To elucidate the transcriptional events downstream of V600EBRAF/MEK signalling we performed gene expression profiling of A375 melanoma cells treated with potent and selective inhibitors of V600EBRAF and MEK (PLX4720 and PD184352 respectively). Using a stringent Bayesian approach, we identified 69 transcripts that appear to be direct transcriptional targets of this pathway and whose expression changed after 6 h of pathway inhibition. We also identified several additional genes whose expression changed after 24 h of pathway inhibition and which are likely to be indirect transcriptional targets of the pathway. Several of these were confirmed by demonstrating their expression to be similarly regulated when BRAF was depleted using RNA interference, and by using qRT-PCR in other BRAF mutated melanoma lines. Many of these genes are transcription factors and feedback inhibitors of the ERK pathway and are also regulated by MEK signalling in NRAS mutant cells. This study provides a basis for understanding the molecular processes that are regulated by V600EBRAF/MEK signalling in melanoma cells.

Transcription factories : gene expression in unions?

Transcription is a fundamental step in gene expression, yet it remains poorly understood at a cellular level. Visualization of transcription sites and active genes has led to the suggestion that transcription occurs at discrete sites in the nucleus, termed transcription factories, where multiple active RNA polymerases are concentrated and anchored to a nuclear substructure. However, this concept is not universally accepted. This Review discusses the experimental evidence in support of the transcription factory model and the evidence that argues against such a spatially structured view of transcription. The transcription factory model has implications for the regulation of transcription initiation and elongation, for the organization of genes in the genome, for the co-regulation of genes and for genome instability.

Improving national hospice/palliative care service symptom outcomes systematically through point-of-care data collection, structured feedback and benchmarking

PURPOSE Every health care sector including hospice/palliative care needs to systematically improve services using patient-defined outcomes. Data from the national Australian Palliative Care Outcomes Collaboration aims to define whether hospice/palliative care patients' outcomes and the consistency of these outcomes have improved in the last 3 years. METHODS Data were analysed by clinical phase (stable, unstable, deteriorating, terminal). Patient-level data included the Symptom Assessment Scale and the Palliative Care Problem Severity Score. Nationally collected point-of-care data were anchored for the period July-December 2008 and subsequently compared to this baseline in six 6-month reporting cycles for all services that submitted data in every time period (n = 30) using individual longitudinal multi-level random coefficient models. RESULTS Data were analysed for 19,747 patients (46 % female; 85 % cancer; 27,928 episodes of care; 65,463 phases). There were significant improvements across all domains (symptom control, family care, psychological and spiritual care) except pain. Simultaneously, the interquartile ranges decreased, jointly indicating that better and more consistent patient outcomes were being achieved. CONCLUSION These are the first national hospice/palliative care symptom control performance data to demonstrate improvements in clinical outcomes at a service level as a result of routine data collection and systematic feedback.

Optimal HMM filtering and decision feedback equalisation for differential encoded transmission systems

In this paper conditional hidden Markov model (HMM) filters and conditional Kalman filters (KF) are coupled together to improve demodulation of differential encoded signals in noisy fading channels. We present an indicator matrix representation for differential encoded signals and the optimal HMM filter for demodulation. The filter requires O(N3) calculations per time iteration, where N is the number of message symbols. Decision feedback equalisation is investigated via coupling the optimal HMM filter for estimating the message, conditioned on estimates of the channel parameters, and a KF for estimating the channel states, conditioned on soft information message estimates. The particular differential encoding scheme examined in this paper is differential phase shift keying. However, the techniques developed can be extended to other forms of differential modulation. The channel model we use allows for multiplicative channel distortions and additive white Gaussian noise. Simulation studies are also presented.

Improving criteria and feedback in student assessment in law

Spurred on by both the 1987 Pearce Report1 and the general changes to higher education spawned by the “Dawkins revolution” from 1988, there has been much critical self-evaluation leading to profound improvements to the quality of teaching in Australian law schools.2 Despite the changes there are still areas of general law teaching practice which have lagged behind recent developments in our understanding of what constitutes high quality teaching. One such area is assessment criteria and feedback. The project Improving Feedback in Student Assessment in Law is an attempt to remedy this. It aims to produce a manual containing key principles for the design of assessment and the provision of feedback, with practical yet flexible ideas and illustrations which law teachers may adopt or modify. Most of the examples have been developed by teachers at the University of Melbourne Law School. The project was supported in 1996 by a Committee for the Advancement of University Teaching grant and the manual will be published late in 1997.3 This note summarises the core principles which are elaborated further in the manual.

Stochastic output feedback model predictive control

This paper addresses the issue of output feedback model predictive control for linear systems with input constraints and stochastic disturbances. We show that the optimal policy uses the Kalman filter for state estimation, but the resultant state estimates are not utilized in a certainty equivalence control law

Learning-based Relevance Feedback for Web-based Relation Completion

In a pilot application based on web search engine calledWeb-based Relation Completion (WebRC), we propose to join two columns of entities linked by a predefined relation by mining knowledge from the web through a web search engine. To achieve this, a novel retrieval task Relation Query Expansion (RelQE) is modelled: given an entity (query), the task is to retrieve documents containing entities in predefined relation to the given one. Solving this problem entails expanding the query before submitting it to a web search engine to ensure that mostly documents containing the linked entity are returned in the top K search results. In this paper, we propose a novel Learning-based Relevance Feedback (LRF) approach to solve this retrieval task. Expansion terms are learned from training pairs of entities linked by the predefined relation and applied to new entity-queries to find entities linked by the same relation. After describing the approach, we present experimental results on real-world web data collections, which show that the LRF approach always improves the precision of top-ranked search results to up to 8.6 times the baseline. Using LRF, WebRC also shows performances way above the baseline.