Protein monoubiquitination and polyubiquitination generate structural diversity to control distinct biological processes

Ubiquitination involves the attachment of ubiquitin (Ub) to lysine residues on substrate proteins or itself, which can result in protein monoubiquitination or polyubiquitination. Polyubiquitination through different lysines (seven) or the N-terminus of Ub can generate different protein-Ub structures. These include monoubiquitinated proteins, polyubiqutinated proteins with homotypic chains through a particular lysine on Ub or mixed polyubiquitin chains generated by polymerization through different Ub lysines. The ability of the ubiquitination pathway to generate different protein-Ub structures provides versatility of this pathway to target proteins to different fates. Protein ubiquitination is catalyzed by Ub-conjugating and Ub-ligase enzymes, with different combinations of these enzymes specifying the type of Ub modification on protein substrates. How Ub-conjugating and Ub-ligase enzymes generate this structural diversity is not clearly understood. In the current review, we discuss mechanisms utilized by the Ub-conjugating and Ub-ligase enzymes to generate structural diversity during protein ubiquitination, with a focus on recent mechanistic insights into protein monoubiquitination and polyubiquitination.

Critical timescales and time intervals for coupled linear processes

In 1991, McNabb introduced the concept of mean action time (MAT) as a finite measure of the time required for a diffusive process to effectively reach steady state. Although this concept was initially adopted by others within the Australian and New Zealand applied mathematics community, it appears to have had little use outside this region until very recently, when in 2010 Berezhkovskii and coworkers rediscovered the concept of MAT in their study of morphogen gradient formation. All previous work in this area has been limited to studying single–species differential equations, such as the linear advection–diffusion–reaction equation. Here we generalise the concept of MAT by showing how the theory can be applied to coupled linear processes. We begin by studying coupled ordinary differential equations and extend our approach to coupled partial differential equations. Our new results have broad applications including the analysis of models describing coupled chemical decay and cell differentiation processes, amongst others.

Lignocellulosics as a renewable feedstock for chemical industry : chemical hydrolysis and pretreatment processes

Lignocellulosic materials including agricultural, municipal and forestry residues, and dedicated bioenergy crops offer significant potential as a renewable feedstock for the production of fuels and chemicals. These products can be chemically or functionally equivalent to existing products that are produced from fossil-based feedstocks. To unlock the potential of lignocellulosic materials, it is necessary to pretreat or fractionate the biomass to make it amenable to downstream processing. This chapter explores current and developing technologies for the pretreatment and fractionation of lignocellulosic biomass for the production of chemicals and fuels.

Queer theory, media studies and editorial processes in queer student media

Australian queer (GLBTIQ) university student activist media is an important site of self-representation. Community media is a significant site for the development of queer identity, community and a key part of queer politics. This paper reviews my research into queer student media, which is grounded in a queer theoretical perspective. Rob Cover argues that queer theoretical approaches that study media products fail to consider the material contexts that contribute to their construction. I use an ethnographic approach to examine how editors construct queer identity and community in queer student media. My research contributes to queer media scholarship by addressing the gap that Cover identifies, and to the rich scholarship on negotiations of queer community.

Efficient route update and maintenance processes for multipath routing in large-scale industrial wireless sensor networks

Reliable communications is one of the major concerns in wireless sensor networks (WSNs). Multipath routing is an effective way to improve communication reliability in WSNs. However, most of existing multipath routing protocols for sensor networks are reactive and require dynamic route discovery. If there are many sensor nodes from a source to a destination, the route discovery process will create a long end-to-end transmission delay, which causes difficulties in some time-critical applications. To overcome this difficulty, the efficient route update and maintenance processes are proposed in this paper. It aims to limit the amount of routing overhead with two-tier routing architecture and introduce the combination of piggyback and trigger update to replace the periodic update process, which is the main source of unnecessary routing overhead. Simulations are carried out to demonstrate the effectiveness of the proposed processes in improvement of total amount of routing overhead over existing popular routing protocols.

Silver Gelatin Print: A group exhibition curated by Karen Milder that investigates and captures the traditional processes using photograms, liquid emulsion, toning, hand-colouring and film. Part of the Queensland Festival of Photography 4 (QFP4).

Pillar of salt: (3 hand-applied silver gelatin photographs) Statement: For women moving into new experiences and spaces, loss and hardship is often a price to be paid. These courageous women look back to things they have overcome in order to continue to grow.

Automated risk mitigation in business processes

This paper proposes a concrete approach for the automatic mitigation of risks that are detected during process enactment. Given a process model exposed to risks, e.g. a financial process exposed to the risk of approval fraud, we enact this process and as soon as the likelihood of the associated risk(s) is no longer tolerable, we generate a set of possible mitigation actions to reduce the risks' likelihood, ideally annulling the risks altogether. A mitigation action is a sequence of controlled changes applied to the running process instance, taking into account a snapshot of the process resources and data, and the current status of the system in which the process is executed. These actions are proposed as recommendations to help process administrators mitigate process-related risks as soon as they arise. The approach has been implemented in the YAWL environment and its performance evaluated. The results show that it is possible to mitigate process-related risks within a few minutes.

Procuring OSM : base-line models of off-site manufacture business processes in Australia

A pressing cost issue facing construction is the procurement of off-site pre-manufactured assemblies. In order to encourage Australian adoption of off-site manufacture (OSM), a new approach to underlying processes is required. The advent of object oriented digital models for construction design assumes intelligent use of data. However, the construction production system relies on traditional methods and data sources and is expected to benefit from the application of well-established business process management techniques. The integration of the old and new data sources allows for the development of business process models which, by capturing typical construction processes involving OSM, provides insights into such processes. This integrative approach is the foundation of research into the use of OSM to increase construction productivity in Australia. The purpose of this study is to develop business process models capturing the procurement, resources and information flow of construction projects. For each stage of the construction value chain, a number of sub-processes are identified. Business Process Modelling Notation (BPMN), a mainstream business process modelling standard, is used to create base-line generic construction process models. These models identify OSM decision-making points that could provide cost reductions in procurement workflow and management systems. This paper reports on phase one of an on-going research aiming to develop a proto-type workflow application that can provide semi-automated support to construction processes involving OSM and assist in decision-making in the adoption of OSM thus contributing to a sustainable built environment.

Real-time risk monitoring in business processes : a sensor-based approach

This article proposes an approach for real-time monitoring of risks in executable business process models. The approach considers risks in all phases of the business process management lifecycle, from process design, where risks are defined on top of process models, through to process diagnosis, where risks are detected during process execution. The approach has been realized via a distributed, sensor-based architecture. At design-time, sensors are defined to specify risk conditions which when fulfilled, are a likely indicator of negative process states (faults) to eventuate. Both historical and current process execution data can be used to compose such conditions. At run-time, each sensor independently notifies a sensor manager when a risk is detected. In turn, the sensor manager interacts with the monitoring component of a business process management system to prompt the results to process administrators who may take remedial actions. The proposed architecture has been implemented on top of the YAWL system, and evaluated through performance measurements and usability tests with students. The results show that risk conditions can be computed efficiently and that the approach is perceived as useful by the participants in the tests.

Submission to National Inquiry into Children in Immigration Detention from The Australian Psychological Society

Executive Summary The Australian Psychological Society categorically condemns the practice of detaining child asylum seekers and their families, on the grounds that it is not commensurate with psychological best practice concerning children’s development and mental health and wellbeing. Detention of children in this fashion is also arguably a violation of the UN Convention on the Rights of the Child. A thorough review of relevant psychological theory and available research findings from international research has led the Australian Psychological Society to conclude that: • Detention is a negative socialisation experience. • Detention is accentuates developmental risks. • Detention threatens the bonds between children and significant caregivers. • Detention limits educational opportunities. • Detention has traumatic impacts on children of asylum seekers. • Detention reduces children’s potential to recover from trauma. • Detention exacerbates the impacts of other traumas. • Detention of children from these families in many respects is worse for them than being imprisoned. In the absence of any indication from the Australian Government that it intends in the near future to alter the practice of holding children in immigration detention, the Australian Psychological Society’s intermediate position is that the facilitation of short-term and long-term psychological development and wellbeing of children is the basic tenet upon which detention centres should be audited and judged. Based on that position, the Society has identified a series of questions and concerns that arise directly from the various psychological perspectives that have been brought to bear on estimating the effects of detention on child asylum seekers. The Society argues that, because these questions and concerns relate specifically to improvement and maintenance of child detainees’ educational, social and psychological wellbeing, they are legitimate matters for the Inquiry to consider and investigate. • What steps are currently being taken to monitor the psyc hological welfare of the children in detention? In particular, what steps are being taken to monitor the psychological wellbeing of children arriving from war-torn countries? • What qualifications and training do staff who care for children and their families in detention centres have? What knowledge do they have of psychological issues faced by people who have been subjected to traumatic experiences and are suffering high degrees of anxiety, stress and uncertainty? • What provisions have been made for psycho-educational assessment of children’s specific learning needs prior to their attending formal educational programmes? • who are suffering chronic and/or vicarious trauma as a result of witnessing threatening behaviour whilst in detention? • What provisions have been made for families who have been seriously affected by displacement to participate in family therapy? • What critical incident debriefing procedures are in place for children who have witnessed their parents, other family members, or social acquaintances engaging in acts of self-harm or being harmed while in detention? What psychotherapeutic support is in place for children who themselves have been harmed or have engaged in self- harmful acts while in detention? • What provisions are in place for parenting programmes that provide support for parents of children under extremely difficult psychological and physical circumstances? • What efforts are being made to provide parents with the opportunity to model traditional family roles for children, such as working to earn an income, meal preparation, other household duties, etc.? • What opportunities are in place for the assessment of safety issues such as bullying, and sexual or physical abuse of children or their mothers in detention centres? • How are resources distributed to children and families in detention centres? • What socialization opportunities are available either within detention centres or in the wider community for children to develop skills and independence, engage in social activities, participate in cultural traditions, and communicate and interaction with same-age peers and adults from similar ethnic and religious backgrounds? • What access do children and families have to videos, music and entertainment from their cultures of origin? • What provisions are in place to ensure the maintenance of privacy in a manner commensurate with usual cultural practice? • What is the Government’s rationale for continuing to implement a policy of mandatory detention of child asylum seekers that on the face of it is likely to have a pernicious impact on these children’s mental health? • In view of the evidence on the potential long-term impact of mandatory detention on children, what processes may be followed by Government to avoid such a practice and, more importantly, to develop policies and practices that will have a positive impact on these children’s psychological development and mental health?

Implementing green business processes : the importance of functional affordances of information systems

An environmentally sustainable and thus green business process is one that delivers organizational value whilst also exerting a minimal impact on the natural environment. Recent works from the field of Information Systems (IS) have argued that information systems can contribute to the design and implementation of sustainable business processes. While prior research has investigated how information systems can be used in order to support sustainable business practices, there is still a void as to the actual changes that business processes have to undergo in order to become environmentally sustainable, and the specific role that information systems play in enabling this change. In this paper, we provide a conceptualization of environmentally sustainable business processes, and discuss the role of functional affordances of information systems in enabling both incremental and radical changes in order to make processes environmentally sustainable. Our conceptualization is based on (a) a fundamental definition of the concept of environmental sustainability, grounded in two basic components:the environmental source and sink functions of any project or activity, and (b) the concept of functional affordances, which describe the potential uses originating in the material properties of information systems in relation to their use context. In order to illustrate the application of our framework and provide a first evaluation, we analyse two examples from prior research where information systems impacted on the sustainability of business processes.

Configuring processes and business documents : an integrated approach to enterprise systems collaboration

Enterprise Systems (ES) provide standardized, off-theshelf support for operations and management within organizations. With the advent of ES based on a serviceoriented architecture (SOA) and an increasing demand of IT-supported interorganizational collaboration, implementation projects face paradigmatically new challenges. The configuration of ES is costly and error-prone. Dependencies between business processes and business documents are hardly explicit and foster component proliferation instead of reuse. Configurative modeling can support the problem in two ways: First, conceptual modeling abstracts from technical details and provides more intuitive access and overview. Second, configuration allows the projection of variants from master models providing manageable variants with controlled flexibility. We aim at tackling the problem by proposing an integrated model-based framework for configuring both, processes and business documents, on an equal basis; as together, they constitute the core business components of an ES.

The rise of birds and mammals: are microevolutionary processes sufficient for macroevolution?

It is a basis of darwinian evolution that the microevolutionary mechanisms that can be studied in the present are sufficient to account for macroevolution. However, this idea needs to be tested explicitly, as highlighted here by the example of the superceding of dinosaurs and pterosaurs by birds and placental mammals that occurred near the Cretaceous/Tertiary boundary approximately 65 million years ago. A major problem for testing the sufficiency of microevolutionary processes is that independent ideas (such as the existence of an extraterrestrial impact, and the extinction of dinosaurs) were linked without the evidence for each idea being evaluated separately. Here, we suggest and discuss five testable models for the times and divergences of modern mammals and birds. Determination of the model that best represents these events will enable the role of microevolutionary mechanisms to be evaluated. The question of the sufficiency of microevolutionary processes for macroevolution is solvable, and available evidence supports an important role for biological processes in the initial decline of dinosaurs and pterosaurs.

A catchment modelling approach integrating surface and groundwater processes, land use and distribution of nutrients : Elimbah Creek, southeast Queensland

As the world’s population is growing, so is the demand for agricultural products. However, natural nitrogen (N) fixation and phosphorus (P) availability cannot sustain the rising agricultural production, thus, the application of N and P fertilisers as additional nutrient sources is common. It is those anthropogenic activities that can contribute high amounts of organic and inorganic nutrients to both surface and groundwaters resulting in degradation of water quality and a possible reduction of aquatic life. In addition, runoff and sewage from urban and residential areas can contain high amounts of inorganic and organic nutrients which may also affect water quality. For example, blooms of the cyanobacterium Lyngbya majuscula along the coastline of southeast Queensland are an indicator of at least short term decreases of water quality. Although Australian catchments, including those with intensive forms of land use, show in general a low export of nutrients compared to North American and European catchments, certain land use practices may still have a detrimental effect on the coastal environment. Numerous studies are reported on nutrient cycling and associated processes on a catchment scale in the Northern Hemisphere. Comparable studies in Australia, in particular in subtropical regions are, however, limited and there is a paucity in the data, in particular for inorganic and organic forms of nitrogen and phosphorus; these nutrients are important limiting factors in surface waters to promote algal blooms. Therefore, the monitoring of N and P and understanding the sources and pathways of these nutrients within a catchment is important in coastal zone management. Although Australia is the driest continent, in subtropical regions such as southeast Queensland, rainfall patterns have a significant effect on runoff and thus the nutrient cycle at a catchment scale. Increasingly, these rainfall patterns are becoming variable. The monitoring of these climatic conditions and the hydrological response of agricultural catchments is therefore also important to reduce the anthropogenic effects on surface and groundwater quality. This study consists of an integrated hydrological–hydrochemical approach that assesses N and P in an environment with multiple land uses. The main aim is to determine the nutrient cycle within a representative coastal catchment in southeast Queensland, the Elimbah Creek catchment. In particular, the investigation confirms the influence associated with forestry and agriculture on N and P forms, sources, distribution and fate in the surface and groundwaters of this subtropical setting. In addition, the study determines whether N and P are subject to transport into the adjacent estuary and thus into the marine environment; also considered is the effect of local topography, soils and geology on N and P sources and distribution. The thesis is structured on four components individually reported. The first paper determines the controls of catchment settings and processes on stream water, riverbank sediment, and shallow groundwater N and P concentrations, in particular during the extended dry conditions that were encountered during the study. Temporal and spatial factors such as seasonal changes, soil character, land use and catchment morphology are considered as well as their effect on controls over distributions of N and P in surface waters and associated groundwater. A total number of 30 surface and 13 shallow groundwater sampling sites were established throughout the catchment to represent dominant soil types and the land use upstream of each sampling location. Sampling comprises five rounds and was conducted over one year between October 2008 and November 2009. Surface water and groundwater samples were analysed for all major dissolved inorganic forms of N and for total N. Phosphorus was determined in the form of dissolved reactive P (predominantly orthophosphate) and total P. In addition, extracts of stream bank sediments and soil grab samples were analysed for these N and P species. Findings show that major storm events, in particular after long periods of drought conditions, are the driving force of N cycling. This is expressed by higher inorganic N concentrations in the agricultural subcatchment compared to the forested subcatchment. Nitrate N is the dominant inorganic form of N in both the surface and groundwaters and values are significantly higher in the groundwaters. Concentrations in the surface water range from 0.03 to 0.34 mg N L..1; organic N concentrations are considerably higher (average range: 0.33 to 0.85 mg N L..1), in particular in the forested subcatchment. Average NO3-N in the groundwater has a range of 0.39 to 2.08 mg N L..1, and organic N averages between 0.07 and 0.3 mg N L..1. The stream bank sediments are dominated by organic N (range: 0.53 to 0.65 mg N L..1), and the dominant inorganic form of N is NH4-N with values ranging between 0.38 and 0.41 mg N L..1. Topography and soils, however, were not to have a significant effect on N and P concentrations in waters. Detectable phosphorus in the surface and groundwaters of the catchment is limited to several locations typically in the proximity of areas with intensive animal use; in soil and sediments, P is negligible. In the second paper, the stable isotopes of N (14N/15N) and H2O (16O/18O and 2H/H) in surface and groundwaters are used to identify sources of dissolved inorganic and organic N in these waters, and to determine their pathways within the catchment; specific emphasis is placed on the relation of forestry and agriculture. Forestry is predominantly concentrated in the northern subcatchment (Beerburrum Creek) while agriculture is mainly found in the southern subcatchment (Six Mile Creek). Results show that agriculture (horticulture, crops, grazing) is the main source of inorganic N in the surface waters of the agricultural subcatchment, and their isotopic signature shows a close link to evaporation processes that may occur during water storage in farm dams that are used for irrigation. Groundwaters are subject to denitrification processes that may result in reduced dissolved inorganic N concentrations. Soil organic matter delivers most of the inorganic N to the surface water in the forested subcatchment. Here, precipitation and subsequently runoff is the main source of the surface waters. Groundwater in this area is affected by agricultural processes. The findings also show that the catchment can attenuate the effects of anthropogenic land use on surface water quality. Riparian strips of natural remnant vegetation, commonly 50 to 100 m in width, act as buffer zones along the drainage lines in the catchment and remove inorganic N from the soil water before it enters the creek. These riparian buffer zones are common in most agricultural catchments of southeast Queensland and are indicated to reduce the impact of agriculture on stream water quality and subsequently on the estuary and marine environments. This reduction is expressed by a significant decrease in DIN concentrations from 1.6 mg N L..1 to 0.09 mg N L..1, and a decrease in the �15N signatures from upstream surface water locations downstream to the outlet of the agricultural subcatchment. Further testing is, however, necessary to confirm these processes. Most importantly, the amount of N that is transported to the adjacent estuary is shown to be negligible. The third and fourth components of the thesis use a hydrological catchment model approach to determine the water balance of the Elimbah Creek catchment. The model is then used to simulate the effects of land use on the water balance and nutrient loads of the study area. The tool that is used is the internationally widely applied Soil and Water Assessment Tool (SWAT). Knowledge about the water cycle of a catchment is imperative in nutrient studies as processes such as rainfall, surface runoff, soil infiltration and routing of water through the drainage system are the driving forces of the catchment nutrient cycle. Long-term information about discharge volumes of the creeks and rivers do, however, not exist for a number of agricultural catchments in southeast Queensland, and such information is necessary to calibrate and validate numerical models. Therefore, a two-step modelling approach was used to calibrate and validate parameters values from a near-by gauged reference catchment as starting values for the ungauged Elimbah Creek catchment. Transposing monthly calibrated and validated parameter values from the reference catchment to the ungauged catchment significantly improved model performance showing that the hydrological model of the catchment of interest is a strong predictor of the water water balance. The model efficiency coefficient EF shows that 94% of the simulated discharge matches the observed flow whereas only 54% of the observed streamflow was simulated by the SWAT model prior to using the validated values from the reference catchment. In addition, the hydrological model confirmed that total surface runoff contributes the majority of flow to the surface water in the catchment (65%). Only a small proportion of the water in the creek is contributed by total base-flow (35%). This finding supports the results of the stable isotopes 16O/18O and 2H/H, which show the main source of water in the creeks is either from local precipitation or irrigation waters delivered by surface runoff; a contribution from the groundwater (baseflow) to the creeks could not be identified using 16O/18O and 2H/H. In addition, the SWAT model calculated that around 68% of the rainfall occurring in the catchment is lost through evapotranspiration reflecting the prevailing long-term drought conditions that were observed prior and during the study. Stream discharge from the forested subcatchment was an order of magnitude lower than discharge from the agricultural Six Mile Creek subcatchment. A change in land use from forestry to agriculture did not significantly change the catchment water balance, however, nutrient loads increased considerably. Conversely, a simulated change from agriculture to forestry resulted in a significant decrease of nitrogen loads. The findings of the thesis and the approach used are shown to be of value to catchment water quality monitoring on a wider scale, in particular the implications of mixed land use on nutrient forms, distributions and concentrations. The study confirms that in the tropics and subtropics the water balance is affected by extended dry periods and seasonal rainfall with intensive storm events. In particular, the comprehensive data set of inorganic and organic N and P forms in the surface and groundwaters of this subtropical setting acquired during the one year sampling program may be used in similar catchment hydrological studies where these detailed information is missing. Also, the study concludes that riparian buffer zones along the catchment drainage system attenuate the transport of nitrogen from agricultural sources in the surface water. Concentrations of N decreased from upstream to downstream locations and were negligible at the outlet of the catchment.

How collaborative technology supports cognitive processes in collaborative process modeling : a capabilities-gains-outcome model

We examine which capabilities technologies provide to support collaborative process modeling. We develop a model that explains how technology capabilities impact cognitive group processes, and how they lead to improved modeling outcomes and positive technology beliefs. We test this model through a free simulation experiment of collaborative process modelers structured around a set of modeling tasks. With our study, we provide an understanding of the process of collaborative process modeling, and detail implications for research and guidelines for the practical design of collaborative process modeling.