hSSB1 (NABP2/ OBFC2B) is required for the repair of 8-oxo-guanine by the hOGG1-mediated base excision repair pathway

The maintenance of genome stability is essential to prevent loss of genetic information and the development of diseases such as cancer. One of the most common forms of damage to the genetic code is the oxidation of DNA by reactive oxygen species (ROS), of which 8-oxo-7,8-dihydro-guanine (8-oxoG) is the most frequent modification. Previous studies have established that human single-stranded DNA-binding protein 1 (hSSB1) is essential for the repair of double-stranded DNA breaks by the process of homologous recombination. Here we show that hSSB1 is also required following oxidative damage. Cells lacking hSSB1 are sensitive to oxidizing agents, have deficient ATM and p53 activation and cannot effectively repair 8-oxoGs. Furthermore, we demonstrate that hSSB1 forms a complex with the human oxo-guanine glycosylase 1 (hOGG1) and is important for hOGG1 localization to the damaged chromatin. In vitro, hSSB1 binds directly to DNA containing 8-oxoguanines and enhances hOGG1 activity. These results underpin the crucial role hSSB1 plays as a guardian of the genome.

How serious are they? The use of data linkage to explore different definitions of serious road crash injuries

Over recent years, the focus in road safety has shifted towards a greater understanding of road crash serious injuries in addition to fatalities. Police reported crash data are often the primary source of crash information; however, the definition of serious injury within these data is not consistent across jurisdictions and may not be accurately operationalised. This study examined the linkage of police-reported road crash data with hospital data to explore the potential for linked data to enhance the quantification of serious injury. Data from the Queensland Road Crash Database (QRCD), the Queensland Hospital Admitted Patients Data Collection (QHAPDC), Emergency Department Information System (EDIS), and the Queensland Injury Surveillance Unit (QISU) for the year 2009 were linked. Nine different estimates of serious road crash injury were produced. Results showed that there was a large amount of variation in the estimates of the number and profile of serious road crash injuries depending on the definition or measure used. The results also showed that as the definition of serious injury becomes more precise the vulnerable road users become more prominent. These results have major implications in terms of how serious injuries are identified for reporting purposes. Depending on the definitions used, the calculation of cost and understanding of the impact of serious injuries would vary greatly. This study has shown how data linkage can be used to investigate issues of data quality. It has also demonstrated the potential improvements to the understanding of the road safety problem, particularly serious injury, by conducting data linkage.

Using an ‘interpretative model’ for contextual design of heritage landscape databases: The case of St Helena Island National Park in Queensland, Australia

Due to the increasing speed of landscape changes and the massive development of computer technologies, the methods of representing heritage landscapes using digital tools have become a worldwide concern in conservation research. The aim of this paper is to demonstrate how an ‘interpretative model’ can be used for contextual design of heritage landscape information systems. This approach is explored through building a geographic information system database for St Helena Island national park in Moreton Bay, South East Queensland, Australia. Stakeholders' interpretations of this landscape were collected through interviews, and then used as a framework for designing the database. The designed database is a digital inventory providing contextual descriptions of the historic infrastructure remnants on St Helena Island. It also reveals the priorities of different sites in terms of historic research, landscape restoration, and tourism development. Additionally, this database produces thematic maps of the intangible heritage values, which could be used for landscape interpretation. This approach is different from the existing methods because building a heritage information system is deemed as an interpretative activity, rather than a value-free replication of the physical environment. This approach also shows how a cultural landscape methodology can be used to create a flexible information system for heritage conservation. The conclusion is that an ‘interpretative model’ of database design facilitates a more explicit focus on information support, and is a potentially effective approach to user-centred design of geographic information systems.

Poisoning for production: how effective is fox baiting in south-eastern Australia?

1. The European red fox Vulpes vulpes represents a continuing threat to both livestock and native vertebrates in Australia, and is commonly managed by setting ground-level baits impregnated with 1080 (sodium fluoroacetate) poison. However, the long-term effectiveness of such control campaigns is likely to be limited due to the ability of foxes to disperse over considerable distances and to swiftly recolonize areas from where they had been removed. 2. To investigate the effectiveness of fox baiting in a production landscape, we assessed the potential for foxes to reinvade baited farm property areas within the jurisdiction of the Molong Rural Lands Protection Board (RLPB), an area of 815 000 ha on the central tablelands of New South Wales, Australia. The spatial distribution and timing of fox baiting campaigns between 1998 and 2002 was estimated from RLPB records and mapped using Geographical Information System software. The effectiveness of the control campaign was assessed on the basis of the likely immigration of foxes from non-baited farms using immigration distances calculated from published relationships between dispersal distance and home range size. 3. Few landholders undertook baiting campaigns in any given year, and the area baited was always so small that no baited property would have been sufficiently far from an unbaited property to have been immune from immigrating individuals. It is likely, therefore, that immigration onto farms negated any long-term effects of baiting operations. This study highlights some of the key deficiencies in current baiting practices in south-eastern Australia and suggests that pest management programmes should be monitored using such methods to ensure they achieve their goals.

Construction of microsatellite linkage maps for Corymbia

The genus Corymbia is closely related to the genus Eucalyptus, and like Eucalyptus contains tree species that are important for sub-tropical forestry. Corymbia's close relationship with Eucalyptus suggests genetic studies in Corymbia should benefit from transfer of genetic information from its more intensively studied relatives. Here we report a genetic map for Corymbia spp. based on microsatellite markers identified de novo in Corymbia sp or transferred from Eucalyptus. A framework consensus map was generated from an outbred F 2 population (n = 90) created by crossing two unrelated Corymbia torelliana x C. citriodora subsp. variegata F1 trees. The map had a total length of 367 cM (Kosambi) and was composed of 46 microsatellite markers distributed across 13 linkage groups (LOD 3). A high proportion of Eucalyptus microsatellites (90%) transferred to Corymbia. Comparative analysis between the Corymbia map and a published Eucalyptus map identified eight homeologous linkage groups in Corymbia with 13 markers mapping on one or both maps. Further comparative analysis was limited by low power to detect linkage due to low genome coverage in Corymbia, however, there was no convincing evidence for chromosomal structural differences because instances of non-synteny were associated with large distances on the Eucalyptus map. Segregation distortion was primarily restricted to a single linkage group and due to a deficit of hybrid genotypes, suggesting that hybrid inviability was one factor shaping the genetic composition of the F2 population in this inter-subgeneric hybrid. The conservation of microsatellite loci and synteny between Corymbia and Eucalyptus suggests there will be substantial value in exchanging information between the two groups.

Trapping to monitor tephritid movement: Results, best practice, and assessment of alternatives

Movement of tephritid flies underpins their survival, reproduction, and ability to establish in new areas and is thus of importance when designing effective management strategies. Much of the knowledge currently available on tephritid movement throughout landscapes comes from the use of direct or indirect methods that rely on the trapping of individuals. Here, we review published experimental designs and methods from mark-release-recapture (MRR) studies, as well as other methods, that have been used to estimate movement of the four major tephritid pest genera (Bactrocera, Ceratitis, Anastrepha, and Rhagoletis). In doing so, we aim to illustrate the theoretical and practical considerations needed to study tephritid movement. MRR studies make use of traps to directly estimate the distance that tephritid species can move within a generation and to evaluate the ecological and physiological factors that influence dispersal patterns. MRR studies, however, require careful planning to ensure that the results obtained are not biased by the methods employed, including marking methods, trap properties, trap spacing, and spatial extent of the trapping array. Despite these obstacles, MRR remains a powerful tool for determining tephritid movement, with data particularly required for understudied species that affect developing countries. To ensure that future MRR studies are successful, we suggest that site selection be carefully considered and sufficient resources be allocated to achieve optimal spacing and placement of traps in line with the stated aims of each study. An alternative to MRR is to make use of indirect methods for determining movement, or more correctly, gene flow, which have become widely available with the development of molecular tools. Key to these methods is the trapping and sequencing of a suitable number of individuals to represent the genetic diversity of the sampled population and investigate population structuring using nuclear genomic markers or non-recombinant mitochondrial DNA markers. Microsatellites are currently the preferred marker for detecting recent population displacement and provide genetic information that may be used in assignment tests for the direct determination of contemporary movement. Neither MRR nor molecular methods, however, are able to monitor fine-scale movements of individual flies. Recent developments in the miniaturization of electronics offer the tantalising possibility to track individual movements of insects using harmonic radar. Computer vision and radio frequency identification tags may also permit the tracking of fine-scale movements by tephritid flies by automated resampling, although these methods come with the same problems as traditional traps used in MRR studies. Although all methods described in this chapter have limitations, a better understanding of tephritid movement far outweighs the drawbacks of the individual methods because of the need for this information to manage tephritid populations.

A high-density consensus map of barley linking DArT markers to SSR, RFLP and STS loci and agricultural traits

Background: Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results: The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion: Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

Liquefaction Hazard Mapping of Bangalore, South India

his paper presents identification and mapping of vulnerable and safe zones for liquefaction hazard. About 850 bore logs data collected from geotechnical investigation reports have been used to estimate the liquefaction factor of safety for Bangalore Mahanagara palike (BMP) area of about 220 km(2). Liquefaction factor of safety is arrived based on surface level peak ground acceleration presented by Anbazhagan and Sitharam(5) and liquefaction resistance, using corrected standard penetration test (SPT) N values. The estimated factor of safety against liquefaction is used to estimate liquefaction potential index and liquefaction severity index. These values are mapped using Geographical information system (GIS) to identify the vulnerable and safe zones in Bangalore. This study shows that more than 95% of the BMP area is safe against liquefaction potential. However the western part of the BMP is not safe against liquefaction, as it may be subjected to liquefaction with probability of 35 to 65%. Three approaches used in this study show that 1) mapping least factor of safety irrespective of depth may be used to find liquefiable area for worst case. 2) mapping liquefaction potential index can be used to assess the liquefaction severity of the area by considering layer thickness and factor of safety and 3) mapping of liquefaction severity index can be used to access the probability of liquefaction of area.

Surveillance protocols for management of invasive plants: modelling Chilean needle grass (Nassella neesiana) in Australia

Aim: To develop a surveillance support model that enables prediction of areas susceptible to invasion, comparative analysis of surveillance methods and intensity and assessment of eradication feasibility. To apply the model to identify surveillance protocols for generalized invasion scenarios and for evaluating surveillance and control for a context-specific plant invasion. Location: Australia. Methods: We integrate a spatially explicit simulation model, including plant demography and dispersal vectors, within a Geographical Information System. We use the model to identify effective surveillance protocols using simulations of generalized plant life-forms spreading via different dispersal mechanisms in real landscapes. We then parameterize the surveillance support model for Chilean needle grass [CNG; Nassella neesiana (Trin. & Rupr.) Barkworth], a highly invasive tussock grass, which is an eradication target in south-eastern Queensland, Australia. Results: General surveillance protocols that can guide rapid response surveillance were identified; suitable habitat that is susceptible to invasion through particular dispersal syndromes should be targeted for surveillance using an adaptive seek-and-destroy method. The search radius of the adaptive method should be based on maximum expected dispersal distances. Protocols were used to define a surveillance strategy for CNG, but simulations indicated that despite effective and targeted surveillance, eradication is implausible at current intensities. Main conclusions: Several important surveillance protocols emerged and simulations indicated that effectiveness can be increased if they are followed in rapid response surveillance. If sufficient data are available, the surveillance support model should be parameterized to target areas susceptible to invasion and determine whether surveillance is effective and eradication is feasible. We discovered that for CNG, regardless of a carefully designed surveillance strategy, eradication is implausible at current intensities of surveillance and control and these efforts should be doubled if they are to be successful. This is crucial information in the face of environmentally and economically damaging invasive species and large, expensive and potentially ineffective control programmes.

Interactions between a Trawl fishery and spatial closures for biodiversity conservation in the Great Barrier Reef World Heritage Area, Australia.

Background: The Queensland East Coast Otter Trawl Fishery (ECOTF) for penaeid shrimp fishes within Australia's Great Barrier Reef World Heritage Area (GBRWHA). The past decade has seen the implementation of conservation and fisheries management strategies to reduce the impact of the ECOTF on the seabed and improve biodiversity conservation. New information from electronic vessel location monitoring systems (VMS) provides an opportunity to review the interactions between the ECOTF and spatial closures for biodiversity conservation. Methodology and Results: We used fishing metrics and spatial information on the distribution of closures and modelled VMS data in a geographical information system (GIS) to assess change in effort of the trawl fishery from 2001-2009 and to quantify the exposure of 70 reef, non-reef and deep water bioregions to trawl fishing. The number of trawlers and the number of days fished almost halved between 2001 and 2009 and new spatial closures introduced in 2004 reduced the area zoned available for trawl fishing by 33%. However, we found that there was only a relatively minor change in the spatial footprint of the fishery as a result of new spatial closures. Non-reef bioregions benefited the most from new spatial closures followed by deep and reef bioregions. Conclusions/Significance: Although the catch of non target species remains an issue of concern for fisheries management, the small spatial footprint of the ECOTF relative to the size of the GBRWHA means that the impact on benthic habitats is likely to be negligible. The decline in effort as a result of fishing industry structural adjustment, increasing variable costs and business decisions of fishers is likely to continue a trend to fish only in the most productive areas. This will provide protection for most benthic habitats without any further legislative or management intervention.

Design and testing of stand-specific bucking instructions for use on modern cut-to-length harvesters

This study addresses three important issues in tree bucking optimization in the context of cut-to-length harvesting. (1) Would the fit between the log demand and log output distributions be better if the price and/or demand matrices controlling the bucking decisions on modern cut-to-length harvesters were adjusted to the unique conditions of each individual stand? (2) In what ways can we generate stand and product specific price and demand matrices? (3) What alternatives do we have to measure the fit between the log demand and log output distributions, and what would be an ideal goodness-of-fit measure? Three iterative search systems were developed for seeking stand-specific price and demand matrix sets: (1) A fuzzy logic control system for calibrating the price matrix of one log product for one stand at a time (the stand-level one-product approach); (2) a genetic algorithm system for adjusting the price matrices of one log product in parallel for several stands (the forest-level one-product approach); and (3) a genetic algorithm system for dividing the overall demand matrix of each of the several log products into stand-specific sub-demands simultaneously for several stands and products (the forest-level multi-product approach). The stem material used for testing the performance of the stand-specific price and demand matrices against that of the reference matrices was comprised of 9 155 Norway spruce (Picea abies (L.) Karst.) sawlog stems gathered by harvesters from 15 mature spruce-dominated stands in southern Finland. The reference price and demand matrices were either direct copies or slightly modified versions of those used by two Finnish sawmilling companies. Two types of stand-specific bucking matrices were compiled for each log product. One was from the harvester-collected stem profiles and the other was from the pre-harvest inventory data. Four goodness-of-fit measures were analyzed for their appropriateness in determining the similarity between the log demand and log output distributions: (1) the apportionment degree (index), (2) the chi-square statistic, (3) Laspeyres quantity index, and (4) the price-weighted apportionment degree. The study confirmed that any improvement in the fit between the log demand and log output distributions can only be realized at the expense of log volumes produced. Stand-level pre-control of price matrices was found to be advantageous, provided the control is done with perfect stem data. Forest-level pre-control of price matrices resulted in no improvement in the cumulative apportionment degree. Cutting stands under the control of stand-specific demand matrices yielded a better total fit between the demand and output matrices at the forest level than was obtained by cutting each stand with non-stand-specific reference matrices. The theoretical and experimental analyses suggest that none of the three alternative goodness-of-fit measures clearly outperforms the traditional apportionment degree measure. Keywords: harvesting, tree bucking optimization, simulation, fuzzy control, genetic algorithms, goodness-of-fit

Suunnittelunäkemys metsäorganisaatioissa ja sen vaikutus tietojärjestelmälle asetettaviin vaatimuksiin

Department of Forest Resource Management in the University of Helsinki has in years 2004?2007 carried out so-called SIMO -project to develop a new generation planning system for forest management. Project parties are organisations doing most of Finnish forest planning in government, industry and private owned forests. Aim of this study was to find out the needs and requirements for new forest planning system and to clarify how parties see targets and processes in today's forest planning. Representatives responsible for forest planning in each organisation were interviewed one by one. According to study the stand-based system for managing and treating forests continues in the future. Because of variable data acquisition methods with different accuracy and sources, and development of single tree interpretation, more and more forest data is collected without field work. The benefits of using more specific forest data also calls for use of information units smaller than tree stand. In Finland the traditional way to arrange forest planning computation is divided in two elements. After updating the forest data to present situation every stand unit's growth is simulated with different alternative treatment schedule. After simulation, optimisation selects for every stand one treatment schedule so that the management program satisfies the owner's goals in the best possible way. This arrangement will be maintained in the future system. The parties' requirements to add multi-criteria problem solving, group decision support methods as well as heuristic and spatial optimisation into system make the programming work more challenging. Generally the new system is expected to be adjustable and transparent. Strict documentation and free source code helps to bring these expectations into effect. Variable growing models and treatment schedules with different source information, accuracy, methods and the speed of processing are supposed to work easily in system. Also possibilities to calibrate models regionally and to set local parameters changing in time are required. In future the forest planning system will be integrated in comprehensive data management systems together with geographic, economic and work supervision information. This requires a modular method of implementing the system and the use of a simple data transmission interface between modules and together with other systems. No major differences in parties' view of the systems requirements were noticed in this study. Rather the interviews completed the full picture from slightly different angles. In organisation the forest management is considered quite inflexible and it only draws the strategic lines. It does not yet have a role in operative activity, although the need and benefits of team level forest planning are admitted. Demands and opportunities of variable forest data, new planning goals and development of information technology are known. Party organisations want to keep on track with development. One example is the engagement in extensive SIMO-project which connects the whole field of forest planning in Finland.

Hospital in the Nursing Home program reduces emergency department presentations and hospital admissions from residential aged care facilities in Queensland, Australia: A quasi-experimental study

Background There has been considerable publicity regarding population ageing and hospital emergency department (ED) overcrowding. Our study aims to investigate impact of one intervention piloted in Queensland Australia, the Hospital in the Nursing Home (HiNH) program, on reducing ED and hospital attendances from residential aged care facilities (RACFs). Methods A quasi-experimental study was conducted at an intervention hospital undertaking the program and a control hospital with normal practice. Routine Queensland health information system data were extracted for analysis. Results Significant reductions in the number of ED presentations per 1000 RACF beds (rate ratio (95 % CI): 0.78 (0.67–0.92); p = 0.002), number of hospital admissions per 1000 RACF beds (0.62 (0.50–0.76); p < 0.0001), and number of hospital admissions per 100 ED presentations (0.61 (0.43–0.85); p = 0.004) were noticed in the experimental hospital after the intervention; while there were no significant differences between intervention and control hospitals before the intervention. Pre-test and post-test comparison in the intervention hospital also presented significant decreases in ED presentation rate (0.75 (0.65–0.86); p < 0.0001) and hospital admission rate per RACF bed (0.66 (0.54–0.79); p < 0.0001), and a non-significant reduction in hospital admission rate per ED presentation (0.82 (0.61–1.11); p = 0.196). Conclusions Hospital in the Nursing Home program could be effective in reducing ED presentations and hospital admissions from RACF residents. Implementation of the program across a variety of settings is preferred to fully assess the ongoing benefits for patients and any possible cost-savings.

Plants of Central Queensland: Identification and Uses of Native and Introduced Species

Conservation and sustainable productivity are vital issues for Australia. In order to manage vegetation well from an agricultural, recreational or conservation point of view, an understanding of individual plant species is important. Plants of Central Queensland provides a guide for identifying and understanding the plants of the region so that pastoralists and others can be better equipped to manage the vegetation resource of our grazing lands. Central Queensland straddles the Tropic of Capricorn, although many of the plants in the book will also be found outside this area, as shown by their distribution maps. The book provides information on the habit, distribution, foliage and fruits of 525 plant species. Informative notes highlighting declared, poisonous, weed and medicinal plants are included, and plants useful for bees and bush tucker are also noted. These are the most important plants you might see if you live in or travel through central Queensland. This book has an easy-to-read, non-botanical format, with helpful photographs and distribution maps that greatly aid anyone interested in the vegetation of central Queensland. It is based on a previous work of the same title but is greatly expanded, incorporating information on an additional 285 plant species.

Urban Growth Analysis Using Spatial and Temporal Data

Urban growth identification, quantification, knowledge of rate and the trends of growth would help in regional planning for better infrastructure provision in environmentally sound way. This requires analysis of spatial and temporal data, which help in quantifying the trends of growth on spatial scale. Emerging technologies such as Remote Sensing, Geographic Information System (GIS) along with Global Positioning System (GPS) help in this regard. Remote sensing aids in the collection of temporal data and GIS helps in spatial analysis. This paper focuses on the analysis of urban growth pattern in the form of either radial or linear sprawl along the Bangalore - Mysore highway. Various GIS base layers such as builtup areas along the highway, road network, village boundary etc. were generated using collateral data such as the Survey of India toposheet, etc. Further, this analysis was complemented with the computation of Shannon's entropy, which helped in identifying prevalent sprawl zone, rate of growth and in delineating potential sprawl locations. The computation Shannon's entropy helped in delineating regions with dispersed and compact growth. This study reveals that the Bangalore North and South taluks contributed mainly to the sprawl with 559% increase in built-up area over a period of 28 years and high degree of dispersion. The Mysore and Srirangapatna region showed 128% change in built-up area and a high potential for sprawl with slightly high dispersion. The degree of sprawl was found to be directly proportional to the distances from the cities.