Mapping a candidate gene (MdMYB10) for red flesh and foliage colour in apple

BACKGROUND Integrating plant genomics and classical breeding is a challenge for both plant breeders and molecular biologists. Marker-assisted selection (MAS) is a tool that can be used to accelerate the development of novel apple varieties such as cultivars that have fruit with anthocyanin through to the core. In addition, determining the inheritance of novel alleles, such as the one responsible for red flesh, adds to our understanding of allelic variation. Our goal was to map candidate anthocyanin biosynthetic and regulatory genes in a population segregating for the red flesh phenotypes. RESULTS We have identified the Rni locus, a major genetic determinant of the red foliage and red colour in the core of apple fruit. In a population segregating for the red flesh and foliage phenotype we have determined the inheritance of the Rni locus and DNA polymorphisms of candidate anthocyanin biosynthetic and regulatory genes. Simple Sequence Repeats (SSRs) and Single Nucleotide Polymorphisms (SNPs) in the candidate genes were also located on an apple genetic map. We have shown that the MdMYB10 gene co-segregates with the Rni locus and is on Linkage Group (LG) 09 of the apple genome. CONCLUSION We have performed candidate gene mapping in a fruit tree crop and have provided genetic evidence that red colouration in the fruit core as well as red foliage are both controlled by a single locus named Rni. We have shown that the transcription factor MdMYB10 may be the gene underlying Rni as there were no recombinants between the marker for this gene and the red phenotype in a population of 516 individuals. Associating markers derived from candidate genes with a desirable phenotypic trait has demonstrated the application of genomic tools in a breeding programme of a horticultural crop species.

Mapping Hydrophobicity on the Protein Molecular Surface at Atom-Level Resolution

A precise representation of the spatial distribution of hydrophobicity, hydrophilicity and charges on the molecular surface of proteins is critical for the understanding of the interaction with small molecules and larger systems. The representation of hydrophobicity is rarely done at atom-level, as this property is generally assigned to residues. A new methodology for the derivation of atomic hydrophobicity from any amino acid-based hydrophobicity scale was used to derive 8 sets of atomic hydrophobicities, one of which was used to generate the molecular surfaces for 35 proteins with convex structures, 5 of which, i.e., lysozyme, ribonuclease, hemoglobin, albumin and IgG, have been analyzed in more detail. Sets of the molecular surfaces of the model proteins have been constructed using spherical probes with increasingly large radii, from 1.4 to 20 A˚, followed by the quantification of (i) the surface hydrophobicity; (ii) their respective molecular surface areas, i.e., total, hydrophilic and hydrophobic area; and (iii) their relative densities, i.e., divided by the total molecular area; or specific densities, i.e., divided by property-specific area. Compared with the amino acid-based formalism, the atom-level description reveals molecular surfaces which (i) present an approximately two times more hydrophilic areas; with (ii) less extended, but between 2 to 5 times more intense hydrophilic patches; and (iii) 3 to 20 times more extended hydrophobic areas. The hydrophobic areas are also approximately 2 times more hydrophobicity-intense. This, more pronounced "leopard skin"-like, design of the protein molecular surface has been confirmed by comparing the results for a restricted set of homologous proteins, i.e., hemoglobins diverging by only one residue (Trp37). These results suggest that the representation of hydrophobicity on the protein molecular surfaces at atom-level resolution, coupled with the probing of the molecular surface at different geometric resolutions, can capture processes that are otherwise obscured to the amino acid-based formalism.

A copia-like element in Pisum demonstrates the uses of dispersed repeated sequences in genetic analysis

A DNA sequence between two legumin genes in Pisum is a member of the copia-like class of retrotransposons and represents one member of a polymorphic and heterogeneous dispersed repeated sequence family in Pisum. This sequence can be exploited in genetic studies either by RFLP analysis where several markers can be scored together, or the segregation of individual elements can be followed after PCR amplification of specific members.

Spatial mapping and map exploitation : a bio-inspired engineering perspective

Probabilistic robot mapping techniques can produce high resolution, accurate maps of large indoor and outdoor environments. However, much less progress has been made towards robots using these maps to perform useful functions such as efficient navigation. This paper describes a pragmatic approach to mapping system development that considers not only the map but also the navigation functionality that the map must provide. We pursue this approach within a bio-inspired mapping context, and use esults from robot experiments in indoor and outdoor environments to demonstrate its validity. The research attempts to stimulate new research directions in the field of robot mapping with a proposal for a new approach that has the potential to lead to more complete mapping and navigation systems.

Small angle X-ray scattering mapping and kinetics study of sub-critical CO2 sorption by two Australian coals

Time- and position-resolved synchrotron small angle X-ray scattering data were acquired from samples of two Australian coal seams: Bulli seam (Bulli 4, Ro=1.42%, Sydney Basin), which naturally contains CO2 and Baralaba seam (Ro=0.67%, Bowen Basin), a potential candidate for sequestering CO2. This experimental approach has provided unique, pore-size-specific insights into the kinetics of CO2 sorption in the micro- and small mesopores (diameter 5 to 175 Å) and the density of the sorbed CO2 at reservoir-like conditions of temperature and hydrostatic pressure. For both samples, at pressures above 5 bar, the density of CO2 confined in pores was found to be uniform, with no densification in near-wall regions. In the Bulli 4 sample, CO2 first flooded the slit pores between polyaromatic sheets. In the pore-size range analysed, the confined CO2 density was close to that of the free CO2. The kinetics data are too noisy for reliable quantitative analysis, but qualitatively indicate faster kinetics in mineral-matter-rich regions. In the Baralaba sample, CO2 preferentially invaded the smallest micropores and the confined CO2 density was up to five times that of the free CO2. Faster CO2 sorption kinetics was found to be correlated with higher mineral matter content but, the mineral-matter-rich regions had lower-density CO2 confined in their pores. Remarkably, the kinetics was pore-size dependent, being faster for smaller pores. These results suggest that injection into the permeable section of an interbedded coal-clastic sequence could provide a viable combination of reasonable injectivity and high sorption capacity.

Eruption centres of the Hamilton area of the Newer Volcanics Province, Victoria, Australia: Pinpointing volcanoes from a multifaceted approach to landform mapping

Volcanic eruption centres of the mostly 4.5 Ma-5000 BP Newer Volcanics Province in the Hamilton area of southeastern Australia were examined in detail using a multifaceted approach, including ground truthing and analysis of ArcGIS Total Magnetic Intensity and seamless geology data, NASA Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) digital elevation models and Google Earth satellite image interpretation. Sixteen eruption centres were recognised in the Hamilton area, including three previously unrecorded volcanoes-one of which, the Cas Maar, constitutes the northernmost maar-cone volcanic complex in the Western Plains subprovince. Seven previously allocated eruption centres were placed into question based on field and laboratory observations. Three phases of volcanic activity have been suggested by other authors and are interpreted to correlate with ages of >4 Ma, ca 2 Ma and <0.5 Ma, which may be further subdivided based on preservation of outcrop. Geochemical compositions of the dominantly basaltic products become increasingly alkaline and enriched in incompatible elements from Phases 1 to 2, with Phase 3 eruptions both covering the entire geochemical range and extending into increasingly enriched compositions. This research highlights the importance of a multifaceted approach to landform mapping and demonstrates that additional volcanic centres may yet be discovered in the Newer Volcanics Province

Understanding Connectivity between Groundwater Chemistry Data and Geological Stratigraphy via 3D Sub-surface Visualization and Analysis

This paper describes the 3D Water Chemistry Atlas - an open source, Web-based system that enables the three-dimensional (3D) sub-surface visualization of ground water monitoring data, overlaid on the local geological model. Following a review of existing technologies, the system adopts Cesium (an open source Web-based 3D mapping and visualization interface) together with a PostGreSQL/PostGIS database, for the technical architecture. In addition a range of the search, filtering, browse and analysis tools were developed that enable users to interactively explore the groundwater monitoring data and interpret it spatially and temporally relative to the local geological formations and aquifers via the Cesium interface. The result is an integrated 3D visualization system that enables environmental managers and regulators to assess groundwater conditions, identify inconsistencies in the data, manage impacts and risks and make more informed decisions about activities such as coal seam gas extraction, waste water extraction and re-use.

Curriculum mapping of the Spatial Science Program, QUT : what was the cartography journey?

There are currently a number of issues of great importance affecting universities and the way in which their programs are now offered. Many issues are largely being driven top-down and impact both at a university-wide and at an individual discipline level. This paper provides a brief history of cartography and digital mapping education at the Queensland University of Technology (QUT). It also provides an overview of what is curriculum mapping and presents some interesting findings from the program review process. Further, this review process has triggered discussion and action for the review, mapping and embedding of graduate attributes within the spatial science major program. Some form of practical based learning is expected in vocationally oriented degrees that lead to professional accreditation and are generally regarded as a good learning exposure. With the restructure of academic programs across the Faculty of Built Environment and Engineering in 2006, spatial science and surveying students now undertake a formal work integrated learning unit. There is little doubt that students acquire the skills of their discipline (mapping science, spatial) by being immersed in the industry culture- learning how to process information and solve real-world problems within context. The broad theme of where geo-spatial mapping skills are embedded in this broad-based tertiary education course are examined with some focused discussion on the learning objectives, outcomes and examples of some student learning experiences

Mapping personal trip OD from probe data

The paper analyses the expected value of OD volumes from probe with fixed error, error that is proportional to zone size and inversely proportional to zone size. To add realism to the analysis, real trip ODs in the Tokyo Metropolitan Region are synthesised. The results show that for small zone coding with average radius of 1.1km, and fixed measurement error of 100m, an accuracy of 70% can be expected. The equivalent accuracy for medium zone coding with average radius of 5km would translate into a fixed error of approximately 300m. As expected small zone coding is more sensitive than medium zone coding as the chances of the probe error envelope falling into adjacent zones are higher. For the same error radii, error proportional to zone size would deliver higher level of accuracy. As over half (54.8%) of the trip ends start or end at zone with equivalent radius of ≤ 1.2 km and only 13% of trips ends occurred at zones with equivalent radius ≥2.5km, measurement error that is proportional to zone size such as mobile phone would deliver higher level of accuracy. The synthesis of real OD with different probe error characteristics have shown that expected value of >85% is difficult to achieve for small zone coding with average radius of 1.1km. For most transport applications, OD matrix at medium zone coding is sufficient for transport management. From this study it can be drawn that GPS with error range between 2 and 5m, and at medium zone coding (average radius of 5km) would provide OD estimates greater than 90% of the expected value. However, for a typical mobile phone operating error range at medium zone coding the expected value would be lower than 85%. This paper assumes transmission of one origin and one destination positions from the probe. However, if multiple positions within the origin and destination zones are transmitted, map matching to transport network could be performed and it would greatly improve the accuracy of the probe data.

Graduate Attribute Mapping With the Extended CDIO Framework

The CDIO (Conceive-Design-Implement-Operate) Initiative has been globally recognised as an enabler for engineering education reform. With the CDIO process, the CDIO Standards and the CDIO Syllabus, many scholarly contributions have been made around cultural change, curriculum reform and learning environments. In the Australasian region, reform is gaining significant momentum within the engineering education community, the profession, and higher education institutions. This paper presents the CDIO Syllabus cast into the Australian context by mapping it to the Engineers Australia Graduate Attributes, the Washington Accord Graduate Attributes and the Queensland University of Technology Graduate Capabilities. Furthermore, in recognition that many secondary schools and technical training institutions offer introductory engineering technology subjects, this paper presents an extended self-rating framework suited for recognising developing levels of proficiency at a preparatory level. A demonstrator mapping tool has been created to demonstrate the application of this extended graduate attribute mapping framework as a precursor to an integrated curriculum information model.

An extended CDIO syllabus framework with preparatory engineering proficiencies

The CDIO Initiative has been globally recognised as an enabler for engineering education reform. With the CDIO process, the CDIO Standards and the CDIO Syllabus, many scholarly contributions have been made around cultural change, curriculum reform and learning environments. In the Australasian region, reform is gaining significant momentum within the engineering education community, the profession, and higher education institutions. This paper presents the CDIO Syllabus cast into the Australian context by mapping it to the Engineers Australia Graduate Attributes, the Washington Accord Graduate Attributes and the Queensland University of Technology Graduate Capabilities. Furthermore, in recognition that many secondary schools and technical training institutions offer introductory engineering technology subjects, this paper presents an extended self-rating framework suited for recognising developing levels of proficiency at a preparatory level. The framework is consistent with conventional application to undergraduate programs and professional practice, but adapted for the preparatory context. As with the original CDIO framework with proficiency levels, this extended framework is informed by Bloom’s Educational Objectives. A proficiency evaluation of Queensland Study Authority’s Engineering Technology senior syllabus is demonstrated indicating proficiency levels embedded within this secondary school subject within a preparatory scope. Through this extended CDIO framework, students and faculty have greater awareness and access to tools to promote (i) student engagement in their own graduate capability development, (ii) faculty engagement in course and program design, through greater transparency and utility of the continuum of graduate capability development with associate levels of proficiency, and the context in which they exist in terms of pre-tertiary engineering studies; and (iii) course maintenance and quality audit methodology for the purpose of continuous improvement processes and program accreditation.

Value-mapping for major economic infrastructure projects

The establishment of corporate objectives regarding economic, environmental, social, and ethical responsibilities, to inform business practice, has been gaining credibility in the business sector since the early 1990’s. This is witnessed through (i) the formation of international forums for sustainable and accountable development, (ii) the emergence of standards, systems, and frameworks to provide common ground for regulatory and corporate dialogue, and (iii) the significant quantum of relevant popular and academic literature in a diverse range of disciplines. How then has this move towards greater corporate responsibility become evident in the provision of major urban infrastructure projects? The gap identified, in both academic literature and industry practice, is a structured and auditable link between corporate intent and project outcomes. Limited literature has been discovered which makes a link between corporate responsibility; project performance indicators (or critical success factors) and major infrastructure provision. This search revealed that a comprehensive mapping framework, from an organisation’s corporate objectives through to intended, anticipated and actual outcomes and impacts has not yet been developed for the delivery of such projects. The research problem thus explored is ‘the need to better identify, map and account for the outcomes, impacts and risks associated with economic, environmental, social and ethical outcomes and impacts which arise from major economic infrastructure projects, both now, and into the future’. The methodology being used to undertake this research is based on Checkland’s soft system methodology, engaging in action research on three collaborative case studies. A key outcome of this research is a value-mapping framework applicable to Australian public sector agencies. This is a decision-making methodology which will enable project teams responsible for delivering major projects, to better identify and align project objectives and impacts with stated corporate objectives.

The use of high dynamic range luminance mapping in the assessment, understanding and defining of visual issues in post occupancy building assessment

The international focus on embracing daylighting for energy efficient lighting purposes and the corporate sector’s indulgence in the perception of workplace and work practice “transparency” has spurned an increase in highly glazed commercial buildings. This in turn has renewed issues of visual comfort and daylight-derived glare for occupants. In order to ascertain evidence, or predict risk, of these events; appraisals of these complex visual environments require detailed information on the luminances present in an occupant’s field of view. Conventional luminance meters are an expensive and time consuming method of achieving these results. To create a luminance map of an occupant’s visual field using such a meter requires too many individual measurements to be a practical measurement technique. The application of digital cameras as luminance measurement devices has solved this problem. With high dynamic range imaging, a single digital image can be created to provide luminances on a pixel-by-pixel level within the broad field of view afforded by a fish-eye lens: virtually replicating an occupant’s visual field and providing rapid yet detailed luminance information for the entire scene. With proper calibration, relatively inexpensive digital cameras can be successfully applied to the task of luminance measurements, placing them in the realm of tools that any lighting professional should own. This paper discusses how a digital camera can become a luminance measurement device and then presents an analysis of results obtained from post occupancy measurements from building assessments conducted by the Mobile Architecture Built Environment Laboratory (MABEL) project. This discussion leads to the important realisation that the placement of such tools in the hands of lighting professionals internationally will provide new opportunities for the lighting community in terms of research on critical issues in lighting such as daylight glare and visual quality and comfort.

Value-mapping inputs

This research aims to increase understanding of and delivery to qualitative (or intangible) outcomes and impacts of major economic infrastructure projects (i.e. bridges, roads, water infrastructure and the like), and the role of stakeholder engagement in this process.-------- Recent doctoral research completed at the Queensland University of Technology by the author investigated how the principles of corporate responsibility are applied in the construction sector. This related specifically to major economic infrastructure projects (hereafter referred to as major projects), with particular regard to urban transportation projects. One outcome of this past research was a value-mapping framework which enables organisations to track project outcomes to pre-existing corporate objectives, and report on these throughout the project life-cycle. Two recommendations for future research from that work formed the basis for this current research: • How can qualitative measurables be better integrated into decision-making on major economic infrastructure projects? • How can non-contractual stakeholders be more effectively engaged with on these projects? The link between these two areas may relate to the stakeholders’ role in qualitative indicator identification and measurement. This is a key point for future investigation.---------- The aim of this research is thus to further investigate these two areas, with the intent of (i) better defining the research direction; (ii) identifying potential research partners; and (iii) identify possible sources of future funding.