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.

MYB transcription factors that colour our fruit

Anthocyanin concentration is a primary determinant of plant colour. Fruit anthocyanin biosynthesis is controlled by a distinct clade of R2R3 MYB transcription factors. In apple, three recent papers describe the discovery of MYB genes activating skin, flesh and foliage anthocyanic colour. These findings lead the way to new approaches in the breeding and biotechnological development of fruit with new colour patterns.

High temperature reduces apple fruit colour via modulation of the anthocyanin regulatory complex

The biosynthesis of anthocyanin in many plants is affected by environmental conditions. In apple (Malus×domestica Borkh.), concentrations of fruit anthocyanins are lower under hot climatic conditions. We examined the anthocyanin accumulation in the peel of maturing 'Mondial Gala' and 'Royal Gala' apples, grown in both temperate and hot climates, and using artificial heating of on-tree fruit. Heat caused a dramatic reduction of both peel anthocyanin concentration and transcripts of the genes of the anthocyanin biosynthetic pathway. Heating fruit rapidly reduced expression of the R2R3 MYB transcription factor (MYB10) responsible for coordinative regulation for red skin colour, as well as expression of other genes in the transcriptional activation complex. A single night of low temperatures is sufficient to elicit a large increase in transcription of MYB10 and consequently the biosynthetic pathway. Candidate genes that can repress anthocyanin biosynthesis did not appear to be responsible for reductions in anthocyanin content. We propose that temperature-induced regulation of anthocyanin biosynthesis is primarily caused by altered transcript levels of the activating anthocyanin regulatory complex.

Environmental regulation of leaf colour in red 35S : PAP1 Arabidopsis thaliana

High-temperature, low-light (HTLL) treatment of 35S:PAP1 Arabidopsis thaliana over-expressing the PAP1 (Production of Anthocyanin Pigment 1) gene results in reversible reduction of red colouration, suggesting the action of additional anthocyanin regulators. High-performance liquid chromatography (HPLC), liquid chromatography mass spectrometry (LCMS) and Affimetrix®-based microarrays were used to measure changes in anthocyanin, flavonoids, and gene expression in response to HTLL. HTLL treatment of control and 35S:PAP1 A. thaliana resulted in a reversible reduction in the concentrations of major anthocyanins despite ongoing over-expression of the PAP1 MYB transcription factor. Twenty-one anthocyanins including eight cis-coumaryl esters were identified by LCMS. The concentrations of nine anthocyanins were reduced and those of three were increased, consistent with a sequential process of anthocyanin degradation. Analysis of gene expression showed down-regulation of flavonol and anthocyanin biosynthesis and of transport-related genes within 24 h of HTLL treatment. No catabolic genes up-regulated by HTLL were found. Reductions in the concentrations of anthocyanins and down-regulation of the genes of anthocyanin biosynthesis were achieved by environmental manipulation, despite ongoing over-expression of PAP1. Quantitative PCR showed reduced expression of three genes (TT8, TTG1 and EGL3) of the PAP1 transcriptional complex, and increased expression of the potential transcriptional repressors AtMYB3, AtMYB6 and AtMYBL2 coincided with HTLL-induced down-regulation of anthocyanin biosynthesis. HTLL treatment offers a model system with which to explore anthocyanin catabolism and to discover novel genes involved in the environmental control of anthocyanins.

Summarisation of short-term and long-term videos using texture and colour

We present a novel approach to video summarisation that makes use of a Bag-of-visual-Textures (BoT) approach. Two systems are proposed, one based solely on the BoT approach and another which exploits both colour information and BoT features. On 50 short-term videos from the Open Video Project we show that our BoT and fusion systems both achieve state-of-the-art performance, obtaining an average F-measure of 0.83 and 0.86 respectively, a relative improvement of 9% and 13% when compared to the previous state-of-the-art. When applied to a new underwater surveillance dataset containing 33 long-term videos, the proposed system reduces the amount of footage by a factor of 27, with only minor degradation in the information content. This order of magnitude reduction in video data represents significant savings in terms of time and potential labour cost when manually reviewing such footage.

Colour by numbers in Excel 2007 : solving algebraic equations without algebra

This is an update of an earlier paper, and is written for Excel 2007. A series of Excel 2007 models is described. The more advanced versions allow solution of f(x)=0 by examining change of sign of function values. The function is graphed and change of sign easily detected by a change of colour. Relevant features of Excel 2007 used are Names, Scatter Chart and Conditional Formatting. Several sample Excel 2007 models are available for download, and the paper is intended to be used as a lesson plan for students having some familiarity with derivatives. For comparison and reference purposes, the paper also presents a brief outline of several common equation-solving strategies as an Appendix.

The influence of colour and sound on neuronal activation during visual object naming

This paper investigates how neuronal activation for naming photographs of objects is influenced by the addition of appropriate colour or sound. Behaviourally, both colour and sound are known to facilitate object recognition from visual form. However, previous functional imaging studies have shown inconsistent effects. For example, the addition of appropriate colour has been shown to reduce antero-medial temporal activation whereas the addition of sound has been shown to increase posterior superior temporal activation. Here we compared the effect of adding colour or sound cues in the same experiment. We found that the addition of either the appropriate colour or sound increased activation for naming photographs of objects in bilateral occipital regions and the right anterior fusiform. Moreover, the addition of colour reduced left antero-medial temporal activation but this effect was not observed for the addition of object sound. We propose that activation in bilateral occipital and right fusiform areas precedes the integration of visual form with either its colour or associated sound. In contrast, left antero-medial temporal activation is reduced because object recognition is facilitated after colour and form have been integrated.

Technicolouring the fridge : reducing food waste through uses of colour-coding and cameras

Domestic food wastage is a growing problem for the environment and food security. Some causes of domestic food wastes are attributed to a consumer’s behaviours during food purchasing, storage and consumption, such as: excessive food purchases and stockpiling in storage. Recent efforts in human-computer interaction research have examined ways of influencing consumer behaviour. The outcomes have led to a number of interventions that assist users with performing everyday tasks. The Internet Fridge is an example of such an intervention. However, new pioneering technologies frequently confront barriers that restrict their future impact in the market place, which has prompted investigations into the effectiveness of behaviour changing interventions used to encourage more sustainable practices. In this paper, we investigate and compare the effectiveness of two interventions that encourage behaviour change: FridgeCam and the Colour Code Project. We use FridgeCam to examine how improving a consumer’s food supply knowledge can reduce food stockpiling. We use the Colour Code Project to examine how improving consumer awareness of food location can encourage consumption of forgotten foods. We explore opportunities to integrate these interventions into commercially available technologies, such as the Internet Fridge, to: (i) increase the technology’s benefit and value to users, and (ii) promote reduced domestic food wastage. We conclude that interventions improving consumer food supply and location knowledge can promote behaviours that reduce domestic food waste over a longer term. The implications of this research present new opportunities for existing and future technologies to play a key role in reducing domestic food waste.

The Catlin Seaview Survey – kilometre-scale seascape assessment, and monitoring of coral reef ecosystems

1.Marine ecosystems provide critically important goods and services to society, and hence their accelerated degradation underpins an urgent need to take rapid, ambitious and informed decisions regarding their conservation and management. 2.The capacity, however, to generate the detailed field data required to inform conservation planning at appropriate scales is limited by time and resource consuming methods for collecting and analysing field data at the large scales required. 3.The ‘Catlin Seaview Survey’, described here, introduces a novel framework for large-scale monitoring of coral reefs using high-definition underwater imagery collected using customized underwater vehicles in combination with computer vision and machine learning. This enables quantitative and geo-referenced outputs of coral reef features such as habitat types, benthic composition, and structural complexity (rugosity) to be generated across multiple kilometre-scale transects with a spatial resolution ranging from 2 to 6 m2. 4.The novel application of technology described here has enormous potential to contribute to our understanding of coral reefs and associated impacts by underpinning management decisions with kilometre-scale measurements of reef health. 5.Imagery datasets from an initial survey of 500 km of seascape are freely available through an online tool called the Catlin Global Reef Record. Outputs from the image analysis using the technologies described here will be updated on the online repository as work progresses on each dataset. 6.Case studies illustrate the utility of outputs as well as their potential to link to information from remote sensing. The potential implications of the innovative technologies on marine resource management and conservation are also discussed, along with the accuracy and efficiency of the methodologies deployed.

Geochemistry-based coral palaeoclimate studies and the potential of ‘non-traditional’ (non-massive Porites) corals : recent developments and future progression

Understanding the natural variability of the Earth's climate system and accurately identifying potential anthropogenic influences requires long term, geographically distributed records of key climate indicators, such as temperature and precipitation that extend prior to the last 400. years of the Holocene. Reef corals provide an excellent source of high resolution climate records, and importantly represent the tropical marine environment where palaeoclimate data are urgently required. Recent decades have seen significant improvement in our understanding of coral biomineralisation, the associated uptake of geochemical proxies and methods of identifying and understanding the effects of both early and late, post depositional diagenetic alteration. These processes all have significant implications for interpreting geochemical proxies relevant to palaeoclimatic reconstructions. This paper reviews the current 'state of the art' in terms of coral based palaeoclimate reconstructions and highlights a key remaining problem. The majority of coral based palaeoclimate research has been derived from massive colonies of Porites. However, massive Porites are not globally abundant and may not provide material of a particular age of interest in those regions where they are present. Therefore, there is great potential for alternate coral genera to act as complimentary climate archives. While it remains critical to consider five key factors - vital effects, differential growth morphologies, geochemical heterogeneity in the skeletal ultrastructure, transfer equation selection and diagenetic screening of skeletal material - in order to allow the highest level of accuracy in coral palaeoclimate reconstructions, it is also important to develop alternate taxa for palaeoclimate studies in regions where Porites colonies are absent or rare. Currently as many as nine genera other than Porites have proven at least limited utility in palaeothermometry, most of which are found in the Atlantic/Caribbean region where massive Porites do not exist. Even branching taxa such as Acropora have significant potential to preserve environmental archives. Increasing this capability will greatly expand the number of potential geochemical archives available for longer term temporal records of palaeoclimate.

Understanding Uncertainties in Non-Linear Population Trajectories: A Bayesian Semi-Parametric Hierarchical Approach to Large-Scale Surveys of Coral Cover

Recently, attempts to improve decision making in species management have focussed on uncertainties associated with modelling temporal fluctuations in populations. Reducing model uncertainty is challenging; while larger samples improve estimation of species trajectories and reduce statistical errors, they typically amplify variability in observed trajectories. In particular, traditional modelling approaches aimed at estimating population trajectories usually do not account well for nonlinearities and uncertainties associated with multi-scale observations characteristic of large spatio-temporal surveys. We present a Bayesian semi-parametric hierarchical model for simultaneously quantifying uncertainties associated with model structure and parameters, and scale-specific variability over time. We estimate uncertainty across a four-tiered spatial hierarchy of coral cover from the Great Barrier Reef. Coral variability is well described; however, our results show that, in the absence of additional model specifications, conclusions regarding coral trajectories become highly uncertain when considering multiple reefs, suggesting that management should focus more at the scale of individual reefs. The approach presented facilitates the description and estimation of population trajectories and associated uncertainties when variability cannot be attributed to specific causes and origins. We argue that our model can unlock value contained in large-scale datasets, provide guidance for understanding sources of uncertainty, and support better informed decision making

Capturing natural-colour 3D models of insects for species discovery and diagnostics

Collections of biological specimens are fundamental to scientific understanding and characterization of natural diversity - past, present and future. This paper presents a system for liberating useful information from physical collections by bringing specimens into the digital domain so they can be more readily shared, analyzed, annotated and compared. It focuses on insects and is strongly motivated by the desire to accelerate and augment current practices in insect taxonomy which predominantly use text, 2D diagrams and images to describe and characterize species. While these traditional kinds of descriptions are informative and useful, they cannot cover insect specimens "from all angles" and precious specimens are still exchanged between researchers and collections for this reason. Furthermore, insects can be complex in structure and pose many challenges to computer vision systems. We present a new prototype for a practical, cost-effective system of off-the-shelf components to acquire natural-colour 3D models of insects from around 3 mm to 30 mm in length. ("Natural-colour" is used to contrast with "false-colour", i.e., colour generated from, or applied to, gray-scale data post-acquisition.) Colour images are captured from different angles and focal depths using a digital single lens reflex (DSLR) camera rig and two-axis turntable. These 2D images are processed into 3D reconstructions using software based on a visual hull algorithm. The resulting models are compact (around 10 megabytes), afford excellent optical resolution, and can be readily embedded into documents and web pages, as well as viewed on mobile devices. The system is portable, safe, relatively affordable, and complements the sort of volumetric data that can be acquired by computed tomography. This system provides a new way to augment the description and documentation of insect species holotypes, reducing the need to handle or ship specimens. It opens up new opportunities to collect data for research, education, art, entertainment, biodiversity assessment and biosecurity control. © 2014 Nguyen et al.

Environmental colour and well-being

Significance of colour schemes in appraisal of the urban aesthetic has been traditionally recognised by design professionals. However, the proven psychological and emotional impacts of urban colour remain overlooked in design thinking. This paper argues that health-conscious approach to environmental colour design requires consideration of phenomenological human needs in addition to aesthetic and stylistic preferences of a designer. A body of knowledge accumulated in environmental colour psychology provides a foundation for a shift in the environmental colour design. Though, some architectural critics suggest that design professionals have little understanding of how different aspects of colour psychology can be integrated in design process. Lack of an explicit design methodology has been described as a main constraint to applicability of the related knowledge in design process. Understanding the notion of environmental colour is essential in developing health-conscious approach to environmental colour design. Therefore, this paper is primarily focused on conceptualisation of environmental colour and experiential environmental colour design. Additionally, a role of environmental colour design in the delivery of health-enhancing environments and balanced sensorial experiences is briefly discussed.

Non-market use and non-use values for preserving ecosystem services over time : a choice experiment application to coral reef ecosystems in New Caledonia

Non-use values (i.e. economic values assigned by individuals to ecosystem goods and services unrelated to current or future uses) provide one of the most compelling incentives for the preservation of ecosystems and biodiversity. Assessing the non-use values of non-users is relatively straightforward using stated preference methods, but the standard approaches for estimating non-use values of users (stated decomposition) have substantial shortcomings which undermine the robustness of their results. In this paper, we propose a pragmatic interpretation of non-use values to derive estimates that capture their main dimensions, based on the identification of a willingness to pay for ecosystem protection beyond one's expected life. We empirically test our approach using a choice experiment conducted on coral reef ecosystem protection in two coastal areas in New Caledonia with different institutional, cultural, environmental and socio-economic contexts. We compute individual willingness to pay estimates, and derive individual non-use value estimates using our interpretation. We find that, a minima, estimates of non-use values may comprise between 25 and 40% of the mean willingness to pay for ecosystem preservation, less than has been found in most studies.