Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant

Background Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. Methods We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. Key Results Assembly of the 221 746 sequence reads resulted in 12 442 contigs. Over 50 % (6183) of 12 442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. Conclusions This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.

An ecological footprint for an early learning centre : identifying opportunities for early childhood sustainability education through interdisciplinary research

In this study, engineers and educators worked together to adapt and apply the ecological footprint (EF) methodology to an early learning centre in Brisbane, Australia. Results were analysed to determine how environmental impact can be reduced at the study site and more generally across early childhood settings. It was found that food, transport and energy consumption had the largest impact on the centre’s overall footprint. In transport and energy, early childhood centres can reduce their impact through infrastructure and cultural change, in association with changed curriculum strategies. Building design, the type of energy purchased and appliance usage can all be modified to reduce the energy footprint. The transport footprint can be reduced through more families using active and public transport, which can be encouraged by providing information, support and facilities and appropriate siting of new centres. Introducing the concept of ecological footprint in early childhood education may be an effective way to educate children, staff and parents on the links between the food they eat, land usage and environmental impact. This study responds directly to the call in this journal for research focused on early childhood education and for more to be made of interdisciplinary research opportunities.

Sequential release of BMP-7 and VEGF from the PLGA/AK-Gelatin Composite Scaffolds

Vascular endothelial growth factor (VEGF) and bone morphogenetic proteins (BMP-7) are key regulators of angiogenesis and osteogenesis during bone regeneration. The aim of this study was to investigate the possibility of realizing sequential release of the two growth factors using a novel composite scaffold. Poly(lactic-co-glycolic acid) (PLGA)-Akermanite (AK) microspheres were used to make the composite scaffold, which was then loaded with BMP-7, followed by embedding in a gelatin hydrogel matrix loaded with VEGF. The release profiles of the growth factors were studied and selected osteogenic related markers of bone marrow stromal cells (BMSCs) were analysed. It was shown that the composite scaffolds exhibited a fast initial burst release of VEGF within the first 3 days and a sustained slow release of BMP-7 over the full period of 20 days. The in vitro proliferation and differentiation of the BMSCs cultured in the osteogenic medium were enhanced by 1 to 2 times, resulting from the additionally and sequentially release of growth factors from the PLGA-AK/gelatin composite scaffolds.

Hypoxia-mimicking mesoporous bioactive glass scaffolds with controllable cobalt ion release for bone tissue engineering

Low oxygen pressure (hypoxia) plays an important role in stimulating angiogenesis; there are, however, few studies to prepare hypoxia-mimicking tissue engineering scaffolds. Mesoporous bioactive glass (MBG) has been developed as scaffolds with excellent osteogenic properties for bone regeneration. Ionic cobalt (Co) is established as a chemical inducer of hypoxia-inducible factor (HIF)-1α, which induces hypoxia-like response. The aim of this study was to develop hypoxia-mimicking MBG scaffolds by incorporating ionic Co2+ into MBG scaffolds and investigate if the addition of Co2+ ions would induce a cellular hypoxic response in such a tissue engineering scaffold system. The composition, microstructure and mesopore properties (specific surface area, nano-pore volume and nano-pore distribution) of Co-containing MBG (Co-MBG) scaffolds were characterized and the cellular effects of Co on the proliferation, differentiation, vascular endothelial growth factor (VEGF) secretion, HIF-1α expression and bone-related gene expression of human bone marrow stromal cells (BMSCs) in MBG scaffolds were systematically investigated. The results showed that low amounts of Co (< 5%) incorporated into MBG scaffolds had no significant cytotoxicity and that their incorporation significantly enhanced VEGF protein secretion, HIF-1α expression, and bone-related gene expression in BMSCs, and also that the Co-MBG scaffolds support BMSC attachment and proliferation. The scaffolds maintain a well-ordered mesopore channel structure and high specific surface area and have the capacity to efficiently deliver antibiotics drugs; in fact, the sustained released of ampicillin by Co-MBG scaffolds gives them excellent anti-bacterial properties. Our results indicate that incorporating cobalt ions into MBG scaffolds is a viable option for preparing hypoxia-mimicking tissue engineering scaffolds and significantly enhanced hypoxia function. The hypoxia-mimicking MBG scaffolds have great potential for bone tissue engineering applications by combining enhanced angiogenesis with already existing osteogenic properties.

Grounded Media: Expanding the Scope of Ecological Art Practices Within New Media Arts Culture

‘Grounded Media’ is a form of art practice focused around the understanding that our ecological crisis is also a cultural crisis, perpetuated by our sense of separation from the material and immaterial ecologies upon which we depend. This misunderstanding of relationships manifests not only as environmental breakdown, but also in the hemorrhaging of our social fabric. ‘Grounded Media’ is consistent with an approach to media art making that I name ‘ecosophical’ and ‘praxis-led’ – which seeks through a range of strategies, to draw attention to the integrity, diversity and efficacy of the biophysical, social and electronic environments of which we are an integral part. It undertakes this through particular choices of location, interaction design,participative strategies and performative direction. This form of working emerged out of the production of two major projects, Grounded Light [8] and Shifting Intimacies [9] and is evident in a recent prototypical wearable art project called In_Step [6]. The following analysis and reflections will assist in promoting new, sustainable roles for media artists who are similarly interested in attuning their practices.

'Homes for Life' : a critical ecological study of an independent living project

In this paper, an ‘ecological’ lens is applied to an independent living project aiming to provide ‘homes for life’ for adult children with disabilities. The qualities of the project as ecological praxis are highlighted along with the implications for an open-ended enquiry into ecologies for and of the interior. In terms of the ecological concern for intimate modes of being, interior design is shown to be well placed through its association with environments in which people spend most of their life and through powerful concepts such as ‘interiority’ and ‘home’ which link to fundamental existential notions of ‘self ’ and ‘identity’. However, despite the interior being a significant generative force, this has not happened to the exclusion of other disciplines. Ignoring territorial urges to claim areas and concepts as one’s own, the paper describes how the project has actively encouraged design disciplines to trespass in each other’s territories. Ecologies for and of the interior, while recognising the need for discipline emphasis, also demand an integrated and collective approach through what is in effect transdisciplinary practice.

Cyclin-dependent kinase-mediated phosphorylation of RBP1 and pRb promotes their dissociation to mediate release of the SAP30·mSin3·HDAC transcriptional repressor complex

Eukaryotic cell cycle progression is mediated by phosphorylation of protein substrates by cyclin-dependent kinases (CDKs). A critical substrate of CDKs is the product of the retinoblastoma tumor suppressor gene, pRb, which inhibits G1-S phase cell cycle progression by binding and repressing E2F transcription factors. CDK-mediated phosphorylation of pRb alleviates this inhibitory effect to promote G1-S phase cell cycle progression. pRb represses transcription by binding to the E2F transactivation domain and recruiting the mSin3·histone deacetylase (HDAC) transcriptional repressor complex via the retinoblastoma-binding protein 1 (RBP1). RBP1 binds to the pocket region of pRb via an LXCXE motif and to the SAP30 subunit of the mSin3·HDAC complex and, thus, acts as a bridging protein in this multisubunit complex. In the present study we identified RBP1 as a novel CDK substrate. RBP1 is phosphorylated by CDK2 on serines 864 and 1007, which are N- and C-terminal to the LXCXE motif, respectively. CDK2-mediated phosphorylation of RBP1 or pRb destabilizes their interaction in vitro, with concurrent phosphorylation of both proteins leading to their dissociation. Consistent with these findings, RBP1 phosphorylation is increased during progression from G 1 into S-phase, with a concurrent decrease in its association with pRb in MCF-7 breast cancer cells. These studies provide new mechanistic insights into CDK-mediated regulation of the pRb tumor suppressor during cell cycle progression, demonstrating that CDK-mediated phosphorylation of both RBP1 and pRb induces their dissociation to mediate release of the mSin3·HDAC transcriptional repressor complex from pRb to alleviate transcriptional repression of E2F.

Government initiative and start-up firms’ eco-innovation : A case study through the ecological modernisation lens

Government programs to finance small firms or start-ups have attracted a little empirical attention. From an economical perspective, the effect of government grants is evaluated by a measure of innovation or firm productivity. Yet, this paper takes a different approach from economical view aiming to address the research question “How do start ups firms view the relationship between government grants and their co-efficient innovation effort?” Semi-structured interviews with grant recipients (start-up business owners revealed that the grants assist firms to leverage their resource limitations but at the same time the grants also act as a major roadblock for their product development success.

Processpedia : an ecological environment for BPM stakeholders' collaboration

Purpose: The purpose of this paper is to clarify how end-users’ tacit knowledge can be captured and integrated in an overall business process management (BPM) approach. Current approaches to support stakeholders’ collaboration in the modelling of business processes envision an egalitarian environment where stakeholders interact in the same context, using the same languages and sharing the same perspectives on the business process. Therefore, such stakeholders have to collaborate in the context of process modelling using a language that some of them do not master, and have to integrate their various perspectives. Design/methodology/approach: The paper applies the SECI knowledge management process to analyse the problems of traditional top-down BPM approaches and BPM collaborative modelling tools. Besides, the SECI model is also applied to Wikipedia, a successful Web 2.0-based knowledge management environment, to identify how tacit knowledge is captured in a bottom-up approach. Findings – The paper identifies a set of requirements for a hybrid BPM approach, both top-down and bottom-up, and describes a new BPM method based on a stepwise discovery of knowledge. Originality/value: This new approach, Processpedia, enhances collaborative modelling among stakeholders without enforcing egalitarianism. In Processpedia tacit knowledge is captured and standardised into the organisation’s business processes by fostering an ecological participation of all the stakeholders and capitalising on stakeholders’ distinctive characteristics.

Machine vision toolbox for MATLAB, release 3 [Software]

The Toolbox, combined with MATLAB ® and a modern workstation computer, is a useful and convenient environment for investigation of machine vision algorithms. For modest image sizes the processing rate can be sufficiently ``real-time'' to allow for closed-loop control. Focus of attention methods such as dynamic windowing (not provided) can be used to increase the processing rate. With input from a firewire or web camera (support provided) and output to a robot (not provided) it would be possible to implement a visual servo system entirely in MATLAB. Provides many functions that are useful in machine vision and vision-based control. Useful for photometry, photogrammetry, colorimetry. It includes over 100 functions spanning operations such as image file reading and writing, acquisition, display, filtering, blob, point and line feature extraction, mathematical morphology, homographies, visual Jacobians, camera calibration and color space conversion.

Robotics toolbox for MATLAB, release 9 [Software]

The ninth release of the Toolbox, represents over fifteen years of development and a substantial level of maturity. This version captures a large number of changes and extensions generated over the last two years which support my new book “Robotics, Vision & Control”. The Toolbox has always provided many functions that are useful for the study and simulation of classical arm-type robotics, for example such things as kinematics, dynamics, and trajectory generation. The Toolbox is based on a very general method of representing the kinematics and dynamics of serial-link manipulators. These parameters are encapsulated in MATLAB ® objects - robot objects can be created by the user for any serial-link manipulator and a number of examples are provided for well know robots such as the Puma 560 and the Stanford arm amongst others. The Toolbox also provides functions for manipulating and converting between datatypes such as vectors, homogeneous transformations and unit-quaternions which are necessary to represent 3-dimensional position and orientation. This ninth release of the Toolbox has been significantly extended to support mobile robots. For ground robots the Toolbox includes standard path planning algorithms (bug, distance transform, D*, PRM), kinodynamic planning (RRT), localization (EKF, particle filter), map building (EKF) and simultaneous localization and mapping (EKF), and a Simulink model a of non-holonomic vehicle. The Toolbox also including a detailed Simulink model for a quadcopter flying robot.