A concise approach to the polycyclic scaffold of frondosin D

Frondosins A−E, 1−5 (Figure 1), are a family of related marine sesquiterpenoids first isolated in their dextro-rotatory form from the sponge Dysidea frondosa.(1a) Additionally, levo-rotatory frondosins A and D were isolated from an unidentified Eurospongia species.(1b) Frondosins A−E are compounds of interest due to their promising interleukin-8 (IL-8) affinity and protein kinase C inhibition.(1a) IL-8 antagonists are of particular interest in view of their antiinflammatory,(2a) anti-HIV,(1b, 2b) and antitumor(2c-2f) properties. To date, frondosins A, B, and C have been synthesized.(3) Notwithstanding these successes, the frondosins have proved quite a formidable synthetic challenge, and as of yet, there has been no synthesis of frondosin D or E. In this report, we describe our approaches to the molecular scaffold of frondosins D. This work has culminated in a very effective means of producing the trimethylbicyclo[5.4.0]undecane ring system common to all frondosins (shown in bold, Figure 1).

Tandem B1 SINE retro-elements may provide a basis for natural antisense transcription in the Magi1 locus of the mouse (Mus musculus)

Transposable elements, which are DNA sequences that can move between different sites in genomes, comprise approximately 40% of the genome of mammals and are emerging as important contributors to biological diversity. Here we report a transcription unit lying within intron 1 of the murine Magi1 (membrane associated guanylate kinase inverted 1) gene that codes for a cell-cell junction scaffolding protein. The transcription unit, termed Magi1OS (Magi1 Opposite Strand), originates from a region with tandem B1 short interspersed nuclear elements (SINEs) and is an antisense gene to Magi1. Mag1OS transcription initiates in a proximal B1 element that shows only 4% divergence from the consensus sequence, indicating that it has been recently inserted into the mouse genome and could be replication competent. Moreover, a chimaeric transcript may result from intra-chromosomal interaction and trans-splicing of the Magi1 antisense transcript (Magi1OS) and Ghrl, which codes for the multifunctional peptide hormone ghrelin. These two genes are 20 megabases apart on chromosome 6 and are transcribed in opposite directions. We propose that the Magi1OS locus may serve as a useful model system to study exaptation and retrotransposition of B1 SINEs, as well as to examine the mechanisms of intra-chromosomal trans-splicing.

A sub‒domain smoothed Galerkin method for solid mechanics problems

A sub‒domain smoothed Galerkin method is proposed to integrate the advantages of mesh‒free Galerkin method and FEM. Arbitrarily shaped sub‒domains are predefined in problems domain with mesh‒free nodes. In each sub‒domain, based on mesh‒free Galerkin weak formulation, the local discrete equation can be obtained by using the moving Kriging interpolation, which is similar to the discretization of the high‒order finite elements. Strain smoothing technique is subsequently applied to the nodal integration of sub‒domain by dividing the sub‒domain into several smoothing cells. Moreover, condensation of DOF can also be introduced into the local discrete equations to improve the computational efficiency. The global governing equations of present method are obtained on the basis of the scheme of FEM by assembling all local discrete equations of the sub‒domains. The mesh‒free properties of Galerkin method are retained in each sub‒domain. Several 2D elastic problems have been solved on the basis of this newly proposed method to validate its computational performance. These numerical examples proved that the newly proposed sub‒domain smoothed Galerkin method is a robust technique to solve solid mechanics problems based on its characteristics of high computational efficiency, good accuracy, and convergence.

Considering the economic value of natural design elements at city scale

With increasing signs of climate change and the influence of national and international carbon-related laws and agreements, governments all over the world are grappling with how to rapidly transition to low-carbon living. This includes adapting to the impacts of climate change that are very likely to be experienced due to current emission levels (including extreme weather and sea level changes), and mitigating against further growth in greenhouse gas emissions that are likely to result in further impacts. Internationally, the concept of ‘Biophilic Urbanism’, a term coined by Professors Tim Beatley and Peter Newman to refer to the use of natural elements as design features in urban landscapes, is emerging as a key component in addressing such climate change challenges in rapidly growing urban contexts. However, the economics of incorporating such options is not well understood and requires further attention to underpin a mainstreaming of biophilic urbanism. Indeed, there appears to be an ad hoc, reactionary approach to creating economic arguments for or against the design, installation or maintenance of natural elements such as green walls, green roofs, streetscapes, and parklands. With this issue in mind, this paper will overview research as part of an industry collaborative research project that considers the potential for using a number of environmental economic valuation techniques that have evolved over the last several decades in agricultural and resource economics, to systematically value the economic value of biophilic elements in the urban context. Considering existing literature on environmental economic valuation techniques, the paper highlights opportunities for creating a standardised language for valuing biophilic elements. The conclusions have implications for expanding the field of environmental economic value to support the economic evaluations and planning of the greater use of natural elements in cities. Insights are also noted for the more mature fields of agricultural and resource economics.

An exploration into retrofitting cities with natural design elements - learning from the city of Berlin, Germany

Natural design features in the built environment or biophilic elements are emerging as a potential response to the challenges of climate change, urbanisation and population pressures which have invited issues such as rising urban heat island effect, rising pollution, increased congestion, among others. This concept of living cities was made popular by Professor Tim Beatley in his book titled ‘Biophilic Urbanism’. Evidence of biophilic urbanism can be seen in some cities from around the globe since decoupling environmental pressures from future development is a priority on many agendas. Berlin is an example of a modern economy that has adopted an ecological sustainable development approach to reduce environmental degradation while driving innovation and employment.

The Six Core Elements of Business Process Management

The previous chapters gave an insightful introduction into the various facets of Business Process Management. We now share a rich understanding of the essential ideas behind designing and managing processes for organizational purposes. We have also learned about the various streams of research and development that have influenced contemporary BPM. As a matter of fact, BPM has become a holistic management discipline. As such, it requires that a plethora of facets needs to be addressed for its successful und sustainable application. This chapter provides a framework that consolidates and structures the essential factors that constitute BPM as a whole. Drawing from research in the field of maturity models, we suggest six core elements of BPM: strategic alignment, governance, methods, information technology, people, and culture. These six elements serve as the structure for this BPM Handbook.

Greening Buildings : How can the performance of existing commercial buildings be improved?

Efforts to improve the performance of commercial buildings have often focused on encouraging green design, construction and building operation; however, the business case is not very compelling if considering the energy cost savings alone. In recent years green building has been driven by a sense that it will improve the productivity of occupants, something with even greater economic returns than energy savings. Reducing energy demand in commercial buildings in a way that encourages greater productivity is not yet well understood as it involves a set of complex and interdependent factors. This project investigates these factors and focuses on the performance of and interaction between: green design elements, indoor environment quality, tenant/ leasing agreements and culture, occupant experience, and building management practices.

A detailed investigation of nominally 2-D radical-farming scramjet combustion

This paper reports on an investigation of the flow/chemistry coupling inside a nominally two-dimensional inlet-fuelled scramjet configuration. The experiments were conducted at a freestream Mach number of 7.3 and a total flow enthalpy of 4.3MJ/kg corresponding to a Mach 9.7 flight condition. The phenomenon of radical-farming has been studied in detail using two-dimensional OH* chemiluminescence imaging and emission spectroscopy. High signal levels of excited OH (OH*) were detected behind the first shock reflections inside the combustion chamber upstream of any measurable pressure rise from combustion, which occurred towards the rear of the combustor. The production of OH in the first hot pocket initiates the ignition process and then accelerates the combustion process in the next downstream hot pocket. This was confirmed by numerical simulations of premixed hydrogen/air flow through the scramjet. Chemical kinetics analyses reveal that the ignition process is governed by the interaction between various reaction groups leading to a chainbranching explosion for low mean temperature and pressure combustion flowfields.

Biophilic urbanism : harnessing natural elements to enhance the performance of constructed assets

Creating climate resilient, low-carbon urban environments and assets is a policy goal of many governments and city planners today, and an important issue for constructed asset owners. Stakeholders and decision makers in urban environments are also responding to growing evidence that cities need to increase their densities to reduce their footprint in the face of growing urban populations. Meanwhile, research is highlighting the importance of balancing such density with urban nature, to provide a range of health and wellbeing benefits to residents as well as to mitigate the environmental and economic impacts of heavily built up, impervious urban areas. Concurrently achieving this suite of objectives requires the coordination and cooperation of multiple stakeholder groups, with urban development and investment increasingly involving many private and public actors. Strategies are needed that can provide ‘win-win’ outcomes to benefit these multiple stakeholders, and provide immediate benefits while also addressing the emerging challenges of climate change, resource shortages and urban population growth. Within this context, ‘biophilic urbanism’ is emerging as an important design principle for buildings and urban areas. Through the use of a suite of natural design elements, biophilic urbanism has the potential to address multiple pressures related to climate change, increasing urban populations, finite resources and human’s inherent need for contact with nature. The principle directs the creation of urban environments that are conducive to life, delivering a range of benefits to stakeholders including building owners, occupiers and the surrounding community. This paper introduces the principle of biophilic urbanism and discusses opportunities for improved building occupant experience and performance of constructed assets, as well as addressing other sustainability objectives including climate change mitigation and adaptation. The paper presents an emerging process for considering biophilic design opportunities at different scales and highlights implications for the built environment industry. This process draws on findings of a study of leading cities internationally and learnings related to economic and policy considerations. This included literature review, two stakeholder workshops, and extensive industry consultation, funded by the Sustainable Built Environment National Research Centre through core project partners Western Australian Department of Finance, Parsons Brinckerhoff, Townsville City Council CitySolar Program, Green Roofs Australasia, and PlantUp.

Nanostructured metal hydrides for hydrogen storage studied by in situ synchrotron and neutron diffraction

This work was focused on studies of the metal hydride materials having a potential in building hydrogen storage systems with high gravimetric and volumetric efficiencies of H storage and formed / decomposed with high rates of hydrogen exchange. In situ diffraction studies of the metal-hydrogen systems were explored as a valuable tool in probing both the mechanism of the phase-structural transformations and their kinetics. Two complementary techniques, namely Neutron Powder Diffraction (NPD) and Synchrotron X-ray diffraction (SR XRD) were utilised. High pressure in situ NPD studies were performed at D2 pressures reaching 1000 bar at the D1B diffractometer accommodated at Institute Laue Langevin, Grenoble. The data of the time resolved in situ SR XRD were collected at the Swiss Norwegian Beam Lines, ESRF, Grenoble in the pressure range up to 50 bar H2 at temperatures 20-400°C. The systems studied by NPD at high pressures included deuterated Al-modified Laves-type C15 ZrFe2-xAlx intermetallics with x = 0.02; 0.04 and 0.20 and the CeNi5-D2 system. D content, hysteresis of H uptake and release, unit cell expansion and stability of the hydrides systematically change with Al content. Deuteration exhibited a very fast kinetics; it resulted in increase of the unit cells volumes reaching 23.5 % for ZrFe1.98Al0.02D2.9(1) and associated with exclusive occupancy of the Zr2(Fe,Al)2 tetrahedra. For CeNi5 deuteration yielded a hexahydride CeNi5D6.2 (20°C, 776 bar D2) and was accompanied by a nearly isotropic volume expansion reaching 30.1% (∆a/a=10.0%; ∆c/c=7.5%). Deuterium atoms fill three different interstitial sites including Ce2Ni2, Ce2Ni3 and Ni4. Significant hysteresis was observed on the first absorption-desorption cycle. This hysteresis decreased on the absorption-desorption cycling. A different approach to the development of H storage systems is based on the hydrides of light elements, first of all the Mg-based ones. These systems were studied by SR XRD. Reactive ball milling in hydrogen (HRBM) allowed synthesis of the nanostructured Mg-based hydrides. The experimental parameters (PH2, T, energy of milling, ball / sample ratio and balls size), significantly influence rate of hydrogenation. The studies confirmed (a) a completeness of hydrogenation of Mg into MgH2; (b) indicated a partial transformation of the originally formed -MgH2 into a metastable -MgH2 (a ratio / was 3/1); (c) yielded the crystallite size for the main hydrogenation product, -MgH2, as close to 10 nm. Influence of the additives to Mg on the structure and hydrogen absorption/desorption properties and cycle behaviour of the composites was established and will be discussed in the paper.

High-level expression of Rhodotorula gracilis d-amino acid oxidase in Pichia pastoris

By combining gene design and heterologous over-expression of Rhodotorula gracilis D-amino acid oxidase (RgDAO) in Pichia pastoris, enzyme production was enhanced by one order of magnitude compared to literature benchmarks, giving 350 kUnits/l of fed-batch bioreactor culture with a productivity of 3.1 kUnits/l h. P. pastoris cells permeabilized by freeze-drying and incubation in 2-propanol (10% v/v) produce a highly active (1.6 kUnits/g dry matter) and stable oxidase preparation. Critical bottlenecks in the development of an RgDAO catalyst for industrial applications have been eliminated.

Stepwise engineering of a Pichia pastoris D-amino acid oxidase whole cell catalyst

Trigonopsis variabilis D-amino acid oxidase (TvDAO) is a well characterized enzyme used for cephalosporin C conversion on industrial scale. However, the demands on the enzyme with respect to activity, operational stability and costs also vary with the field of application. Processes that use the soluble enzyme suffer from fast inactivation of TvDAO while immobilized oxidase preparations raise issues related to expensive carriers and catalyst efficiency. Therefore, oxidase preparations that are more robust and active than those currently available would enable a much broader range of economically viable applications of this enzyme in fine chemical syntheses. A multi-step engineering approach was chosen here to develop a robust and highly active Pichia pastoris TvDAO whole-cell biocatalyst. As compared to the native T. variabilis host, a more than seven-fold enhancement of the intracellular level of oxidase activity was achieved in P. pastoris through expression optimization by codon redesign as well as efficient subcellular targeting of the enzyme to peroxisomes. Multi copy integration further doubled expression and the specific activity of the whole cell catalyst. From a multicopy production strain, about 1.3 x 103 U/g wet cell weight (wcw) were derived by standard induction conditions feeding pure methanol. A fed-batch cultivation protocol using a mixture of methanol and glycerol in the induction phase attenuated the apparent toxicity of the recombinant oxidase to yield final biomass concentrations in the bioreactor of >or= 200 g/L compared to only 117 g/L using the standard methanol feed. Permeabilization of P. pastoris using 10% isopropanol yielded a whole-cell enzyme preparation that showed 49% of the total available intracellular oxidase activity and was notably stabilized (by three times compared to a widely used TvDAO expressing Escherichia coli strain) under conditions of D-methionine conversion using vigorous aeration. Stepwise optimization using a multi-level engineering approach has delivered a new P. pastoris whole cell TvDAO biocatalyst showing substantially enhanced specific activity and stability under operational conditions as compared to previously reported preparations of the enzyme. The production of the oxidase through fed-batch bioreactor culture and subsequent cell permeabilization is high-yielding and efficient. Therefore this P. pastoris catalyst has been evaluated for industrial purposes.

Simulation of plant cell shrinkage during drying : A SPH–DEM approach

Plant based dried food products are popular commodities in global market where much research is focused to improve the products and processing techniques. In this regard, numerical modelling is highly applicable and in this work, a coupled meshfree particle-based two-dimensional (2-D) model was developed to simulate micro-scale deformations of plant cells during drying. Smoothed Particle Hydrodynamics (SPH) was used to model the viscous cell protoplasm (cell fluid) by approximating it to an incompressible Newtonian fluid. The visco-elastic characteristic of the cell wall was approximated to a Neo-Hookean solid material augmented with a viscous term and modelled with a Discrete Element Method (DEM). Compared to a previous work [H. C. P. Karunasena, W. Senadeera, Y. T. Gu and R. J. Brown, Appl. Math. Model., 2014], this study proposes three model improvements: linearly decreasing positive cell turgor pressure during drying, cell wall contraction forces and cell wall drying. The improvements made the model more comparable with experimental findings on dried cell morphology and geometric properties such as cell area, diameter, perimeter, roundness, elongation and compactness. This single cell model could be used as a building block for advanced tissue models which are highly applicable for product and process optimizations in Food Engineering.

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.

Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants

Background We describe novel plasmid vectors for transient gene expression using Agrobacterium, infiltrated into Nicotiana benthamiana leaves. We have generated a series of pGreenII cloning vectors that are ideally suited to transient gene expression, by removing elements of conventional binary vectors necessary for stable transformation such as transformation selection genes. Results We give an example of expression of heme-thiolate P450 to demonstrate effectiveness of this system. We have also designed vectors that take advantage of a dual luciferase assay system to analyse promoter sequences or post-transcriptional regulation of gene expression. We have demonstrated their utility by co-expression of putative transcription factors and the promoter sequence of potential target genes and show how orthologous promoter sequences respond to these genes. Finally, we have constructed a vector that has allowed us to investigate design features of hairpin constructs related to their ability to initiate RNA silencing, and have used these tools to study cis-regulatory effect of intron-containing gene constructs. Conclusion In developing a series of vectors ideally suited to transient expression analysis we have provided a resource that further advances the application of this technology. These minimal vectors are ideally suited to conventional cloning methods and we have used them to demonstrate their flexibility to investigate enzyme activity, transcription regulation and post-transcriptional regulatory processes in transient assays.