Self-assembled hyperbranched polymer - gold nanoparticle hybrids : understanding the effect of polymer coverage on assembly size and SERS performance

In the past few years, remarkable progress has been made in unveiling novel and unique optical properties of strongly coupled plasmonic nanostructures. However, application of such plasmonic nanostructures in biomedicine remains challenging due to the lack of facile and robust assembly methods for producing stable nanostructures. Previous attempts to achieve plasmonic nano-assemblies using molecular ligands were limited due to the lack of flexibility that could be exercised in forming them. Here, we report the utilization of tailor-made hyperbranched polymers (HBP) as linkers to assemble gold nanoparticles (NPs) into nano-assemblies. The ease and flexibility in tuning the particle size and number of branch ends of a HBP makes it an ideal candidate as a linker, as opposed to DNA, small organic molecules and linear or dendrimeric polymers. We report a strong correlation of polymer (HBP) concentration with the size of the hybrid nano-assemblies and “hot-spot” density. We have shown that such solutions of stable HBP-gold nano-assemblies can be barcoded with various Raman tags to provide improved surface-enhanced Raman scattering (SERS) compared with non-aggregated NP systems. These Raman barcoded hybrid nano-assemblies, with further optimization of NP shape, size and “hot-spot” density, may find application as diagnostic tools in nanomedicine.

Procuring OSM : base-line models of off-site manufacture business processes in Australia

A pressing cost issue facing construction is the procurement of off-site pre-manufactured assemblies. In order to encourage Australian adoption of off-site manufacture (OSM), a new approach to underlying processes is required. The advent of object oriented digital models for construction design assumes intelligent use of data. However, the construction production system relies on traditional methods and data sources and is expected to benefit from the application of well-established business process management techniques. The integration of the old and new data sources allows for the development of business process models which, by capturing typical construction processes involving OSM, provides insights into such processes. This integrative approach is the foundation of research into the use of OSM to increase construction productivity in Australia. The purpose of this study is to develop business process models capturing the procurement, resources and information flow of construction projects. For each stage of the construction value chain, a number of sub-processes are identified. Business Process Modelling Notation (BPMN), a mainstream business process modelling standard, is used to create base-line generic construction process models. These models identify OSM decision-making points that could provide cost reductions in procurement workflow and management systems. This paper reports on phase one of an on-going research aiming to develop a proto-type workflow application that can provide semi-automated support to construction processes involving OSM and assist in decision-making in the adoption of OSM thus contributing to a sustainable built environment.

Urban renewal, migration and memories : the affordances of place-based pedagogies for developing immigrant students’ literate repertoires

This paper reports on the new literacy demands in the middle years of schooling project in which the affordances of placed-based pedagogy are being explored through teacher inquiries and classroom-based design experiments. The school is located within a large-scale urban renewal project in which houses are being demolished and families relocated. The original school buildings have recently been demolished and replaced by a large ‘superschool’ which serves a bigger student population from a wider area. Drawing on both quantitative and qualitative data, the teachers reported that the language literacy learning of students (including a majority of students learning English as a second language) involved in the project exceeded their expectations. The project provided the motivation for them to develop their oral language repertoires, by involving them in processes such as conducting interviews with adults for their oral histories, through questioning the project manager in regular meetings, and through reporting to their peers and the wider community at school assemblies. At the same time students’ written and multimodal documentation of changes in the neighbourhood and the school grounds extended their literate and semiotic repertoires as they produced books, reports, films, powerpoints, visual designs and models of structures.

Synthesis of discrete allyl-functional polyethylene glycol for efficient hydrophilization of dihydr (polydimethylsiloxane)

Amphiphilic poly(ethylene glycol)-block-pol (dimethylsiloxane)-block-poly(ethylene glycol)(PEG-block-PDMS block-PEG) triblock copolymers have been successfully prepared via hydrosilylation using discrete and polydisperse PEG of various chain lengths. Facile synthesis of discrete PEG (dPEG) is achieved via systematic tosylation and etherification of lower glycols. Amphiphilicity of the dPEG block-PDMS-block-dPEG triblock copolymer is illustrated by dynamic light scattering (DLS) and measurement of the critical micelle concentration (CMC).

Experimental study of load bearing cold-formed steel wall systems under fire conditions

Light Gauge Steel Framing (LSF) walls made of cold-formed and thin-walled steel lipped channel studs with plasterboard linings on both sides are commonly used in commercial, industrial and residential buildings. However, there is limited data about their structural and thermal performance under fire conditions while past research showed contradicting results about the benefits of using cavity insulation. A new composite wall panel was recently proposed to improve the fire resistance rating of LSF walls, where an insulation layer was used externally between the plasterboards on both sides of the wall frame instead of using it in the cavity. In this research 11 full scale tests were conducted on conventional load bearing steel stud walls with and without cavity insulation, and the new composite panel system to study their thermal and structural performance under standard fire conditions. These tests showed that the use of cavity insulation led to inferior fire performance of walls, and provided supporting research data. They demonstrated that the use of insulation externally in a composite panel enhanced the thermal and structural performance of LSF walls and increased their fire resistance rating. This paper presents the details of the LSF wall tests and the thermal and structural performance data and fire resistance rating of load-bearing wall assemblies lined with varying plasterboard-insulation configurations under two different load ratios. Fire test results including the time–temperature and deflection profiles are presented along with the failure times and modes.

Fatigue behaviour of corrugated roofing under cycling wind loading

Low cycle fatigue cracking of light gauge metal roofing was investigated by testing a number of two-span corrugated roofing assemblies with different spans and fastening systems under cyclic uplift wind loading. Fatigue results correlated quite well with the corresponding static results reported earlier, and revealed the dependence of fatigue behaviour on the fastening system used. A comparison was made of one fastening system with the other regarding fatigue performance .

Behaviour and design of crest-fixed profiled steel roof claddings under wind uplift

Profiled steel roof claddings in Australia are commonly made of very thin high tensile steel and are crest-fixed with screw fasteners. At present the design of these claddings is entirely based on testing. In order to improve the understanding of the behaviour of these claddings under wind uplift, and thus the design methods, a detailed investigation consisting of a finite element analysis and laboratory experiments was carried out on two-span roofing assemblies of three common roofing profiles. It was found that the failure of the roof cladding system was due to a local failure (dimpling of crests/pull-through) at the fasteners. This paper presents the details of the investigation, the results and then proposes a design method based on the strength of the screwed connections, for which testing of small-scale roofing models and/or using a simple design formula is recommended.

Reconstruction of the ancestral marsupial karyotype from comparative gene maps

BACKGROUND: The increasing number of assembled mammalian genomes makes it possible to compare genome organisation across mammalian lineages and reconstruct chromosomes of the ancestral marsupial and therian (marsupial and eutherian) mammals. However, the reconstruction of ancestral genomes requires genome assemblies to be anchored to chromosomes. The recently sequenced tammar wallaby (Macropus eugenii) genome was assembled into over 300,000 contigs. We previously devised an efficient strategy for mapping large evolutionarily conserved blocks in non-model mammals, and applied this to determine the arrangement of conserved blocks on all wallaby chromosomes, thereby permitting comparative maps to be constructed and resolve the long debated issue between a 2n=14 and 2n=22 ancestral marsupial karyotype. RESULTS: We identified large blocks of genes conserved between human and opossum, and mapped genes corresponding to the ends of these blocks by fluorescence in situ hybridization (FISH). A total of 242 genes was assigned to wallaby chromosomes in the present study, bringing the total number of genes mapped to 554 and making it the most densely cytogenetically mapped marsupial genome. We used these gene assignments to construct comparative maps between wallaby and opossum, which uncovered many intrachromosomal rearrangements, particularly for genes found on wallaby chromosomes X and 3. Expanding comparisons to include chicken and human permitted the putative ancestral marsupial (2n=14) and therian mammal (2n=19) karyotypes to be reconstructed. CONCLUSIONS: Our physical mapping data for the tammar wallaby has uncovered the events shaping marsupial genomes and enabled us to predict the ancestral marsupial karyotype, supporting a 2n=14 ancestor. Futhermore, our predicted therian ancestral karyotype has helped to understand the evolution of the ancestral eutherian genome.

Computational model of membrane fission catalyzed by ESCRT-III

ESCRT-III proteins catalyze membrane fission during multi vesicular body biogenesis, budding of some enveloped viruses and cell division. We suggest and analyze a novel mechanism of membrane fission by the mammalian ESCRT-III subunits CHMP2 and CHMP3. We propose that the CHMP2-CHMP3 complexes self-assemble into hemi-spherical dome-like structures within the necks of the initial membrane buds generated by CHMP4 filaments. The dome formation is accompanied by the membrane attachment to the dome surface, which drives narrowing of the membrane neck and accumulation of the elastic stresses leading, ultimately, to the neck fission. Based on the bending elastic model of lipid bilayers, we determine the degree of the membrane attachment to the dome enabling the neck fission and compute the required values of the protein-membrane binding energy. We estimate the feasible values of this energy and predict a high efficiency for the CHMP2-CHMP3 complexes in mediating membrane fission. We support the computational model by electron tomography imaging of CHMP2-CHMP3 assemblies in vitro. We predict a high efficiency for the CHMP2-CHMP3 complexes in mediating membrane fission.

Hybrid polymer/metal nanoparticles with surface enhanced raman tracking for potential use in nanomedicine

This project was a preliminary step towards the development of novel methods for early stage cancer diagnosis and treatment. Diagnostic imaging agents with high Raman signal enhancement were developed based on tailored assemblies of gold nanoparticles, which demonstrated potential for non-invasive detection from deep under the skin surface. Specifically designed polymers were employed to assemble gold nanoparticles into controlled morphologies including dimers, nanochains, nanoplates, globular and core-satellite nanostructures. Our findings suggest that the Raman enhancement is strongly dependent on assembly morphology and can be tuned to adapt to the requirements of the diagnostic agent.

Assembly and annotation of a non-model gastropod (Nerita melanotragus) transcriptome: a comparison of De novo assemblers

Background The sequencing, de novo assembly and annotation of transcriptome datasets generated with next generation sequencing (NGS) has enabled biologists to answer genomic questions in non-model species with unprecedented ease. Reliable and accurate de novo assembly and annotation of transcriptomes, however, is a critically important step for transcriptome assemblies generated from short read sequences. Typical benchmarks for assembly and annotation reliability have been performed with model species. To address the reliability and accuracy of de novo transcriptome assembly in non-model species, we generated an RNAseq dataset for an intertidal gastropod mollusc species, Nerita melanotragus, and compared the assembly produced by four different de novo transcriptome assemblers; Velvet, Oases, Geneious and Trinity, for a number of quality metrics and redundancy. Results Transcriptome sequencing on the Ion Torrent PGM™ produced 1,883,624 raw reads with a mean length of 133 base pairs (bp). Both the Trinity and Oases de novo assemblers produced the best assemblies based on all quality metrics including fewer contigs, increased N50 and average contig length and contigs of greater length. Overall the BLAST and annotation success of our assemblies was not high with only 15-19% of contigs assigned a putative function. Conclusions We believe that any improvement in annotation success of gastropod species will require more gastropod genome sequences, but in particular an increase in mollusc protein sequences in public databases. Overall, this paper demonstrates that reliable and accurate de novo transcriptome assemblies can be generated from short read sequencers with the right assembly algorithms. Keywords: Nerita melanotragus; De novo assembly; Transcriptome; Heat shock protein; Ion torrent

Supramolecular organization in fluorene/indenofluorene-oligothiophene alternating conjugated copolymers

A series of conjugated copolymers containing fluorene or indenofluorene units alternating with oligothiophene segments, with potential interest for use as the active layer in field-effect transistors, is investigated. Atomic force microscopy analysis of the morphology of thin deposits shows either the formation of fibrillar structures, which are the signature of long-range π stacking, or the presence of untextured aggregates, resulting from disordered assembly. These morphologies are interpreted in terms of the supramolecular organization of the conjugated chains. Molecular modeling simulations indicate that the commensurability between the lengths of the monomer units and the presence of alkyl side groups are the two key structural factors governing the chain organization into highly ordered assemblies. The most favorable structures are those combining fluorene (indenofluorene) units with unsubstituted bithiophene (terthiophene) segments.

Profiled steel roof claddings under high wind forces

Profiled steel roof claddings in Australia and its neighbouring countries are commonly made of very thin high tensile steel and are crest-fixed intermittently with screw fasteners. The failure of the roof cladding systems was due to a local failure (dimpling of crests I pull-through) at the fasteners under wind uplift Cyclic wind uplift during cyclones causes fatigue cracking to occur at the fastener holes which leads to pull-through failures at lower load levels. At present the design of these claddings is entirely based on testing. In order to improve the understanding of the behaviour and the design and test methods of these claddings under wind uplift loading during storms and cyclones, a detailed investigation consisting of finite element analyses, static and fatigue experiments and cyclonic wind modelling was carried out on two-span roofing assemblies of three common roofing profiles. This paper presents the details of this investigation and its important results.

Optimizing de novo transcriptome assembly and extending genomic resources for striped catfish (Pangasianodon hypophthalmus)

Striped catfish (Pangasianodon hypophthalmus) is a commercially important freshwater fish used in inland aquaculture in the Mekong Delta, Vietnam. The culture industry is facing a significant challenge however from saltwater intrusion into many low topographical coastal provinces across the Mekong Delta as a result of predicted climate change impacts. Developing genomic resources for this species can facilitate the production of improved culture lines that can withstand raised salinity conditions, and so we have applied high-throughput Ion Torrent sequencing of transcriptome libraries from six target osmoregulatory organs from striped catfish as a genomic resource for use in future selection strategies. We obtained 12,177,770 reads after trimming and processing with an average length of 97 bp. De novo assemblies were generated using CLC Genomic Workbench, Trinity and Velvet/Oases with the best overall contig performance resulting from the CLC assembly. De novo assembly using CLC yielded 66,451 contigs with an average length of 478 bp and N50 length of 506 bp. A total of 37,969 contigs (57%) possessed significant similarity with proteins in the non-redundant database. Comparative analyses revealed that a significant number of contigs matched sequences reported in other teleost fishes, ranging in similarity from 45.2% with Atlantic cod to 52% with zebrafish. In addition, 28,879 simple sequence repeats (SSRs) and 55,721 single nucleotide polymorphisms (SNPs) were detected in the striped catfish transcriptome. The sequence collection generated in the current study represents the most comprehensive genomic resource for P. hypophthalmus available to date. Our results illustrate the utility of next-generation sequencing as an efficient tool for constructing a large genomic database for marker development in non-model species.

Hydrogen-bonded supramolecular polymers as self-healing hydrogels: Effect of a bulky adamantyl substituent in the ureido-pyrimidinone monomer

In an attempt to generate supramolecular assemblies able to function as self-healing hydrogels, a novel ureido-pyrimidinone (UPy) monomer, 2-(N ′-methacryloyloxyethylureido)-6-(1-adamantyl)-4[1H]-pyrimidinone, was synthesized and then copolymerized with N,N-dimethylacrylamide at four different feed compositions, using a solution of lithium chloride in N,N-dimethylacetamide as the polymerization medium. The assembling process in the resulting copolymers is based on crosslinking through the reversible quadruple hydrogen bonding between side-chain UPy modules. The adamantyl substituent was introduced in order to create a “hydrophobic pocket” that may protect the hydrogen bonds against the disruptive effect of water molecules. Upon hydration to equilibrium, all copolymers generated typical hydrogels when their concentration in the hydrated system was at least 15%. The small-deformation rheometry showed that all hydrated copolymers were hydrogels that maintained a solid-like behavior, and that their extrusion through a syringe needle did not affect significantly this behavior, suggesting a self-healing capacity in these materials. An application as injectable substitutes for the eye's vitreous humor was proposed