Occurrence of LINE, gypsy-like, and copia-like retrotransposons in the clonally propagated sweet potato (Ipomoea batatas L.)

Retrotransposons are a class of transposable elements that represent a major fraction of the repetitive DNA of most eukaryotes. Their abundance stems from their expansive replication strategies. We screened and isolated sequence fragments of long terminal repeat (LTR), gypsy-like reverse transcriptase (rt) and gypsy-like envelope (env) domains, and two partial sequences of non-LTR retrotransposons, long interspersed element (LINE), in the clonally propagated allohexaploid sweet potato (Ipomoea batatas (L.) Lam.) genome. Using dot-blot hybridization, these elements were found to be present in the ~1597 Mb haploid sweet potato genome with copy numbers ranging from ~50 to ~4100 as observed in the partial LTR (IbLtr-1) and LINE (IbLi-1) sequences, respectively. The continuous clonal propagation of sweet potato may have contributed to such a multitude of copies of some of these genomic elements. Interestingly, the isolated gypsy-like env and gypsy-like rt sequence fragments, IbGy-1 (~2100 copies) and IbGy-2 (~540 copies), respectively, were found to be homologous to the Bagy-2 cDNA sequences of barley (Hordeum vulgare L.). Although the isolated partial sequences were found to be homologous to other transcriptionally active elements, future studies are required to determine whether they represent elements that are transcriptionally active under normal and (or) stressful conditions.

Microscopic and spectroscopic investigation of poly(3-hexylthiophene) interaction with carbon nanotubes

The inclusion of carbon nanotubes in polymer matrix has been proposed to enhance the polymer’s physical and electrical properties. In this study, microscopic and spectroscopic techniques are used to investigate the interaction between poly(3-hexylthiophene) (P3HT) and nanotubes and the reciprocal modification of physical properties. The presence of P3HT-covered nanotubes dispersed in the polymer matrix has been observed by atomic force microscopy and transmission electron microscopy. Then, the modification of P3HT optical properties due to nanotube inclusion has been evidenced with spectroscopic techniques like absorption and Raman spectroscopy. The study is completed with detailed nanoscale analysis by scanning probe techniques. The ordered self assembly of polymer adhering on the nanotube is unveiled by showing an example of helical wrapping of P3HT. Scanning tunneling spectroscopy study provides information on the electronic structure of nanotube-polymer assembly, revealing the charge transfer from P3HT to the nanotube.

Extreme ultraviolet (EUV) degradation of poly(olefin sulfone)s : towards applications as EUV photoresists

Poly(olefin sulfone)s, formed by the reaction of sulfur dioxide (SO2) and an olefin, are known to be highly susceptible to degradation by radiation and thus have been identified as candidate materials for chain scission-based extreme ultraviolet lithography (EUVL) resist materials. In order to investigate this further, the synthesis and characterisation of two poly(olefin sulfone)s namely poly(1-pentene sulfone) (PPS) and poly(2-methyl-1-pentene sulfone) (PMPS), was achieved and the two materials were evaluated for possible chain scission EUVL resist applications. It was found that both materials possess high sensitivities to EUV photons; however; the rates of outgassing were extremely high. The only observed degradation products were found to be SO2 and the respective olefin suggesting that depolymerisation takes place under irradiation in a vacuum environment. In addition to depolymerisation, a concurrent conversion of SO2 moieties to a sulfide phase was observed using XPS.

The undirected feedback vertex set problem has a Poly(k) Kernel

Resolving a noted open problem, we show that the Undirected Feedback Vertex Set problem, parameterized by the size of the solution set of vertices, is in the parameterized complexity class Poly(k), that is, polynomial-time pre-processing is sufficient to reduce an initial problem instance (G, k) to a decision-equivalent simplified instance (G', k') where k' � k, and the number of vertices of G' is bounded by a polynomial function of k. Our main result shows an O(k11) kernelization bound.

Properties of lignin and poly(hydroxybutyrate) blends

The Queensland University of Technology (QUT) allows the presentation of a thesis for the Degree of Doctor of Philosophy in the format of published or submitted papers, where such papers have been published, accepted or submitted during the period of candidature. This thesis is composed of Seven published/submitted papers and one poster presentation, of which five have been published and the other two are under review. This project is financially supported by the QUTPRA Grant. The twenty-first century started with the resurrection of lignocellulosic biomass as a potential substitute for petrochemicals. Petrochemicals, which enjoyed the sustainable economic growth during the past century, have begun to reach or have reached their peak. The world energy situation is complicated by political uncertainty and by the environmental impact associated with petrochemical import and usage. In particular, greenhouse gasses and toxic emissions produced by petrochemicals have been implicated as a significant cause of climate changes. Lignocellulosic biomass (e.g. sugarcane biomass and bagasse), which potentially enjoys a more abundant, widely distributed, and cost-effective resource base, can play an indispensible role in the paradigm transition from fossil-based to carbohydrate-based economy. Poly(3-hydroxybutyrate), PHB has attracted much commercial interest as a plastic and biodegradable material because some its physical properties are similar to those of polypropylene (PP), even though the two polymers have quite different chemical structures. PHB exhibits a high degree of crystallinity, has a high melting point of approximately 180°C, and most importantly, unlike PP, PHB is rapidly biodegradable. Two major factors which currently inhibit the widespread use of PHB are its high cost and poor mechanical properties. The production costs of PHB are significantly higher than for plastics produced from petrochemical resources (e.g. PP costs $US1 kg-1, whereas PHB costs $US8 kg-1), and its stiff and brittle nature makes processing difficult and impedes its ability to handle high impact. Lignin, together with cellulose and hemicellulose, are the three main components of every lignocellulosic biomass. It is a natural polymer occurring in the plant cell wall. Lignin, after cellulose, is the most abundant polymer in nature. It is extracted mainly as a by-product in the pulp and paper industry. Although, traditionally lignin is burnt in industry for energy, it has a lot of value-add properties. Lignin, which to date has not been exploited, is an amorphous polymer with hydrophobic behaviour. These make it a good candidate for blending with PHB and technically, blending can be a viable solution for price and reduction and enhance production properties. Theoretically, lignin and PHB affect the physiochemical properties of each other when they become miscible in a composite. A comprehensive study on structural, thermal, rheological and environmental properties of lignin/PHB blends together with neat lignin and PHB is the targeted scope of this thesis. An introduction to this research, including a description of the research problem, a literature review and an account of the research progress linking the research papers is presented in Chapter 1. In this research, lignin was obtained from bagasse through extraction with sodium hydroxide. A novel two-step pH precipitation procedure was used to recover soda lignin with the purity of 96.3 wt% from the black liquor (i.e. the spent sodium hydroxide solution). The precipitation process is presented in Chapter 2. A sequential solvent extraction process was used to fractionate the soda lignin into three fractions. These fractions, together with the soda lignin, were characterised to determine elemental composition, purity, carbohydrate content, molecular weight, and functional group content. The thermal properties of the lignins were also determined. The results are presented and discussed in Chapter 2. On the basis of the type and quantity of functional groups, attempts were made to identify potential applications for each of the individual lignins. As an addendum to the general section on the development of composite materials of lignin, which includes Chapters 1 and 2, studies on the kinetics of bagasse thermal degradation are presented in Appendix 1. The work showed that distinct stages of mass losses depend on residual sucrose. As the development of value-added products from lignin will improve the economics of cellulosic ethanol, a review on lignin applications, which included lignin/PHB composites, is presented in Appendix 2. Chapters 3, 4 and 5 are dedicated to investigations of the properties of soda lignin/PHB composites. Chapter 3 reports on the thermal stability and miscibility of the blends. Although the addition of soda lignin shifts the onset of PHB decomposition to lower temperatures, the lignin/PHB blends are thermally more stable over a wider temperature range. The results from the thermal study also indicated that blends containing up to 40 wt% soda lignin were miscible. The Tg data for these blends fitted nicely to the Gordon-Taylor and Kwei models. Fourier transform infrared spectroscopy (FT-IR) evaluation showed that the miscibility of the blends was because of specific hydrogen bonding (and similar interactions) between reactive phenolic hydroxyl groups of lignin and the carbonyl group of PHB. The thermophysical and rheological properties of soda lignin/PHB blends are presented in Chapter 4. In this chapter, the kinetics of thermal degradation of the blends is studied using thermogravimetric analysis (TGA). This preliminary investigation is limited to the processing temperature of blend manufacturing. Of significance in the study, is the drop in the apparent energy of activation, Ea from 112 kJmol-1 for pure PHB to half that value for blends. This means that the addition of lignin to PHB reduces the thermal stability of PHB, and that the comparative reduced weight loss observed in the TGA data is associated with the slower rate of lignin degradation in the composite. The Tg of PHB, as well as its melting temperature, melting enthalpy, crystallinity and melting point decrease with increase in lignin content. Results from the rheological investigation showed that at low lignin content (.30 wt%), lignin acts as a plasticiser for PHB, while at high lignin content it acts as a filler. Chapter 5 is dedicated to the environmental study of soda lignin/PHB blends. The biodegradability of lignin/PHB blends is compared to that of PHB using the standard soil burial test. To obtain acceptable biodegradation data, samples were buried for 12 months under controlled conditions. Gravimetric analysis, TGA, optical microscopy, scanning electron microscopy (SEM), differential scanning calorimetry (DSC), FT-IR, and X-ray photoelectron spectroscopy (XPS) were used in the study. The results clearly demonstrated that lignin retards the biodegradation of PHB, and that the miscible blends were more resistant to degradation compared to the immiscible blends. To obtain an understanding between the structure of lignin and the properties of the blends, a methanol-soluble lignin, which contains 3× less phenolic hydroxyl group that its parent soda lignin used in preparing blends for the work reported in Chapters 3 and 4, was blended with PHB and the properties of the blends investigated. The results are reported in Chapter 6. At up to 40 wt% methanolsoluble lignin, the experimental data fitted the Gordon-Taylor and Kwei models, similar to the results obtained soda lignin-based blends. However, the values obtained for the interactive parameters for the methanol-soluble lignin blends were slightly lower than the blends obtained with soda lignin indicating weaker association between methanol-soluble lignin and PHB. FT-IR data confirmed that hydrogen bonding is the main interactive force between the reactive functional groups of lignin and the carbonyl group of PHB. In summary, the structural differences existing between the two lignins did not manifest itself in the properties of their blends.

Poly[tetra-mu-aqua-diaquatetrakis[mu-(E)-2-nitrocinnamato]tetrarubidium]

In the structure of the title compound [Rb4(C9H6NO4)4(H~2~O)6]n, the asymmetric unit comprises four rubidium complex cations, two of which have an RbO7 coordination polyhedron with a monocapped distorted octahedral stereochemistry and two of which have a distorted RbO6 octahedral coordination. The bonding about both the seven-coordinate centres is similar, comprising one monodentate water molecule together with three bridging water molecules and three carboxylate O-atom donors, two of which are bridging. The environments about the six-coordinate cations are also similar, comprising a monodentate nitro O-atom donor, a bridging water molecule and four bridging carboxylate O-atom donors [overall Rb-O range, 2.849(2)-3.190(2)A]. The coordination leads to a two-dimensional polymeric structure extending parallel to (001), which is stabilized by interlayer water O-H...O hydrogen-bonding associations to water, carboxyl and nitro O-atom acceptors, together with weak inter-ring pi--pi interactions [minimum ring centroid separation = 3.5319(19)A].

Charting the system : the integrated master schedule as a multi-level and poly-temporal boundary object in complex projects

This paper investigates the use of visual artifacts to represent a complex adaptive system (CAS). The integrated master schedule (IMS) is one of those visuals widely used in complex projects for scheduling, budgeting, and project management. In this paper, we discuss how the IMS outperforms the traditional timelines and acts as a ‘multi-level and poly-temporal boundary object’ that visually represents the CAS. We report the findings of a case study project on the way the IMS mapped interactions, interdependencies, constraints and fractal patterns in a complex project. Finally, we discuss how the IMS was utilised as a complex boundary object by eliciting commitment and development of shared mental models, and facilitating negotiation through the layers of multiple interpretations from stakeholders.

The influence of architecture on degradation and tissue ingrowth into three-dimensional poly(lactic-co-glycolic acid) scaffolds in vitro and in vivo

The in vitro and in vivo degradation properties of poly(lactic-co-glycolic acid) (PLGA) scaffolds produced by two different technologies - thermally induced phase separation (TIPS), and solvent casting and particulate leaching (SCPL) were compared. Over 6 weeks, in vitro degradation produced changes in SCPL scaffold dimension, mass, internal architecture and mechanical properties. TIPS scaffolds produced far less changes in these parameters providing significant advantages over SCPL. In vivo results were based on a microsurgically created arteriovenous (AV) loop sandwiched between two TIPS scaffolds placed in a polycarbonate chamber under rat groin skin. Histologically, a predominant foreign body giant cell response and reduced vascularity was evident in tissue ingrowth between 2 and 8 weeks in TIPS scaffolds. Tissue death occurred at 8 weeks in the smallest pores. Morphometric comparison of TIPS and SCPL scaffolds indicated slightly better tissue ingrowth but greater loss of scaffold structure in SCPL scaffolds. Although advantageous in vitro, large surface area:volume ratios and varying pore sizes in PLGA TIPS scaffolds mean that effective in vivo (AV loop) utilization will only be achieved if the foreign body response can be significantly reduced so as to allow successful vascularisation, and hence sustained tissue growth, in pores less than 300 μm. © 2005 Elsevier Ltd. All rights reserved.

Expression Pattern of the Alpha-Kafirin Promoter Coupled with a Signal Peptide from Sorghum bicolor L. Moench

Regulatory sequences with endosperm specificity are essential for foreign gene expression in the desired tissue for both grain quality improvement and molecular pharming. In this study, promoters of seed storage α-kafirin genes coupled with signal sequence (ss) were isolated from Sorghum bicolor L. Moench genomic DNA by PCR. The α-kafirin promoter (α-kaf) contains endosperm specificity-determining motifs, prolamin-box, the O2-box 1, CATC, and TATA boxes required for α-kafirin gene expression in sorghum seeds. The constructs pMB-Ubi-gfp and pMB-kaf-gfp were microprojectile bombarded into various sorghum and sweet corn explants. GFP expression was detected on all explants using the Ubi promoter but only in seeds for the α-kaf promoter. This shows that the α-kaf promoter isolated was functional and demonstrated seed-specific GFP expression. The constructs pMB-Ubi-ss-gfp and pMB-kaf-ss-gfp were also bombarded into the same explants. Detection of GFP expression showed that the signal peptide (SP)::GFP fusion can assemble and fold properly, preserving the fluorescent properties of GFP.

An investigation into the effect of amphiphilic siloxane oligomers on dermal fibroblasts

This study investigates the effect of well-defined poly(dimethylsiloxane)-poly(ethylene glycol) (PDMS-PEG) ABA linear block co-oligomers on the proliferation of human dermal fibroblasts. The co-oligomers assessed ranged in molecular weight (MW) from 1335 to 5208 Da and hydrophilic-lipophilic balance (HLB) from 5.9 to 16.6 by varying the number of both PDMS and PEG units. In general, it was found that co-oligomers of low MW or intermediate hydrophilicity significantly reduced fibroblast proliferation. A linear relationship between down-regulation of fibroblast proliferation, and the ratio HLB/MW was observed at concentrations of 0.1 and 1.0 wt % of the oligomers. This enabled the structures with highest efficiency to be determined. These results suggest the possible use of the PEG-PDMS-PEG block co-oligomers as an alternative to silicone gels for hypertrophic scar remediation.

Environmental degradation of lignin/poly(hydroxybutyrate) blends

Blends of lignin and poly(hydroxybutyrate) (PHB) were obtained by melt extrusion. They were buried in a garden soil for up to 12 months, and the extent and mechanism of degradation were investigated by gravimetric analysis, thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and Fourier transform infra-red spectroscopy (FTIR) over the entire range of compositions. The PHB films were disintegrated and lost 45 wt% of mass within 12 months. This value dropped to 12 wt% of mass when only 10 wt% of lignin was present, suggesting that lignin both inhibited and slowed down the rate of PHB degradation. TGA and DSC indicated structural changes, within the lignin/PHB matrix, with burial time, while FTIR results confirmed the fragmentation of the PHB polymer. XPS revealed an accumulation of biofilms on the surface of buried samples, providing evidence of a biodegradation mechanism. Significant surface roughness was observed with PHB films due to microbial attack caused by both loosely and strongly associated micro-organisms. The presence of lignin in the blends may have inhibited the colonisation of the micro-organisms and caused the blends to be more resistant to microbial attack. Analysis suggested that lignin formed strong hydrogen bonds with PHB in the buried samples and it is likely that the rate of breakdown of PHB is reduced, preventing rapid degradation of the blends.