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Brown rot fungi are notoriously copper-tolerant, which makes them difficult to control with copper-based wood preservatives. Brown rot fungi are also unique because they have evolved a bilateral strategy for decay. Their initial attack involves the production of hydroxyl free radicals to increase wood porosity, followed by an enzymatic onslaught of glycoside hydrolases that free the sugars locked within cellulose and hemicellulose. Our molecular understanding of these biological processes, however, has been hampered by our limited knowledge of the underlying genetic mechanisms. To address this knowledge gap, high-throughput, short-read sequencing was used to conduct a comprehensive analysis of the genomics and transcriptomics of wood decay and copper tolerance in the brown rot fungus Fibroporia radiculosa. The results were impressively informative. In the genomic study, the sequences of 9262 genes were predicted and gene function was assigned to 5407 of the genes. An examination of target motifs showed that 1213 of the genes encoded products with extracellular functions. By mining these genomic annotations, 187 genes were identified with putative roles in lignocellulose degradation and copper tolerance. The transcriptomic study quantified gene expression of the fungus growing on wood treated with a copper-based preservative. At day 31, the fungus was adapting to the preservative, and the wood showed no strength loss. At day 154, the preservative effects were gone, and the fungus was actively degrading the wood, which exhibited 52% strength loss. A total of 917 differentially expressed genes were identified, 108 of which appeared to be regulating wood decay and preservative tolerance. Genes that showed increased expression at day 31 were involved in oxalate metabolism, hydroxyl free radical production by the enzyme laccase, energy production, xenobiotic detoxification, copper resistance, stress response, and pectin degradation. Genes that exhibited higher expression at day 154 were involved in wood polysaccharide degradation, hexose transport, oxalate catabolism, catabolism of laccase substrates, proton reduction, re-modeling the glucan sheath, and shoring up the plasma membrane for acid shock. These newly discovered genes represent a significant step towards accelerating a genome-wide understanding of brown rot decay and tolerance to wood preservatives.

Isoxaben is a preemergence (PRE) broadleaf herbicide used in turf and ornamentals. Field, greenhouse, and laboratory research evaluated this herbicide for PRE control of selected broadleaves in turf, suspected postemergence (POST) herbicidal effects, and the influence of application timings and rates on soil residual. During seed germination in moist filter paper, isoxaben concentrations required for 50% inhibition of radicle growth (GR50) were 0.013, 0.010, 0.008, 0.008, and 0.007 ppm for dandelion, buckhorn plantain, white clover, black medic, and common lespedeza, respectively. In greenhouse experiments, isoxaben applied POST at 2.24 kg ai/ha suppressed the growth of Florida betony, black medic and white clover by 45, 65, and 66%, respectively, and reduced regrowth of Florida betony by 71%. In soil bioassays, yellow rocket control from isoxaben applied in fall was approximately 20 and 30% greater than spring-applied isoxaben at 3 and 6 MAT, respectively. Buckhorn plantain control from fall treatments at 3 MAT was approximately 15% higher than spring-applied isoxaben at 3 MAT. Application timings did not influence control of spotted spurge, a less sensitive weed. Isoxaben applied to turf in spring at 1.12 kg/ha provided > 90% control of buckhorn plantain, dandelion, and corn speedwell at 4 MAT. Fall applied isoxaben at the same rate provided total control of common chickweed, corn speedwell and henbit at 3 MAT and 80 to 90% control of white sweet clover and buckhorn plantain that germinated the following spring. Double (spring followed by fall) application of isoxaben to turf appeared to enhance broadleaf weed control in some instances. Dissipation of isoxaben in the top 3.8 cm of a Ross silt-loam soil as affected by spring, fall, and spring followed by fall applications was determined using high performance liquid chromatography (HPLC) analysis. Isoxaben residues in soil decreased by 55 and 92% by 3 and 6 MAT, respectively, for spring teatments, and decreased 29 and 52% by 3 and 6 MAT for fall treatments, respectively. A soil-bioassay study correlated well with chemical analysis of isoxaben residues, as the correlation coefficients were 0.85 and 0.89 for yellow rocket and buckhorn plantain, respectively. / Ph. D.

This study addressed two aspects of ecological theory developed primarily in North America and examined these theories using an Australian passerine as a model species. The first theory concerns the mechanisms by which habitat fragmentation affects avian populations. I investigated the mechanisms causing the decline of the Brown Treecreeper (Climacteris picumnus) in fragmented habitat, and specifically considered the effects of isolation and habitat degradation, which are potentially important in Australian woodlands, and edge (patch size), which are important in North America. Brown Treecreeper groups were as productive in isolated patches as in connected patches of habitat regardless of patch size, yet unpaired males were common in isolated fragments of habitat. I conducted a field experiment that confirmed that female dispersal was disrupted among isolated fragments. Thus, my results suggested Brown Treecreepers were declining due to disruption of dispersal by habitat fragmentation rather than degradation or edge effects. I compared the results of an individual-based, spatially explicit simulation model to field observations and concluded that territory spatial arrangement and matrix composition altered dispersal success, recruitment, and subsequent population growth. With the aid of a geographic information system, I determined that both landscape factors (fragmentation patterns within 4.5-km) and habitat characteristics (cavity density) explained Brown Treecreeper presence and absence from random locations in woodland habitat. The birds appear to be absent from suitable habitat in unsuitable landscapes. The second theory I addressed concerns the maintenance of avian cooperative breeding. The most widely accepted models to explain cooperative breeding suggest that individuals that delay dispersal obtain a payoff under conditions in which the quality of breeding positions varies greatly. These models arose chiefly from a few long-term studies in North American. This is an unfortunate bias because the occurrence of cooperative breeding among birds of Gondwanan origin is 22%, whereas the worldwide incidence is only 3%. I used demographic and habitat data to examine the influence of habitat and cooperative breeding on Brown Treecreeper fitness. Group size affected one component of fitness and habitat variables affected another. High cavity density may be favorable due to intense inter-specific competition for suitable cavities, which Brown Treecreepers require for roosting and nesting. Low tree density may be advantageous by favoring ground foraging, in which Brown Treecreepers frequently engage. Experimental manipulations of important habitat variables are needed to determine whether variability in these ecological factors is critical in maintaining group formation in this species. / Ph. D.

Cyanate ester thermosetting resins are a novel family of materials for high technology and aerospace applications. The high glass transition temperatures available from cured cyanate ester networks and subsequently, their resistances to corrosive materials make these resins attractive for harsh environmental applications. These features of cyanate ester resins presented a threefold opportunity for investigation, namely: 1) establish a characterization technique for the long term mechanical properties of the cured resins, 2) develop a method for determining the effect of physical and chemical aging on these mechanical properties, and 3) evaluate the AroCy® B-10 cyanate ester resin from Ciba-Geigy for use in applications where temperatures could easily reach 177°C (300°F). Dynamic mechanical analysis used in a step isothermal mode was developed to characterize the mechanical properties of the cured resin and a family of isothermal modulus curves was established. These data were then shifted, following WLF theory, to create a master curve of storage modulus with respect to measurement frequency. The resultant master curves allowed the prediction of long term mechanical behavior of the resin networks via short duration, accelerated experimental tests. The test methodology and experimental procedures were especially useful in determining the effects of physical and chemical aging on the mechanical properties of the resin. Cured resins were aged in oxidative and inert atmospheres (air and nitrogen, respectively) for varying time and temperature to study the suitability of cyanate ester resins for harsh environmental applications. After aging, the samples were tested by DMA, DSC and TGA and master curves of their mechanical behavior were generated. The results were then grouped to form a family of master curves as a function of atmosphere, time and temperature. This approach allowed for the separation of the competing chemical and physical degradation processes and established the practical application conditions for this class of cross-linked polymers. Using the techniques established above, a model cyanate ester resin was selected based upon its chemical simplicity and availability. AroCy® B-10 cyanate ester resin manufactured commercially by Ciba-Geigy was evaluated for its application where temperatures could easily reach 177C. While this material was clearly unacceptable for the stated application conditions (especially in an oxygen rich atmosphere), its investigation provided experimental confirmation of the techniques developed. The test procedures and performance evaluation techniques described allow for the systematic assessment of not only the cyanate ester class of networking polymers, but any glass forming material, and a separation methodology for their concomitant chemical and physical degradation pathways. / Ph. D.

Doctor of Philosophy / Enhancing and recycling plastic are two important focuses in plastics research. In this dissertation, enhancing the property of polyetherimide (PEI) is first discussed, and two methods are introduced. Later, a new recycling strategy, the degradation-upcycling (Deg-Up) strategy, is presented. The potential of Deg-Up is evaluated on three plastics: polystyrene (PS), polyethylene (PE), and polypropylene (PP). These plastics serve broad applications in daily life, such as Styrofoam, food containers, shopping bags, garden decorations, and furniture. PEI, a powerful plastic resilient to high temperature and strength, is broadly used in aerospace, defense technology, space exploration, and transportation. However, PEI can only be processed at high temperatures, and PEI films can be easily dissolved or compromised in many solvents, such as solmethine, chloroform, and furanidin. Water is not permeable in PEI, and therefore, it is strongly demanded to modify the PEI structure, giving PEI new and improved properties for water filtration and purification. We have investigated two methods for modifying PEI. Influencers affecting the PEI film's performance are also studied. Plastic upcycling, which converts low-value wastes to high-value chemical products, is a vital technology that mitigates the environmental crisis and the plastic recycling problem. However, effective plastic upcycling improving waste value with good selectivity toward products with ten-fold or even greater value is uncommon due to the lack of upcycling theories/methodologies. This dissertation presents a new upcycling strategy; the degradation-upcycling strategy (Deg-Up) comprises degradation reactions yielding preliminary chemicals and upcycling reactions converting the preliminary chemicals to desired high-value products. Based on the Deg-Up strategy, PS is converted to fragrances and drug precursors, and PE and PP are Deg-Up to fats and soaps. The economic and industrial possibilities are also discussed through a preliminary industrial design and an economic analysis.

Major vehicle manufacturers are committed to expand their electrified vehicle fleet in upcoming years to meet fuel efficiency goals. Understanding the effect of the charge/discharge cycle profiles on battery durability is important to the implementation of batteries in electrified vehicles and to the design of appropriate battery testing protocols. In this work, commercial high-power prismatic lithium ion cells were cycled using a pulse-heavy profile and a simple square-wave profile to investigate the effect of cycle profile on the capacity fade of the battery. The pulse-heavy profile was designed to simulate on-road conditions for a typical hybrid electric vehicle, while the simplified square-wave profile was designed to have the same charge throughput as the pulse-heavy profile, but with lower peak currents. The batteries were cycled until each battery achieved a combined throughput of 100 kAh. Reference Performance Tests were conducted periodically to monitor the state of the batteries through the course of the testing. The results indicate that, for the batteries tested, the capacity fade for the two profiles was very similar and was 11 % ± 0.5 % compared to beginning of life. The change in internal resistance of the batteries over the course of the testing was also monitored and found to increase 21% and 12% compared to beginning of life for the pulse-heavy and square-wave profiles respectively. Cycling tests on coin cells with similar electrode chemistries as well as development of a first principles, physics based model were done in order to understand the underlying cause of the observed degradation. The results from the coin cells and the model suggest that the loss of active material in the electrodes due to the charge transfer process is the primary cause of degradation while the loss of cyclable lithium due to side reactions plays a secondary role. These results also indicate that for high power cells, the capacity degradation associated with the charge-sustaining mode of operation can be studied with relatively simple approximations of complex drive cycles. / Ph. D. / Major vehicle manufacturers are committed to expand their electrified vehicle fleet in upcoming years to meet fuel efficiency goals. Understanding the effect of the charge/discharge cycle profiles on battery durability is important to the implementation of batteries in electrified vehicles and to the design of appropriate battery testing protocols. In this work, commercial lithium ion cells were tested using two profiles with the same energy transfer; a pulse-heavy profile to simulate on-road conditions for a typical hybrid electric vehicle, and a simplified square-wave profile with the same charge flow as the pulse-heavy profile, but with lower currents. Cycling tests on coin cells with similar electrode chemistries as well as development of a first principles, physics based model were done in order to understand the underlying cause of the degradation. The results suggest that the degradation observed is not dependent on the type of profile used. These results also indicate that for high power cells, the capacity degradation associated with the charge-sustaining mode of operation can be studied with relatively simple approximations of complex drive cycles.

Yes / The realisation that unregulated activation of the Janus kinase–signal transducer and activator of transcription (JAK–STAT) pathway is a key driver of a wide range of diseases has identified its components as targets for therapeutic intervention by small molecule inhibitors and biologicals. In this review, we discuss JAK-STAT signalling pathway inhibition by the inducible inhibitor “suppressor of cytokine signaling 3 (SOCS3), its role in diseases such as myeloproliferative disorders, and its function as part of a multi-subunit E3 ubiquitin ligase complex. In addition, we highlight potential applications of these insights into SOCS3-based therapeutic strategies for management of conditions such as vascular re-stenosis associated with acute vascular injury, where there is strong evidence that multiple processes involved in disease progression could be attenuated by localized potentiation of SOCS3 expression levels. / British Heart Foundation; Chief Scientist's Office; NHS Greater Glasgow and Clyde Research Endowment Fund; BBSRC

Yes / The level of glutamine (Gln) deamidation in bone collagen provides information on the diagenetic history of bone but, in order to accurately assess the extent of Gln deamidation, it is important to minimise the conditions that may induce deamidation during the sample preparation. Here we report the results of a preliminary investigation of the variability in glutamine deamidation levels in an archaeological bone due to: a) sampling location within a bone; b) localised diagenesis; and c) sample preparation methods. We then investigate the effects of pre-treatment on three bone samples: one modern, one Medieval and one Pleistocene. The treatment of bone with acidic solutions was found to both induce deamidation and break down the collagen fibril structure. This is particularly evident in the Pleistocene material (~80,000 years BP) considered in this study. We show that ethylenediaminetetraacetic acid (EDTA), when used as an alternative to hydrochloric acid (HCl) demineralisation, induces minimal levels of deamidation and maintains the collagen fibril structure. Areas of bone exhibiting localised degradation are shown to be correlated with an increase in the levels of Gln deamidation. This indicates that the extent of Gln deamidation could provide a marker for diagenesis but that sampling is important, and that, whenever possible, subsamples should be taken from areas of the bone that are visually representative of the bone as a whole. Although validation of our observations will require analysis of a larger sample set, deamidation measurements could be a valuable screening tool to evaluate the suitability of bone for further destructive collagen analyses such as isotopic or DNA analysis, as well as assessing the overall preservation of bone material at a site. The measure of bone preservation may be useful to help conservators identify bones that may require special long-term storage conditions. / NERC (NE/J500197/1), Yorkshire Forward - Northern Way Initiative, Science City York, Gordon and Betty Moore Foundation, Leverhulme Trust