Soil-pile interaction of pile embedded in deep layered marine sediment under seismic excitation

This research provides validated Finite Element techniques to analyse pile foundations under seismic loads. The results show that the capability of the technique to capture the important pile response which includes kinematic and inertial interaction effects, effects of soil stiffness and depth on pile deflection patterns and permanent deformations.

UafB is a serine-rich repeat adhesin of Staphylococcus saprophyticus that mediates binding to fibronectin, fibrinogen and human uroepithelial cells

Staphylococcus saprophyticus is an important cause of urinary tract infection (UTI), particularly among young women, and is second only to uropathogenic Escherichia coli as the most frequent cause of UTI. The molecular mechanisms of urinary tract colonization by S. saprophyticus remain poorly understood. We have identified a novel 6.84 kb plasmid-located adhesin-encoding gene in S. saprophyticus strain MS1146 which we have termed uro-adherence factor B (uafB). UafB is a glycosylated serine-rich repeat protein that is expressed on the surface of S. saprophyticus MS1146. UafB also functions as a major cell surface hydrophobicity factor. To characterize the role of UafB we generated an isogenic uafB mutant in S. saprophyticus MS1146 by interruption with a group II intron. The uafB mutant had a significantly reduced ability to bind to fibronectin and fibrinogen. Furthermore, we show that a recombinant protein containing the putative binding domain of UafB binds specifically to fibronectin and fibrinogen. UafB was not involved in adhesion in a mouse model of UTI; however, we observed a striking UafB-mediated adhesion phenotype to human uroepithelial cells. We have also identified genes homologous to uafB in other staphylococci which, like uafB, appear to be located on transposable elements. Thus, our data indicate that UafB is a novel adhesin of S. saprophyticus that contributes to cell surface hydrophobicity, mediates adhesion to fibronectin and fibrinogen, and exhibits tropism for human uroepithelial cells.

DNA binding study of isophorone in rats and mice

Following isophorone exposure, in a 2-year study with F344 rats and B6C3F1 mice performed under the National Toxicology Program (NTP), an elevated incidence of tumors was observed in male rats (kidney tumors) and male mice (liver tumors). Female rats and mice showed no elevation of tumor rates by isophorone (NTP 1986).

The effects of geochemical conditions on the establishment and growth of mangrove seedlings in acid sulfate soil environments

Acid sulfate soils (ASS) is a stress factor that is responsible for the failure of some mangrove restoration projects, including abandoned aquaculture ponds converted from mangrove ecosystems. Through experimental and field studies, this research provides a better understanding of the biogeochemistry of ASS disturbance and the response of mangrove seedlings (Rhizophoraceae) under high metal levels and acidic conditions. This study found that mangrove restorations under ASS disturbance can work but with lower numbers of survived seedlings. To prevent toxicity under high levels of metal, seedlings retained metals in their roots and sparingly distributed them into aerial parts with low mobility. The presence of high levels of potential acidity parameters would allow pyrite to oxidise, thus increasing metal levels and acidity, which in turn affected the survival and growth of the seedlings.

Diverse urban plantings managed with sufficient resource availability can increase plant productivity and arthropod diversity

Buildings structures and surfaces are explicitly being used to grow plants, and these “urban plantings” are generally designed for aesthetic value. Urban plantings also have the potential to contribute significant “ecological values” by increasing urban habitat for animals such as arthropods and by increasing plant productivity. In this study, we evaluated how the provision of these additional ecological values is affected by plant species richness; the availability of essential resources for plants, such as water, light, space; and soil characteristics. We sampled 33 plantings located on the exterior of three buildings in the urban center of Brisbane, Australia (subtropical climatic region) over 2, 6 week sampling periods characterized by different temperature and rainfall conditions. Plant cover was estimated as a surrogate for productivity as destructive sampling of biomass was not possible. We measured weekly light levels (photosynthetically active radiation), plant CO2 assimilation, soil CO2 efflux, and arthropod diversity. Differences in plant cover were best explained by a three-way interaction of plant species richness, management water regime and sampling period. As the richness of plant species increased in a planter, productivity and total arthropod richness also increased significantly—likely due to greater habitat heterogeneity and quality. Overall we found urban plantings can provide additional ecological values if essential resources are maintained within a planter such as water, light and soil temperature. Diverse urban plantings that are managed with these principles in mind can contribute to the attraction of diverse arthropod communities, and lead to increased plant productivity within a dense urban context.

The plasticity of NBS resistance genes in sorghum is driven by multiple evolutionary processes

Background Increased disease resistance is a key target of cereal breeding programs, with disease outbreaks continuing to threaten global food production, particularly in Africa. Of the disease resistance gene families, the nucleotide-binding site plus leucine-rich repeat (NBS-LRR) family is the most prevalent and ancient and is also one of the largest gene families known in plants. The sequence diversity in NBS-encoding genes was explored in sorghum, a critical food staple in Africa, with comparisons to rice and maize and with comparisons to fungal pathogen resistance QTL. Results In sorghum, NBS-encoding genes had significantly higher diversity in comparison to non NBS-encoding genes and were significantly enriched in regions of the genome under purifying and balancing selection, both through domestication and improvement. Ancestral genes, pre-dating species divergence, were more abundant in regions with signatures of selection than in regions not under selection. Sorghum NBS-encoding genes were also significantly enriched in the regions of the genome containing fungal pathogen disease resistance QTL; with the diversity of the NBS-encoding genes influenced by the type of co-locating biotic stress resistance QTL. Conclusions NBS-encoding genes are under strong selection pressure in sorghum, through the contrasting evolutionary processes of purifying and balancing selection. Such contrasting evolutionary processes have impacted ancestral genes more than species-specific genes. Fungal disease resistance hot-spots in the genome, with resistance against multiple pathogens, provides further insight into the mechanisms that cereals use in the “arms race” with rapidly evolving pathogens in addition to providing plant breeders with selection targets for fast-tracking the development of high performing varieties with more durable pathogen resistance.

Spatially varying ground motion effects on seismic response of adjacent structures considering soil-structure interaction

Spatial variation of seismic ground motions is caused by incoherence effect, wave passage, and local site conditions. This study focuses on the effects of spatial variation of earthquake ground motion on the responses of adjacent reinforced concrete (RC) frame structures. The adjacent buildings are modeled considering soil-structure interaction (SSI) so that the buildings can be interacted with each other under uniform and non-uniform ground motions. Three different site classes are used to model the soil layers of SSI system. Based on fast Fourier transformation (FFT), spatially correlated non-uniform ground motions are generated compatible with known power spectrum density function (PSDF) at different locations. Numerical analyses are carried out to investigate the displacement responses and the absolute maximum base shear forces of adjacent structures subjected to spatially varying ground motions. The results are presented in terms of related parameters affecting the structural response using three different types of soil site classes. The responses of adjacent structures have changed remarkably due to spatial variation of ground motions. The effect can be significant on rock site rather than clay site.

Development of a transient, high-level expression platform for protein production in plants

Plants are an attractive alternative to conventional expression systems for the production of recombinant proteins and useful biologics, however, the economic viability of plant made proteins is strongly yield dependent. This study aimed to improve transgene expression levels in the plant host Nicotiana benthamiana using the Agroinfiltration transient expression platform. Independent investigation of the physical, chemical and genetic features associated with Agroinfiltration identified factors that improved transformation frequencies, elevated transgene expression levels and ultimately improved protein yield. The major outcome of this research was a novel hyper-expression system for biofarming recombinant proteins in plants.

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.