Hypermethylation of the 5 ' CpG island of the gene encoding the serine protease Testisin promotes its loss in testicular tumorigenesis

The Testisin gene (PRSS21) encodes a glycosylphosphatidylinositol (GPI)-linked serine protease that exhibits testis tissue-specific expression. Loss of Testisin has been implicated in testicular tumorigenesis, but its role in testis biology and tumorigenesis is not known. Here we have investigated the role of CpG methylation in Testisin gene inactivation and tested the hypothesis that Testisin may act as a tumour suppressor for testicular tumorigenesis. Using sequence analysis of bisulphite-treated genomic DNA, we find a strong relationship between hypermethylation of a 385 bp 50 CpG rich island of the Testisin gene, and silencing of the Testisin gene in a range of human tumour cell lines and in 100% (eight/eight) of testicular germ cell tumours. We show that treatment of Testisin-negative cell lines with demethylating agents and/or a histone deacetylase inhibitor results in reactivation of Testisin gene expression, implicating hypermethylation in Testisin gene silencing. Stable expression of Testisin in the Testisin-negative Tera-2 testicular cancer line suppressed tumorigenicity as revealed by inhibition of both anchorage-dependent cell growth and tumour formation in an SCID mouse model of testicular tumorigenesis. Together, these data show that loss of Testisin is caused, at least in part, by DNA hypermethylation and histone deacetylation, and suggest a tumour suppressor role for Testisin in testicular tumorigenesis.

Stochastic models for mainland-island metapopulations in static and dynamic landscapes

This paper has three primary aims: to establish an effective means for modelling mainland-island metapopulations inhabiting a dynamic landscape: to investigate the effect of immigration and dynamic changes in habitat on metapopulation patch occupancy dynamics; and to illustrate the implications of our results for decision-making and population management. We first extend the mainland-island metapopulation model of Alonso and McKane [Bull. Math. Biol. 64:913-958,2002] to incorporate a dynamic landscape. It is shown, for both the static and the dynamic landscape models, that a suitably scaled version of the process converges to a unique deterministic model as the size of the system becomes large. We also establish that. under quite general conditions, the density of occupied patches, and the densities of suitable and occupied patches, for the respective models, have approximate normal distributions. Our results not only provide us with estimates for the means and variances that are valid at all stages in the evolution of the population, but also provide a tool for fitting the models to real metapopulations. We discuss the effect of immigration and habitat dynamics on metapopulations, showing that mainland-like patches heavily influence metapopulation persistence, and we argue for adopting measures to increase connectivity between this large patch and the other island-like patches. We illustrate our results with specific reference to examples of populations of butterfly and the grasshopper Bryodema tuberculata.

Bryophyte propagule banks in a feldmark on subantarctic Macquarie Island

Subantarctic Macquarie Island has substantial areas of feldmark on its plateau above 200 m altitude. Samples of the substrate (5.5 cm in depth) from bare areas of feldmark contained viable propagules of bryophyte species found at adjacent and distant sites on the island. In laboratory conditions propagules of 15 bryophyte taxa germinated, allowing interpretation of reasons for bare patches in feldmark: bryophytes were successful at colonizing stable ground but when surface movement was present, burial and/or damage of propagules and young plants prevented colonization. Spherical moss polsters found in cryoturbatic areas in feldmark, however, represent a growth form that can tolerate surface movement. A conceptual model illustrating processes associated with colonization dynamics of bryophytes on feldmark terraces is presented. Ten of the 15 germinated taxa were nonlocal taxa which currently grow in plant communities at lower and hence warmer altitudes on Macquarie Island. The presence of viable propagules of these taxa provide an immediate and constant potential for dramatic vegetation change with climate change.

Poly(methyl methacrylate) model study of optical surface quality after excimer laser photorefractive keratectomy

Purpose: To evaluate lenses produced by excimer laser ablation of poly(methyl methacrylate) (PMMA) plates. Setting: University research laboratory. Methods: Two Nidek EC-5000 scanning-slit excimer laser systems were used to ablate plane-parallel plates of PMMA. The ablated lenses were examined by focimetry, interferometry, and mechanical surface profiling. Results: The spherical optical powers of the lenses matched the expected values, but the cylindrical powers were generally lower than intended. Interferometry revealed marked irregularity in the surface of negative corrections, which often had a positive “island” at their center. Positive corrections were generally smoother. These findings were supported by the results of mechanical profiling. Contrast sensitivity measurements carried out when observing through ablated lenses whose power had been neutralized with a suitable spectacle lens of opposite sign confirmed that the surface irregularities of the ablated lenses markedly reduced contrast sensitivity over a range of spatial frequencies. Conclusion: Improvements in beam delivery systems seem desirable.

Evaluating the urban heat island for cities of Emilia-Romagna region through numerical simulations

Lo scopo di questo studio è la comprensione della dinamica dello strato limite urbano per città dell’Emilia Romagna tramite simulazioni numeriche. In particolare, l’attenzione è posta sull’ effetto isola di calore, ovvero sulla differenza di temperatura dell’aria in prossimità del suolo fra zone rurali e urbane dovuta all’urbanizzazione. Le simulazioni sono state effettuate con il modello alla mesoscala "Weather Research and Forecasting" (WRF), accoppiato con le parametrizzazioni urbane "Building Effect Parametrization" (BEP) e "Building Energy Model" (BEM), che agiscono a vari livelli verticali urbani. Il periodo di studio riguarda sei giorni caldi e senza copertura nuvolosa durante un periodo di heat wave dell’anno 2015. La copertura urbana è stata definita con il "World Urban Databes and Access Portal Tools" (WUDAPT), un metodo che permette di classificare le aree urbane in dieci "urban climate zones" (UCZ), attraverso l’uso combinato di immagini satellitari e "training areas" manualmente definite con il software Google Earth. Sono state svolte diverse simulazioni a domini innestati, con risoluzione per il dominio più piccolo di 500 m, centrato sulla città di Bologna. Le differenze fra le simulazioni riguardano la presenza o l’assenza delle strutture urbane, il metodo di innesto e tipo di vegetazione rurale. Inoltre, è stato valutato l’effetto dovuto alla presenza di pannelli fotovoltaici sopra i tetti di ogni edificio e le variazioni che i pannelli esercitano sullo strato limite urbano. Per verificare la bontà del modello, i dati provenienti dalle simulazioni sono stati confrontati con misure provenienti da 41 stazioni all’interno dell’area di studio. Le variabili confrontate sono: temperatura, umidità relativa, velocità e direzione del vento. Le simulazioni sono in accordo con i dati osservativi e riescono a riprodurre l’effetto isola di calore: la differenza di temperatura fra città e zone rurali circostanti è nulla durante il giorno; al contrario, durante la notte l’isola di calore è presente, e in media raggiunge il massimo valore di 4°C alle 1:00. La presenza dei pannelli fotovoltaici abbassa la temperatura a 2 metri dell’aria al massimo di 0.8°C durante la notte, e l’altezza dello strato limite urbano dell’ordine 200mrispetto al caso senza pannelli. I risultati mostrano come l’uso di pannelli fotovoltaici all’interno del contesto urbano ha molteplici benefici: infatti, i pannelli fotovoltaici riescono a ridurre la temperatura durante un periodo di heat wave, e allo stesso tempo possono parzialmente sopperire all’alto consumo energetico, con una conseguente riduzione del consumo di combustibili fossili.

Planktonic foraminiferal d18O and d13C values, derived sea-surface temperatures from d18O and selected planktonic foraminiferal species for core P69 of Hawke Bay off eastern North Island

Recent evidence suggests that the Subtropical Convergence (STC) zone east of New Zealand shifted little from its modern position along Chatham Rise during the last glaciation, and that offshore surface waters north of the STC zone cooled only slightly. However, at nearshore core site P69 (2195 m depth), 115 km off the east coast of North Island and ca 300 km north of the modern STC zone, planktonic foraminiferal species, transfer function data and stable oxygen and carbon isotope records suggest that surface waters were colder by up to 6°C during the late last glacial period compared to the Holocene, and included a strong upwelling signature. Presently site P69 is bathed by south-flowing subtropical waters in the East Cape Current. The nearshore western end of Chatham Rise supports a major bathymetric depression, the Mernoo Saddle, through which some exchange between northern subtropical and southern subantarctic water presently occurs. It is proposed that as a result of much intensified current flows south of the Rise during the last glaciation, a consequence of more compressed subantarctic water masses, lowered sea level, and an expanded and stronger Westerly Wind system, there was accelerated leakage northwards of both Australasian Subantarctic Water and upwelled Antarctic Intermediate Water over Mernoo Saddle in a modified and intensified Southland Current. The expanded cold water masses displaced the south-flowing warm East Cape Current off southeastern North Island, and offshore divergence was accompanied by wind-assisted upwelling of nutrient-rich waters in the vicinity of P69. A comparable kind of inshore cold water jetting possibly characterised most glacial periods since the latest Miocene, and may account for the occasional occurrence of subantarctic marine fossils in onland late Cenozoic deposits north of the STC zone, rather than invoking wholesale major oscillations of the oceanic STC itself.

King George Island TanDEM-X DEM, link to GeoTIFF

We have generated a new digital elevation model for entire King George Island, Antarctica, using summer TanDEM-X bistatic SAR satellite data. The data was processed using differential SAR interferometry with an older DEM as reference. 4 TanDEM-X scenes from January 2012 were used as input. The new DEM was referenced to and validated against DGPS measurements. Height values are given in reference to ellipsoid (WGS84).

Theory and Practice in Sustainability Science: Influence of Urban Form on the Urban Heat Island and Implications for Urban Systems

As the world population continues to grow past seven billion people and global challenges continue to persist including resource availability, biodiversity loss, climate change and human well-being, a new science is required that can address the integrated nature of these challenges and the multiple scales on which they are manifest. Sustainability science has emerged to fill this role. In the fifteen years since it was first called for in the pages of Science, it has rapidly matured, however its place in the history of science and the way it is practiced today must be continually evaluated. In Part I, two chapters address this theoretical and practical grounding. Part II transitions to the applied practice of sustainability science in addressing the urban heat island (UHI) challenge wherein the climate of urban areas are warmer than their surrounding rural environs. The UHI has become increasingly important within the study of earth sciences given the increased focus on climate change and as the balance of humans now live in urban areas.

In Chapter 2 a novel contribution to the historical context of sustainability is argued. Sustainability as a concept characterizing the relationship between humans and nature emerged in the mid to late 20th century as a response to findings used to also characterize the Anthropocene. Emerging from the human-nature relationships that came before it, evidence is provided that suggests Sustainability was enabled by technology and a reorientation of world-view and is unique in its global boundary, systematic approach and ambition for both well being and the continued availability of resources and Earth system function. Sustainability is further an ambition that has wide appeal, making it one of the first normative concepts of the Anthropocene.

Despite its widespread emergence and adoption, sustainability science continues to suffer from definitional ambiguity within the academe. In Chapter 3, a review of efforts to provide direction and structure to the science reveals a continuum of approaches anchored at either end by differing visions of how the science interfaces with practice (solutions). At one end, basic science of societally defined problems informs decisions about possible solutions and their application. At the other end, applied research directly affects the options available to decision makers. While clear from the literature, survey data further suggests that the dichotomy does not appear to be as apparent in the minds of practitioners.

In Chapter 4, the UHI is first addressed at the synoptic, mesoscale. Urban climate is the most immediate manifestation of the warming global climate for the majority of people on earth. Nearly half of those people live in small to medium sized cities, an understudied scale in urban climate research. Widespread characterization would be useful to decision makers in planning and design. Using a multi-method approach, the mesoscale UHI in the study region is characterized and the secular trend over the last sixty years evaluated. Under isolated ideal conditions the findings indicate a UHI of 5.3 ± 0.97 °C to be present in the study area, the magnitude of which is growing over time.

Although urban heat islands (UHI) are well studied, there remain no panaceas for local scale mitigation and adaptation methods, therefore continued attention to characterization of the phenomenon in urban centers of different scales around the globe is required. In Chapter 5, a local scale analysis of the canopy layer and surface UHI in a medium sized city in North Carolina, USA is conducted using multiple methods including stationary urban sensors, mobile transects and remote sensing. Focusing on the ideal conditions for UHI development during an anticyclonic summer heat event, the study observes a range of UHI intensity depending on the method of observation: 8.7 °C from the stationary urban sensors; 6.9 °C from mobile transects; and, 2.2 °C from remote sensing. Additional attention is paid to the diurnal dynamics of the UHI and its correlation with vegetation indices, dewpoint and albedo. Evapotranspiration is shown to drive dynamics in the study region.

Finally, recognizing that a bridge must be established between the physical science community studying the Urban Heat Island (UHI) effect, and the planning community and decision makers implementing urban form and development policies, Chapter 6 evaluates multiple urban form characterization methods. Methods evaluated include local climate zones (LCZ), national land cover database (NCLD) classes and urban cluster analysis (UCA) to determine their utility in describing the distribution of the UHI based on three standard observation types 1) fixed urban temperature sensors, 2) mobile transects and, 3) remote sensing. Bivariate, regression and ANOVA tests are used to conduct the analyses. Findings indicate that the NLCD classes are best correlated to the UHI intensity and distribution in the study area. Further, while the UCA method is not useful directly, the variables included in the method are predictive based on regression analysis so the potential for better model design exists. Land cover variables including albedo, impervious surface fraction and pervious surface fraction are found to dominate the distribution of the UHI in the study area regardless of observation method.

Chapter 7 provides a summary of findings, and offers a brief analysis of their implications for both the scientific discourse generally, and the study area specifically. In general, the work undertaken does not achieve the full ambition of sustainability science, additional work is required to translate findings to practice and more fully evaluate adoption. The implications for planning and development in the local region are addressed in the context of a major light-rail infrastructure project including several systems level considerations like human health and development. Finally, several avenues for future work are outlined. Within the theoretical development of sustainability science, these pathways include more robust evaluations of the theoretical and actual practice. Within the UHI context, these include development of an integrated urban form characterization model, application of study methodology in other geographic areas and at different scales, and use of novel experimental methods including distributed sensor networks and citizen science.

Breeding success and traits of equal and unequal pairs of little penguins (Eudyptula minor) on Phillip Island during 2001-2008

According to life-history theory, individuals optimize their decisions in order to maximize their fitness. This raises a conflict between parents, which need to cooperate to ensure the propagation of their genes but at the same time need to minimize the associated costs. Trading-off between benefits and costs of a reproduction is one of the major forces driving demographic trends and has shaped several different parental care strategies. Using little penguins (Eudyptula minor) as a model, we investigated whether individuals of a pair provide equal parental effort when raising offspring and whether their behavior was consistent over 8 years of contrasting resource availability. Using an automated identification system, we found that 72% of little penguin pairs exhibited unforced (i.e., that did not result from desertion of 1 parent) unequal partnership through the postguard stage. This proportion was lower in favorable years. Although being an equal pair appeared to be a better strategy, it was nonetheless the least often observed. Individuals that contributed less than their partner were not less experienced (measured by age), and gender did not explain differences between partners. Furthermore, birds that contributed little or that contributed a lot tended to be consistent in their level of contribution across years. We suggest that unequal effort during breeding may reflect differences in individual quality, and we encourage future studies on parental care to consider this consistent low and high contributor behavior when investigating differences in pair investment into its offspring. Key words: attendance patterns, individual quality, meal size, parental care, reproductive costs, seabirds.

Results of wave modelling for Moreton Bay, Southeast Queensland, and a reef lagoon off Lizard Island, Great Barrier Reef, Australia

The distribution, abundance, behaviour, and morphology of marine species is affected by spatial variability in the wave environment. Maps of wave metrics (e.g. significant wave height Hs, peak energy wave period Tp, and benthic wave orbital velocity URMS) are therefore useful for predictive ecological models of marine species and ecosystems. A number of techniques are available to generate maps of wave metrics, with varying levels of complexity in terms of input data requirements, operator knowledge, and computation time. Relatively simple "fetch-based" models are generated using geographic information system (GIS) layers of bathymetry and dominant wind speed and direction. More complex, but computationally expensive, "process-based" models are generated using numerical models such as the Simulating Waves Nearshore (SWAN) model. We generated maps of wave metrics based on both fetch-based and process-based models and asked whether predictive performance in models of benthic marine habitats differed. Predictive models of seagrass distribution for Moreton Bay, Southeast Queensland, and Lizard Island, Great Barrier Reef, Australia, were generated using maps based on each type of wave model. For Lizard Island, performance of the process-based wave maps was significantly better for describing the presence of seagrass, based on Hs, Tp, and URMS. Conversely, for the predictive model of seagrass in Moreton Bay, based on benthic light availability and Hs, there was no difference in performance using the maps of the different wave metrics. For predictive models where wave metrics are the dominant factor determining ecological processes it is recommended that process-based models be used. Our results suggest that for models where wave metrics provide secondarily useful information, either fetch- or process-based models may be equally useful.

Hydrochemical properties of groundwater samples in Semarang area, Java Island, Indonesia (1992, 1993, 2003, 2006, and 2007)

In Semarang City, groundwater has been exploited as a natural resource since 1841. The groundwater exploited in deep wells is concentrated in confined aquifers. The previous hydrogeological model was developed in one unit of aquifer and refined then by using several hydrostratigraphical units following a regional hydrogeological map without any further analysis. At present, there is a lack of precise hydrogeological model which integrates geological and hydrogeological data, in particular for multiple aquifers in Semarang. Thus, the aim of this paper is to develop a hydrogeological model for the multiple aquifers in Semarang using an integrated data approach. Groundwater samples in the confined aquifers have been analyzed to define the water type and its lateral distribution. Two hydrogeological cross sections were then created based on several borelog data to define a hydrostratigraphical unit (HSU). The HSU result indicates the hydrogeological model of Semarang consists of two aquifers, three aquitards, and one aquiclude. Aquifer 1 is unconfined, while Aquifer 2 is confined. Aquifer 2 is classified into three groups (2a, 2b, and 2c) based on analyses of major ion content and hydrostratigraphical cross sections.

Heat fluxes and surface radiation measurements from Samoylov Island, Lena Delta, Siberia, October 2007 to March 2008

In this study, we present the winter time surface energy balance at a polygonal tundra site in northern Siberia based on independent measurements of the net radiation, the sensible heat flux and the ground heat flux from two winter seasons. The latent heat flux is inferred from measurements of the atmospheric turbulence characteristics and a model approach. The long-wave radiation is found to be the dominant factor in the surface energy balance. The radiative losses are balanced to about 60 % by the ground heat flux and almost 40 % by the sensible heat fluxes, whereas the contribution of the latent heat flux is small. The main controlling factors of the surface energy budget are the snow cover, the cloudiness and the soil temperature gradient. Large spatial differences in the surface energy balance are observed between tundra soils and a small pond. The ground heat flux released at a freezing pond is by a factor of two higher compared to the freezing soil, whereas large differences in net radiation between the pond and soil are only observed at the end of the winter period. Differences in the surface energy balance between the two winter seasons are found to be related to differences in snow depth and cloud cover which strongly affect the temperature evolution and the freeze-up at the investigated pond.

Terrain Controls and Landscape-Scale Susceptibility Modelling of Active-Layer Detachments, Sabine Peninsula, Melville Island, Nunavut

Modelling the susceptibility of permafrost slopes to disturbance can identify areas at risk to future disturbance and result in safer infrastructure and resource development in the Arctic. In this study, we use terrain attributes derived from a digital elevation model, an inventory of permafrost slope disturbances known as active-layer detachments (ALDs) and generalised additive modelling to produce a map of permafrost slope disturbance susceptibility for an area on northern Melville Island, in the Canadian High Arctic. By examining terrain variables and their relative importance, we identified factors important for initiating slope disturbance. The model was calibrated and validated using 70 and 30 per cent of a data-set of 760 mapped ALDs, including disturbed and randomised undisturbed samples. The generalised additive model calibrated and validated very well, with areas under the receiver operating characteristic curve of 0.89 and 0.81, respectively, demonstrating its effectiveness at predicting disturbed and undisturbed samples. ALDs were most likely to occur below the marine limit on slope angles between 3 and 10° and in areas with low values of potential incoming solar radiation (north-facing slopes).

The Role of Corals on Tsunami Dynamics in an Island Setting: A Case Study of Tutuila Island

Thesis (Ph.D.)--University of Washington, 2016-07

Upper crustal structure of Madeira Island revealed from ambient noise tomography

We present the first image of the Madeira upper crustal structure, using ambient seismic noise tomography. 16 months of ambient noise, recorded in a dense network of 26 seismometers deployed across Madeira, allowed reconstructing Rayleigh wave Green's functions between receivers. Dispersion analysis was performed in the short period band from 1.0 to 4.0 s. Group velocity measurements were regionalized to obtain 2D tomographic images, with a lateral resolution of 2.0 km in central Madeira. Afterwards, the dispersion curves, extracted from each cell of the 2D group velocity maps, were inverted as a function of depth to obtain a 3D shear wave velocity model of the upper crust, from the surface to a depth of 2.0 km. The obtained 3D velocity model reveals features throughout the island that correlates well with surface geology and island evolution.