Down-regulation of transmembrane carbonic anhydrases in renal cell carcinoma cell lines by wild-type von Hippel-Lindau transgenes

To discover genes involved in von Hippel-Lindau (VHL)-mediated carcinogenesis, we used renal cell carcinoma cell lines stably transfected with wild-type VHL-expressing transgenes. Large-scale RNA differential display technology applied to these cell lines identified several differentially expressed genes, including an alpha carbonic anhydrase gene, termed CA12. The deduced protein sequence was classified as a one-pass transmembrane CA possessing an apparently intact catalytic domain in the extracellular CA module. Reintroduced wild-type VHL strongly inhibited the overexpression of the CA12 gene in the parental renal cell carcinoma cell lines. Similar results were obtained with CA9, encoding another transmembrane CA with an intact catalytic domain. Although both domains of the VHL protein contribute to regulation of CA12 expression, the elongin binding domain alone could effectively regulate CA9 expression. We mapped CA12 and CA9 loci to chromosome bands 15q22 and 17q21.2 respectively, regions prone to amplification in some human cancers. Additional experiments are needed to define the role of CA IX and CA XII enzymes in the regulation of pH in the extracellular microenvironment and its potential impact on cancer cell growth.

Mineral surfaces and bioavailability of heavy metals: A molecular-scale perspective

There is a continual influx of heavy metal contaminants and pollutants into the biosphere from both natural and anthropogenic sources. A complex variety of abiotic and biotic processes affects their speciation and distribution, including adsorption onto and desorption from mineral surfaces, incorporation in precipitates or coprecipitates, release through the dissolution of minerals, and interactions with plants and microbes. Some of these processes can effectively isolate heavy metals from the biosphere, whereas others cause their release or transformation to different species that may be more (or less) bioavailable and/or toxic to organisms. Here we focus on abiotic adsorption and precipitation or coprecipitation processes involving the common heavy metal contaminant lead and the metalloids arsenic and selenium in mine tailings and contaminated soils. We have used extremely intense x-rays from synchrotron sources and a structure-sensitive method known as x-ray absorption fine structure (XAFS) spectroscopy to determine the molecular-level speciation of these elements at concentrations of 50 to several thousand ppm in the contaminated environmental samples as well as in synthetic sorption samples. Our XAFS studies of As and Pb in the mine tailings show that up to 50% of these contaminants in the samples studied may be present as adsorbed species on mineral surfaces, which makes them potentially more bioavailable than when present in sparingly soluble solid phases. Our XAFS studies of Se(VI) sorption on Fe2+-containing sulfates show that this element undergoes redox reactions that transform it into less bioavailable and less toxic species. This type of information on molecular-level speciation of heavy metal and metalloid contaminants in various environmental settings is needed to prioritize remediation efforts and to assess their potential hazard to humans and other organisms.

Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection.

Pseudomonas aeruginosa, an opportunistic human pathogen, is a major causative agent of mortality and morbidity in immunocompromised patients and those with cystic fibrosis genetic disease. To identify new virulence genes of P. aeruginosa, a selection system was developed based on the in vivo expression technology (IVET) that was first reported in Salmonella system. An adenine-requiring auxotrophic mutant strain of P. aeruginosa was isolated and found avirulent on neutropenic mice. A DNA fragment that can complement the mutant strain, containing purEK operon that is required for de novo biosynthesis of purine, was sequenced and used in the IVET vector construction. By applying the IVET selection system to a neutropenic mouse infection model, genetic loci that are specifically induced in vivo were identified. Twenty-two such loci were partially sequenced and analyzed. One of them was a well-studied virulence factor, pyochelin receptor (FptA), that is involved in iron acquisition. Fifteen showed significant homology to reported sequences in GenBank, while the remaining six did not. One locus, designated np20, encodes an open reading frame that shares amino acid sequence homology to transcriptional regulators, especially to the ferric uptake regulator (Fur) proteins of other bacteria. An insertional np20 null mutant strain of P. aeruginosa did not show a growth defect on laboratory media; however, its virulence on neutropenic mice was significantly reduced compared with that of a wild-type parent strain, demonstrating the importance of the np20 locus in the bacterial virulence. The successful isolation of genetic loci that affect bacterial virulence demonstrates the utility of the IVET system in identification of new virulence genes of P. aeruginosa.

The Gaia-ESO Survey: The analysis of high-resolution UVES spectra of FGK-type stars

Context. The ongoing Gaia-ESO Public Spectroscopic Survey is using FLAMES at the VLT to obtain high-quality medium-resolution Giraffe spectra for about 105 stars and high-resolution UVES spectra for about 5000 stars. With UVES, the Survey has already observed 1447 FGK-type stars. Aims. These UVES spectra are analyzed in parallel by several state-of-the-art methodologies. Our aim is to present how these analyses were implemented, to discuss their results, and to describe how a final recommended parameter scale is defined. We also discuss the precision (method-to-method dispersion) and accuracy (biases with respect to the reference values) of the final parameters. These results are part of the Gaia-ESO second internal release and will be part of its first public release of advanced data products. Methods. The final parameter scale is tied to the scale defined by the Gaia benchmark stars, a set of stars with fundamental atmospheric parameters. In addition, a set of open and globular clusters is used to evaluate the physical soundness of the results. Each of the implemented methodologies is judged against the benchmark stars to define weights in three different regions of the parameter space. The final recommended results are the weighted medians of those from the individual methods. Results. The recommended results successfully reproduce the atmospheric parameters of the benchmark stars and the expected Teff-log  g relation of the calibrating clusters. Atmospheric parameters and abundances have been determined for 1301 FGK-type stars observed with UVES. The median of the method-to-method dispersion of the atmospheric parameters is 55 K for Teff, 0.13 dex for log  g and 0.07 dex for [Fe/H]. Systematic biases are estimated to be between 50−100 K for Teff, 0.10−0.25 dex for log  g and 0.05−0.10 dex for [Fe/H]. Abundances for 24 elements were derived: C, N, O, Na, Mg, Al, Si, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Y, Zr, Mo, Ba, Nd, and Eu. The typical method-to-method dispersion of the abundances varies between 0.10 and 0.20 dex. Conclusions. The Gaia-ESO sample of high-resolution spectra of FGK-type stars will be among the largest of its kind analyzed in a homogeneous way. The extensive list of elemental abundances derived in these stars will enable significant advances in the areas of stellar evolution and Milky Way formation and evolution.

Enriching plant diversity in grasslands by large-scale experimental sward disturbance and seed addition along gradients of land-use intensity

Aims The relationship between biodiversity and ecosystem functioning is among the most active areas of ecological research. Furthermore, enhancing the diversity of degraded ecosystems is a major goal in applied restoration ecology. In grasslands, many species may be locally absent due to dispersal or microsite limitation and may therefore profit from mechanical disturbance of the resident vegetation. We established a seed addition and disturbance experiment across several grassland sites of different land use to test whether plant diversity can be increased in these grasslands. Additionally, the experiment will allow us testing the consequences of increased plant diversity for ecosystem processes and for the diversity of other taxa in real-world ecosystems. Here we present details of the experimental design and report results from the first vegetation survey one year after disturbance and seed addition. Moreover, we tested whether the effects of seed addition and disturbance varied among grassland depending on their land use or pre-disturbance plant diversity. Methods A full-factorial experiment was installed in 73 grasslands in three regions across Germany. Grasslands were under regular agricultural use, but varied in the type and the intensity of management, thereby representing the range of management typical for large parts of Central Europe. The disturbance treatment consisted of disturbing the top 10 cm of the sward using a rotavator or rotary harrow. Seed addition consisted of sowing a high-diversity seed mixture of regional plant species. These species were all regionally present, but often locally absent, depending on the resident vegetation composition and richness of each grassland. Important findings One year after sward disturbance it had significantly increased cover of bare soil, seedling species richness and numbers of seedlings. Seed addition had increased plant species richness, but only in combination with sward disturbance. The increase in species richness, when both seed addition and disturbance was applied, was higher at high land-use intensity and low resident diversity. Thus, we show that at least the early recruitment of many species is possible also at high land-use intensity, indicating the potential to restore and enhance biodiversity of species-poor agricultural grasslands. Our newly established experiment provides a unique platform for broad-scale research on the land-use dependence of future trajectories of vegetation diversity and composition and their effects on ecosystem functioning.

Drivers of multi-scale plant community structure in agricultural field margins of South Korea

This data set describes the distribution of a total of 90 plant species growing on field margins of an agricultural landscape in the Haean-myun catchment in South Korea. We conducted our survey between July and August 2011 in 100 sampling plots, covering the whole catchment. In each plot we measured three environmental variables: slope, width of the field margin, and management type (i.e. "managed" for field margins that had signs of management activities from the ongoing season such as cutting or spraying herbicides and "unmanaged" for field margins that had been left untouched in the season). For the botanical survey each plot was sampled using three subplots of one square meter per subplot; subplots were 4 m apart from each other. In each subplot, we estimated three different vegetation characteristics: vegetation cover (i.e. the percentage of ground covered by vegetation), species richness (i.e. the number of observed species) and species abundance (i.e. the number of observed individuals / species). We calculated the percentage of the non-farmed habitats by creating buffer zones of 100, 200, 300, 400 and 500 m radii around each plot using data provided by (Seo et al. 2014). Non-farmed habitats included field margins, fallows, forest, riparian areas, pasture and grassland.

Initial soil properties and biomass after experimental grazing and warming in mesic and wet sites, Adventdalen valley, Spitzbergen

High-latitude ecosystems store large amounts of carbon (C); however, the C storage of these ecosystems is under threat from both climate warming and increased levels of herbivory. In this study we examined the combined role of herbivores and climate warming as. drivers of CO2 fluxes in two typical high-latitude habitats (mesic heath and wet meadow). We hypothesized that both herbivory and climate warming would reduce the C sink strength of Arctic tundra through their combined effects on plant biomass and gross ecosystem photosynthesis and on decomposition rates and the abiotic environment. To test this hypothesis we employed experimental warming (via International Tundra Experiment [ITEX] chambers) and grazing (via captive Barnacle Geese) in a three-year factorial field experiment. Ecosystem CO2 fluxes (net ecosystem exchange of CO2, ecosystem respiration, and gross ecosystem photosynthesis) were measured in all treatments at varying intensity over the three growing seasons to capture the impact of the treatments on a range of temporal scales (diurnal, seasonal, and interannual). Grazing and warming treatments had markedly different effects on CO2 fluxes in the two tundra habitats. Grazing caused a strong reduction in CO2 assimilation in the wet meadow, while warming reduced CO2 efflux from the mesic heath. Treatment effects on net ecosystem exchange largely derived from the modification of gross ecosystem photosynthesis rather than ecosystem respiration. In this study we have demonstrated that on the habitat scale, grazing by geese is a strong driver of net ecosystem exchange of CO2, with the potential to reduce the CO2 sink strength of Arctic ecosystems. Our results highlight that the large reduction in plant biomass due to goose grazing in the Arctic noted in several studies can alter the C balance of wet tundra ecosystems. We conclude that herbivory will modulate direct climate warming responses of Arctic tundra with implications for the ecosystem C balance; however, the magnitude and direction of the response will be habitat-specific.

Geological map of Heimefrontfjella, Dronning Maud Land, Antarctica (Scale 1:250,000)

The geological overview map was compiled from 15 geological maps (1 : 25,000) and is based on Jacobs et al. 1996. The topographic basemaps were adapted from unpublished 1:250,000 provisional topographic maps, Institut f. Angewandte Geodäsie, Frankfurt, 1983. Part of the contour lines are from Radarsat (Liu et al. 2001).

Calcareous plankton response to orbital and millennial-scale climate changes from ODP Leg 161-975

The paleoenvironmental conditions through MIS 15-9 at the Mediterranean Ocean Drilling Program (ODP) Site 975 were interpreted by high resolution study of calcareous plankton assemblages compared with available d18O and d13C records and high resolution paleoclimate proxies from the Atlantic Ocean. Sea Surface Temperatures (SSTs) have been estimated from planktonic foraminiferal assemblages using the artificial neural networks method. Calcareous plankton varied dominantly on a glacial-interglacial scale as testified by the SST record, foraminiferal diversity, total coccolith abundance and changes in warm-water calcareous nannofossil taxa. A general increase in foraminiferal diversity and of total coccolith abundance is observed during interglacials. Warmest SSTs are reached during MIS 11, while MIS 12 and MIS 10 represent the coldest intervals of the studied record. During MIS 12, one of the most extreme glacials of the last million years, occurrence of Globorotalia inflata and of neogloboquadrinids indicates a shoaling of the interface between Atlantic inflowing and Mediterranean outflowing waters. Among calcareous nannofossils the distribution of Gephyrocapsa margereli-G. muellerae > 4 µm also supports a reduced Atlantic-Mediterranean exchange during MIS 12. Superimposed on glacial-interglacial variability, six short-terms coolings are recognized during MIS 12 and 10, which appear comparable in their distribution and amplitude to the Heinrich - type events documented in the Atlantic Ocean in the same interval. During these H-type events, N. pachyderma (s) and G. margereli-G. muellerae > 4 µm increase as a response to the enhanced inflow of cold Atlantic water into the Mediterranean via the Strait of Gibraltar. Mediterranean surface water hydrography appears to have been most severely affected at Termination V during the H-type event Ht4, possibly as a response to a large volume of Atlantic meltwater inflow via the Strait of Gibraltar and/or to freshwater/terrigenous input deriving from local mountain glaciers. Three additional SST coolings are recorded through MIS 14-16, but these are not well correlated with Heinrich - type events documented in the Atlantic Ocean in the same interval; during these cooling episodes only the subpolar Turborotalita quinqueloba increases. These results highlight the sensitive response of the Mediterranean basin to millennial-scale climate variations related to Northern Hemisphere ice-sheet instability and support the hypothesis that the tight connection between high latitude climate dynamics and Mediterranean sea surface water features can be traced through the Middle Pleistocene.

On the Geometry of Rectifiable Sets with Carleson and Poincare-type inequlaities

Thesis (Ph.D.)--University of Washington, 2016-06

Change in abundance of dugongs in Shark Bay, Ningaloo and Exmouth Gulf, Western Australia: evidence for large-scale migration

The third in a series of five-yearly aerial surveys for dugongs in Shark Bay, Ningaloo Reef and Exmouth Gulf was conducted in July 1999. The first two surveys provided evidence of an apparently stable population of dugongs, with similar to 1000 animals in each of Exmouth Gulf and Ningaloo Reef, and 10000 in Shark Bay. We report estimates of less than 200 for each of Exmouth Gulf and Ningaloo Reef and similar to 14000 for Shark Bay. This is an apparent overall increase in the dugong population over this whole region, but with a distributional shift of animals to the south. The most plausible hypothesis to account for a large component of this apparent population shift is that animals in Exmouth Gulf and Ningaloo Reef moved to Shark Bay, most likely after Tropical Cyclone Vance impacted available dugong forage in the northern habitat. Bias associated with survey estimate methodology, and normal changes in population demographics may also have contributed to the change. The movement of large numbers of dugongs over the scale we suggest has important management implications. First, such habitat-driven shifts in regional abundance will need to be incorporated in assessing the effectiveness of marine protected areas that aim to protect dugongs and their habitat. Second, in circumstances where aerial surveys are used to estimate relative trends in abundance of dugongs, animal movements of the type we propose could lead to errors in interpretation.

The igneous charnockite—high-K alkali-calcic I-type granite—incipient charnockite association in Trivandrum Block, southern India

The Pan-African (640 Ma) Chengannoor granite intrudes the NW margin of the Neoproterozoic high-grade metamorphic terrain of the Trivandrum Block (TB), southern India, and is spatially associated with the Cardamom hills igneous charnockite massif (CM). Geochemical features characterize the Chengannoor granite as high-K alkali-calcic I-type granite. Within the constraints imposed by the high temperature, anhydrous, K-rich nature of the magmas, comparison with recent experimental studies on various granitold source compositions, and trace- and rare-earth-element modelling, the distinctive features of the Chengannoor granite reflect a source rock of igneous charnockitic nature. A petrogenetic model is proposed whereby there was a period of basaltic underplating; the partial melting of this basaltic lower crust formed the CM charnockites. The Chengannoor granite was produced by the partial melting of the charnoenderbites from the CM, with subsequent fractionation dominated by feldspars. In a regional context, the Chengannoor I-type granite is considered as a possible heat source for the near-UHT nature of metamorphism in the northern part of the TB. This is different from previous studies, which favoured CM charnockite as the major heat source. The Occurrence of incipient charnockites (both large scale as well as small scale) adjacent to the granite as well as pegmatites (which contain CO2, CO2-H2O, F and other volatiles), suggests that the fluids expelled from the alkaline magma upon solidification generated incipient charnockites through fluid-induced lowering of water activity. Thus the granite and associated alkaline pegmatites acted as conduits for the transfer of heat and volatiles in the Achankovil Shear Zone area, causing pervasive as well as patchy charnockite formation. The transport Of CO2 by felsic melts through the southern Indian middle crust is suggested to be part of a crustal-scale fluid system that linked mantle heat and CO2 input with upward migration of crustally derived felsic melts and incipient charnockite formation, resulting in an igneous charnockite - I-type granite - incipient charnockite association.

Subcellular localization of mammalian type II membrane proteins

Application of a computational membrane organization prediction pipeline, MemO, identified putative type II membrane proteins as proteins predicted to encode a single alpha-helical transmembrane domain (TMD) and no signal peptides. MemO was applied to RIKEN's mouse isoform protein set to identify 1436 non-overlapping genomic regions or transcriptional units (TUs), which encode exclusively type II membrane proteins. Proteins with overlapping predicted InterPro and TMDs were reviewed to discard false positive predictions resulting in a dataset comprised of 1831 transcripts in 1408 TUs. This dataset was used to develop a systematic protocol to document subcellular localization of type II membrane proteins. This approach combines mining of published literature to identify subcellular localization data and a high-throughput, polymerase chain reaction (PCR)-based approach to experimentally characterize subcellular localization. These approaches have provided localization data for 244 and 169 proteins. Type II membrane proteins are localized to all major organelle compartments; however, some biases were observed towards the early secretory pathway and punctate structures. Collectively, this study reports the subcellular localization of 26% of the defined dataset. All reported localization data are presented in the LOCATE database (http://www.locate.imb.uq.edu.au).