High-resolution terrestrial permian-triassic eventostratigraphic boundary in western Guizhou and eastern Yunnan, southwestern China

The adjoining area of western Guizhou and eastern Yunnan Provinces in southwest China is an ideal place to investigate the feasibility of correlating marine and nonmarine Permian–Triassic boundary (PTB) sequences, as it contains outcrop sections of shallow marine, marginal marine (or paralic), and terrestrial PTB sections, all in close geographic proximity. This paper documents for the first time multiple stratigraphic data from several well-preserved terrestrial PTB sections in the area and attempts to use these data to define, locate, and correlate the PTB in the area. A study of the spores and pollen and vegetation types across the terrestrial PTB sections in the study area suggests three distinct evolutionary stages across the boundary: Stage 1 (Xuanwei Formation) is characterised by Late Permian or Paleozoic-type ferns and pteridosperms (85.0%), with a few gymnosperms (15.0%); stage 2 is marked by an abrupt drop of sporopollen elements of Late Permian aspects, coupled with the appearance of fungal spores and limited Early Triassic palynomorphs; stage 3 (top Xuanwei Formation and Kayitou Formation) is dominated by gymnosperm pollen (58.8%) of clearly Early Triassic aspect, although still retaining limited ferns and pteridosperms. The three biotic stages seem to well correspond with the changing trend of the δ13Corg curves from the same sections, which is characterized by a sharp drop just before the PTB, followed by a short term partial recovery across the boundary, and then succeeded by a gradual decline after the PTB in the Early Triassic. Combining evidence from eventostratigraphic (i.e., the succession of boundary clay beds), biostratigraphic (using both macroplants and palynomorphs), and chemostratigraphic (i.e., organic carbon isotope excursion signals), we propose that a high-resolution PTB succession, closely correlatable to its marine counterpart at the Meishan section in eastern China, is recognisable at the terrestrial PTB sections in the western Guizhou–eastern Yunnan area in southwest China.

Method design and validation for the determination of uranium levels in human urine using high-resolution alpha spectrometry

Quantification of uranium in human urine is a valuable technique for assessing occupational and public exposure to uranium. A reliable method has been developed and validated in the ARPANSA Radiochemistry Laboratory by means of standard radiochemical separation and purification techniques and measurement using high-resolution alpha spectrometry. This method can be used to evaluate the levels of naturally occurring ²³⁴U, ²³⁵U and ²³⁸U in urine. Method design and validation is the process of defining an analytical requirement, and then confirming that the method under consideration has performance capabilities consistent with what the application requires. The method was designed to measure levels down to 2 mBq/day of total uranium, corresponding to approximately 1/100th of the annual committed effective dose of 20 mSv. Validation tests were developed to assess selectivity, accuracy, recovery and quantification of uncertainty. The radiochemical recovery of this method was measured using ²³²U tracer. The typical minimum detectable concentration for total uranium for 24-h urine samples is approximately 0.6 mBq/day or 0.019 μg/day.

Use of high resolution digital multi-spectral imagery to assess the distribution of disease caused by Phytophthora cinnamomi on heathland at Anglesea, Victoria

Disease caused by the soilborne plant pathogen Phytophthora cinnamomi causes long-term floristic and structural changes in native vegetation communities in Australia. Key components of the management of this disease are to know where it occurs and the rate at which it spreads. The distribution of P. cinnamomi has generally been assessed as locality points of infestation and mapping the extent of diseased vegetation in any area is difficult and costly. This study was undertaken in P. cinnamomi-infested heathland communities in southern Victoria, Australia, where the symptoms of P. cinnamomi arise as a mosaic within healthy vegetation. We investigated the potential to improve the efficiency and effectiveness of mapping and monitoring vegetation affected by P. cinnamomi using digital multi-spectral imaging. This technique was developed for the purposes of monitoring vegetation and provides a single, seamless ortho-rectified digital image over the total area of interest. It is used to spatially quantify small differences in the characteristics of vegetation. In this study, the symptoms of disease caused by P. cinnamomi infestation were related to differences in the imagery and were used to map areas of infestation. Comparison of the digital multi-spectral imaging indications with on-ground observations gave moderate accuracy between the datasets (κ = 0.49) for disease and healthy indications. This study demonstrates the ability of the technique to determine disease extent over broad areas in native vegetation and provides a non-invasive, cost effective tool for management.

RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3'-end processing in Saccharomyces cerevisiae

We describe methods for obtaining a quantitative description of RNA processing at high resolution in budding yeast. As a model gene expression system, we constructed tetON (for induction studies) and tetOFF (for repression, derepression, and RNA degradation studies) yeast strains with a series of reporter genes integrated in the genome under the control of a tetO7 promoter. Reverse transcription and quantitative real-time-PCR (RT-qPCR) methods were adapted to allow the determination of mRNA abundance as the average number of copies per cell in a population. Fluorescence in situ hybridization (FISH) measurements of transcript numbers in individual cells validated the RT-qPCR approach for the average copy-number determination despite the broad distribution of transcript levels within a population of cells. In addition, RT-qPCR was used to distinguish the products of the different steps in splicing of the reporter transcripts, and methods were developed to map and quantify 3′-end cleavage and polyadenylation. This system permits pre-mRNA production, splicing, 3′-end maturation and degradation to be quantitatively monitored with unprecedented kinetic detail, suitable for mathematical modeling. Using this approach, we demonstrate that reporter transcripts are spliced prior to their 3′-end cleavage and polyadenylation, that is, cotranscriptionally.

Rapid detection of SMARCB1 sequence variation using high resolution melting

Background : Rhabdoid tumors are rare cancers of early childhood arising in the kidney, central nervous system and other organs. The majority are caused by somatic inactivating mutations or deletions affecting the tumor suppressor locus SMARCB1 [OMIM 601607]. Germ-line SMARCB1 inactivation has been reported in association with rhabdoid tumor, epitheloid sarcoma and familial schwannomatosis, underscoring the importance of accurate mutation screening to ascertain recurrence and transmission risks. We describe a rapid and sensitive diagnostic screening method, using high resolution melting (HRM), for detecting sequence variations in SMARCB1. Methods : Amplicons, encompassing the nine coding exons of SMARCB1, flanking splice site sequences and the 5' and 3' UTR, were screened by both HRM and direct DNA sequencing to establish the reliability of HRM as a primary mutation screening tool. Reaction conditions were optimized with commercially available HRM mixes. Results : The false negative rate for detecting sequence variants by HRM in our sample series was zero. Nine amplicons out of a total of 140 (6.4%) showed variant melt profiles that were subsequently shown to be false positive. Overall nine distinct pathogenic SMARCB1 mutations were identified in a total of 19 possible rhabdoid tumors. Two tumors had two distinct mutations and two harbored SMARCB1 deletion. Other mutations were nonsense or frame-shifts. The detection sensitivity of the HRM screening method was influenced by both sequence context and specific nucleotide change and varied from 1: 4 to 1:1000 (variant to wild-type DNA). A novel method involving digital HRM, followed by re-sequencing, was used to confirm mutations in tumor specimens containing associated normal tissue. Conclusions : This is the first report describing SMARCB1 mutation screening using HRM. HRM is a rapid, sensitive and inexpensive screening technology that is likely to be widely adopted in diagnostic laboratories to facilitate whole gene mutation screening.

Corner Inlet and Nooramunga Habitat Mapping Project – Part 2 : High resolution mapping and change detection analysis using 2011 Rapid Eye Satellite Image compared to 2009 ALOS Satellite Image

Building on a habitat mapping project completed in 2011, Deakin University was commissioned by Parks Victoria (PV) to apply the same methodology and ground-truth data to a second, more recent and higher resolution satellite image to create habitat maps for areas within the Corner Inlet and Nooramunga Marine and Coastal Park and Ramsar area. A ground-truth data set using in situ video and still photographs was used to develop and assess predictive models of benthic marine habitat distributions incorporating data from both RapidEye satellite imagery (corrected for atmospheric and water column effects by CSIRO) and LiDAR (Light Detection and Ranging) bathymetry. This report describes the results of the mapping effort as well as the methodology used to produce these habitat maps.

Overall accuracies of habitat classifications were good, with error rates similar to or better than the earlier classification (>73 % and kappa values > 0.58 for both study localities). The RapidEye classification failed to accurately detect Pyura and reef habitat classes at the Corner Inlet locality, possibly due to differences in spectral frequencies. For comparison, these categories were combined into a ‘non-seagrass’ category, similar to the one used at the Nooramunga locality in the original classification. Habitats predicted with highest accuracies differed from the earlier classification and were Posidonia in Corner Inlet (89%), and bare sediment (no-visible seagrass class) in Nooramunga (90%). In the Corner Inlet locality reef and Pyura habitat categories were not distinguishable in the repeated classification and so were combined with bare sediments. The majority of remaining classification errors were due to the misclassification of Zosteraceae as bare sediment and vice versa. Dominant habitats were the same as those from the 2011 classification with some differences in extent. For the Corner Inlet study locality the no-visible seagrass category remained the most extensive (9059 ha), followed by Posidonia (5,513 ha) and Zosteraceae (5,504 ha). In Nooramunga no-visible seagrass (6,294 ha), Zosteraceae (3,122 ha) and wet saltmarsh (1,562 ha) habitat classes were most dominant.

Change detection analyses between the 2009 and 2011 imagery were undertaken as part of this project, following the analyses presented in Monk et al. (2011) and incorporating error estimates from both classifications. These analyses indicated some shifts in classification between Posidonia and Zosteraceae as well as a general reduction in the area of Zosteraceae. Issues with classification of mixed beds were apparent, particularly in the main Posidonia bed at Nooramunga where a mosaic of Zosteraceae and Posidonia was seen that was not evident in the ALOS classification. Results of a reanalysis of the 1998-2009 change detection illustrating effects of binning of mixed beds is also provided as an appendix.

This work has been successful in providing baseline maps at an improved level of detail using a repeatable method meaning that any future changes in intertidal and shallow water marine habitats may be assessed in a consistent way with quantitative error assessments. In wider use, these maps should also allow improved conservation planning, advance fisheries and catchment management, and progress infrastructure planning to limit impacts on the Inlet environment.

Trabecular and cortical bone density and architecture in women after 60 days of bed rest using high-resolution pQCT: WISE 2005

Prolonged bed rest is used to simulate the effects of spaceflight and causes disuse-related loss of bone. While bone density changes during bed rest have been described, there are no data on changes in bone microstructure. Twenty-four healthy women aged 25 to 40 years participated in 60 days of strict 6-degree head-down tilt bed rest (WISE 2005). Subjects were assigned to either a control group (CON, n = 8), which performed no countermeasures; an exercise group (EXE, n = 8), which undertook a combination of resistive and endurance training; or a nutrition group (NUT, n = 8), which received a high-protein diet. Density and structural parameters of the distal tibia and radius were measured at baseline, during, and up to 1 year after bed rest by high-resolution peripheral quantitative computed tomography (HR-pQCT). Bed rest was associated with reductions in all distal tibial density parameters (p < 0.001), whereas only distal radius trabecular density decreased. Trabecular separation increased at both the distal tibia and distal radius (p < 0.001), but these effects were first significant after bed rest. Reduction in trabecular number was similar in magnitude at the distal radius (p = 0.021) and distal tibia (p < 0.001). Cortical thickness decreased at the distal tibia only (p < 0.001). There were no significant effects on bone structure or density of the countermeasures (p ≥ 0.057). As measured with HR-pQCT, it is concluded that deterioration in bone microstructure and density occur in women during and after prolonged bed rest. The exercise and nutrition countermeasures were ineffective in preventing these changes.