Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.

In single stranded (+)-sense RNA viruses, RNA structural elements (SEs) play essential roles in the infection process from replication to encapsidation. Using selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) and covariation analysis, we explore the structural features of the third genome segment of cucumber mosaic virus (CMV), RNA3 (2216 nt), both in vitro and in plant cell lysates. Comparing SHAPE-Seq and covariation analysis results revealed multiple SEs in the coat protein open reading frame and 3' untranslated region. Four of these SEs were mutated and serially passaged in Nicotiana tabacum plants to identify biologically selected changes to the original mutated sequences. After passaging, loop mutants showed partial reversion to their wild-type sequence and SEs that were structurally disrupted by mutations were restored to wild-type-like structures via synonymous mutations in planta. These results support the existence and selection of virus open reading frame SEs in the host organism and provide a framework for further studies on the role of RNA structure in viral infection. Additionally, this work demonstrates the applicability of high-throughput chemical probing in plant cell lysates and presents a new method for calculating SHAPE reactivities from overlapping reverse transcriptase priming sites

Using airborne LiDAR Survey to explore historic-era archaeological landscapes of Montserrat in the eastern Caribbean

This article describes what appears to be the first archaeological application of airborne LiDAR survey to historic-era landscapes in the Caribbean archipelago, on the island of Montserrat. LiDAR is proving invaluable in extending the reach of traditional pedestrian survey into less favorable areas, such as those covered by dense neotropical forest and by ashfall from the past two decades of active eruptions by the Soufrière Hills volcano, and to sites in localities that are inaccessible on account of volcanic dangers. Emphasis is placed on two aspects of the research: first, the importance of ongoing, real-time interaction between the LiDAR analyst and the archaeological team in the field; and second, the advantages of exploiting the full potential of the three-dimensional LiDAR point cloud data for purposes of the visualization of archaeological sites and features

Prevalence and Distribution of Ranavirus in Amphibians From

Several infectious diseases are threatening amphibian species worldwide and have resulted in massmortality events across the globe. An emerging group of viral pathogens (ranaviruses) are documented to cause die-offs in amphibian populations worldwide, including in several regions of the U.S. Unfortunately, large gaps remain in our understanding of the distribution of this systemic pathogen in the U.S., including within the state of Oklahoma. To address this gap in our understanding, we carried out surveys of this infectious pathogen across 14 sites in seven southeastern Oklahoma counties in spring 2015, screening 17 amphibian species from this region. Using liver and tail tissue samples collected from individual amphibians, we screened for the presence and infection load of ranavirus. Of the 390 samples, 84 (21.5%) tested positive for ranavirus, with infection prevalence varying among species surveyed. Notably, the family Bufonidae had no samples that tested positive for ranavirus, whereas the remaining families had an infection prevalence ranging from 14–50%. Despite an overall infection prevalence of 21.5%, we detected no clinical signs of ranavirosis and all sampled individuals appeared outwardly healthy. These results provide data on the geographic and host distribution of ranavirus in southeastern Oklahoma, as well as the first documented cases of the pathogen in three species of anurans: Gastrophryne carolinensis (Eastern Narrow-mouthed Toad), G. olivacea (Western Narrow-mouthed Toad), and Pseudacris fouquettei (Cajun Chorus Frog). With widespread ranavirus infection, there is potential for transmission from abundant, widespread species to more vulnerable, state-threatened amphibians

Field Studies of Crater Gradation in Gusev Crater and Meridiani Planum Using the Mars Exploration Rovers

The Mars Exploration Rovers Spirit and Opportunity investigated numerous craters since landing in Gusev crater (14.569degS, 175.473degE) and Meridiani Planum (1.946degS, 354.473degE) over the first 400 sols of their missions [1-4]. Craters at both sites are simple structures and vary in size and preservation state. Comparing observed and expected pristine morphology and using process-specific gradational signatures around terrestrial craters as a template [5-7] allows distinguishing gradation processes whose relative importance fundamentally differs from those responsible for most crater modification on the Earth

Accelerated Thermokarst Formation in the McMurdo Dry Valleys, Antarctica

Thermokarst is a land surface lowered and disrupted by melting ground ice. Thermokarst is a major driver of landscape change in the Arctic, but has been considered to be a minor process in Antarctica. Here, we use ground-based and airborne LiDAR coupled with timelapse imaging and meteorological data to show that 1) thermokarst formation has accelerated in Garwood Valley, Antarctica; 2) the rate of thermokarst erosion is presently,10 times the average Holocene rate; and 3) the increased rate of thermokarst formation is driven most strongly by increasing insolation and sediment/albedo feedbacks. This suggests that sediment enhancement of insolation-driven melting may act similarly to expected increases in Antarctic air temperature (presently occurring along the Antarctic Peninsula), and may serve as a leading indicator of imminent landscape change in Antarctica that will generate thermokarst landforms similar to those in Arctic periglacial terrains

Insights into the subsurface structure of the Caloris basin, Mercury, from assessments of mechanical layering and changes in long-wavelength topography

The volcanic plains that fill the Caloris basin, the largest recognized impact basin on Mercury, are deformed by many graben and wrinkle ridges, among which the multitude of radial graben of Pantheon Fossae allow us to resolve variations in the depth extent of associated faulting. Displacement profiles and displacement-to-length scaling both indicate that faults near the basin center are confined to a ~ 4-km-thick mechanical layer, whereas faults far from the center penetrate more deeply. The fault scaling also indicates that the graben formed in mechanically strong material, which we identify with dry basalt-like plains. These plains were also affected by changes in long-wavelength topography, including undulations with wavelengths of up to 1300 km and amplitudes of 2.5 to 3 km. Geographic correlation of the depth extent of faulting with topographic variations allows a first-order interpretation of the subsurface structure and mechanical stratigraphy in the basin. Further, crosscutting and superposition relationships among plains, faults, craters, and topography indicate that development of long-wavelength topographic variations followed plains emplacement, faulting, and much of the cratering within the Caloris basin. As several examples of these topographic undulations are also found outside the basin, our results on the scale, structural style, and relative timing of the topographic changes have regional applicability and may be the surface expression of global-scale interior processes on Mercury

Insights into the subsurface structure of the Caloris basin, Mercury, from assessments of mechanical layering and changes in long-wavelength topography

The volcanic plains that fill the Caloris basin, the largest recognized impact basin on Mercury, are deformed by many graben and wrinkle ridges, among which the multitude of radial graben of Pantheon Fossae allow us to resolve variations in the depth extent of associated faulting. Displacement profiles and displacement-to-length scaling both indicate that faults near the basin center are confined to a ~ 4-km-thick mechanical layer, whereas faults far from the center penetrate more deeply. The fault scaling also indicates that the graben formed in mechanically strong material, which we identify with dry basalt-like plains. These plains were also affected by changes in long-wavelength topography, including undulations with wavelengths of up to 1300 km and amplitudes of 2.5 to 3 km. Geographic correlation of the depth extent of faulting with topographic variations allows a first-order interpretation of the subsurface structure and mechanical stratigraphy in the basin. Further, crosscutting and superposition relationships among plains, faults, craters, and topography indicate that development of long-wavelength topographic variations followed plains emplacement, faulting, and much of the cratering within the Caloris basin. As several examples of these topographic undulations are also found outside the basin, our results on the scale, structural style, and relative timing of the topographic changes have regional applicability and may be the surface expression of global-scale interior processes on Mercury

Snapshot of Mathematical Background Demographics of a Broad Cohort of First Year Chemistry Science Students

A case study of the background mathematical skills of a varied group of first year chemistry students (n = 455) is presented. Potential student demographic factors, including school leaver, mature age, non-English speaking background, and pre-requisite or prior assumed mathematical and chemistry knowledge, were examined. The student cohort had a diverse background in mathematical knowledge with only 53% meeting the pre-requisite mathematics admission criteria used in Queensland. A voluntary survey was completed by some students (n = 57) from the total cohort, which identified the individual mathematical background of students, their perception of the importance of mathematical skills in their study and their confidence with mathematics. The survey responses indicated that students generally did not have high confidence with their mathematical skills; especially for those with poorer mathematics backgrounds. Interestingly, all students were in strong agreement regarding the importance of mathematics to their study of chemistry. Correlation of the student mathematics background with a chemistry diagnostic test revealed that prior achievement in mathematics impacted on performance within chemistry. We propose that integration of foundational and enabling mathematical skills with curriculum would build student confidence and is more likely to have success in enabling science students to engage and succeed