RNASTAR: An RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs

Automated RNA alignment algorithms often fail to recapture the essential conserved sites that are critical for function. To assist in the refinement of these algorithms, we manually curated a set of 148 alignments with a total of 9600 unique sequences, in which each alignment was backed by at least one crystal or NMR structure. These alignments included both naturally and artificially selected molecules. We used principles of isostericity to improve the alignments from an average of 83%–94% isosteric base pairs. We expect that this alignment collection will assist in a wide range of benchmarking efforts and provide new insight into evolutionary principles governing change in RNA structural motifs. The improved alignments have been contributed to the Rfam database.

<i>Tex 19</i> Paralogs Exhibit a Gonad and Placenta-Specific Expression in the Mouse

We have previously suggested that TEX19, a mammalian-specific protein of which two paralogs exist in rodents, could be implicated in stem cell self-renewal and pluripotency. We have established here the expression profiles of Tex19.1 and Tex19.2 during mouse development and adulthood. We show that both genes are coexpressed in the ectoderm and then in primordial germ cells (PGCs). They are also coexpressed in the testis from embryonic day 13.5 to adulthood, whereas only Tex19.1 transcripts are detected in the developing and adult ovary as well as in the placenta and its precursor tissue, the ectoplacental cone. The presence of both Tex19.1 and Tex19.2 in PGCs, gonocytes and spermatocytes opens the possibility that these two genes could play redundant functions in male germ cells. Furthermore, the placental expression of Tex19.1 can explain why Tex19.1 knockout mice show embryonic lethality, in addition to testis defects.

Synovial sarcoma leading to a paraesophageal abscess in a child.

Synovial sarcoma (SS) is an uncommon malignant neoplasm arising from primitive pluripotential mesenchyme primarily affecting the soft tissues of the extremities. Rarely other locations are involved, including the mediastinum.

The Metabolomic Approach Identifies a Biological Signature of Low-dose Chronic Exposure to Cesium 137

Reports have described apparent biological effects of (137)Cs (the most persistent dispersed radionuclide) irradiation in people living in Chernobyl-contaminated territory. The sensitive analytical technology described here should now help assess the relation of this contamination to the observed effects. A rat model chronically exposed to (137)Cs through drinking water was developed to identify biomarkers of radiation-induced metabolic disorders, and the biological impact was evaluated by a metabolomic approach that allowed us to detect several hundred metabolites in biofluids and assess their association with disease states. After collection of plasma and urine from contaminated and non-contaminated rats at the end of the 9-months contamination period, analysis with a LC-MS system detected 742 features in urine and 1309 in plasma. Biostatistical discriminant analysis extracted a subset of 26 metabolite signals (2 urinary, 4 plasma non-polar, and 19 plasma polar metabolites) that in combination were able to predict from 68 up to 94% of the contaminated rats, depending on the prediction method used, with a misclassification rate as low as 5.3%. The difference in this metabolic score between the contaminated and non-contaminated rats was highly significant (P = 0.019 after ANOVA cross-validation). In conclusion, our proof-of-principle study demonstrated for the first time the usefulness of a metabolomic approach for addressing biological effects of chronic low-dose contamination. We can conclude that a metabolomic signature discriminated (137)Cs-contaminated from control animals in our model. Further validation is nevertheless required together with full annotation of the metabolic indicators.

Bone mineral density and hormonal status in adolescent athletic girls

The aim of this study was to determine the relationships of bone mineral density (BMD) and content (BMC) with selected fasting hormones in adolescents with different exercise training patterns. The participants were female athletes of weight-loaded (n=23) and weight-supported (n=24) sports, and 33 non-athletic girls aged 13–15 years. BMD (g/cm2) and BMC (g) at the femoral neck (FN) and lumbar spine (LS) were measured. Venous blood samples were drawn to determine the concentration of insulin-like growth factor-1 (IGF-1), IGF binding protein-3 (IGFBP-3), estradiol, visfatin, adiponectin, leptin, insulin, and glucose. After adjusting for age, height, and body mass, the relationships of BMD variables with IGF-1, IGF-1/IGFBP-3 molar ratio, estradiol, and leptin levels remained significant only in the weight-loaded sport group (r=0.41–0.60; p<0.05). Adiponectin was inversely correlated to FN and LS BMD and BMC (r=–0.47–0.62; p<0.05) in weight-supported sport group only, but after adjustments for age, height, and body mass, these associations disappeared. In this study, concentrations of visfatin, a fairly new adipocytokine, were not related to bone parameters in adolescent girls with different training patterns.

Melissa Croteau and Carolyn Jess-Cooke (eds). <em>Apocalyptic Shakespeare: Essays on Visions of Chaos and Revelation in Recent Film Adaptations</em>. Jefferson, NC: McFarland, 2009.

Do As the Romans: Greco-Roman Iconography in Eleanor Antin’s Last Days of Pompeii

How Does the Use of Trademarks by Third-Party Sellers Affect Online Search?

Firms that sell via a direct channel and via indirect channels have to decide whether to allow third-party sellers to use trademarked brand names of products in their advertising. This question has been particularly controversial for advertising on search engines. In June 2009, Google started allowing any third-party reseller of a product to use a trademark such as “DoubleTree” in the text of its ad, even if the reseller did not have the trademark holder's permission. We study the effects of this change empirically within the hotel industry. We find some evidence that allowing third-party sellers to use a trademark in their online search advertising weakly reduced the likelihood of a consumer clicking on a trademark holder's paid search ads. However, the decrease in paid clicks was outweighed by a large increase in consumers clicking on the unpaid links to the hotelier's website within the main search results. Our evidence shows that when a third-party seller focuses on a trademarked brand in its ads, the ads become less distinct, and customers are more likely to ignore the advertised offers and buy from the direct channel

Animal Use and Lessons Learned in the U.S. High Production Volume Chemicals Challenge Program

Launched by the U.S. Environmental Protection Agency (EPA) in 1998, the High Production Volume (HPV) Challenge Program was developed to address the perceived gap in basic hazard information for the 2,800 chemicals produced or imported into the United States in quantities of ≥ 1 million pounds per year. Health and environmental effects data obtained from either existing information or through new vertebrate animal testing were voluntarily submitted by chemical companies (sponsors) to the U.S. EPA. Despite the potential for extensive animal testing, animal welfare guidelines were not provided until after the start of the program.

Managing the Risks of Extreme Weather: IPCC Special Report

The number of hot days and nights very likely has increased globally in recent years, according to a special report1 focused solely on extreme weather events from the Intergovernmental Panel on Climate Change (IPCC),2 while the number of cold days has decreased. The future looks similar, the IPCC panel says: If countries continue to increase emissions of carbon dioxide (CO2)—the greenhouse gas produced by human activities in the greatest quantities—deadly heat waves and heavy precipitation events will occur more often. Devastating tropical cyclones, on the other hand, are likely to remain the same or even decrease. A summary report for policy makers was released 18 November 2011 in advance of the February 2012 publication of the full IPCC Special Report Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation (SREX). Several aspects of SREX are designed to inform governments and other decision makers struggling to develop climate-change adaptation plans. The report offers adaptation measures that planners can implement to protect human health during extreme weather events. These include “low-regrets” activities that provide benefits now and under a variety of future scenarios, such as installing systems that warn people of impending disasters and improving systems for health surveillance, drinking water, and drainage. This publication represents the first time that IPCC working groups I (which focuses on the physical science basis of climate change) and II (which focuses on impacts, adaptation, and vulnerability) have collaborated on a report, says SREX coordinating lead author Sonia I. Seneviratne, an assistant professor at the Institute for Atmospheric and Climate Science, ETH Zurich. It also includes several lead authors from the disaster risk management community. “I think the report allows a better integration of information all the way from the physical projections of climate extremes to disaster management and climate adaptation options. This should make it particularly valuable for decision makers,” Seneviratne says. The analysis concludes that extreme weather events will particularly affect sectors closely tied to climate: water, agriculture, food security, forestry, health, and tourism. The severity of human health impacts from climate extremes will reflect how prepared or how vulnerable a community is. For example, people living in areas with rapid and unplanned urbanization, environmental degradation, and poverty are more vulnerable to the hazards of extreme climate events than those living in better-planned, better-protected, and higher-income communities. After a disaster, the summary notes, planners should focus on reconstruction that improves a community’s resistance to weather- and climate-related disasters rather than recreating or even worsening existing vulnerabilities. The report helps untangle some of the confusion nonscientists feel when reading news reports about blockbuster blizzards at the same time the Earth is supposedly warming.3 Gerald A. Meehl, senior scientist at the National Center for Atmospheric Research (NCAR) and a lead author on the near-term climate change chapter for the forthcoming IPCC Fifth Assessment Report (due by 2014), explains that the very nature of global warming exacerbates extreme weather events of all kinds—not just heat-related events. “We know that CO2 traps heat in the atmosphere,” Meehl says. “That causes things to warm up, and warmer air holds more moisture, which means there is more moisture available as a source for precipitation in storms.” Precipitation intensity increases, he says, even though the overall number of storms may not increase. Even in a much warmer climate, Meehl adds, there will still be record cold temperatures and snow storms. However, as the atmosphere continues to warm, “extreme cold will occur less frequently than extreme heat,”4 he says. At least one scientist thinks the SREX underestimates the extent to which human activity affects climate. Kevin Trenberth, distinguished senior scientist in the Climate Analysis Section at the NCAR, says the report “inherently assumes a null hypothesis of no human influence. In reality, many studies have shown otherwise.” Combined with short-term data sets that often contain variabilities and the fact that many models don’t accurately simulate certain extremes such as tropical storms and monsoons, the message would appear to be there is no human influence, according to Trenberth. “The result of the null hypothesis is that the errors from imperfect models and data fall on the side of saying there is no human influence when there really is,” he says. “This is a fundamental issue with the science community as well as public perceptions. . . . The result has been the appearance of overwhelming uncertainties and paralysis of action.” Changes in the mean, variance, or shape of weather probability distributions—or some combination of those three—could mean a change in the number and severity of extreme weather events.