MOST detects variability on tau Bootis possibly induced by its planetary companion

(abridged) There is considerable interest in the possible interaction between parent stars and giant planetary companions in 51 Peg-type systems. We demonstrate from MOST satellite photometry and Ca II K line emission that there has been a persistent, variable region on the surface of tau Boo A which tracked its giant planetary companion for some 440 planetary revolutions and lies ~68deg (phi=0.8) in advance of the sub-planetary point. The light curves are folded on a range of periods centered on the planetary orbital period and phase dependent variability is quantified by Fourier methods and by the mean absolute deviation (MAD) of the folded data for both the photometry and the Ca II K line reversals. The region varies in brightness on the time scale of a rotation by ~1 mmag. In 2004 it resembled a dark spot of variable depth, while in 2005 it varied between bright and dark. Over the 123 planetary orbits spanned by the photometry the variable region detected in 2004 and in 2005 are synchronised to the planetary orbital period within 0.0015 d. The Ca II K line in 2001, 2002 and 2003 also shows enhanced K-line variability centered on phi=0.8, extending coverage to some 440 planetary revolutions. The apparently constant rotation period of the variable region and its rapid variation make an explanation in terms of conventional star spots unlikely. The lack of complementary variability at phi=0.3 and the detection of the variable region so far in advance of the sub-planetary point excludes tidal excitation, but the combined photometric and Ca II K line reversal results make a good case for an active region induced magnetically on the surface of tau Boo A by its planetary companion.Comment: 7 pages, 7 figures; accepted for publication in A&

Warm spring reduced carbon cycle impact of the 2012 US summer drought

The global terrestrial carbon sink offsets one-third of the world’s fossil fuel emissions, but the strength of this sink is highly sensitive to large-scale extreme events. In 2012, the contiguous United States experienced exceptionally warm temperatures and the most severe drought since the Dust Bowl era of the 1930s, resulting in substantial economic damage. It is crucial to understand the dynamics of such events because warmer temperatures and a higher prevalence of drought are projected in a changing climate. Here, we combine an extensive network of direct ecosystem flux measurements with satellite remote sensing and atmospheric inverse modeling to quantify the impact of the warmer spring and summer drought on biosphere-atmosphere carbon and water exchange in 2012. We consistently find that earlier vegetation activity increased spring carbon uptake and compensated for the reduced uptake during the summer drought, which mitigated the impact on net annual carbon uptake. The early phenological development in the Eastern Temperate Forests played a major role for the continental-scale carbon balance in 2012. The warm spring also depleted soil water resources earlier, and thus exacerbated water limitations during summer. Our results show that the detrimental effects of severe summer drought on ecosystem carbon storage can be mitigated by warming-induced increases in spring carbon uptake. However, the results also suggest that the positive carbon cycle effect of warm spring enhances water limitations and can increase summer heating through biosphere–atmosphere feedbacks.Data deposition: The eddy-covariance data are available in the AmeriFlux data archive at the Carbon Dioxide Information Analysis Center at the Oak Ridge National Laboratory (cdiac.ornl.gov/ftp/ameriflux/data). This is the publisher’s final pdf. The article is published by National Academy of Sciences and can be found at: http://www.pnas.org/Keywords: ecosystem fluxes, eddy covariance, carbon uptake, biosphere, seasonal climate anomalies, atmosphere feedback

Gene-specific ACMG/AMP classification criteria for germline APC variants: recommendations from the ClinGen InSIGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel

Purpose The Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel (VCEP) was established by the International Society for Gastrointestinal Hereditary Tumours and the Clinical Genome Resource, who set out to develop recommendations for the interpretation of germline APC variants underlying Familial Adenomatous Polyposis, the most frequent hereditary polyposis syndrome. Methods Through a rigorous process of database analysis, literature review, and expert elicitation, the APC VCEP derived gene-specific modifications to the ACMG/AMP (American College of Medical Genetics and Genomics and Association for Molecular Pathology) variant classification guidelines and validated such criteria through the pilot classification of 58 variants. Results The APC-specific criteria represented gene- and disease-informed specifications, including a quantitative approach to allele frequency thresholds, a stepwise decision tool for truncating variants, and semiquantitative evaluations of experimental and clinical data. Using the APC-specific criteria, 47% (27/58) of pilot variants were reclassified including 14 previous variants of uncertain significance (VUS). Conclusion The APC-specific ACMG/AMP criteria preserved the classification of well-characterized variants on ClinVar while substantially reducing the number of VUS by 56% (14/25). Moving forward, the APC VCEP will continue to interpret prioritized lists of VUS, the results of which will represent the most authoritative variant classification for widespread clinical use

A Continuous Measure of Gross Primary Production for the Conterminous U.S. Derived from MODIS and AmeriFlux Data

The quantification of carbon fluxes between the terrestrial biosphere and the atmosphere is of scientific importance and also relevant to climate-policy making. Eddy covariance flux towers provide continuous measurements of ecosystem-level exchange of carbon dioxide spanning diurnal, synoptic, seasonal, and interannual time scales. However, these measurements only represent the fluxes at the scale of the tower footprint. Here we used remotely-sensed data from the Moderate Resolution Imaging Spectroradiometer (MODIS) to upscale gross primary productivity (GPP) data from eddy covariance flux towers to the continental scale. We first combined GPP and MODIS data for 42 AmeriFlux towers encompassing a wide range of ecosystem and climate types to develop a predictive GPP model using a regression tree approach. The predictive model was trained using observed GPP over the period 2000-2004, and was validated using observed GPP over the period 2005-2006 and leave-one-out cross-validation. Our model predicted GPP fairly well at the site level. We then used the model to estimate GPP for each 1 km x 1 km cell across the U.S. for each 8-day interval over the period from February 2000 to December 2006 using MODIS data. Our GPP estimates provide a spatially and temporally continuous measure of gross primary production for the U.S. that is a highly constrained by eddy covariance flux data. Our study demonstrated that our empirical approach is effective for upscaling eddy flux GPP data to the continental scale and producing continuous GPP estimates across multiple biomes. With these estimates, we then examined the patterns, magnitude, and interannual variability of GPP. We estimated a gross carbon uptake between 6.91 and 7.33 Pg C yr{sup -1} for the conterminous U.S. Drought, fires, and hurricanes reduced annual GPP at regional scales and could have a significant impact on the U.S. net ecosystem carbon exchange. The sources of the interannual variability of U.S. GPP were dominated by these extreme climate events and disturbances

Curated multiple sequence alignment for the Adenomatous Polyposis Coli (APC) gene and accuracy of in silico pathogenicity predictions.

Computational algorithms are often used to assess pathogenicity of Variants of Uncertain Significance (VUS) that are found in disease-associated genes. Most computational methods include analysis of protein multiple sequence alignments (PMSA), assessing interspecies variation. Careful validation of PMSA-based methods has been done for relatively few genes, partially because creation of curated PMSAs is labor-intensive. We assessed how PMSA-based computational tools predict the effects of the missense changes in the APC gene, in which pathogenic variants cause Familial Adenomatous Polyposis. Most Pathogenic or Likely Pathogenic APC variants are protein-truncating changes. However, public databases now contain thousands of variants reported as missense. We created a curated APC PMSA that contained >3 substitutions/site, which is large enough for statistically robust in silico analysis. The creation of the PMSA was not easily automated, requiring significant querying and computational analysis of protein and genome sequences. Of 1924 missense APC variants in the NCBI ClinVar database, 1800 (93.5%) are reported as VUS. All but two missense variants listed as P/LP occur at canonical splice or Exonic Splice Enhancer sites. Pathogenicity predictions by five computational tools (Align-GVGD, SIFT, PolyPhen2, MAPP, REVEL) differed widely in their predictions of Pathogenic/Likely Pathogenic (range 17.5-75.0%) and Benign/Likely Benign (range 25.0-82.5%) for APC missense variants in ClinVar. When applied to 21 missense variants reported in ClinVar and securely classified as Benign, the five methods ranged in accuracy from 76.2-100%. Computational PMSA-based methods can be an excellent classifier for variants of some hereditary cancer genes. However, there may be characteristics of the APC gene and protein that confound the results of in silico algorithms. A systematic study of these features could greatly improve the automation of alignment-based techniques and the use of predictive algorithms in hereditary cancer genes

Deliberate Introductions of Species: Research Needs

Research questions about introductions Several research questions need to be answered to help ensure that proposed introductions are done wisely and safely. Guarding against risks without sacrificing benefits: How can the potential benefits and costs of introductions best be evaluated in economic, environmental, and social terms? Should all introductions be regulated? How different must organisms or recipient ecosystems be from those assessed previously to warrant independent assessment? When is it appropriate to assess and regulate taxa other than species? What are appropriate ecological and political boundaries for regulation? Alternatives to introductions: How and when can indigenous organisms be domesticated so that they can substitute for proposed uses of nonindigenous organisms? How can the retention of indigenous species and natural food webs be integrated into agroecosystems so that the risk of pest problems is minimized? Purposeful introductions: What common guidelines can be developed for deliberate introductions of all kinds of organisms? Have screening procedures differed for introductions that proved successful or harmful? How can the potential for nonindigenous organisms to disrupt ecosystem processes be assessed and reduced? Can the demand for introductions be reduced by improving the effectiveness of introductions that are attempted? Reducing negative impacts: When can reduction of human-caused disturbance within natural areas be used to control nonindigenous species impacts? Can subtle, indirect effects of potential introductions be predicted? Can enough be learned from the population growth lags, booms, and crashes of previously introduced organisms to make useful generalizations? Should special guidelines accompany release of sterile forms, which may pose less risk than fertile organisms? Can protocols be developed to predict when an introduced species will hybridize with natives and what the ecological and economic consequences of such hybridization might be? Should special guidelines related to invasion and hybridization potential be added to those that already regulate release of genetically engineered organisms

Warm spring reduced carbon cycle impact of the 2012 US summer drought.

The global terrestrial carbon sink offsets one-third of the world's fossil fuel emissions, but the strength of this sink is highly sensitive to large-scale extreme events. In 2012, the contiguous United States experienced exceptionally warm temperatures and the most severe drought since the Dust Bowl era of the 1930s, resulting in substantial economic damage. It is crucial to understand the dynamics of such events because warmer temperatures and a higher prevalence of drought are projected in a changing climate. Here, we combine an extensive network of direct ecosystem flux measurements with satellite remote sensing and atmospheric inverse modeling to quantify the impact of the warmer spring and summer drought on biosphere-atmosphere carbon and water exchange in 2012. We consistently find that earlier vegetation activity increased spring carbon uptake and compensated for the reduced uptake during the summer drought, which mitigated the impact on net annual carbon uptake. The early phenological development in the Eastern Temperate Forests played a major role for the continental-scale carbon balance in 2012. The warm spring also depleted soil water resources earlier, and thus exacerbated water limitations during summer. Our results show that the detrimental effects of severe summer drought on ecosystem carbon storage can be mitigated by warming-induced increases in spring carbon uptake. However, the results also suggest that the positive carbon cycle effect of warm spring enhances water limitations and can increase summer heating through biosphere-atmosphere feedbacks

Carbon-Water Interactions during Warm Spring and Summer Drought

ISSN:1029-7006ISSN:1607-796

Warm spring reduced carbon cycle impact of the 2012 US summer drought

The global terrestrial carbon sink offsets one-third of the world's fossil fuel emissions, but the strength of this sink is highly sensitive to large-scale extreme events. In 2012, the contiguous United States experienced exceptionally warm temperatures and the most severe drought since the Dust Bowl era of the 1930s, resulting in substantial economic damage. It is crucial to understand the dynamics of such events because warmer temperatures and a higher prevalence of drought are projected in a changing climate. Here, we combine an extensive network of direct ecosystem flux measurements with satellite remote sensing and atmospheric inverse modeling to quantify the impact of the warmer spring and summer drought on biosphereatmosphere carbon and water exchange in 2012. We consistently find that earlier vegetation activity increased spring carbon uptake and compensated for the reduced uptake during the summer drought, which mitigated the impact on net annual carbon uptake. The early phenological development in the Eastern Temperate Forests played a major role for the continental-scale carbon balance in 2012. The warm spring also depleted soil water resources earlier, and thus exacerbated water limitations during summer. Our results show that the detrimental effects of severe summer drought on ecosystem carbon storage can be mitigated by warming-induced increases in spring carbon uptake. However, the results also suggest that the positive carbon cycle effect of warm spring enhances water limitations and can increase summer heating through biosphere-atmosphere feedbacks.</p