Radiation damage to nucleoprotein complexes in macromolecular crystallography

Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein-DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07-44.63 MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1-C and sugar-phosphate C-O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses

The effect of irradiation-induced disorder on the conductivity and critical temperature of the organic superconductor κ\kappa-(BEDT-TTF)2_2Cu(SCN)2_2

We have introduced defects into clean samples of the organic superconductor $\kappa$-(BEDT-TTF)$_2$Cu(SCN)$_2$ in order to determine their effect on the temperature dependence of the conductivity and the critical temperature $T_{\rm c}$. We find a violation of Matthiessen's rule that can be explained by a model of the conductivity involving a defect-assisted interlayer channel which acts in parallel with the band-like conductivity. We observe an unusual dependence of $T_{\rm c}$ on residual resistivity which is not consistent with the generalised Abrikosov-Gor'kov theory for an order parameter with a single component, providing an important constraint on models of the superconductivity in this material

Confirmation of two extended objects along the line of sight to PKS1830-211 with ESO-VLT adaptive optics imaging

We report on new high-resolution near-infrared images of the gravitationally lensed radio source PKS1830-211, a quasar at z=2.507. These adaptive optics observations, taken with the Very Large Telescope (VLT), are further improved through image deconvolution. They confirm the presence of a second object along the line of sight to the quasar, in addition to the previously known spiral galaxy. This additional object is clearly extended in our images. However, its faint luminosity does not allow to infer any photometric redshift. If this galaxy is located in the foreground of PKS1830-211, it complicates the modeling of this system and decreases the interest in using PKS1830-211 as a means to determine H0 via the time delay between the two lensed images of the quasar.Comment: Accepted in A&A Letter

Development of a bioavailability‐based risk assessment approach for nickel in freshwater sediments

To assess nickel (Ni) toxicity and behavior in freshwater sediments, a large‐scale laboratory and field sediment testing program was conducted. The program used an integrative testing strategy to generate scientifically based threshold values for Ni in sediments and to develop integrated equilibrium partitioning‐based bioavailability models for assessing risks of Ni to benthic ecosystems. The sediment testing program was a multi‐institutional collaboration that involved extensive laboratory testing, field validation of laboratory findings, characterization of Ni behavior in natural and laboratory conditions, and examination of solid phase Ni speciation in sediments. The laboratory testing initiative was conducted in 3 phases to satisfy the following objectives: 1) evaluate various methods for spiking sediments with Ni to optimize the relevance of sediment Ni exposures; 2) generate reliable ecotoxicity data by conducting standardized chronic ecotoxicity tests using 9 benthic species in sediments with low and high Ni binding capacity; and, 3) examine sediment bioavailability relationships by conducting chronic ecotoxicity testing in sediments that showed broad ranges of acid volatile sulfides, organic C, and Fe. A subset of 6 Ni‐spiked sediments was deployed in the field to examine benthic colonization and community effects. The sediment testing program yielded a broad, high quality data set that was used to develop a Species Sensitivity Distribution for benthic organisms in various sediment types, a reasonable worst case predicted no‐effect concentration for Ni in sediment (PNECsediment), and predictive models for bioavailability and toxicity of Ni in freshwater sediments. A bioavailability‐based approach was developed using the ecotoxicity data and bioavailability models generated through the research program. The tiered approach can be used to fulfill the outstanding obligations under the European Union (EU) Existing Substances Risk Assessment, EU Registration, Evaluation, Authorisation, and Regulation of Chemicals (REACH), and other global regulatory initiatives. Integr Environ Assess Manag 2016;12:735–746. © 2015 SETACKey PointsA comprehensive, representative sediment toxicity database is available to support risk assessment of Ni in freshwater sediments.Sediment Ni ecotoxicity data were gathered from studies that used spiking approaches that resulted in Ni‐enriched sediments resembling naturally contaminated sediments, thus increasing their relevance.Bioavailability of Ni in sediments, which is controlled by acid volatile sulfides (AVS), varies among different species, with actively bioturbating species showing a lower slope in the relationship between decreasing toxicity with increasing AVS.A bioavailability‐based, tiered approach is presented, where the first tier involves comparison of ambient total Ni concentrations with a RWC threshold value of 136 mg Ni/kg. Site‐specific AVS can be used to calculate a site‐specific threshold if ambient Ni is greater than 136 mg Ni/kg.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134197/1/ieam1720.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134197/2/ieam1720_am.pd

Experimental philosophy leading to a small scale digital data base of the conterminous United States for designing experiments with remotely sensed data

Research using satellite remotely sensed data, even within any single scientific discipline, often lacked a unifying principle or strategy with which to plan or integrate studies conducted over an area so large that exhaustive examination is infeasible, e.g., the U.S.A. However, such a series of studies would seem to be at the heart of what makes satellite remote sensing unique, that is the ability to select for study from among remotely sensed data sets distributed widely over the U.S., over time, where the resources do not exist to examine all of them. Using this philosophical underpinning and the concept of a unifying principle, an operational procedure for developing a sampling strategy and formal testable hypotheses was constructed. The procedure is applicable across disciplines, when the investigator restates the research question in symbolic form, i.e., quantifies it. The procedure is set within the statistical framework of general linear models. The dependent variable is any arbitrary function of remotely sensed data and the independent variables are values or levels of factors which represent regional climatic conditions and/or properties of the Earth's surface. These factors are operationally defined as maps from the U.S. National Atlas (U.S.G.S., 1970). Eighty-five maps from the National Atlas, representing climatic and surface attributes, were automated by point counting at an effective resolution of one observation every 17.6 km (11 miles) yielding 22,505 observations per map. The maps were registered to one another in a two step procedure producing a coarse, then fine scale registration. After registration, the maps were iteratively checked for errors using manual and automated procedures. The error free maps were annotated with identification and legend information and then stored as card images, one map to a file. A sampling design will be accomplished through a regionalization analysis of the National Atlas data base (presently being conducted). From this analysis a map of homogeneous regions of the U.S.A. will be created and samples (LANDSAT scenes) assigned by region

K-band Spectroscopy of Clusters in NGC 4038/4039

Integral field spectroscopy in the K-band (1.9-2.4um) was performed on four IR-bright star clusters and the two nuclei in NGC 4038/4039 (``The Antennae''). Two of the clusters are located in the overlap region of the two galaxies, and together comprise ~25% of the total 15um and ~10% of the total 4.8 GHz emission from this pair of merging galaxies. The other two clusters, each of them spatially resolved into two components, are located in the northern galaxy, one in the western and one in the eastern loop of blue clusters. Comparing our analysis of Brgamma, CO band-heads, He I (2.058um), Halpha (from archival HST data), and V-K colors with stellar population synthesis models indicates that the clusters are extincted (A_V ~ 0.7 - 4.3 mags) and young, displaying a significant age spread (4-13 Myrs). The starbursts in the nuclei are much older (65 Myrs), with the nucleus of NGC 4038 displaying a region of recent star formation northward of its K-band peak. Using our derived age estimates and assuming the parameters of the IMF (Salpeter slope, upper mass cut-off of 100 M_sun, Miller-Scalo between 1 M_sun and 0.1 M_sun), we find that the clusters have masses between 0.5 and 5 * 10^6M_sun.Comment: 10 pages, 3 figures, ApJ accepte

Zonation investigation Strawberry Hill intertidal region

Keywords: Zoo451; Strawberry Hill; Zonation; Distribution; Postelsia palmaeformis; Verongia thiona; Lissodendoryx noxiosa; Halichondria panacea; Oplitospongia pennata; Flustrella cervicus; Allopora porphyra; Pisaster ochraceous; Tonicella lineata; Pachycheles rudis; Balanus Pachycheles; Ophlitaspongia pennata; Flustrella cervicis; Pisaster ochraceu

Growing Things Rare, Foreign, and Tender : The Early Nineteenth-Century Greenhouse at Gore Place, Waltham Massachusetts

Excavations and ground penetrating radar at Gore Place in Waltham, Massachusetts, uncovered part of an early 19th-century greenhouse (ca. 1806 to the early 1840s) constructed by Christopher and Rebecca Gore. Documentary, archaeological, and geophysical data suggest that the greenhouse was a formal space intended to display exotic plants and that it was built in the relatively new lean-to style, with a tall back wall and a short front wall. The artifact assemblage included tools and small finds related to the greenhouse operation, as well as the remains of at least 149 planting pots. The greenhouse was constructed during a period of intense interest in agricultural experimentation by members of the Massachusetts commercial and political elite, including Gore. Scholars have argued that these men used the positive associations of agriculture to offset some of the contemporary negative connotations of commerce. This article examines the greenhouse in the light of this scientific agricultural movement but also argues that the greenhouse was an extension of the social space of the house and posits that Rebecca Gore may have played a significant role in managing it