Chapter sixteen: Rodents and other vertebrate invaders in the United States

Contents 16.1 Introduction 381 16.2 Assessing impacts of rodents and other vertebrate invaders 385 16.3 Accounts of some important vertebrate invaders 38616.3.1 Norway rant (Rattus norvegicus) 38616.3.2 Roof Rat (Rattus rattus) 38716.3.3 Polynesian rat (Rattus exulans) 38816.3.4 House mouse (Mus Musculus) 38816.3.5 Nutria (Myocastor coypus) 38916.3.6 Gambian giant pouched rat (Cricetomys gambianus) 39016.3.7 Feral swine (Sus scofa) 39016.3.8 Small Indian Mongoose (Herpestes javanicus) 39116.3.9 Rock pigeon (Columba livia) 39216.3.10 House sparrow (Passer domesticus) 39316.3.11 European starling (Sturnus vulgaris) 39316.3.12 Monk parakeet (Myiopsitta monachus) 39416.3.13 Brown tree snake (Boiga irregularis) 39516.3.14 Burmese python (Python molurus bivittatus) 39616.3.15 Coqui frog (Eleutherodactylus coqui) 39716.3.16 Sea lamprey (Petromyzon marinus) 39716.3.17 European and Asian carp (Cyprinidae) 398 16.4 Offshore Threats 399 16.5 Discussion 400 Acknowledgements 401 References 40

Chapter sixteen: Rodents and other vertebrate invaders in the United States

Contents 16.1 Introduction 381 16.2 Assessing impacts of rodents and other vertebrate invaders 385 16.3 Accounts of some important vertebrate invaders 38616.3.1 Norway rant (Rattus norvegicus) 38616.3.2 Roof Rat (Rattus rattus) 38716.3.3 Polynesian rat (Rattus exulans) 38816.3.4 House mouse (Mus Musculus) 38816.3.5 Nutria (Myocastor coypus) 38916.3.6 Gambian giant pouched rat (Cricetomys gambianus) 39016.3.7 Feral swine (Sus scofa) 39016.3.8 Small Indian Mongoose (Herpestes javanicus) 39116.3.9 Rock pigeon (Columba livia) 39216.3.10 House sparrow (Passer domesticus) 39316.3.11 European starling (Sturnus vulgaris) 39316.3.12 Monk parakeet (Myiopsitta monachus) 39416.3.13 Brown tree snake (Boiga irregularis) 39516.3.14 Burmese python (Python molurus bivittatus) 39616.3.15 Coqui frog (Eleutherodactylus coqui) 39716.3.16 Sea lamprey (Petromyzon marinus) 39716.3.17 European and Asian carp (Cyprinidae) 398 16.4 Offshore Threats 399 16.5 Discussion 400 Acknowledgements 401 References 40

All-Atomic Molecular Dynamic Studies of Human and Drosophila CDK8: Insights into Their Kinase Domains, the LXXLL Motifs, and Drug Binding Site

Cyclin-dependent kinase 8 (CDK8) and its regulatory partner Cyclin C (CycC) play conserved roles in modulating RNA polymerase II (Pol II)-dependent gene expression. To understand the structure and function relations of CDK8, we analyzed the structures of human and Drosophila CDK8 proteins using molecular dynamics simulations, combined with functional analyses in Drosophila. Specifically, we evaluated the structural differences between hCDK8 and dCDK8 to predict the effects of the LXXLL motif mutation (AQKAA), the P154L mutations, and drug binding on local structures of the CDK8 proteins. First, we have observed that both the LXXLL motif and the kinase activity of CDK8 are required for the normal larval-to-pupal transition in Drosophila. Second, our molecular dynamic analyses have revealed that hCDK8 has higher hydrogen bond occupation of His149-Asp151 and Asp151-Asn156 than dCDK8. Third, the substructure of Asp282, Phe283, Arg285, Thr287 and Cys291 can distinguish human and Drosophila CDK8 structures. In addition, there are two hydrogen bonds in the LXXLL motif: a lower occupation between L312 and L315, and a relatively higher occupation between L312 and L316. Human CDK8 has higher hydrogen bond occupation between L312 and L316 than dCDK8. Moreover, L312, L315 and L316 in the LXXLL motif of CDK8 have the specific pattern of hydrogen bonds and geometries, which could be crucial for the binding to nuclear receptors. Furthermore, the P154L mutation dramatically decreases the hydrogen bond between L312 and L315 in hCDK8, but not in dCDK8. The mutations of P154L and AQKAA modestly alter the local structures around residues 154. Finally, we identified the inhibitor-induced conformational changes of hCDK8, and our results suggest a structural difference in the drug-binding site between hCDK8 and dCDK8. Taken together, these results provide the structural insights into the roles of the LXXLL motif and the kinase activity of CDK8 in vivo

Hierarchical cluster analysis of polychlorinated dioxins and furans in Michigan, USA, soils: Evaluation of industrial and background congener profiles

As part of the University of Michigan Dioxin Exposure Study, soil samples were collected from 766 residential properties near the Tittabawassee River between Midland and Saginaw; near the Dow Chemical Facility in Midland; and, for comparison, in the other areas of Midland and Saginaw Counties and in Jackson and Calhoun Counties, all located in the state of Michigan, USA. A total of 2,081 soil samples were analyzed for 17 polychlorinated dibenzo- p -dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs). In order to better understand the distribution and sources of the PCDD/F congeners in the study area, hierarchical cluster analysis (HCA) was used to statistically group samples with similar congener patterns. The analysis yielded a total of 13 clusters, including: 3 clusters among the soils impacted by contamination present in the Tittabawassee River sediments, a cluster comprised mainly of samples collected within the depositional area of the Dow incinerator complex, a small cluster of samples with elevated 2,3,7,8-tetrachlorinated dibenzo- p -dioxin (TCDD), and several clusters exhibiting background patterns. The clusters related to the Tittabawassee River floodplain contamination all contained elevated PCDF levels and were differentiated from one another primarily by their relative concentrations of higher-chlorinated PCDDs, a difference likely related to both extent and timing of impacts from Tittabawassee sediments. The background clusters appear to be related to combustion processes and are differentiated, in part, by their relative fractions of TCDD. Thus, HCA was useful for identifying congener profile characteristics in both contaminated and background soil samples. Environ. Toxicol. Chem. 2010;29:64–72. © 2009 SETACPeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/64530/1/24_ftp.pd

Chapter nine: Understanding Declines in Rusty Blackbirds

The Rusty Blackbird (Euphagus carolinus), a formerly common breeding species of boreal wetlands, has exhibited the most marked decline of any North American landbird. North American Breeding Bird Survey (BBS) trends in abundance are estimated to be ‒12.5%/yr. over the last 40 years, which is tantamount to a \u3e95% cumulative decline. Trends in abundance calculated from Christmas Bird Counts (CBC) for a similar period indicate a range-wide decline of ‒5.6%/yr. Qualitative analyses of ornithological accounts suggest the species has been declining for over a century. Several studies document range retraction in the southern boreal forest, whereas limited data suggest that abundance may be more stable in more northerly areas. The major hypotheses for the decline include degradation of boreal habitats from logging and agricultural development, mercury contamination, and wetland desiccation resulting from global warming. Other likely reasons for decline include loss or degradation of wooded wetlands of the southeastern U.S and mortality associated with abatement efforts targeting nuisance blackbirds. In addition, the patchy breeding distribution of this species may inhibit population consolidation, causing local populations to crash when reduced to low levels. Progress in understanding the causes and mechanisms for observed declines has remained limited until recently. Here we present initial attempts to understand the habitat requirements of Rusty Blackbirds and offer specific predictions associated with each of the hypotheses for decline as a way of guiding future research

The University of Michigan Dioxin Exposure Study: Population Survey Results and Serum Concentrations for Polychlorinated Dioxins, Furans, and Biphenyls

Background: The University of Michigan Dioxin Exposure Study was undertaken to address concerns that the discharge of polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs) from the Dow Chemical Company in the Midland, Michigan, area had resulted in contamination of soils in the Tittabawassee River floodplain and the city of Midland, leading to an increase in residents’ body burdens of these compounds. Objective: In this article we present descriptive statistics from the resident survey and sampling of human serum, household dust, and soil and compare them with other published values. Methods: From a multistage random sample of populations in four areas of Midland and Saginaw counties and from a distant referent population, we interviewed 946 adults, who also donated blood for analysis of PCDDs, PCDFs, and polychlorinated biphenyls (PCBs). Samples of household dust and house perimeter soil were collected from consenting subjects who owned their property. Results: All five study populations were comparable in age, race, sex, and length of residence in their current home. Regional differences existed in employment history, personal contact with contaminated soils, and consumption of fish and game from contaminated areas. Median soil concentrations were significantly increased around homes in the Tittabawassee River floodplain (11.4 ppt) and within the city of Midland (58.2 ppt) compared with the referent population (3.6 ppt). Median serum toxic equivalencies were significantly increased in people who lived in the floodplain (23.2 ppt) compared with the referent population (18.5 ppt). Conclusions: Differences in serum dioxin concentrations among the populations were small but statistically significant. Regression modeling is needed to identify whether the serum concentrations of PCDDs, PCDFs, and PCBs are associated with contaminated soils, household dust, and other factors

KL Estimation of the Power Spectrum Parameters from the Angular Distribution of Galaxies in Early SDSS Data

We present measurements of parameters of the 3-dimensional power spectrum of galaxy clustering from 222 square degrees of early imaging data in the Sloan Digital Sky Survey. The projected galaxy distribution on the sky is expanded over a set of Karhunen-Loeve eigenfunctions, which optimize the signal-to-noise ratio in our analysis. A maximum likelihood analysis is used to estimate parameters that set the shape and amplitude of the 3-dimensional power spectrum. Our best estimates are Gamma=0.188 +/- 0.04 and sigma_8L = 0.915 +/- 0.06 (statistical errors only), for a flat Universe with a cosmological constant. We demonstrate that our measurements contain signal from scales at or beyond the peak of the 3D power spectrum. We discuss how the results scale with systematic uncertainties, like the radial selection function. We find that the central values satisfy the analytically estimated scaling relation. We have also explored the effects of evolutionary corrections, various truncations of the KL basis, seeing, sample size and limiting magnitude. We find that the impact of most of these uncertainties stay within the 2-sigma uncertainties of our fiducial result.Comment: Fig 1 postscript problem correcte

Uniform electron gases

We show that the traditional concept of the uniform electron gas (UEG) --- a homogeneous system of finite density, consisting of an infinite number of electrons in an infinite volume --- is inadequate to model the UEGs that arise in finite systems. We argue that, in general, a UEG is characterized by at least two parameters, \textit{viz.} the usual one-electron density parameter $\rho$ and a new two-electron parameter $\eta$. We outline a systematic strategy to determine a new density functional $E(\rho,\eta)$ across the spectrum of possible $\rho$ and $\eta$ values.Comment: 8 pages, 2 figures, 5 table