Kootenai River Operational Loss Assessment Methodology and its Application to Habitat Restoration

Libby dam regulates in-stream flow of the Kootenai River through Montana, Idaho, and into Canada. The floodplain and associated biotic communities are strongly influenced by riverine system alterations. In order to assist with habitat restoration work, an assessment tool was developed that defines ecologically functional impacts to the Kootenai River floodplain and its vegetative, aquatic, and wildlife communities. This assessment tool includes; hydrologic models for historic flows, anthropomorphic floodplain alterations, post-dam flows, and sturgeon flow releases; an Index of Biological Integrity for insect and avian communities; vegetative cover estimates within sample plots; and an index of human disturbance. In addition, summary indices of ecological integrity were compiled. This assessment tool is being used to identify areas on the Kootenai River for habitat restoration and/or protection. Some of the tool’s uses and implications are identified

Unravelling the Dodecahedral Spaces

The hyperbolic dodecahedral space of Weber and Seifert has a natural non-positively curved cubulation obtained by subdividing the dodecahedron into cubes. We show that the hyperbolic dodecahedral space has a 6-sheeted irregular cover with the property that the canonical hypersurfaces made up of the mid-cubes give a very short hierarchy. Moreover, we describe a 60-sheeted cover in which the associated cubulation is special. We also describe the natural cubulation and covers of the spherical dodecahedral space (aka Poincar\'e homology sphere).Comment: 15 pages + 6 pages appendix, 7 figures, 4 table

Cysteines and N-glycosylation sites conserved among all alphaherpesviruses regulate membrane fusion in herpes simplex virus 1 infection

© 2017 American Society for Microbiology. Neurotropism is a defining characteristic of alphaherpesvirus pathogenicity. Glycoprotein K (gK) is a conserved virion glycoprotein of all alphaherpesviruses that is not found in other herpesvirus subfamilies. The extracellular amino terminus of gK has been shown to be important to the ability of the prototypic alphaherpesvirus herpes simplex virus 1 (HSV-1) to enter neurons via axonal termini. Here, we determined the role of the two conserved N-linked glycosylation (N48 and N58) sites of gK in virus-induced cell fusion and replication. We found that N-linked glycosylation is important to the regulation of HSV-1-induced membrane fusion since mutating N58 to alanine (N58A) caused extensive virus-induced cell fusion. Due to the known contributions of N-linked glycosylation to protein processing and correct disulfide bond formation, we investigated whether the conserved extracellular cysteine residues within the amino terminus of gK contributed to the regulation of HSV-1-induced membrane fusion. We found that mutation of C37 and C114 residues led to a gK-null phenotype characterized by very small plaque formation and drastic reduction in infectious virus production, while mutation of C82 and C243 caused extensive virus-induced cell fusion. Comparison of N-linked glycosylation and cysteine mutant replication kinetics identified disparate effects on infectious virion egress from infected cells. Specifically, cysteine mutations caused defects in the accumulation of infectious virus in both the cellular and supernatant fractions, while glycosylation site mutants did not adversely affect virion egress from infected cells. These results demonstrate a critical role for the N glycosylation sites and cysteines for the structure and function of the amino terminus of gK

A cold metal-poor cloud traced by a weak MgII absorption at z~0.45. First detection of SiI, CaI and FeI in a QSO absorber

We present the observations of a weak MgII absorption system detected at z~0.452 in the UVES high resolution spectrum of the QSO HE0001-2340. The weaker of the two MgII components forming the system shows associated absorptions due to SiI, CaI and FeI observed for the first time in a QSO spectrum. We investigate the nature of this absorber by comparing its properties with those of different classes of absorbers (weak MgII, Damped Ly-alpha systems and local interstellar clouds) and reproducing its ionization conditions with photoionization models. The observed absorber belongs to the class of weak MgII systems on the basis of its equivalent width, however the relative strength of commonly observed transitions deviates significantly from those of the above mentioned absorbers. A rough estimate of the probability to cross such a system with a QSO line of sight is P~0.03. The presence of rare neutral transitions suggests that the cloud is shielded by a large amount of neutral hydrogen. A detailed comparison of the observed column densities with the average properties of damped Ly-alpha systems and local interstellar cold clouds shows, in particular, deficient MgII/MgI and CaII/CaI ratios in our cloud. The results of photoionization models indicate that the cloud could be ionized by the UV background. However, a simple model of a single cloud with uniform density cannot reproduce the observed ionic abundance ratios, suggesting a more complex density structure for the absorber. Supposing that ionization corrections are negligible, the most puzzling result is the underabundance of magnesium with respect to iron which is hard to explain both with nucleosynthesis and with differential dust depletion. [Abridged]Comment: 7 pages, 9 figures. A&A in pres

Proteomics reveals multiple routes to the osteogenic phenotype in mesenchymal stem cells

<p>Abstract</p> <p>Background</p> <p>Recently, we demonstrated that human mesenchymal stem cells (hMSC) stimulated with dexamethazone undergo gene focusing during osteogenic differentiation (<it>Stem Cells Dev </it>14(6): 1608–20, 2005). Here, we examine the protein expression profiles of three additional populations of hMSC stimulated to undergo osteogenic differentiation via either contact with pro-osteogenic extracellular matrix (ECM) proteins (collagen I, vitronectin, or laminin-5) or osteogenic media supplements (OS media). Specifically, we annotate these four protein expression profiles, as well as profiles from naïve hMSC and differentiated human osteoblasts (hOST), with known gene ontologies and analyze them as a tensor with modes for the expressed proteins, gene ontologies, and stimulants.</p> <p>Results</p> <p>Direct component analysis in the gene ontology space identifies three components that account for 90% of the variance between hMSC, osteoblasts, and the four stimulated hMSC populations. The directed component maps the differentiation stages of the stimulated stem cell populations along the differentiation axis created by the difference in the expression profiles of hMSC and hOST. Surprisingly, hMSC treated with ECM proteins lie closer to osteoblasts than do hMSC treated with OS media. Additionally, the second component demonstrates that proteomic profiles of collagen I- and vitronectin-stimulated hMSC are distinct from those of OS-stimulated cells. A three-mode tensor analysis reveals additional focus proteins critical for characterizing the phenotypic variations between naïve hMSC, partially differentiated hMSC, and hOST.</p> <p>Conclusion</p> <p>The differences between the proteomic profiles of OS-stimulated hMSC and ECM-hMSC characterize different transitional phenotypes en route to becoming osteoblasts. This conclusion is arrived at via a three-mode tensor analysis validated using hMSC plated on laminin-5.</p

Fibrinolytic-deficiencies predispose hosts to septicemia from a catheter-associated UTI

Catheter-associated urinary tract infections (CAUTIs) are amongst the most common nosocomial infections worldwide and are difficult to treat partly due to development of multidrug-resistance from CAUTI-related pathogens. Importantly, CAUTI often leads to secondary bloodstream infections and death. A major challenge is to predict when patients will develop CAUTIs and which populations are at-risk for bloodstream infections. Catheter-induced inflammation promotes fibrinogen (Fg) and fibrin accumulation in the bladder which are exploited as a biofilm formation platform by CAUTI pathogens. Using our established mouse model of CAUTI, here we identified that host populations exhibiting either genetic or acquired fibrinolytic-deficiencies, inducing fibrin deposition in the catheterized bladder, are predisposed to severe CAUTI and septicemia by diverse uropathogens in mono- and poly-microbial infections. Furthermore, here we found that Enterococcus faecalis, a prevalent CAUTI pathogen, uses the secreted protease, SprE, to induce fibrin accumulation and create a niche ideal for growth, biofilm formation, and persistence during CAUTI

Reconstructing the intergalactic UV background with QSO absorption lines

We present a new approach to constrain the spectral energy distribution of the intergalactic UV background observationally by studying metal absorption systems. We study single-component metal line systems exhibiting various well-measured species. Among the observed transitions at least two ratios of ionization stages from the same element are required, e.g. CIII/CIV and SiIII/SiIV. For each system photoionization models are constructed varying the spectrum of the ionizing radiation. The spectral energy distribution can then be constrained by comparing the models with the observed column density ratios. Extensive tests with artificial absorbers show that the spectrum of the ionizing radiation cannot be reconstructed unambiguously, but it is possible to constrain the main characteristics of the spectrum. Furthermore, the resulting physical parameters of the absorber, such as ionization parameter, metallicity, and relative abundances, may depend strongly on the adopted ionizing spectrum. Even in case of well-fitting models the uncertainties can be as high as ~0.5 dex for the ionization parameter and up to ~1.5 dex for the metallicity. Therefore, it is essential to know the hardness of the UV background when estimating the metallicity of the intergalactic medium. Applying the procedure to a small sample of 3 observed single-component metal line systems yields a soft ionizing radiation at z > 2 and a slightly harder spectrum at z < 2. The resulting energy distributions exhibit strong HeII Ly alpha re-emission features suggesting that reprocessing by intergalactic HeII is important. Comparing to UV background spectra from the literature indicates that the recent model of Madau & Haardt (2009) including sawtooth modulation due to reprocessing by intergalactic HeII with delayed helium reionization fits the investigated systems very well.Comment: accepted for publication by A&

A Population of Dust-rich Quasars at z ~ 1.5

We report Herschel SPIRE (250, 350, and 500 μm) detections of 32 quasars with redshifts 0.5 ≤z < 3.6 from the Herschel Multi-tiered Extragalactic Survey (HerMES). These sources are from a MIPS 24 μm flux-limited sample of 326 quasars in the Lockman Hole Field. The extensive multi-wavelength data available in the field permit construction of the rest-frame spectral energy distributions (SEDs) from ultraviolet to the mid-infrared for all sources, and to the far-infrared (FIR) for the 32 objects. Most quasars with Herschel FIR detections show dust temperatures in the range of 25-60 K, with a mean of 34 K. The FIR luminosities range from 10^(11.3) to 10^(13.5) L_☉, qualifying most of their hosts as ultra- or hyper-luminous infrared galaxies. These FIR-detected quasars may represent a dust-rich population, but with lower redshifts and fainter luminosities than quasars observed at ~1 mm. However, their FIR properties cannot be predicted from shorter wavelengths (0.3-20 μm, rest frame), and the bolometric luminosities derived using the 5100 Å index may be underestimated for these FIR-detected quasars. Regardless of redshift, we observed a decline in the relative strength of FIR luminosities for quasars with higher near-infrared luminosities

Extended Lyman alpha emission around bright quasars

Quasars trace the most massive structures at high redshifts and their presence may influence the evolution of the massive host galaxies. We study the extended Lyman alpha emission line regions (EELRs) around seven bright, mostly radio-quiet quasars (QSOs) at 2.7<z<4.5, and compare luminosities with EELRs around radio-loud QSOs reported in the literature. Using integral field spectroscopy, we analyse the morphology and kinematics of the quiescent Lya EELRs around the QSOs. We find evidence for the presence of EELRs around four radio-quiet and one radio-loud QSO. All EELRs appear asymmetric and the optically brightest QSOs also have the brightest Lya nebulae. For the two brightest nebulae we find velocities between ~600 km s^-1 at the QSO position to ~200 km s^-1 at a distance of 3-4 arcsec from the QSO and surface flux densities up to 2-3*10^{-16} erg cm^-2 s^-1 arcsec^-2. The five EELRs have total Lya luminosities which correspond to ~0.5% of the luminosities from the QSOs broad Lya emission lines. This fraction is an order of magnitude smaller than found for EELRs around radio-loud, steep spectrum QSOs reported in the literature. While the nebulae luminosities are correlated with the QSO Lya luminosities, we find that nebulae luminosities are not correlated with the central QSO ionising fluxes. The presence of gas in the EELRs can be interpreted based on two competing scenarios: either from quasar feedback mechanisms, or from infalling matter. Apart from these two effects, the Lya flux around radio-loud objects can be enhanced due to interactions with the radio jets. The relatively fainter nebulae around radio-quiet QSOs compared to lobe-dominated radio-loud QSOs can be ascribed to this effect, or to significant differences in the environments between the two classes.Comment: 15 pages, A&A accepted. Section 4 revise