Regional and seasonal patterns of epipelagic fish assemblages from the central California Current

The coastal Pacific Ocean off northern and central California encompasses the strongest seasonal upwelling zone in the California Current ecosystem. Headlands and bays here generate complex circulation features and confer unusual oceanographic complexity. We sampled the coastal epipelagic fish community of this region with a surface trawl in the summer and fall of 2000–05 to assess patterns of spatial and temporal community structure. Fifty-three species of fish were captured in 218 hauls at 34 fixed stations, with clupeiform species dominating. To examine spatial patterns, samples were grouped by location relative to a prominent headland at Point Reyes and the resulting two regions, north coast and Gulf of the Farallones, were plotted by using nonmetric multidimensional scaling. Seasonal and interannual patterns were also examined, and representative species were identified for each distinct community. Seven oceanographic variables measured concurrently with trawling were plotted by principal components analysis and tested for correlation with biotic patterns. We found significant differences in community structure by region, year, and season, but no interaction among main effects. Significant differences in oceanographic conditions mirrored the biotic patterns, and a match between biotic and hydrographic structure was detected. Dissimilarity between assemblages was mostly the result of differences in abundance and frequency of occurrence of about twelve common species. Community patterns were best described by a subset of hydrographic variables, including water depth, distance from shore, and any one of several correlated variables associated with upwelling intensity. Rather than discrete communities with clear borders and distinct member species, we found gradients in community structure and identified stations with similar fish communities by region and by proximity to features such as the San Francisco Bay

Structural diversity in the type IV pili of multidrug-resistant Acinetobacter

Acinetobacter baumannii is a Gram-negative coccobacillus found primarily in hospital settings that has recently emerged as a source of hospital-acquired infections. A. baumannii expresses a variety of virulence factors, including type IV pili, bacterial extracellular appendages often essential for attachment to host cells. Here, we report the high resolution structures of the major pilin subunit, PilA, from three Acinetobacter strains, demonstrating thatA. baumannii subsets produce morphologically distinct type IV pilin glycoproteins. We examine the consequences of this heterogeneity for protein folding and assembly as well as host-cell adhesion by Acinetobacter. Comparisons of genomic and structural data with pilin proteins from other species of soil gammaproteobacteria suggest that these structural differences stem from evolutionary pressure that has resulted in three distinct classes of type IVa pilins, each found in multiple species

Altered gut microbiota in infants is associated with respiratory syncytial virus disease severity

© 2020 The Author(s). Background: Respiratory syncytial virus (RSV) is the number one cause of lower respiratory tract infections in infants. There are still no vaccines or specific antiviral therapies against RSV, mainly due to the inadequate understanding of RSV pathogenesis. Recent data suggest a role for gut microbiota community structure in determining RSV disease severity. Our objective was to determine the gut microbial profile associated with severe RSV patients, which could be used to help identify at-risk patients and develop therapeutically protective microbial assemblages that may stimulate immuno-protection. Results: We enrolled 95 infants from Le Bonheur during the 2014 to 2016 RSV season. Of these, 37 were well-babies and 58 were hospitalized with RSV. Of the RSV infected babies, 53 remained in the pediatric ward (moderate) and 5 were moved to the pediatric intensive care unit at a later date (severe). Stool samples were collected within 72 h of admission; and the composition of gut microbiota was evaluated via 16S sequencing of fecal DNA. There was a significant enrichment in S24_7, Clostridiales, Odoribacteraceae, Lactobacillaceae, and Actinomyces in RSV (moderate and severe) vs. controls. Patients with severe RSV disease had slightly lower alpha diversity (richness and evenness of the bacterial community) of the gut microbiota compared to patients with moderate RSV and healthy controls. Beta diversity (overall microbial composition) was significantly different between all RSV patients (moderate and severe) compared to controls and had significant microbial composition separating all three groups (control, moderate RSV, and severe RSV). Conclusions: Collectively, these data demonstrate that a unique gut microbial profile is associated with RSV disease and with severe RSV disease with admission to the pediatric intensive care unit. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of severe RSV disease

Halo Star Streams in the Solar Neighborhood

We have assembled a sample of halo stars in the solar neighborhood to look for halo substructure in velocity and angular momentum space. Our sample includes red giants, RR Lyrae, and red horizontal branch stars within 2.5 kpc of the Sun with [Fe/H] less than -1.0. It was chosen to include stars with accurate distances, space velocities, and metallicities as well as well-quantified errors. We confirm the existence of the streams found by Helmi and coworkers, which we refer to as the H99 streams. These streams have a double-peaked velocity distribution in the z direction. We use the results of modeling of the H99 streams by Helmi and collaborators to test how one might use v_z velocity information and radial velocity information to detect kinematic substructure in the halo. We find that detecting the H99 streams with radial velocities alone would require a large sample. We use the velocity distribution of the H99 streams to estimate their age. From our model of the progenitor of the H99 streams, we determine that it was accreted between 6 and 9 Gyr ago. The H99 streams have [alpha/Fe] abundances similar to other halo stars in the solar neighborhood, suggesting that the gas that formed these stars were enriched mostly by Type II SNe. We have also discovered in angular momentum space two other possible substructures, which we refer to as the retrograde and prograde outliers. The retrograde outliers are likely to be halo substructure, but the prograde outliers are most likely part of the smooth halo. The retrograde outliers have significant structure in the v_phi direction and show a range of [alpha/Fe]. The methods presented in this paper can be used to exploit the kinematic information present in future large databases like RAVE, SDSSII/SEGUE, and Gaia.Comment: 46 pages, 13 figures, and 9 tables. Minor changes to text to match proofed version of the paper. Low resolution figures. High resolution version at http://www.astro.wisc.edu/~kepley/solar_streams.p

IL-4Rα on dendritic cells in neonates and Th2 immunopathology in respiratory syncytial virus infection

© Society for Leukocyte Biology. Respiratory syncytial virus (RSV) is one of the leading causes of bronchiolitis in children, and severe RSV infection early in life has been associated with asthma development. Using a neonatal mouse model, we have shown that down-regulation of IL-4 receptor α (IL-4Rα) with antisense oligonucleotides in the lung during neonatal infection protected from RSV immunopathophysiology. Significant down-regulation of IL-4Rα was observed on pulmonary CD11b+ myeloid dendritic cells (mDCs) suggesting a role for IL-4Rα on mDCs in the immunopathogenesis of neonatal RSV infection. Here, we demonstrated that neonatal CD11b+ mDCs expressed higher levels of IL-4Rα than their adult counterparts. Because CD11b+ mDCs mainly present antigens to CD4+ T cells, we hypothesized that increased expression of IL- 4Rα on neonatal CD11b+ mDCs was responsible for Th2 - biased RSV immunopathophysiology. Indeed, when IL-4Rα was selectively deleted from CD11b+ mDCs, the immunopathophysiology typically observed following RSV reinfection was ablated, including Th2 inflammation, airway-mucus hyperproduction, and pulmonary dysfunction. Further, overexpression of IL-4Rα on adult CD11b+ DCs and their adoptive transfer into adult mice was able to recapitulate the Th2-biased RSV immunopathology typically observed only in neonates infected with RSV. IL-4Rα levels on CD11c+ cells were inversely correlated with maturation status of CD11b+ mDCs upon RSV infection. Our data demonstrate that developmentally regulated IL-4Rα expression is critical for the maturity of pulmonary CD11b+ mDCs and the Th2-biased immunopathogenesis of neonatal RSV infection

A framework for experimental-data-driven assessment of Magnetized Liner Inertial Fusion stagnation image metrics

A variety of spherical crystal x-ray imager (SCXI) diagnostics have been developed and fielded on Magnetized Liner Inertial Fusion (MagLIF) experiments at the Sandia National Laboratories Z-facility. These different imaging modalities provide detailed insight into different physical phenomena such as mix of liner material into the hot fuel, cold liner emission, or reduce impact of liner opacity. However, several practical considerations ranging from the lack of a consistent spatial fiducial for registration to different point-spread-functions and tuning crystals or using filters to highlight specific spectral regions make it difficult to develop broadly applicable metrics to compare experiments across our stagnation image database without making significant unverified assumptions. We leverage experimental data for a model-free assessment of sensitivities to instrumentation-based features for any specified image metric. In particular, we utilize a database of historical and recent MagLIF data including $N_{\text{scans}} = 139$ image plate scans gathered across $N_{\text{exp}} = 67$ different experiments to assess the impact of a variety of features in the experimental observations arising from uncertainties in registration as well as discrepancies in signal-to-noise ratio and instrument resolution. We choose a wavelet-based image metric known as the Mallat Scattering Transform for the study and highlight how alternate metric choices could also be studied. In particular, we demonstrate a capability to understand and mitigate the impact of signal-to-noise, image registration, and resolution difference between images. This is achieved by utilizing multiple scans of the same image plate, sampling random translations and rotations, and applying instrument specific point-spread-functions found by ray tracing to high-resolution datasets, augmenting our data in an effectively model-free fashion.Comment: 17 pages, 14 figure

Early Ocean Distribution of Juvenile Chinook Salmon in an Upwelling Ecosystem

Extreme variability in abundance of California salmon populations is often ascribed to ocean conditions, yet relatively little is known about their marine life-history. To investigate which ocean conditions influence their distribution and abundance, we surveyed juvenile Chinook salmon (Oncorhynchus tshawytscha) within the California Current (central California (37o 30’ N) to Newport, Oregon (44o 00’ N)) for a two-week period over three summers (2010-2012). At each station, we measured chlorophyll a as an indicator of primary productivity, acoustic-based metrics of zooplankton density as an indicator of potential prey availability, and physical characteristics such as bottom depth, temperature, and salinity. We also measured fork lengths and collected genetic samples from each salmon that was caught. Genetic stock identification revealed that the majority of juvenile salmon were from the Central Valley and the Klamath Basin (91-98%). We constructed generalized logistic-linear negative binomial hurdle models and chose the best model(s) using AIC to determine which covariates influenced salmon presence and, at locations where salmon were present, determined the variables that influenced their abundance. The probability of salmon presence was highest in shallower waters with high chlorophyll a concentration and close to an individual’s natal river. Catch abundance was primarily influenced by year, mean fork length, and proximity to natal rivers. At the scale of sampling stations, presence and abundance was not related to acoustic indices of zooplankton density. In the weeks to months following ocean entry, California’s juvenile Chinook salmon population appears to be primarily constrained to coastal waters near natal river outlets

Fashionably Late? Building up the Milky Way's Inner Halo

Using a sample of 248 metal-poor stars (RR Lyraes, red giants and RHB stars) which is remarkable for the accuracy of its 6-D kinematical data, we find a new component for the local halo which has an axial ratio c/a ~ 0.2, a similar flattening to the thick disk. It has a small prograde rotation but is supported by velocity anisotropy, and contains more intermediate-metallicity stars (with -1.5 < [Fe/H] < -1.0) than the rest of our sample. We suggest that this component was formed quite late, during or after the formation of the disk. It formed either from the gas that was accreted by the last major mergers experienced by the Galaxy, or by dynamical friction of massive infalling satellite(s) with the halo and possibly the stellar disk or thick disk. The remainder of the stars in our sample exhibit a clumpy distribution in energy and angular momentum, suggesting that the early, chaotic conditions under which the inner halo formed were not violent enough to erase the record of their origins. The clumpy structure suggests that a relatively small number of progenitors were responsible for building up the inner halo, in line with theoretical expectations. We find a difference in mean binding energy between the RR Lyrae variables and the red giants in our sample, suggesting that more of the RR Lyraes in the sample belong to the outer halo, and that the outer halo may be somewhat younger, as first suggested by Searle and Zinn (1978). We also find that the RR Lyrae mean rotation is more negative than the red giants, which is consistent with the recent result of Carollo et al.(2007) that the outer halo has a retrograde rotation and with the difference in kinematics seen between RR Lyraes and BHB stars by Kinman et al.(2007).Comment: 16 pages, 10 figures, this version accepted by Ap