Seagrass rhizosphere microenvironment alters plant-associated microbial community composition

© 2018 Society for Applied Microbiology and John Wiley & Sons Ltd The seagrass rhizosphere harbors dynamic microenvironments, where plant-driven gradients of O2 and dissolved organic carbon form microhabitats that select for distinct microbial communities. To examine how seagrass-mediated alterations of rhizosphere geochemistry affect microbial communities at the microscale level, we applied 16S rRNA amplicon sequencing of artificial sediments surrounding the meristematic tissues of the seagrass Zostera muelleri together with microsensor measurements of the chemical conditions at the basal leaf meristem (BLM). Radial O2 loss (ROL) from the BLM led to ∼ 300 µm thick oxic microzones, wherein pronounced decreases in H2S and pH occurred. Significantly higher relative abundances of sulphate-reducing bacteria were observed around the meristematic tissues compared to the bulk sediment, especially around the root apical meristems (RAM; ∼ 57% of sequences). Within oxic microniches, elevated abundances of sulphide-oxidizing bacteria were observed compared to the bulk sediment and around the RAM. However, sulphide oxidisers within the oxic microzone did not enhance sediment detoxification, as rates of H2S re-oxidation here were similar to those observed in a pre-sterilized root/rhizome environment. Our results provide novel insights into how chemical and microbiological processes in the seagrass rhizosphere modulate plant-microbe interactions potentially affecting seagrass health

Toxin inhibition in <i>C. crescentus</i> VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding

Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct interaction with the antitoxin. Here, we determine crystal structures of the complete 90 kDa heterooctameric VapBC1 complex from Caulobacter crescentus CB15 both in isolation and bound to its cognate DNA operator sequence at 1.6 and 2.7 Å resolution, respectively. DNA binding is associated with a dramatic architectural rearrangement of conserved TA interactions in which C-terminal extended structures of the antitoxin VapB1 swap positions to interlock the complex in the DNA-bound state. We further show that a pseudo-palindromic protein sequence in the antitoxin is responsible for this interaction and required for binding and inactivation of the VapC1 toxin dimer. Sequence analysis of 4127 orthologous VapB sequences reveals that such palindromic protein sequences are widespread and unique to bacterial and archaeal VapB antitoxins suggesting a general principle governing regulation of VapBC TA systems. Finally, a structure of C-terminally truncated VapB1 bound to VapC1 reveals discrete states of the TA interaction that suggest a structural basis for toxin activation in vivo

Comparison of NTF Experimental Data with CFD Predictions from the Third AIAA CFD Drag Prediction Workshop

Recently acquired experimental data for the DLR-F6 wing-body transonic transport con figuration from the National Transonic Facility (NTF) are compared with the database of computational fluid dynamics (CFD) predictions generated for the Third AIAA CFD Drag Prediction Workshop (DPW-III). The NTF data were collected after the DPW-III, which was conducted with blind test cases. These data include both absolute drag levels and increments associated with this wing-body geometry. The baseline DLR-F6 wing-body geometry is also augmented with a side-of-body fairing which eliminates the flow separation in this juncture region. A comparison between computed and experimentally observed sizes of the side-of-body flow-separation bubble is included. The CFD results for the drag polars and separation bubble sizes are computed on grids which represent current engineering best practices for drag predictions. In addition to these data, a more rigorous attempt to predict absolute drag at the design point is provided. Here, a series of three grid densities are utilized to establish an asymptotic trend of computed drag with respect to grid convergence. This trend is then extrapolated to estimate a grid-converged absolute drag level

sUPRa is a dual-color reporter for unbiased quantification of the unfolded protein response with cellular resolution

The unfolded protein response (UPR) maintains proteostasis upon endoplasmic reticulum (ER) stress, and is initiated by a range of physiological and pathological processes. While there have been advances in developing fluorescent reporters for monitoring individual signaling pathways of the UPR, this approach may not capture a cell’s overall UPR activity. Here we describe a novel sensor of UPR activity, sUPRa, which is designed to report the global UPR. sUPRa displays excellent response characteristics, outperforms reporters of individual UPR pathways in terms of sensitivity and kinetics, and responds to a range of different ER stress stimuli. Furthermore, sUPRa’s dual promoter and fluorescent protein design ensures that both UPR-active and inactive cells are detected, and controls for reporter copy number. Using sUPRa, we reveal UPR activation in layer 2/3 pyramidal neurons of mouse cerebral cortex following a period of sleep deprivation. sUPRa affords new opportunities for quantifying physiological UPR activity with cellular resolution

Analysis of interactions between ribosomal proteins and RNA structural motifs

<p>Abstract</p> <p>Background</p> <p>One important goal of structural bioinformatics is to recognize and predict the interactions between protein binding sites and RNA. Recently, a comprehensive analysis of ribosomal proteins and their interactions with rRNA has been done. Interesting results emerged from the comparison of r-proteins within the small subunit in <it>T. thermophilus </it>and <it>E. coli</it>, supporting the idea of a core made by both RNA and proteins, conserved by evolution. Recent work showed also that ribosomal RNA is modularly composed. Motifs are generally single-stranded sequences of consecutive nucleotides (ssRNA) with characteristic folding. The role of these motifs in protein-RNA interactions has been so far only sparsely investigated.</p> <p>Results</p> <p>This work explores the role of RNA structural motifs in the interaction of proteins with ribosomal RNA (rRNA). We analyze composition, local geometries and conformation of interface regions involving motifs such as tetraloops, kink turns and single extruded nucleotides. We construct an interaction map of protein binding sites that allows us to identify the common types of shared 3-D physicochemical binding patterns for tetraloops. Furthermore, we investigate the protein binding pockets that accommodate single extruded nucleotides either involved in kink-turns or in arbitrary RNA strands. This analysis reveals a new structural motif, called <it>tripod</it>.</p> <p>It corresponds to small pockets consisting of three aminoacids arranged at the vertices of an almost equilateral triangle. We developed a search procedure for the recognition of tripods, based on an empirical tripod fingerprint.</p> <p>Conclusion</p> <p>A comparative analysis with the overall RNA surface and interfaces shows that contact surfaces involving RNA motifs have distinctive features that may be useful for the recognition and prediction of interactions.</p

Summary of the Third AIAA CFD Drag Prediction Workshop

The workshop focused on the prediction of both absolute and differential drag levels for wing-body and wing-al;one configurations of that are representative of transonic transport aircraft. The baseline DLR-F6 wing-body geometry, previously utilized in DPW-II, is also augmented with a side-body fairing to help reduce the complexity of the flow physics in the wing-body juncture region. In addition, two new wing-alone geometries have been developed for the DPW-II. Numerical calculations are performed using industry-relevant test cases that include lift-specific and fixed-alpha flight conditions, as well as full drag polars. Drag, lift, and pitching moment predictions from previous Reynolds-Averaged Navier-Stokes computational fluid Dynamics Methods are presented, focused on fully-turbulent flows. Solutions are performed on structured, unstructured, and hybrid grid systems. The structured grid sets include point-matched multi-block meshes and over-set grid systems. The unstructured and hybrid grid sets are comprised of tetrahedral, pyramid, and prismatic elements. Effort was made to provide a high-quality and parametrically consistent family of grids for each grid type about each configuration under study. The wing-body families are comprised of a coarse, medium, and fine grid, while the wing-alone families also include an extra-fine mesh. These mesh sequences are utilized to help determine how the provided flow solutions fair with respect to asymptotic grid convergence, and are used to estimate an absolute drag of each configuration

Optical effects of abaxial anthocyanin on absorption of red wavelengths by understorey species: revisiting the back-scatter hypothesis

A red/purple coloration of lower (abaxial) leaf surfaces is commonly observed in deeply-shaded understorey plants, especially in the tropics. However, the functional significance of red abaxial coloration, including its role in photosynthetic adaptation, remains unclear. The objective of this study was to test the back-scatter hypothesis for abaxial leaf coloration, which posits that red pigments internally reflect/scatter red light transmitted by the upper leaf surface back into the mesophyll, thereby enhancing photon capture in light-limited environments. Abaxially red/non-red variegated leaves of Begonia heracleifolia (Cham. & Schltdl.) were used to compare reflectance spectra and chlorophyll fluorescence profiles of abaxially anthocyanic (red) and acyanic (non-red) tissues under red light. Photosynthetic gas exchange in response to red light was also compared for abaxially red/non-red leaf sections. The results did not support a back-scattering function, as anthocyanic leaf surfaces were not more reflective of red light than acyanic surfaces. Anthocyanic tissues also did not exhibit any increases in the mesophyll absorbance of red light, or increased photosynthetic gas exchange under red light at any intensity, relative to acyanic tissues. These results suggest that abaxial anthocyanins do not significantly enhance the absorption of red light in the species tested, and alternative functions are discussed

Summary of the Fourth AIAA CFD Drag Prediction Workshop

Results from the Fourth AIAA Drag Prediction Workshop (DPW-IV) are summarized. The workshop focused on the prediction of both absolute and differential drag levels for wing-body and wing-body-horizontal-tail configurations that are representative of transonic transport air- craft. Numerical calculations are performed using industry-relevant test cases that include lift- specific flight conditions, trimmed drag polars, downwash variations, dragrises and Reynolds- number effects. Drag, lift and pitching moment predictions from numerous Reynolds-Averaged Navier-Stokes computational fluid dynamics methods are presented. Solutions are performed on structured, unstructured and hybrid grid systems. The structured-grid sets include point- matched multi-block meshes and over-set grid systems. The unstructured and hybrid grid sets are comprised of tetrahedral, pyramid, prismatic, and hexahedral elements. Effort is made to provide a high-quality and parametrically consistent family of grids for each grid type about each configuration under study. The wing-body-horizontal families are comprised of a coarse, medium and fine grid; an optional extra-fine grid augments several of the grid families. These mesh sequences are utilized to determine asymptotic grid-convergence characteristics of the solution sets, and to estimate grid-converged absolute drag levels of the wing-body-horizontal configuration using Richardson extrapolation

Proximity to Sports Facilities and Sports Participation for Adolescents in Germany

Objectives - To assess the relationship between proximity to specific sports facilities and participation in the corresponding sports activities for adolescents in Germany. Methods - A sample of 1,768 adolescents aged 11–17 years old and living in 161 German communities was examined. Distances to the nearest sports facilities were calculated as an indicator of proximity to sports facilities using Geographic Information Systems (GIS). Participation in specific leisure-time sports activities in sports clubs was assessed using a self-report questionnaire and individual-level socio-demographic variables were derived from a parent questionnaire. Community-level socio-demographics as covariates were selected from the INKAR database, in particular from indicators and maps on land development. Logistic regression analyses were conducted to examine associations between proximity to the nearest sports facilities and participation in the corresponding sports activities. Results - The logisitic regression analyses showed that girls residing longer distances from the nearest gym were less likely to engage in indoor sports activities; a significant interaction between distances to gyms and level of urbanization was identified. Decomposition of the interaction term showed that for adolescent girls living in rural areas participation in indoor sports activities was positively associated with gym proximity. Proximity to tennis courts and indoor pools was not associated with participation in tennis or water sports, respectively. Conclusions - Improved proximity to gyms is likely to be more important for female adolescents living in rural areas

Lazarus1, a DUF300 Protein, Contributes to Programmed Cell Death Associated with Arabidopsis acd11 and the Hypersensitive Response

Programmed cell death (PCD) is a necessary part of the life of multi-cellular organisms. A type of plant PCD is the defensive hypersensitive response (HR) elicited via recognition of a pathogen by host resistance (R) proteins. The lethal, recessive accelerated cell death 11 (acd11) mutant exhibits HR-like accelerated cell death, and cell death execution in acd11 shares genetic requirements for HR execution triggered by one subclass of R proteins