Physiological relevance of a trna-dependent mechanism for membrane modification in enterococcus faecium

Enterococci were once thought to be harmless, commensal organisms that colonize the gastrointestinal tract of humans and other mammals. In the last 30 years, however, concern has grown in the clinical setting over two particular species, Enterococcus faecalis and Enterococcus faecium, which are frequently found to be the etiologic agents of nosocomial infections. Aminoacyl-phosphatidylglycerol synthases (aaPGSs) are integral membrane proteins that add amino acids to phosphatidylglycerol (PG) in the cellular envelope of bacteria. Addition of amino acids to PG confers resistance to various therapeutic antimicrobial agents, and contributes to evasion of the host immune response in a number of clinically relevant microorganisms. E. faecium possesses two distinct aaPGSs: aaPGS1 and aaPGS2. In addition, another gene coding for a putative hydrolase (pHyd) is located in the same operon as aaPGS2, and has no known function. To investigate the physiological relevance of aa-PG formation, and the function of aaPGS1, aaPGS2, and pHyd in E. faecium, we generated individual knockouts of these genes using a markerless deletion strategy. Deletion of aaPGS1 did not noticeably alter lipid aminoacylation, whereas deletion of aaPGS2 led to a loss of aa-PG synthesis. Deletion of pHyd also led to a loss of lipid aminoacylation; however, additional experiments are needed to verify that expression of aaPGS2 (which resides just downstream in the same operon) is unaffected in the pHyd-deletion strain. Development of the mutant strains described here will enable us to investigate additional phenotypes associated with these genes, and to determine whether aa-PG formation contributes to antibiotic resistance in E. faecium as in several other pathogenic microorganisms

Methods for Estimating The Diagonal of Matrix Functions

Many applications such as path integral evaluation in Lattice Quantum Chromodynamics (LQCD), variance estimation of least square solutions and spline ts, and centrality measures in network analysis, require computing the diagonal of a function of a matrix, Diag(f(A)) where A is sparse matrix, and f is some function. Unfortunately, when A is large, this can be computationally prohibitive. Because of this, many applications resort to Monte Carlo methods. However, Monte Carlo methods tend to converge slowly. One method for dealing with this shortcoming is probing. Probing assumes that nodes that have a large distance between them in the graph of A, have only a small weight connection in f(A). to determine the distances between nodes, probing forms Ak. Coloring the graph of this matrix will group nodes that have a high distance between them together, and thus a small connection in f(A). This enables the construction of certain vectors, called probing vectors, that can capture the diagonals of f(A). One drawback of probing is in many cases it is too expensive to compute and store A^k for the k that adequately determines which nodes have a strong connection in f(A). Additionally, it is unlikely that the set of probing vectors required for A^k is a subset of the probing vectors needed for Ak+1. This means that if more accuracy in the estimation is required, all previously computed work must be discarded. In the case where the underlying problem arises from a discretization of a partial dierential equation (PDE) onto a lattice, we can make use of our knowledge of the geometry of the lattice to quickly create hierarchical colorings for the graph of A^k. A hierarchical coloring is one in which colors for A^{k+1} are created by splitting groups of nodes sharing a color in A^k. The hierarchical property ensures that the probing vectors used to estimate Diag(f(A)) are nested subsets, so if the results are inaccurate the estimate can be improved without discarding the previous work. If we do not have knowledge of the intrinsic geometry of the matrix, we propose two new classes of methods that improve on the results of probing. One method seeks to determine structural properties of the matrix f(A) by obtaining random samples of the columns of f(A). The other method leverages ideas arising from similar problems in graph partitioning, and makes use of the eigenvectors of f(A) to form effective hierarchical colorings. Our methods have thus far seen successful use in computational physics, where they have been applied to compute observables arising in LQCD. We hope that the renements presented in this work will enable interesting applications in many other elds

Governing beyond the metropolis: Placing the rural in city-region development

Despite a select group of urban centres generating a disproportionate amount of global economic output, significant attention is being devoted to the impact of urban-economic processes on interstitial spaces lying between metropolitan areas. Nevertheless, there remains a noticeable silence in city-region debate concerning how rural spaces are conceptualised, governed and represented. In this paper we draw on recent city-region developments in England and Wales to suggest a paralysis of city-region policymaking has ensued from policy elites constantly swaying between a spatially-selective, city-first, agglomeration perspective on city-regionalism and a spatially-inclusive, region-first, scalar approach which fragments and divides territorial space along historical lines. In the final part we provide a typology of functionally dominant city-region constructs which we suggest offers a way out from the paralysis that currently grips city-region policymaking

Review of standards for biodegradable plastic bags.

The Single Use Carrier Bags Charges (England) Order 2015 requires retailers to charge at least 5p for each single use carrier bag, except where exempted. Under section 18 of that order, the Secretary of State must— (a) complete a review of industry standards for the biodegradability of lightweight plastic material; and (b) lay a copy of a report before Parliament setting out the conclusions of the review, in particular— (i) whether it appears to the Secretary of State that there exists an industry standard appropriate for the purposes of an exclusion from the obligations specified in Part 2 on grounds of biodegradability; and (ii) if so, how that exclusion would be implemented. That review has now been completed. It found that there are a number of standards for plastic bag biodegradability. We will need to conduct further work before any of these could be used to exempt certain types of carrier bags on grounds of biodegradability. By the end of May 2016 retailers are required to report the number of bags that have been supplied, and the uses to which the proceeds of the charge have been put, after reasonable costs are deducted. The Government will use that opportunity to consider the early impacts of the charge. The Government will continue to consider the technical specification for a genuinely biodegradable bag, and will at that point further report on how an exemption for such a biodegradable bag can be implemented

Climate drives loss of phylogenetic diversity in a grassland community

© 2019 National Academy of Sciences. All rights reserved. While climate change has already profoundly influenced biodiversity through local extinctions, range shifts, and altered interactions, its effects on the evolutionary history contained within sets of coexisting species—or phylogenetic community diversity—have yet to be documented. Phylogenetic community diversity may be a proxy for the diversity of functional strategies that can help sustain ecological systems in the face of disturbances. Under climatic warming, phylogenetic diversity may be especially vulnerable to decline in plant communities in warm, water-limited regions, as intensified water stress eliminates drought-intolerant species that may be relicts of past wetter climates and may be distantly related to coexisting species. Here, we document a 19-y decline of phylogenetic diversity in a grassland community as moisture became less abundant and predictable at a critical time of the year. This decline was strongest in native forbs, particularly those with high specific leaf area, a trait indicating drought sensitivity. This decline occurred at the small spatial scale where species interact, but the larger regional community has so far been buffered against loss of phylogenetic diversity by its high levels of physical and biotic heterogeneity

Understanding the Predictability of Gesture Parameters from Speech and their Perceptual Importance

Gesture behavior is a natural part of human conversation. Much work has focused on removing the need for tedious hand-animation to create embodied conversational agents by designing speech-driven gesture generators. However, these generators often work in a black-box manner, assuming a general relationship between input speech and output motion. As their success remains limited, we investigate in more detail how speech may relate to different aspects of gesture motion. We determine a number of parameters characterizing gesture, such as speed and gesture size, and explore their relationship to the speech signal in a two-fold manner. First, we train multiple recurrent networks to predict the gesture parameters from speech to understand how well gesture attributes can be modeled from speech alone. We find that gesture parameters can be partially predicted from speech, and some parameters, such as path length, being predicted more accurately than others, like velocity. Second, we design a perceptual study to assess the importance of each gesture parameter for producing motion that people perceive as appropriate for the speech. Results show that a degradation in any parameter was viewed negatively, but some changes, such as hand shape, are more impactful than others. A video summarization can be found at https://youtu.be/aw6-_5kmLjY.Comment: To be published in the Proceedings of the 20th ACM International Conference on Intelligent Virtual Agents (IVA 20

16S and 18S rRNA Gene Metabarcoding Provide Congruent Information on the Responses of Sediment Communities to Eutrophication

Metabarcoding analyses of bacterial and eukaryotic communities have been proposed as efficient tools for environmental impact assessment. It has been unclear, however, to which extent these analyses can provide similar or differing information on the ecological status of the environment. Here, we used 16S and 18S rRNA gene metabarcoding to compare eutrophication-induced shifts in sediment bacterial and eukaryotic community structure in relation to a range of porewater, sediment and bottom-water geochemical variables, using data obtained from six stations near a former rainbow trout farm in the Archipelago Sea (Baltic Sea). Shifts in the structure of both community types were correlated with a shared set of variables, including porewater ammonium concentrations and the sediment depth-integrated oxygen consumption rate. Distance-based redundancy analyses showed that variables typically employed in impact assessments, such as bottom water nutrient concentrations, explained less of the variance in community structure than alternative variables (e.g., porewater NH4+ inventories and sediment depth-integrated O2 consumption rates) selected due to their low collinearity (up to 40 vs. 58% of the variance explained, respectively). In monitoring surveys where analyses of both bacterial and eukaryotic communities may be impossible, either 16S or 18S rRNA gene metabarcoding can serve as reliable indicators of wider ecological impacts of eutrophication.Peer reviewe

3D Imaging and Mechanical Modeling of Helical Buckling in Medicago truncatula Plant Roots

We study the primary root growth of wild-type Medicago truncatula plants in heterogeneous environments using 3D time-lapse imaging. The growth medium is a transparent hydrogel consisting of a stiff lower layer and a compliant upper layer. We find that the roots deform into a helical shape just above the gel layer interface before penetrating into the lower layer. This geometry is interpreted as a combination of growth-induced mechanical buckling modulated by the growth medium and a simultaneous twisting near the root tip. We study the helical morphology as the modulus of the upper gel layer is varied and demonstrate that the size of the deformation varies with gel stiffness as expected by a mathematical model based on the theory of buckled rods. Moreover, we show that plant-to-plant variations can be accounted for by biomechanically plausible values of the model parameters

3D Imaging and Mechanical Modeling of Helical Buckling in Medicago truncatula Plant Roots

We study the primary root growth of wild-type Medicago truncatula plants in heterogeneous environments using 3D time-lapse imaging. The growth medium is a transparent hydrogel consisting of a stiff lower layer and a compliant upper layer. We find that the roots deform into a helical shape just above the gel layer interface before penetrating into the lower layer. This geometry is interpreted as a combination of growth-induced mechanical buckling modulated by the growth medium and a simultaneous twisting near the root tip. We study the helical morphology as the modulus of the upper gel layer is varied and demonstrate that the size of the deformation varies with gel stiffness as expected by a mathematical model based on the theory of buckled rods. Moreover, we show that plant-to-plant variations can be accounted for by biomechanically plausible values of the model parameters