The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict

Bacterial genomes commonly contain ‘addiction’ gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin–antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive ‘rock-paper-scissors’ dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes

Geometric Classification of Conformal Anomalies in Arbitrary Dimensions

We give a complete geometric description of conformal anomalies in arbitrary, (necessarily even) dimension. They fall into two distinct classes: the first, based on Weyl invariants that vanish at integer dimensions, arises from finite -- and hence scale-free -- contributions to the effective gravitational action through a mechanism analogous to that of the (gauge field) chiral anomaly. Like the latter, it is unique and proportional to a topological term, the Euler density of the dimension, thereby preserving scale invariance. The contributions of the second class, requiring introduction of a scale through regularization, are correlated to all local conformal scalar polynomials involving powers of the Weyl tensor and its derivatives; their number increases rapidly with dimension. Explicit illustrations in dimensions 2, 4 and 6 are provided.Comment: Brandeis BRX--343, SISSA 14/93/E

Sunshine Of Mine

https://digitalcommons.library.umaine.edu/mmb-vp/2982/thumbnail.jp

On Silicon Group Elements Ejected by Supernovae Type Ia

There is compelling evidence that the peak brightness of a Type Ia supernova is affected by the electron fraction Ye at the time of the explosion. The electron fraction is set by the aboriginal composition of the white dwarf and the reactions that occur during the pre explosive convective burning. To date, determining the makeup of the white dwarf progenitor has relied on indirect proxies, such as the average metallicity of the host stellar population. In this paper, we present analytical calculations supporting the idea that the electron fraction of the progenitor systematically influences the nucleosynthesis of silicon group ejecta in Type Ia supernovae. In particular, we suggest the abundances generated in quasi nuclear statistical equilibrium are preserved during the subsequent freezeout. This allows one to potential recovery of Ye at explosion from the abundances recovered from an observed spectra. We show that measurement of 28Si, 32S, 40Ca, and 54Fe abundances can be used to construct Ye in the silicon rich regions of the supernovae. If these four abundances are determined exactly, they are sufficient to recover Ye to 6 percent. This is because these isotopes dominate the composition of silicon-rich material and iron rich material in quasi nuclear statistical equilibrium. Analytical analysis shows that the 28Si abundance is insensitive to Ye, the 32S abundance has a nearly linear trend with Ye, and the 40Ca abundance has a nearly quadratic trend with Ye. We verify these trends with post-processing of 1D models and show that these trends are reflected in model synthetic spectra.Comment: Submitted to the Ap

Decline and Fall at the White House

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/67262/2/10.1177_009365027700400103.pd

Fine particle pH and the partitioning of nitric acid during winter in the northeastern United States

Particle pH is a critical but poorly constrained quantity that affects many aerosol processes and properties, including aerosol composition, concentrations, and toxicity. We assess PM1 pH as a function of geographical location and altitude, focusing on the northeastern U.S., based on aircraft measurements from the Wintertime Investigation of Transport, Emissions, and Reactivity campaign (1 February to 15 March 2015). Particle pH and water were predicted with the ISORROPIA-II thermodynamic model and validated by comparing predicted to observed partitioning of inorganic nitrate between the gas and particle phases. Good agreement was found for relative humidity (RH) above 40%; at lower RH observed particle nitrate was higher than predicted, possibly due to organic-inorganic phase separations or nitrate measurement uncertainties associated with low concentrations (nitrate \u3c 1 µg m−3). Including refractory ions in the pH calculations did not improve model predictions, suggesting they were externally mixed with PM1 sulfate, nitrate, and ammonium. Sample line volatilization artifacts were found to be minimal. Overall, particle pH for altitudes up to 5000 m ranged between −0.51 and 1.9 (10th and 90th percentiles) with a study mean of 0.77 ± 0.96, similar to those reported for the southeastern U.S. and eastern Mediterranean. This expansive aircraft data set is used to investigate causes in variability in pH and pH-dependent aerosol components, such as PM1 nitrate, over a wide range of temperatures (−21 to 19°C), RH (20 to 95%), inorganic gas, and particle concentrations and also provides further evidence that particles with low pH are ubiquitous

Comparison of Two Methodologies for Calibrating Satellite Instruments in the Visible and Near Infrared

Traditionally, satellite instruments that measure Earth-reflected solar radiation in the visible and near infrared wavelength regions have been calibrated for radiance response in a two-step method. In the first step, the spectral response of the instrument is determined using a nearly monochromatic light source, such a lamp-illuminated monochromator. Such sources only provide a relative spectral response (RSR) for the instrument, since they do not act as calibrated sources of light nor do they typically fill the field-of-view of the instrument. In the second step, the instrument views a calibrated source of broadband light, such as lamp-illuminated integrating sphere. In the traditional method, the RSR and the sphere spectral radiance are combined and, with the instrument's response, determine the absolute spectral radiance responsivity of the instrument. More recently, an absolute calibration system using widely tunable monochromatic laser systems has been developed, Using these sources, the absolute spectral responsivity (ASR) of an instrument can be determined on a wavelength-hy-wavelength basis. From these monochromatic ASRs. the responses of the instrument bands to broadband radiance sources can be calculated directly, eliminating the need for calibrated broadband light sources such as integrating spheres. Here we describe the laser-based calibration and the traditional broad-band source-based calibration of the NPP VIIRS sensor, and compare the derived calibration coefficients for the instrument. Finally, we evaluate the impact of the new calibration approach on the on-orbit performance of the sensor

The effectiveness of beach mega-nourishment, assessed over three management epochs

Resilient coastal protection requires adaptive management strategies that build with nature to maintain long-term sustainability. With increasing pressures on shorelines from urbanisation, industrial growth, sea-level rise and changing storm climates soft approaches to coastal management are implemented to support natural habitats and maintain healthy coastal ecosystems. The impact of a beach mega-nourishment along a frontage of interactive natural and engineered systems that incorporate soft and hard defences is explored. A coastal evolution model is applied to simulate the impact of different hypothetical mega-nourishment interventions to assess their impacts’ over 3 shoreline management planning epochs: present-day (0–20 years), medium-term (20–50 years) and long-term (50–100 years). The impacts of the smaller interventions when appropriately positioned are found to be as effective as larger schemes, thus making them more cost-effective for present-day management. Over time the benefit from larger interventions becomes more noticeable, with multi-location schemes requiring a smaller initial nourishment to achieve at least the same benefit as that of a single-location scheme. While the longer-term impact of larger schemes reduces erosion across a frontage the short-term impact down drift of the scheme can lead to an increase in erosion as the natural sediment drift becomes interrupted. This research presents a transferable modelling tool to assess the impact of nourishment schemes for a variety of sedimentary shorelines and highlights both the positive and negative impact of beach mega-nourishment

Unraveling metastable Markovian open quantum systems

We analyze the dynamics of metastable Markovian open quantum systems by unraveling their average dynamics into stochastic trajectories. We use quantum reset processes as examples to illustrate metastable phenomenology, including a simple three-state model whose metastability is of classical type, and a two-qubit model that features a metastable decoherence-free subspace. In the three-state model, the trajectories exhibit classical metastable phenomenology: fast relaxation into distinct phases and slow transitions between them. This extends the existing correspondence between classical and quantum metastability. It enables the computation of committors for the quantum phases, and the mechanisms of rare transitions between them. For the two-qubit model, the decoherence-free subspace appears in the unraveled trajectories as a slow manifold on which the quantum state has a continuous slow evolution. This provides a classical (nonmetastable) analog of this quantum effect. We discuss the general implications of these results, and we highlight the useful role of quantum reset processes for analysis of quantum trajectories in metastable systems

Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women.

We compared the gut microbial populations in 100 women, from rural Ghana and urban US [50% lean (BMI < 25 kg/m2) and 50% obese (BMI ≥ 30 kg/m2)] to examine the ecological co-occurrence network topology of the gut microbiota as well as the relationship of short chain fatty acids (SCFAs) with obesity. Ghanaians consumed significantly more dietary fiber, had greater microbial alpha-diversity, different beta-diversity, and had a greater concentration of total fecal SCFAs (p-value < 0.002). Lean Ghanaians had significantly greater network density, connectivity and stability than either obese Ghanaians, or lean and obese US participants (false discovery rate (FDR) corrected p-value ≤ 0.01). Bacteroides uniformis was significantly more abundant in lean women, irrespective of country (FDR corrected p < 0.001), while lean Ghanaians had a significantly greater proportion of Ruminococcus callidus, Prevotella copri, and Escherichia coli, and smaller proportions of Lachnospiraceae, Bacteroides and Parabacteroides. Lean Ghanaians had a significantly greater abundance of predicted microbial genes that catalyzed the production of butyric acid via the fermentation of pyruvate or branched amino-acids, while obese Ghanaians and US women (irrespective of BMI) had a significantly greater abundance of predicted microbial genes that encoded for enzymes associated with the fermentation of amino-acids such as alanine, aspartate, lysine and glutamate. Similar to lean Ghanaian women, mice humanized with stool from the lean Ghanaian participant had a significantly lower abundance of family Lachnospiraceae and genus Bacteroides and Parabacteroides, and were resistant to obesity following 6-weeks of high fat feeding (p-value < 0.01). Obesity-resistant mice also showed increased intestinal transcriptional expression of the free fatty acid (Ffa) receptor Ffa2, in spite of similar fecal SCFAs concentrations. We demonstrate that the association between obesity resistance and increased predicted ecological connectivity and stability of the lean Ghanaian microbiota, as well as increased local SCFA receptor level, provides evidence of the importance of robust gut ecologic network in obesity