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Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a

Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on microbial communities in CCB, a mesocosm experiment was implemented in a stoichiometrically imbalanced pond, Lagunita, which has an average TN:TP ratio of 122 (atomic). The experiment had four treatments, each with five spatial replicates – unamended controls and three fertilization treatments with different nitrogen:phosphorus (N:P) regimes (P only, N:P = 16 and N:P = 75 by atoms). In the water column, quantitative PCR of the 16S rRNA gene indicated that P enrichment alone favored proliferation of bacterial taxa with high rRNA gene copy number, consistent with a previously hypothesized but untested connection between rRNA gene copy number and P requirement. Bacterial and microbial eukaryotic community structure was investigated by pyrosequencing of 16S and 18S rRNA genes from the planktonic and surficial sediment samples. Nutrient enrichment shifted the composition of the planktonic community in a treatment-specific manner and promoted the growth of previously rare bacterial taxa at the expense of the more abundant, potentially endemic, taxa. The eukaryotic community was highly enriched with phototrophic populations in the fertilized treatment. The sediment microbial community exhibited high beta diversity among replicates within treatments, which obscured any changes due to fertilization. Overall, these results showed that nutrient stoichiometry can be an important factor in shaping microbial community structure.

ContributorsLee, Zarraz (Author) / Poret-Peterson, Amisha (Author) / Siefert, Janet L. (Author) / Kaul, Drishti (Author) / Moustafa, Ahmed (Author) / Allen, Andrew E. (Author) / Dupont, Chris L. (Author) / Eguiarte, Luis E. (Author) / Souza, Valeria (Author) / Elser, James (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / School of Earth and Space Exploration (Contributor)
Created2017-05-30
Description

Cell-sediment separation methods can potentially enable determination of the elemental composition of microbial communities by removing the sediment elemental contribution from bulk samples. We demonstrate that a separation method can be applied to determine the composition of prokaryotic cells. The method uses chemical and physical means to extract cells from

Cell-sediment separation methods can potentially enable determination of the elemental composition of microbial communities by removing the sediment elemental contribution from bulk samples. We demonstrate that a separation method can be applied to determine the composition of prokaryotic cells. The method uses chemical and physical means to extract cells from benthic sediments and mats. Recovery yields were between 5% and 40%, as determined from cell counts. The method conserves cellular element contents to within 30% or better, as assessed by comparing C, N, P, Mg, Al, Ca, Ti, Mn, Fe, Ni, Cu, Zn, and Mo contents in Escherichia coli. Contamination by C, N, and P from chemicals used during the procedure was negligible. Na and K were not conserved, being likely exchanged through the cell membrane as cations during separation. V, Cr, and Co abundances could not be determined due to large (>100%) measurement uncertainties. We applied this method to measure elemental contents in extremophilic communities of Yellowstone National Park hot springs. The method was generally successful at separating cells from sediment, but does not discriminate between cells and detrital biological or noncellular material of similar density. This resulted in Al, Ti, Mn, and Fe contamination, which can be tracked using proxies such as metal:Al ratios. With these caveats, we present the first measurements, to our knowledge, of the elemental abundances of a chemosynthetic community. The communities have C:N ratios typical of aquatic microorganisms, are low in P, and their metal abundances vary between hot springs by orders of magnitude.

ContributorsNeveu, Marc (Author) / Poret-Peterson, Amisha (Author) / Lee, Zarraz (Author) / Anbar, Ariel (Author) / Elser, James (Author) / College of Liberal Arts and Sciences (Contributor) / School of Earth and Space Exploration (Contributor) / School of Life Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor)
Created2014-07-01
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Description
Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory,

Open-ended evolution (OEE) is relevant to a variety of biological, artificial and technological systems, but has been challenging to reproduce in silico. Most theoretical efforts focus on key aspects of open-ended evolution as it appears in biology. We recast the problem as a more general one in dynamical systems theory, providing simple criteria for open-ended evolution based on two hallmark features: unbounded evolution and innovation. We define unbounded evolution as patterns that are non-repeating within the expected Poincare recurrence time of an isolated system, and innovation as trajectories not observed in isolated systems. As a case study, we implement novel variants of cellular automata (CA) where the update rules are allowed to vary with time in three alternative ways. Each is capable of generating conditions for open-ended evolution, but vary in their ability to do so. We find that state-dependent dynamics, regarded as a hallmark of life, statistically out-performs other candidate mechanisms, and is the only mechanism to produce open-ended evolution in a scalable manner, essential to the notion of ongoing evolution. This analysis suggests a new framework for unifying mechanisms for generating OEE with features distinctive to life and its artifacts, with broad applicability to biological and artificial systems.
Created2017-04-20
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Description

Cataclysmic Variables (CVs) are close binary star systems with one component a white dwarf (WD) and the other a larger cooler star that fills its Roche Lobe. The cooler star is losing mass through the inner Lagrangian point of the binary and some unknown fraction of this material is accreted

Cataclysmic Variables (CVs) are close binary star systems with one component a white dwarf (WD) and the other a larger cooler star that fills its Roche Lobe. The cooler star is losing mass through the inner Lagrangian point of the binary and some unknown fraction of this material is accreted by the WD. One consequence of the WDs accreting material, is the possibility that they are growing in mass and will eventually reach the Chandrasekhar Limit. This evolution could result in a Supernova Ia (SN Ia) explosion and is designated the Single Degenerate Progenitor (SD) scenario. This paper is concerned with the SD scenario for SN Ia progenitors. One problem with the single degenerate scenario is that it is generally assumed that the accreting material mixes with WD core material at some time during the accretion phase of evolution and, since the typical WD has a carbon-oxygen CO core, the mixing results in large amounts of carbon and oxygen being brought up into the accreted layers. The presence of enriched carbon causes enhanced nuclear fusion and a Classical Nova explosion.

Both observations and theoretical studies of these explosions imply that more mass is ejected than is accreted. Thus, the WD in a Classical Nova system is losing mass and cannot be a SN Ia progenitor. However, the composition in the nuclear burning region is important and, in new calculations reported here, the consequences to the WD of no mixing of accreted material with core material have been investigated so that the material involved in the explosion has only a Solar composition. WDs with a large range in initial masses and mass accretion rates have been evolved. I find that once sufficient material has been accreted, nuclear burning occurs in all evolutionary sequences and continues until a thermonuclear runaway (TNR) occurs and the WD either ejects a small amount of material or its radius grows to about 10[superscript 12] cm and the evolution is ended. In all cases where mass ejection occurs, the mass of the ejecta is far less than the mass of the accreted material. Therefore, all the WDs are growing in mass. It is also found that the accretion time to explosion can be sufficiently short for a 1.0M[subscript ⊙] WD that recurrent novae can occur on a low mass WD. This mass is lower than typically assumed for the WDs in recurrent nova systems. Finally, the predicted surface temperatures when the WD is near the peak of the explosion imply that only the most massive WDs will be significant X-ray emitters at this time.

Created2014-02-25
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Description

The occurrence of nonliquid and liquid physical states of submicron atmospheric particulate matter (PM) downwind of an urban region in central Amazonia was investigated. Measurements were conducted during two intensive operating periods (IOP1 and IOP2) that took place during the wet and dry seasons of the GoAmazon2014/5 campaign. Air masses

The occurrence of nonliquid and liquid physical states of submicron atmospheric particulate matter (PM) downwind of an urban region in central Amazonia was investigated. Measurements were conducted during two intensive operating periods (IOP1 and IOP2) that took place during the wet and dry seasons of the GoAmazon2014/5 campaign. Air masses representing variable influences of background conditions, urban pollution, and regional- and continental-scale biomass burning passed over the research site. As the air masses varied, particle rebound fraction, an indicator of physical state, was measured in real time at ground level using an impactor apparatus. Micrographs collected by transmission electron microscopy confirmed that liquid particles adhered, while nonliquid particles rebounded. Relative humidity (RH) was scanned to collect rebound curves.

When the apparatus RH matched ambient RH, 95 % of the particles adhered as a campaign average. Secondary organic material, produced for the most part by the oxidation of volatile organic compounds emitted from the forest, produces liquid PM over this tropical forest. During periods of anthropogenic influence, by comparison, the rebound fraction dropped to as low as 60 % at 95 % RH. Analyses of the mass spectra of the atmospheric PM by positive-matrix factorization (PMF) and of concentrations of carbon monoxide, total particle number, and oxides of nitrogen were used to identify time periods affected by anthropogenic influences, including both urban pollution and biomass burning. The occurrence of nonliquid PM at high RH correlated with these indicators of anthropogenic influence. A linear model having as output the rebound fraction and as input the PMF factor loadings explained up to 70 % of the variance in the observed rebound fractions. Anthropogenic influences can contribute to the presence of nonliquid PM in the atmospheric particle population through the combined effects of molecular species that increase viscosity when internally mixed with background PM and increased concentrations of nonliquid anthropogenic particles in external mixtures of anthropogenic and biogenic PM.

ContributorsBateman, Adam P. (Author) / Gong, Zhaoheng (Author) / Harder, Tristan H. (Author) / de Sa, Suzane S. (Author) / Wang, Bingbing (Author) / Castillo, Paulo (Author) / China, Swarup (Author) / Liu, Yingjun (Author) / O'Brien, Rachel E. (Author) / Palm, Brett B. (Author) / Shiu, Hung-Wei (Author) / Cirino, Glauber G. (Author) / Thalman, Ryan (Author) / Adachi, Kouji (Author) / Alexander, M. Lizabeth (Author) / Artaxo, Paulo (Author) / Bertram, Allan K. (Author) / Buseck, Peter (Author) / Gilles, Mary K. (Author) / Jimenez, Jose L. (Author) / Laskin, Alexander (Author) / Manzi, Antonio O. (Author) / Sedlacek, Arthur (Author) / Souza, Rodrigo A. F. (Author) / Wang, Jian (Author) / Zaveri, Rahul (Author) / Martin, Scot T. (Author) / College of Liberal Arts and Sciences (Contributor) / School of Earth and Space Exploration (Contributor) / School of Molecular Sciences (Contributor)
Created2017-02-06
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Description
A major conceptual step forward in understanding the logical architecture of living systems was advanced by von Neumann with his universal constructor, a physical device capable of self-reproduction. A necessary condition for a universal constructor to exist is that the laws of physics permit physical universality, such that any transformation

A major conceptual step forward in understanding the logical architecture of living systems was advanced by von Neumann with his universal constructor, a physical device capable of self-reproduction. A necessary condition for a universal constructor to exist is that the laws of physics permit physical universality, such that any transformation (consistent with the laws of physics and availability of resources) can be caused to occur. While physical universality has been demonstrated in simple cellular automata models, so far these have not displayed a requisite feature of life—namely open-ended evolution—the explanation of which was also a prime motivator in von Neumann’s formulation of a universal constructor. Current examples of physical universality rely on reversible dynamical laws, whereas it is well-known that living processes are dissipative. Here we show that physical universality and open-ended dynamics should both be possible in irreversible dynamical systems if one entertains the possibility of state-dependent laws. We demonstrate with simple toy models how the accessibility of state space can yield open-ended trajectories, defined as trajectories that do not repeat within the expected Poincaré recurrence time and are not reproducible by an isolated system. We discuss implications for physical universality, or an approximation to it, as a foundational framework for developing a physics for life.
Created2017-09-01
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Description
Cuatro Ciénegas Basin (CCB) is a desert ecosystem that hosts a large diversity of water bodies. Many surface waters in this basin have imbalanced nitrogen (N) to phosphorus (P) stoichiometry (total N:P > 100 by atoms), where P is likely to be a limiting nutrient. To investigate the effects of

Cuatro Ciénegas Basin (CCB) is a desert ecosystem that hosts a large diversity of water bodies. Many surface waters in this basin have imbalanced nitrogen (N) to phosphorus (P) stoichiometry (total N:P > 100 by atoms), where P is likely to be a limiting nutrient. To investigate the effects of nutrient stoichiometry on planktonic and sediment ecosystem components and processes, we conducted a replicated in situ mesocosm experiment in Lagunita, a shallow pond located in the southwest region of the basin. Inorganic N and P were periodically added to mesocosms under three different N:P regimes (P only, N:P = 16 and N:P = 75) while the control mesocosms were left unamended. After three weeks of fertilization, more than two thirds of the applied P was immobilized into seston or sediment. The rapid uptake of P significantly decreased biomass C:P and N:P ratios, supporting the hypothesis that Lagunita is P-limited. Meanwhile, simultaneous N and P enrichment significantly enhanced planktonic growth, increasing total planktonic biomass by more than 2-fold compared to the unenriched control. With up to 76% of added N sequestered into the seston, it is suspected that the Lagunita microbial community also experienced strong N-limitation. However, when N and P were applied at N:P = 75, the microbes remained in a P-limitation state as in the untreated control. Two weeks after the last fertilizer application, seston C:P and N:P ratios returned to initial levels but chlorophyll a and seston C concentrations remained elevated. Additionally, no P release from the sediment was observed in the fertilized mesocosms. Overall, this study provides evidence that Lagunita is highly sensitive to nutrient perturbation because the biota is primarily P-limited and experiences a secondary N-limitation despite its high TN:TP ratio. This study serves as a strong basis to justify the need for protection of CCB ecosystems and other low-nutrient microbe-dominated systems from anthropogenic inputs of both N and P.
ContributorsLee, Zarraz (Author) / Steger, Laura (Author) / Corman, Jessica (Author) / Neveu, Marc (Author) / Poret-Peterson, Amisha (Author) / Souza, Valeria (Author) / Elser, James (Author) / College of Liberal Arts and Sciences (Contributor) / School of Life Sciences (Contributor) / School of Earth and Space Exploration (Contributor)
Created2015-04-16
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Description
The unusual physical properties and formation conditions attributed to h-, i-, m-, and n-nanodiamond polymorphs has resulted in their receiving much attention in the materials and planetary science literature. Their identification is based on diffraction features that are absent in ordinary cubic (c-) diamond (space group: Fd-3m). We show, using

The unusual physical properties and formation conditions attributed to h-, i-, m-, and n-nanodiamond polymorphs has resulted in their receiving much attention in the materials and planetary science literature. Their identification is based on diffraction features that are absent in ordinary cubic (c-) diamond (space group: Fd-3m). We show, using ultra-high-resolution transmission electron microscope (HRTEM) images of natural and synthetic nanodiamonds, that the diffraction features attributed to the reported polymorphs are consistent with c-diamond containing abundant defects. Combinations of {113} reflection and <011> rotation twins produce HRTEM images and d-spacings that match those attributed to h-, i-, and m-diamond. The diagnostic features of n-diamond in TEM images can arise from thickness effects of c-diamonds. Our data and interpretations strongly suggest that the reported nanodiamond polymorphs are in fact twinned c-diamond. We also report a new type of twin (<121> rotational), which can give rise to grains with dodecagonal symmetry. Our results show that twins are widespread in diamond nanocrystals. A high density of twins could strongly influence their applications.
ContributorsNemeth, Peter (Author) / Garvie, Laurence (Author) / Buseck, Peter (Author) / College of Liberal Arts and Sciences (Contributor) / School of Earth and Space Exploration (Contributor) / Center for Meteorite Studies (Contributor)
Created2015-12-16
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Description
The unified model of active galactic nuclei (AGNs) has provided a successful explanation for the observed diversity of AGNs in the local universe. However, recent analysis of multi-wavelength spectral and image data suggests that the unified model is only a partial theory of AGNs, and may need to be augmented

The unified model of active galactic nuclei (AGNs) has provided a successful explanation for the observed diversity of AGNs in the local universe. However, recent analysis of multi-wavelength spectral and image data suggests that the unified model is only a partial theory of AGNs, and may need to be augmented to remain consistent with all observations. Recent studies using high spatial resolution ground-and space-based observations of local AGNs show that Seyfert class and the "core" (r less than or similar to 1 kpc) host-galaxy morphology are correlated. Currently, this relationship has only been established qualitatively, by visual inspection of the core morphologies of low-redshift (z < 0.035) Seyfert host galaxies. We re-establish this empirical relationship in Hubble Space Telescope optical imaging by visual inspection of a catalog of 85 local (D < 63 Mpc) Seyfert galaxies. We also attempt to re-establish the core morphology-Seyfert class relationship using an automated, non-parametric technique that combines both existing classification parameter methods (the adapted CAS and G-M-20) and a new method which implements the Source Extractor software for feature detection in unsharp-mask images. This new method is designed explicitly to detect dust features in the images. We use our automated approach to classify the morphology of the AGN cores and determine that Sy2 galaxies visually appear, on average, to have more dust features than Sy1. With the exception of this "dustiness" however, we do not measure a strong correlation between the dust morphology and the Seyfert class of the host galaxy using quantitative techniques. We discuss the implications of these results in the context of the unified model.
ContributorsRutkowski, Michael (Author) / Hegel, P. R. (Author) / Kim, Hwihyun (Author) / Windhorst, Rogier (Author) / Tamura, Kazuyuki (Author) / College of Liberal Arts and Sciences (Contributor) / School of Earth and Space Exploration (Contributor)
Created2013-10-28
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Description
Quantum weak measurements with states both pre- and post-selected offer a window into a hitherto neglected sector of quantum mechanics. A class of such systems involves time dependent evolution with transitions possible. In this paper we explore two very simple systems in this class. The first is a toy model

Quantum weak measurements with states both pre- and post-selected offer a window into a hitherto neglected sector of quantum mechanics. A class of such systems involves time dependent evolution with transitions possible. In this paper we explore two very simple systems in this class. The first is a toy model representing the decay of an excited atom. The second is the tunneling of a particle through a barrier. The post-selection criteria are chosen as follows: at the final time, the atom remains in its initial excited state for the first example and the particle remains behind the barrier for the second. We then ask what weak values are predicted in the physical environment of the atom (to which no net energy has been transferred) and in the region beyond the barrier (to which the particle has not tunneled). Thus, just as the dog that didn't bark in Arthur Conan Doyle's story Silver Blaze gave Sherlock Holmes meaningful information about the dog's non-canine environment, here we probe whether the particle that has not decayed or has not tunneled can provide measurable information about physical changes in the environment. Previous work suggests that very large weak values might arise in these regions for long durations between pre- and post-selection times. Our calculations reveal some distinct differences between the two model systems.
Created2014-06-13