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At least 775 records · Page 43

Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography

Abstract Wetlands store 20–30% of the world’s soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.

Environmental Sciences & Ecology↗

Growth rate as a link between microbial diversity and soil biogeochemistry

The growth rate of a microorganism is a simple yet profound way to quantify its impact on the world. The absolute growth rate of a microbial population reflects rates of resource assimilation, biomass production, and element transformation, some of the many ways that organisms affect Earth’s ecosystems and climate. Microbial fitness in the environment depends on the ability to reproduce quickly when conditions are favorable and adopt a survival physiology when conditions worsen, which cells coordinate by adjusting their relative growth rate. At the population level, relative growth rate is a sensitive metric of fitness, linking survival and reproduction to the ecology and evolution of populations. Techniques combining ‘omics and stable isotope probing enable sensitive measurements of growth rates of microbial assemblages and individual taxa in soil. Microbial ecologists can explore how the growth rates of taxa with known traits and evolutionary histories respond to changes in resource availability, environmental conditions, and interactions with other organisms. We anticipate that quantitative and scalable data on the growth rates of soil microorganisms, coupled with measurements of biogeochemical fluxes, will allow scientists to test and refine ecological theory and advance process-based models of carbon flux, nutrient uptake, and ecosystem productivity. Finally, measurements of in situ microbial growth rates provide insights into the ecology of populations and can be used to quantitatively link microbial diversity to soil biogeochemistry.

54 ENVIRONMENTAL SCIENCES↗

Forecasting and modeling of the COVID-19 pandemic in the USA with a timed intervention model

We propose a novel Timed Intervention S, P, E, I, Q, R, D model for projecting the possible futures of the COVID-19 pandemic in the USA. The proposed model introduces a series of timed interventions that can account for the influence of real time changes in government policy and social norms. We consider three separate types of interventions: (i) Protective interventions: Where population moves from susceptible to protected corresponding to mask mandates, stay-at-home orders and/or social distancing. (ii) Release interventions: Where population moves from protected to susceptible corresponding to social distancing mandates and practices being lifted by policy or pandemic fatigue. (iii) Vaccination interventions: Where population moves from susceptible, protected, and exposed to recovered (meaning immune) corresponding to the mass immunization of the U.S. Population. By treating the pandemic with timed interventions, we are able to model the pandemic extremely effectively, as well as directly predicting the course of the pandemic under differing sets of intervention schedules. We show that without prompt effective protective/vaccination interventions the pandemic will be extended significantly and result in many millions of deaths in the U.S.

60 APPLIED LIFE SCIENCES↗

Counting generations in birth and death processes with competing Erlang and exponential waiting times

Lymphocyte populations, stimulated in vitro or in vivo, grow as cells divide. Stochastic models are appropriate because some cells undergo multiple rounds of division, some die, and others of the same type in the same conditions do not divide at all. If individual cells behave independently, then each cell can be imagined as sampling from a probability density of times to division and death. The exponential density is the most mathematically and computationally convenient choice. It has the advantage of satisfying the memoryless property, consistent with a Markov process, but it overestimates the probability of short division times. With the aim of preserving the advantages of a Markovian framework while improving the representation of experimentally-observed division times, we consider a multi-stage model of cellular division and death. We use Erlang-distributed (or, more generally, phase-type distributed) times to division, and exponentially distributed times to death. We classify cells into generations, using the rule that the daughters of cells in generation n are in generation n + 1. In some circumstances, our representation is equivalent to established models of lymphocyte dynamics. We find the growth rate of the cell population by calculating the proportions of cells by stage and generation. The exponent describing the late-time cell population growth, and the criterion for extinction of the population, differs from what would be expected if N steps with rate λ were equivalent to a single step of rate λ/N. We link with a published experimental dataset, where cell counts were reported after T cells were transferred to lymphopenic mice, using Approximate Bayesian Computation. In the comparison, the death rate is assumed to be proportional to the generation and the Erlang time to division for generation 0 is allowed to differ from that of subsequent generations. The multi-stage representation is preferred to a simple exponential in posterior distributions, and the mean time to first division is estimated to be longer than the mean time to subsequent divisions.

59 BASIC BIOLOGICAL SCIENCES↗

Gas phase protonated nicotine is a mixture of pyridine- and pyrrolidine-protonated conformers: implications for its native structure in the nicotinic acetylcholine receptor

The infrared (IR) spectra of gas phase protonated nicotine has been measured in the never-before probed N–H “fingerprint region” (3200–3500 cm -1 ). The protonated molecules generated by an electrospray source are thermalized in the first ion trap with water vapor and He gas at a pre-determined temperature prior to being probed by IR spectroscopy in the second ion trap at 4 K. The IR spectra exhibit two N–H stretching bands which are assigned to the pyridine and pyrrolidine protomers with the aid of high-level electronic structure calculations. This finding is in sharp contrast to previous spectroscopic studies that suggested a single population of the pyridine protomer. The relative populations of the two protomers vary by changing the temperature of the thermalizing trap from 180-300 K. The relative conformer populations at 240 K and 300 K are well reproduced by the theoretical calculations, unequivocally determining that gas phase nicotine is a 3 : 2 mixture of both pyridine and pyrrolidine protomers at room temperature. The thermalizing anhydrous vapor does not result in any population change. It rather demonstrates the catalytic role of water in achieving equilibrium between the two protomers. The combination of IR spectroscopy and electronic structure calculations establish the small energy difference between the pyridine and pyrrolidine protomers in nicotine. Finally, one of the gas phase nicotine pyrrolidine protomers has the closest conformational resemblance among all low-lying energy isomers with the X-ray structure of nicotine in the nicotinic acetylcholine receptor (nAChR).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A multifrequency characterization of the extragalactic hard X-ray sky

Context: Nowadays, we know that the origin of the cosmic X-ray background (CXB) is mainly due to the integrated emission of active galactic nuclei. Therefore, in order to obtain a precise estimate of the contribution of different source classes to the CXB, it is crucial to achieve full characterization of the hard-X ray sky. Aims: We present a multifrequency analysis of all sources listed in the third release of the Palermo Swift-BAT hard X-ray catalog (3PBC) with the goal of (i) identifying and classifying the largest number of sources adopting multifrequency criteria, with particular emphasis on extragalactic populations and (ii) extracting sources belonging to the class of Seyfert galaxies to present here the release of the second version of the Turin-SyCAT. Methods: We outline a classification scheme based on radio, infrared (IR), and optical criteria that allows us to distinguish between unidentified and unclassified hard X-ray sources, as well as to classify those sources belonging to the Galactic and the extragalactic populations. Results: Our revised version of the 3PBC lists 1176 classified, 820 extragalactic, and 356 Galactic sources, as well as 199 unclassified and 218 unidentified sources. According to our analysis, the hard X-ray sky is mainly populated by Seyfert galaxies and blazars. For the blazar population, we report trends between the hard X-ray and the gamma-ray emissions based on the fact that a large fraction of them also have a counterpart detected by the Fermi satellite. These trends are all in agreement with the expectations of inverse Compton models which are widely adopted to explain the blazar broadband emission. For the Seyfert galaxies, we present the second version of the Turin-SyCAT, including a total of 633 Seyfert galaxies, with 282 new sources corresponding to an increase of ~80% with respect to the previous release. Comparing the hard X-ray and the infrared emissions of Seyfert galaxies, we confirm that there is no clear difference between the flux distribution of the infrared-to-hard X-ray flux ratio of Seyfert galaxies Type 1 and Type 2. However, there is a significant trend between the mid-IR flux and hard X-ray flux, confirming previous statistical results in the literature. Conclusions: We provide two catalog tables. The first is the revised version of the 3PBC catalog based on our multifrequency analyses. The second catalog table is a release of the second version of the Turin-SyCAT catalog. Finally, we highlight that extensive soft X-ray data are already available in the form of the Swift archive which can be used to search for potential counterparts of unidentified hard X-ray sources. All these datasets will be reduced and analyzed in a forthcoming analysis to determine the precise position of low-energy counterparts in the 0.5–10 keV energy range for 3PBC sources that can be targets of future optical spectroscopic campaigns; this is necessary to obtain their precise classification.

79 ASTRONOMY AND ASTROPHYSICS↗

Deep optical imaging of star-forming blue early-type galaxies: Color map structures and faint features indicative of recent mergers

Blue early-type galaxies with galaxy-scale ongoing star formation are interesting targets in order to understand the stellar mass buildup in elliptical and S0 galaxies in the local Universe. We study the star-forming population of blue early-type galaxies to understand the origin of star formation in these otherwise red and dead stellar systems. The legacy survey imaging data taken with the dark energy camera in the g, r, and z bands for 55 star-forming blue early-type galaxies were examined, and g – r color maps were created. We identified low surface brightness features near 37 galaxies, faint-level interaction signatures near 15 galaxies, and structures indicative of recent merger activity in the optical color maps of all 55 galaxies. These features are not visible in the shallow Sloan Digital Sky Survey imaging data in which these galaxies were originally identified. Low surface brightness features found around galaxies could be remnants of recent merger events. The star-forming population of blue early-type galaxies could be post-merger systems that are expected to be the pathway for the formation of elliptical galaxies. We hypothesize that the star-forming population of blue early-type galaxies is a stage in the evolution of early-type galaxies. The merger features will eventually disappear, fuel for star formation will cease, and the galaxy will move to the passive population of normal early-type galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗

Mobility Gaps between Low-Income and Not Low-Income Households: A Case Study in New York State

Understanding the travel challenges faced by low-income residents has always been and continues to be one of the most important transportation equity topics. This study aims to explore the mobility gaps between low-income households (HHs) and not low-income HHs, and how the gaps vary within different socio-demographic population groups in New York State (NYS). The latest National Household Travel Survey data was used as the primary data source for the analysis. The study first employed the K-prototype clustering algorithm to categorize the HHs in NYS based on their socio-demographic attributes. Five population groups were identified based on nine different household (HH) features such as HH size, vehicle ownership, and elderly status of its members. Then, the mobility differences, measured by trip frequency, trip distance, travel time, and person miles traveled, were examined among the five population groups. Results suggest that the individuals in low-income HHs consistently took fewer trips and made shorter trips compared to their not low-income counterparts in NYS. The travel distance gaps were most obvious among white HHs with more vehicles than drivers. In addition, while the population from low-income HHs made shorter trips on average (2.7 mi shorter per trip), they experienced longer travel time than those from not low-income HHs (1.8 min longer per trip). These key findings provide a deeper understanding of the travel behavior disparities between low-income and not low-income households. The findings could also support policymakers and transportation planners in addressing the critical needs of residents in low-income households in NYS and provide inputs for designing a more equitable transportation system.

Liu, Yuandong↗

Preparation of high orbital angular momentum Rydberg states by optical-millimeter-wave STIRAP

Rydberg states of molecules are intrinsically challenging to study due to the presence of fast non-radiative decay pathways, such as predissociation. However, selectively exciting Rydberg states with values of the orbital angular momentum (ℓ) ℓ ≳ 3 is a productive strategy to minimize this rapid decay and to populate molecular Rydberg states with lifetimes that approach those of atoms. Here, in this proof-of-principle demonstration, we transfer population to an nf Rydberg state of the calcium atom by stimulated Raman adiabatic passage, in which an optical and a millimeter-wave field couple the initial and final states via an intermediate nd Rydberg state. Numerical simulations reproduce the observed time and frequency dependences of the population transfer and suggest the utility of this scheme to populate high-ℓ Rydberg states of molecules.

74 ATOMIC AND MOLECULAR PHYSICS↗

Nonlinear coupling of whistler waves to oblique electrostatic turbulence enabled by cold plasma

Kinetic simulations and theory demonstrate that whistler waves can excite oblique, short-wavelength fluctuations through secondary drift instabilities if a population of sufficiently cold plasma is present. The excited modes lead to heating of the cold populations and damping of the primary whistler waves. The instability threshold depends on the density and temperature of the cold population and can be relatively small if the temperature of the cold population is sufficiently low. Furthermore, this mechanism may thus play a significant role in controlling amplitude of whistlers in the regions of the Earth's magnetosphere where cold background plasma of sufficient density is present.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A quantum trajectory picture of single photon absorption and energy transport in photosystem II

Here, we use quantum trajectory theory to study the dynamics of the first step in photosynthesis for a single photon interacting with photosystem II (PSII). By considering individual trajectories we are able to look beyond the ensemble average dynamics to compute the PSII system evolution conditioned upon individual photon counting measurements. Measurements of the transmitted photon beam strongly affects the system state, since detection of an outgoing photon confirms that the PSII must be in the electronic ground state, while a null measurement implies it is in an excited electronic state. We show that under ideal conditions, observing the null result transforms a state with a low excited state population to a state with nearly all population contained in the excited states. We study the PSII dynamics conditioned on such photon counting for both a pure excitonic model of PSII and a more realistic model with exciton-phonon coupling to a dissipative phononic environment. In the absence of such coupling, we show that the measured fluorescence rates show oscillations constituting a photon-counting witness of excitonic coherence. Excitonic coupling to the phonon environment has a strong effect on the observed rates of fluorescence, damping the oscillations. Addition of non-radiative decay and incoherent transitions to radical pair states in the reaction center to the phononic model allows extraction of a quantum efficiency of 92.5% from the long-time evolution, consistent with bulk experimental measurements.

Coherent states↗

The impact of long-range dispersal on gene surfing

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: Depending on the tail of the dispersal distance distribution, diversity can be either preserved (i.e., many variants survive) or lost (i.e., one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.

59 BASIC BIOLOGICAL SCIENCES↗

Growth instabilities shape morphology and genetic diversity of microbial colonies

Abstract Cellular populations assume an incredible variety of shapes ranging from circular molds to irregular tumors. While we understand many of the mechanisms responsible for these spatial patterns, little is known about how the shape of a population influences its ecology and evolution. Here, we investigate this relationship in the context of microbial colonies grown on hard agar plates. This a well-studied system that exhibits a transition from smooth circular disks to more irregular and rugged shapes as either the nutrient concentration or cellular motility is decreased. Starting from a mechanistic model of colony growth, we identify two dimensionless quantities that determine how morphology and genetic diversity of the population depend on the model parameters. Our simulations further reveal that population dynamics cannot be accurately described by the commonly-used surface growth models. Instead, one has to explicitly account for the emergent growth instabilities and demographic fluctuations. Overall, our work links together environmental conditions, colony morphology, and evolution. This link is essential for a rational design of concrete, biophysical perturbations to steer evolution in the desired direction.

Golden, Alexander↗

Urban morphology and urban water demand: a case study in the land constrained Los Angeles region using urban growth modeling

The interactions between population growth, urban morphology, and water demand have important implications for water resources and supply in urban regions. Water use for irrigation comprises a significant fraction of urban water demand, and is potentially influenced by long-term changes in urban morphology. To investigate this, we used spatially explicit projections of urban land development intensity (fraction impervious area) generated from a 30 m resolution urban growth model for the Los Angeles (LA) region. Recent historical data on water use and high resolution landcover were used to establish relationships between green area, urban development intensity, and outdoor water demand. These relationships were then used to project outdoor and total water demand in 2100 using the urban growth model outputs. We considered two different population scenarios informed by the shared socioeconomic pathway (SSP) projections for the region (SSP3 and SSP5), and three scenarios of urban development intensification. Our analysis is resolved for over 80 water providers in the region, from the urban core to suburban fringe, and highlights diverse demand responses influenced by initial urban form and water demand attributes. Assumptions about outdoor water use factors based on recent water supply data were found to be nearly as influential on future outdoor demand as the urban growth scenario settings. Compared to previous studies, our work is unique in coherently linking high resolution SSP population scenarios, urban land cover evolution, and urban water demand projections, demonstrating the approach for the LA region—the largest population center in the western United States.

54 ENVIRONMENTAL SCIENCES↗

Island of misfit tortoises: waif gopher tortoise health assessment following translocation

Translocation, the intentional movement of animals from one location to another, is a common management practice for the gopher tortoise (Gopherus polyphemus). Although the inadvertent spread of pathogens is a concern with any translocation effort, waif tortoises—individuals that have been collected illegally, injured and rehabilitated or have unknown origins—are generally excluded from translocation efforts due to heightened concerns of introducing pathogens and subsequent disease to naïve populations. However, repurposing these long-lived animals for species recovery is desirable when feasible, and introducing waif tortoises may bolster small populations facing extirpation. The objective of this study was to assess the health of waif tortoises experimentally released at an isolated preserve in Aiken County, SC, USA. Our assessments included visual examination, screening for 14 pathogens using conventional or quantitative polymerase chain reaction (qPCR) and haematological evaluation. Of the 143 individuals assessed in 2017 and 2018, most individuals (76%; n = 109 of 143) had no overt clinical evidence of disease and, when observed, clinical findings were mild. In both years, we detected two known tortoise pathogens, Mycoplasma agassizii and Mycoplasma testudineum, at a prevalence of 10.2–13.9% and 0.0–0.8%, respectively. Additionally, we found emydid Mycoplasma, a bacterium commonly found in box turtles (Terrapene spp.), in a single tortoise that showed no clinical evidence of infection. The presence of nasal discharge was an important, but imperfect, predictor of Mycoplasma spp. infection in translocated tortoises. Hemogram data were comparable with wild populations. Our study is the first comprehensive effort to assess pathogen prevalence and hemogram data of waif gopher tortoises following translocation. Although caution is warranted and pathogen screening necessary, waif tortoises may be an important resource for establishing or augmenting isolated populations when potential health risks can be managed.

60 APPLIED LIFE SCIENCES↗

The predicted properties of helium-enriched globular cluster progenitors at high redshift

Globular cluster progenitors may have been detected by Hubble Space Telescope, and are predicted to be observable with James Webb Space Telescope (JWST) and ground-based extremely large telescopes with adaptive optics. This has the potential to elucidate the issue of globular cluster formation and the origins of significantly helium-enriched subpopulations, a problem in Galactic astronomy with no satisfactory theoretical solution. Given this context, we use model stellar tracks and isochrones to investigate the predicted observational properties of helium-enriched stellar populations in globular cluster progenitors. We find that, relative to helium-normal populations, helium-enriched (ΔY = +0.12) stellar populations similar to those inferred in the most massive globular clusters, are expected, modulo some rapid fluctuations in the first ~30 Myr, to be brighter and redder in the rest frame. At fixed age, stellar mass, and metallicity, a helium-enriched population is predicted to converge to being ~0.40 mag brighter at $\lambda \approx 2.0\, {\mu \rm m}$, and to be 0.30-mag redder in the JWST–NIRCam colour (F070W - F200W), and to actually be fainter for $\lambda \lesssim 0.50 \, {\mu \rm m}$. Separately, we find that the time-integrated shift in ionizing radiation is a negligible $\sim \!5{{\ \rm per\ cent}}$, though we show that the Lyman-α escape fraction could end up higher for helium-enriched stars.

79 ASTRONOMY AND ASTROPHYSICS↗

Unveiling the star formation history of the Upper Scorpius association through its kinematics

ABSTRACT Stellar associations can be discerned as overdensities of sources not only in the physical space but also in the velocity space. The common motion of their members, gradually eroded by the galactic tidal field, is partially reminiscent of the initial kinematic structure. Using recent data from Gaia EDR3, combined with radial velocities from GALAH and APOGEE, we traced back the present positions of stars belonging to Upper Scorpius (USCO), a subgroup of Scorpius–Centaurus, the nearest OB association. About one half of the subgroup (the ‘clustered’ population) appears composed of many smaller entities, which were in a more compact configuration in the past. The presence of a kinematic duality is reflected into an age spread between this younger clustered population and an older diffuse population, in turn confirmed by a different fraction fD of disc-bearing stars (fD = 0.24 ± 0.02 versus fD = 0.10 ± 0.01). Star formation in USCO appears to have lasted more than 10 Myr and proceeded in small groups that, after a few Myr, dissolve in the field of the older population but retain for some time memory of their initial structure. The difference of ages inferred through isochrones and kinematics, in this regard, could provide a powerful tool to quantify the time-scale of gas removal.

79 ASTRONOMY AND ASTROPHYSICS↗

The distribution of [α/Fe] in the Milky Way disc

ABSTRACT Using a sample of red giant stars from the Apache Point Observatory Galactic Evolution Experiment (APOGEE) Data Release 16, we infer the conditional distribution $p([\alpha /{\rm Fe}]\, |\, [{\rm Fe}/{\rm H}])$ in the Milky Way disk for the α-elements Mg, O, Si, S, and Ca. In each bin of [Fe/H] and Galactocentric radius R, we model p([α/Fe]) as a sum of two Gaussians, representing ‘low-α’ and ‘high-α’ populations with scale heights $z_1=0.45\, {\rm kpc}$ and $z_2=0.95\, {\rm kpc}$, respectively. By accounting for age-dependent and z-dependent selection effects in APOGEE, we infer the [α/Fe] distributions that would be found for a fair sample of long-lived stars covering all z. Near the Solar circle, this distribution is bimodal at sub-solar [Fe/H], with the low-α and high-α peaks clearly separated by a minimum at intermediate [α/Fe]. In agreement with previous results, we find that the high-α population is more prominent at smaller R, lower [Fe/H], and larger |z|, and that the sequence separation is smaller for Si and Ca than for Mg, O, and S. We find significant intrinsic scatter in [α/Fe] at fixed [Fe/H] for both the low-α and high-α populations, typically ∼0.04-dex. The means, dispersions, and relative amplitudes of this two-Gaussian description, and the dependence of these parameters on R, [Fe/H], and α-element, provide a quantitative target for chemical evolution models and a test for hydrodynamic simulations of disk galaxy formation. We argue that explaining the observed bimodality will probably require one or more sharp transitions in the disk’s gas accretion, star formation, or outflow history in addition to radial mixing of stellar populations.

79 ASTRONOMY AND ASTROPHYSICS↗