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At least 19 records

Species-specific ribosomal RNA-FISH identifies interspecies cellular-material exchange, active-cell population dynamics and cellular localization of translation machinery in clostridial cultures and co-cultures

ABSTRACT The development of synthetic microbial consortia in recent years has revealed that complex interspecies interactions, notably the exchange of cytoplasmic material, exist even among organisms that originate from different ecological niches. Although morphogenetic characteristics, viable RNA and protein dyes, and fluorescent reporter proteins have played an essential role in exploring such interactions, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to further investigate interactions in synthetic or semisynthetic consortia. Despite its maturity, several challenges exist in using rRNA-FISH as a tool to quantify individual species population dynamics and interspecies interactions using high-throughput instrumentation such as flow cytometry. In this work, we resolve such challenges and apply rRNA-FISH to double and triple co-cultures of Clostridium acetobutylicum, Clostridium ljungdahlii, and Clostridium kluyveri . In pursuing our goal to capture each organism’s population dynamics, we demonstrate dynamic rRNA, and thus ribosome, exchange between the three species leading to the formation of hybrid cells. We also characterize the localization patterns of the translation machinery in the three species, identifying distinct, dynamic localization patterns among them. Our data also support the use of rRNA-FISH to assess the culture’s health and expansion potential, and, here again, our data find surprising differences among the three species examined. Taken together, our study argues for rRNA-FISH as a valuable and accessible tool for quantitative exploration of interspecies interactions, especially in organisms which cannot be genetically engineered or in consortia where selective pressures to maintain recombinant species cannot be used. IMPORTANCE Though dyes and fluorescent reporter proteins have played an essential role in identifying microbial species in co-cultures, we hypothesized that ribosomal RNA-fluorescence in situ hybridization (rRNA-FISH) could be adapted and applied to quantitatively probe complex interactions between organisms in synthetic consortia. Despite its maturity, several challenges existed before rRNA-FISH could be used to study Clostridium co-cultures of interest. First, species-specific probes for Clostridium acetobutylicum and Clostridium ljungdahlii had not been developed. Second, “state-of-the-art” labeling protocols were tedious and often resulted in sample loss. Third, it was unclear if FISH was compatible with existing fluorescent reporter proteins. We resolved these key challenges and applied the technique to co-cultures of C. acetobutylicum , C. ljungdahlii , and Clostridium kluyveri . We demonstrate that rRNA-FISH is capable of identifying rRNA/ribosome exchange between the three organisms and characterized rRNA localization patterns in each. In combination with flow cytometry, rRNA-FISH can capture sub-population dynamics in co-cultures.

Hill, John D.

Host population dynamics influence Leptospira spp. transmission patterns among Rattus norvegicus in Boston, Massachusetts, US

Leptospirosis (caused by pathogenic bacteria in the genus Leptospira ) is prevalent worldwide but more common in tropical and subtropical regions. Transmission can occur following direct exposure to infected urine from reservoir hosts, or a urine-contaminated environment, which then can serve as an infection source for additional rats and other mammals, including humans. The brown rat, Rattus norvegicus , is an important reservoir of Leptospira spp. in urban settings. We investigated the presence of Leptospira spp. among brown rats in Boston, Massachusetts and hypothesized that rat population dynamics in this urban setting influence the transportation, persistence, and diversity of Leptospira spp. We analyzed DNA from 328 rat kidney samples collected from 17 sites in Boston over a seven-year period (2016–2022); 59 rats representing 12 of 17 sites were positive for Leptospira spp. We used 21 neutral microsatellite loci to genotype 311 rats and utilized the resulting data to investigate genetic connectivity among sampling sites. We generated whole genome sequences for 28 Leptospira spp. isolates obtained from frozen and fresh tissue from some of the 59 positive rat kidneys. When isolates were not obtained, we attempted genomic DNA capture and enrichment, which yielded 14 additional Leptospira spp. genomes from rats. We also generated an enriched Leptospira spp. genome from a 2018 human case in Boston. We found evidence of high genetic structure among rat populations that is likely influenced by major roads and/or other dispersal barriers, resulting in distinct rat population groups within the city; at certain sites these groups persisted for multiple years. We identified multiple distinct phylogenetic clades of L. interrogans among rats that were tightly linked to distinct rat populations. This pattern suggests L. interrogans persists in local rat populations and its transportation is influenced by rat population dynamics. Finally, our genomic analyses of the Leptospira spp. detected in the 2018 human leptospirosis case in Boston suggests a link to rats as the source. These findings will be useful for guiding rat control and human leptospirosis mitigation efforts in this and other similar urban settings.

Stone, Nathan E.

Galactic civilizations - Population dynamics and interstellar diffusion

A model is developed of the interstellar diffusion of galactic civilizations which takes into account the population dynamics of such civilizations. The problem is formulated in terms of potential theory, with a family of nonlinear partial differential and difference equations specifying population growth and diffusion for an organism with advantageous genes that undergoes random dispersal while increasing in population locally, and a population at zero population growth. In the case of nonlinear diffusion with growth and saturation, it is found that the colonization wavefront from the nearest independently arisen galactic civilization can have reached the earth only if its lifetime exceeds 2.6 million years, or 20 million years if discretization can be neglected. For zero population growth, the corresponding lifetime is 13 billion years. It is concluded that the earth is uncolonized not because interstellar spacefaring civilizations are rare, but because there are too many worlds to be colonized in the plausible colonization lifetime of nearby civilizations, and that there exist no very old galactic civilizations with a consistent policy of the conquest of inhabited worlds.

Newman, W. I.

Second Cancers After Fractionated Radiotherapy: Stochastic Population Dynamics Effects

When ionizing radiation is used in cancer therapy it can induce second cancers in nearby organs. Mainly due to longer patient survival times, these second cancers have become of increasing concern. Estimating the risk of solid second cancers involves modeling: because of long latency times, available data is usually for older, obsolescent treatment regimens. Moreover, modeling second cancers gives unique insights into human carcinogenesis, since the therapy involves administering well characterized doses of a well studied carcinogen, followed by long-term monitoring. In addition to putative radiation initiation that produces pre-malignant cells, inactivation (i.e. cell killing), and subsequent cell repopulation by proliferation can be important at the doses relevant to second cancer situations. A recent initiation/inactivation/proliferation (IIP) model characterized quantitatively the observed occurrence of second breast and lung cancers, using a deterministic cell population dynamics approach. To analyze ifradiation-initiated pre-malignant clones become extinct before full repopulation can occur, we here give a stochastic version of this I I model. Combining Monte Carlo simulations with standard solutions for time-inhomogeneous birth-death equations, we show that repeated cycles of inactivation and repopulation, as occur during fractionated radiation therapy, can lead to distributions of pre-malignant cells per patient with variance >> mean, even when pre-malignant clones are Poisson-distributed. Thus fewer patients would be affected, but with a higher probability, than a deterministic model, tracking average pre-malignant cell numbers, would predict. Our results are applied to data on breast cancers after radiotherapy for Hodgkin disease. The stochastic IIP analysis, unlike the deterministic one, indicates: a) initiated, pre-malignant cells can have a growth advantage during repopulation, not just during the longer tumor latency period that follows; b) weekend treatment gaps during radiotherapy, apart from decreasing the probability of eradicating the primary cancer, substantially increase the risk of later second cancers.

Sachs, Rainer K.

Population dynamics of transgenic strain Escherichia coli Z905/pPHL7 in freshwater and saline lake water microcosms with differing microbial community structures

Populations of Escherichia coli Z905/pPHL7, a transgenic microorganism, were heterogenic in the expression of plasmid genes when adapting to the conditions of water microcosms of various mineralization levels and structure of microbial community. This TM has formed two subpopulations (ampicillin-resistant and ampicillin-sensitive) in every microcosm. Irrespective of mineralization level of a microcosm, when E. coli Z905/pPHL7 alone was introduced, the ampicillin-resistant subpopulation prevailed, while introduction of the TM together with indigenous bacteria led to the dominance of the ampicillin-sensitive subpopulation. A high level of lux gene expression maintained longer in the freshwater microcosms than in sterile saline lake water microcosms. A horizontal gene transfer has been revealed between the jointly introduced TM and Micrococcus sp. 9/pSH1 in microcosms with the Lake Shira sterile water. c2005 COSPAR. Published by Elsevier Ltd. All rights reserved.

Ecosystem

Population dynamics during cell proliferation and neuronogenesis in the developing murine neocortex

During the development of the neocortex, cell proliferation occurs in two specialized zones adjacent to the lateral ventricle. One of these zones, the ventricular zone, produces most of the neurons of the neocortex. The proliferating population that resides in the ventricular zone is a pseudostratified ventricular epithelium (PVE) that looks uniform in routine histological preparations, but is, in fact, an active and dynamically changing population. In the mouse, over the course of a 6-day period, the PVE produces approximately 95% of the neurons of the adult neocortex. During this time, the cell cycle of the PVE population lengthens from about 8 h to over 18 h and the progenitor population passes through a total of 11 cell cycles. This 6-day, 11-cell cycle period comprises the "neuronogenetic interval" (NI). At each passage through the cell cycle, the proportion of daughter cells that exit the cell cycle (Q cells) increases from 0 at the onset of the NI to 1 at the end of the NI. The proportion of daughter cells that re-enter the cell cycle (P cells) changes in a complementary fashion from 1 at the onset of the NI to 0 at the end of the NI. This set of systematic changes in the cell cycle and the output from the proliferative population of the PVE allows a quantitative and mathematical treatment of the expansion of the PVE and the growth of the cortical plate that nicely accounts for the observed expansion and growth of the developing neocortex. In addition, we show that the cells produced during a 2-h window of development during specific cell cycles reside in a specific set of laminae in the adult cortex, but that the distributions of the output from consecutive cell cycles overlap. These dynamic events occur in all areas of the PVE underlying the neocortex, but there is a gradient of maturation that begins in the rostrolateral neocortex near the striatotelencephalic junction and which spreads across the surface of the neocortex over a period of 24-36 h. The presence of the gradient across the hemisphere is a possible source of positional information that could be exploited during development to establish the areal borders that characterize the adult neocortex.

Non-NASA Center

Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts

Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning to be incorporated into predictive modeling, high-frequency ocean virus dynamics remain understudied due to methodological challenges. Here we sampled stratified Bermuda Atlantic Time Series (BATS) waters for 112 hours at sub-daily 4- (surface) or 12- (deep chlorophyll maximum) hour intervals, purified viral particles from these samples, sequenced their metagenomes, and used the resulting data to characterize high-frequency virus community dynamics. Aggregated community diversity metrics changed with depth, but were not statistically significant temporally at a fixed location. However, finer-scale population-level analyses revealed both depth and temporal change, including physicochemical depth-driven differences and, in surface waters, thousands of viral populations that exhibited statistically significant diel rhythms. Statistical analyses revealed three main archetypes of temporal dynamics that themselves differed in abundance patterns, host predictions, viral taxonomy, and gene functions. Among these, highlights include viruses resembling an archetype with a night peaking pattern in activity that include an over-representation of viruses that putatively infect Prochlorococcus, a phototrophic cyanobacteria. Together, these efforts provide baseline community- and population-scale short-time-frame observations relevant to future climate state modeling.

Carrillo, Alfonso [The Ohio State University, Colu

Galactic civilizations: Population dynamics and interstellar diffusion

The interstellar diffusion of galactic civilizations is reexamined by potential theory; both numerical and analytical solutions are derived for the nonlinear partial differential equations which specify a range of relevant models, drawn from blast wave physics, soil science, and, especially, population biology. An essential feature of these models is that, for all civilizations, population growth must be limited by the carrying capacity of the environment. Dispersal is fundamentally a diffusion process; a density-dependent diffusivity describes interstellar emigration. Two models are considered: the first describing zero population growth (ZPG), and the second which also includes local growth and saturation of a planetary population, and for which an asymptotic traveling wave solution is found.

Newman, W. I.

Remotely Sensing Larval Population Dynamics of Rice Field Anophelines

The primary objective of both studies was to determine if RS and GIS techniques could be used to distinguish between high and low larval-producing rice fields in California. Results of the first study suggested that early-season green-up and proximity to livestock pastures were positively correlated with high larval abundance. Based on the early-season spectral differences between high and low larval-producing fields, it appeared that canopy development and tillering influenced mosquito habitat quality. At that time, rice fields consisted of a mixture of plants and water, a combination that allowed An. freeborni females to lay eggs in partial sunlight, protected from both predators and wind. This established a population earlier in the season than in other, 'less-green' fields where tillering and plant emergence was too minimal for ovipositioning. The study also indicated the importance of the distance that a mosquito would have to fly in order to take a bloodmeal prior to ovipositing. These associations were fully explored in an expanded study two years later. The second study confirmed the positive relationship between early season canopy development and larval abundance, and also demonstrated the relationship between abundance and distance-to-pasture. The association between greenness (as measured using NDVI), distance-to-pasture, and abundance is illustrated. The second study also indicated the siginificance of the landscape context of rice fields for larval production. Fields that included opportunities for feeding and resting within the flight range of the mosquito had higher abundances than did fields that were in a homogeneous rice area.

Beck, Louisa R.

Dynamic population balance in molecular-level simulations of hypersonic flows

This report summarizes the work towards developing stochastic weighted particle methods (SWPM) for future application in hypersonic flows. Extensive changes to Sandia’s direct simulation Monte Carlo (DSMC) solver, SPARTA (Stochastic Particle Real Time Analyzer), were made to enable the necessary particle splitting and reduction capabilities for SWPM. The results from one-dimensional Couette and Fourier flows suggest that SWPM can reproduce the correct transport for a large range of Knudsen numbers with adequate accuracy. The associated velocity and temperature profiles are in good agreement with DSMC. An issue with particle placement during particle number reduction, is identified, to which, a simple but effective solution based on minimizing the center of mass error is proposed. High Mach wheel flows are simulated using the SWPM and DSMC methods. SWPM is capable of providing nearly an order of magnitude increase in efficiency over DSMC while retaining high accuracy.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

New Species of Fire Discovered: Fingering Flamelets Form a Dynamic Population

Poets and artists have long used fire as a metaphor for life. At the NASA Glenn Research Center, recent experiments in a subcritical Rayleigh number flow channel demonstrated that this analogy holds up surprisingly well when tools developed to characterize a biological population are applied to a class of fire that occurs in near-extinction, weakly convective environments (such as microgravity) or in vertically confined spaces (such as our apparatus). Under these conditions, the flame breaks into numerous 'flamelets" that form a Turing-type reaction-diffusion fingering pattern as they spread across the fuel. It is standard practice on U.S. spacecraft for the astronaut crew to turn off the ventilation to help extinguish a fire, both to eliminate the fresh oxygen supply and to reduce the distribution of the smoke. When crew members think that the fire is fully extinguished, they reactivate the ventilation system to clear the smoke. However, some flamelets can survive, and our experiments have demonstrated that flamelets quickly grow into a large fire when ventilation increases.

Olson, Sandra L.

Ultrafast population and structural dynamics of a Ni-bipyridine photoredox catalyst reveal a significant deactivation pathway

The ultrafast excited state pathways and dynamics of NiII-bipyridine complexes influence the yield of photochemical processes involved in their catalytic cross-coupling reactions. Here we present ultrafast Ni K x-ray emission spectroscopy (XES) and x-ray solution scattering (XSS) of a NiII-bipyridine aryl halide complex, [Ni(t-Bubpy)(o-tol)Br], to quantify the excited state population dynamics and structural changes of the pre-catalyst. Due to the local spin-sensitivity of XES, the population dynamics of metal-to-ligand charge transfer (MLCT) and metal-centered (MC) excited states is established. A rapid ground state recovery pathway is newly identified, representing a significant deactivation pathway during photocatalysis. Furthermore, the pseudotetrahedral structure of the long-lived MC excited state is unambiguously identified and refined by XSS. The results advance our understanding of the ultrafast relaxation mechanisms that impact the photocatalytic mechanism and yield for NiII-bipyridine aryl halide cross-coupling catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH

An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality

Abstract Body size is one of the most important traits governing individual‐level demographic rates and modulating population‐level processes. Multiple size‐dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size‐dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM 2 ) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex, size‐structured demographic rates from imperfect observations. We apply the IPM 2 in the context of invasive European green crab ( Carcinus maenas ), a species for which individual body size strongly regulates both the observation‐generating process and latent, population dynamics. The IPM 2 facilitates the distinct estimation of green crab size‐structured harvest and natural mortality rates, parameters for which no explicit data is collected and that are unidentifiable in component datasets of the integrated population model. The model represents how the green crab population changes over time, providing the first estimates of size‐structured abundance of this high‐priority species. By forecasting the stable size distribution and equilibrium population size under varying removal efforts, we demonstrate that extremely high levels of removal effort can reduce the equilibrium green crab population size. Yet these high mortality rates also shift the stable size distribution and increase the equilibrium abundance of smaller crabs, since size‐selective removal alters intraspecific interactions. The ecological outcome of this shift in size structure will be variable, as green crab size modulates only some of its interactions with other species. These results highlight the value of the IPM 2 framework for inferring complex population dynamics with information needs that outpace information in individual observational datasets, providing a path forward for accurate assessment of conservation programs.

Keller, Abigail G. [Department of Environment Scie

Non-equilibrium rate theory for polariton relaxation dynamics

We derive an analytic expression of the non-equilibrium Fermi’s golden rule (NE-FGR) expression for a Holstein–Tavis–Cumming Hamiltonian, a universal model for many molecules collectively coupled to the optical cavity. These NE-FGR expressions capture the full-time-dependent behavior of the rate constant for transitions from polariton states to dark states. The rate is shown to be reduced to the well-known frequency domain-based equilibrium Fermi’s golden rule (E-FGR) expression in the equilibrium and collective limit and is shown to retain the same scaling with the number of sites in non-equilibrium and non-collective cases. We use these NE-FGR to perform population dynamics with a time-non-local and time-local quantum master equation and obtain accurate population dynamics from the initially occupied upper or lower polariton states. Furthermore, NE-FGR significantly improves the accuracy of the population dynamics when starting from the lower polariton compared to the E-FGR theory, highlighting the importance of the non-Markovian behavior and the short-time transient behavior in the transition rate constant.

Chemical dynamics

Propagating synthetic populations with dynamic Bayesian networks: a framework for long-horizon demographic forecasting

This study presents a dynamic demographic microsimulator using dynamic Bayesian networks to forecast long–term changes in household and individual life events. Leveraging longitudinal Panel Study of Income Dynamics (PSID) data, two networks for individuals and households were modeled to simulate transitions in employment, income, education, marriage, childbirth, leaving the parental home, home ownership, mortality, and household formation or dissolution. Across 1,000 simulation runs spanning 24 years, household–level outcomes remain highly accurate and individual–level predictions reasonable. Although accuracy naturally declines with projection horizon, performance remains promising at both levels. This study addresses a key limitation of existing population synthesis models, which typically generate only a single static snapshot of the population. In conclusion, by introducing a framework that propagates cross-sectional outputs into the future, the microsimulator enables the tracking of demographic evolution over time, enhances realism in population-based simulations, and supplies credible inputs to agent-based travel demand models.

Demographic modeling

Climate Predicts Geographic and Temporal Variation in Mosquito-Borne Disease Dynamics on Two Continents

Climate drives population dynamics through multiple mechanisms, which can lead to seemingly context-dependent effects of climate on natural populations. For climate-sensitive diseases such as dengue, chikungunya, and Zika, climate appears to have opposing effects in different contexts. Here we show that a model, parameterized with laboratory measured climate-driven mosquito physiology, captures three key epidemic characteristics across ecologically and culturally distinct settings in Ecuador and Kenya: the number, timing, and duration of outbreaks. The model generates a range of disease dynamics consistent with observed Aedes aegypti abundances and laboratory-confirmed arboviral incidence with variable accuracy (28–85% for vectors, 44–88%for incidence). The model predicted vector dynamics better in sites with a smaller proportion of young children in the population, lower mean temperature, and homes with piped water and made of cement. Models with limited calibration that robustly capture climate-virus relationships can help guide intervention efforts and climate change disease projections.

Climate-change ecology

Analytic rate theory of polariton relaxation that explains long polariton lifetime

Hybridization of a molecular exciton with a quantized photon creates a polariton. Despite extensive experimental investigations, the apparent lifetime of the exciton–polariton is not well-understood. For this work, we examined the steady-state population dynamics for a Holstein–Tavis–Cumming Hamiltonian to illuminate the long-term polaritonic dynamics and lifetime of the exciton–polariton in an optical cavity. For a realistic description of polariton relaxation, cavity loss and various exciton decay channels are included in the model. We found that in the presence of weak but finite exciton loss, the apparent lifetime of the lower polariton coincides with the out-of-cavity exciton lifetime and is independent of cavity-matter detuning. This is a simple explanation for the experimentally observed lifetimes for exciton polaritons and theoretically justifies the dark state reservoir hypothesis. Furthermore, if the upper polariton is initially populated, the system reaches the steady state very quickly, leading to single-exponential polariton relaxation. Starting from the lower polariton leads to a longer pre-steady-state time period, leading to double-exponential relaxation. Finally, we considered the effect of site orientational disorders and the exciton frequency disorderers. Under the collective limit, the effects of this disorder can be included in Fermi’s golden rule population dynamics without explicit sampling. For the exciton energy disorders, numerical calculations are needed. Our theoretical framework is applicable to interpret exciton–polariton experiments, especially related to the measured apparent lifetime of polaritons.

Chemical dynamics

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Simpson, Abigayle