Asynchrony between virus diversity and antibody selection limits influenza virus evolution.

Funder: H2020 European Research Council; FundRef: http://dx.doi.org/10.13039/100010663; Grant(s): Naviflu:818353Seasonal influenza viruses create a persistent global disease burden by evolving to escape immunity induced by prior infections and vaccinations. New antigenic variants have a substantial selective advantage at the population level, but these variants are rarely selected within-host, even in previously immune individuals. Using a mathematical model, we show that the temporal asynchrony between within-host virus exponential growth and antibody-mediated selection could limit within-host antigenic evolution. If selection for new antigenic variants acts principally at the point of initial virus inoculation, where small virus populations encounter well-matched mucosal antibodies in previously-infected individuals, there can exist protection against reinfection that does not regularly produce observable new antigenic variants within individual infected hosts. Our results provide a theoretical explanation for how virus antigenic evolution can be highly selective at the global level but nearly neutral within-host. They also suggest new avenues for improving influenza control

Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses

Ambient temperature and humidity strongly affect inactivation rates of enveloped viruses, but a mechanistic, quantitative theory of these effects has been elusive. We measure the stability of SARS-CoV-2 on an inert surface at nine temperature and humidity conditions and develop a mechanistic model to explain and predict how temperature and humidity alter virus inactivation. We find SARS-CoV-2 survives longest at low temperatures and extreme relative humidities (RH); median estimated virus half-life is >24 hr at 10°C and 40% RH, but ∼1.5 hr at 27°C and 65% RH. Our mechanistic model uses fundamental chemistry to explain why inactivation rate increases with increased temperature and shows a U-shaped dependence on RH. The model accurately predicts existing measurements of five different human coronaviruses, suggesting that shared mechanisms may affect stability for many viruses. The results indicate scenarios of high transmission risk, point to mitigation strategies, and advance the mechanistic study of virus transmission

Space and diversification: a theoretical perspective

Alguns dos padrões ecológicos mais consistentemente encontrados na natureza, como as relações espécie-área e as distribuições de rank-abundância, podem ser previstas por uma classe de modelos neutros. Nesse contexto, neutralidade quer dizer que há equivalência demográfica entre os indivíduos de todas as espécies. Para os modelos dessa classe, extinções causadas por flutuações demográficas são contrabalanceadas por algum mecanismo de especiação. Cada modo de especiação deixa uma marca nos padrões ecológicos emergentes. Foi mostrado que um modelo com uma implementação mecanística de especiação gera padrões de diversidade que dependem de limites geográficos. Eu usei simulações baseadas em indivíduos com uma implementação mecanística de especiação para investigar se padrões espaciais intrínsecos das comunidades poderiam transformar os padrões de biodiversidade. Eu descobri que existe uma transição de fase no modo de especiação que depende da estrutura espacial da comunidade. Uma gama extensa de padrões encontrados na natureza puderam ser unificados em um único modelo dada essa transição de fase. Relações entre riqueza e idade de um clado podem ser melhor compreendidas considerando-se o efeito previsto de desaceleração crítica da diversificação. Uma nova interpretação foi dado ao efeito \"Clado Morto Andando\", característico dos períodos seguintes a extinções em massa. Uma redefinição objetiva e biologicamente razoável para especiação alopátrica é explorada, graças às propriedades da transição de fase descrita. Eu proponho a existência de um \"crédito de especiação\", e exploro suas possíveis implicações para a conservação a longo prazo da biodiversidadeSome of the most consistent ecological patterns encountered in nature, such as species-area relationships and rank-abundance distributions, can be predicted from a class of neutral models. In this context, neutrality means demographic equivalence between individuals of all species. Within this class of neutral models, species extinction by demographic fluctuations is counterbalanced by some speciation mechanism. Each particular speciation mode leaves an imprint in the resulting patterns. A model with a mechanistic speciation implementation was shown to generate patterns dependent on geographic constraints. I used individual based simulations with a mechanistic speciation implementation to investigate whether the intrinsic spatial patterning of organisms could transform biodiversity patterns. I found out that there is a phase transition on speciation modes that is dependent on the spatial structure of the community. An extended range of the biodiversity patterns found in nature can be unified into a single model because of this phase transition. Clade richness and age relationships may be understood by the predicted critical slowdowns in diversification. A new interpretation is given to the post mass extinction \"Dead Clade Walking\" effect. An objective and biologically reasonable redefinition of allopatric speciation is explored by exploiting the phase transition. I propose the \"speciation credit\" effect, and its potential implications for long term biodiversity conservatio

The emergent properties of diverse organism ensembles: from slime molds to protocells

Many crucial features of biological systems emerge from self-organized patterns.Moreover, to understand ecological succession and evolutionary change in systems with emergent properties, we must contend with how self-organized patterns are affected by individuals that follow divergent interaction rules. Here we use cellular slime molds as a model system to investigate emergent biological properties in the context of heterogeneous individuals. Slime molds have a complex life cycle with a unicellular foraging stage and a multicellular dispersal stage. First, we show that slime mold cells spontaneously self-organize into cells that aggregate and follow multicellular development and loner cells that stay behind. We then theoretically explore the ecological consequences of this self-organized partitioning in the context of differentially aggregative strains. Second, we show that self-organization also plays a role in the foraging stage of the slime mold life cycle. Cells spontaneously partition into fast, polarized cells and slow unpolarized cells. This behavioral differentiation powers the expansion of the slime mold colony and determines the outcomes of their interaction with bacterial prey. Altogether we reveal that individual behavioral variation is often the result of self-organization but also determines further self-organized patterns that feed into the emergent properties of the system. Third, we look at a different system altogether — early chromosomes in protocells — and show that competition between genes with different replication efficiencies might have driven the organization of the genome into chromosomes

Data and code for “Structured foraging of soil predators unveils functional responses to bacterial defenses”

This dataset is too large to download directly from this item page. You can access and download the data via Globus at this link: https://app.globus.org/file-manager?destination_id=dc43f461-0ca7-4203-848c-33a9fc00a464&destination_path=%2F5cey-ce46%2FMicroscopy images are part of a paper entitled "Structured foraging of soil predators unveils functional responses to bacterial defenses" by Fernando Rossine, Gabriel Vercelli, Corina Tarnita, and Thomas Gregor. For detailed acquisition methods see the paper. Experiments were performed between 2019 and 2020 at Princeton University. Two types of images are provided, macroscopic and microscopic widefiled Images. Macroscopic images all show Petri dishes covered in fluorescent bacteria being consumed by amoebae. Images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum. Images used for the creation of a profile were all taken within 30 minutes of each other. Within each directory numbered images are independent replicates. The raw video directory contains time series for dishes under drug treatments. Each numbered folder is a sequence of photos (taken 30 minutes apart of each other) of a single dish. Microscopic images all show amoebae consuming bacteria on a petri dish. The 45 minute videos show either edge cells (located at the edge of amoebae colonies), or inner cells (located 2.5 millimeters towards the center of the colony, from the edge). Videos are confocal stacks, with bacteria showing in green and amoebae appearing as black holes within the bacterial lawn. As was for the macroscopic images, images are shown for D. discoideum, P. violaceum, and A. castellanii. Images depicting drug treatments (Nystatin and Fluorouracil) were obtained using D. discoideum.National Science Foundation (NSF): Fernando Rossine, Corina E Tarnita NSF RoL: FELS: EAGER-1838331; National Science Foundation (NSF): Thomas Gregor Center for the Physics of Biological function (PHY-1734030); HHS | NIH | National Institute of General Medical Sciences (NIGMS): Thomas Gregor R01 GM097275findBoundaries.m graph.R makeRegistration.m README.txt Image_files.zip (see link below

Structured foraging of soil predators unveils functional responses to bacterial defenses

International audiencePredators and their foraging strategies often determine ecosystem structure and function. Yet, the role of protozoan predators in microbial soil ecosystems remains elusive despite the importance of these ecosystems to global biogeochemical cycles. In particular, amoebae—the most abundant soil protozoan predator of bacteria—remineralize soil nutrients and shape the bacterial community. However, their foraging strategies and their role as microbial ecosystem engineers remain unknown. Here, we present a multiscale approach, connecting microscopic single-cell analysis and macroscopic whole ecosystem dynamics, to expose a phylogenetically widespread foraging strategy, in which an amoeba population spontaneously partitions between cells with fast, polarized movement and cells with slow, unpolarized movement. Such differentiated motion gives rise to efficient colony expansion and consumption of the bacterial substrate. From these insights, we construct a theoretical model that predicts how disturbances to amoeba growth rate and movement disrupt their predation efficiency. These disturbances correspond to distinct classes of bacterial defenses, which allows us to experimentally validate our predictions. All considered, our characterization of amoeba foraging identifies amoeba mobility, and not amoeba growth, as the core determinant of predation efficiency and a key target for bacterial defense systems

Structured foraging of soil predators unveils functional responses to bacterial defenses

Predators and their foraging strategies often determine ecosystem structure and function. Yet, the role of protozoan predators in microbial soil ecosystems remains elusive despite the importance of these ecosystems to global biogeochemical cycles. In particular, amoebae -- the most abundant soil protozoan predators of bacteria -- remineralize soil nutrients and shape the bacterial community. However, their foraging strategies and their role as microbial ecosystem engineers remain unknown. Here we present a multi-scale approach, connecting microscopic single-cell analysis and macroscopic whole ecosystem dynamics, to expose a phylogenetically widespread foraging strategy, in which an amoeba population spontaneously partitions between cells with fast, polarized movement and cells with slow, unpolarized movement. Such differentiated motion gives rise to efficient colony expansion and consumption of the bacterial substrate. From these insights we construct a theoretical model that predicts how disturbances to amoeba growth rate and movement disrupt their predation efficiency. These disturbances correspond to distinct classes of bacterial defenses, which allows us to experimentally validate our predictions. All considered, our characterization of amoeba foraging identifies amoeba mobility, and not amoeba growth, as the core determinant of predation efficiency and a key target for bacterial defense systems

Eco-evolutionary significance of “loners”

International audienceLoners-individuals out of sync with a coordinated majority-occur frequently in nature. Are loners incidental byproducts of large-scale coordination attempts, or are they part of a mosaic of life-history strategies? Here, we provide empirical evidence of naturally occurring heritable variation in loner behavior in the model social amoeba Dictyostelium discoideum. We propose that Dictyostelium loners-cells that do not join the multicellular life stagearise from a dynamic population-partitioning process, the result of each cell making a stochastic, signal-based decision. We find evidence that this imperfectly synchronized multicellular development is affected by both abiotic (environmental porosity) and biotic (signaling) factors. Finally, we predict theoretically that when a pair of strains differing in their partitioning behavior coaggregate, cross-signaling impacts slime-mold diversity across spatiotemporal scales. Our findings suggest that loners could be critical to understanding collective and social behaviors, multicellular development, and ecological dynamics in D. discoideum. More broadly, across taxa, imperfect coordination of collective behaviors might be adaptive by enabling diversification of life-history strategies