Salinity detection by Hydrobia ulvae (Pennant) and Potamopyrgus jenkinsi Smith (Gastropoda:Prosobranchia)

Both Hydrobia ulvae (Pennant) and Potamopyrgus jenkinsi Smith climb vertically in the laboratory but stop or crawl horizontally if presented with a sharp salinity drop. 50% of Hydrobia ulvae respond to a difference of 18–26% from the original solution. 50% of Potamopyrgus jenkinsi respond to a difference of 53–55%. In both species, the response is impaired at high temperatures, and in Hydrobia ulvae it is also impaired at low temperatures. From 9–22 °C no temperature influence is evident.From acclimation experiments it is suggested that the snails respond not to the gradient across the interface, but to the gradient between body fluids and the upper solution presented. Snails respond to non-ionic gradients when these are presented either as density gradients or as solutions separated by a semi-permeable membrane, and it is argued that they detect osmotic pressure directly. The sense organs are probably located in the tentacles.     

Environmental Drivers of the Canadian Arctic Megabenthic Communities

Environmental gradients and their influence on benthic community structure vary over different spatial scales; yet, few studies in the Arctic have attempted to study the influence of environmental gradients of differing spatial scales on megabenthic communities across continental-scales. The current project studied for the first time how megabenthic community structure is related to several environmental factors over 2000 km of the Canadian Arctic, from the Beaufort Sea to northern Baffin Bay. Faunal trawl samples were collected between 2007 and 2011 at 78 stations from 30 to 1000 m depth and patterns in biomass, density, richness, diversity, and taxonomic composition were examined in relation to indirect/spatial gradients (e.g., depth), direct gradients (e.g., bottom oceanographic variables), and resource gradients (e.g., food supply proxies). Six benthic community types were defined based on their biomass-based taxonomic composition. Their distribution was significantly, but moderately, associated with large-scale (100–1000 km) environmental gradients defined by depth, physical water properties (e.g., bottom salinity), and meso-scale (10–100 km) environmental gradients defined by substrate type (hard vs. soft) and sediment organic carbon content. We did not observe a strong decline of bulk biomass, density and richness with depth or a strong increase of those community characteristics with food supply proxies, contrary to our hypothesis. We discuss how local- to meso-scale environmental conditions, such as bottom current regimes and polynyas, sustain biomass-rich communities at specific locations in oligotrophic and in deep regions of the Canadian Arctic. This study demonstrates the value of considering the scales of variability of environmental gradients when interpreting their relevance in structuring of communities.     

Sudden motility reversal indicates sensing of magnetic field gradients in Magnetospirillum magneticum AMB-1 strain

Many motile unicellular organisms have evolved specialized behaviors for detecting and responding to environmental cues such as chemical gradients (chemotaxis) and oxygen gradients (aerotaxis). Magnetotaxis is found in magnetotactic bacteria and it is defined as the passive alignment of these cells to the geomagnetic field along with active swimming. Herein we show that Magnetospirillum magneticum (AMB-1) show a unique set of responses that indicates they sense and respond not only to the direction of magnetic fields by aligning and swimming, but also to changes in the magnetic field or magnetic field gradients. We present data showing that AMB-1 cells exhibit sudden motility reversals when we impose them to local magnetic field gradients. Our system employs permalloy (Ni₈₀Fe₂₀) islands to curve and diverge the magnetic field lines emanating from our custom-designed Helmholtz coils in the vicinity of the islands (creating a drop in the field across the islands). The three distinct movements we have observed as they approach the permalloy islands are: unidirectional, single reverse and double reverse. Our findings indicate that these reverse movements occur in response to magnetic field gradients. In addition, using a permanent magnet we found further evidence that supports this claim. Motile AMB-1 cells swim away from the north and south poles of a permanent magnet when the magnet is positioned less than ∼30 mm from the droplet of cells. All together, these results indicate previously unknown response capabilities arising from the magnetic sensing systems of AMB-1 cells. These responses could enable them to cope with magnetic disturbances that could in turn potentially inhibit their efficient search for nutrients.     

The use of visual information by house flies,Musca domestica (Diptera: Muscidae), foraging in resource patches

Summary House flies, Musca domestica, respond to visual contrasts on the substrate if a resource is associated with the contrasting patterns. Visible resource patch boundaries serve as a signal to flies that they are about to leave a rewarding patch. Searching flies respond to such visual information by walking along the resource patch boundary and turning back into the patch at its edge. This edge detection and response serve as a mechanism for flies with visual cues to stay in a rewarding patch and locate more resources within it. The intensity of their response correlates with the quality of the resource. In the absence of visual cues, patch shape affects foraging success; flies find more resources in circular than in linear resource distributions. The effects of visual cues, however, render patch shape unimportant. Various substrate contrasts are effective as resource information for flies: dark (e.g., green) figures on bright (e.g., white) backgrounds or bright figures on dark backgrounds. Responses to substrate contrasts measured in this study indicate that, over the short term, house flies can learn a visual cue associated with a food source.     

Robust Spatial Sensing of Mating Pheromone Gradients by Yeast Cells

Projecting or moving up a chemical gradient is a universal behavior of living organisms. We tested the ability of S. cerevisiae a-cells to sense and respond to spatial gradients of the mating pheromone α-factor produced in a microfluidics chamber; the focus was on bar1Δ strains, which do not degrade the pheromone input. The yeast cells exhibited good accuracy with the mating projection typically pointing in the correct direction up the gradient (∼80% under certain conditions), excellent sensitivity to shallow gradients, and broad dynamic range so that gradient-sensing was relatively robust over a 1000-fold range of average α-factor concentrations. Optimal directional sensing occurred at lower concentrations (5 nM) close to the K_d of the receptor and with steeper gradient slopes. Pheromone supersensitive mutations (sst2Δ and ste2^300Δ) that disrupt the down-regulation of heterotrimeric G-protein signaling caused defects in both sensing and response. Interestingly, yeast cells employed adaptive mechanisms to increase the robustness of the process including filamentous growth (i.e. directional distal budding) up the gradient at low pheromone concentrations, bending of the projection to be more aligned with the gradient, and forming a more accurate second projection when the first projection was in the wrong direction. Finally, the cells were able to amplify a shallow external gradient signal of α-factor to produce a dramatic polarization of signaling proteins at the front of the cell. Mathematical modeling revealed insights into the mechanism of this amplification and how the supersensitive mutants can disrupt accurate polarization. Together, these data help to specify and elucidate the abilities of yeast cells to sense and respond to spatial gradients of pheromone.     

Modeling robustness tradeoffs in yeast cell polarization induced by spatial gradients

Cells localize (polarize) internal components to specific locations in response to external signals such as spatial gradients. For example, yeast cells form a mating projection toward the source of mating pheromone. There are specific challenges associated with cell polarization including amplification of shallow external gradients of ligand to produce steep internal gradients of protein components (e.g. localized distribution), response over a broad range of ligand concentrations, and tracking of moving signal sources. In this work, we investigated the tradeoffs among these performance objectives using a generic model that captures the basic spatial dynamics of polarization in yeast cells, which are small. We varied the positive feedback, cooperativity, and diffusion coefficients in the model to explore the nature of this tradeoff. Increasing the positive feedback gain resulted in better amplification, but also produced multiple steady-states and hysteresis that prevented the tracking of directional changes of the gradient. Feedforward/feedback coincidence detection in the positive feedback loop and multi-stage amplification both improved tracking with only a modest loss of amplification. Surprisingly, we found that introducing lateral surface diffusion increased the robustness of polarization and collapsed the multiple steady-states to a single steady-state at the cost of a reduction in polarization. Finally, in a more mechanistic model of yeast cell polarization, a surface diffusion coefficient between 0.01 and 0.001 μm(2)/s produced the best polarization performance, and this range is close to the measured value. The model also showed good gradient-sensitivity and dynamic range. This research is significant because it provides an in-depth analysis of the performance tradeoffs that confront biological systems that sense and respond to chemical spatial gradients, proposes strategies for balancing this tradeoff, highlights the critical role of lateral diffusion of proteins in the membrane on the robustness of polarization, and furnishes a framework for future spatial models of yeast cell polarization.     

Mariprofundus ferrooxydans PV-1 the first genome of a marine Fe(II) oxidizing Zetaproteobacterium

Mariprofundus ferrooxydans PV-1 has provided the first genome of the recently discovered Zetaproteobacteria subdivision. Genome analysis reveals a complete TCA cycle, the ability to fix CO(2), carbon-storage proteins and a sugar phosphotransferase system (PTS). The latter could facilitate the transport of carbohydrates across the cell membrane and possibly aid in stalk formation, a matrix composed of exopolymers and/or exopolysaccharides, which is used to store oxidized iron minerals outside the cell. Two-component signal transduction system genes, including histidine kinases, GGDEF domain genes, and response regulators containing CheY-like receivers, are abundant and widely distributed across the genome. Most of these are located in close proximity to genes required for cell division, phosphate uptake and transport, exopolymer and heavy metal secretion, flagellar biosynthesis and pilus assembly suggesting that these functions are highly regulated. Similar to many other motile, microaerophilic bacteria, genes encoding aerotaxis as well as antioxidant functionality (e.g., superoxide dismutases and peroxidases) are predicted to sense and respond to oxygen gradients, as would be required to maintain cellular redox balance in the specialized habitat where M. ferrooxydans resides. Comparative genomics with other Fe(II) oxidizing bacteria residing in freshwater and marine environments revealed similar content, synteny, and amino acid similarity of coding sequences potentially involved in Fe(II) oxidation, signal transduction and response regulation, oxygen sensation and detoxification, and heavy metal resistance. This study has provided novel insights into the molecular nature of Zetaproteobacteria.     

Quorum sensing regulation in bacteria of the family enterobacteriaceae

Bacteria are able to sense an increase in population density and can respond to it by coordinated regulation of the expression of certain sets of genes in the total population of bacteria. This specific mode of regulation is known as Quorum Sensing (QS). The QS systems include low-molecular-weight signaling molecules of different chemical nature and the regulatory proteins that interact with the signaling molecules. The QS systems are global regulators of bacterial gene expression. They play an important role in controlling metabolic processes in bacteria. This review describes QS systems in members of the bacterial family Enterobacteriaceae functioning with the involvement of various signaling molecules, including N-acyl-homoserine lactones, AI-2, AI-3, peptides, and indole. The differences of the QS system in these bacteria from those in other taxonomic groups of bacteria are discussed. Data on the role of different types of QS systems in the regulation of different cellular processes in bacteria, i.e., their virulence, the synthesis of enzymes and antibiotics, biofilm formation, apoptosis, etc. are presented.     

Nematode Indicators of Organic Enrichment

The organisms of the soil food web, dependent on resources from plants or on amendment from other sources, respond characteristically to enrichment of their environment by organic matter. Primary consumers of the incoming substrate, including bacteria, fungi, plant-feeding nematodes, annelids, and some microarthropods, are entry-level indicators of enrichment. However, the quantification of abundance and biomass of this diverse group, as an indicator of resource status, requires a plethora of extraction and assessment techniques. Soluble organic compounds are absorbed by bacteria and fungi, while fungi also degrade more recalcitrant sources. These organisms are potential indicators of the nature of incoming substrate, but current methods of biomass determination do not reliably indicate their community composition. Guilds of nematodes that feed on bacteria (e.g., Rhabditidae, Panagrolaimidae) and fungi (e.g., Aphelenchidae, Aphelenchoididae) are responsive to changes in abundance of their food. Through direct herbivory, plant-feeding nematodes (e.g., many species of Tylenchina) also contribute to food web resources. Thus, analysis of the nematode community of a single sample provides indication of carbon flow through an important herbivore channel and through channels mediated by bacteria and fungi. Some nematode guilds are more responsive than others to resource enrichment. Generally, those bacterivores with short lifecycles and high reproductive potential (e.g., Rhabditidae) most closely mirror the bloom of bacteria or respond most rapidly to active plant growth. The feeding habits of some groups remain unclear. For example, nematodes of the Tylenchidae may constitute 30% or more of the individuals in a soil sample; further study is necessary to determine which resource channels they portray and the appropriate level of taxonomic resolution for this group. A graphic representation of the relative biomass of bacterivorous, fungivorous, and herbivorous nematodes provides a useful tool for assessing the importance of the bacterial, fungal, and plant resource channels in an extant food web.     

Spatial distribution of microalgae in marine systems: A reaction–diffusion model

In this paper, we have proposed a reaction–diffusion system of partial differential equations which model the plankton-nutrient interaction mediated by a toxin-determined functional response. It has been established that microalgae, a clean and green source of energy, can be potentially used for carbon capture and sequestration. The common biofuels (bio-diesel and ethanol) are efficiently extracted from microalgae of different shapes and sizes. A spatio-temporal model has been presented to guide exploration and harvesting of microalgae (e.g., dinoflagellates, cilliates, chlorella, etc.). The spatial distribution of the phytoplankton (microalgae) is determined by growth pattern of the biotic subsystem (phytoplankton and zooplankton); e.g., whether it is oscillatory or aperiodic. The model incorporates a toxin-determined functional response of the zooplankton, which can be parametrized for specific phytoplankton–zooplankton combinations in different aquatic bodies such as ponds, seas, and oceans. The present model does not take into account higher zooplankton’s role in maintaining the core subsystem. The temporal model is analytically investigated in terms of the existence criteria and stability analysis (both linear and nonlinear) of the possible equilibria and the spatio-temporal model is studied in terms of global stability, Turing instability and existence of Hopf-bifurcation which help us to explore the dynamical behavior of the spatial model system. Numerical simulations are carried out to support the obtained theoretical results. Simulation experiments and computed densities thereof (equal densities are codes by same color) suggest that the spatial distribution of microalgae is complex; e.g., spatial density of microalgae varies chaotically for certain parameter sets. Harvesting schedule can be designed based on information thus derived. It should be implemented carefully in case the spatial density distribution is chaotic.The sustainability of the marine system for future use has been the prime concern. Parameters of harvesting strategy (time, intensity and technology) are determined in such a way that exploitation causes minimal damage to the environment and the yield of the harvest is maximal. Future studies would consider larger carnivorous fishes (e.g., Squids, Dolphins) on system’s dynamics. The effect of oceanic noise and colloidal swarming of zooplankton in the presence of bacteria will also be incorporated.     

Analysis of the signal transduction properties of a module of spatial sensing in eukaryotic chemotaxis

The movement of cells in response to a gradient in chemical concentration—known as chemotaxis—is crucial for the proper functioning of uni-and multicellular organisms. How a cell senses the chemical concentration gradient surrounding it, and what signal is transmitted to its motion apparatus is known as gradient sensing. The ability of a cell to sense gradients persists even when the cell is immobilized (i.e., its motion apparatus is deactivated). This suggests that important features of gradient sensing can be studied in isolation, decoupling this phenomenon from the movement of the cell. A mathematical model for gradient sensing in Dictyostelium cells and neutrophils was recently proposed. This consists of an adaptation/spatial sensing module. This spatial sensing module feeds into an amplification module, magnifying the effects of the former. In this paper, we analyze the spatial sensing module in detail and examine its signal transduction properties. We examine the response of this module to several inputs of experimental and biological relevance.     

Genome Analysis of Planctomycetes Inhabiting Blades of the Red Alga Porphyra umbilicalis

Porphyra is a macrophytic red alga of the Bangiales that is important ecologically and economically. We describe the genomes of three bacteria in the phylum Planctomycetes (designated P1, P2 and P3) that were isolated from blades of Porphyra umbilicalis (P.um.1). These three Operational Taxonomic Units (OTUs) belong to distinct genera; P2 belongs to the genus Rhodopirellula, while P1 and P3 represent undescribed genera within the Planctomycetes. Comparative analyses of the P1, P2 and P3 genomes show large expansions of distinct gene families, which can be widespread throughout the Planctomycetes (e.g., protein kinases, sensors/response regulators) and may relate to specific habitat (e.g., sulfatase gene expansions in marine Planctomycetes) or phylogenetic position. Notably, there are major differences among the Planctomycetes in the numbers and sub-functional diversity of enzymes (e.g., sulfatases, glycoside hydrolases, polysaccharide lyases) that allow these bacteria to access a range of sulfated polysaccharides in macroalgal cell walls. These differences suggest that the microbes have varied capacities for feeding on fixed carbon in the cell walls of P.um.1 and other macrophytic algae, although the activities among the various bacteria might be functionally complementary in situ. Additionally, phylogenetic analyses indicate augmentation of gene functions through expansions arising from gene duplications and horizontal gene transfers; examples include genes involved in cell wall degradation (e.g., κ-carrageenase, alginate lyase, fucosidase) and stress responses (e.g., efflux pump, amino acid transporter). Finally P1 and P2 contain various genes encoding selenoproteins, many of which are enzymes that ameliorate the impact of environmental stresses that occur in the intertidal habitat.     

Proteomic Approach for Characterization of Hop-Inducible Proteins in Lactobacillus brevis

Resistance to hops is a prerequisite for the capability of lactic acid bacteria to grow in beer and thus cause beer spoilage. Bactericidal hop compounds, mainly iso-α-acids, are described as ionophores which exchange H⁺ for cellular divalent cations, e.g., Mn²⁺, and thus dissipate ion gradients across the cytoplasmic membrane. The acid stress response of Lactobacillus brevis TMW 1.465 and hop adaptation in its variant L. brevis TMW 1.465A caused changes at the level of metabolism, membrane physiology, and cell wall composition. To identify the basis for these changes, a proteomic approach was taken. The experimental design allowed the discrimination of acid stress and hop stress. A strategy for improved protein identification enabled the identification of 84% of the proteins investigated despite the lack of genome sequence data for this strain. Hop resistance in L. brevis TMW 1.465A implies mechanisms to cope with intracellular acidification, mechanisms for energy generation and economy, genetic information fidelity, and enzyme functionality. Interestingly, the majority of hop-regulated enzymes are described as manganese or divalent cation dependent. Regulation of the manganese level allows fine-tuning of the metabolism, which enables a rapid response to environmental (stress) conditions. The hop stress response indicates adaptations shifting the metabolism into an energy-saving mode by effective substrate conversion and prevention of exhaustive protein de novo synthesis. The findings further demonstrate that hop stress in bacteria not only is associated with proton motive force depletion but obviously implies divalent cation limitation.     

Microbiology of flooded rice paddies

Flooded rice paddies are one of the major biogenic sources of atmospheric methane. Apart from this contribution to the 'greenhouse' effect, rice paddy soil represents a suitable model system to study fundamental aspects of microbial ecology, such as diversity, structure, and dynamics of microbial communities as well as structure-function relationships between microbial groups. Flooded rice paddy soil can be considered as a system with three compartments (oxic surface soil, anoxic bulk soil, and rhizosphere) characterized by different physio-chemical conditions. After flooding, oxygen is rapidly depleted in the bulk soil. Anaerobic microorganisms, such as fermentative bacteria and methanogenic archaea, predominate within the microbial community, and thus methane is the final product of anaerobic degradation of organic matter. In the surface soil and the rhizosphere well-defined microscale chemical gradients can be measured. The oxygen profile seems to govern gradients of other electron acceptors (e.g., nitrate, iron(III), and sulfate) and reduced compounds (e.g., ammonium, iron(II), and sulfide). These gradients provide information about the activity and spatial distribution of functional groups of microorganisms. This review presents the current knowledge about the highly complex microbiology of flooded rice paddies. In Section 2 we describe the predominant microbial groups and their function with particular regard to bacterial populations utilizing polysaccharides and simple sugars, and to the methanogenic archaea. Section 3 describes the spatial and temporal development of microscale chemical gradients measured in experimentally defined model systems, including gradients of oxygen and dissolved and solid-phase iron(III) and iron(II). In Section 4, the results of measurements of microscale gradients of oxygen, pH, nitrate-nitrite, and methane in natural rice fields and natural rice soil cores taken to the laboratory will be presented. Finally, perspectives of future research are discussed (Section 5).     

Response of Nitrosospira sp. Strain AF-Like Ammonia Oxidizers to Changes in Temperature, Soil Moisture Content, and Fertilizer Concentration

Very little is known regarding the ecology of Nitrosospira sp. strain AF-like bacteria, a unique group of ammonia oxidizers within the Betaproteobacteria. We studied the response of Nitrosospira sp. strain AF-like ammonia oxidizers to changing environmental conditions by applying molecular methods and physiological measurements to Californian grassland soil manipulated in the laboratory. This soil is naturally high in Nitrosospira sp. strain AF-like bacteria relative to the much-better-studied Nitrosospira multiformis-like ammonia-oxidizing bacteria. Increases in temperature, soil moisture, and fertilizer interacted to reduce the relative abundance of Nitrosospira sp. strain AF-like bacteria, although they remained numerically dominant. The overall abundance of ammonia-oxidizing bacteria increased with increasing soil moisture and decreased with increasing temperature. Potential nitrification activity was altered by interactions among temperature, soil moisture, and fertilizer, with activity tending to be higher when soil moisture and temperature were increased. The increase in potential nitrification activity with increased temperature was surprising, given that the overall abundance of ammonia-oxidizing bacteria decreased significantly under these conditions. This observation suggests that (i) Nitrosospira sp. strain AF-like bacteria may respond to increased temperature with an increase in activity, despite a decrease in abundance, or (ii) that potential nitrification activity in these soils may be due to organisms other than bacteria (e.g., archaeal ammonia oxidizers), at least under conditions of increased temperature.     

Landscape-scale patterns of shrub-species abundance in California chaparral – The role of topographically mediated resource gradients

We examine the degree to which landscape-scale spatial patterns of shrub-species abundance in California chaparral reflect topographically mediated environmental conditions, and evaluate whether these patterns correspond to known ecophysiological plant processes. Regression tree models are developed to predict spatial patterns in the abundance of 12 chaparral shrub and tree species in three watersheds of the Santa Ynez Mountains, California. The species response models are driven by five variables: average annual soil moisture, seasonal variability in soil moisture, average annual photosynthetically active radiation, maximum air temperature over the dry season (May–October), and substrate rockiness. The energy and moisture variables are derived by integrating high resolution (10 m) digital terrain data and daily climate observations with a process-based hydro-ecological model (RHESSys). Field-sampled data on species abundance are spatially integrated with the distributed environmental variables for developing and evaluating the species response models.The species considered are differentially distributed along topographically-mediated environmental gradients in ways that are consistent with known ecophysiological processes. Spatial patterns in shrub abundance are most strongly associated with annual soil moisture and solar radiation. Substrate rockiness is also closely associated with the establishment of certain species, such as Adenostoma fasciculatum and Arctostaphylos glauca. In general, species that depend on fire for seedling recruitment (e.g., Ceanothous megacarpus) occur at high abundance in xeric environments, whereas species that do not depend on fire (e.g., Heteromeles arbutifolia) occur at higher abundance in mesic environments. Model performance varies between species and is related to life history strategies for regeneration. The scale of our analysis may be less effective at capturing the processes that underlie the establishment of species that do not depend on fire for recruitment. Analysis of predication errors in relation to environmental conditions and the abundance of potentially competing species suggest factors not explicitly considered in the species response models.     

Spatial differentiation in the vegetative mycelium of Aspergillus niger

Fungal mycelia are exposed to heterogenic substrates. The substrate in the central part of the colony has been (partly) degraded, whereas it is still unexplored at the periphery of the mycelium. We here assessed whether substrate heterogeneity is a main determinant of spatial gene expression in colonies of Aspergillus niger. This question was addressed by analyzing whole-genome gene expression in five concentric zones of 7-day-old maltose- and xylose-grown colonies. Expression profiles at the periphery and the center were clearly different. More than 25% of the active genes showed twofold differences in expression between the inner and outermost zones of the colony. Moreover, 9% of the genes were expressed in only one of the five concentric zones, showing that a considerable part of the genome is active in a restricted part of the colony only. Statistical analysis of expression profiles of colonies that had either been or not been transferred to fresh xylose-containing medium showed that differential expression in a colony is due to the heterogeneity of the medium (e.g., genes involved in secretion, genes encoding proteases, and genes involved in xylose metabolism) as well as to medium-independent mechanisms (e.g., genes involved in nitrate metabolism and genes involved in cell wall synthesis and modification). Thus, we conclude that the mycelia of 7-day-old colonies of A. niger are highly differentiated. This conclusion is also indicated by the fact that distinct zones of the colony grow and secrete proteins, even after transfer to fresh medium.     

Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations

Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.     

Genetic Drift Suppresses Bacterial Conjugation in Spatially Structured Populations

Conjugation is the primary mechanism of horizontal gene transfer that spreads antibiotic resistance among bacteria. Although conjugation normally occurs in surface-associated growth (e.g., biofilms), it has been traditionally studied in well-mixed liquid cultures lacking spatial structure, which is known to affect many evolutionary and ecological processes. Here we visualize spatial patterns of gene transfer mediated by F plasmid conjugation in a colony of Escherichia coli growing on solid agar, and we develop a quantitative understanding by spatial extension of traditional mass-action models. We found that spatial structure suppresses conjugation in surface-associated growth because strong genetic drift leads to spatial isolation of donor and recipient cells, restricting conjugation to rare boundaries between donor and recipient strains. These results suggest that ecological strategies, such as enforcement of spatial structure and enhancement of genetic drift, could complement molecular strategies in slowing the spread of antibiotic resistance genes.     

Discrete Element Framework for Modelling Extracellular Matrix,Deformable Cells and Subcellular Components

This paper presents a framework for modelling biological tissues based on discrete particles. Cell components (e.g. cell membranes, cell cytoskeleton, cell nucleus) and extracellular matrix (e.g. collagen) are represented using collections of particles. Simple particle to particle interaction laws are used to simulate and control complex physical interaction types (e.g. cell-cell adhesion via cadherins, integrin basement membrane attachment, cytoskeletal mechanical properties). Particles may be given the capacity to change their properties and behaviours in response to changes in the cellular microenvironment (e.g., in response to cell-cell signalling or mechanical loadings). Each particle is in effect an ‘agent’, meaning that the agent can sense local environmental information and respond according to pre-determined or stochastic events. The behaviour of the proposed framework is exemplified through several biological problems of ongoing interest. These examples illustrate how the modelling framework allows enormous flexibility for representing the mechanical behaviour of different tissues, and we argue this is a more intuitive approach than perhaps offered by traditional continuum methods. Because of this flexibility, we believe the discrete modelling framework provides an avenue for biologists and bioengineers to explore the behaviour of tissue systems in a computational laboratory.