Biomedical subjects

Mark A Lewis

Publications and source records attributed to Mark A Lewis.

18 recordsLinked to original sources

PubMed2006

Epizootics of wild fish induced by farm fish.

The continuing decline of ocean fisheries and rise of global fish consumption has driven aquaculture growth by 10% annually over the last decade. The association of fish farms with disease emergence in sympatric wild fish stocks remains one of the most controversial and unresolved threats aquaculture poses to coastal ecosystems and fisheries. We report a comprehensive analysis of the spread and impact of farm-origin parasites on the survival of wild fish populations. We mathematically coupled extensive data sets of native parasitic sea lice (Lepeophtheirus salmonis) transmission and pathogenicity on migratory wild juvenile pink (Oncorhynchus gorbuscha) and chum (Oncorhynchus keta) salmon. Farm-origin lice induced 9-95% mortality in several sympatric wild juvenile pink and chum salmon populations. The epizootics arise through a mechanism that is new to our understanding of emerging infectious diseases: fish farms undermine a functional role of host migration in protecting juvenile hosts from parasites associated with adult hosts. Although the migratory life cycles of Pacific salmon naturally separate adults from juveniles, fish farms provide L. salmonis novel access to juvenile hosts, in this case raising infection rates for at least the first approximately 2.5 months of the salmon's marine life (approximately 80 km of the migration route). Spatial segregation between juveniles and adults is common among temperate marine fishes, and as aquaculture continues its rapid growth, this disease mechanism may challenge the sustainability of coastal ecosystems and economies.

Animals↗

PubMed2006

A nonlocal continuum model for biological aggregation.

We construct a continuum model for biological aggregations in which individuals experience long-range social attraction and short-range dispersal. For the case of one spatial dimension, we study the steady states analytically and numerically. There exist strongly nonlinear states with compact support and steep edges that correspond to localized biological aggregations, or clumps. These steady-state clumps are reached through a dynamic coarsening process. In the limit of large population size, the clumps approach a constant density swarm with abrupt edges. We use energy arguments to understand the nonlinear selection of clump solutions, and to predict the internal density in the large population limit. The energy result holds in higher dimensions as well, and is demonstrated via numerical simulations in two dimensions.

Algorithms↗

PubMed2006

Mechanistic home range models capture spatial patterns and dynamics of coyote territories in Yellowstone.

Patterns of space-use by individuals are fundamental to the ecology of animal populations influencing their social organization, mating systems, demography and the spatial distribution of prey and competitors. To date, the principal method used to analyse the underlying determinants of animal home range patterns has been resource selection analysis (RSA), a spatially implicit approach that examines the relative frequencies of animal relocations in relation to landscape attributes. In this analysis, we adopt an alternative approach, using a series of mechanistic home range models to analyse observed patterns of territorial space-use by coyote packs in the heterogeneous landscape of Yellowstone National Park. Unlike RSAs, mechanistic home range models are derived from underlying correlated random walk models of individual movement behaviour, and yield spatially explicit predictions for patterns of space-use by individuals. As we show here, mechanistic home range models can be used to determine the underlying determinants of animal home range patterns, incorporating both movement responses to underlying landscape heterogeneities and the effects of behavioural interactions between individuals. Our analysis indicates that the spatial arrangement of coyote territories in Yellowstone is determined by the spatial distribution of prey resources and an avoidance response to the presence of neighbouring packs. We then show how the fitted mechanistic home range model can be used to correctly predict observed shifts in the patterns of coyote space-use in response to perturbation.

Animals↗

PubMed2006

A spatially explicit model for an Allee effect: why wolves recolonize so slowly in Greater Yellowstone.

A reduced probability of finding mates at low densities is a frequently hypothesized mechanism for a component Allee effect. At low densities dispersers are less likely to find mates and establish new breeding units. However, many mathematical models for an Allee effect do not make a distinction between breeding group establishment and subsequent population growth. Our objective is to derive a spatially explicit mathematical model, where dispersers have a reduced probability of finding mates at low densities, and parameterize the model for wolf recolonization in the Greater Yellowstone Ecosystem (GYE). In this model, only the probability of establishing new breeding units is influenced by the reduced probability of finding mates at low densities. We analytically and numerically solve the model to determine the effect of a decreased probability in finding mates at low densities on population spread rate and density. Our results suggest that a reduced probability of finding mates at low densities may slow recolonization rate.

Acclimatization↗

PubMed2006

A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: analysis of a "highly twisted" benzimidazole-diamidine.

A general strategy for the rapid structural analysis of DNA binding ligands is described as it was applied to the study of RT29, a benzimidazole-diamidine compound containing a highly twisted diphenyl ether linkage. By combining the existing high-throughput fluorescent intercalator displacement (HT-FID) assay developed by Boger et al. and a high-resolution (HR) host-guest crystallographic technique, a system was produced that was capable of determining detailed structural information pertaining to RT29-DNA interactions within approximately 3 days. Our application of the HT/HR strategy immediately revealed that RT29 has a preference for 4-base pair (bp), A.T-rich sites (AATT) and a similar tolerance and affinity for three A-T-bp sites (such as ATTC) containing a G.C bp. On the basis of these selectivities, oligonucleotides were designed and the host-guest crystallographic method was used to generate diffraction quality crystals. Analysis of the resulting crystal structures revealed that the diphenyl ether moiety of RT29 undergoes conformational changes that allow it to adopt a crescent shape that now complements the minor groove structure. The presence of a G.C bp in the RT29 binding site of ATTC did not overly perturb its interaction with DNA-the compound adjusted to the nucleobases that were available through water-mediated interactions. Our analyses suggest that the HT/HR strategy may be used to expedite the screening of novel minor groove binding compounds leading to a direct, HR structural determination.

Base Pairing↗

PubMed2006

Effects of heterogeneity on spread and persistence in rivers.

The question how aquatic populations persist in rivers when individuals are constantly lost due to downstream drift has been termed the "drift paradox." Recent modeling approaches have revealed diffusion-mediated persistence as a solution. We study logistically growing populations with and without a benthic stage and consider spatially varying growth rates. We use idealized hydrodynamic equations to link river cross-sectional area to flow speed and assume heterogeneity in the form of alternating patches, i.e., piecewise constant conditions. We derive implicit formulae for the persistence boundary and for the dispersion relation of the wave speed. We explicitly discuss the influence of flow speed, cross-sectional area and benthic stage on both persistence and upstream invasion speed.

Animals↗

PubMed2006

A comparison of continuous and discrete-time West Nile virus models.

The first recorded North American epidemic of West Nile virus was detected in New York state in 1999, and since then the virus has spread and become established in much of North America. Mathematical models for this vector-transmitted disease with cross-infection between mosquitoes and birds have recently been formulated with the aim of predicting disease dynamics and evaluating possible control methods. We consider discrete and continuous time versions of the West Nile virus models proposed by Wonham et al. [Proc. R. Soc. Lond. B 271:501-507, 2004] and by Thomas and Urena [Math. Comput. Modell. 34:771-781, 2001], and evaluate the basic reproduction number as the spectral radius of the next-generation matrix in each case. The assumptions on mosquito-feeding efficiency are crucial for the basic reproduction number calculation. Differing assumptions lead to the conclusion from one model [Wonham, M.J. et al., [Proc. R. Soc. Lond. B] 271:501-507, 2004] that a reduction in bird density would exacerbate the epidemic, while the other model [Thomas, D.M., Urena, B., Math. Comput. Modell. 34:771-781, 2001] predicts the opposite: a reduction in bird density would help control the epidemic.

Algorithms↗

PubMed2006

Fluorescent intercalator displacement analyses of DNA binding by the peptide-derived natural products netropsin, actinomycin, and bleomycin.

The response of the high-throughput fluorescent intercalator displacement (HT-FID) assay reported recently by Boger et al. to peptide-based DNA binding intercalators and metal complexes was examined through the study of actinomycin and Co(III).bleomycin-B2. Along with a validation of netropsin that illustrated the good laboratory-to-laboratory reproducibility of the assay, our examination of actinomycin revealed results for a four base pair cassette library of DNA hairpins that paralleled the known DNA site-selectivity of this agent and also indicated the involvement of the flanking sequences of the hairpin oligonucleotide. In addition, for Co(III).bleomycin-B2 the established cleavage site-selectivity for 5'-GT and 5'-GC sites was correlated to drug-DNA association in this binding-only assay; our results also suggest a tetranucleotide site-selectivity for metallobleomycin involving cross-strand, 'back-to-back' 5'-GT and 5'-GC sites such as 5'-ACGT and 5'-ACGC.

Anti-Bacterial Agents↗

PubMed2006

Transmission assumptions generate conflicting predictions in host-vector disease models: a case study in West Nile virus.

This review synthesizes the conflicting outbreak predictions generated by different biological assumptions in host-vector disease models. It is motivated by the North American outbreak of West Nile virus, an emerging infectious disease that has prompted at least five dynamical modelling studies. Mathematical models have long proven successful in investigating the dynamics and control of infectious disease systems. The underlying assumptions in these epidemiological models determine their mathematical structure, and therefore influence their predictions. A crucial assumption is the host-vector interaction encapsulated in the disease-transmission term, and a key prediction is the basic reproduction number, R(0). We connect these two model elements by demonstrating how the choice of transmission term qualitatively and quantitatively alters R(0) and therefore alters predicted disease dynamics and control implications. Whereas some transmission terms predict that reducing the host population will reduce disease outbreaks, others predict that this will exacerbate infection risk. These conflicting predictions are reconciled by understanding that different transmission terms apply biologically only at certain population densities, outside which they can generate erroneous predictions. For West Nile virus, R(0) estimates for six common North American bird species indicate that all would be effective outbreak hosts.

Animals↗

PubMed2005

Transmission dynamics of parasitic sea lice from farm to wild salmon.

Marine salmon farming has been correlated with parasitic sea lice infestations and concurrent declines of wild salmonids. Here, we report a quantitative analysis of how a single salmon farm altered the natural transmission dynamics of sea lice to juvenile Pacific salmon. We studied infections of sea lice (Lepeophtheirus salmonis and Caligus clemensi) on juvenile pink salmon (Oncorhynchus gorbuscha) and chum salmon (Oncorhynchus keta) as they passed an isolated salmon farm during their seaward migration down two long and narrow corridors. Our calculations suggest the infection pressure imposed by the farm was four orders of magnitude greater than ambient levels, resulting in a maximum infection pressure near the farm that was 73 times greater than ambient levels and exceeded ambient levels for 30 km along the two wild salmon migration corridors. The farm-produced cohort of lice parasitizing the wild juvenile hosts reached reproductive maturity and produced a second generation of lice that re-infected the juvenile salmon. This raises the infection pressure from the farm by an additional order of magnitude, with a composite infection pressure that exceeds ambient levels for 75 km of the two migration routes. Amplified sea lice infestations due to salmon farms are a potential limiting factor to wild salmonid conservation.

Animal Migration↗

PubMed2005

Spreading speeds as slowest wave speeds for cooperative systems.

It is well known that in many scalar models for the spread of a fitter phenotype or species into the territory of a less fit one, the asymptotic spreading speed can be characterized as the lowest speed of a suitable family of traveling waves of the model. Despite a general belief that multi-species (vector) models have the same property, we are unaware of any proof to support this belief. The present work establishes this result for a class of multi-species model of a kind studied by Lui [Biological growth and spread modeled by systems of recursions. I: Mathematical theory, Math. Biosci. 93 (1989) 269] and generalized by the authors [Weinberger et al., Analysis of the linear conjecture for spread in cooperative models, J. Math. Biol. 45 (2002) 183; Lewis et al., Spreading speeds and the linear conjecture for two-species competition models, J. Math. Biol. 45 (2002) 219]. Lui showed the existence of a single spreading speed c(*) for all species. For the systems in the two aforementioned studies by the authors, which include related continuous-time models such as reaction-diffusion systems, as well as some standard competition models, it sometimes happens that different species spread at different rates, so that there are a slowest speed c(*) and a fastest speed c(f)(*). It is shown here that, for a large class of such multi-species systems, the slowest spreading speed c(*) is always characterized as the slowest speed of a class of traveling wave solutions.

Alleles↗

PubMed2004

An epidemiological model for West Nile virus: invasion analysis and control applications.

Infectious diseases present ecological and public health challenges that can be addressed with mathematical models. Certain pathogens, however, including the emerging West Nile virus (WN) in North America, exhibit a complex seasonal ecology that is not readily analysed with standard epidemiological methods. We develop a single-season susceptible-infectious-removed (SIR) model of WN cross-infection between birds and mosquitoes, incorporating specific features unique to WN ecology. We obtain the disease reproduction number, R0, and show that mosquito control decreases, but bird control increases, the chance of an outbreak. We provide a simple new analytical and graphical method for determining, from standard public health indicators, necessary mosquito control levels. We extend this method to a seasonally variable mosquito population and outline a multi-year model framework. The model's numerical simulations predict disease levels that are consistent with independent data.

Animals↗

PubMed2003

Spatially-explicit matrix models. A mathematical analysis of stage-structured integrodifference equations.

This paper is concerned with mathematical analysis of the 'critical domain-size' problem for structured populations. Space is introduced explicitly into matrix models for stage-structured populations. Movement of individuals is described by means of a dispersal kernel. The mathematical analysis investigates conditions for existence, stability and uniqueness of equilibrium solutions as well as some bifurcation behaviors. These mathematical results are linked to species persistence or extinction in connected habitats of different sizes or fragmented habitats; hence the framework is given for application of such models to ecology. Several approximations which reduce the complexity of integrodifference equations are given. A simple example is worked out to illustrate the analytical results and to compare the behavior of the integrodifference model to that of the approximations.

Algorithms↗

PubMed2002

An ounce of prevention or a pound of cure: bioeconomic risk analysis of invasive species.

Numbers of non-indigenous species--species introduced from elsewhere - are increasing rapidly worldwide, causing both environmental and economic damage. Rigorous quantitative risk-analysis frameworks, however, for invasive species are lacking. We need to evaluate the risks posed by invasive species and quantify the relative merits of different management strategies (e.g. allocation of resources between prevention and control). We present a quantitative bioeconomic modelling framework to analyse risks from non-indigenous species to economic activity and the environment. The model identifies the optimal allocation of resources to prevention versus control, acceptable invasion risks and consequences of invasion to optimal investments (e.g. labour and capital). We apply the model to zebra mussels (Dreissena polymorpha), and show that society could benefit by spending up to US$324 000 year(-1) to prevent invasions into a single lake with a power plant. By contrast, the US Fish and Wildlife Service spent US$825 000 in 2001 to manage all aquatic invaders in all US lakes. Thus, greater investment in prevention is warranted.

Animals↗

PubMed2002

Home range formation in wolves due to scent marking.

Social carnivores, such as wolves and coyotes, have distinct and well-defined home ranges. During the formation of these home ranges scent marks provide important cues regarding the use of space by familiar and foreign packs. Previous models for territorial pattern formation have required a den site as the organizational center around which the territory is formed. However, well-defined wolf home ranges have been known to form in the absence of a den site, and even in the absence of surrounding packs. To date, the quantitative models have failed to describe a mechanism for such a process. In this paper we propose a mechanism. It involves interaction between scent marking and movement behavior in response to familiar scent marks. We show that the model yields distinct home ranges by this new means, and that the spatial profile of these home ranges is different from those arising from the territorial interactions with den sites.

Animals↗

PubMed2002

Spreading speed and linear determinacy for two-species competition models.

One crucial measure of a species' invasiveness is the rate at which it spreads into a competitor's environment. A heuristic spread rate formula for a spatially explicit, two-species competition model relies on 'linear determinacy' which equates spread rate in the full nonlinear model with spread rate in the system linearized about the leading edge of the invasion. However, linear determinacy is not always valid for two-species competition; it has been shown numerically that the formula only works for certain values of model parameters when the model is diffusive Lotka-Volterra competition [2]. This paper derives a set of sufficient conditions for linear determinacy in spatially explicit two-species competition models. These conditions can be interpreted as requiring sufficiently large dispersal of the invader relative to dispersal of the out-competed resident and sufficiently weak interactions between the resident and the invader. When these conditions are not satisfied, spread rate may exceed linearly determined predictions. The mathematical methods rely on the application of results established in a companion paper [11].

Animals↗

PubMed2002

Analysis of linear determinacy for spread in cooperative models.

The discrete-time recursion system u_[n+1]=Q[u_n] with u_n(x) a vector of population distributions of species and Q an operator which models the growth, interaction, and migration of the species is considered. Previously known results are extended so that one can treat the local invasion of an equilibrium of cooperating species by a new species or mutant. It is found that, in general, the resulting change in the equilibrium density of each species spreads at its own asymptotic speed, with the speed of the invader the slowest of the speeds. Conditions on Q are given which insure that all species spread at the same asymptotic speed, and that this speed agrees with the more easily calculated speed of a linearized problem for the invader alone. If this is true we say that the recursion has a single speed and is linearly determinate. The conditions are such that they can be verified for a class of reaction-diffusion models.

Animals↗

PubMedDate not supplied

Dental mission trips.

Explore the source record for details and available documents.

Dental Care↗