Lethal mutagenesis in a structured environment

We analyze how lethal mutagenesis operates in a compartmentalized host. We assume that different compartments receive different amounts of mutagen and that virions can migrate among compartments. We address two main questions: (1) To what extent can refugia, i.e., compartments that receive little mutagen, prevent extinction? (2) Does migration among compartments limit the effectiveness of refugia? We find that if there is little migration, extinction has to be achieved separately in all compartments. In this case, the total dose of mutagen administered to the host needs to be so high that the mutagen is effective even in the refugia. By contrast, if migration is extensive, then lethal mutagenesis is effective as long as the average growth in all compartments is reduced to below replacement levels. The effectiveness of migration is governed by the ratio of virion replication and death rates, R₀. The smaller R₀, the less migration is necessary to neutralize refugia and the less mutagen is necessary to achieve extinction at high migration rates.     

Discrete and continuous mathematical models of DNA branch migration

DNA junctions, known as Holliday junctions, are intermediates in genetic recombination between DNAs. In this structure, two double-stranded DNA helices with similar sequence are joined at a branch point. The branch point can move along these helices when strands with the same sequence are exchanged. Such branch migration is modeled as a random walk. First, we model this process discretely, such that the motion of the branch is represented as transfer between discrete compartments. This is useful in analysing the results of DNA branch migration on junction comprised of synthetic oligonucleotides. The limit in which larger numbers of smaller steps go to continuous motion of the branch is also considered. We show that the behavior of the continuous system is very similar to that of the discrete system when there are more than just a few compartments. Thus, even branch migration on oligonucleotides can be viewed as a continuous process. One consequence of this is that a step size must be assumed when determining rate constants of branch migration.We compare migration where forward and backward movements of the branch are equally probable to biased migration where one direction is favored over the other. In the latter case larger differences between the discrete and continuous cases are predicted, but the differences are still small relative to the experimental error associated with experiments to measure branch migration in oligonucleotides.     

Viral infection in internally structured hosts. I. Conditions for persistent infection

For a virus population within its host, two important levels of structure can be considered: multiple cell types which can be infected, and tissue types or body compartments which may be coupled via movement. We develop a model with both types of structure. Migration between compartments can create "sources" and "sinks" within the virus population, where realized viral growth rate and abundance is lowered in some compartments compared to what would be observed in isolation. Using both analytical and numerical methods, we investigate how this within-host spatial structure affects the conditions for persistent viral infection. We find that migration between compartments makes the establishment of infection more difficult than it would be in the absence of migration, implying that within-host spatial structure combined with viral movement decreases the likelihood of viral establishment. If migration is symmetrical and compartments are heterogeneous, an increase in migration rates between compartments generally makes establishment less likely. This may help to explain the tissue specificity observed for many viruses. There are, however, important exceptions to this result. These include circumstances where the virus initially invades a compartment that is unfavorable to population growth and migration is necessary to infect other parts of the host body. Stochastic aspects of viral establishment may also favor increased migration as it tends to dampen the amplitude of fluctuations in population size during the initial transient phase of establishment.     

Spatial Heterogeneity in Drug Concentrations Can Facilitate the Emergence of Resistance to Cancer Therapy

Acquired resistance is one of the major barriers to successful cancer therapy. The development of resistance is commonly attributed to genetic heterogeneity. However, heterogeneity of drug penetration of the tumor microenvironment both on the microscopic level within solid tumors as well as on the macroscopic level across metastases may also contribute to acquired drug resistance. Here we use mathematical models to investigate the effect of drug heterogeneity on the probability of escape from treatment and the time to resistance. Specifically we address scenarios with sufficiently potent therapies that suppress growth of all preexisting genetic variants in the compartment with the highest possible drug concentration. To study the joint effect of drug heterogeneity, growth rate, and evolution of resistance, we analyze a multi-type stochastic branching process describing growth of cancer cells in multiple compartments with different drug concentrations and limited migration between compartments. We show that resistance is likely to arise first in the sanctuary compartment with poor drug penetrations and from there populate non-sanctuary compartments with high drug concentrations. Moreover, we show that only below a threshold rate of cell migration does spatial heterogeneity accelerate resistance evolution, otherwise deterring drug resistance with excessively high migration rates. Our results provide new insights into understanding why cancers tend to quickly become resistant, and that cell migration and the presence of sanctuary sites with little drug exposure are essential to this end.     

Compartmentalization of surface envelope glycoprotein of human immunodeficiency virus type 1 during acute and chronic infection

Human immunodeficiency virus type 1 is characterized by extensive genetic heterogeneity. Having previously demonstrated that, in the peripheral blood, the initial viral population is more homogeneous than at subsequent stages of infection, we have extended our studies to tissue samples, allowing comparisons between viral populations in peripheral blood and tissues during both the acute and chronic stages of infection. We found that homogeneity in gp120 sequences during the acute infection phase is not just restricted to the peripheral blood but also extends to other tissue compartments. However, in chronically infected individuals, heterogeneous and distinct viral populations were found in different compartments. We therefore conclude that the dominant and homogeneous viral population observed during the acute infection phase is likely to infiltrate lymphoid tissues and form the genetic bases for subsequent diversification. It is therefore likely that the compartmentalization of viral sequences observed in chronically infected patients reflects a gradual diversification of a common dominant viral variant rather than the preferential migration of distinct viral populations to different tissue compartments at the beginning of infection.     

Sequential recruitment of neutrophils into lung and bronchoalveolar lavage fluid in LPS-induced acute lung injury

Infiltration of activated neutrophils [polymorphonuclear leukocytes (PMN)] into the lung is an important component of the inflammatory response in acute lung injury. The signals required to direct PMN into the different compartments of the lung have not been fully elucidated. In a murine model of LPS-induced lung injury, we investigated the sequential recruitment of PMN into the pulmonary vasculature, lung interstitium, and alveolar space. Mice were exposed to aerosolized LPS and bronchoalveolar lavage fluid (BAL), and lungs were harvested at different time points. We developed a flow cytometry-based technique to assess in vivo trafficking of PMN in the intravascular and extravascular lung compartments. Aerosolized LPS induced consistent PMN migration into all lung compartments. We found that sequestration in the pulmonary vasculature occurred within the first hour. Transendothelial migration into the interstitial space started 1 h after LPS exposure and increased continuously until a plateau was reached between 12 and 24 h. Transepithelial migration into the alveolar air space was delayed, as the first PMN did not appear until 2 h after LPS, reaching a peak at 24 h. Transendothelial migration and transepithelial migration were inhibited by pertussis toxin, indicating involvement of Galphai-coupled receptors. These findings confirm LPS-induced migration of PMN into the lung. For the first time, distinct transmigration steps into the different lung compartments are characterized in vivo.     

Freshwater and coastal migration patterns in the silver‐stage eel Anguilla anguilla

The unimpeded downstream movement patterns and migration success of small female and male Anguilla anguilla through a catchment in north‐west Europe were studied using an acoustic hydrophone array along the River Finn and into the Foyle Estuary in Ireland. Twenty silver‐stage A. anguilla (total length, L_T, range: 332–520 mm) were trapped 152 km upstream from a coastal marine sea‐lough outlet and internally tagged with acoustic transmitters of which 19 initiated downstream migration. Migration speed was highly influenced by river flow within the freshwater (FW) compartment. Anguilla anguilla activity patterns were correlated with environmental influences; light, tidal direction and lunar phase all influenced the initiation of migration of tagged individuals. Migration speed varied significantly between upstream and lower river compartments. Individuals migrated at a slower speed in transitional water and sea‐lough compartments compared with the FW compartment. While 88·5% survival was recorded during migration through the upper 121 km of the river and estuary, only 26% of A. anguilla which initiated downstream migration were detected at the outermost end of the acoustic array. Telemetry equipment functioned efficiently, including in the sea‐lough, so this suggests high levels of mortality during sea‐lough migration, or less likely, long‐term sea‐lough residence by silver A. anguilla emigrants. This has important implications for eel management plans.     

Membrane ruffles in cell migration: indicators of inefficient lamellipodia adhesion and compartments of actin filament reorganization

During epithelial cell migration, membrane ruffles can be visualized by phase contrast microscopy as dark waves arising at the leading edge of lamellipodia that move centripetally toward the main cell body. Despite the common use of the term membrane ruffles, their structure, molecular composition, and the mechanisms leading to their formation remained largely unknown. We show here that membrane ruffles differ from the underlying cell lamella by more densely packed bundles of actin filaments that are enriched in the actin cross-linkers filamin and ezrin, pointing to a specific bundling process based on these cross-linkers. The accumulation of phosphorylated, that is, inactivated, cofilin in membrane ruffles suggests that they are compartments of inhibited actin filament turnover. High Rac1 and low RhoA activities were found under conditions of suboptimal integrin-ligand interaction correlating with low lamellipodia persistence, inefficient migration, and high ruffling rates. Based on these findings, we define membrane ruffles as distinct compartments of specific composition that form as a consequence of inefficient lamellipodia adhesion.     

Endothelial cell migration directs testis cord formation

While the molecular cues initiating testis determination have been identified in mammals, the cellular interactions involved in generating a functional testis with cord and interstitial compartments remain poorly understood. Previous studies have shown that testis cord formation relies on cell migration from the adjacent mesonephros, and have implicated immigrant peritubular myoid cells in this process. Here, we used recombinant organ culture experiments to show that immigrant cells are endothelial, not peritubular myoid or other interstitial cells. Inhibition of endothelial cell migration and vascular organisation using a blocking antibody to VE-cadherin, also disrupted the development of testis cords. Our data reveal that migration of endothelial cells is required for testis cord formation, consistent with increasing evidence of a broader role for endothelial cells in establishing tissue architecture during organogenesis.     

The migration of blood cells of the bone marrow through the sinusoidal wall

Electron microscopic observations on the mechanically undisturbed guinea pig bone marrow show that the sinusoidal lining is continuous. There are neither intercellular nor intracellular apertures allowing free communication between the extravascular and intravascular compartments. A transient migration pore is only formed during the diapedetic transit of blood cells. Serial sections show that this aperture is transcellular. A functional continuity of the sinusoidal lining appears to be maintained during the diapedesis of blood cells, which is evident from the absence of a significant extravascular leakage of plasma during this process.     

Morphological intergration between development compartments in the Drosophila wing

Abstract. Developmental integration is the covariation among morphological structures due to connections between the developmental processes that built them. Here we use the methods of geometric morphometrics to study integration in the wing of Drosophila melanogaster . In particular, we focus on the hypothesis that the anterior and posterior wing compartments are separate developmental units that vary independently. We measured both variation among genetically diverse individuals and random differences between body sides of single individuals (fluctuating asymmetry, FA). For both of these sources of variation, the patterns of variation identified by principal component analyses all involved landmarks in both the anterior and posterior compartments simultaneously. Analyses focusing exclusively on the covariation between the anterior and posterior compartments, by the partial least-squares method, revealed pervasive integration of the two compartments, for both individual variation and FA. These analyses clearly indicate that the anterior and posterior compartments are not separate units of variation, but that the covariation between compartments is sufficient to account for nearly all the variation throughout the entire wing. We conclude that variation among individuals as well as the developmental perturbations responsible for FA generate shape variation primarily through developmental processes that are integrated across both compartments. In contrast, much less of the shape variation in our sample can be attributed to the localized processes that establish the identity of particular wing veins.     

Translation initiation factors and active sites of protein synthesis co-localize at the leading edge of migrating fibroblasts

Cell migration is a highly controlled essential cellular process, often dysregulated in tumour cells, dynamically controlled by the architecture of the cell. Studies involving cellular fractionation and microarray profiling have previously identified functionally distinct mRNA populations specific to cellular organelles and architectural compartments. However, the interaction between the translational machinery itself and cellular structures is relatively unexplored. To help understand the role for the compartmentalization and localized protein synthesis in cell migration, we have used scanning confocal microscopy, immunofluorescence and a novel ribopuromycylation method to visualize translating ribosomes. In the present study we show that eIFs (eukaryotic initiation factors) localize to the leading edge of migrating MRC5 fibroblasts in a process dependent on TGN (trans-Golgi network) to plasma membrane vesicle transport. We show that eIF4E and eIF4GI are associated with the Golgi apparatus and membrane microdomains, and that a proportion of these proteins co-localize to sites of active translation at the leading edge of migrating cells.     

Phenotypic consequences of nonrandom migration in the Jirels of Nepal

The phenotypic structure of human populations is shaped by a number of factors such as population size and marital migration. This paper examines the impact of migration on the between-village phenotypic differentiation of the Jirels, a tribal group of eastern Nepal. Data on stature and five cranial measurements for 526 individuals (males and females) are utilized to illustrate the patterns of phenotypic variation. A permutation method is used to generate the phenotypic consequences of random migration constrained to observed levels of movement. The results suggest that Jirel migration is nonrandom and that it produces higher levels of phenotypic differentiation than would result from a random migration process.     

The endosomal adaptor protein APPL1 impairs the turnover of leading edge adhesions to regulate cell migration

Cell migration is a complex process that requires the integration of signaling events that occur in distinct locations within the cell. Adaptor proteins, which can localize to different subcellular compartments, where they bring together key signaling proteins, are emerging as attractive candidates for controlling spatially coordinated processes. However, their function in regulating cell migration is not well understood. In this study, we demonstrate a novel role for the adaptor protein containing a pleckstrin-homology (PH) domain, phosphotyrosine-binding (PTB) domain, and leucine zipper motif 1 (APPL1) in regulating cell migration. APPL1 impairs migration by hindering the turnover of adhesions at the leading edge of cells. The mechanism by which APPL1 regulates migration and adhesion dynamics is by inhibiting the activity of the serine/threonine kinase Akt at the cell edge and within adhesions. In addition, APPL1 significantly decreases the tyrosine phosphorylation of Akt by the nonreceptor tyrosine kinase Src, which is critical for Akt-mediated cell migration. Thus, our results demonstrate an important new function for APPL1 in regulating cell migration and adhesion turnover through a mechanism that depends on Src and Akt. Moreover, our data further underscore the importance of adaptor proteins in modulating the flow of information through signaling pathways.     

Resolution of multiple endosomal compartments associated with the internalization of epidermal growth factor and transferrin

Morphological studies have indicated divergent pathways for the endocytosis of epidermal growth factor (EGF) and transferrin (Tf). In order to obtain biochemical evidence for the pathways associated with the endocytosis of EGF and Tf, a series of Percoll density gradients were employed to separate individual cellular components. Subcellular fractionation of murine fibroblasts exposed to a 2-min pulse of either 125I-Tf or 125I-EGF results in the detection of a total of six cellular compartments related to the internalization process of these ligands. The results of kinetic analysis of the entry of EGF into five membranous fractions is consistent with a model in which ligand is transferred sequentially from the plasma membrane through three distinct prelysosomal environments prior to reaching secondary lysosomes. Each prelysosomal compartment exhibits distinct density and temporal properties in a Percoll density gradient and may represent preexisting endocytic vesicles and/or specific domains of a continuous tubular structure, vesicularized during the process of cell disruption. In addition, the observed differential migration on Percoll density gradients of Tf and EGF containing compartments indicates that the majority of cell bound Tf segregates from EGF and enters a compartment lacking EGF within 5 min of internalization.     

Leukotriene B4-induced neutrophil-mediated endothelial leakage in vitro and in vivo.

The vascular leakage of macromolecules seen in several models after application of leukotriene B4 (LTB4) is mediated by neutrophil granulocytes. We describe here an in vitro assay for this event. Human umbilical vein endothelial cells were grown on polycarbonate filters separating luminal and abluminal compartments of fluid. Both clearance rate of fluorescein isothiocyanate albumin and neutrophil migration through the endothelial monolayer were increased when LTB4 (10-100 nM) was added to the abluminal compartment. However, if LTB4 was instead added to the luminal compartments together with the neutrophils, no migration or change in clearance could be detected. These findings were confirmed in vivo in the cheek pouches of anesthetized hamsters, where extravascular application of LTB4 induced intravascular adhesion of neutrophils, accompanied by neutrophil-dependent vascular leakage. On the other hand, intravascular deposition of LTB4 with micropipettes induced adhesion of leukocytes but no leakage. In conclusion, the presence of neutrophils adhering to endothelium does not necessarily imply the development of neutrophil-mediated vascular leakage. Instead, the leakage appears connected to the process of neutrophil chemotaxis.     

Estimation of Monod model parameters by hybrid differential evolution

A hybrid method based on evolutionary algorithms is developed in this study. Two additional operations, an acceleration operation and a migration operation, are embedded into the original version of differential evolution. These two operations are used for the improvement of the convergence speed without decreasing the diversity among the individuals. The acceleration operation is used to speed up convergence. However, the migration operation is used to increase the diversity among the individuals. The hybrid method is applied to estimate the parameters of the Monod model of a recombinant fermentation process. The model profiles based on ᇆ% variations of the initial concentrations of glucose can fit the experimental observations satisfactorily.     

Population-scale drivers of individual arrival times in migratory birds

1. In migratory species, early arrival on the breeding grounds can often enhance breeding success. Timing of spring migration is therefore a key process that is likely to be influenced both by factors specific to individuals, such as the quality of winter and breeding locations and the distance between them, and by annual variation in weather conditions before and during migration. 2. The Icelandic black-tailed godwit Limosa limosa islandica population is currently increasing and, throughout Iceland, is expanding into poorer quality breeding areas. Using a unique data set of arrival times in Iceland in different years for individuals of known breeding and wintering locations, we show that individuals breeding in lower quality, recently occupied and colder areas arrive later than those from traditionally occupied areas. The population is also expanding into new wintering areas, and males from traditionally occupied winter sites also arrive earlier than those occupying novel sites. 3. Annual variation in timing of migration of individuals is influenced by large-scale weather systems (the North Atlantic Oscillation), but between-individual variation is a stronger predictor of arrival time than the NAO. Distance between winter and breeding sites does not influence arrival times. 4. Annual variation in timing of migration is therefore influenced by climatic factors, but the pattern of individual arrival is primarily related to breeding and winter habitat quality. These habitat effects on arrival patterns are likely to operate through variation in individual condition and local-scale density-dependent processes. Timing of migration thus appears to be a key component of the intricate relationship between wintering and breeding grounds in this migratory system.     

The migration game in habitat network: the case of tuna

Long-distance migration is a widespread process evolved independently in several animal groups in terrestrial and marine ecosystems. Many factors contribute to the migration process and of primary importance are intra-specific competition and seasonality in the resource distribution. Adaptive migration in direction of increasing fitness should lead to the ideal free distribution (IFD) which is the evolutionary stable strategy of the habitat selection game. We introduce a migration game which focuses on migrating dynamics leading to the IFD for age-structured populations and in time varying habitats, where dispersal is costly. The model predicts migration dynamics between these habitats and the corresponding population distribution. When applied to Atlantic bluefin tunas, it predicts their migration routes and their seasonal distribution. The largest biomass is located in the spawning areas which have also the largest diversity in the age-structure. Distant feeding areas are occupied on a seasonal base and often by larger individuals, in agreement with empirical observations. Moreover, we show that only a selected number of migratory routes emerge as those effectively used by tunas.     

Convergence to the island-model coalescent process in populations with restricted migration

In this article we apply some graph-theoretic results to the study of coalescence in a structured population with migration. The graph is the pattern of migration among subpopulations, or demes, and we use the theory of random walks on graphs to characterize the ease with which ancestral lineages can traverse the habitat in a series of migration events. We identify conditions under which the coalescent process in populations with restricted migration, such that individuals cannot traverse the habitat freely in a single migration event, nonetheless becomes identical to the coalescent process in the island migration model in the limit as the number of demes tends to infinity. Specifically, we first note that a sequence of symmetric graphs with Diaconis-Stroock constant bounded above has an unstructured Kingman-type coalescent in the limit for a sample of size two from two different demes. We then show that circular and toroidal models with long-range but restricted migration have an upper bound on this constant and so have an unstructured-migration coalescent in the limit. We investigate the rate of convergence to this limit using simulations.