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.     

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populations, we have investigated the performance of different phasing methods designed for nominally ‘unrelated’ individuals. We find that SHAPEIT2 produces much lower switch error rates in all cohorts compared to other methods, including those designed specifically for isolated populations. In particular, when large amounts of IBD sharing is present, SHAPEIT2 infers close to perfect haplotypes. Based on these results we have developed a general strategy for phasing cohorts with any level of implicit or explicit relatedness between individuals. First SHAPEIT2 is run ignoring all explicit family information. We then apply a novel HMM method (duoHMM) to combine the SHAPEIT2 haplotypes with any family information to infer the inheritance pattern of each meiosis at all sites across each chromosome. This allows the correction of switch errors, detection of recombination events and genotyping errors. We show that the method detects numbers of recombination events that align very well with expectations based on genetic maps, and that it infers far fewer spurious recombination events than Merlin. The method can also detect genotyping errors and infer recombination events in otherwise uninformative families, such as trios and duos. The detected recombination events can be used in association scans for recombination phenotypes. The method provides a simple and unified approach to haplotype estimation, that will be of interest to researchers in the fields of human, animal and plant genetics.     

The Emergence of Two Functions for Spatial Devices in Nicaraguan Sign Language

The emergence of a new sign language since the late 1970s in Nicaragua enables us to capture the effects of successive cohorts of learners on an emerging grammar and to observe how elements are reshaped from one form and function to another. Here we document the contrastive use of a device that has been found to be central to the grammars of sign languages: the spatial modulation of signs. In Nicaraguan Sign Language, this device has two primary functions: expressing the participants of events (that is, indicating who), and describing locations and orientations of referents (that is, indicating where). We ask whether the two uses reduce to a single construction type, or if the more abstract who construction derived from the more iconic and concrete where construction. We compare the first two successive cohorts of deaf signers to acquire the language in its first decade. We find that as learners created new constructions to meet the new functions, they did not simply apply an already developed form more broadly, nor did they develop the more abstract application from the more iconic one. Instead, the more abstract who construction appears to have conventionalized first. Thus, the forms either emerged independently, or split very early in the 1980s, before either had developed as a consistently applied form.     

The Regional Concentrations of S-Adenosyl-l-Methionine, S-Adenosyl-l-Homocysteine, and Adenosine in Rat Brain

Abstract: The concentrations of S -adenosyl- l -methionine (SAM), S -adenosyl- l -homocysteine (SAH), and adenosine (Ado) were determined in whole brain and rat brain regions by HPLC. The whole brain contains, respectively, 22 nmol, 1 nmol, and 64 nmol of SAM, SAH, and Ado per g of wet tissue. Their distribution indicated that SAM and SAH levels are highest in brainstem, whereas the Ado level is highest in cortex. With aging the SAM concentrations decrease in whole brain, brainstem, and hypothalamus (–25%) and SAH levels increase by 90% in striatum and by 160% in cerebellum, while Ado levels are increased in all regions by 100–180%.     

Emergence patterns of Plecoptera in a stream in Oregon, USA

Forty-three species of Plecoptera were collected from emergence traps in an Oregon woodland stream. Adults occurred during every month of the year, but the largest numbers and most species emerged from April to June. Temporal separation of con-generic species occurred within the suborder of Filipalpia, but not in Setipalpia. Some species of Nemoura had split emergence periods. The onset of emergence for a species from year to year generally varied by less than 2 weeks. Peak emergence occurred at least 1-2 weeks after the start ofthe emergence period.     

Holocene Demographic Changes and the Emergence of Complex Societies in Prehistoric Australia

A continental-scale model of Holocene Australian hunter-gatherer demography and mobility is generated using radiocarbon data and geospatial techniques. Results show a delayed expansion and settlement of much of Australia following the termination of the late Pleistocene until after 9,000 years ago (or 9ka). The onset of the Holocene climatic optimum (9-6ka) coincides with rapid expansion, growth and establishment of regional populations across ~75% of Australia, including much of the arid zone. This diffusion from isolated Pleistocene refugia provides a mechanism for the synchronous spread of pan-continental archaeological and linguistic attributes at this time (e.g. Pama-Nyungan language, Panaramitee art style, backed artefacts). We argue longer patch residence times were possible at the end of the optimum, resulting in a shift to more sedentary lifestyles and establishment of low-level food production in some parts of the continent. The onset of El Niño - Southern Oscillation (ENSO; 4.5-2ka) restricted low-level food production, and resulted in population fragmentation, abandonment of marginal areas, and reduction in ranging territory of ~26%. Importantly, climate amelioration brought about by more pervasive La Niña conditions (post-2ka), resulted in an intensification of the mobility strategies and technological innovations that were developed in the early- to mid-Holocene. These changes resulted in population expansion and utilization of the entire continent. We propose that it was under these demographically packed conditions that the complex social and religious societies observed at colonial contact were formed.     

The Genetic Relatedness in Groups of Joint-Nesting Taiwan Yuhinas: Low Genetic Relatedness with Preferences for Male Kin

The relative importance of direct and indirect fitness and, thus, the role of kinship in the evolution of social behavior is much debated. Studying the genetic relatedness of interacting individuals is crucial to improving our understanding of these issues. Here, we used a seven-year data set to study the genetic structure of the Taiwan yuhina (Yuhina brunneciceps), a joint-nesting passerine. Ten microsatellite loci were used to investigate the pair-wised relatedness among yuhina breeding group members. We found that the average genetic relatedness between same-sex group members was very low (0.069 for male dyads and 0.016 for female dyads). There was also a low ratio of closely-related kin (r>0.25) in the cooperative breeding groups of yuhinas (21.59% and 9.68% for male and female dyads, respectively). However, the relatedness of male dyads within breeding groups was significantly higher than female dyads. Our results suggest that yuhina cooperation is maintained primarily by direct fitness benefits to individuals; however, kin selection might play a role in partner choice for male yuhinas. Our study also highlights an important, but often neglected, question: Why do animals form non-kin groups, if kin are available? We use biological market theory to propose an explanation for group formation of unrelated Taiwan yuhinas.     

Marine Plastic Pollution in Waters around Australia: Characteristics,Concentrations, and Pathways

Plastics represent the vast majority of human-made debris present in the oceans. However, their characteristics, accumulation zones, and transport pathways remain poorly assessed. We characterised and estimated the concentration of marine plastics in waters around Australia using surface net tows, and inferred their potential pathways using particle-tracking models and real drifter trajectories. The 839 marine plastics recorded were predominantly small fragments (“microplastics”, median length = 2.8 mm, mean length = 4.9 mm) resulting from the breakdown of larger objects made of polyethylene and polypropylene (e.g. packaging and fishing items). Mean sea surface plastic concentration was 4256.4 pieces km⁻², and after incorporating the effect of vertical wind mixing, this value increased to 8966.3 pieces km⁻². These plastics appear to be associated with a wide range of ocean currents that connect the sampled sites to their international and domestic sources, including populated areas of Australia''s east coast. This study shows that plastic contamination levels in surface waters of Australia are similar to those in the Caribbean Sea and Gulf of Maine, but considerably lower than those found in the subtropical gyres and Mediterranean Sea. Microplastics such as the ones described here have the potential to affect organisms ranging from megafauna to small fish and zooplankton.     

Evaluating Spatial Overlap and Relatedness of White-tailed Deer in a Chronic Wasting Disease Management Zone

Wildlife disease transmission, at a local scale, can occur from interactions between infected and susceptible conspecifics or from a contaminated environment. Thus, the degree of spatial overlap and rate of contact among deer is likely to impact both direct and indirect transmission of infectious diseases such chronic wasting disease (CWD) or bovine tuberculosis. We identified a strong relationship between degree of spatial overlap (volume of intersection) and genetic relatedness for female white-tailed deer in Wisconsin’s area of highest CWD prevalence. We used volume of intersection as a surrogate for contact rates between deer and concluded that related deer are more likely to have contact, which may drive disease transmission dynamics. In addition, we found that age of deer influences overlap, with fawns exhibiting the highest degree of overlap with other deer. Our results further support the finding that female social groups have higher contact among related deer which can result in transmission of infectious diseases. We suggest that control of large social groups comprised of closely related deer may be an effective strategy in slowing the transmission of infectious pathogens, and CWD in particular.     

Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation

On its own, a single cell cannot exert more than a microscopic influence on its immediate surroundings. However, via strength in numbers and the expression of cooperative phenotypes, such cells can enormously impact their environments. Simple cooperative phenotypes appear to abound in the microbial world, but explaining their evolution is challenging because they are often subject to exploitation by rapidly growing, non-cooperative cell lines. Population spatial structure may be critical for this problem because it influences the extent of interaction between cooperative and non-cooperative individuals. It is difficult for cooperative cells to succeed in competition if they become mixed with non-cooperative cells, which can exploit the public good without themselves paying a cost. However, if cooperative cells are segregated in space and preferentially interact with each other, they may prevail. Here we use a multi-agent computational model to study the origin of spatial structure within growing cell groups. Our simulations reveal that the spatial distribution of genetic lineages within these groups is linked to a small number of physical and biological parameters, including cell growth rate, nutrient availability, and nutrient diffusivity. Realistic changes in these parameters qualitatively alter the emergent structure of cell groups, and thereby determine whether cells with cooperative phenotypes can locally and globally outcompete exploitative cells. We argue that cooperative and exploitative cell lineages will spontaneously segregate in space under a wide range of conditions and, therefore, that cellular cooperation may evolve more readily than naively expected.     

Contributions of Hydrology to Vesicular Stomatitis Virus Emergence in the Western USA

Ecosystems - Relationships between environmental variables associated with the spread of vector-borne pathogens, such as RNA viruses transmitted to humans and animals, remain poorly understood....     

Seasonal and Spatial Variability in Lake Michigan Sediment Small-Subunit rRNA Concentrations

We have used molecular biological methods to study the distribution of microbial small-subunit rRNAs (SSU rRNAs), in relation to chemical profiles, in offshore Lake Michigan sediments. The sampling site is at a depth of 100 m, with temperatures of 2 to 4°C year-round. RNA extracted from sediment was probed with radiolabeled oligonucleotides targeting bacterial, archaeal, and eukaryotic SSU rRNAs, as well as with a universal probe. The coverage of these probes in relation to the present sequence database is discussed. Because ribosome production is growth rate regulated, rRNA concentrations are an indicator of the microbial populations active in situ. Over a 1-year period, changes in sedimentary SSU rRNA concentrations followed seasonal changes in surface water temperature and SSU rRNA concentration. Sedimentary depth profiles of oxygen, reduced manganese and iron, and sulfate changed relatively little from season to season, but the nitrate concentration was approximately fivefold higher in April and June 1997 than at the other times sampling was done. We propose that sediment microbial SSU rRNA concentrations at our sampling site are influenced by seasonal inputs from the water column, particularly the settling of the spring diatom bloom, and that the timing of this input may be modulated by grazers, such that ammonia becomes available to sediment microbes sooner than fresh organic carbon. Nitrate production from ammonia by autotrophic nitrifying bacteria, combined with low activity of heterotrophic denitrifying bacteria in the absence of readily degradable organic carbon, could account for the cooccurrence of high nitrate and low SSU rRNA concentrations.     

The Recent Emergence of Plague: A Process of Felonious Evolution

Yersinia pestis, the causative agent of bubonic plague, evolved from closely related Yersinia pseudotuberculosis within the past 20,000 years, an event that corresponds to the end of the last ice age and distribution of Homo sapiens throughout the world. Y. pseudotuberculosis causes chronic but generally mild enteropathogenic infections whereas plague is the most devastating acute disease experienced by mankind. The very recent evolution of plague from its progenitor assures close genomic homogeneity between the two species and thus high probability that disparities in DNA sequence mediate dramatic differences in symptoms of infection. The purpose of this minireview is to define salient distinctions between the genomes of Y. pestis and Y. pseudotuberculosis and to equate unique functions to respective acute and chronic mechanisms of virulence. The significance of these processes is then related to the procedures the organisms use to survive when between hosts (i.e., the flea vector colonized by Y. pestis and natural environments including soil and water in the case of Y. pseudotuberculosis). Next, an attempt is made to order the various mutational events that caused the recent emergence of Y. pestis as a distinct species. Finally, selective pressures such as predatory soil nematodes are considered that possibly influenced the early evolution of those yersiniae now pathogenic to humans.     

Spatial Interaction Among Nontoxic Phytoplankton, Toxic Phytoplankton, and Zooplankton: Emergence in Space and Time

In homogeneous environments, by overturning the possibility of competitive exclusion among phytoplankton species, and by regulating the dynamics of overall plankton population, toxin-producing phytoplankton (TPP) potentially help in maintaining plankton diversity—a result shown recently. Here, I explore the competitive effects of TPP on phytoplankton and zooplankton species undergoing spatial movements in the subsurface water. The spatial interactions among the species are represented in the form of reaction-diffusion equations. Suitable parametric conditions under which Turing patterns may or may not evolve are investigated. Spatiotemporal distributions of species biomass are simulated using the diffusivity assumptions realistic for natural planktonic systems. The study demonstrates that spatial movements of planktonic systems in the presence of TPP generate and maintain inhomogeneous biomass distribution of competing phytoplankton, as well as grazer zooplankton, thereby ensuring the persistence of multiple species in space and time. The overall results may potentially explain the sustainability of biodiversity and the spatiotemporal emergence of phytoplankton and zooplankton species under the influence of TPP combined with their physical movement in the subsurface water.     

Implications of Seedling Emergence to Site Restoration following Bauxite Mining in Western Australia

Seedling emergence of 12 selected northern jarrah (Eucalyptus marginata Donn ex Smith) forest species were investigated to assist Alcoa of Australia Ltd. in maximizing the establishment of topsoil species in rehabilitated bauxite mining sites. The species, which encompassed a range of seed weights (0.024 mg to 87 mg), plant families, seed-storage types, life forms, and germination requirements, were placed on the soil surface and at depths of 1, 2, 5, 10, and 15 cm under controlled conditions in a glasshouse. Ability to emerge from deep burial was found to depend on seed size for species that annually release their seed to the topsoil but not for species that store their seed on the plant. All selected species were capable of emerging from 2 cm depth of burial, but eight of the 12 species were either unable to emerge from 5 cm or showed a significant reduction in emergence from 5 cm depth of burial compared to optimally buried seed. This group included two small-seeded species, Stylidium calcaratum and Chamaescilla corymbosa; the major forest dominant, Eucalyptus marginata; the serotinous canopy-borne seed of Hakea amplexicaulis; and the wind-dispersed seed of Xanthorrhoea gracilis. A few seeds of the legume species Kennedia coccinea, Acacia pulchella, and Bossiaea aquifolium established seedlings from depths of 15 cm. Currently, Alcoa removes the upper 15 cm of topsoil separately from the underlying soil prior to the commencement of mining. This topsoil is respread at a similar depth following mining as part of the rehabilitation procedure. It is recommended that Alcoa continue to strip topsoil to a depth of 15 cm but investigate the option of re-spreading topsoil onto rehabilitated pits at a shallower depth to maximize establishment via the soil seed bank.     

Mixing Carrots and Sticks to Conserve Forests in the Brazilian Amazon: A Spatial Probabilistic Modeling Approach

Annual forest loss in the Brazilian Amazon had in 2012 declined to less than 5,000 sqkm, from over 27,000 in 2004. Mounting empirical evidence suggests that changes in Brazilian law enforcement strategy and the related governance system may account for a large share of the overall success in curbing deforestation rates. At the same time, Brazil is experimenting with alternative approaches to compensate farmers for conservation actions through economic incentives, such as payments for environmental services, at various administrative levels. We develop a spatially explicit simulation model for deforestation decisions in response to policy incentives and disincentives. The model builds on elements of optimal enforcement theory and introduces the notion of imperfect payment contract enforcement in the context of avoided deforestation. We implement the simulations using official deforestation statistics and data collected from field-based forest law enforcement operations in the Amazon region. We show that a large-scale integration of payments with the existing regulatory enforcement strategy involves a tradeoff between the cost-effectiveness of forest conservation and landholder incomes. Introducing payments as a complementary policy measure increases policy implementation cost, reduces income losses for those hit hardest by law enforcement, and can provide additional income to some land users. The magnitude of the tradeoff varies in space, depending on deforestation patterns, conservation opportunity and enforcement costs. Enforcement effectiveness becomes a key determinant of efficiency in the overall policy mix.     

The Effect of Spatial Distributions of Mycoparasites on Biocontrol Efficacy: a Modelling Approach

The spatial distribution of propagules in soil is an important factor in determining the ability of mycoparasites to control soilborne plant pathogens. The assumptions of uniform, random and aggregated propagule distribution were used to evaluate the importance of spatial distribution patterns of propagules of a mycoparasite. For the random and uniform cases explicit expressions were obtained for the average distance between propagules. Average distances among propagules are 40-50% smaller for the random compared to the uniform distribution. For the aggregated case no explicit expression is possible and numerical simulations were used to generate spatial distributions. The consequences for host inactivation by the mycoparasite were evaluated using a simple model of omnidirectional and constant growth of the mycoparasite. A random distribution of propagules gave a considerably slower rate of inactivation than the uniform distribution. Numerical simulations were made to generate comparable patterns of host inactivation for aggregated distributions in which propagule clusters were located at random in three-dimensional space and the distances between propagules with centres followed a normal distribution. The number of propagule centres and propagules/centre varied for a given inoculum density. Parameters were estimated from published data for sclerotia of Sclerotium minor inactivation at different densities of macroconidia of Sporidesmium sclerotivorum. Differences in host inactivation between the uniform and random distributions were small but both gave poor predictions of the field data at low and high densities. The aggregated distribution gave an improved fit for the higher propagule densities but no improvement at the lower. In studying the dynamics of mycoparasites it may be more significant epidemiologically to design treatments based on differences in mean distances between propagules rather than population densities. Density-dependent effects on growth rate need more attention in models and studies on mycoparasite ecology.