Development of an index of abundance for pygmy rabbit populations

The pygmy rabbit (Brachylagus idahoensis) is a cryptic, burrowing lagomorph of conservation concern for which an efficient method to monitor populations is needed for conservation planning. We developed an index of abundance based on density of active burrow systems at 7 sites (57.2–118.5 ha) in east central Idaho. We conducted censuses of burrow systems and used mark-resight surveys of 80 radio-collared individuals to estimate density of rabbits. At 5 sites, we also used a second method to estimate rabbit numbers based on presence of tracks in snow around burrow systems. We evaluated patterns of burrow use by individuals and examined the relationship between vegetation structure and density of rabbits. Density of active burrow systems varied from 0.19 to 3.46 per ha, and density of rabbits ranged from 0.02 to 0.46 per ha. Number of burrow systems used by individuals increased with density of available burrows, which supported a nonlinear relationship between abundance of burrows and rabbits. Population density increased curvilinearly with density of active burrows accounting for >75% of the variation (r² = 0.79) in population estimates across sites. We documented a positive relationship between visual obstruction of vegetation and density of rabbits across 6 of the study sites. Our results suggest that density of burrows can serve as an index for monitoring changes in abundance of pygmy rabbits in east central Idaho and that this index also might be useful for monitoring changes in relative abundance over time at other locations. To assess abundance at larger spatial scales or across different regions, the index should be calibrated under regional conditions and site-level covariates should be evaluated. © 2011 The Wildlife Society.     

Linyphiid spider populations in sustainable wheat-clover bi-cropping compared to conventional wheat-growing practice

Linyphiid web densities in wheat-clover bi-crop systems where winter wheat was grown in an under-storey of white clover were compared with web densities estimated in conventional wheat-growing systems. The web densities in the wheat-clover bi-crop systems were on average between 200 and 250 webs per square-metre when the densities peaked, while the estimated average web density peak levels under conventional growing practices were 100–150 webs per square-metre. Repeated Measure anova tests show significant differences between the estimated mean web density levels of the bi-crop systems compared to the mean density levels of the conventional growing systems in two consecutive growing seasons. Particularly, Bathyphantes gracilis and Tenuiphantes tenuis took advantage of the more heterogeneous conditions with high secondary vegetation layer density and high food animal supply in the bi-crop plots compared to the more homogeneous conditions under conventional wheat-growing practices with low food animal supply. Structural equation modelling with a data set pooled from four different wheat-growing practices shows that the linyphiid juvenile production is influenced by the number of collembolans accessible as food animals for the adult females. The modelling demonstrates the importance of the detritus food chain, particularly for the juvenile recruitment.     

The influence of weather and microclimate on Dalbulus maidis (Homoptera: Cicadellidae) flight activity and the incidence of diseases within maize and bean monocultures and bicultures in tropical America

Mixed cropping systems in tropical America have been shown to be less prone than monocultures to damage from pathogens carried by insects. This finding formed the basis for a series of experiments conducted in Costa Rica to evaluate the hypothesis that mixed cropping systems create a physical environment that influences vector movement and consequently the spread of leafhopper-borne pathogens. The principle finding of the study is that both the mixture of plants and planting density have little influence on the spread of pathogens by Dalbulus maidis, an oligophagus leafhopper which prefers maize, within maize and bean single and mixed cropping systems. Leafhopper flight activity proved similar for high and low density monocultures and bicultures. The number of leafhoppers immigrating to and emigrating from a field appears dependent on the size of the field, not the density of maize plants. Single and mixed crops with the same density of maize plants were equally prone to damage by pathogens carried by leafhoppers. The lower percentage infection in high density than in low density maize treatments resulted from fewer vectors per plant in the former.     

Cell density sensing and size determination

The social amoeba Dictyostelium discoideum is one of the leading model systems used to study how cells count themselves to determine the number and/or density of cells. In this review, we describe work on three different cell-density sensing systems used by Dictyostelium. The first involves a negative feedback loop in which two secreted signals inhibit cell proliferation during the growth phase. As the cell density increases, the concentrations of the secreted factors concomitantly increase, allowing the cells to sense their density. The two signals act as message authenticators for each other, and the existence of two different signals that require each other for activity may explain why previous efforts to identify autocrine proliferation-inhibiting signals in higher eukaryotes have generally failed. The second system involves a signal made by growing cells that is secreted only when they starve. This then allows cells to sense the density of just the starving cells, and is an example of a mechanism that allows cells in a tissue to sense the density of one specific cell type. The third cell density counting system involves cells in aggregation streams secreting a signal that limits the size of fruiting bodies. Computer simulations predicted, and experiments then showed, that the factor increases random cell motility and decreases cell-cell adhesion to cause streams to break up if there are too many cells in the stream. Together, studies on Dictyostelium cell density counting systems will help elucidate how higher eukaryotes regulate the size and composition of tissues.     

Predictions of bone remodeling around dental implant systems

This study presents the implementation of a mathematical bone remodeling algorithm to bone adaptation in the premolar area of the mandible around various dental implant systems, and thus sheds a new perspective to the complex interactions in dental implant mechanics. A two-dimensional, plane strain model of the bone was built from a CT-scan. The effect of implant contour on internal bone remodeling was investigated by considering four dental implant systems with contours similar to commercially available ones and another four with cylindrical and conical cross-sections. The remodeling algorithm predicts non-homogeneous density/elastic modulus distribution; and, implant contour has some effect on how this is distributed. Bone density is predicted to increase on the tips of the threads of the implants, but to decrease inside the grooves. Threadless implants favor to develop a softer bone around their periphery, compared to implant systems that have threads. The overall contour (dimensions and the shape) of an implant affect the bone density redistribution, but the differences between different implant systems are relatively small.     

Herbivore regulation and irreversible vegetation change in semi-arid grazing systems

Models made to explain sudden and irreversible vegetation shifts in semi-arid grasslands typically assume that herbivore density is independent of the state of the vegetation, e.g., under the control of humans. We relax this assumption and investigate the mathematical implications of vegetation-regulated herbivore population dynamics. We show that irreversible vegetation change may also occur in systems where herbivore population dynamics are affected by changes in plant standing crop. Our analysis furthermore shows that irreversible vegetation change may occur for a larger set of soil and climatic conditions when herbivore numbers are independent of the vegetation, as compared to systems where vegetation density determines herbivore population size. Hence, our analysis suggests that irreversible vegetation change is less likely to occur in systems with natural herbivore population dynamics than in systems where humans control herbivore density.     

Evolutionary feedback mediated through population density, illustrated with viruses in chemostats

A cornerstone of evolutionary ecology is that population density affects adaptation: r and K selection is the obvious example. The reverse is also appreciated: adaptation impacts population density. Yet, empirically demonstrating a direct connection between population density and adaptation is challenging. Here, we address both evolution and ecology of population density in models of viral (bacteriophage) chemostats. Chemostats supply nutrients for host cell growth, and the hosts are prey for viral reproduction. Two different chemostat designs have profoundly different consequences for viral evolution. If host and virus are confined to the same chamber, as in a predator-prey system, viral regulation of hosts feeds back to maintain low viral density (measured as infections per cell). Viral adaptation impacts host density but has a small effect on equilibrium viral density. More interesting are chemostats that supply the viral population with hosts from a virus-free refuge. Here, a type of evolutionary succession operates: adaptation at low viral density leads to higher density, but high density then favors competitive ability. Experiments support these models with both phenotypic and molecular data. Parallels to these designs exist in many natural systems, so these experimental systems may yield insights to the evolution and regulation of natural populations.     

Host-parasite population dynamics under combined frequency- and density-dependent transmission

Many host‐parasite models assume that transmission increases linearly with host population density (‘density‐dependent transmission’), but various alternative transmission functions have been proposed in an effort to capture the complexity of real biological systems. The most common alternative (usually applied to sexually transmitted parasites) assumes instead that the rate at which hosts contact one another is independent of population density, leading to ‘frequency‐dependent’ transmission. This straight‐forward distinction generates fundamentally different dynamics (e.g. deterministic, parasite‐driven extinction with frequency‐ but not density‐dependence). Here, we consider the situation where transmission occurs through two different types of contact, one of which is density‐dependent (e.g. social contacts), the other density‐independent (e.g. sexual contacts). Drawing on a range of biological examples, we propose that this type of contact structure may be widespread in natural populations. When our model is characterized mainly by density‐dependent transmission, we find that allowing even small amounts of transmission to occur through density‐independent contacts leads to the possibility of deterministic, parasite‐driven extinction (and lowers the threshold for parasite persistence). Contrastingly, allowing some density‐dependent transmission to occur in a model characterized mainly by density‐independent contacts (i.e. by frequency‐dependent transmission) does not affect the extinction threshold, but does increase the likelihood of parasite persistence. The idea that directly transmitted parasites exploit different types of host contact is not new, but here we show that the impact on dynamics can be fundamental even in the simplest cases. For example, in systems where density‐dependent transmission is normally assumed de facto, we show that parasite‐driven extinction can occur if a small amount of transmission occurs through density‐independent contacts. Many empirical studies are still guided by the traditional density/frequency dichotomy, but our combined transmission function may provide a better model for systems in which both types of transmission occur.     

Engineering challenges in high density cell culture systems

High density cell culture systems offer the advantage of production of bio-pharmaceuticals in compact bioreactors with high volumetric production rates; however, these systems are difficult to design and operate. First of all, the cells have to be retained in the bioreactor by physical means during perfusion. The design of the cell retention is the key to performance of high density cell culture systems. Oxygenation and media design are also important for maximizing the cell number. In high density perfusion reactors, variable cell density, and hence the metabolic demand, require constant adjustment of perfusion rates. The use of cell specific perfusion rate (CSPR) control provides a constant environment to the cells resulting in consistent production. On-line measurement of cell density and metabolic activities can be used for the estimation of cell densities and the control of CSPR. Issues related to mass transfer and mixing become more important at high cell densities. Due to the difference in mass transfer coefficients for oxygen and CO₂, a significant accumulation of dissolved CO₂ is experienced with silicone tubing aeration. Also, mixing is observed to decrease at high densities. Base addition, if not properly done, could result in localized cell lysis and poor culture performance. Non-uniform mixing in reactors promotes the heterogeneity of the culture. Cell aggregation results in segregation of the cells within different mixing zones. This paper discusses these issues and makes recommendations for further development of high density cell culture bioreactors.     

Root length dynamics in agroforestry with Gliricidia sepium as compared to sole cropping in the semi-deciduous rainforest zone of West Africa

Tree root systems may improve soil fertility through carbon inputs, uptake of leachable nutrients and maintenance of soil biomass, but can at the same time reduce crop yields by competition for water and nutrients. Quantitative information about the positive and negative effects of tree roots and their changes in space and time are necessary for the optimization of agroforestry associations. An alley cropping experiment was layed out as a randomized complete block design on a Plinthic Lixisol/Ferralic Cambisol with Gliricidia sepium hedgerows at 5 m distance, including a sole cropping control. The development of root systems was monitored by sequential soil coring (eight samplings) during one year, with maize and groundnut as crops. Additional information is presented from a single sampling for rice during the foregoing year. Pronounced fluctuations of live root length density indicated an important variability in the nutrient and water uptake capacity of the vegetation. At low total root length density, the hedgerows affected the root development in the agroforestry plots directly by the presence of their root systems. At high root length density, they affected root development mainly by improving crop root growth and influencing the composition of the spontaneous vegetation. The root length density of the hedgerows was too low to compete with the crops for soil resources. The hedgerows tended to increase root length densities in the subsoil when few roots were present, thus possibly reducing the risk of nutrient leaching. However, the length density of the perennial root systems decreased during the cropping season, presumably as an effect of repeated pruning, and attained minimum values almost at the same time as the crops. Trees with denser root systems which are less frequently pruned may be more efficient in achieving closer nutrient cycles, though at the cost of higher root competition with crops.     

Quorum-sensing regulation of gene expression: Fundamental and applied aspects and the role in bacterial communication

Quorum sensing (QS) is a specific type of regulation of gene expression in bacteria; it is dependent on the population density. QS systems include two obligate components: a low-molecular-weight regulator (autoinducer), readily diffusible through the cytoplasmic membrane, and a regulatory receptor protein, which interacts with the regulator. As the bacterial population reaches a critical level of density, autoinducers accumulate to a necessary threshold value and abrupt activation (induction) of certain genes and operons occurs. By means of low-molecular-weight regulators, bacteria accomplish communication between cells belonging to the same or different species, genera, and even families. QS systems have been shown to play a key role in the regulation of various metabolic processes in bacteria and to function as global regulators of the expression of bacterial genes. Data are presented on different types of QS systems present in bacteria of various taxonomic groups, on the species specificity of these systems, and on communication of bacteria by means of QS systems. The possibility is considered of using QS regulation systems as targets while combating bacterial infections; other applied aspects of QS investigation are discussed.     

Quorum-sensing regulation of gene expression: fundamental and applied aspects and the role in bacterial communication

Quorum sensing (QS) is a specific type of regulation of gene expression in bacteria; it is dependent on the population density. QS systems include two obligate components: a low-molecular-weight regulator (autoinducer), readily diffusible through the cytoplasmic membrane, and a regulatory receptor protein, which interacts with the regulator. As the bacterial population reaches a critical level of density, autoinducers accumulate to a necessary threshold value and abrupt activation (induction) of certain genes and operons occurs. By means of low-molecular-weight regulators, bacteria accomplish communication between cells belonging to the same or different species, genera, and even families. QS systems have been shown to play a key role in the regulation of various metabolic processes in bacteria and to function as global regulators of the expression of bacterial genes. Data are presented on different types of QS systems present in bacteria of various taxonomic groups, on the species specificity of these systems, and on communication of bacteria by means of QS systems. The possibility is considered of using QS regulation systems as targets while combating bacterial infections; other applied aspects of QS investigation are discussed.     

Electrophysiology of growth control and acupuncture

Bioelectric fields have been shown to interact with morphogens and guide growth control. The morphogenetic singularity theory published a decade ago suggests that organizing centers have high density of gap junctions and high electrical conductance. They are the singular points in morphogen gradient and bioelectric field. A growth control system originates from a network of organizing centers containing under-differentiated cells and retains its regulatory functions after embryogenesis. The formation and maintenance of all the physiological systems are directly dependent on the activity of the growth control system. The evolutionary origin of the growth control system is likely to have preceded all the other physiological systems. Its genetic blueprint might have served as a template from which the newer systems evolved. The growth control signal transduction is embedded in the activity of the function-based physiological systems. The regulation of most physiological processes is through growth control mechanisms such as hypertrophy, hyperplasia, atrophy, and apoptosis. Acupuncture points, which also have high electrical conductance and high density of gap junctions, originate from organizing centers. This theory can explain the distribution and non-specific activation of organizing centers and many research results in acupuncture. In several 'prospective blind trials', recent research results have supported its corollary on the role of singularity and separatrix in morphogenesis, the predictions on the high electric conductance and the high density of gap junctions at the organizing centers. These advances have broad implications in biomedical sciences.     

Plant population dynamics, pollinator foraging, and the selection of self-fertilization

Many flowering plants rely on pollinators, self-fertilization, or both for reproduction. We model the consequences of these features for plant population dynamics and mating system evolution. Our mating systems-based population dynamics model includes an Allee effect. This often leads to an extinction threshold, defined as a density below which population densities decrease. Reliance on generalist pollinators who primarily visit higher density plant species increases the extinction threshold, whereas autonomous modes of selfing decrease and can eliminate the threshold. Generalist pollinators visiting higher density plant species coupled with autonomous selfing may introduce an effect where populations decreasing in density below the extinction threshold may nonetheless persist through selfing. The extinction threshold and selfing at low density result in populations where individuals adopting a single reproductive strategy exhibit mating systems that depend on population density. The ecological and evolutionary analyses provide a mechanism where prior selfing evolves even though inbreeding depression is greater than one-half. Simultaneous consideration of ecological and evolutionary dynamics confirms unusual features (e.g., evolution into extinction or abrupt increases in population density) implicit in our separate consideration of ecological and evolutionary scenarios. Our analysis has consequences for understanding pollen limitation, reproductive assurance, and the evolution of mating systems.     

Unravelling the role of mate density and sex ratio in competition for pollen

Mate density and sex ratio are commonly used concepts in pollination biology, but are not always clearly distinguished. Here we propose that mate density should only capture the number of male‐phase flowers in a defined area and ignore female‐phase flowers. Sex ratio is the ratio of male and female‐phase flowers in a defined area and captures female–female competition. We use a spatially explicit simulation model to quantify the effect of variation in mate density and sex ratio for plant–pollinator systems characterized by combinations of high or low rates of pollen loss and deposition from pollinator to stigma and then assess the size of pollination neighbourhoods. In efficient systems with relatively little pollen loss, female–female competition is of overriding importance. In contrast, in wasteful systems with high pollen loss rates, mate density becomes the dominant factor and sex ratio is no longer consequential. These patterns were observed at both landscape and local scales. Systems with low deposition and low pollen loss rates are associated with large pollination neighbourhoods, which decline with increasing deposition and pollen loss rates. These results show that mate density and sex ratio should carefully be distinguished and highlight the complex way in which pollen loss interacts with deposition rate, which has not previously been appreciated.     

Density dependence,spatial scale and patterning in sessile biota

Sessile biota can compete with or facilitate each other, and the interaction of facilitation and competition at different spatial scales is key to developing spatial patchiness and patterning. We examined density and scale dependence in a patterned, soft sediment mussel bed. We followed mussel growth and density at two spatial scales separated by four orders of magnitude. In summer, competition was important at both scales. In winter, there was net facilitation at the small scale with no evidence of density dependence at the large scale. The mechanism for facilitation is probably density dependent protection from wave dislodgement. Intraspecific interactions in soft sediment mussel beds thus vary both temporally and spatially. Our data support the idea that pattern formation in ecological systems arises from competition at large scales and facilitation at smaller scales, so far only shown in vegetation systems. The data, and a simple, heuristic model, also suggest that facilitative interactions in sessile biota are mediated by physical stress, and that interactions change in strength and sign along a spatial or temporal gradient of physical stress.     

Prevalence and distribution of Aeromonas hydrophila in the United States.

The abundance of Aeromonas hydrophila was measured in 147 natural aquatic habitats in 30 states and Puerto Rico. Viable cell counts were used to estimate density at all sites by using Rimler-Shotts medium, a differential presumptive medium for A. hydrophila. Temperature, pH, conductivity, salinity, and turbidity were measured simultaneously with water sample collection. The density of A. hydrophila was higher in lotic than in lentic systems. Saline systems had higher densities of A. hydrophila than did freshwater systems. A. hydrophila could not be isolated from extremely saline, thermal, or polluted waters, even though it was found over wide ranges of salinity, conductivity, temperature, pH, and turbidity. Of the water quality parameters measured, only conductivity was significantly regressed with density of A. hydrophila.     

Prevalence and distribution of Aeromonas hydrophila in the United States.

The abundance of Aeromonas hydrophila was measured in 147 natural aquatic habitats in 30 states and Puerto Rico. Viable cell counts were used to estimate density at all sites by using Rimler-Shotts medium, a differential presumptive medium for A. hydrophila. Temperature, pH, conductivity, salinity, and turbidity were measured simultaneously with water sample collection. The density of A. hydrophila was higher in lotic than in lentic systems. Saline systems had higher densities of A. hydrophila than did freshwater systems. A. hydrophila could not be isolated from extremely saline, thermal, or polluted waters, even though it was found over wide ranges of salinity, conductivity, temperature, pH, and turbidity. Of the water quality parameters measured, only conductivity was significantly regressed with density of A. hydrophila.     

Pair distribution functions in small systems: implications for protein structure analysis.

A general formula is derived for the relation between the pair correlation function and the histogram of interparticle distances in small nonuniform systems. The formula is applied to random packings of spheres in a spherical container, which are generated by a Monte Carlo method. When measured properly, the resultant correlation functions are very similar to ones in bulk systems with the same volume fraction of particles. In contrast, the density is very nonuniform as a function of distance from the center of the container. The variation is an order of magnitude for the number density of particle centers, or severalfold for the occupied volume fraction. It is described how these results can be used to analyze the forces that determine protein structure.