resevol: An R package for spatially explicit models of pesticide resistance given evolving pest genomes.

The evolution of pesticide resistance is a widespread problem with potentially severe consequences for global food security. We introduce the resevol R package, which simulates individual-based models of pests with evolving genomes that produce complex, polygenic, and covarying traits affecting pest life history and pesticide resistance. Simulations are modelled on a spatially-explicit and highly customisable landscape in which crop and pesticide application and rotation can vary, making the package a highly flexible tool for both general and tactical models of pest management and resistance evolution. We present the key features of the resevol package and demonstrate its use for a simple example simulating pests with two covarying traits. The resevol R package is open source under GNU Public License. All source code and documentation are available on GitHub.

Predicting transition from selective withdrawal to entrainment in two-fluid stratified systems.

Selective withdrawal is a desired phenomenon in transferring oil from large caverns in the U.S. Strategic Petroleum Reserve (SPR), because entrainment of oil at the time during withdrawal poses a risk of contaminating the environment. Motivated to understand selective withdrawal in an SPR-like orientation, we performed experiments in order to investigate the critical submergence depth as a function of critical flow rate. For the experiments, a tube was positioned through a liquid-liquid interface that draws the lower liquid upward, avoiding entrainment of the upper fluid. Analysis of the normal stress balance across the interface produced a Weber number, utilizing dynamic pressure scaling, that predicted the transition to entrainment. Additionally, an inviscid flow analysis was performed assuming an ellipsoidal control volume surface that produced a linear relationship between the Weber number and the scaled critical submergence depth. This analytical model was validated using the experimental data, resulting in a robust model for predicting transition from selective withdrawal to entrainment.

Melting barriers to faunal exchange across ocean basins.

Accelerated loss of sea ice in the Arctic is opening routes connecting the Atlantic and Pacific Oceans for longer periods each year. These changes may increase the ease and frequency with which marine birds and mammals move between the Pacific and Atlantic Ocean basins. Indeed, recent observations of birds and mammals suggest these movements have intensified in recent decades. Reconnection of the Pacific and Atlantic Ocean basins will present both challenges to marine ecosystem conservation and an unprecedented opportunity to examine the ecological and evolutionary consequences of interoceanic faunal exchange in real time. To understand these changes and implement effective conservation of marine ecosystems, we need to further develop modeling efforts to predict the rate of dispersal and consequences of faunal exchange. These predictions can be tested by closely monitoring wildlife dispersal through the Arctic Ocean and using modern methods to explore the ecological and evolutionary consequences of these movements.

Variation in partner benefits in a shrimp-sea anemone symbiosis.

Symbiotic interactions, where two species occur in close physical proximity for the majority of the participants' lifespans, may constrain the fitness of one or both of the participants. Host choice could result in lineage divergence in symbionts if fitness benefits vary across the interaction with hosts. Symbiotic interactions are common in the marine environment, particularly in the most diverse marine ecosystems: coral reefs. However, the variation in symbiotic interactions that may drive diversification is poorly understood in marine systems. We measured the fecundity of the symbiotic shrimp Periclimenes yucatanicus on two anemone hosts on coral reefs in Panama, and found that while fecundity varies among host species, this variation is explained largely by host size, not species. This suggests that shrimp on larger hosts may have higher fitness regardless of host species, which in turn could drive selection for host choice, a proposed driver of diversification in this group.

Ecological drivers and habitat associations of estuarine bivalves.

Community composition of the infaunal bivalve fauna of the St. Lucie Estuary and southern Indian River Lagoon, eastern Florida was sampled quarterly for 10 years as part of a long-term benthic monitoring program. A total of 38,514 bivalves of 137 taxa were collected and identified. We utilized this data, along with sediment samples and environmental measurements gathered concurrently, to assess the community composition, distribution, and ecological drivers of the infaunal bivalves of this estuary system. Salinity had the strongest influence on bivalve assemblage across the 15 sites, superseding the influences of sediment type, water turbidity, temperature and other environmental parameters. The greatest diversity was found in higher salinity euhaline sites, while the greatest abundance of individual bivalves was found in medium salinity mixohaline sites, the lowest diversity and abundances were found in the low salinity oligohaline sites, demonstrating a strong positive association between salinity and diversity/abundance. Water management decisions for the estuary should incorporate understanding of the role of salinity on bivalve diversity, abundance, and ecosystem function.

Species and size diversity in protective services offered by coral guard-crabs.

Coral guard-crabs in the genus Trapezia are well-documented defenders of their pocilloporid coral hosts against coral predators such as the Crown-of-Thorns seastar (Acanthaster planci complex). The objectives of this study were to examine the protective services of six species of Trapezia against corallivory, and the extent of functional diversity among these Trapezia species. Studies conducted in Mo'orea, French Polynesia showed the Trapezia-coral mutualism protected the host corals from multiple predators through functional diversity in the assemblage of crab symbionts. Species differed in their defensive efficacy, but species within similar size classes shared similar abilities. Smaller-size Trapezia species, which were previously thought to be ineffective guards, play important defensive roles against small corallivores. We also measured the benefits of this mutualism to corals in the midst of an Acanthaster outbreak that reduced the live coral cover on the fore reef to less than 4%. The mutualism may positively affect the reef coral demography and potential for recovery during adverse predation events through shelter of multiple species of small corals near the host coral. Our results show that while functional diversity is supported within the genus, some Trapezia species may be functionally equivalent within the same size class, decreasing the threat of gaps in coral protection caused by absence or replacement of any single Trapezia species.

Housekeeping mutualisms: do more symbionts facilitate host performance?

Mutualisms often involve one host supporting multiple symbionts, whose identity, density and intraguild interactions can influence the nature of the mutualism and performance of the host. However, the implications of multiple co-occurring symbionts on services to a host have rarely been quantified. In this study, we quantified effects of decapod symbionts on removal of sediment from their coral host. Our field survey showed that all common symbionts typically occur as pairs and never at greater abundances. Two species, the crab Trapezia serenei and the shrimp Alpheus lottini, were most common and co-occurred more often than expected by chance. We conducted a mesocosm experiment to test for effects of decapod identity and density on sediment removal. Alone, corals removed 10% of sediment, but removal increased to 30% and 48% with the presence of two and four symbionts, respectively. Per-capita effects of symbionts were independent of density and identity. Our results suggest that symbiont density is restricted by intraspecific competition. Thus, increased sediment removal from a coral host can only be achieved by increasing the number of species of symbionts on that coral, even though these species are functionally equivalent. Symbiont diversity plays a key role, not through added functionality but by overcoming density limitation likely imposed by intraspecific mating systems.

Multiple defender effects: synergistic coral defense by mutualist crustaceans.

The majority of our understanding of mutualisms comes from studies of pairwise interactions. However, many hosts support mutualist guilds, and interactions among mutualists make the prediction of aggregate effects difficult. Here, we apply a factorial experiment to interactions of 'guard' crustaceans that defend their coral host from seastar predators. Predation was reduced by the presence of mutualists (15% reduction in predation frequency and 45% in volume of coral consumed). The frequency of attacks with both mutualists was lower than with a single species, but it did not differ significantly from the expected frequency of independent effects. In contrast, the combined defensive efficacy of both mutualist species reduced the volume of coral tissue lost by 73%, significantly more than the 38% reduction expected from independent defensive efforts, suggesting the existence of a cooperative synergy in defensive behaviors of 'guard' crustaceans. These emergent 'multiple defender effects' are statistically and ecologically analogous to the emergent concept of 'multiple predator effects' known from the predation literature.

Benefits for plants in ant-plant protective mutualisms: a meta-analysis.

Costs and benefits for partners in mutualistic interactions can vary greatly, but surprisingly little is known about the factors that drive this variation across systems. We conducted a meta-analysis of ant-plant protective mutualisms to quantify the effects of ant defenders on plant reproductive output, to evaluate if reproductive effects were predicted from reductions in herbivory and to identify characteristics of the plants, ants and environment that explained variation in ant protection. We also compared our approach with two other recent meta-analyses on ant-plant mutualisms, emphasizing differences in our methodology (using a weighted linear mixed effects model) and our focus on plant reproduction rather than herbivore damage. Based on 59 ant and plant species pairs, ant presence increased plant reproductive output by 49% and reduced herbivory by 62%. The effects on herbivory and reproduction within systems were positively correlated, but the slope of this relationship (0.75) indicated that tolerance to foliar herbivory may be a common plant response to absence of ant guards. Furthermore, the relationship between foliar damage and reproduction varied substantially among systems, suggesting that herbivore damage is not a reliable surrogate for fitness consequences of ant protection. Studies that experimentally excluded ants reported a smaller effect of ant protection on plant reproduction than studies that relied upon natural variation in ant presence, suggesting that study methods can affect results in these systems. Of the ecological variables included in our analysis, only plant life history (i.e., annual or perennial) explained variation in the protective benefit of mutualistic ants: presence of ants benefitted reproduction of perennials significantly more than that of annuals. These results contrast with other quantitative reviews of these relationships that did not include plant life history as an explanatory factor and raise several questions to guide future research on ant-plant protection mutualisms.

Epidemiology of community-acquired meticillin-resistant Staphylococcus aureus obtained from the UK West Midlands region.

SUMMARY: Between January 2005 and December 2005, 199 meticillin-resistant Staphylococcus aureus (MRSA) isolates were obtained from non-hospitalised patients presenting skin and soft tissue infections to local general practitioners. The study area incorporated 57 surgeries from three Primary Care Trusts in the Lichfield, Tamworth, Burntwood, North and East Birmingham regions of Central England, UK. Following antibiotic susceptibility testing, pulsed-field gel electrophoresis, Panton-Valentine leukocidin gene detection and SCCmec element assignment, 95% of the isolates were shown to be related to hospital epidemic strains EMRSA-15 and EMRSA-16. In total 87% of the isolate population harboured SCCmec IV, 9% had SCCmec II and 4% were identified as carrying novel SCCmec IIIa(-mecI). When mapped to patient home postcode, a diverse distribution of isolates harbouring SCCmec II and SCCmec IV was observed; however, the majority of isolates harbouring SCCmec IIIa(-mecI) were from patients residing in the north-west of the study region, highlighting a possible localised clonal group. Transmission of MRSA from the hospital setting into the surrounding community population, as demonstrated by this study, warrants the need for targeted patient screening and decolonisation in both the clinical and community environments.

Patient safety during medication administration: the influence of organizational and individual variables on unsafe work practices and medication errors.

Medication errors are a leading cause of unintended harm to patients, both in Australia and internationally, and there is now a concerted attempt to identify and correct individual and workplace factors that encourage medication errors. The current study used structural equation modelling to measure organizational climate and to test a model with hypothesized links between climate and unsafe medication administration behaviours. The study also examined the possible mediating role of stress and morale. Data were collected from 176 nurses working in rural areas in Australia. The model provided a reasonable fit to the data with organizational climate accounting for 39% of the variance in individual distress, which in turn explained 7% of the variance in self-reported violations. The only variable that made a direct contribution to errors was violations, which accounted for 24% of the variance in medication errors. These findings highlight the importance of monitoring the state of the whole health system. Deficiencies at the organizational level affect the psychological well-being of hospital employees, and distressed employees are more likely to engage in substandard work practices that ultimately endanger the patients under their care.

Revegetation of an abandoned uranium millsite on the Colorado Plateau, Arizona.

We attempted to restore native plants on disturbed sites at a former uranium mill on the Colorado Plateau near Tuba City, AZ. Four-wing saltbush [Atriplex canescens (Pursh) Nutt.] was successfully established in compacted caliche soil and in unconsolidated dune soil when transplants were irrigated through the first summer with 20 L/plant/wk. The caliche soil was ripped before planting to improve water-holding capacity. The diploid saltbush variety, angustifolia, had higher survival and growth than the common tetraploid variety, occidentalis, especially on dune soil. The angustifolia variety grew to 0.3 to 0.4 m3 per plant over 3 yr even though irrigation was provided only during the establishment year. By contrast, direct seeding of a variety of native forbs, grasses, and shrubs yielded poor results, despite supplemental irrigation throughout the first summer. In this arid environment (precipitation = 100 to 200 mm/yr), the most effective revegetation strategy is to establish keystone native shrubs, such as four-wing saltbush, using transplants and irrigation during the establishment year, rather than attempting to establish a diverse plant community all at once.

Cross-regulation of C/EBP alpha and PPAR gamma controls the transcriptional pathway of adipogenesis and insulin sensitivity.

Mice deficient in C/EBP alpha have defective development of adipose tissue, but the precise role of C/EBP alpha has not been defined. Fibroblasts from C/EBP alpha(-/-) mice undergo adipose differentiation through expression and activation of PPAR gamma, though several clear defects are apparent. C/EBP alpha-deficient adipocytes accumulates less lipid, and they do not induce endogenous PPAR gamma, indicating that cross-regulation between C/EBP alpha and PPAR gamma is important in maintaining the differentiated state. The cells also show a complete absence of insulin-stimulated glucose transport, secondary to reduced gene expression and tyrosine phosphorylation for the insulin receptor and IRS-1. These results define multiple roles for C/EBP alpha in adipogenesis and show that cross-regulation between PPAR gamma and C/EBP alpha is a key component of the transcriptional control of this cell lineage.

Michigan versus Kevorkian.

Our personal reflections on the Michigan versus Kevorkian trial highlight the following issues: 1) the switch from physician-assisted suicide to euthanasia, 2) the television showing of the death, 3) the dropping of the prosecution of the charge of physician-assisted suicide, 4) Kevorkian serving as his own defense attorney, trying to argue that ALS was a secondary cause of Thomas Youk's death, 5) Kevorkian's attempt to employ a logical syllogism to demonstrate that euthanasia need not be murder, 6) Kevorkian's initial reference to the civil rights tradition but sudden change to the medical analogy of Nazi medicine: a final solution, 7) the insistence of Kevorkian on "all or nothing" sentencing, 8) the irony of Kevorkian being finally convicted by a prosecutor who was elected on a platform of not prosecuting Kevorkian, 9) Kevorkian hiring a lawyer after the verdict is in, and 10) Kevorkian's threat to starve himself to death if sent to prison.

A conserved region in the first intron of the insulin receptor gene binds nuclear proteins during adipocyte differentiation.

The insulin receptor gene is induced 8 to 10-fold during adipocyte differentiation. Plasmids containing the promoter, exon 1 and a portion of the first intron from either the mouse or human gene are able to modulate the expression of an insulin receptor/CAT gene 3 to 7-fold during differentiation. We have shown that several nuclear proteins from both preadipocyte and adipocyte nuclear extracts bind to two discrete sites within a 278-bp region in the 5' end of the first intron. Sequence comparison between the first intron of the human gene and the mouse gene shows two regions of sequence identity which correspond to the protein binding regions detected by DNase footprinting. One of these sites binds proteins that are enriched in adipocyte nuclear extracts and can be competed by adipose regulatory element, ARE6.

A case-comparison of intermittent exotropia and quality of life measurements.

A Vision Quality of Life Questionnaire that combines the SF-20 and a Vision Quality Scale developed by the authors was pilot tested in a case-comparison of extreme groups, patients with intermittent exotropia (IXT) and those with no vision problems (Non-IXT), at the University of Houston (UH) Optometry Clinic. The purposes of the study were to measure the internal consistency reliability and examine the validity-related evidence of vision function associated with the instrument. The pilot study involved mailing the instrument to 52 patients in each group (IXT and Non-IXT patients). IXT patients were then frequency-matched by age and separately by sex, to control for confounding variables, to Non-IXT group patients. The Cronbach's Alpha internal consistency reliability of both scales was acceptable at > 0.70 for both the IXT and Non-IXT groups. The Wilcoxon signed ranks test was used to determine validity-related evidence. The differences between groups on the SF-20 (p = 0.0276) and Vision Function Scale (VFS) (p = 0.0385) confirm that the scales discriminate between IXT and Non-IXT populations. Two conclusions can be drawn from the pretesting and pilot testing of the SF-20 and the VFS: (1) both have acceptable internal consistency reliability scores, and (2) both show validity-related evidence that they can discriminate vision function between IXT and Non-IXT patient populations.

Proximal enhancer of the human insulin receptor gene binds the transcription factor Sp1.

The insulin receptor is a growth regulator present on the surface of most cells that transmits a mitogenic signal in response to insulin. Thus, the gene for the insulin receptor is constitutively expressed at low levels in all cells. We characterize a constitutive enhancer element that is present in the proximal promoter of the human insulin receptor gene. We have localized the enhancer to a 26-base-pair (26-bp) sequence from -528 to -503. When this sequence is inserted into the proximal promoter, a three- to fourfold increase in promoter activity is observed, and when two copies are inserted, a five- to sixfold increase is seen. Electrophoretic mobility shift analysis demonstrates that nuclear factors binding to this sequence are found in many different cell types. At least two proteins with different specificities bind within this 26-bp sequence. The identity of the predominant binding protein is Sp1, because an oligonucleotide composed of an Sp1 consensus binding sequence can compete for several of the DNA-protein complexes. In addition, we demonstrate that purified Sp1 can bind to the 26-bp oligonucleotide and that this complex comigrates with a DNA-protein complex formed with a HeLa nuclear extract. Finally, an antibody to human Sp1 protein is able to bind to the enhancer DNA/HeLa protein complex and supershift this complex. These findings suggest that this sequence corresponds to a general element that may contribute to the ubiquitous expression of the human insulin receptor gene.

Transcriptional regulation of the insulin receptor gene promoter.

The insulin receptor is a highly regulated promoter. A schematic of several of the elements so far identified is shown in Figure 4. The gene has a basic "housekeeping" promoter which controls low level expression in all cells. This promoter seems to be regulated by the transcription factor, Sp1 at several locations upstream. There are in addition several potential Sp1 binding sites in the first intron. Specific enhancers are present to allow increased expression in certain cell types or in response to hormones. Several potential enhancers have been identified including a potential GRE binding site, muscle specific binding protein, and adipocyte binding protein. Clearly additional elements need to be identified in order to elucidate the complexed interactions which are required for appropriate regulation of the insulin receptor.

Transactivation of the human insulin receptor gene by the CAAT/enhancer binding protein.

Within human insulin receptor gene there are three consensus binding sites for the CAAT/enhancer binding protein (C/EBP). Two sites are located in the 5' flanking region and the other is in the first intron. We have studied the ability of these sequences to be regulated by C/EBP. A eukaryotic expression vector containing these sequences can be transactivated in a dose-dependent manner by a C/EBP expression vector when co-transfected into NIH-3T3 cells. In addition, double stranded oligonucleotides corresponding to two of these sequences can bind C/EBP in a gel retardation assay. These two oligonucleotides can complete with each other to bind C/EBP. These findings suggest that this transcription factor may play a role in the regulation of insulin receptor gene expression in vivo.