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.

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.

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.

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.

Two mutant alleles of the insulin receptor gene in a patient with extreme insulin resistance.

Insulin receptor complementary DNA has been cloned from an insulin-resistant patient with leprechaunism whose receptors exhibited multiple abnormalities in insulin binding. The patient is a compound heterozygote, having inherited two different mutant alleles of the insulin receptor gene. One allele contains a missense mutation encoding the substitution of glutamic acid for lysine at position 460 in the alpha subunit of the receptor. The second allele has a nonsense mutation causing premature chain termination after amino acid 671 in the alpha subunit, thereby deleting both the transmembrane and tyrosine kinase domains of the receptor. Interestingly, the father is heterozygous for this nonsense mutation and exhibits a moderate degree of insulin resistance. This raises the possibility that mutations in the insulin receptor gene may account for the insulin resistance in some patients with non-insulin-dependent diabetes mellitus.

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.

Differential protooncogene expression characterizes histopathologically indistinguishable tumors of the peripheral nervous system.

We have found highly predictable patterns of protooncogene expression in cell lines and tumor tissue of neuroblastoma (NB), a tumor of the peripheral nervous system (PNS). These patterns make it possible to recognize two different genetically definable subgroups among histopathologically indistinguishable tumors. Additionally, we have identified a difference in neurotransmitter biosynthetic enzyme activity in these two subgroups of NB. The patterns of protooncogene expression and neurotransmitter biosynthetic enzymes suggests that these tumors arise in different cells of the PNS.

Indistinguishable patterns of protooncogene expression in two distinct but closely related tumors: Ewing's sarcoma and neuroepithelioma.

Genetic characterization of human tumors promises new insights of biological importance and clinical relevance. We have found that two solid tumors, peripheral neuroepithelioma and Ewing's sarcoma of bone, which share a common cytogenetic rearrangement, are characterized by an indistinguishable and highly reproducible pattern of protooncogene expression. c-myc, N-myc, c-myb, and c-mil/raf-1 are all expressed at similar levels in these tumors. c-fes and c-sis expression was not detected in any specimens of either tumor. In contrast, the protooncogene c-ets-1, located near the breakpoint of the chromosomal translocation in these tumors, is variable in its expression. We also detected high levels of choline acetyltransferase in these tumors, which suggests a common neural origin. Since it is likely that the clinical behavior and therapeutic responsiveness of tumors relate closely to their biological and genetic features, the pattern of protooncogene expression of individual tumors may provide a novel basis for their characterization.

Step conductance increases in bilayer membranes induced by antibody-antigen-complement action.

A sharp rise in the electrical conductance of lipid bilayer membranes was observed following the addition of antigen (bovine serum), antibody (rabbit anti-bovine serum), and complement to the neighboring aqueous phases. At low concentrations, step increases in the conductivity occurred which are consistent with the appearance of about 2.2 nm holes in the membrane. Probably attack or lysis of the lipid bilayer by complement is responsible.

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.

Structural and functional analysis of the insulin receptor promoter.

The insulin receptor plays a critical role in the maintenance of glucose homeostasis. Regulation of this key function must be under stringent controls. In order to study the regulation of insulin receptor gene expression, we have cloned, sequenced and characterized its promoter. The first exon of the insulin receptor gene is embedded in an unusual segment of DNA composed of Alu repeats. The promoter has the characteristics typical of a housekeeping gene. It is GC-rich and has multiple start sites of transcription. A 574 base pair fragment immediately upstream of the translation initiation site contains promoter activity when transfected into eukaryotic cell lines. Deletion analysis was performed to study promoter function. These studies showed that only 150 base pairs of promoter sequence were necessary for promoter function. This region contains three potential binding sites for the transcription factor, Sp1 and a TC box sequence. Furthermore, the fragment functions equally well in either orientation. We have defined an element in this region with enhancer function for both its homologous and a heterologous promoter. In addition, this region seems to contribute some degree of tissue specificity to insulin receptor gene expression.

Mutations in insulin-receptor gene in insulin-resistant patients.

Defects in insulin-receptor function have been associated with insulin-resistant states such as obesity and non-insulin-dependent diabetes mellitus (NIDDM). Several types of mutations in the insulin-receptor gene have been identified in patients with genetic syndromes of extreme insulin resistance. In some patients, insulin resistance results from a decrease in the number of insulin receptors on the cell surface. In one patient with leprechaunism (leprechaun/Minn-1), there is greater than 90% decrease in the levels of insulin-receptor mRNA. This patient is a compound heterozygote for two mutations in the insulin-receptor gene, both of which act in a cis-dominant fashion to decrease levels of mRNA transcribed from that allele. In one allele, there is a nonsense mutation at codon 897. All 22 exons of the other allele have a normal sequence, so that the mutation in this allele appears to map outside the coding sequence of the gene. Impaired insertion in the plasma membrane also causes insulin resistance. In two sisters (patients A-5 and A-8) with type A extreme insulin resistance, there is an 80-90% decrease in the number of insulin receptors expressed on the surface of their cells. Both sisters, whose parents are first cousins, are homozygous for a point mutation in which valine is substituted for phenylalanine at position 382 in the alpha-subunit of the insulin receptor. This mutation retards the posttranslational processing of the receptor and impairs the transport of receptors to the cell surface. Another patient with leprechaunism (leprechaun/Ark-1) is a compound heterozygote with two different mutant alleles of the insulin-receptor gene. In the allele derived from the father, there is a nonsense mutation at codon 672 that truncates the insulin receptor by deleting the COOH-terminal of the alpha-subunit and the entire beta-subunit. This truncated receptor, lacking a transmembrane domain, appears not to be expressed at the plasma membrane. In leprechaun/Ark-1, there is a missense mutation in the allele of the insulin-receptor gene derived from the mother. This point mutation results in substitution of glutamic acid for lysine at position 460 in the COOH-terminal half of the alpha-subunit. This mutation increases receptor affinity and impairs the ability of acid pH to dissociate insulin from the receptor within the endosome. There is a defect in recycling the receptor back to the plasma membrane associated with this defect. This results in an accelerated rate of receptor degradation and a consequent decrease in the number of receptors on the cell surface in vivo.(ABSTRACT TRUNCATED AT 400 WORDS)

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.

Vasoactive intestinal polypeptide and the innervation of the human lacrimal gland.

Vasoactive intestinal polypeptide (VIP) is a biologically active neuropeptide found in both the peripheral and the central nervous systems. Previous studies have shown that VIP-like immunoreactive nerves are present in the uveal tissues of the human eye. The distribution of VIP-like immunoreactivity of the human lacrimal gland and sphenopalatine ganglion was studied. A lacy network of VIP-like immunoreactive nerve fibers was found in the lacrimal gland and was predominantly located along the basilar surface of the acinar epithelium and in the interstitial connective tissue of the gland. This pattern of innervation was nearly identical to the distribution of cholinesterase-positive fibers in human lacrimal glands. The VIP-like immunoreactive cell bodies were found throughout the sphenopalatine ganglion obtained at autopsy. The distribution of VIP-like immunoreactive nerves in the human lacrimal gland and sphenopalatine ganglion was generally similar to that described in mammalian and avian systems, although some differences were noted. Vasoactive intestinal polypeptide may represent an important cotransmitter or neuromodulator for the facial parasympathetic nerves that supply the eye and the lacrimal gland.

Translocation breakpoint mapping: molecular and cytogenetic studies of chromosome 22.

A number of clinically significant human diseases are associated with rearrangements of chromosome #22. These include the t(9;22) of chronic myelogenous leukemia (CML), the t(8;22) of Burkitt's lymphoma (BL), the t(11;22)(q23;q11) constitutional rearrangement and the t(11;22) of Ewing's sarcoma (ES) and neuroepithelioma (NE). All of these translocations have breakpoints in 22q11. Using a molecular cytogenetic approach and various cloned portions of the lambda light chain gene as probe, we have assigned a linear order within 22q11 to these breakpoints. Using chromosomal in situ hybridization we have determined that the 22q11 breakpoint in BL2, a t(8;22) Burkitt's lymphoma is proximal to the breakpoint of the t(9;22) of CML. We have demonstrated that the 22q11 breakpoint of PA682, another t(8;22) BL cell line, interrupts the lambda light chain locus. Using a combination of variable and constant region probes and PA682 cells, we have shown that the lambda light chain locus is oriented such that V lambda is proximal to C lambda in 22q11. Our results for the constitutional t(11;22) indicate that the 22q11 breakpoint is distal to that of BL, proximal both to that of CML and ES and, in addition, it interrupts the C lambda gene cluster. Our studies of the 22q11 breakpoint of the t(11;22) of ES and NE suggest that they are the most distal of the breakpoints we studied on chromosome #22.

Immunological studies of propionyl CoA carboxylase in livers and fibroblasts of patients with propionic acidemia.

Antiserum prepared against homogeneous pig heart propionyl CoA carboxylase cross-reacted with human propionyl CoA carboxylase, and was used to demonstrate the presence of immunological cross-reacting material in extracts from the livers of three patients and from fibroblasts of four patients with propionic acidemia representing three major propionyl CoA carboxylase-deficient genetic complementation groups, pcc A, pcc C and bio. Since the quantity of cross-reacting material in the propionyl CoA carboxylase-deficient livers and enzyme-deficient fibroblast cell lines was comparable to that in normal tissues while showing less than five percent of the normal enzyme activity, these patients must synthesize normal or near-normal quantities of an enzymatically inactive propionyl CoA carboxylase protein. In addition, no appreciable change in the amount of cross-reacting material was found in the biotin-responsive bio fibroblasts after incubation with supplemental biotin despite a sixteen-fold increase in enzyme activity suggesting that the defect in the bio mutant involves the activation rather than the synthesis of a pre-existing normal apoenzyme.

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.

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.

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.