Direct electrical detection of hybridization at DNA-modified silicon surfaces

Electrochemical impedance spectroscopy was used to investigate the changes in interfacial electrical properties that arise when DNA-modified Si(111) surfaces are exposed to solution-phase DNA oligonucleotides with complementary and non-complementary sequences. The n- and p-type silicon(111) samples were covalently linked to DNA molecules via direct Si?C linkages without any intervening oxide layer. Exposure to solutions containing DNA oligonucleotides with the complementary sequence produced significant changes in both real and imaginary components of the electrical impedance, while exposure to DNA with non-complementary sequences generated negligible responses. These changes in electrical properties were corroborated with fluorescence measurements and were reproduced in multiple hybridization-denaturation cycles. The ability to detect DNA hybridization is strongly frequency-dependent. Modeling of the response and comparison of results on different silicon bulk doping shows that the sensitivity to DNA hybridization arises from DNA-induced changes in the resistance of the silicon substrate and the resistance of the molecular layers.     

Simulation as experiment: a philosophical reassessment for biological modeling

Some scientific modelers suggest that complex simulation models that mimic biological processes should have a limited place in ecological and evolutionary studies. However, complex simulation models can have a role that is different from that of simpler models that are designed to be fit to data. Simulation can be viewed as another kind of experimental system and should be analyzed as such. Here, I argue that current discussions in the philosophy of science and in the physical sciences fields about the use of simulation as an experimental system have important implications for biology, especially complex sciences such as evolution and ecology. Simulation models can be used to mimic complex systems, but unlike nature, can be manipulated in ways that would be impossible, too costly or unethical to do in natural systems. Simulation can add to theory development and testing, can offer hypotheses about the way the world works and can give guidance as to which data are most important to gather experimentally.     

Tumour-expressed CD43 (sialophorin) mediates tumourmesothelial cell adhesion

Mesothelial cell intercellular adhesion molecule-1 (ICAM-1) has recently been shown to play a role in tumour cell adherence to the peritoneum. However, solid tumours poorly express its most ubiquitous ligand, beta2 integrin. The aim of this study was to investigate the role of the beta2 integrin subunit and CD43, a known ligand for ICAM-1, in the development of peritoneal metastases. beta2 Integrin subunit and CD43 expression was assessed on a number of tumour cell lines. Adhesion of SW1222 and PSN-1 cells to human peritoneal mesothelial cells was investigated using a fluorometric assay incorporating an inhibitory antibody to beta2 integrin and CD43. beta2 Integrin expression was not inducible on these tumour cell lines, but Western blotting demonstrated CD43 expression in all the cancer cell lines examined and cell surface expression was confirmed by flow cytometry. The anti-CD43 antibody significantly reduced adhesion of PSN-1 and SW1222 cells to HPMC, however beta2 integrin inhibition did not reduce tumour cell adhesion. CD43 is expressed by a variety of carcinoma cell lines, and plays a role in tumour cell-peritoneal adhesion probably via interactions with its putative ligand ICAM-1.     

Rapid population decline in red knots: fitness consequences of decreased refuelling rates and late arrival in Delaware Bay

Most populations of migrant shorebirds around the world are in serious decline, suggesting that vital condition-dependent rates such as fecundity and annual survival are being affected globally. A striking example is the red knot (Calidris canutus rufa) population wintering in Tierra del Fuego, which undertakes marathon 30,000 km hemispheric migrations annually. In spring, migrant birds forage voraciously on horseshoe crab eggs in Delaware Bay in the eastern USA before departing to breed in Arctic polar deserts. From 1997 to 2002 an increasing proportion of knots failed to reach threshold departure masses of 180-200 g, possibly because of later arrival in the Bay and food shortage from concurrent over-harvesting of crabs. Reduced nutrient storage, especially in late-arriving birds, possibly combined with reduced sizes of intestine and liver during refuelling, had severe fitness consequences for adult survival and recruitment of young in 2000-2002. From 1997 to 2002 known survivors in Delaware Bay were heavier at initial capture than birds never seen again, annual survival of adults decreased by 37% between May 2000 and May 2001, and the number of second-year birds in wintering flocks declined by 47%. Population size in Tierra del Fuego declined alarmingly from 51,000 to 27,000 in 2000-2002, seriously threatening the viability of this subspecies. Demographic modelling predicts imminent endangerment and an increased risk of extinction of the subspecies without urgent risk-averse management.     

Reduced oxygen at high altitude limits maximum size

The trend towards large size in marine animals with latitude, and the existence of giant marine species in polar regions have long been recognized, but remained enigmatic until a recent study showed it to be an effect of increased oxygen availability in sea water of a low temperature. The effect was apparent in data from 12 sites worldwide because of variations in water oxygen content controlled by differences in temperature and salinity. Another major physical factor affecting oxygen content in aquatic environments is reduced pressure at high altitude. Suitable data from high-altitude sites are very scarce. However, an exceptionally rich crustacean collection, which remains largely undescribed, was obtained by the British 1937 expedition from Lake Titicaca on the border between Peru and Bolivia in the Andes at an altitude of 3809 m. We show that in Lake Titicaca the maximum length of amphipods is 2-4 times smaller than other low-salinity sites (Caspian Sea and Lake Baikal).     

A plasma membrane syntaxin is phosphorylated in response to the bacterial elicitor flagellin

In vivo pulse labeling of suspension-cultured Arabidopsis cells with [32P]orthophosphate allows a systematic analysis of dynamic changes in protein phosphorylation. Here, we use this technique to investigate signal transduction events at the plant plasma membrane triggered upon perception of microbial elicitors of defense responses, using as a model elicitor flg22, a peptide corresponding to the most conserved domain of bacterial flagellin. We demonstrate that two-dimensional gel electrophoresis in conjunction with mass spectrometry is a suitable tool for the identification of intrinsic membrane proteins, and we show that among them a syntaxin, AtSyp122, is phosphorylated rapidly in response to flg22. Although incorporation of radioactive phosphate into the protein only occurs significantly after elicitation, immunoblot analysis after two-dimensional gel separation indicates that the protein is also phosphorylated prior to elicitation. These results indicate that flg22 elicits either an increase in the rate of turnover of phosphate or an additional de novo phosphorylation event. In vitro, phosphorylation of AtSyp122 is calcium-dependent. In vitro phosphorylated peptides separated by two-dimensional thin layer chromatography comigrate with two of the three in vivo phosphopeptides, indicating that this calcium-dependent phosphorylation is biologically relevant. These results indicate a regulatory link between elicitor-induced calcium fluxes and the rapid phosphorylation of a syntaxin. Because syntaxins are known to be important in membrane fusion and exocytosis, we hypothesize that one of the functions of the calcium signal is to stimulate exocytosis of defense-related proteins and compounds.     

Spatial processes in the evolution of resistance in Helicoverpa zea (Lepidoptera: Noctuidae) to Bt transgenic corn and cotton in a mixed agroecosystem: a biology-rich stochastic simulation model

A simulation model is developed to examine the role of spatial processes in the evolution of resistance in Helicoverpa zea populations to Bt corn and Bt cotton. The model is developed from the stochastic spatially explicit Heliothis virescens model described by Peck et al. (1999), to accommodate a spatial mix of two host crops (corn and cotton), and to reflect the agronomic practices, as well as the spatial and temporal population dynamics of H. zea, in eastern North Carolina. The model suggests that selection for resistance is more intense in Bt cotton fields than in Bt corn fields. It further suggests that local gene frequencies are highly dependent on local deployment levels of Bt crops despite the high mobility of the adult insects. Region-wide average gene frequencies depend on the region-wide level of Bt deployment, so incomplete technology adoption slows the rate of resistance evolution. However, on a local scale, H. zea populations in clusters of fields in which Bt use is high undergo far more rapid evolution than populations in neighboring clusters of fields in which Bt use is low. The model suggests that farm-level refuge requirements are important for managing the risk of resistance. The model can be used as an aid in designing plans for monitoring for resistance by suggesting the appropriate distribution of monitoring locations, which should focus on areas of highest Bt crop deployment. The findings need to be placed in the context of the input parameters, many of which are uncertain or highly variable in nature, and therefore, a thorough sensitivity analysis is warranted.     

Sensitivity analysis of a spatially-explicit stochastic simulation model of the evolution of resistance in Helicoverpa zea (Lepidoptera: Noctuidae) to Bt transgenic corn and cotton

The sensitivities of a model simulating the evolution of resistance in Helicoverpa zea to Bt toxins in transgenic crops were investigated by examining effects of each of the model parameters on the frequency of resistance alleles after 8 yr. The functional dominance of resistance alleles and the initial frequency of those alleles had a major impact on resistance evolution. The survival of susceptible insects on the transgenic crops and the population dynamics of the insect, driven by winter survival and reproductive rates, were also important. In addition, agricultural practices including the proportion of the acreage planted to corn, and the larval threshold for spraying cotton fields affected the R-allele frequency. Many of these important parameters are inherently variable or cannot be measured with accuracy, so model output cannot be interpreted as being a forecast. However, this analysis is useful in focusing empirical research on those aspects of the insects' life system that have the largest effects on resistance development, and indicates ways in which to improve products and agricultural practices to increase the expected time to resistance. The model can thus be used as a scientific basis for devising a robust resistance management strategy for Bt crops.     

Directed proteomics identifies a plant-specific protein rapidly phosphorylated in response to bacterial and fungal elicitors

The perception of microbial signal molecules is part of the strategy evolved by plants to survive attacks by potential pathogens. To gain a more complete understanding of the early signaling events involved in these responses, we used radioactive orthophosphate to pulse-label suspension-cultured cells of Arabidopsis in conjunction with two-dimensional gel electrophoresis and mass spectrometry to identify proteins that are phosphorylated rapidly in response to bacterial and fungal elicitors. One of these proteins, AtPhos43, and related proteins in tomato and rice, are phosphorylated within minutes after treatment with flagellin or chitin fragments. By measuring (32)P incorporation into AtPhos43 immunoprecipitated from extracts of elicitor-treated hormone and defense-response mutants, we found that phosphorylation of AtPhos43 after flagellin treatment but not chitin treatment is dependent on FLS2, a receptor-like kinase involved in flagellin perception. Induction by both elicitors is not dependent on salicylic acid or EDS1, a putative lipase involved in defense signaling.