The slow road to the eukaryotic genome

The eukaryotic genome is a mosaic of eubacterial and archaeal genes in addition to those unique to itself. The mosaic may have arisen as the result of two prokaryotes merging their genomes, or from genes acquired from an endosymbiont of eubacterial origin. A third possibility is that the eukaryotic genome arose from successive events of lateral gene transfer over long periods of time. This theory does not exclude the endosymbiont, but questions whether it is necessary to explain the peculiar set of eukaryotic genes. We use phylogenetic studies and reconstructions of ancestral first appearances of genes on the prokaryotic phylogeny to assess evidence for the lateral gene transfer scenario. We find that phylogenies advanced to support fusion can also arise from a succession of lateral gene transfer events. Our reconstructions of ancestral first appearances of genes reveal that the various genes that make up the eukaryotic mosaic arose at different times and in diverse lineages on the prokaryotic tree, and were not available in a single lineage. Successive events of lateral gene transfer can explain the unusual mosaic structure of the eukaryotic genome, with its content linked to the immediate adaptive value of the genes its acquired. Progress in understanding eukaryotes may come from identifying ancestral features such as the eukaryotic splicesome that could explain why this lineage invaded, or created, the eukaryoticniche.

The challenges for molecular nutrition research 1: linking genotype to healthy nutrition

Nutrition science finds itself at a major crossroad. On the one hand we can continue the current path, which has resulted in some substantial advances, but also many conflicting messages which impair the trust of the general population, especially those who are motivated to improve their health through diet. The other road is uncharted and is being built over the many exciting new developments in life sciences. This new era of nutrition recognizes the complex relation between the health of the individual, its genome, and the life-long dietary exposure, and has lead to the realisation that nutrition is essentially a gene - environment interaction science. This review on the relation between genotype, diet and health is the first of a series dealing with the major challenges in molecular nutrition, analyzing the foundations of nutrition research. With the unravelling of the human genome and the linking of its variability to a multitude of phenotypes from " healthy'' to an enormously complex range of predispositions, the dietary modulation of these propensities has become an area of active research. Classical genetic approaches applied so far in medical genetics have steered away from incorporating dietary effects in their models and paradoxically, most genetic studies analyzing diet-associated phenotypes and diseases simply ignore diet. Yet, a modest but increasing number of studies are accounting for diet as a modulator of genetic associations. These range from observational cohorts to intervention studies with prospectively selected genotypes. New statistical and bioinformatics approaches are becoming available to aid in design and evaluation of these studies. This review discusses the various approaches used and provides concrete recommendations for future research.

The rough guide to the Moon and Mars

Space is a dangerous place for humans, once we step beyond the rotection of Earth’s atmosphere and magnetic field. Galactic cosmic rays and bursts of charged particles from the Sun damaging to health happen with alarming frequency – the Apollo astronauts were very lucky. Understanding the physics of radiation from distinct sources in space will be useful to help future space voyagers plan journeys in greater safety, and produce effective shields for these unavoidable events on journeys to Mars or beyond.

Trypsin IV or mesotrypsin and p23 cleave protease-activated receptors 1 and 2 to induce inflammation and hyperalgesia

Although principally produced by the pancreas to degrade dietary proteins in the intestine, trypsins are also expressed in the nervous system and in epithelial tissues, where they have diverse actions that could be mediated by protease-activated receptors (PARs). We examined the biological actions of human trypsin IV (or mesotrypsin) and rat p23, inhibitor-resistant forms of trypsin. The zymogens trypsinogen IV and pro-p23 were expressed in Escherichia coli and purified to apparent homogeneity. Enteropeptidase cleaved both zymogens, liberating active trypsin IV and p23, which were resistant to soybean trypsin inhibitor and aprotinin. Trypsin IV cleaved N-terminal fragments of PAR(1), PAR(2), and PAR(4) at sites that would expose the tethered ligand (PAR(1) = PAR(4) > PAR(2)). Trypsin IV increased [Ca(2+)](i) in transfected cells expressing human PAR(1) and PAR(2) with similar potencies (PAR(1), 0.5 microm; PAR(2), 0.6 microm). p23 also cleaved fragments of PAR(1) and PAR(2) and signaled to cells expressing these receptors. Trypsin IV and p23 increased [Ca(2+)](i) in rat dorsal root ganglion neurons that responded to capsaicin and which thus mediate neurogenic inflammation and nociception. Intraplantar injection of trypsin IV and p23 in mice induced edema and granulocyte infiltration, which were not observed in PAR (-/-)(1)(trypsin IV) and PAR (-/-)(2) (trypsin IV and p23) mice. Trypsin IV and p23 caused thermal hyperalgesia and mechanical allodynia and hyperalgesia in mice, and these effects were absent in PAR (-/-)(2) mice but maintained in PAR (-/-)(1) mice. Thus, trypsin IV and p23 are inhibitor-resistant trypsins that can cleave and activate PARs, causing PAR(1)- and PAR(2)-dependent inflammation and PAR(2)-dependent hyperalgesia.

Novel probiotics and prebiotics : road to the market

Novel probiotics and prebiotics designed to manipulate the gut microbiota for improving health outcomes are in demand as the importance of the gut microbiota in human health is revealed. The regulations governing introduction of novel probiotics and prebiotics vary by geographical region. Novel foods and foods with health claims fall under specific regulations in several countries. The paper reviews the main requirements of the regulations in the EU, USA, Canada and Japan. We propose a number of areas that need to be addressed in any safety assessment of novel probiotics and prebiotics. These include publication of the genomic sequence, antibiotic resistance profiling, selection of appropriate in vivo model, toxicological studies (including toxin production) and definition of target population.

Aqueous peroxyl radical exposure to THP-1 cells causes glutathione loss followed by protein oxidation and cell death without increased caspase-3 activity

Protein oxidation within cells exposed to oxidative free radicals has been reported to occur in an uninhibited manner with both hydroxyl and peroxyl radicals. In contrast, THP-1 cells exposed to peroxyl radicals (ROO center dot) generated by thermo decomposition of the azo compound AAPH showed a distinct lag phase of at least 6 h, during which time no protein oxidation or cell death was observed. Glutathione appears to be the source of the lag phase as cellular levels were observed to rapidly decrease during this period. Removal of glutathione with buthionine sulfoxamine eliminated the lag phase. At the end of the lag phase there was a rapid loss of cellular MTT reducing activity and the appearance of large numbers of propidium iodide/annexin-V staining necrotic cells with only 10% of the cells appearing apoptotic (annexin-V staining only). Cytochrome c was released into the cytoplasm after 12 h of incubation but no increase in caspase-3 activity was found at any time points. We propose that the rapid loss of glutathione caused by the AAPH peroxyl radicals resulted in the loss of caspase activity and the initiation of protein oxidation. The lack of caspase-3 activity appears to have caused the cells to undergo necrosis in response to protein oxidation and other cellular damage. (c) 2007 Elsevier B.V. All rights reserved.

Enhanced sensitivity to rapamycin following long-term oestrogen deprivation in MCF-7, T-47-D and ZR-75-1 human breast cancer cells

Human breast cancer cells (MCF-7, T-47-D and ZR-75-1) can adapt to circumvent any reduced growth rate during long-term oestrogen deprivation, and this provides three model systems to investigate mechanisms of endocrine resistance in breast cancer. In this paper we report consistent differences in the effects of three growth inhibitors following long-term oestrogen deprivation in all three cell models. Long-term oestrogen deprivation of MCF-7, T-47-D and ZR-75-1 cells resulted in reduced growth inhibition by PD98059 (2–10 µg/ml), implying a loss of dependence on mitogen-activated protein kinase pathways for growth. The growth inhibitor LY294002 (2–10 µM) inhibited growth of both oestrogen-maintained and oestrogen-deprived cells with similar dose–responses, implying continued similar dependence on phosphoinositide 3-kinase (PI3K) pathways with no alteration after adaptation to oestrogen independent growth. However, by contrast, long-term oestrogen deprivation resulted in an increased sensitivity to growth inhibition by rapamycin, which was not reduced by readdition of oestradiol. The enhanced inhibition of long-term oestrogen-deprived MCF-7-ED, T-47-D-ED and ZR-75-1-ED cell growth by combining rapamycin with LY294002 at concentrations where each alone had little effect, offers preclinical support to the development of therapeutic combinations of rapamycin analogues with other PI3K inhibitors in endocrine-resistant breast cancer.

Accumulated metal speciation in earthworm populations with multi-generational exposure to metalliferous soils: cell fractionation and high energy synchrotron analyses

Predicting metal bioaccumulation and toxicity in soil organisms is complicated by site-specific biotic and abiotic parameters. In this study we exploited tissue fractionation and digestion techniques, combined with X-ray absorption spectroscopy (XAS), to investigate the whole-body and subcellular distributions, ligand affinities, and coordination chemistry of accumulated Pb and Zn in field populations of the epigeic earthworm Lumbricus rubellus inhabiting three contrasting metalliferous and two unpolluted soils. Our main findings were (i) earthworms were resident in soils with concentrations of Pb and Zn ranging from 1200 to 27 000 mg kg(-1) and 200 to 34 000 mg kg(-1), respectively; (ii) Pb and Zn primarily accumulated in the posterior alimentary canal in nonsoluble subcellular fractions of earthworms; (iii) site-specific differences in the tissue and subcellular partitioning profiles of populations were observed, with earthworms from a calcareous site partitioning proportionally more Pb to their anterior body segments and Zn to the chloragosome-rich subcellular fraction than their acidic-soil inhabiting counterparts; (iv) XAS indicated that the interpopulation differences in metal partitioning between organs were not accompanied by qualitative differences in ligand-binding speciation, because crystalline phosphate-containing pyromorphite was a predominant chemical species in the whole-worm tissues of all mine soil residents. Differences in metal (Pb, Zn) partitioning at both organ and cellular levels displayed by field populations with protracted histories of metal exposures may reflect their innate ecophysiological responses to essential edaphic variables, such as Ca2+ status. These observations are highly significant in the challenging exercise of interpreting holistic biomarker data delivered by "omic" technologies.

Sonic to ultrasonic Q of sandstones and limestones: Laboratory measurements at in situ pressures

Laboratory measurements of the attenuation and velocity dispersion of compressional and shear waves at appropriate frequencies, pressures, and temperatures can aid interpretation of seismic and well-log surveys as well as indicate absorption mechanisms in rocks. Construction and calibration of resonant-bar equipment was used to measure velocities and attenuations of standing shear and extensional waves in copper-jacketed right cylinders of rocks (30 cm in length, 2.54 cm in diameter) in the sonic frequency range and at differential pressures up to 65 MPa. We also measured ultrasonic velocities and attenuations of compressional and shear waves in 50-mm-diameter samples of the rocks at identical pressures. Extensional-mode velocities determined from the resonant bar are systematically too low, yielding unreliable Poisson's ratios. Poisson's ratios determined from the ultrasonic data are frequency corrected and used to calculate the sonic-frequency compressional-wave velocities and attenuations from the shear- and extensional-mode data. We calculate the bulk-modulus loss. The accuracies of attenuation data (expressed as 1000/Q, where Q is the quality factor) are +/- 1 for compressional and shear waves at ultrasonic frequency, +/- 1 for shear waves, and +/- 3 for compressional waves at sonic frequency. Example sonic-frequency data show that the energy absorption in a limestone is small (Q(P) greater than 200 and stress independent) and is primarily due to poroelasticity, whereas that in the two sandstones is variable in magnitude (Q(P) ranges from less than 50 to greater than 300, at reservoir pressures) and arises from a combination of poroelasticity and viscoelasticity. A graph of compressional-wave attenuation versus compressional-wave velocity at reservoir pressures differentiates high-permeability (> 100 mD, 9.87 X 10(-14) m(2)) brine-saturated sandstones from low-permeability (< 100 mD, 9.87 X 10 (14) m(2)) sandstones and shales.

Food-chain transfer of cadmium and zinc from contaminated Urtica dioica to Helix aspersa and Lumbricus terrestris

The present study examines the potential of Urtica dioica as an ecologically relevant species for use in ecotoxicological testing. It is prevalent in degraded ecosystems and is a food source for invertebrates. Urtica dioica grown in hydroponic solutions containing from less than 0.003 to 5.7 mg Cd/L or from 0.02 to 41.9 mg Zn/L accumulated metals resulting in leaf tissue concentrations in the range of 0.10 to 24.9 mg Cd/kg or 22.5 to 2,772.0 mg Zn/kg. No toxicological effects were apparent except at the highest concentrations tested, suggesting that this species may be an important pathway for transfer of metals to primary plant consumers. Helix aspersa and Lumbricus terrestris were fed the Cd- and Zn-rich leaves of U. dioica for six and four weeks, respectively. Cadmium and Zn body load increased with increasing metal concentration in the leaves (p < 0.001). Ratios of invertebrate metal concentration to leaf metal concentration were in the range of 1:0.03 to 1:1.4 for Cd and 1:0.2 to 1:2.8 for Zn in H. aspersa and 1:0.002 to 1:3.9 for Cd and 1:0.2 to 1:8.8 for Zn in L. terrestris. Helix aspersa Cd and Zn tissue concentrations (15.5 and 1,220.2 mg/kg, respectively) were approximately threefold those in L. terrestris when both species were fed nettle leaves with concentrations of approximately 23 mg Cd/ kg and 3,400 mg Zn/kg. Models demonstrate that L. terrestris Cd tissue concentrations (r(2) = 0.74, p < 0.001) and H. aspersa Zn tissue concentrations (r(2) = 0.69, p < 0.001) can be estimated from concentrations of Cd and Zn within the leaves of U. dioica and suggest that reasonably reproducible results can be obtained using these species for ecotoxicological testing.

Investigating the causes of the response of the thermohaline circulation to past and future climate changes

The Atlantic thermohaline circulation (THC) is an important part of the earth's climate system. Previous research has shown large uncertainties in simulating future changes in this critical system. The simulated THC response to idealized freshwater perturbations and the associated climate changes have been intercompared as an activity of World Climate Research Program (WCRP) Coupled Model Intercomparison Project/Paleo-Modeling Intercomparison Project (CMIP/PMIP) committees. This intercomparison among models ranging from the earth system models of intermediate complexity (EMICs) to the fully coupled atmosphere-ocean general circulation models (AOGCMs) seeks to document and improve understanding of the causes of the wide variations in the modeled THC response. The robustness of particular simulation features has been evaluated across the model results. In response to 0.1-Sv (1 Sv equivalent to 10(6) ms(3) s(-1)) freshwater input in the northern North Atlantic, the multimodel ensemble mean THC weakens by 30% after 100 yr. All models simulate sonic weakening of the THC, but no model simulates a complete shutdown of the THC. The multimodel ensemble indicates that the surface air temperature could present a complex anomaly pattern with cooling south of Greenland and warming over the Barents and Nordic Seas. The Atlantic ITCZ tends to shift southward. In response to 1.0-Sv freshwater input, the THC switches off rapidly in all model simulations. A large cooling occurs over the North Atlantic. The annual mean Atlantic ITCZ moves into the Southern Hemisphere. Models disagree in terms of the reversibility of the THC after its shutdown. In general, the EMICs and AOGCMs obtain similar THC responses and climate changes with more pronounced and sharper patterns in the AOGCMs.

Donepezil for the symptomatic treatment of patients with mild to moderate Alzheimer's disease: a meta-analysis of individual patient data from randomised controlled trials

Background: The objective was to evaluate the efficacy and tolerability of donepezil (5 and 10 mg/day) compared with placebo in alleviating manifestations of mild to moderate Alzheimer's disease (AD). Method: A systematic review of individual patient data from Phase II and III double-blind, randomised, placebo-controlled studies of up to 24 weeks and completed by 20 December 1999. The main outcome measures were the ADAS-cog, the CIBIC-plus, and reports of adverse events. Results: A total of 2376 patients from ten trials were randomised to either donepezil 5 mg/day (n = 821), 10 mg/day (n = 662) or placebo (n = 893). Cognitive performance was better in patients receiving donepezil than in patients receiving placebo. At 12 weeks the differences in ADAS-cog scores were 5 mg/day-placebo: - 2.1 [95% confidence interval (CI), - 2.6 to - 1.6; p < 0.001], 10 mg/day-placebo: - 2.5 ( - 3.1 to - 2.0; p < 0.001). The corresponding results at 24 weeks were - 2.0 ( - 2.7 to - 1.3; p < 0.001) and - 3.1 ( - 3.9 to - 2.4; p < 0.001). The difference between the 5 and 10 mg/day doses was significant at 24 weeks (p = 0.005). The odds ratios (OR) of improvement on the CIBIC-plus at 12 weeks were: 5 mg/day-placebo 1.8 (1.5 to 2.1; p < 0.001), 10 mg/day-placebo 1.9 (1.5 to 2.4; p < 0.001). The corresponding values at 24 weeks were 1.9 (1.5 to 2.4; p = 0.001) and 2.1 (1.6 to 2.8; p < 0.001). Donepezil was well tolerated; adverse events were cholinergic in nature and generally of mild severity and brief in duration. Conclusion: Donepezil (5 and 10 mg/day) provides meaningful benefits in alleviating deficits in cognitive and clinician-rated global function in AD patients relative to placebo. Increased improvements in cognition were indicated for the higher dose. Copyright © 2004 John Wiley & Sons, Ltd.