Regional differences in effects of APOE ε4 on cognitive impairment in non-demented subjects.

BACKGROUND: The APOE ε4 allele is a risk factor for Alzheimer's disease (AD). APOE ε4 is common in non-demented subjects with cognitive impairment. In both healthy people and people with AD, its prevalence has a north-south gradient across Europe. In the present study, we investigated whether the relation between the APOE ε4 allele and cognitive impairment varied across Northern, Middle and Southern Europe. We also investigated whether a north-south gradient existed in subjects with subjective cognitive impairment (SCI), amnestic mild cognitive impairment (MCI) and non-amnestic MCI. METHODS: Data from 16 centers across Europe were analyzed. RESULTS: A north-south gradient in APOE ε4 prevalence existed in the total sample (62.7% for APOE ε4 carriers in the northern region, 42.1% in the middle region, and 31.5% in the southern region) and in subjects with SCI and amnestic MCI separately. Only in Middle Europe was the APOE ε4 allele significantly associated with poor performance on tests of delayed recall and learning, as well as with the amnestic subtype of MCI. CONCLUSION: The APOE ε4 allele frequencies in subjects with SCI and amnestic MCI have a north-south gradient. The relation between the APOE ε4 allele and cognition is region dependent.

Microporous membrane liquid-liquid extraction coupled on-line with normal-phase liquid chromatography for the determination of cationic surfactants in river and waste water.

Membrane-based continuous liquid-liquid extraction combined on-line with normal-phase liquid chromatography is proposed for the determination of cationic surfactants in complex aqueous samples. The technique has the potential for complete automation. Selective enrichment of cationic surfactants from spiked river water and waste-water samples with simultaneous removal of matrix constituents, followed by a quantitative transfer of the extract onto a liquid chromatographic column and separation of the surfactant homologues yielding low detection limits, has been realised. The homologues of alkyldimethylbenzylammonium chloride (Dodigen 226) were chosen as model compounds in the method development. Dodigen homologues were ion-paired with heptanoic acid and extracted into chlorobutane by means of microporous membrane liquid-liquid extraction. It was thereby possible to attain an enrichment of over 250 times for one of the homologues, viz. the concentration in the organic liquid is 250 times higher than in the original sample. Detection limits for the three best-detected homologues of the mixture were in the range 0.7-5 microg/l in spiked river water samples. Ion-pair normal-phase liquid chromatography, again with heptanoic acid as counter-ion, gave the necessary separation of the surfactant homologues.

Automated liquid membrane extraction for high-performance liquid chromatography of Ropivacaine metabolites in urine.

An automatic method for the determination of metabolites of Ropivacaine in urine was set up. It utilizes supported liquid membrane extraction for sample clean-up and enrichment, followed by ion-pair chromatography determination using UV detection. The extraction was very selective with no observed interfering compounds from the urine matrix, permitting simple isocratic chromatographic analysis. The detection limits for spiked urine samples were 2-18 nM for the different compounds. The repeatability was 1-3% (RSD) with an internal standard that was also extracted, and about twice without this standard. A throughput of 3.3 samples per hour was achieved and the liquid membrane was stable for more than a week.

Resource-niche complementarity and autotrophic compensation determines ecosystem-level responses to increased cladoceran species richness.

This study examines the relationship between cladoceran species richness and ecosystem functioning. I conducted an experiment in which four cladocerans, Daphnia. magna, D. longispina, D. pulex and Chydorus sphaericus, were cultured in microcosms using different species combinations and levels of species richness. The results demonstrate that even within this closely related group of organisms the effects on ecosystem-level variables, such as total algae and zooplankton biomass, per capita productivity, and nutrient concentrations, as well as phytoplankton community structure, were highly variable between different combinations of these species. Since only four species where involved in this study, species-specific effects dominated the general relationship between species richness and ecosystem functioning. Particular combinations of species resulted in effects that indicated more efficient grazing. These effects, which were most pronounced in combinations including both D. magna and C. sphaericus, were manifested as an indirect effect as the prey community shifted towards grazing-resistant species. As a result, the productivity of the prey community decreased, because phytoplankton species with lower per capita productivity became more dominant. I suggest that the primary mechanism that caused this significant effect was complementarity in prey-size use of D. magna and C. sphaericus. In terms of prey-size range, D. pulex and D. longispina were redundant when D. magna was present and were quickly out-competed by the latter despite higher per capita filtering efficiency. The results show that different mechanisms are important for different combinations of species. Furthermore, the ability of the prey community to respond to changes of consumer species composition is an important factor in experiments in which consumer species richness is experimentally manipulated.

Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates.

The free energy of the stacking-unstacking process of deoxyribodinucleoside monophosphates in aqueous solution has been investigated by potential of mean force calculations along a reaction coordinate, defined by the distance between the glycosidic nitrogen atoms of the bases. The stacking-unstacking process of a ribodinucleoside monophosphate was observed to be well characterized by this coordinate, which has the advantage that it allows for a dynamical backbone and flexible bases. All 16 naturally occurring DNA dimers composed of the adenine, cytosine, guanine, or thymine bases in both the 5' and the 3' positions were studied. From the free-energy profiles we observed the deepest minima for the stacked states of the purine-purine dimers, but good stacking was also observed for the purine-pyrimidine and pyrimidine-purine dimers. Substantial stacking ability was found for the dimers composed of a thymine base and a purine base and also for the deoxythymidylyl-3',5'-deoxythymidine dimer. Very poor stacking was observed for the dCpdC dimer. Conformational properties and solvent accessibility are discussed for the stacked and unstacked dimers. The potential of mean force profiles of the stacking-unstacking process for the DNA dimers are compared with the RNA dimers.

Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics.

Molecular dynamics simulations were carried out on two conformations of the dinucleoside monophosphate guanylyl-3',5'-uridine (GpU) in aqueous solution with one sodium counterion. One stacked conformation and one with the C3'-O3'-P-O5' backbone torsion angle twisted 180 degrees to create an unstacked conformation. We observed a relatively stable behavior of the stacked conformation, which remained stacked throughout the simulation, whereas the unstacked conformation showed major changes in the backbone torsion and glycosidic angles. During the simulation the unstacked conformation transformed into a more stacked form and then back again to an unstacked one. The calculated correlation times for rotational diffusion from the molecular dynamics simulations are in agreement with fluorescence anisotropy and nuclear magnetic resonance data. As expected, the correlation times for rotational diffusion of the unstacked conformation were observed to be longer than for the stacked conformation. The 2'OH group may contribute in stabilizing the stacked conformation, where the O2'-H...O4' hydrogen bond occurred in 82.7% of the simulation.

Glass transition in DNA from molecular dynamics simulations.

Molecular dynamics simulations of the oligonucleotide duplex d(CGCGCG)2 in aqueous solution are used to investigate the glass transition phenomenon. The simulations were performed at temperatures in the 20 K to 340 K range. The mean square atomic fluctuations showed that the behavior of the oligonucleotide duplex was harmonic at low temperatures. A glass transition temperature at 223 K to 234 K was inferred for the oligonucleotide duplex, which is in agreement with experimental observations. The largest number of hydrogen bounds between the polar atoms of the oligonucleotide duplex and the water molecules was obtained at the glass transition temperature. With increasing temperature we observed a decrease in the average lifetime of the hydrogen bonds to water molecules.

Internal mobility of the oligonucleotide duplexes d(TCGCG)2 and d(CGCGCG)2 in aqueous solution from molecular dynamics simulations.

In this paper we present longitudinal relaxation times, order parameters and effective correlation times for the base and sugar carbons in both strands of the oglionucleotide duplexes d(TCGCG)2 and d(CGCGCG)2, as calculated from 400 ps molecular dynamics trajectories in aqueous solution. The model-free approach (Lipari and Szabo, 1982) was used to determine the amplitudes and time scales of the internal motion. Comparisons were made with NMR relaxation measurements (Borer et al., 1994). The order parameters could acceptably be reproduced, and the effective correlation times were found to be lower than the experimental estimates. Reasonable T1 relaxation times were obtained in comparison with experiment for the nonterminal nucleosides. The T1 relaxation times were found to depend mainly on the order parameters and overall rotational correlation time.

Solvent influence on base stacking.

In this paper we present a detailed analysis of the base-stacking phenomenon in different solvents, using nanosecond molecular dynamics simulations. The investigation focuses on deoxyribo- and ribodinucleoside monophosphates in aqueous and organic solutions. Organic solvents with a low dielectric constant, such as chloroform, and solvents with intermediate dielectric constants, such as dimethyl sulfoxide and methanol, were analyzed. This was also done for water, which is highly polar and has a high dielectric constant. Structural parameters such as the sugar puckering and the base-versus-base orientations, as well as the energetics of the solute-solvent interactions, were examined in the different solvents. The obtained data demonstrate that base stacking is favored in the high dielectric aqueous solution, followed by methanol and dimethyl sulfoxide with intermediate dielectric constants, and chloroform, with a low dielectric constant.

On the truncation of long-range electrostatic interactions in DNA.

Long-range interactions are known to play an important role in highly polar biomolecules like DNA. In molecular dynamics simulations of nucleic acids and proteins, an accurate treatment of the long-range interactions are crucial for achieving stable nanosecond trajectories. In this report, we evaluate the structural and dynamic effects on a highly charged oligonucleotide in aqueous solution from different long-range truncation methods. Two group-based truncation methods, one with a switching function and one with a force-switching function were found to fail to give accurate stable trajectories close to the crystal structure. For these group-based truncation methods, large root mean square (rms) deviations from the initial structure were obtained and severe distortions of the oligonucleotide were observed. Another group-based truncation scheme, which used an abrupt truncation at 8. 0 A or at 12.0 A was also investigated. For the short cutoff distance, the conformations deviated far away from the initial structure and were significantly distorted. However, for the longer cutoff, where all necessary electrostatic interactions were included, the trajectory was quite stable. For the particle mesh Ewald (PME) truncation method, a stable DNA simulation with a heavy atom rms deviation of 1.5 A was obtained. The atom-based truncation methods also resulted in stable trajectories, according to the rms deviation from the initial B-DNA structure, of between 1.5 and 1.7 A for the heavy atoms. In these stable simulations, the heavy atom rms deviations were approximately 0.6-1.0 A lower for the bases than for the backbone. An increase of the cutoff radius from 8 to 12 A decreased the rms deviation by approximately 0.2 A for the atom-based truncation method with a force-shifting function, but increased the computational time by a factor of 2. Increasing the cutoff from 12 to 18 A for the atom-based truncation method with a force-shifting function requires 2-3 times more computational time, but did not significantly change the rms deviation. Similar rms deviations from the initial structure were found for the atom-based method with a force-shifting function and for the PME method. The computational cost was longer for the PME method with a cutoff of 12. 0 A for the direct space nonbonded calculations than for the atom-based truncation method with a force-shifting function and a cutoff of 12.0 A. If a nonperiodic boundary, e.g., a spherical boundary, was used, a considerable speedup could be achieved. From the rms fluctuations, the terminal nucleotides and especially the cytidines were found to be more flexible than the nonterminal nucleotides. The B-DNA form of the oligonucleotide was maintained throughout the simulations and is judged to depend on the parameters of the energy function and not on the truncation method used to handle the long-range electrostatic interactions. To perform accurate and stable simulations of highly charged biological macromolecules, we recommend that the atom-based force-shift method or the PME method should be used for the long-range electrostatics interactions.

A cross-comparison of a large dataset of genes.

SUMMARY: We make available a large cross-comparison for 16 of the completely sequenced genomes and additional eukaryotic genes. The alignments were performed at the protein level using liberal similarity bounds in order to capture as many significant alignments as possible. This dataset will be updated as new genomes become available.

Phenotypic diversity and ecosystem functioning in changing environments: a theoretical framework.

Biodiversity plays a vital role for ecosystem functioning in a changing environment. Yet theoretical approaches that incorporate diversity into classical ecosystem theory do not provide a general dynamic theory based on mechanistic principles. In this paper, we suggest that approaches developed for quantitative genetics can be extended to ecosystem functioning by modeling the means and variances of phenotypes within a group of species. We present a framework that suggests that phenotypic variance within functional groups is linearly related to their ability to respond to environmental changes. As a result, the long-term productivity for a group of species with high phenotypic variance may be higher than for the best single species, even though high phenotypic variance decreases productivity in the short term, because suboptimal species are present. In addition, we find that in the case of accelerating environmental change, species succession in a changing environment may become discontinuous. Our work suggests that this phenomenon is related to diversity as well as to the environmental disturbance regime, both of which are affected by anthropogenic activities. By introducing new techniques for modeling the aggregate behavior of groups of species, the present approach may provide a new avenue for ecosystem analysis.

On-line supported liquid membrane-liquid chromatography with a phenol oxidase-based biosensor as a selective detection unit for the determination of phenols in blood plasma.

The potential of on-line combination of supported liquid membrane extraction and column liquid chromatography with a phenol oxidase-based biosensor as a selective detection unit has been investigated for the determination of phenols in human plasma. The phenols are selectively extracted into a porous PTFE (polytetraflouroethene) membrane impregnated with a water-immiscible organic solvent and further into an alkaline acceptor phase. Via an ion-exchange interface, the analytes are transferred to a reversed-phase column where they are separated and detected using the biosensor. No sample pretreatment before the extraction, except centrifugation, is made. Due to the high selectivity both in the extraction and in the detection steps and to the fact that the demands on the chromatographic separation are low, a quick separation using an eluent with a low concentration of organic modifier can be made, without affecting the biosensor response. Detection limits below the 50 microg/l level in blood plasma were obtained for the three model compounds, phenol, p-cresol and 4-chlorophenol.