Complete and draft genome sequences of six members of the Aquificales.

The Aquificales are widespread in marine and terrestrial hydrothermal environments. Here, we report the complete and draft genome sequences of six new members of the Aquificales: two marine species, Persephonella marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East Pacific Rise, 9 degrees 50.3'N, 104 degrees 17.5'W, and the Eastern Lau Spreading Center, 176 degrees 11.5'W, 20 degrees 45.8'S, respectively), and four terrestrial isolates, Sulfurihydrogenibium azorense strain Az-Fu1, Sulfurihydrogenibium yellowstonense strain SS-5, and Sulfurihydrogenibium strain Y03AOP1 (from Furnas, Azores, Portugal, and Calcite Springs and Obsidian Pool in Yellowstone National Park, United States, respectively), and the only thermoacidophilic isolate, Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool). Significant differences among the different species exist that include nitrogen metabolism, hydrogen utilization, chemotaxis, and signal transduction, providing insights into their ecological niche adaptations.

Temporal aggregation bias and inference of causal regulatory networks.

Time course experiments with microarrays have begun to provide a glimpse into the dynamic behavior of gene expression. In a typical experiment, scientists use microarrays to measure the abundance of mRNA at discrete time points after the onset of a stimulus. Recently, there has been much work on using these data to infer causal regulatory networks that model how genes influence each other. However, microarray studies typically have slow sampling rates that can lead to temporal aggregation of the signal. That is, each successive sampling point represents the sum of all signal changes since the previous sample. In this paper, we show that temporal aggregation can bias algorithms for causal inference and lead them to discover spurious relations that would not be found if the signal were sampled at a much faster rate. We discuss the implications of temporal aggregation on inference, the problems it creates, and potential directions for solutions.

Revising regulatory networks: from expression data to linear causal models.

Discovering the complex regulatory networks that govern mRNA expression is an important but difficult problem. Many current approaches use only expression data from microarrays to infer the likely network structure. However, this ignores much existing knowledge because for a given organism and system under study, a biologist may already have a partial model of gene regulation. We propose a method for revising and improving these initial models, which may be incomplete or partially incorrect, with expression data. We demonstrate our approach by revising a model of photosynthesis regulation proposed by a biologist for Cyanobacteria. Applied to wild type expression data, our system suggested several modifications consistent with biological knowledge. Applied to a mutant strain, our system correctly modified the disabled gene. Power experiments with synthetic data that indicate that reliable revision is feasible even with a small number of samples.

A semiempirical study of the optimized ground and excited state potential energy surfaces of retinal and its protonated Schiff base.

The electronic ground and first excited states of retinal and its Schiff base are optimized for the first time using the semiempirical AM1 Hamiltonian. The barrier for rotation about the C(11)-C(12) double bond is characterized by variation of both the twist angle delta(C(10)-C(11)-C(12)-C(13)) and the bond length d(C(11)-C(12)). The potential energy surface is obtained by varying these two parameters. The calculated ground state rotational barrier is equal to 15.6 kcal/mol for retinal and 20.5 kcal/mol for its Schiff base. The all-trans conformation is more stable by 3.7 kcal/mol than the 11-cis geometry. For the first excited state, S(1,) the 90 degrees twisted geometry represents a saddle point for retinal with the rotational barrier of 14.6 kcal/mol. In contrast, this conformation is an energy minimum for the Schiff base. It can be easily reached at room temperature from the planar minima since it is separated from them by a barrier of only 0.6 kcal/mol. The 90 degrees minimum conformation is more stable than the all-trans by 8.6 kcal/mol. We are thus able to present a reaction path on the S(1) surface of the retinal Schiff base with an almost barrier-less geometrical relaxation into a twisted minimum geometry, as observed experimentally. The character of the ground and first excited singlet states underscores the need for the inclusion of double excitations in the calculations.

Proton pumps: mechanism of action and applications.

Recent progress in understanding the molecular structures and mechanisms of action of proton pumps has paved the way to their novel applications in biotechnology. Proton pumps, bacteriorhodopsin and ATP synthases in particular, are capable of continuous, renewable conversion of light to chemical, mechanical or electrical energy, which can be used in macro- or nano-scale devices. The capability of protein systems incorporated into liposomes to generate ATP, which can be used to drive chemical reactions and to act as molecular motors has been already demonstrated. Other possible applications of such biochemical devices include targeted drug delivery and biocatalytic reactors. All these devices might prove superior to their inorganic alternatives.

Models of risk and choice: challenge or danger.

A dimensional model of perceived risk and a model of risk acceptance based on risk rates are proposed in this paper. In line with the proposed model of perceived risk, risk is a linear combination of the three basic dimensions of a risky situation: the amount and probability of loss and the amount of gain. It is assumed that psychological transformations are made on these dimensions. According to the model of acceptance, acceptance is judged by making a trade-off between perceived risk and the amount of gain. These models have been investigated in two experiments, in which risk judgments and acceptance rates for a set of descriptions of risky investments were collected from managers in Poland. The proposed dimensional model of perceived risk was compared to the distributional models of risk and to the risk models based on the expectation principle. The best fit was obtained for the proposed model. It was also found that perceived risk was useful in predicting acceptance rates. Better fits were obtained for the models of acceptance, based on perceived risk, than for the expected/weighted utility models, including bilinear models.

Computer simulation of ion channel gating: the M(2) channel of influenza A virus in a lipid bilayer.

The transmembrane fragment of the influenza virus M(2) protein forms a homotetrameric channel that transports protons. In this paper, we use molecular dynamics simulations to help elucidate the mechanism of channel gating by four histidines that occlude the channel lumen in the closed state. We test two competing hypotheses. In the "shuttle" mechanism, the delta nitrogen atom on the extracellular side of one histidine is protonated by the incoming proton, and, subsequently, the proton on the epsilon nitrogen atom is released on the opposite side. In the "water-wire" mechanism, the gate opens because of electrostatic repulsion between four simultaneously biprotonated histidines. This allows for proton transport along the water wire that penetrates the gate. For each system, composed of the channel embedded in a hydrated phospholipid bilayer, a 1.3-ns trajectory was obtained. It is found that the states involved in the shuttle mechanism, which contain either single-protonated histidines or a mixture of single-protonated histidines plus one biprotonated residue, are stable during the simulations. Furthermore, the orientations and dynamics of water molecules near the gate are conducive to proton transfer. In contrast, the fully biprotonated state is not stable. Additional simulations show that if only two histidines are biprotonated, the channel deforms but the gate remains closed. These results support the shuttle mechanism but not the gate-opening mechanism of proton gating in M(2).

Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study.

Folding of the capped LQQLLQQLLQL peptide is investigated at the water-hexane interface by molecular dynamics simulations for 161.5 ns. Initially placed in the aqueous phase as a beta-strand, the peptide rapidly adsorbs to the interface, where it adopts an amphipathic conformation. The marginal presence of nonamphipathic structures throughout the complete trajectory indicates that the corresponding conformations are strongly disfavored at the interface. It is further suggestive that folding in an interfacial environment proceeds through a pathway of successive amphipathic intermediates. The energetic and entropic penalties involved in the conformational changes along this pathway markedly increase the folding time scales of LQQLLQQLLQL, explaining why the alpha-helix, the hypothesized lowest free energy structure for a sequence with a hydrophobic periodicity of 3.6, has not been reached yet. The formation of a type I beta-turn at the end of the simulation confirms the importance of such motifs as initiation sites allowing the peptide to coalesce towards a secondary structure. Proteins 1999;36:383-399.

Hypothesis: volatile anesthetics produce immobility by acting on two sites approximately five carbon atoms apart.

UNLABELLED: All series of volatile and gaseous compounds contain members that can produce anesthesia, as defined by the minimum alveolar anesthetic concentration (MAC) required to produce immobility in response to a noxious stimulus. For unhalogenated n-alkanes, cycloalkanes, aromatic compounds, and n-alkanols, potency (1 MAC) increases by two-to threefold with each carbon addition in the series (e.g., ethanol is twice as potent as methanol). Total fluorination (perfluorination) of n-alkanes essentially eliminates anesthetic potency: only CF4 is anesthetic (MAC = 66.5 atm), which indicates that fluorine atoms do not directly influence sites of anesthetic action. Fluorine may enhance the anesthetic action of other moieties, such as the hydrogen atom in CHF3 (MAC = 1.60 atm), but, consistent with the notion that the fluorine atoms do not directly influence sites of anesthetic action, adding -(CF2)n moieties does not further increase potency (e.g., CHF2-CF3 MAC = 1.51 atm). Similarly, adding -(CF2)n moieties to perfluorinated alkanols (CH2OH-[CF2]nF) does not increase potency. However, adding a second terminal hydrogen atom (e.g., CHF2-CHF2 or CH2OH-CHF2) produces series in which the addition of each -CF2- "spacer" in the middle of the molecule increases potency two- to threefold, as in each unhalogenated series. This parallel stops at four or five carbon atom chain lengths. Further increases in chain length (i.e., to CHF2[CF2]4CHF2 or CHF2[CF2]5CH2OH) decrease or abolish potency (i.e., a discontinuity arises). This leads to our hypothesis that the anesthetic moieties (-CHF2 and -CH2OH) interact with two distinct, spatially separate, sites. Both sites must be influenced concurrently to produce a maximal anesthetic (immobility) effect. We propose that the maximal potency (i.e., for CHF2[CF2]2CHF2 and CHF2[CF2]3CH2OH) results when the spacing between the anesthetic moieties most closely matches the distance between the two sites of action. This reasoning suggests that a distance equivalent to a four or five carbon atom chain, approximately 5 A, separates the two sites. IMPLICATIONS: Volatile anesthetics may produce immobility by a concurrent action on two sites five carbon atom lengths apart.

Minimum alveolar anesthetic concentration of fluorinated alkanols in rats: relevance to theories of narcosis.

UNLABELLED: The Meyer-Overton hypothesis predicts that the potency of conventional inhaled anesthetics correlates inversely with lipophilicity: minimum alveolar anesthetic concentration (MAC) x the olive oil/gas partition coefficient equals a constant of approximately 1.82 +/- 0.56 atm (mean +/- SD), whereas MAC x the octanol/gas partition coefficient equals a constant of approximately 2.55 +/- 0.65 atm. MAC is the minimum alveolar concentration of anesthetic required to eliminate movement in response to a noxious stimulus in 50% of subjects. Although MAC x the olive oil/gas partition coefficient also equals a constant for normal alkanols from methanol through octanol, the constant (0.156 +/- 0.072 atm) is one-tenth that found for conventional anesthetics, whereas the product for MAC x the octanol/gas partition coefficient (1.72 +/- 1.19) is similar to that for conventional anesthetics. These normal alkanols also have much greater affinities for water (saline/gas partition coefficients equaling 708 [octanol] to 3780 [methanol]) than do conventional anesthetics. In the present study, we examined whether fluorination lowers alkanol saline/gas partition coefficients (i.e., decreases polarity) while sustaining or increasing lipid/gas partition coefficients, and whether alkanols with lower saline/gas partition coefficients had products of MAC x olive oil or octanol/gas partition coefficients that approached or exceeded those of conventional anesthetics. Fluorination decreased saline/gas partition coefficients to as low as 0.60 +/- 0.08 (CF3[CF2]6CH2OH) and, as hypothesized, increased the product of MAC x the olive oil or octanol/gas partition coefficients to values equaling or exceeding those found for conventional anesthetics. We conclude that the greater potency of many alkanols (greater than would be predicted from conventional inhaled anesthetics and the Meyer-Overton hypothesis) is associated with their greater polarity. IMPLICATIONS: Inhaled anesthetic potency correlates with lipophilicity, but potency of common alkanols is greater than their lipophilicity indicates, in part because alkanols have a greater hydrophilicity--i.e., a greater polarity.

Regional and subcellular distribution of a neutral and basic amino acid transporter in forebrain neurons containing nitric oxide synthase.

The neutral and basic amino acid transporter (NBAT) facilitates sodium-independent transport of L-amino acids in renal and intestinal epithelial cells and has been postulated to play a similar role in neurons. In previous studies, NBAT has been detected within enteric and brainstem autonomic neurons in a distribution similar to that of constitutive nitric oxide synthase (cNOS). Furthermore, L-arginine, the required precursor for nitric oxide synthesis, is an excellent NBAT substrate. Together, these findings suggest that NBAT may play a role in the regulation of nitric oxide synthesis, through the control of precursor availability. To gain insight into the potential physiological role of NBAT in central neurons, we used an antipeptide antiserum to examine the light and electron microscopic immunocytochemical localization of NBAT in the rat forebrain and to compare this distribution with that of cNOS. Immunolabeling for NBAT was detected within perikarya and dendrite-like processes that were most numerous in the frontal and cingulate cortex, the ventral striatum, the central amygdala, and the bed nucleus of the stria terminalis. Labeled varicose axonal processes were distributed most densely in the agranular insular cortex and the paraventricular nuclei of the thalamus and hypothalamus (PVH). Electron microscopy showed that immunogold labeling for NBAT was distributed along plasmalemmal and vacuolar membranes within somata, dendrites, and axonal profiles. Many of the NBAT-containing somata and dendrites contained detectable cNOS. Our results suggest that expression of NBAT may provide specific populations of cNOS-containing forebrain neurons with a unique mechanism for regulating somatodendritic synthesis of nitric oxide.

The localization of the brain-specific inorganic phosphate transporter suggests a specific presynaptic role in glutamatergic transmission.

Molecular cloning has recently identified a vertebrate brain-specific Na+-dependent inorganic phosphate transporter (BNPI). BNPI has strong sequence similarity to EAT-4, a Caenorhabditis elegans protein implicated in glutamatergic transmission. To characterize the physiological role of BNPI, we have generated an antibody to the protein. Immunocytochemistry of rat brain sections shows a light microscopic pattern that is suggestive of reactivity in nerve terminals. Excitatory projections are labeled prominently, and ultrastructural analysis confirms that BNPI localizes almost exclusively to terminals forming asymmetric excitatory-type synapses. Although BNPI depends on a Na+ gradient and presumably functions at the plasma membrane, both electron microscopy and biochemical fractionation show that BNPI associates preferentially with the membranes of small synaptic vesicles. The results provide anatomic evidence of a specific presynaptic role for BNPI in glutamatergic neurotransmission, consistent with the phenotype of eat-4 mutants. Because an enzyme known as the phosphate-activated glutaminase produces glutamate for release as a neurotransmitter, BNPI may augment excitatory transmission by increasing cytoplasmic phosphate concentrations within the nerve terminal and hence increasing glutamate synthesis. Expression of BNPI on synaptic vesicles suggests a mechanism for neural activity to regulate the function of BNPI.

Concentrations of anesthetics across the water-membrane interface; the Meyer-Overton hypothesis revisited.

The free energies of transferring a variety of anesthetic and nonanesthetic compounds across water-oil and water-membrane interfaces were obtained using computer simulations. Anesthetics exhibit greatly enhanced concentrations at these interfaces, compared to nonanesthetics. The substitution of the interfacial solubilites of the anesthetics for their bulk lipid solubilities in the Meyer-Overton relation, was found to give a better correlation, indicating that the potency of an anesthetic is directly proportional to its solubility at the interface.

Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study.

The conformational equilibria of the acetyl and methyl amide terminally blocked L-alanine, L-leucine and L-glutamine amino acids are examined in vacuum, in bulk water, and at the water-hexane interface, using multi-nanosecond molecular dynamics simulations. The two-dimensional probability distribution functions of finding the peptides at different dihedral angles of the backbone, phi and psi, are calculated, and free energy differences between different conformational states are determined. All three peptides are interfacially active, i.e. tend to accumulate at the interface even though they are not amphiphilic. Conformational states stable in both gas phase and water are also stable in the interfacial environment. Their populations, however, cannot be simply predicted from the knowledge of conformational equilibria in the bulk phases, indicating that the interface exerts a unique effect on the peptides. Conformational preferences in the interfacial environment arise from the interplay between electrostatic and hydrophobic effects. As in an aqueous solution, electrostatic solute-solvent interactions lead to the stabilization of more polar peptide conformations. The hydrophobic effect is manifested at the interface by a tendency to segregate polar and nonpolar moieties of the solute into the aqueous and the hexane phases, respectively. For the terminally blocked glutamine, this favors conformations for which such a segregation is compatible with the formation of strong, backbone-side chain intramolecular hydrogen bonds on the hexane side of the interface. The influence of the hydrophobic effect can be also noted in the orientational preferences of the peptides at the interface. The terminally blocked leucine is oriented such that its nonpolar side chain is buried in hexane, whereas the polar side chain of glutamine is immersed in water. The free energies of rotating the peptides along the axis parallel to the interface by more than 90 degrees are substantial. This indicates that peptide folding at interfaces is strong by driven by the tendency to adopt amphiphilic structures.

Transient cavities in liquids and the nature of the hydrophobic effect.

The size distributions of transient cavities in water and organic liquids, obtained from computer simulations, have provided a new means to analyze the nature of the hydrophobic effect and to evaluate the adequacy of different analytical models of this effect. The poor solubility of non-polar solutes in water is attributed to a low probability of finding in water cavities of atomic and molecular size. It has been shown that water applies more force per unit area of cavity surface than do hydrocarbon liquids. Models that successfully capture the main characteristics of the hydrophobic effect must at least include information about the density and the radial distribution of oxygen atoms in liquid water. One such model, quantitatively accurate for molecular solutes of arbitrary shape, is presented.

Folding and translocation of the undecamer of poly-L-leucine across the water-hexane interface. A molecular dynamics study.

The undecamer of poly-L-leucine at the water-hexane interface is studied by molecular dynamics simulations. This represents a simple model relevant to folding and insertion of hydrophobic peptides into membranes. The peptide, initially placed in a random coil conformation on the aqueous side of the system, rapidly translocates toward the hexane phase and undergoes interfacial folding into an alpha-helix in the subsequent 36 ns. Folding is nonsequential and highly dynamic. The initially formed helical segment at the N-terminus of the undecamer becomes transiently broken and, subsequently, reforms before the remainder of the peptide folds from the C-terminus. The formation of intramolecular hydrogen bonds during the folding of the peptide is preceded by a dehydration of the participating polar groups, as they become immersed in hexane. Folding proceeds through a short-lived intermediate, a 3(10)-helix, which rapidly interconverts to an alpha-helix. Both helices contribute to the equilibrium ensemble of folded structures. The helical peptide is largely buried in hexane, yet remains adsorbed at the interface. Its preferred orientation is parallel to the interface, although the perpendicular arrangement with the N-terminus immersed in hexane is only slightly less favorable. In contrast, the reversed orientation is highly unfavorable, because it would require dehydration of C-terminus carbonyl groups that do not participate in intramolecular hydrogen bonding. For the same reason, the transfer of the undecamer from the interface to the bulk hexane is also unfavorable. The results suggest that hydrophobic peptides fold in the interfacial region and, simultaneously, translocate into the nonpolar side of the interface. It is further implied that peptide insertion into the membrane is accomplished by rotating from the parallel to the perpendicular orientation, most likely in such a way that the N-terminus penetrates the bilayer.

The dopamine transporter: comparative ultrastructure of dopaminergic axons in limbic and motor compartments of the nucleus accumbens.

The dopamine transporter (DAT) regulates extracellular dopamine concentrations, transports neurotoxins, and acts as a substrate for cocaine reinforcement. These functions are known to differ in the limbic-associated shell and motor-associated core compartments of the nucleus accumbens (NAc). Previous studies have shown differential expression of DAT in the NAc shell and core but were limited in resolution to the regional level. Thus, it is not known whether there are differences in the amount, subcellular localization, or plasmalemmal targeting of DAT within individual dopaminergic axons in the two regions. We used high-resolution electron microscopic immunocytochemistry to investigate these possibilities. We show that in both the shell and core, DAT immunogold labeling is present in tyrosine hydroxylase-immunoreactive varicose axons that form symmetric synapses. Within these labeled axons, most DAT gold particles are located on extrasynaptic plasma membranes, but some are associated with intracellular membranes. Dopaminergic axons in the shell contain lower mean densities of both total DAT gold particles (per square micron) and plasmalemmal DAT gold particles (per micron) than those in the core. Within labeled axons in the NAc shell and core, however, there are no detectable differences in the subcellullar distribution of DAT or the percentage of total DAT gold particles that are located on plasma membranes. These studies are the first to examine and compare the subcellular localization of DAT in the NAc shell and core. As a result, they identify intrinsic, cell-specific differences in the expression of DAT within dopaminergic axons in these functionally distinct striatal compartments.

Adsorption and solvation of ethanol at the water liquid-vapor interface: a molecular dynamics study.

The free energy profiles of methanol and ethanol at the water liquid-vapor interface at 310K were calculated using molecular dynamics computer simulations. Both alcohols exhibit a pronounced free energy minimum at the interface and, therefore, have positive adsorption at this interface. The surface excess was computed from the Gibbs adsorption isotherm and was found to be in good agreement with experimental results. Neither compound exhibits a free energy barrier between the bulk and the surface adsorbed state. Scattering calculations of ethanol molecules from a gas phase thermal distribution indicate that the mass accommodation coefficient is 0.98, and the molecules become thermalized within 10 ps of striking the interface. It was determined that the formation of the solvation structure around the ethanol molecule at the interface is not the rate-determining step in its uptake into water droplets. The motion of an ethanol molecule in a water lamella was followed for 30 ns. The time evolution of the probability distribution of finding an ethanol molecule that was initially located at the interface is very well described by the diffusion equation on the free energy surface.