The interactive effects of hypoxemia, hyperoxia, and temperature on the gill morphology of goldfish (Carassius auratus)

Acclimation of crucian carp and goldfish to temperatures below 15°C causes covering of the gill lamellae by a mass of cells termed the interlamellar cell mass (ILCM). Here we explore the cues underlying gill remodeling (removal or growth of an ILCM) and specifically test the hypotheses that 1) depletion of internal O(2) stores in the absence of any change in external O(2) status can trigger the removal of the ILCM in goldfish acclimated to 7°C, 2) exposing fish acclimated to 25°C to an abundance of O(2) (hyperoxia) can reverse the gill remodeling (i.e., cause the covering of lamellae by an expansion of the ILCM), and 3) neuroepithelial cells (NECs) are involved in signaling the shedding of the ILCM. Hypoxemia induced by phenylhydrazine (anemia) or 5% CO caused a decrease in the ILCM from 80% to 23% and 35%, respectively. Hyperoxia exposure at 25°C caused an increase to 67% of total ILCM and a smaller decrease in the size of the ILCM when fish were transferred from 7 to 25°C. Daily sodium cyanide injections were used to stimulate NECs; this treatment led to a significant decrease in the ILCM. Thus, the three major conclusions of this study are 1) that gill remodeling can occur during periods of internal hypoxemia, 2) that O(2) supply and demand may be a significant driving force shaping gill remodeling in goldfish, and 3) the NECs may play a role in triggering the shedding of the ILCM during hypoxia.     

The effects of dissolved oxygen levels on the metabolic interaction between digestion and locomotion in Cyprinid fishes with different locomotive and digestive performances

To test whether the effects of water oxygen concentration ([O(2)]) on the metabolic interaction between locomotion and digestion differ between fish species with different locomotive and digestive behaviours in normoxia, we investigated the swimming performance of fasted and fed fish at water [O(2)] of 1, 2 and 8 (normoxia) mg L(-1) (2.5, 5 and 20 kPa) at 25°C in three juvenile Cyprinidae fish species: goldfish (Carassius auratus), common carp (Cyprinus carpio) and qingbo (Spinibarbus sinensis). Digestion, taxon and water [O(2)] all had significant effects on the pre-exercise oxygen consumption rate [Formula: see text] and the swimming performance (P < 0.05). Among the three fishes, qingbo showed the highest swimming performance and the lowest feeding [Formula: see text] at the saturated water [O(2)], and its active oxygen consumption rate [Formula: see text] and critical swimming speed (U (crit)) decreased the most with decreases in water [O(2)]. Qingbo exhibited a locomotion-priority metabolic mode at all three water [O(2)]. Digestion was sacrificed to locomotion in a postprandial swimming situation, but fed qingbo could not maintain their U (crit) at water [O(2)] of 2 and 1 mg L(-1). Goldfish showed the lowest swimming performance and the highest feeding [Formula: see text] at the saturated water [O(2)]. They exhibited a digestion-priority metabolic mode at high water [O(2)]. However, with a decrease in water [O(2)], the feeding [Formula: see text] decreased more acutely than the respiratory capacity; thus, digestion and locomotion performed independently in a postprandial swimming situation (i.e., an additive metabolic mode) at a water [O(2)] of 1 mg L(-1). The common carp showed moderate and balanced swimming performance and feeding [Formula: see text] at the saturated water [O(2)], and exhibited an additive metabolic mode at all 3 water [O(2)], because digestion, swimming and respiratory capacities decreased in parallel with the decrease in water [O(2)].     

The effects of gill remodeling on transepithelial sodium fluxes and the distribution of presumptive sodium-transporting ionocytes in goldfish (Carassius auratus)

Goldfish, Carassius auratus, adaptively remodel their gills in response to changes in ambient oxygen and temperature, altering the functional lamellar surface area to balance the opposing requirements for respiration and osmoregulation. In this study, the effects of thermal- and hypoxia-mediated gill remodeling on branchial Na⁺ fluxes and the distribution of putative Na⁺-transporting ionocytes in goldfish were assessed. When assessed either in vitro (isolated gill arches) or in vivo at a common water temperature, the presence of an interlamellar cell mass (ILCM) in fish acclimated to 7°C clearly decreased Na⁺ efflux across the gill relative to fish maintained at 25°C and lacking an ILCM. However, loss of the ILCM in 7°C-acclimated fish exposed to hypoxia led to a decrease in Na⁺ efflux (assessed under hypoxic conditions) despite the apparent large increases in functional lamellar surface area. Goldfish possessing an ILCM were able to sustain Na⁺ uptake, albeit at a lower rate matched to efflux, owing to the re-distribution of ionocytes expressing genes thought to be involved in Na⁺ uptake [Na⁺/H⁺ exchanger isoform 3 (NHE3) and V- type H⁺-ATPase] to the edge of the ILCM where they can establish contact with the surrounding environment. NHE-expressing cells co-localized with Na⁺/K⁺-ATPase expression, suggesting a role for NHE in Na⁺-uptake in the goldfish. Implications of the ILCM on ion fluxes in the goldfish are discussed.     

Lack of histamine type-1 receptors impairs the thermal response of respiration during hypoxia in mice (Mus musculus)

Thermoregulation and the hypoxic ventilatory response are modulated by histamine type-1 (H1) receptors in the brain. In this study, we tested the hypothesis that activation of H1 receptors is required for the thermal control of ventilation during normoxia and hypoxia, using conscious male wild-type and H1 receptor-knockout (H1RKO) mice (Mus musculus). Under normoxic conditions, hyperthermia (39 degrees C) decreased minute ventilation (V (E)) and oxygen consumption [Formula: see text] in both genotypes, suggesting that H1 receptors are not involved in thermal ventilatory control during normoxia. Pa(CO2) was unchanged in both hyperthermia and normothermia, suggesting that the thermal decrease in V (E) is optimized by metabolic demand. Acute hypoxic gas exposure (7% O(2)+3% CO(2) in N(2)) increased, and then decreased, V (E) in wild-type mice; this increase was augmented and sustained by hyperthermia. Hypoxic gas exposure reduced [Formula: see text] and [Formula: see text] in wild-type mice at both body temperatures; the reduced [Formula: see text] during combined hyperthermia and hypoxia was higher than during normothermia and hypoxia. In H1RKO mice, hyperthermia did not augment the V (E) response to hypoxia, and did not affect [Formula: see text] and [Formula: see text] during hypoxia. In conclusion, histamine participates in the thermal increase of ventilation during hypoxia by activating H1 receptors.     

The interactive effects of exercise and gill remodeling in goldfish (Carassius auratus)

Gill remodeling in goldfish (Carassius auratus) is accomplished by the appearance or retraction of a mass of cells (termed the interlamellar cell mass or ILCM) between adjacent lamellae. Given the presumed effects of gill remodeling on diffusing capacity, the goals of the current study were (1) to determine the consequences of increased aerobic O(2) demand (swimming) on gill remodelling and (2) to assess the consequences of the presence or absence of the ILCM on aerobic swimming capacity. Fish acclimated to 7?°C exhibited a marked increase in the ILCM which occupied, on average, 70.0?±?4.1?% of the total interlamellar channel area in comparison to an average ILCM area of only 28.3?±?0.9?% in fish acclimated to 25?°C. Incrementally increasing swimming velocity in fish at 7?°C to achieve a maximum aerobic swimming speed (U (CRIT)) within approximately 3?h resulted in a marked loss of the ILCM area to 44.8?±?3.5?%. Fish acclimated to 7?°C were subjected to 35?min swimming trials at 30, 60 or 80?% U (CRIT) revealing that significant loss of the ILCM occurred at swimming speeds exceeding 60?% U (CRIT). Prior exposure of cold water-acclimated fish to hypoxia to induce shedding of the ILCM did not affect swimming performance when assessed under normoxic conditions (control fish U (CRIT)?=?2.34?±?0.30 body lengths s(-1); previously hypoxic fish U (CRIT)?=?2.99?±?0.14 body lengths s(-1)) or the capacity to raise rates of O(2) consumption with increasing swimming speeds. Because shedding of ILCM during U (CRIT) trials complicated the interpretation of experiments designed to evaluate the impact of the ILCM on swimming performance, additional experiments using a more rapid 'ramp' protocol were performed to generate swimming scores. Neither prior hypoxia exposure nor a previous swim to U (CRIT) (both protocols are known to cause loss of the ILCM) affected swimming scores (the total distance swum during ramp U (CRIT) trials). However, partitioning all data based on the extent of ILCM coverage upon cessation of the swimming trial revealed that fish with less than 40?% ILCM coverage exhibited a significantly greater swimming score (539?±?86?m) than fish with greater than 50?% ILCM coverage (285?±?70?m). Thus, while loss of the ILCM at swimming speeds exceeding 60?% U (CRIT) confounds the interpretation of experiments designed to assess the impact of the ILCM on swimming performance, we suggest that the shedding of the ILCM, in itself, coupled with improved swimming scores in fish exhibiting low ILCM coverage (<40?%), provide evidence that the ILCM in goldfish acclimated to cold water (7?°C) is indeed an impediment to aerobic swimming capacity.     

Shear conditions in clavulanic acid production by Streptomyces clavuligerus in stirred tank and airlift bioreactors

In biochemical processes involving filamentous microorganisms, the high shear rate may damage suspended cells leading to viability loss and cell disruption. In this work, the influence of the shear conditions in clavulanic acid (CA) production by Streptomyces clavuligerus was evaluated in a 4-dm(3) conventional stirred tank (STB) and in 6-dm(3) concentric-tube airlift (ALB) bioreactors. Batch cultivations were performed in a STB at 600 and 800 rpm and 0.5 vvm (cultivations B1 and B2) and in ALB at 3.0 and 4.1 vvm (cultivations A1 and A2) to define two initial oxygen transfer conditions in both bioreactors. The average shear rate ([Formula: see text]) of the cultivations was estimated using correlations of recent literature based on experimental data of rheological properties of the broth (consistency index, K, and flow index, n) and operating conditions, impeller speed (N) for STB and superficial gas velocity in the riser (UGR) for ALB. In the same oxygen transfer condition, the [Formula: see text] values for ALB were higher than those obtained in STB. The maximum [Formula: see text] presented a strong correlation with a maximum consistency index (K (max)) of the broth. Close values of maximum CA production were obtained in cultivations A1 and A2 (454 and 442 mg L(-1)) with similar maximum [Formula: see text] values of 4,247 and 4,225 s(-1). In cultivations B1 and B2, the maximum CA production of 269 and 402 mg L(-1) were reached with a maximum [Formula: see text] of 904 and 1,786 s(-1). The results show that high values of average shear rate increase the CA production regardless of the oxygen transfer condition and bioreactor model.     

Mapping of redox state of mitochondrial cytochromes in live cardiomyocytes using Raman microspectroscopy

This paper presents a nonivasive approach to study redox state of reduced cytochromes [Formula: see text], [Formula: see text] and [Formula: see text] of complexes II and III in mitochondria of live cardiomyocytes by means of Raman microspectroscopy. For the first time with the proposed approach we perform studies of rod- and round-shaped cardiomyocytes, representing different morphological and functional states. Raman mapping and cluster analysis reveal that these cardiomyocytes differ in the amounts of reduced cytochromes [Formula: see text], [Formula: see text] and [Formula: see text]. The rod-shaped cardiomyocytes possess uneven distribution of reduced cytochromes [Formula: see text], [Formula: see text] and [Formula: see text] in cell center and periphery. Moreover, by means of Raman spectroscopy we demonstrated the decrease in the relative amounts of reduced cytochromes [Formula: see text], [Formula: see text] and [Formula: see text] in the rod-shaped cardiomyocytes caused by H(2)O(2)-induced oxidative stress before any visible changes. Results of Raman mapping and time-dependent study of reduced cytochromes of complexes II and III and cytochrome [Formula: see text] in cardiomyocytes are in a good agreement with our fluorescence indicator studies and other published data.     

Copper(I)-alkyl sulfide and -cysteine tri-nuclear clusters as models for metallo proteins: a structural density functional analysis

After having set up the computational methodology for Cu(I)-sulfur systems as models for copper proteins, namely using the simple ligands H(2)S, HS(-), CH(3)SH, and CH(3)S(-), the Cu(I)-Cysteine systems have been investigated: [Cu(I)( S -H(2)Cys) (n) ](+) (H(2)Cys, cysteine, NH(2),SH,COOH) [Cu(I)( S -HCys) (n) ](1-) (n) (NH(2),S(-),COOH). Finally, the structures for bi-nuclear [Formula: see text] (Et, CH(2)CH(3)), [Formula: see text] and tri-nuclear [Cu(I)( S -SH)](3), [Formula: see text], [Formula: see text], [Formula: see text], [Formula: see text] (NH(2),SH,COOH), [Formula: see text] (NH(2),S(-),COOH, and NH(2),SH,COO(-)), as well as [Formula: see text] (NH(2),S(-),COO(-)), were also optimized to mimic the active center for a metallo-chaperone copper transport protein (CopZ). The X-ray structures for the biomolecules were matched fairly well as regards the Cu-S bond distances and Cu…Cu contact distances in the case the model cysteine S atom is deprotonated. Upon protonation of ligand S atoms, the conformation of clusters is altered and might bring about the di- and tri-nuclear core breakage. These findings suggest that subtle protonation/deprotonation steps, i.e. small and/or local pH changes play a significant role for copper transport processes.     

Branchial and extra-branchial ammonia excretion in goldfish (Carassius auratus) following thermally induced gill remodeling

Under cold acclimated conditions, goldfish (Carassius auratus) express an interlamellar cell mass (ILCM) which limits diffusive ion loss but may also impede branchial ammonia excretion (J(amm)). In the present study, goldfish were subjected to a 2-week 5 or 25 °C acclimation in order to modulate the degree of ILCM gill coverage and determine potential effects on J(amm). 25 °C-fish displayed gill coverage which was significantly lower than the 5 °C-fish, though the ILCM was not completely absent in these fish. 5 °C-fish demonstrated J(amm) values approximately 60% lower than those of 25 °C-fish. The magnitude of anterior (branchial) J(amm) strongly correlated with gill coverage (r(2)=0.83), suggesting that the ILCM may impede branchial J(amm). Divided chamber experiments demonstrated that relative to the 25 °C-fish, 5 °C-fish relied more upon posterior routes of excretion. In response to high external ammonia (HEA; 1.5mM NH(4)HCO(3)) exposures, 25 °C-fish displayed ammonia uptake while 5 °C-fish maintained excretion against HEA, suggesting that the ILCM may act as a barrier preventing ammonia uptake. In summary, the ILCM appears to impede branchial J(amm), such that 5 °C-rely more on extra-branchial routes of excretion. We hypothesize that gill remodeling in these fish may be intimately tied to physiological adjustments on the whole-body scale.     

Unifying Time to Contact Estimation and Collision Avoidance across Species

The [Formula: see text]-function and the [Formula: see text]-function are phenomenological models that are widely used in the context of timing interceptive actions and collision avoidance, respectively. Both models were previously considered to be unrelated to each other: [Formula: see text] is a decreasing function that provides an estimation of time-to-contact (ttc) in the early phase of an object approach; in contrast, [Formula: see text] has a maximum before ttc. Furthermore, it is not clear how both functions could be implemented at the neuronal level in a biophysically plausible fashion. Here we propose a new framework - the corrected modified Tau function - capable of predicting both [Formula: see text]-type ("[Formula: see text]") and [Formula: see text]-type ("[Formula: see text]") responses. The outstanding property of our new framework is its resilience to noise. We show that [Formula: see text] can be derived from a firing rate equation, and, as [Formula: see text], serves to describe the response curves of collision sensitive neurons. Furthermore, we show that [Formula: see text] predicts the psychophysical performance of subjects determining ttc. Our new framework is thus validated successfully against published and novel experimental data. Within the framework, links between [Formula: see text]-type and [Formula: see text]-type neurons are established. Therefore, it could possibly serve as a model for explaining the co-occurrence of such neurons in the brain.     

Complete determination of the Pin1 catalytic domain thermodynamic cycle by NMR lineshape analysis

The phosphorylation-specific peptidyl-prolyl isomerase Pin1 catalyzes the isomerization of the peptide bond preceding a proline residue between cis and trans isomers. To best understand the mechanisms of Pin1 regulation, rigorous enzymatic assays of isomerization are required. However, most measures of isomerase activity require significant constraints on substrate sequence and only yield rate constants for the cis isomer, [Formula: see text] and apparent Michaelis constants, [Formula: see text]. By contrast, NMR lineshape analysis is a powerful tool for determining microscopic rates and populations of each state in a complex binding scheme. The isolated catalytic domain of Pin1 was employed as a first step towards elucidating the reaction scheme of the full-length enzyme. A 24-residue phosphopeptide derived from the amyloid precurser protein intracellular domain (AICD) phosphorylated at Thr668 served as a biologically-relevant Pin1 substrate. Specific (13)C labeling at the Pin1-targeted proline residue provided multiple reporters sensitive to individual isomer binding and on-enzyme catalysis. We have performed titration experiments and employed lineshape analysis of phosphopeptide (13)C-(1)H constant time HSQC spectra to determine [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] for the catalytic domain of Pin1 acting on this AICD substrate. The on-enzyme equilibrium value of [E·trans]/[E·cis]?=?3.9 suggests that the catalytic domain of Pin1 is optimized to operate on this substrate near equilibrium in the cellular context. This highlights the power of lineshape analysis for determining the microscopic parameters of enzyme catalysis, and demonstrates the feasibility of future studies of Pin1-PPIase mutants to gain insights on the catalytic mechanism of this important enzyme.     

Robustness and information propagation in attractors of random boolean networks

Attractors represent the long-term behaviors of Random Boolean Networks. We study how the amount of information propagated between the nodes when on an attractor, as quantified by the average pairwise mutual information ([Formula: see text]), relates to the robustness of the attractor to perturbations ([Formula: see text]). We find that the dynamical regime of the network affects the relationship between [Formula: see text] and [Formula: see text]. In the ordered and chaotic regimes, [Formula: see text] is anti-correlated with [Formula: see text], implying that attractors that are highly robust to perturbations have necessarily limited information propagation. Between order and chaos (for so-called "critical" networks) these quantities are uncorrelated. Finite size effects cause this behavior to be visible for a range of networks, from having a sensitivity of 1 to the point where [Formula: see text] is maximized. In this region, the two quantities are weakly correlated and attractors can be almost arbitrarily robust to perturbations without restricting the propagation of information in the network.     

Fracture Faces in the Cell Envelope of Escherichia coli

Freeze-fracturing of Escherichia coli cells in the presence of 30% (v/v) glycerol resulted in a double cleavage of the cell envelope exposing two convex and two concave fracture faces ([Formula: see text], [Formula: see text] and [Formula: see text], [Formula: see text]) with characteristic patterns. Complementary replicas revealed the relationship of the fracture faces to their corresponding fracture planes. The inner fracture plane splits the plasma membrane at one particular level. Apparently the outer fracture plane was located in the outer part of the wall, as it was separated by a layer ([Formula: see text]) from the fractured profile (CW1) presumably corresponding to the murein layer. The outer fracture plane did alternate toward the cell periphery, exposing complementary smooth areas ([Formula: see text] and [Formula: see text]). When cells were freeze-fractured in the absence of glycerol, the outer cell surface appeared as an etching face rather than a fracture face. A schematic representation of the relative location of the different fracture faces in the E. coli cell envelope is given.     

Critical motor number for fractional steps of cytoskeletal filaments in gliding assays

In gliding assays, filaments are pulled by molecular motors that are immobilized on a solid surface. By varying the motor density on the surface, one can control the number [Formula: see text] of motors that pull simultaneously on a single filament. Here, such gliding assays are studied theoretically using Brownian (or Langevin) dynamics simulations and taking the local force balance between motors and filaments as well as the force-dependent velocity of the motors into account. We focus on the filament stepping dynamics and investigate how single motor properties such as stalk elasticity and step size determine the presence or absence of fractional steps of the filaments. We show that each gliding assay can be characterized by a critical motor number, [Formula: see text]. Because of thermal fluctuations, fractional filament steps are only detectable as long as [Formula: see text]. The corresponding fractional filament step size is [Formula: see text] where [Formula: see text] is the step size of a single motor. We first apply our computational approach to microtubules pulled by kinesin-1 motors. For elastic motor stalks that behave as linear springs with a zero rest length, the critical motor number is found to be [Formula: see text], and the corresponding distributions of the filament step sizes are in good agreement with the available experimental data. In general, the critical motor number [Formula: see text] depends on the elastic stalk properties and is reduced to [Formula: see text] for linear springs with a nonzero rest length. Furthermore, [Formula: see text] is shown to depend quadratically on the motor step size [Formula: see text]. Therefore, gliding assays consisting of actin filaments and myosin-V are predicted to exhibit fractional filament steps up to motor number [Formula: see text]. Finally, we show that fractional filament steps are also detectable for a fixed average motor number [Formula: see text] as determined by the surface density (or coverage) of the motors on the substrate surface.     

Limits to the rate of adaptive substitution in sexual populations

In large populations, many beneficial mutations may be simultaneously available and may compete with one another, slowing adaptation. By finding the probability of fixation of a favorable allele in a simple model of a haploid sexual population, we find limits to the rate of adaptive substitution, [Formula: see text], that depend on simple parameter combinations. When variance in fitness is low and linkage is loose, the baseline rate of substitution is [Formula: see text], where [Formula: see text] is the population size, [Formula: see text] is the rate of beneficial mutations per genome, and [Formula: see text] is their mean selective advantage. Heritable variance [Formula: see text] in log fitness due to unlinked loci reduces [Formula: see text] by [Formula: see text] under polygamy and [Formula: see text] under monogamy. With a linear genetic map of length [Formula: see text] Morgans, interference is yet stronger. We use a scaling argument to show that the density of adaptive substitutions depends on [Formula: see text], [Formula: see text], [Formula: see text], and [Formula: see text] only through the baseline density: [Formula: see text]. Under the approximation that the interference due to different sweeps adds up, we show that [Formula: see text], implying that interference prevents the rate of adaptive substitution from exceeding one per centimorgan per 200 generations. Simulations and numerical calculations confirm the scaling argument and confirm the additive approximation for [Formula: see text]; for higher [Formula: see text], the rate of adaptation grows above [Formula: see text], but only very slowly. We also consider the effect of sweeps on neutral diversity and show that, while even occasional sweeps can greatly reduce neutral diversity, this effect saturates as sweeps become more common-diversity can be maintained even in populations experiencing very strong interference. Our results indicate that for some organisms the rate of adaptive substitution may be primarily recombination-limited, depending only weakly on the mutation supply and the strength of selection.     

The biosynthesis of 4-hydroxycoumarin and dicoumarol by Aspergillus fumigatus Fresenius

A strain of Aspergillus fumigatus Fresenius, isolated from spoiled hay, converts melilotic acid (o-hydroxyphenylpropionic acid) and o-coumaric acid into 4-hydroxycoumarin and dicoumarol. The sequence is shown to be melilotic acid (I) [Formula: see text] coumaric acid (IV) [Formula: see text] beta-hydroxymelilotic acid (II) [Formula: see text] beta-oxomelilotic acid (III) [Formula: see text] 4-hydroxycoumarin (VI), on the basis of (1) studies on the formation of postulated intermediates, (2) experiments with isotopically labelled materials and (3) sequential enzyme induction. In the presence of semicarbazide, o-coumaraldehyde is formed from o-coumaric acid: there is no evidence, however, that this lies on the normal metabolic pathway.     

Application of DFT methods to the study of the coordination environment of the VO2+ ion in V?proteins

Density functional theory (DFT) methods were used to simulate the environment of vanadium in several V proteins, such as vanadyl-substituted carboxypeptidase (sites A and B), vanadyl-substituted chloroplast F(1)-ATPase (CF(1); site 3), the reduced inactive form of vanadium bromoperoxidase (VBrPO; low- and high-pH sites), and vanadyl-substituted imidazole glycerol phosphate dehydratase (IGPD; sites α, β, and γ). Structural, electron paramagnetic resonance, and electron spin echo envelope modulation parameters were calculated and compared with the experimental values. All the simulations were performed in water within the framework of the polarizable continuum model. The angular dependence of [Formula: see text] and [Formula: see text] on the dihedral angle θ between the V=O and N-C bonds and on the angle φ between the V=O and V-N bonds, where N is the coordinated aromatic nitrogen atom, was also found. From the results it emerges that it is possible to model the active site of a vanadium protein through DFT methods and determine its structure through the comparison between the calculated and experimental spectroscopic parameters. The calculations confirm that the donor sets of sites B and A of vanadyl-substituted carboxypeptidase are [[Formula: see text], H(2)O, H(2)O, H(2)O] and [N(His)(||), N(His)(⊥), [Formula: see text], H(2)O], and that the donor set of site 3 of CF(1)-ATPase is [[Formula: see text], OH(Thr), H(2)O, H(2)O, [Formula: see text]]. For VBrPO, the coordination modes [N(His)(||), N(His)(∠), OH(Ser), H(2)O, H(2)O(ax)] for the low-pH site and [N(His)(||), N(His)(∠), OH(Ser), OH(-), H(2)O(ax)] or [N(His)(||), N(His)(∠), [Formula: see text], H(2)O] for the high-pH site, with an imidazole ring of histidine strongly displaced from the equatorial plane, can be proposed. Finally, for sites α, β, and γ of IGPD, the subsequent deprotonation of one, two, and three imidazole rings of histidine and the participation of a carboxylate group of a glutamate residue ([N(His)(||), [Formula: see text], H(2)O, H(2)O], [N(His)(||), N(His)(||), [Formula: see text], H(2)O], and [N(His)(||), N(His)(||), [Formula: see text], OH(-), [Formula: see text]], respectively) seems to be the most plausible hypothesis.     

Specificity of Hpa II and Hae III DNA methylases

The methylases M.HaeIII and M.HpaII recognize the tetranucleotide sequences [Formula: see text] and [Formula: see text] respectively, in DNA, and transfer a methyl group from S-adenosylmethionine to the 5-position of cytosine on each strand as indicated by the asterisks. Restriction endonuclease R.HaeIII does not cleave the methylated sequence [Formula: see text] but can cleave [Formula: see text] in which methylation is introduced on the unnatural external cytosine positions. Similarly, R.HpaII does not cleave [Formula: see text] but can cleave [Formula: see text].Images     

Architecture of the Outer Membrane of Escherichia coli III. Protein-Lipopolysaccharide Complexes in Intramembraneous Particles

In a previous paper (A. Verkleij, L. van Alphen, J. Bijvelt, and B. Lugtenberg, Biochim. Biophys. Acta 466:269-282, 1977) we have hypothesized that particles on the outer fracture face of the outer membrane ([Formula: see text]), with corresponding pits on the inner fracture face of the outer membrane ([Formula: see text]), consist of lipopolysaccharide (LPS) aggregates stabilized by divalent cations and that they might contain protein and/or phospholipid. In the present paper the roles of LPS, cations, and proteins in these [Formula: see text] particles are described more extensively, using a strain that lacks the major outer membrane proteins, b, c, and d (b(-) c(-) d(-)), and has a reduction in the number of [Formula: see text] particles of 75%. To study the role of divalent cations in the formation of [Formula: see text] particles, these b(-) c(-) d(-) cells were grown or incubated with Ca(2+), Mg(2+), or putrescine. The presence of Ca(2+) resulted in the appearance of many [Formula: see text] particles and [Formula: see text] pits. Mg(2+) and putrescine were less effective than Ca(2+). Introduction of these particles was not accompanied by alterations in the relative amounts of LPS and cell envelope proteins. Ca(2+) treatment of a heptoseless derivative of a b(-) c(-) d(-) strain did not result in morphological changes. Incubation of Ca(2+)-treated cells with ethylenediaminetetraacetate caused the disappearance of the introduced particles as well as the release of more than 60% of the cellular LPS. These results strongly support the hypothesis that LPS is involved in the formation of [Formula: see text] particles and [Formula: see text] pits. The roles of various outer membrane proteins in the formation of [Formula: see text] particles were studied by comparing the freeze-fracture morphology of b(-) c(-) d(-) cells with that of cells which contain one of the outer membrane proteins b, c, d, and e or the receptor protein for bacteriophage lambda. The results showed that the presence of any of these five proteins in a b(-) c(-) d(-) background resulted in a large increase in the number of [Formula: see text] particles and [Formula: see text] pits, indicating that these proteins are, independent of each other, involved in the formation of [Formula: see text] particles and [Formula: see text] pits. The simplest explanation for the results is that in wild-type cells each particle consists of LPS complexed with some molecules of a single protein species, stabilized by either divalent cations or polyamines. It is hypothesized that the outer membrane of the wild-type cell contains a heterogeneous population of particles, of which 75% consists of protein b-LPS, protein c-LPS, and protein d-LPS particles. A function of these particles as aqueous pores is proposed.     

(13)C NMR Reveals No Evidence of n-π* Interactions in Proteins

An [Formula: see text] interaction between neighboring carbonyl groups has been postulated to stabilize protein structures. Such an interaction would affect the [Formula: see text]C chemical shielding of the carbonyl groups, whose paramagnetic component is dominated by [Formula: see text] and [Formula: see text] excitations. Model compound calculations indicate that both the interaction energetics and the chemical shielding of the carbonyl group are instead dominated by a classical dipole-dipole interaction. A set of high-resolution protein structures with associated carbonyl [Formula: see text]C chemical shift assignments verifies this correlation and provides no evidence for an inter-carbonyl [Formula: see text] interaction.