Evaluation of monocyte subsets and markers of activation in leprosy reactions

Understanding host immune pathways associated with tissue damage during reactions are of upmost importance to the development of immune intervention strategies. The participation of monocytes in leprosy reactions was evaluated by determining the frequency of monocyte subsets and the degree of cellular activation through the expression of MHCII and the co-stimulatory molecules CD40, CD80, CD86. Leprosy subjects with or without reactions were included in this cross-sectional study. Peripheral blood mononuclear cell were isolated and stained ex vivo to determine monocyte subsets and the degree of cellular activation by flow cytometry. Intermediate monocytes were increased in leprosy patients with reactions when compared to patients without reactions. Although no difference was detected in the frequency of monocyte subsets between type 1 and 2 reactions, the expression of CD80 was increased in monocytes from patients with type 1 reactions and CD40 was higher in paucibacillary subjects presenting type 1 reactions. Moreover, CD86 and MHC II expression were higher in intermediate monocytes when compared to the other subsets in leprosy reaction types 1 and 2. Intermediate monocyte activation with CD86 and MHCII expression is involved with both type 1 and 2 reactions, whereas CD80 and CD40 expression is related to type 1 reactions.     

Functional homogeneity of P-700 in cyclic and non-cyclic electron transport reactions in thylakoids

The photoinduced turnover of P-700 (the reaction center chlorophyll a of photosystem I) in higher plant thylakoids was examined at room temperature by observation of the kinetics and amplitude of the transmission signal at 700 nm. The concentration of P-700 functional in cyclic and non-cyclic electron transfer reactions was compared. For the cyclic reactions mediated by N-methylphenazonium-p-methosulfate, 2,3,5,6-tetramethylphenylenediamine, 2,6-dichlorophenolindophenol and N,N,N′,N′-tetramethylphenylenediamine and non-cyclic reactions utilizing either methylviologen or NADP⁺ as acceptor, the illuminated steady-state concentration of P-700⁺ was shown to be similar. The data support the concept of a homogeneous pool of P-700 that is capable of interaction in both cyclic and non-cyclic electron transfer reactions and are consistent with previous data obtained in vivo.The amplitude and kinetics of the P-700 signal were found to be very dependent upon the composition of the reaction medium and differences were noted for turnover in the cyclic and non-cyclic reactions. Specifically, at white light saturation, the addition of low concentrations of divalent cations, such as Mg²⁺ or Ca²⁺, had no effect on the signal amplitude during the cyclic reactions, but, in confirmation of previous work, caused an attenuation of the signal amplitude during non-cyclic flow. At low light intensities, the divalent cations caused a similar reduction in redox level of P-700 in the steady-state during non-cyclic flow and also reduced the rate of P-700 photooxidation in the cyclic reactions. The concentration of divalent cation that reduced the signal amplitude of P-700⁺ during non-cyclic flow was compared with that required for the stimulation of the variable component of fluorescence, and it was shown to be similar with half maximal effects at 1 mM Mg²⁺. The observations confirm that divalent cations control non-cyclic electron transport by an activation of Photosystem II in addition to regulating the distribution of excitation energy between the two photosystems.     

Millifluidics for Chemical Synthesis and Time-resolved Mechanistic Studies

Procedures utilizing millifluidic devices for chemical synthesis and time-resolved mechanistic studies are described by taking three examples. In the first, synthesis of ultra-small copper nanoclusters is described. The second example provides their utility for investigating time resolved kinetics of chemical reactions by analyzing gold nanoparticle formation using in situ X-ray absorption spectroscopy. The final example demonstrates continuous flow catalysis of reactions inside millifluidic channel coated with nanostructured catalyst.     

Organization of SNAREs within the Golgi Stack

Antero- and retrograde cargo transport through the Golgi requires a series of membrane fusion events. Fusion occurs at the cis- and trans-side and along the rims of the Golgi stack. Four functional SNARE complexes have been identified mediating lipid bilayer merger in the Golgi. Their function is tightly controlled by a series of reactions involving vesicle tethering and SM proteins. This network of protein interactions spatially and temporally determines the specificity of transport vesicle targeting and fusion within the Golgi.At steady state, the Golgi maintains its structural and functional organization despite a massive lipid and protein flow. A balanced anterograde and retrograde membrane flow are required to constantly recycle the transport machinery and cargo containers (vesicles). In the absence of efficient recycling, directional net cargo transport would cease and the Golgi would collapse. Thus, transport vesicles constantly leave and enter at both sides of the Golgi stack and bud and fuse along the rims of the cisternae. To maintain the compartmental identity, vesicle fusion occurs in a specific and orchestrated manner. These fusion events are mediated by a cascade of reactions centered around the membrane fusion proteins SNAREs (SNAP receptors) (Söllner et al. 1993b).     

Flow through a rough,shallow reef

This paper presents a simple model of wave-driven flow through a coral reef that is characterized by a shallow, wide reef crest and a deeper, but frictional lagoon. Assuming that the dominant momentum balances are between quadratic drag and barotropic pressure gradients, along-lagoon and cross-reef flows are coupled through continuity and through a setup of the water surface in the lagoon that varies in the along-reef direction. Scaling of the governing equations shows that this flow is governed by a single parameter P that expresses the competing effects of cross-reef and along-lagoon drag. When P < 1, the cross-reef flow is nearly constant, whereas when P > 1, only that portion of the reef closest to the pass through the reef crest through which fluid exists the lagoon supports cross-reef flows.     

Studies of enzyme reactions in open systems

An experimental arrangement is described which allows studies of the temporal performance of enzyme reactions (also reactions of complexes of enzyme chains) under conditions of open systems. The various steady-state properties of such open systems can be recognized by measuring their input and output [1,2]. The various levels of flowing equilibria are perturbed by applying molecular modulators to the system, and the data obtained are compared to those found in closed systems. In order to prove the accuracy of the experimental configuration, the determination of K_m in a one-substrate reaction is carried out in the open system, using only one concentration of substrate at various flow rates.     

Pyridine nucleotides and H2 as electron donors to the respiratory and photosynthetic electron-transfer chains and to nitrogenase in Anabaena heterocysts

The pathways through which NADPH, NADH and H₂ provide electrons to nitrogenase were examined in anaerobically isolated heterocysts. Electron donation in freeze-thawed heterocysts and in heterocyst fractions was studied by measuring O₂ uptake, acetylene reduction and reduction of horse heart cytochrome c. In freeze-thawed heterocysts and membrane fractions, NADH and H₂ supported cyanide-sensitive, respiratory O₂ uptake and light-enhanced, cyanide-insensitive uptake of O₂ resulting from electron donation to O₂ at the reducing side of Photosystem I. Membrane fractions also catalyzed NADH-dependent reduction of cytochrome c. In freeze-thawed heterocysts and soluble fractions from heterocysts, NADPH donated electrons in dark reactions to O₂ or cytochrome c through a pathway involving ferredoxin:NADP reductase; these reactions were only slightly influenced by cyanide or illumination. In freeze-thawed heterocysts provided with an ATP-generating system, NADH or H₂ supported slow acetylene reduction in the dark through uncoupler-sensitive reverse electron flow. Upon illumination, enhanced rates of acetylene reduction requiring the participation of Photosystem I were observed with NADH and H₂ as electron donors. Rapid NADPH-dependent acetylene reduction occurred in the dark and this activity was not influenced by illumination or uncoupler. A scheme summarizing electron-transfer pathways between soluble and membrane components is presented.     

Characterization and multi-step transketolase-ω-transaminase bioconversions in an immobilized enzyme microreactor (IEMR) with packed tube

The concept of de novo metabolic engineering through novel synthetic pathways offers new directions for multi-step enzymatic synthesis of complex molecules. This has been complemented by recent progress in performing enzymatic reactions using immobilized enzyme microreactors (IEMR). This work is concerned with the construction of de novo designed enzyme pathways in a microreactor synthesizing chiral molecules. An interesting compound, commonly used as the building block in several pharmaceutical syntheses, is a single diastereoisomer of 2-amino-1,3,4-butanetriol (ABT). This chiral amino alcohol can be synthesized from simple achiral substrates using two enzymes, transketolase (TK) and transaminase (TAm). Here we describe the development of an IEMR using His₆-tagged TK and TAm immobilized onto Ni-NTA agarose beads and packed into tubes to enable multi-step enzyme reactions. The kinetic parameters of both enzymes were first determined using single IEMRs evaluated by a kinetic model developed for packed bed reactors. The K_m(app) for both enzymes appeared to be flow rate dependent, while the turnover number k_cat was reduced 3 fold compared to solution-phase TK and TAm reactions. For the multi-step enzyme reaction, single IEMRs were cascaded in series, whereby the first enzyme, TK, catalyzed a model reaction of lithium-hydroxypyruvate (HPA) and glycolaldehyde (GA) to l-erythrulose (ERY), and the second unit of the IEMR with immobilized TAm converted ERY into ABT using (S)-α-methylbenzylamine (MBA) as amine donor. With initial 60 mM (HPA and GA each) and 6 mM (MBA) substrate concentration mixture, the coupled reaction reached approximately 83% conversion in 20 min at the lowest flow rate. The ability to synthesize a chiral pharmaceutical intermediate, ABT in relatively short time proves this IEMR system as a powerful tool for construction and evaluation of de novo pathways as well as for determination of enzyme kinetics.     

CONSTRICTOR: Constraint Modification Provides Insight into Design of Biochemical Networks

Advances in computational methods that allow for exploration of the combinatorial mutation space are needed to realize the potential of synthetic biology based strain engineering efforts. Here, we present Constrictor, a computational framework that uses flux balance analysis (FBA) to analyze inhibitory effects of genetic mutations on the performance of biochemical networks. Constrictor identifies engineering interventions by classifying the reactions in the metabolic model depending on the extent to which their flux must be decreased to achieve the overproduction target. The optimal inhibition of various reaction pathways is determined by restricting the flux through targeted reactions below the steady state levels of a baseline strain. Constrictor generates unique in silico strains, each representing an “expression state”, or a combination of gene expression levels required to achieve the overproduction target. The Constrictor framework is demonstrated by studying overproduction of ethylene in Escherichia coli network models iAF1260 and iJO1366 through the addition of the heterologous ethylene-forming enzyme from Pseudomonas syringae. Targeting individual reactions as well as combinations of reactions reveals in silico mutants that are predicted to have as high as 25% greater theoretical ethylene yields than the baseline strain during simulated exponential growth. Altering the degree of restriction reveals a large distribution of ethylene yields, while analysis of the expression states that return lower yields provides insight into system bottlenecks. Finally, we demonstrate the ability of Constrictor to scan networks and provide targets for a range of possible products. Constrictor is an adaptable technique that can be used to generate and analyze disparate populations of in silico mutants, select gene expression levels and provide non-intuitive strategies for metabolic engineering.     

Generation and interaction of intense counterpropagating plasma flows

Results are presented from experimental studies of the parameters of two counterpropagating (colliding) plasma flows generated by discharges in crossed electric and magnetic fields. It is shown that the conversion efficiency of the energy deposited in the discharges into the energy of directed plasma flows is 0.3–0.6. For discharge current pulses with a duration of ∼10 μs, the energy flux density in the plasma flow reaches ∼10 J/cm² and the total energy of the flow is on the order of 300 J. The density of deuterons in the flows is ∼10¹⁵ cm⁻³, and the flow velocity is ≤2×10⁷ cm/s. The total number of particles carried by the flows is about 10¹⁹. The possibility of using counterpropagating plasma flows to study reactions involving light nuclei (dd, pd, dt, and dHe reactions) in the range of ultralow collision energies is discussed. __________ Translated from Fizika Plazmy, Vol. 29, No. 8, 2003, pp. 714–721. Original Russian Text Copyright ? 2003 by Dudkin, Nechaev, Padalko, Bystritsky, Stolupin, Bystritskii, Voznyak.     

Intrinsic Levanase Activity of Bacillus subtilis 168 Levansucrase (SacB)

Levansucrase catalyzes the synthesis of fructose polymers through the transfer of fructosyl units from sucrose to a growing fructan chain. Levanase activity of Bacillus subtilis levansucrase has been described since the very first publications dealing with the mechanism of levan synthesis. However, there is a lack of qualitative and quantitative evidence regarding the importance of the intrinsic levan hydrolysis of B. subtilis levansucrase and its role in the levan synthesis process. Particularly, little attention has been paid to the long-term hydrolysis products, including its participation in the final levan molecules distribution. Here, we explored the hydrolytic and transferase activity of the B. subtilis levansucrase (SacB) when levans produced by the same enzyme are used as substrate. We found that levan is hydrolyzed through a first order exo-type mechanism, which is limited to a conversion extent of around 30% when all polymer molecules reach a structure no longer suitable to SacB hydrolysis. To characterize the reaction, Isothermal Titration Calorimetry (ITC) was employed and the evolution of the hydrolysis products profile followed by HPLC, GPC and HPAEC-PAD. The ITC measurements revealed a second step, taking place at the end of the reaction, most probably resulting from disproportionation of accumulated fructo-oligosaccharides. As levanase, levansucrase may use levan as substrate and, through a fructosyl-enzyme complex, behave as a hydrolytic enzyme or as a transferase, as demonstrated when glucose and fructose are added as acceptors. These reactions result in a wide variety of oligosaccharides that are also suitable acceptors for fructo-oligosaccharide synthesis. Moreover, we demonstrate that SacB in the presence of levan and glucose, through blastose and sucrose synthesis, results in the same fructooligosaccharides profile as that observed in sucrose reactions. We conclude that SacB has an intrinsic levanase activity that contributes to the final levan profile in reactions with sucrose as substrate.     

The topology of genome-scale metabolic reconstructions unravels independent modules and high network flexibility

The topology of metabolic networks is recognisably modular with modules weakly connected apart from sharing a pool of currency metabolites. Here, we defined modules as sets of reversible reactions isolated from the rest of metabolism by irreversible reactions except for the exchange of currency metabolites. Our approach identifies topologically independent modules under specific conditions associated with different metabolic functions. As case studies, the E.coli iJO1366 and Human Recon 2.2 genome-scale metabolic models were split in 103 and 321 modules respectively, displaying significant correlation patterns in expression data. Finally, we addressed a fundamental question about the metabolic flexibility conferred by reversible reactions: “Of all Directed Topologies (DTs) defined by fixing directions to all reversible reactions, how many are capable of carrying flux through all reactions?”. Enumeration of the DTs for iJO1366 model was performed using an efficient depth-first search algorithm, rejecting infeasible DTs based on mass-imbalanced and loopy flux patterns. We found the direction of 79% of reversible reactions must be defined before all directions in the network can be fixed, granting a high degree of flexibility.     

Simulations of a longitudinal glow discharge in a hot air flow at atmospheric pressure

A one-dimensional axisymmetric time-dependent model of a discharge in a gas flow is developed. The model includes a fairly complete set of plasmochemical reactions and describes the heating and gasdynamic expansion of a plasma channel in air. The processes governing the distribution of nitrogen molecules in the N₂(C ³Π_u, v) state over vibrational levels are considered. The parameters of a longitudinal glow discharge in a hot (T ₀ = 1500?3000 K) air flow at atmospheric pressure are calculated. It is found that gas preheating considerably influences the parameters of the discharge channel. The results of calculations are compared with the experimental data.     

Stoichiometric analysis of self-maintaining metabolisms

This paper presents an extension of stoichiometric analysis in systems where the catalytic compounds (enzymes) are also intermediates of the metabolic network (dual property), so they are produced and degraded by the reaction network itself. To take this property into account, we introduce the definition of enzyme-maintaining mode, a set of reactions that produces its own catalyst and can operate at stationary state. Moreover, an enzyme-maintaining mode is defined as elementary with respect to a given reaction if the removal of any of the remaining reactions causes the cessation of any steady state flux through this reference reaction. These concepts are applied to determine the network structure of a simple self-maintaining system.     

Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions

The wobble uridine of certain bacterial and mitochondrial tRNAs is modified, at position 5, through an unknown reaction pathway that utilizes the evolutionarily conserved MnmE and GidA proteins. The resulting modification (a methyluridine derivative) plays a critical role in decoding NNG/A codons and reading frame maintenance during mRNA translation. The lack of this tRNA modification produces a pleiotropic phenotype in bacteria and has been associated with mitochondrial encephalomyopathies in humans. In this work, we use in vitro and in vivo approaches to characterize the enzymatic pathway controlled by the Escherichia coli MnmE•GidA complex. Surprisingly, this complex catalyzes two different GTP- and FAD-dependent reactions, which produce 5-aminomethyluridine and 5-carboxymethylamino-methyluridine using ammonium and glycine, respectively, as substrates. In both reactions, methylene-tetrahydrofolate is the most probable source to form the C5-methylene moiety, whereas NADH is dispensable in vitro unless FAD levels are limiting. Our results allow us to reformulate the bacterial MnmE•GidA dependent pathway and propose a novel mechanism for the modification reactions performed by the MnmE and GidA family proteins.     

Galactosaminogalactan secreted from Aspergillus fumigatus and Aspergillus flavus induces platelet activation

Platelets are meanwhile recognized as versatile elements within the immune system and appear to play a key role in the innate immune response to pathogens including fungi. Previous experiments revealed platelet activation by direct contact with the hyphal-associated polysaccharide galactosaminogalactan (GAG). Since secreted fungal products may also be relevant and trigger immune reactions or thrombosis, we screened culture supernatants (SN) of human-pathogenic fungi for their capacity to activate platelets. For that purpose, platelets were incubated with SN from various fungal species; platelet activation and GAG deposition on the surface of platelets were detected by flow cytometry and electron and confocal microscopy, Culture supernatants of Aspergillus fumigatus and flavus isolates were potent platelet stimulators in a dose- and time-dependent manner, while SN of other Aspergillus species and all tested mucormycete species did not significantly induce platelet activation. The capacity of culture SN to activate platelets was dependent on fungal production of GAG and deposition of secreted GAG on the platelet surface; supernatants from mucormycetes or mutants of A. fumigatus lacking GAG secretion did not affect platelet activity. These results suggest that invading fungi can stimulate platelets not only locally through direct interactions with fungal hyphae, but can also act over a certain distance through secreted GAG.     

Studies on three microsomal electron transfer enzyme systems: Specificity of electron flow pathways

The routes of microsomal electron flow to the three terminal oxidative enzymes, the mixed function oxidase, the fatty acyl CoA desaturase, and the lipid peroxidase have been examined by the use of specific antibodies, by alteration of electron transfer enzyme levels, and with the inhibitor NADP⁺. From these studies a number of conclusions are drawn: (1) NADH-supported lipid peroxidation utilizes NADH-cytochrome b₅ reductase, but electron flow does not go via cytochrome b₅. (2) The positive modifier effect of type I substrates on NADPH-driven cytochrome P-450 reduction is seen also with NADH-supported cytochrome P-450 reductase activity. The latter reaction proceeds via cytochrome b₅ while the former does not. (3) Cross-reactivity can occur between NADH-cytochrome b₅ reductase and NADPH-cytochrome c reductase, but at a rate too slow to support most reactions. (4) Cytochrome b₅ appears to exist in two pools; one pool is readily inhibited by antibody and the other pool is either inaccessible to or incompletely inhibited by antibody. The various cytochrome b₅-dependent reactions show different abilities to use the noninhibited hemoprotein. NADH-cytochrome c reductase activity and NADH-synergism appear to utilize only the former pool and are completely inhibitable by antibody. Other NADH-supported reactions (Δ⁹-desaturation and mixedfunction oxidation) utilize the total cytochrome b₅ population. Fortification studies show that the extra bound cytochrome b₅ is distributed in the same manner as the endogenous cytochrome b₅.     

Energy transfer and molecular switching. I. The nerve action potential

In previous papers (Barrett, 1977b, 1980), the concept of chemical paramemetric excitation was applied to a number of diverse chemical phenomena and contrasted with the concept of chemical resonance, which is a special case of parametric excitation. In the present paper, its status as the fundamental concept of energy transfer and molecular switching is indicated, providing a mechanically sound explanation of nerve excitation at a basic level.The mechanism addressed by the parametric excitation concept is intermediate between macroscopic models of membrane assymetry and molecular models. No assumptions are made concerning the related macroscopic processes, but a systematic approach to organizational aspects of the processes involved in energy transfer is proposed.The chemical analog of the Manley-Rowe relations, which are the power conservation relations for parametrically excited electrical networks, is also derived. The demonstration of such Manley-Rowe relations for chemical systems indicates, for the first time, an explanation for the directionality of flow of power, and thus designates a pumping role. The generalized Manley-Rowe relations translated into flow, reaction, as well as oscillatory system terms, are suggested to be a universal law. Non-linearity is due to the coupling of three systems—each separately describable by Onsager linear relations—by the generalized Manley-Rowe conditions relating flows/reactions/oscillations.All phenomena considered are treated in accordance with a principle of power transfer optimization (Odum & Pinkerton, 1955). Parametric excitation involves three-body interaction, with one system as energy donor, the pump, another as energy receiving, the idler, and a third as mediator of this energy flow, the signal. A conservation law is mandatory for flows/reactions/oscillations, ω_i so that ω_pump= ω_idler±ω_signal. The macroscopic structure, which sets up the conditions for this law to be in operation, may be of diverse kinds, e.g. membrane-bounded compartments, macromolecules capable of multiple conformations and bound cations, etc. All are non-linear.     

The effect of inhibitors on the electron flow triggering photo-phobic reactions in cyanophyceae

1. Since photo-phobic reactions in the blue green alga Phormidium uncinatum seem to be triggered by changes of electron flow rates into or out of an electron pool situated in the electron transport chain between photosystem II and I, the effect of inhibitors affecting the electron transport chain has been studied.
2. Dose response curves of the phobic reaction have been measured by varying the trap energy in double beam light trap experiments with constant pairs of monochromatic light. From these dose response curves the effects of the inhibitors on both types of phobic reactions, i.e. exit reactions and entrance reactions, have been calculated.
3. Dibromothymoquinone (DBMIB) inhibits the electron transport between the electron pool and photosystem I by preventing the reoxidation of plastoquinone. The phobic entrance reaction, which results in an emptying of the light trap, is triggered by changes in the electron flow out of the pool; thus it is more effected by DBMIB than the exit reaction, which is mediated by the electron transport into the pool.
4. The phobic exit reaction, which results in accumulations in the light trap, is triggered by changes in the electron flow into the electron pool via photosystem II. 3-[3,4-dichlorophenyl]-1,1-dimethylurea (DCMU) inhibits the electron transport near photosystem II; thus it affects the exit reaction more than the entrance reaction.