Acetylated nucleosome assembly on telomeric DNAs

The role of histone N-terminal domains on the thermodynamic stability of nucleosomes assembled on several different telomeric DNAs as well as on 'average' sequence DNA and on strong nucleosome positioning sequences, has been studied by competitive reconstitution. We find that histone tails hyperacetylation favors nucleosome formation, in a similar extent for all the examined sequences. On the contrary, removal of histone terminal domains by selective trypsinization causes a decrease of nucleosome stability which is smaller for telomeres compared to the other sequences examined, suggesting that telomeric sequences have only minor interactions with histone tails. Micrococcal nuclease kinetics shows enhanced accessibility of acetylated nucleosomes formed both on telomeric and 'average' sequence DNAs. These results suggest a more complex role for histone acetylation than the decrease of electrostatic interactions between DNA and histones.     

Biodegradation kinetics of microcystins-LR crude extract by Lysinibacillus boronitolerans strain CQ5

As the most common variant of microcystins (MCs), microcystin-LR (MCLR) is a kind of toxins produced by some species of harmful cyanobacteria and more and more attention has been paid to it. Biodegradation has been extensively investigated and recognized to be a cost-efficient and environmentally benign method for MC clean-up. In order to further research the growth characteristics of strain and the biodegradation characteristics of MCLR, it is necessary to use the dynamic mathematical models as powerful and useful tools. In this study, strain CQ5 was screened and identified by morphological observation, physiological and biochemical tests, and 16S rDNA sequence analysis. The kinetic models of cell growth and MCLR degradation were established with the Gompertz model and revised Monod kinetic model. The results showed that strain CQ5 had the closest phylogenetic similarity to Lysinibacillus boronitolerans (T-10a, AB199591) in the phylogenetic tree, with 99% bootstrap support. Strain CQ5 could utilize MCLR as the carbon and nitrogen source for growth. When the initial pH value was 7 and the inoculation amount was 3%, strain CQ5 grew well in MSM, in which the MCLR crude extract was used as the carbon and nitrogen source of strain CQ5. Within 244 h, the MCLR concentration changed from 14.12 to 1.57 μg/L and its degradation rate could reach 88.88%. The growth curve fitted with the Gompertz growth model (Nt = 1.3119 * exp(−0.1237 * exp(−6.6341t)), R2 > 0.99). The process of MCLR degradation agreed with the first-order reaction kinetic equation (lnS = 2.64764 − 0.01537t, R2 > 0.99). The linkage relationship between MCLR concentration, cell density, and MCLR degradation rate was consistent with the revised Monod equation (V = 0.342S, R2 > 0.97) at low substrate concentration, where Vmax/ Ks was 0.342. The dynamic relationship in which strain CQ5 degraded MCLR and used it as the carbon and nitrogen source to promote its own growth could be explained by the equation S = 14.12 e− 0.342 Nt (N = 1.08). The growth of strain CQ5 and MCLR concentration in degradation system could be simulated and predicted by the dynamic mathematical models in this study. And the predicted results were very consistent. These results could provide theoretical reference for studying the mechanism of MCLR biodegradation and promote the engineering application of strain CQ5.     

Pharmacological activities of crude acetone extract and purified constituents of Salvia moorcraftiana Wall.

The crude acetone extract of aerial parts of Salvia moorcraftiana Wall. was screened for various biological activities including Lemna bioassay, antifungal, antibacterial, leishmanicidal, insecticidal activities and brine shrimp cytotoxicity. It was found to possess strong phytotoxic activity against Lemna aequinoctials Welve. and moderate antifungal activity against animal and plant pathogens. The purified chemical constituents were tested for enzyme inhibition activity. Two constituents (compounds 3 and 8) were found to be effective inhibitors of alpha-glucosidase.     

Factors affecting the kinetics of light emission from crude and purified firefly luciferase.

Crude and purified firefly luciferase have been used to assay ATP from 0.2 pmol to 2 μmol. Over this range of ATP concentrations, there is a large change in the kinetics of light emission. At the lowest concentrations of ATP, light emission rises to a maximum and remains constant for a minute or longer. As the concentration of ATP is increased, the peak light intensity increases and the decay rate of light increases significantly. This is true for both the crude as well as the purified enzyme. High concentration of sodium arsenate as well as other salts inhibit the peak light emission and prevent the decay in light intensity which is due to product inhibition. It is possible to obtain almost any type of kinetics by manipulating the experimental conditions.     

A 54 kDa cysteine protease purified from the crude extract of Neodiplostomum seoulense adult worms

As a preliminary study for the explanation of pathobiology of Neodiplostomum seoulense infection, a 54 kDa protease was purified from the crude extract of adult worms by sequential chromatographic methods. The crude extract was subjected to DEAE-Sepharose Fast Flow column, and protein was eluted using 25 mM Tris-HCl (pH 7.4) containing 0.05, 0.1, 0.2 and 0.4 M NaCl in stepwise elution. The 0.2 M NaCl fraction was further purified by Q-Sepharose chromatography and protein was eluted using 20 mM sodium acetate (pH 6.4) containing 0.05, 0.1, 0.2 and 0.3 M NaCl, respectively. The 0.1M NaCl fraction showed a single protein band on SDS-PAGE carried out on a 7.5-15% gradient gel. The proteolytic activities of the purified enzyme were specifically inhibited by L-trans-epoxy-succinylleucylamide (4-guanidino) butane (E-64) and iodoacetic acid. The enzyme, cysteine protease, showed the maximum proteolytic activity at pH 6.0 in 0.1 M buffer, and degraded extracellular matrix proteins such as collagen and fibronectin with different activities. It is suggested that the cysteine protease may play a role in the nutrient uptake of N. seoulense from the host intestine.     

Effectivity of crude versus purified mycobacterial secretory proteins as immunogen for optimum antibody production

Monospecific antibodies have been successfully utilized in antigen detection, which is better indicator of active infection. Mycobacterium tuberculosis excretory secretory (M tb ES) antigens such as ES 31, ES 41 and ES 43 (31 kDa, 41 kDa and 43 kDa protein, respectively) have been shown to be present in Mycobacterium tuberculosis H37Ra culture filtrate and are of diagnostic interest. To study the immunogenic potential of crude versus purified antigen, goat was immunized with M tb detergent soluble sonicate (DSS) antigen as well as purified antigen fraction (ESAS 7) containing ES 31 antigen. Both anti-DSS IgG antibody and anti ESAS 7 IgG antibody were found to be reactive with ES 31 antigen upto 1 ng concentration of antibody by ELISA. Crude DSS antigen was found to be quite effective in producing high titre antibodies and showed further high reactivity with other ES antigens (ES 41 and ES 43) of diagnostic interest.     

Calcium-sensitivity of the microtubule reassembly system. Difference between crude brain extract and purified microtubular proteins

Microtubule reassembly in crude extracts of porcine brain was inhibited by 10(-5) M Ca2+, wherease 10(-3) M Ca2+ was required for inhibition of the reassembly from purified microtubular proteins. This accounts for the apparent discrepancies between the results reported by other investigators. Furthermore, the Ca-sensitivity of the purified microtubular proteins was nearly completely recovered on addition of a fraction obtained from crude brain extract.     

Characterization of a phospholipase C activity regulated by the purified Gh in reconstitution systems.

Recently, we have reported that the isolated guanine nucleotide-binding regulatory protein, Gh, couples to the alpha 1-adrenergic receptor (Im, M.-J., and Graham, R. M. (1990) J. Biol. Chem. 265, 18944-18951 and Im, M.-J., Riek, R.P., and Graham, R. M. (1990) J. Biol. Chem. 265, 18952-18960) and has a molecular mass of approximately 74 kDa, and the approximately 50-kDa protein which is copurified probably regulates guanine nucleotide binding of the 74-kDa GTP-binding protein. In this paper, we describe the role of purified Gh in the regulation of phospholipase C in the reconstitution system. The stimulation of phospholipase C activity by Gh effectively occurred at a low calcium concentration (less than or equal to 2 microM), but the phospholipase C (PLC) itself required at least 50-100 times more calcium to become fully activated. The characteristic nature of phospholipase C stimulation by Gh is its response to the calcium concentration. Thus, the enzyme activity changes in narrow submicromolar ranges and reaches maximal stimulation, but it does not extend to the levels above those stimulated by calcium alone. The calcium concentrations for the maximal stimulation of phospholipase C activity were 10-20 microM with phospholipid vesicles and 100-200 microM with detergent solution. These calcium concentrations were further decreased when Gh and phospholipase C were co-reconstituted into the phospholipid vesicles or in the detergent solution. The maximal stimulations of the PLC activity were reached at less than 5 microM calcium in both the vesicles and the detergent solution. The changes of calcium concentration for the activation of PLC are quite different from those obtained by reconstituting PLC-beta 1 with Gq-like G-proteins (Smarcka, A. V., Hepler, J. R., Brown, K. O., and Sternweis, P. C. (1991) Science 251, 804-807 and Taylor, S. J., Chae, H. Z., Rhee, S. G., and Exton, J. H. (1991) Nature 350, 516-518). The phospholipase C activity was stimulated in a Gh concentration-dependent manner in the presence of GTP gamma S. The phospholipase C activity was activated by Gh alpha in the presence of aluminum fluoride, but not by Gh beta. Furthermore, a Gh.PLC complex can be induced by incubation with aluminum fluoride in a detergent solution and partially purified without the dissociation of related proteins. Thus, our reconstitution studies show that the pattern of stimulation of PLC by AIF-4-activated Gh in the ternary complex is similar to the stimulation of PLC activated by Gh in both detergent solution and phospholipid vesicles.     

Chromatin reconstitution on small DNA rings. II. DNA supercoiling on the nucleosome

DNA supercoiling on the nucleosome was investigated by relaxing with topoisomerase I mono- and dinucleosomes reconstituted on small DNA rings. Besides 359 base-pair (bp) rings whose linking differences were integers, two additional series of rings with fractional differences, 341 and 354 bp in size, were used. Mononucleosomes reconstituted on 359 bp rings were found to relax into a single mononucleosome form. In contrast, 341 and 354 bp mononucleosomes relaxed into a mixture of two forms, corresponding to two adjacent topoisomers. The observation that the ratio between these two forms was, within each ring series, virtually independent of the initial linking number of the topoisomer used for the reconstitution suggested that each partition reflected an equilibrium. Comparison with the equilibria observed for the same rings in the absence of histones showed that the formation of a single nucleosome is associated with a linking number change of -1.1(+/-0.1) turn. Dinucleosomes, in contrast, were not relaxed to completion and do not reach equilibria. The corresponding linking number change per nucleosome was, however, estimated to be similar to the above figure, in agreement with previous data from the literature obtained with circular chromatins containing larger numbers of nucleosomes. DNA structure in mononucleosomes was subsequently investigated by means of high-resolution electron microscopy and gel electrophoresis. It was found that the above linking number reduction could be ascribed to a particle with a large open extranucleosomal DNA loop and with no more than 1.5 turns of a superhelix around the histone core. A theoretical model of a nucleosome on a small ring was constructed in which one part of the DNA was wrapped around a cylinder and the other part was free to vary both in torsion and flexion. The linking number reduction predicted was found to be most consistent with experimental data when the twist of the DNA in the superhelix was between 10.5 and 10.65 pb per turn, suggesting that wrapping on the nucleosome does not alter the twist of the DNA significantly. A lower estimate of the linking number reduction associated with a two-turn nucleosome was also derived, based on an analysis of recent data obtained upon treatment of reconstituted minichromosomes with gyrase. The value, 1.6 turns, set a lower limit of 10.44 bp per turn for the twist of nucleosomal DNA, in agreement with the above estimate.(ABSTRACT TRUNCATED AT 400 WORDS)     

Component proteins in crude extract of adult Paragonimus westermani purified by immunoaffinity chromatography using monoclonal antibodies.

The nature of 2 component proteins in crude saline extract of adult Paragonimus westermani was investigated. By immunoaffinity chromatography using monoclonal antibodies (MAb) as ligands, the proteins were purified from the crude extract. Band 1 protein in disc-polyacrylamide gel electrophoresis (PAGE) was purified by PFCK-136 MAb. The protein, known to have molecular mass of 440 kDa, was composed of 23, 46 and 92 kDa subunits when observed by reducing SDS-PAGE and SDS-PAGE/immunoblot. This protein was originated from eggs of the worm as revealed by immunohistochemical staining with PFCK-136 Mab. Another affinity purified protein utilizing PFCK-44 MAb was the band 4 protein of 17 kDa in disc-PAGE. This was a monomer protein in reducing SDS-PAGE and SDS-PAGE/immunoblot. The protein was produced at intestinal epithelium of the worm.     

Classical versus stochastic kinetics modeling of biochemical reaction systems

We study fundamental relationships between classical and stochastic chemical kinetics for general biochemical systems with elementary reactions. Analytical and numerical investigations show that intrinsic fluctuations may qualitatively and quantitatively affect both transient and stationary system behavior. Thus, we provide a theoretical understanding of the role that intrinsic fluctuations may play in inducing biochemical function. The mean concentration dynamics are governed by differential equations that are similar to the ones of classical chemical kinetics, expressed in terms of the stoichiometry matrix and time-dependent fluxes. However, each flux is decomposed into a macroscopic term, which accounts for the effect of mean reactant concentrations on the rate of product synthesis, and a mesoscopic term, which accounts for the effect of statistical correlations among interacting reactions. We demonstrate that the ability of a model to account for phenomena induced by intrinsic fluctuations may be seriously compromised if we do not include the mesoscopic fluxes. Unfortunately, computation of fluxes and mean concentration dynamics requires intensive Monte Carlo simulation. To circumvent the computational expense, we employ a moment closure scheme, which leads to differential equations that can be solved by standard numerical techniques to obtain more accurate approximations of fluxes and mean concentration dynamics than the ones obtained with the classical approach.     

Lack of reconstitution of nude mice alloreactivity by purified interleukin 2 and induction of non-H-2-specific effector cells by crude supernatants

To verify or to challenge the reports indicating that IL-2 was the only molecule involved in the reconstitution of nu/nu mice alloreactivity in vitro, Balb/c (H-2d) nu/nu spleen cells were primed in culture against C57/B16 (H-2b) in the presence of crude IL-2-containing supernatants or purified IL-2. The generation of cytotoxic effectors was evaluated against a panel of 51Cr-labeled target cells. Although crude IL-2-containing supernatants sustained the generation of cytotoxic effectors, purified "natural" IL-2 (from different origins) and recombinant IL-2 were not able to do so. Con A or PHA were identified as cofactors synergizing with IL-2 to induce effectors from nu/nu spleen cells. These effectors efficiently lysed EL4 (H-2b, tumor line), but not mitogen-induced blast cells from the same strain. They also lysed targets bearing irrelevant allogenic H-2 specificities. Cold competition experiments confirmed the lack of H-2 specificity of such effectors: lysis of EL4 cells (H-2b) was inhibited strongly by YAC-1 cells (H-2a, very sensitive to NK lysis) or P815 cells (H-2d, autologous to the nu/nu effectors). Our results clearly challenge earlier conclusions and indicate that IL-2 alone does not reconstitute nude mice alloreactivity. Crude supernatants containing IL-2 and mitogen induce nonspecific effectors with patterns of reactivity similar to those of activated natural killers. We think that the cytotoxicity observed in these conditions in nude mice results from the mitogenic triggering of some kind of prethymic killer cells which subsequently are expanded by IL-2.     

Aldehyde PEGylation kinetics: a standard protein versus a pharmaceutically relevant single chain variable fragment

The mPEG-aldehyde PEGylation with two different PEG sizes and two proteins was experimentally determined with respect to yield, conversion, and selectivity. The kinetic behavior of these PEGylation reactions was simulated using a numerically solved set of differential equations. We show that the assumption of an inactivation of mPEG-aldehyde is crucial for the simulation of the overall PEGylation and that the inactivation is pH-dependent. We further demonstrate that ideal PEGylation parameters such as pH, temperature, reaction time, and protein concentration need to be chosen carefully depending on the protein and PEG size. In terms of selectivity and yield, we show that the reaction should be stopped before the highest mono-PEG concentration is reached. Moreover, room temperature and a slightly acidic pH of approximately 6 are good starting points. In conclusion, selectivity can be optimized choosing a shorter reaction time and a reduced reaction temperature.     

Analysis of kinetics in noisy systems: application to single molecule tethered particle motion

In the tethered particle motion method the length of a DNA molecule is monitored by measuring the range of diffusion of a microsphere tethered to the surface of a microscope coverslip through the DNA molecule itself. Looping of DNA (induced by binding of a specific protein) can be detected with this method and the kinetics of the looping/unlooping processes can be measured at the single molecule level. The microsphere's position variance represents the experimental variable reporting on the polymer length. Therefore, data windowing is required to obtain position variance from raw position data. Due to the characteristic diffusion time of the microsphere, the low-pass filtering required to attain a good signal/noise ratio (S/N) in the discrimination of looped versus unlooped state impacts significantly the measurement's time resolution. Here we present a method for measuring lifetimes based on half-amplitude thresholding and then correcting the kinetic measurements, taking into account low S/N (leading to false events) and limited time resolution (leading to missed events). This method allows an accurate and unbiased estimation of the kinetic parameters under investigation, independently of the choice of the window used for variance calculation, with potential applications to other single molecule measurements with low S/N.     

Chromatin reconstitution on small DNA rings. IV. DNA supercoiling and nucleosome sequence preference.

Nucleosome formation on inverted repeats or on some alternations of purines and pyrimidines can be inhibited in vitro by DNA supercoiling through their supercoiling-induced structural transitions to cruciforms or Z-form DNA, respectively. We report here, as a result of study of single nucleosome reconstitutions on a DNA minicircle, that a physiological level of DNA supercoiling can also enhance nucleosome sequence preference. The 357 base-pair minicircle was composed of a promoter of phage SP6 RNA polymerase joined to a 256 base-pair fragment containing a sea urchin 5 S RNA gene. Nucleosome formation on the promoter was found to be enhanced on a topoisomer with in vivo superhelix density when compared to topoisomers of lower or higher superhelical densities, to the nicked circle, or to the linear DNA. In contrast, nucleosomes at other positions appeared to be insensitive to supercoiling. This observation relied on a novel procedure for the investigation of nucleosome positioning. The reconstituted circular chromatin was first linearized using a restriction endonuclease, and the linear chromatin so obtained was electrophoresed as nucleoprotein in a polyacrylamide gel. The gel showed well-fractionated bands whose mobilities were a V-like function of nucleosome positions, with the nucleosome near the middle migrating less. This behavior is similar to that previously observed for complexes of sequence-specific DNA-bending proteins with circularly permuted DNA fragments, and presumably reflects the change in the direction of the DNA axis between the entrance and the exit of the particle. Possible mechanisms for such supercoiling-induced modulation of nucleosome formation are discussed in the light of the supercoiling-dependent susceptibility to cleavage of the naked minicircle with S1 and Bal31 nucleases; and a comparison between DNase I cleavage patterns of the modulated nucleosome and of another, non-modulated, overlapping nucleosome.     

Influence of a cyanobacterial crude extract containing microcystin-LR on the physiology and antioxidative defence systems of different spinach variants

Plants can be contaminated with cyanobacterial toxins during spray irrigation of lake water containing toxic cyanobacteria. Here, long-term effects of cyanobacterial crude extract (containing microcystin-LR) on the growth and physiology of different spinach (Spinacia oleracea) variants under semifield conditions were investigated. Changes in antioxidative enzyme activities, and in glutathione, ascorbate and tocopherol contents were investigated to assess the reaction of the antioxidative defence systems in spinach to toxin exposure. In addition to severe morphological effects, such as growth inhibition and chlorosis, the generation of oxidative stress was observed at the cellular level. In response to the negative effects of oxidative stress, plants stimulated an antioxidative system consisting of an enzyme network with superoxide dismutases, peroxidases, catalases, glutathione S-transferases and glutathione reductases, as well as a set of low-molecular-weight antioxidants, including glutathione, ascorbate and tocopherols. Exposure of spinach to cyanobacterial crude extract affected germination, growth and morphology, as well as antioxidative response parameters. Different variants of the same plant reacted in different ways to certain toxicants.     

Comparative kinetics of thiol oxidation in two distinct free-radical generating systems: SIN-1 versus AAPH

Abstract

To study oxidative stress in biological systems, chemical compounds capable of producing free radicals have been widely used. Here, we compared two free-radical generators, 3-morpholinosydnonimine (SIN-1) and 2,2′-azo-bis(2-amidinopropane) hydrochloride (AAPH), by measuring the thiol oxidation kinetics of various thiols. We found that SIN-1 is >?30 times potent in causing thiol oxidation than AAPH. Kinetic simulations revealed that in the SIN-1 system (0.1 mM), superoxide, nitrogen dioxide and carbonate radicals are the major reactive species which, in combination, induce ～50% of thiol molecules to undergo one-electron oxidation, thereby forming the thiyl radical which propagates further thiol oxidation by direct coupling with thiolates. Similarly, the alkyl peroxyl radical derived from AAPH (3 mM) initiates comparable extent of one-electron oxidation and formation of the thiyl radical. In conclusion, our study provides experimental and theoretical evidence that SIN-1 is mainly an one-electron oxidizing agent that can be functionally mimicked by AAPH.