Diagnostic of an ionized gas by recording linearly polarized radiation

The degree of linear polarization of radiation from an ionized gas is calculated analytically. The analytical results on the resonant transition in Al XII atoms agree (to within 4%) with the numerical results obtained from the ATOM code. The applicability of the analytic expressions derived to the analysis of the degree of linear polarization of radiation from this atomic transition and the related excitation cross section is discussed. The plots of the degree of linear polarization of radiation from an ionized gas as a function of the electron parameters are presented. The question of whether the spectropolarimetry can provide an independent optical diagnostic tool is discussed.     

Adsorption of ionized and neutral pentachlorophenol to phosphatidylcholine membranes

We have studied adsorption of pentachlorophenol (PCP) to phosphatidylcholine (PC) membranes by measuring the electrophoretic mobility of multilayered lipid vesicles in PCP solutions. PC vesicles become negatively charged due to the adsorption of ionized PCP, and we have found that their zeta potential depends upon the ionic strength and pH of the aqueous suspension. We have shown that the experimental results can be adequately accounted for in terms of a two-component Langmuir-Stern-Grahame adsorption model assuming that the 'PCP adsorption sites' are occupied either by the neutral (HA) or the ionized (A-) species. The characteristics of adsorption isotherms of the PCP - PC membrane are as follows: the association constants are KA = 55,000 dm3/mol, KHA = 279,000 dm3/mol; 4.3 PC molecules make up each PCP adsorption site at saturation; the linear partition coefficients are beta HA = (15.5 +/- 0.7) x 10(-5) m and beta A = (3.0 +/- 0.3) x 10(-5) m. The properties of PCP adsorption isotherms for PC membranes predict an increased pKa value of membrane-bound PCP, which has been observed in related studies.     

Emergence of structural patterns in neutral trophic networks

Interaction networks are central elements of ecological systems and have very complex structures. Historically, much effort has focused on niche-mediated processes to explain these structures, while an emerging consensus posits that both niche and neutral mechanisms simultaneously shape many features of ecological communities. However, the study of interaction networks still lacks a comprehensive neutral theory. Here we present a neutral model of predator-prey interactions and analyze the structural characteristics of the simulated networks. We find that connectance values (complexity) and complexity-diversity relationships of neutral networks are close to those observed in empirical bipartite networks. High nestedness and low modularity values observed in neutral networks fall in the range of those from empirical antagonist bipartite networks. Our results suggest that, as an alternative to niche-mediated processes that induce incompatibility between species ("niche forbidden links"), neutral processes create "neutral forbidden links" due to uneven species abundance distributions and the low probability of interaction between rare species. Neutral trophic networks must be seen as the missing endpoint of a continuum from niche to purely stochastic approaches of community organization.     

Summary statistics of neutral mutations in longitudinal DNA samples

Longitudinal samples of DNA sequences are the DNA sequences sampled from the same population at different time points. For fast evolving organisms, e.g. RNA virus, these kind of samples have increasingly been used to study the evolutionary process in action. Longitudinal samples provide some interesting new summary statistics of genetic variation, such as the frequency of mutation of size i in one sample and size j in another, the average number of mutations accumulated since the common ancestor of two sequences each from a different sample, and number of private, shared and fixed mutations within samples. To make the results more applicable, we used in this study a general two-sample model, which assumes two longitudinal samples were taken from the same measurably evolving population. Inspired by the HIV study, we also studied a two-sample-two-stage model, which is a special case of two-sample model and assumes a treatment after the first sampling instantaneously changes the population size. We derived the formulas for calculating statistical properties, e.g. expectations, variances and covariances, of these new summary statistics under the two models. Potential applications of these results were discussed.     

Enhancement of ethene removal from waste gas by stimulating nitrification

The treatment of poorly water soluble waste gas compounds,such as ethene, is associated with low substrateconcentration levels in the liquid phase. This lowconcentration level might hamper the optimal development ofa microbial population. In this respect, the possible benefit ofintroducing nitrifying activity in the heterotrophic removal ofethene at moderate concentrations (< 1000 ppm) from awaste gas was investigated. Nitrifying activity is known to beassociated with (i) the production of soluble microbialproducts, which can act as (co-)substrates for heterotrophicmicro-organisms and (ii) the co-oxidation of ethene. Theused reactor configuration was a packed granular activatedcarbon biobed inoculated with the heterotrophic strain Mycobacterium E3. The nitrifying activity was introduced byregular submersion in a nitrifying medium prepared from (i)compost or (ii) activated sludge. In both cases a clearenhancement of the volumetric removal rate of ethene couldbe observed. When combined with a NH₃ dosage on adaily basis, a gradual increase of the volumetric removal rateof ethene could be observed. For a volumetric loading rateof 3 kg ethene-COD·m^-3·d^-1, the volumetric removal rate could thus be increased with a factor1.8, i.e. from 0.72 to a level of 1.26 kgethene-COD·m^-3·d^-1.     

Residual electron momentum and energy in a gas ionized by a short high-power laser pulse

A study is made of the nonadiabatic dynamics of photoelectrons produced during interaction of an elliptically polarized, high-power laser pulse with a gas. Expressions for the so-called residual momentum and energy of the electrons (i.e., the mean electron momentum and energy after the passage of the pulse through the gas) are derived. The residual electron momentum and energy are investigated analytically as functions of the gas and laser parameters. A relationship is established between the residual energy and the electron temperature tensor.     

The determination of acetaldehyde in blological samples by head-space gas chromatography

A method for the determination of acetaldehyde (AcH) in biological samples by head-space gas chromatography is presented. Human venous blood (antecubital), rat blood (heart-punctured) rat liver (freeze-clamped), and rat and mouse brain (freeze-clamped) were used as the biological samples. The method involves two steps, in the first of which the samples are deproteinized with perchloric acid (PCA). Rat blood can, alternatively, be hemolyzed with water. In the second step, the deproteinized supernatant or hemolyzed blood is pipetted into a serum bottle, which is sealed with a rubber stopper and brought to 65°C in a sampling turntable. Head-space samples are then automatically taken for GLC analysis. Ethanol causes a nonenzymatic formation of AcH in the PCA supernatants of liver and brain, which can be inhibited by the use of thiourea. This reaction is minor in the blood supernatants and cannot be inhibited there by thiourea. The method described measures the total AcH content without regard to any binding. Some of the AcH in rat blood was shown to be bound.     

Thermodynamic and structural studies of carbohydrate binding by the agrin-G3 domain

Agrin is a key heparan sulfate proteoglycan involved in the development and maintenance of synaptic junctions between nerves and muscles. Agrin's important functions include clustering acetylcholine receptors on the postsynaptic membranes of muscles and binding to the muscle protein alpha-dystroglycan through its glycan chains. ITC and NMR were used to study the interactions of the C-terminal domain, agrin-G3, with carbohydrates implicated in agrin's functions. Sialic acid caps the glycan chains of alpha-dystroglycan and occurs as a posttranslational modification on the muscle-specific kinase component of the agrin receptor. We found that agrin-G3 binds sialic acid in a Ca2+-dependent manner. ITC data indicate that binding is exothermic and occurs with a 1:1 stoichiometry. NMR chemical shift changes map the sialic acid binding site to the loops that control the domain's acetylcholine receptor clustering activity. By contrast, the glycosaminoglycans heparin and heparan sulfate bind independently of Ca2+. Binding is endothermic, and the binding site spans about 12 saccharide units. The binding site for heparin occupies a similar location but is distinct from that for sialic acid. NMR translational diffusion experiments show that agrin-G3 binds heparin with a 2:1 stoichiometry. Comparisons between the muscle (B0) and neuronal (B8) isoforms of the agrin domain showed very similar Ca2+ and carbohydrate binding properties. Our work identifies agrin-G3 as a functional analogue of the concanavalin A-type lectins, highlights functional similarities between agrin and laminin G domains, and provides mechanistic clues about the roles of carbohydrates in agrin's functions.     

Determination of acetaldehyde in biological samples by gas chromatography with electron-capture detection

A simple specific assay was developed for the determination of acetaldehyde in biological samples. Acetaldehyde was derivatized to 2,4-dinitrophenylhydrazone, which was determined by gas chromatography with electron-capture detection. The use of this detection method is an important device to which no one drew notice. This procedure was very simple and so sensitive that as little as 500 fmol of acetaldehyde could be measured in aqueous solution. The calibration curve of acetaldehyde was linear at least up to 40 μM. Its recoveries from human plasma and rat liver homogenate were 96.5 and 95.7%, respectively.     

Quantification of sodium dodecyl sulfate in microliter biochemical samples by gas chromatography

A novel gas chromatography (GC) method has been developed to accurately quantitate sodium dodecyl sulfate (SDS) in aqueous biochemical samples. This method is based on the quantitative conversion of SDS to 1-dodecanol in the GC injection port at elevated temperature, and the thermal degradation product 1-dodecanol was analyzed to determine SDS concentration. It was found that the addition of guanidinium chloride (GnHCl) to SDS samples (via direct dilution with GnHCl/MeOH solution) is necessary to ensure accurate quantitation. The presence of GnHCl enables quantitative conversion of SDS to 1-dodecanol, improves sensitivity, and virtually eliminates interference from proteins and other chemicals commonly present in biochemical samples. The method features direct analysis of diluted SDS samples, is free from interference, and is capable of quantifying less than 1 ng SDS in biochemical samples. It is also suitable for samples with limited volume, with as little as 1 microl sample being sufficient for quantitation.     

Enhancement of the structural stability of full-length clostridial collagenase by calcium ions

The clostridial collagenases G and H are multidomain proteins. For collagen digestion, the domain arrangement is likely to play an important role in collagen binding and hydrolysis. In this study, the full-length collagenase H protein from Clostridium histolyticum was expressed in Escherichia coli and purified. The N-terminal amino acid of the purified protein was Ala31. The expressed protein showed enzymatic activity against azocoll as a substrate. To investigate the role of Ca(2+) in providing structural stability to the full-length collagenase H, biophysical measurements were conducted using the recombinant protein. Size exclusion chromatography revealed that the Ca(2+) chelation by EGTA induced interdomain conformational changes. Dynamic light scattering measurements showed an increase in the percent polydispersity as the Ca(2+) was chelated, suggesting an increase in protein flexibility. In addition to these conformational changes, differential scanning fluorimetry measurements revealed that the thermostability was decreased by Ca(2+) chelation, in comparison with the thermal melting point (T(m)). The melting point changed from 54 to 49°C by the Ca(2+) chelation, and it was restored to 54°C by the addition of excess Ca(2+). These results indicated that the interdomain flexibility and the domain arrangement of full-length collagenase H are reversibly regulated by Ca(2+).     

Enhancement of glomerular mesangial cell neutral proteinase secretion by macrophages: role of interleukin 1

We have examined the ability of rat mesangial cells to regulate neutral proteinase production in vitro. Mesangial cells constitutively produced gelatinase when cultured in serum-free medium, and enzyme production by these cells was inhibited by cycloheximide. Coculture with thioglycollate-elicited rat peritoneal macrophages resulted in enhanced gelatinase production. The increase in enzyme released correlated directly with the number of macrophages added. Conditioned medium from LPS-activated peritoneal macrophages also enhanced gelatinase production in a dose-dependent manner. Fractionation of these macrophage supernatants on Sephacryl S-200 revealed a predominant fraction of gelatinase-enhancing activity in a m.w. range between 10,000 and 20,000. These data suggested that the enhanced mesangial cell gelatinase production was mediated through the action of interleukin 1. This was confirmed by the finding that purified interleukin 1, prepared from LPS-stimulated rat peritoneal macrophages, stimulated mesangial cells to secrete gelatinase in a dose-dependent manner. These findings may be of significance in the understanding of the pro-inflammatory role of macrophages in immune-mediated glomerulonephritis.     

Role of carbohydrate moiety in carboxypeptidase Y: structural study of mutant enzyme lacking carbohydrate moiety.

To study the roles of the carbohydrate moiety in the function of carboxypeptidase Y, asparagine residues at 13, 87, 168, and 368, the four-consensus N-linked glycosylation sites, were altered to alanine with site-directed mutagenesis. The mutant enzyme of 51 kDa completely lost the carbohydrate moiety which was present in the 61-kDa wild-type enzyme. Structural studies of the mutant enzyme showed that it maintained the native-like structure; hydrolytic activity, and substrate specificity of the mutant enzyme analogous to those of the wild-type enzyme. Susceptibility of the mutant enzyme toward proteolysis and pressure denaturation was reduced by 10-20%. It is concluded that the carbohydrate moiety functions to maintain the structural integrity of the enzyme under stressed.     

New structural variation in evolutionary searches of RNA neutral networks

RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets of RNA sequences that fold into the same structure. Our work extends and deepens previous studies on neutral networks. First, we show that even the 1-mutant neighborhood of a given sequence (genotype) G0 with structure (phenotype) P contains many structural variants that are not close to P. This holds for biological and generic RNA sequences alike. Second, we analyze the relation between new structures in the 1-neighborhoods of genotypes Gk that are only a moderate Hamming distance k away from G0, and the structure of G0 itself, both for biological and for generic RNA structures. Third, we analyze the relation between mutational robustness of a sequence and the distances of structural variants near this sequence. Our findings underscore the role of neutral networks in evolutionary innovation, and the role that high robustness can play in diminishing the potential for such innovation.     

Localization of neutral N-linked carbohydrate chains in pig zona pellucida glycoprotein ZPC.

Zona pellucida, a transparent envelope surrounding the mammalian oocyte, plays important roles in fertilization and consists of three glycoproteins; ZPA, ZPB and ZPC. In pig, neutral complex-type N-linked chains obtained from a ZPB/ZPC mixture possess sperm-binding activity. We have recently reported that among neutral N-linked chains triantennary and tetraantennary chains have a sperm-binding activity stronger than that of diantennary chains. Triantennary and tetraantennary chains are localized at the second of the three N-glycosylation sites of ZPB. In this study, we focused on the localization of neutral N-linked chains in ZPC. ZPB and ZPC can not be separated from each other unless the acidic N-acetyllactosamine regions of their carbohydrate chains are removed by endo-beta-galactosidase digestion. A large part of the acidic N-linked chains becomes neutral by the digestion, but the main neutral N-linked chains are not susceptible to the enzyme. N-glycanase digestion indicated that ZPC has three N-glycosylation sites. Three glycopeptides each containing one of the N-glycosylation sites were obtained by tryptic digestion of ZPC and the N-glycosylation sites were revealed as Asn124, Asn146 and Asn271. The carbohydrate structures of the neutral N-linked chains from each glycopeptide were characterized by two-dimensional sugar mapping analysis taking into consideration the structures of the main, intact neutral N-linked chains of ZPB/ZPC mixture reported previously. Triantennary and tetraantennary chains were found mainly at Asn271 of ZPC, whereas diantennary chains were present at all three N-glycosylation sites. Thus, ZPC has tri-antennary and tetra-antennary chains as well as ZPB, but the localization of the chains is different from that in ZPB.     

Estimation of neutral lipid and carbohydrate quotas in microalgae using adaptive interval observers

Under stress conditions, microalgae are known to accumulate large amounts of neutral lipids and carbohydrates, which can be used for biofuel production. However, on-line measurement of microalgal biochemical composition is a difficult task which makes the microalgal process rather difficult to manage. In this paper, we propose a so called adaptive interval observer for the on-line estimation of neutral lipid and carbohydrate quotas in microalgae. The observer is based on a change of coordinates that involves a time-varying gain. We introduce dynamics for the gain, whose trajectory converges toward a predefined optimal value (which maximizes the convergence rate of the observer). The observer performance is illustrated with experimental data of Isochrysis sp. cultures under nitrogen limitations and day–night cycle. The proposed observer design appears to be a suitable robust estimation technique.