A method for concentrating organic dyes: colorimetric measurements of nitric oxides and sialic acids

A new method for extraction and concentration of organic dyes that uses a reagent composed of a nonionic detergent mixed with an alcohol is described. We have observed that water-soluble organic dyes are also soluble in nonionic detergents and can be extracted by adding salt, which separates the dye–detergent component from the aqueous phase. We have also found that mixing nonionic detergents with alcohols markedly reduces their viscosity and produces stable, free-flowing, and effective reagents for color extraction. On the basis of these observations, we used a mixture of Triton X-100 and 1-butanol and observed that water-soluble natural and synthetic chromophores, as well as dyes generated in biochemical reactions, can be extracted, concentrated, and analyzed spectrophotometrically. Trypan blue and phenol red are used as examples of synthetic dyes, and red wine is used as an example of phenolic plant pigments. Applications for quantification of nitric oxides and sialic acids are described in more detail and show that as little as 0.15 nmol of nitric oxide and 0.20 nmol of sialic acid can be detected. A major advantage of this method is its ability to concentrate chromophores from dye-containing solutions that otherwise cannot be measured because of their low concentrations.     

Membrane-active metabolites produced by soil actinomycetes using chromatic phospholipid/polydiacetylene vesicles

Increased resistance of pathogens toward existing antibiotics has compelled the research efforts to introduce new antimicrobial substances. Drugs with new and less resistant-prone targets to antimicrobial activity have a high priority for drug development activities. Cell membrane seems to be a potential target for new antibiotic agent development to overcome resistance. In this study, A total number of 67 actinomycetes were isolated from the soil samples collected from desert, farming and mineral parts of Iran. We used a chromatic sensor as a membrane model that was set up for the target of antimicrobial metabolites of actinomycetes isolated from the soil. The sensors particles were composed of phospholipid and polymerized polydiacetylene (PDA) lipids. These polymers exhibited color change following interaction with membrane-active metabolites. The color change was due to structural disorder in the lipids following their interaction with membrane-active metabolites. The resultant color change was recorded by fluorescent microscope and easily recognizable by naked eye as well. Sixteen strains were isolated which produced antimicrobial metabolites and were effective against test microorganisms (Escherichia coli, Candida albicans and Saccharomyces cerevisiae ). A total number of 3 out of 16 strains produced membrane-active metabolites. These 3 strains were identified using 16s rRNA as Streptomyces sp and submitted to GenBank (accession no. JN180853; JN180854; JN180855).     

NMR and NQR parameters of the SiC-doped on the (4,4) <Emphasis Type="Italic">armchair</Emphasis> single-walled BPNT: a computational study

The structural properties, NMR and NQR parameters in the pristine and silicon carbide (SiC) doped boron phosphide nanotubes (BPNTs) were calculated using DFT methods (BLYP, B3LYP/6-31G*) in order to evaluate the influence of SiC-doped on the (4,4) armchair BPNTs. Nuclear magnetic resonance (NMR) parameters including isotropic (CS^I) and anisotropic (CS^A) chemical shielding parameters for the sites of various ¹³C, ²⁹Si, ¹¹B, and ³¹P atoms and quadrupole coupling constant (C _Q ), and asymmetry parameter (η _Q ) at the sites of various ¹¹B nuclei were calculated in pristine and SiC- doped (4,4) armchair boron phosphide nanotubes models. The calculations indicated that doping of ¹¹B and ³¹P atoms by C and Si atoms had a more significant influence on the calculated NMR and NQR parameters than did doping of the B and P atoms by Si and C atoms. In comparison with the pristine model, the SiC- doping in Si_PC_B model of the (4,4) armchair BPNTs reduces the energy gaps of the nanotubes and increases their electrical conductance. The NMR results showed that the B and P atoms which are directly bonded to the C atoms in the SiC-doped BPNTs have significant changes in the NMR parameters with respect to the B and P atoms which are directly bonded to the Si atoms in the SiC-doped BPNTs. The NQR results showed that in BPNTs, the B atoms at the edges of nanotubes play dominant roles in determining the electronic behaviors of BPNTs. Also, the NMR and NQR results detect that the Fig. 1b (Si_PC_B) model is a more reactive material than the pristine and the Fig. 1a (Si_BC_p) models of the (4,4) armchair BPNTs.     

Activity of the Bcr GTPase-activating domain is regulated through direct protein/protein interaction with the Rho guanine nucleotide dissociation inhibitor

The cycling of Rac GTPases, alternating between an active GTP- and an inactive GDP-bound state, is controlled by guanine nucleotide exchange factors, GTPase-activating proteins (GAPs), and guanine nucleotide dissociation inhibitors (GDIs). Little is known about how these controlling activities are coordinated. Studies using null mutant mice have demonstrated that Bcr and Abr are two physiologically important GAPs for Rac. Here, we report that in the presence of RhoGDIalpha, Bcr is unable to convert Rac-GTP to Rac-GDP because RhoGDI forms a direct protein complex with Bcr. Interestingly, RhoGDIalpha binds to the GAP domain in Bcr and Abr, a domain that also binds to Rac-GTP and catalyzes conversion of the bound GTP to GDP on Rac. The presence of activated Rac diminished the Bcr/RhoGDIalpha interaction. Moreover, a Bcr mutant that lacks the ability to promote hydrolysis of Rac-GTP bound to its GAP domain did not bind to RhoGDIalpha in cell lysates, indicating that binding of RhoGDIalpha and Rac-GTP to the Bcr GAP domain is mutually exclusive. Our results provide the first identification of a protein that regulates BcrGAP activity.     

Scaleable downstream recovery of nematodes used as biopesticides.

This study assesses the suitability of sieving as a scaleable technique for the separation of adult nematodes from infective juveniles, the latter is an effective bioinsecticide whereas the former is waste material resulting from the fermentation process. Batch and semibatch experiments using conventional flow-assisted wet sieving and a novel cross-flow sieving technique were used to study the separation of juveniles from adult nematodes. The experiments were carried out using small-scale devices and the data were analyzed in terms of the screen effectiveness factor. The results were used to identify the sieve size and operating conditions for optimum juvenile recovery. It was found that, for a given species of nematode, optimum recovery was achieved when sieving was carried out in the cross-flow mode, the maximum recovery being a function of the size of the screen. Industrial-scale self-cleaning equipment capable of large-scale continuous screening was used to confirm the capacity of the small-scale operation for scale-up. Experimental results with this unit showed that in continuous operation sieving time is an additional parameter that influences separation performance.     

gamma-Turn types prediction in proteins using the support vector machines

Recently, two different models have been developed for predicting gamma-turns in proteins by Kaur and Raghava [2002. An evaluation of beta-turn prediction methods. Bioinformatics 18, 1508-1514; 2003. A neural-network based method for prediction of gamma-turns in proteins from multiple sequence alignment. Protein Sci. 12, 923-929]. However, the major limitation of previous methods is inability in predicting gamma-turns types. Thus, there is a need to predict gamma-turn types using an approach which will be useful in overall tertiary structure prediction. In this work, support vector machines (SVMs), a powerful model is proposed for predicting gamma-turn types in proteins. The high rates of prediction accuracy showed that the formation of gamma-turn types is evidently correlated with the sequence of tripeptides, and hence can be approximately predicted based on the sequence information of the tripeptides alone.     

Biophysical characterization of an integrin-targeted lipopolyplex gene delivery vector

Nonviral gene delivery vectors now show good therapeutic potential: however, detailed characterization of the composition and macromolecular organization of such particles remains a challenge. This paper describes experiments to elucidate the structure of a ternary, targeted, lipopolyplex synthetic vector, the LID complex. This consists of a lipid component, Lipofectin (L) (1:1 DOTMA:DOPE), plasmid DNA (D), and a dual-function, cationic peptide component (I) containing DNA condensation and integrin-targeting sequences. Fluorophore-labeled lipid, peptide, and DNA components were used to formulate the vector, and the stoichiometry of the particles was established by fluorescence correlation spectroscopy (FCS). The size of the complex was measured by FCS, and the sizes of LID, L, LD, and ID complexes were measured by dynamic light scattering (DLS). Fluorescence quenching experiments and freeze-fracture electron microscopy were then used to demonstrate the arrangement of the lipid, peptide, and DNA components within the complex. These experiments showed that the cationic portion of the peptide, I, interacts with the plasmid DNA, resulting in a tightly condensed DNA-peptide inner core; this is surrounded by a disordered lipid layer, from which the integrin-targeting sequence of the peptide partially protrudes.     

Development of fast Fourier transformation continuous cyclic voltammetry as a highly sensitive detection system for ultra trace monitoring of penicillin V

Fast continuous cyclic voltammetry was used as a detection method for penicillin V in a flow injection system. Additionally, a special computer-based numerical calculation method (using fast Fourier transformation) providing enhancement of the analyte signal and noise reduction is introduced here. During the measurements, the potential waveform (consisting of the potential steps of cleaning, stripping, and the potential ramp) was continuously applied to an Au disk microelectrode (12.5 microm in radius). In particular, the effects of accumulation potential, sweep rate, and delay time on the sensitivity and selectivity of the method were investigated. Eventually, the stripping time was found to be less than 300 ms, the detection limit of the method was 7.0x10(-12) M, and the associated relative standard deviation at 5.0x10(-6) M penicillin V was 2.3 for eight runs.