Dye-decolorization of a newly isolated strain Bacillus amyloliquefaciens W36.

Dye-decolorization is one of the most important steps in dye-polluted wastewater treatment. The dye-decolorization bacteria were isolated from active sludge collected from wastewater treating pond of a dyeing and printing plant using serial dilution method. Among the 44 bacteria isolates from the active sludge, the strain Bacillus amyloliquefaciens W36 was found to have strong ability in dye-decolorization. The effects of carbon source, nitrogen sources, C/N, metal ions, temperature, pH, and rotation speed for dye-decolorization were investigated. The optimum decolorization conditions were that the strain was grown in enriched mineral salt medium (EMSM) using maltose 1 g/L, (NH4)2SO4 1 g/L as carbon and nitrogen source respectively, supplemented with 100 mg/L different dyes (pH 6.0), at 30 °C, 200 rpm from 48 to 96 h. The bacteria could aerobically decolorize dyes, such as Coomassie brilliant blue (95.42%), Bromcresol purple (93.34%), Congo red (72.37%) and Sarranine (61.7%), within 96 h. The dyes decolorization products were analyzed by ultra-violet and visible (UV-vis) spectroscopy before and after decolorization, which indicated that the four dyes were significantly degraded by the strain. The results indicated that the bacteria Bacillus amyloliquefaciens W36 could be used in dye-polluted wastewater treatment.

Molecular modeling to investigate the binding of Congo red toward GNNQQNY protofibril and in silico virtual screening for the identification of new aggregation inhibitors.

Understanding the nature of the recognition between amyloid protofibrils and dye molecules at the molecular level is essential to improving instructive guides for designing novel molecular probes or new inhibitors. However, the atomic details of the binding between dyes and amyloid fibrils are still not fully understood. In this study, molecular docking, consensus scoring, molecular dynamics (MD), and molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analyses were integrated to investigate the binding between Congo red (CR) and the GNNQQNY protofibril from yeast prion protein Sup35 and to further evaluate their binding stabilities and affinities. Our results reveal that there are four CR binding sites located on GNNQQNY protofibril surface. These four CR binding sites adopt dual binding modes by which CR binding with its long axis parallel and perpendicular to the long axis of the protofibril. In addition, CR was also found to bind to the edge of the protofibril via hydrophobic/aromatic and hydrogen-bonding interactions, which is inferred as the possible inhibition mechanism to prevent the elongation of the protofibril from the addition of incoming peptides. Virtual screening from National Cancer Institute (NCI) database obtained three hit compounds with higher binding affinity than CR to the edge of the protofibril due to the fact that the central parts of these compounds are able to form additional hydrogen bonds with the protofibril. The results of the study could be useful for the development of new molecular probes or inhibitors for clinical applications.

A small molecule inhibitor of Pot1 binding to telomeric DNA.

Chromosome ends are complex structures, consisting of repetitive DNA sequence terminating in an ssDNA overhang with many associated proteins. Because alteration of the regulation of these ends is a hallmark of cancer, telomeres and telomere maintenance have been prime drug targets. The universally conserved ssDNA overhang is sequence-specifically bound and regulated by Pot1 (protection of telomeres 1), and perturbation of Pot1 function has deleterious effects for proliferating cells. The specificity of the Pot1/ssDNA interaction and the key involvement of this protein in telomere maintenance have suggested directed inhibition of Pot1/ssDNA binding as an efficient means of disrupting telomere function. To explore this idea, we developed a high-throughput time-resolved fluorescence resonance energy transfer (TR-FRET) screen for inhibitors of Pot1/ssDNA interaction. We conducted this screen with the DNA-binding subdomain of Schizosaccharomyces pombe Pot1 (Pot1pN), which confers the vast majority of Pot1 sequence-specificity and is highly similar to the first domain of human Pot1 (hPOT1). Screening a library of ∼20 000 compounds yielded a single inhibitor, which we found interacted tightly with sub-micromolar affinity. Furthermore, this compound, subsequently identified as the bis-azo dye Congo red (CR), was able to competitively inhibit hPOT1 binding to telomeric DNA. Isothermal titration calorimetry and NMR chemical shift analysis suggest that CR interacts specifically with the ssDNA-binding cleft of Pot1, and that alteration of this surface disrupts CR binding. The identification of a specific inhibitor of ssDNA interaction establishes a new pathway for targeted telomere disruption.

Diseases of protein conformation: what do in vitro experiments tell us about in vivo diseases?

Certain human diseases are associated with proteins that misfold and exhibit decreased solubility under physiological conditions. They result either from mutations that change the amino acid sequence of a protein, or from misfolded wild-type proteins, such as in Parkinson's disease and Alzheimer's disease. One subset--the amyloidoses--cause extracellular deposits that stain with the dye Congo red. Another subset is associated with intracellular deposits with non-Congophilic nuclear or cytoplasmic inclusions. Purified, recombinantly produced versions of some of the proteins that form intracellular aggregates can also display Congophilia, as well as other properties associated with the in vivo amyloidoses when examined under non-physiological conditions in vitro. Some of these purified proteins or protein fragments have never been identified as pathogenic in humans or animals. Despite potentially shared thermodynamic and kinetic processes involving the target molecules, the biology of these two subsets differs significantly.

Effects of Ocimum gratissimum L essential oil at subinhibitory concentrations on virulent and multidrug-resistant Shigella strains from Lagos, Nigeria.

Ocimum gratissimum leaf extracts have been extensively demonstrated to be effective against the various aetiologic agents of diarrhoea, including Shigellae. However, the mechanism of the shigellocidal action of this plant remains to be understood. This study investigated the effects of O. gratissimum essential oil (EO) at subinhibitory concentrations of 0.75 and 1.0 microg/ml on virulence and multidrug-resistant strains of 22 Shigella isolates from Nigeria. Compared with untreated Shigella strains, O. gratissimum EO caused significant decreases (p<0.01) in extracellular protease activity, o-lipopolysaccharide rhamnose content and incidence of invasiveness mediated as keratoconjunctivitis in guinea pig. The disparity in extracellular protease activity and o-lipopolysacharide rhamnose between the two treatment groups was also found to be significant (p<0.05), suggesting greater anti-virulent effects of O. gratissimum oil at 1.0 microg/ml. Antibiotic susceptibility testing revealed that the EO of O. gratissimum reduced the MICs of antibiotics to which Shigellae showed resistance by 9.8-53.1% and fluoroquinolones by 18.2-45.5%. The results of this study strongly suggest inhibition of extracellular protease and expression of O-LPS rhamnose in Shigellae by O. gratissimum EO. The future use of O. gratissimum- antibiotic combinations as a therapeutic measure against shigellosis is discussed.

Factors affecting haemolysin production and congo red binding in Salmonella enterica serovar Typhimurium DT 98.

Differences in haemolysin expression were observed in a strain of Salmonella enterica serovar Typhimurium definitive phage type (DT) 98 cultured under various conditions. Haemolysin expression was optimal in cultures grown micro-aerobically. The zones of haemolysis were wider after longer periods of incubation. Haemolysin production varied after growth in the following media (greatest to least): brain heart infusion (BHI) broth > nutrient broth (NB)>trypticase soy broth (TSB)> M-9 glucose medium. Haemolysin production correlated directly with Congo red binding in nutrient broth. On Congo red blood agar, colonies were smaller, with dark centres and wider zones of haemolysis. Culture-cell-free haemolysin activity was higher, but cell-bound haemolysin activity was very low in growth medium supplemented with Congo red. Boiled tea extract at 25% v/v (of 25% w/v tea infusion) in PBS and nutrient broth was bactericidal to S. Typhimurium DT 98. The addition of boiled tea extract to growth medium inhibited haemolysin production by S. Typhimurium DT 98 at higher concentrations (6-12.5% v/v) but stimulated haemolysin production at lower concentrations (1.5-3% v/v). The pre-treatment of bacterial cell suspensions with lower concentrations of tea extract (1.5-3% v/v) also altered the Congo red binding, which showed an inverse correlation in nutrient broth.

Enhanced anti-Shigella activity of erythromycin supplemented with sulfadiazine.

Sulfadiazine enhanced the anti-Shigella activity of erythromycin. Erythromycin passes through the type III secretion apparatus and suppresses the growth of invasive Shigella organisms. Sulfadiazine enhanced this effect at the concentration under minimum inhibitory concentration and it came from not only the folate-inhibiting activity but also from a new function. It has proved that sulfadiazine stimulated type III secretion in Shigella as determined from the secretion of the pathogenic protein IpaB. As Congo red induced secretion of Ipa proteins and uptake of erythromycin through the type III secretion gate, sulfadiazine which is similar to Congo red in chemical structure may induce the uptake in the same way.

Inhibition of fibril formation in beta-amyloid peptide by a novel series of benzofurans.

A series of benzofuran derivatives have been identified as inhibitors of fibril formation in the beta-amyloid peptide. The activity of these compounds has been assessed by a novel fibril-formation-specific immunoassay and for their effects on the production of a biologically active fibril product. The inhibition afforded by the compounds seems to be associated with their binding to beta-amyloid, as identified by scintillation proximity binding assay. Binding assays and NMR studies also indicate that the inhibition is associated with self-aggregation of the compounds. There is a close correlation between the activity of the benzofurans as inhibitors of fibril formation and their ability to bind to beta-amyloid. Non-benzofuran inhibitors of the fibril formation process do not seem to bind to the same site on the beta-amyloid molecule as the benzofurans. Thus a specific recognition site might exist for benzofurans on beta-amyloid, binding to which seems to interfere with the ability of the peptide to form fibrils.

Detection and differentiation of iron-responsive avirulent mutants on Congo red agar.

Agar medium containing Congo red dye differentiates virulent and avirulent colonies of Shigella, Vibrio cholerae, Escherichia coli, and Neisseria meningitidis. Like virulent plague bacilli, wild-type cells of these species absorb the dye and produce red colonies. Mutants or colonial variants have been isolated that fail to absorb the dye and produce colorless colonies. These mutants exhibit reduced virulence in the chicken embryo model, but their virulence is enhanced by supplementation with iron. Of those species tested, only Neisseria gonorrhoeae isolates failed to grow in the presence of this dye. Inhibition of growth by Congo red may thus provide a simple means for differentiating gonococci from other Neisseria.