Advances in bacterial adsorption and transport of aromatic compounds / 生物工程学报

Aromatic compounds are a class of organic compounds with benzene ring(s). Aromatic compounds are hardly decomposed due to its stable structure and can be accumulated in the food cycle, posing a great threat to the ecological environment and human health. Bacteria have a strong catabolic ability to degrade various refractory organic contaminants (e.g., polycyclic aromatic hydrocarbons, PAHs). The adsorption and transportation are prerequisites for the catabolism of aromatic compounds by bacteria. While remarkable progress has been made in understanding the metabolism of aromatic compounds in bacterial degraders, the systems responsible for the uptake and transport of aromatic compounds are poorly understood. Here we summarize the effect of cell-surface hydrophobicity, biofilm formation, and bacterial chemotaxis on the bacterial adsorption of aromatic compounds. Besides, the effects of outer membrane transport systems (such as FadL family, TonB-dependent receptors, and OmpW family), and inner membrane transport systems (such as major facilitator superfamily (MFS) transporter and ATP-binding cassette (ABC) transporter) involved in the membrane transport of these compounds are summarized. Moreover, the mechanism of transmembrane transport is also discussed. This review may serve as a reference for the prevention and remediation of aromatic pollutants.

Comparative effect of ciprofloxacin and moxifloxacin on the modulation of bile acid profiles and gut microbiota in rats

Abstract Fluoroquinolones are an important class of antimicrobial agents to manage infectious diseases. However, knowledge about how host bile acids are modified by fluoroquinolones is limited. We investigated and compared the impact of fluoroquinolones on circulating bile acid profiles and gut microbiota from in vivo studies. We administered ciprofloxacin (100 mg/kg/day) or moxifloxacin (40 mg/kg/day) orally to male Wistar rats for seven days. Fifteen bile acids (BAs) from the serum and large intestine were quantified by HPLC-MS/MS. The diversity of gut microbiota after ciprofloxacin and moxifloxacin treatment was analyzed using high-throughput, next-generation sequencing technology. The two fluoroquinolone-treated groups had different BA profiles. Ciprofloxacin significantly reduced the hydrophobicity index of the BA pool, reduced secondary BAs, and increased taurine-conjugated primary BAs in both the serum and large intestine as compared with moxifloxacin. Besides, ciprofloxacin treatment altered intestinal microbiota with a remarkable increase in Firmicutes to Bacteroidetes ratio, while moxifloxacin exerted no effect. What we found suggests that different fluoroquinolones have a distinct effect on the host BAs metabolism and intestinal bacteria, and therefore provide guidance on the selection of fluoroquinolones to treat infectious diseases.

Lipophilicity Descriptors Correlate Uniquely with Pharmacokinetic and Blood-Brain Barrier Penetration Parameters for Selected Antipsychotic Drugs

Lipophilicity is an important physicochemical parameter of biological relevance; although its in- vivo predictive capability is dependent on accuracy and reliability of platforms used for its determination. This work examines biomimetic attribute of isocratic chromatographic hydrophobicity index (ICHI), experimental logarithm of octanol ­ water partition coefficient (LogP) and some computed lipophilicity indices for eight (8) selected antipsychotic agents and their predictive capability in drug discovery. The retention behavior of 5 first-generation and 3 second-generation antipsychotics was determined on reversed-phase chromatographic platform using methanol-phosphate buffer (pH 6.8) mobile phase. The retardation factor obtained was transformed to Rm, and plotted against volume fraction of organic modifier in the mobile phase to generate linear graph whose x- intercept is ICHI. Experimental LogP values were curled from literature while computed LogP were obtained using respective software. The experimentally determined LogPoctanol/water and ICHI were first correlated with index of brain permeability (BBB); before all lipophilicity indices were comparatively evaluated and correlated with in-vivo-normalized pharmacokinetic parameters curled from literature. ICHI gave better correlation with BBB index (r = 0.976) compared to Log Poctanol/water (r = 0.557). Comparative lipophilicity evaluation shows clustered pattern for second generation antipsychotics compared to first generation. In vivo correlation was poorer for the 8 drugs (r < 0.7), better with subset of phenothiazine homologues (r = 0.51 to 0.97). The ALogP, LogPoctanol/water, cLogP and ICHI gave highest correlation with the pharmacokinetic parameters. The biomimetic attributes of ICHI is better than for LogPoctanol/water in predicting brain permeability, but lower for in-vivo pharmacokinetic prediction.

Comparative analysis of virulence factors & biotypes of Gardnerella vaginalis isolated from the genital tract of women with & without bacterial vaginosis

Background & objectives: Bacterial vaginosis (BV) involves the presence of a thick vaginal multispecies biofilm, where Gardnerella vaginalis is the predominant species. The reason for an increase in the number of G. vaginalis which are usually present as normal flora of the female genital tract in cases of BV, is not known. Hence, the objective of the present study was to compare the biotypes and virulence factors of G. vaginalis isolated from the genital tract of women with and without BV. Methods: High vaginal swabs collected from 811 women of reproductive age were cultured. G. vaginalis isolates were biotyped and tested for adherence to vaginal epithelial cells, biofilm formation, agglutination of human red blood cells (RBCs), protease production, phospholipase production and surface hydrophobicity. Results: Of the isolates from women with BV, 83.3 per cent (60/72) showed good adherence, 78.4 per cent (58/74) produced biofilm, 82.9 per cent (63/76) produced phospholipase, 67.1 per cent (51/76) produced protease, 77.3 per cent (58/75) were positive for surface hydrophobicity and 61.6 per cent (45/73) were positive for haemagglutination of human RBC. In case of G. vaginalis from non-BV women, 25 per cent (15/60) isolates showed good adherence, 18.4 per cent (9/49) biofilm production, 35 per cent (21/60) phospholipase, 36.6 per cent (22/60) protease, 41.7 per cent (25/60) surface hydrophobicity and 10.1 per cent (6/59) agglutination of human RBCs. Maximum number of isolates belonged to biotypes 6, 2 and 3. Biotype 3 was more associated with non-BV rather than BV; biotype 6, 2 and 1 were more associated with cases of BV. Maximum virulence factors were expressed by biotypes 6, 2 and 1. Interpretation & conclusions: Virulence factors were more expressed by G. vaginalis isolates obtained from women with BV rather than from non-BV. Biotypes 6, 2 and 1 were more associated with cases of BV and expressed maximum virulence factors.

Preparation and characterization of drug-loaded polymer-lipid hybrid nanoparticles with tunable surface hydrophobicity / 药学学报

The surface hydrophobicity of nanoparticles plays an important role in drug delivery process. The aim of this study was to verify the feasibility of using self-assembly method to prepare drug-loaded nanoparticles with tunable surface hydrophobicity. Here, Soluplus was selected as the polymeric carrier to prepare panobinostat (PNB) loaded micelles. Three different monoglycerides, glycerly monooleate (GMO), glycerly linoleate (GML) and glycerly linolenate (GMLO), were used to modify the surface of PNB-Soluplus micelles to prepare polymer-lipid hybrid nanoparticles (PLHNs). The effect of monoglyceride type and amount on the physico-chemical properties of PNB-loaded PLHNs was investigated, and the surface hydrophobicity of PLHNs was characterized by Rose Bengal (RB) binding method and mucin particle method. The results suggested that compared with the PNB-Soluplus micelles (particle size 77.97 ± 0.78 nm, zeta potential 0.44 ± 0.29 mV, entrapment efficiency 99.45% ± 1.47%, the RB binding constant (K) value 0.008 ± 0.002, the increased particle size after mixing with mucin particles 7.90 ± 1.41 nm), surface hydrophobicity of the PLHNs increased significantly when modified by GMO, GML, GMLO, with K values of 0.055 ± 0.010, 0.050 ± 0.011 and 0.058 ± 0.008, respectively. The increased particle sizes after mixing with mucin particles were 17.37 ± 4.48 nm, 22.60 ± 2.10 nm and 25.13 ± 3.89 nm, respectively. Among them, the physico-chemical properties of the GMLO modified PNB-loaded PLHNs (particle size 81.60 ± 4.52 nm, zeta potential 0.77 ± 0.03 mV, entrapment efficiency 99.59% ± 0.20%) kept constant, thus GMLO was selected to further investigate the effect of GMLO mass ratio (1%-3%) to Soluplus on the properties of the nanoparticles. While no statistical significant difference in particle size, zeta potential, entrapment efficiency or in vitro release behavior was found when GMLO ratio increased, the surface lipophilicity of the PLHNs, as characterized by K values and the increased particle sizes after mixing with mucin particles, increased almost linearly with the increase of GMLO amount. In conclusion, we demonstrated that drug-loaded PLHNs based on Soluplus and GMLO can be prepared by self-assembly method, and the surface hydrophobicity was tunable by modifying the mass ratio of GMLO to Soluplus. This approach could be used for related basic science research aiming to elucidate the effect of surface hydrophobicity on in vivo behavior of drug-loaded system.

Elastin increases biofilm and extracellular matrix production of Aspergillus fumigatus

Abstract Aspergillus fumigatus is an opportunistic saprobe fungus that accounts for 90% of cases of pulmonary aspergillosis in immunosuppressed patients and is known for its angiotropism. When it reaches the respiratory tract, A. fumigatus interacts with structural components and blood vessels of the lungs, such as elastin. To understand the effect of this structural component, we examined the effect of elastin on the production and development of the biofilm of A. fumigatus. In RPMI containing 10 mg/mL of elastin, a significant increase (absorbance p < 0.0001; dry weight p < 0.0001) in the production of biofilm was observed in comparison to when RPMI was used alone, reaching a maximum growth of 18.8 mg (dry weight) of biofilm in 72 h. In addition, elastin stimulates the production (p = 0.0042) of extracellular matrix (ECM) and decreases (p = 0.005) the hydrophobicity during the development of the biofilm. These results suggest that elastin plays an important role in the growth of A. fumigatus and that it participates in the formation of thick biofilm.

Root canal irrigants influence the hydrophobicity and adherence of Staphylococcus epidermidis to root canal dentin: an in vitro study

OBJECTIVES: To determine the effect of root canal irrigants on the hydrophobicity and adherence of Staphylococcus epidermidis (S. epidermidis) to root canal dentin in vitro. MATERIALS AND METHODS: Root dentin blocks (n = 60) were randomly divided into 4 groups based on the irrigation regimen: group 1, saline; group 2, 5.25% sodium hypochlorite (NaOCl); group 3, 5.25% NaOCl followed by 17% ethylenediaminetetraacetic acid (EDTA); group 4, same as group 3 followed by 2% chlorhexidine (CHX). The hydrophobicity of S. epidermidis to root dentin was calculated by cell surface hydrophobicity while the adherence was observed by fluorescence microscopy, and bacteria were quantified using ImageJ software (National Institutes of Health). Statistical analysis of the data was done using Kruskal-Wallis test and Mann-Whitney U test (p = 0.05). RESULTS: The hydrophobicity and adherence of S. epidermidis to dentin were significantly increased after irrigating with group 3 (NaOCl-EDTA) (p < 0.05), whereas in group 4 (NaOCl-EDTA-CHX) both hydrophobicity and adherence were significantly reduced (p < 0.05). CONCLUSIONS: The adherence of S. epidermidis to dentin was influenced differently by root canal irrigants. Final irrigation with CHX reduces the bacterial adherence and may impact biofilm formation.

Influence of Cell Surface Hydrophobicity on Adhesion and Biofilm Formation in Candida albicans and Several Bacterial Species

The purpose of this study is to investigate the correlation of cell surface hydrophobicity (CSH) and biofilm formation or adhesion in Candida albicans (C. albicans) and several pathogenic bacteria. All of C. albicans (n=82) and 7 bacterial species (Escherichia coli, n=25; Klebsiella pneumoniae, n=33; Morganella morganii, n=21; Proteus mirabilis, n=33; Proteus vulgaris, n=12; Pseudomonas aeruginosa, n=31; Staphylococcus aureus, n=31) were isolated clinically. CSH was quantified with microbial adhesion to hydrocarbons. Biofilm formation was determined by tetrazolium salt reduction assay. Adhesion assay was performed by counting colonies after culture the microbes adhered to HeLa cells. Although high CSH-expressing bacterial species showed greater adherence to HeLa cells and larger amounts of biofilm formation on polystyrene, the significant relationships within same species were not shown. In C. albicans, however, strong positive correlations were observed between CSH and biofilm formation (r =0.708; p < 0.05) or cell adhesion (r =0.509; p < 0.05). These results suggest that hydrophobic force of bacteria may play a minor role in adhesion and biofilm formation, but CSH of C. albicans may be an important factor for adherence on surface and biofilm forming process.

Cell surface hydrophobicity and biofilm formation of candida yeast species in different culture media / Hidrofobicidade da superfície celular e formação de biofilme de Candida sp em diferentes meios de cultura

Cell surface adhesion is considered an essential step in the spread, infection and persistence of Candida yeasts in the host. Their ability to adhere on biotic and abiotic surfaces depends on several factors, including hydrophobicity. Once attached, these yeasts are capable of growing in biofilms, which are constituted of structured communities of encapsulated cells within an extracellular matrix, resistant to antifungal agents. In this context, this study aimed to analyze the cell surface hydrophobicity and specific biofilm formation of six Candida strains in different culture media: Sabouraud dextrose broth (SDB), artificial saliva (AS), Roswell Park Memorial Institute medium (RPMI 1640) and N-acetylglucosamine-yeast nitrogen base proline (NYP). Six yeasts of the genus Candida were studied: three C. albicans (Ca): Ca ATCC 10231 and the clinical isolates Ca34 and Ca05 and C. parapsilosis (Cp): Cp ATCC 22019 and the clinical isolates Cp120 and Cp38. Hydrophobicity was calculated as the percentage reduction in turbidity of the aqueous phase, due to the retention of the hydrophobic cells in hydrocarbon by the hydrocarbon-water biphasic assay following the MATH (Microbial Adhesion to Hydrocarbon) method. The biofilm formation index was calculated as the optical density obtained by the growth of the yeasts in the culture media in a polystyrene microtiter plate, subsequently stained with 1% violet crystal. The results showed that hydrophobicity varied according to the media and the yeasts studied, and two of these (Ca34 and Ca10231) presented significant variation between the media. A more hydrophobic character was observed in yeasts grown on RPMI-1640 medium, and those grown on Sabouraud dextrose broth appeared more hydrophilic. The specific biofilm formation index was more intense for RPMI 1640 than in other media, which was expected, due to its ability to induce the transition between yeast-hyphae morphology, which is one of the key factors involved in the adhesion of C. albicans on different surfaces. RPMI 1640 was the best medium for obtaining biofilm in vitro, due to its greater hydrophobicity, which can enhance cell adhesion to the polystyrene plate, and due to its nutrient content, necessary for complete cell growth and biofilm formation.

A adesão é considerada um passo essencial para a disseminação, infecção e persistência das leveduras do gênero Candida nos hospedeiros. A habilidade dessas leveduras em se aderir a superfícies bióticas e abióticas depende de fatores, incluindo a hidrofobicidade da superfície celular. Uma vez aderidas, estas leveduras são capazes de crescer como biofilmes, os quais são caracterizados como comunidades estruturadas de células encapsuladas dentro de uma matriz extracelular, resistentes a drogas antifúngicas. Neste contexto, objetivou-se analisar a hidrofobicidade da superfície celular e a formação específica de biofilme de Candida spp. em diferentes meios de cultura: caldo Sabouraud dextrose (CSD), saliva artificial (SA), Roswell Park Memorial Institute medium (RPMI 1640) e N-acetylglucosamineyeast nitrogen base-proline (NYP). Foram estudadas seis leveduras do gênero Candida, sendo três C. albicans (Ca): Ca ATCC 10231 e os isolados clínicos Ca34 e Ca05 e C. parapsilosis (Cp): Cp ATCC 22019 e os isolados clínicos Cp120 e Cp38. A hidrofobicidade foi calculada como a porcentagem da redução da turbidez da fase aquosa, devido a retenção das células hidrofóbicas no hidrocarboneto pelo método bifásico água-hidrocarboneto MATH (Teste de Adesão Microbiana a Hidrocarbonetos). O índice de formação de biofilme foi calculado com as densidades ópticas obtidas por meio do crescimento das leveduras nos meios de cultura em poços de placa de microtitulação de poliestireno e posteriormente corados com cristal violeta a 1%. Os resultados demonstraram que a hidrofobicidade variou de acordo com os meios e as leveduras estudadas, sendo que duas (Ca34 e Ca10231) apresentaram variação significativa entre os meios. Foi verificado um caráter mais hidrofóbico das células crescidas em RPMI 1640 e mais hidrofílico nas células crescidas em caldo Sabouraud dextrose. A formação específica de biofilme apresentou-se mais intensa em RPMI 1640 do que nos outros meios, o que já era esperado pela sua capacidade de induzir o processo de transição levedura-hifa, o qual é considerado um dos fatores cruciais envolvidos na adesão de leveduras. Com os resultados obtidos, infere-se que o RPMI 1640 é o melhor meio para obtenção de biofilme in vitro, pois as células foram mais hidrofóbicas, o que pode aumentar a adesão das

Physical and chemical quality, biodiversity, and thermodynamic prediction of adhesion of bacterial isolates from a water purification system: a case study

ABSTRACT The objective of this study was to evaluate the quality of water purification system and identify the bacteria this system, predict bacterial adherence according to the hydrophobicity of these microorganisms and of the polypropylene distribution loop for purified water. The assessment of drinking water that supplies the purification system allowed good-quality physical, chemical, and microbiological specifications. The physicochemical specifications of the distributed purified water were approved, but the heterotrophic bacteria count was higher than allowed (>2 log CFU mL-1).The sanitation of the storage tank with chlorine decreased the number of bacteria adhered to the surface (4.34 cycles log). By sequencing of the 16SrDNA genes, six species of bacteria were identified. The contact angle was determined and polypropylene surface and all bacteria were considered to be hydrophilic, and adhesion was thermodynamically unfavorable. This case study showed the importance of monitoring the water quality in the purified water systems and the importance of sanitization with chemical agents. The count of heterotrophic bacteria on the polypropylene surface was consistent with the predicted thermodynamics results because the number of adhered cells reached approximate values of 5 log CFU cm-2.

Effect of plasma surface treatment of poly(dimethylsiloxane) on the permeation of pharmaceutical compounds / 药物分析学报

This paper addresses the modification of poly(dimethylsiloxane), i.e. PDMS, using plasma surface treatment and a novel application of the membrane created. A set of model compounds were analysed to determine their permeation through PDMS, both with and without plasma treatment. It was found that plasma treatment reduced permeation for the majority of compounds but had little effect on some compounds, such as caffeine, with results indicating that polarity plays an important role in permeation, as is seen in human skin. Most importantly, a direct correlation was observed between plasma-modified permeation data and literature data through calculation of membrane permeability (Kp) values suggesting plasma-modified silicone membrane (PMSM) could be considered as a suitable in vivo replacement to predict clinical skin permeation.

Study on the Effect of Hydrophilic/Hydrophobic Nano-silica with Different Adding Amount on the Stability of Glycyrrhetinic Acid Lipo-emulsion / 中国药房

OBJECTIVE:To study the effect of hydrophilic/hydrophobic nano-silica with different adding amount on the stabili-ty of lipo-emulsion. METHODS:Glycyrrhetinic acid lipo-emulsion 4 mL was taken,respectively adding into 0.5%,1.0%,1.5%(m/m,the same below) hydrophilic nSiO2,and 0.4%,0.75,1.0% hydrophobic nSiO2,incubating 2 h in 30 ℃ water;the same batch of Glycyrrhetinic acid lipo-emulsion was treated as blank control. The forms were observed under electron microscopy after treatment,absorbance value was determined,the stability parameter (KE) was calculated according to the absorbance value,then the adding amount of nSiO2 was optimized,3 batches of preparations was prepared,and the verification test was conducted. RE-SULTS:The spherical structure was Glycyrrhetinic acid lipo-emulsion in the electron microscopy,the substance wrapping its sur-face white ring (fully wrapped) or semi-circular structure (not fully wrapped) was nSiO2. KE of hydrophilic nSiO2 were 4.66%, 5.01% and -2.08%,and KE of hydrophobic nSiO2 were 3.02%,4.51% and 7.24%. The optimized adding amount of hydrophilic nSiO2 was 0.2%,0.3% and 0.4%,hydrophobic nSiO2 was 0.1%,0.2% and 0.3%;KE were 6.19%,3.05%,7.84%,8.42%, 2.41%,2.93%,respectively. The optimal adding amount was 0.3% hydrophilic nSiO2 and 0.2% hydrophobic nSiO2;the 3 batches of preparation showed the optimum stability in its own adding amount. CONCLUSIONS:Both hydrophilic and hydrophobic nSiO2 can improve the stability of Glycyrrhetinic acid lipo-emulsion,and preferably 0.3%,0.2%.

Effect of plasma surface treatment of poly(dimethylsiloxane) on the permeation of pharmaceutical compounds / 药物分析学报

This paper addresses the modification of poly(dimethylsiloxane), i.e. PDMS, using plasma surface treatment and a novel application of the membrane created. A set of model compounds were analysed to determine their permeation through PDMS, both with and without plasma treatment. It was found that plasma treatment reduced permeation for the majority of compounds but had little effect on some compounds, such as caffeine, with results indicating that polarity plays an important role in permeation, as is seen in human skin. Most importantly, a direct correlation was observed between plasma-modified permeation data and literature data through calculation of membrane permeability (Kp) values suggesting plasma-modified silicone membrane (PMSM) could be considered as a suitable in vivo replacement to predict clinical skin permeation.

Influence of Aae Autotransporter Protein on Adhesion and Biofilm Formation by Aggregatibacter actinomycetemcomitans

Abstract The periodontopathogen Aggregatibacter actinomycetemcomitans colonizes oral cavity by binding to and invading epithelial cells as well as by participating in biofilms formed on hard surfaces. Aae, an autotransporter protein, is implicated in bacterial adhesion to epithelial cells. Due to the multiple functions of bacterial autotransporter proteins, this study aimed to evaluate the role of aae in A. actinomycetemcomitans ability to adhere to both saliva-coated hydroxyapatite (SHA) and biofilm. An aae null mutant was constructed. Its hydrophobic properties as well as its ability to adhere to epithelial cells, SHA and to form biofilm were evaluated and compared with the parental strain, A. actinomycetemcomitans VT1169. The aae null mutant showed reduced hydrophobicity, as well as decreased binding to SHA and biofilm formation compared to the parental strain. These data suggest that aae mediates A. actinomycetemcomitans adhesion to epithelial cells and may be involved in biofilm formation and interaction with adsorbed salivary proteins.

Resumo O peridontopatógeno Aggregatibacter actinomycetemcomitans coloniza a cavidade oral aderindo e invadindo as células epiteliais e participando da formação de biofilme em superfícies duras. Aae, uma proteína autotransportadora está relacionada com a adesão bacteriana às células epiteliais. Devido às múltiplas funções desempenhadas por proteínas bacterianas autotransportadoras, este estudo teve como objetivo avaliar o papel de aae de A. actinomycetemcomitans tanto na capacidade de aderir à hidroxiapatita recoberta por saliva (SHA), quanto a de formar biofilme. Um mutante nulo aae foi construído. Suas propriedades hidrofóbicas, bem como a sia capacidade para aderir às células epiteliais, à SHA e para formar biofilme foram avaliadas e comparadas com a cepa -mãe, A. Actinomycetemcomitans VT1169. O mutante nulo aae apresentou redução de hidrofobicidade, assim como diminuição da adesão à SHA e na formação de biofilme, quando comparado à cepa parental. Estes dados sugerem que aae media a adesão de A. Actinomycetemcomitans às células epiteliais e pode também estar envolvida na formação de biofilme e na interação com proteínas salivares adsorvidas.

In vitro biofilm formation in ESBL producing Escherichia coli isolates from cage birds

Objective To determine biofilm and hydrophobicity formation ratios in extended spectrum beta lactamases (ESBL) synthesizing Escherichia coli isolates which were isolated from feces samples of 150 cage bird species randomly taken from pet shops in Hatay province, Turkey. Methods In vitro biofilm production of 4 ESBL positive isolates were performed by Congo Red Agar (CRA), Standard Tube (ST) and Microtitre Plate (MP) methods while their hydrophobicity were examined by bacterial adhesion to hydrocarbon (BATH) test. Results In the examined isolates, while biofilm production was found to be negative by CRA method, highest biofilm producing strain, among 4 bacteria was determined to be A42 by ST and MP methods. The Scanning Electron Microscopy (SEM) also displayed these confirmed findings. The hydrophobicity values of strains were determined to be between 22.45% and 26.42%. Conclusions As a result, biofilm formation in cage bird feces originated ESBL positive Escherichia coli isolates was performed for the first time in Turkey. In order to present the relation between pathogenicity and biofilm production in animal originated ESBL positive isolates, further studies are required.

50 years of amino acid hydrophobicity scales: revisiting the capacity for peptide classification

BACKGROUND: Physicochemical properties are frequently analyzed to characterize protein-sequences of known and unknown function. Especially the hydrophobicity of amino acids is often used for structural prediction or for the detection of membrane associated or embedded ß-sheets and α-helices. For this purpose many scales classifying amino acids according to their physicochemical properties have been defined over the past decades. In parallel, several hydrophobicity parameters have been defined for calculation of peptide properties. We analyzed the performance of separating sequence pools using 98 hydrophobicity scales and five different hydrophobicity parameters, namely the overall hydrophobicity, the hydrophobic moment for detection of the α-helical and ß-sheet membrane segments, the alternating hydrophobicity and the exact ß-strand score. RESULTS: Most of the scales are capable of discriminating between transmembrane α-helices and transmembrane ß-sheets, but assignment of peptides to pools of soluble peptides of different secondary structures is not achieved at the same quality. The separation capacity as measure of the discrimination between different structural elements is best by using the five different hydrophobicity parameters, but addition of the alternating hydrophobicity does not provide a large benefit. An in silico evolutionary approach shows that scales have limitation in separation capacity with a maximal threshold of 0.6 in general. We observed that scales derived from the evolutionary approach performed best in separating the different peptide pools when values for arginine and tyrosine were largely distinct from the value of glutamate. Finally, the separation of secondary structure pools via hydrophobicity can be supported by specific detectable patterns of four amino acids. CONCLUSION: It could be assumed that the quality of separation capacity of a certain scale depends on the spacing of the hydrophobicity value of certain amino acids. Irrespective of the wealth of hydrophobicity scales a scale separating all different kinds of secondary structures or between soluble and transmembrane peptides does not exist reflecting that properties other than hydrophobicity affect secondary structure formation as well. Nevertheless, application of hydrophobicity scales allows distinguishing between peptides with transmembrane α-helices and ß-sheets. Furthermore, the overall separation capacity score of 0.6 using different hydrophobicity parameters could be assisted by pattern search on the protein sequence level for specific peptides with a length of four amino acids.

In vitro biofilm formation in ESBL producing Escherichia coli isolates from cage birds

OBJECTIVE@#To determine biofilm and hydrophobicity formation ratios in extended spectrum beta lactamases (ESBL) synthesizing Escherichia coli isolates which were isolated from feces samples of 150 cage bird species randomly taken from pet shops in Hatay province, Turkey.@*METHODS@#In vitro biofilm production of 4 ESBL positive isolates were performed by Congo Red Agar (CRA), Standard Tube (ST) and Microtitre Plate (MP) methods while their hydrophobicity were examined by bacterial adhesion to hydrocarbon (BATH) test.@*RESULTS@#In the examined isolates, while biofilm production was found to be negative by CRA method, highest biofilm producing strain, among 4 bacteria was determined to be A42 by ST and MP methods. The Scanning Electron Microscopy (SEM) also displayed these confirmed findings. The hydrophobicity values of strains were determined to be between 22.45% and 26.42%.@*CONCLUSIONS@#As a result, biofilm formation in cage bird feces originated ESBL positive Escherichia coli isolates was performed for the first time in Turkey. In order to present the relation between pathogenicity and biofilm production in animal originated ESBL positive isolates, further studies are required.

The effects of lemon essential oil,limonene and tea polyphenols on cell surface hydrophobicity and adher-ence of Streptococcus mutans / 实用口腔医学杂志

Objective:To explore the effects of the natural plant ingredients lemon essential oil(LEO),limonene(LIM)and tea poly-phenols(TP)on the cell surface hydrophobicity and adherence of Streptococcus mutans(S.mutans).Methods:S.mutans were treated by sub-minimal inhibitory concentration(MIC)levels of LEO,LIMand TP respectively.Adsorption to hexadecane was used to measure the hydrophobic interaction of S.mutans.A classical 96-cell microtitre plate production assay using crystal violet staining was employed to visualize the adherence of S.mutans to hard tissue surface.Results:LEO,LIMand TP at sub-MIC levels could inhibit the cell sur-face hydrophobicity and adherence of S.mutans in a dose-dependent manner(P <0.05).At 1 /2 MIC and 1 /20 MIC,the inhibitary effect of LEO was stronger than that of LIMand TP(P <0.05).Conclusion:LEO may possess anticariogenic potential.

Effect of Sub-minimal Inhibitory Concentration of Chlorhexidine on Biofilm Formation and Coaggregation of Early Colonizers, Streptococci and Actinomycetes

Chlorhexidine has long been used in mouth washes for the control of dental caries, gingivitis and dental plaque. Minimal inhibitory concentration (MIC) is the lowest concentration of an antimicrobial substance to inhibit the growth of bacteria. Concentrations lower than the MIC are called sub minimal inhibitory concentrations (sub-MICs). Many studies have reported that sub-MICs of antimicrobial substances can affect the virulence of bacteria. The aim of this study was to investigate the effect of sub-MIC chlorhexidine on biofilm formation and coaggregation of oral early colonizers, such as Streptococcus gordonii, Actinomyces naeslundii and Actinomyces odontolyticus. The biofilm formation of S. gordonii, A. naeslundii and A. odontolyticus was not affected by sub-MIC chlorhexidine. However, the biofilm formation of S. mutans increased after incubation with sub-MIC chlorhexidine. In addition, cell surface hydrophobicity of S. mutans treated with sub-MIC of chlorhexidine, decreased when compared with the group not treated with chlorhexidine. However, significant differences were seen with other bacteria. Coaggregation of A. naeslundii with A. odontolyticus reduced by sub-MIC chlorhexidine, whereas the coaggreagation of A. naeslundii with S. gordonii remained unaffected. These results indicate that sub-MIC chlorhexidine could influence the binding properties, such as biofilm formation, hydrophobicity and coaggregation, in early colonizing streptococci and actinomycetes.

Sanitização de cenoura minimamente processada com nanopartículas de prata / Sanitization of minimally processed carrot with silver nanoparticles

A produção de cenoura em grande escala na região de Rio Paranaíba coloca essa região em posição de destaque no cenário nacional. No entanto, é relatado que ocorre significativa quantidade de sobras após a colheita. O aproveitamento do material descartado na cadeia de alimentos pode se concretizar pelo processamento mínimo, como uma alternativa de agregação de valor. A etapa de sanitização é de extrema importância durante a produção de vegetais minimamente processados. Nesse contexto, objetivou-se estudar o efeito antimicrobiano de nanopartículas de prata na sanitização de cenoura minimamente processada, obtida a partir do aproveitamento das sobras de cenouras da colheita da cidade de Rio Paranaíba, bem como o estudo da termodinâmica de adesão de diferentes estirpes bacterianas na superfície da cenoura sanitizada. Observou-se que as nanopartículas de prata (6mg L^-1)apresentaram bons resultados, quando comparadas aos sanitizantes hipoclorito de sódio (100mg L^-1) e dicloroisocianurato de sódio (150mg L^-1), na descontaminação da cenoura minimamente processada sobre microrganismos mesófilos aeróbios; Pseudomonasspp.; bactérias láticas; e coliformes a 35ºC. Verificou-se também que a superfície da cenoura apresenta características hidrofílicas que podem dificultar a adesão bacteriana. Esse fato foi confirmado na avaliação de termodinâmica de adesão, que foi desfavorável paraStaphylococcus aureus, Escherichia colie Listeria innocua, sendo mais desfavorável para as interações envolvendo as superfícies de cenoura sanitizadas com nanopartículas de prata.

The carrot production on a large scale in the region of Rio Paranaiba places the region in a prominent position on the national scene. However, it is reported that a significant amount of scraps occurs after harvest. The use of discarded material in the food chain can be realized by minimal processing, as an alternative of adding value. A sanitization step is very important during the production of minimally processed vegetables. In this context, this research aimed to study the antimicrobial effect of silver nanoparticles in the sanitization of minimal processing carrot from discarded carrot harvested at Rio Paranaiba city, as well as study the thermodynamics adhesion for different bacterial strains in sanitized carrot surface. It was observed that silver nanoparticles (6mg L^-1) showed good results when was compared to sodium hypochlorite (100mg L^-1) and sodium dichloroisocyanurate (150mg L^-1) in reducing populations of aerobic mesophilic microorganism;Pseudomonasspp. lactic acid bacteria and coliforms at 35ºC present in carrot. It was also found that the surface of carrot has hydrophilic characteristics which can prevent bacterial adhesion. This fact was confirmed that thermodynamic evaluation of adhesion that was unfavorable for Staphylococcus aureus, Escherichia coliand Listeria innocua, and more thermodynamically unfavorable for interactions involving carrot surfaces sanitized with silver nanoparticles.