High Resolution Melting Analysis (HRM-PCR) - method and its application

DNA denaturation with High Resolution Melting PCR-HRM is a method based on the identification of differences in the denaturation of PCR reaction products in the presence of fluorescent dyes. It is used to detect genetic variation in nucleic acid sequences in many branches of science, medicine and industry. This article is a review of the current literature of the methodology, applications and development of HRM analysis, which, thanks to its advantages such as speed, low cost, flexibility and simplicity, has found many applications, and its spectrum is still expanding.

HRM-PCR in medical diagnostic

High resolution melting (HRM) is a method based on the identification of differences in the denaturation of PCR reaction products in the presence of fluorescent dyes. It allows for a detailed analysis of the genetic profiles. In addition this analysis is low-cost, single-step, closed-tube and has high sensitivity. HRM found applications in diagnostics, laboratory and clinical researches. This article is a literature review of the applications of HRM analysis in medicine.

A benzimidazole-based ruthenium(IV) complex inhibits Pseudomonas aeruginosa biofilm formation by interacting with siderophores and the cell envelope, and inducing oxidative stress

Pseudomonas aeruginosa biofilm-associated infections are a serious medical problem, and new compounds and therapies acting through novel mechanisms are much needed. Herein, the authors report a ruthenium(IV) complex that reduces P. aeruginosa PAO1 biofilm formation by 84%, and alters biofilm morphology and the living-to-dead cell ratio at 1 mM concentration. Including the compound in the culture medium altered the pigments secreted by PAO1, and fluorescence spectra revealed a decrease in pyoverdine. Scanning electron microscopy showed that the ruthenium complex did not penetrate the bacterial cell wall, but accumulated on external cell structures. Fluorescence quenching experiments indicated strong binding of the ruthenium complex to both plasmid DNA and bovine serum albumin. Formamidopyrimidine DNA N-glycosylase (Fpg) protein digestion of plasmid DNA isolated after ruthenium(IV) complex treatment revealed the generation of oxidative stress, which was further proved by the observed upregulation of catalase and superoxide dismutase gene expression.

Adaptation of bacteria Escherichia coli in presence of quaternary ammonium ionic liquids

This paper presents the adaptation of Escherichia coli Gram-negative bacteria to increased concentrations of ionic liquids. Theophylline-based quaternary ammonium salts were used as an example of an ionic liquid that on the one hand includes an anion of natural origin and on the other hand is characterized by amphiphilic properties due to aliphatic chains in its structure. Theophylline-based ionic liquids can be synthesized relatively cheaply and easily and can exhibit strong antibacterial properties depending on the alkyl chain length. These compounds can also strongly affect bacterial membrane properties, including changes in electrokinetic potential as well as net surface charge. The experiments performed in this study succeeded in obtaining bacterial cultures growing at a tetradecyltrimethylammonium theophyllinate concentration three times higher than the minimum inhibition and bactericidal concentration. The adapted bacteria were characterized by intriguing changes in morphology and grew in the form of almost one-millimeter spheres in a liquid medium. It was shown that cultivation of adapted bacteria with tetradecyltrimethylammonium theophyllinate resulted in changes in the lipid membrane composition and protein patterns of the bacterial lysates, depending on the ionic liquid concentration. This study also revealed that such bacterial adaptation can increase sensitivity to antibiotics by affecting membrane properties like ionophores. These results can be potentially important with regard to synergistic or antagonistic action with other bactericidal compounds like antibiotics and nanoparticles.

Bacterial Communities from the Arsenic Mine in Złoty Stok, Sudety Mountains, Poland

Investigations of bacterial communities and characterization of mineralogy of the environment in the Złoty Stok As-Au deposit were carried out. PXRD analysis revealed the presence of picropharmacolite as the most common secondary arsenic mineral in the mine. Total DNA was extracted from slime streams or slime biofilms samples to investigate the bacterial communities. PCR amplification of 16S rDNA was performed followed by subcloning of its products. Over 170 clones were analyzed by means of RFLP method. Eight group of clones representing different restriction patterns were identified. The nucleotide sequences of their inserts suggest that bacteria present in the mine environment belong to: Flavobacteria, Sphingobacteriia, Bacteroides, Proteobacteria, Mollicutes and Firmicutes. The metagenomic approach allows to demonstrate a higher diversity of microbiota than classical microbiological studies of cultivable isolates.

Different antibacterial activity of novel theophylline-based ionic liquids - Growth kinetic and cytotoxicity studies

The aim of this study was to investigate novel theophylline-based ionic liquids and their cytotoxic effects towards model Gram-positive and Gram-negative bacteria (Bacillus cereus and Escherichia coli, respectively). Growth kinetics, respiratory rates and dehydrogenase activities were studied in the presence of ionic liquids at concentrations ranging from 10 to 1000mg/L. Additionally, the influence of ionic liquids on bacterial cells associated with specific interactions based on the structure of cell wall was evaluated. This effect was assessed by viability tests and scanning electron microscope observations. The obtained results confirmed that ionic liquids exhibit different levels of toxicity in relation to Gram-positive and Gram-negative bacteria. Those effects are associated with the chemical structure of the cationic species of the ionic liquids and their critical micelle concentration value. It was established that the presence of an alkyl or allyl group increased the toxicity, whereas the presence of an aryl group in the cation decreased the toxic effect of ILs. Results presented in this study also revealed unexpected effects of self-aggregation of E. coli cells. Overall, it was established that the studied ILs exhibited higher toxicity towards Gram-positive bacteria due to different interactions between the ILs and the cell membranes. These findings may be of importance for the design of ILs with targeted antimicrobial properties.

Monitoring of Virulence Genes, Drug-Resistance in Campylobacter coli Isolated from Golden Retrievers

The investigation was performed on 75 of Golden Retriever puppies. Faecal samples were collected on the 42 day of the puppies life (control). Probiotic preparation was administered on 43 day of the puppies life and 10 days after the application of the probiotic, faecal samples were collected again (on 53 day of puppies life). All isolates of Campylobacter coli isolated prior to the administration of the probiotic were found to contain the cadF gene responsible for adhesion, as well as, the flaA gene influencing motility of the examined bacteria. Significant differences (P < 0.05) were recorded only in the case of enrofloxacin.

Oxidative stress in bacteria (Pseudomonas putida) exposed to nanostructures of silicon carbide

Silicon carbide (SiC) nanostructures produced by combustion synthesis can cause oxidative stress in the bacterium Pseudomonas putida. The results of this study showed that SiC nanostructures damaged the cell membrane, which can lead to oxidative stress in living cells and to the loss of cell viability. As a reference, micrometric SiC was also used, which did not exhibit toxicity toward cells. Oxidative stress was studied by analyzing the activity of peroxidases, and the expression of the glucose-6-phosphate dehydrogenase gene (zwf1) using real-time PCR and northern blot techniques. Damage to nucleic acid was studied by isolating and hydrolyzing plasmids with the formamidopyrimidine [fapy]-DNA glycosylase (also known as 8-oxoguanine DNA glycosylase) (Fpg), which is able to detect damaged DNA. The level of viable microbial cells was investigated by propidium iodide and acridine orange staining.

Adsorption studies of the gram-negative bacteria onto nanostructured silicon carbide

In this study, we demonstrated a significant adsorption of Pseudomonas putida bacteria onto aggregates of nanofibers (NFSiC) and nanorods (NRSiC) of silicon carbide (SiC) in aqueous suspensions. Langmuir and Freundlich isotherms were used to quantify adsorption affinities. It was found that adsorption of the bacteria strongly depended on the structure of the silicon carbide and the pH of the aqueous solution, which affected the isoelectric point of both the silicon carbide and the bacterial cells. The strongest affinity of bacteria was noted in the case of NRSiC aggregates. Affinity was inversely proportional to pH. Similarly, the adsorption of bacteria to the surface of the aggregates increased with decreasing pH. For NFSiC, the affinity of the bacteria for the surface of the aggregates was also inversely proportional to pH. However, adsorption increased at higher pH values. This discrepancy was explained by microscopic analysis, which showed that the bacterial cells were both adsorbed onto and trapped by NFSiC. The adsorption of bacteria onto a micrometric silicon carbide reference material was significantly smaller than adsorption onto nanostructured SiC.

The Prevalence of Campylobacter spp. and Occurrence of Virulence Genes Isolated from Dogs

This study was conducted to determine the prevalence of Campylobacter spp. isolated from dogs' faecal samples. From June 2012 to June 2013, a total of 210 faecal samples from pet dogs living in different kennels (n = 210) were collected by the owners in Greater Poland Voivodeship, Poznań District, Poland. The study revealed that 105 out of 210 faecal samples (50%) contained Campylobacter. The highest prevalence of Campylobacter spp. occurred in spring (81%), followed by winter (64%). The cadF gene was found in 100% of the isolates tested. The occurrence of the other genes was variable. The isolates from young dogs were characterised by higher occurrence of virulence genes.