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Photodynamic inactivation of microorganisms known as antibacterial photodynamic therapy (APDT) is one of the most promising and innovative approaches for the destruction of pathogenic microorganisms. Among the photosensitizers (PSs), compounds based on cationic porphyrins/metalloporphyrins are most successfully used to inactivate microorganisms. Series of meso-substituted cationic pyridylporphyrins and metalloporphyrins with various peripheral groups in the third and fourth positions of the pyrrole ring have been synthesized in Armenia. The aim of this work was to determine and test the most effective cationic porphyrins and metalloporphyrins with high photoactivity against Gram negative and Gram positive microorganisms. It was shown that the synthesized cationic pyridylporphyrins/metalloporphyrins exhibit a high degree of phototoxicity towards both types of bacteria, including the methicillin-resistant S. aureus strain. Zinc complexes of porphyrins are more phototoxic than metal-free porphyrin analogs. The effectiveness of these Zn–metalloporphyrins on bacteria is consistent with the level of singlet oxygen generation. It was found that the high antibacterial activity of the studied cationic porphyrins/metalloporphyrins depends on four factors: the presence in the porphyrin macrocycle of a positive charge (+4), a central metal atom (Zn${}^{2+})$ and hydrophobic peripheral functional groups as well as high values of quantum yields of singlet oxygen. The results indicate that meso-substituted cationic pyridylporphyrins/metalloporphyrins can find wider application in photoinactivation of bacteria than anionic or neutral PSs usually used in APDT.

The experimental and computational study of bacterial thioredoxin, an E. coli protein, at THz frequencies is presented. The absorption spectrum of the entire protein in water was studied numerically in the terahertz range (0.1 – 2 THz). In our work, the initial X-ray molecular structure of thioredoxin was optimized using the molecular dynamical (MD) simulations at room temperature and atmospheric pressure. The effect of a liquid content of a bacterial cell was taken into account explicitly via the simulation of water molecules using the TIP3P water model. Using atomic trajectories from the room-temperature MD simulations, thioredoxin's THz vibrational spectrum and the absorption coefficient were calculated in a quasi harmonic approximation.

For our terahertz transmission measurements, we used solutions of thioredoxin in distilled water obtained from Sigma. The experimental and simulated signatures are correlated and dominant peaks are close in frequencies. The results of this study demonstrate that terahertz spectroscopy is a promising tool in generating spectral data for cellular components of bio agents such as bacterial cells and spores.

Bacterial resistance is today a matter of great medical concern, so it is urgent to investigate alternatives to alleviate it. Photodynamic inactivation (PDI) is a method that has been endorsed to inactivate different pathogens, including bacteria, fungi and viruses. PDI is achieved by using a photosensitizer (PS) molecule which generates reactive oxygen species under visible or UV radiation. We use visible light and UV-A radiation to excite four commercial PSs (methylene blue, rose bengal, riboflavin and curcumin), and nanoparticles synthesized in our laboratory. Despite these PSs having been thoroughly studied in the past by other research groups, in order to compare their effects in an appropriate way, we matched the number of photons they absorb. We found that methylene blue leads to the major inactivation of Escherichia coli. Furthermore, we evaluated the production of singlet oxygen and hydroxyl radicals in the photoinactivation process.

This study presents the first report on enhanced bacterial inactivation of E. coli by RF-plasma pretreated cotton with high surface area CuO powders compared with non-pretreated cotton textiles. The high surface area CuO (65 m/g) powder was fully characterized. The E. coli inactivation proceeded in the dark and was accelerated under visible and sunlight irradiation even at very low levels of visible light irradiation. The effect the RF-plasma pretreatment of the cotton on the binding of CuO, applied light dose, and initial E. coli concentration on the inactivation kinetics of E. coli is reported.

The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated and the associated THz signature was derived theoretically. The tRNA that binds amino acid tyrosine (tRNA_tyr) was studied. Here, the molecular structure was optimized using the potential energy minimization and molecular dynamical (MD) simulations. Solvation effects (water molecules) were also included explicitly in the MD simulations. To verify that realistic molecular signatures were simulated, a parallel experimental study of tRNAs of E. coli was also conducted. Two very similar molecules, valine and tyrosine tRNA were investigated experimentally. Samples were prepared in the form of water solutions with the concentrations in the range 0.01-1 mg/ml. A strong correlation of the measured THz signatures associated with valine tRNA and tyrosine tRNA was observed. These findings are consistent with the structural similarity of the two tRNAs. The calculated THz signature of the tyrosine tRNA of E. coli reproduces many features of our measured spectra, and, therefore, provides valuable new insights into bio-agent detection.

Mapping of putative promoters within the entire genome of Escherichia coli (E. coli) by means of pattern-recognition software PlatProm revealed several thousand of sites having high probability to perform promoter function. Along with the expected promoters located upstream of coding sequences, PlatProm identified more than a thousand potential promoters for antisense transcription and several hundred very similar signals within coding sequences having the same direction with the genes. Since recently developed ChIP–chip technology also testified the presence of intragenic RNA polymerase binding sites, such distribution of putative promoters is likely to be a general biological phenomenon reflecting yet undiscovered regulatory events. Here, we provide experimental evidences that two internal promoters are recognized by bacterial RNA polymerase. One of them is located within the hns coding sequence and may initiate synthesis of RNA from the antisense strand. Another one is found within the overlapping genes htgA/yaaW and may control the production of a shortened mRNA or an RNA-product complementary to mRNA of yaaW. Both RNA-products can form secondary structures with free energies of folding close to those of small regulatory RNAs (sRNAs) of the same length. Folding propensity of known sRNAs was further compared with that of antisense RNAs (aRNAs), predicted in E. coli as well as in Salmonella typhimurium (S. typhimurium). Slightly lower stability observed for aRNAs assumes that their structural compactness may be less significant for biological function.

The performance of a nanoscale sensor is not limited by the sensitivity of the sensor itself but rather by the diffusion time required for target molecules to reach to the extremely small sensor surface. In this work, we developed a carbon nanotube device that performed the dual functions of concentrating and detecting microorganisms in a sample solution. The sensor surface area was increased by fabricating a carbon nanotube network device using thermal chemical vapor deposition and standard microfabrication techniques. The target Escherichia coli (E. coli) cells were concentrated at the sensor surface via dielectrophoretic concentration by the carbon nanotube network channels. After 10 min of collection, the chip was washed with ample amounts of a clean buffer solution, and only the E. coli cells that were bound to the antibodies remained on the sensor surface. The binding of E. coli to the CNT network device decreased the conductance, presumably due to an increase in the scattering at the sensor surface. The detection limit and the time required for microorganism detection was greatly improved by combining dielectrophoresis with the carbon nanotube devices.

The purpose of the present study was to asses the thermal inactivation of E. coli and coliform during the kneading step, in hot water, in the making process of Oaxaca cheese – a fresh pasta filata Mexican cheese. A three-strain cocktail of E. coli isolated from industrial Oaxaca cheeses was used for the assay. Three batches of pasteurised and, then, inoculated milk were processed into Oaxaca cheese following a traditional open-vat process until before the kneading step. At this point, the process was halted and a simulated kneading step at 55 °C for 15 min was carried out. Counts of E. coli and coliform were performed on the curd after 0, 5, 10 and 15 min of the begining of the sumulated kneading. The data of these counts were analysed using linear regression, and the correspondent D_55°C values were calculated. The heating taking place during the kneading can reduce considerably the population of E. coli and coliform of the curd. However, it did not eliminate entirely the risk of foodborne illness in Oaxaca cheese.

Antibacterial activity of alkaloids of two medicinal plants Fumaria bastardii and Fumaria capreolata was evaluated by two diffusion methods, wells method and disks method, against four bacterial stocks resistant to antibiotics isolated from infected patients in hospital. The tested strains are S.aureus S56, K. pneumoniae E47, P. aeruginosa 604 and E. coli. The contents of alkaloids were 2,42% and 1,17% in Fumaria bastardii and Fumaria capreolata respectively. Both alkaloid extracts showed a high antibacterial activity against the four strains tested. However P. aeruginosa was the least susceptible strain. Extract of F. bastardii was the most active one showing a higher activity excepted against P. aeruginosa which was most susceptible to F. capreolata extract. A synergy effect was observed between alkaloids of F. bastardii and the SXT on K. pneumonia and between alkaloids of F. capreolata and the SXT on P. aeruginosa 604.