A mechanistic simulation of induced DNA damage in a bacterial cell by X- and gamma rays: a parameter study

Mechanistic Monte Carlo simulations calculating DNA damage caused by ionizing radiation are highly dependent on the simulation parameters. In the present study, using the Geant4-DNA toolkit, the impact of different parameters on DNA damage induced in a bacterial cell by X- and gamma-ray irradiation was investigated. Three geometry configurations, including the simple (without DNA details), the random (a random multiplication of identical DNA segments), and the fractal (a regular replication of DNA segments using fractal Hilbert curves), were simulated. Also, three physics constructors implemented in Geant4-DNA, i.e., G4EmDNAPhysics_option2, G4EmDNAPhysics_option4, and G4EmDNAPhysics_option6, with two energy thresholds of 17.5 eV and 5-37.5 eV were compared for direct DNA damage calculations. Finally, a previously developed mathematical model of cell repair called MEDRAS (Mechanistic DNA Repair and Survival) was employed to compare the impact of physics constructors on the cell survival curve. The simple geometry leads to undesirable results compared to the random and fractal ones, highlighting the importance of simulating complex DNA structures in mechanistic simulation studies. Under the same conditions, the DNA damage calculated in the fractal geometry was more consistent with the experimental data. All physics constructors can be used alternatively with the fractal geometry, provided that an energy threshold of 17.5 eV is considered for recording direct DNA damage. All physics constructors represent a similar behavior in generating cell survival curves, although the slopes of the curves are different. Since the inverse of the slope of a bacterial cell survival curve (i.e., the D10-value) is highly sensitive to the simulation parameters, it is not logical to determine an optimal set of parameters for calculating the D10-value by Monte Carlo simulation.

Trends in single-impact electrochemistry for bacteria analysis

Single-impact electrochemistry for the analysis of bacteria is a powerful technique for biosensing applications at the single-cell scale. The sensitivity of this electro-analytical method has been widely demonstrated based on chronoamperometric measurements at an ultramicroelectrode polarized at the appropriate potential of redox species in solution. Furthermore, the most recent studies display a continuous improvement in the ability of this sensitive electrochemical method to identify different bacterial strains with better selectivity. To achieve this, several strategies, such as the presence of a redox mediator, have been investigated for detecting and identifying the bacterial cell through its own electrochemical behavior. Both the blocking electrochemical impacts method and electrochemical collisions of single bacteria with a redox mediator are reported in this review and discussed through relevant examples. An original sensing strategy for virulence factors originating from pathogenic bacteria is also presented, based on a recent proof of concept dealing with redox liposome single-impact electrochemistry. The limitations, applications, perspectives, and challenges of single-impact electrochemistry for bacteria analysis are briefly discussed, based on the most significant published data.

Distinct mechanisms in the heteroaggregation of silver nanoparticles with mineral and microbial colloids

Attachment to solids is an important process for determining nanomaterial transport and their fate in environments. Here we revealed distinct behaviours in the attachment of silver nanoparticles (AgNPs) to kaolin and bacterial cells. We found preferential attachment of AgNPs to the edges of kaolin. Decreasing pH or adding metal ions promoted AgNP-kaolin attachment due to the increase of positive charge on kaolin's surfaces. Multivalent cations (Mg²⁺ and Ca²⁺) induced stronger enhancement than monovalent cations (Na⁺, K⁺ and Ag⁺), which demonstrated the positive role of electrostatic interaction in AgNP-kaolin attachment. However, the presence of metal ions inhibited AgNP binding to bacterial cells. The inhibitive effect was significantly correlated with solubility product of metal ions, which implied a chemical reaction mechanism in AgNP-cell attachment. In kaolin system, humic acid (HA) can considerably inhibit AgNP attachment and diminish the enhanced effects induced by metal ions. In contrast, in bacterial cell system, HA reduced the inhibitive effect of metal ions for AgNP adsorption, although HA itself had negligible effect on AgNP-cell attachment. Taken together, our results demonstrated the contribution of electrostatic attraction versus chemical interaction to the attachment of AgNPs to kaolin or bacterial cells, providing fundamental support to understand the attachment of nanomaterials to inorganic and organic solids in the environments.

Harmaline and its Derivatives Against the Infectious Multi-Drug Resistant Escherichia coli

BACKGROUND

Multidrug resistance (MDR) is a major challenge in the treatment of infectious diseases. The MDR in urinary tract infection causing bacteria, such as Escherichia coli, has made treatment of UTI very difficult.

OBJECTIVE

The aims of the current study were to synthesize a library of harmaline derivatives, and to evaluate their activity against various strains of multi-drug resistance (MDR) E. coli.

METHOD

Harmaline derivatives were synthesized by the reaction of harmaline (1) with various acid halides and anhydrides. These compounds were subjected to susceptibility determination by in vitro MTT assay. The changes in morphology of the bacterial cells after the treatment with harmaline (1) and its new derivatives 2 and 3 were studied through scanning electron, atomic force and fluorescence microscopy. Effect of harmaline and its derivatives on the production of Reactive Oxygen Species (ROS) in MDR E. coli was assessed through lucigenin chemiluminescence assays.

RESULTS

The selected compounds assisted the fluorescently labeled dye DiBAC4(3) to bind to the lipid rich intra-cellular entities, and thus produced a sharp green fluorescence by easily penetrating into the compound-induced depolarized membrane of MDR E. coli. These compounds have also triggered a significant generation of ROS from bacterial cells as compared to the conventional antibiotics. The current study demonstrated that harmaline (1), and its derivatives 2 and 3 were identified as anti-MDR agents against MDR strains of E. coli. Antibacterial effect of compounds 1-3 on MDR E. coli is possibly due to membrane depolarization due to ROS-induced damage to the bacterial cell membrane.

CONCLUSION

Harmaline and its derivatives were identified as anti-MDR agents against various highly resistant and Pakistani MDR clinical isolates of E. coli. These compounds may serve as the leads for further studies towards the development of treatment against the infections caused by MDR E. coli.

Methods for studying RNA localization in bacteria

The subcellular localization of RNA transcripts provides important insights into biological processes. Hence, understanding the mechanisms underlying RNA targeting is a high priority aim of modern cell biology. The advancements in imaging techniques, such as in situ hybridization and live-cell imaging, coupled with the evolution in optical microscopy led to the discovery that bacterial RNAs, despite the lack of nucleus, are specifically localized. Here we describe the methods used to study RNA localization in bacteria and their applications and discuss their advantages and limitations.

Membrane interaction of antimicrobial peptides using E. coli lipid extract as model bacterial cell membranes and SFG spectroscopy

Supported lipid bilayers are used as a convenient model cell membrane system to study biologically important molecule-lipid interactions in situ. However, the lipid bilayer models are often simple and the acquired results with these models may not provide all pertinent information related to a real cell membrane. In this work, we use sum frequency generation (SFG) vibrational spectroscopy to study molecular-level interactions between the antimicrobial peptides (AMPs) MSI-594, ovispirin-1 G18, magainin 2 and a simple 1,2-dipalmitoyl-d62-sn-glycero-3-phosphoglycerol (dDPPG)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) bilayer. We compared such interactions to those between the AMPs and a more complex dDPPG/Escherichia coli (E. coli) polar lipid extract bilayer. We show that to fully understand more complex aspects of peptide-bilayer interaction, such as interaction kinetics, a heterogeneous lipid composition is required, such as the E. coli polar lipid extract. The discrepancy in peptide-bilayer interaction is likely due in part to the difference in bilayer charge between the two systems since highly negative charged lipids can promote more favorable electrostatic interactions between the peptide and lipid bilayer. Results presented in this paper indicate that more complex model bilayers are needed to accurately analyze peptide-cell membrane interactions and demonstrates the importance of using an appropriate lipid composition to study AMP interaction properties.

Antimicrobial activity of low-pressure plasma treatment against selected foodborne bacteria and meat microbiota

The effects of helium and argon plasma treatments on inactivation of both pure bacterial cultures inoculated onto the surface of agarized media and the surface microbiota of meat were investigated. Cold plasmas were generated by high voltage discharge at low pressure (20 kPa) for 2, 5, and 10 min. The number of viable microorganisms was determined using a plate count method. Morphological changes were observed using scanning electron microscopy (SEM). Microbial log reduction depended on time of exposure and type of gas used. After a 10-min treatment with helium plasma, the total number of microorganisms, yeasts and molds, and psychrotrophic microorganisms was reduced in the range of 1.14-1.48 log cycles for pork and 0.98-2.09 log cycles for beef. A significant reduction of 2.00 log for Bacillus subtilis and Yersinia enterocolitica was achieved within 2 min of helium plasma treatment. Similar results were obtained for Staphylococcus aureus, Escherichia coli and Pseudomonas fluorescens after 5 min and 10 min of exposure. SEM revealed disruption and lysis of E. coli cells treated with helium plasma for 10 min, suggesting a bactericidal effect.

Protein targeting via mRNA in bacteria

Proteins of all living organisms must reach their subcellular destination to sustain the cell structure and function. The proteins are transported to one of the cellular compartments, inserted into the membrane, or secreted across the membrane to the extracellular milieu. Cells have developed various mechanisms to transport proteins across membranes, among them localized translation. Evidence for targeting of Messenger RNA for the sake of translation of their respective protein products at specific subcellular sites in many eukaryotic model organisms have been accumulating in recent years. Cis-acting RNA localizing elements, termed RNA zip-codes, which are embedded within the mRNA sequence, are recognized by RNA-binding proteins, which in turn interact with motor proteins, thus coordinating the intracellular transport of the mRNA transcripts. Despite the rareness of conventional organelles, first and foremost a nucleus, pieces of evidence for mRNA localization to specific subcellular domains, where their protein products function, have also been obtained for prokaryotes. Although the underlying mechanisms for transcript localization in bacteria are yet to be unraveled, it is now obvious that intracellular localization of mRNA is a common mechanism to spatially localize proteins in both eukaryotes and prokaryotes. This article is part of a Special Issue entitled: Protein trafficking and secretion in bacteria. Guest Editors: Anastassios Economou and Ross Dalbey.