Determination of the size of lipid rafts studied through single-molecule FRET simulations.

Fluorescence resonance energy transfer (FRET) is a high-resolution technique that allows the characterization of spatial and temporal properties of biological structures and mechanisms. In this work, we developed an in silico single-molecule FRET methodology to study the dynamics of fluorophores inside lipid rafts. We monitored the fluorescence of a single acceptor molecule in the presence of several donor molecules. By looking at the average fluorescence, we selected events with single acceptor and donor molecules, and we used them to determine the raft size in the range of 5-16 nm. We conclude that our method is robust and insensitive to variations in the diffusion coefficient, donor density, or selected fluorescence threshold.

How Useful are Antimicrobial Peptide Properties for Predicting Activity, Selectivity, and Potency?

Antimicrobial peptides (AMPs) are recognized for their potential application as new generation antibiotics, however, up to date, they have not been widely commercialized as expected. Although current bioinformatic tools can predict antimicrobial activity based on only amino acid sequences with astounding accuracy, peptide selectivity and potency are not foreseeable. This, in turn, creates a bottleneck not only in the discovery and isolation of promising candidates but, most importantly, in the design and development of novel synthetic peptides. In this paper, we discuss the challenges faced when trying to predict peptide selectivity and potency, based on peptide sequence, structure and relevant biophysical properties such as length, net charge and hydrophobicity. Here, pore-forming alpha-helical antimicrobial peptides family isolated from anurans was used as the case study. Our findings revealed no congruent relationship between the predicted peptide properties and reported microbial assay data, such as minimum inhibitory concentrations against microorganisms and hemolysis. In many instances, the peptides with the best physicochemical properties performed poorly against microbial strains. In some cases, the predicted properties were so similar that differences in activity amongst peptides of the same family could not be projected. Our general conclusion is that antimicrobial peptides of interest must be carefully examined since there is no universal strategy for accurately predicting their behavior.

Biophysical characterization of the insertion of two potent antimicrobial peptides-Pin2 and its variant Pin2[GVG] in biological model membranes.

The aim of this study was to investigate the factors that govern the activity and selectivity of two potent antimicrobial peptides (AMPs) using lipid membrane models of bacterial, erythrocyte and fungal cells. These models were used in calcein liposome leakage experiments to explore peptide efficiency. The AMPs (Pin2 and its variant Pin2[GVG]) showed highest affinity towards the bacterial models in the nanomolar range, followed by the erythrocyte and fungal systems. The presence of sterols modulated the variant's selectivity, while the wild type was unaffected. Liposome leakage experiments with Fluorescein Isothiocyanate-dextran (FITC)-dextran conjugates indicated that pore size depended on peptide concentration. Dynamic Light Scattering revealed peptide aggregation in aqueous solution, and that aggregate size was related to activity. The interacting peptides did not alter liposome size, suggesting pore forming activity rather than detergent activity. Atomic Force Microscopy showed differential membrane absorption, being greater in the bacterial model compared to the mammalian model, and pore-like defects were observed. Electrophysiological assays with the Tip-Dip Patch Clamp method provided evidence of changes in the electrical resistance of the membrane. Membrane potential experiments showed that liposomes were also depolarized in the presence of the peptides. Both peptides increased the Laurdan Generalized Polarization of the bacterial model indicating increased viscosity, on the contrary, no effect was observed with the erythrocyte and the fungal models. Peptide membrane insertion and pore formation was corroborated with Langmuir Pressure-Area isotherms and Brewster Angle Microscopy. Finally, molecular dynamics simulations were used to get an insight into the molecular mechanism of action.

X-ray spectra and doses.

Using the Monte Carlo method the x-ray spectrum produced by 150keV electrons colliding with W, Rh and Mo targets were calculated. The x-ray spectra were calculated to 20, 50, and 100cm from the focal point. In order to analyze the effect of the filter, calculations were carried out with and without filter. The spectra were used to estimate the Kerma in air, the Ambient dose equivalent, and the Personal dose equivalent. The spectra were integrated in energy to obtain the total photon fluences. Calculated spectra depend on the type of target having the continuous spectrum due to bremsstrahlung and the characteristics x-rays. The Al filter eliminates the low-energy photons; however no effect is noticed when the photon energy is larger than 40keV. The largest effect of dose reduction due to the filter was noticed to 20cm for the Kerma in air.

Design of an explosive detection system using Monte Carlo method.

Regardless the motivation terrorism is the most important risk for the national security in many countries. Attacks with explosives are the most common method used by terrorists. Therefore several procedures to detect explosives are utilized; among these methods are the use of neutrons and photons. In this study the Monte Carlo method an explosive detection system using a 241AmBe neutron source was designed. In the design light water, paraffin, polyethylene, and graphite were used as moderators. In the work the explosive RDX was used and the induced gamma rays due to neutron capture in the explosive was estimated using NaI(Tl) and HPGe detectors. When light water is used as moderator and HPGe as the detector the system has the best performance allowing distinguishing between the explosive and urea. For the final design the Ambient dose equivalent for neutrons and photons were estimated along the radial and axial axis.