Assessment of the nucleotide modifications in the high-resolution cryo-electron microscopy structure of the Escherichia coli 50S subunit.

Post-transcriptional ribosomal RNA (rRNA) modifications are present in all organisms, but their exact functional roles and positions are yet to be fully characterized. Modified nucleotides have been implicated in the stabilization of RNA structure and regulation of ribosome biogenesis and protein synthesis. In some instances, rRNA modifications can confer antibiotic resistance. High-resolution ribosome structures are thus necessary for precise determination of modified nucleotides' positions, a task that has previously been accomplished by X-ray crystallography. Here, we present a cryo-electron microscopy (cryo-EM) structure of the Escherichia coli 50S subunit at an average resolution of 2.2 Å as an additional approach for mapping modification sites. Our structure confirms known modifications present in 23S rRNA and additionally allows for localization of Mg2+ ions and their coordinated water molecules. Using our cryo-EM structure as a testbed, we developed a program for assessment of cryo-EM map quality. This program can be easily used on any RNA-containing cryo-EM structure, and an associated Coot plugin allows for visualization of validated modifications, making it highly accessible.

High-resolution cost-effective compact portable inverted light microscope.

Commercial high-resolution optical microscopes are essential for microscopy imaging; however, they are expensive and bulky, which limits their use in point-of-care devices, resource-limited areas, and real-time imaging of a sample in a large apparatus. In this study, we report a novel compact (10 cm × 5 cm × 5 cm, without the light source) lightweight (∼0.5 kg) submicron-resolution inverted optical microscope at low cost (∼$ 300). Our technique utilises the proximity of the image sensor to a commercial microscope objective lens for compactness of the microscope. The use of an image sensor with a small pixel size helps to reduce the information loss, which provides high-resolution images. Moreover, our technique offers a freedom to tailor the design of microscope according to the required resolution, cost, and portability for specific applications, which makes it a suitable candidate for affordable point-of-care devices. Images of several micron-to-submicron scale patterns and spherical beads are acquired to observe the resolution and quality of the images obtained using our microscope. In addition, we demonstrate the applications of our microscope in various fields such as recording of high-speed water microdroplet formation inside a microfluidic device, high-resolution live cell imaging inside an incubator, and real-time imaging of crack propagation in a sample under stretching by a material testing system (MTS). Therefore, this portable and inexpensive microscope provides the essential functionalities of a bulky expensive high-performance microscope at a lower cost. LAY DESCRIPTION: Microscope is an essential tool in research allowing for observation of microsized objects and life forms. Contemporary commercial high-resolution microscopes have long optical paths involving series of lenses and filters. Although this configuration precisely corrects for optical distortions and produces clear images, it makes modern microscopes very costly and bulky, restricting their usage to low-funded research laboratories and at remote places. We have developed a simple digital microscope with high-resolution but with much smaller size and lighter in weight at low cost by removing the long optical terrain. Our microscope consists of a commercial microscope objective lens for magnification and semiconductor image sensor with small pixels placed right after the lens, both of which are affordable and easily available. The small pixel size helps to translate the magnified analogue sample image to high-resolution digital image. In our paper, we show that our microscope can view micro and submicron-sized patterns and beads. Moreover, our fist-sized microscope can be placed inside an incubator for real-time imaging of cells or rotated sideways for recording submicron-sized crack generation due stretching of novel materials, both of which could not be accomplished with the 2 feet tall laboratory microscopes.

Assessment of synergistic antibacterial activity of combined biosurfactants revealed by bacterial cell envelop damage.

Besides potential surface activity and some beneficial physical properties, biosurfactants express antibacterial activity. Bacterial cell membrane disrupting ability of rhamnolipid produced by Pseudomonas aeruginosa C2 and a lipopeptide type biosurfactant, BS15 produced by Bacillus stratosphericus A15 was examined against Staphylococcus aureus ATCC 25923 and Escherichia coli K8813. Broth dilution technique was followed to examine minimum inhibitory concentration (MIC) of both the biosurfactants. The combined effect of rhamnolipid and BS15 against S. aureus and E. coli showed synergistic activity by expressing fractional inhibitory concentration (FIC) index of 0.43 and 0.5. Survival curve of both the bacteria showed bactericidal activity after treating with biosurfactants at their MIC obtained from FIC index study as it killed >90% of initial population. The lesser value of MIC than minimum bactericidal concentration (MBC) of the biosurfactants also supported their bactericidal activity against both the bacteria. Membrane permeability against both the bacteria was supported by amplifying protein release, increasing of cell surface hydrophobicity, withholding capacity of crystal violet dye and leakage of intracellular materials. Finally cell membrane disruption was confirmed by scanning electron microscopy (SEM). All these experiments expressed synergism and effective bactericidal activity of the combination of rhamnolipid and BS15 by enhancing the bacterial cell membrane permeability. Such effect of the combination of rhamnolipid and BS15 could make them promising alternatives to traditional antibiotic in near future.

Transmutation of Personal Glucose Meters into Portable and Highly Sensitive Microbial Pathogen Detection Platform.

Herein, for the first time, we presented a simple and general approach by using personal glucose meters (PGM) for portable and ultrasensitive detection of microbial pathogens. Upon addition of pathogenic bacteria, glucoamylase-quaternized magnetic nanoparticles (GA-QMNPS) conjugates were disrupted by the competitive multivalent interactions between bacteria and QMNPS, resulting in the release of GA. After magnetic separation, the free GA could catalyze the hydrolysis of amylose into glucose for quantitative readout by PGM. In such way, PGM was transmuted into a bacterial detection device and extremely low detection limits down to 20 cells mL(-1) was achieved. More importantly, QMNPS could inhibit the growth of the bacteria and destroy its cellular structure, which enabled bacteria detection and inhibition simultaneously. The simplicity, portability, sensitivity and low cost of presented work make it attractive for clinical applications.

Rice husk based porous carbon loaded with silver nanoparticles by a simple and cost-effective approach and their antibacterial activity.

In this paper, we chose rice husk as raw material and synthesized successfully porous carbon loaded with silver nanoparticles (RH-Ag) composites by simple and cost-effective method. The as-prepared RH-Ag composites have a BET-specific surface area of 1996 m(2) g(-1) and result in strong capacity of bacteria adsorption. The result of antibacterial study indicated that the RH-Ag system displayed antibacterial activity that was two times better than pure Ag NPs. Our study demonstrates that the antibacterial activity of RH-Ag composites may be attributed to their strong adsorption ability with bacteria and result in the disorganization of the bacterial membrane ultrastructure. In addition, RH-Ag system was found to be durative slow-releasing of silver ions and biocompatible for human skin keratinocytes cells. In terms of these advantages, the RH-Ag composites have potential application in antibacterial infections and therapy.

Assessment of titanium dioxide nanoparticle effects in bacteria: association, uptake, mutagenicity, co-mutagenicity and DNA repair inhibition.

Due to their unique properties, the use of nanoparticles (NPs) is expanding; these same properties may affect their potential risk to humans. However, standard methods for genotoxicity assessment may not be adequate for NPs; altered tests reported here have been developed to address perceived inadequacies. The bacterial reverse mutation assay is an essential part of the battery of tests to determine genotoxicity. The utility of this test for assessing NPs is currently questioned, due to negative results seemingly caused by failure of particle uptake. To probe uptake issues, we examined the physical state in different media, dose and time dependent association, uptake and mutagenicity of titanium dioxide (TiO2) NPs in Salmonella typhimurium and Escherichia coli. The NPs suspended in water were characterized using dynamic light scattering, NP tracking analysis and transmission electron microscopy. NP association with bacteria was assessed by flow cytometry. Association was found to be time and dose dependent, with maximal association by 60 min. Therefore mutagenicity was assessed after a 60 min pre-incubation in a miniaturized assay demonstrating enhanced sensitivity. To assess potential indirect effects on bacterial mutagenicity, the effect of TiO2 NPs on the action of standard mutagens or on DNA repair capability was also investigated. TiO2 NPs did not affect mutant yields in standard strains of S. typhimurium or E. coli, including those detecting oxidative damage, using the modified methods. Nor did TiO2 NPs affect the action of standard mutagens or DNA excision repair capability. Despite particle association with the bacteria, subsequent analysis using electron microscopy and energy dispersive x-ray spectroscopy indicated that the NPs were not internalized. This work demonstrates that additional studies, including flow cytometry, are valuable tools for understanding the action of NPs in biological systems.

Effect of extracted housefly pupae peptide mixture on chilled pork preservation.

The peptide mixture from housefly pupae has broad spectrum antimicrobial activity but has not previously been reported as a food preservative. In this study, the preservation effects of a housefly pupae peptide mixture, nisin, and sodium dehydroacetate (DHA-S) on the number of mesophilic aerobic bacteria (MAB), total volatile basic nitrogen (TVB-N), and pH value of chilled pork were compared. All results showed that a good preservation effect was observed among 3 treatments with the peptide mixture of housefly pupae, nisin, and DHA-S and that there was no significant difference among them. These results indicate that housefly peptide mixture has a great potential as a food preservative. The results of scanning electron microscope and transmission electron microscopy suggest that the primary mechanism of housefly pupae peptide mixture may be bacterial cytoplasmic membrane lysis and pores induced in the membranes. Practical Applications: Peptide mixture extracted from housefly pupae using low-cost and simple method has broad spectrum antimicrobial activity. According to the effect on chilled pork preservation, extracted housefly peptide mixture has a great potential as a food preservative.

Novel and economical purification of recombinant proteins: intein-mediated protein purification using in vivo polyhydroxybutyrate (PHB) matrix association.

This work combines two well-established technologies to generate a breakthrough in protein production and purification. The first is the production of polyhydroxybutyrate (PHB) granules in engineered strains of Escherichia coli. The second is a recently developed group of self-cleaving affinity tags based on protein splicing elements known as inteins. By combining these technologies with a PHB-specific binding protein, a self-contained protein expression and purification system has been developed. In this system, the PHB-binding protein effectively acts as an affinity tag for desired product proteins. The tagged product proteins are expressed in E. coli strains that also produce intracellular PHB granules, where they bind to the granules via the PHB-binding tag. The granules and attached proteins can then be easily recovered following cell lysis by simple mechanical means. Once purified, the product protein is self-cleaved from the granules and released into solution in a substantially purified form. This system has been successfully used at laboratory scale to purify several active test proteins at reasonable yield. By allowing the bacterial cells to effectively produce both the affinity resin and tagged target protein, the cost associated with the purification of recombinant proteins could be greatly reduced. It is expected that this combination of improved economics and simplicity will constitute a significant breakthrough in both large-scale production of purified proteins and enzymes and high-throughput proteomics studies of peptide libraries.

A Bayesian method for classification of images from electron micrographs.

Particle classification is an important component of multivariate statistical analysis methods that has been used extensively to extract information from electron micrographs of single particles. Here we describe a new Bayesian Gibbs sampling algorithm for the classification of such images. This algorithm, which is applied after dimension reduction by correspondence analysis or by principal components analysis, dynamically learns the parameters of the multivariate Gaussian distributions that characterize each class. These distributions describe tilted ellipsoidal clusters that adaptively adjust shape to capture differences in the variances of factors and the correlations of factors within classes. A novel Bayesian procedure to objectively select factors for inclusion in the classification models is a component of this procedure. A comparison of this algorithm with hierarchical ascendant classification of simulated data sets shows improved classification over a broad range of signal-to-noise ratios.

Energetic and spatial parameters for gating of the bacterial large conductance mechanosensitive channel, MscL.

MscL is multimeric protein that forms a large conductance mechanosensitive channel in the inner membrane of Escherichia coli. Since MscL is gated by tension transmitted through the lipid bilayer, we have been able to measure its gating parameters as a function of absolute tension. Using purified MscL reconstituted in liposomes, we recorded single channel currents and varied the pressure gradient (P) to vary the tension (T). The tension was calculated from P and the radius of curvature was obtained using video microscopy of the patch. The probability of being open (Po) has a steep sigmoidal dependence on T, with a midpoint (T1/2) of 11.8 dyn/cm. The maximal slope sensitivity of Po/Pc was 0.63 dyn/cm per e-fold. Assuming a Boltzmann distribution, the energy difference between the closed and fully open states in the unstressed membrane was DeltaE = 18.6 kBT. If the mechanosensitivity arises from tension acting on a change of in-plane area (DeltaA), the free energy, TDeltaA, would correspond to DeltaA = 6.5 nm2. MscL is not a binary channel, but has four conducting states and a closed state. Most transition rates are independent of tension, but the rate-limiting step to opening is the transition between the closed state and the lowest conductance substate. This transition thus involves the greatest DeltaA. When summed over all transitions, the in-plane area change from closed to fully open was 6 nm2, agreeing with the value obtained in the two-state analysis. Assuming a cylindrical channel, the dimensions of the (fully open) pore were comparable to DeltaA. Thus, the tension dependence of channel gating is primarily one of increasing the external channel area to accommodate the pore of the smallest conducting state. The higher conducting states appear to involve conformational changes internal to the channel that don't involve changes in area.

Assessment of molecular sieving across bacterial outer membrane of Pseudomonas.

The role of the permeability barrier of the outer membrane of Pseudomonas was re-evaluated based on the physical theory of molecular sieving in view of its intrinsic antibiotic resistance. We developed a set of analytical procedures based on parametric and non-parametric statistical tests to evaluate, validate and adopt the better among a set of competing non-linear models of diffusion. The molecular mass dependence of uptake of non-electrolytes in bacteria yielded a quantitative measure to distinguish between sieving mechanisms and specific uptake/efflux mechanisms. The experimental data, supported by the physical model of DEAE-Sephadex and various analytical models and extensive simulation of the errors, both in measurement and models, yielded evidence consistent with the relaxation of the outer membrane matrix barrier in Pseudomonas.

Assessment of uncoupling by amiloride analogs.

The amiloride analogs N5-methyl-N5-isobutylamiloride, N5-ethyl-N5-isopropylamiloride, and N5,N5-hexamethyleneamiloride are frequently used to investigate NaH exchange on the premise that they are highly specific inhibitors of the NaH-antiporters. We assessed the relative protonophoric activity of these compounds in reconstituted and native membrane vesicles, using acridine orange fluorescence to measure intravesicular pH. All the compounds tested were found to be potent protonophores at concentrations which are normally used to demonstrate inhibition of NaH exchange. Uncoupling was dependent on both the pH of the assay system and the total amount of lipid present. At the pH optima, which lay in a range from 7.5 to 8.5, these amiloride analogs were more potent uncouplers than the classical protonophore carbonyl cyanide m-chlorophenylhydrazone. Therefore, extreme care must be taken in the interpretation of results obtained using these or similar derivatives of amiloride.

Positions of proteins S14, S18 and S20 in the 30 S ribosomal subunit of Escherichia coli.

A map of the 30 S ribosomal subunit is presented giving the positions of 15 of its 21 proteins. The components located in the map are S1, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S14, S15, S18 and S20.