SciCombinator

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Concept: Bacteriophage MS2

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To use a MS2 bacteriophage model to compare three hand-drying methods, paper towels (PT), a warm air dryer (WAD) and a jet air dryer (JAD), for their potential to disperse viruses and contaminate the immediate environment during use.

Concepts: Virus, Bacteriophage MS2, RNA, Microbiology, Bacteriophage

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We show that viruslike particles (VLPs) reassembled in vitro with the RNA bacteriophage MS2 coat protein and an RNA conjugate encompassing a siRNA and a known capsid assembly signal can be targeted to HeLa cells by covalent attachment of human transferrin. The siRNA VLPs protect their cargoes from nuclease, have a double-stranded conformation in the capsid and carry multiple drug and targeting ligands. The relative efficiency of VLP reassembly has been assessed, and conditions have been determined for larger scale production. Targeted VLPs have been purified away from unmodified VLPs for the first time allowing improved analysis of the effects of this synthetic virion system. The particles enter cells via receptor-mediated endocytosis and produce siRNA effects at low nanomolar concentrations. Although less effective than a commercial cationic lipid vector at siRNA delivery, the smaller amounts of internalized RNA with VLP delivery had an effect as good as if not better than the lipid transfection route. This implies that the siRNAs delivered by this route are more accessible to the siRNA pathway than identical RNAs delivered in complex lipid aggregates. The data suggest that the MS2 system continues to show many of the features that will be required to create an effective targeted drug delivery system. The fluorescence assays of siRNA effects described here will facilitate the combinatorial analysis of both future formulations and dosing regimes.

Concepts: Virus-like particle, Small interfering RNA, Protein, DNA, Bacteriophage MS2, Microbiology, RNA

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Ferrate [Fe(VI); FeO(4)(2-)] is an emerging oxidizing agent capable of controlling chemical and microbial water contaminants. Here, inactivation of MS2 coliphage by Fe(VI) was examined. The inactivation kinetics observed in individual batch experiments was well described by a Chick-Watson model with first-order dependences on disinfectant and infective phage concentrations. The inactivation rate constant k(i) at a Fe(VI) dose of 1.23 mgFe/L (pH 7.0, 25 °C) was 2.27(±0.05) L/(mgFe × min), corresponding to 99.99% inactivation at a Ct of ∼4 (mgFe × min)/L. Measured k(i) values were found to increase with increasing applied Fe(VI) dose (0.56-2.24 mgFe/L), increasing temperature (5-30 °C), and decreasing pH conditions (pH 6-11). The Fe(VI) dose effect suggested that an unidentified Fe byproduct also contributed to inactivation. Temperature dependence was characterized by an activation energy of 39(±6) kJ mol(-1), and k(i) increased >50-fold when pH decreased from 11 to 6. The pH effect was quantitatively described by parallel reactions with HFeO(4)(-) and FeO(4)(2-). Mass spectrometry and qRT-PCR analyses demonstrated that both capsid protein and genome damage increased with the extent of inactivation, suggesting that both may contribute to phage inactivation. Capsid protein damage, localized in the two regions containing oxidant-sensitive cysteine residues, and protein cleavage in one of the two regions may facilitate genome damage by increasing Fe(VI) access to the interior of the virion.

Concepts: Chemical kinetics, Chemical reaction, Walter Fiers, Enzyme, RNA, Bacteriophage MS2, Bacteriophage, Microbiology

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Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) has frequently been proposed as an enabling technology for simplified diagnostic tests for RNA viruses. However, common detection techniques used for LAMP and RT-LAMP have drawbacks, including: poor discrimination capability, inability to multiplex targets, high rates of false positives, and (in some cases) the requirement of opening reaction tubes post-amplification. Here, we present a simple technique that allows closed-tube, target-specific detection, based on inclusion of a dye-labeled primer that is incorporated into a target-specific amplicon if the target is present. A short, complementary quencher hybridizes to unincorporated primer upon cooling down at the end of the reaction, thereby quenching fluorescence of any unincorporated primer. Our technique, which we term QUASR (for Quenching of Unincorporated Amplification Signal Reporters, read “quasar”), does not significantly reduce the amplification efficiency or sensitivity of RT-LAMP. Equipped with a simple LED excitation source and a colored plastic gel filter, the naked eye or a camera can easily discriminate between positive and negative QUASR reactions, which produce a difference in signal of approximately 10:1 without background subtraction. We demonstrate that QUASR detection is compatible with complex sample matrices such as human blood, using a novel LAMP primer set for bacteriophage MS2 (a model RNA virus particle). Furthermore, we demonstrate single-tube duplex detection of West Nile virus (WNV) and chikungunya virus (CHIKV) RNA.

Concepts: Bacteriophage MS2, DEET, West Nile virus, Bacteriophage, Virus, Genome, RNA, Microbiology

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Norovirus outbreaks are associated with the consumption of contaminated shellfish, and so efficient methods to recover and detect infectious norovirus in shellfish are important. The Proteinase K digestion method used to recover norovirus from shellfish, as described in the ISO 15216, would be a good candidate but its impact on the virus capsid integrity and thus infectivity was never examined. The aim of this study was to assess the impact of the Proteinase K digestion method, and of the heat treatment component of the method alone, on norovirus (genogroups I and II) and MS2 bacteriophage capsid integrity. A slightly modified version of the ISO method was used. RT-qPCR was used for virus detection following digestion of accessible viral RNA using RNases. MS2 phage infectivity was measured using a plaque assay. The effect of shellfish digestive glands (DG) on recovery was evaluated. In the presence of shellfish DG, a reduction in MS2 phage infectivity of about 1 log10 was observed after the Proteinase K digestion method and after heat treatment component alone. For norovirus GII and MS2 phage, there was no significant loss of genome following the Proteinase K digestion method but there was a significant 0.24 log10 loss of norovirus GI. In the absence of shellfish DG, the reduction in MS2 phage infectivity was about 2 log10, with the addition of RNases resulting in a significant loss of genome for all tested viruses following complete Proteinase K digestion method and the heat treatment alone. While some protective effect from the shellfish DG on viruses was observed, the impact on capsid integrity and infectivity suggests that this method, while suitable for norovirus genome detection, may not completely preserve virus infectivity.

Concepts: DNA, Walter Fiers, Genome, Virus, Bacteriophage MS2, Microbiology, RNA, Bacteriophage

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A series of full-scale testing was performed at the City of Lathrop Consolidated Treatment Facility to determine the “concentration times time” (Ct) value for free chlorine disinfection of nitrified membrane bioreactor (MBR) effluent to achieve more than 5-log virus inactivation. The full-scale testing consisted of tracer study, chlorine decay study, and virus seeding study. The virus seeding study was performed at a flow rate of 1 million gallons/day (3,800 m3/min), which corresponded to a theoretical contact time of 117 min in the chlorine contact basin. It was found that Ct values as small as 3 mg·min/L were sufficient to achieve 5-log inactivation of MS2 bacteriophage in this study, which is comparable to the results of previous bench- and pilot-scale free chlorine disinfection studies on nitrified MBR effluent (3 to 40 mg·min/L), as well as those of pilot- and full-scale studies on granular media-filtered nitrified effluent (2 to 22 mg·min/L).

Concepts: Bacteriophages, Time, Walter Fiers, RNA, Chlorine, Microbiology, Bacteriophage MS2, Bacteriophage

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Silver nanoparticles (AgNPs) have been reported as an effective alternative for controlling a broad-spectrum of pathogenic viruses. We developed a micrometer-sized silica hybrid composite decorated with AgNPs (AgNP-SiO2) to prevent the inherent aggregation of AgNPs, and facilitated their recovery from environmental media after use. The production process had a high-yield, and fabrication was cost-effective. We evaluated the antiviral capabilities of Ag30-SiO2 particles against two model viruses, bacteriophage MS2 and murine norovirus (MNV), in four different types of water (deionized, tap, surface, and ground). MNV was more susceptible to Ag30-SiO2 particles in all four types of water compared to MS2. Furthermore, several water-related factors, including temperature and organic matter content, were shown to affect the antimicrobial capabilities of Ag30-SiO2 particles. The modified Hom model was the best-fit disinfection model for MNV disinfection in the different types of water. Additionally, this study demonstrated that the effects of a certain level of physical obstacles in water were negligible in regards to the use of Ag30-SiO2 particles. Thus, effective use of AgNPs in water disinfection processes can be achieved using our novel hybrid composites to inactivate various waterborne viruses.

Concepts: Effect, Bacteriophages, Walter Fiers, Virus, RNA, Bacteriophage MS2, Bacteriophage, Microbiology

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In bacteriophage research and therapy, most applications ask for highly purified phage suspensions. The standard technique for this is ultracentrifugation using cesium chloride gradients. This technique is cumbersome, elaborate and expensive. Moreover, it is unsuitable for the purification of large quantities of phage suspensions.The protocol described here, uses anion-exchange chromatography to bind phages to a stationary phase. This is done using an FLPC system, combined with Convective Interaction Media (CIM®) monoliths. Afterward, the column is washed to remove impurities from the CIM® disk. By using a buffer solution with a high ionic strength, the phages are subsequently eluted from the column and collected. In this way phages can be efficiently purified and concentrated.This protocol can be used to determine the optimal buffers, stationary phase chemistry and elution conditions, as well as the maximal capacity and recovery of the columns.

Concepts: Bacteriophage MS2, Bacteriophages, Chromatography, Gas chromatography, Phage therapy, Bacteriophage, Analytical chemistry

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The inactivation efficacy of bacteriophage MS2 by simulated sunlight irradiation was investigated to understand the effects of MS2 aggregation and adsorption to particles in solutions with different components. Kaolinite and Microcystis aeruginosa were used as model inorganic and organic particles, respectively. Lower pH and di-valent ions (Ca2+) were main factors on the aggregation and inactivation of MS2. In the presence of both particles, there was no significant impact on the MS2 inactivation efficacy by kaolinite (10-200mM) or Microcystis aeruginosa (102-105Cells/mL) in 1mM NaCl at pH 7. However at lower pH 3, MS2 aggregates formed in the particle-free and kaolinite-containing solutions, caused lower inactivation since the outer viruses of aggregation protect the inner viruses. In addition, more MS2 adsorbed on Microcystis aeruginosa at lower pH (3 and 4). Microcystis aeruginosa would act as a potential photosensitizer for ROS production to inactivate the adsorbed MS2, since extracellular organic matter (EOM) of Microcystis aeruginosa was detected in this study, which has been reported to produce ROS under solar irradiation. At pH 7, Na+ had no effect on the inactivation of MS2, because MS2 was stable and dispersed even at 200mM Na+. MS2 aggregated and adsorbed on particles even at 10mM Ca2+ and led to lower inactivation. Kaolinite cannot offer enough protection to adsorbed MS2 as aggregation and Microcystis aeruginosa acts as potential photosensitizer to produce ROS and inactivate the adsorbed MS2 at high concentration of Ca2+. In particle-free solution, SRNOM inhibited MS2 inactivation by shielding the sunlight and coating MS2 to increase its survival.

Concepts: Effectiveness, Aggregate, Bacteriophage MS2, PH, Chemistry, Concentration, Solution, Bacteriophage

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MS2 phage-like particles (MS2 PLP) are artificially constructed pseudo-viral particles derived from bacteriophage MS2. They are able to carry a specific single stranded RNA (ssRNA) sequence of choice inside their capsid, thus protecting it against the effects of ubiquitous nucleases. Such particles are able to mimic ssRNA viruses and, thus, may serve as the process control for molecular detection and quantification of such agents in several kinds of matrices, vaccines and vaccine candidates, drug delivery systems, and systems for the display of immunologically active peptides or nanomachines. Currently, there are several different in vivo plasmid-driven packaging systems for production of MS2 PLP. In order to combine all the advantages of the available systems and to upgrade and simplify the production and purification of MS2 PLP, a one-plasmid double-expression His-tag system was designed. The described system utilizes a unique fusion insertional mutation enabling purification of particles using His-tag affinity. Using this new production system, highly pure MS2 PLP can be quickly produced and purified by a fast performance liquid chromatography (FPLC) approach. The system can be easily adapted to produce other MS2 PLP with different properties.

Concepts: Genome, Protein, Bacteriophage, Genetics, Bacteriophage MS2, Microbiology, DNA, RNA