Design of a self-regulating mRNA gene circuit.

Protein expression in vivo is predominately controlled via regulatory feedback mechanisms that adjust the level of mRNA transcription. However for positive sense single-stranded RNA viruses, protein expression is often controlled via secondary structural elements, such as internal ribosomal entry sites, that are encoded within the mRNA. The self-regulation of mRNA translation observed in this class of viruses suggests that it may be possible to design mRNAs that self-regulate their protein expression, enabling the creation of mRNAs for vaccines and other synthetic biology applications where protein levels in the cell can be tightly controlled without feedback to a transcriptional mechanism. As a proof of concept, I design a polycistronic mRNA based on bacteriophage MS2, where the upstream gene is capable of repressing synthesis of the downstream gene. Using a computational tool that simulates ribosome kinetics and the co-translational folding of the mRNA in response, I show that mutations to the mRNA can be identified which enhance the efficiency of the translation and the repression of the downstream gene. The results of this study open up the possibility of designing bespoke mRNA gene circuits in which the amount of protein synthesised in cells are self-regulated for therapeutic or antigenic purposes.

Exploring the Effects of Intersubunit Interface Mutations on Virus-Like Particle Structure and Stability.

Virus-like particles (VLPs) from bacteriophage MS2 provide a platform to study protein self-assembly and create engineered systems for drug delivery. Here, we aim to understand the impact of intersubunit interface mutations on the local and global structure and function of MS2-based VLPs. In previous work, our lab identified locally supercharged double mutants [T71K/G73R] that concentrate positive charge at capsid pores, enhancing uptake into mammalian cells. To study the effects of particle size on cellular internalization, we combined these double mutants with a single point mutation [S37P] that was previously reported to switch particle geometry from T = 3 to T = 1 icosahedral symmetry. These new variants retained their enhanced cellular uptake activity and could deliver small-molecule drugs with efficacy levels similar to our first-generation capsids. Surprisingly, these engineered triple mutants exhibit increased thermostability and unexpected geometry, producing T = 3 particles instead of the anticipated T = 1 assemblies. Transmission electron microscopy revealed various capsid assembly states, including wild-type (T = 3), T = 1, and rod-like particles, that could be accessed using different combinations of these point mutations. Molecular dynamics experiments recapitulated the structural rationale in silico for the single point mutation [S37P] forming a T = 1 virus-like particle and showed that this assembly state was not favored when combined with mutations that favor rod-like architectures. Through this work, we investigated how interdimer interface dynamics influence VLP size and morphology and how these properties affect particle function in applications such as drug delivery.

Deciphering the Thermal Stability of Bacteriophage MS2-Derived Virus-like Particle and Its Engineered Variant.

RNA bacteriophage MS2-derived virus-like particles (VLPs) have been widely used in biomedical research as model systems to study virus assembly, structure-function relationships, vaccine development, and drug delivery. Considering the diverse utility of these VLPs, a systemic engineering approach has been utilized to generate smaller particles with optimal serum stability and tissue penetrance. Additionally, it is crucial to demonstrate the overall stability of these mini MS2 VLPs, ensuring cargo protection until they reach their target cell/organ. However, no detailed analysis of the thermal stability and heat-induced disassembly of MS2 VLPs has yet been attempted. In this work, we investigated the thermal stability of both wild-type (WT) MS2 VLP and its "mini" variant containing S37P mutation (mini MS2 VLP). The mini MS2 VLP exhibits a higher capsid melting temperature (Tm) when compared to its WT MS2 VLP counterpart, possibly attributed to its smaller interdimer angle. Our study presents that the thermal unfolding of MS2 VLPs follows a sequential process involving particle destabilization, nucleic acid exposure/melting, and disassembly of VLP. This observation underscores the disruption of cooperative intersubunit interactions and protein-nucleic acid interactions, shedding light on the mechanism of heat-induced VLP disassembly.

Transformation of a Viral Capsid from Nanocages to Nanotubes and Then to Hydrogels: Redirected Self-Assembly and Effects on Immunogenicity.

The ability to manipulate the self-assembly of proteins is essential to understanding the mechanisms of life and beneficial to fabricating advanced nanomaterials. Here, we report the transformation of the MS2 phage capsid from nanocages to nanotubes and then to nanotube hydrogels through simple point mutations guided by interfacial interaction redesign. We demonstrate that site 70, which lies in the flexible FG loop of the capsid protein (CP), is a "magic" site that can largely dictate the final morphology of assemblies. By varying the amino acid at site 70, with the aid of a cysteine-to-alanine mutation at site 46, we achieved the assembly of double-helical or single-helical nanotubes in addition to nanocages. Furthermore, an additional cysteine substitution on the surface of nanotubes mediated their cross-linking to form hydrogels with reducing agent responsiveness. The hierarchical self-assembly system allowed for the investigation of morphology-related immunogenicity of MS2 CPs, which revealed dramatic differences among nanocages, nanotubes, and nanotube hydrogels in terms of immune response types, antibody levels and T cell functions. This study provides insights into the assembly manipulation of protein nanomaterials and the customized design of nanovaccines and drug delivery systems.

Influence of suspended particles and dissolved organic matters on virus enrichment in reclaimed water by two-step tangential flow ultrafiltration: Phenomena and mechanisms.

Enteric virus concentration in large-volume water samples is crucial for detection and essential for assessing water safety. Certain dissolution and suspension components can affect the enrichment process. In this study, tangential flow ultrafiltration (TFUF) was used as an enrichment method for recovering enteric virus in water samples. Interestingly, the bacteriophage MS2 recovery in reclaimed water and the reclaimed water without particles were higher than that in ultrapure water. The simulated reclaimed water experiments showed that humic acid (HA) (92.16% ± 4.32%) and tryptophan (Try) (81.50 ± 7.71%) enhanced MS2 recovery, while the presence of kaolin (Kaolin) inhibited MS2 recovery with an efficiency of 63.13% ± 11.17%. Furthermore, Atomic force microscopy (AFM) revealed that the MS2-HA cluster and the MS2-Try cluster had larger roughness values on the membrane surface, making it difficult to be eluted, whereas MS2-Kaolin cluster had compact surfaces making it difficult to be eluted. Additionally, the MS2-HA cluster is bound to the membrane by single hydrogen bond with SO, whereas both the MS2-Try cluster and the MS2-Kaolin cluster are bound to the membrane by two hydrogen bonds, making eluting MS2 challenging. These findings have potential implications for validating standardized methods for virus enrichment in water samples.

Massively parallel dissection of RNA in RNA-protein interactions in vivo.

Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to biology. Here, we present massively parallel RNA assay combined with immunoprecipitation (MPRNA-IP) for in vivo high-throughput dissection of RNA-protein interactions and describe statistical models for identifying RNA domains and parsing the structural contributions of RNA. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, MPRNA-IP is able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest, including the long noncoding RNA NORAD, bacteriophage MS2 RNA, and human telomerase RNA, and we use it to interrogate the hitherto unknown sequence or structural RNA-binding preferences of the DNA-looping factor CTCF. By integrating systematic mutation analysis with crosslinking immunoprecipitation, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions in vivo.

Photostability and photodynamic antimicrobial profile of dye extracts from four (4) plants: prospects for eco-friendly low-cost food disinfection and topical biomedical applications.

In this study, photostability and photodynamic antimicrobial performance of dye extracts from Hibiscus sabdariffa (HS) calyces, Sorghum bicolor (SB) leaf sheaths, Lawsonia inermis (LI) leaves and Curcuma longa (CL) roots were investigated in Acetate-HCl (AH) Buffer (pH 4.6), Tris Base-HCl (TBH) Buffer (pH 8.6), distilled water (dH2O), and Phosphate Buffer Saline (PBS, pH 7.2) using Bacillus subtilis as model for gram positive bacteria, Escherichia coli as model for gram negative bacteria, phage MS2 as model for non-envelope viruses and phage phi6 as model for envelope viruses including SARS CoV-2 which is the causative agent of COVID-19. Our results showed that the photostability of the dye extracts is in the decreasing order of LI > CL > SB > HS. The dye extract-HS is photostable in dH2O but bleaches in buffers-AH, TBH and PBS. The rate of bleaching is higher in AH compared to in TBH and PBS. The bleaching and buffers affected the photodynamic and non-photodynamic antimicrobial activity of the dye extracts. The photodynamic antibacterial activity of the dye extracts is in the decreasing order of CL > HS > LI > SB while the non-photodynamic antibacterial activity is in the decreasing order of LI > CL > HS > SB. The non-photodynamic antiviral activity pattern observed is the same as that of non-photodynamic antibacterial activity observed. However, the photodynamic antiviral activity of the dye extracts is in the decreasing order of CL > LI > HS > SB. Given their performance, the dye extracts maybe mostly suitable for environmental applications including fresh produce and food disinfection, sanitation of hands and contact surfaces where water can serve as diluent for the extracts and the microenvironment is free of salts.

Effects of chemically-reductive trace gas contaminants on non-thermal plasma inactivation of an airborne virus.

Transmission of airborne infectious diseases poses great risk for public health and socio-economic stability, thus, there is a need for an effective control method targeting the spread and transmission of pathogenic aerosols. The existence of chemically-reductive trace air contaminants in animal agriculture may affect the oxidation inactivation process of pathogens. In this study, we report how the presence of such gasses impacts the effectiveness of using non-thermal plasma (NTP) within a packed-bed dielectric barrier discharge reactor to inactivate MS2 bacteriophage. Inactivation of the aerosolized bacteriophage is determined by the combination of viability and polymerase chain reaction assays. Using a plasma power source with a voltage of 20 kV and frequency of 350 Hz, after differentiating and excluding the physical removal effects of viral aerosols potentially caused by plasma, the baseline inactivation of MS2 aerosol in air has been determined based on an overall air flow rate of 200 Liters per minute and plasma discharge power of 1.8 W. When either ammonia or hydrogen sulfide gas is introduced into the airstream at a concentration of 1 part per million, the NTP virus inactivation efficiency is reduced to around 0.5-log from the 1-log baseline inactivation in air alone. Higher concentrations of those gasses will not further inhibit the effectiveness of plasma inactivation.

Refining and in-situ growth of polyaniline endows the cellulose fibers with electrical stimulation sterilization.

Bacteria and virus infections have posed a great threat to public health and personnel safety. For realizing rapid sterilization of the bacteria and virus, electrical stimulation sterilization was adopted to endow cellulose fibers with instantaneous antibacterial and antiviral properties. In the proposed strategy, the fiber is fluffed by mechanical refining, and then by means of the hydrogen bond between hydroxyl and aniline, the polyaniline (PANI) directionally grows vertically along the fine fibers via in-situ oxidative polymerization. Benefiting from the conductive polyaniline nanorod arrays on the fiber stem, the paper made from PANI modified refined fibers (PANI/BCF/P) exhibited excellent antibacterial and antiviral activity, the inhibition rates against S. aureus, E. coli, and bacteriophage MS2 can up to 100 %, 100 %, and 99.89 %, respectively when a weak voltage (2.5 V) was applied within 20 min. This study provides a feasible path for plant fiber to achieve efficient antibacterial and antiviral activity with electrical stimulation, which is of great significance for the preparation of electroactive antibacterial and antiviral green health products.

The dsRNA isolated from Escherichia coli infected with the MS2 bacteriophage induces the production of interferons.

Viral infections pose a significant threat to public health, and the production of interferons represents one of the most critical antiviral innate immune responses of the host. Consequently, the screening and identification of compounds or reagents that induce interferon production are of paramount importance. This study commenced with the cultivation of host bacterium 15,597, followed by the infection of Escherichia coli with the MS2 bacteriophage. Utilizing the J2 capture technique, a class of dsRNA mixtures (MS2+15,597) was isolated from the E. coli infected with the MS2 bacteriophage. Subsequent investigations were conducted on the immunostimulatory activity of the MS2+15,597 mixture. The results indicated that the dsRNA mixtures (MS2+15,597) extracted from E. coli infected with the MS2 bacteriophage possess the capability to activate innate immunity, thereby inducing the production of interferon-ß. These dsRNA mixtures can activate the RIG-I and TLR3 pattern recognition receptors, stimulating the expression of interferon stimulatory factors 3/7, which in turn triggers the NF-κB signaling pathway, culminating in the cellular production of interferon-ß to achieve antiviral effects. This study offers novel insights and strategies for the development of broad-spectrum antiviral drugs, potentially providing new modalities for future antiviral therapies.

Virus-like particles derived from bacteriophage MS2 as antigen scaffolds and RNA protective shells.

The versatile potential of bacteriophage MS2-derived virus-like particles (VLPs) in medical biotechnology has been extensively studied during the last 30 years. Since the first reports showing that MS2 VLPs can be produced at high yield and relatively easily engineered, numerous applications have been proposed. Particular effort has been spent in developing MS2 VLPs as protective capsules and delivery platforms for diverse molecules, such as chemical compounds, proteins and nucleic acids. Among these, two are particularly noteworthy: as scaffolds displaying heterologous epitopes for vaccine development and as capsids for encapsulation of foreign RNA. In this review, we summarize the progress in developing MS2 VLPs for these two areas.

Hollow, nanosized protein particles have many potential uses. If they can be appropriately engineered, they may for example be able to carry therapeutic cargoes to diseased cells or be used as a vaccine where appropriate antigens are mounted on their external surface. Many viruses offer a ready-made protein particle, the capsid, which can be made hollow by exclusion of the viral genetic material. MS2 is a virus that targets bacteria ­ a bacteriophage ­ which is well characterized and has been developed over many years for a number of applications. It has particular promise for development as a vaccine and for RNA delivery, both of which are reviewed here.

Purification of Single-Stranded RNA Bacteriophages and Host Receptors for Structural Determination Using Cryo-Electron Microscopy.

Single-stranded RNA bacteriophages (ssRNA phages) are small viruses with a compact genome (~3-4 kb) that infect gram-negative bacteria via retractile pili. These phages have been applied in various fields since their discovery approximately 60 years ago. To understand their biology, it is crucial to analyze the structure of mature virions. Cryo-electron microscopy (cryo-EM) has been employed to determine the structures of two ssRNA phages, MS2 and Qß. This chapter presents a method for purifying these two phages and their receptor, the F-pilus, to allow examination using cryo-EM.

Impact of different hand-drying methods on surrounding environment: aerosolization of virus and bacteria, and transfer to surfaces.

BACKGROUND: In recent years, hand drying has been highlighted as a key step in appropriate hand hygiene, as moisture on hands can increase the transfer of micro-organisms from hands to surfaces and vice versa. AIM: To understand bacterial and viral aerosolization following hand drying, and study the transfer of micro-organisms from hands to surfaces after drying using different methods. METHODS: Groups of five volunteers had their hands pre-washed with soap, rinsed and dried, then inoculated with a concentrated mixture of Pseudomonas fluorescens and MS2 bacteriophage. Volunteers entered an empty washroom, one at a time, and rinsed their hands with water or washed their hands with soap prior to drying with a jet dryer or paper towels. Each volunteer applied one hand successively to various surfaces, while their other hand was sampled using the glove juice method. Both residual bacteria and viruses were quantified from the washroom air, surface swabs and hand samples. FINDINGS: P. fluorescens and MS2 bacteriophages were rarely aerosolized while drying hands for any of the drying methods studied. Results also showed limited, and similar, transfer of both micro-organisms studied on to surfaces for all drying methods. CONCLUSION: The use of jet dryers or paper towels produces low levels of aerosolization when drying hands in a washroom. Similarly, all drying methods result in low transfer to surfaces. While the coronavirus disease 2019 pandemic raised concerns regarding public washrooms, this study shows that all methods tested are hygienic solutions for dry washed hands.

Mitigation of viruses of concern and bacteriophage surrogates via common unit processes for water reuse: A meta-analysis.

Water reuse is a growing global reality. In regulating water reuse, viruses have come to the fore as key pathogens due to high shedding rates, low infectious doses, and resilience to traditional wastewater treatments. To demonstrate the high log reductions required by emerging water reuse regulations, cost and practicality necessitate surrogates for viruses for use as challenge organisms in unit process evaluation and monitoring. Bacteriophage surrogates that are mitigated to the same or lesser extent than viruses of concern are routinely used for individual unit process testing. However, the behavior of these surrogates over a multi-barrier treatment train typical of water reuse has not been well-established. Toward this aim, we performed a meta-analysis of log reductions of common bacteriophage surrogates for five treatment processes typical of water reuse treatment trains: advanced oxidation processes, chlorination, membrane filtration, ozonation, and ultraviolet (UV) disinfection. Robust linear regression was applied to identify a range of doses consistent with a given log reduction of bacteriophages and viruses of concern for each treatment process. The results were used to determine relative conservatism of surrogates. We found that no one bacteriophage was a representative or conservative surrogate for viruses of concern across all multi-barrier treatments (encompassing multiple mechanisms of virus mitigation). Rather, a suite of bacteriophage surrogates provides both a representative range of inactivation and information about the effectiveness of individual processes within a treatment train. Based on the abundance of available data and diversity of virus treatability using these five key water reuse treatment processes, bacteriophages MS2, phiX174, and Qbeta were recommended as a core suite of surrogates for virus challenge testing.

Heat inactivation of aqueous viable norovirus and MS2 bacteriophage.

AIMS: This study aimed to compare the heat inactivation kinetics of viable human norovirus with the surrogate, MS2 bacteriophage as well as assess the decay of the RNA signal. METHODS AND RESULTS: Human intestinal enteroids were used to analyze the heat inactivation kinetics of viable human norovirus compared to the surrogate MS2 bacteriophage, which was cultured using a plaque assay. Norovirus decay rates were 0.22 min-1, 0.68 min-1, and 1.11 min-1 for 50°C, 60°C, and 70°C, respectively, and MS2 bacteriophage decay rates were 0.0065 min-1, 0.045 min-1, and 0.16 min-1 for 50°C, 60°C, and 70°C, respectively. Norovirus had significantly higher decay rates than MS2 bacteriophage at all tested temperatures (P = .002-.007). No decrease of RNA titers as measured by reverse transcription-PCR for both human norovirus and MS2 bacteriophage over time was observed, indicating molecular methods do not accurately depict viable human norovirus after heat inactivation and treatment efficiency is underestimated. CONCLUSIONS: Overall, our data demonstrate that MS2 bacteriophage is a conservative surrogate to measure heat inactivation and potentially overestimates the infectious risk of norovirus. Furthermore, this study corroborates that measuring viral RNA titers, as evaluated by PCR methods, does not correlate with the persistence of viable norovirus under heat inactivation.

Ozone, hydrogen peroxide, and peroxymonosulfate disinfection of MS2 coliphage in water.

The control of viruses in water is critical to preventing the spread of infectious viral diseases. Many oxidants can inactivate viruses, and this study aims to systematically compare the disinfection effects of ozone (O3), peroxymonosulfate (PMS), and hydrogen peroxide (H2O2) on MS2 coliphage. The effects of oxidant dose and contact time on disinfection were explored, as were the disinfection effects of three oxidizing agents in secondary effluent. The 4-log inactivation of MS2 coliphage required 0.05 mM O3, 0.5 mM PMS, or 25 mM H2O2 with a contact time of 30 min. All three oxidants achieved at least 4-log disinfection within 30 min, and O3 required only 0.5 min. In secondary effluent, all three oxidants also achieved 4-log inactivation of MS2 coliphage. Excitation-emission matrix (EEM) results indicate that all three oxidants removed dissolved organic matter synchronously and O3 oxidized dissolved organic matter more thoroughly while maintaining disinfection efficacy. Considering the criteria of oxidant dose, contact time, and disinfection efficacy in secondary effluent, O3 is the best choice for MS2 coliphage disinfection among the three oxidants.

Microplastics as potential barriers to ultraviolet light emitting diode inactivation of MS2 bacteriophage: Influence of water-quality parameters.

Microplastics have emerged as a concerning contaminant in drinking water sources, potentially interacting with pathogenic microorganisms and affecting the disinfection processes. In this study, MS2 was selected as an alternative for the human enteric virus. The influence of microplastics polyvinylchloride (MPs-PVC) on ultraviolet light emitting diode (UV-LED) inactivation of MS2 was investigated under various water chemistry conditions, such as MPs-PVC concentration, pH, salinity, and humic acid concentration. The results revealed that higher concentrations of MPs-PVC led to the reduced inactivation of MS2 by decreased UV transmittance, hindering the disinfection process. Additionally, the inactivation efficiency of MS2 in the presence of MPs-PVC was influenced by pH, and acidic solution (pH at 4, 5, and 6) exhibited higher efficiency compared to alkaline solution (pH at 8 and 9) and neutral solution (pH at 7). The low Na+ concentrations (0-50 mM) had a noticeable effect on MS2 inaction efficiency in the presence of MPs-PVC, while the addition of Ca2+ posed an insignificant effect due to the preferential interaction with MPs-PVC. Furthermore, the inactivation rate of MS2 initially increased and then decreased with increasing the concentration of humic acid, which was significantly different without MPs-PVC. These findings shed light on the complex interactions between MPs-PVC and MS2 in the UV-LED disinfection process under various water-quality parameters, contributing to drinking water safety and treatment.

Insights of phytoremediation mechanisms for viruses based on in-vitro, in-vivo and in-silico assessments of selected herbal plants.

Waterborne pathogenic viruses present unrelenting challenges to the global health and wastewater treatment industry. Phytoremediation offers promising solutions for wastewater treatment through plant-based technologies. This study investigated antiviral mechanisms in-vivo using bacteriophages MS2 and T4 as surrogates for effective herbs screened in-vitro from three embryophytes (Ocimum basilicum, Mentha sp., Plectranthus amboinicus), two macrophytes (Eichhornia crassipes, Pistia stratiotes) and a perennial grass (Cyperus rotundas). In-silico virtual screening predicted antiviral phytochemicals for further antiviral potency assessment. Results suggested in-vitro antiviral activities of embryophytes and macrophytes were higher (43-62%) than grass (21-26%). O. basilicum (OB, 57-62%) and P. stratiotes (PS, 59-60%) exhibited the highest antiviral activities. In-vivo tests showed notable virus reduction (>60%) in culture solution, attributed to rhizofiltration (66-74%) and phytoinactivation/phytodegradation (63-84%). In-silico analysis identified rutin as a primary antiviral phytochemical for MS2 (-9.7 kcal/mol) and T4 (-10.9 kcal/mol), correlating with dose-response inactivation (∼58-62%). In-vivo tests suggested additional phytocompounds may contribute to viral inactivation, presenting new opportunities for herb-based wastewater treatment solutions. Consequently, this study not only demonstrates the antiviral capabilities of OB and PS but also introduces an innovative approach for addressing viral contaminants in water.

Ozone and photodynamic inactivation of norovirus surrogate bacteriophage MS2 in fresh Brazilian berries and surfaces.

This study assessed the efficacy of ozone (bubble diffusion in water; 6.25 ppm) and photodynamic inactivation (PDT) using curcumin (75 µM) as photosensitizer (LED emission 430-470 nm; 33.6 mW/cm2 irradiance; 16.1, 20.2, and 24.2 J/cm2 light dose) against the Norovirus surrogate bacteriophage MS2 in Brazilian berries (black mulberry and pitanga) and surfaces (glass and stainless steel). Contaminated berries and surfaces were immersed in ozonized water or exposed to PDT-curcumin for different time intervals. Transmission electron microscopy was used to assess the effects of the treatments on MS2 viral particles. The MS2 inactivation by ozone and PDT-curcumin varied with the fruit and the surface tested. Ozone reduced the MS2 titer up to 3.6 log PFU/g in black mulberry and 4.1 log PFU/g in pitanga. On surfaces, the MS2 reduction by ozone reached 3.6 and 4.8 log PFU/cm2 on glass and stainless steel, respectively. PDT-curcumin reduced the MS2 3.2 and 4.8 log PFU/g in black mulberry and pitanga and 2.7 and 3.3 log PFU/cm2 on glass and stainless steel, respectively. MS2 particles were disintegrated by exposure of MS2 to ozone and PDT-curcumin on pitanga. Results can contribute to establishing effective practices for controlling NoV in fruits and surfaces, estimated based on MS2 bacteriophage behavior.