Protocol for an in vitro assay to study HIV-1 Tat methylation.

A critical virus-encoded regulator of HIV-1 transcription is the Tat protein, which is required to potently activate transcription. Tat is regulated by a wide variety of post-translational modifications. This protocol describes an in vitro assay to study Tat methylation. We describe steps for incorporation of radioactive methyl groups into Tat protein, visualization by gel analysis, Coomassie blue stain, gel drying, and detection by autoradiography. This protocol can also be used to assess methylation in other proteins such as histones. For complete details on the use and execution of this protocol, please refer to Boehm et al. (2023).1.

A flow cytometry-based assay to investigate HIV-1 expression in SMYD5 shRNA containing primary CD4+ T cells.

Delivering small hairpin RNAs (shRNAs) and the HIV-1 virus to primary CD4+ T cells with high transduction efficiency and high cell viability can be challenging. Here, we present a flow cytometry-based assay to knock down the host protein SMYD5 by shRNA and study the HIV-1 virus specifically in shRNA-containing cells. We describe steps for purifying CD4+ T cells, activating them with CD3/CD28 Dynabeads, transfection of plasmids into HEK293T cells, spinoculation with two different viruses, and analysis by flow cytometry. For complete details on the use and execution of this protocol, please refer to Boehm et al.1.

Combined Effect of Plasma-Activated Water and Topotecan in Glioblastoma Cells.

The increase in cancer diagnoses and cancer deaths, severe side effects of existing treatments and resistance to traditional treatments have generated a need for new anticancer treatments. Glioblastoma multiforme (GBM) is the most common, malignant and aggressive brain cancer. Despite many innovations regarding GBM treatment, the final outcome is still very poor, making it necessary to develop new therapeutic approaches. Cold atmospheric plasma (CAP) as well as plasma-activated liquids (PAL) are being studied as new possible approaches against cancer. The anticancer activity of PAL such as "plasma-activated water" (PAW) is dependent on the reactive chemical compounds present in the solution. Possible combinatory effects with conventional therapies, such as chemotherapeutics, may expand the potential of PAL for cancer treatment. We aim to explore the therapeutic properties of a combination of PAW and topotecan (TPT), an antineoplastic agent with major cytotoxic effects during the S phase of the cell cycle, on a GBM cancer cell line (U-251mg). Combined treatments with PAW and TPT showed a reduction in the metabolic activity and cell mass, an increase in apoptotic cell death and a reduction in the long-term survival. Single applications of PAW+TPT treatments showed a cytotoxic effect in the short term and an antiproliferative effect in the long term, warranting future exploration of combining PAW with chemotherapeutic agents as new therapeutic approaches.

The lysine methyltransferase SMYD5 amplifies HIV-1 transcription and is post-transcriptionally upregulated by Tat and USP11.

A successful HIV-1 cure strategy may require enhancing HIV-1 latency to silence HIV-1 transcription. Modulators of gene expression show promise as latency-promoting agents in vitro and in vivo. Here, we identify Su(var)3-9, enhancer-of-zeste, and trithorax (SET) and myeloid, Nervy, and DEAF-1 (MYND) domain-containing protein 5 (SMYD5) as a host factor required for HIV-1 transcription. SMYD5 is expressed in CD4+ T cells and activates the HIV-1 promoter with or without the viral Tat protein, while knockdown of SMYD5 decreases HIV-1 transcription in cell lines and primary T cells. SMYD5 associates in vivo with the HIV-1 promoter and binds the HIV trans-activation response (TAR) element RNA and Tat. Tat is methylated by SMYD5 in vitro, and in cells expressing Tat, SMYD5 protein levels are increased. The latter requires expression of the Tat cofactor and ubiquitin-specific peptidase 11 (USP11). We propose that SMYD5 is a host activator of HIV-1 transcription stabilized by Tat and USP11 and, together with USP11, a possible target for latency-promoting therapy.

Efficacy of plasma activated saline in a co-culture infection control model.

Plasma activated liquids have demonstrated antimicrobial effects and receive increasing attention due to the potential to strengthen the armoury of novel approaches against antibiotic resistant bacteria. However, the antibacterial activity and cytotoxic effects of these solutions need to be understood and balanced before exposure to humans. In this study, the antibacterial effects of plasma activated saline (PAS) were tested against Gram negative and positive bacteria, and HaCaT keratinocytes were used for cytotoxicity studies. For the first time, a co-culture model between these bacteria and eukaryotic cells under the influence of PAS has been described. Exposure of saline to plasma resulted in high concentrations of nitrate, hydrogen peroxide and a reduction of pH. PAS caused high antibacterial effects in the co-culture model, accompanied by high cytotoxic effects to the monolayer of mammalian cells. We present evidence and provide a deeper understanding for the hypothesis that upon treatment with PAS, chemical species generated in the liquid mediate high antimicrobial effects in the co-culture setup as well as mitochondrial depolarization and glutathione depletion in HaCaT cells and cell lysis due to acidic pH. In conclusion, PAS retains strong antibacterial effects in a co-culture model, which may have unintended negative biological effects on mammalian cells.

Cell death induced in glioblastoma cells by Plasma-Activated-Liquids (PAL) is primarily mediated by membrane lipid peroxidation and not ROS influx.

Since first identified in 1879, plasma, the fourth state of matter, has been developed and utilised in many fields. Nonthermal atmospheric plasma, also known as cold plasma, can be applied to liquids, where plasma reactive species such as reactive Oxygen and Nitrogen species and their effects can be retained and mediated through plasma-activated liquids (PAL). In the medical field, PAL is considered promising for wound treatment, sterilisation and cancer therapy due to its rich and relatively long-lived reactive species components. This study sought to identify any potential antagonistic effect between antioxidative intracellularly accumulated platinum nanoparticles (PtNPs) and PAL. We found that PAL can significantly reduce the viability of glioblastoma U-251MG cells. This did not involve measurable ROS influx but instead lead to lipid damage on the plasma membrane of cells exposed to PAL. Although the intracellular antioxidative PtNPs showed no protective effect against PAL, this study contributes to further understanding of principle cell killing routes of PAL and discovery of potential PAL-related therapy and methods to inhibit side effects.

Biomolecules as Model Indicators of In Vitro and In Vivo Cold Plasma Safety.

The potential applications for cold plasma in medicine are extensive, from microbial inactivation and induction of apoptosis in cancer cells to stimulating wound healing and enhancing the blood coagulation cascade. The safe bio-medical application of cold plasma and subsequent effect on complex biological pathways requires precision and a distinct understanding of how physiological redox chemistry is manipulated. Chemical modification of biomolecules such as carbohydrates, proteins, and lipids treated with cold plasma have been characterized, however, the context of how alterations of these molecules affect cell behavior or in vivo functionality has not been determined. Thus, this study examines the cytotoxic and mutagenic effects of plasma-treated molecules in vitro using CHO-K1 cells and in vivo in Galleria mellonella larvae. Specifically, albumin, glucose, cholesterol, and arachidonic acid were chosen as representative biomolecules, with established involvement in diverse bioprocesses including; cellular respiration, intracellular transport, cell signaling or membrane structure. Long- and short-term effects depended strongly on the molecule type and the treatment milieu indicating the impact of chemical and physical modifications on downstream biological pathways. Importantly, absence of short-term toxicity did not always correlate with absence of longer-term effects, indicating the need to comprehensively assess ongoing effects for diverse biological applications.

The effect of atmospheric cold plasma treatment on the antigenic properties of bovine milk casein and whey proteins.

Casein, ß-lactoglobulin and α-lactalbumin are major milk protein allergens. In the present study, the structural modifications and antigenic response of these bovine milk allergens as induced by non-thermal treatment by atmospheric cold plasma were investigated. Spark discharge (SD) and glow discharge (GD), as previously characterized cold plasma systems, were used for protein treatments. Casein, ß-lactoglobulin and α-lactalbumin were analyzed before and after plasma treatment using SDS-PAGE, FTIR, UPLC-MS/MS and ELISA. SDS-PAGE results revealed a reduction in the casein and α-lactalbumin intensity bands after SD or GD treatments; however, the ß-lactoglobulin intensity band remained unchanged. FTIR studies revealed alterations in protein secondary structure induced by plasma, particularly contents of ß-sheet and ß-turn. The UPLC-MS/MS results showed that the amino acid compositions decreased after plasma treatments. ELISA of casein and α-lactalbumin showed a decrease in antigenicity post plasma treatment, whereas ELISA of ß-lactoglobulin showed an increase in antigenicity. The study indicates that atmospheric cold plasma can be tailored to mitigate the risk of bovine milk allergens in the dairy processing and ingredients sectors.

Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.

The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/µL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.

Effects of cold plasma on wheat grain microbiome and antimicrobial efficacy against challenge pathogens and their resistance.

The safety and quality of cereal grain supplies are adversely impacted by microbiological contamination, with novel interventions required to maximise whole grains safety and stability. The microbiological contaminants of wheat grains and the efficacy of Atmospheric Cold Plasma (ACP) for potential to control these risks were investigated. The evaluations were performed using a contained reactor dielectric barrier discharge (DBD) system; samples were treated for 0-20 min using direct and indirect plasma exposure. Amplicon-based metagenomic analysis using bacterial 16S rRNA gene and fungal 18S rRNA gene with internal transcribed spacer (ITS) region was performed to characterize the change in microbial community composition in response to ACP treatment. The antimicrobial efficacy of ACP against a range of bacterial and fungal contaminants of wheat, was assessed to include individual isolates from grains as challenge pathogens. ACP influenced wheat microbiome composition, with a higher microbial diversity as well as abundance found on the untreated control grain samples. Culture and genomic approaches revealed different trends for mycoflora detection and control. A challenge study demonstrated that using direct mode of plasma exposure with 20 min of treatment significantly reduced the concentration of all pathogens. Overall, reduction levels for B. atrophaeus vegetative cells were higher than for all fungal species tested, whereas B. atrophaeus spores were the most resistant to ACP among all microorganisms tested. Of note, repeating sub-lethal plasma treatment did not induce resistance to ACP in either B. atrophaeus or A. flavus spores. ACP process control could be tailored to address diverse microbiological risks for grain stability and safety.

Assessing the Biological Safety of Atmospheric Cold Plasma Treated Wheat Using Cell and Insect Models.

Atmospheric cold plasma (ACP) is under investigation for an extensive range of biocontrol applications in food biosystems. However, the development of a novel intervention technology requires a thorough evaluation of the potential for negative effects and the implications for the human and animal food chains' safety. The evaluations were performed using a contained, high-voltage, dielectric barrier discharge plasma system. The cytotoxicity of two types of food models-a liquid model (wheat model medium (WMM)) vs. a solid model (wheat grain extract (WGE)) was compared in vitro using the mammalian cell line CHO-K1. The residual toxicity of ACP treatment of grains for food purposes was assessed using the invertebrate model Tribolium castaneum, by feeding the beetles with flour produced from ACP-treated wheat grains. The cytotoxic effects and changes in the chemistry of the ACP-treated samples were more pronounced in samples treated in a liquid form as opposed to actual wheat grains. The feeding trial using T. castaneum demonstrated no negative impacts on the survivability or weight profiles of insects. Investigations into the interactions of plasma-generated species with secondary metabolites in the food matrices are necessary to ensure the safety of plasma for food applications.

FOXO1 promotes HIV latency by suppressing ER stress in T cells.

Quiescence is a hallmark of CD4+ T cells latently infected with human immunodeficiency virus 1 (HIV-1). While reversing this quiescence is an effective approach to reactivate latent HIV from T cells in culture, it can cause deleterious cytokine dysregulation in patients. As a key regulator of T-cell quiescence, FOXO1 promotes latency and suppresses productive HIV infection. We report that, in resting T cells, FOXO1 inhibition impaired autophagy and induced endoplasmic reticulum (ER) stress, thereby activating two associated transcription factors: activating transcription factor 4 (ATF4) and nuclear factor of activated T cells (NFAT). Both factors associate with HIV chromatin and are necessary for HIV reactivation. Indeed, inhibition of protein kinase R-like ER kinase, an ER stress sensor that can mediate the induction of ATF4, and calcineurin, a calcium-dependent regulator of NFAT, synergistically suppressed HIV reactivation induced by FOXO1 inhibition. Thus, our studies uncover a link of FOXO1, ER stress and HIV infection that could be therapeutically exploited to selectively reverse T-cell quiescence and reduce the size of the latent viral reservoir.

Inactivation Efficacies and Mechanisms of Gas Plasma and Plasma-Activated Water against Aspergillus flavus Spores and Biofilms: a Comparative Study.

Atmospheric cold plasma (ACP) treatment is an emerging food technology for product safety and quality retention, shelf-life extension, and sustainable processing. The activated chemical species of ACP can act rapidly against microorganisms without leaving chemical residues on food surfaces. The main objectives of this study were to investigate the efficiency and mechanisms of inactivation of fungal spores and biofilms by ACP and to understand the effects of the gas-mediated and liquid-mediated modes of application against important fungal contaminants. Aspergillus flavus was selected as the model microorganism. A. flavus spores were exposed to either gas plasma (GP) or plasma-activated water (PAW), whereas gas plasma alone was used to treat A. flavus biofilms. This study demonstrated that both GP and PAW treatments independently resulted in significant decreases of A. flavus metabolic activity and spore counts, with maximal reductions of 2.2 and 0.6 log10 units for GP and PAW, respectively. The characterization of the reactive oxygen and nitrogen species in PAW and spore suspensions indicated that the concentration of secondary reactive species was an important factor influencing the antimicrobial activity of the treatment. The biofilm study showed that GP had detrimental effects on biofilm structure; however, the initial inoculum concentration prior to biofilm formation can be a crucial factor influencing the fungicidal effects of ACP.IMPORTANCE The production of mycotoxin-free food remains a challenge in both human and animal food chains. A. flavus, a mycotoxin-producing contaminant of economically important crops, was selected as the model microorganism to investigate the efficiency and mechanisms of ACP technology against fungal contaminants of food. Our study directly compares the antifungal properties of gas plasma (GP) and plasma-activated water (PAW) against fungi as well as reporting the effects of ACP treatment on biofilms produced by A. flavus.

The Effect of Plasma Treated Water Unit Processes on the Food Quality Characteristics of Fresh-Cut Endive.

This study evaluated the impact of a defined plasma treated water (PTW) when applied to various stages within fresh-cut endive processing. The quality characteristic responses were investigated to establish the impact of the PTW unit processes and where PTW may be optimally applied in a model process line to retain or improve produce quality. Different stages of application of PTW within the washing process were investigated and compared to tap water and chlorine dioxide. Fresh-cut endive (Cichorium endivia L.) samples were analyzed for retention of food quality characteristics. Measurements included color, texture, and nitrate quantification. Effects on tissue surface and cell organelles were observed through scanning electron and atomic force microscopy. Overall, the endive quality characteristics were retained by incorporating PTW in the washing process. Furthermore, promising results for color and texture characteristics were observed, which were supported by the microscopic assays of the vegetal tissue. While ion chromatography detected high concentrations of nitrite and nitrate in PTW, these did not affect the nitrate concentration of the lettuce tissue post-processing and were below the concentrations within EU regulations. These results provide a pathway to scale up the industrial application of PTW to improve and retain quality characteristic retention of fresh leafy products, whilst also harnessing the plasma functionalized water as a process intervention for reducing microbial load at multiple points, whether on the food surface, within the process water or on food-processing surfaces.

Efficacy of cold plasma functionalised water for improving microbiological safety of fresh produce and wash water recycling.

Atmospheric cold plasma (ACP) is an effective method for microbiological decontamination. This study evaluated an alternative water-based decontamination approach for inactivation of bacterial population from fresh produce and in the wash water generated from fresh produce washing. The study characterised ACP inactivation of attached Listeria innocua and Pseudomonas fluorescens inoculated on lettuce in comparison to chlorine treatment. P. fluorescens was sensitive to ACP treatment and was reduced below detection limit within 3 min of treatment. L. innocua population was reduced by ∼2.4 Log10 CFU/g after 5 min of treatment; showing similar inactivation efficacy to chlorine treatment. The microbial load in wash water was continuously decreased and was below detection limits after 10 min of ACP treatment. Micro-bubbling along with agitation assisted the bacterial detachment and distribution of reactive species, thus increasing bacterial inactivation efficacy from fresh produce and wash water. A shift in pH of plasma functionalised water was observed along with high concentration of nitrate and ozone with a relative amount of nitrites which increased with plasma exposure time. Further, L. innocua treated at different independent pH conditions showed minimal or no effect of pH on ACP bacterial inactivation efficacy. Aqueous ACP treatment poses a promising alternative for decontamination of fresh produce and the associated wash-waters which could be applied in the food industry to replace continuous chlorine dosing of process waters.

Degradation kinetics of cold plasma-treated antibiotics and their antimicrobial activity.

Antibiotics, such as ofloxacin (OFX) and ciprofloxacin (CFX), are often detected in considerable concentrations in both wastewater effluents and surface water. This poses a risk to non-target organisms and to human health. The aim of this work was to study atmospheric cold plasma (ACP) degradation of antibiotics in water and meat effluent and to explore any residual antimicrobial activity of samples submitted to the plasma process. The results revealed that ACP successfully degraded the studied antibiotics and that the reaction mechanism is principally related to attack by hydroxyl radicals and ozone. According to the disk diffusion assay, the activity of both antibiotics was considerably reduced by the plasma treatment. However, a microdilution method demonstrated that CFX exhibited higher antimicrobial activity after ACP treatment than the corresponding control revealing a potentially new platform for future research to improve the efficiency of conventional antibiotic treatments. Importantly, short-term exposures to sub-lethal concentrations of the antibiotic equally reduced bacterial susceptibility to both ACP treated and untreated CFX. As a remediation process, ACP removal of antibiotics in complex wastewater effluents is possible. However, it is recommended that plasma encompass degradant structure activity relationships to ensure that biological activity is eliminated against non-target organisms and that life cycle safety of antibiotic compounds is achieved.

The Effect of Atmospheric Cold Plasma on Bacterial Stress Responses and Virulence Using Listeria monocytogenes Knockout Mutants.

Listeria monocytogenes is an opportunistic intracellular pathogen commonly associated with serious infections and multiple food-borne outbreaks. In this study, we investigated the influence of atmospheric cold plasma (80 kV, 50 Hz) on L. monocytogenes (EGD-e) and its knockout mutants of sigB, rsbR, prfA, gadD, and lmo0799 genes at different treatment time intervals. Further, to ascertain if sub-lethal environmental stress conditions could influence L. monocytogenes survival and growth responses, atmospheric cold plasma (ACP) resistance was evaluated for the cultures exposed to cold (4°C) or acid (pH 4) stress for 1 h. The results demonstrate that both wild-type and knockout mutants were similarly affected after 1 min exposure to ACP (p > 0.05), with a difference in response noted only after 3 min of treatment. While all L. monocytogenes strains exposed to acid/cold stress were hypersensitive to ACP treatment and were significantly reduced or inactivated within 1 min of treatment (p < 0.05). The results indicate sigB and prfA are important for general stress resistance and biofilm, respectively, loss of these two genes significantly reduced bacterial resistance to ACP treatment. In addition, exposure to sub-lethal 1min ACP increased the gene expression of stress associated genes. SigB showed the highest gene expression, increasing by 15.60 fold, followed by gadD2 (7.19) and lmo0799 (8.6) after 1 min exposure. Overall, an increase in gene expression was seen in all stress associated genes analyzed both at 1 min treatment; while long treatment time reduced the gene expression and some cases down-regulated prfA and gadD3 gene expression. By comparing the response of mutants under ACP exposure to key processing parameters, the experimental results presented here provide a baseline for understanding the bacterial genetic response and resistance to cold plasma stress and offers promising insights for optimizing ACP applications.

Efficacy of Cold Plasma for Direct Deposition of Antibiotics as a Novel Approach for Localized Delivery and Retention of Effect.

Antimicrobial coating of medical devices has emerged as a potentially effective tool to prevent or ameliorate device-related infections. In this study the plasma deposition process for direct deposition of pharmaceutical drugs on to a range of surfaces and the retention of structure function relationship and antimicrobial efficacy against mono-species biofilms were investigated. Two selected sample antibiotics-ampicillin and gentamicin, were deposited onto two types of surfaces-polystyrene microtiter plates and stainless steel coupons. The antimicrobial efficacy of the antibiotic-coated surfaces was tested against challenge populations of both planktonic and sessile Escherichia coli and Pseudomonas aeruginosa, with responses monitored for up to 14 days. The plasma deposition process bonded the antibiotic to the surfaces, with localized retention of antibiotic activity. The antibiotics deposited on the test surfaces retained a good efficacy against planktonic cells, and importantly prevented biofilm formation of attached cells for up to 96 h. The antibiotic rapidly eluted from the surface of antibiotic-coated surfaces to the surrounding medium, with retention of effect in this surrounding milieu for up to 2 weeks. Control experiments established that there was no independent antimicrobial or growth promoting effect of the plasma deposition process, where there was no antibiotic in the helium plasma assisted delivery stream. Apart from the flexibility offered through deposition on material surfaces, there was no additive or destructive effect associated with the helium assisted plasma deposition process on the antibiotic. The plasma assisted process was a viable mean of coating clinically relevant materials and developing innovative functional materials with retention of antibiotic activity, without employing a linker or plasma modified polymer, thus minimizing bio-compatibility issues for medical device materials. This offers potential to prevent or control instrumented or non-permanent device associated infection localized to the surgical or implant site.

Cold atmospheric plasma is a viable solution for treating orthopedic infection: a review.

Bacterial infection and antibiotic resistance are major threats to human health and very few solutions are available to combat this eventuality. A growing number of studies indicate that cold (non-thermal) plasma treatment can be used to prevent or eliminate infection from bacteria, bacterial biofilms, fungi and viruses. Mechanistically, a cold plasma discharge is composed of high-energy electrons that generate short-lived reactive oxygen and nitrogen species which further react to form more stable compounds (NO2, H2O2, NH2Cl and others) depending on the gas mixture and plasma parameters. Cold plasma devices are being developed for medical applications including infection, cancer, plastic surgery applications and more. Thus, in this review we explore the potential utility of cold plasma as a non-antibiotic approach for treating post-surgical orthopedic infections.