Functional and transcriptional profiling of non-coding RNAs in yeast reveal context-dependent phenotypes and in trans effects on the protein regulatory network.

Non-coding RNAs (ncRNAs), including the more recently identified Stable Unannotated Transcripts (SUTs) and Cryptic Unstable Transcripts (CUTs), are increasingly being shown to play pivotal roles in the transcriptional and post-transcriptional regulation of genes in eukaryotes. Here, we carried out a large-scale screening of ncRNAs in Saccharomyces cerevisiae, and provide evidence for SUT and CUT function. Phenotypic data on 372 ncRNA deletion strains in 23 different growth conditions were collected, identifying ncRNAs responsible for significant cellular fitness changes. Transcriptome profiles were assembled for 18 haploid ncRNA deletion mutants and 2 essential ncRNA heterozygous deletants. Guided by the resulting RNA-seq data we analysed the genome-wide dysregulation of protein coding genes and non-coding transcripts. Novel functional ncRNAs, SUT125, SUT126, SUT035 and SUT532 that act in trans by modulating transcription factors were identified. Furthermore, we described the impact of SUTs and CUTs in modulating coding gene expression in response to different environmental conditions, regulating important biological process such as respiration (SUT125, SUT126, SUT035, SUT432), steroid biosynthesis (CUT494, SUT053, SUT468) or rRNA processing (SUT075 and snR30). Overall, these data capture and integrate the regulatory and phenotypic network of ncRNAs and protein-coding genes, providing genome-wide evidence of the impact of ncRNAs on cellular homeostasis.

Effect of different types of adhesive systems on the bond strength and marginal integrity of composite restorations in cavities prepared with the erbium laser-a systematic review.

There are inconclusive results regarding etching and bonding protocol to achieve optimal bond strength and marginal integrity of adhesive composite resin restorations in erbium laser prepared cavities. This systematic review aimed to consider which adhesive system protocol may be optimal in achieving the bond strength and marginal integrity in erbium laser-prepared cavities, comparable to that obtained with conventional method of cavity preparation. This review was developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement with literature search based on all publications during the period January1, 2000-October 10, 2020, in three databases: MEDLINE, Google Scholar and ScienceDirect. The necessary information was extracted by two independent authors. The search resulted in 139 articles from all databases, and a total of thirty-one articles met the inclusion criteria. The results indicated that the selection of adhesives depending on their pH and composition and the laser pulse duration and pulse energy used plays an important role in predicting the adhesion and marginal integrity. The 10-MDP containing moderate self-etch adhesives has demonstrated predictable outcomes. Longer pulse durations used for cavity preparations may indicate the use of etch-and-rinse (EnR) or moderate self-etch adhesives (SEA) to allow better resin infiltration in deep craters formed due to laser irradiation. However, further studies with more standardizations in relation to adhesives and laser parameters are needed.

The influence of delivery power losses and full operating parametry on the effectiveness of diode visible-near infra-red (445-1064 nm) laser therapy in dentistry-a multi-centre investigation.

The development of protocols for laser-assisted therapy demands strict compliance with comprehensive operating parametry. The purpose of this investigation was to examine the accuracy of correlation between laser control panel and fibre emission power values in a selection of diode dental lasers. Through retrospective analysis using successive systematic review and meta-analysis, it is clear that there is inconsistency in the details, and possible inaccuracies in laser power applied and associated computed data. Through a multi-centre investigation, 38 semi-conductor ("diode") dental laser units were chosen, with emission wavelengths ranging from 445 to 1064 nm. Each unit had been recently serviced according to manufacturer's recommendations, and delivery fibre assembly checked for patency and correct alignment with the parent laser unit. Subject to the output capacity of each laser, four average power values were chosen using the laser control panel-100 mW, 500 mW, 1.0 W, and 2.0 W. Using a calibrated power meter, the post-fibre emission power value was measured, and a percentage power loss calculated. For each emission, a series of six measurements were made and analysed to investigate sources of power losses along the delivery fibre, and to evaluate the precision of power loss determinations. Statistical analysis of a dataset comprising % deviations from power setting levels was performed using a factorial ANOVA model, and this demonstrated very highly significant differences between devices tested and emission power levels applied (p < 10-142 and < 10-52 respectively). The devices × emission power interaction effect was also markedly significant (p < 10-66), and this confirmed that differences observed in these deviations for each prior power setting parameter were dependent on the device employed for delivery. Power losses were found to be negatively related to power settings applied. Significant differences have emerged to recommend the need to standardize a minimum set of parameters that should form the basis of comparative research into laser-tissue interactions, both in vitro and in vivo.

Large-scale profiling of noncoding RNA function in yeast.

Noncoding RNAs (ncRNAs) are emerging as key regulators of cellular function. We have exploited the recently developed barcoded ncRNA gene deletion strain collections in the yeast Saccharomyces cerevisiae to investigate the numerous ncRNAs in yeast with no known function. The ncRNA deletion collection contains deletions of tRNAs, snoRNAs, snRNAs, stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs) and other annotated ncRNAs encompassing 532 different individual ncRNA deletions. We have profiled the fitness of the diploid heterozygous ncRNA deletion strain collection in six conditions using batch and continuous liquid culture, as well as the haploid ncRNA deletion strain collections arrayed individually onto solid rich media. These analyses revealed many novel environmental-specific haplo-insufficient and haplo-proficient phenotypes providing key information on the importance of each specific ncRNA in every condition. Co-fitness analysis using fitness data from the heterozygous ncRNA deletion strain collection identified two ncRNA groups required for growth during heat stress and nutrient deprivation. The extensive fitness data for each ncRNA deletion strain has been compiled into an easy to navigate database called Yeast ncRNA Analysis (YNCA). By expanding the original ncRNA deletion strain collection we identified four novel essential ncRNAs; SUT527, SUT075, SUT367 and SUT259/691. We defined the effects of each new essential ncRNA on adjacent gene expression in the heterozygote background identifying both repression and induction of nearby genes. Additionally, we discovered a function for SUT527 in the expression, 3' end formation and localization of SEC4, an essential protein coding mRNA. Finally, using plasmid complementation we rescued the SUT075 lethal phenotype revealing that this ncRNA acts in trans. Overall, our findings provide important new insights into the function of ncRNAs.

Rapid prototyping of microbial production strains for the biomanufacture of potential materials monomers.

Bio-based production of industrial chemicals using synthetic biology can provide alternative green routes from renewable resources, allowing for cleaner production processes. To efficiently produce chemicals on-demand through microbial strain engineering, biomanufacturing foundries have developed automated pipelines that are largely compound agnostic in their time to delivery. Here we benchmark the capabilities of a biomanufacturing pipeline to enable rapid prototyping of microbial cell factories for the production of chemically diverse industrially relevant material building blocks. Over 85 days the pipeline was able to produce 17 potential material monomers and key intermediates by combining 160 genetic parts into 115 unique biosynthetic pathways. To explore the scale-up potential of our prototype production strains, we optimized the enantioselective production of mandelic acid and hydroxymandelic acid, achieving gram-scale production in fed-batch fermenters. The high success rate in the rapid design and prototyping of microbially-produced material building blocks reveals the potential role of biofoundries in leading the transition to sustainable materials production.

Infectious Diseases Specialty Intervention Is Associated With Better Outcomes Among Privately Insured Individuals Receiving Outpatient Parenteral Antimicrobial Therapy.

BACKGROUND: Outpatient parenteral antimicrobial therapy (OPAT) can be managed by specialists in infectious diseases (ID) or by other physicians. Better management of OPAT can reduce the likelihood of readmission or emergency department (ED) use. The relative success of ID specialists and other physicians in managing OPAT has received little study. METHODS: We analyzed a national database of insurance claims for privately insured individuals under age 65, locating inpatient acute-care stays in 2013 and 2014 that were followed by OPAT. Through propensity scoring, patients who received outpatient ID intervention (ID-led OPAT) were matched 1-to-1 with those who did not (Other OPAT). We estimated regression models of hospital and ED admissions and of total healthcare payments over the first 30 days after discharge. RESULTS: The final analytic sample of 8200 observations was well balanced on clinical and demographic characteristics. Soft-tissue infection and osteomyelitis were the most common infections in the index event, each affecting more than 40% of individuals. Relative to those with Other OPAT, people with ID-led OPAT had lower odds of an ED admission (odds ratio [OR] 0.449, 95% confidence interval [CI] 0.311-0.645) or hospitalization (OR 0.661, 95% CI 0.557-0.791) over 30 days, and they accumulated $1488 less in total healthcare payments (95% CI -2 688.56--266.58). CONCLUSIONS: Among privately insured individuals below age 65, ID consultations during OPAT are associated with large and significant reductions in the rates of ED admission and hospital admission in the 30 days after index events, as well as lower total healthcare spending.

A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae.

Eukaryotic genomes are extensively transcribed, generating many different RNAs with no known function. We have constructed 1502 molecular barcoded ncRNA gene deletion strains encompassing 443 ncRNAs in the yeast Saccharomyces cerevisiae as tools for ncRNA functional analysis. This resource includes deletions of small nuclear RNAs (snRNAs), transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and other annotated ncRNAs as well as the more recently identified stable unannotated transcripts (SUTs) and cryptic unstable transcripts (CUTs) whose functions are largely unknown. Specifically, deletions have been constructed for ncRNAs found in the intergenic regions, not overlapping genes or their promoters (i.e., at least 200 bp minimum distance from the closest gene start codon). The deletion strains carry molecular barcodes designed to be complementary with the protein gene deletion collection enabling parallel analysis experiments. These strains will be useful for the numerous genomic and molecular techniques that utilize deletion strains, including genome-wide phenotypic screens under different growth conditions, pooled chemogenomic screens with drugs or chemicals, synthetic genetic array analysis to uncover novel genetic interactions, and synthetic dosage lethality screens to analyze gene dosage. Overall, we created a valuable resource for the RNA community and for future ncRNA research.

Correction to: Outpatient erbium:YAG (2940 nm) laser treatment for snoring: a prospective study on 40 patients.

In the originally published article, the name of the first author was incorrectly labeled. Given name is Isabelle and family name is Fini Storchi.

Outpatient erbium:YAG (2940 nm) laser treatment for snoring: a prospective study on 40 patients.

Snoring is a sleep phenomenon due to the partial upper airway obstruction during sleep which causes vibration of the tissues of the rhino-oro-hypopharynx and less frequently the larynx. This study evaluated the use and effectiveness of the erbium:YAG 2940-nm laser as an adjunctive in providing treatment for patients suffering from chronic snoring-related sleep disorders. A prospective study of 40 consecutive patients with snoring and sleep disorders was performed, assessing data before and after three Er:YAG laser treatment sessions. During laser treatment, the pain was almost absent. There were no side effects, except a very mild sore throat in 1 out of 40 patients. The patient's evaluation of satisfaction of the results obtained after the treatments showed that 85% of cases were very satisfied, 5 patients (12.5%) reported being fairly satisfied with the treatment and only 1 subject (2.5%) was not satisfied. Mallampati, Friedman Tongue Position, and degree of O (oropharynx) at nose oropharynx hypopharynx and larynx classification were significantly decreased after the laser sessions. The decrease of Epworth Sleepiness Scale and Visual Analogue Scale for loudness of snoring, waking up during sleep because of snoring, dry mouth on waking, and choking was all statistically significant. The incidence of dreaming during the night also raised significantly; 30/40 (75%) of cases perceived less tightness in their throat and better breathing after treatment. These results were stable at 20 months follow-up (14-24 q) in 72% of cases. Nonsurgical and non-invasive Er:YAG laser treatment demonstrated to be a valid procedure in reducing the loudness of snoring.

Non-coding RNAs and disease: the classical ncRNAs make a comeback.

Many human diseases have been attributed to mutation in the protein coding regions of the human genome. The protein coding portion of the human genome, however, is very small compared with the non-coding portion of the genome. As such, there are a disproportionate number of diseases attributed to the coding compared with the non-coding portion of the genome. It is now clear that the non-coding portion of the genome produces many functional non-coding RNAs and these RNAs are slowly being linked to human diseases. Here we discuss examples where mutation in classical non-coding RNAs have been attributed to human disease and identify the future potential for the non-coding portion of the genome in disease biology.

808-nm laser therapy with a flat-top handpiece photobiomodulates mitochondria activities of Paramecium primaurelia (Protozoa).

Photobiomodulation is proposed as a non-linear process, and only low-level laser therapy (LLLT) is assumed to stimulate exposed cells, whereas high powered laser and fluences can cause negative effects, exhausting the cell's energy reserve as a consequence of excessive photon-based stimulation. In our work, we investigated and compared the effects of 808-nm diode laser (CW) with a new flat-top handpiece. To this purpose, we tested the photobiomodulation effects of 1 and 3 J/cm(2) fluence, both generated by 100 mW or 1 W of laser power and of 64 J/cm(2) of fluence generated by 100 mW, 1 W, 1.5 W or 2 W, as expressed through oxygen consumption and ATP synthesis of Paramecium. Data collected indicates the incremental consumption of oxygen through irradiation with 3 J/cm(2)-100 mW or 64 J/cm(2)-1 W correlates with an increase in Paramecium ATP synthesis. The Paramecium respiration was inhibited by fluences 64 J/cm(2)-100 mW or 64 J/cm(2)-2 W and was followed by a decrease in the endogenous ATP concentration. The 1 J/cm(2)-100 mW or 1 W and 3 J/cm(2)-1 W did not affect mitochondrial activity. The results show that the fluence of 64 J/cm(2)-1 W more than the 3 J/cm(2)-100 mW causes greater efficiency in Paramecium mitochondria respiratory chain activity. Our results suggest that thanks to flat-top handpiece we used, high fluences by high-powered laser have to be reconsidered as an effective and non-invasive therapy. Possible associated benefits of deeper tissue penetration would increase treatment effectiveness and reduced irradiation time.

The protozoan, Paramecium primaurelia, as a non-sentient model to test laser light irradiation: The effects of an 808nm infrared laser diode on cellular respiration.

Photobiomodulation (PBM) has been used in clinical practice for more than 40 years. Unfortunately, conflicting literature has led to the labelling of PBM as a complementary or alternative medicine approach. However, past and ongoing clinical and research studies by reputable investigators have re-established the merits of PBM as a genuine medical therapy, and the technique has, in the last decade, seen an exponential increase in the numbers of clinical instruments available, and their applications. This resurgence has led to a clear need for appropriate experimental models to test the burgeoning laser technology being developed for medical applications. In this context, an ethical model that employs the protozoan, Paramecium primaurelia, is proposed. We studied the possibility of using the measure of oxygen consumption to test PBM by irradiation with an infrared or near-infrared laser. The results show that an 808nm infrared laser diode (1W; 64J/cm²) affects cellular respiration in P. primaurelia, inducing, in the irradiated cells, a significantly (p < 0.05) increased oxygen consumption of about 40%. Our findings indicate that Paramecium can be an excellent tool in biological assays involving infrared and near-infrared PBM, as it combines the advantages of in vivo results with the practicality of in vitro testing. This test represents a fast, inexpensive and straightforward assay, which offers an alternative to both traditional in vivo testing and more expensive mammalian cellular cultures.

On the expansion of ribosomal proteins and RNAs in eukaryotes.

While the ribosome constitution is similar in all biota, there is a considerable increase in size of both ribosomal proteins (RPs) and RNAs in eukaryotes as compared to archaea and bacteria. This is pronounced in the large (60S) ribosomal subunit (LSU). In addition to enlargement (apparently maximized already in lower eukarya), the RP changes include increases in fraction, segregation and clustering of basic residues, and decrease in hydrophobicity. The acidic fraction is lower in eukaryote as compared to prokaryote RPs. In all eukaryote groups tested, the LSU RPs have significantly higher content of basic residues and homobasic segments than the SSU RPs. The vertebrate LSU RPs have much higher sequestration of basic residues than those of bacteria, archaea and even of the lower eukarya. The basic clusters are highly aligned in the vertebrate, but less in the lower eukarya, and only within families in archaea and bacteria. Increase in the basicity of RPs, besides helping transport to the nucleus, should promote stability of the assembled ribosome as well as the association with translocons and other intracellular matrix proteins. The size and GC nucleotide bias of the expansion segments of large LSU rRNAs also culminate in the vertebrate, and should support ribosome association with the endoplasmic reticulum and other intracellular networks. However, the expansion and nucleotide bias of eukaryote LSU rRNAs do not clearly correlate with changes in ionic parameters of LSU ribosomal proteins.

Toxoplasma gondii: prevalence in species and genotypes of British bats (Pipistrellus pipistrellus and P. pygmaeus).

Few studies have investigated Toxoplasma gondii infections in bat populations and none have reported its presence in protected British bat species. Using a collection of dead/euthanased bats collected from Lancashire, UK, two species of bats (Pipistrellus pipistrellus and Pipistrellus pygmaeus) were tested using a highly sensitive SAG1-PCR method specific for detection of T. gondii DNA (n=77; 71 P. pipistrellus and 6 P. pygmaeus). Whilst some potential bias may exist in the sampling strategy, an overall prevalence of 10.39% (±6.06%; 95%CI) was detected. All P. pipistrellus, were also genotyped using eleven polymorphic microsatellite loci to determine their local population structure. The programme STRUCTURE revealed that the majority of individuals (83%) were derived from one interbreeding population, and the remaining individuals (17%) had mixed genetic origins. There was no significant difference in the frequency of T. gondii infection or geographical distribution between subclusters. As all British bats are insectivorous, the routes of infection with T. gondii remain elusive. However, the locally large and panmictic gene pool suggests that intraspecies transmission could be applicable.

Dimers of G-protein coupled receptors as versatile storage and response units.

The status and use of transmembrane, extracellular and intracellular domains in oligomerization of heptahelical G-protein coupled receptors (GPCRs) are reviewed and for transmembrane assemblies also supplemented by new experimental evidence. The transmembrane-linked GPCR oligomers typically have as the minimal unit an asymmetric ~180 kDa pentamer consisting of receptor homodimer or heterodimer and a G-protein αßγ subunit heterotrimer. With neuropeptide Y (NPY) receptors, this assembly is converted to ~90 kDa receptor monomer-Gα complex by receptor and Gα agonists, and dimers/heteropentamers are depleted by neutralization of Gαi subunits by pertussis toxin. Employing gradient centrifugation, quantification and other characterization of GPCR dimers at the level of physically isolated and identified heteropentamers is feasible with labeled agonists that do not dissociate upon solubilization. This is demonstrated with three neuropeptide Y (NPY) receptors and could apply to many receptors that use large peptidic agonists.

Full operating parameter recording as an essential component of the reproducibility of laser-tissue interaction and treatments.

BACKGROUND: The number and diversity of published peer-reviewed studies in the discipline of laser dentistry have grown considerably during the past 10 years. OBJECTIVES: Within primary research, the development of protocols to guide and formulate clinical practice demands precision and ease of reproducibility. Errors in data acquisition and management may become amplified as the applied randomized clinical trials (RCTs) forge new levels of clinical diversity and predictability in the use of laser photonic energy in both ablative (surgical) and sub-ablative (photobiomodulation (PBM) or photodynamic therapy (PDT)) applications. MATERIAL AND METHODS: A comprehensive range of empirical and computational operating parameters must be included in published studies to facilitate the uniformity of powerand time-related values of laser irradiation. RESULTS: Choosing the correct "tissue irradiation parameters" is difficult and depends on the pathology and symptoms, the surface area to be treated, laser wavelength, the thermal relaxation time of each targeted tissue, and controlling penetration depth of the light into tissues. Therefore, to allow the reproducibility of the results, it is recommended that authors mention with the greatest care and clarity the irradiation parameters used in their study. CONCLUSION: This paper outlines the concerns felt regarding the general shortfalls and proposes a minimum range of laser operating parameters that should be represented in future peer-reviewed publications.

Photothermal Effects of High-Energy Photobiomodulation Therapies: An In Vitro Investigation.

The purpose of this study was to investigate photothermal aspects of photobiomodulation therapies (PBMT) in vitro to assist in the development of safe clinical parameters with respect to higher-power devices with large surface applicators. Laser wavelengths in the range of 650 nm-1064 nm were investigated using a thermal camera. Thermographic measures of surface and sub-surface temperature variations of similar lean porcine muscle tissue samples were recorded for a series of calibrated experiments. A thermal comparison was then made between Flat-top and Gaussian beam spatial distribution devices. Outcome data were subjected to statistical analysis using an ANOVA model. Results acquired at similar parameters of irradiance indicated that the application of the 980 nm wavelength was associated with the highest rise in temperature, which decreased with other wavelengths in the order 980 > 1064 ≈ 650 >>> 810 nm (p < 5 × 10-20). All wavelengths assessed were associated with a significant temperature increase, and with the exception of 810 nm, all exceeded the threshold of a 6 °C rise within the prescribed parameter limits. Optical scanning by movement of the applied source over a relevant area was found to offer effective mitigation of these temperature increases. An extended discussion is presented, analysing the clinical significance of the study outcomes. Recommendations are made within the limits of this in vitro study in order to assist future clinical investigations.

Anti-biofilm and bystander effects of antimicrobial photo-sonodynamic therapy against polymicrobial periopathogenic biofilms formed on coated orthodontic mini-screws with zinc oxide nanoparticles.

BACKGROUND: The present study evaluated the anti-biofilm and bystander effects of antimicrobial photo-sonodynamic therapy (aPSDT) on the polymicrobial periopathogenic biofilms formed on mini-screws coated with zinc oxide nanoparticles (ZnONPs). MATERIALS AND METHODS: Thirty orthodontic identical mini-screws were divided into 6 groups (n = 5) as follows: 1. negative control: uncoated mini-screw + phosphate-buffered saline (PBS), 2. positive control: uncoated mini-screw + 0.2% CHX, 3. coating control: coated mini-screw + PBS, 4. antimicrobial photodynamic therapy (aPDT): coated mini-screw+light emitting diode (LED), 5. Antimicrobial sonodynamic therapy (aSDT): coated mini-screw+ultrasound waves, and 6. aPSDT: coated mini-screw+LED+ultrasound waves. Electrostatic spray-assisted vapor deposition was employed to coat ZnONPs on titanium mini-screws. The biofilm inhibition test was used to assess the anti-biofilm efficacy against polymicrobial periopathogenic biofilms including Porphyromonas gingivitis, Prevotella intermedia, and Aggregatibacter actinomycetemcomitans, and the results were shown as the percent reduction of Log10 colony-forming unit (CFU)/mL. Following each treatment, the gene expression levels of TNF-α, IL-1ß, and IL-6 were evaluated on human gingival fibroblast (HGF) cells via quantitative real-time polymerase chain reaction (qRT-PCR) to reveal the bystander effects of aPSDT on HGF cells. RESULTS: A significant reduction in log10 CFU/mL of periopathogens was observed in groups treated with aPDT, aSDT, aPSDT, and 0.2% CHX up to 6.81, 6.63, 5.02, and 4.83 log, respectively, when compared with control groups (P<0.05). 0.2% CHX and aPSDT groups demonstrated significantly higher capacity in eliminating the periopathogen biofilm compared with other groups (P<0.05). The qRT-PCR showed that the expression level of inflammatory cytokines was significantly down regulated in aPDT, aSDT, and aPSDT groups (P<0.05). CONCLUSION: It was found that the ZnONPs-mediated aPSDT could significantly reduce periopathogen biofilm as well as the expression level of inflammatory cytokines.

Effects of Kojic Acid-mediated Sonodynamic Therapy as a Matrix Metalloprotease-9 Inhibitor against Oral Squamous Cell Carcinoma: A Bioinformatics Screening and in vitro Analysis.

BACKGROUND: Oral squamous cell carcinoma (OSCC) is a type of cancer that is responsible for a significant amount of morbidity and mortality worldwide. Researchers are searching for promising therapeutic methods to manage this cancer. In this study, an in silico approach was used to evaluate the activity of sonodynamic therapy (SDT) based on the use of Kojic acid as a sonosensitizer to inhibit matrix metalloprotease-9 (MMP-9) in OSCC. MATERIALS AND METHODS: The three-dimensional structure of MMP-9 was predicted and validated by computational approaches. The possible functional role of MMP-9 was determined in terms of Gene Ontology (GO) enrichment analysis. In silico, molecular docking was then performed to evaluate the binding energies of Kojic acid with MMP-9, and ADME parameters and toxicity risks were predicted. The pharmacokinetics and drug-likeness properties of Kojic acid were assessed. Moreover, after the determination of the cytotoxicity effect of Kojic acid-mediated SDT, the change of mmp-9 gene expression was assessed on OSCC cells. RESULTS: The results of the study showed that Kojic acid could efficiently interact with MMP-9 protein with a strong binding affinity. Kojic acid obeyed Lipinski's rule of five without violation and exhibited drug-likeness. The cytotoxic effects of Kojic acid and ultrasound waves on the OSCC cells were dose-dependent, and the lowest expression level of the mmp-9 gene was observed in SDT. CONCLUSIONS: Overall, Kojic acid-mediated SDT as an MMP-9 inhibitor can be a promising adjuvant treatment for OSCC. The study highlights the potential of in silico approaches to evaluate therapeutic methods for cancer treatment.

Enhancement of hypericin nanoparticle-mediated sonoinduced disruption of biofilm and persister cells of Streptococcus mutans by dermcidin-derived peptide DCD-1L.

BACKGROUND: Streptococcus mutans is considered a major significant contributor to dental caries and its effective removal is difficult due to the formation of biofilm. Therefore, the development of adjuvant therapeutic strategies with anti-biofilm properties is a promising approach. In the present study, we examined the effect of dermcidin-derived peptide DCD-1 L on the antibacterial activity of hypericin nanoparticle (HypNP)-mediated antimicrobial sonodynamic therapy (aSDT) against persister cells growing- and biofilm cultures of S. mutans. MATERIALS AND METHODS: Following synthesis and confirmation of HypNP, the fractional inhibitory concentration (FIC) index of HypNP and DCD-1 L was determined by checkerboard assay. Cellular uptake of HypNP-DCD-1 L and generation of endogenous reactive oxygen species (ROS) were assessed and followed by the determination of antimicrobial sonoactivity of HypNP-DCD-1 L against persister cells growing- and biofilm cultures of S. mutans. The water-insoluble extracellular polysaccharide (EPS) and expression of the gtfD, comDE, and smuT genes were then evaluated in persister cells growing- and biofilm cultures of S. mutans. RESULTS: There was a synergistic activity in the combination of HypNP and DCD-1 L against S. mutans with an FIC index value of 0.37. The HypNP-DCD-1L-mediated aSDT also displayed the highest cellular uptake and endogenous ROS generation by bacterial cells. When biofilm and persister cells of S. mutans were treated with HypNP-DCD-1 L and subsequently exposed to ultrasound waves, 5.1 log and 3.8 log reductions, respectively, in bacterial numbers were observed (P<0.05). According to the data, EPS in both persister cells growing- and biofilm cultures of S. mutans were significantly decreased after exposure to the HypNP-DCD-1L-mediated aSDT (P<0.05). In addition, the quantitative real-time PCR data illustrated the high level of similarities in very low-expression profiles of the gtfD before and after all treated groups for persister cells. While, following HypNP-DCD-1L-mediated aSDT treatment, the expression levels of gtfD, comDE, and smuT were significantly lower in treated persister cells growing- and biofilm cultures of S. mutans in comparison with control groups (P<0.05). CONCLUSIONS: Combined, the results of this study indicate that ultrasound waves-activated HypNP-DCD-1 L can sonoinactivate S. mutans biofilms and persister cells, as well as reduce effectively pathogenicity potency of S. mutans. Hence, HypNP-DCD-1L-mediated aSDT may be proposed as a promising adjunctive therapeutic approach for dental caries.