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OBJECTIVE: The objective of this study was to investigate the mediators and the resident peritoneal cells involved in the neutrophil migration (NM) induced by mineral trioxide aggregate (MTA) in mice. STUDY DESIGN: MTA (25 mg/cavity) was injected into normal and pretreated peritoneal cavities (PC) with indomethacin (IND), dexamethasone (DEX), BWA4C, U75302, antimacrophage inflammatory protein-2 (MIP-2), and anti-interleukin-1[beta] (IL-1[beta]) antibodies and the NM was determined. The role of macrophage (MO) and mast cells (MAST) was determined by administration of thioglycollate 3% or 48/80 compound, respectively. The concentration of IL-1[beta] and MIP-2 exudates was measured by ELISA. RESULTS: MTA induced dose- and time-dependent NM into mice PC, with the participation of MO and MAST. NM was inhibited by DEX, BWA4C, and U75302, as well as anti-MIP-2 and anti-IL-1[beta] antibodies. In the exudates, IL-1[beta] and MIP-2 were detected. CONCLUSIONS: This study suggests that MTA induces NM via a mechanism dependent on MAST and MO mediated by IL-1[beta], MIP-2, and LTB[4]. [ABSTRACT FROM AUTHOR]

Calcium silicate-based sealers are bioactive materials that release ions when in contact with body fluids. Therefore, this study aims mapping/trace bone formation markers released by MTA Fillapex, BioRoot RCS, and experimental tricalcium silicate-based sealer (CEO) into subcutaneous tissues, bloodstream and body organs. Toward, polyethylene tubes filled with sealers were implanted into connective tissue of Wistar rats. On days 7, 15, 30, and 45 after implantation, blood samples were collected to measure calcium (Ca 2+ ), phosphorus (P), and alkaline phosphatase (ALP) levels. Thereafter, the animals were killed, and the brain, liver, kidneys, and subcutaneous tissue were removed and processed to determine the concentrations of Ca 2+ and P by ICP-OES. Similar Ca 2+ levels were observed in subcutaneous tissue for all groups, although, at 45 days, it was identified a reduction in Ca 2+ serum levels of CEO compared to those two other sealers and an increase in Ca 2+ levels in the liver compared to those released by MTA Fillapex. In contrast, no trace of P was detected in any tissue; moreover, plasma P and ALP serum levels of MTA Fillapex were higher at day 30. Our findings showed that Ca 2+ were identified in local tissues, bloodstream, and organs from all sealers. The up-regulation of bone marker levels promoted by sealers can modify body homeostasis and induce tissue damage. Besides, MTA Fillapex was associated with a raise of bone marker levels, suggesting a possible systemic effect. The sealer composition can affect not only the local repair process but also the systemic health., (© 2024. The Author(s), under exclusive licence to The Society of The Nippon Dental University.)

Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for causing Coronavirus Disease-2019 (COVID-19), a heterogeneous clinical condition that manifests varying symptom severity according to the demographic profile of the studied population. While many studies have focused on the spread of COVID-19 in large urban centers in Brazil, few have evaluated medium or small cities in the Northeast region. The aims of this study were: (i) to identify risk factors for mortality from SARS-CoV-2 infection, (ii) to evaluate the gene expression patterns of key immune response pathways using nasopharyngeal swabs of COVID-19 patients, and (iii) to identify the circulating SARS-CoV-2 variants in the residents of a medium-sized city in Northeast Brazil. A total of 783 patients infected with SARS-CoV-2 between May 2020 and August 2021 were included in this study. Clinical-epidemiological data from patients who died and those who survived were compared. Patients were also retrospectively divided into three groups based on disease severity: asymptomatic, mild, and moderate/severe. Samples were added to a qPCR array for analyses of 84 genes involved with immune response pathways and sequenced using the Oxford Nanopore MinION technology. Having pre-existing comorbidity; being male; having cardiovascular disease, diabetes, and/or chronic obstructive pulmonary disease; and PCR cycle threshold (Ct) values under 22 were identified as risk factors for mortality. Analysis of the expression profiles of inflammatory pathway genes showed that the greater the infection severity, the greater the activation of inflammatory pathways, triggering the cytokine storm and downregulating anti-inflammatory pathways. Viral genome analysis revealed the circulation of multiple lineages, such as B.1, B.1.1.28, Alpha, and Gamma, suggesting that multiple introduction events had occurred over time. This study's findings help identify the specific strains and increase our understanding of the true state of local health. In addition, our data demonstrate that epidemiological and genomic surveillance together can help formulate public health strategies to guide governmental actions.

Objectives: This study aimed to evaluate the influence of different polymerisation methods of acrylic resin for ocular prostheses on the subcutaneous tissue inflammatory response of rats., Methods: The study was conducted at the Basic Sciences Department, Araçatuba Dental School, São Paulo State University (UNESP), Brazil, from 2016 to 2018. The samples were prepared by water bath (WB), microwave energy (MW) or autopolymerisation (AP) (n = 20 samples per group). The inflammatory response (cell count and immunohistochemical analysis of interleukin [IL]-1β, IL-6, tumour necrosis factor [TNF]-α, IL-17 and macrophage inflammatory protein-3α) was analysed by the implantation of a sample from each group in the subcutaneous tissue of 20 Wistar rats and evaluated after seven, 15, 30 and 60 days. The quantitative and qualitative data were analysed using analysis of variance and Tukey tests ( P <0.05) and visual comparison, respectively., Results: There was a moderate inflammatory infiltrate for the MW and AP groups and a light infiltrate for the WB group after seven days. The inflammatory infiltrate and the immunolabeling of tested targets decreased gradually during the 60-day period. The AP group had the highest immunolabeling of TNF-α (seven days), IL-1β and IL-17 (at 15 and 30 days) and IL-6 (at 30 and 60 days). The WB and MW groups showed greater immunolabeling at 15 and 30 days, while the MW group also had high results at 60 days., Conclusion: Polymerisation by microwave energy and by chemical activation resulted in a higher inflammatory response., Competing Interests: CONFLICT OF INTEREST The authors declare no conflicts of interest., (© Copyright 2022, Sultan Qaboos University Medical Journal, All Rights Reserved.)

This study aimed to investigate the antimicrobial and biological properties of Ambroxol associated with glycerin (GLI), propylene glycol (PG), and polyethylene glycol (PEG) as a possible vehicle for an experimental tricalcium silicate sealer, with the intention of developing a new biomaterial. Mouse undifferentiated dental pulp cells (OD-21) were cultured, and the effects of different association on cell proliferation and inflammatory cytokine production were investigated. Antimicrobial adhesion of Enterococcus faecalis to setting sealers at 2 h was evaluated. Polyethylene tubes containing experimental sealers and empty tubes were implanted into dorsal connective tissues of 12 male 3- to 4-months-old Wistar rats (250-280 g). After 7 and 30 days, the tubes were removed and processed for histological and immunohistochemical analyses. ANOVA followed by Bonferroni correction and ANOVA followed by Tukey test was used for parametric data and Kruskal-Wallis followed by Dunn for nonparametric (p < 0.05). Cell proliferation was dose-dependent, since all association were cytotoxic at higher concentrations; however, Ambroxol-PEG showed significantly higher cytotoxicity than other association (p < 0.05). In addition, irrespective of the association, no cytokine production was observed in vitro. Ambroxol-GLI reduced bacterial viability, whereas Ambroxol-PEG increased (p < 0.05). Histological examination showed no significant difference in the inflammatory response (p > 0.05) and mineralization ability in all association. Additionally, IL-1β and TNF-α were upregulated on Ambroxol-PEG in relation to Control at 07 days (p < 0.05). Ambroxol-GLI was the best vehicle for experimental tricalcium silicate sealer, as it promoted an increase in antimicrobial activity without altering the inflammatory response or mineralization ability., (© 2021. The Author(s).)

The study evaluated the influence of cycles and methods of an ocular prosthesis resin on cytotoxicity toward human conjunctival cells. Resins were polymerized by water bath (WB, 74 °C or 100 °C for 30 min to 9 h), microwave (MW, 1200 W, 3 to 14 min and 30 s at 0 to 720 W), or autopolymerization (AP, room temperature for 20 min ± 60 °C for 30 min). Degree of conversion (DC), cytotoxicity, level of inflammatory mediators, gene expression of different markers, and apoptosis were evaluated. Data were submitted to ANOVA and Tukey test (p < 0.05). WB with longer processing time at higher temperature had highest DC (85.6%) and higher TGF β1-gene expression (1.39); long cycle low power MW showed lowest DC (69.6%), lower cell proliferation (85.4%, MTT), and large IL-2 release (39,297 ng/mL). AP with additional processing time showed lower cell proliferation (75.3%, Alamar Blue), and AP polymerized at room temperature showed higher CASP 9-gene expression (1.21). AP methods showed higher IL-6 release (>277 pg/mL). Short cycle medium power MW had higher IL-23 release (534.2 pg/mL). MW (long and short cycles) and AP polymerizations have triggered a more intense inflammatory response. Among methods recommended by the manufacturer, WB showed high DC and less cytotoxicity., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Objectives: This study compared the cytotoxicity, biocompatibility, and tenascin immunolabeling of a new ready-to-use hydraulic sealer (Bio-C Sealer) with MTA-Fillapex and white MTA-Angelus., Materials and Methods: L929 fibroblasts were cultivated and exposed to undiluted and diluted material extracts. Polyethylene tubes with or without (the control) the materials were implanted into the dorsa of rats. At 7 days and 30 days, the rats were euthanized, and the specimens were prepared for analysis; inflammation and immunolabeling were measured, and statistical analysis was performed ( p < 0.05)., Results: MTA-Fillapex exhibited greater cytotoxicity than the other materials at all time points ( p < 0.05). The undiluted Bio-C Sealer exhibited greater cytocompatibility at 6 and 48 hours than white MTA-Angelus, with higher cell viability than in the control ( p < 0.05). White MTA-Angelus displayed higher cell viability than the control at 24 hours, and the one-half dilution displayed similar results at both 6 and 48 hours ( p < 0.05). At 7 days and 30 days, the groups exhibited moderate inflammation with thick fibrous capsules and mild inflammation with thin fibrous capsules, respectively ( p > 0.05). At 7 days, moderate to strong immunolabeling was observed ( p > 0.05). After 30 days, the control and MTA-Fillapex groups exhibited strong immunolabeling, the white MTA-Angelus group exhibited moderate immunolabeling ( p > 0.05), and the Bio-C Sealer group exhibited low-to-moderate immunolabeling, differing significantly from the control ( p < 0.05)., Conclusions: Bio-C Sealer and white MTA-Angelus exhibited greater cytocompatibility than MTA-Fillapex; all materials displayed adequate biocompatibility and induced tenascin immunolabeling., Competing Interests: Conflict of Interest: No potential conflict of interest relevant to this article was reported., (Copyright © 2021. The Korean Academy of Conservative Dentistry.)

New X-ray crystallography and cryo-electron microscopy (cryo-EM) approaches yield vast amounts of structural data from dynamic proteins and their complexes. Modeling the full conformational ensemble can provide important biological insights, but identifying and modeling an internally consistent set of alternate conformations remains a formidable challenge. qFit efficiently automates this process by generating a parsimonious multiconformer model. We refactored qFit from a distributed application into software that runs efficiently on a small server, desktop, or laptop. We describe the new qFit 3 software and provide some examples. qFit 3 is open-source under the MIT license, and is available at https://github.com/ExcitedStates/qfit-3.0., (© 2020 The Protein Society.)

Background: Although silver nanoparticles (SNP) have proven antimicrobial activity against different types of microorganisms, the effect of SNP incorporation into acrylic resin to control Candida albicans biofilm formation aiming at the prevention of Candida-associated denture stomatitis has not yet been fully elucidated., Objectives: This study aimed to evaluate the antimicrobial effect of an acrylic resin containing SNP on C. albicans biofilm growth, the flexural strength of this material and tissue reaction in the subcutaneous connective tissue of rats to SNP., Method: SNP were synthesized through silver nitrate reduction by sodium citrate. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) were used to verify the size and colloidal stability. SNP were added to acrylic resin monomer (Lucitone 550) at 0.05, 0.5 and 5 vol%. The antimicrobial effect against C. albicans (ATCC 10231) was investigated by the enumeration of colony-forming units (CFUs) and SEM. The three-point bending test was performed to analyze the flexural strength. Tissue reaction was evaluated after 7 and 60 days of implantation in the connective tissue of Wistar rats., Results: Spherical particles of 5 and 10 nm were obtained. SNP at 0.05 and 0.5% incorporated into acrylic resin was effective in reducing C. albicans biofilm growth (p < .001). SEM revealed that the material was able to disrupt C. albicans biofilm formation and did not reduce the flexural strength compared to control (p > .05). The inflammatory response observed 60 days after implantation SNP in the subcutaneous tissue was similar to control., Conclusion: It was concluded that SNP addition at 0.05 and 0.5% into acrylic resin exhibited antimicrobial effects against C. albicans biofilm, did not interfere in the flexural strength and may be considered biocompatible., (Copyright © 2020 Elsevier B.V. All rights reserved.)

Objective: To evaluate the prevalence of HPV DNA detection in fresh tissue from oral leukoplakia by Linear Array assay, and its correlation with p16 INK4a immunoexpression in the northwest region of the São Paulo state, Brazil., Patients and Methods: Fifty patients diagnosed with oral leukoplakia were included in the study. Sociodemographic, clinicopathologic and lifestyle data, fresh tissue and formalin fixed paraffin embedded (FFPE) tissue samples were collected. The fresh tissue was stored at -80 °C and then submitted to further viral DNA detection by the Linear Array method. Immunohistochemical analysis for the p16 INK4a expression was performed., Results: Of the 50 patients included in the study, 62 % were men, and the age ranged from 25 to 82 years. Twenty-three (46 %) were elderly, 46 % were middle-aged adults, and only 12 % were young adults. Most patients were smokers (76 %), 14 % were former smokers, and 10 % were non-smokers. Most patients (56 %) were current drinkers, 22 % were ex-drinkers and 22 % were non-drinkers. Thirty-two percent of the lesions presented some degree of dysplasia. No lesions were positive to HPV by Linear Array detection. Thirty (60 %) OL had p16-low immunoexpression and 20 (40 %) had p16-high immunoexpression., Conclusion: HPV was not identified in the population studied. The high p16 INK4a immunoexpression is not dependent on HPV in oral leukoplakia. Broader epidemiological studies are required to clarify the geographic variability in the prevalence of HPV in head and neck squamous cell carcinoma and oral potentially malignant lesions., Competing Interests: Declaration of Competing Interest The authors declare that there is no potential conflict of interest regarding this work., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Background: Oral fibroblast immunological responses to bacterial stimuli are well known. However, there are few studies about pulp fibroblasts from deciduous teeth (HDPF) responses, which are important for the treatment of pulp infections in children. The aim of this study was to evaluate expression and production of inflammatory cytokines and chemokines by HDPF when challenged with bacterial antigens normally present in advanced caries lesions., Methods: Triplicate HDPF from 4 children (n = 4; 2 boys and 2 girls) were cultured by explant technique and challenged or not with Escherichia coli lipopolysaccharide/1 μg/mL (EcLPS) or Enterococcus faecalis lipoteichoic acid/1 μg/mL (EfLTA) for 6 and 24 h. Most of published studies employed immortalized cells, i.e., without checking possible gender and genetic variables. mRNA expression and protein production were evaluated by RT-qPCR and ELISA MILLIPLEX®, respectively, for Interleukin (IL)-1α, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IL-17, Chemokine C-C motif ligand 2/monocyte chemoattractant protein 1 (CCL2/MCP-1), Chemokine C-C motif ligand 3/macrophage inflammatory protein 1-alpha (CCL3/MIP1-α), Chemokine C-C motif ligand 5/ regulated on activation, normal T cell expressed and secreted (CCL5/RANTES), C-X-C motif chemokine 12/ stromal cell-derived factor 1 (CXCL12/SDF-1), Tumor Necrosis Factor-alpha (TNF-α), Interferon-gamma (IFN γ), Vascular Endothelial Growth Factor (VEGF), Colony stimulating factor 1 (CSF-1) and Macrophage colony-stimulating factor (M-CSF)., Results: EcLPS increased IL-1α, IL-1β, IL-8, CCL2, CCL5, TNF-α and CSF-1 mRNA and protein levels while EfLTA was only able to positively regulate gene expression and protein production of IL-8., Conclusion: The results of the present study confirmed our hypothesis, since pulp fibroblasts from deciduous teeth are capable of increasing gene expression and protein production after being stimulated with EcLPS and EfLTA.

Aim: To evaluate the cytotoxicity and inflammatory response of different types of provisional restorative materials to mice gingival fibroblasts., Methods: Cytotoxicity of provisional material discs (thermal-polymerized acrylic resin; auto-polymerized acrylic resin; bisacrylic resin; nano-ceramic resin for CAD/CAM and prefabricated polymer block for CAD/CAM) to Mice (Balb/c) gingival cell were investigated under direct and indirect contact (extracts) at 24, 48 and 72 h, using the MTT and Alamar blue assays. Materials extracts (24 h) were applied to the cell culture (indirect contact) or cells were seeded on discs of provisional materials, and the cytotoxicity and production of IL-6, IL-1β and TNF-α after 24, 48 and 72 h were analyzed through MTT, Alamar Blue® and ELISA. Culture medium was used as control for indirect contact assay (extract) and the surfaces of the wells without discs of provisional materials were used as control for direct contact assay. Results were analysed statistically by ANOVA followed by the Bonferroni-Test correction. Statistically significant differences were considered if P was < .05., Results: Auto-polymerized and bisacrylic resins (direct contact) reduced cell viability after 24, 48 and 72 h compared to control (P < .05). Indirect contact (extract) was not cytotoxic to cells at all periods compared to control (P > .05). Auto-polymerized and bisacrylic resins increased IL-6, IL-1β and TNF-α levels mainly at 24 h when compared to the other materials (P < .001)., Conclusion: Auto-polymerized and bisacrylic were more cytotoxic to mice gingival fibroblasts. CAD/CAM nano ceramic resin and prefabricated polymer blocks are more predictable materials to preserve the periodontal soft tissues., Competing Interests: Declaration of Competing Interest Manuscript title “Cytotoxicity and inflammatory response of different types of provisional restorative materials” The authors whose names are listed immediately below certify that they have NO affiliations with or involvement in any organization or entity with any financial interest (such as honoraria; educational grants; participation in speakers’ bureaus; membership, employment, consultancies, stock ownership, or other equity interest; and expert testimony or patent-licensing arrangements), or non-financial interest (such as personal or professional relationships, affiliations, knowledge or beliefs) in the subject matter or materials discussed in this manuscript., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Motivation: Over the last few years, the field of protein structure prediction has been transformed by increasingly accurate contact prediction software. These methods are based on the detection of coevolutionary relationships between residues from multiple sequence alignments (MSAs). However, despite speculation, there is little evidence of a link between contact prediction and the physico-chemical interactions which drive amino-acid coevolution. Furthermore, existing protocols predict only a fraction of all protein contacts and it is not clear why some contacts are favoured over others. Using a dataset of 863 protein domains, we assessed the physico-chemical interactions of contacts predicted by CCMpred, MetaPSICOV and DNCON2, as examples of direct coupling analysis, meta-prediction and deep learning., Results: We considered correctly predicted contacts and compared their properties against the protein contacts that were not predicted. Predicted contacts tend to form more bonds than non-predicted contacts, which suggests these contacts may be more important than contacts that were not predicted. Comparing the contacts predicted by each method, we found that metaPSICOV and DNCON2 favour accuracy, whereas CCMPred detects contacts with more bonds. This suggests that the push for higher accuracy may lead to a loss of physico-chemically important contacts. These results underscore the connection between protein physico-chemistry and the coevolutionary couplings that can be derived from MSAs. This relationship is likely to be relevant to protein structure prediction and functional analysis of protein structure and may be key to understanding their utility for different problems in structural biology., Availability and Implementation: We use publicly available databases. Our code is available for download at https://opig.stats.ox.ac.uk/., Supplementary Information: Supplementary information is available at Bioinformatics online., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Although the effectiveness of some mouthwashes has been proven, phytotherapy is still a field to be explored as an alternative to commercial products., Objective: To evaluate, in vitro, the cytotoxicity and efficacy of two solutions based on citronella oil (CN), on S. aureus and C. albicans biofilms (in formation-adhesion phase and 24 h-biofilm formation) on acrylic resin and nickel-chromium alloy samples (one trademark of each material), compared to two alcohol-free commercial mouthwashes., Material and Methods: Two solutions containing CN at concentrations of 5x and 10x the minimum bactericidal/fungicidal concentration (MBC/MFC) were prepared by microdilution. After contamination of the samples surfaces with these microorganisms, the mouthwashes (CN - 5x and 10x; CHX - 0,12% alcohol-free chlorhexidine and LT - alcohol-free essential oils) were evaluated. Mouthwash simulation was performed for 1 min at two moments, the first simulation after 4 h of microbial adhesion and 24 h-biofilm formation, and the second simulation, 6 h after the first simulation. For biofilm quantification, the number of cultured cells was evaluated by CFUs. The cytotoxicity assay was performed on HaCat epithelial cells and quantified by the MTT method., Results: Tested solutions completely inhibited the growth of both microorganisms in the adhesion phase. All solutions showed inhibitory activity against 24 h-biofilm formation. However, CN led to greater microbial reduction, regardless of the surface of the sample. All solutions demonstrated a toxic effect. However, after serial dilution, CN presented the lowest cytotoxic effect., Conclusion: Citronella had a lower cytotoxic effect and a higher action compared to commercial solutions., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis., Competing Interests: The authors declare no competing interest.

While template-free protein structure prediction protocols now produce good quality models for many targets, modelling failure remains common. For these methods to be useful it is important that users can both choose the best model from the hundreds to thousands of models that are commonly generated for a target, and determine whether this model is likely to be correct. We have developed Random Forest Quality Assessment (RFQAmodel), which assesses whether models produced by a protein structure prediction pipeline have the correct fold. RFQAmodel uses a combination of existing quality assessment scores with two predicted contact map alignment scores. These alignment scores are able to identify correct models for targets that are not otherwise captured. Our classifier was trained on a large set of protein domains that are structurally diverse and evenly balanced in terms of protein features known to have an effect on modelling success, and then tested on a second set of 244 protein domains with a similar spread of properties. When models for each target in this second set were ranked according to the RFQAmodel score, the highest-ranking model had a high-confidence RFQAmodel score for 67 modelling targets, of which 52 had the correct fold. At the other end of the scale RFQAmodel correctly predicted that for 59 targets the highest-ranked model was incorrect. In comparisons to other methods we found that RFQAmodel is better able to identify correct models for targets where only a few of the models are correct. We found that RFQAmodel achieved a similar performance on the model sets for CASP12 and CASP13 free-modelling targets. Finally, by iteratively generating models and running RFQAmodel until a model is produced that is predicted to be correct with high confidence, we demonstrate how such a protocol can be used to focus computational efforts on difficult modelling targets. RFQAmodel and the accompanying data can be downloaded from http://opig.stats.ox.ac.uk/resources., Competing Interests: The authors have declared that no competing interests exist.

Background: Maternal periodontal disease leads to low birth weight (LBW), insulin resistance (IR), increased TNF-α levels, and alterations in insulin signaling in adult offspring. TNF-α has been associated with the stimulation of IKKβ/NF-κB, resulting in the decreased expression of GLUT4. Another mechanism that may be involved in decreasing GLUT4 expression is DNA methylation. This study aimed to evaluate in the adult offspring of rats with periodontal disease: IR, inflammatory pathways, DNA methylation, and expression of GLUT4., Methods: Female Wistar rats were distributed into control and experimental periodontal disease groups. Seven days after induction of periodontal disease, both groups were mated with healthy male rats. After weaning, male offspring were distributed into control offspring (CN-o) and periodontal disease offspring (PED-o) groups. Body weights were measured from 0-75 days of age. At day 75, the following were measured in the offspring: IR (HOMA-IR index); TNF-α and NF-κBp65 content in the gastrocnemius muscle (GM) by western blotting; IKKα/β, JNK, ERK 1/2, NF-κBp65, and NF-κBp50 phosphorylation status in the GM by western blotting; DNA methylation by restriction digest and real-time PCR(qAMP); and expression of GLUT4 mRNA in the GM by real-time PCR., Results: LBW, IR, increases in TNF-α, IKKα/β, ERK 1/2, NF-κBp65, and NF-κBp50 decreased expression of GLUT4 mRNA were observed in the PED-o rats. No differences were identified in JNK phosphorylation status and DNA methylation in the evaluated regions of the GLUT4-encoding gene Slc2a4., Conclusion: Maternal periodontal disease causes LBW, IR, activation of inflammatory pathways, and decreased GLUT4 expression in the GM of adult offspring., (© 2019 American Academy of Periodontology.)

Background: This study was undertaken to analyze if different preparation and exposure periods of eluates from ocular prosthesis acrylic resin influence the cytotoxicity for conjunctival cells., Methods: Twenty-four acrylic resin specimens were divided, according to the period of eluate exposure to Chang conjunctival cells (24 and 72 hours). Eluates were prepared in four different ways: 24, 48, and 72 hours of resin specimen immersion in medium and 24 hours of immersion in water, followed by 24 hours of immersion in medium. MTT assay was used to evaluate the cytotoxic effect. The production of IL-1β, IL-6, TNF-α, and chemokine macrophage inflammatory protein 1α was evaluated by ELISA, while the mRNA expression of type IV collagen (COL IV), transforming growth factor β (TGF-β), and matrix metalloproteinase 9 (MMP9) were evaluated by real-time RT-PCR technique. The statistical analysis was carried out using ANOVA with Bonferroni post-hoc test and the student’s t-test (p < 0.05)., Results: Significant quantities of IL-6 (4.594 pg/mL) and mRNA expression of COL IV (1.58) were verified at 72 hours of eluate exposure to cells, as compared to 24 hours. After the 72-hour exposure of eluates to cells, lower cell proliferation (88.4%) and higher IL-6 quantities (12.374 pg/mL), as well as mRNA expression of COL IV (2.21), TGF-β (2.02), and MMP9 (5.75) were observed, which corresponded to 72 hours of a specimen immersed in medium., Conclusion: Longer periods of eluate preparation and exposure from the acrylic resin to cells are related to higher production of proinflammatory cytokines and extracellular matrix proteins.

Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multitemperature crystallography could therefore augment the structure-based drug design toolbox.

Motivation: Recent advances in co-evolution techniques have made possible the accurate prediction of protein structures in the absence of a template. Here, we provide a general approach that further utilizes co-evolution constraints to generate better fragment libraries for fragment-based protein structure prediction., Results: We have compared five different fragment library generation programmes on three different datasets encompassing over 400 unique protein folds. We show that considering the secondary structure of the fragments when assembling these libraries provides a critical way to assess their usefulness to structure prediction. We then use co-evolution constraints to improve the fragment libraries by enriching them with fragments that satisfy constraints and discarding those that do not. These improved libraries have better precision and lead to consistently better modelling results., Availability and Implementation: Data is available for download from: http://opig.stats.ox.ac.uk/resources. Flib-Coevo is available for download from: https://github.com/sauloho/Flib-Coevo., Supplementary Information: Supplementary data are available at Bioinformatics online.

Motivation: Most current de novo structure prediction methods randomly sample protein conformations and thus require large amounts of computational resource. Here, we consider a sequential sampling strategy, building on ideas from recent experimental work which shows that many proteins fold cotranslationally., Results: We have investigated whether a pseudo-greedy search approach, which begins sequentially from one of the termini, can improve the performance and accuracy of de novo protein structure prediction. We observed that our sequential approach converges when fewer than 20 000 decoys have been produced, fewer than commonly expected. Using our software, SAINT2, we also compared the run time and quality of models produced in a sequential fashion against a standard, non-sequential approach. Sequential prediction produces an individual decoy 1.5-2.5 times faster than non-sequential prediction. When considering the quality of the best model, sequential prediction led to a better model being produced for 31 out of 41 soluble protein validation cases and for 18 out of 24 transmembrane protein cases. Correct models (TM-Score > 0.5) were produced for 29 of these cases by the sequential mode and for only 22 by the non-sequential mode. Our comparison reveals that a sequential search strategy can be used to drastically reduce computational time of de novo protein structure prediction and improve accuracy., Availability and Implementation: Data are available for download from: http://opig.stats.ox.ac.uk/resources. SAINT2 is available for download from: https://github.com/sauloho/SAINT2., Contact: saulo.deoliveira@dtc.ox.ac.uk., Supplementary Information: Supplementary data are available at Bioinformatics online.

Objectives: The aim of this study was to determine whether the presence of single or multiple apical periodontitis (AP) alters blood cell counts and cytokine production., Material and Methods: Thirty rats were divided into three groups: a control group comprising rats without AP, a group called 1AP comprising rats with AP in one tooth, and a group called 4AP comprising rats with AP in four teeth. Endodontic infection was induced by pulp exposure of the first right maxillary molar in the 1AP group or by exposing the first and second right maxillary and mandibular molars in the 4AP group. A blood count and cytokine levels were obtained 30 days after infection by collecting blood by cardiac puncture. The maxillae were dissected and stained with hematoxylin and eosin to evaluate the inflammatory infiltrate. The data were tabulated and subjected to statistical analysis (P < 0.05)., Results: Histological analysis showed a predominance of mononuclear inflammatory cells. In blood, significant increase of leukocytes, lymphocytes, and tumor necrosis factor alpha (TNF-α) in 4AP compared with the control and 1AP groups (P < 0.05) was observed. In addition, significant decrease of interleukin-4 (IL-4) in 1AP and 4AP groups compared with the control was observed (P < 0.05)., Conclusions: In the rat model, the presence of multiple AP can affect health by increasing lymphocyte and TNF-α levels in the blood., Clinical Relevance: The presence of endodontic infections can interfere with the blood profile, altering systemic health.

Evidence show that stress hormones can influence cancer progression, but its role in carcinogenesis is poorly understood. In this study, we used a new method based on oral carcinogenesis model in rats to test the hypothesis that physiological levels of stress hormones in the normal tissue microenvironment would have significant predictive value for chemically induced cancer occurrence. Male Wistar rats were submitted to a tongue biopsy for measuring not-stress induced levels of norepinephrine, corticosterone, adrenocorticotropic hormone (ACTH) and brain-derived neurotrophic factor (BDNF) in the tissue before carcinogenic induction. Rats were treated with the 4-nitroquinoline-1-oxide (4NQO) chemical carcinogen for twenty weeks and then euthanized for microscopic evaluation of the tongue lesions. Increased pre-carcinogen norepinephrine concentrations and reduced basal corticosterone levels in the normal tissue microenvironment were predictive for oral squamous cell carcinoma (OSCC) occurrence. Likewise, increased pre-carcinogen norepinephrine levels in the normal microenvironment were associated a lower expression of pCDKN2a-p16 in OSCCs. Post-carcinogen levels of corticosterone and BDNF in oral leukoplakia tissues (precursor lesion of OSCC) and post-carcinogen corticosterone concentrations in OSCCs were higher than basal levels in the normal mucosa. Increased norepinephrine concentrations in OSCCs were associated to a greater tumor volume and thickness. Furthermore, higher levels of norepinephrine, ACTH and BDNF in OSCCs were associated to a lesser intensity of the lymphoplasmocytic infiltrate. This study shows that pre-carcinogen stress hormones levels in the normal microenvironment may be predictive for chemically induced cancer in rats. Moreover, chemical carcinogenesis can promote stressor-like effects with hormonal changes in the tissue microenvironment, which may be associated to tumor progression., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The Structural T-cell Receptor Database (STCRDab; http://opig.stats.ox.ac.uk/webapps/stcrdab) is an online resource that automatically collects and curates TCR structural data from the Protein Data Bank. For each entry, the database provides annotations, such as the α/β or γ/δ chain pairings, major histocompatibility complex details, and where available, antigen binding affinities. In addition, the orientation between the variable domains and the canonical forms of the complementarity-determining region loops are also provided. Users can select, view, and download individual or bulk sets of structures based on these criteria. Where available, STCRDab also finds antibody structures that are similar to TCRs, helping users explore the relationship between TCRs and antibodies., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Introduction: Many endodontic sealers are available, but the search for the ideal sealer continues. This study evaluated the cytotoxicity and biocompatibility of Sealer Plus, a new resin epoxy-based endodontic sealer containing calcium hydroxide. AH Plus, Endofill, and SimpliSeal endodontics sealers were used for comparison., Methods: L929 fibroblasts were cultured, and an MTT assay was used to determine the cytotoxicity of the sealer extracts at 6, 24, 48, and 72 hours. Tubes containing materials or empty tubes for control were inserted into the subcutaneous tissues of 20 rats. After 7 and 30 days, the rats were killed, and the tubes were removed with the surrounding tissues for histologic analysis. The data were submitted to statistical tests (P < .05)., Results: Undiluted Sealer Plus exhibited less cytotoxicity compared with other undiluted extracts at 6 hours (P < .05), and cell viability was higher for all Sealer Plus extracts after 24 hours (P < .05). At 48 hours, the undiluted and ½ Sealer Plus dilution were the extracts with less cytotoxicity (P < .05). At 72 hours, cell viability was higher for the undiluted and ½ Sealer Plus dilution compared with the other sealers (P < .05). At 7 days, Endofill and SimpliSeal had higher inflammation compared with the control and Sealer Plus (P < .05); AH Plus had moderate inflammation (P > .05). At 30 days, control, Sealer Plus, and AH Plus had less inflammation (P < .05). The fibrous capsule was thick at 7 days and thin at 30 days, except for SimpliSeal., Conclusions: In general, Sealer Plus promoted greater cell viability and was more biocompatible compared with the other sealers., (Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.)

Introduction: Our previous studies have shown that periapical lesions (PLs) in rats cause systemic disorders such as increased tumor necrosis factor-α plasma levels, insulin resistance, and impairment in insulin signal transduction in muscle tissue. However, the mechanisms involved in these alterations are not fully understood. Under chronic inflammatory conditions such as obesity, it has been shown that the skeletal muscle is affected by inflammation, and the number of resident macrophages that are associated with impairments of insulin action and sensitivity is increased. This study aimed to investigate the presence of macrophages, activation of inflammatory pathways in muscle tissue, glycemia, and insulinemia of rats with PLs., Methods: Sixty Wistar rats were distributed into a control group; a group with 1 PL (1PL), which was induced in the right maxillary first molar; and a group with 4 PLs (4PL), which were induced in the right upper and lower first and second molars. We quantified macrophage content by immunohistochemistry for the F4/80 protein. We evaluated Jun N-terminal kinase and IKKα/β phosphorylation status in the muscle tissue by Western blotting. Serum levels of lipopolysaccharide (LPS) and HSP70 and plasma levels of glucose and insulin were assessed by using commercial kits., Results: The 1PL and 4PL groups showed increase in macrophage content, IKKα/β, and Jun N-terminal kinase phosphorylation status, serum LPS and HSP70 levels, and insulin resistance and no changes in glycemia and insulinemia compared with the control group. There was no difference in these parameters between the 1PL and 4PL groups., Conclusions: PLs promoted an increase in macrophage infiltration, activation of inflammatory pathways in muscle tissue, and serum concentrations of HSP70 and LPS in rats. The present study improves the knowledge on the impact of oral inflammations on the development of systemic alteration, which can induce insulin resistance., (Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.)

Background: The aim of this study was to evaluate the effects of photodynamic therapy with curcumin (PDT) comparatively to 5% sodium hypochlorite (NaOCl) and saline solution on cell viability and cytokine (IL-1β and IL-6) production by mouse fibroblasts., Methods: Sixty seconds of pre-irradiation time with curcumin 500mg/L and Led wavelength (λ) 480nm, 72Jcm(2), for 300s was used for PDT. Solutions were diluted in culture medium DMEM (1×10(4) cells) and placed into 24-well cell culture plates with mouse fibroblasts L-929. Culture medium was used as control. After 6, 24 and 48h, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide assay (MTT) was used to evaluate the cell viability and the supernatant was collected for cytokine evaluation using enzyme-linked immunosorbent assay (ELISA). The results were statistically analyzed by ANOVA and BonFerroni correction (p<0.05) for MTT and Kruskal-Wallis test and Dunn (p<0.05) for ELISA., Results: PDT and saline solution presented low cytotoxic effect similar to the control group (p>0.05) while 5% NaOCl was more cytotoxic than PDT (p<0.05) in all periods of time. All materials similarly expressed IL-1β and IL-6 regardless to the experimental period (p<0.05)., Conclusions: PDT with curcumin was not cytotoxic to L929 fibroblasts differently from 5% NaOCl. In all groups occurred similar expression of IL-1β and IL-6., (Copyright © 2016 Elsevier B.V. All rights reserved.)