Metatranscriptomic analysis shows functional alterations in subgingival biofilm in young smokers with periodontitis: a pilot study.

OBJECTIVE: This study aimed to assess the influence of smoking on the subgingival metatranscriptomic profile of young patients affected by stage III/IV and generalized periodontal disease. METHODOLOGY: In total, six young patients, both smokers and non-smokers (n=3/group), who were affected by periodontitis were chosen. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines for case-control reporting were followed. Periodontal clinical measurements and subgingival biofilm samples were collected. RNA was extracted from the biofilm and sequenced via Illumina HiSeq. Differential expression analysis used Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and differentially expressed genes were identified using the Sleuth package in R, with a statistical cutoff of ≤0.05. RESULTS: This study found 3351 KEGGs in the subgingival biofilm of both groups. Smoking habits altered the functional behavior of subgingival biofilm, resulting in 304 differentially expressed KEGGs between groups. Moreover, seven pathways were modulated: glycan degradation, galactose metabolism, glycosaminoglycan degradation, oxidative phosphorylation, peptidoglycan biosynthesis, butanoate metabolism, and glycosphingolipid biosynthesis. Smoking also altered antibiotic resistance gene levels in subgingival biofilm by significantly overexpressing genes related to beta-lactamase, permeability, antibiotic efflux pumps, and antibiotic-resistant synthetases. CONCLUSION: Due to the limitations of a small sample size, our data suggest that smoking may influence the functional behavior of subgingival biofilm, modifying pathways that negatively impact the behavior of subgingival biofilm, which may lead to a more virulent community.

Unlocking the biosynthetic potential and taxonomy of the Antarctic microbiome along temporal and spatial gradients.

Extreme environments, such as Antarctica, select microbial communities that display a range of evolutionary strategies to survive and thrive under harsh environmental conditions. These include a diversity of specialized metabolites, which have the potential to be a source for new natural product discovery. Efforts using (meta)genome mining approaches to identify and understand biosynthetic gene clusters in Antarctica are still scarce, and the extent of their diversity and distribution patterns in the environment have yet to be discovered. Herein, we investigated the biosynthetic gene diversity of the biofilm microbial community of Whalers Bay, Deception Island, in the Antarctic Peninsula and revealed its distribution patterns along spatial and temporal gradients by applying metagenome mining approaches and multivariable analysis. The results showed that the Whalers Bay microbial community harbors a great diversity of biosynthetic gene clusters distributed into seven classes, with terpene being the most abundant. The phyla Proteobacteria and Bacteroidota were the most abundant in the microbial community and contributed significantly to the biosynthetic gene abundances in Whalers Bay. Furthermore, the results highlighted a significant correlation between the distribution of biosynthetic genes and taxonomic diversity, emphasizing the intricate interplay between microbial taxonomy and their potential for specialized metabolite production.IMPORTANCEThis research on antarctic microbial biosynthetic diversity in Whalers Bay, Deception Island, unveils the hidden potential of extreme environments for natural product discovery. By employing metagenomic techniques, the research highlights the extensive diversity of biosynthetic gene clusters and identifies key microbial phyla, Proteobacteria and Bacteroidota, as significant contributors. The correlation between taxonomic diversity and biosynthetic gene distribution underscores the intricate interplay governing specialized metabolite production. These findings are crucial for understanding microbial adaptation in extreme environments and hold significant implications for bioprospecting initiatives. The study opens avenues for discovering novel bioactive compounds with potential applications in medicine and industry, emphasizing the importance of preserving and exploring these polyextreme ecosystems to advance biotechnological and pharmaceutical research.

Postpandemic Rebound in Noninvasive Group a Streptococcal Disease is not Synchronous with Winter RSV and Influenza Epidemics.

An increase in invasive group A Streptococcus infections was reported in 2022, associated with intense respiratory virus circulation. We describe a marked increase of noninvasive group A Streptococcus infections. Although the rise coincided with epidemics of respiratory syncytial virus and influenza, it continued after detection of these viruses fell to low levels, suggesting that other factors have contributed to this epidemiologic change.

Metatranscriptomic analysis shows functional alterations in subgingival biofilm in young smokers with periodontitis: a pilot study

Abstract This study aimed to assess the influence of smoking on the subgingival metatranscriptomic profile of young patients affected by stage III/IV and generalized periodontal disease. Methodology In total, six young patients, both smokers and non-smokers (n=3/group), who were affected by periodontitis were chosen. The STROBE (Strengthening the Reporting of Observational Studies in Epidemiology) guidelines for case-control reporting were followed. Periodontal clinical measurements and subgingival biofilm samples were collected. RNA was extracted from the biofilm and sequenced via Illumina HiSeq. Differential expression analysis used Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, and differentially expressed genes were identified using the Sleuth package in R, with a statistical cutoff of ≤0.05. Results This study found 3351 KEGGs in the subgingival biofilm of both groups. Smoking habits altered the functional behavior of subgingival biofilm, resulting in 304 differentially expressed KEGGs between groups. Moreover, seven pathways were modulated: glycan degradation, galactose metabolism, glycosaminoglycan degradation, oxidative phosphorylation, peptidoglycan biosynthesis, butanoate metabolism, and glycosphingolipid biosynthesis. Smoking also altered antibiotic resistance gene levels in subgingival biofilm by significantly overexpressing genes related to beta-lactamase, permeability, antibiotic efflux pumps, and antibiotic-resistant synthetases. Conclusion Due to the limitations of a small sample size, our data suggest that smoking may influence the functional behavior of subgingival biofilm, modifying pathways that negatively impact the behavior of subgingival biofilm, which may lead to a more virulent community.

The reconciliation between the experimental and calculated octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine using atomistic molecular dynamics: an open question.

The octanol-water partition coefficient of 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC) was investigated using atomistic molecular dynamics simulations via thermodynamic integration and multistate Bennett acceptance ratio methods. The GAFF and CHARMM36 force fields were used with six water models widely used in molecular dynamics simulations. The OPC4 water model provided the best agreement with the experimental octanol-water partition coefficient of DPPC using the two force fields. However, there is still plenty of room for improvement in water models with correct estimation of surface tension that uses better and suitable non-bonded interaction parameters between water-water and water-DPPC. The Gibbs free energy of transferring DPPC from octanol to water phase was calculated to be 19.8 ± 0.3 and 20.2 ± 0.3 kcal mol-1, giving a partition coefficient of 14.5 ± 0.4 and 14.8 ± 0.3 for the GAFF and CHARMM36 force fields, respectively. This study reinforces the importance of developing new water models that reproduce experimental surface tensions to reconcile the water-water and water-DPPC non-bonded interactions and the existing discrepancy between experimental measurements of amphiphilic molecules that are important in many areas of scientific applications and industry such as biophysics, surfactant, colloids, membranes, medicine, nanotechnology, and food and pharmaceutical industries, and so on. It raises two important open questions: Is the experimental octanol-water partition coefficient of DPPC reliable? Or is its calculation accurate using the OPC4 water model? With respect to the experimental measurements, there may be non-treated aspects such as the formation of aggregates in aqueous phase and limit of detection of the applied method. And, in the calculation, some effects are not possible to be considered in a correct way or viable time such as calculating quantum effects, sampling all conformations, considering phase transitions, and correctly evaluating the intermolecular forces to estimate an accurate surface tension.Communicated by Ramaswamy H. Sarma.

Absolute binding free energies of the antiviral peptide ATN-161 with protein targets of SARS-CoV-2.

The interactions of the antiviral pentapeptide ATN-161 with the closed and open conformations of the α5ß1 integrin, the SARS-CoV-2 major protease, and the omicron variant spike protein complexed with hACE2 were studied using molecular docking and molecular dynamics simulation. Molecular docking was performed to obtain ATN-161 binding poses with these studied protein targets. Subsequently, molecular dynamics simulations were performed to verify the ligand stability at the binding site of each protein target. Pulling simulations, umbrella sampling, and weighted histogram analysis method were used to obtain the potential of mean force of each system and calculate the Gibbs free energy of binding for the ATN-161 peptide in each binding site of these protein targets. The results showed that ATN-161 binds to α5ß1 integrin in its active and inactive form, binds weakly to the omicron variant spike protein complexed with hACE2, and strongly binds to the main protease target.Communicated by Ramaswamy H. Sarma.

Structural changes and adaptative evolutionary constraints in FLOWERING LOCUS T and TERMINAL FLOWER1-like genes of flowering plants.

Regulation of flowering is a crucial event in the evolutionary history of angiosperms. The production of flowers is regulated through the integration of different environmental and endogenous stimuli, many of which involve the activation of different genes in a hierarchical and complex signaling network. The FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1) gene family is known to regulate important aspects of flowering in plants. To better understand the pivotal events that changed FT and TFL1 functions during the evolution of angiosperms, we reconstructed the ancestral sequences of FT/TFL1-like genes and predicted protein structures through in silico modeling to identify determinant sites that evolved in both proteins and allowed the adaptative diversification in the flowering phenology and developmental processes. In addition, we demonstrate that the occurrence of destabilizing mutations in residues located at the phosphatidylcholine binding sites of FT structure are under positive selection, and some residues of 4th exon are under negative selection, which is compensated by the occurrence of stabilizing mutations in key regions and the P-loop to maintain the overall protein stability. Our results shed light on the evolutionary history of key genes involved in the diversification of angiosperms.

Aging is accompanied by T-cell stiffening and reduced interstitial migration through dysfunctional nuclear organization.

Age-associated changes in T-cell function play a central role in immunosenescence. The role of aging in the decreased T-cell repertoire, primarily because of thymic involution, has been extensively studied. However, increasing evidence indicates that aging also modulates the mechanical properties of cells and the internal ordering of diverse cell components. Cellular functions are generally dictated by the biophysical phenotype of cells, which itself is also tightly regulated at the molecular level. Based on previous evidence suggesting that the relative nuclear size contributes to variations of T-cell stiffness, here we examined whether age-associated changes in T-cell migration are dictated by biophysical parameters, in part through nuclear cytoskeleton organization and cell deformability. In this study, we first performed longitudinal analyses of a repertoire of 111 functional, biophysical and biomolecular features of the nucleus and cytoskeleton of mice CD4+ and CD8+ T cells, in both naive and memory state. Focusing on the pairwise correlations, we found that age-related changes in nuclear architecture and internal ordering were correlated with T-cell stiffening and declined interstitial migration. A similarity analysis confirmed that cell-to-cell variation was a direct result of the aging process and we applied regression models to identify biomarkers that can accurately estimate individuals' age. Finally, we propose a biophysical model for a comprehensive understanding of the results: aging involves an evolution of the relative nuclear size, in part through DNA-hypomethylation and nuclear lamin B1, which implies an increased cell stiffness, thus inducing a decline in cell migration.

Light regulates xylem cell differentiation via PIF in Arabidopsis.

The balance between cell proliferation and differentiation in the cambium defines the formation of plant vascular tissues. As cambium cells proliferate, subsets of daughter cells differentiate into xylem or phloem. TDIF-PXY/TDR signaling is central to this process. TDIF, encoded by CLE41 and CLE44, activates PXY/TDR receptors to maintain proliferative cambium. Light and water are necessary for photosynthesis; thus, vascular differentiation must occur upon light perception to facilitate the transport of water and minerals to the photosynthetic tissues. However, the molecular mechanism controlling vascular differentiation in response to light remains elusive. In this study we show that the accumulation of PIF transcription factors in the dark promotes TDIF signaling and inhibits vascular cell differentiation. On the contrary, PIF inactivation by light leads to a decay in TDIF activity, which induces vascular cell differentiation. Our study connects light to vascular differentiation and highlights the importance of this crosstalk to fine-tune water transport.

Lung surfactant negatively affects the photodynamic inactivation of bacteria-in vitro and molecular dynamic simulation analyses.

In the context of the rapid increase of antibiotic-resistant infections, in particular of pneumonia, antimicrobial photodynamic therapy (aPDT), the microbiological application of photodynamic therapy (PDT), comes in as a promising treatment alternative since the induced damage and resultant death are not dependent on a specific biomolecule or cellular pathway. The applicability of aPDT using the photosensitizer indocyanine green with infrared light has been successfully demonstrated for different bacterial agents in vitro, and the combination of pulmonary delivery using nebulization and external light activation has been shown to be feasible. However, there has been little progress in obtaining sufficient in vivo efficacy results. This study reports the lung surfactant as a significant suppressor of aPDT in the lungs. In vitro, the clinical surfactant Survanta® reduced the aPDT effect of indocyanine green, Photodithazine®, bacteriochlorin-trizma, and protoporphyrin IX against Streptococcus pneumoniae. The absorbance and fluorescence spectra, as well as the photobleaching profile, suggested that the decrease in efficacy is not a result of singlet oxygen quenching, while a molecular dynamics simulation showed an affinity for the polar head groups of the surfactant phospholipids that likely impacts uptake of the photosensitizers by the bacteria. Methylene blue is the exception, likely because its high water solubility confers a higher mobility when interacting with the surfactant layer. We propose that the interaction between lung surfactant and photosensitizer must be taken into account when developing pulmonary aPDT protocols.

Effects of different cultivation conditions on the production of ß-cyclocitral and ß-ionone in Microcystis aeruginosa.

BACKGROUND: Cyanobacteria blooms have become a major environmental problem and concern because of secondary metabolites produced by cyanobacteria released into the water. Cyanobacteria produce volatile organic compounds (VOCs), such as the compounds ß-cyclocitral and ß-ionone, which comprise odors, off-flavors, defense compounds, as well as growth regulators. Therefore, the general objective of this work was to evaluate the VOCs produced by two strains of Microcystis aeruginosa, differing in their ability to produce microcystins (LTPNA 01-non-producing and LTPNA 08-toxin-producing). The analysis of VOC production was carried out in (1) normal culture conditions, (2) under different light intensities (LI), and (3) after the external application of ß-ionone in both cultures. RESULTS: The results showed that ß-cyclocitral and ß-ionone are produced in all growth phases of LTPNA 01 and LTPNA 08. Both strains were producers of ß-cyclocitral and ß-ionone in normal culture conditions. It was observed that the ß-cyclocitral concentration was higher than ß-ionone in all light intensities investigated in this study. Additionally, the strain LTPNA 01 produced more ß-cyclocitral than LTPNA 08 at almost all times and LIs analyzed. However, the strain LTPNA 08 produced more ß-ionone, mainly at the initial times. In addition, the experiment results with the external addition of ß-ionone in the cultures showed that the strain LTPNA 01 produced more ß-cyclocitral in control conditions than in treatment. Nonetheless, ß-ionone production was higher in treatment conditions in LTPNA 08, indicating that the addition of ß-ionone may favor the production of these compounds and inhibit the production of ß-cyclocitral. CONCLUSION: Our results showed that some abiotic factors, such as different light intensities and external application of ß-ionone, can be triggers that lead to the production of VOCs.

Effect of Grinding and Regenerative Heat Treatment on the Fracture Resistance of a Zirconia/Porcelain Veneer Interface.

PURPOSE: To experimentally assess the effect of regenerative heat treatment (HT) on yttria-stabilized tetragonal zirconia polycrystalline ceramic (Y-TZP) to guarantee veneer adhesion strength. MATERIALS AND METHODS: One surface of bar-shaped Y-TZP specimens was ground (G) with a diamond stone, while the control samples (C) were not. Groups C900 and G900 were submitted to HT at 900°C for 60 min, whereas groups C1000 and G1000 were submitted to HT at 1000°C for 30 min. The treated surfaces were characterized by x-ray diffractometry (XRD), scanning electron microscopy (SEM), and optical and mechanical profilometry. The energy release rate through interface fracture was determined by a four-point bending test on notched Y-TZP veneered specimens. XRD was refined by the Rietveld method, mean roughness (Ra) and energy release rate were submitted to two-way ANOVA (a = 0.05), and the images were analyzed descriptively. RESULTS: The monoclinic phase (vol%), means of Ra (µm), and the energy release rate (J/m2) were, respectively: C = 1.2/0.17/6.8, C900 = 0.0/0.18/6.6, C1000 = 0.0/0.18/7.6, G = 2.6/1.16/8.3, G900 = 0.0/1.07/8.0, and G1000 = 0.0/1.01/5.7. The surface fraction of monoclinic zirconia increased by grinding and decreased by HT. Ra also increased after grinding (p < 0.005) but remained unaltered after HT (p = 0.22). Increased irregularity was observed in the G groups and a subtle smoothing of the surface after HT. After the fracture of the bilayers, a residual amount of porcelain could be seen on the zirconia surface in all groups. The energy release rate was statistically equal among all groups (p > 0.05). CONCLUSION: Heat treatment after grinding completely restored the tetragonal phase of zirconia without altering the energy release rate during interfacial fracture.

Assessment of the influence of psychosocial factors on musculoskeletal disorder symptom intensity.

BACKGROUND: Previous studies have observed that psychosocial factors are associated with an increase in work-related musculoskeletal disorders (WMSDs) in European countries. However, the influence of psychosocial factors on the WMSD symptoms has not been studied in detail. Additionally, working conditions differ between developing and developed countries. OBJECTIVE: In this study, the influence of psychosocial factors on WMSD symptoms among men and women in the footwear industry in northeastern Brazil is investigated. METHODS: A questionnaire survey was conducted to evaluate workers' perceptions of psychosocial factors and WMSD symptoms. The influence of psychosocial factors on WMSD symptom trends was observed through ordinal logistic regression models. RESULTS: It was found that different psychosocial factors are related to WMSD symptom intensification. Factors such as "job insecurity" and "low social support," which are not associated with the worsening of WMSD symptoms in developed countries, showed a noticeable influence in the sample analyzed. CONCLUSION: These findings may be associated with differences in working conditions and economic problems in developing countries, suggesting that some psychosocial factors have a different effect on workers' perceptions in developing countries.

Reversion of fruit-dependent inhibition of flowering in Citrus requires sprouting of buds with epigenetically silenced CcMADS19.

In Citrus, the response to environmental floral inductive signals is inhibited by the presence of developing fruits. The mechanism involves epigenetic activation of the CcMADS19 locus (FLC orthologue), encoding a floral repressor. To understand how this epigenetic regulation is reverted to allow flowering in the following season, we have forced precocious sprouting of axillary buds in fruit-bearing shoots, and examined the competence to floral inductive signals of old and new leaves derived from them. We have found that CcMADS19 is enriched in repressive H3K27me3 marks in young, but not old leaves, revealing that axillary buds retain a silenced version of the floral repressor that is mitotically transmitted to the newly emerging leaves, which are able to induce flowering. Therefore, we propose that flowering in Citrus is necessarily preceded by vegetative sprouting, so that the competence to respond to floral inductive signals is reset in the new leaves.

Recent Open Issues in Coarse Grained Force Fields.

This viewpoint intends to show recent open issues of using coarse grained models in molecular dynamics simulation. It reviews the current knowledge of the comparison between experimental and simulation data of structural and physical chemical properties that depend on the hydrophilic and hydrophobic behavior of the molecule.

Fruit-dependent epigenetic regulation of flowering in Citrus.

In many perennial plants, seasonal flowering is primarily controlled by environmental conditions, but in certain polycarpic plants, environmental signals are locally gated by the presence of developing fruits initiated in the previous season through an unknown mechanism. Polycarpy is defined as the ability of plants to undergo several rounds of reproduction during their lifetime, alternating vegetative and reproductive meristems in the same individual. To understand how fruits regulate flowering in polycarpic plants, we focused on alternate bearing in Citrus trees that had been experimentally established as fully flowering or nonflowering. We found that the presence of the fruit causes epigenetic changes correlating with the induction of the CcMADS19 floral repressor, which prevents the activation of the floral promoter CiFT2 even in the presence of the floral inductive signals. By contrast, newly emerging shoots display an opposite epigenetic scenario associated with CcMADS19 repression, thereby allowing the activation of CiFT2 the following cold season.

New insights into exogenous surfactant as a carrier of pulmonary therapeutics.

As an organ system, the lung has unique advantages and disadvantages for localized drug delivery. Its direct contact with the external environment allows for the upper airways to be easily accessible to intrapulmonary delivery. However, its complex branching structure makes direct delivery to the peripheral airways challenging. This review will discus the utility of exogenous surfactant, a lipoprotein complex currently used to treat neonatal respiratory distress syndrome, as a carrier for pulmonary therapeutics to enhance the delivery of these drugs to the deeper regions of the lung. The focus is to provide an update on the many tools available to develop new surfactant-based therapeutics using computer modeling, in vitro approaches, and in vivo testing, which may ultimately lead to clinical trials. Two clinical conditions, Acute Respiratory Distress Syndrome and Bacterial Pneumonia are utilized throughout as prototypical examples of pulmonary conditions in which surfactant drug combination may be beneficial. Consequently, the pharmaceuticals discussed are primarily those with antimicrobial or anti-inflammatory activities.

Genome Assembly of a Highly Aldehyde-Resistant Saccharomyces cerevisiae SA1-Derived Industrial Strain.

Here, we report the genome assembly of a Saccharomyces cerevisiae SA1-derived haploid (FMY097) indigenous strain isolated from a Brazilian ethanol distillery. FMY097 was recently reported to be a highly aldehyde-resistant strain capable of producing bioethanol in the presence of up to 40 mM furfural and 80 mM 5-hydroxymethylfurfural.