Crosstalk between Regnase-1 and -3 shapes mast cell survival and cytokine expression.

Post-transcriptional regulation of immune-related transcripts by RNA-binding proteins (RBPs) impacts immune cell responses, including mast cell functionality. Despite their importance in immune regulation, the functional role of most RBPs remains to be understood. By manipulating the expression of specific RBPs in murine mast cells, coupled with mass spectrometry and transcriptomic analyses, we found that the Regnase family of proteins acts as a potent regulator of mast cell physiology. Specifically, Regnase-1 is required to maintain basic cell proliferation and survival, whereas both Regnase-1 and -3 cooperatively regulate the expression of inflammatory transcripts upon activation, with Tnf being a primary target in both human and mouse cells. Furthermore, Regnase-3 directly interacts with Regnase-1 in mast cells and is necessary to restrain Regnase-1 expression through the destabilization of its transcript. Overall, our study identifies protein interactors of endogenously expressed Regnase factors, characterizes the regulatory interplay between Regnase family members in mast cells, and establishes their role in the control of mast cell homeostasis and inflammatory responses.

Human antibodies in Mexico and Brazil neutralizing tick-borne flaviviruses.

Flaviviruses such as dengue virus (DENV), Zika virus (ZIKV), and yellow fever virus (YFV) are spread by mosquitoes and cause human disease and mortality in tropical areas. In contrast, Powassan virus (POWV), which causes severe neurologic illness, is a flavivirus transmitted by ticks in temperate regions of the Northern hemisphere. We find serologic neutralizing activity against POWV in individuals living in Mexico and Brazil. Monoclonal antibodies P002 and P003, which were derived from a resident of Mexico (where POWV is not reported), neutralize POWV lineage I by recognizing an epitope on the virus envelope domain III (EDIII) that is shared with a broad range of tick- and mosquito-borne flaviviruses. Our findings raise the possibility that POWV, or a flavivirus closely related to it, infects humans in the tropics.

The bacterial lysate OM-85 engages Toll-like receptors 2 and 4 triggering an immunomodulatory gene signature in human myeloid cells.

OM-85 is a bacterial lysate used in clinical practice to reduce duration and frequency of recurrent respiratory tract infections. Whereas knowledge of its regulatory effects in vivo has substantially advanced, the mechanisms of OM-85 sensing remain inadequately addressed. Here, we show that the immune response to OM-85 in the mouse is largely mediated by myeloid immune cells through Toll-like receptor (TLR) 4 in vitro and in vivo. Instead, in human immune cells, TLR2 and TLR4 orchestrate the response to OM-85, which binds to both receptors as shown by surface plasmon resonance assay. Ribonucleic acid-sequencing analyses of human monocyte-derived dendritic cells reveal that OM-85 triggers a pro-inflammatory signature and a unique gene set, which is not induced by canonical agonists of TLR2 or TLR4 and comprises tolerogenic genes. A largely overlapping TLR2/4-dependent gene signature was observed in individual subsets of primary human airway myeloid cells, highlighting the robust effects of OM-85. Collectively, our results suggest caution should be taken when relating murine studies on bacterial lysates to humans. Furthermore, our data shed light on how a standardized bacterial lysate shapes the response through TLR2 and TLR4, which are crucial for immune response, trained immunity, and tolerance.

Relationship between smoking and mental health in educational settings with high smoking rates: a cohort study among Danish youth.

BACKGROUND: Smoking and poor mental health in youth represent important public health priorities. This study aimed to (i) compare tobacco-related behaviors and mental health in two educational settings with high smoking rates: vocational education and training (VET) schools and preparatory basic education (PBE) schools, and (ii) examine associations between smoking at school start and mental health 5 months later. METHODS: Data were obtained from baseline (N = 1843) and follow-up (N = 1039) assessments conducted as part of a school-based trial in two rounds (baseline in August 2018 and August 2019). Students' characteristics were presented by adjusted prevalences. Logistic regression analyses assessed associations between smoking and measures of mental health: school-related well-being, overall loneliness, and stress. RESULTS: More PBE students than VET students reported daily smoking (40% vs. 27%), nicotine dependence, perceived benefits of smoking (e.g., stress reduction: 41% vs. 33%), low smoking-related self-efficacy (e.g., ability to resist smoking if offered by a friend: 20% vs. 32%), school-related loneliness, and low school connectedness (25% vs. 11%). Daily smokers at VET and PBE schools had lower odds of school-related loneliness (AOR = 0.51, 95% CI: 0.35-0.74) and higher odds of stress (AOR = 2.75, 95% CI: 2.00-3.80). Smoking was associated with better classmate relations in VET schools but not in PBE schools. CONCLUSIONS: Our study suggested that students in PBE schools constitute a more vulnerable group in terms of smoking and mental health compared with students in VET schools. Smoking seemed to prevent loneliness in school but was associated with heightened stress levels.

Genetic Variability Impacts Genotoxic and Transcriptome Responses in the Human Colon after the Consumption of Processed Red Meat Products and Those with Added Phytochemical Extracts.

The PHYTOME study investigated the effect of consuming processed meat products on outcomes related to colorectal cancer risk without testing the impact of genetic variability on these responses. This research aims to elucidate the genetic impact on apparent total N-nitroso compound (ATNC) excretion, colonic DNA adduct formation, ex vivo-induced DNA damage, and gene expression changes in colon biopsies of healthy participants. Through a systematic literature review, candidate polymorphisms were selected and then detected using TaqMan and PCR analysis. The effect of genotype on study outcomes was determined via a linear mixed model and analysis of variance. Machine learning was used to evaluate relative allele importance concerning genotoxic responses, which established a ranking of the most protective alleles and a combination of genotypes (gene scores). Participants were grouped by GSTM1 genotype and differentially expressed genes (DEGs), and overrepresented biological pathways were compared between groups. Stratifying participants by ten relevant genes revealed significant variations in outcome responses. After consumption of processed red meat, variations in NQO1 and COMT impacted responses in ATNC levels (µmol/L) (+9.56 for wildtype vs. heterozygous) and DNA adduct levels (pg/µg DNA) (+1.26 for variant vs. wildtype and +0.43 for variant vs. heterozygous), respectively. After phytochemicals were added to the meat, GSTM1 variation impacted changes in DNA adduct levels (-6.12 for deletion vs. wildtype). The gene scores correlated with these responses and DEGs were identified by GSTM1 genotype. The altered pathways specific to the GSTM1 wildtype group included 'metabolism', 'cell cycle', 'vitamin D receptor', and 'metabolism of water-soluble vitamins and co-factors'. Genotype impacted both the potential genotoxicity of processed red meat and the efficacy of protective phytochemical extracts.

Away from the herd: loneliness as a dysfunction of social alignment.

The tendency of all humans to experience loneliness at some point in their lives implies that it serves an adaptive function. Building on biological theories of herding in animals, according to which collective movement emerges from local interactions that are based on principles of attraction, repulsion and alignment, we propose an approach that synthesizes these principles with theories of loneliness in humans. We present here the 'herding model of loneliness' that extends these principles into the psychological domain. We hold that these principles serve as basic building blocks of human interactions and propose that distorted attraction and repulsion tendencies may lead to inability to align properly with others, which may be a core component in loneliness emergence and perpetuation. We describe a neural model of herding in humans and suggest that loneliness may be associated with altered interactions between the gap/error detection, reward signaling, threat and observation-execution systems. The proposed model offers a framework to predict the behavior of lonely individuals and thus may inform intervention designs for reducing loneliness intensity.

Post-interaction neuroplasticity of inter-brain networks underlies the development of social relationship.

Inter-brain coupling has been increasingly recognized for its role in supporting connectedness during social communication. Here we investigate whether inter-brain coupling is plastic and persists beyond the offset of social interaction, facilitating the emergence of social closeness. Dyads were concurrently scanned using functional near infrared spectroscopy (fNIRS) while engaging in a task that involved movement synchronization. To assess post-interaction neuroplasticity, participants performed a baseline condition with no interaction before and after the interaction. The results reveal heightened inter-brain coupling in neural networks comprising the inferior frontal gyrus (IFG) and dorsomedial prefrontal cortex in the post-task compared to the pre-task baseline. Critically, the right IFG emerged as a highly connected hub, with post-task inter-brain coupling in this region predicting the levels of motivation to connect socially. We suggest that post-interactions inter-brain coupling may reflect consolidation of socially related cues, underscoring the role of inter-brain plasticity in fundamental aspects of relationship development.

Do school-based smoking preventive interventions have unintended effects? Post hoc analysis of the Focus cluster randomised controlled trial.

OBJECTIVES: Public health interventions are designed to improve specific health-related outcomes; however, they may also produce negative side effects, such as substitution use, psychological or social harms. Knowledge about the unintended effects of school-based smoking preventive interventions is sparse. Hence, this study examined these potential unintended effects of the smoking-reducing intervention, Focus, among students in the vocational education and training setting. DESIGN: Cluster randomised controlled trial stratified by school type with 5 months follow-up. SETTING AND PARTICIPANTS: Across Denmark, eight schools were randomised to the intervention group (n=844 students, response proportion 76%) and six schools to the control group (n=815 students, response proportion 75%). This study focused solely on students who smoked at baseline (N=491). INTERVENTIONS: The intervention was developed systematically based on theory and a thoroughly mixed-methods needs assessment. Intervention components included a comprehensive school tobacco policy (smoke-free school hours) supported by a 3-day course for school staff and launched by an edutainment session for students; class-based lessons and a quit-and-win competition; and individual telephone smoking cessation support. OUTCOMES: Alternative tobacco and nicotine products (regular use of smokeless tobacco, hookah and e-cigarettes), regular cannabis use, boredom and loneliness at school, stress and perceived stigmatisation among smokers. RESULTS: We found no statistically significant unintended effects of the intervention. Nonetheless, insignificant findings indicated that students in the intervention group were less likely to be bored during school hours (OR 0.59, 95% CI 0.32 to 1.10) and experience stress (OR 0.62, 95% CI 0.35 to 1.10), but more likely to report feeling stigmatised compared with the control group (OR 1.55, 95% CI 0.71 to 3.40). CONCLUSIONS: Overall, findings suggested no unintended effects of the Focus trial with respect to substitution use, psychological, nor group or social harms. Future research is encouraged to report potential harmful outcomes of smoking preventive interventions, and interventions should be aware of the possible stigmatisation of smokers. TRIAL REGISTRATION NUMBER: ISRCTN16455577.

Novel plant-associated genomoviruses from the Brazilian Cerrado biome.

The discovery rate of new plant viruses has increased due to studies involving high-throughput sequencing (HTS), particularly for single-stranded DNA viruses of the family Genomoviridae. We carried out an HTS-based survey of genomoviruses in a wide range of native and exotic trees grown in the Brazilian Cerrado biome, and the complete genome sequences of two novel members of the family Genomoviridae from two distinct genera were determined. Specific primers were designed to detect these genomoviruses in individual samples. A new gemykolovirus (Tecoma stans associated gemykolovirus) was detected in Tecoma stans, and a new gemykibivirus (Ouratea duparquetiana associated gemykibivirus) was detected in Ouratea duparquetiana. A gemykrogvirus related to Gila monster associated gemykrogvirus (80% pairwise identity) was also detected in foliar samples of Trembleya parviflora. Our pilot study paves the way for a better characterization of this diverse collection of genomoviruses as well as their interactions with the associated tree species.

Correction: Bischoff et al. The Effects of the Food Additive Titanium Dioxide (E171) on Tumor Formation and Gene Expression in the Colon of a Transgenic Mouse Model for Colorectal Cancer. Nanomaterials 2022, 12, 1256.

In the published publication [...].

Translation, cross-cultural adaptation, reliability, and construct validity of the Brazilian Portuguese version of the Basic Psychological Needs in Exercise Scale.

RESULTS: 59 patients were included (61% with COPD and 39% with ILD). BPNES factor scores were not significantly different between raters' assessments (p > 0.05). The internal consistency was 0.70 for autonomy, 0.76 for competence, and 0.80 for relatedness. Inter-rater and test-retest reliability were good to very good for autonomy (ICC = 0.78, 95%CI 0.62-0.87; ICC = 0.75, 95%CI 0.57-0.86, respectively), competence (ICC = 0.81, 95%CI 0.68-0.89; ICC = 0.65, 95%CI 0.43-0.80, respectively), and relatedness (ICC = 0.79, 95%CI 0.65-0.88; ICC = 0.70, 95%CI 0.50-0.83, respectively). Significant correlations were observed between BPNES factors and quality of life, anxiety, depression, and functional status. In conclusion, this study confirmed the reliability and construct validity of the Brazilian Portuguese version of the BPNES in patients with COPD and ILD.

CATCH-UP: A High-Throughput Upstream-Pipeline for Bulk ATAC-Seq and ChIP-Seq Data.

Assay for transposase-accessible chromatin (ATAC) and chromatin immunoprecipitation (ChIP), coupled with next-generation sequencing (NGS), have revolutionized the study of gene regulation. A lack of standardization in the analysis of the highly dimensional datasets generated by these techniques has made reproducibility difficult to achieve, leading to discrepancies in the published, processed data. Part of this problem is due to the diverse range of bioinformatic tools available for the analysis of these types of data. Secondly, a number of different bioinformatic tools are required sequentially to convert raw data into a fully processed and interpretable output, and these tools require varying levels of computational skills. Furthermore, there are many options for quality control that are not uniformly employed during data processing. We address these issues with a complete assay for transposase-accessible chromatin sequencing (ATAC-seq) and chromatin immunoprecipitation sequencing (ChIP-seq) upstream pipeline (CATCH-UP), an easy-to-use, Python-based pipeline for the analysis of bulk ChIP-seq and ATAC-seq datasets from raw fastq files to visualizable bigwig tracks and peaks calls. This pipeline is simple to install and run, requiring minimal computational knowledge. The pipeline is modular, scalable, and parallelizable on various computing infrastructures, allowing for easy reporting of methodology to enable reproducible analysis of novel or published datasets.

Analysis of cell-specific transcriptional responses in human colon tissue using CIBERSORTx.

Diet is an important determinant of overall health, and has been linked to the risk of various cancers. To understand the mechanisms involved, transcriptomic responses from human intervention studies are very informative. However, gene expression analysis of human biopsy material only represents the average profile of a mixture of cell types that can mask more subtle, but relevant cell-specific changes. Here, we use the CIBERSORTx algorithm to generate single-cell gene expression from human multicellular colon tissue. We applied the CIBERSORTx to microarray data from the PHYTOME study, which investigated the effects of different types of meat on transcriptional and biomarker changes relevant to colorectal cancer (CRC) risk. First, we used single-cell mRNA sequencing data from healthy colon tissue to generate a novel signature matrix in CIBERSORTx, then we determined the proportions and gene expression of each separate cell type. After comparison, cell proportion analysis showed a continuous upward trend in the abundance of goblet cells and stem cells, and a continuous downward trend in transit amplifying cells after the addition of phytochemicals in red meat products. The dietary intervention influenced the expression of genes involved in the growth and division of stem cells, the metabolism and detoxification of enterocytes, the translation and glycosylation of goblet cells, and the inflammatory response of innate lymphoid cells. These results show that our approach offers novel insights into the heterogeneous gene expression responses of different cell types in colon tissue during a dietary intervention.

MAGNETO: Cell type marker panel generator from single-cell transcriptomic data.

Single-cell RNA sequencing experiments produce data useful to identify different cell types, including uncharacterized and rare ones. This enables us to study the specific functional roles of these cells in different microenvironments and contexts. After identifying a (novel) cell type of interest, it is essential to build succinct marker panels, composed of a few genes referring to cell surface proteins and clusters of differentiation molecules, able to discriminate the desired cells from the other cell populations. In this work, we propose a fully-automatic framework called MAGNETO, which can help construct optimal marker panels starting from a single-cell gene expression matrix and a cell type identity for each cell. MAGNETO builds effective marker panels solving a tailored bi-objective optimization problem, where the first objective regards the identification of the genes able to isolate a specific cell type, while the second conflicting objective concerns the minimization of the total number of genes included in the panel. Our results on three public datasets show that MAGNETO can identify marker panels that identify the cell populations of interest better than state-of-the-art approaches. Finally, by fine-tuning MAGNETO, our results demonstrate that it is possible to obtain marker panels with different specificity levels.

Exploring the Experiences and Impacts of Research Role-Emerging Placements in Physiotherapy.

Purpose: Research role-emerging placements (RREPs) have been integrated into placement offerings in Canadian physiotherapy programmes. The purpose of the present study is to describe the experiences and impacts of RREPs completed by graduates of Canadian physiotherapy programmes. Methods: Participants were recruited by purposive sampling and completed semi-structured interviews to explore their RREP experiences. Themes were identified using thematic analysis and collaboratively analyzed using the DEPICT model. Results: Eleven participants who completed RREPs during their Canadian physiotherapy programmes (three men, eight women; aged 26.9 [SD 2.7] years) took part in this study. The participants expressed the RREP was a valuable experience. Four themes emerged from the data: (1) Motivators for selecting an RREP included interest in research or a medical injury, (2) The RREP experience involved benefits and challenges, (3) Impacts of completing an RREP, and (4) RREP participant suggestions. Conclusions: RREPs are valuable placement opportunities for learners in Canadian physiotherapy programmes facilitating the development of essential competencies in a non-traditional setting. RREPs could be considered as a placement opportunity for other allied health programmes, as the skills gained are beneficial for all health care professionals.

Objectif: les stages de recherche dans un rôle émergent (SRRÉ) sont intégrés aux offres de stage des programmes de physiothérapie canadiens. La présente étude visait à décrire les expériences et les effets des SRRÉ effectués par les diplômés des programmes de physiothérapie canadiens. Méthodologie: les chercheurs ont recruté les participants par échantillonnage dirigé et ont effectué des entrevues semi-structurées pour explorer leurs expériences de SRRÉ. Ils ont extrait les thèmes au moyen d'une analyse thématique et en ont fait une analyse coopérative à l'aide du modèle DEPICT. Résultats: onze participants qui ont effectué des SRRÉ pendant leur programme de physiothérapie au Canada (trois hommes, huit femmes; 26,9 ± 2,7 ans) ont participé à l'étude. Ils ont trouvé que leur SRRÉ avait été une expérience précieuse. Ils ont tiré quatre thèmes des données : 1) les motivations pour sélectionner un SRRÉ incluaient l'intérêt pour la recherche ou une lésion médicale, 2) l'expérience du SRRÉ comportait des avantages et des difficultés, 3) les répercussions d'avoir effectué un SRRÉ et 4) les suggestions des participants aux SRRÉ. Conclusions: les SRRÉ sont de précieuses occasions de stage pour les apprenants des programmes de physiothérapie canadiens, ce qui a facilité l'acquisition de compétences essentielles dans un milieu non traditionnel. Les SRRÉ pourraient être considérés comme des occasions de stage dans des programmes de santé connexes, car les compétences acquises sont bénéfiques pour tous les professionnels de la santé.

Response of Soybean Cultivars to Oxidative Stress caused by Meloidogyne javanica.

The present study aimed to investigate the response of soybean cultivars with different susceptibility levels to the root-knot nematode Meloidogyne javanica at varied time intervals by analyzing the initial plant-nematode interaction using antioxidant enzymes as oxidative stress markers. A 4 × 4 × 2 factorial method with 5 repetitions was used to analyze 4 soybean cultivars at 4 different collection times-6, 12, 24, and 48 h-with and without M. javanica inoculation. The parameters evaluated were the activities of antioxidant enzymes phenol peroxidase (POX) and ascorbate peroxidase (APX); the concentrations of hydrogen peroxide (H2O2) and malondialdehyde (MDA); and the number of M. javanica juveniles penetrated into each plant. H2O2 concentration varied among the cultivars with and without inoculation and at different collection times as indicated by MDA concentration and POX and APX activities, demonstrating a rapid response of the host to an infection by M. javanica. Oxidative stress caused by M. javanica did not vary among the soybean cultivars regardless of their susceptibility level; however, the antioxidant enzymes POX and APX responded according to the susceptibility level of the cultivars.

Autopsy for Medical Diagnostics: Finding the Cause of Sudden Unexpected Death through Investigation of the Cardiac Conduction System by Serial Sections.

Sudden unexpected death (SUD) is a fatal event that occurs in an apparently healthy subject in a way that such an abrupt outcome could have not been predicted. SUD-including sudden intrauterine unexplained death (SIUD), sudden neonatal unexpected death (SNUD), sudden infant death syndrome (SIDS), sudden unexpected death of the young (SUDY), and sudden unexpected death in the adult (SUDA)-occurs as the first manifestation of an unknown underlying disease or within a few hours of the presentation of a disease. SUD is a major unsolved, shocking form of death that occurs frequently and can happen at any time without warning. For each case of SUD, a review of clinical history data and performance of a complete autopsy, particularly focused on the study of the cardiac conduction system, were carried out according to the necropsy protocol devised by the Lino Rossi Research Center, Università degli Studi di Milano, Italy. Research cases collected and selected for this study were represented by 75 SUD victims that were subdivided into 15 SIUD, 15 SNUD, 15 SUDY, and 15 SUDA victims. After a routine autopsy and clinical history analysis, death remained unexplained, and hence a diagnosis of SUD was assigned to 75 subjects, which included 45 females (60%) and 30 (40%) males ranging in age from 27 gestational weeks to 76 years. Serial sections of the cardiac conduction system disclosed frequent congenital alterations of the cardiac conduction system in fetuses and infants. An age-related significant difference in distribution among the five age-related groups was detected for the following anomalies of the conduction system: central fibrous body (CFB) islands of conduction tissue, fetal dispersion, resorptive degeneration, Mahaim fiber, CFB cartilaginous meta-hyperplasia, His bundle septation, sino-atrial node (SAN) artery fibromuscular thickening, atrio-ventricular junction hypoplasia, intramural right bundle branch, and SAN hypoplasia. The results are useful for understanding the cause of death for all SUD cases that were unexpected and would have otherwise remained unexplained, so as to motivate medical examiners and pathologists to perform more in-depth studies.

Impact of Processing Method and Storage Time on Phytochemical Concentrations in an Antioxidant-Rich Food Mixture.

Foods high in phytochemicals are known for their role in the prevention of chronic disease development, but after processing and storage, such food products may lose part of their functionality as these compounds are sensitive to the impact of processing temperature and the type of methods applied. Therefore, we measured the levels of vitamin C, anthocyanins, carotenoids, catechins, chlorogenic acid, and sulforaphane in a complex blend of fruits and vegetables, and when applied to a dry food product, after exposure to different processing methods. These levels were compared between pasteurized, pascalized (high-pressure processing), and untreated conditions. Furthermore, we established the effect of freezing and storage time on the stability of these compounds. The results showed that pascalization better preserved vitamin C and sulforaphane, whereas pasteurization resulted in higher concentrations of chlorogenic acid, carotenoids, and catechins. For samples which were frozen and thawed immediately after processing, pascalization was the optimal treatment for higher contents of lutein, cyanidin-3-glucoside, quercetin-3-glucoside, delphinidin-3-glucoside, peonidin-3-glucoside, and epicatechin gallate. Ultimately, the optimal processing method to preserve phytochemicals in fruit and vegetable products is as complex as the blend of compounds, and this decision-making would best be led by the prioritized nutrient aim of an antioxidant food product.

GTAC enables parallel genotyping of multiple genomic loci with chromatin accessibility profiling in single cells.

Understanding clonal evolution and cancer development requires experimental approaches for characterizing the consequences of somatic mutations on gene regulation. However, no methods currently exist that efficiently link high-content chromatin accessibility with high-confidence genotyping in single cells. To address this, we developed Genotyping with the Assay for Transposase-Accessible Chromatin (GTAC), enabling accurate mutation detection at multiple amplified loci, coupled with robust chromatin accessibility readout. We applied GTAC to primary acute myeloid leukemia, obtaining high-quality chromatin accessibility profiles and clonal identities for multiple mutations in 88% of cells. We traced chromatin variation throughout clonal evolution, showing the restriction of different clones to distinct differentiation stages. Furthermore, we identified switches in transcription factor motif accessibility associated with a specific combination of driver mutations, which biased transformed progenitors toward a leukemia stem cell-like chromatin state. GTAC is a powerful tool to study clonal heterogeneity across a wide spectrum of pre-malignant and neoplastic conditions.