Miracle-dz/UniFAR-FTUs huggingface dataset:
Substrate mediated elastic coupling between motile cells modulates inter–cell interactions and enhances cell–cell contact

The mechanical micro–environment of cells and tissues influences key aspects of cell structure and function including cell motility. For proper tissue development, cells need to migrate, interact with other neighbouring cells and form contacts, each of which require the cell to exert physical forces. Cells are known to exert contractile forces on underlying soft substrates. These stresses result in substrate deformation that can affect migratory behavior of cells as well as provide an avenue for cells to sense each other and coordinate their motion. The role of substrate mechanics, particularly its stiffness, in such biological processesis therefore a subject of active investigation. Recent progress in experimental techniques have enabled key insights into pairwise mechanical interactions that control cell motility when they move on compliant soft substrates. Analysis and modeling of such systemsis however still in its nascent stages. Motivated by the role modeling is expected to play in interpreting, informing and guiding experiments, we build a biophysical model for cell migration and cell–cell interactions. Our focus is on situations highly relevant to tissue engineering and regenerative medicine –when substrate traction stresses induced by motile cells enable substrate deformation and serve as a medium of communication. Using a generalizable agent–basedmodel, we compute key metrics of cell motile behavior such as the number of cell–cell contacts over a given time, dispersion of cell trajectories, and probability of permanent cell contact, and analyze how these depend on a cell motility parameter and on substrate stiffness. Our results provide a framework towards modeling the manner in which cells may sense each other mechanically via the substrate and use this information to generate coordinated movements across much longer length scales. Our results also provide a foundation to analyze experiments on the phenomenon known as durotaxis where single cells move preferentially towards regions of high stiffness on patterned substrates.
Critical Assessment of Metaproteome Investigation (CAMPI): A Multi-Lab Comparison of Established Workflows

Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carried out the first community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluated the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observed that variability at the peptide level was predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappeared at the protein group level. While differences were observed for predicted community composition, similar functional profiles were obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments.
Exploration of polyyne biosynthetic gene cluster diversity in bacteria leads to the discovery of the Pseudomonas polyyne protegencin

Natural products that possess alkyne or polyyne moieties have been isolated from a variety of biological sources. In bacteria their biosynthesis has been defined, however, the distribution of polyyne biosynthetic gene clusters (BGCs), and their evolutionary relationship to alkyne biosynthesis, have not been addressed. We explored the distribution of alkyne biosynthesis gene cassettes throughout bacteria, revealing evidence of multiple horizontal gene transfer events. Investigating the evolutionary connection between alkyne and polyyne biosynthesis identified a monophyletic clade possessing a conserved seven-gene cassette for polyyne biosynthesis. Mapping the diversity of these conserved genes revealed a phylogenetic clade representing a polyyne BGC in Pseudomonas, pgn, and subsequent pathway mutagenesis and analytical chemistry characterised the associated metabolite, protegencin. In addition to unifying and expanding our knowledge of polyyne diversity, our results show that alkyne and polyyne biosynthetic gene clusters are promiscuous within bacteria. Systematic mapping of conserved biosynthetic genes across bacterial genomic diversity has proven to be a successful method for discovering natural products.
Molecular basis for SPIN·DOC-Spindlin1 engagement and its role in transcriptional inhibition

Spindlin1 is a transcriptional coactivator with three Tudor-like domains, of which the first and second Tudors are engaged in histone methylation readout, while the function of the third Tudor is largely unknown. Recent studies revealed that the transcriptional co-activator activity of Spindlin1 could be attenuated by SPIN•DOC. Here we solved the crystal structure of SPIN•DOC-Spindlin1 complex, revealing that a hydrophobic motif, DOCpep3 (256-281), of SPIN•DOC interacts with Tudor 3 of Spindlin1 and completes its β-barrel fold. Massive hydrophobic contacts and hydrogen bonding interactions ensure a high affinity DOCpep3-Spindlin1 engagement with a binding Kd of 30 nM. Interestingly, we characterized two more K/R-rich motifs of SPIN•DOC, DOCpep1 (187-195) and DOCpep2 (228-239), which bind to Spindlin1 at lower affinities with Kd values of 78 μM and 31 μM, respectively. Structural and binding studies revealed that DOCpep1 and DOCpep2 competitively bind to the aromatic cage of Spindlin1 Tudor 2 that is responsible for H3K4me3 readout. Although DOCpep3-Spindlin1 engagement is compatible with histone readout, an extended SPIN•DOC fragment containing DOCpep1 and DOCpep2 inhibits histone or TCF4 binding by Spindin1 due to introduced competition. This inhibitory effect is more pronounced for weaker binding targets but not for strong ones such as H3 “K4me3-K9me3” bivalent mark. Our RT-qPCR experiment showed that the removal of the hydrophobic motif or the K/R-rich region compromised the inhibitory effects of SPIN•DOC on Spindlin1-mediated transcriptional activation. In sum, here we revealed multivalent engagement between SPIN•DOC and Spindlin1, in which a hydrophobic motif acts as the primary binding site for stable SPIN•DOC-Spindlin1 association, while two more neighboring K/R-rich motifs further modulate the target selectivity of Spindlin1 via competitive inhibition, therefore attenuating the transcriptional co-activator activities of Spindlin1 through affecting its chromatin association.
An Investigation of the Mechanism for a Novel Influenza Inhibitor Designed to Target the Import of PB1

A novel inhibitor of PB1 import, referred to here as GM30, previously displayed nuclear retention of viral nucleoprotein (NP), which spurred the question of whether the compound directly or indirectly blocked viral ribonucleoprotein (vRNP) complex export. vRNPs are exported from the nucleus via exportin 1 (XPO1). Using verdinexor (VNXR), a direct inhibitor of vRNP export that binds to XPO1 and also blocks nuclear factor kappa B (NF-κB) export, we found that GM30 does not block nuclear export of NF-κB. GM30 likewise demonstrated high nuclear retention of NP but not as much as the direct inhibition of nuclear export by VNXR. When the compound was added hours after infection, the compound lost its ability to block nuclear export but VNXR retained its ability to block nuclear export. GM30 is therefore likely an indirect inhibitor of nuclear export because it disrupts the vRNP complex formation and impedes export from the nucleus by reducing nuclear import of PB1.
Oxaliplatin resistance in colorectal cancer enhances TRAIL sensitivity via death receptor 4 upregulation and lipid raft localization

Colorectal cancer (CRC) remains a leading cause of cancer death, and its mortality is associated with metastasis and chemoresistance. We demonstrate that oxaliplatin-resistant CRC cells are sensitized to TRAIL-mediated apoptosis. Oxaliplatin-resistant cells exhibited transcriptional downregulation of caspase-10, but this had minimal effects on TRAIL sensitivity following CRISPR-Cas9 deletion of caspase-10 in parental cells. Sensitization effects in oxaliplatin-resistant cells were found to be a result of increased DR4, as well as significantly enhanced DR4 palmitoylation and translocation into lipid rafts. Raft perturbation via nystatin and resveratrol significantly altered DR4/raft colocalization and TRAIL sensitivity. Blood samples from metastatic CRC patients were treated with TRAIL liposomes, and a 57% reduction of viable CTCs was observed. Increased DR4/lipid raft colocalization in CTCs was found to correspond with increased oxaliplatin resistance and increased efficacy of TRAIL liposomes. To our knowledge, this is the first study to investigate the role of lipid rafts in primary CTCs. Impact Statement Oxaliplatin-resistant colorectal cancer cells exhibit unregulated death receptor 4 expression with increased receptor palmitoylation and translocation into lipid rafts, increasing their sensitivity to apoptosis via TRAIL.
Mechanism of REST/NRSF regulation of clustered protocadherin α genes

Repressor element-1 silencing transcription factor (REST) or neuron-restrictive silencer factor (NRSF) is a zinc-finger (ZF) containing transcriptional repressor that recognizes thousands of neuron-restrictive silencer elements (NRSEs) in mammalian genomes. How REST/NRSF regulates gene expression remains incompletely understood. Here, we investigate the binding pattern and regulation mechanism of REST/NRSF in the clustered protocadherin (PCDH) genes. We find that REST/NRSF directionally forms base-specific interactions with NRSEs via tandem ZFs in an anti-parallel manner but with striking conformational changes. In addition, REST/NRSF recruitment to the HS5-1 enhancer leads to the decrease of long-range enhancer-promoter interactions and downregulation of the clustered PCDHα genes. Thus, REST/NRSF represses PCDHα gene expression through directional binding to a repertoire of NRSEs within the distal enhancer and variable target genes.
Elementary teachers’ cognitive processes and metacognitive strategies during self-directed online learning

ABSTRACT This study involves an in-depth examination of Canadian elementary teachers’ cognitive processes and metacognitive strategies they used during a self-directed online learning experience. The virtual revisit think aloud, a methodology that combines a retrospective procedure with screen recording technology, was used to capture verbalisations from 13 elementary teachers as they used an online database. Resulting think aloud protocols and post-task interviews were analysed using qualitative methods. An inductive approach to analysis led to six themes related to the types of cognitive processes and metacognitive strategies teachers use during self-directed online learning: connecting to practice, tweaking and adapting, narrowing the focus, skimming through, reading for depth, and source credibility. The teachers in this study demonstrated a non-linear iterative process in which they continuously planned, monitored, and evaluated their learning during the self-directed online learning experience. Implications for teacher learning and research are discussed.
Stories of Forgiveness

ABSTRACT Miranda Fricker argues that paradigm-based explanations take a more direct and transparent route to the same destination as State of Nature storytelling, offering hypotheses about the basic purpose of a practice while dispensing with distracting narrative elements. I argue that narratives of forgiveness are not simply dispensable; they but offer a form of emotional and evaluative understanding to which there is no more direct route.
Underneath the veneer of techno-positivity – exploring teachers’ perspectives on technology use in Further Education and Training

ABSTRACT This qualitative study explores the views of nine teachers working in the Further Education and Training in Ireland regarding the use of technology. Drawing on in-depth interviews, thematic analysis exposed a techno-positive perspective and a hierarchy of technologies with newer technologies being valued more. A sort of ‘intangible’ quality is ascribed to technology, which we labelled ‘techno-magic’. The study uncovered a phenomenon of ‘techno-guilt’ where teachers blamed themselves for not using new technologies. The study concludes that there needs to be a new dialogue that moves beyond pro/anti-technology and empowers teachers to approach technology with a more critical perspective.
Exploring Relationships Between Anthropometry, Body Composition, Maturation, and Selection for Competition: A Study in Youth Soccer Players

Purpose The purpose of this study was to analyze variations of selection for competition between late and early mature players and test the relationships between anthropometry, body composition, maturation, and selection for competition. Methods Seventy-nine youth soccer players from under-11 to under-14 participated in this study, over 6 months. Body composition and maturity offset were estimated based on anthropometric data collected. Participants were also monitored for their number of matches as starters and time of play accrued in minutes. Results Minutes played had large correlation coefficients with maturity offset (r = 0.58), and leg length and sitting height interaction (r = 0.56). Multiple linear regression explained 35% of the variation in minutes played (p < 0.001, R2 = 0.41, R2adjusted = 0.35, RMSE = 334.8), but only 12% of the variation in matches as starter (p = 0.04, R2 = 0.21, R2adjusted = 0.12, RMSE = 5.47) between above and below the median of the maturity offset was accounted for, respectively. Conclusions Although maturation may play a role in the minutes of play accrued and matches as starters in young, it is not necessarily determining. A significant amount of the variation in the minutes of play accrued of players can be accounted for when considering body composition and anthropometric data.
Motivational Interviewing and Glycemic Control in Adolescents With Poorly Controlled Type 1 Diabetes: A Randomized Controlled Pilot Trial

A multicenter randomized controlled pilot trial investigated whether motivational interviewing (MI) by diabetes physicians improves glycemic control and variability in the context of follow-up for adolescent patients with poorly controlled type 1 diabetes. Patients (n = 47) aged 12 to 15.9 years who showed poor glycemic control (HbA1c >75 mmol/mol/9.0%) were randomized to standard education (SE) only or MI+SE, with study physicians randomized to employ MI+SE (N = 24 patients) or SE only (N = 23). For one year of follow-up, the main outcome measurements were obtained at three-month visits (HbA1c) or six-monthly: time in range (TIR) and glycemic variability (CV). Mean adjusted 12-month change in HbA1c was similar between the MI+SE and SE-only group (-3.6 vs. -1.0 mmol/mol), and no inter-group differences were visible in the mean adjusted 12-month change in TIR (-0.8 vs. 2.6%; P = 0.53) or CV (-0.5 vs. -6.2; P = 0.26). However, the order of entering the study correlated significantly with the 12-month change in HbA1c in the MI+SE group (r = -0.5; P = 0.006) and not in the SE-only group (r = 0.2; P = 0.4). No link was evident between MI and changes in quality of life. The authors conclude that MI’s short-term use by diabetes physicians managing adolescents with poorly controlled type 1 diabetes was not superior to SE alone; however, improved skills in applying the MI method at the outpatient clinic may produce greater benefits in glycemic control.
Deep Learning Reveals Key Immunosuppression Genes and Distinct Immunotypes in Periodontitis

Background Periodontitis is a chronic immuno-inflammatory disease characterized by inflammatory destruction of tooth-supporting tissues. Its pathogenesis involves a dysregulated local host immune response that is ineffective in combating microbial challenges. An integrated investigation of genes involved in mediating immune response suppression in periodontitis, based on multiple studies, can reveal genes pivotal to periodontitis pathogenesis. Here, we aimed to apply a deep learning (DL)-based autoencoder (AE) for predicting immunosuppression genes involved in periodontitis by integrating multiples omics datasets. Methods Two periodontitis-related GEO transcriptomic datasets (GSE16134 and GSE10334) and immunosuppression genes identified from DisGeNET and HisgAtlas were included. Immunosuppression genes related to periodontitis in GSE16134 were used as input to build an AE, to identify the top disease-representative immunosuppression gene features. Using K-means clustering and ANOVA, immune subtype labels were assigned to disease samples and a support vector machine (SVM) classifier was constructed. This classifier was applied to a validation set (Immunosuppression genes related to periodontitis in GSE10334) for predicting sample labels, evaluating the accuracy of the AE. In addition, differentially expressed genes (DEGs), signaling pathways, and transcription factors (TFs) involved in immunosuppression and periodontitis were determined with an array of bioinformatics analysis. Shared DEGs common to DEGs differentiating periodontitis from controls and those differentiating the immune subtypes were considered as the key immunosuppression genes in periodontitis. Results We produced representative molecular features and identified two immune subtypes in periodontitis using an AE. Two subtypes were also predicted in the validation set with the SVM classifier. Three “master” immunosuppression genes, PECAM1, FCGR3A, and FOS were identified as candidates pivotal to immunosuppressive mechanisms in periodontitis. Six transcription factors, NFKB1, FOS, JUN, HIF1A, STAT5B, and STAT4, were identified as central to the TFs-DEGs interaction network. The two immune subtypes were distinct in terms of their regulating pathways. Conclusion This study applied a DL-based AE for the first time to identify immune subtypes of periodontitis and pivotal immunosuppression genes that discriminated periodontitis from the healthy. Key signaling pathways and TF-target DEGs that putatively mediate immune suppression in periodontitis were identified. PECAM1, FCGR3A, and FOS emerged as high-value biomarkers and candidate therapeutic targets for periodontitis.
Euthanasia Through Cervical Dislocation or CO2 Might Affect Keel Bone Fracture Prevalence in 30-Week-Old Laying Hens

Laying hens are susceptible to keel bone fractures due to continuous endogenous calcium resorption for eggshell formation. Although it is assumed that external trauma to the keel bone, e.g., due to collisions, is the main cause for fractures, accumulated forces or asymmetric load on a weakened bone might contribute to the high keel bone fracture prevalence found in commercial laying hens. The objective of this study was to investigate whether forces applied to the keel due to involuntary convulsions and uncontrolled wing flapping during euthanasia have the potential to cause keel bone fractures. Two hundred and seventy Dekalb White laying hens were euthanized at 30 weeks of age using cervical dislocation (n = 60) or CO2 (n = 210). All hens were radiographed immediately before and after euthanasia. Radiographs were compared side by side to detect new fractures. Four out of the 270 hens (1.5%) obtained a fracture during euthanasia. Specifically, 0.95% of hens euthanized with CO2 (2 out of 210) and 3.3% of hens euthanized through cervical dislocation (2 out of 60) obtained a euthanasia-induced fracture. All four hens with a euthanasia-induced fracture had signs of damage to the keel before euthanasia, indicating that pre-existing fractures could affect fracture susceptibility. Based on our results, we cannot rule out that convulsions during euthanasia can cause keel bone fractures in laying hens. In studies investigating keel bone integrity in birds euthanized with CO2 or cervical dislocation, fracture prevalence might be overestimated. Future research is needed to assess whether euthanasia might be more likely to cause keel bone fractures in older birds and to quantify the frequency and strength of convulsions as a potential cause of fractures.
The Arabidopsis SMALL AUXIN UP RNA32 Protein Regulates ABA-Mediated Responses to Drought Stress

SMALL AUXIN UP-REGULATED RNAs (SAURs) are recognized as auxin-responsive genes involved in the regulation of abiotic stress adaptive growth. Among the growth-limiting factors, water-deficit condition significantly affects plant growth and development. The putative function of SAUR family member AtSAUR32 has the potential to diminish the negative impact of drought stress, but the exact function and mode of action remain unclear in Arabidopsis. In the current study, AtSAUR32 gene was cloned and functionally analyzed. AtSAUR32 localized to the plasma membrane and nucleus was dominantly expressed in roots and highly induced by abscisic acid and drought treatment at certain time points. The stomatal closure and seed germination of saur32 were less sensitive to ABA relative to AtSAUR32-overexpressed line (OE32-5) and wild type (WT). Moreover, the saur32 mutant under drought stress showed increased ion leakage while quantum yield of photosystem II (ΦPSII) and endogenous ABA accumulation were reduced, along with the expression pattern of ABA/stress-responsive genes compared with WT and the OE32-5 transgenic line. Additionally, yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that AtSAUR32 interacted with clade-A PP2C proteins (AtHAI1 and AtAIP1) to regulate ABA sensitivity in Arabidopsis. Taken together, these results indicate that AtSAUR32 plays an important role in drought stress adaptation via mediating ABA signal transduction.
Helicobacter hepaticus Induce Colitis in Male IL-10−/− Mice Dependent by Cytolethal Distending Toxin B and via the Activation of Jak/Stat Signaling Pathway

It has been well documented that cytolethal distending toxin (CDT) from Helicobacter hepaticus (H. hepaticus), Campylobacter jejuni (C. jejuni) and other Gram-negative intestinal pathogens is linked to the inflammatory bowel disease (IBD). However, the mechanisms underlying the progression of H. hepaticus induced colitis remains unclear. In this study, male B6.129P2-IL10tm1Cgn /J mice were infected by H. hepaticus and ΔCdtB H. hepaticus for 6, 12, 18, and 24 weeks. Histopathology, H. hepaticus colonization levels, expression of inflammatory cytokines, signaling pathways, and content of NO in proximal colon were examined. We found that Cytolethal distending toxin subunit B (CdtB) deletion had no influence on colonization ability of H. hepaticus in colon of B6.129P2-IL10tm1cgn /J mice, and there was no significant difference in abundance of colonic H. hepaticus over infection duration. H. hepaticus aggravated rectocele and proximal colonic inflammation, especially at 24 WPI, while ΔCdtB H. hepaticus could not cause significant symptom. Furthermore, mRNA levels of Il-6, Tnf-α, Il-1β, and iNOS significantly increased in the proximal colon of H. hepaticus-infected mice compared to ΔCdtB H. hepaticus infected group from 12 WPI to 24 WPI. In addition, the elevated content of NO and activated Stat3 and Jak2 in colon were observed in H. hepaticus infected mice. These data demonstrated that CdtB promote colitis development in male B6.129P2-IL10tm1Cgn /J mice by induction of inflammatory response and activation of Jak-Stat signaling pathway.