Phytosulfokine contributes to suspension culture of Cunninghamia lanceolata through its impact on redox homeostasis.

BACKGROUND: Suspension culture is widely used in the establishment of efficient plant regeneration systems, as well as in the mass production of plant secondary metabolites. However, the establishment of a suspension culture system of Cunninghamia lanceolata is genotype-dependent given that proembryogenic masses (PEMs) are prone to browning during this process in recalcitrant genotypes. Previously, we reported that the plant peptide hormone phytosulfokine (PSK) can tremendously decrease the hydrogen peroxide (H2O2) level and help to initiate somatic embryogenesis (SE) in recalcitrant C. lanceolata genotypes. However, to date, no studies have revealed whether or how PSK may contribute to the establishment of a suspension culture system in these recalcitrant genotypes. RESULTS: Here, we demonstrated that exogenous application of PSK effectively inhibited PEM browning during suspension culture in a recalcitrant genotype of C. lanceolata. Comparative time-series transcriptome profiling showed that redox homeostasis underwent drastic fluctuations when PEMs were cultured in liquid medium, while additional PSK treatment helped to maintain a relatively stable redox homeostasis. Interestingly, PSK seemed to have a dual effect on peroxidases (PRXs), with PSK simultaneously transcriptionally repressing ROS-producing PRXs and activating ROS-scavenging PRXs. Furthermore, determination of H2O2 and MDA content, as well as cell viability, showed that exogenous PSK treatment inhibited PEM browning and safeguarded PEM suspension culture by decreasing the H2O2 level and increasing PEM activity. CONCLUSIONS: Collectively, these findings provide a valuable tool for the future establishment of large-scale C. lanceolata PEM suspension culture without genotype limitations.

A comprehensive analysis of the role of QPRT in breast cancer.

To explore the clinical role of QPRT in breast cancer. The gene expression, methylation levels and prognostic value of QPRT in breast cancer was analyzed using TCGA data. Validation was performed using the data from GEO dataset and TNMPLOT database. Meta analysis method was used to pool the survival data for QPRT. The predictive values of QPRT for different drugs were retrieved from the ROC plot. The expression differences of QPRT in acquired drug-resistant and sensitive cell lines were analyzed using GEO datasets. GO and KEGG enrichment analysis were conducted for those genes which were highly co-expressed with QPRT in tissue based on TCGA data and which changed after QPRT knockdown. Timer2.0 was utilized to explore the correlation between QPRT and immune cells infiltration, and the Human Protein Atlas was used to analyse QPRT's single-cell sequencing data across different human tissues. The expression of QPRT in different types of macrophages, and the expression of QPRT were analysed after coculturing HER2+ breast cancer cells with macrophages. Additionally, TargetScan, Comparative Toxicogenomics and the connectivity map were used to research miRNAs and drugs that could regulate QPRT expression. Cytoscape was used to map the interaction networks between QPRT and other proteins. QPRT was highly expressed in breast cancer tissue and highly expressed in HER2+ breast cancer patients (P < 0.01). High QPRT expression levels were associated with worse OS, DMFS, and RFS (P < 0.01). Two sites (cg02640602 and cg06453916) were found to be potential regulators of breast cancer (P < 0.01). QPRT might predict survival benefits in breast cancer patients who received taxane or anthracycline. QPRT was associated with tumour immunity, especially in macrophages. QPRT may influence the occurrence and progression of breast cancer through the PI3K-AKT signalling pathway, Wnt signalling pathway, and cell cycle-related molecules.

Scaling logical density of DNA storage with enzymatically-ligated composite motifs.

DNA is a promising candidate for long-term data storage due to its high density and endurance. The key challenge in DNA storage today is the cost of synthesis. In this work, we propose composite motifs, a framework that uses a mixture of prefabricated motifs as building blocks to reduce synthesis cost by scaling logical density. To write data, we introduce Bridge Oligonucleotide Assembly, an enzymatic ligation technique for synthesizing oligos based on composite motifs. To sequence data, we introduce Direct Oligonucleotide Sequencing, a nanopore-based technique to sequence short oligos, eliminating common preparatory steps like DNA assembly, amplification and end-prep. To decode data, we introduce Motif-Search, a novel consensus caller that provides accurate reconstruction despite synthesis and sequencing errors. Using the proposed methods, we present an end-to-end experiment where we store the text "HelloWorld" at a logical density of 84 bits/cycle (14-42× improvement over state-of-the-art).

The development of clinical reasoning throughout the training and career of psychiatrists in Singapore.

Objectives: The current study sought to explain how different professional experiences led Singaporean psychiatrists to alter their clinical reasoning processes as their careers evolved from psychiatry residents to senior consultant psychiatrists. Methods: The current qualitative study interviewed 26 clinicians at various stages of their psychiatric career, spanning residents to senior psychiatrists.  The authors used a constructivist grounded theory approach to structure the collection and analysis of data. Analyses produced a dense theoretical explanation rooted in the experiences of participants. Results: Several differences emerged between the way psychiatry residents and senior psychiatrists explained their reasoning process and the experiences on which they based their preference. Residents preferred using deductive logic-driven frameworks that were diagnosis-centric, because of the pressures they experienced during their training and assessments. Senior psychiatrists emphasized a more holistic and problem-centric approach. Participants attributed the changes that occurred over time to practical experiences, such as their greater clinical responsibility and independence, and individual experiences, such as growing sensitivity to the clinical reasoning process or their growing propensity for professional reflectiveness. These changes manifest as an increase in repertoire and flexibility in deployment of different clinical reasoning strategies. Conclusions: It is important for trainees to be aware of the deductive and inductive modes of clinical reasoning during supervision and to be comfortable with shifting clinical focus from diagnoses to specific individual problems. Training programs should provide and plan adequate longitudinal clinical exposure to develop clinical reasoning abilities in a way that allows consequences of decisions to be explored. Continued faculty development to ease the diversification of clinical reasoning skills should be encouraged, as should reflectivity in the learners during clinical supervision.

Clinical Impact of Root Canal Treatment Combined with Eugenol Cement on Acute Pulpitis and its Influence on Inflammatory Factor Levels.

Background: Acute pulpitis poses a significant clinical challenge. Traditional root canal treatment has been a standard approach, and the incorporation of adjunctive therapies, such as eugenol cement, presents a potential avenue for enhanced efficacy and reduced complications. Objective: This study aimed to assess the clinical efficacy of root canal treatment combined with eugenol cement for acute pulpitis and its impact on inflammatory factor levels. Design: The study employed a parallel, randomized, controlled, experimental design. Setting: The research was conducted at Suzhou Ninth People's Hospital. Participants: A total of 92 patients diagnosed with acute pulpitis and seeking treatment at our hospital between August 2020 and November 2021 were included in the study. Interventions: Participants were randomly assigned to two groups with 46 patients in each group: the control group receiving traditional root canal treatment and the experimental group receiving root canal treatment combined with eugenol cement. Primary Outcome Measures: The primary outcomes assessed included (1) treatment efficiency, (2) masticatory function, (3) complications, and levels of inflammatory factors. Results: In the study, root canal treatment combined with eugenol cement showed superior efficacy (95.7% vs. 76.1%, P < .05) compared to root canal treatment alone. After one month, both groups exhibited reduced bleeding and gingival indices, with a more significant reduction in the experimental group (P < .05). The combined treatment significantly improved masticatory efficiency and occlusal strength (P < .05). The experimental group had a lower complication rate (6.5% vs. 26.1%, P < .05) and reduced inflammatory markers (IL-6, IL-8, TNF-α, LTB4) compared to the control group (P < .05). Conclusions: Root canal treatment plus eugenol cement enhances masticatory function, reduces complications and inflammatory response in patients with acute pulpitis, alleviates dental pain and looseness, and mitigates inflammatory responses with fewer adverse effects.

Accel-Align: a fast sequence mapper and aligner based on the seed-embed-extend method.

BACKGROUND: Improvements in sequencing technology continue to drive sequencing cost towards $100 per genome. However, mapping sequenced data to a reference genome remains a computationally-intensive task due to the dependence on edit distance for dealing with INDELs and mismatches introduced by sequencing. All modern aligners use seed-filter-extend methodology and rely on filtration heuristics to reduce the overhead of edit distance computation. However, filtering has inherent performance-accuracy trade-offs that limits its effectiveness. RESULTS: Motivated by algorithmic advances in randomized low-distortion embedding, we introduce SEE, a new methodology for developing sequence mappers and aligners. While SFE focuses on eliminating sub-optimal candidates, SEE focuses instead on identifying optimal candidates. To do so, SEE transforms the read and reference strings from edit distance regime to the Hamming regime by embedding them using a randomized algorithm, and uses Hamming distance over the embedded set to identify optimal candidates. To show that SEE performs well in practice, we present Accel-Align an SEE-based short-read sequence mapper and aligner that is 3-12[Formula: see text] faster than state-of-the-art aligners on commodity CPUs, without any special-purpose hardware, while providing comparable accuracy. CONCLUSIONS: As sequencing technologies continue to increase read length while improving throughput and accuracy, we believe that randomized embeddings open up new avenues for optimization that cannot be achieved by using edit distance. Thus, the techniques presented in this paper have a much broader scope as they can be used for other applications like graph alignment, multiple sequence alignment, and sequence assembly.

Interleukin-6 produced by enteric neurons regulates the number and phenotype of microbe-responsive regulatory T cells in the gut.

The immune and enteric nervous (ENS) systems monitor the frontier with commensal and pathogenic microbes in the colon. We investigated whether FoxP3+ regulatory T (Treg) cells functionally interact with the ENS. Indeed, microbe-responsive RORγ+ and Helios+ subsets localized in close apposition to nitrergic and peptidergic nerve fibers in the colon lamina propria (LP). Enteric neurons inhibited in vitro Treg (iTreg) differentiation in a cell-contact-independent manner. A screen of neuron-secreted factors revealed a role for interleukin-6 (IL-6) in modulating iTreg formation and their RORγ+ proportion. Colonization of germfree mice with commensals, especially RORγ+ Treg inducers, broadly diminished colon neuronal density. Closing the triangle, conditional ablation of IL-6 in neurons increased total Treg cells but decreased the RORγ+ subset, as did depletion of two ENS neurotransmitters. Our findings suggest a regulatory circuit wherein microbial signals condition neuronal density and activation, thus tuning Treg cell generation and immunological tolerance in the gut.

Denatured corona proteins mediate the intracellular bioactivities of nanoparticles via the unfolded protein response.

Biomolecular corona formed on nanoparticles (NPs) influences the latter's in vivo biological effects. Nanomaterials with different physicochemical properties exert similar adverse effects, such as cytotoxicity, suggesting the existence of ubiquitous signals during various corona formations that mediate common and fundamental cellular events. Here, we discover the involvement of the unfolded protein response (UPR) and recruited chaperones in the corona. Specially, heat shock protein 90 kDa α class B member 1 (Hsp90ab1) is abundantly enriched in the corona, accompanied by substantial aggregation of misfolded protein on particles intracellularly. Further analysis reveals the particulate matter 2.5 (PM2.5) and metal-containing particles are more capable of denaturing proteins. The recruited Hsp90ab1 activates diverse NPs' pathological behaviour by heat stress response (HSR), which were significantly reversed by geldanamycin (GA), the inhibitor of Hsp90ab1. Murine lung inflammation induced by PM2.5 and iron oxide NPs (Fe3O4NPs) is suppressed by GA, highlighting that Hsp90ab1-mediated UPR is a potential target for the treatment of environmental pollution-related illnesses. Based on our findings, the UPR and Hsp90ab1 presented in the corona of particles initiate fundamental intracellular reactions that lead to common pathological outcomes, which may provide new insights for understanding nanotoxicity and designing therapeutic approaches for diseases associated with environmental pollution.

Development and application of a nonbinary SNP-based microhaplotype panel for paternity testing involving close relatives.

Paternity testing involving close relatives is facing challenges in the field of forensic genetics. Microhaplotype has been proposed as a promising genetic marker for their low mutation rates and high discrimination power recently. In this study, we selected 30 microhaplotypes from 1000 genome projects, including one non-binary SNP, and other six microhaplotypes from published studies containing only binary SNPs to established a panel of microhaplotypes for paternity testing. Most microhaplotypes generated a high effective number of alleles (Ae) with the harmonic mean value of Ae of 3.91 and the arithmetic mean value of heterozygosity of 0.74, respectively. We collected 54 unrelated individuals and 53 samples from six extended families. It was noting that 13 samples from six extended families were unrelated so they were also included in unrelated individuals. The pedigrees of 38 parent-child duos, 55 uncle/aunt/grandparent-child duos (non-biological parent-child duos) and 29 full sibling pairs were constructed based on 53 samples from six extended families. The genotype and haplotype results demonstrated that the combined power of discrimination (CPD) reached 0.99999999999999999999999999999999799 and the cumulative probability of exclusion (CPE) reached 0.999999999999548. The combined probability of excluding relatives (uncle/aunt/grandparent) (CPER) was 0.999999993 (>0.9999), indicating that our panel had good effectiveness in preventing the misinterpretation of close relatives being biological parents. For 38 parent-child duos, the CPI by using the microhaplotypes panel was higher than the one by using Goldeneye 20A kit due to higher polymorphism and more loci in our panel. For 55 non-biological parent-child duos, the CPIs by using STR loci could not help determine 9 non-biological parent-child duos as "exclusions" of paternity while the CPIs by using microhaplotype loci could not help exclude the parenthood of 4 non-biological parent-child duos (CPI > 0.0001). Using the CPI derived from both datasets of STRs and microhaplotypes, all the non-biological parent-child duos could be considered as exclusions. The efficiency of excluding close relatives for this panel was evaluated by analyzing the parameters of 2000 simulated pairs, and the effectiveness was 0.988 at the threshold of t1 = 4 and t2 = -4. Moreover, the average Log10 combined full sibling index (CFSI) for all 29 full sibling pairs was about 7.55 after physical linkage taken account. These data demonstrated that this nonbinary SNPs-based microhaplotype panel has advantages in paternity testing, especially in STR mutated or close relatives involved cases.

Gut-Innervating Nociceptor Neurons Regulate Peyer's Patch Microfold Cells and SFB Levels to Mediate Salmonella Host Defense.

Gut-innervating nociceptor sensory neurons respond to noxious stimuli by initiating protective responses including pain and inflammation; however, their role in enteric infections is unclear. Here, we find that nociceptor neurons critically mediate host defense against the bacterial pathogen Salmonella enterica serovar Typhimurium (STm). Dorsal root ganglia nociceptors protect against STm colonization, invasion, and dissemination from the gut. Nociceptors regulate the density of microfold (M) cells in ileum Peyer's patch (PP) follicle-associated epithelia (FAE) to limit entry points for STm invasion. Downstream of M cells, nociceptors maintain levels of segmentous filamentous bacteria (SFB), a gut microbe residing on ileum villi and PP FAE that mediates resistance to STm infection. TRPV1+ nociceptors directly respond to STm by releasing calcitonin gene-related peptide (CGRP), a neuropeptide that modulates M cells and SFB levels to protect against Salmonella infection. These findings reveal a major role for nociceptor neurons in sensing and defending against enteric pathogens.

Growing Trans-Species Islets in Tumor Extract-Remodeled Testicles.

Although pancreatic islet transplantation holds promise for the treatment of type I diabetes, its application has been significantly hampered by transplant rejection. Here, an approach is demonstrated to support trans-species islet beta cells from a rat to grow and function in the body of a mouse host while overcoming graft rejection. This approach, which builds on remodeling of the mouse testicle by local injection of a tumor homogenate, establishes an immunosuppressive and proregenerative niche in the testicle. This remodeling proves necessary and effective in shaping the testicle into a unique site to accommodate xenograft cells. Rat pancreatic beta cells-from both the insulinoma (cancer cells) and pancreatic islet (normal tissue)-survive, grow, and form a desirable morphology in the remodeled mouse testicle. Notably, when hyperglycemia is induced in the host body, these xenografts secrete insulin to regulate the blood glucose level in mice for as long as 72 days. Furthermore, no graft rejection, acute inflammation, or safety risks are observed throughout the study. In summary, it is demonstrated that the growth of xenogeneic insulinoma cells in a mouse testicle might serve as an alternative approach for islet transplantation.

Pillararene-Containing Polymers with Tunable Conductivity Based on Host-Guest Complexations.

Regulating the conductivity of conducting polymers has spurred increasing studies, aiming at meeting different demands in various fields, including chemosensors, photovoltaic cells, and so on. Herein, linear pillar[5]arene-containing conjugated polymers were designed and synthesized via metathesis cyclopolymerization of pillar[5]arene-functionalized 1,6-heptadiyne. Upon addition of an ionic guest, such polymers could form inclusion complexes, of which the glass transition temperature decreased dramatically. With the aid of ionic guest and host-guest complexations between the pendant pillararenes and guest, these supramolecular materials exhibited tunable conductivity from 10-12 to 10-3 S·cm-1 at 30 °C. In addition, compared with the polymers without pendant pillar[5]arenes, such polymers showed better compatibility with the ionic guest, which could prevent the leakage of the latter one and was good for the conductivity of the material.

Plant Lectins Activate the NLRP3 Inflammasome To Promote Inflammatory Disorders.

Plant-derived dietary lectins have been reported to be involved in the pathogenesis of several inflammatory diseases, including inflammatory bowel disease, diabetes, rheumatoid arthritis, and celiac disease, but little is known about the molecular mechanisms underlying lectin-induced inflammation. In this study, we showed that plant lectins can induce caspase-1 activation and IL-1ß secretion via the NLRP3 inflammasome. Lectins were internalized and subsequently escaped from the lysosome and then translocated to the endoplasmic reticulum. Endoplasmic reticulum-loaded plant lectins then triggered Ca2+ release and mitochondrial damage, and inhibition of Ca2+ release and mitochondrial reactive oxygen species by chemical inhibitors significantly suppressed NLRP3 inflammasome activation. In vivo, plant lectin-induced inflammation and tissue damage also depended on the NLRP3 inflammasome. Our findings indicate that plant lectins can act as an exogenous "danger signal" that can activate the NLRP3 inflammasome and suggest that dietary lectins might promote inflammatory diseases via the NLRP3 inflammasome.

Dopamine controls systemic inflammation through inhibition of NLRP3 inflammasome.

Inflammasomes are involved in diverse inflammatory diseases, so the activation of inflammasomes needs to be tightly controlled to prevent excessive inflammation. However, the endogenous regulatory mechanisms of inflammasome activation are still unclear. Here, we report that the neurotransmitter dopamine (DA) inhibits NLRP3 inflammasome activation via dopamine D1 receptor (DRD1). DRD1 signaling negatively regulates NLRP3 inflammasome via a second messenger cyclic adenosine monophosphate (cAMP), which binds to NLRP3 and promotes its ubiquitination and degradation via the E3 ubiquitin ligase MARCH7. Importantly, in vivo data show that DA and DRD1 signaling prevent NLRP3 inflammasome-dependent inflammation, including neurotoxin-induced neuroinflammation, LPS-induced systemic inflammation, and monosodium urate crystal (MSU)-induced peritoneal inflammation. Taken together, our results reveal an endogenous mechanism of inflammasome regulation and suggest DRD1 as a potential target for the treatment of NLRP3 inflammasome-driven diseases.

RNA viruses promote activation of the NLRP3 inflammasome through a RIP1-RIP3-DRP1 signaling pathway.

The NLRP3 inflammasome functions as a crucial component of the innate immune system in recognizing viral infection, but the mechanism by which viruses activate this inflammasome remains unclear. Here we found that inhibition of the serine-threonine kinases RIP1 (RIPK1) or RIP3 (RIPK3) suppressed RNA virus-induced activation of the NLRP3 inflammasome. Infection with an RNA virus initiated assembly of the RIP1-RIP3 complex, which promoted activation of the GTPase DRP1 and its translocation to mitochondria to drive mitochondrial damage and activation of the NLRP3 inflammasome. Notably, the RIP1-RIP3 complex drove the NLRP3 inflammasome independently of MLKL, an essential downstream effector of RIP1-RIP3-dependent necrosis. Together our results reveal a specific role for the RIP1-RIP3-DRP1 pathway in RNA virus-induced activation of the NLRP3 inflammasome and establish a direct link between inflammation and cell-death signaling pathways.

Omega-3 fatty acids prevent inflammation and metabolic disorder through inhibition of NLRP3 inflammasome activation.

Omega-3 fatty acids (ω-3 FAs) have potential anti-inflammatory activity in a variety of inflammatory human diseases, but the mechanisms remain poorly understood. Here we show that stimulation of macrophages with ω-3 FAs, including eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA), and other family members, abolished NLRP3 inflammasome activation and inhibited subsequent caspase-1 activation and IL-1ß secretion. In addition, G protein-coupled receptor 120 (GPR120) and GPR40 and their downstream scaffold protein ß-arrestin-2 were shown to be involved in inflammasome inhibition induced by ω-3 FAs. Importantly, ω-3 FAs also prevented NLRP3 inflammasome-dependent inflammation and metabolic disorder in a high-fat-diet-induced type 2 diabetes model. Our results reveal a mechanism through which ω-3 FAs repress inflammation and prevent inflammation-driven diseases and suggest the potential clinical use of ω-3 FAs in gout, autoinflammatory syndromes, or other NLRP3 inflammasome-driven inflammatory diseases.

Identifying responsive modules by mathematical programming: an application to budding yeast cell cycle.

High-throughput biological data offer an unprecedented opportunity to fully characterize biological processes. However, how to extract meaningful biological information from these datasets is a significant challenge. Recently, pathway-based analysis has gained much progress in identifying biomarkers for some phenotypes. Nevertheless, these so-called pathway-based methods are mainly individual-gene-based or molecule-complex-based analyses. In this paper, we developed a novel module-based method to reveal causal or dependent relations between network modules and biological phenotypes by integrating both gene expression data and protein-protein interaction network. Specifically, we first formulated the identification problem of the responsive modules underlying biological phenotypes as a mathematical programming model by exploiting phenotype difference, which can also be viewed as a multi-classification problem. Then, we applied it to study cell-cycle process of budding yeast from microarray data based on our biological experiments, and identified important phenotype- and transition-based responsive modules for different stages of cell-cycle process. The resulting responsive modules provide new insight into the regulation mechanisms of cell-cycle process from a network viewpoint. Moreover, the identification of transition modules provides a new way to study dynamical processes at a functional module level. In particular, we found that the dysfunction of a well-known module and two new modules may directly result in cell cycle arresting at S phase. In addition to our biological experiments, the identified responsive modules were also validated by two independent datasets on budding yeast cell cycle.