VThunter: a database for single-cell screening of virus target cells in the animal kingdom.

Viral infectious diseases are a devastating and continuing threat to human and animal health. Receptor binding is the key step for viral entry into host cells. Therefore, recognizing viral receptors is fundamental for understanding the potential tissue tropism or host range of these pathogens. The rapid advancement of single-cell RNA sequencing (scRNA-seq) technology has paved the way for studying the expression of viral receptors in different tissues of animal species at single-cell resolution, resulting in huge scRNA-seq datasets. However, effectively integrating or sharing these datasets among the research community is challenging, especially for laboratory scientists. In this study, we manually curated up-to-date datasets generated in animal scRNA-seq studies, analyzed them using a unified processing pipeline, and comprehensively annotated 107 viral receptors in 142 viruses and obtained accurate expression signatures in 2 100 962 cells from 47 animal species. Thus, the VThunter database provides a user-friendly interface for the research community to explore the expression signatures of viral receptors. VThunter offers an informative and convenient resource for scientists to better understand the interactions between viral receptors and animal viruses and to assess viral pathogenesis and transmission in species. Database URL: https://db.cngb.org/VThunter/.

Voluntariness, timing, and consistency in adolescent routine disclosure and lying to parents.

INTRODUCTION: Whether adolescents' routine disclosure to parents is voluntary is assumed but rarely assessed. Researchers also have not examined whether disclosure and lying are premeditated, occurring before rather than after disclosure or lying, and whether adolescents use a single strategy consistently rather than applying multiple strategies when deciding whether to disclose or lie about their activities. This study investigated these significant gaps in the literature and tested whether voluntariness (for disclosure), timing, consistency, and parental psychological control are associated with lessons learned from disclosure and lying. METHODS: Narrative interviews were conducted in 2014-2015 with 131 primarily middle-class, mostly White US early and middle adolescents and college students (M's = 12.74, 15.81, 20.41 years). Narrated disclosure and lying interviews were reliably coded for voluntariness, timing, consistency, and lessons learned. Parental psychological control was assessed using an online survey. RESULTS: Disclosure was primarily strategic or voluntary and less often involuntary. Lying occurred more often before the narrated event, whereas disclosure occurred more often after. Youth typically reported using other strategies besides the elicited one. Disclosing after was associated with lessons learned. Voluntary disclosure was associated with psychological growth, and psychological control was associated with negative self-lessons. CONCLUSIONS: Disclosure and lying are complex and nuanced, varying in their timing, consistency, and voluntariness. These features contribute to adolescents' meaning-make from disclosure and lying. The findings have implications for future research on disclosure and secrecy.

Efficient Electrocatalytic Oxidation of Glycerol to Formate Coupled with Nitrate Reduction over Cu-doped NiCo Alloy Supported on Nickel Foam.

Electrooxidation of biomass-derived glycerol which is regarded as a main byproduct of industrial biodiesel production, is an innovative strategy to produce value-added chemicals, but currently showcases slow kinetics, limited Faraday efficiency, and unclear catalytic mechanism. Herein, we report high-efficiency electrooxidation of glycerol into formate via a Cu doped NiCo alloy catalyst supported on nickel foam (Cu-NiCo/NF) in a coupled system paired with nitrate reduction. The designed Cu-NiCo/NF delivers only 1.23 V vs. RHE at 10 mA cm-2, and a record Faraday efficiency of formate of 93.8%. The superior performance is ascribed to the rapid generation of NiIII-OOH and CoIII-OOH and favorable coupling of surface *O with reactive intermediates. Using Cu-NiCo/NF as a bifunctional catalyst, the coupled system synchronously produces NH3 and formate, showing 290 mV lower than the coupling of hydrogen evolution reaction, together with excellent long-term stability for up to 144 h. This work lays out new guidelines and reliable strategies from catalyst design to system coupling for biomass-derived electrochemical refinery.

Ferrocene-Based Polymeric Nanoparticles Carrying Doxorubicin for Oncotherapeutic Combination of Chemotherapy and Ferroptosis.

Mono-chemotherapy has significant side effects and unsatisfactory efficacy, limiting its clinical application. Therefore, a combination of multiple treatments is becoming more common in oncotherapy. Chemotherapy combined with the induction of ferroptosis is a potential new oncotherapy. Furthermore, polymeric nanoparticles (NPs) can improve the antitumor efficacy and decrease the toxicity of drugs. Herein, a polymeric NP, mPEG-b-PPLGFc@Dox, is synthesized to decrease the toxicity of doxorubicin (Dox) and enhance the efficacy of chemotherapy by combining it with the induction of ferroptosis. First, mPEG-b-PPLGFc@Dox is oxidized by endogenous H2 O2 and releases Dox, which leads to an increase of H2 O2 by breaking the redox balance. The Fe(II) group of ferrocene converts H2 O2 into ·OH, inducing subsequent ferroptosis. Furthermore, glutathione peroxidase 4, a biomarker of ferroptosis, is suppressed and the lipid peroxidation level is elevated in cells incubated with mPEG-b-PPLGFc@Dox compared to those treated with Dox alone, indicating ferroptosis induction by mPEG-b-PPLGFc@Dox. In vivo, the antitumor efficacy of mPEG-b-PPLGFc@Dox is higher than that of free Dox. Moreover, the loss of body weight in mice treated mPEG-b-PPLGFc@Dox is lower than in those treated with free Dox, indicating that mPEG-b-PPLGFc@Dox is less toxic than free Dox. In conclusion, mPEG-b-PPLGFc@Dox not only has higher antitumor efficacy but it reduces the damage to normal tissue.

PacBio full-length transcriptome analysis provides new insights into transcription of chloroplast genomes.

Chloroplast and mitochondrial DNA (cpDNA and mtDNA) are apart from nuclear DNA (nuDNA) in a eukaryotic cell. The transcription system of chloroplasts differs from those of mitochondria and eukaryotes. In contrast to nuDNA and animal mtDNA, the transcription of cpDNA is still not well understood, primarily due to the unresolved identification of transcription initiation sites (TISs) and transcription termination sites (TTSs) on the genome scale. In the present study, we characterized the transcription of chloroplast (cp) genes with greater accuracy and comprehensive information using PacBio full-length transcriptome data from Arabidopsis thaliana. The major findings included the discovery of four types of artifacts, the validation and correction of cp gene annotations, the exact identification of TISs that start with G, and the discovery of polyA-like sites as TTSs. Notably, we proposed a new model to explain cp transcription initiation and termination at the whole-genome level. Four types of artifacts, degraded RNAs and splicing intermediates deserve the attention from researchers working with PacBio full-length transcriptome data, as these contaminant sequences can lead to incorrect downstream analysis. Cp transcription initiates at multiple promoters and terminates at polyA-like sites. Our study provides new insights into cp transcription and new clues to study the evolution of promoters, TISs, TTSs and polyA tails of eukaryotic genes.

House dust mite-induced endoplasmic reticulum stress mediates MUC5AC hypersecretion via TBK1 in airway epithelium.

Purpose: Endoplasmic reticulum (ER) stress regulates mucus hypersecretion, and may activate downstream factors via TBK1 signaling to induce gene expression. However, it remains unclear whether ER stress promotes airway mucus secretion through the TBK1 pathway. We aimed to investigate the role of the TBK1 pathway in the regulation of MUC5AC expression in a mouse model of house dust mite (HDM)-induced allergic asthma. Materials and Methods: Mice with HDM-induced asthma and human bronchial epithelial BEAS-2B cells were treated with amlexanox, an anti-allergy drug (25 µM), or 4-PBA (10 mM). Tissue and cell samples were collected. Tissue samples were stained with hematoxylin and eosin (H&E) or periodic acid Schiff (PAS) to evaluate pathology. Protein expression was analyzed by western blotting and immunofluorescence. Results: Mice exposed to HDM presented ER stress and hypersecretion of mucus Muc5ac from airway epithelial cells (p < 0.001). Similar results were observed in BEAS-2B cells following exposure to HDM. Both in vivo and in vitro studies revealed that HDM-induced ER stress induced MUC5AC overexpression via TBK1 signaling. Amlexanox and 4-PBA markedly reduced mucus production and weakened the TBK1 signal, which mediates MUC5AC hypersecretion. Conclusion: TBK1 plays a pivotal role in HDM-induced ER stress, leading to overproduction of MUC5AC in the asthmatic airway epithelium. The overproduction of MUC5AC can be significantly decreased by inhibiting TBK1 or ER stress using 4-PBA. These findings highlight potential target-specific therapies for patients with chronic allergic asthma.

Transboundary milRNAs: Indispensable molecules in the process of Trichoderma breve T069 mycoparasitism of Botrytis cinerea.

Despite the increasing number of fungal microRNA-like small RNAs (milRNAs) being identified and reported, profiling of milRNAs in biocontrol fungi and their roles in the mycoparasitism of pathogenic fungi remains limited. Therefore, in this study, we constructed a GFP fluorescence strain to evaluate the critical period of mycoparasitism in the interaction system between T. breve T069 and B. cinerea. The results showed that the early stage of Trichoderma mycoparasitism occurred 12 h after hyphal contact and was characterized by hyphal parallelism, whereas the middle stage lasted 36 h was characterized by wrapping. The late stage of mycoparasitism occurred at 72 h was characterized by the degradation of B. cinerea mycelia. We subsequently identified the sRNAs of T. breve T069 and B. cinerea during the critical period of mycoparasitism using high-throughput sequencing. In ltR1, 45 potential milRNA targets were identified for 243 genes, and 73 milRNAs targeted 733 genes in ltR3. Additionally, to identify potential transboundary miRNAs in T. breve T069, we screened for miRNAs that were exclusively expressed and had precursor structures in the T. breve T069 genome but were absent in the B. cinerea genome. Next, we predicted the target genes of B. cinerea. Our findings showed that 14 potential transboundary milRNAs from T. breve T069 targeted 41 genes in B. cinerea. Notably, cme-MIR164a-p5_1ss17CT can target 15 genes, including Rim15 (BCIN_15g00280), Nop53 (BCIN_12g03770), Skn7 (BCIN_02g08650), and Vel3 (BCIN_03g06410), while ppe-MIR477b-p3_1ss11TC targeted polyketide synthase (BCIN_03g04360, PKS3). The target gene of PC-5p-27397_41 was a non-ribosomal peptide synthetase (BCIN_01g03730, Bcnrps6). PC-3p-0029 (Tri-milR29) targeted chitin synthetase 7. These genes play crucial roles in normal mycelial growth and pathogenicity of B. cinerea. In conclusion, this study highlights the significance of milRNAs in Trichoderma mycoparasitism of B. cinerea. This discovery provides a new strategy for the application of miRNAs in the prevention and treatment of fungal pathogens.

Comparison of Transcriptome between Tolerant and Susceptible Rice Cultivar Reveals Positive and Negative Regulators of Response to Rhizoctonia solani in Rice.

Rice (Oryza sativa L.) is one of the world's most crucial food crops, as it currently supports more than half of the world's population. However, the presence of sheath blight (SB) caused by Rhizoctonia solani has become a significant issue for rice agriculture. This disease is responsible for causing severe yield losses each year and is a threat to global food security. The breeding of SB-resistant rice varieties requires a thorough understanding of the molecular mechanisms involved and the exploration of immune genes in rice. To this end, we conducted a screening of rice cultivars for resistance to SB and compared the transcriptome based on RNA-seq between the most tolerant and susceptible cultivars. Our study revealed significant transcriptomic differences between the tolerant cultivar ZhengDao 22 (ZD) and the most susceptible cultivar XinZhi No.1 (XZ) in response to R. solani invasion. Specifically, the tolerant cultivar showed 7066 differentially expressed genes (DEGs), while the susceptible cultivar showed only 60 DEGs. In further analysis, we observed clear differences in gene category between up- and down-regulated expression of genes (uDEGs and dDEGs) based on Gene Ontology (GO) classes in response to infection in the tolerant cultivar ZD, and then identified uDEGs related to cell surface pattern recognition receptors, the Ca2+ ion signaling pathway, and the Mitogen-Activated Protein Kinase (MAPK) cascade that play a positive role against R. solani. In addition, DEGs of the jasmonic acid and ethylene signaling pathways were mainly positively regulated, whereas DEGs of the auxin signaling pathway were mainly negatively regulated. Transcription factors were involved in the immune response as either positive or negative regulators of the response to this pathogen. Furthermore, our results showed that chloroplasts play a crucial role and that reduced photosynthetic capacity is a critical feature of this response. The results of this research have important implications for better characterization of the molecular mechanism of SB resistance and for the development of resistant cultivars through molecular breeding methods.

Patterns of Reasons for Not Disclosing Personal Activities and Feelings to Mothers and Fathers among Ethnically Diverse Adolescents.

Adolescents' routine disclosure and self (non)disclosure to parents have been distinguished conceptually, but rarely empirically. Using latent profile analyses (LPA), these two types of (non)disclosure were operationalized and examined in terms of the patterns of reasons middle adolescents endorsed for not disclosing personal activities and personal feelings to mothers and fathers and their correlates. This was studied in a sample of 489 U.S. Chinese, Mexican, and European heritage middle adolescents (Mage = 16.37, SD = 0.77, 55% females). Three profiles emerged for both mothers and fathers: A majority profile for mothers consisting of adolescents who viewed personal activities and feelings as personal (i.e., private and not harmful), and much smaller sanction-driven and self-conscious profiles. With fathers, personal concerns were separated in the private profile, which also emphasized that fathers would not listen or understand, a harmless profile, and as with mothers, a sanction-driven profile. Overall, but varying in frequency for different profiles, middle adolescents emphasized personal concerns for not disclosing routine personal activities and psychological concerns for self nondisclosure. The profiles also differed by ethnicity/race, generational status, and trust in mothers and fathers. The father private profile and sanction-driven profiles with both parents were associated with more depressive symptoms and problem behavior relative to the other profiles. The results provide insight into why middle adolescents of diverse ethnicities do not disclose personal information to parents.

SnRK1A-mediated phosphorylation of a cytosolic ATPase positively regulates rice innate immunity and is inhibited by Ustilaginoidea virens effector SCRE1.

Rice false smut caused by Ustilaginoidea virens is becoming one of the most recalcitrant rice diseases worldwide. However, the molecular mechanisms underlying rice immunity against U. virens remain unknown. Using genetic, biochemical and disease resistance assays, we demonstrated that the xb24 knockout lines generated in non-Xa21 rice background exhibit an enhanced susceptibility to the fungal pathogens U. virens and Magnaporthe oryzae. Consistently, flg22- and chitin-induced oxidative burst and expression of pathogenesis-related genes in the xb24 knockout lines were greatly attenuated. As a central mediator of energy signaling, SnRK1A interacts with and phosphorylates XB24 at Thr83 residue to promote ATPase activity. SnRK1A is activated by pathogen-associated molecular patterns and positively regulates plant immune responses and disease resistance. Furthermore, the virulence effector SCRE1 in U. virens targets host ATPase XB24. The interaction inhibits ATPase activity of XB24 by blocking ATP binding to XB24. Meanwhile, SCRE1 outcompetes SnRK1A for XB24 binding, and thereby suppresses SnRK1A-mediated phosphorylation and ATPase activity of XB24. Our results indicate that the conserved SnRK1A-XB24 module in multiple crop plants positively contributes to plant immunity and uncover an unidentified molecular strategy to promote infection in U. virens and a novel host target in fungal pathogenesis.

Social identity and contamination: Young children are more willing to eat native contaminated foods.

Ingesting dangerous substances can lead to illness, or even death, meaning that it is critical for humans to learn how to avoid potentially dangerous foods. However, young children are notoriously bad at choosing foods; they are willing to put nonfoods and disgust elicitors into their mouths. Because food choice is inherently social, we hypothesized that social learning and contamination might separately influence children's decisions about whether to eat or avoid a food. Here, we asked how children reason about foods that are contaminated by someone from within versus outside their culture. We presented 3- to 11-year-olds (N = 534) with videos of native and foreign speakers eating snacks. In Studies 1a and 1b, one speaker contaminated her food and the other did not, and we asked children (a) which food they would prefer to eat, (b) how germy each food was, and (c) which food would make them sick. Although children rated the contaminated food as germier regardless of whether it was contaminated by a foreign speaker (Study 1a) or by a native speaker (Study 1b), children were more likely to report that they would avoid eating foreign contaminated food compared with native contaminated food. In Study 2, we used a non-forced-choice method and found converging evidence that children attend to both culture and contamination when making food choices but that with age they place more weight on contamination status.

Towards understanding the biosynthetic pathway for ustilaginoidin mycotoxins in Ustilaginoidea virens.

Ustilaginoidins, toxic to plants, animals and human, are one of major types of mycotoxins produced by Ustilaginoidea virens. In this study, a gene cluster containing the polyketide synthase gene UvPKS1 was analysed via gene replacement and biochemical studies to determine ustilaginoidin biosynthetic pathway in U. virens. UvPKS1 was first proven to be responsible for the first step of ustilaginoidin biosynthesis, since neither ustilaginoidin derivatives nor intermediates were produced when UvPKS1 was deleted. Replacement of ugsO greatly reduced ustilaginoidin production but increased the ratios of dehydrogenated/hydrogenated ustilagioidin derivatives. The enhanced growth rate of the ΔugsO mutant indicates that accumulation of certain ustilaginoidin derivatives may adversely affect mycelial growth in U. virens. Deletion of ugsT encoding a putative MFS transporter disrupted the ability to generate ustilaginoidins. The ustilaginoidin derivatives produced in the ΔugsJ mutant all lack C3-methyl, indicating that UgsJ is responsible for C3-methylation. Only monomeric intermediates, such as 3-methyl-dihydro-nor-rubrofusarin, but no ustilaginoidin derivatives were generated in the ΔugsL mutant, indicating that UgsL is responsible for the dimerization of nor-rubrofusarin derivatives to produce ustilaginoidins. However, ugsR2 deletion had no dramatic effect on ustilaginoidin biosynthesis. Together, biochemical analyses with bioinformatics and chemoinformatics uncover a multiple-step enzyme-catalysed pathway for ustilaginoidin biosynthesis in U. virens.

Winter plant phenology in the alpine meadow on the eastern Qinghai-Tibetan Plateau.

Background and Aims: There is no knowledge of winter plant phenology and its controlling factors on the Qinghai-Tibetan Plateau (QTP). Thus, we conducted a 4 year winter phenology and growth dynamics study in the alpine meadow on the eastern QTP. Methods: From November 2013 to March 2017, the phenology of the 'winter-growth' and 'winter-green' species was recorded every 5 d. In November-February from 2014 to 2015, the above-ground biomass (AGB) in random plots was calculated to distinguish different growth patterns among winter growing species. The percentage of winter abundance relative to the summer population for forbs and the percentage of absolute coverage for grasses (W/S) were calculated to describe the importance of the winter population to the summer population. The soil moisture (SM) and soil temperature (ST) were used to explore the controlling factors on the AGB. Pearson's correlation analysis between winter phenology data and environmental variables, including air temperature (Tair), snow cover fraction (SCF), SM and ST, was used to investigate the factors affecting winter phenology during November-February from 2014 to 2017. Key Results: There were 107 species in total in the sites, including ten 'winter-growth' species and four 'winter-green' species. Among the 'winter-green' species, Festuca ovina and Deschampsia cespitosa were the dominant species in the sites. The 'winter-growth' species grew new leaves or ramets or transitioned to reproductive growth. Gentiana spathulifolia even flowered in winter. 'Winter-growth' made important contributions to the annual AGB, e.g. winter growth of G. spathulifolia accounted for 23.26 % of its annual AGB, while 14.74 % of the annual AGB of G. crassuloides was from winter growth. In addition, winter warming and snowfall reduction under global climate change on the eastern QTP may decrease the AGB increment of the 'winter-growth' and delay the green-up onset date of 'winter-green' species. Also, winter warming and snowfall reduction may advance the first flowering date of 'winter-growth' species. Conclusions: In contrast to previous views that plants on the QTP were generally considered to remain dormant in winter, our study revealed that alpine meadow plants had strong winter growth which suggested the importance of re-evaluating the dynamics of ecosystem function of alpine meadow, including its contribution to the global carbon balance. It was also shown that soil moisture availability is more important than warmer temperature in controlling the green-up onset of 'winter-green' species on the eastern QTP, which contrasts with the traditional view that warmer winters could advance green-up. As snowmelt is the only source of soil water in winter, the prediction of the green-up trend may be further complicated by snowfall variation in winter.

ClC-3 promotes angiotensin II-induced reactive oxygen species production in endothelial cells by facilitating Nox2 NADPH oxidase complex formation.

Recent evidence suggests that ClC-3, a member of the ClC family of Cl- channels or Cl-/H+ antiporters, plays a critical role in NADPH oxidase-derived reactive oxygen species (ROS) generation. However, the underling mechanisms remain unclear. In this study we investigated the effects and mechanisms of ClC-3 on NADPH oxidase activation and ROS generation in endothelial cells. Treatment with angiotensin II (Ang II, 1 µmol/L) significantly elevated ClC-3 expression in cultured human umbilical vein endothelial cells (HUVECs). Furthermore, Ang II treatment increased ROS production and NADPH oxidase activity, an effect that could be significantly inhibited by knockdown of ClC-3, and further enhanced by overexpression of ClC-3. SA-ß-galactosidase staining showed that ClC-3 silencing abolished Ang II-induced HUVEC senescence, whereas ClC-3 overexpression caused the opposite effects. We further showed that Ang II treatment increased the translocation of p47phox and p67phox from the cytosol to membrane, accompanied by elevated Nox2 and p22phox expression, which was significantly attenuated by knockdown of ClC-3 and potentiated by overexpression of ClC-3. Moreover, overexpression of ClC-3 increased Ang II-induced phosphorylation of p47phox and p38 MAPK in HUVECs. Pretreatment with a p38 inhibitor SB203580 abolished ClC-3 overexpression-induced increase in p47phox phosphorylation, as well as NADPH oxidase activity and ROS generation. Our results demonstrate that ClC-3 acts as a positive regulator of Ang II-induced NADPH oxidase activation and ROS production in endothelial cells, possibly via promoting both Nox2/p22phox expression and p38 MAPK-dependent p47phox/p67phox membrane translocation, then increasing Nox2 NADPH oxidase complex formation.

Comparative Analyses of Methanogenic and Methanotrophic Communities Between Two Different Water Regimes in Controlled Wetlands on the Qinghai-Tibetan Plateau, China.

Wetlands are an important methane (CH4) emission source. CH4 is mainly produced during the biogeochemical process, in which methanogens and methanotrophs both play important roles. However, little is known how these two microbial communities change under different water regimes. In this study, the diversity and abundance of methanogens and methanotrophs in wetlands on Qinghai-Tibetan Plateau with different water contents (a high water content site DZ2-14-3 and a low water content site DZ2-14-4) were studied by using phylogenetic analysis and quantitative PCR based on mcrA gene and pmoA gene. A total of 16 methanogenic operational taxonomic units (OTUs) and 9 methanotrophic OTUs are obtained. For methanogens, Fen cluster (58.0%) and Methanosaetaceae (20.3%) are the dominant groups in high moisture samples, whereas Methanosaetaceae (32.4%), Methanosarcinaceae (29.4%), and Methanobacteriaceae (22.1%) are prevalent in low moisture samples. Methylobacter (90.0%) of type I methanotrophs are overwhelmingly dominant in high moisture samples, while Methylocystis (53.3%) and Methylomonas (42.2%) belonging to types II and I methanotrophs are the predominant groups in low moisture samples. Furthermore, qPCR analysis revealed that the abundance of methanogens and methanotrophs were higher in high moisture samples than that in low moisture samples. Overall, this comparative study between wetlands controlled by two different water regimes on the Qinghai-Tibetan Plateau provides fundamental data for further research on microbial functions within extreme ecosystems.

ISL1 and JMJD3 synergistically control cardiac differentiation of embryonic stem cells.

ISL1 is expressed in cardiac progenitor cells and plays critical roles in cardiac lineage differentiation and heart development. Cardiac progenitor cells hold great potential for clinical and translational applications. However, the mechanisms underlying ISL1 function in cardiac progenitor cells have not been fully elucidated. Here we uncover a hierarchical role of ISL1 in cardiac progenitor cells, showing that ISL1 directly regulates hundreds of potential downstream target genes that are implicated in cardiac differentiation, through an epigenetic mechanism. Specifically, ISL1 promotes the demethylation of tri-methylation of histone H3K27 (H3K27me3) at the enhancers of key downstream target genes, including Myocd and Mef2c, which are core cardiac transcription factors. ISL1 physically interacts with JMJD3, a H3K27me3 demethylase, and conditional depletion of JMJD3 leads to impaired cardiac progenitor cell differentiation, phenocopying that of ISL1 depletion. Interestingly, ISL1 is not only responsible for the recruitment of JMJD3 to specific target loci during cardiac progenitor differentiation, but also modulates its demethylase activity. In conclusion, ISL1 and JMJD3 partner to alter the cardiac epigenome, instructing gene expression changes that drive cardiac differentiation.

Pathogenicity Genes in Ustilaginoidea virens Revealed by a Predicted Protein-Protein Interaction Network.

Rice false smut, caused by Ustilaginoidea virens, produces significant losses in rice yield and grain quality and has recently emerged as one of the most important rice diseases worldwide. Despite its importance in rice production, relatively few studies have been conducted to illustrate the complex interactome and the pathogenicity gene interactions. Here a protein-protein interaction network of U. virens was built through two well-recognized approaches, interolog- and domain-domain interaction-based methods. A total of 20 217 interactions associated with 3305 proteins were predicted after strict filtering. The reliability of the network was assessed computationally and experimentally. The topology of the interactome network revealed highly connected proteins. A pathogenicity-related subnetwork involving up-regulated genes during early U. virens infection was also constructed, and many novel pathogenicity proteins were predicted in the subnetwork. In addition, we built an interspecies PPI network between U. virens and Oryza sativa, providing new insights for molecular interactions of this host-pathogen pathosystem. A web-based publicly available interactive database based on these interaction networks has also been released. In summary, a proteome-scale map of the PPI network was described for U. virens, which will provide new perspectives for finely dissecting interactions of genes related to its pathogenicity.

Unraveling the contributions of prosodic patterns and individual traits on cross-linguistic perception of Spanish sentence modality.

Cross-linguistic perception is known to be molded by native and second language (L2) experiences. Yet, the role of prosodic patterns and individual characteristics on how speakers of tonal languages perceive L2 Spanish sentence modalities remains relatively underexplored. This study addresses the gap by analyzing the auditory performance of 75 Mandarin speakers with varying levels of Spanish proficiency. The experiment consisted of four parts: the first three collected sociolinguistic profiles and assessed participants' pragmatic competence and musical abilities. The last part involved an auditory gating task, where participants were asked to identify Spanish broad focus statements and information-seeking yes/no questions with different stress patterns. Results indicated that the shape of intonation contours and the position of the final stressed syllable significantly impact learners' perceptual accuracy, with effects modulated by utterance length and L2 proficiency. Moreover, individual differences in pragmatic and musical competence were found to refine auditory and cognitive processing in Mandarin learners, thereby influencing their ability to discriminate question-statement contrasts. These findings reveal the complex interplay between prosodic and individual variations in L2 speech perception, providing novel insights into how speakers of tonal languages process intonation in a non-native Romance language like Spanish.

Evaluation of thyroid-disrupting effects of bisphenol F and bisphenol S on zebrafish (Danio rerio) using anti-transthyretin monoclonal antibody-based immunoassays.

The thyroid disrupting chemicals (TDCs) have raised great concerns due to their adverse impacts on thyroid hormones (THs). In this study, we investigated the thyroid-disrupting effects of bisphenol F (BPF) and bisphenol S (BPS), two major BPA substitutes, on adult zebrafish (Danio rerio). Firstly, anti-transthyretin (TTR) monoclonal antibody (anti-TTR mAb) was prepared and used to establish an indirect ELISA, which had a working range of 15.6∼1000 ng/mL of a detection limit of 6.1 ng/mL. The immunoassays based on anti-TTR mAb showed that exposure to BPF (10 and 100 µg/L) and BPS (100 µg/L) significantly elevated the levels of TTR protein in the plasma, liver, and brain tissues. Moreover, immunofluorescence showed that 100 µg/L BPF and BPS induced the production of TTR protein in liver and brain tissues. In addition, BPF and BPS increased THs levels and damaged thyroid tissue structure in adult female zebrafish. Especially, 100 µg/L BPF significantly increased T4 and T3 levels by 2.05 and 1.14 times, and induced pathological changes of thyroid follicles. The changes in the expression levels of genes involved in the hypothalamus-pituitary-thyroid (HPT) axis further illustrated that BPF and BPS had significant adverse effects on THs homeostasis and thyroid function in zebrafish. Therefore, TTR immunoassays could be used for the evaluation of thyroid-disrupting effects in fish and BPF exhibited greater disruption than BPS.

Trichoderma-derived emodin competes with ExpR and ExpI of Pectobacterium carotovorum subsp. carotovorum to biocontrol bacterial soft rot.

BACKGROUND: Quorum sensing inhibitors (QSIs) are an emerging control tool that inhibits the quorum sensing (QS) system of pathogenic bacteria. We aimed to screen for potential QSIs in the metabolites of Trichoderma and to explore their inhibitory mechanisms. RESULTS: We screened a strain of Trichoderma asperellum LN004, which demonstrated the ability to inhibit the color development of Chromobacterium subtsugae CV026, primarily attributed to the presence of emodin as its key QSI component. The quantitative polymerase chain reaction with reverse transcription results showed that after emodin treatment of Pectobacterium carotovorum subsp. carotovorum (Pcc), plant cell wall degrading enzyme-related synthetic genes were significantly downregulated, and the exogenous enzyme synthesis gene negative regulator (rsmA) was upregulated 3.5-fold. Docking simulations indicated that emodin could be a potential ligand for ExpI and ExpR proteins because it exhibited stronger competition than the natural ligands in Pcc. In addition, western blotting showed that emodin attenuated the degradation of n-acylhomoserine lactone on the ExpR protein and protected it. Different concentrations of emodin reduced the activity of pectinase, cellulase, and protease in Pcc by 20.81%-72.21%, 8.38%-52.73%, and 3.57%-47.50%. Lesion size in Chinese cabbages, carrots and cherry tomatoes following Pcc infestation was reduced by 10.02%-68.57%, 40.17%-88.56% and 11.36%-86.17%. CONCLUSION: Emodin from T. asperellum LN004 as a QSI can compete to bind both ExpI and ExpR proteins, interfering with the QS of Pcc and reducing the production of virulence factors. The first molecular mechanism reveals the ability of emodin as a QSI to competitively inhibit two QS proteins simultaneously. © 2023 Society of Chemical Industry.