Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes.

mRNA translation relies on identifying translation initiation sites (TISs) in mRNAs. Alternative TISs are prevalent across plant transcriptomes, but the mechanisms for their recognition are unclear. Using ribosome profiling and machine learning, we developed models for predicting alternative TISs in the tomato (Solanum lycopersicum). Distinct feature sets were predictive of AUG and nonAUG TISs in 5' untranslated regions and coding sequences, including a novel CU-rich sequence that promoted plant TIS activity, a translational enhancer found across dicots and monocots, and humans and viruses. Our results elucidate the mechanistic and evolutionary basis of TIS recognition, whereby cis-regulatory RNA signatures affect start site selection. The TIS prediction model provides global estimates of TISs to discover neglected protein-coding genes across plant genomes. The prevalence of cis-regulatory signatures across plant species, humans, and viruses suggests their broad and critical roles in reprogramming the translational landscape.

Stratifying TAD boundaries pinpoints focal genomic regions of regulation, damage, and repair.

Advances in chromatin mapping have exposed the complex chromatin hierarchical organization in mammals, including topologically associating domains (TADs) and their substructures, yet the functional implications of this hierarchy in gene regulation and disease progression are not fully elucidated. Our study delves into the phenomenon of shared TAD boundaries, which are pivotal in maintaining the hierarchical chromatin structure and regulating gene activity. By integrating high-resolution Hi-C data, chromatin accessibility, and DNA double-strand breaks (DSBs) data from various cell lines, we systematically explore the complex regulatory landscape at high-level TAD boundaries. Our findings indicate that these boundaries are not only key architectural elements but also vibrant hubs, enriched with functionally crucial genes and complex transcription factor binding site-clustered regions. Moreover, they exhibit a pronounced enrichment of DSBs, suggesting a nuanced interplay between transcriptional regulation and genomic stability. Our research provides novel insights into the intricate relationship between the 3D genome structure, gene regulation, and DNA repair mechanisms, highlighting the role of shared TAD boundaries in maintaining genomic integrity and resilience against perturbations. The implications of our findings extend to understanding the complexities of genomic diseases and open new avenues for therapeutic interventions targeting the structural and functional integrity of TAD boundaries.

The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model.

Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distribution evolves to regulate spatio-temporal gene expression and consequent heritable phenotypic variation. In this study, chromatin accessibility profiles and gene expression profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish and medaka), and chicken. Transcription factor binding sites clustered regions (TFCRs) at different embryonic stages were characterized to investigate regulatory evolution. The study revealed dynamic changes in TFCR distribution during embryonic development and species evolution. The synchronization between TFCR complexity and gene expression was assessed across species using RegulatoryScore. Additionally, an explainable machine learning model highlighted the importance of the distance between TFCR and promoter in the coordinated regulation of TFCRs on gene expression. Our results revealed the developmental and evolutionary dynamics of TFCRs during embryonic development from fish, chicken to mammals. These data provide valuable resources for exploring the relationship between transcriptional regulation and phenotypic differences during embryonic development.

dbEmbryo multi-omics database for analyses of synergistic regulation in early mammalian embryo development.

During early mammalian embryo development, different epigenetic marks undergo reprogramming and play crucial roles in the mediation of gene expression. Currently, several databases provide multi-omics information on early embryos. However, how interconnected epigenetic markers function together to coordinate the expression of the genetic code in a spatiotemporal manner remains difficult to analyze, markedly limiting scientific and clinical research. Here, we present dbEmbryo, an integrated and interactive multi-omics database for human and mouse early embryos. dbEmbryo integrates data on gene expression, DNA methylation, histone modifications, chromatin accessibility, and higher-order chromatin structure profiles for human and mouse early embryos. It incorporates customized analysis tools, such as "multi-omics visualization," "Gene&Peak annotation," "ZGA gene cluster," "cis-regulation," "synergistic regulation," "promoter signal enrichment," and "3D genome." Users can retrieve gene expression and epigenetic profile patterns to analyze synergistic changes across different early embryo developmental stages. We showed the uniqueness of dbEmbryo among extant databases containing data on early embryo development and provided an overview. Using dbEmbryo, we obtained a phase-separated model of transcriptional control during early embryo development. dbEmbryo offers web-based analytical tools and a comprehensive resource for biologists and clinicians to decipher molecular regulatory mechanisms of human and mouse early embryo development.

EpiCarousel: memory- and time-efficient identification of metacells for atlas-level single-cell chromatin accessibility data.

SUMMARY: Recent technical advancements in single-cell chromatin accessibility sequencing (scCAS) have brought new insights to the characterization of epigenetic heterogeneity. As single-cell genomics experiments scale up to hundreds of thousands of cells, the demand for computational resources for downstream analysis grows intractably large and exceeds the capabilities of most researchers. Here, we propose EpiCarousel, a tailored Python package based on lazy loading, parallel processing, and community detection for memory- and time-efficient identification of metacells, i.e. the emergence of homogenous cells, in large-scale scCAS data. Through comprehensive experiments on five datasets of various protocols, sample sizes, dimensions, number of cell types, and degrees of cell-type imbalance, EpiCarousel outperformed baseline methods in systematic evaluation of memory usage, computational time, and multiple downstream analyses including cell type identification. Moreover, EpiCarousel executes preprocessing and downstream cell clustering on the atlas-level dataset with 707 043 cells and 1 154 611 peaks within 2 h consuming <75 GB of RAM and provides superior performance for characterizing cell heterogeneity than state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: The EpiCarousel software is well-documented and freely available at https://github.com/biox-nku/epicarousel. It can be seamlessly interoperated with extensive scCAS analysis toolkits.

Translation initiation landscape profiling reveals hidden open-reading frames required for the pathogenesis of tomato yellow leaf curl Thailand virus.

Plant viruses with densely packed genomes employ noncanonical translational strategies to increase the coding capacity for viral function. However, the diverse translational strategies used make it challenging to define the full set of viral genes. Here, using tomato yellow leaf curl Thailand virus (TYLCTHV, genus Begomovirus) as a model system, we identified genes beyond the annotated gene sets by experimentally profiling in vivo translation initiation sites (TISs). We found that unanticipated AUG TISs were prevalent and determined that their usage involves alternative transcriptional and/or translational start sites and is associated with flanking mRNA sequences. Specifically, two downstream in-frame TISs were identified in the viral gene AV2. These TISs were conserved in the begomovirus lineage and led to the translation of different protein isoforms localized to cytoplasmic puncta and at the cell periphery, respectively. In addition, we found translational evidence of an unexplored gene, BV2. BV2 is conserved among TYLCTHV isolates and localizes to the endoplasmic reticulum and plasmodesmata. Mutations of AV2 isoforms and BV2 significantly attenuated disease symptoms in tomato (Solanum lycopersicum). In conclusion, our study pinpointing in vivo TISs untangles the coding complexity of a plant viral genome and, more importantly, illustrates the biological significance of the hidden open-reading frames encoding viral factors for pathogenicity.

Compressible and Elastic Reduced Graphene Oxide Sponge for Stable and Dendrite-Free Lithium Metal Anodes.

Dendritic Li deposition, an unstable solid-electrolyte interphase (SEI), and a nearly infinite relative volume change during cycling are three major obstacles to the practical application of Li metal batteries. Herein, we introduce a compressible and elastic reduced graphene oxide sponge (rGO-S) to simultaneously eliminate Li dendrite growth, stabilize the SEI, and accommodate the volume change. The volume change is contained by compressing and expanding the rGO-S anode, which effectively releases the Li plating-induced stress during cycling. The smooth and dense Li metal is deposited on rGO-S without dendrites, which preserves the SEI, reduces consumption of the electrolyte, and prevents the formation of Li debris. The half-cells employing rGO-S show a steady and high Coulombic efficiency. The Li@rGO-S symmetric cells demonstrate excellent cycling stability over 1200 cycles with a low overpotential. When paired with LiFePO4 (LFP), the Li@rGO-S||LFP full cells exhibit a high specific capacity (150.3 mAh g-1 at 1C), superior rate performance, and good capacity retention.

Simultaneous Dual-Gene Test of Methicillin-Resistant Staphylococcus Aureus using an Argonaute-Centered Portable and Visual Biosensor.

The development of novel method for drug-resistant bacteria detection is imperative. A simultaneous dual-gene Test of methicillin-resistant Staphylococcus aureus (MRSA) is developed using an Argonaute-centered portable biosensor (STAR). This is the first report concerning Argonaute-based pathogenic bacteria detection. Simply, the species-specific mecA and nuc gene are isothermally amplified using loop-mediated isothermal amplification (LAMP) technique, followed by Argonaute-based detection enabled by its programmable, guided, sequence-specific recognition and cleavage. With the strategy, the targeted nucleic acid signals gene are dexterously converted into fluorescent signals. STAR is capable of detecting the nuc gene and mecA gene simultaneously in a single reaction. The limit of detection is 10 CFU/mL with a dynamic range from 10 to 107 CFU/mL. The sample-to-result time is <65 min. This method is successfully adapted to detect clinical samples, contaminated foods, and MRSA-infected animals. This work broadens the reach of Argonaute-based biosensing and presents a novel bacterial point-of-need (PON) detection platform.

Linkage and association mapping in multi-parental populations reveal the genetic basis of carotenoid variation in maize kernels.

Carotenoids are indispensable to plants and critical components of the human diet. The carotenoid metabolic pathway is conserved across plant species, but our understanding of the genetic basis of carotenoid variation remains limited for the seeds of most cereal crops. To address this issue, we systematically performed linkage and association mapping for eight carotenoid traits using six recombinant inbred line (RIL) populations. Single linkage mapping (SLM) and joint linkage mapping (JLM) identified 77 unique additive QTLs and 104 pairs of epistatic QTLs. Among these QTLs, we identified 22 overlapping hotspots of additive and epistatic loci, highlighting the important contributions of some QTLs to carotenoid levels through additive or epistatic mechanisms. A genome-wide association study based on all RILs detected 244 candidate genes significantly associated with carotenoid traits, 23 of which were annotated as carotenoid pathway genes. Effect comparisons suggested that a small number of loci linked to pathway genes have substantial effects on carotenoid variation in our tested populations, but many loci not associated with pathway genes also make important contributions to carotenoid variation. We identified ZmPTOX as the causal gene for a QTL hotspot (Q10/JLM10/GWAS019); this gene encodes a putative plastid terminal oxidase that produces plastoquinone-9 used by two enzymes in the carotenoid pathway. Natural variants in the promoter and second exon of ZmPTOX were found to alter carotenoid levels. This comprehensive assessment of the genetic mechanisms underlying carotenoid variation establishes a foundation for rewiring carotenoid metabolism and accumulation for efficient carotenoid biofortification.

Platycodin D2 enhances P21/CyclinA2-mediated senescence of HCC cells by regulating NIX-induced mitophagy.

BACKGROUND: Hepatocellular carcinoma (HCC) cells usually show strong resistance to chemotherapy, which not only reduces the efficacy of chemotherapy but also increases the side effects. Regulation of autophagy plays an important role in tumor treatment. Cell senescence is also an important anti-cancer mechanism, which has become an important target for tumor treatment. Therefore, it is of great clinical significance to find anti-HCC drugs that act through this new mechanism. Platycodin D2 (PD2) is a new saponin compound extracted from the traditional Chinese medicine Platycodon grandiflorum. PURPOSE: Our study aimed to explore the effects of PD2 on HCC and identify the underlying mechanisms. METHODS: First, the CCK8 assay was used to detect the inhibitory effect of PD2 on HCC cells. Then, different pathways of programmed cell death and cell cycle regulators were measured. In addition, we assessed the effects of PD2 on the autophagy and senescence of HCC cells by flow cytometry, immunofluorescence staining, and Western blotting. Finally, we studied the in vivo effect of PD2 on HCC cells by using a mouse tumor-bearing model. RESULTS: Studies have shown that PD2 has a good anti-tumor effect, but the specific molecular mechanism has not been clarified. In this study, we found that PD2 has no obvious toxic effect on normal hepatocytes, but it can significantly inhibit the proliferation of HCC cells, induce mitochondrial dysfunction, enhance autophagy and cell senescence, upregulate NIX and P21, and downregulate CyclinA2. Gene silencing and overexpression indicated that PD2 induced mitophagy in HCC cells through NIX, thereby activating the P21/CyclinA2 pathway and promoting cell senescence. CONCLUSIONS: These results indicate that PD2 induces HCC cell death through autophagy and aging. Our findings provide a new strategy for treating HCC.

Zinc finger protein ZBTB17 controls cellular senescence via interacting with nuclear receptor RXRA and its downstream calcium signaling.

Cellular senescence is broadly known as a stable cell cycle arrest accompanied by a senescence-associated secretory phenotype (SASP). In the past decades, calcium signaling has emerged as a key mediator of cellular senescence. However, the transcriptional regulation of calcium signaling during cellular senescence remains partially understood. We have previously identified the nuclear receptor RXRA as a key senescence repressor through inhibiting the endoplasmic reticulum (ER) calcium release channel inositol 1,4,5-trisphosphate receptor, type 2 (ITPR2) mediated intracellular calcium signaling. Nevertheless, as a transcriptional recruiter, the mechanism by which RXRA inhibits ITPR2 during cellular senescence remains unclear. Here we identified the zinc finger protein ZBTB17 can interact with RXRA. Interestingly, knockdown of ZBTB17 induces a cascade of RXRA-dependent intracellular calcium signaling, mitochondrial membrane potential (MMP), reactive oxygen species (ROS) accumulation, DNA damages, and ultimately cellular senescence. Moreover, the signaling and senescence phenotype induced by knocking down of ZBTB17 can also be abolished after silencing ITPR2. Altogether, our work provides a new mechanism controlling intracellular calcium signaling and cellular senescence and unveils novel insight toward the role of zinc finger proteins.

Transcriptome analysis reveals tissue-specific responses of Mytilus unguiculatus to Vibrio alginolyticus infection.

Mytilus unguiculatus is an important economic bivalve species with wide consumption and aquaculture value. Disease is one of the primary limiting factors in mussel aquaculture, thus understanding the response of different tissues of M. unguiculatus to pathogens is crucial for disease prevention and control. In this study, we investigated the physiological and transcriptomic responses of the gills, adductor muscle, and mantle of M. unguiculatus infected with Vibrio alginolyticus. The results showed that V. alginolyticus infection caused inflammation and tissue structure changes in the gill, adductor muscle and mantle of M. unguiculatus. Meanwhile, the activities of superoxide dismutase and catalase in the three tissues increased, while the total antioxidant capacity decreased, suggesting that M. unguiculatus have an activated defense mechanism against infection-induced oxidative stress, despite a compromised total antioxidant capacity. Transcriptomic studies reveal that infected M. unguiculatus exhibits upregulation of endocytosis, lysosome activity, cellular apoptosis, and immune-related signaling pathways, indicating that M. unguiculatus responds to pathogen invasion by upregulating efferocytosis. Compared with the gill and adductor muscle, the mantle had a higher level of mytimycin, mytilin and myticin, and the three tissues also increased the expression of mytimycin to cope with the invasion of pathogens. In addition, the analysis of genes related to taste transduction pathways and muscle contraction and relaxation found that after infection with V. alginolyticus, M. unguiculatus may reduce appetite by inhibiting taste transduction in the gill, while improving muscle contraction of the adductor muscle and keeping the shell closed, to resist further invasion of pathogens and reduce the risk of pathogen transmission in the population.

Comparative performance of contact plate metod and swab method for surface microbial contamination on medical fabrics.

BACKGROUND: The contact plate method is widely accepted and used in various fields where hygiene and contamination levels are crucial. Evidence regarding the applicability of the contact plate method for sampling fabric microbial contamination levels in real medical environments was limited. This study aimed to assess the applicability of the contact plate method for detecting microbial contamination on medical fabrics in a real healthcare environment, thereby providing a benchmark for fabric microbial sampling methods. METHODS: In a level three obstetrics ward of a hospital, twenty-four privacy curtains adjacent to patient beds were selected for this study. The contact plate and swab method were used to collect microbial samples from the privacy curtains on the 1st, 7th, 14th, and 28th days after they were hung. The total colony count on each privacy curtain surface was calculated, and microbial identification was performed. RESULTS: After excluding the effects of time, room type, and curtain location on the detected microbial load, the linear mixed-effects model analysis showed that contact plate method yielded lower colony counts compared to swab method (P < 0.001). However, the contact plate method isolated more microbial species than swab method (P < 0.001). 291 pathogenic strains were isolated using the contact plate method and 133 pathogenic strains were isolated via the swab method. There was no difference between the two sampling methods in the detection of gram-negative bacteria (P = 0.089). Furthermore, the microbial load on curtains in double-occupancy rooms was lower than those in triple-occupancy rooms (P = 0.021), and the microbial load on curtains near windows was lower than that near doors (P = 0.004). CONCLUSION: Contact plate method is superior to swab method in strain isolation. Swab method is more suitable for evaluating the bacterial contamination of fabrics.

The design, synthesis and bioactivity evaluation of novel androgen receptor degraders based on hydrophobic tagging.

Prostate Cancer (PCa) easily progress to metastatic Castration-Resistant Prostate Cancer (mCRPC) that remains a significant cause of cancer-related death. Androgen receptor (AR)-dependent transcription is a major driver of prostate tumor cell proliferation. Proteolysis-targeting chimaera (PROTAC) technology based on Hydrophobic Tagging (HyT) represents an intriguing strategy to regulate the function of therapeutically androgen receptor proteins. In the present study, we have designed, synthesized, and evaluated a series of PROTAC-HyT AR degraders using AR antagonists, RU59063, which were connected with adamantane-based hydrophobic moieties by different alkyl chains. Compound D-4-6 exhibited significant AR protein degradation activity, with a degradation rate of 57 % at 5 µM and nearly 90 % at 20 µM in 24 h, and inhibited the proliferation of LNCaP cells significantly with an IC50 value of 4.77 ± 0.26 µM in a time-concentration-dependent manner. In conclusion, the present study lays the foundation for the development of a completely new class of therapeutic agents for the treatment of mCRPC, and further design and synthesis of AR-targeting degraders are currently in progress for better degradation rate.

Spatiotemporal variations in soil pollution by polycyclic aromatic hydrocarbons over a 20-year economic boom in different districts of a heavy industrial city in North China.

Urbanization-related human activities, such as population aggregation, rapid industrial expansion, and intensified traffic, are key factors that impact local polycyclic aromatic hydrocarbon emissions and their associated health risks. Consequently, regions with varying degrees of urbanization within a megacity may exhibit diverse spatiotemporal patterns in the presence and distribution of soil polycyclic aromatic hydrocarbons, resulting in different levels of ecological risks for local inhabitants following the same period of development. In this study, we measured the concentrations of 16 polycyclic aromatic hydrocarbons in soil samples collected from industrial district and rural district in Tianjin (China) in 2018, and compared with polycyclic aromatic hydrocarbon data in 2001 from a previous study to characterize these regional variations in occurrence, source, and human risk of polycyclic aromatic hydrocarbons induced by urbanization with time and space. The results indicate the 20-year rapid urbanization and industrialization has differentially affected the composition, distribution and sources of polycyclic aromatic hydrocarbons in soils from different economic functional zones in Tianjin. Additionally, its impact on health risks in rural district appeared to be more significant than that in industrial district.

Copper-zinc nanoparticle-decorated nitrogen-doped carbon composite for electrochemical determination of triclosan.

A new sensor based on copper-zinc bimetal embedded and nitrogen-doped carbon-based composites (CuZn@NC) was prepared for triclosan (TCS) detection by pyrolyzing the precursor of Cu-Zn binuclear metal-organic framework (MOF). The performance for detecting TCS was evaluated using linear scanning voltammetry (LSV) and differential pulse voltammetry (DPV), and the proton and electron numbers during TCS oxidation have been proved to be one-to-one. The results indicated that CuZn@NC can present a satisfactory analysis performance for TCS detection. Under the optimized conditions, the linear response range was 0.2-600 µM and the detection limit was 47.9 nM. The sensor presented good stability (signal current dropped only 2.5% after 21 days) and good anti-interference of inorganic salts and small molecular organic acids. The good recovery (97.5-104.1%) for detecting spiked TCS in commercial products (toothpaste and hand sanitizer) suggested its potential for routine determination of TCS in real samples.

The Application of Piecewise Regularization Reconstruction to the Calibration of Strain Beams.

Standard beams are mainly used for the calibration of strain sensors using their load reconstruction models. However, as an ill-posed inverse problem, the solution to these models often fails to converge, especially when dealing with dynamic loads of different frequencies. To overcome this problem, a piecewise Tikhonov regularization method (PTR) is proposed to reconstruct dynamic loads. The transfer function matrix is built both using the denoised excitations and the corresponding responses. After singular value decomposition (SVD), the singular values are divided into submatrices of different sizes by utilizing a piecewise function. The regularization parameters are solved by optimizing the piecewise submatrices. The experimental result shows that the MREs of the PTR method are 6.20% at 70 Hz and 5.86% at 80 Hz. The traditional Tikhonov regularization method based on GCV exhibits MREs of 28.44% and 29.61% at frequencies of 70 Hz and 80 Hz, respectively, whereas the L-curve-based approach demonstrates MREs of 29.98% and 18.42% at the same frequencies. Furthermore, the PREs of the PTR method are 3.54% at 70 Hz and 3.73% at 80 Hz. The traditional Tikhonov regularization method based on GCV exhibits PREs of 27.01% and 26.88% at frequencies of 70 Hz and 80 Hz, respectively, whereas the L-curve-based approach demonstrates PREs of 29.50% and 15.56% at the same frequencies. All in all, the method proposed in this paper can be extensively applied to load reconstruction across different frequencies.

Model of predicting fear of cancer recurrence in patients with digestive tract cancer: A cross-sectional study.

AIMS: To investigate the incidence of fear of cancer recurrence in patients with digestive tract cancers analyse its influencing factors, and further establish a visual risk prediction model. DESIGN: A cross-sectional study. METHODS: A cross-sectional survey was conducted among 570 patients with digestive tract tumours admitted to a local hospital, from May 2023 to December 2023 by convenient sampling method. Univariate analysis and logistic analysis were performed on the influencing factors, and the risk prediction nomogram model of fear of cancer recurrence in patients with digestive tract cancer was constructed by using R 4.1.3 software. ROC curve was used to evaluate the differentiation of the nomogram model. The calibration curve and Hosmer-Lemeshow goodness of fit test were used to evaluate the consistency of the model. This study was reported using the TRIPOD checklist. RESULTS: In this study, 272 (47.7%) patients developed fear of recurrence. The risk prediction model of recurrence fear column chart for digestive tract cancer patients incorporated six variables of gender, therapy, alimentary tract haemorrhage, pain, depression and social support. The C-statistic was (.976), and the calibration curve showed that the predicted probability was more in line with the actual probability of occurrence, and the decision curve showed that the predictive model had better practicality. CONCLUSION: The column-line diagram prediction model constructed in this study is effective and facilitates timely intervention and management by healthcare professionals based on their risk factors. IMPACT: Nomogram is helpful to calculate the risk probability of FCR in patients with digestive tract cancer, identify FCR patients in time, and formulate comprehensive and personalized countermeasures, to provide a good quality of life and prolong the survival cycle of patients with digestive tract cancer. PATIENT OR PUBLIC CONTRIBUTION: Participants were hospitalized patients or patients with digestive tract cancer undergoing follow-up. First of all, before the investigation and research, a team is formed to discuss the concept, research purpose, method, significance, etc., and determine the research tools. Second, by reasonably explaining the study to patients to seek informed consent from the patient and sign it, patients filled in the questionnaire independently. For patients with low education levels who could not fill in the questionnaire, the team members made objective explanations to help them choose reasonable options.

Genome-Wide Identification, Expression Analysis under Abiotic Stress and Co-Expression Analysis of MATE Gene Family in Torreya grandis.

The multidrug and toxin efflux (MATE) family participates in numerous biological processes and plays important roles in abiotic stress responses. However, information about the MATE family genes in Torreya grandis remains unclear. In this study, our genome-wide investigation identified ninety MATE genes in Torreya grandis, which were divided into five evolutionary clades. TgMATE family members are located on eleven chromosomes, and a total of thirty TgMATEs exist in tandem duplication. The promoter analysis showed that most TgMATEs contain the cis-regulatory elements associated with stress and hormonal responses. In addition, we discovered that most TgMATE genes responded to abiotic stresses (aluminum, drought, high temperatures, and low temperatures). Weighted correlation network analysis showed that 147 candidate transcription factor genes regulated the expression of 14 TgMATE genes, and it was verified through a double-luciferase assay. Overall, our findings offer valuable information for the characterization of the TgMATE gene mechanism in responding to abiotic stress and exhibit promising prospects for the stress tolerance breeding of Torreya grandis.

Ecological effect of microplastics on soil microbe-driven carbon circulation and greenhouse gas emission: A review.

Soil organic carbon (SOC) pool, the largest part of terrestrial ecosystem, controls global terrestrial carbon balance and consequently presented carbon cycle-climate feedback in climate projections. Microplastics, (MPs, <5 mm) as common pollutants in soil ecosystems, have an obvious impact on soil-borne carbon circulation by affecting soil microbial processes, which play a central role in regulating SOC conversion. In this review, we initially presented the sources, properties and ecological risks of MPs in soil ecosystem, and then the differentiated effects of MPs on the component of SOC, including dissolved organic carbon, soil microbial biomass carbon and easily oxidized organic carbon varying with the types and concentrations of MPs, the soil types, etc. As research turns into a broader perspective, greenhouse gas emissions dominated by the mineralization of SOC coming into view since it can be significantly affected by MPs and is closely associated with soil microbial respiration. The pathways of MPs impacting soil microbes-driven carbon conversion include changing microbial community structure and composition, the functional enzyme's activity and the abundance and expression of functional genes. However, numerous uncertainties still exist regarding the microbial mechanisms in the deeper biochemical process. More comprehensive studies are necessary to explore the affected footprint and provide guidance for finding the evaluation criterion of MPs affecting climate change.