Deciphering the intricate hierarchical gene regulatory network: unraveling multi-level regulation and modifications driving secondary cell wall formation.

Wood quality is predominantly determined by the amount and the composition of secondary cell walls (SCWs). Consequently, unraveling the molecular regulatory mechanisms governing SCW formation is of paramount importance for genetic engineering aimed at enhancing wood properties. Although SCW formation is known to be governed by a hierarchical gene regulatory network (HGRN), our understanding of how a HGRN operates and regulates the formation of heterogeneous SCWs for plant development and adaption to ever-changing environment remains limited. In this review, we examined the HGRNs governing SCW formation and highlighted the significant key differences between herbaceous Arabidopsis and woody plant poplar. We clarified many confusions in existing literatures regarding the HGRNs and their orthologous gene names and functions. Additionally, we revealed many network motifs including feed-forward loops, feed-back loops, and negative and positive autoregulation in the HGRNs. We also conducted a thorough review of post-transcriptional and post-translational aspects, protein-protein interactions, and epigenetic modifications of the HGRNs. Furthermore, we summarized how the HGRNs respond to environmental factors and cues, influencing SCW biosynthesis through regulatory cascades, including many regulatory chains, wiring regulations, and network motifs. Finally, we highlighted the future research directions for gaining a further understanding of molecular regulatory mechanisms underlying SCW formation.

Regulation of regeneration in Arabidopsis thaliana.

We employed several algorithms with high efficacy to analyze the public transcriptomic data, aiming to identify key transcription factors (TFs) that regulate regeneration in Arabidopsis thaliana. Initially, we utilized CollaborativeNet, also known as TF-Cluster, to construct a collaborative network of all TFs, which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder (CoSE) algorithms. Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration. We further applied principal component analysis and gene ontology (GO) enrichment analysis to reduce the subnetworks from nine to three, namely subnetworks 1, 12, and 17. Searching for TF-binding sites in the promoters of the co-expressed and co-regulated (CCGs) genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each subnetwork. Finally, six potential candidate TFs-WOX9A, LEC2, PGA37, WIP5, PEI1, and AIL1 from subnetwork 1-were identified, and their roles in somatic embryogenesis (GO:0010262) and regeneration (GO:0031099) were discussed, so were the TFs in Subnetwork 12 and 17 associated with regeneration. The TFs identified were also assessed using the CIS-BP database and Expression Atlas. Our analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to regeneration. The tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest. Supplementary Information: The online version contains supplementary material available at 10.1007/s42994-023-00121-9.

The influence of preoperative urodynamic parameters on clinical results in patients with benign prostatic hyperplasia after transurethral resection of the prostate.

PURPOSE: To identify the urodynamic parameters affecting the clinical outcomes of transurethral resection of the prostate(TURP) surgery for patients with benign prostatic hyperplasia(BPH) by multifactor analysis and establish a regression model with diagnostic values. METHODS: The medical records of patients who underwent TURP surgery for BPH between December 2018 and September 2021 were collected from the urology department of the Second Affiliated Hospital of Kunming Medical University, Kunming, China. The patients' clinical data and urodynamic parameters were collected before surgery. The urodynamic parameters affecting surgical efficacy were identified by multifactor analysis, and a regression model with diagnostic values was established and evaluated. RESULTS: A total of 201 patients underwent TURP, of whom 144 had complete preoperative urodynamic data. Each urodynamic factor was subjected to multifactor analysis, and the bladder contractility index (BCI), bladder outflow obstruction index (BOOI), bladder residual urine, and bladder compliance (BC) were found to be independent influence factors on the efficacy of TURP in patients with BPH. The diagnostic value of the regression model was analyzed by receiver operating characteristics (ROC) analysis, and it was found that the AUC = 0.939 (95% CI 0.886-0.972), for which the sensitivity and specificity were 95.19% and 80%, respectively. CONCLUSIONS: The regression model had high diagnostic sensitivity and specificity in predicting the efficacy of surgery, and the diagnostic value was higher than that of individual urodynamic factors. Therefore, BCI, BOOI, bladder residual urine, and BC should be considered as independent influence factors on the efficacy of TURP surgery for BPH.

Effect of preoperative prophylactic antibiotic use on postoperative infection after percutaneous nephrolithotomy in patients with negative urine culture: a single-center randomized controlled trial.

PURPOSE: To compare the effects of different preoperative antibiotic prophylaxis (ABP) regimens on the incidence of sepsis after percutaneous nephrolithotomy (PCNL) in patients with negative urine culture. METHODS: A single-center, randomized controlled trial (June 2022-December 2023) included 120 patients with negative preoperative urine cultures for upper urinary tract stones who underwent PCNL (chictr.org.cn; ChiCTR2200059047). The experimental group and the control group were respectively given different levofloxacin-based preoperative ABP regimes, including 3 days before surgery and no ABP before surgery. Both groups were given a dose of antibiotics before the operation. The primary outcome was differences in the incidence of postoperative sepsis. RESULTS: A total of 120 subjects were included, including 60 patients in the experimental group and 60 patients in the control group. The baseline characteristics of the two groups were comparable and intraoperative characteristics also did not differ. The sepsis rate was not statistically different between the experimental and control groups (13.3% vs.13.3%, P = 1.0). A multivariate logistic regression analysis revealed that body mass index (BMI) (OR = 1.3; 95% CI = 1.1-1.6; P = 0.003) and operating time (OR = 1.1; 95% CI = 1.0-1.1; P = 0.012) were independent risk factors of sepsis. CONCLUSION: Our study showed that prophylactic antibiotic administration for 3 days before surgery did not reduce the incidence of postoperative sepsis in patients with negative urine cultures undergoing PCNL. For this subset of patients, we recommend that a single dose of antibiotics be given prior to the commencement of surgery seems adequate.

TGPred: efficient methods for predicting target genes of a transcription factor by integrating statistics, machine learning and optimization.

Four statistical selection methods for inferring transcription factor (TF)-target gene (TG) pairs were developed by coupling mean squared error (MSE) or Huber loss function, with elastic net (ENET) or least absolute shrinkage and selection operator (Lasso) penalty. Two methods were also developed for inferring pathway gene regulatory networks (GRNs) by combining Huber or MSE loss function with a network (Net)-based penalty. To solve these regressions, we ameliorated an accelerated proximal gradient descent (APGD) algorithm to optimize parameter selection processes, resulting in an equally effective but much faster algorithm than the commonly used convex optimization solver. The synthetic data generated in a general setting was used to test four TF-TG identification methods, ENET-based methods performed better than Lasso-based methods. Synthetic data generated from two network settings was used to test Huber-Net and MSE-Net, which outperformed all other methods. The TF-TG identification methods were also tested with SND1 and gl3 overexpression transcriptomic data, Huber-ENET and MSE-ENET outperformed all other methods when genome-wide predictions were performed. The TF-TG identification methods fill the gap of lacking a method for genome-wide TG prediction of a TF, and potential for validating ChIP/DAP-seq results, while the two Net-based methods are instrumental for predicting pathway GRNs.

Characteristics of Salvia miltiorrhiza methylome and the regulatory mechanism of DNA methylation in tanshinone biosynthesis.

Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value. Its roots produce a group of diterpenoid lipophilic bioactive components, termed tanshinones. Biosynthesis and regulation of tanshinones has attracted widespread interest. However, the methylome of S. miltiorrhiza has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely unknown. Here we report single-base resolution DNA methylomes from roots and leaves. Comparative analysis revealed differential methylation patterns for CG, CHG, and CHH contexts and the association between DNA methylation and the expression of genes and small RNAs. Lowly methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in S. miltiorrhiza. DNA methylation variation analysis showed that CHH methylation contributed mostly to the difference. Go enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_root. Tanshinone biosynthesis-related enzyme genes, such as DXS2, CMK, IDI1, HMGR2, DXR, MDS, CYP76AH1, 2OGD25, and CYP71D373, were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in March. Consistently, gene expression was up-regulated in S. miltiorrhiza roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone production. It suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in S. miltiorrhiza through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.

Heritable epigenetic modification of BpPIN1 is associated with leaf shapes in Betula pendula.

The new variety Betula pendula 'Dalecarlica', selected from Betula pendula, shows high ornamental value owing to its lobed leaf shape. In this study, to identify the genetic components of leaf shape formation, we performed bulked segregant analysis and molecular marker-based fine mapping to identify the causal gene responsible for lobed leaves in B. pendula 'Dalecarlica'. The most significant variations associated with leaf shape were identified within the gene BpPIN1 encoding a member of the PIN-FORMED family, responsible for the auxin efflux carrier. We further confirmed the hypomethylation at the promoter region promoting the expression level of BpPIN1, which causes stronger and longer veins and lobed leaf shape in B. pendula 'Dalecarlica'. These results indicated that DNA methylation at the BpPIN1 promoter region is associated with leaf shapes in B. pendula. Our findings revealed an epigenetic mechanism of BpPIN1 in the regulation of leaf shape in Betula  Linn. (birch), which could help in the molecular breeding of ornamental traits.

The Influence of Preoperative Hydronephrosis on the Prognosis after Radical Cystectomy among Patients with Different Pathological Stages of Bladder Cancer.

INTRODUCTION: Preoperative hydronephrosis is closely associated with the prognosis of patients with bladder cancer. This study assesses the effect of preoperative hydronephrosis on the prognosis after radical cystectomy (RC) among patients with different pathological stages of bladder urothelial carcinoma. METHODS: We retrospectively analyzed the clinical data of 231 patients who underwent RC because of bladder urothelial carcinoma at our institution from January 2013 to December 2017. The overall survival (OS) in patients with or without preoperative hydronephrosis was followed up and compared, and the prognostic role that preoperative hydronephrosis played in patients with different pathological stages of bladder cancer was analyzed. Multivariate analysis was performed with the help of Cox proportional hazards regression models, the postoperative survival was analyzed with the help of Kaplan-Meier plots and log-rank test, and the p values of multiple testing were corrected using the Bonferroni correction. RESULTS: Of 231 patients, 96 were patients with preoperative hydronephrosis and 115 patients had died by the end of the follow-up. Survival analysis found the 3- and 5-year survival rates after radical surgery of patients with preoperative hydronephrosis were significantly lower than those of patients without preoperative hydronephrosis (p < 0.001). Multivariate analysis found preoperative hydronephrosis, T stage of tumor, and lymphatic metastasis were independent influencing factors of postoperative OS (p < 0.05). Survival analysis of subgroups according to pathological stages found in pT3-4N0M0 patients had a significant difference in postoperative survival between the group with preoperative hydronephrosis and the group without preoperative hydronephrosis (p < 0.0001). CONCLUSION: The results indicate that preoperative hydronephrosis mainly affects postoperative OS in the patients whose pathological stage of bladder cancer is pT3-4N0M0.

Bacterium-enabled transient gene activation by artificial transcription factors for resolving gene regulation in maize.

Understanding gene regulatory networks is essential to elucidate developmental processes and environmental responses. Here, we studied regulation of a maize (Zea mays) transcription factor gene using designer transcription activator-like effectors (dTALes), which are synthetic Type III TALes of the bacterial genus Xanthomonas and serve as inducers of disease susceptibility gene transcription in host cells. The maize pathogen Xanthomonas vasicola pv. vasculorum was used to introduce 2 independent dTALes into maize cells to induced expression of the gene glossy3 (gl3), which encodes a MYB transcription factor involved in biosynthesis of cuticular wax. RNA-seq analysis of leaf samples identified, in addition to gl3, 146 genes altered in expression by the 2 dTALes. Nine of the 10 genes known to be involved in cuticular wax biosynthesis were upregulated by at least 1 of the 2 dTALes. A gene previously unknown to be associated with gl3, Zm00001d017418, which encodes aldehyde dehydrogenase, was also expressed in a dTALe-dependent manner. A chemically induced mutant and a CRISPR-Cas9 mutant of Zm00001d017418 both exhibited glossy leaf phenotypes, indicating that Zm00001d017418 is involved in biosynthesis of cuticular waxes. Bacterial protein delivery of dTALes proved to be a straightforward and practical approach for the analysis and discovery of pathway-specific genes in maize.

The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine.

Epigenetics has been revealed to play a crucial role in the long-term memory in plants. However, little is known about whether the epigenetic modifications occur with age progressively in conifers. Here, we present the single-base resolution DNA methylation landscapes of the 25-gigabase Chinese pine (Pinus tabuliformis) genome at different ages. The result shows that DNA methylation is closely coupled with the regulation of gene transcription. The age-dependent methylation profile with a linearly increasing trend is the most significant pattern of DMRs between ages. Two segments at the five-prime end of the first ultra-long intron in DAL1, a conservative age biomarker in conifers, shows a gradual decline of CHG methylation as the age increased, which is highly correlated with its expression profile. Similar high correlation is also observed in nine other age marker genes. Our results suggest that DNA methylation serves as an important epigenetic signature of developmental age in conifers.

Autotetraploidization Alters Morphology, Photosynthesis, Cytological Characteristics and Fruit Quality in Sour Jujube (Ziziphus acidojujuba Cheng et Liu).

Artificially induced polyploidization is one of the most effective techniques for improving the biological properties and creating new cultivars of fruit trees. Up to now, systematic research on the autotetraploid of sour jujube (Ziziphus acidojujuba Cheng et Liu) has not been reported. 'Zhuguang' is the first released autotetraploid sour jujube induced with colchicine. The objective of this study was to compare the differences in the morphological, cytological characteristics, and fruit quality between diploid and autotetraploid. Compared with the original diploid, 'Zhuguang' showed dwarf phenotypes and decreased tree vigor. The sizes of the flowers, pollen, stomata, and leaves of 'Zhuguang' were larger. Perceptible darker green leaves were observed in 'Zhuguang' trees owing to increased chlorophyll contents, which led to higher photosynthesis efficiency and bigger fruit. The pollen activities and the contents of ascorbic acid, titratable acid, and soluble sugar in the autotetraploid were lower than those in diploids. However, the cyclic adenosine monophosphate content in autotetraploid fruit was significantly higher. The sugar/acid ratio of autotetraploid fruit was higher than that of diploid fruit, which made the autotetraploid fruit taste different and better. The results indicated that the autotetraploid we generated in sour jujube could greatly meet the goals of our multi-objective optimized breeding strategies for improving sour jujube, which includes tree dwarfing, increased photosynthesis efficiency, and better nutrient values and flavors as well as more bioactive compounds. Needless to say, the autotetraploid can also serve as material for generating valuable triploids or other types of polyploids and are also instrumental in studying the evolution of both sour jujube and Chinese jujube (Ziziphus jujuba Mill.).

High temperature inhibited the accumulation of anthocyanin by promoting ABA catabolism in sweet cherry fruits.

Color is an essential appearance characteristic of sweet cherry (Prunus avium L.) fruits and mainly determined by anthocyanin. Temperature plays an important role in the regulation of anthocyanin accumulation. In this research, anthocyanin, sugar, plant hormone and related gene expression were analyzed using physiological and transcriptomic methods in order to reveal the effects of high temperature on fruit coloring and the related mechanism. The results showed that high temperature severely inhibited anthocyanin accumulation in fruit peel and slowed the coloring process. The total anthocyanin content in fruit peel increased by 455% and 84% after 4 days of normal temperature treatment (NT, 24°C day/14°C night) and high temperature treatment (HT, 34°C day/24°C night), respectively. Similarly, the contents of 8 anthocyanin monomers were significantly higher in NT than in HT. HT also affected the levels of sugars and plant hormones. The total soluble sugar content increased by 29.49% and 16.81% in NT and HT, respectively, after 4 days of treatment. The levels of ABA, IAA and GA20 also increased in both the two treatments but more slowly in HT. Conversely, the contents of cZ, cZR and JA decreased more rapidly in HT than in NT. The results of the correlation analysis showed that the ABA and GA20 contents were significantly correlated with the total anthocyanin contents. Further transcriptome analysis showed that HT inhibited the activation of structural genes in anthocyanin biosynthesis as well as the repression of CYP707A and AOG, which dominated the catabolism and inactivation of ABA. These results indicate that ABA may be a key regulator in the high-temperature-inhibited fruit coloring of sweet cherry. High temperature induces higher ABA catabolism and inactivation, leading to lower ABA levels and finally resulting in slow coloring.

Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa.

Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13-17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18-20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.

PuHox52 promotes coordinated uptake of nitrate, phosphate, and iron under nitrogen deficiency in Populus ussuriensis.

It is of great importance to better understand how trees regulate nitrogen (N) uptake under N deficiency conditions which severely challenge afforestation practices, yet the underlying molecular mechanisms have not been well elucidated. Here, we functionally characterized PuHox52, a Populus ussuriensis HD-ZIP transcription factor, whose overexpression greatly enhanced nutrient uptake and plant growth under N deficiency. We first conducted an RNA sequencing experiment to obtain root transcriptome using PuHox52-overexpression lines of P. ussuriensis under low N treatment. We then performed multiple genetic and phenotypic analyses to identify key target genes of PuHox52 and validated how they acted against N deficiency under PuHox52 regulation. PuHox52 was specifically induced in roots by N deficiency, and overexpression of PuHox52 promoted N uptake, plant growth, and root development. We demonstrated that several nitrate-responsive genes (PuNRT1.1, PuNRT2.4, PuCLC-b, PuNIA2, PuNIR1, and PuNLP1), phosphate-responsive genes (PuPHL1A and PuPHL1B), and an iron transporter gene (PuIRT1) were substantiated to be direct targets of PuHox52. Among them, PuNRT1.1, PuPHL1A/B, and PuIRT1 were upregulated to relatively higher levels during PuHox52-mediated responses against N deficiency in PuHox52-overexpression lines compared to WT. Our study revealed a novel regulatory mechanism underlying root adaption to N deficiency where PuHox52 modulated a coordinated uptake of nitrate, phosphate, and iron through 'PuHox52-PuNRT1.1', 'PuHox52-PuPHL1A/PuPHL1B', and 'PuHox52-PuIRT1' regulatory relationships in poplar roots.

Molecular Mechanisms of Diverse Auxin Responses during Plant Growth and Development.

The plant hormone auxin acts as a signaling molecule to regulate numerous developmental processes throughout all stages of plant growth. Understanding how auxin regulates various physiological and developmental processes has been a hot topic and an intriguing field. Recent studies have unveiled more molecular details into how diverse auxin responses function in every aspect of plant growth and development. In this review, we systematically summarized and classified the molecular mechanisms of diverse auxin responses, and comprehensively elaborated the characteristics and multilevel regulation mechanisms of the canonical transcriptional auxin response. On this basis, we described the characteristics and differences between different auxin responses. We also presented some auxin response genes that have been genetically modified in plant species and how their changes impact various traits of interest. Finally, we summarized some important aspects and unsolved questions of auxin responses that need to be focused on or addressed in future research. This review will help to gain an overall understanding of and some insights into the diverse molecular mechanisms of auxin responses in plant growth and development that are instrumental in harnessing genetic resources in molecular breeding of extant plant species.

Protein Kinase CK2 Controls CD8+ T Cell Effector and Memory Function during Infection.

Protein kinase CK2 is a serine/threonine kinase composed of two catalytic subunits (CK2α and/or CK2α') and two regulatory subunits (CK2ß). CK2 promotes cancer progression by activating the NF-κB, PI3K/AKT/mTOR, and JAK/STAT pathways, and also is critical for immune cell development and function. The potential involvement of CK2 in CD8+ T cell function has not been explored. We demonstrate that CK2 protein levels and kinase activity are enhanced upon mouse CD8+ T cell activation. CK2α deficiency results in impaired CD8+ T cell activation and proliferation upon TCR stimulation. Furthermore, CK2α is involved in CD8+ T cell metabolic reprogramming through regulating the AKT/mTOR pathway. Lastly, using a mouse Listeria monocytogenes infection model, we demonstrate that CK2α is required for CD8+ T cell expansion, maintenance, and effector function in both primary and memory immune responses. Collectively, our study implicates CK2α as an important regulator of mouse CD8+ T cell activation, metabolic reprogramming, and differentiation both in vitro and in vivo.

PtrWOX13A Promotes Wood Formation and Bioactive Gibberellins Biosynthesis in Populus trichocarpa.

WUSCHEL-related homeobox (WOX) genes are plant-specific transcription factors (TFs) involved in multiple processes of plant development. However, there have hitherto no studies on the WOX TFs involved in secondary cell wall (SCW) formation been reported. In this study, we identified a Populus trichocarpa WOX gene, PtrWOX13A, which was predominantly expressed in SCW, and then characterized its functions through generating PtrWOX13A overexpression poplar transgenic lines; these lines exhibited not only significantly enhanced growth potential, but also remarkably increased SCW thicknesses, fiber lengths, and lignin and hemicellulose contents. However, no obvious change in cellulose content was observed. We revealed that PtrWOX13A directly activated its target genes through binding to two cis-elements, ATTGATTG and TTAATSS, in their promoter regions. The fact that PtrWOX13A responded to the exogenous GAs implies that it is responsive to GA homeostasis caused by GA inactivation and activation genes (e.g., PtrGA20ox4, PtrGA2ox1, and PtrGA3ox1), which were regulated by PtrWOX13A directly or indirectly. Since the master switch gene of SCW formation, PtrWND6A, and lignin biosynthesis regulator, MYB28, significantly increased in PtrWOX13A transgenic lines, we proposed that PtrWOX13A, as a higher hierarchy TF, participated in SCW formation through controlling the genes that are components of the known hierarchical transcription regulation network of poplar SCW formation, and simultaneously triggering a gibberellin-mediated signaling cascade. The discovery of PtrWOX13A predominantly expressed in SCW and its regulatory functions in the poplar wood formation has important implications for improving the wood quality of trees via genetic engineering.