The Characterization of G-Quadruplexes in Tobacco Genome and Their Function under Abiotic Stress.

Tobacco is an ideal model plant in scientific research. G-quadruplex is a guanine-rich DNA structure, which regulates transcription and translation. In this study, the prevalence and potential function of G-quadruplexes in tobacco were systematically analyzed. In tobacco genomes, there were 2,924,271,002 G-quadruplexes in the nuclear genome, 430,597 in the mitochondrial genome, and 155,943 in the chloroplast genome. The density of the G-quadruplex in the organelle genome was higher than that in the nuclear genome. G-quadruplexes were abundant in the transcription regulatory region of the genome, and a difference in G-quadruplex density in two DNA strands was also observed. The promoter of 60.4% genes contained at least one G-quadruplex. Compared with up-regulated differentially expressed genes (DEGs), the G-quadruplex density in down-regulated DEGs was generally higher under drought stress and salt stress. The G-quadruplex formed by simple sequence repeat (SSR) and its flanking sequence in the promoter region of the NtBBX (Nitab4.5_0002943g0010) gene might enhance the drought tolerance of tobacco. This study lays a solid foundation for further research on G-quadruplex function in tobacco and other plants.

Genome-wide identification and expression analysis of NF-Y gene family in tobacco (Nicotiana tabacum L.).

Nuclear factor Y (NF-Y) gene family is an important transcription factor composed of three subfamilies of NF-YA, NF-YB and NF-YC, which is involved in plant growth, development and stress response. In this study, 63 tobacco NF-Y genes (NtNF-Ys) were identified in Nicotiana tabacum L., including 17 NtNF-YAs, 30 NtNF-YBs and 16 NtNF-YCs. Phylogenetic analysis revealed ten pairs of orthologues from tomato and tobacco and 25 pairs of paralogues from tobacco. The gene structure of NtNF-YAs exhibited similarities, whereas the gene structure of NtNF-YBs and NtNF-YCs displayed significant differences. The NtNF-Ys of the same subfamily exhibited a consistent distribution of motifs and protein 3D structure. The protein interaction network revealed that NtNF-YC12 and NtNF-YC5 exhibited the highest connectivity. Many cis-acting elements related to light, stress and hormone response were found in the promoter of NtNF-Ys. Transcriptome analysis showed that more than half of the NtNF-Y genes were expressed in all tissues, and NtNF-YB9/B14/B15/B16/B17/B29 were specifically expressed in roots. A total of 15, 12, 5, and 6 NtNF-Y genes were found to respond to cold, drought, salt, and alkali stresses, respectively. The results of this study will lay a foundation for further study of NF-Y genes in tobacco and other Solanaceae plants.

Bacterial dynamic of flue-cured tobacco leaf surface caused by change of environmental conditions.

Microorganisms present on the surface of tobacco leaves play a significant role in shaping the composition of the tobacco microbial ecosystem, which undergoes continuous changes throughout the curing process. In the present study, a total of four distinct tobacco curing periods were selected for sampling, namely the fresh, yellowing, leaf-drying, and stem-drying stages. The bacterial 16S rRNA gene sequences of the collected samples were subsequently analyzed to identify operational taxonomic units (OTUs). The findings indicated that the complete dataset of leaf microbial samples was clustered, resulting in the identification of 1,783 operational taxonomic units (OTUs). Furthermore, the analysis of diversity revealed a pattern of initially increasing and subsequently decreasing community diversity. Redundancy Analysis (RDA) and weighted gene correlation networks for analysis (WGCNA) were employed in conjunction with environmental factors to assign OTUs to 22 modules for functional analysis. Additionally, a classification model utilizing the random forest algorithm was utilized to identify seven marker microorganisms (Escherichia coli, Faecalibacterium prausnitzii, Faecalibacterium, Escherichia-Shigella, Peptostreptococcaceae, Peptostreptococcales-Tissierellales, and Proteobacteria) that exhibited discriminative characteristics across different time periods. This study aimed to investigate the dynamic changes in the bacterial community throughout the curing process and their impact on the community's function. Additionally, certain bacteria were identified as potential markers for detecting changes in the curing stage. These findings offer a novel opportunity to accurately regulate the curing environment, thereby enhancing the overall quality of tobacco leaf curing.

Polyploid Genome Assembly Provides Insights into Morphological Development and Ascorbic Acid Accumulation of Sauropus androgynus.

Sauropus androgynus (S. androgynus) (2n = 4x = 52) is one of the most popular functional leafy vegetables in South and Southeast Asia. With its rich nutritional and pharmaceutical values, it has traditionally had widespread use for dietary and herbal purposes. Here, the genome of S. androgynus was sequenced and assembled, revealing a genome size of 1.55 Gb with 26 pseudo-chromosomes. Phylogenetic analysis traced back the divergence of Sauropus from Phyllanthus to approximately 29.67 million years ago (Mya). Genome analysis revealed that S. androgynus polyploidized around 20.51 Mya and shared a γ event about 132.95 Mya. Gene function analysis suggested that the expansion of pathways related to phloem development, lignin biosynthesis, and photosynthesis tended to result in the morphological differences among species within the Phyllanthaceae family, characterized by varying ploidy levels. The high accumulation of ascorbic acid in S. androgynus was attributed to the high expression of genes associated with the L-galactose pathway and recycling pathway. Moreover, the expanded gene families of S. androgynus exhibited multiple biochemical pathways associated with its comprehensive pharmacological activity, geographic adaptation and distinctive pleasurable flavor. Altogether, our findings represent a crucial genomic asset for S. androgynus, casting light on the intricate ploidy within the Phyllanthaceae family.

Pulmonary embolism following urological non-oncological surgery: The clinical features, management, and long-term follow-up outcome from a tertiary hospital of China.

Objective: To evaluate the clinical features, treatment, and outcomes of pulmonary embolism (PE) after urological non-oncological surgery in a tertiary hospital of China. Methods: A total of eight patients who suffered from PE after urological non-oncological surgery from 2016 to 2019 were recruited to the study. Clinical data such as symptoms, vital signs, electrocardiogram, echocardiography, and computed tomographic pulmonary arteriography (CTPA) were reviewed. In addition, the management and long-term follow-up outcome of PE were reported. Pulmonary Embolism Quality of Life (PEmb-QoL) questionnaire was applied for five patients to evaluate health-related quality of life after PE. Results: All patients survived during their hospitalization, and five patients were contacted during follow-up. Five of the eight patients were anticoagulated regularly until the re-examination results of CTPA and lower extremities ultrasound were normal. The period of anticoagulant sustained at least one month for each patient. The long-term follow-up outcomes showed that PE had little impact on the patients' quality of life. Conclusions: The study demonstrated that the prognosis of PE patients was not as terrible as feared when treated immediately in the ward. Early diagnosis and treatment of PE is vital for prognosis. However, further verifications based on the results of large studies are still needed.

Establishment of Prediction Models for Venous Thromboembolism in Non-Oncological Urological Inpatients - A Single-Center Experience.

Purpose: Venous thromboembolism (VTE) comprises deep venous thrombosis (DVT) and pulmonary embolism (PE), which can lead to death. VTE is an insidious disease with no specific symptoms and overlooked readily. We aimed to establish prediction models for VTE in non-oncological urological inpatients to aid urologists to better identify VTE patients. Patients and Methods: A retrospective analysis of 1453 inpatients was carried out. The risk factors for VTE had been clarified in our previous study. A stepwise regression method was used to screen the relevant influencing factors for VTE and construct a logistic regression prediction model to predict VTE. To validate the accuracy of the model, data from 291 patients from another cohort were used for external validation. Results: A total of 1453 inpatients were enrolled. Five potential risk factors (previous VTE; treatment with anticoagulants or anti-platelet agents before hospital admission; D-dimer ≥0.89 µg/mL; lower-extremity swelling; chest symptoms) were selected by multivariable analysis with p < 0.05. These five risk factors were used to build a logistic regression prediction model. When p < 0.1 in the multivariable logistic regression model, two additional risk factors were added: Caprini score ≥5 and complications, and all seven risk factors were used to build another prediction model. Internal verification showed the cutoff values, sensitivity, and specificity of the two models to be 0.02474, 0.941, 0.816 (model 1) and 0.03824, 0.941, and 0.820 (model 2), respectively. Both models had good predictive ability, but prediction accuracy was 43.0% for both when using the data of the additional 291 inpatients in the two models. Conclusion: Two novel prediction models were built to predict VTE in non-oncological urological inpatients. This is a new method for VTE screening, and internal validation showed a good performance. External validation results were suboptimal but may provide clues for subsequent VTE screening.

Transcriptomic analysis of bladder tissue in a rat model of ketamine-induced bladder fibrosis.

INTRODUCTION: Ketamine-induced cystitis (KIC) is a disease caused by ketamine that can cause lower urinary tract symptoms (LUTS). Its end-stage is bladder contracture, which is related to bladder fibrosis and poses a serious burden to patient lives. METHODS: We established a KIC model in female Sprague Dawley rats and verified bladder fibrosis in the model by Masson trichrome staining and western blot analysis. The bladders of the rats from the ketamine and control groups were used to perform transcriptome analysis. In particular, association analysis with metabolomics was also used to determine the potential mechanisms of ketamine-induced bladder fibrosis. RESULTS: A total of 685 differentially expressed messenger RNAs, 71 differentially expressed long noncoding RNAs, 23 differentially expressed microRNAs, and 68 differentially expressed circular RNAs were identified. We found that ribosome, Wnt signaling, vascular endothelial growth factor signaling, cytoskeleton organization, and cytoskeletal protein binding may be potential pathways in ketamine-induced bladder fibrosis as identified by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. In addition, the mitogen-activated protein kinase pathway appeared to be closely related to the development of ketamine-induced bladder fibrosis according to association analysis. CONCLUSIONS: In this study, using transcriptomic and correlation analyses of metabolomics, we identified pathways that may be potential targets for the prevention and treatment of ketamine-induced bladder fibrosis.

Incidence and Risk Factors of Venous Thromboembolism in Patients After Transurethral Resection of the Prostate (TURP).

OBJECTIVE: Venous thromboembolism (VTE) in patients following transurethral resection of the prostate (TURP) has been overlooked for many years. This research was aimed to investigate the incidence and risk factors of VTE in patients after TURP. METHODS: A total of 451 patients who underwent TURP between January 2017 and December 2020 were retrospectively analyzed. Clinical data of the patients were collected, such as basic demographic data, prostate volume, creatinine values, hemoglobin values, surgery duration, Caprini score, international prostate symptom score (IPSS), quality of life (QOL) score, plasma D-dimer levels, and so on. Univariate analysis and multivariate logistic regression were performed to identify the potential risk factors of VTE. Venous ultrasonography of lower extremities was performed routinely to detect VTE for patients after TURP. RESULTS: In total, 36 (8%) out of the 451 patients suffered from VTE. A total of 12 (2.7%) patients were confirmed with deep venous thrombosis (DVT). Two patients (0.4%) were identified with pulmonary embolism (PE). Twenty-two (4.9%) patients were suffered from superficial venous thrombosis. Furthermore, according to the results of multivariate stepwise logistic regression analysis, having a history of VTE (adjusted odds ratio [aOR] = 10.980, 95% CI = 2.265-53.223), complicated with postoperative bladder hematoma (aOR = 6.302, 95% CI = 2.265-17.532), D-dimer >1.25 mg/L (aOR = 4.402, 95% CI = 1.798-10.774), and age >65 (aOR = 3.106, 95% CI = 1.084-8.893) were independent risk factors of VTE after TURP. In addition, the nomogram prediction model is a useful auxiliary prevention tool of VTE. CONCLUSION: The incidence of VTE is severely underestimated in patients following TURP. A lot of asymptomatic VTEs have been overlooked. Early detection and diagnosis of VTE are essential. Nevertheless, further verifications based on the results of large-scaled studies are still needed.

Ketamine Induced Bladder Fibrosis Through MTDH/P38 MAPK/EMT Pathway.

Purpose: Ketamine is an anesthetic in clinical, but it has also been used as an abusing drug due to its low price and hallucinogenic effects. It is proved that ketamine abusing would cause multiple system damage including the urinary system, which is called ketamine-induced cystitis (KIC). Bladder fibrosis is late stage in KIC and threaten abusers' life. This study aimed to investigate the molecular mechanism of ketamine-induced bladder fibrosis. Methods: Female Sprague Dawley (SD) rats were randomly divided into 3 groups. 2 groups were treated with tail vein injection of ketamine (25 mg/kg/day, 50 mg/kg/day ketamine hydrochloride solution, respectively) for 12 weeks, whereas the control group was treated with normal saline solution. In each group, rat bladders were extracted and samples were examined for pathological and morphological alterations via hematoxylin and eosin (HE) staining, Masson's trichrome staining and immunohistochemistry (IHC). SV-HUC-1 cells were treated with different concentrations of ketamine solution (0, 0.1, 0.5, 1 mmol/L). Rat bladder and SV-HUC-1 cells were extracted protein and RNA for Western blot and RT-PCR detection. Metadherin (MTDH) siRNAs and overexpression plasmids were used to knock down and overexpress the relative genes. P38 mitogen-activated protein kinase (MAPK) inhibitor was utilized to inhibit the MAPK pathway. Results: Rats in the ketamine group exhibited fibrosis compared to rats of the control group and fibrosis were also markedly upregulated in SV-HUC-1 cells after treated with ketamine, which were ketamine concentration-dependent. After treating with ketamine in SV-HUC-1 cells, there was an increase expression of MTDH, epithelial-mesenchymal transition (EMT) markers, P38 MAPK. MTDH knockdown would suppresses P38 MAPK/EMT pathway to inhibit fibrosis, however, MTDH overexpression could promote the pathway in SV-HUC-1 cells. Conclusion: In rats and SV-HUC-1 cells ketamine-treated models, MTDH can regulate EMT through the P38 MAPK pathway to regulate the process of bladder fibrosis.

Sulfidation of zerovalent iron for improving the selectivity toward Cr(VI) in oxic water: Involvements of FeSx.

Recognition of the general roles of FeSx in selectivity of zerovalent iron (ZVI) toward target contaminants is of great significance but challenging, especially in oxic water system. Herein, the ZVI amended with Na2S2O3 (i.e., S-ZVINa2S2O3) and Na2S2O4 (i.e., S-ZVINa2S2O4) were applied for the sequestration of Cr(VI) and corresponding FeSx involvements were explored. Results revealed that the largest effect for S-ZVINa2S2O3 and S-ZVINa2S2O4 observed at S/Fe molar ratio of 0.05 were 7.9- and 11.6- folds increase in removal rate (kobs) of Cr(VI), respectively. respectively. Correspondingly, the electron efficiency (EE) of S-ZVI for reducing Cr(VI) were mainly from 2.1- to 2.4- folds greater than that that of the ZVIH2O. Further, this work suggested that the improved selectivity of ZVI toward Cr(VI) by sulfidation should be mainly ascribed to the involvements of FeSx, which could tune the reactive sites and corrosion products of ZVI for synergistically improving the mass transfer of Cr(VI) and subsequent electron transfer from iron core to Cr(VI). Overall, this work offers a new platform for improving ZVI selectivity for water decontamination.

Application value of D-dimer testing and Caprini risk assessment model (RAM) to predict venous thromboembolism (VTE) in Chinese non-oncological urological inpatients: a retrospective study from a tertiary hospital.

BACKGROUND: The Caprini risk assessment model (RAM) and D-dimer testing have been widely used in the prediction of venous thromboembolism (VTE). However, the clinical significance of these testing options are limited in non-oncological urological inpatients because of the low specificity. METHODS: This retrospective study included 1,453 patients who were admitted to the non-oncological unit of the Department of Urology, Xiangya Hospital, Central South University, from January 2018 to December 2018. The highest score of Caprini RAM and the highest D-dimer level were collected in this retrospective study. Ultrasound examinations of the lower extremities or computed tomographic pulmonary arteriography (CTPA) were applied to patients who were suspected of having VTE, if necessary. RESULTS: A total of 1,453 patients were collected in this study, which included 34 VTE and 1,419 non-VTE patients. The threshold of D-dimer was 0.89 µg/mL, according to the receiver operating characteristic (ROC) curve, with a sensitivity of 82.4%, a specificity of 83.3%, and a negative predictive value (NPV) of 99.5%. The cut-off of the Caprini RAM was 5, with a sensitivity of 76.5%, a specificity of 58.7%, and an NPV of 99.0%. The area under the curve (AUC) was higher for D-dimer (0.86) than for the Caprini score (0.73). CONCLUSIONS: The application of 0.89 µg/mL and a score of 5 as cut-offs for D-dimer testing and Caprini RAM, respectively, could safely decrease the proportion of Chinese non-oncological urological inpatients who needed to undergo further examinations. These new findings may enhance the application value of D-dimer testing and Caprini RAM for Chinese non-oncological urological inpatients.