Polygalacturonase gene family analysis identifies FcPG12 as a key player in fig (Ficus carica L.) fruit softening.

BACKGROUND: The fig (Ficus carica L.) tree has high economic value. However, its fruit have a short shelf life due to rapid softening. Polygalacturonases (PGs) are essential hydrolases, responsible for the pectin degradation that plays a key role in fruit softening. However, fig PG genes and their regulators have not yet been characterized. RESULTS: In this study, 43 FcPGs were identified in the fig genome. They were non-uniformly distributed on 13 chromosomes, and tandem repeat PG gene clusters were found on chromosomes 4 and 5. Ka/Ks calculation and collinear analysis indicated negative selection as the main driver of FcPG family expansion. Fourteen FcPGs were found expressed in fig fruit with FPKM values > 10, of which seven were positively correlated, and three, negatively correlated with fruit softening. Eleven FcPGs were upregulated and two downregulated in response to ethephon treatment. FcPG12, a member of the tandem repeat cluster on chromosome 4, was selected for further analyses due to its sharp increment in transcript abundance during fruit softening and its response to ethephon treatment. Transient overexpression of FcPG12 led to decreased fig fruit firmness and increased PG enzyme activity in the tissue. Two ethylene response factor (ERF)-binding GCC-box sites were found on the FcPG12 promoter. Yeast one-hybrid and dual luciferase assays showed that FcERF5 binds directly to the FcPG12 promoter and upregulates its expression. Transient overexpression of FcERF5 upregulated FcPG12 expression, thereby increasing PG activity and fruit softening. CONCLUSIONS: Our study identified FcPG12 as a key PG gene in fig fruit softening, and its direct positive regulation by FcERF5. The results provide new information on the molecular regulation of fig fruit softening.

Risk, Prognostic Factors and Nomograms for Bone Metastasis in Young Females with Breast Cancer: A Large Cohort Retrospective Study.

Purpose: To determine the incidence of bone metastasis (BM) in young female patients with breast cancer (BC) and develop 2 robust nomograms for BM in young female patients with BC. Methods: We searched and downloaded the data from young (age ≤40 years) female patients with bone cancer from the Surveillance, Epidemiology, and End Results (SEER) database between 2010 and 2015. Univariate and multivariate analyses were performed to screen the potential diagnostic variables and prognostic factors for BM. The diagnostic and prognostic nomograms were generated and evaluated by the area under the receiver operating characteristic (ROC) curve (AUC), calibration curves, and decision curve analysis (DCA). Results: A total of 13 347 young female patients with BC were identified; of these, 462 were initially diagnosed as having BM. The independent risk factors for BM in young female patients with BC were tumor size, BC subtype, American Joint Committee on Cancer (AJCC) T stage, AJCC N stage, age and marital status. The independent prognostic factors in these patients were tumor size, subtype, surgery performed, lung metastasis, liver metastasis and brain metastasis. The AUC values of the diagnostic nomogram were 0.803 (95% CI; 0.795-0.811) and 0.813 (95% CI; 0.800-0.825) in the training and validation cohorts, respectively. The time-dependent AUC values of prognostic nomogram were 0.850, 0.853, and 0.824 at 2, 3 and 4 years in the training cohort, and also >0.700 in the validation cohort. For both nomograms, the discrimination was higher than all independent variables. Calibration curve and decision curve analysis (DCA) indicated that both nomograms had favorable calibration and clinical utilization. Finally, a risk stratification system was generated and the 3 risk subgroups showed significantly distinct prognoses. Conclusions: A total of 2 nomograms were developed to assess the risk for and in prognosis of young female patients with BC with BM (BCBM).

Overexpression of four MiTFL1 genes from mango delays the flowering time in transgenic Arabidopsis.

BACKGROUND: TERMINAL FLOWER 1 (TFL1) belongs to the phosphatidylethanolamine-binding protein (PEBP) family, which is involved in inflorescence meristem development and represses flowering in several plant species. In the present study, four TFL1 genes were cloned from the mango (Mangifera indica L.) variety 'SiJiMi' and named MiTFL1-1, MiTFL1-2, MiTFL1-3 and MiTFL1-4. RESULTS: Sequence analysis showed that the encoded MiTFL1 proteins contained a conserved PEBP domain and belonged to the TFL1 group. Expression analysis showed that the MiTFL1 genes were expressed in not only vegetative organs but also reproductive organs and that the expression levels were related to floral development. Overexpression of the four MiTFL1 genes delayed flowering in transgenic Arabidopsis. Additionally, MiTFL1-1 and MiTFL1-3 changed the flower morphology in some transgenic plants. Yeast two-hybrid (Y2H) analysis showed that several stress-related proteins interacted with MiTFL1 proteins. CONCLUSIONS: The four MiTFL1 genes exhibited a similar expression pattern, and overexpression in Arabidopsis resulted in delayed flowering. Additionally, MiTFL1-1 and MiTFL1-3 overexpression affected floral organ development. Furthermore, the MiTFL1 proteins could interact with bHLH and 14-3-3 proteins. These results indicate that the MiTFL1 genes may play an important role in the flowering process in mango.

Isolation and Functional Characterization of Two SHORT VEGETATIVE PHASE Homologous Genes from Mango.

The SHORT VEGETATIVE PHASE (SVP) gene is a transcription factor that integrates flowering signals and plays an important role in the regulation of flowering time in many plants. In this study, two full-length cDNA sequences of SVP homologous genes-MiSVP1 and MiSVP2-were obtained from 'SiJiMi' mango. Sequence analysis showed that the MiSVPs had typical MADS-box domains and were highly conserved between each other. The analysis of expression patterns showed that the MiSVPs were expressed during flower development and highly expressed in vegetative tissues, with low expression in flowers/buds. The MiSVPs could responded to low temperature, NaCl, and PEG treatment. Subcellular localization revealed that MiSVP1 and MiSVP2 were localized in the nucleus. Transformation of Arabidopsis revealed that overexpression of MiSVP1 delayed flowering time, overexpression of MiSVP2 accelerated flowering time, and neither MiSVP1 nor MiSVP2 had an effect on the number of rosette leaves. Overexpression of MiSVP1 increased the expression of AtFLC and decreased the expression of AtFT and AtSOC1, and overexpression of MiSVP2 increased the expression levels of AtSOC1 and AtFT and decreased the expression levels of AtFLC. Point-to-point and bimolecular fluorescence complementation (BiFC) assays showed that MiSVP1 and MiSVP2 could interact with SEP1-1, SOC1D, and AP1-2. These results suggest that MiSVP1 and MiSVP2 may play a significant roles in the flowering process of mango.

Novel nomogram to predict risk of bone metastasis in newly diagnosed thyroid carcinoma: a population-based study.

BACKGROUND: The aim of this study was to develop and validate a visual nomogram for predicting the risk of bone metastasis (BM) in newly diagnosed thyroid carcinoma (TC) patients. METHODS: The demographics and clinicopathologic variables of TC patients from 2010 to 2015 in the Surveillance, Epidemiology and End Results (SEER) database were retrospectively reviewed. Chi-squared (χ2) test and logistic regression analysis were performed to identify independent risk factors. Based on that, a predictive nomogram was developed and validated for predicting the risk of BM in TC patients. The C-index was used to compute the predictive performance of the nomogram. Calibration curves and decision curve analysis (DCA) were furthermore used to evaluate the clinical value of the nomogram. RESULTS: According to the inclusion and exclusion criteria, the data of 14,772 patients were used to analyze in our study. After statistical analysis, TC patients with older age, higher T stage, higher N stage, poorly differentiated, follicular thyroid carcinoma (FTC) and black people had a higher risk of BM. We further developed a nomogram with a C-index of 0.925 (95%CI,0.895-0.948) in the training set and 0.842 (95%CI,0.777-0.907) in the validation set. The calibration curves and decision curve analysis (DCA) also demonstrated the reliability and accuracy of the clinical prediction model. CONCLUSIONS: The present study developed a visual nomogram to accurately identify TC patients with high risk of BM, which might help to further provide more individualized clinical decision guidelines.

Diagnostic and prognostic nomograms for bone metastasis in hepatocellular carcinoma.

BACKGROUND: Bone metastasis (BM) is one of the common sites of hepatocellular carcinoma (HCC), and the prognosis of BM patients is worse than patients without it. Our study aimed to identify predictors and prognostic factors of BM in HCC patients and develop two nomograms to quantify the risk of BM and the prognosis of HCC patients with BM. METHODS: We retrospectively reviewed the data of patients who were diagnosed as HCC between 2010 and 2015 in the Surveillance, Epidemiology, and End Results (SEER) database. Independent predictors for BM from HCC patients were determined by the univariate and multivariate logistic regression analysis. Independent prognostic factors for HCC patients with BM were identified by univariate and multivariate Cox regression analysis. Two nomograms were established and evaluated by calibration curves, receiver operating characteristic (ROC) curve, and decision curve analysis (DCA). RESULTS: Nine thousand and forty-seven patients were included. The independent risk factors of BM in newly diagnosed HCC patients are sex, grade, T stage, and N stage. The independent prognostic factors for HCC patients with BM are radiotherapy, chemotherapy, and lung metastasis. The AUC of diagnostic nomogram were 0.726 in the training set and 0.629 in the testing set. For the prognostic nomogram, the AUCs of 6-, 9-, and 12-months were 0.753, 0.799, and 0.732 in the training set and 0.698, 0.770, and 0.823 in the validation set. The calibration curve and DCA indicated the good performance of the nomogram. CONCLUSIONS: Two nomograms were established to predict the incidence of BM in HCC patients and the prognosis of HCC patients with BM, respectively. Both nomograms have satisfactory accuracy, and clinical utility may benefit for clinical decision-making.

Prognostic role of the preoperative neutrophil-to-lymphocyte ratio and albumin for 30-day mortality in patients with postoperative acute pulmonary embolism.

BACKGROUND: This retrospective study aimed to investigate the prognostic value of the neutrophil-to-lymphocyte ratio (NLR) and albumin for 30-day mortality in patients with postoperative acute pulmonary embolism (PAPE). METHODS: We retrospectively reviewed the medical records of 101 patients with PAPE admitted from September 1, 2012, to March 31, 2019. The characteristics, surgical information, admission examination data and mortality within 30 days after PAPE were obtained from our electronic medical recording system and follow-up. The associations between the NLR, PLR, and other predictors and 30-day mortality were analyzed with univariate and multivariate analyses. Then, the nomogram including the independent predictors was established and evaluated. RESULTS: Twenty-four patients died within 30 days, corresponding to a 30-day mortality rate of 23.8%. The results of the multivariate analysis indicated that both the NLR and albumin were independent predictors for 30-day mortality in patients with PAPE. The probability of death increased by approximately 17.1% (OR = 1.171, 95% CI: 1.073-1.277, P = 0.000) with a one-unit increase in the NLR, and the probability of death decreased by approximately 15.4% (OR = 0.846, 95% CI: 0.762c-0.939, P = 0.002) with a one-unit increase in albumin. The area under the curve of the nomogram was 0.888 (95% CI: 0.812-0.964). CONCLUSION: Our findings showed that an elevated NLR and decreased albumin were related to poor prognosis in patients with PAPE. The NLR and albumin were independent prognostic factors for PAPE.

A comparison study of posterior cervical percutaneous endoscopic ventral bony decompression and simple dorsal decompression treatment in cervical spondylotic radiculopathy caused by cervical foraminal and/or lateral spinal stenosis: a clinical retrospective study.

BACKGROUND: Percutaneous endoscopic cervical decompression (PECD) is an ideal minimally invasive decompression technique for the treatment of cervical spondylotic radiculopathy (CSR). However, the mainstream is the resection of dorsal bone and removal of free nucleus pulposus. The necessity of excision of ventral osteophytes and hyperplastic ligaments in the treatment of CSR caused by cervical foraminal and/or lateral spinal stenosis (CFa/oLSS) to be discussed. METHODS: We performed a retrospective study of 46 patients with CSR caused by CFa/oLSS from January 2017 to November 2018. These patients received posterior percutaneous endoscopic cervical decompression-ventral bony decompression (PPECD-VBD)(23 cases, classified as VBD group) or posterior percutaneous endoscopic cervical decompression-simple dorsal decompression (PPECD-SDD)(23 cases, classified as SDD group). Following surgery, we recorded Visual Analogue Scale (VAS), Neck Disable Index (NDI), Japanese Orthopaedic Association (JOA) Scores and myodynamia. We further evaluated the changes of cervical curvature and cervical spine motion in the VBD group and recorded the operation time and complications during the follow-up of each patient. RESULTS: All patients underwent successful operations, with an average follow-up time of 16.53 ± 9.90 months. The excellent and good rates in the VBD and SDD groups were 91.29 and 60.87%, respectively. In the SDD group, neck-VAS, arm-VAS, and NDI scores were significantly higher than those of the VBD group at 1 day, 6 months, and 12 months after surgery (P < 0.05), while the JOA scores and improvement rate of JOA were significantly lower than those of the VBD group (P < 0.05). There were no significant differences in terms of angular displacement (AD), horizontal displacement (HD), segmental angle (SA) and cervical curvature (CA) before and after the operation in the VBD group (P > 0.05). CONCLUSION: PPECD-VBD was significantly better than PPECD-SDD as well as PPECD-VBD had no significant effects on cervical spine stability or cervical curvature.

Effects of neoadjuvant chemotherapy on respiratory function in patients with breast cancer.

OBJECTIVE: To evaluate changes in chest X-rays, pulmonary function tests (PFTs) and quality of life in female breast cancer patients who had been treated with four cycles of neoadjuvant chemotherapy consisting of a regimen of cyclophosphamide, epirubicin and 5-fluorouracil (CEF regimen), and to determine the correlation between pulmonary function parameters and declined quality of life. METHODS: Twenty-nine eligible female patients diagnosed with breast cancer at the first visit who were 20-60 years old, were classified as the American Society of Anesthesiologists (ASA) I-II and patients whose body mass index (BMI) <30 kg/m2 were recruited and subjected to chest X-ray examinations, PFTs and the European Organization for Research and Treatment of Cancer Quality of Life Questionnaire C30 (EORTC QLQ-C30) questionnaire before and after receiving 4 cycles of the CEF regimen. RESULTS: In this study, chest X-rays showed no abnormal changes after chemotherapy, but significant decreases in carbon monoxide diffusing capacity (DLCO) and percentage of the DLCO predicted value (DLCO%) (P<0.001). A significant increase in maximal ventilatory volume (MVV) (P=0.004) was observed, and most patients experienced dyspnea (P=0.031) and fatigue (P<0.001). However, there was no significant correlation between the changes in these PFTs parameters and the results of the EORTC QLQ-C30 (P>0.05). CONCLUSIONS: Neoadjuvant chemotherapy can reduce lung diffusion function and quality of life in females with breast cancer.

[Influence of dexamethasone on the incidence of postoperative nausea and vomiting in breast cancer patients with neoadjuvant chemotherapy].

OBJECTIVE: To evaluate the influence of dexamethasone on the incidence of postoperative nausea and vomiting (PONV) in patients undergoing modified radical mastectomy with neoadjuvant chemotherapy. METHODS: In a prospective trial, 280 female (18-60 years) breast cancer patients undergoing modified radical mastectomy with neoadjuvent chemotherapy were randomized to two groups: one with dexamethasone (Group D) and one without dexamethasone (Group C, n=140). In each group, anesthesia was maintained with volatile anesthesia or total intravenous anesthesia (TIVA): TIVA (propofol) without dexamethasone (Subgroup CP); volatile anesthesia (sevoflurane) without dexamethasone (Subgroup CS); TIVA with 10 mg dexamethasone intravenously before anesthetic induction (Subgroup DP); volatile anesthesia with 10 mg dexamethasone intravenously before anesthetic induction (Subgroup DS). A standard general anesthetic technique was used. All the patients received 8 mg of ondansetron intravenously 30 minutes before the end of surgical procedures. The incidence of PONV during the 24-hour postoperative period was recorded. A Logistic regression analysis was conducted to examine relevant factors for PONV. The tested factors were: age, body mass index (BMI), duration of surgery, postoperative pain, history of motion sickness/PONV, with or without dexamethasone and anesthetic regimen. RESULTS: There was a significant lower incidence of PONV in the patients who received dexamethasone than in those who received placebo during the 24-hour postoperative period (11.4% vs. 20.7%, P=0.034). In the early postoperative period (0-2 h) dexamethasone reduced the incidence of PONV ( 1.4%vs.6.4%, P=0.031), but in the late postoperative period (2-24 h) the difference of the incidence was insignificantly (10.7% vs. 17.9%, P=0.088). No differences were found between TIVA and volatile anesthesia in the 24-hour postoperative period. Dexamethasone was effective to prevent PONV(OR=0.447, P=0.030), and history of PONV or motion sickness was the risk factor of PONV (OR=15.730, P<0.001). CONCLUSION: Dexamethasone prevents PONV effectively in patients undergoing modified radical mastectomy with neoadjuvant chemotherapy, and TIVA cannot decrease the incidence of PONV in the 24-hour postoperative period in those patients.

Population genomic analysis of clinical ST15 Klebsiella pneumoniae strains in China.

ST15 Klebsiella pneumoniae (Kpn) is a growing public health concern in China and worldwide, yet its genomic and evolutionary dynamics in this region remain poorly understood. This study comprehensively elucidates the population genomics of ST15 Kpn in China by analyzing 287 publicly available genomes. The proportion of the genomes increased sharply from 2012 to 2021, and 92.3% of them were collected from the Yangtze River Delta (YRD) region of eastern China. Carbapenemase genes, including OXA-232, KPC-2, and NDM, were detected in 91.6% of the studied genomes, and 69.2% of which were multidrug resistant (MDR) and hypervirulent (hv). Phylogenetic analysis revealed four clades, C1 (KL112, 59.2%), C2 (mainly KL19, 30.7%), C3 (KL48, 0.7%) and C4 (KL24, 9.4%). C1 appeared in 2007 and was OXA-232-producing and hv; C2 and C4 appeared between 2005 and 2007, and both were KPC-2-producing but with different levels of virulence. Transmission clustering detected 86.1% (n = 247) of the enrolled strains were grouped into 55 clusters (2-159 strains) and C1 was more transmissible than others. Plasmid profiling revealed 88 plasmid clusters (PCs) that were highly heterogeneous both between and within clades. 60.2% (n = 53) of the PCs carrying AMR genes and 7 of which also harbored VFs. KPC-2, NDM and OXA-232 were distributed across 14, 4 and 1 PCs, respectively. The MDR-hv strains all carried one of two homologous PCs encoding iucABCD and rmpA2 genes. Pangenome analysis revealed two major coinciding accessory components predominantly located on plasmids. One component, associated with KPC-2, encompassed 15 additional AMR genes, while the other, linked to OXA-232, involved seven more AMR genes. This study provides essential insights into the genomic evolution of the high-risk ST15 CP-Kpn strains in China and warrants rigorous monitoring.

Effects of γ-oryzanol on motor function in a spinal cord injury model.

Objective: Spinal cord injury (SCI) is caused by disease or trauma and results in a partial or complete loss of motor or sensory function below the injury level. Most patients with SCI are young, and long-term disability imposes both psychological and financial burdens. Rice is the most abundant source of γ-oryzanol, which exhibits both antioxidant and anti-inflammatory properties. γ-Oryzanol has been shown to cross the blood-brain barrier in an intact form and have beneficial effects on brain function. To the best of our knowledge, this is the first study to report the effect of γ-oryzanol on motor function recovery in mice after SCI. Methods: Mice were randomly divided into three groups: the sham group, the injury group, and the γ-oryzanol-treated group that received an intraperitoneal γ-oryzanol (100 mg/kg) injection every 2 days for 42 days after SCI. The effect of γ-oryzanol was assessed through various approaches. Behavioral tests were performed using Basso mouse scale scores and gait analysis. Hematoxylin and eosin staining, Luxol fast blue staining, magnetic resonance imaging ,and immunofluorescence staining were used to observe the lesion area changes, demyelination, axonal regeneration, and scar tissue formation. The levels of inflammatory cytokines in the peripheral blood of mice were assessed by enzyme-linked immunosorbent assay. Results: Behavioral tests showed that γ-oryzanol treatment improved gait following SCI. Pathological examination revealed that demyelination at the site of injury improved with γ-oryzanol treatment and was accompanied by the retention of axons associated with motor function and reduced scarring. Additionally, γ-oryzanol treatment decreased the serum levels of pro-inflammatory factors. Conclusions: Studies have shown that γ-oryzanol promotes motor function recovery in mice after SCI. Therefore, γ-oryzanol might be the latent target for SCI therapy.

Advances in sequencing and key character analysis of mango (Mangifera indica L.).

Mango (Mangifera indica L.) is an important fruit crop in tropical and subtropical countries associated with many agronomic and horticultural problems, such as susceptibility to pathogens, including powdery mildew and anthracnose, poor yield and quality, and short shelf life. Conventional breeding techniques exhibit significant limitations in improving mango quality due to the characteristics of long ripening, self-incompatibility, and high genetic heterozygosity. In recent years, much emphasis has been placed on identification of key genes controlling a certain trait through genomic association analysis and directly breeding new varieties through transgene or genotype selection of offspring. This paper reviews the latest research progress on the genome and transcriptome sequencing of mango fruit. The rapid development of genome sequencing and bioinformatics provides effective strategies for identifying, labeling, cloning, and manipulating many genes related to economically important traits. Preliminary verification of the functions of mango genes has been conducted, including genes related to flowering regulation, fruit development, and polyphenol biosynthesis. Importantly, modern biotechnology can refine existing mango varieties to meet the market demand with high economic benefits.

Ectopic expression of two CAULIFLOWER genes from mango caused early flowering in Arabidopsis.

APETALA1 (AP1), CAULIFLOWER (CAL) and FRUITFULL (FUL) were homologous genes with redundant functions in the process of flower transformation and floral development in Arabidopsis. Two CALs genes, MiCAL1 and MiCAL2, were cloned from mango (Mangifera indica L.). Their full-length sequences contained 717 bp and 714 bp, encoding 239 and 238 amino acids, respectively. Both the MiCAL1 and MiCAL2 proteins contained typical MADS-box and K-box domains and therefore belonged to the CAL-like protein family. MiCAL1 and MiCAL2 were expressed in all tissues at the inflorescence elongation stage and flowering stage, with the highest expression in the leaves at the flowering stage. They had similar expression patterns during flower development, with the highest expression levels in leaves during flower differentiation and the lowest expression levels during fruit development. Overexpression of MiCAL1 and MiCAL2 resulted in significantly earlier flowering in Arabidopsis. Overexpression of MiCAL1 resulted in terminal flowers with normal flower organs, while overexpression of MiCAL2 induced partially variation in floral organs but had no effect on inflorescences. Yeast two-hybrid (Y2H) experiments showed that MiCAL1 and MiCAL2 can interact with several flower-related proteins as well as stress response proteins, such as SEP1, SVP1, SVP2, SOC1G and Di19-4. These results suggest that these two MiCALs genes may have an important influence on mango flowering.

Score for the Risk and Overall Survival of Lung Metastasis in Patients First Diagnosed With Soft Tissue Sarcoma: A Novel Nomogram-Based Risk Assessment System.

Background: Metastatic soft tissue sarcoma (STS) patients have a poor prognosis with a 3-year survival rate of 25%. About 30% of them present lung metastases (LM). This study aimed to construct 2 nomograms to predict the risk of LM and overall survival of STS patients with LM. Materials and Methods: The data of patients were derived from the Surveillance, Epidemiology, and End Results database during the period of 2010 to 2015. Logistic and Cox analysis was performed to determine the independent risk factors and prognostic factors of STS patients with LM, respectively. Afterward, 2 nomograms were, respectively, established based on these factors. The performance of the developed nomogram was evaluated with receiver operating characteristic curves, area under the curve (AUC) calibration curves, and decision curve analysis (DCA). Results: A total of 7643 patients with STS were included in this study. The independent predictors of LM in first-diagnosed STS patients were N stage, grade, histologic type, and tumor size. The independent prognostic factors for STS patients with LM were age, N stage, surgery, and chemotherapy. The AUCs of the diagnostic nomogram were 0.806 in the training set and 0.799 in the testing set. For the prognostic nomogram, the time-dependent AUC values of the training and testing set suggested a favorable performance and discrimination of the nomogram. The 1-, 2-, and 3-year AUC values were 0.698, 0.718, and 0.715 in the training set, and 0.669, 0.612, and 0717 in the testing set, respectively. Furthermore, for the 2 nomograms, calibration curves indicated satisfactory agreement between prediction and actual survival, and DCA indicated its clinical usefulness. Conclusion: In this study, grade, histology, N stage, and tumor size were identified as independent risk factors of LM in STS patients, age, chemotherapy surgery, and N stage were identified as independent prognostic factors of STS patients with LM, these developed nomograms may be an effective tool for accurately predicting the risk and prognosis of newly diagnosed patients with LM.

Genome-Wide Analysis of Anthocyanin Biosynthesis Regulatory WD40 Gene FcTTG1 and Related Family in Ficus carica L.

WD40 proteins serve as crucial regulators in a broad spectrum of plant developmental and physiological processes, including anthocyanin biosynthesis. However, in fig (Ficus carica L.), neither the WD40 family nor any member involved in anthocyanin biosynthesis has been elucidated. In the present study, 204 WD40 genes were identified from the fig genome and phylogenetically classified into 5 clusters and 12 subfamilies. Bioinformatics analysis prediction localized 109, 69, and 26 FcWD40 proteins to the cytoplasm, nucleus and other cellular compartments, respectively. RNA-seq data mining revealed 127 FcWD40s expressed at FPKM > 10 in fig fruit. Most of these genes demonstrated higher expression in the early stages of fruit development. FcWD40-97 was recruited according to three criteria: high expression in fig fruit, predicted nuclear localization, and closest clustering with TTG1s identified in other plants. FcWD40-97, encoding 339 amino acids including 5 WD-repeat motifs, showed 88.01 and 87.94% amino acid sequence similarity to apple and peach TTG1, respectively. The gene is located on fig chromosome 4, and is composed of 1 intron and 2 exons. Promoter analysis revealed multiple light-responsive elements, one salicylic acid-responsive element, three methyl jasmonate-responsive elements, and one MYB-binding site involved in flavonoid biosynthesis gene regulation. FcWD40-97 was in the FPKM > 100 expression level group in fig fruit, and higher expression was consistently found in the peel compared to the flesh at the same development stages. Expression level did not change significantly under light deprivation, whereas in leaves and roots, its expression was relatively low. Transient expression verified FcWD40-97's localization to the nucleus. Yeast two-hybrid (Y2H) and biomolecular fluorescence complementation (BiFC) assays revealed that FcWD40-97 interacts with FcMYB114, FcMYB123, and FcbHLH42 proteins in vitro and in vivo, showing that FcWD40-97 functions as a member of the MYB-bHLH-WD40 (MBW) complex in anthocyanin-biosynthesis regulation in fig. We therefore renamed FcWD40-97 as FcTTG1. Our results provide the first systematic analysis of the FcWD40 family and identification of FcTTG1 in fig pigmentation.

APETALA2/ethylene responsive factor in fruit ripening: Roles, interactions and expression regulation.

Insects and animals are attracted to, and feed on ripe fruit, thereby promoting seed dispersal. As a vital vitamin and nutrient source, fruit make up an indispensable and enjoyable component of the human diet. Fruit ripening involves a series of physiological and biochemical changes in, among others, pigmentation, chlorophyll (Chl) degradation, texture, sugar accumulation, and flavor. Growing evidence indicates that the coordinated and ordered trait changes during fruit ripening depend on a complex regulatory network consisting of transcription factors, co-regulators, hormonal signals, and epigenetic modifications. As one of the predominant transcription factor families in plants and a downstream component of ethylene signaling, more and more studies are showing that APETALA2/ethylene responsive factor (AP2/ERF) family transcription factors act as critical regulators in fruit ripening. In this review, we focus on the regulatory mechanisms of AP2/ERFs in fruit ripening, and in particular the recent results on their target genes and co-regulators. We summarize and discuss the role of AP2/ERFs in the formation of key fruit-ripening attributes, the enactment of their regulatory mechanisms by interaction with other proteins, their role in the orchestration of phytohormone-signaling networks, and the epigenetic modifications associated with their gene expression. Our aim is to provide a multidimensional perspective on the regulatory mechanisms of AP2/ERFs in fruit ripening, and a reference for understanding and furthering research on the roles of AP2/ERF in fruit ripening.

Study of bacterial community succession and reconstruction of the core lactic acid bacteria to enhance the flavor of paocai.

Paocai is a widely consumed traditional Chinese fermented vegetable product. To study the effects of bacterial community succession and core microbial reconstruction on the flavor of paocai, culture-dependent and culture-independent methods were used to analyze the bacterial community structure of naturally fermented paocai. HPLC and GC-MS were used to investigate changes in flavor compounds during the fermentation of paocai. Key odorants were identified by olfactometry combined with GC-MS. The results showed that dominant bacteria in the paocai fermentation were mostly cultivable. Leuconostoc mesenteroides, Weissella cibaria, and Lactococcus lactis appeared at the start of fermentation, Leu. mesenteroides, L. lactis, Lactiplantibacillus plantarum, and Levilactobacillus brevis appeared in the middle of fermentation, and L. plantarum dominated fermentation in the late stage. Leuconostoc mesenteroides CPTCC 1R3 (LEM), Weissella cibaria CPTCC 1R15 (WC), Levilactobacillus brevis CPTCC 3R8 (LB), and Lactiplantibacillus plantarum CPTCC 5R10 (LP) were screened from naturally fermented paocai and used for microbial reconstruction, revealing that the growth and fermentation profiles of the strains were closely related to the evolution of the bacterial community. Paocai inoculated with LEM had the following characteristics: fast fermentation, quickly disappearance of pungent odor of the raw materials, and the improved flavor and taste. Paocai inoculated with WC and LB contained ethanol and mannitol, but inoculated strains were poorly acid-tolerated. However, they can be used as auxiliary strains to enhance the flavor of paocai. Sample inoculated with LP resulted in slow fermentation and massive acid production. Mixed culture fermentation of paocai has more advantages than pure culture fermentation. Leu. mesenteroides and L. plantarum were the core microorganisms related to the flavor formation of paocai. These findings contributed to the better understanding of mechanisms underlie in the microbial community succession and flavor formation during paocai fermentation.

A Novel Nomogram for Predicting Cancer-Specific Survival in Patients With Spinal Chordoma: A Population-Based Analysis.

BACKGROUND: Chordoma is a rare malignant bone tumor, and the survival prediction for patients with chordoma is difficult. The objective of this study was to construct and validate a nomogram for predicting cancer-specific survival (CSS) in patients with spinal chordoma. METHODS: A total of 316 patients with spinal chordoma were identified from the SEER database between 1998 and 2015. The independent prognostic factors for patients with spinal chordoma were determined by univariate and multivariate Cox analyses. The prognostic nomogram was established for patients with spinal chordoma based on independent prognostic factors. Furthermore, we performed internal and external validations for this nomogram. RESULTS: Primary site, disease stage, histological type, surgery, and age were identified as independent prognostic factors for patients with spinal chordoma. A nomogram for predicting CSS in patients with spinal chordoma was constructed based on the above 5 variables. In the training cohort, the area under the curve for predicting 1-, 3-, and 5-year CSS were 0.821, 0.856, and 0.920, respectively. The corresponding area under the curve in the validation cohort were 0.728, 0.804, and 0.839, respectively. The calibration curves of the nomogram showed a high degree of agreement between the predicted and the actual results, and the decision curve analysis further demonstrated the satisfactory clinical utility of the nomogram. CONCLUSIONS: The prognostic nomogram provides a considerably more accurate prediction of prognosis for patients with spinal chordoma. Clinicians can use it to categorize patients into different risk groups and make personalized treatment methods.

Bone Metastasis in Renal Cell Carcinoma Patients: Risk and Prognostic Factors and Nomograms.

BACKGROUND: Bone metastasis (BM) is one of the common sites of renal cell carcinoma (RCC), and patients with BM have a poorer prognosis. We aimed to develop two nomograms to quantify the risk of BM and predict the prognosis of RCC patients with BM. METHODS: We reviewed patients with diagnosed RCC with BM in the Surveillance, Epidemiology, and End Results (SEER) database from 2010 to 2015. Multivariate logistic regression analysis was used to determine independent factors to predict BM in RCC patients. Univariate and multivariate Cox proportional hazards regression analyses were used to determine independent prognostic factors for BM in RCC patients. Two nomograms were established and evaluated by calibration curve, receiver operating characteristic (ROC) curve, and decision curve analysis (DCA). RESULTS: The study included 37,554 patients diagnosed with RCC in the SEER database, 537 of whom were BM patients. BM's risk factors included sex, tumor size, liver metastasis, lung metastasis, brain metastasis, N stage, T stage, histologic type, and grade in RCC patients. Currently, independent prognostic factors for RCC with BM included grade, histologic type, N stage, surgery, brain metastasis, and lung metastasis. The calibration curve, ROC curve, and DCA showed good performance for diagnostic and prognostic nomograms. CONCLUSIONS: Nomograms were established to predict the risk of BM in RCC and the prognosis of RCC with BM, separately. These nomograms strengthen each patient's prognosis-based decision making, which is critical in improving the prognosis of patients.