Integrated mass spectrometry imaging and single-cell transcriptome atlas strategies provide novel insights into taxoid biosynthesis and transport in Taxus mairei stems.

Taxol, which is a widely used important chemotherapeutic agent, was originally isolated from Taxus stem barks. However, little is known about the precise distribution of taxoids and the transcriptional regulation of taxoid biosynthesis across Taxus stems. Here, we used MALDI-IMS analysis to visualize the taxoid distribution across Taxus mairei stems and single-cell RNA sequencing to generate expression profiles. A single-cell T. mairei stem atlas was created, providing a spatial distribution pattern of Taxus stem cells. Cells were reordered using a main developmental pseudotime trajectory which provided temporal distribution patterns in Taxus stem cells. Most known taxol biosynthesis-related genes were primarily expressed in epidermal, endodermal, and xylem parenchyma cells, which caused an uneven taxoid distribution across T. mairei stems. We developed a single-cell strategy to screen novel transcription factors (TFs) involved in taxol biosynthesis regulation. Several TF genes, such as endodermal cell-specific MYB47 and xylem parenchyma cell-specific NAC2 and bHLH68, were implicated as potential regulators of taxol biosynthesis. Furthermore, an ATP-binding cassette family transporter gene, ABCG2, was proposed as a potential taxoid transporter candidate. In summary, we generated a single-cell Taxus stem metabolic atlas and identified molecular mechanisms underpinning the cell-specific transcriptional regulation of the taxol biosynthesis pathway.

DcERF109 regulates shoot branching by participating in strigolactone signal transduction in Dendrobium catenatum.

Shoot branching fundamentally influences plant architecture and agricultural yield. However, research on shoot branching in Dendrobium catenatum, an endangered medicinal plant in China, remains limited. In this study, we identified a transcription factor DcERF109 as a key player in shoot branching by regulating the expression of strigolactone (SL) receptors DWARF 14 (D14)/ DECREASED APICAL DOMINANCE 2 (DAD2). The treatment of D. catenatum seedlings with GR24rac/TIS108 revealed that SL can significantly repress the shoot branching in D. catenatum. The expression of DcERF109 in multi-branched seedlings is significantly higher than that of single-branched seedlings. Ectopic expression in Arabidopsis thaliana demonstrated that overexpression of DcERF109 resulted in significant shoot branches increasing and dwarfing. Molecular and biochemical assays demonstrated that DcERF109 can directly bind to the promoters of AtD14 and DcDAD2.2 to inhibit their expression, thereby positively regulating shoot branching. Inhibition of DcERF109 by virus-induced gene silencing (VIGS) resulted in decreased shoot branching and improved DcDAD2.2 expression. Moreover, overexpression of DpERF109 in A. thaliana, the homologous gene of DcERF109 in Dendrobium primulinum, showed similar phenotypes to DcERF109 in shoot branch and plant height. Collectively, these findings shed new insights into the regulation of plant shoot branching and provide a theoretical basis for improving the yield of D. catenatum.

Comparison of long-term bowel symptoms after laparoscopic radical hysterectomy versus abdominal radical hysterectomy in patients with cervical cancer.

INTRODUCTION AND HYPOTHESIS: The objective of this study was to compare the long-term bowel symptoms between laparoscopic radical hysterectomy (LRH) and abdominal radical hysterectomy (ARH) in patients with cervical cancer. METHODS: A total of 207 patients who underwent radical hysterectomy (79 underwent LRH and 128 underwent ARH) at Peking University First Hospital from January 2010 to August 2020 were enrolled and their bowel symptoms were investigated using the Colorectal Anal Distress Inventory-8 (CRADI-8) of the Pelvic Floor Distress Inventory-20. The prevalence and severity of bowel symptoms were compared in the LRH and ARH groups, and multivariate analysis was performed to determine the factors associated with bowel symptoms. RESULTS: There was no difference in the CRADI-8 scores between the two groups. However, the prevalence of straining at stool was significantly higher in the ARH group than in the LRH group (19.5% versus 1.3%, p<0.001), and the score was significantly higher in the ARH group than in the LRH group too (0.4 versus 0, p<0.001). The prevalence of incomplete defecation was significantly higher in the ARH group than in the LRH group (13.3% versus 3.8%, p=0.029), and the ARH group also had a significantly higher score than the LRH group (0.3 versus 0.1, p=0.028). Multivariate analysis showed that ARH and postoperative interval were independent risk factors for the development of straining at stool. CONCLUSIONS: Patients with cervical cancer who underwent ARH may be more likely to develop symptoms related to constipation than those who underwent LRH. This finding has to be interpreted with caution owing to the study design.

Bioinformatics-assisted, integrated omics studies on medicinal plants.

The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein-protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.

Integrated assessment of the clinical and biological value of ferroptosis-related genes in multiple myeloma.

BACKGROUND: Ferroptosis is an iron-dependent mode of cell death that could be induced by erastin and exert antitumor effects. However, the clinical and biological roles of ferroptosis-related gene (FRG) signature and the therapeutic value of erastin in multiple myeloma (MM) remained unknown. METHODS: Clinical and gene expression data of MM subjects were extracted from the Gene Expression Omnibus (GEO) public database. Univariable cox analysis was applied to determine FRGs related to survival and the least absolute shrinkage and selection operator (LASSO) regression analysis was used to develop a prognostic model. Prediction accuracy of the model was estimated by receiver operating characteristic (ROC) curves. Functional pathway enrichments and infiltrating immune status were also analyzed. We conducted in vitro experiments to investigate the combination therapy of erastin and doxorubicin. RESULTS: 17 FRGs were strongly associated with patient survival and 11 genes were identified to construct the prognostic model. ROC curves indicated great predictive sensitivity and specificity of the model in all cohorts. Patients were divided into low- and high-risk groups by median risk score in each cohort and the survival of the low-risk group was significantly superior than that of the high-risk group. We also observed a close relevance between functional pathways and immune infiltration with risk scores. Moreover, we combined erastin and doxorubicin in our in vitro experiments and found synergetic antitumor effects of the two agents, and the underlying mechanism is the overgeneration of intracellular Reactive Oxygen Species (ROS). CONCLUSIONS: We demonstrated the important value of ferroptosis in patient prognosis and as a potential antitumor target for MM.

Integrative analysis identifies CXCL11 as an immune-related prognostic biomarker correlated with cell proliferation and immune infiltration in multiple myeloma microenvironment.

PURPOSE: The interaction between tumor cells and tumor microenvironment (TME) has an important impact on progression and prognosis of multiple myeloma (MM), and has been proven to be promising therapeutic targets. This study intended to explore the relationship between TME and prognosis and identify valuable biomarkers of MM. METHODS: The transcriptomic and clinical information of MM retrieved from the Gene Expression Omnibus (GEO) were used to establish the model. The curve of Kaplan-Meier survival and the time-dependent receiver operating characteristic (ROC) were used to appraise the predictive ability. A nomogram was established for clinical application. Furthermore, the CIBERSORT algorithm was used to investigate the relation between IRGPI with the infiltration of immune cells. We also used histology, as well as in vitro and in vivo experiments to validate these findings. RESULTS: The results demonstrated an immune-related gene-based prognostic index (IRGPI) combined with clinical information. Patients were separated into high- and low-risk groups based on risk score, which had significantly difference in survival status and immune infiltrations. Furthermore, we identified CXCL11 as a key factor, which positively promotes the progression of MM and correlate with macrophage M2-like polarization and tumor immune cells infiltration. CONCLUSION: Our findings suggest the IRGPI significantly demonstrate the differential prognosis and prediction of immune cells infiltration. It provides some insights into the complex interaction between myeloma tumor cells and the TME, as well as in the development of a novel biomarker target for anti-MM therapy.

Assessment of long-term sexual function of cervical cancer survivors after treatment: A cross-sectional study.

OBJECTIVES: This study aimed to investigate the long-term sexual function of patients with cervical cancer who underwent treatment and to explore influential factors. METHODS: This retrospective cross-sectional study was conducted at Peking University First Hospital in (Beijing, China). A total of 207 patients, who were diagnosed with Stage IA-IIA cervical cancer and had undergone surgical treatment (some patients had also been treated with adjuvant radiotherapy and chemotherapy) between January 2010 and August 2020, completed questionnaires via telephone. The median time since diagnosis was 54 (range, 13-138) months. Sexual function was assessed using the validated short form of Pelvic Organ Prolapse/Urinary Incontinence Sexual Questionnaire (PISQ-12). The multivariate logistic regression analysis was performed to determine factors influencing sexual function after treatment. RESULTS: The mean preoperative PISQ-12 score was 39.42 ± 3.922, and the mean postoperative PISQ-12 score was 32.60 ± 6.592, indicating a significant decrease in postoperative PISQ-12 score compared with preoperation (p < 0.001). In total, 49.8% of the patients had sexual dysfunction after treatment. According to the results of the multivariate logistic regression analysis, longer follow-up (months), ovariectomy, lack of hormone replacement therapy after ovariectomy and adjuvant radiotherapy were significantly associated with sexual dysfunction after treatment (p < 0.05). There was no significant correlation among surgical method, tumor stage, adjuvant chemotherapy, and sexual dysfunction after treatment. CONCLUSIONS: The sexual function of cervical cancer survivors significantly decreased after treatment, which was related to the length of follow-up, ovariectomy, and adjuvant radiotherapy. Hormone replacement therapy after ovariectomy can help patients to improve their sexual function.

Genome-Wide Identification of AP2/ERF Transcription Factor Family and Functional Analysis of DcAP2/ERF#96 Associated with Abiotic Stress in Dendrobium catenatum.

APETALA2/Ethylene Responsive Factor (AP2/ERF) family plays important roles in reproductive development, stress responses and hormone responses in plants. However, AP2/ERF family has not been systematically studied in Dendrobium catenatum. In this study, 120 AP2/ERF family members were identified for the first time in D. catenatum, which were divided into four groups (AP2, RAV, ERF and DREB subfamily) according to phylogenetic analysis. Gene structures and conserved motif analysis showed that each DcAP2/ERF family gene contained at least one AP2 domain, and the distribution of motifs varied among subfamilies. Cis-element analysis indicated that DcAP2/ERF genes contained abundant cis-elements related to hormone signaling and stress response. To further identify potential genes involved in drought stress, 12 genes were selected to detect their expression under drought treatment through qRT-PCR analysis and DcAP2/ERF#96, a nuclear localized ethylene-responsive transcription factor, showed a strong response to PEG treatment. Overexpression of DcAP2/ERF#96 in Arabidopsis showed sensitivity to ABA. Molecular, biochemical and genetic assays indicated that DcAP2ERF#96 interacts with DREB2A and directly inhibits the expression of P5CS1 in response to the ABA signal. Taken together, our study provided a molecular basis for the intensive study of DcAP2/ERF genes and revealed the biological function of DcAP2ERF#96 involved in the ABA signal.

Identification of a prognostic metabolic gene signature in diffuse large B-cell lymphoma.

Diffuse large B-cell lymphoma (DLBCL) is a clinically diverse disease. Given the numerous genetic mutations and variations associated with it, a prognostic gene signature that can be related to the overall survival (OS) is a clinical implication. We used the mRNA expression profiles and clinicopathological data of patients with DLBCL from the Gene Expression Omnibus (GEO) database to identify a metabolism-related gene signature. Using LASSO regression analysis, a novel 13-metabolic gene signature was identified to evaluate prognosis. The information gathered was used to construct the nomogram model to improve risk stratification and quantify risk factors for individual patients. We performed gene set enrichment analysis to identify the enriched signalling axes to further understand the underlying biological pathways. The receiver operating characteristic (ROC) curve revealed a satisfactory performance in the training cohorts. The model also showed clinical benefit when compared to the standard prognostic factors (P < .05) in validation cohorts. This study aimed to combine metabolic dysregulation with clinical features of patients with DLBCL to generate a prognostic model that might not only indicate the value of the metabolic microenvironment for prognostic stratification but also improve the decision-making during individual therapy.

Establishment of a prognostic ferroptosis-related gene profile in acute myeloid leukaemia.

Acute myeloid leukaemia (AML) is a heterogeneous disease with a difficult to predict prognosis. Ferroptosis, an iron-induced programmed cell death, is a promising target for cancer therapy. Nevertheless, not much is known about the relationship between ferroptosis-related genes and AML prognosis. Herein, we retrieved RNA profile and corresponding clinical data of AML patients from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Univariate Cox analysis was employed to identify ferroptosis-related genes significantly associated with AML prognosis. Next, the least absolute shrinkage and selection operator (LASSO) regression was employed to establish a prognostic ferroptosis-related gene profile. 12 ferroptosis-related genes were screened to generate a prognostic model, which stratified patients into a low- (LR) or high-risk (HR) group. Using Kaplan-Meier analysis, we demonstrated that the LR patients exhibited better prognosis than HR patients. Moreover, receiver operating characteristic (ROC) curve analysis confirmed that the prognostic model showed good predictability. Functional enrichment analysis indicated that the infiltration of regulatory T cells (Treg) differed vastly between the LR and HR groups. Our prognostic model can offer guidance into the accurate prediction of AML prognosis and selection of personalized therapy in clinical practice.

Tissue-specific study across the stem of Taxus media identifies a phloem-specific TmMYB3 involved in the transcriptional regulation of paclitaxel biosynthesis.

Taxus stem barks can be used for extraction of paclitaxel. However, the composition of taxoids across the whole stem and the stem tissue-specificity of paclitaxel biosynthesis-related enzymes remain largely unknown. We used cultivated Taxus media trees for analyses of the chemical composition and protein of major stem tissues by an integrated metabolomic and proteomic approach, and the role of TmMYB3 in paclitaxel biosynthesis was investigated. The metabolomic landscape analysis showed differences in stem tissue-specific accumulation of metabolites. Phytochemical analysis revealed that there is high accumulation of paclitaxel in the phloem. Ten key enzymes involved in paclitaxel biosynthesis were identified, most of which are predominantly produced in the phloem. The full-length sequence of TmMYB3 and partial promoter sequences of five paclitaxel biosynthesis-related genes were isolated. Several MYB recognition elements were found in the promoters of TBT, DBTNBT and TS. Further in vitro and in vivo investigations indicated that TmMYB3 is involved in paclitaxel biosynthesis by activating the expression of TBT and TS. Differences in the taxoid composition of different stem tissues suggest that the whole stem of T. media has potential for biotechnological applications. Phloem-specific TmMYB3 plays a role in the transcriptional regulation of paclitaxel biosynthesis, and may explain the phloem-specific accumulation of paclitaxel.

Omic analysis of the endangered Taxaceae species Pseudotaxus chienii revealed the differences in taxol biosynthesis pathway between Pseudotaxus and Taxus yunnanensis trees.

BACKGROUND: Taxol is an efficient anticancer drug accumulated in Taxus species. Pseudotaxus chienii is an important member of Taxaceae, however, the level of six taxoids in P. chienii is largely unknown. RESULTS: High accumulation of 10-DAB, taxol, and 7-E-PTX suggested that P. chienii is a good taxol-yielding species for large-scale cultivation. By the omics approaches, a total of 3,387 metabolites and 61,146 unigenes were detected and annotated. Compared with a representative Taxus tree (Taxus yunnanensis), most of the differentially accumulated metabolites and differential expressed genes were assigned into 10 primary and secondary metabolism pathways. Comparative analyses revealed the variations in the precursors and intermediate products of taxol biosynthesis between P. chienii and T. yunnanensis. Taxusin-like metabolites highly accumulated in P. chienii, suggesting a wider value of P. chienii in pharmaceutical industry. CONCLUSIONS: In our study, the occurrence of taxoids in P. chienii was determined. The differential expression of key genes involved in the taxol biosynthesis pathway is the major cause of the differential accumulation of taxoids. Moreover, identification of a number of differentially expressed transcription factors provided more candidate regulators of taxol biosynthesis. Our study may help to reveal the differences between Pseudotaxus and Taxus trees, and promote resource utilization of the endangered and rarely studied P. chienii.

Enhanced Salt Tolerance of Rhizobia-inoculated Soybean Correlates with Decreased Phosphorylation of the Transcription Factor GmMYB183 and Altered Flavonoid Biosynthesis.

Soybean (Glycine max (L.) Merrill) is an important component of the human diet and animal feed, but soybean production is limited by abiotic stresses especially salinity. We recently found that rhizobia inoculation enhances soybean tolerance to salt stress, but the underlying mechanisms are unaddressed. Here, we used quantitative phosphoproteomic and metabonomic approaches to identify changes in phosphoproteins and metabolites in soybean roots treated with rhizobia inoculation and salt. Results revealed differential regulation of 800 phosphopeptides, at least 32 of these phosphoproteins or their homologous were reported be involved in flavonoid synthesis or trafficking, and 27 out of 32 are transcription factors. We surveyed the functional impacts of all these 27 transcription factors by expressing their phospho-mimetic/ablative mutants in the roots of composite soybean plants and found that phosphorylation of GmMYB183 could affect the salt tolerance of the transgenic roots. Using data mining, ChIP and EMSA, we found that GmMYB183 binds to the promoter of the soybean GmCYP81E11 gene encoding for a Cytochrome P450 monooxygenase which contributes to the accumulation of ononin, a monohydroxy B-ring flavonoid that negatively regulates soybean tolerance to salinity. Phosphorylation of GmMYB183 was inhibited by rhizobia inoculation; overexpression of GmMYB183 enhanced the expression of GmCYP81E11 and rendered salt sensitivity to the transgenic roots; plants deficient in GmMYB183 function are more tolerant to salt stress as compared with wild-type soybean plants, these results correlate with the transcriptional induction of GmCYP81E11 by GmMYB183 and the subsequent accumulation of ononin. Our findings provide molecular insights into how rhizobia enhance salt tolerance of soybean plants.

Genomic Sequence Resource of Alternaria alternata Strain B3 Causing Leaf Blight on Ophiopogon japonicus.

Black spot of Ophiopogon japonicus is an economically important disease, which can result in significant losses of both yield and quality of this traditional Chinese medicinal plant. The disease is caused by the small-spored fungal pathogen Alternaria alternata, a necrotrophic fungus that is ubiquitously distributed in the environment. Here, we present the draft whole-genome sequence of A. alternata strain B3 that caused black spot on O. japonicus. The assembly consists of 76 contigs with an estimated genome size of 33.8 Mb. Furthermore, we identified genes that may be associated with the pathogenicity, such as carbohydrate-active enzymes, secreted proteins, and secondary metabolite gene clusters. This genome resource will provide a useful source for future research on the evolution of pathogenicity of A. alternata and phylogenomic analysis in delineating phylogenetic lineages within the genus Alternaria.

First Draft Genome Sequence Resource of Colletotrichum liriopes Causing Leaf Anthracnose on Ophiopogon japonicus.

Leaf anthracnose of Ophiopogon japonicus is an important disease that can significantly reduce the quality and economic value of this traditional Chinese medicinal plant. The disease is caused by Colletotrichum liriopes, a necrotrophic fungus that belongs to the Glomerellaceae family of the Sordariomycetes class. Here, we present the draft whole-genome sequence of the C. liriopes strain A2 that caused leaf anthracnose on O. japonicus. The assembly consists of 407 contigs with an estimated genome size of 53.1 Mb. Furthermore, we identified 670 carbohydrate-active enzymes, 1,377 secreted proteins, and 60 secondary metabolite gene clusters, which may be associated with the pathogenicity of this pathogen. This genome resource will provide a valuable resource for future research on the pathogenesis of C. liriopes and comparative genome analyses within genus Colletotrichum.

Bioactive compounds induced in Physalis angulata L. by methyl-jasmonate: an investigation of compound accumulation patterns and biosynthesis-related candidate genes.

KEY MESSAGE: We employed both metabolomic and transcriptomic approaches to explore the accumulation patterns of physalins, flavonoids and chlorogenic acid in Physalis angulata and revealed the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Physalis angulata L. is an annual Solanaceae plant with a number of medicinally active compounds. Despite the potential pharmacological benefits of P. angulata, the scarce genomic information regarding this plant has limited the studies on the mechanisms of bioactive compound biosynthesis. To facilitate the basic understanding of the main chemical constituent biosynthesis pathways, we performed both metabolomic and transcriptomic approaches to reveal the genes associated with the biosynthesis of bioactive compounds under methyl-jasmonate (MeJA) treatment. Untargeted metabolome analysis showed that most physalins, flavonoids and chlorogenic acid were significantly upregulated. Targeted HPLC-MS/MS analysis confirmed variations in the contents of two important representative steroid derivatives (physalins B and G), total flavonoids, neochlorogenic acid, and chlorogenic acid between MeJA-treated plants and controls. Transcript levels of a few steroid biosynthesis-, flavonoid biosynthesis-, and chlorogenic acid biosynthesis-related genes were upregulated, providing a potential explanation for MeJA-induced active ingredient synthesis in P. angulata. Systematic correlation analysis identified a number of novel candidate genes associated with bioactive compound biosynthesis. These results may help to elucidate the regulatory mechanism underlying MeJA-induced active compound accumulation and provide several valuable candidate genes for further functional study.

An RNAi suppressor activates in planta virus-mediated gene editing.

RNA-guided CRISPR/Cas9 technology has been developed for gene/genome editing (GE) in organisms across kingdoms. However, in planta delivery of the two core GE components, Cas9 and small guide RNA (sgRNA), often involves time-consuming and labor-intensive production of transgenic plants. Here we show that Foxtail mosaic virus, a monocot- and dicot-infecting potexvirus, can simultaneously express Cas9, sgRNA, and an RNAi suppressor to efficiently induce GE in Nicotiana benthamiana through a transgenic plant-free manner.

Cladribine with Granulocyte Colony-Stimulating Factor, Cytarabine, and Aclarubicin Regimen in Refractory/Relapsed Acute Myeloid Leukemia: A Phase II Multicenter Study.

LESSONS LEARNED: Studies targeting cladribine in combination with granulocyte colony-stimulating factor, low-dose cytarabine, and aclarubicin (C-CAG) regimen in relapsed and refractory acute myeloid leukemia (R/R AML) are limited. The complete remission rate after two cycles of C-CAG regimen was 67.6%, and 1-year overall survival and disease-free survival rates were 59.7% and 72.9%, respectively. The C-CAG regimen is significantly effective against R/R AML with a low hematological toxicity and thus serves as an alternative treatment for R/R AML. BACKGROUND: The optimal salvage chemotherapy regimen for relapsed and refractory acute myeloid leukemia (R/R AML) remains uncertain. Therefore, a phase II study was conducted for the prospective evaluation of the efficacy and safety of the purine analog cladribine in combination with granulocyte colony-stimulating factor (G-CSF), low-dose cytarabine, and aclarubicin (C-CAG) regimen for patients with R/R AML. METHODS: A total of 34 patients received C-CAG regimen for salvage treatment as follows: cladribine 5 mg/m2 , days 1-5; G-CSF 300 µg, days 0-9; aclarubicin 10 mg, days 3-6; cytarabine 10 mg/m2 every 12 hours, subcutaneously, days 3-9; 4 weeks per cycle. Patients were allowed to withdraw from the study if complete remission (CR) was not achieved after two courses of chemotherapy. If conditions were right, the patients achieving CR were recommended to receive allogeneic hematopoietic stem cell transplantation. Otherwise, they were treated for a total of six cycles unless disease progression or unacceptable side effects were observed or they withdrew their consent. RESULTS: All patients received at least two cycles of C-CAG regimen chemotherapy. After two cycles of C-CAG, 23 patients (67.6%) achieved CR, and 5 patients had partial remission (14.7%). At a median follow-up of 15 months (range, 3-38 months), the 1-year overall survival (OS) and disease-free survival (DFS) rates were 59.7% (95% confidence interval [CI], 42.6%-76.8%) and 72.9% (95% CI, 54.3%-91.5%), respectively. The most common adverse effect was myelosuppression. Nonhematological toxicities were mild, and no treatment-related deaths occurred. CONCLUSION: Preliminary data indicate that the C-CAG regimen chemotherapy is significantly effective against R/R AML with a high remission rate and a low hematological toxicity. Thus, it may serve as an alternative treatment for R/R AML.

Complete chloroplast genomes of four Physalis species (Solanaceae): lights into genome structure, comparative analysis, and phylogenetic relationships.

BACKGROUND: Physalis L. is a genus of herbaceous plants of the family Solanaceae, which has important medicinal, edible, and ornamental values. The morphological characteristics of Physalis species are similar, and it is difficult to rapidly and accurately distinguish them based only on morphological characteristics. At present, the species classification and phylogeny of Physalis are still controversial. In this study, the complete chloroplast (cp) genomes of four Physalis species (Physalis angulata, P. alkekengi var. franchetii, P. minima and P. pubescens) were sequenced, and the first comprehensive cp genome analysis of Physalis was performed, which included the previously published cp genome sequence of Physalis peruviana. RESULTS: The Physalis cp genomes exhibited typical quadripartite and circular structures, and were relatively conserved in their structure and gene synteny. However, the Physalis cp genomes showed obvious variations at four regional boundaries, especially those of the inverted repeat and the large single-copy regions. The cp genomes' lengths ranged from 156,578 bp to 157,007 bp. A total of 114 different genes, 80 protein-coding genes, 30 tRNA genes, and 4 rRNA genes, were observed in four new sequenced Physalis cp genomes. Differences in repeat sequences and simple sequence repeats were detected among the Physalis cp genomes. Phylogenetic relationships among 36 species of 11 genera of Solanaceae based on their cp genomes placed Physalis in the middle and upper part of the phylogenetic tree, with a monophyletic evolution having a 100% bootstrap value. CONCLUSION: Our results enrich the data on the cp genomes of the genus Physalis. The availability of these cp genomes will provide abundant information for further species identification, increase the taxonomic and phylogenetic resolution of Physalis, and assist in the investigation and utilization of Physalis plants.

Investigating microRNA-mediated regulation of the nascent nuclear transcripts in plants: a bioinformatics workflow.

Most of the microRNAs (miRNAs) play their regulatory roles through posttranscriptional target decay or translational inhibition. For both plants and animals, these regulatory events were previously considered to take place in cytoplasm, as mature miRNAs were observed to be exported to the cytoplasm for Argonaute (AGO) loading and subsequent target binding. Recently, this notion was challenged by increasing pieces of evidence in the animal cells that uncovered the nuclear importation and action of the AGO-associated miRNAs. The nuclear-localized regulatory mode was also reported for the plant miRNAs. However, evidence is still lacking to show the universality and conservation of the miRNA-mediated regulation in the plant nuclei. Here, we introduced a bioinformatics workflow for genome-wide investigation of miRNA-guided, cleavage-based regulation of the nascent nuclear transcripts. Facilitated by the tool package PmiRNTSA (Plant microRNA-mediated nascent transcript slicing analyzer), plant biologists could perform a comprehensive search for the miRNA slicing sites located within the introns or the exon-intron/intron-exon junctions of the target transcripts, which are supported by degradome sequencing data. The results enable the researchers to examine the co-transcriptional regulatory model of the miRNAs for a specific plant species. Moreover, a case study was performed to search for the slicing sites located within the exon-intron/intron-exon junctions in two model plants. A case study was performed to show the feasibility and reliability of our workflow. Together, we hope that this work could inspire much more innovative research efforts to expand the current understanding of the miRNA action modes in plants.