Efficiency of therapeutic plasma exchange in critically ill systemic rheumatologic diseases: A single-center 9-year experience.

INTRODUCTION: Therapeutic plasma exchange (TPE), an effective method to eliminate harmful soluble mediators associated with tissue injury, serves as a crucial intervention for systemic rheumatologic diseases (SRDs). However, its value in critically ill SRDs remains uncertain. This retrospective study aims to evaluate the efficacy of TPE in SRDs. METHODS: Critically ill SRD patients admitted to the department of intensive care unit of a large tertiary hospital receiving TPE from January 2011 to December 2019 were included. RESULTS: A total of 91 critically ill SRD patients received TPE were enrolled. Their mean age was 47.67 ± 16.35 years with a female predominance (n = 68). Significant decrease in SOFA score post-TPE treatment was observed (p < 0.05). There were no TPE-related fatalities. Improvement was observed in 64 (70.32%) patients. CONCLUSION: This study shows favorable clinical outcomes. TPE may be an acceptable treatment option for critically ill SRD patients.

Endogenous retroviral solo-LTRs in human genome.

Human endogenous retroviruses (HERVs) are derived from the infection and integration of exogenetic retroviruses. HERVs account for 8% of human genome, and the majority of HERVs are solitary LTRs (solo-LTRs) due to homologous recombination. Multiple findings have showed that solo-LTRs could provide an enormous reservoir of transcriptional regulatory sequences involved in diverse biological processes, especially carcinogenesis and cancer development. The link between solo-LTRs and human diseases still remains poorly understood. This review focuses on the regulatory modules of solo-LTRs, which contribute greatly to the diversification and evolution of human genes. More importantly, although inactivating mutations, insertions and deletions have been identified in solo-LTRs, the inherited regulatory elements of solo-LTRs initiate the expression of chimeric lncRNA transcripts, which have been reported to play crucial roles in human health and disease. These findings provide valuable insights into the evolutionary and functional mechanisms underlying the presence of HERVs in human genome. Taken together, in this review, we will present evidences showing the regulatory and encoding capacity of solo-LTRs as well as the significant impact on various aspects of human biology.

Visible-Light-Induced C-H Cyanoalkylation of Azauracils with Cycloketone Oxime Esters via Catalytic EDA Complex.

Photoexcitation electron donor-acceptor (EDA) complexes provide an effective approach to produce radicals under mild conditions, while the catalytic version of EDA complex photoactivation remains scarce. Herein, we report a visible-light-induced organophotocatalytic pathway for the cyanoalkylation of azauracils using inexpensive and readily available 1,4-diazabicyclo[2.2.2]octane (DABCO) as a catalytic electron donor. This synthetic method exhibits exceptional compatibility with various functional groups and presents 34 examples in high yields. The efficient cyanoalkylation offers an environmentally friendly and sustainable route toward enhancing the structural and functional diversity of azauracils.

Bloodstream infection clusters for critically ill patients: analysis of two-center retrospective cohorts.

BACKGROUND: Bloodstream infections (BSI) are highly prevalent in hospitalized patients requiring intensive care. They are among the most serious infections and are highly associated with sepsis or septic shock, which can lead to prolonged hospital stays and high healthcare costs. This study aimed at establishing an easy-to-use nomogram for predicting the prognosis of patients with BSI. METHODS: In retrospective study, records of patients with BSI admitted to the intensive care unit (ICU) over the period from Jan 1st 2016 to Dec 31st 2021 were included. We used data from two different China hospitals as development cohort and validation cohort respectively. The demographic and clinical data of patients were collected. Based on all baseline data, k-means algorithm was applied to discover the groups of BSI phenotypes with different prognostic outcomes, which was confirmed by Kaplan-Meier analysis and compared using log-rank tests. Univariate Cox regression analyses were used to estimate the risk of clusters. Random forest was used to identified discriminative predictors in clusters, which were utilized to construct nomogram based on multivariable logistic regression in the discovery cohort. For easy clinical applications, we developed a bloodstream infections clustering (BSIC) score according to the nomogram. The results were validated in the validation cohort over a similar period. RESULTS: A total of 360 patients in the discovery cohort and 310 patients in the validation cohort were included in statistical analyses. Based on baseline variables, two distinct clusters with differing prognostic outcomes were identified in the discovery cohort. Population in cluster 1 was 211 with a ICU mortality of 17.1%, while population in cluster 2 was 149 with an ICU mortality of 41.6% (p < 0.001). The survival analysis also revealed a higher risk of death for cluster 2 when compared with cluster 1 (hazard ratio: 2.31 [95% CI, 1.53 to 3.51], p < 0.001), which was confirmed in validation cohort. Four independent predictors (vasoconstrictor use before BSI, mechanical ventilation (MV) before BSI, Deep vein catheterization (DVC) before BSI, and antibiotic use before BSI) were identified and used to develop a nomogram. The nomogram and BSIC score showed good discrimination with AUC of 0.96. CONCLUSION: The developed score has potential applications in the identification of high-risk critically ill BSI patients.

Identification of keystone taxa in rhizosphere microbial communities using different methods and their effects on compounds of the host Cinnamomum migao.

Exploring keystone taxa affecting microbial community stability and host function is crucial for understanding ecosystem functions. However, identifying keystone taxa from humongous microbial communities remains challenging. We collected 344 rhizosphere and bulk soil samples from the endangered plant C. migao for 2 years consecutively. Used high-throughput sequencing 16S rDNA and ITS to obtain the composition of bacterial and fungal communities. We explored keystone taxa and the applicability and limitations of five methods (SPEC-OCCU, Zi-Pi, Subnetwork, Betweenness, and Module), as well as the impact of microbial community domain, time series, and rhizosphere boundary on the identification of keystone taxa in the communities. Our results showed that the five methods, identified abundant keystone taxa in rhizosphere and bulk soil microbial communities. However, the keystone taxa shared by the rhizosphere and bulk soil microbial communities over time decreased rapidly decrease in the five methods. Among five methods on the identification of keystone taxa in the rhizosphere community, Module identified 113 taxa, SPEC-OCCU identified 17 taxa, Betweenness identified 3 taxa, Subnetwork identified 3 taxa, and Zi-Pi identified 4 taxa. The keystone taxa are mainly conditionally rare taxa, and their ecological functions include chemoheterotrophy, aerobic chemoheterotrophy, nitrate reduction, and anaerobic photoautotrophy. The results of the random forest model and structural equation model predict that keystone taxa Mortierella and Ellin6513 may have an effects on the accumulation of 1, 4, 7, - Cycloundecatriene, 1, 5, 9, 9-tetramethyl-, Z, Z, Z-, beta-copaene, bicyclogermacrene, 1,8-Cineole in C. migao fruits, but their effects still need further evidence. Our study evidence an unstable microbial community in the bulk soil, and the definition of microbial boundary and ecologically functional affected the identification of keystone taxa in the community. Subnetwork and Module are more in line with the definition of keystone taxa in microbial ecosystems in terms of maintaining community stability and hosting function.

The potential mechanism of ursolic acid in the treatment of bladder cancer based on network pharmacology and molecular docking.

OBJECTIVE: This study explored the potential molecular mechanisms of ursolic acid (UA) in bladder cancer treatment using network pharmacology and molecular docking. METHODS: The Traditional Chinese Medicine Systems Pharmacology and UniProt databases were used to screen potential targets of UA. Relevant bladder cancer target genes were extracted using the GeneCards database. All data were pooled and intercrossed to obtain common target genes of UA and bladder cancer. Gene Ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed. Molecular docking was conducted to verify the possible binding conformation between UA and bladder cancer cells. Then, in vitro experiments were performed to further validate the predicted results. RESULTS: UA exerts anti-tumor effects on bladder cancer through multiple targets and pathways. Molecular docking indicated that UA undergoes stable binding with the proteins encoded by the top six core genes (STAT3, VEGFA, CASP3, TP53, IL1B, and CCND1). The in vitro experiments verified that UA can induce bladder cancer cell apoptosis by regulating the PI3K/Akt signaling pathway. CONCLUSIONS: Our study illustrated the potential mechanism of UA in bladder cancer based on network pharmacology and molecular docking. The results will provide scientific references for follow-up studies and clinical treatment.

Mathematical modeling of optimal coagulant dosage for tofu preparation using MgCl2.

To explore the association between the optimal coagulant for tofu and the components of soybeans,30 different kinds of soybeans were selected, and tested for their optimal coagulant MgCl2 content. The optimal amount of coagulant was taken as the dependent variable, and the soybean Composition were taken as independent variables for the correlation analysis. The results showed that there was a positive correlation between the optimal coagulant content and the content of histidine, 7S ß-conglycinin, B1aB1bB2B3B4 of 11 s glycincin, and α'-subunit of 7S ß-conglycinin, negative correlation with lysine. The regression formula is y = -1.186 + 3.457*B1aB1bB2B3B4 + 2.304*7S + 0.351*histidine - 0.084*lysine + 4.696*α', and the model is validated to be within 10 % of the error value and has a high degree of confidence. This study provides theoretical support for realizing the green production of traditional soybean products.

Analysis of winter diet in Guizhou golden monkey (Rhinopithecus brelichi) using DNA metabarcoding data.

The Guizhou golden monkey (Rhinopithecus brelichi) is a critically endangered wildlife species, and understanding its diet composition may be useful for assessing its feeding strategies. DNA metabarcoding was used to determine the dietary diversity of R. brelichi. DNA was extracted from 31 faecal samples and amplified chloroplast rbcL and mitochondrial COI DNA was sequenced using the Illumina NovaSeq platform. A comparative analysis of the sequences revealed that the five most abundant plant genera were Magnolia, Morinda, Viburnum, Tetradium and Eurya. In winter, R. brelichi mostly consumed shrubs, herbs and shrubs/trees according to the habit of plant genera with higher abundances comparatively. The five most abundant families in animal diet were Psychodidae, Trichinellidae, Staphylinidae, Scarabaeidae and Trichoceridae. This study is the first to show the composition of the winter animal diets of R. brelichi based on DNA metabarcoding. These results provide an important basis for understanding the diet of wild R. brelichi, which inhabits only the Fanjingshan National Nature Reserve, China.

A Case Report of Concurrent Transplant Renal Artery Stenosis, Renal Cell Carcinoma, and Papillary Thyroid Cancer After Renal Transplantation: A Literature Review.

BACKGROUND: Kidney transplantation is the preferred treatment option for eligible patients with end-stage renal disease. With advanced transplantation technology and novel immunosuppressive agents, kidney transplant recipients survive significantly longer. However, the chance of developing malignant tumors has increased, posing a serious challenge to the survival of transplanted kidneys and patients. CASE PRESENTATION: We report a male patient (the patient's informed consent has been obtained) who underwent kidney transplantation 23 years ago. Subsequently, he developed transplant renal artery stenosis, primary renal clear cell carcinoma, and papillary thyroid cancer. The narrowed blood vessels were dilated through percutaneous transluminal angioplasty, and the malignant tumor was removed surgically. Currently, antirejection drugs are regularly taken, and the transplanted kidney function is good. The patient is satisfied with his living conditions. CONCLUSIONS: Hypertension that is difficult to control after kidney transplantation should be suspected as a possibility of graft vascular stenosis. When B-ultrasound cannot accurately diagnose it, magnetic resonance angiography should be used as early as possible to clarify the diagnosis and relieve the stenosis before graft dysfunction. Transplantation patients have a high incidence of malignant tumors after surgery, and the risk increases with the prolongation of the disease course. The focus should be on symptomatic treatment of related diseases, and antirejection drugs can be reduced or not reduced as appropriate.

Development of a TLR-Based Model That Can Predict Prognosis, Tumor Microenvironment, and Drug Response for Esophageal Squamous Cell Carcinoma.

The toll-like receptor (TLR) family is an important class of proteins involved in the immune response. However, little is known about the association between TLRs and Esophageal squamous cell cancer (ESCC). We explored differentially expressed genes (DEGs) between ESCC and esophagus tissues in TCGA and GTEx database. By taking the intersection with TLR gene set and using univariate Cox analysis and multivariate Cox regression analysis to discriminate the hub genes, we created a TLR-prognostic model. Our model separated patients with ESCC into high- and low-risk score (RS) groups. Prognostic analysis was performed with Kaplan-Meier curves. The two groups were also compared regarding tumor immune microenvironment and drug sensitivity. Six hub genes (including CD36, LGR4, MAP2K3, NINJ1, PIK3R1, and TRAF3) were screened to construct a TLR-prognostic model. High-RS group had a worse survival (p < 0.01), lower immune checkpoint expression (p < 0.05), immune cell abundance (p < 0.05) and decreased sensitivity to Epirubicin (p < 0.001), 5-fluorouracil (p < 0.0001), Sorafenib (p < 0.01) and Oxaliplatin (p < 0.05). We constructed a TLR-based model, which could be used to assess the prognosis of patients with ESCC, provide new insights into drug treatment for ESCC patients and investigate the TME and drug response.

EGFR mediates epithelial­mesenchymal transition through the Akt/GSK-3ß/Snail signaling pathway to promote liver cancer proliferation and migration.

Epidermal growth factor receptor (EGFR) is expressed in various types of cancer and is associated with the malignant biological behavior of cancer cells. In the present study, the expression of EGFR in hepatocellular carcinoma (HCC) tissues and liver cancer cells was detected by immunohistochemical staining, western blotting and immunofluorescence. Furthermore, a lentivirus was transduced into HepG2 liver cancer cells to knock down EGFR expression. Cell proliferation and migration, and the expression levels of epithelial-mesenchymal transition (EMT) markers were assessed by EdU staining, Cell Counting Kit-8, colony formation, wound healing and Transwell assays, and western blotting. The results revealed that EGF/EGFR can mediate EMT through the Akt/glycogen synthase kinase-3ß (GSK-3ß)/Snail signaling pathway to promote HepG2 cell proliferation and migration. Inhibition of the activation of the EGFR signaling pathway can help to partially reverse the EMT phenotype, and inhibit the proliferation and migration of HepG2 cells. In conclusion, the EGFR/Akt/GSK-3ß/Snail signaling pathway serves an important role in HCC progression, and inhibition of the activation of the EGFR signaling pathway may be a valuable strategy in liver cancer treatment.

Fine-tuning rice heading date through multiplex editing of the regulatory regions of key genes by CRISPR-Cas9.

Heading date (or flowering time) is a key agronomic trait that affects seasonal and regional adaption of rice cultivars. An unoptimized heading date can either not achieve a high yield or has a high risk of encountering abiotic stresses. There is a strong demand on the mild to moderate adjusting the heading date in breeding practice. Genome editing is a promising method which allows more precise and faster changing the heading date of rice. However, direct knock out of major genes involved in regulating heading date will not always achieve a new germplasm with expected heading date. It is still challenging to quantitatively adjust the heading date of elite cultivars with best adaption for broader region. In this study, we used a CRISPR-Cas9 based genome editing strategy called high-efficiency multiplex promoter-targeting (HMP) to generate novel alleles at cis-regulatory regions of three major heading date genes: Hd1, Ghd7 and DTH8. We achieved a series of germplasm with quantitative variations of heading date by editing promoter regions and adjusting the expression levels of these genes. We performed field trials to screen for the best adapted lines for different regions. We successfully expanded an elite cultivar Ningjing8 (NJ8) to a higher latitude region by selecting a line with a mild early heading phenotype that escaped from cold stress and achieved high yield potential. Our study demonstrates that HMP is a powerful tool for quantitatively regulating rice heading date and expanding elite cultivars to broader regions.

Embracing Large Natural Data: Enhancing Medical Image Analysis via Cross-domain Fine-tuning.

With the rapid advancements of big data and computer vision, many large-scale natural visual datasets are proposed, such as ImageNet-21K, LAION-400M, and LAION-2B. These large-scale datasets significantly improve the robustness and accuracy of models in the natural vision domain. However, the field of medical images continues to face limitations due to relatively small-scale datasets. In this paper, we propose a novel method to enhance medical image analysis across domains by leveraging pre-trained models on large natural datasets. Specifically, a Cross-Domain Transfer Module (CDTM) is proposed to transfer natural vision domain features to the medical image domain, facilitating efficient fine-tuning of models pre-trained on large datasets. In addition, we design a Staged Fine-Tuning (SFT) strategy in conjunction with CDTM to further improve the model performance. Experimental results demonstrate that our method achieves state-of-the-art performance on multiple medical image datasets through efficient fine-tuning of models pre-trained on large natural datasets. The code is available at https://github.com/qklee-lz/CDTM.

Comparison of robot-assisted thoracic surgery versus video-assisted thoracic surgery in the treatment of lung cancer: a systematic review and meta-analysis of prospective studies.

Introduction: Previous studies have compared robot-assisted thoracic surgery(RATS) with video-assisted thoracic surgery (VATS) in the treatment of patients with lung cancer, but results were conflicting. The present meta-analysis aimed to compare the clinical outcomes of RATS with VATS in the treatment of patients with lung cancer. Materials and methods: Web of Science, PubMed, Cochrane Library and Embase were comprehensively searched for randomized controlled trials or prospective cohort studies comparing the clinical outcomes of RATS and VATS from inception to 22 July 2023. The Cochrane Risk of Bias tool was used to assess risk of bias. Meta-analyses of length of hospital stay, postoperative duration of drainage, postoperative complications, operative time, conversion, estimated blood loss, the number of dissected lymph nodes and stations, 30-day readmission and 30-day mortality were performed. Results: In total 5 studies were included in the meta-analysis. A total of 614 patients were included, of which 299 patients were treated by RATS and 315 patients treated by VATS. Blood loss was significantly less in RATS group than that in VATS (MD = -17.14, 95% CI -29.96 ~ -4.33, P = 0.009). More nodes stations were dissected in RATS group compared with VATS group(MD= 1.07, 95% CI 0.79 ~ 1.36, P < 0.001). No significant difference occurred between RATS and VATS in length of hospital stay(MD= -0.19, 95% CI -0.98~0.61), readmission(OR=0.74, 95%CI 0.36~1.51, P=0.41), operative time(MD=11.43 95% CI -8.41~31.26, P=0.26), conversion(OR=0.58, 95% CI 0.29~1.17, P=0.13), number of dissected lymph nodes(MD=0.98, 95% CI -0.02~1.97, P=0.05), upstaging rate(OR =0.67, 95% CI 0.38 ~ 1.18, P =0.16, I2 = 0%), time of chest tube drainage (MD= -0.34, 95%CI -0.84~0.15, P=0.17), post-operative complications(OR=0.76, 95% CI 0.52~ 1.11, P=0.16) and total cost(MD = 3103.48, 95% CI -575.78 ~ 6782.74, P=0.1, I2 = 99%). Conclusion: RATS is a feasible and safe treatment that can achieve better surgical outcomes compared with VATS in terms of short-term outcomes. Except of higher total cost, RATS has obvious advantage in lymphadenectomy and control of intraoperative bleeding. However, large sample and long follow-up randomized clinical trials comparing RATS with VATS are still necessary to better demonstrate the advantages of RATS for lung cancer. Systematic review registration: https://www.crd.york.ac.uk/prospero/, Identifier CRD42023446653.

The Small Auxin-Up RNA SAUR10 Is Involved in the Promotion of Seedling Growth in Rice.

Small auxin-up-regulated RNAs (SAURs) are genes rapidly activated in response to auxin hormones, significantly affecting plant growth and development. However, there is limited information available about the specific functions of SAURs in rice due to the presence of extensive redundant genes. In this study, we found that OsSAUR10 contains a conserved downstream element in its 3' untranslated region that causes its transcripts to be unstable, ultimately leading to the immediate degradation of the mRNA in rice. In our investigation, we discovered that OsSAUR10 is located in the plasma membrane, and its expression is regulated in a tissue-specific, developmental, and hormone-dependent manner. Additionally, we created ossaur10 mutants using the CRISPR/Cas9 method, which resulted in various developmental defects such as dwarfism, narrow internodes, reduced tillers, and lower yield. Moreover, histological observation comparing wild-type and two ossaur10 mutants revealed that OsSAUR10 was responsible for cell elongation. However, overexpression of OsSAUR10 resulted in similar phenotypes to the wild-type. Our research also indicated that OsSAUR10 plays a role in regulating the expression of two groups of genes involved in auxin biosynthesis (OsYUCCAs) and auxin polar transport (OsPINs) in rice. Thus, our findings suggest that OsSAUR10 acts as a positive plant growth regulator by contributing to auxin biosynthesis and polar transport.

Composition, functional, and niche differentiation of fungal communities in the rhizosphere and root endosphere of Cinnamomum migao in southwestern China.

AIMS: Roots are key parts of plant material circulation and energy flow, creating two distinct niches for the plant microbiome, such as the rhizosphere and root endosphere, which interact to maintain plant growth and health. In this study, two niches of plant rhizosphere and root endosphere were selected to study the composition and differences of fungi communities in order to better understand how differences in the structure and function of plant fungi communities affect plant health. METHODS AND RESULTS: The community structure, diversity, and ecological function of fungi in the rhizosphere and root endosphere of Cinnamomum migao were studied using high-throughput sequencing techniques, traditional culture methods, and the FUNGuild database. The results of the analysis of alpha diversity showed that the diversity of rhizosphere fungal communities in C. migao was much higher than that of root endosphere communities. Some similarities and differences were noted between the two niche fungal communities, and some fungi had niche preferences. Functional prediction results demonstrated that fungi in the rhizosphere and root endosphere adopt multiple trophic modes, mostly saprophytic fungi. CONCLUSIONS: This study provided a basis for an in-depth understanding of the structural variation, niche differentiation, and function of plant root-related fungal microbiota. We believe that it could provide guidance on the subsequent development of beneficial fungi.

Transcriptome Analysis Reveals Candidate Genes Involved in Gibberellin-Induced Fruit Development in Rosa roxburghii.

Gibberellins (GAs) play indispensable roles in the fruit development of horticultural plants. Unfortunately, the molecular basis behind GAs regulating fruit development in R. roxburghii remains obscure. Here, GA3 spraying to R. roxburghii 'Guinong 5' at full-bloom promoted fruit size and weight, prickle development, seed abortion, ascorbic acid accumulation, and reduction in total soluble sugar. RNA-Seq analysis was conducted to generate 45.75 Gb clean reads from GA3- and non-treated fruits at 120 days after pollination. We obtained 4275 unigenes belonging to differently expressed genes (DEGs). Gene ontology and the Kyoto Encyclopedia of Genes and Genomes displayed that carbon metabolism and oxidative phosphorylation were highly enriched. The increased critical genes of DEGs related to pentose phosphate, glycolysis/gluconeogenesis, and citrate cycle pathways might be essential for soluble sugar degradation. Analysis of DEGs implicated in ascorbate revealed the myoinositol pathway required to accumulate ascorbic acid. Finally, DEGs involved in endogenous phytohormones and transcription factors, including R2R3 MYB, bHLH, and WRKY, were determined. These findings indicated that GA3-trigged morphological alterations might be related to the primary metabolites, hormone signaling, and transcription factors, providing potential candidate genes that could be guided to enhance the fruit development of R. roxburghii in practical approaches.

Streptomyces chengmaiensis sp. nov., isolated from the stem of a mangrove plant in Hainan.

A novel Streptomyces strain, designated as HNM0663T, was isolated from the stem of a mangrove plant (Avicennia marina) collected from the coast of Chengmai city, Hainan Island, PR China. On the basis of the alignment of 16S rRNA gene sequences, strain HNM0663T was closely related to Streptomyces lichenis LCR6-01T (98.67 %), Streptomyces nanningensis YIM 33098T (98.12 %) and Streptomyces palmae CMU-AB204T (97.93 %). Genome-based comparisons showed that strain HNM0663T was distinguished from its closest related species with 80.3 % average nucleotide identity and 20.2 % digital DNA-DNA hybridization values. The main cellular fatty acids were iso-C16 : 0, iso-C15 : 0 and anteiso-C15 : 0. The main menaquinones were MK-9 (H6), MK-9 (H4) and MK-8 (H4). The predominant phospholipids contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylcholine. Based on these polyphasic taxonomy results, strain HNM0663T should represent a novel Streptomyces species, for which the name Streptomyces chengmaiensis sp. nov. is proposed. The type strain is HNM 0663T (=CCTCC AA 2019075T=LMG 31909T).

Highly efficient Agrobacterium rhizogenes-mediated transformation for functional analysis in woodland strawberry.

BACKGROUND: The diploid woodland strawberry (Fragaria vesca) is an excellent model plant for investigating economically significant traits and several genetic resources within the Rosaceae family. Agrobacterium rhizogenes-mediated hairy root transformation is an alternative for exploring gene functions, especially the genes specifically expressed in roots. However, the hairy root transformation has not been established in strawberry. RESULTS: Here, we described an efficient and rapid hairy root transgenic system for strawberry using A. rhizogenes. Strain of A. rhizogenes MSU440 or C58C1 was the most suitable for hairy root transformation. The transformation efficiency was highest when tissues contained hypocotyls as explants. The optimal procedure involves A. rhizogenes at an optical density (OD600) of 0.7 for 10 min and co-cultivation duration for four days, achieving a transgenic efficiency of up to 71.43%. An auxin responsive promoter DR5ver2 carrying an enhanced green fluorescent protein (eGFP) marker was transformed by A. rhizogenes MSU440, thereby generating transgenic hairy roots capable of high eGFP expression in root tip and meristem of strawberry where auxin accumulated. Finally, this system was applied for functional analysis using jGCaMP7c, which could sense calcium signals. A significant upsurge in eGFP expression in the transgenic hairy roots was displayed after adding calcium chloride. The results suggested that this approach was feasible for studying specific promoters and could be a tool to analyze gene functions in the roots of strawberries. CONCLUSION: We established a rapid and efficient hairy root transformation in strawberry by optimizing parameters, which was adequate for promoter analysis and functional characterization of candidate genes in strawberry and other rosaceous plants.

Genome-wide identification and expression analyses of the pectate lyase (PL) gene family in Fragaria vesca.

BACKGROUND: Pectate lyase (PL, EC 4.2.2.2), as an endo-acting depolymerizing enzyme, cleaves α-1,4-glycosidic linkages in esterified pectin and involves a broad range of cell wall modifications. However, the knowledge concerning the genome-wide analysis of the PL gene family in Fragaria vesca has not been thoroughly elucidated. RESULTS: In this study, sixteen PLs members in F. vesca were identified based on a genome-wide investigation. Substantial divergences existed among FvePLs in gene duplication, cis-acting elements, and tissue expression patterns. Four clusters were classified according to phylogenetic analysis. FvePL6, 8 and 13 in cluster II significantly contributed to the significant expansions during evolution by comparing orthologous PL genes from Malus domestica, Solanum lycopersicum, Arabidopsis thaliana, and Fragaria×ananassa. The cis-acting elements implicated in the abscisic acid signaling pathway were abundant in the regions of FvePLs promoters. The RNA-seq data and in situ hybridization revealed that FvePL1, 4, and 7 exhibited maximum expression in fruits at twenty days after pollination, whereas FvePL8 and FvePL13 were preferentially and prominently expressed in mature anthers and pollens. Additionally, the co-expression networks displayed that FvePLs had tight correlations with transcription factors and genes implicated in plant development, abiotic/biotic stresses, ions/Ca2+, and hormones, suggesting the potential roles of FvePLs during strawberry development. Besides, histological observations suggested that FvePL1, 4 and 7 enhanced cell division and expansion of the cortex, thus negatively influencing fruit firmness. Finally, FvePL1-RNAi reduced leaf size, altered petal architectures, disrupted normal pollen development, and rendered partial male sterility. CONCLUSION: These results provide valuable information for characterizing the evolution, expansion, expression patterns and functional analysis, which help to understand the molecular mechanisms of the FvePLs in the development of strawberries.