bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep Learning of Liver Contrast-Enhanced Ultrasound to Predict Microvascular Invasion and Prognosis in Hepatocellular Carcinoma
Authors: Zhang Yafang , Wei Qingyue , Huang Yini , Yao Zhao , Yan Cuiju , Zou Xuebin , Han Jing , Li Qing , Mao Rushuang , Liao Ying , Cao Lan , Lin Min , Zhou Xiaoshuang , Tang Xiaofeng , Hu Yixin , Li Lingling , Wang Yuanyuan , Yu Jinhua , Zhou Jianhua
Published: July 2022

Background and Aims

Microvascular invasion (MVI) is a well-known risk factor for poor prognosis in hepatocellular carcinoma (HCC). This study aimed to develop a deep convolutional neural network (DCNN) model based on contrast-enhanced ultrasound (CEUS) to predict MVI, and thus to predict prognosis in patients with HCC.

Methods

A total of 436 patients with surgically resected HCC who underwent preoperative CEUS were retrospectively enrolled. Patients were divided into training (n = 301), validation (n = 102), and test (n = 33) sets. A clinical model (Clinical model), a CEUS video-based DCNN model (CEUS-DCNN model), and a fusion model based on CEUS video and clinical variables (CECL-DCNN model) were built to predict MVI. Survival analysis was used to evaluate the clinical performance of the predicted MVI.

Results

Compared with the Clinical model, the CEUS-DCNN model exhibited similar sensitivity, but higher specificity (71.4% vs. 38.1%, p = 0.03) in the test group. The CECL-DCNN model showed significantly higher specificity (81.0% vs. 38.1%, p = 0.005) and accuracy (78.8% vs. 51.5%, p = 0.009) than the Clinical model, with an AUC of 0.865. The Clinical predicted MVI could not significantly distinguish OS or RFS (both p > 0.05), while the CEUS-DCNN predicted MVI could only predict the earlier recurrence (hazard ratio [HR] with 95% confidence interval [CI 2.92 [1.1–7.75], p = 0.024). However, the CECL-DCNN predicted MVI was a significant prognostic factor for both OS (HR with 95% CI: 6.03 [1.7–21.39], p = 0.009) and RFS (HR with 95% CI: 3.3 [1.23–8.91], p = 0.011) in the test group.

Conclusions

The proposed CECL-DCNN model based on preoperative CEUS video can serve as a noninvasive tool to predict MVI status in HCC, thereby predicting poor prognosis.
Superficial Temporal Artery and Vein as Alternative Recipient Vessels for Intraoral Reconstruction With Free Flaps to Avoid the Cervical Approach With the Resulting Need for Double Flap Transfer in Previously Treated Necks
Authors: Ritschl Lucas M. , Niu Minli , Pippich Katharina , Schuh Philia , Rommel Niklas , Fichter Andreas M. , Wolff Klaus-Dietrich , Weitz Jochen
Published: July 2022

Background

Microvascular reconstruction remains challenging in previously operated and irradiated patients, especially when double flaps seem to be the only solution due to osteoradionecrosis. An alternative reconstructive option could be microvascular anastomosis to the temporal vessels to avoid the obligatory cervical incision.

Methods and Materials

All consecutive cases between January 2013 and 2020 that underwent either mandibular resection and reconstruction with a free fibula flap (FFF) and another soft tissue flap (group I) or pure intraoral resection and reconstruction with an FFF or radial forearm flap (RFF) with temporal microvascular anastomosis (group II) were included. Patients’ general information, indication and extent of surgery, time of ischemia, time of total surgery, and duration of hospital stay as well as incidence of complications were retrospectively recorded and analyzed.

Results

Seventeen (group I) and 11 (group II) cases were included. In group I, FFF was combined with RFF (n = 9), anterolateral thigh flap (ALT, n = 7), or latissimus dorsi flap (n = 1). Group II consisted of six FFFs and five RFFs. Operation time and hospitalization duration were significantly shorter in group II (p < 0.001 and p = 0.025), whereas ischemic time of FFF was significantly shorter in group I (p = 0.002). All patients in group I required a tracheostomy, while only four cases in group II did (p = 0.004). The complication rate regarding hematoma removal, revision of anastomosis, flap loss, delirium, sepsis, pleural effusion, pneumonia, and pulmonary artery embolism showed no significant differences between the two groups.

Conclusions

The superficial temporal vessels served as versatile recipient vessels for intraoral mandibular and soft tissue reconstruction and led to reduced operation time, hospitalization duration, and indication for a primary tracheostomy. Thus, this approach may help to avoid cervical incision for reconstruction in irradiated patients.
FEV Maintains Homing and Expansion by Activating ITGA4 Transcription in Primary and Relapsed AML
Authors: Zhang Jubin , Qi Lijuan , Wang Tanzhen , An Jingnan , Zhou Biqi , Fang Yanglan , Liu Yujie , Shan Meng , Hong Dengli , Wu Depei , Xu Yang , Liu Tianhui
Published: July 2022

Acute myeloid leukemia (AML) is an aggressive hematological malignancy that recurs in approximately 50% of cases. Elevated homing and uncontrolled expansion are characteristics of AML cells. Here, we identified that Fifth Ewing Variant (FEV) regulates the homing and expansion of AML cells. We found that FEV was re-expressed in 30% of primary AML samples and in almost all relapsed AML samples, and FEV expression levels were significantly higher in relapsed samples compared to primary samples. Interference of FEV expression in AML cell lines delayed leukemic progression and suppressed homing and proliferation. Moreover, FEV directly activated integrin subunit alpha 4 (ITGA4) transcription in a dose-dependent manner. Inhibition of integrin α4 activity with natalizumab (NZM) reduced the migration and colony-forming abilities of blasts and leukemic-initiating cells (LICs) in both primary and relapsed AML. Thus, our study suggested that FEV maintains the homing and expansion of AML cells by activating ITGA4 transcription and that targeting ITGA4 inhibits the colony-forming and migration capacities of blasts and LICs. Thus, these findings suggested that the FEV-ITGA4 axis may be a therapeutic target for both primary and relapsed AML.
Tumor-Associated Microenvironment of Adult Gliomas: A Review
Authors: Di Nunno Vincenzo , Franceschi Enrico , Tosoni Alicia , Gatto Lidia , Bartolini Stefania , Brandes Alba Ariela
Published: July 2022

The glioma-associated tumor microenvironment involves a multitude of different cells ranging from immune cells to endothelial, glial, and neuronal cells surrounding the primary tumor. The interactions between these cells and glioblastoma (GBM) have been deeply investigated while very little data are available on patients with lower-grade gliomas. In these tumors, it has been demonstrated that the composition of the microenvironment differs according to the isocitrate dehydrogenase status (mutated/wild type), the presence/absence of codeletion, and the expression of specific alterations including H3K27 and/or other gene mutations. In addition, mechanisms by which the tumor microenvironment sustains the growth and proliferation of glioma cells are still partially unknown. Nonetheless, a better knowledge of the tumor-associated microenvironment can be a key issue in the optic of novel therapeutic drug development.
A Nomogram Model to Predict Post-Progression Survival in Esophageal Squamous Cell Carcinoma Patients With Recurrence After Radical Resection
Authors: Leng Changsen , Cui Yingying , Chen Junying , Wang Kexi , Yang Hong , Wen Jing , Fu Jianhua , Liu Qianwen
Published: July 2022

Background

Esophageal squamous cell carcinoma (ESCC) is characterized clinically by frequent recurrence, leading to a poor prognosis after radical surgery. The aim of this study was to identify a prognostic nomogram to predict the post-progression survival (PPS) of ESCC patients based on the features of primary tumor and recurrence.

Methods

A total of 234 ESCC patients who underwent recurrence after radical surgery were enrolled in this study. The independent prognostic factors screened by the univariate and multivariate Cox regression analysis were subsequently used to construct a nomogram. The predictive performance of the nomogram was evaluated with the concordance index (C-index), decision curve, and the area under the receiver operating characteristic curve (AUC) and validated in two validation cohorts. The Kaplan-Meier curves of different recurrence patterns were analyzed.

Results

The prognostic nomogram of PPS was established by integrating independent prognostic factors, including age, body mass index, number of lymph node dissection, recurrence pattern, and recurrence treatment. The nomogram demonstrated good performance, with C-index values of 0.756, 0.817, and 0.730 for the training and two validation cohorts. The 1-year AUC values were 0.773, 0.798, and 0.735 and 3-year AUC values were 0.832, 0.871, and 0.791, respectively. Furthermore, we found that patients with bone metastasis displayed the worst PPS compared to other isolated recurrence patterns.

Conclusion

We constructed a nomogram to reliably predict PPS, which would be valuable to provide individual managements for ESCC patients after radical surgery.
Effect of Breast Milk Oral Care on Mechanically Ventilated Preterm Infants: A Systematic Review and Meta-Analysis of Randomized Controlled Trials
Authors: Cai Meiling , Lin Lingyu , Peng Yanchun , Chen Liangwan , Lin Yanjuan
Published: July 2022

Background

The benefits of breast milk oral care in mechanically ventilated preterm infants remain controversial. This study aimed to systematically review the evidence on the benefits of breast milk oral care in mechanically ventilated preterm infants.

Methods

The randomized controlled trials of breast milk oral care for mechanically ventilated preterm infants were searched in EMBASE, PubMed, Cochrane Library, Web of Science, WANFANG Date and China National Knowledge Infrastructure databases. The retrieval language was limited to Chinese and English, and the final search was conducted until March 2022. Outcome measures included ventilator-associated pneumonia (VAP), mechanical ventilation time (MVT), length of stay (LOS), necrotizing enterocolitis (NEC), late-onset sepsis, mortality during hospitalization, time of full intestinal feeding and time of full oral feeding. Two researchers independently screened the literature, extracted the data, and conducted the literature quality assessment. Meta-analysis was mainly performed using RevMan 5.3.

Results

Eight articles involving 1,046 preterm infants were included. Our meta-analysis showed that compared with the control group, breast milk oral care could reduce the incidence of VAP [RR = 0.41, 95% CI (0.23, 0.75), P = 0.003] and NEC [RR = 0.54, 95% CI (0.30, 0.95), P = 0.03], and shorten the MVT [MD = −0.45, 95% CI (−0.73, −0.18), P = 0.001] and LOS [MD = −5.74, 95% CI (−10.39, −1.10), P = 0.02]. There were no significant differences in the mortality during hospitalization [RR = 0.94, 95% CI (0.67, 1.33), P = 0.74], the incidence of late-onset sepsis [RR = 0.79, 95% CI (0.40, 1.59), P = 0.51], the time of full intestinal feeding [MD = −2.42, 95% CI (−5.37, 0.52), P = 0.11] and the time of full oral feeding [MD = −3.40, 95% CI (−10.70, 3.91), P = 0.36] between the two groups.

Conclusions

Oral care of breast milk can reduce the incidence of VAP and NEC, shorten MVT and LOS in mechanically ventilated preterm infants. However, due to the quality and quantity limitations of the included studies, larger sample size and more strictly designed clinical trials are still needed in the future to further confirm the findings of this study.
External Evaluation of Population Pharmacokinetic Models of Busulfan in Chinese Adult Hematopoietic Stem Cell Transplantation Recipients
Authors: Huang Huiping , Liu Qingxia , Zhang Xiaohan , Xie Helin , Liu Maobai , Chaphekar Nupur , Wu Xuemei
Published: July 2022

Objective: Busulfan (BU) is a bi-functional DNA-alkylating agent used in patients undergoing hematopoietic stem cell transplantation (HSCT). Over the last decades, several population pharmacokinetic (pop PK) models of BU have been established, but external evaluation has not been performed for almost all models. The purpose of the study was to evaluate the predictive performance of published pop PK models of intravenous BU in adults using an independent dataset from Chinese HSCT patients, and to identify the best model to guide personalized dosing.

Methods: The external evaluation methods included prediction-based diagnostics, simulation-based diagnostics, and Bayesian forecasting. In prediction-based diagnostics, the relative prediction error (PE%) was calculated by comparing the population predicted concentration (PRED) with the observations. Simulation-based diagnostics included the prediction- and variability-corrected visual predictive check (pvcVPC) and the normalized prediction distribution error (NPDE). Bayesian forecasting was executed by giving prior one to four observations. The factors influencing the model predictability, including the impact of structural models, were assessed.

Results: A total of 440 concentrations (110 patients) were obtained for analysis. Based on prediction-based diagnostics and Bayesian forecasting, preferable predictive performance was observed in the model developed by Huang et al. The median PE% was -1.44% which was closest to 0, and the maximum F20 of 57.27% and F30 of 72.73% were achieved. Bayesian forecasting demonstrated that prior concentrations remarkably improved the prediction precision and accuracy of all models, even with only one prior concentration.

Conclusion: This is the first study to comprehensively evaluate published pop PK models of BU. The model built by Huang et al. had satisfactory predictive performance, which can be used to guide individualized dosage adjustment of BU in Chinese patients.
Semi-PBPK Modeling and Simulation to Evaluate the Local and Systemic Pharmacokinetics of OC-01(Varenicline) Nasal Spray
Authors: Wu Xiaofei , Zhang Fan , Yu Mengyang , Ding Faming , Luo Jinghui , Liu Bo , Li Yuan , Li Zhiping , Wang Hongyun
Published: July 2022

This study aimed to build a nasal semi-physiologically based pharmacokinetic (PBPK) model to predict the intranasal pharmacokinetic (PK) of the OC-01(varenicline) nasal spray and accelerate the development of this drug. Based on the physiology of the human upper respiratory system, the semi-PBPK model was established and validated using systemic plasma PK data of varenicline previously observed in Americans and Chinese. Drug concentrations, both in respiratory tissue and plasma circulation system, were well simulated, and it was indicated that local concentration at the target site (nasal cavity) was significantly higher than that of plasma when OC-01 nasal spray was administered. The nasal semi-PBPK model successfully depicted the absorption and distribution of intranasal varenicline in the respiratory tissues and provided an alternative to clinical PK study of OC-01 nasal spray in Chinese. Meanwhile the current study presented a viable framework for predicting respiratory concentrations for other novel nasal spray drugs by semi-PBPK modeling.
Qingluo Tongbi Formula Alleviates Hepatotoxicity Induced by Tripterygium wilfordii Hook. F. by Regulating Excessive Mitophagy Through the PERK-ATF4 Pathway
Authors: Zhang Linluo , Zhou Jie , Feng Zhe , Jiang Baoping , Li Changqing , Zhou Lingling , Zhou Xueping
Published: July 2022

Qingluo Tongbi Formula (QTF) is an empirical formula of Chinese medicine master Zhongying Zhou for the treatment of rheumatoid arthritis. Although including Tripterygium wilfordii Hook. F. (TW), it has not shown liver toxicity in clinical application for many years. Our previous studies have shown that QTF can significantly reduce TW-caused hepatotoxicity, but the mechanism is still unclear. This study aimed to explore the important roles of mitophagy and endoplasmic reticulum stress (ERS) and the relationship between them in QTF in alleviating TW-induced hepatotoxicity. In vivo, C57BL/6J female mice were used to build a model of TW-induced liver toxicity; Then mice were randomly divided into control, TW, TW + RG, TW + PN, TW + SA, TW + BM, and QTF groups. After intragastric administration for 7 days, the levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST) and lactate dehydrogenase (LDH) in serum were detected; H and E staining, Oil Red O staining, transmission electron microscopy, Western blotting, and RT-qPCR were used to detect the pathological changes in liver tissue, the levels of ERS and mitophagy related proteins and genes, including GRP78, PERK, DRP1, LC3, etc., In vitro, triptolide (TP), catalpol (CAT), and panax notoginseng saponins (PNS), the main active ingredients of QTF, were selected. The mitophagy inhibitor, ERS inhibitor, and PERK inhibitor were used to further study the relationship between TW-induced ERS and mitophagy in HepaRG cells. The results showed that, QTF reduced excessive mitophagy and ERS in TW-induced hepatotoxicity in C57BL/6J mice, and the attenuating effects of RG and PN in QTF were most obvious, and they also significantly restrained the TW-induced ERS and mitophagy by the PERK-ATF4 pathway. Furthermore, PNS was superior to CAT in inhibiting the expression levels of GRP78, PERK, and ATF4, while CAT was superior to PNS in reversing the expression levels of DRP1, P62, and LC3. The combination of CAT and PNS had the best attenuating effect and the most significant regulation on ERS and mitophagy. In conclusion, QTF can alleviate TW-induced hepatotoxicity by differentially downregulating the PERK-ATF4 pathway and excessive mitophagy by different components.
Steamed Panax notoginseng and its Saponins Inhibit the Migration and Induce the Apoptosis of Neutrophils in a Zebrafish Tail-Fin Amputation Model
Authors: Xiong Yin , Halima Mahmoud , Che Xiaoyan , Zhang Yiming , Schaaf Marcel J. M. , Li Minghui , Gao Min , Guo Liqun , Huang Yan , Cui Xiuming , Wang Mei
Published: July 2022

Panax notoginseng (PN) is a Chinese medicinal herb that is traditionally used to treat inflammation and immune-related diseases. Its major active constituents are saponins, the types and levels of which can be changed in the process of steaming. These differences in saponins are causally relevant to the differences in the therapeutic efficacies of raw and steamed PN. In this study, we have prepared the extracts of steamed PN (SPNE) with 70% ethanol and investigated their immunomodulatory effect using a zebrafish tail-fin amputation model. A fingerprint-effect relationship analysis was performed to uncover active constituents of SPNE samples related to the inhibitory effect on neutrophil number. The results showed that SPNE significantly inhibited the neutrophil number at the amputation site of zebrafish larvae. And SPNE extracts steamed at higher temperatures and for longer time periods showed a stronger inhibitory effect. Ginsenosides Rh1, Rk3, Rh4, 20(S)-Rg3, and 20(R)-Rg3, of which the levels were increased along with the duration of steaming, were found to be the major active constituents contributing to the neutrophil-inhibiting effect of SPNE. By additionally investigating the number of neutrophils in the entire tail of zebrafish larvae and performing TUNEL assays, we found that the decreased number of neutrophils at the amputation site was due to both the inhibition of their migration and apoptosis-inducing effects of the ginsenosides in SPNE on neutrophils. Among them, Rh1 and 20(R)-Rg3 did not affect the number of neutrophils at the entire tail, suggesting that they only inhibit the migration of neutrophils. In contrast, ginsenosides Rk3, Rh4, 20(S)-Rg3, and SPNE did not only inhibit the migration of neutrophils but also promoted neutrophilic cell death. In conclusion, this study sheds light on how SPNE, in particular the ginsenosides it contains, plays a role in immune modulation.
Nutritional Regulation of Muscle Stem Cells in Exercise and Disease: The Role of Protein and Amino Acid Dietary Supplementation
Authors: Beaudry Kayleigh M , Binet Emileigh R. , Collao Nicolás , De Lisio Michael
Published: July 2022

Human skeletal muscle is a remarkedly plastic tissue that has a high capacity to adapt in response to various stimuli. These adaptations are due in part to the function of muscle-resident stem/progenitor cells. Skeletal muscle regeneration and adaptation is facilitated by the activation and expansion of muscle stem cells (MuSCs). MuSC fate is regulated by signals released from cells in their niche, such as fibro-adipogenic progenitors (FAPs), as well as a variety of non-cellular niche components. Sufficient dietary protein consumption is critical for maximizing skeletal muscle adaptation to exercise and maintaining skeletal muscle in disease; however, the role of dietary protein in altering MuSC and FAP responses to exercise in healthy populations and skeletal muscle disease states requires more research. The present review provides an overview of this emerging field and suggestions for future directions. The current literature suggests that in response to resistance exercise, protein supplementation has been shown to increase MuSC content and the MuSC response to acute exercise. Similarly, protein supplementation augments the increase in MuSC content following resistance training. Endurance exercise, conversely, is an area of research that is sparse with respect to the interaction of protein supplementation and exercise on muscle stem/progenitor cell fate. Initial evidence suggests that protein supplementation augments the early myogenic response to acute endurance exercise but does not enhance the MuSC response to endurance training. Resistance training increases the number of proliferating FAPs with no additional effect of protein supplementation. Future research should continue to focus on the nutritional regulation of skeletal muscle stem/progenitor cell fate paired with studies examining the effects of exercise on a variety of human populations.
Current Understanding of Molecular Pathophysiology of Heart Failure With Preserved Ejection Fraction
Authors: Budde Heidi , Hassoun Roua , Mügge Andreas , Kovács Árpád , Hamdani Nazha
Published: July 2022

Heart Failure (HF) is the most common cause of hospitalization in the Western societies. HF is a heterogeneous and complex syndrome that may result from any dysfunction of systolic or diastolic capacity. Abnormal diastolic left ventricular function with impaired relaxation and increased diastolic stiffness is characteristic of heart failure with preserved ejection fraction (HFpEF). HFpEF accounts for more than 50% of all cases of HF. The prevalence increases with age: from around 1% for those aged <55 years to >10% in those aged 70 years or over. Nearly 50% of HF patients have HFrEF and the other 50% have HFpEF/HFmrEF, mainly based on studies in hospitalized patients. The ESC Long-Term Registry, in the outpatient setting, reports that 60% have HFrEF, 24% have HFmrEF, and 16% have HFpEF. To some extent, more than 50% of HF patients are female. HFpEF is closely associated with co-morbidities, age, and gender. Epidemiological evidence suggests that HFpEF is highly represented in older obese women and proposed as ‘obese female HFpEF phenotype’. While HFrEF phenotype is more a male phenotype. In addition, metabolic abnormalities and hemodynamic perturbations in obese HFpEF patients appear to have a greater impact in women then in men (Sorimachi et al., European J of Heart Fail, 2022, 22). To date, numerous clinical trials of HFpEF treatments have produced disappointing results. This outcome suggests that a “one size fits all” approach to HFpEF may be inappropriate and supports the use of tailored, personalized therapeutic strategies with specific treatments for distinct HFpEF phenotypes. The most important mediators of diastolic stiffness are the cardiomyocytes, endothelial cells, and extracellular matrix (ECM). The complex physiological signal transduction networks that respond to the dual challenges of inflammatory and oxidative stress are major factors that promote the development of HFpEF pathologies. These signalling networks contribute to the development of the diseases. Inhibition and/or attenuation of these signalling networks also delays the onset of disease. In this review, we discuss the molecular mechanisms associated with the physiological responses to inflammation and oxidative stress and emphasize the nature of the contribution of most important cells to the development of HFpEF via increased inflammation and oxidative stress.
Non-destructive Evaluation of the Quality Characteristics of Pomegranate Kernel Oil by Fourier Transform Near-Infrared and Mid-Infrared Spectroscopy
Authors: Okere Emmanuel E. , Arendse Ebrahiema , Nieuwoudt Helene , Perold Willem J. , Opara Umezuruike Linus
Published: July 2022

The pomegranate kernel oil has gained global awareness due to the health benefits associated with its consumption; these benefits have been attributed to its unique fatty acid composition. For quality control of edible fats and oils, various analytical and calorimetric methods are often used, however, these methods are expensive, labor-intensive, and often require specialized sample preparation making them impractical on a commercial scale. Therefore, objective, rapid, accurate, and cost-effective methods are required. In this study, Fourier transformed near-infrared (FT-NIR) and mid-infrared (FT-MIR) spectroscopy as a fast non-destructive technique was investigated and compared to qualitatively and quantitatively predict the quality attributes of pomegranate kernel oil (cv. Wonderful, Acco, Herskawitz). For qualitative analysis, principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) was applied. Based on OPLS-DA, FT-MIR spectroscopy resulted in 100% discrimination between oil samples extracted from different cultivars. For quantitative analysis, partial least squares regression was used for model development over the NIR region of 7,498–940 and 6,102–5,774 cm−1 and provided the best prediction statistics for total carotenoid content (R2, coefficient of determination; RMSEP, root mean square error of prediction; RPD, residual prediction deviation; R2 = 0.843, RMSEP = 0.019 g β-carotene/kg, RPD = 2.28). In the MIR region of 3,996–1,118 cm−1, models developed using FT-MIR spectroscopy gave the best prediction statistics for peroxide value (R2 = 0.919, RMSEP = 1.05 meq, RPD = 3.54) and refractive index (R2 = 0.912, RMSEP = 0.0002, RPD = 3.43). These results demonstrate the potential of infrared spectroscopy combined with chemometric analysis for rapid screening of pomegranate oil quality attributes.
Genome-Wide Identification, Characterization, and Comparative Analysis of NLR Resistance Genes in Coffea spp.
Authors: Santos Mariana de Lima , Resende Mário Lúcio Vilela de , Alves Gabriel Sérgio Costa , Huguet-Tapia Jose Carlos , Resende Márcio Fernando Ribeiro de Júnior , Brawner Jeremy Todd
Published: July 2022

The largest family of disease resistance genes in plants are nucleotide-binding site leucine-rich repeat genes (NLRs). The products of these genes are responsible for recognizing avirulence proteins (Avr) of phytopathogens and triggering specific defense responses. Identifying NLRs in plant genomes with standard gene annotation software is challenging due to their multidomain nature, sequence diversity, and clustered genomic distribution. We present the results of a genome-wide scan and comparative analysis of NLR loci in three coffee species (Coffea canephora,Coffea eugenioidesand their interspecific hybridCoffea arabica). A total of 1311 non-redundant NLR loci were identified inC. arabica, 927 inC. canephora, and 1079 inC. eugenioides, of which 809, 562, and 695 are complete loci, respectively. The NLR-Annotator tool used in this study showed extremely high sensitivities and specificities (over 99%) and increased the detection of putative NLRs in the reference coffee genomes. The NLRs loci in coffee are distributed among all chromosomes and are organized mostly in clusters. TheC. arabicagenome presented a smaller number of NLR loci when compared to the sum of the parental genomes (C. canephora, andC. eugenioides). There are orthologous NLRs (orthogroups) shared between coffee, tomato, potato, and reference NLRs and those that are shared only among coffee species, which provides clues about the functionality and evolutionary history of these orthogroups. Phylogenetic analysis demonstrated orthologous NLRs shared betweenC. arabicaand the parental genomes and those that were possibly lost. The NLR family members in coffee are subdivided into two main groups: TIR-NLR (TNL) and non-TNL. The non-TNLs seem to represent a repertoire of resistance genes that are important in coffee. These results will support functional studies and contribute to a more precise use of these genes for breeding disease-resistant coffee cultivars.
Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort
Authors: Masocha Valerie F. , Liu Hongmei , Zhan Pingshan , Wang Kaikai , Zeng Ao , Shen Sike , Schneider Harald
Published: July 2022

Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.
Promoting the Development of Astragalus mongholicus Bunge Industry in Guyang County (China) Based on MaxEnt and Remote Sensing
Authors: Zhang Ru , Zhang Mingxu , Yan Yumei , Chen Yuan , Jiang Linlin , Wei Xinxin , Zhang Xiaobo , Li Huanting , Li Minhui
Published: July 2022

To provide high-quality Astragalus mongholicus Bunge to domestic and foreign markets and maintain sustainable development of the A. mongholicus industry, Firstly, we evaluated the impact of environmental factors and planting areas on the A. mongholicus industry. The maximum entropy method (MaxEnt) was utilized to simulate the suitability distribution of A. mongholicus and establish the relationship between the active component contents of A. mongholicus and ecological factors through linear regression analysis. The random forest algorithm was subsequently used to perform feature selection and classification extraction on Sentinel-2 imagery covering the study area. Furthermore, the planting, processing, and sales of A. mongholicus in Guyang County were investigated, and the roles of stakeholders in the value chains were analyzed. The results demonstrated that precipitation of the warmest quarter, minimum temperature of the coldest month, standard deviation of seasonal temperature changes, range of mean annual temperature, and mean diurnal range [mean of monthly (max temp - min temp)] were the five environmental variables that contributed the most to the growth of A. mongholicus. The most influential factor on the distribution of high-quality A. mongholicus was the mean temperature of the coldest quarter. The classification results of image features showed that the planting areas of A. mongholicus was consistent with the suitable planting areas predicted by MaxEnt, which can provide data support to the relevant departments for the macro development of the A. mongholicus industry. In the production of A. mongholicus, 10 value chains were constructed, and the study demonstrated that the behavior of stakeholders, target markets, and the selected planting area had a significant impact on the quality of A. mongholicus.
Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza
Authors: Dai Shuang-feng , Zhu Xun-ge , Hutang Ge-rang , Li Jia-yue , Tian Jia-qi , Jiang Xian-hui , Zhang Dan , Gao Li-zhi
Published: July 2022

Genome size variation and evolutionary forces behind have been long pursued in flowering plants. The genus Oryza, consisting of approximately 25 wild species and two cultivated rice, harbors eleven extant genome types, six of which are diploid (AA, BB, CC, EE, FF, and GG) and five of which are tetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL). To obtain the most comprehensive knowledge of genome size variation in the genus Oryza, we performed flow cytometry experiments and estimated genome sizes of 166 accessions belonging to 16 non-AA genome Oryza species. k-mer analyses were followed to verify the experimental results of the two accessions for each species. Our results showed that genome sizes largely varied fourfold in the genus Oryza, ranging from 279 Mb in Oryza brachyantha (FF) to 1,203 Mb in Oryza ridleyi (HHJJ). There was a 2-fold variation (ranging from 570 to 1,203 Mb) in genome size among the tetraploid species, while the diploid species had 3-fold variation, ranging from 279 Mb in Oryza brachyantha (FF) to 905 Mb in Oryza australiensis (EE). The genome sizes of the tetraploid species were not always two times larger than those of the diploid species, and some diploid species even had larger genome sizes than those of tetraploids. Nevertheless, we found that genome sizes of newly formed allotetraploids (BBCC-) were almost equal to totaling genome sizes of their parental progenitors. Our results showed that the species belonging to the same genome types had similar genome sizes, while genome sizes exhibited a gradually decreased trend during the evolutionary process in the clade with AA, BB, CC, and EE genome types. Comparative genomic analyses further showed that the species with different rice genome types may had experienced dissimilar amplification histories of retrotransposons, resulting in remarkably different genome sizes. On the other hand, the closely related rice species may have experienced similar amplification history. We observed that the contents of transposable elements, long terminal repeats (LTR) retrotransposons, and particularly LTR/Gypsy retrotransposons varied largely but were significantly correlated with genome sizes. Therefore, this study demonstrated that LTR retrotransposons act as an active driver of genome size variation in the genus Oryza.
Assessing the Potential of Using the Langdon 5D(5B) Substitution Line for the Introgression of Aegilops tauschii Into Durum Wheat
Authors: Othmeni Manel , Grewal Surbhi , Walker Jack , Yang Cai-yun , King Ian P. , King Julie
Published: July 2022

Aegilops tauschii, the D-genome donor of hexaploid wheat, provides a source of genetic variation that could be used for tetraploid (durum) wheat improvement. In addition to the genes for wheat quality on the D-genome, which differentiate between bread and durum wheats in terms of end-use properties, genes coding for resistances to biotic and abiotic stresses are also present on the D-genome which would be useful in durum wheat. The introgression of Ae. tauschii into durum wheat, however, requires cytogenetic manipulation to induce homoeologous chromosome pairing to promote recombination. For this purpose, the introgression of Ae. tauschii into durum wheat was performed through a bridge cross of the wild species to the Langdon 5D(5B) disomic substitution line that lacks the Ph1 locus present on chromosome 5B, followed by a cross of the F1 to the durum wheat cultivar Om Rabi 5. Subsequent generations were self-fertilized, and these were screened for D-genome introgressions using (i) D-genome-specific Kompetitive Allele-Specific PCR (KASP) markers and (ii) KASP markers polymorphic between the 5D chromosomes of wheat, present in the Langdon 5D(5B) substitution line, and of Ae. tauschii. Homozygous introgression lines were confirmed using genomic and fluorescence in situ hybridization. The results showed that the use of the Langdon 5D(5B) disomic substitution line did not promote D-genome introgression across all linkage groups with only a limited success in the introgression of Ae. tauschii 5D segments into durum wheat.
Auxin Coordinates Achene and Receptacle Development During Fruit Initiation in Fragaria vesca
Authors: Tian Yunhe , Xin Wei , Lin Juncheng , Ma Jun , He Jun , Wang Xuhui , Xu Tongda , Tang Wenxin
Published: July 2022

In strawberries, fruit set is considered as the transition from the quiescent ovary to a rapidly growing fruit. Auxin, which is produced from the fertilized ovule in the achenes, plays a key role in promoting the enlargement of receptacles. However, detailed regulatory mechanisms for fruit set and the mutual regulation between achenes and receptacles are largely unknown. In this study, we found that pollination promoted fruit development (both achene and receptacle), which could be stimulated by exogenous auxin treatment. Interestingly, auxin was highly accumulated in achenes, but not in receptacles, after pollination. Further transcriptome analysis showed that only a small portion of the differentially expressed genes induced by pollination overlapped with those by exogenous auxin treatment. Auxin, but not pollination, was able to activate the expression of growth-related genes, especially in receptacles, which resulted in fast growth. Meanwhile, those genes involved in the pathways of other hormones, such as GA and cytokinin, were also regulated by exogenous auxin treatment, but not pollination. This suggested that pollination was not able to activate auxin responses in receptacles but produced auxin in fertilized achenes, and then auxin might be able to transport or transduce from achenes to receptacles and promote fast fruit growth at the early stage of fruit initiation. Our work revealed a potential coordination between achenes and receptacles during fruit set, and auxin might be a key coordinator.
Flavonoid Accumulation Varies in Medicago truncatula in Response to Mercury Stress
Authors: Alvarez-Rivera Gerardo , Sanz Aurora , Cifuentes Alejandro , Ibánez Elena , Paape Timothy , Lucas M. Mercedes , Pueyo José J.
Published: July 2022

Mercury (Hg) contamination is increasing worldwide in both wild ecosystems and agricultural soils due to natural processes, but mostly to anthropic activities. The molecular mechanisms involved in Hg toxicity and tolerance in plants have been extensively studied; however, the role of flavonoids in response to Hg stress remains to be investigated. We conducted a metabolomic study to analyze the changes induced at the secondary metabolite level in three Hg-tolerant and one Hg-sensitive Medicago truncatula cultivars. A total of 46 flavonoid compounds, classified into five different flavonoid families: anthocyanidins, flavones, isoflavones, pterocarpan flavonoids, and flavanones, along with their respective glycoconjugate derivatives, were identified in leaf and root tissues. The synthesis of free isoflavones, followed by monoglycosylation and further malonylation was shown to be characteristic of root samples, whereas higher glycosylation, followed by further acylation with coumaric and ferulic acid was characteristic of leaf tissues. While minor changes were observed in leaves, significant quantitative changes could be observed in roots upon Hg treatment. Some flavonoids were strongly upregulated in roots, including malonylglucosides of biochanin A, formononetin and medicarpin, and aglycones biochanin, daidzein, and irisolidone. Hg tolerance appeared to be mainly associated to the accumulation of formononetin MalGlc, tricin GlcAGlcA, and afrormosin Glc II in leaves, whereas aglycone accumulation was associated with tolerance to Hg stress in roots. The results evidence the alteration of the flavonoid metabolic profile and their glycosylation processes in response to Hg stress. However, notable differences existed between varieties, both in the basal metabolic profile and in the response to treatment with Hg. Overall, we observed an increase in flavonoid production in response to Hg stress, and Hg tolerance appeared to be associated to a characteristic glycosylation pattern in roots, associated with the accumulation of aglycones and monoglycosylated flavonoids. The findings are discussed in the context of the flavonoid biosynthetic pathway to provide a better understanding of the role of these secondary metabolites in the response and tolerance to Hg stress in M. truncatula.
Evolutionary and Integrative Analysis of Gibberellin-Dioxygenase Gene Family and Their Expression Profile in Three Rosaceae Genomes (F. vesca, P. mume, and P. avium) Under Phytohormone Stress
Authors: Sabir Irfan Ali , Manzoor Muhammad Aamir , Shah Iftikhar Hussain , Abbas Farhat , Liu Xunju , Fiaz Sajid , Shah Adnan Noor , Jiu Songtao , Wang Jiyuan , Abdullah Muhammad , Zhang Caixi
Published: July 2022

The gibberellin-dioxygenase (GAox) gene family plays a crucial role in regulating plant growth and development. GAoxs, which are encoded by many gene subfamilies, are extremely critical in regulating bioactive GA levels by catalyzing the subsequent stages in the biosynthesis process. Moreover, GAoxs are important enzymes in the GA synthesis pathway, and the GAox gene family has not yet been identified in Rosaceae species (Prunus aviumL.,F. vesca, andP. mume), especially in response to gibberellin and PCa (prohexadione calcium; reduce biologically active GAs). In the current investigation, 399 GAox members were identified in sweet cherry, Japanese apricot, and strawberry. Moreover, they were further classified into six (A-F) subgroups based on phylogeny. According to motif analysis and gene structure, the majority of thePavGAoxgenes have a remarkably well-maintained exon–intron and motif arrangement within the same subgroup, which may lead to functional divergence. In the systematic investigation,PavGAoxgenes have several duplication events, but segmental duplication occurs frequently. A calculative analysis of orthologous gene pairs inPrunus aviumL.,F. vesca, andP. mumerevealed that GAox genes are subjected to purifying selection during the evolutionary process, resulting in functional divergence. The analysis ofcis-regulatory elements in the upstream region of the 140PavGAoxmembers suggests a possible relationship between genes and specific functions of hormone response-related elements. Moreover, thePavGAoxgenes display a variety of tissue expression patterns in diverse tissues, with most of thePavGAoxgenes displaying tissue-specific expression patterns. Furthermore, most of thePavGAoxgenes express significant expression in buds under phytohormonal stresses. Phytohormones stress analysis demonstrated that some ofPavGAoxgenes are responsible for maintaining the GA level in plant-likePav co4017001.1 g010.1.br,Pav sc0000024.1 g340.1.br, andPav sc0000024.1 g270.1.mk. The subcellular localization ofPavGAoxprotein utilizing a tobacco transient transformation system into the tobacco epidermal cells predicted that GFP signals were mostly found in the cytoplasm. These findings will contribute to a better understanding of the GAox gene family’s interaction with prohexadione calcium and GA, as well as provide a strong framework for future functional characterization of GAox genes in sweet cherry.
Red and Blue Light Affect the Formation of Adventitious Roots of Tea Cuttings (Camellia sinensis) by Regulating Hormone Synthesis and Signal Transduction Pathways of Mature Leaves
Authors: Shen Yaozong , Fan Kai , Wang Yu , Wang Hui , Ding Shibo , Song Dapeng , Shen Jiazhi , Li He , Song Yujie , Han Xiao , Qian Wenjun , Ma Qingping , Ding Zhaotang
Published: July 2022

Light is an important environmental factor which affects plant growth, through changes of intensity and quality. In this study, monochromatic white (control), red (660 nm), and blue (430 nm) light-emitting diodes (LEDs) were used to treat tea short cuttings. The results showed the most adventitious roots in blue light treated tea cuttings, but the lowest roots in that treated by red light. In order to explore the molecular mechanism of light quality affecting adventitious root formation, we performed full-length transcriptome and metabolome analyses of mature leaves under three light qualities, and then conducted weighted gene co-expression network analysis (WGCNA). Phytohormone analysis showed that Indole-3-carboxylic acid (ICA), Abscisic acid (ABA), ABA-glucosyl ester (ABA-GE), trans-Zeatin (tZ), and Jasmonic acid (JA) contents in mature leaves under blue light were significantly higher than those under white and red light. A crosstalk regulatory network comprising 23 co-expression modules was successfully constructed. Among them, the “MEblue” module which had a highly positive correlation with ICA (R = 0.92, P = 4e-04). KEGG analysis showed that related genes were significantly enriched in the “Plant hormone signal transduction (ko04075)” pathway. YUC (a flavin-containing monooxygenase), AUX1, AUX/IAA, and ARF were identified as hub genes, and gene expression analysis showed that the expression levels of these hub genes under blue light were higher than those under white and red light. In addition, we also identified 6 auxin transport-related genes, including PIN1, PIN3, PIN4, PILS5, PILS6, and PILS7. Except PILS5, all of these genes showed the highest expression level under blue light. In conclusion, this study elucidated the molecular mechanism of light quality regulating adventitious root formation of tea short cutting through WGCNA analysis, which provided an innovation for “rapid seedling” of tea plants.
Functional Characterization of a 2OGD Involved in Abietane-Type Diterpenoids Biosynthetic Pathway in Salvia miltiorrhiza
Authors: Hu Zhimin , Ren Li , Bu Junling , Liu Xiuyu , Li Qishuang , Guo Wending , Ma Ying , Wang Jian , Chen Tong , Wang Ling , Jin Baolong , Tang Jinfu , Cui Guanghong , Guo Juan , Huang Luqi
Published: July 2022

Salvia miltiorrhiza is one of the most commonly used Chinese medicinal herbs. Tanshinones, the most abundant lipid-soluble bioactive constituents of S. miltiorrhiza, are a class of structural highly oxidized abietane-type diterpenoids with multiple pharmacological activities. Although several enzymes, including diterpene synthase, cytochrome P450, and Fe(II)/2-oxoglutarate-dependent dioxygenase (2OGD), have been functionally characterized in biosynthesis of abietane-type diterpenoids, the highly oxidized structure and complex secondary metabolic network of tanshinones imply that more oxidases should be characterized. Here, we identified a new 2OGD (Sm2OGD25) from S. miltiorrhiza. Molecular cloning and functional studies in vitro showed that Sm2OGD25 could catalyze the hydroxylation of sugiol at C-15 and C-16 positions to produce hypargenin B and crossogumerin C, respectively. The phylogenetic analysis of the DOXC family demonstrated that Sm2OGD25 belongs to the DOXC54 clade. Furthermore, structural modeling and site-directed mutagenesis characterization revealed the importance of the hydrogen-bonding residue Y339 and the hydrophobic residues (V122, F129, A144, A208, F303, and L344) in substrate binding and enzyme activity. This study will promote further studies on the catalytic characterization of plant 2OGDs and the secondary metabolic biosynthesis network of diterpenoids.