First Report of Fusarium avenaceum Causing Root Rot of Raspberry (Rubus corchorifolius) in China.

Raspberry (Rubus corchorifolius) plants hold historical, economic, and medicinal importance in China (Yang et al. 2022). Raspberries are cultivated to generate income for local farmers in Lintao County, Dingxi City, Gansu Province. However, farmers encountered challenges due to raspberry plants exhibiting root rot disease, resulting in plant death. During a thorough field survey conducted in June 2022, symptoms ranging from leaf yellowing and wilting to necrotic lesions and root rots were observed, where approximately 30% of raspberry plants were affected. Five diseased and healthy plants were collected from the farmers' fields in Lintao (35.53oN, 103.84oE) for pathogen identification. Symptomatic and asymptomatic root tissues were surface sterilized with 75% ethanol for 30 s and 3% NaOCl for 5 min, followed by three rinses in sterile water. Small pieces (0.5 × 0.5 cm) were cut and incubated on potato dextrose agar (PDA) plates at 25°C for 7-10 days. Twenty-two pure Fusarium isolates, which displayed four distinct colony groups morphologically, were obtained. Pathogenicity tests on isolates RB10, RB1, RB30, and RB23, representing each colony group, revealed that RB10 exhibited symptoms similar to those observed in the field. The RB10 strain produced yellowish-white to greyish-white colonies on PDA and was then cultured in a carboxymethylcellulose (CMC) broth for enhanced conidia production (Zhang et al. 2020). Macroconidia were sickle-shaped or slightly curved, with three to five septa (19.2 to 38.5 x 3.1 to 5.8 µm, n =40). Microconidia were oval to ellipsoidal, non-septate or featuring 1 to 2 septa (4.8 to 10.5 x 2.1 to 5.2 µm, n=20). These morphological features indicated the isolate was similar to Fusarium avenaceum (Leslie and Summerell, 2006). For further identification of the strains, genomic regions (ITS-rDNA, TEF-1α, and RPB2) were amplified and sequenced using specific primers ITS1/ITS4, EF-1/EF-2, and 5f2/7cr, respectively (O'Donnell et al. 2010; Uwaremwe et al. 2021; Zarrin et al. 2016). PCR BLASTn queries of NCBI GenBank revealed a 99.8% (522 bp), 99.4% (355 bp) and 99.6% (985 bp) homology with F. avenaceum (MZ724839.1, MN271631.1, and MK185026.1), respectively. Sequences were deposited in GenBank (ITS, OR735571; TEF-1α, PP216660; RPB2, PP857820). One-year-old raspberry seedlings were planted in pots with a sterile soil mix (2:2:1 v/v ratio of soil, peat, and vermiculite) under controlled greenhouse conditions (23-26°C, 16h light/8h dark). A month post-planting, taproots were wounded in six pots and inoculated with 20 ml of conidia suspension (106 conidia/ml), while the other six pots were maintained as controls. After 14 days, RB10-infected plants showed symptoms similar to field observations, while controls remained healthy. The experiment was conducted twice, and re-isolation confirmed both the pathogenicity and identity of the pathogen. In the concatenated phylogenetic tree of ITS, TEF-1α and RPB2, strain RB10 was clustered with the F. avenaceum representative strains KG502, KG431 and F094. Studies revealed F. avenaceum varied pathogenicity across plants (Bugingo, 2022; Moparthi et al. 2020& 2024; Yli-Mattila et al. 2018), and it has been reported to induce raspberry fruit rot (Wang et al. 2017). However, no previous reports linked this fungus to raspberry root rot. This report is crucial for understanding the impact of root rot disease on raspberry cultivation and developing effective management strategies.

Electrophysiological and sick sinus syndrome effects of Remdesivir challenge in guinea-pig hearts.

Remdesivir (RDV) is the first drug approved by the FDA for clinical treatment of hospitalized patients infected with COVID-19 because it has been shown to have good antiviral activity against a variety of viruses, including Arenaviridae and Coronaviridae viral families. However, it has been reported that its clinical treatment leads to the symptoms of sick sinus syndrome such as sinus bradycardia, conduction block, and sinus arrest, but the electrophysiological mechanism of its specific cardiac adverse events is still unclear. We report complementary, experimental, studies of its electrophysiological effects. In wireless cardiac telemetry experiments in vivo and electrocardiographic studies in ex vivo cardiac preparations, RDV significantly caused sinus bradycardia, sinus atrial block, and prolongation of the QT interval in guinea pigs. Dose-dependent effects of RDV on the electrical activities of sinoatrial node (SA node) preparations of guinea pigs were characterised by multielectrode, optical RH237 voltage mapping. These revealed reversibly reduced sinoatrial conduction time (SACT), increased AP durations (APDs), and decreased the pacemaking rate of the SA node. Patch-clamp experiments showed that RDV significantly inhibited the If current of HCN4 channels, resulting in a significant decrease in the spontaneous firing rate of SA node cells, which may underlie the development of sick sinus node syndrome. In addition, RDV significantly inhibits IKr currents in hERG channels, leading to prolongation of the QT interval and playing a role in bradycardia. Therefore, these findings provide insights into the understanding the bradycardia effect of RDV, which may be used as basic theoretical guidance for the intervention of its adverse events, and prompt safety investigations of RDV's cardiac safety in the future.

Acute kidney injury with intravenous colistin sulfate compared with polymyxin B in critically ill patients: A real-world, retrospective cohort study.

BACKGROUND: Polymyxins have re-emerged as a last-resort therapeutic option for infections caused by carbapenem-resistant gram-negative bacteria. Nephrotoxicity induced by polymyxins is a significant limitation of its use in the clinic. Polymyxin B and colistin sulfate are two widely used active formulations of polymyxins. However, there is a lack of studies conducting a comparative assessment of nephrotoxicity between the two formulations. This study aimed to compare the nephrotoxicity of polymyxin B and colistin sulfate in critically ill patients. METHODS: We conducted a retrospective cohort study among critically ill patients who received intravenous polymyxin B or colistin sulfate for over 48 h from January 2017 to January 2024. The primary outcome was the incidence of acute kidney injury (AKI) associated with polymyxins, and the secondary outcome was 30-day all-cause mortality. Additionally, the risk factors of polymyxins-induced AKI and 30-day all-cause mortality were identified by Cox proportional hazard regression analysis. RESULTS: A total of 473 patients were included in this study. The overall incidence of AKI was significantly higher in patients who received polymyxin B compared to those who received colistin sulfate in the unmatched cohort (20.8% vs. 9.0%, p = 0.002) and in the propensity score matching cohort (21.1% vs. 7.0%, p = 0.004), respectively. However, there was no significant difference in 30-day all-cause mortality between the two groups. Polymyxin type, septic shock, and concomitant use of vasopressors were identified as independent risk factors for polymyxin-induced AKI. CONCLUSIONS: The prevalence of AKI was higher among patients who received polymyxin B compared to those treated with colistin sulfate. However, there was no significant difference in 30-day all-cause mortality between the two groups. Further prospective, multicenter studies with larger sample sizes are needed to validate these findings.

Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions.

Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.

Utilizing Artificial Neural Networks for Establishing Hearing-Loss Predicting Models Based on a Longitudinal Dataset and Their Implications for Managing the Hearing Conservation Program.

Background: Though the artificial neural network (ANN) technique has been used to predict noise-induced hearing loss (NIHL), the established prediction models have primarily relied on cross-sectional datasets, and hence, they may not comprehensively capture the chronic nature of NIHL as a disease linked to long-term noise exposure among workers. Methods: A comprehensive dataset was utilized, encompassing eight-year longitudinal personal hearing threshold levels (HTLs) as well as information on seven personal variables and two environmental variables to establish NIHL predicting models through the ANN technique. Three subdatasets were extracted from the afirementioned comprehensive dataset to assess the advantages of the present study in NIHL predictions. Results: The dataset was gathered from 170 workers employed in a steel-making industry, with a median cumulative noise exposure and HTL of 88.40 dBA-year and 19.58 dB, respectively. Utilizing the longitudinal dataset demonstrated superior prediction capabilities compared to cross-sectional datasets. Incorporating the more comprehensive dataset led to improved NIHL predictions, particularly when considering variables such as noise pattern and use of personal protective equipment. Despite fluctuations observed in the measured HTLs, the ANN predicting models consistently revealed a discernible trend. Conclusions: A consistent correlation was observed between the measured HTLs and the results obtained from the predicting models. However, it is essential to exercise caution when utilizing the model-predicted NIHLs for individual workers due to inherent personal fluctuations in HTLs. Nonetheless, these ANN models can serve as a valuable reference for the industry in effectively managing its hearing conservation program.

Machine learning-enabled forward prediction and inverse design of 4D-printed active plates.

Shape transformations of active composites (ACs) depend on the spatial distribution of constituent materials. Voxel-level complex material distributions can be encoded by 3D printing, offering enormous freedom for possible shape-change 4D-printed ACs. However, efficiently designing the material distribution to achieve desired 3D shape changes is significantly challenging yet greatly needed. Here, we present an approach that combines machine learning (ML) with both gradient-descent (GD) and evolutionary algorithm (EA) to design AC plates with 3D shape changes. A residual network ML model is developed for the forward shape prediction. A global-subdomain design strategy with ML-GD and ML-EA is then used for the inverse material-distribution design. For a variety of numerically generated target shapes, both ML-GD and ML-EA demonstrate high efficiency. By further combining ML-EA with a normal distance-based loss function, optimized designs are achieved for multiple irregular target shapes. Our approach thus provides a highly efficient tool for the design of 4D-printed active composites.

Operative treatment of isolated epiphyseal fracture of the distal fibula: 1 case report and literature review.

Pediatric ankle injuries are common; ankle epiphyseal fractures are also common in children. But isolated distal epiphyseal fibular fractures of the distal fibula are clinically rare. We describe one unusual case of an adolescent with a completely displaced Salter-Harris type II distal fibular epiphyseal fracture. The attempt of closed reduction failed, and the patient required open reduction and internal fixation. The localized periosteum and the superior peroneal retinaculum were avulsed from the distal fibular metaphysis, with the peroneal tendons underneath exposed but no obvious subluxation. To the best of our knowledge, this combination of injuries has not been previously reported.

Computational synthesis of locomotive soft robots by topology optimization.

Locomotive soft robots (SoRos) have gained prominence due to their adaptability. Traditional locomotive SoRo design is based on limb structures inspired by biological organisms and requires human intervention. Evolutionary robotics, designed using evolutionary algorithms (EAs), have shown potential for automatic design. However, EA-based methods face the challenge of high computational cost when considering multiphysics in locomotion, including materials, actuations, and interactions with environments. Here, we present a design approach for pneumatic SoRos that integrates gradient-based topology optimization with multiphysics material point method (MPM) simulations. This approach starts with a simple initial shape (a cube with a central cavity). The topology optimization with MPM then automatically and iteratively designs the SoRo shape. We design two SoRos, one for walking and one for climbing. These SoRos are 3D printed and exhibit the same locomotion features as in the simulations. This study presents an efficient strategy for designing SoRos, demonstrating that a purely mathematical process can produce limb-like structures seen in biological organisms.

A pilot clinical risk model to predict polymyxin-induced nephrotoxicity: a real-world, retrospective cohort study.

OBJECTIVES: Polymyxin-induced nephrotoxicity (PIN) is a major safety concern and challenge in clinical practice, which limits the clinical use of polymyxins. This study aims to investigate the risk factors and to develop a scoring tool for the early prediction of PIN. METHODS: Data on critically ill patients who received intravenous polymyxin B or colistin sulfate for over 24 h were collected. Logistic regression with the least absolute shrinkage and selection operator (LASSO) was used to identify variables that are associated with outcomes. The eXtreme Gradient Boosting (XGB) classifier algorithm was used to further visualize factors with significant differences. A prediction model for PIN was developed through binary logistic regression analysis and the model was assessed by temporal validation and external validation. Finally, a risk-scoring system was developed based on the prediction model. RESULTS: Of 508 patients, 161 (31.6%) patients developed PIN. Polymyxin type, loading dose, septic shock, concomitant vasopressors and baseline blood urea nitrogen (BUN) level were identified as significant predictors of PIN. All validation exhibited great discrimination, with the AUC of 0.742 (95% CI: 0.696-0.787) for internal validation, of 0.708 (95% CI: 0.605-0.810) for temporal validation and of 0.874 (95% CI: 0.759-0.989) for external validation, respectively. A simple risk-scoring tool was developed with a total risk score ranging from -3 to 4, corresponding to a risk of PIN from 0.79% to 81.24%. CONCLUSIONS: This study established a prediction model for PIN. Before using polymyxins, the simple risk-scoring tool can effectively identify patients at risk of developing PIN within a range of 7% to 65%.

Identification of octyl gallate, a novel apoptosis-inducing compound for colon cancer therapy, from Sanguisorba officinalis L. by cell membrane chromatography and UHPLC-(Q)TOF-MS/MS.

Colon cancer is a common gastrointestinal malignancy that ranks third in incidence among gastrointestinal cancers. Therefore, screening bioactive compounds for treatment of colon cancer is urgently needed. Sanguisorba officinalis L. (SO) has been demonstrated that the extractions or monomers possess potential anti-tumor effect. In this study, we firstly used cell membrane chromatography (CMC) and ultra-performance liquid chromatography coupled with (quadrupole) time-of-flight mass spectrometry (UHPLC-(Q) TOF-MS/MS) to identify a novel active ingredient, octyl gallate (OG), from SO methanol extract (SO-MtOH). HCT116 and SW620 cells lines were used for in vitro research, which showed OG presents great anti-colon cancer effect by inhibiting proliferation, inducing apoptosis, and repressing the migration and invasion. Furthermore, SW620 bearing athymic nude mice was used to investigate the potential antitumor activity in vivo, which exhibited OG treatment remarkably lessened the tumor volume. Mechanism studies showed that OG downregulated the PI3K/AKT/mTOR signaling axis and induced apoptosis by upregulating the Bax/Bcl-2 protein and the cleaved caspase-3, caspase-9. In conclusion, our research innovatively applied the method of CMC to intriguingly unearth the potential anti-colon cancer ingredient OG and demonstrated its the great antineoplastic activity, which provide a new insight for researchers efficiently developing the novel apoptosis-inducing compound for colon cancer therapy.

Noninvasive cardiac hemodynamics monitoring of acute myocardial ischemia in rats using near-infrared spectroscopy: A pilot study.

Noninvasive and real-time optical detection of cardiac hemodynamics dysfunction during myocardial ischemia remains challenging. In this study, we developed a near-infrared spectroscopy device to monitor rats' myocardial hemodynamics. The well-designed system can accurately reflect the hemodynamics changes by the classic upper limb ischemia test. Systemic hypoxia by disconnecting to the ventilator and cardiac ischemia by coronary artery slipknot ligation was conducted to monitor myocardial hemodynamics. When systemic hypoxia occurred, ΔHbR and ΔtHb increased significantly, whereas ΔHbO decreased rapidly. When coronary blood flow was obstructed by slipknots, cardiothoracic ΔHbO immediately begins to decline, while ΔHbR also significantly increases. Simultaneously, SpO2 did not show any obvious changes during myocardial ischemia, while SpO2 decreased significantly during systemic hypoxia. These results demonstrated that cardiothoracic hemodynamics stemmed from myocardial ischemia. This pilot study demonstrated the practicality of noninvasive, low-cost optical monitoring for cardiac oxygenation dysfunction in rats.

Michael Addition-Elimination Ring-Opening Polymerization.

A cyclic thioenone system capable of controlled ring-opening polymerization (ROP) is presented that leverages a reversible Michael addition-elimination (MAE) mechanism. The cyclic thioenone monomers are easy to access and modify and for the first time incorporate the dynamic reversibility of MAE with chain-growth polymerization. This strategy features mild polymerization conditions, tunable functionalities, controlled molecular weights (Mn), and narrow dispersities. The obtained polythioenones exhibit excellent optical transparency and good mechanical properties and can be depolymerized to recover the original monomers. Density functional theory (DFT) calculations of model reactions offer insights into the role of monomer conformation in the polymerization process, as well as explaining divergent reactivity observed in seven-membered thiepane (TP) and eight-membered thiocane (TC) ring systems. Collectively, these findings demonstrate the feasibility of MAE mechanisms in ring-opening polymerization and provide important guidelines toward future monomer designs.

Progress and breakthroughs in human kidney organoid research.

The three-dimensional (3D) kidney organoid is a breakthrough model for recapitulating renal morphology and function in vitro, which is grown from stem cells and resembles mammalian kidney organogenesis. Currently, protocols for cultivating this model from induced pluripotent stem cells (iPSCs) and patient-derived adult stem cells (ASCs) have been widely reported. In recent years, scientists have focused on combining cutting-edge bioengineering and bioinformatics technologies to improve the developmental accuracy of kidney organoids and achieve high-throughput experimentation. As a remarkable tool for mechanistic research of the renal system, kidney organoid has both potential and challenges. In this review, we have described the evolution of kidney organoid establishment methods and highlighted the latest progress leading to a more sophisticated kidney transformation research model. Finally, we have summarized the main applications of renal organoids in exploring kidney disease.

Design of Apoptotic Cell-Inspired Particles as a Blood Coagulation Test.

The blood coagulation test is an indispensable test for monitoring the blood coagulation and fibrinolysis functions. Currently, activated partial thromboplastin time (APTT) is the most widely used approach to coagulation testing. However, APTT reagents need to be optimized due to the fact that they are unstable, highly variable, and cannot be easily controlled. In this study, we created apoptotic cell-inspired methacryloyloxyethyl phosphorylserine (MPS) particles for blood coagulation as an alternative to conventional APTT reagents. Particle size could be controlled by changing the concentration of the polymer. The blood coagulation ability of particles was stable at different environmental temperatures. Moreover, the procoagulant activity could be enhanced by increasing the concentration to 0.06 mg/mL and reducing the size of the particles to around 900 nm. Fibrin clotted by particles showed no significant difference from that formed by APTT regent Actin FSL. We propose that MPS particles are a potential alternative to Actin FS for the application of blood coagulation tests.

Proteomic, single-cell and bulk transcriptomic analysis of plasma and tumor tissues unveil core proteins in response to anti-PD-L1 immunotherapy in triple negative breast cancer.

BACKGROUND: Anti-PD-1/PD-L1 treatment has achieved durable responses in TNBC patients, whereas a fraction of them showed non-sensitivity to the treatment and the mechanism is still unclear. METHODS: Pre- and post-treatment plasma samples from triple negative breast cancer (TNBC) patients treated with immunotherapy were measured by tandem mass tag (TMT) mass spectrometry. Public proteome data of lung cancer and melanoma treated with immunotherapy were employed to validate the findings. Blood and tissue single-cell RNA sequencing (scRNA-seq) data of TNBC patients treated with or without immunotherapy were analyzed to identify the derivations of plasma proteins. RNA-seq data from IMvigor210 and other cancer types were used to validate plasma proteins in predicting response to immunotherapy. RESULTS: A random forest model constructed by FAP, LRG1, LBP and COMP could well predict the response to immunotherapy. The activation of complement cascade was observed in responders, whereas FAP and COMP showed a higher abundance in non-responders and negative correlated with the activation of complements. scRNA-seq and bulk RNA-seq analysis suggested that FAP, COMP and complements were derived from fibroblasts of tumor tissues. CONCLUSIONS: We constructe an effective plasma proteomic model in predicting response to immunotherapy, and find that FAP+ and COMP+ fibroblasts are potential targets for reversing immunotherapy resistance.

Myasthenia gravis with tongue muscle atrophy: A case series.

Here, we presented 6 patients who were admitted to our institution and diagnosed as myasthenia gravis (MG) with tongue muscle atrophy. All these 6 patients developed symptoms of bulbar muscle weakness in acetylcholine receptor antibodies positive MG (AChR-MG) (3/6), muscle-specific receptor tyrosine kinase antibodies positive MG (MuSK-MG) (1/6), and sero-negative MG (2/6). Most of patients had "triple-furrowed" tongue except for patient 2 with irregular atrophy of tongue muscle. Tongue muscle atrophy occurs in patients with MuSK-MG, AChR-MG, and sero-negative MG. Atrophied tongue muscles of five patients with MG were reversible after immunotherapy.

Neonatal Filaggrin Genetic Screening and Counseling to Prevent Atopic Dermatitis in High-Risk Infants.

Background: Mutations in filaggrin (FLG), the gene that codes for the skin barrier protein, have been shown to be associated with atopic dermatitis (AD). Objective: The objectives of this study were to determine the effects of genetic counseling and parental education on infants at a high risk of AD. Methods: We enrolled 7521 newborns in Taiwan from January 1, 2016, to March 30, 2020, and all of them received genetic testing encompassing 20 known FLG mutations. The genetic counseling and AD prevention and care team consisted of pediatricians, dermatologists, social workers, and genetic counselors. The counseling was arranged for at least 30 minutes within 45 days after delivery. Results: A total of 2963 high-risk infants (39.4%) were identified. Homozygous c.1432C>T was the most commonly identified mutation. A total of 418 neonates' parents were stratified into counseling and noncounseling groups, where the effect of parental education was evaluated. The genetically stratified parental education program was effective in preventing AD development by 63.3% in high-risk infants before 12 months of life (P < 0.0001). Conclusion: Genetic stratification and parental education are effective in preventing the development of AD in high-risk infants before 12 months of life.

Association of the AhR, ARNT, and AhRR gene polymorphisms and cord blood AhR levels with elevated cord blood IgE susceptibility in Taiwan mother-infant pairs: a nested case-control study.

The roles of aryl hydrocarbon receptor (AhR), AhR-nuclear translocator (ARNT), and AhR repressor (AhRR) genes in the elevation of cord blood IgE (CbIgE) remained unclear. Our aims were to determine the polymorphisms of AhR, ARNT, and AhRR genes, cord blood AhR (CBAhR) level, and susceptibility to elevation of CbIgE. 206 infant-mother pairs with CbIgE>=0.35 IU/ml and 421 randomly selected controls recruited from our previous study. Genotyping was determined using TaqMan assays. Statistical analysis showed AhR rs2066853 (GG vs. AA+AG: adjusted OR (AOR)=1.5, 95%CI=1.10-2.31 and AOR=1.60, 95%CI=1.06-2.43, respectively) and the combination of AhR rs2066853 and maternal total IgE (mtIgE)>=100 IU/ml were significantly correlated with CbIgE>=0.35 IU/ml or CbIgE>=0.5 IU/ml. CBAhR in a random subsample and CbIgE levels were significantly higher in infants with rs2066853GG genotype. We suggest that infant AhR rs2066853 and their interactions with mtIgE>=100 IU/ml significantly correlate with elevated CbIgE, but AhRR and ARNT polymorphisms do not.

Concatenated ScaA and TSA56 Surface Antigen Sequences Reflect Genome-Scale Phylogeny of Orientia tsutsugamushi: An Analysis Including Two Genomes from Taiwan.

Orientia tsutsugamushi is an obligate intracellular bacterium associated with trombiculid mites and is the causative agent of scrub typhus, a life-threatening febrile disease. Strain typing of O. tsutsugamushi is based on its immunodominant surface antigen, 56-kDa type-specific antigen (TSA56). However, TSA56 gene sequence-based phylogenetic analysis is only partially congruent with core genome-based phylogenetic analysis. Thus, this study investigated whether concatenated surface antigen sequences, including surface cell antigen (Sca) proteins, can reflect the genome-scale phylogeny of O. tsutsugamushi. Complete genomes were obtained for two common O. tsutsugamushi strains in Taiwan, TW-1 and TW-22, and the core genome/proteome was identified for 11 O. tsutsugamushi strains. Phylogenetic analysis was performed using maximum likelihood (ML) and neighbor-joining (NJ) methods, and the congruence between trees was assessed using a quartet similarity measure. Phylogenetic analysis based on 691 concatenated core protein sequences produced identical tree topologies with ML and NJ methods. Among TSA56 and core Sca proteins (ScaA, ScaC, ScaD, and ScaE), TSA56 trees were most similar to the core protein tree, and ScaA trees were the least similar. However, concatenated ScaA and TSA56 sequences produced trees that were highly similar to the core protein tree, the NJ tree being more similar. Strain-level characterization of O. tsutsugamushi may be improved by coanalyzing ScaA and TSA56 sequences, which are also important targets for their combined immunogenicity.

Impacts of continuous cropping on the rhizospheric and endospheric microbial communities and root exudates of Astragalus mongholicus.

Astragalus mongholicus is a medicinal plant that is known to decrease in quality in response to continuous cropping. However, the differences in the root-associated microbiome and root exudates in the rhizosphere soil that may lead to these decreases are barely under studies. We investigated the plant biomass production, root-associated microbiota, and root exudates of A. mongholicus grown in two different fields: virgin soil (Field I) and in a long-term continuous cropping field (Field II). Virgin soil is soil that has never been cultivated for A. mongholicus. Plant physiological measurements showed reduced fresh and dry weight of A. mongholicus under continuous cropping conditions (i.e. Field II). High-throughput sequencing of the fungal and bacterial communities revealed differences in fungal diversity between samples from the two fields, including enrichment of potentially pathogenic fungi in the roots of A. mongholicus grown in Field II. Metabolomic analysis yielded 20 compounds in A. mongholicus root exudates that differed in relative abundance between rhizosphere samples from the two fields. Four of these metabolites (2-aminophenol, quinic acid, tartaric acid, and maleamate) inhibited the growth of A. mongholicus, the soil-borne pathogen Fusarium oxysporum, or both. This comprehensive analysis enhances our understanding of the A. mongholicus microbiome, root exudates, and interactions between the two in response to continuous cropping. These results offer new information for future design of effective, economical approaches to achieving food security.