Genome sequencing and comparative genome analysis of Rhizoctonia solani AG-3.

Rhizoctonia solani AG-3 is a plant pathogenic fungus that belongs to the group of multinucleate Rhizoctonia. According to its internal transcribed spacer (ITS) cluster analysis and host range, it is divided into TB, PT, and TM subgroups. AG-3 TB mainly causes tobacco target spots, AG-3 PT mainly causes potato black scurf, and AG-3 TM mainly causes tomato leaf blight. In our previous study, we found that all 36 tobacco target spot strains isolated from Yunnan (Southwest China) were classified into AG-3 TB subgroup, while only two of the six tobacco target spot strains isolated from Liaoning (Northeast China) were classified into AG-3 TB subgroup, and the remaining four strains were classified into AG-3 TM subgroup, which had a unique taxonomic status, and there was no previous report on the whole genome information of AG-3 TM subgroup. In this study, the whole genomes of R. solani AG-3 strains 3T-1 (AG-3 TM isolated from Liaoning) and MJ-102 (AG-3 TB isolated from Yunnan) isolated from tobacco target spot in Liaoning and Yunnan were sequenced by IIumina and PacBio sequencing platforms. Comparative genomic analysis was performed with the previously reported AG-3 PT strain Rhs1AP, revealing their differences in genomes and virulence factors. The results indicated that the genome size of 3T-1 was 42,103,597 bp with 11,290 coding genes and 49.74% GC content, and the genome size of MJ-102 was 41,908,281 bp with 10,592 coding genes and 48.91% GC content. Through comparative genomic analysis with the previously reported strain Rhs1AP (AG-3 PT), it was found that the GC content between the genomes was similar, but the strains 3T-1 and MJ-102 contained more repetitive sequences. Similarly, there are similarities between their virulence factors, but there are also some differences. In addition, the results of collinearity analysis showed that 3T-1 and MJ-102 had lower similarity and longer evolutionary distance with Rhs1AP, but the genetic relationship between 3T-1 and MJ-102 was closer. This study can lay a foundation for studying the molecular pathogenesis and virulence factors of R. solani AG-3, and revealing its genomic composition will also help to develop more effective disease control strategies.

MEOL: A Maximum-Entropy Framework for Options Learning.

Options, the temporally extended courses of actions that can be taken at varying time scale, have provided a concrete, key framework for learning levels of temporal abstraction in hierarchical tasks. While methods of learning options end-to-end is well researched, how to explore good options and actions simultaneously is still challenging. We address this issue by maximizing reward augmented with entropies of both option and action selection policy in options learning. To this end, we reveal our novel optimization objective by reformulating options learning from perspective of probabilistic inference and propose a soft options iteration method to guarantee convergence to the optimum. In implementation, we propose an off-policy algorithm called the maximum-entropy options critic (MEOC) and evaluate it on series of continuous control benchmarks. Comparative results demonstrate that our method outperforms baselines in efficiency and final result on most benchmarks, and the performance exhibits superiority and robustness especially on complex tasks. Ablated studies further explain that entropy maximization on hierarchical exploration promotes learning performance through efficient options specialization and multimodality in action level.

Deep-Learning Density Functional Perturbation Theory.

Calculating perturbation response properties of materials from first principles provides a vital link between theory and experiment, but is bottlenecked by the high computational cost. Here, a general framework is proposed to perform density functional perturbation theory (DFPT) calculations by neural networks, greatly improving the computational efficiency. Automatic differentiation is applied on neural networks, facilitating accurate computation of derivatives. High efficiency and good accuracy of the approach are demonstrated by studying electron-phonon coupling and related physical quantities. This work brings deep-learning density functional theory and DFPT into a unified framework, creating opportunities for developing ab initio artificial intelligence.

Identification of the toxin components of Rhizoctonia solani AG1-IA and its destructive effect on plant cell membrane structure.

Rice sheath blight is a fungal disease caused mainly by Rhizoctonia solani AG1-IA. Toxins are a major pathogenic factor of R. solani, and some studies have reported their toxin components; however, there is no unified conclusion. In this study, we reported the toxin components and their targets that play a role in R. solani AG1-IA. First, toxins produced by R. solani AG1-IA were examined. Several important phytotoxins, including benzoic acid (BZA), 5-hydroxymethyl-2-furanic aid (HFA), and catechol (CAT), were identified by comparative analysis of secondary metabolites from AG1-IA, AG1-IB, and healthy rice. Follow-up studies have shown that the toxin components of this fungus can rapidly disintegrate the biofilm structure while maintaining the content of host plant membrane components, thereby affecting the organelles, which may also explain the lack of varieties highly resistant to sheath blight.

Risk factors and clinical characteristics of surgical site infections in athletes undergoing Achilles tendon repair surgery.

Achilles tendon ruptures are common in athletes, requiring surgical intervention. However, the risk of surgical site infections (SSIs) post-surgery poses significant challenges. This study aims to analyse the risk factors and microbial aetiology associated with SSIs in athletes undergoing Achilles tendon repair. A comprehensive retrospective analysis was conducted from May 2021 to July 2023. The study included 25 patients with SSIs (case group) and 50 patients without SSIs (control group) post Achilles tendon repair surgery. Inclusion criteria encompassed patients with medically confirmed Achilles tendon ruptures who underwent surgical repair. Exclusion criteria included prior tendon pathologies and significant chronic illnesses. Diagnostic criteria for SSIs involved symptoms like elevated body temperature and localized tenderness, along with laboratory confirmations such as positive microbiological cultures. The study utilized VITEK® 2 for bacterial identification and involved statistical analyses like univariate and multivariate logistic regression. The study identified Staphylococcus aureus as the primary pathogen in SSIs. Significant risk factors included lack of prophylactic antibiotic use, presence of diabetes, open wounds and prolonged surgery duration. Univariate analysis revealed stark contrasts in these factors between infected and non-infected groups, while multivariate analysis underscored their importance in SSI development. S. aureus emerged as the predominant pathogen in SSIs post Achilles tendon repair. Critical risk factors such as absence of prophylactic antibiotics, diabetes, open wounds and extended surgery duration play a vital role in SSIs. Addressing these factors is essential for better postoperative outcomes in Achilles tendon repair surgeries.

Unveiling HSP40/60/70/90/100 gene families and abiotic stress response in Jerusalem artichoke.

Heat shock proteins (HSPs) are essential for plant growth, development, and stress adaptation. However, their roles in Jerusalem artichoke are largely unexplored. Using bioinformatics, we classified 143 HSP genes into distinct families: HSP40 (82 genes), HSP60 (22 genes), HSP70 (29 genes), HSP90 (6 genes), and HSP100 (4 genes). Our analysis covered their traits, evolution, and structures. Using RNA-seq data, we uncovered unique expression patterns of these HSP genes across growth stages and tissues. Notably, HSP40, HSP60, HSP70, HSP90, and HSP100 families each had specific roles. We also studied how these gene families responded to various stresses, from extreme temperatures to drought and salinity, revealing intricate expression dynamics. Remarkably, HSP40 showed remarkable flexibility, while HSP60, HSP70, HSP90, and HSP100 responded specifically to stress types. Moreover, our analysis unveiled significant correlations between gene pairs under stress, implying cooperative interactions. qRT-PCR validation underscored the significance of particular genes such as HtHSP60-7, HtHSP90-5, HtHSP100-2, and HtHSP100-3 in responding to stress. In summary, our study advances the understanding of how HSP gene families collectively manage stresses in Jerusalem artichoke. This provides insights into specific gene functions and broader plant stress responses.

Horizontal and Vertical Transmission of a Mycovirus Closely Related to the Partitivirus RhsV717 That Confers Hypovirulence in Rhizoctonia solani.

Rhizoctonia solani virus717 (RhsV717) was isolated from the Rhizoctonia solani (R. solani) AG-2 strain Rhs717. This study isolated a virus designated as Rhizoctonia solani partitivirus BS-5 (RsPV-BS5) from the R. solani AG-3 strain BS-5, the causal agent of tobacco target spot disease. The virus was identified as a strain of RhsV717. Transmission electron microscopy (TEM) images showed that RsPV-BS5 had virus particles with a diameter of approximately 40 nm. Importantly, it can be horizontally transmitted through hyphal anastomosis and vertically transmitted via sexual basidiospores. Furthermore, this study demonstrated that RsPV-BS5 infection significantly impedes mycelial growth and induces hypovirulence in tobacco leaves. Thus, RsPV-BS5 presents a promising avenue for biocontrolling tobacco target spot disease. Transcriptome analysis unveiled differential expression of four genes related to cell wall-degrading enzymes between two isogenic strains, 06-2-15V and 06-2-15. These findings shed light on the molecular mechanism through which RsPV-BS5 reduces host pathogenicity.

Complete genome sequence of a novel fusarivirus from Rhizoctonia solani AG-3 PT strain 3P-2-2.

Here, we describe a novel mycovirus, tentatively designated as "Rhizoctonia solani fusarivirus 6" (RsFV6), which was discovered in Rhizoctonia solani AG-3 PT strain 3P-2-2. The virus has a single-stranded positive-sense RNA (+ssRNA) genome of 6141 nucleotides containing two open reading frames (ORFs) and a poly(A) tail. ORF1 encodes a large polypeptide of 1,862 amino acids (aa) with conserved RNA-dependent RNA polymerase (RdRp) and helicase (Hel) domains. ORF2 encodes a putative 167-aa protein of unknown function. BLASTp searches revealed that the ORF1-encoded polypeptide showed the highest sequence similarity (70.67% identity) to that of Rhizoctonia solani fusarivirus 3 (RsFV3), which was isolated from Rhizoctonia solani AG-2-2LP. Multiple sequence alignments and phylogenetic analysis based on RdRp and Hel sequences indicated that RsFV6 could be a novel member of the genus Alphafusarivirus family Fusariviridae.

Morphological and molecular characterization of Rhizoctonia solani AG-3 associated with tobacco target leaf spot in China.

Tobacco target leaf spot is a leaf disease that seriously affects both the quantity and quality of commercial tobacco crops and has caused huge economic losses in many countries and also pandemics in China since 2006. The anastomosis group-3 (AG-3) pathogen is divided into different subgroups namely AG-3 PT (potato type), AG-3TB (tobacco type), and AG-3 TM (tomato type), based on their host and the combined data from the ribosomal DNA internal transcribed spacer (rDNA-ITS), rDNA intergenic spacer 1 (rDNA-IGS1) regions, and translation elongation factor 1-α (tef-1α) gene. In this study, we collected tobacco leaves showing target spot symptom from four fields in China. We obtained 49 isolates from southwest China (Yunnan Provinces) and six isolates from northeast China (Liaoning Province). Phylogenetic tree based on rDNA-ITS region indicated that 51 isolates (49 isolates from Yunnan and two isolates from Liaoning) and 4 isolates from Liaoning belonged to AG-3 TB and AG-3 TM, respectively.

Molecular characterization of a novel mitovirus from Rhizoctonia solani AG-4 HGIII strain XMC-IF.

The nucleotide sequence of a viral double-stranded RNA (dsRNA) from Rhizoctonia solani AG-4 HGIII strain XMC-IF (designated as "Rhizoctonia solani mitovirus 106", RsMV-106) was determined. The complete sequence was 2794 bp in length with a 57.50% A + U content and contained a large open reading frame (ORF) when the fungal mitochondrial genetic code was used. The ORF potentially encodes a 95.76-kDa protein containing a conserved domain of an RNA-dependent RNA polymerase (RdRp). BLASTp analysis revealed that the RdRp domain of RsMV-106 shared 47.52-73.24% sequence identity with those of viruses of the genus Duamitovirus and was most similar (73.24% identity) to that of Alternaria alternata mitovirus 1 (AaMV1). Phylogenetic analysis showed that RsMV-106 is a novel member of the genus Duamitovirus, family Mitoviridae. This is the first report of the full genome sequence of a mitovirus associated with R. solani AG-4 HGIII.

Centranthera grandiflore alleviates alcohol-induced oxidative stress and cell apoptosis.

Alcohol liver disease (ALD) has become a global threat to human health. It is associated with a wide range of liver diseases including alcohol fatty liver, steatosis, fibrosis and cirrhosis, and finally leads to liver cancer and even death. Centranthera grandiflora is a traditional Chinese medicinal herb commonly used to treat ALD, but no research about its mechanism is available. This study evaluated the hepatoprotective effect and mechanism of C. grandiflora against alcohol-induced liver injury in mice. We found that the ethanol extracts of C. grandiflora (CgW) alleviated the alcohol-induced liver injury, enhanced the levels of antioxidant enzymes, and reduced the amount of lipid peroxides. CgW also affected cell apoptosis by inhibiting the activity of Bax, cleaved-caspase 3 and cleaved-caspase 9, and increasing the activity of Bcl-2. In conclusion, the results showed that CgW can effectively improve ALD through alleviating oxidative stress and inhibiting cell apoptosis for the first time. This study suggested that C. grandiflora is a promising herbal medicine for ALD treatment.

Distributed adaptive consensus tracking control for heterogeneous nonlinear multi-agent systems.

In this study, our focus is to resolve the consensus problem of heterogeneous nonlinear multi-agent systems. As only some agents access reference information directly, the proposed distributed adaptive consensus controller uses only local information, by employing the command filtered backstepping approach. The uniform, ultimate boundedness of all closed-loop signals and the convergence of consensus tracking error to a small tunable compact set can be obtained using our proposed mechanism. Finally, the formation-tracking problem of nonholonomic unmanned aerial vehicles is solved with the suggested control algorithm.

Rational Design of Heteroanionic Two-Dimensional Materials with Emerging Topological, Magnetic, and Dielectric Properties.

Designing and tuning the physical properties of two-dimensional (2D) materials at the atomic level are crucial to the development of 2D technologies. Here, we introduce heteroanions into metal-centered octahedral structural units of a 2D crystal breaking the Oh symmetry, together with the synergistic effect of anions' electrons and electronegativity, to realize ternary 2D materials with emerging topological, magnetic, and dielectric properties. Using an intrinsic heteroanionic van der Waals layered material, VOCl, as a prototype, 20 2D monolayers VXY (X = B, C, N, O, or F; Y = F, Cl, Br, or I) are obtained and investigated by means of first-principles calculations. The anion engineering in this family significantly reshapes the electronic properties of VOCl, leading to nonmagnetic topological insulators with nontrivial edge states in VCY, ferromagnetic half-semimetals with a nodal ring around the Fermi energy in VNY, and insulators with dielectric constants in VOY higher than that of h-BN. This work demonstrates the rationality and validity of the design strategy of multiple-anion engineering to achieve superior properties in the 2D monolayers with potential application in electronics and spintronics.

Molecular characterization of a novel mycovirus isolated from Rhizoctonia solani AG-1 IA strain 9-11.

The complete genome sequence of a double-stranded RNA (dsRNA) virus, Rhizoctonia solani dsRNA virus 11 (RsRV11), isolated from Rhizoctonia solani AG-1 IA strain 9-11 was determined. The RsRV11 genome is 9,555 bp in length and contains three conserved domains: structural maintenance of chromosomes (SMC) superfamily, phosphoribulokinase (PRK), and RNA-dependent RNA polymerase (RdRp). The RsRV11 genome has two non-overlapping open reading frames (ORFs). ORF1 is predicted to encode a 204.12-kDa protein that shares low but significant amino acid sequence similarity with a putative protein encoded by Rhizoctonia solani RNA virus HN008 (RsRV-HN008). ORF2 potentially encodes a 132.41-kDa protein that contains the conserved domain of the RdRp. Phylogenetic analysis indicated that RsRV11 clustered with RsRV-HN008 in a separate clade from other virus families. This implies that RsRV11 and RsRV-HN008 should be included in a new mycovirus taxon close to the family Megabirnaviridae and that RsRV11 is a new mycovirus.

Upstream and downstream mechanisms for the promoting effects of IGF-1 on differentiation of spermatogonia to primary spermatocytes.

AIM: The aim of this study is to delineate the mechanisms for the promoting the effects of insulin growth factor I (IGF1) on the differentiation of spermatogonia into primary spermatocytes. MAIN METHODS: We used organ culture of testicular fragments from mice to observe the effects of varying agents and siRNAs. Real-time RT-PCR and immunoblotting analysis were employed to quantify expression of genes. Luciferase reporter gene assay was employed for verifying the targeting relationship between miRNA and protein-coding genes. KEY FINDINGS: During spermatogenesis while spermatozoa pass through epididymis and vas deferens for maturation, expression of IGF1 and its receptor IGF1R, p44/ERK1 and p42/ERK2, and PI3K was all upregulated, whereas let-7 miRNA family members let-7a/b/d/e/g/ were downregulated. We established both IGF1 and IGF1R as cognate target genes for let-7; downregulation of let-7 resulted in upregulation of IGF1 and IGF1R during the early stage of differentiation from spermatogonia to primary spermatocytes. Transfection of let-7 inhibited, whereas transfection of anti-let-7 inhibitor enhanced the differentiation. The promoting effect of anti-let-7 was eliminated by PPP to block IGF1R phosphorylation. IGF1 activated ERK1/2 and PI3K and induced differentiation. PPP eliminated the activation of ERK1/2 and PI3K and inhibited the differentiation induced by IGF1. Specific inhibition of ERK1/2 by U0126 or PI3K by LY294002 reduced the IGF1-induced differentiation. Knockdown of ERK1/ERK2 or PI3K by siRNAs also blocked IGF1-induced spermatogenesis. SIGNIFICANCE: Our study therefore identified downregulation of let-7 as an upstream mechanism for IGF1/IGF1R upregulation and activation of ERK1/2 and PI3K as a downstream mechanism mediating the IGF1 signaling cascade promoting differentiation of spermatogonia to primary spermatocytes.

[Application study on inversion diagnosis of F8 gene in hemophilia A].

OBJECTIVE: To establish an effective method of genetic diagnosis on hemophilia A (HA) by detecting the inversion mutation in intron 22 of F8 gene. METHODS: Intron 22 inversion mutation in F8 gene was detected by using long distance-polymerase chain reaction (LD-PCR) and inversion-PCR (I-PCR) in 31 HA patients. The mothers of HA patients with intron 22 inversion mutation were selected to carrier diagnosis and amniotic fluid of the pregnant women with inversion mutation was collected at intermediate stage of gestation, and used to prenatal genetic diagnosis. RESULTS: Seven patients showed F8 gene inversion mutation in thirty-one patients. Three in four mothers of HA patients with intron 22 inversion mutation were diagnosed as carriers. The prenatal diagnosis result indicated that the fetus conceived in the HA-carrier woman was normal individual. CONCLUSION: The detection of intron 22 inversion mutation by LD-PCR and I-PCR is time-saving, and can be used in prenatal diagnosis on HA.