Molecular characterization of a novel mycovirus from binucleate Rhizoctonia AG-A strain A46.

The complete genome sequence of a positive-sense single-stranded RNA (+ ssRNA) virus, Rhizoctonia beny-like virus 1 (RBLV1), isolated from binucleate Rhizoctonia AG-A strain A46, was determined. The RBLV1 genome is 10,280 nt in length and contains a short stretch of adenines at the 3' terminus. It contains a single open reading frame (ORF) encoding a 376.30-kDa protein with viral helicase and RNA-dependent RNA polymerase (RdRp) motifs. The encoded protein exhibited the highest sequence similarity to Rhizoctonia cerealis beny-like virus 0928-1 (RcBeLV 0928-1, 45.25%), with a sequence coverage of 63%. Phylogenetic analysis based on ORF protein sequences revealed that RBLV1 is a novel unclassified mycovirus.

Reassessing the Quantum Yield and Reactivity of Triplet-State Dissolved Organic Matter via Global Kinetic Modeling.

Measuring the quantum yield and reactivity of triplet-state dissolved organic matter (3DOM*) is essential for assessing the impact of DOM on aquatic photochemical processes. However, current 3DOM* quantification methods require multiple fitting steps and rely on steady-state approximations under stringent application criteria, which may introduce certain inaccuracies in the estimation of DOM photoreactivity parameters. Here, we developed a global kinetic model to simulate the reaction kinetics of the hv/DOM system using four DOM types and 2,4,6-trimethylphenol as the probe for 3DOM*. Analyses of residuals and the root-mean-square error validated the exceptional precision of the new model compared to conventional methods. 3DOM* in the global kinetic model consistently displayed a lower quantum yield and higher reactivity than those in local regression models, indicating that the generation and reactivity of 3DOM* have often been overestimated and underestimated, respectively. The global kinetic model derives parameters by simultaneously fitting probe degradation kinetics under different conditions and considers the temporally increasing concentrations of the involved reactive species. It minimizes error propagation and offers insights into the interactions of different species, thereby providing advantages in accuracy, robustness, and interpretability. This study significantly advances the understanding of 3DOM* behavior and provides a valuable kinetic model for aquatic photochemistry research.

Temperature Thresholds of Pyrogenic Dissolved Organic Matter in Heating Experiments Simulating Forest Fires.

Heating temperature (HT) during forest fires is a critical factor in regulating the quantity and quality of pyrogenic dissolved organic matter (DOM). However, the temperature thresholds at which maximum amounts of DOM are produced (TTmax) and at which the DOC gain turns into net DOC loss (TT0) remain unidentified on a component-specific basis. Here, based on solid-state 13C nuclear magnetic resonance, absorbance and fluorescence spectroscopies, and Fourier transform ion cyclotron resonance mass spectrometry, we analyzed variations in DOM composition in detritus and soil with HT (150-500 °C) and identified temperature thresholds for components on structural, fluorophoric, and molecular formula levels. TTmax was similar for detritus and soil and ranged between 225 and 250 °C for bulk dissolved organic carbon (DOC) and most DOM components. TT0 was consistently lower in detritus than in soil. Moreover, temperature thresholds differed across the DOM components. As the HT increased, net loss was observed initially in molecular formulas tentatively associated with carbohydrates and aliphatics, then proteins, peptides, and polyphenolics, and ultimately condensed aromatics. Notably, at temperatures lower than TT0, particularly at TTmax, burning increased the DOC quantity and thus might increase labile substrates to fuel soil microbial community. These composition-specific variations of DOM with temperature imply nonlinear and multiple temperature-dependent wildfire impacts on soil organic matter properties.

Complete nucleotide sequence of a novel alphapartitivirus from Rhizoctonia solani AG-4 HG III isolate SM03.

In this report, the full genome sequence of a novel mycovirus, designated as "Rhizoctonia solani partitivirus SM03" (RsPV-SM03), was determined in Rhizoctonia solani AG-4 HG III isolate SM03. RsPV-SM03 genome consists of two dsRNAs (dsRNA-1 and dsRNA-2), each of them contains one single open reading frame (ORF). ORF1 of dsRNA-1 encodes a putative RNA-dependent RNA polymerase (RdRp), while ORF2 of dsRNA-2 encodes a putative viral coat protein (CP). Phylogenetic analysis indicated that the RdRp and CP of RsPV-SM03 are closely related to those of other members of the genus Alphapartitivirus, family Partitiviridae, suggesting that RsPV-SM03 represents a novel species in the genus Alphapartitivirus.

Complete nucleotide sequence of a novel mycovirus infecting Rhizoctonia fumigata AG-Ba isolate C-314 Baishi.

The complete nucleotide sequence of a novel mycovirus, designated as "Rhizoctonia fumigata bipartite virus 1" (RfBV1), from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi was determined. The genome of RfBV1 is composed of two double-stranded RNAs (dsRNA). dsRNA-1 (2311 bp) contains one open reading frame (ORF), which codes for the putative RNA-dependent RNA polymerase (RdRp) of the virus. dsRNA-2 (1690 bp) contains one ORF, which encodes a putative protein whose function is unknown. Phylogenetic analysis indicated that the RdRp of RfBV1 clustered with several unassigned bipartite viruses belonging to the CThTV-like viruses group, but not the family Amalgaviridae or Partitiviridae. Our study suggests that RfBV1 is a novel mycovirus related to the CThTV-like viruses.

A novel alphapartitivirus from binucleate Rhizoctonia fumigata AG-Ba isolate C-314 Baishi.

The full-length nucleotide sequence and genome organization of a novel mycovirus designated as "Rhizoctonia fumigata partitivirus 1" (RfPV1) from Rhizoctonia fumigata AG-Ba strain C-314 Baishi was determined. The genome of RfPV1 consists of two double-stranded RNAs (dsRNAs): dsRNA1 (2003 bp) and dsRNA2 (1802 bp). Each of the two dsRNAs contains one open reading frame, coding for a putative RNA-dependent RNA polymerase and a coat protein, respectively. The 5' untranslated regions (UTRs) of both dsRNAs were conserved, and the 3'-UTRs of the two dsRNAs had interrupted poly(A) tails, similar to other partitiviruses. Phylogenetic analysis indicated that RfPV1 is a new species in the genus Alphapartitivirus, family Partitiviridae.

Complete genome sequence of a novel mitovirus from binucleate Rhizoctonia AG-K strain FAS2909W.

The full-length AU-rich (63.14%) 2,794-nucleotide sequence of Rhizoctonia mitovirus K1 (RMV-K1) isolated from the binucleate AG-K strain FAS2909W was determined. The positive strand of RMV-K1 contains a large open reading frame (ORF) when the fungal mitochondrial genetic code is used. This ORF was predicted to encode an RdRp protein exhibiting the highest sequence identity (41.77%) to Rhizoctonia solani mitovirus 30. Phylogenetic analysis showed that RMV-K1 is a novel member of the genus Mitovirus, family Mitoviridae.

Pod pepper vein yellows virus, a new recombinant polerovirus infecting Capsicum frutescens in Yunnan province, China.

Pepper vein yellows viruses (PeVYV) are phloem-restricted viruses in the genus Polerovirus, family Luteoviridae. Typical viral symptoms of PeVYV including interveinal yellowing of leaves and upward leaf curling were observed in pod pepper plants (Capsicum frutescens) growing in Wenshan city, Yunnan province, China. The complete genome sequence of a virus from a sample of these plants was determined by next-generation sequencing and RT-PCR. Pod pepper vein yellows virus (PoPeVYV) (MT188667) has a genome of 6015 nucleotides, and the characteristic genome organization of a member of the genus Polerovirus. In the 5' half of its genome (encoding P0 to P4), PoPeVYV is most similar (93.1% nt identity) to PeVYV-3 (Pepper vein yellows virus 3) (KP326573) but diverges greatly in the 3'-part encoding P5, where it is most similar (91.7% nt identity) to tobacco vein distorting virus (TVDV, EF529624) suggesting a recombinant origin. Recombination analysis predicted a single recombination event affecting nucleotide positions 4126 to 5192 nt, with PeVYV-3 as the major parent but with the region 4126-5192 nt derived from TVDV as the minor parent. A full-length clone of PoPeVYV was constructed and shown to be infectious in C. frutescens by RT-PCR and the presence of icosahedral viral particles.

Construction of an infectious full-length cDNA clone of potato aucuba mosaic virus.

Potato aucuba mosaic virus (PAMV), a positive single-strand RNA virus, has one of the longest genomes of the viruses in the genus Potexvirus. In 2019, potato samples with mottle and crinkling symptoms from Huzhou, Zhejiang province, China, were identified to be infected with PAMV, potato virus X (PVX), and potato virus Y (PVY) by transcriptome sequencing. To study the effects of single infection by PAMV, the full-length sequence of PAMV from Huzhou (MT193476) was determined and an infectious full-length cDNA clone was constructed. This cDNA clone was infectious by agro-infiltration, leading to systemic symptoms in Nicotiana benthamiana, tomato, pepper, and potato.

Molecular characterization of a novel mycovirus from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi.

The complete genome sequence of a novel dsRNA virus isolated from Rhizoctonia fumigata AG-Ba isolate C-314 Baishi (designated as Rhizoctonia fumigata virus 1, RfV1) was determined. The RfV1 genome was 9,907 bp in length and contained two open reading frames (ORFs). ORF1 potentially coded for a 198.10-kDa protein (P1). P1 shared low but significant amino acid sequence similarity to the putative protein encoded by Lentinula edodes mycovirus (LeV) ORF1. P1 contained a NUDIX domain, which was also present in the putative proteins encoded by the ORF1s of LeV and Phlebiopsis gigantea large virus 1 (PgLV-1). ORF2 potentially coded for a 146.72-kDa protein (P2) that contained the conserved motifs of the RNA-dependent RNA polymerase (RdRp). ORF1 and ORF2 were overlapping, and it was predicted that ORF2 could be translated as a fusion with ORF1 via a ribosomal -1 frameshifting mechanism. Phylogenetic analysis indicated that RfV1 clustered with PgLV-1, LeV and Rosellinia necatrix megabirnavirus 1 (RnMBV1) in a separate clade independent of other virus genera. We propose that RfV1, along with PgLV-1 and LeV, should be grouped into a new viral genus related to the family Megabirnaviridae. This is the first report of the full-length genome sequence of a novel mycovirus isolated from R. fumigata.

Development, validation, and visualization of a novel nomogram to predict depression risk in patients with stroke.

BACKGROUND: This study aimed to develop and validate a predictive nomogram model applicable to depression risk in stroke patients. METHODS: Participants from the NHANES database (n = 1097) were enrolled from 2005 to 2018; 767 subjects were randomly assigned to the training cohort, and the remaining subjects composed the testing cohort. A nomogram containing the optimal predictors identified by the least absolute shrinkage and selection operator (LASSO) and logistic regression methods was constructed to estimate the probability of depression in stroke patients. To evaluate the performance of the nomogram, the area under the receiver operating characteristic curve (AUC), calibration plot, decision curve analysis (DCA) and internal validation were utilized. RESULTS: Age, family income, trouble sleeping, coronary heart disease, and total cholesterol were included in the nomogram after filtering predictive variables. The AUCs of the nomogram for the training and testing cohorts were 0.782 (95 % CI = 0.742-0.821) and 0.755 (95 % CI = 0.675-0.834), respectively. The calibration plot revealed that the predicted probability was extremely close to the actual probability of depression occurrence in both the training and testing cohorts. DCA revealed that the nomogram model in the training and testing cohorts had a net benefit when the risk thresholds were 0-0.59 and 0-0.375, respectively. LIMITATIONS: This study was limited by the absence of clinical external validation, which hindered the estimation of the nomogram's external applicability. In addition, this study has a cross-sectional design. CONCLUSIONS: A novel nomogram was successfully constructed and proven to be beneficial for identifying individuals at high risk for depression among stroke patients.

Molecular-level carbon traits underlie the multidimensional fine root economics space.

Carbon influences the evolution and functioning of plants and their roots. Previous work examining a small number of commonly measured root traits has revealed a global multidimensionality of the resource economics traits in fine roots considering carbon as primary currency but without considering the diversity of carbon-related traits. To address this knowledge gap, we use data from 66 tree species from a tropical forest to illustrate that root economics space co-varies with a novel molecular-level traits space based on nuclear magnetic resonance. Thinner fine roots exhibit higher proportions of carbohydrates and lower diversity of molecular carbon than thicker roots. Mass-denser fine roots have more lignin and aromatic carbon compounds but less bioactive carbon compounds than lighter roots. Thus, the transition from thin to thick fine roots implies a shift in the root carbon economy from 'do-it-yourself' soil exploration to collaboration with mycorrhizal fungi, while the shift from light to dense fine roots emphasizes a shift from acquisitive to conservative root strategy. We reveal a previously undocumented role of molecular-level carbon traits that potentially undergird the multidimensional root economics space. This finding offers new molecular insight into the diversity of root form and function, which is fundamental to our understanding of plant evolution, species coexistence and adaptations to heterogeneous environments.

Identification of viral particles in the apoplast of Nicotiana benthamiana leaves infected by potato virus X.

The apoplast is the extracellular space for signalling, nutrient transport, and plant-microbe interactions, but little is known about how plant viruses use the foliar apoplast. Proteomic analysis of the apoplasts isolated from potato virus X (PVX)-infected Nicotiana benthamiana plants showed that the coat protein (CP) is the dominant viral component. The presence of the CP in the apoplast was confirmed by western blot, viral nucleic acid was detected by reverse transcription-PCR and northern blot, and viral particles were observed by transmission electron microscopy (TEM). The apoplast from infected leaves was infectious if rubbed onto healthy leaves but not when infiltrated into them. The exosomes were separated from the apoplast fluid by high-speed centrifugation and TEM showed that PVX particles were not associated with the exosomes. These results suggest that PVX virions are released to the N. benthamiana apoplast in a one-way manner and do not share the bidirectional transport of exosomes.

Biological and Genetic Characterization of Pod Pepper Vein Yellows Virus-Associated RNA From Capsicum frutescens in Wenshan, China.

Tombusvirus-like associated RNAs (tlaRNAs) are positive-sense single-stranded RNAs found in plants co-infected with some viruses of the genus Polerovirus. Pod pepper vein yellows virus (PoPeVYV) was recently reported as a new recombinant polerovirus causing interveinal yellowing, stunting, and leaf rolling in Capsicum frutescens plants at Wenshan city, Yunnan province, China. The complete genome sequence of its associated RNA has now been determined by next-generation sequencing and reverse transcription (RT) polymerase chain reaction (PCR). PoPeVYV-associated RNA (PoPeVYVaRNA) (GenBank Accession No. MW323470) has 2970 nucleotides and is closely related to other group II tlaRNAs, particularly tobacco bushy top disease-associated RNA (TBTDaRNA, GenBank Accession No. EF529625). In infection experiments on Nicotiana benthamiana and C. frutescens plants, synergism between PoPeVYVaRNA and PoPeVYV was demonstrated, leading to severe interveinal yellowing of leaves and stunting of plants. The results provide further information on the genetic and biological properties of the various agents associated with pepper vein yellows disease (PeVYD).

Complete nucleotide sequence and genome organization of a Chinese isolate of Tobacco vein distorting virus.

Tobacco bushy top disease is caused by tobacco bushy top virus (TBTV, a member of the genus Umbravirus) which is dependent on tobacco vein-distorting virus (TVDV) to act as a helper virus encapsidating TBTV and enabling its transmission by aphids. Isometric virions from diseased tobacco plants were purified and disease symptoms were reproduced after experimental aphid transmission. The complete genome of TVDV was determined from cloned RT-PCR products derived from viral RNA. It was 5,920 nucleotides (nts) long and had the six major open reading frames (ORFs) typical of a member of the genus Polerovirus. Sequence comparisons showed that it differed significantly from any of the other species in the genus and this was confirmed by phylogenetic analyses of the RdRp and coat protein. SDS-PAGE analysis of purified virions gave two protein bands of about 26 and 59 kDa both of which reacted strongly in Western blots with antiserum produced to prokaryotically expressed TVDV CP showing that the two forms of the TVDV CP were the only protein components of the capsid.

Phylogenetic classification of a group of self-replicating RNAs that are common in co-infections with poleroviruses.

Tombusvirus-like associated RNAs (tlaRNAs) are positive-sense single-stranded RNAs found in plants co-infected with viruses of the genus Polerovirus. TlaRNAs depend upon capsid proteins supplied in trans by the co-infecting polerovirus vector for transmission and intra-host systemic movement. Here, the full-length genomes of five tlaRNAs were determined using a combination of RT-PCR and next-generation sequencing, and evidence is provided for an additional tlaRNA associated with potato leafroll virus. Phylogenetic analyses based on conserved domains of the RdRp placed tlaRNAs as a monophyletic clade clustering with members of the family Tombusviridae and comprising three different subclades. Full-length clones of tlaRNAs from two of three subclades were confirmed to replicate autonomously, and each produces a subgenomic RNA during infection.