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Abstract Passionfruit (Passiflora edulis) is a significant fruit crop in the commercial sector, owing to its high nutritional and medicinal value. The advent of high-throughput genomics sequencing technology has led to the publication of a vast amount of passionfruit omics data, encompassing complete genome sequences and transcriptome data under diverse stress conditions. To facilitate the efficient integration, storage, and analysis of these large-scale datasets, and to enable researchers to effectively utilize these omics data, we developed the first passionfruit genome database (PGD). The PGD platform comprises a diverse range of functional modules, including a genome browser, search function, heatmap, gene expression patterns, various tools, sequence alignment, and batch download, thereby providing a user-friendly interface. Additionally, supplementary practical tools have been developed for the PGD, such as gene family analysis tools, gene ontology (GO) terms, a pathway enrichment analysis, and other data analysis and mining tools, which enhance the data’s utilization value. By leveraging the database’s robust scalability, the intention is to continue to collect and integrate passionfruit omics data in the PGD, providing comprehensive and in-depth support for passionfruit research. The PGD is freely accessible via http://passionfruit.com.cn .

Many geminiviruses, including members of the genus Begomovirus, produce a protein known as C4 or AC4. Whereas C4/AC4 typically consists of more than 80 amino acid residues, a few are much shorter. The significance of these shorter C4/AC4 proteins in viral infection and why the virus maintains their abbreviated length is not yet understood. The AC4 of the begomovirus Tomato leaf curl Hsinchu virus contains only 65 amino acids, but it extends to 96 amino acids when the natural termination codon is replaced with a normal codon. We discovered that both interrupting and extending AC4 were harmful to tomato leaf curl Hsinchu virus (ToLCHsV). The extended AC4 (EAC4) also showed a reduced ability to promote the infection of the heterologous virus Potato virus X than the wild-type AC4. When the wild-type AC4 was fused with yellow fluorescent protein (AC4-YFP), it was predominantly found in chloroplasts, whereas EAC4-YFP was mainly localized to the cell periphery. These results suggest that ToLCHsV's AC4 protein is important for viral infection, and the virus may benefit from the abbreviated length, because it may lead to chloroplast localization. [Graphic: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

IntroductionAccessory breast cancer (ABC) is an extremely rare condition, particularly the presence of triple-negative ABC with ipsilateral invasive in situ breast cancer. Binary breast tumors are controversial in terms of surgical methods and comprehensive treatment.Case presentationWe share the case of a 64-year-old postmenopausal woman who presented with an underarm mass for 3 months. Ultrasonography and computed tomography suggested possible breast cancer with axillary lymph node metastasis. The patient underwent a left modified radical mastectomy combined with axillary lymph node dissection. The postoperative pathology confirmed a binary tumor, prompting us to initiate comprehensive treatment.ConclusionWe present the treatment approach for a rare case of triple-negative para-breast cancer complicated with carcinoma in situ of the breast, hoping to contribute new therapeutic ideas for the treatment of this disease.

Chinese bayberry (Myrica rubra) is an economically significant fruit tree native to eastern Asia and widely planted in south-central China. However, studies about the viruses infecting M. rubra remain largely lacking. In the present study, we employed the metatranscriptomic method to identify viruses in M. rubra leaves exhibiting yellowing and irregular margin symptoms collected in Fuzhou, a city located in China’s Fujian province in the year 2022. As a consequence, a novel member of the genus Totivirus was identified and tentatively named “Myrica rubra associated totivirus 1” (MRaTV1). The genome sequencing of MRaTV1 was determined by overlapping reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The two deduced proteins encoded by MRaTV1 have the highest amino acid (aa) sequence identity to the coat protein (CP) and RNA-dependent RNA polymerase (RdRP) of Panax notoginseng virus A (PNVA), a member of the genus Totivirus within the family Totiviridae, at 49.7% and 61.7%, respectively. According to the results of the phylogenetic tree and the species demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV) for the genus Totivirus, MRaTV1 is considered a new member of the genus Totivirus.

Abstract Objective To investigate the efficacy and clinical application advantage of omental tamponade with vascular pedicle combined with Laparoscopic fenestration for the treatment of diaphragmatic hepatic cyst. Methods A total of 56 patients with diaphragmatic hepatic cysts underwent laparoscopic surgery in a single tertiary academic medical center from January 2010 to October 2020, including 21 patients (non-omental group) underwent laparoscopic fenestration of liver cysts, and 36 patients underwent laparoscopic liver cyst fenestration combined with vascular pedicle omentum tamponade (omental group). The general conditions and follow-up results of the two groups were compared and annalyzed. Results The operation time of the omental group was longer than that of the non-omental group (P = 1.358E-4). There was no significant difference in postoperative complications, postoperative laboratory values and hospital costs (P>0.05). The length of hospital stay in omental group was shorter than that in non-omental group (P = 0.034). In the omental group, recurrence occurred in 1 of 35 patients (4.65%) who were followeded up 12 months after surgery. In the non-omental group, of the 21 patients followed, 3 patients (14.28%) recurred 6 months after surgery, and 8 patients (38.10%) recurred 12 months after surgery. Conclusion It is an effective method to prevent the recurrence of diaphragmatic hepatic cyst after laparoscopic fenestration by packing the cyst with vascularized omentum.

Abstract Rice stripe virus (RSV) is one of the most important viral pathogens of rice in East Asia. The transcription of RSV is initiated by cap-snatching, a mechanism shared by influenza virus (IFV). This lends the possibility that antiviral compounds targeting the cap-snatching of IFV, many of which have been commercially available, may inhibit RSV transcription. A convenient and inexpensive system allowing researchers to test this idea, however, has been unavailable to date. Here, we show that purified RSV performs transcription in vitro and the transcription was readily detectable by nested reverse transcription-polymerase chain reaction (RT-PCR). With this system, we tested the effects of 2,4-dioxo-4-phenylbutanoic acid (DPBA) and pimodivir, two well-known IFV cap-snatching inhibitors, as well as ribavirin, a broad-spectrum antiviral compound whose targets remain elusive. In reaction mixtures containing 2.5 ng/µL of purified RSV, DPBA and pimodivir abolished RSV transcription at a concentration of 10 and 100 µM, respectively. In contrast, no inhibitory effect was detected from ribavirin, even at a concentration as high as 400 µM. These results suggest that at least some cap-snatching inhibitors of IFV are inhibitory to RSV transcription. These compounds, which can be identified with the experimental system described here, may serve as starting points in developing antivirals against RSV or related plant viruses.

Abstract Passionfruit (Passiflora edulis) is widely cultivated in tropical and subtropical regions around the world. Several viruses of the genus Potyvirus pose serious threat to passion fruit production. The origin, dispersal and evolution of these potyviruses, however, are poorly understood. Here, we investigated the genetic structure of telosma mosaic virus (TelMV), a potyvirus that infects passionfruit in East and Southeast Asia, after a survey of its incidence in passionfruit plants of China. The phylogeny inferred from 140 nucleotide sequences of the coat protein (CP) gene of TelMV, including 96 determined in this study, separated this virus into 4 clades. TelMV isolates from passionfruit were placed into Clade 1–3, while those from other plant species into Clade 4. Interestingly, TelMV isolates of passionfruit from Thailand were found in all the three clades of Clade 1–3, but those from China and Vietnam were found exclusively in Clade 1. Nevertheless, TelMV isolates within Clade 1 tended to cluster according to their geographical origin. Geographical populations from Thailand, Taiwan and Hainan islands of China showed significant genetic differences with one another and with those from Guangxi, Fujian, Guangdong, Yunnan and Jiangsu provinces of China. Altogether, these data suggest that several distinct TelMV clades had arisen from the passionfruit of Thailand, but only one of which was dispersed. In expanding its distribution, this clade of TelMV has undergone geography-associated evolution. Further studies on this hypothesis may shed new insights into mechanisms underlying the emergence of potyviral diseases in passionfruit plants.

Abstract Different hypotheses have been proposed to interpret the observed unusual ITS (internal transcribed spacer) sequences in Ophiocordyceps sinensis. The coexistence of diverged ITS paralogs in a single genome was previously shown by amplifying the ITS region from mono-ascospore isolates using specific primers designed for different ITS paralog groups. Among those paralogs, are AT-biased ITS sequences which were hypothesized to result from repeat-induced point mutation (RIP). This is a process that detects and mutates repetitive DNA and frequently leads to epigenetic silencing, and these mutations have been interpreted as pseudogenes. Here we investigate the occurrence and frequency of ITS pseudogenes in populations of O. sinensis using large-scale sampling, and discusses the implications of ITS pseudogenes for fungal phylogenetic and evolutionary studies. Our results demonstrate a wide distribution of ITS pseudogenes amongst different geographic populations, and indicate how ITS pseudogenes can contribute to the reconstruction of the evolutionary history of the species.

Visible light communication (VLC) based on light emitting diodes (LEDs) has attracted much attention because of its high data rate and energy efficiency. However, the shadowing caused by any mobile obstacles could block the light-of-sight (LoS) link which may have a dramatical effect on the indoor VLC channel state information (CSI). Instead of investigating the shadowing channel characteristics, we model the link blockages as the incomplete channel matrix with sparse missing elements and reconstruct the transmitted signal by the ℓ0-minimization with additional constraint on shadowing loss. However, the indoor VLC channel is highly correlated especially in cases with small emitter separation. To further improve the accuracy performance, we design the transmit beamforming to reduce the total coherence. Simulation results illustrate the effectiveness of the proposed signal recovery algorithm with incomplete channel and further significant enhancement via the proposed beamforming design.

Replication of positive-strand RNA viruses [(+)RNA viruses] takes place in membrane-bound viral replication complexes (VRCs). Formation of VRCs requires virus-mediated manipulation of cellular lipid synthesis. Here, we report significantly enhanced brome mosaic virus (BMV) replication and much improved cell growth in yeast cells lacking PAH1 (pah1Δ), the sole yeast ortholog of human LIPIN genes. PAH1 encodes Pah1p (phosphatidic acid phosphohydrolase), which converts phosphatidate (PA) to diacylglycerol that is subsequently used for the synthesis of the storage lipid triacylglycerol. Inactivation of Pah1p leads to altered lipid composition, including high levels of PA, total phospholipids, ergosterol ester, and free fatty acids, as well as expansion of the nuclear membrane. In pah1Δ cells, BMV replication protein 1a and double-stranded RNA localized to the extended nuclear membrane, there was a significant increase in the number of VRCs formed, and BMV genomic replication increased by 2-fold compared to wild-type cells. In another yeast mutant that lacks both PAH1 and DGK1 (encodes diacylglycerol kinase converting diacylglycerol to PA), which has a normal nuclear membrane but maintains similar lipid compositional changes as in pah1Δ cells, BMV replicated as efficiently as in pah1Δ cells, suggesting that the altered lipid composition was responsible for the enhanced BMV replication. We further showed that increased levels of total phospholipids play an important role because the enhanced BMV replication required active synthesis of phosphatidylcholine, the major membrane phospholipid. Moreover, overexpression of a phosphatidylcholine synthesis gene (CHO2) promoted BMV replication. Conversely, overexpression of PAH1 or plant PAH1 orthologs inhibited BMV replication in yeast or Nicotiana benthamiana plants. Competing with its host for limited resources, BMV inhibited host growth, which was markedly alleviated in pah1Δ cells. Our work suggests that Pah1p promotes storage lipid synthesis and thus represses phospholipid synthesis, which in turn restricts both viral replication and cell growth during viral infection.

Identification of the transcription start sites (TSSs) of a virus is of great importance to understand and dissect the mechanism of viral genome transcription but this often requires costly and laborious experiments. Many segmented negative-sense RNA viruses (sNSVs) cleave capped leader sequences from a large variety of mRNAs and use these cleaved leaders as primers for transcription in a conserved process called cap snatching. The recent developments in high-throughput sequencing have made it possible to determine most, if not all, of the capped RNAs snatched by a sNSV. Here, we show that rice stripe tenuivirus (RSV), a plant-infecting sNSV, co-infects Nicotiana benthamiana with two different begomoviruses and snatches capped leader sequences from their mRNAs. By determining the 5′ termini of a single RSV mRNA with high-throughput sequencing, the 5′ ends of almost all the mRNAs of the co-infecting begomoviruses could be identified and mapped on their genomes. The findings in this study provide support for the using of the cap snatching of sNSVs as a tool to map viral TSSs.

Viral pathogens are a major threat to rice production worldwide. Although RNA interference (RNAi) is known to mediate antiviral immunity in plant and animal models, the mechanism of antiviral RNAi in rice and other economically important crops is poorly understood. Here, we report that rice resistance to evolutionarily diverse viruses requires Argonaute18 (AGO18). Genetic studies reveal that the antiviral function of AGO18 depends on its activity to sequester microRNA168 (miR168) to alleviate repression of rice AGO1 essential for antiviral RNAi. Expression of miR168-resistant AGO1a in ago18 background rescues or increases rice antiviral activity. Notably, stable transgenic expression of AGO18 confers broad-spectrum virus resistance in rice. Our findings uncover a novel cooperative antiviral activity of two distinct AGO proteins and suggest a new strategy for the control of viral diseases in rice.

Rice dwarf virus (RDV) replicates in and is transmitted by a leafhopper vector in a persistent-propagative manner. Previous cytopathologic and genetic data revealed that tubular structures, constructed by the nonstructural viral protein Pns10, contain viral particles and are directly involved in the intercellular spread of RDV among cultured leafhopper cells. Here, we demonstrated that RDV exploited these virus-containing tubules to move along actin-based microvilli of the epithelial cells and muscle fibers of visceral muscle tissues in the alimentary canal, facilitating the spread of virus in the body of its insect vector leafhoppers. In cultured leafhopper cells, the knockdown of Pns10 expression due to RNA interference (RNAi) induced by synthesized dsRNA from Pns10 gene strongly inhibited tubule formation and prevented the spread of virus among insect vector cells. RNAi induced after ingestion of dsRNA from Pns10 gene strongly inhibited formation of tubules, preventing intercellular spread and transmission of the virus by the leafhopper. All these results, for the first time, show that a persistent-propagative virus exploits virus-containing tubules composed of a nonstructural viral protein to traffic along actin-based cellular protrusions, facilitating the intercellular spread of the virus in the vector insect. The RNAi strategy and the insect vector cell culture provide useful tools to investigate the molecular mechanisms enabling efficient transmission of persistent-propagative plant viruses by vector insects.

Cell-to-cell movement is essential for plant viruses to systemically infect host plants. Plant viruses encode movement proteins (MP) to facilitate such movement. Unlike the well-characterized MPs of DNA viruses and single-stranded RNA (ssRNA) viruses, knowledge of the functional mechanisms of MPs encoded by double-stranded RNA (dsRNA) viruses is very limited. In particular, many studied MPs of DNA and ssRNA viruses bind non-specifically ssRNAs, leading to models in which ribonucleoprotein complexes (RNPs) move from cell to cell. Thus, it will be of special interest to determine whether MPs of dsRNA viruses interact with genomic dsRNAs or their derivative sRNAs. To this end, we studied the biochemical functions of MP Pns6 of Rice dwarf phytoreovirus (RDV), a member of Phytoreovirus that contains a 12-segmented dsRNA genome. We report here that Pns6 binds both dsRNAs and ssRNAs. Intriguingly, Pns6 exhibits non-sequence specificity for dsRNA but shows preference for ssRNA sequences derived from the conserved genomic 5'- and 3'-terminal consensus sequences of RDV. Furthermore, Pns6 exhibits magnesium-dependent ATPase activities. Mutagenesis identified the RNA binding and ATPase activity sites of Pns6 at the N- and C-termini, respectively. Our results uncovered the novel property of a viral MP in differentially recognizing dsRNA and ssRNA and establish a biochemical basis to enable further studies on the mechanisms of dsRNA viral MP functions.

Marine viruses shape microbial communities with the most genetic diversity in the sea by multiple genetic exchanges and infect multiple marine organisms. Here we provide proof from experimental infection that abalone shriveling syndrome-associated virus (AbSV) can cause abalone shriveling syndrome. This malady produces histological necrosis and abnormally modified macromolecules (hemocyanin and ferritin). The AbSV genome is a 34.952-kilobase circular double-stranded DNA, containing putative genes with similarity to bacteriophages, eukaryotic viruses, bacteria and endosymbionts. Of the 28 predicted open reading frames (ORFs), eight ORF-encoded proteins have identifiable functional homologues. The 4 ORF products correspond to a predicted terminase large subunit and an endonuclease in bacteriophage, and both an integrase and an exonuclease from bacteria. The other four proteins are homologous to an endosymbiont-derived helicase, primase, single-stranded binding (SSB) protein, and thymidylate kinase, individually. Additionally, AbSV exhibits a common gene arrangement similar to the majority of bacteriophages. Unique to AbSV, the viral genome also contains genes associated with bacterial outer membrane proteins and may lack the structural protein-encoding ORFs. Genomic characterization of AbSV indicates that it may represent a transitional form of microbial evolution from viruses to bacteria.