Deciphering the virome of Chunkung (Cnidium officinale) showing dwarfism-like symptoms via a high-throughput sequencing analysis.

BACKGROUND: Viruses have notable effects on agroecosystems, wherein they can adversely affect plant health and cause problems (e.g., increased biosecurity risks and economic losses). However, our knowledge of their diversity and interactions with specific host plants in ecosystems remains limited. To enhance our understanding of the roles that viruses play in agroecosystems, comprehensive analyses of the viromes of a wide range of plants are essential. High-throughput sequencing (HTS) techniques are useful for conducting impartial and unbiased investigations of plant viromes, ultimately forming a basis for generating further biological and ecological insights. This study was conducted to thoroughly characterize the viral community dynamics in individual plants. RESULTS: An HTS-based virome analysis in conjunction with proximity sampling and a tripartite network analysis were performed to investigate the viral diversity in chunkung (Cnidium officinale) plants. We identified 61 distinct chunkung plant-associated viruses (27 DNA and 34 RNA viruses) from 21 known genera and 6 unclassified genera in 14 known viral families. Notably, 12 persistent viruses (7 DNA and 5 RNA viruses) were exclusive to dwarfed chunkung plants. The detection of viruses from the families Partitiviridae, Picobirnaviridae, and Spinareoviridae only in the dwarfed plants suggested that they may contribute to the observed dwarfism. The co-infection of chunkung by multiple viruses is indicative of a dynamic and interactive viral ecosystem with significant sequence variability and evidence of recombination. CONCLUSIONS: We revealed the viral community involved in chunkung. Our findings suggest that chunkung serves as a significant reservoir for a variety of plant viruses. Moreover, the co-infection rate of individual plants was unexpectedly high. Future research will need to elucidate the mechanisms enabling several dozen viruses to co-exist in chunkung. Nevertheless, the important insights into the chunkung virome generated in this study may be relevant to developing effective plant viral disease management and control strategies.

Complete nucleotide sequence of chrysanthemum virus D, a polero-like virus.

A putative new polerovirus, named "chrysanthemum virus D" (ChVD), was detected in a Chrysanthemum morifolium plant in South Korea. The virus was identified by high-throughput sequencing and confirmed by reverse transcription polymerase chain reaction. The entire ChVD genome is composed of 5,963 nucleotides and contains seven open reading frames (ORF0-5 and ORF3a), which are arranged similarly to those of other poleroviruses. These ORFs encode the putative proteins P0-5 and P3a, respectively. Pairwise amino acid sequence comparisons showed that the ChVD P0-5 and P3a proteins have 30.45-75% sequence identity to the corresponding proteins of other members of the genus Polerovirus. Since one of the species demarcation criteria for the genus Polerovirus is > 10% difference in the amino acid sequence of any gene product, the sequence comparisons indicate that ChVD represents a new species in this genus. Phylogenetic analysis of the P1-P2 and P3 amino acid sequences further indicate that ChVD is a novel polerovirus.

Complete genome sequence of a new putative member of the genus Pelarspovirus that infects Quercus aliena Blume in South Korea.

The complete nucleotide sequence of a newly discovered virus infecting Quercus aliena Blume, tentatively named "quercus leafroll virus" (QLRV), was determined through high-throughput and Sanger sequencing. The sequence comprises 3,940 nucleotides, has five open reading frames, and has a typical pelarspovirus genome organization, with neither 3' polyadenylation nor a 5' cap. The proteins encoded by QLRV share 17.9 to 44.2% amino acid sequence identity with known pelarspovirus proteins. The highest amino acid sequence identity values for the RNA-dependent RNA polymerase (RdRp) and coat protein were 67.5% and 55.2%, respectively, which are below the current thresholds for pelarspovirus species demarcation. On the basis of these results, we propose classifying QLRV as a new member of the genus Pelarspovirus, family Tombusviridae.

Molecular characterization of a novel umbra-like virus from Thuja orientalis (arborvitae) in South Korea.

A novel umbra-like virus was identified in arborvitae in South Korea using RNA sequencing (RNA-seq). The virus identified was tentatively named "arborvitae umbra-like virus" (AULV) and contained a 4,300-nucleotide genome organized into four non-structural open reading frames (ORFs). Cloning and Sanger sequencing were used to confirm the viral contig sequence and determine the size of the genome. Genome analysis indicated that ORF2 encodes an RNA-dependent RNA polymerase that is probably expressed through ribosomal frameshifting. ORF3 encodes a putative long-distance movement protein, while the functions of ORFs 1 and 4 are unknown. The virus lacks a coat protein gene. The genome of AULV shares 27.3%-48.4% nucleotide sequence identity with closely related umbraviruses. Phylogenetic analysis based on the complete genome sequences and amino acid sequences of the RNA-dependent RNA polymerase revealed that AULV forms a monophyletic lineage with Guiyang paspalum paspaloides tombus-like virus (GPpTV1). We suggest that AULV is a novel umbra-like virus belonging to the family Tombusviridae.

First report of Kalanchoe Latent Virus naturally infecting common bean (Phaseolus vulgaris L.) in South Korea.

The common bean (Phaseolus vulgaris; family: Fabaceae) is an economically and nutritionally important food crop worldwide (Ganesan et al. 2017). In 2021, several plants collected from different provinces in South Korea had symptoms of viral infections (e.g., mild yellow-greenish speckling, stunting, crinkling, and deformed leaves). To identify the causal pathogens, total RNA was isolated from pooled leaf tissues from all samples (n = 29) for paired-end high-throughput sequencing (HTS). The cDNA library was constructed after eliminating ribosomal RNA using the TruSeq RNA Sample Prep Kit and then sequenced using the Illumina NovaSeq 6000 platform (Macrogen, Korea). The 297,868,156 paired-end clean reads (150 nt) were de novo assembled using Trinity with default parameters. BLASTx was used for the contig analysis, which revealed the pooled samples were infected with several plant viruses (e.g., turnip mosaic virus, zucchini yellow mosaic virus, cucumber mosaic virus, lily mottle virus). Notably, the assembled contigs included a single viral contig (8,472 nt) comprising the nearly complete KLV genome (HTS mean coverage: 39.46%). Kalanchoe latent virus (KLV; genus: Carlavirus; family: Betaflexiviridae) has been detected in Kalanchoë blossfeldiana (Hearon 1982), Chenopodium quinoa (Dinesen et al. 2009), and Graptopetalum paraguayense (Sorrentino et al. 2017). The sequence was most similar (96.28% nucleotide identity; 99% query coverage) to KLV isolate DSMZ PV-0290 (GenBank: OP525283) from Denmark. The contig sequence was validated via reverse transcription-polymerase chain reaction (RT-PCR) using total RNA extracted from the 29 individually stored samples and nine primer sets specific for the KLV contig. All nine contig-specific overlapping fragments were amplified from only a P. vulgaris plant with mild yellowing mosaic symptoms collected on July 6, 2021, in Jeongseon County, South Korea. Additionally, 5' and 3' rapid amplification of cDNA ends (RACE)-specific primers were designed for the KLV contig sequence to determine the terminal ends of the genome of the South Korean KLV isolate using the 5'/3' RACE System (Invitrogen, Carlsbad, CA, USA). All of the amplified and overlapping fragments were cloned into the RBC T&A Cloning Vector (RBC Bioscience, Taipei, Taiwan) and sequenced using the Sanger method. The obtained full-length genomic sequence of the KLV isolate (KLV-SK22) was 8,517 nt long and was deposited in GenBank OQ718816. According to the BLASTn analysis, KLV-SK22 was highly similar (96.30% sequence identity; 100% query coverage) to the DSMZ PV-0290 isolate. Phylogenetic trees constructed on the basis of coat protein and RNA-dependent RNA polymerase amino acid sequences revealed that KLV-SK22 is closely related to the DSMZ PV-0290 and PV-0290B isolates from Denmark, respectively. At the genome and gene levels, the individual sequence identities between the carlaviruses and other KLV isolates were 96.29% to 100% (Adams et al. 2004). Additionally, an RT-PCR analysis using detection primers specific for KLV-SK22 did not detect KLV in 15 samples (P. vulgaris = 3, Glycine max = 8, Pueraria montana = 2, Trifolium repens = 1, and Vigna angularis = 1) randomly collected from different regions in South Korea. Based on these results, KLV infection may not be widespread at this time in South Korea. To the best of our knowledge, this is the first report of KLV in P. vulgaris in South Korea or elsewhere. Our findings will aid future research on the epidemiology and long-term management of KLV-related diseases.

Effect of supercooling on storage ability of different beef cuts in comparison to traditional storage methods.

The effect of supercooling on different beef cuts was evaluated compared with traditional storage methods. Beef striploins and topsides were stored under freezing, refrigeration, or supercooling conditions and their storage ability and quality were analyzed during 28 days of storage. The total aerobic bacteria, pH, and volatile basic nitrogen were higher in the supercooled beef than in the frozen beef, but lower than in the refrigerated one, regardless of the type of cut. In addition, the discoloration of frozen and supercooled beef was slower than that of refrigerated beef. The results in storage stability and color indicate that supercooling can prolong the shelf-life of beef compared to refrigeration due to its temperature characteristic. In addition, supercooling minimized the problems of freezing and refrigeration, including ice crystal formation and enzyme-based deterioration; therefore, the qualities of topside and striploin were less affected. Collectively, these results indicate that supercooling can be a beneficial storage method for extending the shelf-life of different beef cuts.

Effect of cutting time and cooking temperature on physicochemical properties of chicken breast meat emulsion sausage with olive oil.

This study aimed to optimize the emulsification of olive oil in chicken sausage production at varying cutting times (30, 45, and 60 s) and cooking temperatures (63, 73, and 83°C). Pork backfat sausages were prepared as controls, using the same variables. The quality attributes of the sausages were analyzed, and the distribution of lipid droplets was identified using confocal laser scanning microscopy. The combinations of cutting time and cooking temperature in olive oil sausages showed different emulsifying characteristics. Meat emulsion with olive oil at a cutting time of 60 s and cooking temperature of 73°C showed the highest emulsion stability with lowest water and lipid loss (2.49%, P < 0.05). The pH values were lower for olive oil samples than for the controls (5.9 vs. 6.2, P < 0.05). Cutting time of 60 s and cooking temperature of 73°C generated higher hardness, gumminess, and chewiness in olive oil sausages (P < 0.05). The replacement of pork backfat with olive oil resulted in a higher b*, C*, and h values, as well as lower lipid oxidation (P < 0.05). In addition, microstructural images exhibited a finer distribution of lipid droplets in olive oil sausages with a cutting time of 60 s. In conclusion, chicken sausage at a cooking temperature of 73°C and cutting time of 60 s was optimal for producing sausages with olive oil. Given the condition, the sausages produced from olive oil had better emulsion and oxidative stability than sausages produced from pork backfat.

Effect of Temperature Abuse on Quality and Metabolites of Frozen/Thawed Beef Loins.

The objective of this study was to examine the effect of temperature abuse prior to cold storage on changes in quality and metabolites of frozen/thawed beef loin. The aerobic packaged samples were assigned to three groups: refrigeration (4°C) (CR); freezing (-18°C for 6 d) and thawing (20±1°C for 1 d), followed by refrigeration (4°C) (FT); temperature abuse (20°C for 6 h) prior to freezing (-18°C for 6 d) and thawing (20±1°C for 1 d), followed by refrigeration (4°C) (AFT). FT and AFT resulted in higher volatile basic nitrogen (VBN) values than CR (p<0.05), and these values rapidly increased in the final 15 d. Cooking loss decreased significantly with an increase in the storage period (p<0.05). In addition, cooking loss was lower in the FT and AFT groups than in the CR owing to water loss after storage (p<0.05). A scanning electron microscope (SEM) revealed that frozen/thawed beef samples were influenced by temperature abuse in the structure of the fiber at 15 d. Metabolomic analysis showed differences among CR, FT, and AFT from partial least square discriminant analysis (PLS-DA) based on proton nuclear magnetic resonance (1H NMR) profiling. The treatments differed slightly, with higher FT than AFT values in several metabolites (phenylalanine, isoleucine, valine, betaine, and tyrosine). Overall, temperature abuse prior to freezing and during thawing of beef loin resulted in accelerated quality changes.

Efficacy of Bone-Anchored Hearing Aids in Single-Sided Deafness: A Systematic Review.

OBJECTIVES: Bone-anchored hearing aids (BAHAs) have been known to partially restore some of the functions lost in subjects with single-sided deafness (SSD). Our aims in this systemic review were to analyze the present capabilities of BAHAs in the context of SSD, and to evaluate the efficacy of BAHAs in improving speech recognition in noisy conditions, sound localization, and subjective outcomes. DESIGN: A systematic search was undertaken until August 2015 by two independent reviewers, with disagreements resolved by consensus. Among 286 references, we analyzed 14 studies that used both subjective and objective indicators to assess the capabilities of a total of 296 patients in the unaided and aided situations. RESULTS: Although there was "no benefit" of BAHA implantation for sound localization, BAHAs certainly improved subjects' speech discrimination in noisy circumstances. In the six studies that dealt with sound localization, no significant difference was found after the implantation. Twelve studies showed the benefits of BAHAs for speech discrimination in noise. Regarding subjective outcomes of using the prosthesis in patients with SSD (abbreviated profile of hearing aid benefit [APHAB] and the Glasgow hearing aid benefit profile [GHABP], etc.), we noticed an improvement in the quality of life. CONCLUSIONS: This systematic review has indicated that BAHAs may successfully rehabilitate patients with SSD by alleviating the hearing handicap to a certain degree, which could improve patients' quality of life. This report has presented additional evidence of effective auditory rehabilitation for SSD and will be helpful to clinicians counseling patients regarding treatment options for SSD.