Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes.

It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to the strong but ineffective inflammatory response that characterizes severe Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse cell types, including cells without angiotensin-converting enzyme 2 receptors necessary for infection. Proteolytic degradation of SARS-CoV-2 virions is a milestone in host viral clearance, but the impact of remnant viral peptide fragments from high viral loads is not known. Here, we examine the inflammatory capacity of fragmented viral components from the perspective of supramolecular self-organization in the infected host environment. Interestingly, a machine learning analysis to SARS-CoV-2 proteome reveals sequence motifs that mimic host antimicrobial peptides (xenoAMPs), especially highly cationic human cathelicidin LL-37 capable of augmenting inflammation. Such xenoAMPs are strongly enriched in SARS-CoV-2 relative to low-pathogenicity coronaviruses. Moreover, xenoAMPs from SARS-CoV-2 but not low-pathogenicity homologs assemble double-stranded RNA (dsRNA) into nanocrystalline complexes with lattice constants commensurate with the steric size of Toll-like receptor (TLR)-3 and therefore capable of multivalent binding. Such complexes amplify cytokine secretion in diverse uninfected cell types in culture (epithelial cells, endothelial cells, keratinocytes, monocytes, and macrophages), similar to cathelicidin's role in rheumatoid arthritis and lupus. The induced transcriptome matches well with the global gene expression pattern in COVID-19, despite using <0.3% of the viral proteome. Delivery of these complexes to uninfected mice boosts plasma interleukin-6 and CXCL1 levels as observed in COVID-19 patients.

Complete genome sequence of seed-transmitted soybean yellow mottle mosaic virus from soybeans in Korea.

Soybean yellow mottle mosaic virus (SYMMV), a member of the genus Gammacarmovirus, remains poorly understood in terms of its transmission pathway. This study reveals the complete genome sequence of a seed-transmitted isolate, ST-HB56, contributing to the understanding of SYMMV's ecological dynamics.

Complete genome sequence of soybean geminivirus A in soybean in Korea.

Soybean geminivirus A (SGVA), a member of the family Geminiviridae, was detected in a survey of early-stage soybean. The complete genome sequence of SGVA isolate Habin was determined, revealing its characteristics and similarity to Korean and Chinese isolates. This study contributes to understanding the impact of SGVA on soybean production.

First Report of Olive Mild Mosaic Virus in Imported Tulips (Tulipa gesneriana) in Korea.

Tulip cultivation in Korea primarily uses imported bulbs due to the absence of domestic production. To ensure safety and sustainability, Korean authorities have implemented strict phytosanitary measures for five viruses: arabis mosaic virus, tobacco necrosis virus, tobacco ringspot virus, tomato black ring virus, and tomato bushy stunt virus. In April 2021, 86 tulip plants presented symptoms such as chlorotic mottle, mosaic, streak, stripe, yellowing of the leaves, and color breaking on flowers. These samples were collected to investigate the incidence of viruses in four Korean provinces (Gangwon, Gyeongbuk, Gyeongnam, and Chungnam). The leaves and petals from each individual sample (10 mg each) were pooled and ground using liquid nitrogen. Total RNA was extracted using a Maxwell® 16 LEV Plant RNA Kit (Promega, Madison, USA). A cDNA library was constructed using TruSeq Standard Total RNA with Ribo - Zero (Illumina, San Diego, USA) and sequenced on an Illumina NovaSeq 6000 platform (Macrogen, Seoul, Korea) with 100-bp paired-end reads. Trinity software identified tulip breaking virus (TBV), tulip virus X (TVX), and lily symptomless virus (LSV), which are known to occur in Korea (Bak et al. 2023) by de novo assembly of 628 million reads into 498,795 contigs. The contigs were annotated as previously described (Bak et al. 2022). Moreover, a contig (ON758350) related to olive mild mosaic virus (OMMV; genus Alphanecrovirus, family Tombusviridae) was identified through BLASTn analysis. This contig had a 99.27% nucleotide (nt) identity to OMMV PPO-L190209 (KU641010), which was assembled from 201,346 reads and spanned 3,713 bp. To confirm the presence of OMMV, a primer pair (5'-GAATGTCTGGCGTTAAGCG-3'/5'-GTGTCCTGCGCATCATACAC-3') was designed to amplify a 797-bp fragment of the coat protein gene. In RT-PCR, 31.4% (27/86) of samples were positive for OMMV and coinfected with TBV or TBV+LSV. Coinfection with TBV led to chlorotic mottling and stripes, whereas triple coinfection with TBV+LSV produced distinct yellow streaks and mosaic within the lesion boundaries. In contrast, solely TBV infection did not produce such symptoms. The samples infected with OMMV were exclusively collected from Gangwon and Gyeongnam. In each province, an RT-PCR amplicon was cloned, and subsequently sequenced (Bioneer, Daejeon, Korea). The obtained sequences were named CC (OM243091) and GS (OM243092), and they shared 98.6% and 98.9% identity with PPO-L190209 (KU641010), respectively. A bioassay was conducted using a leaf infected with OMMV CC and TBV to inoculate 13 indicator species in triplicate, including Capsicum annuum, Chenopodium amaranticolor, C. quinoa, Cucumis sativus, Nicotiana benthamiana, N. clevelandii, N. glutinosa, N. occidentalis, N. rustica, N. tabacum, Solanum lycopersicum, Tetragonia tetragonioides, and Tulipa gesneriana. The RT-PCR revealed positivity only for OMMV in the upper leaves of N. clevelandii, while all other species were negative with no symptoms. To our knowledge, this is the first report of OMMV occurring in tulips grown from imported bulbs in Korea, with no other known natural hosts such as olive tree (Cardoso et al. 2004), spinach (Gratsia et al. 2012), and corn salad (Verdin et al. 2018). The Korean OMMV isolates exhibited a high nt identity with the foreign isolate, and the samples were collected from farms that rely entirely on bulb imports for cultivation. These suggest that the outbreak of OMMV was likely caused by imported bulbs.

Complete Genome Sequences of Two Apple Stem Grooving Viruses in Cnidium officinale in Korea.

We determined the whole-genome sequences of two apple stem grooving viruses (ASGV) detected in infected Cnidium officinale plants. The analyzed ASGV genomes were 6,494 nucleotides long and encoded two overlapping open reading frames. Phylogenetic analysis revealed the two ASGV isolates to be most closely related to the ASGV isolate Xinjiang-3.

First report of Tulip Virus X infecting tulip (Tulipa gesneriana) in Korea.

Tulip virus X (tulip virus X, TVX) is a member of the genus Potexvirus (family Alphaflexiviridae) and is a positive single-stranded RNA virus. TVX was described first in Scotland (Mowat 1982), followed by several countries (Yamaji et al. 2001; Tzanetakis et al. 2005; Ward et al. 2008; Dees et al. 2011; Sochacki and Komorowska 2012; Wylie et al. 2019). In April 2021, 86 whole tulip plants showing viral symptoms in leaves (mosaic, yellowing, and malformation) and flowers (color breaking) were collected in Chilgok, Chuncheon, Goseong, Yecheon and Yesan, Korea. Furthermore, high-throughput sequencing was performed to identify viruses that infect tulips in Korea. Total RNA was extracted from pooled the leaves and petals using a Maxwell® 16 LEV Plant RNA Kit (Promega, Madison, USA). We constructed a single library using the TruSeq Stranded Total RNA LT Sample Prep Kit for Plant (Illumina, San Diego, USA). The library was 100 bp paired-end sequenced using Illumina's NovaSeq 6000 (Macrogen, Seoul, Korea) and was assembled de novo using Trinity software version trinityrnaseq_r20140717, with default parameters. The contigs were annotated as in previous study (Lee et al. 2020), revealing a single contig each related to TVX, lily symptomless virus (LSV), and tulip breaking virus (TBV) was generated from 648 million total reads. The TVX-related contig (GenBank ON205948) consisting of 6,076 bp showed 99.52% nucleotide identity (6027/6056 bp) with TVX-J (GenBank AB066288). We conducted an RT-PCR assay to validate the presence of viruses with specific primers as TVX-F5093/R5624 (5'-CTATCCGGACTCATTCTACTTC/GTGCGTTCCAGATAAGCTTG-3'), LSV-F7013/R7338 (5'-CTTGGTCGACAGGGACATAAC/GATTGGAATTGTGCTTTTCAGC-3'), and TBV-F7515/R8116 (5'-GTGTGTCATGGATGATTGTTG/CAACTGATTTGCTACCGCTAG-3'). Consequently, TVX were detected in 13 of 86 samples. Moreover, LSV and TBV were detected in 15 and 26 samples, respectively. However, the yellowing and mosaic observed in the TVX infected samples were not observed in the LSV and TBV infected samples. Subsequently, two TVX amplicons were selected, cloned and sequenced. The obtained sequences were 532 bp and were named YS24 and YS38 (GenBank LC664027 and LC664028), respectively. The Korean isolates showed 98.68% (525/532 bp) and 99.62% (530/532 bp) identity with Australian isolate (GenBank MH886522) in BLASTn analysis. To bioassay for TVX, the infected tulip leaf tissue from which YS24 was obtained was used to sap-inoculate, in triplicates, 15 species of indicator plants (Nicotiana benthamiana, N. clevelandii, N. debneyi, N. glutinosa, N. rustica, N. tabacum, Datura stramonium, Glycine max, Phaseolus vulgaris, Chenopodium amaranticolor, C. quinoa, Cucumis sativus, Cu. melo, Gomphrena globosa, and Tetragonia tetragonioides). After 14 days of inoculation, we observed distinct chlorotic spots on inoculated and upper leaves of C. quinoa, but no symptoms were observed in other indicator plants. In RT-PCR assay using TVX-specific primers, only C. quinoa showed a positive reaction. In previous studies, C. amaranticolor, C. quinoa, G. globosa, and N. benthamiana were known as the experimental host of TVX (Dees et al. 2011; Tzanetakis et al. 2005), but only C. quinoa was confirmed to be susceptible to the Korean isolate. Furthermore, transmission electron microscopy revealed typical flexuous rod-shaped viral particles in the inoculated C. quinoa. To our knowledge, this is the first report of TVX infecting tulips in Korea.

The Detection of Plant Viruses in Korean Ginseng (Panax ginseng) through RNA Sequencing.

Korean ginseng (Panax ginseng) is a dicotyledonous, medicinal, perennial plant belonging to the genus Panax of the family Araliaceae. We investigated the occurrence and incidence of plant viruses in Panax ginseng in Korea. A total of 656 leaf samples were combined into one and total RNA was extracted from the polled sample, using RNA sequencing (RNA-Seq), a metatranscriptome analysis of the plant virome was conducted. The virus present in Panax ginseng was confirmed by reverse transcription polymerase chain reaction (RT-PCR) assay using virus-specific primers. In RNA-Seq data analysis, the multiplication protein of four viral contigs including Aristotelia chilensis virus 1 (AcV1), Turnip mosaic virus (TuMV), Watermelon mosaic virus (WMV), and Tobamovirus multiplication protein were discovered. From our metatranscriptome analysis and RT-PCR assay, TuMV and WMV were detected, whereas the three viruses reported in China such as tomato yellow leaf curl China virus; panax notoginseng virus A; and panax virus Y were not found in this study. The distribution of domestic ginseng viruses seems different from that recorded in China. Overall, this is the first plant virome analysis of Panax ginseng in Korea.

Aryl-hydrocarbon receptor binding and the incidence of type 2 diabetes: the Brazilian Longitudinal Study of Adult Health (ELSA-Brasil).

BACKGROUND: Persistent organic pollutants (POPs) may cause diabetes, in part through aryl hydrocarbon receptor (AhR) binding. Ensuing mitochondrial dysfunction is postulated to mediate this effect. We aim to investigate the association of POPs with incident diabetes indirectly by bio-assaying AhR ligand bioactivity and intracellular ATP level induced by participant serum samples. METHODS: In incident case-cohort analyses of one ELSA-Brasil center, 1605 eligible subjects without diabetes at baseline had incident diabetes ascertained by self-report, medication use, OGTT or HbA1c at follow-up 4 years later. We assayed AhR ligand bioactivity (AhRL) and intracellular ATP content, the latter reflecting the presence of mitochondria-inhibiting substances (MIS), following incubation of recombinant mouse Hepa1c1c7 cells with participant sera for 71 incident diabetes cases and 472 randomly selected controls. RESULTS: In multiply-adjusted proportional hazards regression analyses, those with above-median AhRL and below-median MIS-ATP had 69 and 226% greater risk of developing diabetes (HR = 1.69; 95%CI 1.01-2.83 and 3.26; 1.84-5.78), respectively. A strong interaction was seen between the two exposures (HRhigh AhRL/low MIS-ATP vs. low AhRL/high MIS-ATP = 8.15; 2.86-23.2). CONCLUSION: The markedly increased incidence of diabetes seen in those with both higher AhR ligand bioactivity and increased mitochondrial inhibition supports the hypothesis that widespread POPs exposure contributes to the diabetes epidemic.

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi.

Mucormycosis is a life-threatening infection caused by Mucorales fungi. Here we sequence 30 fungal genomes, and perform transcriptomics with three representative Rhizopus and Mucor strains and with human airway epithelial cells during fungal invasion, to reveal key host and fungal determinants contributing to pathogenesis. Analysis of the host transcriptional response to Mucorales reveals platelet-derived growth factor receptor B (PDGFRB) signaling as part of a core response to divergent pathogenic fungi; inhibition of PDGFRB reduces Mucorales-induced damage to host cells. The unique presence of CotH invasins in all invasive Mucorales, and the correlation between CotH gene copy number and clinical prevalence, are consistent with an important role for these proteins in mucormycosis pathogenesis. Our work provides insight into the evolution of this medically and economically important group of fungi, and identifies several molecular pathways that might be exploited as potential therapeutic targets.

The genome sequence of four isolates from the family Lichtheimiaceae.

This study reports the release of draft genome sequences of two isolates of Lichtheimia corymbifera and two isolates of L. ramosa. Phylogenetic analyses indicate that the two L. corymbifera strains (CDC-B2541 and 008-049) are closely related to the previously sequenced L. corymbifera isolate (FSU 9682) while our two L. ramosa strains CDC-B5399 and CDC-B5792 cluster apart from them. These genome sequences will further the understanding of intraspecies and interspecies genetic variation within the Mucoraceae family of pathogenic fungi.

Isavuconazole therapy protects immunosuppressed mice from mucormycosis.

We studied the in vitro and in vivo efficacies of the investigational drug isavuconazole against mucormycosis due to Rhizopus delemar. Isavuconazole was effective, with MIC and minimal fungicidal concentration (MFC) values ranging between 0.125 and 1.00 µg/ml. A high dose of isavuconazole prolonged the survival time and lowered the tissue fungal burden of cyclophosphamide/cortisone acetate-treated mice infected with R. delemar and was as effective as a high-dose liposomal amphotericin B treatment. These results support the further development of this azole against mucormycosis.

NDV-3 protects mice from vulvovaginal candidiasis through T- and B-cell immune response.

We have previously reported that vaccination with rAls3p-N protein of Candida albicans, formulated with alum adjuvant (also designated as NDV-3) protects immunocompetent mice from, lethal disseminated candidiasis and mucosal oropharyngeal candidiasis. NDV-3 vaccine was recently, tested in a Phase 1 clinical trial and found to be safe, well-tolerated, and induced robust humoral and, cellular immune responses with increased interferon (IFN)-gamma and interleukin (IL)-17 secretion. In preparation for a Phase 2 clinical trial against vulvovaginal candidiasis (VVC), we evaluated NDV-3, efficacy in a murine VVC model. Here, NDV-3 induced a strong immune response characterized by high, anti-rAls3p-N serum IgG and vaginal IgA titers. Furthermore, moderate doses of the vaccine (a range of 1-30µg given subcutaneously [SQ] or 0.3-10µg given intramuscularly [IM]) elicited a 10-1000 fold, decrease in vaginal fungal burden vs. control (mice injected with alum adjuvant alone) in both inbred, and outbred mice infected with different clinical C. albicans isolates. Additionally, NDV-3 required both, T and B lymphocytes for efficacy in reducing C. albicans tissue burden, which is followed by a reduction, in neutrophil influx to the affected site. Finally, anti-rAls3p-N antibodies enhanced the ex vivo killing, of C. albicans by neutrophils primed with IFN-gamma. These data indicate that NDV-3 protects mice, from VVC by a mechanism that involves the concerted priming of both humoral and adaptive immune, responses.

Efficacy of liposomal amphotericin B and posaconazole in intratracheal models of murine mucormycosis.

Mucormycosis is a life-threatening fungal infection almost uniformly affecting diabetics in ketoacidosis or other forms of acidosis and/or immunocompromised patients. Inhalation of Mucorales spores provides the most common natural route of entry into the host. In this study, we developed an intratracheal instillation model of pulmonary mucormycosis that hematogenously disseminates into other organs using diabetic ketoacidotic (DKA) or cyclophosphamide-cortisone acetate-treated mice. Various degrees of lethality were achieved for the DKA or cyclophosphamide-cortisone acetate-treated mice when infected with different clinical isolates of Mucorales. In both DKA and cyclophosphamide-cortisone acetate models, liposomal amphotericin B (LAmB) or posaconazole (POS) treatments were effective in improving survival, reducing lungs and brain fungal burdens, and histologically resolving the infection compared with placebo. These models can be used to study mechanisms of infection, develop immunotherapeutic strategies, and evaluate drug efficacies against life-threatening Mucorales infections.

Diabetic murine models for Acinetobacter baumannii infection.

OBJECTIVES: Extremely drug-resistant (XDR; i.e. resistant to all antibiotics except colistin or tigecycline) Acinetobacter baumannii has emerged as one of the most common and highly antibiotic-resistant causes of infection. Diabetes is a risk factor for acquisition of and worse outcomes from A. baumannii infection. We sought to develop diabetic mouse models of A. baumannii bacteraemia and pneumonia and validate these models by comparing the efficacy of antibiotic treatment in these models with the established neutropenic mouse models. METHODS: Diabetic or neutropenic mice were infected via intravenous inoculation or inhalation in an aerosol chamber with an XDR A. baumannii. Treatment with colistin started 24 h after infection and continued daily for 7 days. Survival served as the primary endpoint while tissue bacterial burden and histopathological examination served as secondary endpoints. RESULTS: Lethal infection was achieved for the neutropenic and diabetic mice when infected intravenously or via inhalation. Neutropenic mice were more susceptible to infection than diabetic mice in the pneumonia model and equally susceptible in the bacteraemia model. Both models of bacteraemia were sensitive enough to detect virulence differences among different clinical strains of A. baumannii. In the pneumonia model, colistin treatment was effective in improving survival, reducing lung bacterial burden and histologically resolving the infection compared with placebo only in diabetic mice. CONCLUSIONS: We developed novel models of A. baumannii bacteraemia and pneumonia in diabetic mice. These models can be used to study mechanisms of infection, develop immunotherapeutic strategies and evaluate drug efficacies against highly lethal A. baumannii infections.

Complete Repair of Coarctation of the Aorta and a Ventricular Septal Defect in a 1,480 g Low Birth Weight Neonate.

Although outcomes of neonatal cardiac surgery have dramatically improved in the last two decades, low body weight still constitutes an important risk factor for morbidity and mortality. In particular, cardiac surgery in neonates with very low birth weight (≤1.5 kg) is carried out with greater risk because most organ systems are immature. We report here on a successful case of early one-stage total repair of coarctation of the aorta and a ventricular septal defect in a 1,480 gram neonate.

Outcomes of Sleeve Lobectomy versus Pneumonectomy for Lung Cancer.

BACKGROUND: Sleeve lobectomy for lung cancer in close proximity to or involving the carina is widely accepted. Operative morbidity and mortality rates, recurrence, and survival rates have varied considerably across studies. MATERIALS AND METHODS: From March of 2005 to July of 2010, sleeve lobectomy was performed in 19 patients and pneumonectomy was performed in 20 patients. In this paper, the results of sleeve lobectomy and pneumonectomy for patients with lung cancer will be compared and evaluated. RESULTS: There were no postoperative complications in either group, but there was one mortality in the pneumonectomy group. There was better preservation of pulmonary function in the sleeve lobectomy group than the pneumonectomy group (p=0.066 in FVC, p=0.019 in FEV1). The 3-year survival rates were 46.7% in the sleeve lobectomy group and 54.5% in the pneumonectomy group (p=0.505). The 3-year disease-free survival rates were 38% in the sleeve lobectomy group and 45.8% in the pneumonectomy group (p=0.200). CONCLUSION: Sleeve lobectomy for lung cancer showed low mortality, low bronchial anastomotic complication rates, and good preservation of pulmonary function.

Intramural hematoma of gastric tube after Ivor Lewis operation.

Intramural hematoma of transposed gastric tube after Ivor Lewis operation is an uncommon finding, which is difficult to diagnose and differentiate from perforation at presentation. We report a case of massive intramural hematoma in a transposed gastric tube after an Ivor Lewis operation that was successfully managed with conservative therapy.

Inhibition of lipopolysaccharide-induced inducible nitric oxide synthase expression by a novel compound, mercaptopyrazine, through suppression of nuclear factor-kappaB binding to DNA.

Macrophage cells in response to cytokines and endotoxins produced a large amount of nitric oxide (NO) by expression of inducible nitric oxide synthase (iNOS), resulting in acute or chronic inflammatory disorders including septic hypotension and atherosclerosis. In the present study, we investigated the effect and the mechanism of mercaptopyrazine (MP) in the induction of iNOS and NO production as a culminating factor for several inflammatory disorders. Pretreatment of MP alleviated the mortality of endotoxemic mice receiving a lethal bolus of lipopolysaccharide (LPS), which was associated with the reduced levels of serum nitrite/nitrate and IL-1beta. In RAW264.7 mouse macrophage cells, MP (300microM) inhibited both protein and mRNA levels of iNOS stimulated by LPS/interferon-gamma (IFNgamma) up to 50%. The nuclear factor-kappa B (NF-kappaB)-driven transactivation was also suppressed by MP to the same degree. Treatment of MP reduced the binding of NF-kappaB to the oligonucleotides containing NF-kappaB consensus sequence, while it did not affect the translocation of NF-kappaB to nuclear. Suppression of NF-kappaB activity by MP was completely reversed by a reducing agent, dithiothreitol, implying that MP might oxidize the sulfhydryl group(s) of DNA binding domain of NF-kappaB. In conclusion, MP would be one of interesting candidates or chemical moieties of iNOS expression inhibitor via specific suppression of NF-kappaB binding to DNA, and be useful as a chemopreventive agent or a therapeutic against iNOS-associated inflammatory diseases.

Anti-obesity effects of alpha-lipoic acid mediated by suppression of hypothalamic AMP-activated protein kinase.

AMP-activated protein kinase (AMPK) functions as a fuel sensor in the cell and is activated when cellular energy is depleted. Here we report that alpha-lipoic acid (alpha-LA), a cofactor of mitochondrial enzymes, decreases hypothalamic AMPK activity and causes profound weight loss in rodents by reducing food intake and enhancing energy expenditure. Activation of hypothalamic AMPK reverses the effects of alpha-LA on food intake and energy expenditure. Intracerebroventricular (i.c.v.) administration of glucose decreases hypothalamic AMPK activity, whereas inhibition of intracellular glucose utilization through the administration of 2-deoxyglucose increases hypothalamic AMPK activity and food intake. The 2-deoxyglucose-induced hyperphagia is reversed by inhibiting hypothalamic AMPK. Our findings indicate that hypothalamic AMPK is important in the central regulation of food intake and energy expenditure and that alpha-LA exerts anti-obesity effects by suppressing hypothalamic AMPK activity.

Changes in ghrelin and ghrelin receptor expression according to feeding status.

Ghrelin, a newly identified gut hormone, has been implicated in the regulation of food intake and energy homeostasis. This study was undertaken to investigate changes in expression levels of stomach ghrelin as well as of ghrelin receptor in the hypothalamus and pituitary glands according to feeding state. Stomach ghrelin mRNA levels were increased by 48 h fasting but decreased by re-feeding. The ghrelin receptor mRNA levels of 48 h fasted rats were 8 times higher in the hypothalamus and 3 times higher in the anterior pituitary gland than levels in fed rats. In summary, not only stomach ghrelin, but also hypothalamic ghrelin receptor mRNA expression, increased during a fast. Such as enhanced ghrelin receptor expression could contribute to the amplification of ghrelin action in a negative-energy balance state.