Two complete 1918 influenza A/H1N1 pandemic virus genomes characterized by next-generation sequencing using RNA isolated from formalin-fixed, paraffin-embedded autopsy lung tissue samples along with evidence of secondary bacterial co-infection.

The 1918 influenza pandemic was the most devastating respiratory pandemic in modern human history, with 50-100 million deaths worldwide. Here, we characterized the complete genomes of influenza A virus (IAV) from two fatal cases during the fall wave of 1918 influenza A (H1N1) pandemic in the United States, one from Walter Reed Army Hospital in Washington, DC, and the other from Camp Jackson, SC. The two complete IAV genomes were obtained by combining Illumina deep sequencing data from both total RNA and influenza viral genome-enriched libraries along with Sanger sequencing data from PCR across the sequencing gaps. This study confirms the previously reported 1918 IAV genomes and increases the total number of available complete or near-complete influenza viral genomes of the 1918 pandemic from four to six. Sequence comparisons among them confirm that the genomes of the 1918 pandemic virus were highly conserved during the main wave of the pandemic with geographic separation in North America and Europe. Metagenomic analyses revealed bacterial co-infections in both cases. Interestingly, in the Washington, DC, case, evidence is presented of the first reported Rhodococcus-influenza virus co-infection. IMPORTANCE: This study applied modern molecular biotechnology and high-throughput sequencing to formalin-fixed, paraffin-embedded autopsy lung samples from two fatal cases during the fall wave of the 1918 influenza A (H1N1) pandemic in the United States. Complete influenza genomes were obtained from both cases, which increases the total number of available complete or near-complete influenza genomes of the 1918 pandemic virus from four to six. Sequence analysis confirms that the 1918 pandemic virus was highly conserved during the main wave of the pandemic with geographic separation in North America and Europe. Metagenomic analyses revealed bacterial co-infections in both cases, including the first reported evidence of Rhodococcus-influenza co-infection. Overall, this study offers a detailed view at the molecular level of the very limited samples from the most devastating influenza pandemic in modern human history.

A graph-based pan-genome of Brassica oleracea provides new insights into its domestication and morphotype diversification.

The domestication of Brassica oleracea has resulted in diverse morphological types with distinct patterns of organ development. Here we report a graph-based pan-genome of B. oleracea constructed from high-quality genome assemblies of different morphotypes. The pan-genome harbors over 200 structural variant hotspot regions enriched in auxin- and flowering-related genes. Population genomic analyses revealed that early domestication of B. oleracea focused on leaf or stem development. Gene flows resulting from agricultural practices and variety improvement were detected among different morphotypes. Selective-sweep and pan-genome analyses identified an auxin-responsive small auxin up-regulated RNA gene and a CLAVATA3/ESR-RELATED family gene as crucial players in leaf-stem differentiation during the early stage of B. oleracea domestication and the BoKAN1 gene as instrumental in shaping the leafy heads of cabbage and Brussels sprouts. Our pan-genome and functional analyses further revealed that variations in the BoFLC2 gene play key roles in the divergence of vernalization and flowering characteristics among different morphotypes, and variations in the first intron of BoFLC3 are involved in fine-tuning the flowering process in cauliflower. This study provides a comprehensive understanding of the pan-genome of B. oleracea and sheds light on the domestication and differential organ development of this globally important crop species.

Comprehensive Genome-Wide Identification of the RNA-Binding Glycine-Rich Gene Family and Expression Profiling under Abiotic Stress in Brassica oleracea.

The RNA-binding glycine-rich proteins (RBGs) of the glycine-rich protein family play vital roles in regulating gene expression both at the transcriptional and post-transcriptional levels. However, the members and functions in response to abiotic stresses of the RBG gene family remain unclear in Brassica oleracea. In this study, a total of 19 BoiRBG genes were identified through genome-wide analysis in broccoli. The characteristics of BoiRBG sequences and their evolution were examined. An analysis of synteny indicated that the expansion of the BoiRBG gene family was primarily driven by whole-genome duplication and tandem duplication events. The BoiRBG expression patterns revealed that these genes are involved in reaction to diverse abiotic stress conditions (i.e., simulated drought, salinity, heat, cold, and abscisic acid) and different organs. In the present research, the up-regulation of BoiRBGA13 expression was observed when subjected to both NaCl-induced and cold stress conditions in broccoli. Moreover, the overexpression of BoiRBGA13 resulted in a noteworthy reduction in taproot lengths under NaCl stress, as well as the inhibition of seed germination under cold stress in broccoli, indicating that RBGs play different roles under various stresses. This study provides insights into the evolution and functions of BoiRBG genes in Brassica oleracea and other Brassicaceae family plants.

Construction and Application of an F1-Derived Doubled-Haploid Population and High-Density Genetic Map for Ornamental Kale Breeding.

Ornamental kale (Brassica oleracea var. acephala) is an attractive ornamental plant with a range of leaf colors and shapes. Breeding new varieties of ornamental kale has proven challenging due to its lengthy breeding cycle and the limited availability of genetic markers. In this study, a F1DH ornamental kale population comprising 300 DH lines was constructed using microspore culture. A high-density genetic map was developed by conducting whole-genome sequencing on 150 individuals from the F1DH population. The genetic map contained 1696 bin markers with 982,642 single-nucleotide polymorphisms (SNPs) spanning a total distance of 775.81 cM on all nine chromosomes with an average distance between markers of 0.46 cM. The ornamental kale genetic map contained substantially more SNP markers compared with published genetic maps for other B. oleracea crops. Furthermore, utilizing this high-density genetic map, we identified seven quantitative trait loci (QTLs) that significantly influence the leaf shape of ornamental kale. These findings are valuable for understanding the genetic basis of key agronomic traits in ornamental kale. The F1DH progenies provide an excellent resource for germplasm innovation and breeding new varieties of ornamental kale. Additionally, the high-density genetic map provides crucial insights for gene mapping and unraveling the molecular mechanisms behind important agronomic traits in ornamental kale.

Phakellisins A-E, cyclopeptides from a marine sponge Phakellia sp. guided by LC-MS.

A chemical investigation of the marine sponge Phakellia sp. from the South China Sea yielded five new cyclopeptides, phakellisins A-E (1-5). Structures of these compounds were determined by comprehensive analysis of 1D/2D NMR, HRESIMS/MS spectroscopic data and the advanced Marfey's method. All compounds were evaluated for their cytotoxic activity. Compound 1 showed a strong inhibitory activity against WSU-DLCL-2 cells with an IC50 value of 5.25 ± 0.2 µM by induction of G0/G1 cell cycle arrest and apoptosis.

LC-MS-Guided Isolation of Cyanogripeptides A-C, Cyclolipopeptides with ß-Methyl-Leucine Residues, from an Actinoalloteichus cyanogriseus LHW52806.

Cyanogripeptides A-C (1-3), three new cyclolipopeptides with unusual ß-methyl-leucine residues, were identified from an Actinoalloteichus cyanogriseus LHW52806 using an LC-MS-guided strategy. The structures of compounds 1-3 were elucidated by 1D/2D NMR, HR-MS/MS, and the advanced Marfey's method. The absolute configuration of the ß-methyl-leucine residue was determined by a combination of stereoselective biosynthesis of (2S,3R)-ß-methyl-leucine, racemization to its epimer (2R,3R)-ß-methyl-leucine, and the advanced Marfey's method. The biosynthetic pathway of cyanogripeptides was deduced by analyzing the genome of A. cyanogriseus LHW52806. Compound 3 exhibited antibacterial activity against Helicobacter pylori G27, Helicobacter pylori 26695, and Mycolicibacterium smegmatis ATCC607 with MIC values of 32 µg/mL.

De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Chaenomeles speciosa (Sweet) Nakai Revealed the Existence of Two Structural Isomers.

As a valuable Chinese traditional medicinal species, Chaenomeles speciosa (Sweet) Nakai (C. speciosa) is a natural resource with significant economic and ornamental value. However, its genetic information is not well understood. In this study, the complete mitochondrial genome of C. speciosa was assembled and characterized to explore the repeat sequences, recombination events, rearrangements, and IGT, to predict RNA editing sites, and to clarify the phylogenetic and evolutionary relationship. The C. speciosa mitochondrial genome was found to have two circular chromosomes as its major conformation, with a total length of 436,464 bp and 45.2% GC content. The mitochondrial genome contained 54 genes, including 33 unique protein-coding genes, 18 tRNAs, and 3 rRNA genes. Seven pairs of repeat sequences involving recombination events were analyzed. Both the repeat pairs, R1 and R2, played significant roles in mediating the major and minor conformations. In total, 18 MTPTs were identified, 6 of which were complete tRNA genes. There were 454 RNA editing sites in the 33 protein-coding sequences predicted by the PREPACT3 program. A phylogenetic analysis based on 22 species of mitochondrial genomes was constructed and indicated highly conserved PCG sequences. Synteny analyses showed extensive genomic rearrangements in the mitochondrial genome of C. speciosa and closely related species. This work is the first to report the C. speciosa mitochondrial genome, which is of great significance for conducting additional genetic studies on this organism.

Stephtetrandrine A-D, bisbenzylisoquinoline alkaloids from Stephania tetrandra.

Four undescribed bisbenzylisoquinoline alkaloids, designated as Stephtetrandrine A-D, were isolated from the roots of Stephania tetrandra. Their structures were elucidated by IR, HRESIMS, ECD spectra, 1 D and 2 D NMR spectra and comparison with the literature data. Additional five known compounds (limacine, tetrandrine, N-trans-Feruloyltyramine, 2'-N-chloromethyltetrandrine, 2,2'-N-N-dichloromethyltetrandrine) were also isolated. N-trans-Feruloyltyramine was isolated from Stephania tetrandra for the first time. The isolated compounds were tested for monoamine oxidase, acetylcholinesterase, phosphoinositide 3-kinase α and human hepatoma cell HepG2 inhibitory activities. Stephtetrandrine C showed obvious inhibitory effect on human hepatoma HepG2, with IC50 value of 16.2 µM. Limacine and 2'-N-chloromethyltetrandrine showed moderate monoamine oxidase inhibitory effect with the IC50 values of 37.7 and 29.2 µM, respectively.

Melon shoot organization 1, encoding an AGRONAUTE7 protein, plays a crucial role in plant development.

KEY MESSAGE: A melon gene MSO1 located on chromosome 10 by map-based cloning strategy, which encodes an ARGONAUTE 7 protein, is responsible for the development of shoot organization. Plant endogenous small RNAs (sRNAs) are involved in various plant developmental processes. In Arabidopsis, sRNAs combined with ARGONAUTE (AGO) proteins are incorporated into the RNA-induced silencing complex (RISC), which functions in RNA silencing or biogenesis of trans-acting siRNAs (ta-siRNAs). However, their roles in melon (Cucumis melo L.) are still unclear. Here, the melon shoot organization 1 (mso1) mutant was identified and shown to exhibit pleiotropic phenotypes in leaf morphology and plant architecture. Positional cloning of MSO1 revealed that it encodes a homologue of Arabidopsis AGO7/ZIPPY, which is required for the production of ta-siRNAs. The AG-to-C mutation in the second exon of MSO1 caused a frameshift mutation and significantly reduced its expression. Ectopic expression of MSO1 rescued the Arabidopsis ago7 phenotype. RNA-seq analysis showed that several genes involved in transcriptional regulation and plant hormones were significantly altered in mso1 compared to WT. A total of 304 and 231 miRNAs were identified in mso1 and WT by sRNA sequencing, respectively, and among them, 42 known and ten novel miRNAs were differentially expressed. cme-miR390a significantly accumulated, and the expression levels of the two ta-siRNAs were almost completely abolished in mso1. Correspondingly, their targets, the ARF3 and ARF4 genes, showed dramatically upregulated expression, indicating that the miR390-TAS3-ARF pathway has conserved roles in melon. These findings will help us better understand the molecular mechanisms of MSO1 in plant development in melon.

Axinellasins A-D, Immunosuppressive Cycloheptapeptide Diastereomers, Discovered via a Precursor Ion Scanning-Supercritical Fluid Chromatography Strategy from the Marine Sponge Axinella species.

The precursor ion scanning-supercritical fluid chromatography (PI-SFC) method was applied to explore new methionine sulfoxide-containing cycloheptapeptides, axinellasins A-D (1-4), from the marine sponge Axinella sp. Their structures, including absolute configurations, were elucidated by detailed spectroscopic analyses and X-ray crystallography. The total synthesis of 4 was completed via an Fmoc solid/solution-phase synthesis. Compounds 1-4 exhibited immunosuppressive effects via inhibition of T and B cell proliferation, and 1 and 4 showed better inhibitory activities than their corresponding diastereomers.

CmFSI8/CmOFP13 encoding an OVATE family protein controls fruit shape in melon.

Fruit shape is an important quality and yield trait in melon (Cucumis melo). Although some quantitative trait loci for fruit shape have been reported in in this species, the genes responsible and the underlying mechanisms remain poorly understood. Here, we identified and characterized a gene controlling fruit shape from two melon inbred lines, B8 with long-horn fruit and HP22 with flat-round fruit. Genetic analysis suggested that the shape was controlled by a single and incompletely dominant locus, which we designate as CmFSI8/CmOFP13. This gene was finely mapped to a 53.7-kb interval on chromosome 8 based on bulked-segregant analysis sequencing and map-based cloning strategies. CmFSI8/CmOFP13 encodes an OVATE family protein (OFP) and is orthologous to AtOFP1 and SlOFP20. The transcription level of CmFSI8/CmOFP13 in the ovary of HP22 was significantly higher than that in B8, and sequence analysis showed that a 12.5-kb genomic variation with a retrotransposon insertion identified in the promoter was responsible for elevating the expression, and this ultimately caused the differences in fruit shape. Ectopic overexpression of CmFSI8/CmOFP13 in Arabidopsis led to multiple phenotypic changes, including kidney-shaped leaves and shortened siliques. Taken together, our results demonstrate the involvement of an OFP in regulating fruit shape in melon, and our improved understanding of the molecular mechanisms will enable us to better manipulate fruit shape in breeding.

Anion-driven supramolecular modulation of spin-crossover properties in mononuclear iron(III) Schiff-base complexes.

A series of Fe(III) complexes [Fe(5-F-sal-N-1,4,7,10)]Y (Y = PF6- for 1, Y = ClO4- for 2, Y = I- for 3 and Y = NO3- for 4) have been prepared. Single-crystal X-ray crystallographic studies show that complex 1 crystallizes in the orthorhombic Pna21 space group and complexes 2-4 have an isomorphous structure and crystallize in the same monoclinic space group, P21/n. Complexes 2-4 have two independent molecules (Fe1 and Fe2) in the unit cell. Magnetic susceptibility measurements demonstrated that complexes 1 and 3 showed a gradual one-step SCO behavior (T1/2 for 1 = 177 K and for 3 = 227 K) without thermal hysteresis. The magnetic behavior of 2 shows an incomplete two-step SCO process at T1/2 = 114 K and 170 K, respectively, while 4 is in a high-spin state at all measured temperatures. A careful evaluation of the supramolecular structures of these complexes revealed correlation between the supramolecular packing forces and their SCO behavior. The crystal structure of 1 consists of a three-dimensional (3D) extended network constructed from N-H⋯F and C-H⋯F hydrogen bonds, and C-H⋯π and C⋯C short contacts. In compounds 2-4, the crystal packing is governed by C⋯C, C-H⋯π and p-π interactions for the Fe1 centers and by C-H⋯π/O interactions for the Fe2 centers, which form 1D chains. Additional interactions (C-H⋯F and N-H⋯O/I) connect the neighboring chains and planes to form a complex supramolecular network. The anion⋯π interactions in 4 provide a means for preventing SCO occurring at low temperatures. This suggests that the supramolecular connectivity of the anions influences the magnetic properties.

Lung epithelial and endothelial damage, loss of tissue repair, inhibition of fibrinolysis, and cellular senescence in fatal COVID-19.

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is characterized by respiratory distress, multiorgan dysfunction, and, in some cases, death. The pathological mechanisms underlying COVID-19 respiratory distress and the interplay with aggravating risk factors have not been fully defined. Lung autopsy samples from 18 patients with fatal COVID-19, with symptom onset-to-death times ranging from 3 to 47 days, and antemortem plasma samples from 6 of these cases were evaluated using deep sequencing of SARS-CoV-2 RNA, multiplex plasma protein measurements, and pulmonary gene expression and imaging analyses. Prominent histopathological features in this case series included progressive diffuse alveolar damage with excessive thrombosis and late-onset pulmonary tissue and vascular remodeling. Acute damage at the alveolar-capillary barrier was characterized by the loss of surfactant protein expression with injury to alveolar epithelial cells, endothelial cells, respiratory epithelial basal cells, and defective tissue repair processes. Other key findings included impaired clot fibrinolysis with increased concentrations of plasma and lung plasminogen activator inhibitor-1 and modulation of cellular senescence markers, including p21 and sirtuin-1, in both lung epithelial and endothelial cells. Together, these findings further define the molecular pathological features underlying the pulmonary response to SARS-CoV-2 infection and provide important insights into signaling pathways that may be amenable to therapeutic intervention.

The Association Between Internet Addiction and Anxiety in Nursing Students: A Network Analysis.

Background: Nursing students who suffer from co-occurring anxiety experience added difficulties when communicating and interacting with others in a healthy, positive, and meaningful way. Previous studies have found strong positive correlations between Internet addiction (IA) and anxiety, suggesting that nursing students who report severe IA are susceptible to debilitating anxiety as well. To date, however, network analysis (NA) studies exploring the nature of association between individual symptoms of IA and anxiety have not been published. Objective: This study examined associations between symptoms of IA and anxiety among nursing students using network analysis. Methods: IA and anxiety symptoms were assessed using the Internet Addiction Test (IAT) and the Generalized Anxiety Disorder Screener (GAD-7), respectively. The structure of IA and anxiety symptoms was characterized using "Strength" as a centrality index in the symptom network. Network stability was tested using a case-dropping bootstrap procedure and a Network Comparison Test (NCT) was conducted to examine whether network characteristics differed on the basis of gender and by region of residence. Results: A total of 1,070 nursing students participated in the study. Network analysis showed that IAT nodes, "Academic decline due to Internet use," "Depressed/moody/nervous only while being off-line," "School grades suffer due to Internet use," and "Others complain about your time spent online" were the most influential symptoms in the IA-anxiety network model. Gender and urban/rural residence did not significantly influence the overall network structure. Conclusion: Several influential individual symptoms including Academic declines due to Internet use, Depressed/moody/nervous only while being off-line, School grades suffering due to Internet use and Others complain about one's time spent online emerged as potential targets for clinical interventions to reduce co-occurring IA and anxiety. Additionally, the overall network structure provides a data-based hypothesis for explaining potential mechanisms that account for comorbid IA and anxiety.

Prevalence of problematic Internet use and its association with quality of life among undergraduate nursing students in the later stage of COVID-19 pandemic era in China.

BACKGROUND AND OBJECTIVES: The prevalence of problematic Internet use (PIU) in the post-COVID-19 pandemic era is not known. This cross-sectional study aimed to determine the prevalence of PIU among baccalaureate nursing students (hereafter: nursing students) in the post-COVID-19 era. METHODS: A total of 1070 nursing students were consecutively invited to participate in this study from the nursing schools of five universities. PIU and quality of life (QOL) were assessed using the Internet Addiction Test (IAT) and the World Health Organization Quality of Life Scale Brief Version (WHOQOL-BREF), respectively. t Tests, χ2 , tests, and Kruskal-Wallis tests were used to compare basic demographic and clinical characteristics between participants with and without PIU. Binary logistic regression analysis was used to examine independent correlates. RESULTS: The prevalence of PIU was 23.3% (95% confidence interval [CI]: 20.7%-25.8%). Multiple logistic regression analysis revealed that second- (p = .024) and third-year (p = .012) students were more likely to suffer from PIU compared with first year students. Students with more severe depressive (p = .014) and anxiety symptoms (p = .011) were independently and significantly associated with more severe PIU. After controlling for covariates, nursing students with PIU had a lower overall QOL score (p = .002). CONCLUSION AND SCIENTIFIC SIGNIFICANCE: Problematic Internet use (PIU) was common among nursing students in the post-COVID-19 era. Considering the negative impact of PIU on QOL and academic performance, regular screening should be conducted and effective interventions implemented for nursing students with PIU. This was the first study on the prevalence of PIU among nursing students in the post-COVID-19 era. The findings of this study could help health professionals and education authorities to understand the patterns of PIU and its influence on QOL among nursing students and to allocate health resources and develop effective measures to reduce the risk of PIU in this population.

Network analysis of anxiety and depressive symptoms among nursing students during the COVID-19 pandemic.

BACKGROUND: The 2019 coronavirus disease (COVID-19) pandemic has impacted the mental health and well-being of medical personnel, including nursing students. Network analysis provides a deeper characterization of symptom-symptom interactions in mental disorders. The aim of this study was to elucidate characteristics of anxiety and depressive symptom networks of Chinese nursing students during the COVID-19 pandemic. METHOD: A total of 932 nursing students were included. Anxiety and depressive symptom were measured using the seven-item Generalized Anxiety Disorder Scale (GAD-7) and two-item Patient Health Questionnaire (PHQ-2), respectively. Central symptoms and bridge symptoms were identified via centrality indices and bridge centrality indices, respectively. Network stability was examined using the case-dropping procedure. RESULTS: Irritability, Uncontrollable worry, Trouble relaxing, and Depressed mood had the highest centrality values. Three bridge symptoms (Depressed mood, Nervousness, and Anhedonia) were also identified. Neither gender nor region of residence was associated with network global strength, distribution of edge weights or individual edge weights. LIMITATIONS: Data were collected in a cross-sectional study design, therefore, causal relations and dynamic changes between anxiety and depressive symptoms over time could not be inferred. Generalizability of findings may be limited to Chinese nursing students during a particular phase of the current pandemic. CONCLUSIONS: Irritability, Uncontrollable worry, Trouble relaxing, and Depressed mood constituted central symptoms maintaining the anxiety-depression network structure of Chinese nursing students during the pandemic. Timely, systemic multi-level interventions targeting central symptoms and bridge symptoms may be effective in alleviating co-occurring experiences of anxiety and depression in this population.

The Controversy About the Effects of Different Doses of Corticosteroid Treatment on Clinical Outcomes for Acute Respiratory Distress Syndrome Patients: An Observational Study.

Background: Corticosteroid usage in acute respiratory distress syndrome (ARDS) remains controversial. We aim to explore the correlation between the different doses of corticosteroid administration and the prognosis of ARDS. Methods: All patients were diagnosed with ARDS on initial hospital admission and received systemic corticosteroid treatment for ARDS. The main outcomes were the effects of corticosteroid treatment on clinical parameters and the mortality of ARDS patients. Secondary outcomes were factors associated with the mortality of ARDS patients. Results: 105 ARDS patients were included in this study. Corticosteroid treatment markedly decreased serum interleukin-18 (IL-18) level (424.0 ± 32.19 vs. 290.2 ± 17.14; p = 0.0003) and improved arterial partial pressure of oxygen/fraction of inspired oxygen (PaO2/FiO2) (174.10 ± 65.28 vs. 255.42 ± 92.49; p < 0.0001). The acute physiology and chronic health evaluation (APACHE II) score (16.15 ± 4.41 vs. 14.88 ± 4.57, p = 0.042) decreased significantly on the seventh day after systemic corticosteroid treatment. Interestingly, the serum IL-18 decreased significantly (304.52 ± 286.00 vs. 85.85 ± 97.22, p < 0.0001), whereas the improvement of PaO2/FiO2 (24.78 ± 35.03 vs. 97.17 ± 44.82, p < 0.001) was inconspicuous after systemic corticosteroid treatment for non-survival patients, compared with survival patients. Furthermore, the receiver operating characteristic (ROC) model revealed, when equivalent methylprednisolone usage was 146.5 mg/d, it had the best sensitivity and specificity to predict the death of ARDS. Survival analysis by Kaplan-Meier curves presented the higher 45-day mortality in high-dose corticosteroid treatment group (logrank test p < 0.0001). Multivariate Cox regression analyses demonstrated that serum IL-18 level, APACHE II score, D-dimer, and high-dose corticosteroid treatment were associated with the death of ARDS. Conclusion: Appropriate dose of corticosteroids may be beneficial for ARDS patients through improving the oxygenation and moderately inhibiting inflammatory response. The benefits and risks should be carefully weighed when using high-dose corticosteroid for ARDS. Trial registration: This work was registered in ClinicalTrials.gov. Name of the registry: Corticosteroid Treatment for Acute Respiratory Distress Syndrome. Trial registration number: NCT02819453. URL of trial registry record: https://register.clinicaltrials.gov.