Assembly and comparative analysis of the first complete mitochondrial genome of the invasive water hyacinth, Eichhornia crassipes.

Eichhornia crassipes is an aquatic plant in tropical and subtropical regions, renowned for its notorious invasive tendencies. In this study, we assembled the complete mitogenome of E. crassipes into a single circle molecule of 397,361 bp. The mitogenome has 58 unique genes, including 37 protein-coding genes (PCGs), 18 tRNA genes, three rRNA genes, and 47 % GC content. Sixteen (6.93 %) homologous fragments, ranging from 31 bp to 8548 bp, were identified, indicating the transfer of genetic material from chloroplasts to mitochondria. In addition, we detected positive selection in six PCGs (ccmB, ccmC, ccmFC, nad3, nad4 and sdh4), along with the identification of 782 RNA editing sites across 37 mt-PCGs. These findings suggest a potential contribution to the robust adaptation of this invasive plant to the stressful environment. Lastly, we inferred that phylogenetic conflicts of E. crassipes between the plastome and mitogenome may be attributed to the difference in nucleotide substitution rates between the two organelle genomes. In conclusion, our study provided vital genomic resources for further understanding the invasive mechanism of this species and exploring the dynamic evolution of mitogenomes within the monocot clade.

A useful strategy for synthesis of the disaccharide of OSW-1.

A flexible, efficient, and practical synthesis route was developed to synthesize an OSW-1 disaccharide. The synthesis took 13 steps from l-arabinose and d-xylose derivatives, and the overall yield was 7.2%. The region preferentially protects various d-xylose hydroxides because the TBS group selectively reacts with this hydroxide at low concentrations due to greater activity at the C-4 hydroxyl of d-xylose. Then, high efficiency selectively protects C-2 hydroxyl and C-3 hydroxyl of d-xylose, respectively. The first high yield of glycosylation on an OSW-1 synthesis disaccharide was achieved by taking sulfide donor 4 with ß-PMP anomeric l-arabinose acceptor 12. The cytotoxicity reveals that the analogy has a high IC50 for a variety of cell types. This approach should provide a versatile way to modify OSW-1's disaccharide.

Haplotype-resolved genome assembly provides insights into the evolution of S-locus supergene in distylous Nymphoides indica.

Distyly has evolved independently in numerous animal-pollinated angiosperm lineages. Understanding of its molecular basis has been restricted to a few species, primarily Primula. Here, we investigate the genetic architecture of the single diallelic locus (S-locus) supergene, a linkage group of functionally associated genes, and explore how it may have evolved in distylous Nymphoides indica, a lineage of flowering plants not previously investigated. We assembled haplotype-resolved genomes, used read-coverage-based genome-wide association study (rb-GWAS) to locate the S-locus supergene, co-expression network analysis to explore gene networks underpinning the development of distyly, and comparative genomic analyses to investigate the origins of the S-locus supergene. We identified three linked candidate S-locus genes - NinBAS1, NinKHZ2, and NinS1 - that were only evident in the short-styled morph and were hemizygous. Co-expression network analysis suggested that brassinosteroids contribute to dimorphic sex organs in the short-styled morph. Comparative genomic analyses indicated that the S-locus supergene likely evolved via stepwise duplications and has been affected by transposable element activities. Our study provides novel insight into the structure, regulation, and evolution of the supergene governing distyly in N. indica. It also provides high-quality genomic resources for future research on the molecular mechanisms underlying the striking evolutionary convergence in form and function across heterostylous taxa.

A multicenter prospective study of comprehensive metagenomic and transcriptomic signatures for predicting outcomes of patients with severe community-acquired pneumonia.

BACKGROUND: Severe community-acquired pneumonia (SCAP) results in high mortality as well as massive economic burden worldwide, yet limited knowledge of the bio-signatures related to prognosis has hindered the improvement of clinical outcomes. Pathogen, microbes and host are three vital elements in inflammations and infections. This study aims to discover the specific and sensitive biomarkers to predict outcomes of SCAP patients. METHODS: In this study, we applied a combined metagenomic and transcriptomic screening approach to clinical specimens gathered from 275 SCAP patients of a multicentre, prospective study. FINDINGS: We found that 30-day mortality might be independent of pathogen category or microbial diversity, while significant difference in host gene expression pattern presented between 30-day mortality group and the survival group. Twelve outcome-related clinical characteristics were identified in our study. The underlying host response was evaluated and enrichment of genes related to cell activation, immune modulation, inflammatory and metabolism were identified. Notably, omics data, clinical features and parameters were integrated to develop a model with six signatures for predicting 30-day mortality, showing an AUC of 0.953 (95% CI: 0.92-0.98). INTERPRETATION: In summary, our study linked clinical characteristics and underlying multi-omics bio-signatures to the differential outcomes of patients with SCAP. The establishment of a comprehensive predictive model will be helpful for future improvement of treatment strategies and prognosis with SCAP. FUNDING: National Natural Science Foundation of China (No. 82161138018), Shanghai Municipal Key Clinical Specialty (shslczdzk02202), Shanghai Top-Priority Clinical Key Disciplines Construction Project (2017ZZ02014), Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100).

Integrating host transcriptomic signatures for distinguishing autoimmune encephalitis in cerebrospinal fluid by metagenomic sequencing.

BACKGROUND: The early accurate diagnoses for autoimmune encephalitis (AE) and infectious encephalitis (IE) are essential since the treatments for them are different. This study aims to discover some specific and sensitive biomarkers to distinguish AE from IE at early stage to give specific treatments for good outcomes. RESULTS: We compared the host gene expression profiles and microbial diversities of cerebrospinal fluid (CSF) from 41 patients with IE and 18 patients with AE through meta-transcriptomic sequencing. Significant differences were found in host gene expression profiles and microbial diversities in CSF between patients with AE and patients with IE. The most significantly upregulated genes in patients with IE were enriched in pathways related with immune response such as neutrophil degranulation, antigen processing and presentation and adaptive immune system. In contrast, those upregulated genes in patients with AE were mainly involved in sensory organ development such as olfactory transduction, as well as synaptic transmission and signaling. Based on the differentially expressed genes, a classifier consisting of 5 host genes showed outstanding performance with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.95. CONCLUSIONS: This study provides a promising classifier and is the first to investigate transcriptomic signatures for differentiating AE from IE by using meta-transcriptomic next-generation sequencing technology.

HP1γ Prevents Activation of the cGAS/STING Pathway by Preserving Nuclear Envelope and Genomic Integrity in Colon Adenocarcinoma Cells.

Chronic inflammatory processes in the intestine result in serious conditions such as inflammatory bowel disease (IBD) and cancer. An increased detection of cytoplasmic DNA sensors has been reported in the IBD colon mucosa, suggesting their contribution in mucosal inflammation. Yet, the mechanisms altering DNA homeostasis and triggering the activation of DNA sensors remain poorly understood. In this study, we show that the epigenetic regulator HP1γ plays a role in preserving nuclear envelope and genomic integrity in enterocytic cells, thereby protecting against the presence of cytoplasmic DNA. Accordingly, HP1 loss of function led to the increased detection of cGAS/STING, a cytoplasmic DNA sensor that triggers inflammation. Thus, in addition to its role as a transcriptional silencer, HP1γ may also exert anti-inflammatory properties by preventing the activation of the endogenous cytoplasmic DNA response in the gut epithelium.

Epidermal Barrier Integrity is Associated with Both Skin Microbiome Diversity and Composition in Patients with Acne Vulgaris.

Background: Although the changed lipid environment of the pilosebaceous unit and the growth of lipophilic Cutibacterium acnes (C. acnes) during puberty has long been considered as the trigger of acne vulgaris, the involvement of the interaction between the epidermal barrier integrity and the skin microbiome in this disease has not been fully elucidated. Objective: The aim of this study was to analyze the differences in the epidermal barrier and skin microbiota in patients with acne vulgaris and their correlation. Methods: The skin microbial samples and epidermal barrier data from 74 acne patients and 19 healthy subjects were collected in this cross-sectional study. The microbial diversity was analyzed based on a high-throughput sequencing approach that targets the V3-V4 region of the bacteria 16S ribosomal RNA genes. Results: Compared with healthy controls, acne patients had significantly increased transepidermal water loss (TEWL), pH levels, sebum, porphyrins, and red areas, and reduced skin microbiome diversity according to the goods coverage diversity index (p = 0.021), Shannon diversity index (p = 0.037), and Simpson diversity index (p = 0.023). Moreover, the diversity gradually decreased with the increase in acne grading. Based on the principal coordinate analysis (PCoA) analysis plot, the skin microbiota of acne patients and healthy controls could be divided into two different sets, which could not be used to separate acne patients with different disease severity. Finally, this study found that both TEWL and sebum were negatively associated with the Shannon and Simpson diversity index. Meanwhile, the taxa Enhydrobacter and Stenotrophomonas were positively associated with TEWL, stratum corneum hydration, respectively. Conclusion: This study demonstrated that acne vulgaris exists in patients with both damaged epithelial barriers and associated microbiota dysbiosis; the findings will help improve the understanding of the disease and may contribute to the development of better treatment options.

Microbial and human transcriptional profiling of coronavirus disease 2019 patients: Potential predictors of disease severity.

The high morbidity of patients with coronavirus disease 2019 (COVID-19) brings on a panic around the world. COVID-19 is associated with sex bias, immune system, and preexisting chronic diseases. We analyzed the gene expression in patients with COVID-19 and in their microbiota in order to identify potential biomarkers to aid in disease management. A total of 129 RNA samples from nasopharyngeal, oropharyngeal, and anal swabs were collected and sequenced in a high-throughput manner. Several microbial strains differed in abundance between patients with mild or severe COVID-19. Microbial genera were more abundant in oropharyngeal swabs than in nasopharyngeal or anal swabs. Oropharyngeal swabs allowed more sensitive detection of the causative SARS-CoV-2. Microbial and human transcriptomes in swabs from patients with mild disease showed enrichment of genes involved in amino acid metabolism, or protein modification via small protein removal, and antibacterial defense responses, respectively, whereas swabs from patients with severe disease showed enrichment of genes involved in drug metabolism, or negative regulation of apoptosis execution, spermatogenesis, and immune system, respectively. Microbial abundance and diversity did not differ significantly between males and females. The expression of several host genes on the X chromosome correlated negatively with disease severity. In this way, our analyses identify host genes whose differential expression could aid in the diagnosis of COVID-19 and prediction of its severity via non-invasive assay.

Reactive Oxygen Species-Dependent Innate Immune Mechanisms Control Methicillin-Resistant Staphylococcus aureus Virulence in the Drosophila Larval Model.

Antibiotic-resistant Staphylococcus aureus strains constitute a major public health concern worldwide and are responsible for both health care- and community-associated infections. Here, we establish a robust and easy-to-implement model of oral S. aureus infection using Drosophila melanogaster larvae that allowed us to follow the fate of S. aureus at the whole-organism level as well as the host immune responses. Our study demonstrates that S. aureus infection triggers H2O2 production by the host via the Duox enzyme, thereby promoting antimicrobial peptide production through activation of the Toll pathway. Staphylococcal catalase mediates H2O2 neutralization, which not only promotes S. aureus survival but also minimizes the host antimicrobial response, hence reducing bacterial clearance in vivo. We show that while catalase expression is regulated in vitro by the accessory gene regulatory system (Agr) and the general stress response regulator sigma B (SigB), it no longer depends on these two master regulators in vivo. Finally, we confirm the versatility of this model by demonstrating the colonization and host stimulation capabilities of S. aureus strains belonging to different sequence types (CC8 and CC5) as well as of two other bacterial pathogens, Salmonella enterica serovar Typhimurium and Shigella flexneri. Thus, the Drosophila larva can be a general model to follow in vivo the innate host immune responses triggered during infection by human pathogens. IMPORTANCE The pathogenicity of methicillin-resistant S. aureus (MRSA) strains relies on their ability to produce a wide variety of tightly regulated virulence factors. Current in vivo models to analyze host-pathogen interactions are limited and difficult to manipulate. Here, we have established a robust and reliable model of oral S. aureus infection using Drosophila melanogaster larvae. We show that S. aureus stimulates host immunity through the production of reactive oxygen species (ROS) and antimicrobial peptide (AMP) and that ROS potentialize AMP gene expression. S. aureus catalase plays a key role in this complex environment and acts in vivo independently from SigB and Agr control. We propose that fly larvae can provide a general model for studying the colonization capabilities of human pathogens.

[Role of the Notch signaling pathway in children with tuberculosis].

OBJECTIVE: To study the expression of molecules associated with the Notch signaling pathway in children with tuberculosis, as well as the role of this pathway in the pathogenesis of tuberculosis in children. METHODS: A total of 62 children who were diagnosed with tuberculosis from June 2017 to December 2018 were enrolled as the case group, and 64 healthy children were enrolled as the healthy control group. Peripheral venous blood samples with a volume of 2 mL were collected, and quantitative real-time PCR was used to measure the mRNA expression levels of the molecules associated with the Notch signaling pathway (receptors Notch1-4, ligands Jagged1/2 and DLL1/3/4, and downstream target genes Hes1 and Hey1) in leukocytes. RESULTS: Compared with the healthy control group, the case group had significant increases in the mRNA expression levels of Notch1, Notch2, and DLL4 in leukocytes (P<0.05), while there were no significant differences in the mRNA expression levels of Notch3/4, Jagged1/2, DLL1/3, Hes1, and Hey1 between the two groups (P>0.05). CONCLUSIONS: There are significant increases in the mRNA expression of Notch1/2 and DLL4 in children with tuberculosis, while there are no significant changes in the expression of downstream target genes, suggesting that the Notch signaling pathway, which is activated by the interaction between Notch1/2 and DLL4 after Mycobacterium tuberculosis infection, may play a role in childhood tuberculosis by acting on other target genes, and further studies are needed for clarification.

Burden of tuberculosis in Xinjiang between 2011 and 2015: A surveillance data-based study.

BACKGROUND: Despite the reduction in reported incidence of tuberculosis globally, the burden of pulmonary tuberculosis (PTB) remains high in low- and middle- income countries, including China. The current study aims to evaluate the distribution and trend of PTB incidence in Xinjiang, the region with the highest PTB burden in China. METHODS: We identified all confirmed PTB case records reported to the Chinese TB Information Management System (TBIMS) between 2011 and 2015. We analyzed these records to measure the annual incidence of reported smear-positive PTB cases in Xinjiang and its trend over time. We also analyzed incidence by gender, residential area, and region. Spatial analysis was used to describe the inter-regional disparity of the disease burden during the study period. RESULTS: We identified 212,216 smear-positive PTB cases between 2011 and 2015. The reported incidence increased from 180.8 cases in 2011 to 195.8 cases in 2015 per 100,000 population. The southern region of Xinjiang had the highest disease burden (257.8/100,000 in 2011 and 312.7/100,000 in 2015). More than 60% cases occurred in persons >45 years, and 76% of cases lived in rural areas. CONCLUSION: To reach the goal of elimination and control of TB, more comprehensive STOP TB strategies should be implemented in Xinjiang. Residents in the southern region and rural areas of Xinjiang require particular attention.

Comparative genomic analysis of six new-found integrative conjugative elements (ICEs) in Vibrio alginolyticus.

BACKGROUND: Vibrio alginolyticus is ubiquitous in marine and estuarine environments. In 2012-2013, SXT/R391-like integrative conjugative elements (ICEs) in environmental V. alginolyticus strains were discovered and found to occur in 8.9 % of 192 V. alginolyticus strains, which suggests that V. alginolyticus may be a natural pool possessing resourceful ICEs. However, complete ICE sequences originating from this bacterium have not been reported, which represents a significant barrier to characterizing the ICEs of this bacterium and exploring their relationships with other ICEs. In the present study, we acquired six ICE sequences from five V. alginolyticus strains and performed a comparative analysis of these ICE genomes. RESULTS: A sequence analysis showed that there were only 14 variable bases dispersed between ICEValE0601 and ICEValHN492. ICEValE0601 and ICEValHN492 were treated as the same ICE. ICEValA056-1, ICEValE0601 and ICEValHN492 integrate into the 5' end of the host's prfC gene, and their Int and Xis share at least 97 % identity with their counterparts from SXT. ICEValE0601 or ICEValHN492 contain 50 of 52 conserved core genes in the SXT/R391 ICEs (not s025 or s026). ICEValA056-2, ICEValHN396 and ICEValHN437 have a different tRNA-ser integration site and a distinct int/xis module; however, the remaining backbone genes are highly similar to their counterparts in SXT/R391 ICEs. DNA sequences inserted into hotspot and variable regions of the ICEs are of various sizes. The variable genes of six ICEs encode a large array of functions to bestow various adaptive abilities upon their hosts, and only ICEValA056-1 contains drug-resistant genes. Many variable genes have orthologous and functionally related genes to those found in SXT/R391 ICEs, such as genes coding for a toxin-antitoxin system, a restriction-modification system, helicases and endonucleases. Six ICEs also contain a large number of unique genes or gene clusters that were not found in other ICEs. Six ICEs harbor more abundant transposase genes compared with other parts of their host genomes. A phylogenetic analysis indicated that transposase genes in these ICEs are highly diverse. CONCLUSIONS: ICEValA056-1, ICEValE0601 and ICEValHN492 are typical members of the SXT/R391 family. ICEValA056-2, ICEValHN396 and ICEValHN437 form a new atypical group belonging to the SXT/R391 family. In addition to the many genes found to be present in other ICEs, six ICEs contain a large number of unique genes or gene clusters that were not found in other ICEs. ICEs may serve as a carrier for transposable genetic elements (TEs) and largely facilitate the dissemination of TEs.

[Effects of antibiotics on the transfer frequency of SXT/R391 element of Vibrio alginolyticus].

Objective: We studied the effects of nalidixic acid, norfloxacin and kanamycin on the transfer frequency of SXT/R391 element ICEValA056-1 in Vibrio alginolyticus. Methods: The circular ICEValA056-1 in V. alginolyticus A056 was detected by PCR. Conjugation experiments were conducted between V. alginolyticus A056 and Escherichia coli VB111 to explore the frequency variation of the integrating conjugative elements transfer after donor strain A056 was cultured in Luria Broth containing nalidixic acid or norfloxacin or kanamycin in different concentrations for 15 min or 30 min. Results: Circular ICEValA056-1 was detected in V. alginolyticus A056, indicating that ICEValA056-1 had the potential to transfer. Treatment with 40 µg/mL nalidixic acid for 30 min increased the transfer frequency of ICEValA056-1 to19.59 folds. Treatment with 50 µg/mL norfloxacin for 15 min increased the transfer frequency of ICEValA056-1 to 31.25 folds. The transfer frequency of ICEValA056-1 had no significant changes under treatment with different concentrations of kanamycin for 30 min. Conclusion: This study indicates that some antibiotics can obviously increase the transfer frequency of ICEValA056-1, and that antibiotics abuse and arbitrarily discharge might intensify dissemination of integrating conjugative elements from V. alginolyticus to other bacteria.

Developing Universal Genetic Tools for Rapid and Efficient Deletion Mutation in Vibrio Species Based on Suicide T-Vectors Carrying a Novel Counterselectable Marker, vmi480.

Despite that Vibrio spp. have a significant impact on the health of humans and aquatic animals, the molecular basis of their pathogenesis is little known, mainly due to the limited genetic tools for the functional research of genes in Vibrio. In some cases, deletion of target DNAs in Vibrio can be achieved through the use of suicide vectors. However, these strategies are time-consuming and lack universality, and the widely used counterselectable gene sacB does not work well in Vibrio cells. In this study, we developed universal genetic tools for rapid and efficient deletion mutations in Vibrio species based on suicide T-Vectors carrying a novel counterselectable marker, vmi480. We explored two uncharacterized genes, vmi480 and vmi470, in a genomic island from Vibrio mimicus VM573 and confirmed that vmi480 and vmi470 constitute a two-component toxin-antitoxin system through deletion and expression of vmi480 and vmi470. The product of vmi480 exhibited strong toxicity to Escherichia coli cells. Based on vmi480 and the PBAD or PTAC promoter system, we constructed two suicide T-vectors, pLP11 and pLP12, and each of these vectors contained a multiple cloning region with two AhdI sites. Both vectors linearized by AhdI digestion could be stored and directly ligated with purified PCR products without a digestion step. By using pLP11 and pLP12 coupled with a highly efficient conjugation system provided by E. coli ß2163, six genes from four representative Vibrio species were easily deleted. By using the counterselective marker vmi480, we obtained 3-12 positive colonies (deletion mutants) among no more than 20 colonies randomly selected on counterselection plates. The strategy does not require the digestion of PCR products and suicide vectors every time, and it avoids large-scale screening colonies on counterselective plates. These results demonstrate that we successfully developed universal genetic tools for rapid and efficient gene deletion in Vibrio species.

Pseudoalteromonas xishaensis sp. nov., isolated from Acanthaster planci in the Xisha islands.

A Gram-negative, aerobic, motile by means of single polar flagellum, short rod-shaped marine bacterium, designated strain E418T, was isolated from the spines on the body surface of starfish Acanthaster planci in the Xisha islands, China. Cells of strain E418T were found to grow optimally at pH 7­8, at 25­37 °C, and in the presence of 2­5 % (w/v) NaCl. Phylogenetic analysis based on the comparison of 16S rRNA gene sequences revealed that strain E418T is a member of the genus Pseudoalteromonas. The closest relative to this strain was found to be P. ruthenica LMG 19699T, with a similarity level of 97.7 %. DNA relatedness between the novel isolate and this phylogenetically related species was 57.4 %. Strain E418T decomposed Tween 80, gelatin, and casein, but was unable to decompose starch and grow on DNase Agar. The cellular fatty acid profile consisted of significant amounts of C16:1ω7c/C16:1ω6c, C18:1ω7c/C18:1ω6c, C16:0, and C17:1ω8c. The G+C content of DNA of this strain was determined to be 46.7 mol%. Phenotypic characteristics, phylogenetic analysis and DNA­DNA relatedness data suggest that strain E418T represents a novel species of the genus Pseudoalteromonas, for which the name Pseudoalteromonas xishaensis sp. nov. is proposed. The type strain of P. xishaensis is strain E418T (DSM 25588T = NBRC 108846T = CCTCC AB 2011177T).