Key genes and immune infiltration in chronic spontaneous urticaria: a study of bioinformatics and systems biology.

Background: Chronic spontaneous urticaria (CSU) is defined by the spontaneous occurrence of wheals and/or angioedema for >6 weeks. The pathogenesis involves skin mast cells, but the complex causes of their activation remain to be characterized in detail. Objectives: To explore disease-driving genes and biological pathways in CSU. Methods: Two microarray data sets, e.g., GSE57178 and GSE72540, with mRNA information of skin from CSU patients, were downloaded from the Gene Expression Omnibus (GEO) database. An integrated bioinformatics pipeline including identification of differentially expressed genes (DEGs), functional enrichment analysis, protein-protein interaction (PPI) network analysis, co-expression and drug prediction analysis, and immune and stromal cells deconvolution analyses were applied to identify hub genes and key drivers of CSU pathogenesis. Results: In total, we identified 92 up-regulated and 7 down-regulated genes in CSU lesions. These were significantly enriched in CSU-related pathways such as TNF, NF-κB, and JAK-STAT signaling. Based on PPI network modeling, four genes, i.e., IL-6, TLR-4, ICAM-1, and PTGS-2, were computationally identified as key pathogenic players in CSU. Immune infiltration analyses indicated that dendritic cells, Th2 cells, mast cells, megakaryocyte-erythroid progenitor, preadipocytes, and M1 macrophages were increased in lesional CSU skin. Conclusion: Our results offer new insights on the pathogenesis of CSU and suggest that TNF, NF-κB, JAK-STAT, IL-6, TLR-4, ICAM-1, and PTGS-2 may be candidate targets for novel CSU treatments.

Nocardioides nematodiphilus sp. nov., isolated from rhizosphere of Arabidopsis thaliana.

An actinobacterial strain, designated R-N-C8T, was isolated from the rhizosphere soil of Arabidopsis thaliana collected in Yunnan Province, south-west China. Based on the results of 16S rRNA gene sequence analysis, strain R-N-C8T had highest similarity to Nocardioides terrae CGMCC 1.7056T (96.5%), Nocardioides opuntiae KCTC 19804T (96.3%) and Nocardioides currus IB-3T (96.1%), and lower than 96.0 % similarity to other members of the genus Nocardioides. Phylogenetic trees based on 16S rRNA gene sequences indicated that strain R-N-C8T formed an isolated branch with N. terrae CGMCC 1.7056T and N. opuntiae KCTC 19804T. The polar lipids contained phosphatidylglycerol, diphosphatidylglycerol, one unidentified phosphoglycolipid and four unidentified phospholipids in the cellular membrane. The major fatty acids were identified as iso-C16 : 0, anteiso-C17 : 0, iso-C17 : 0, summed feature 9 (iso-C17 : 1 ω9c and/or C16 : 0 10-methyl) and iso-C15 : 0. The predominant respiratory quinone was MK-8(H4) and ll-diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The genomic DNA G+C content was 70.9 mol%. The orthologous average nucleotide identiy values between N. terrae CGMCC 1.7056T, N. currus IB-3T and strain R-N-C8T were 77.1 and 75.1 %, respectively. DNA-DNA hybridization values between N. terrae CGMCC 1.7056T, N. currus IB-3T and strain R-N-C8T were 20.7 and 19.9 % respectively. Data from phenotypic and genotypic analyses supported that strain R-N-C8T represents a new species of Nocardioides, for which the name Nocardioides nematodiphilus sp. nov. is proposed. The type strain is R-N-C8T (=CGMCC 1.18723T= KCTC 49528T).

First report of 'Candidatus Phytoplasma asteris' associated with witches'-broom disease of Macadamia ternifolia in China.

Macadamia nut (Macadamia ternifolia) was first introduced into China from Australia in 1910, and the main cultivation areas were Yunnan and Guangxi. It can be used as both a fruit and a therapeutic drug, with high economic value. In March 2021, it was observed that the M. ternifolia was showing witches'-broom, leaf yellowing and plexus bud in Dehong Prefecture, Yunnan Province, China. The terminal buds of infected plants were inhibited and the lateral buds are stimulated to germinate into twigs in advance. It was named the M. ternifolia witches'-broom disease, and was found in urban and rural areas of Mangshi, Lianghe, Yingjiang, Mangdong, Longchuan and Longling cities and counties. More than 40% of the plants were infected on the seven areas surveyed. The lateral stems from symptomatic and asymptomatic plants were cut to small pieces. The tissues were treated by fixation, dehydration and spraying-gold. And the tissues were observed under a scanning electron microscope (Hitachi S-3000N) (Pathan et al. 2010). The nearly spherical bodies were found in the phloem sieve cells of symptomatic plants. Symptomatic and asymptomatic plants were collected from seven areas, ddH2O was used as the negative control, and Dodonaea viscose witches'-broom disease plants were used as the positive control. The total plants' DNA extraction was conducted from 0.1 g tissue using the CTAB method (Porebski et al. 1997), and were stored at -20 °C in a refrigerator in the Key Laboratory of Forest Disaster Warning and Control at the Southwest Forestry University. The nested PCR was employed to amplify the 16S rRNA gene with the primers P1/P7 and R16F2/R16R2 (Lee et al. 1993; Schneider et al. 1993). PCR amplicon of 1.8 kb and 1.2 kb were amplified (GenBank accessions MW892818, MW892819, MW892820, MW892821). The direct PCR with primer pairs rp(I)F/ rp(I)R (Lee et al. 2003) specific to the ribosomal protein (rp) gene yielded amplicons of approximately 1.2 kb (GenBank accessions MZ442600, MZ442601, MZ442602, MZ442603). The fragment from 21 samples was consistent with the positive control, confirming the association of phytoplasma with the disease. Interestingly, the phytoplasma/span>16S rRNA gene and rp gene was also amplified from the 4 samples of asymptomatic plant, we speculated that the latent infection and hidden symptoms existed in Macadamia nut (Moslemkhani and Sadeghi 2011). A BLAST analysis of the 16S rRNA sequences of MTWB phytoplasma showed that it has a 99% similarity with Trema laevigata witches'-broom phytoplasma (GenBank accession MG755412). The rp sequence shared 99% identity with 'Salix tetradenia' witches'-broom phytoplasma (GenBank accession KC117314). An analysis with iPhyClassifier showed that the virtual RFLP pattern derived from the query 16S rDNA fragment of MTWB phytoplasma is most similar to the reference pattern of the 16Sr group I, subgroup B (OY-M, GenBank accession AP006628), with a pattern similarity coefficient of 0.99. The phytoplasma is identified as 'Ca. Phytoplasma asteris'-related strain belonging to sub-group 16SrI-B. The phylogenetic tree was constructed based on 16S rRNA gene and rp gene sequences by using MEGA version 6.0 (Tamura et al. 2013) with neighbor-joining (NJ) method and bootstrap support was estimated with 1000 replicates. The result indicated that the MTWB phytoplasma formed a subclade in 16SrI-B and rpI-B respectively. In 2013, Macadamia nut showed leaf hardness phyllody and shoot proliferation caused by 'Ca. Phytoplasma asteris' in Artemisa, Cuba. The concern is that, the macadamia phytoplasma is closely related to the subgroup 16SrI-F, and it is significantly different from the Chinese strains (Pérez-López et al. 2013). In addition, the MTWB phytoplasma was graft-transmitted from infected to healthy plants in nursery conditions (Akhtar et al. 2009; Ikten et al. 2014). And the grafted plants were positive for the phytoplasma in the nested PCR assays. It is noteworthy that the plants were seriously damaged by aphid and it was speculated that the insects of Homoptera caused the spread of the disease by sucking plant sap, thus the aphids that transmits MTWB in China must be determined to control the M. ternifolia witches'-broom disease. To the best of our knowledge, Macadamia nut is a new host plant of 'Ca. Phytoplasma asteris' in China. The newly emerged disease is a threat to Macadamia nut.

Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis.

Background: Although more and more evidence has supported psoriasis is prone to atherosclerosis, the common mechanism of its occurrence is still not fully elucidated. The purpose of this study is to further explore the molecular mechanism of the occurrence of this complication. Methods: The gene expression profiles of psoriasis (GSE30999) and atherosclerosis (GSE28829) were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the common differentially expressed genes (DEGs) of psoriasis and atherosclerosis, three kinds of analyses were performed, namely functional annotation, protein-protein interaction (PPI) network and module construction, and hub gene identification and co-expression analysis. Results: A total of 94 common DEGs (24 downregulated genes and 70 upregulated genes) was selected for subsequent analyses. Functional analysis emphasizes the important role of chemokines and cytokines in these two diseases. In addition, lipopolysaccharide-mediated signaling pathway is closely related to both. Finally, 16 important hub genes were identified using cytoHubba, including LYN, CSF2RB, IL1RN, RAC2, CCL5, IRF8, C1QB, MMP9, PLEK, PTPRC, FYB, BCL2A1, LCP2, CD53, NCF2 and TLR2. Conclusions: Our study reveals the common pathogenesis of psoriasis and atherosclerosis. These common pathways and hub genes may provide new ideas for further mechanism research.

Sphingobacterium lumbrici sp. nov., a novel bacterium isolated from wormcast of Eisenia foetida.

A novel Gram-stain-negative, rod-shaped, non-motile, yellowish bacterium, designated strain 1.3611T, was isolated from the wormcast of Eisenia foetida. The strain grew optimally at 30-37 ℃, at pH 7.0 and with 0-1.0 % (w/v) NaCl. Based on the results of 16S rRNA gene sequence and phylogenetic analyses, strain 1.3611T showed the highest degree of 16S rRNA gene sequence similarity to Sphingobacterium olei HAL-9T (97.0 %), followed by Sphingobacterium alkalisoli Y3L14T (95.8 %). The respiratory quinone of strain 1.3611T was menaquinone-7 (MK-7) and its major cellular fatty acids were iso-C15 : 0 (41.3 %), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c, 22.1 %) and iso-C17 : 0 3-OH (16.2 %). The major polar lipids were sphingophospholipid, phosphatidylethanolamine, four unidentified glycolipids, two unidentified phospholipids and five unidentified polar lipids. The genomic DNA G+C content was 39.0 mol%. The digital DNA-DNA hybridization and average nucleotide identity values between the genomes of strain 1.3611T and S. olei HAL-9T were 37.9 and 88.9 %, respectively. According to the phenotypic and chemotaxonomic phylogenetic results, strain 1.3611T should represent a novel species of the genus Sphingobacterium, for which the name Sphingobacterium lumbrici sp. nov. is proposed, with strain 1.3611T (=KCTC 62980T=CCTCC AB 2018349T) as the type strain.

Morbidity and maternal and infant outcomes of hypertensive disorder in pregnancy in China in 2018.

Hypertensive disorder in pregnancy is a disease that occurs during pregnancy. We aimed to analyze the morbidity and maternal and infant outcomes with respect to the hypertensive disorder in pregnancy in China in 2018. Clinical data of 38 590 cases from 161 hospitals were retrospectively collected. The differences in morbidity and maternal and infant mortality among the major regions and provinces were compared. The overall national average morbidity was 4.74%, and the ratios of gestational hypertension, preeclampsia, eclampsia, chronic hypertension, and chronic hypertension with superimposed preeclampsia were 29.17%, 55.02%, 0.66%, 6.53%, and 8.62%, respectively. The overall maternal mortality was 0.61/100 000, and the case fatality was 0.13%. Morbidity associated with hypertensive disorder in pregnancy was 7.74% in North China, 6.62% in Northwest China, 6.40% in Central China, 5.83% in Northeast China, 4.28% in East China, 3.85% in South China, and 2.88% in Southwest China. The morbidity in each province was 1.62-11.28%. The overall perinatal mortality was 3.59% (81.09% for stillbirths; 18.91% for neonatal deaths). Perinatal mortality decreased with increasing gestational weeks from 24 to 37 + 6 weeks. Perinatal mortality for delivery at 32 weeks of gestation in all regions of the country was <10%. Morbidity varied across regions in China, with the lowest in Southwest and the highest in North China. The low maternal mortality is related to the large-scale development of standardized maternal health care in China. For severe hypertensive disorder patients, gestation should be prolonged to 32 weeks as often as possible for better neonatal survival rates.

Identification of Hub Genes and Immune Infiltration in Psoriasis by Bioinformatics Method.

BACKGROUND: Psoriasis is a chronic, prolonged, and recurrent skin inflammatory disease. However, the pathogenesis of psoriasis is not completely clear, thus we aimed to explore potential molecular basis of it. METHODS: Two datasets were downloaded from the Gene Expression Omnibus database. After identifying the differentially expressed genes of psoriasis skin lesion samples and healthy controls, three kinds of analyses, namely functional annotation, protein-protein interaction (PPI) network, and immune infiltration analyses, were performed. RESULTS: A total of 152 up-regulated genes and 38 down-regulated genes were selected for subsequent analyses. Evaluation of the PPI network identified the most important module containing 13 hub genes. Gene ontology analysis showed that the hub genes have a significant enrichment effect on positive regulation of cell migration, defense response to the other organism and epithelial cell differentiation. KEGG signaling pathway analysis showed that the hub genes were significantly enriched in chemokine signaling, Toll-like receptor signaling pathway, and IL-17 signaling pathway. Compared with the normal control sample, naive B cells, CD8+ T cells, activated memory CD4+ T cells, follicular helper T cells, gamma delta T cells, resting NK cells, monocytes, M0 macrophages, M1 macrophages, activated dendritic cells and neutrophils infiltrated more, while memory B cells, naive CD4+ T cells, regulatory T cells (Tregs), activated NK cells, resting mast cells, and eosinophils infiltrated less. CONCLUSION: To conclude, the hub genes and pathways identified from psoriasis lesions and normal controls along with the immune infiltration profile may provide new insights into the study of psoriasis.

Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis.

BACKGROUND: Melanoma has the highest mortality rate of all skin tumors, and metastases are the major cause of death from it. The molecular mechanism leading to melanoma metastasis is currently unclear. METHODS: With the goal of revealing the underlying mechanism, three data sets with accession numbers GSE8401, GSE46517 and GSE7956 were downloaded from the Gene Expression Omnibus (GEO) database. After identifying the differentially expressed gene (DEG) of primary melanoma and metastatic melanoma, three kinds of analyses were performed, namely functional annotation, protein-protein interaction (PPI) network and module construction, and co-expression and drug-gene interaction prediction analysis. RESULTS: A total of 41 up-regulated genes and 79 down-regulated genes was selected for subsequent analyses. Results of pathway enrichment analysis showed that extracellular matrix organization and proteoglycans in cancer are closely related to melanoma metastasis. In addition, seven pivotal genes were identified from PPI network, including CXCL8, THBS1, COL3A1, TIMP3, KIT, DCN, and IGFBP5, which have all been verified in the TCGA database and clinical specimens, but only CXCL8, THBS1 and KIT had significant differences in expression. CONCLUSIONS: To conclude, CXCL8, THBS1 and KIT may be the hub genes in the metastasis of melanoma and thus may be regarded as therapeutic targets in the future.

Sphingobacterium cavernae sp. nov., a novel bacterium isolated from soil sampled at Tiandong Cave.

A Gram-stain-negative, non-motile and rod-shaped bacterium, designated strain 5.0403-2T, was isolated from a cave soil sample collected from Tiandong Cave, Guizhou Province, south-west PR China. Cells showed positive oxidase and catalase reactions. The predominant isoprenoid quinone was MK-7. The major fatty acids were identified as iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C17 : 0 3OH and summed feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl). The cellular polar lipids contained phosphatidylethanolamine, one unidentified phospholipid, three unidentified phosphoglycolipids and four unidentified lipids. The genomic DNA G+C content was 36.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 5.0403-2T should be assigned to the genus Sphingobacterium. Results of 16S rRNA gene sequence similarity analysis showed that strain 5.0403-2T was most similar to Sphingobacterium bovisgrunnientis KCTC 52685T (98.7 %), Sphingobacterium composti KCTC 12578T (98.0 %) and Sphingobacterium alimentarium DSM 22362T (97.3 %) and less than 95.0 % similar to other species of the genus Sphingobacterium. The average nucleotide identity values between strain 5.0403-2T and S. bovisgrunnientis KCTC 52685T, S. composti KCTC 12578T and S. alimentarium DSM 22362T were 94.2, 82.3 and 77.2 % respectively. The digitalDNA-DNA hybridization values between strain 5.0403-2T and S. bovisgrunnientis KCTC 52685T, S. composti KCTC 12578T and S. alimentarium DSM 22362T were 68.4, 25.6 and 20.7 %. These results indicated that the isolate represented a novel genomic species. The polyphasic taxonomic characteristics indicated that strain 5.0304-2T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium cavernae sp. nov. (type strain 5.0403-2T=KCTC 62981T=CCTCC AB 2019257T) is proposed.

Luteimonas lumbrici sp. nov., a novel bacterium isolated from wormcast.

A Gram-stain-negative, yellow-green bacterium, designated 1.1416T, was isolated from wormcast of Eisenia foetida. The strain was non-motile, rod-shaped, and grew optimally on NA medium at 30 °C, pH 7.0 and with 0 % (w/v) NaCl. On the basis of the 16S rRNA gene sequence and phylogenetic analysis, 1.1416T showed the highest degree of 16S rRNA gene sequence similarity to Luteimonas arsenica 26-35T (96.2 %), followed by Luteimonas lutimaris G3T (96.1 %). The respiratory quinone of 1.1416T was ubiquinone-8 (Q-8), and its major cellular fatty acids were iso-C15 : 0 (39.8 %), summed feature 9 (iso-C17 : 1 ω9c or C16 : 0 10-methyl) (18.6 %). The major polar lipids of 1.1416T were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and six unidentified phospholipids. The genomic DNA G+C content of 1.1416T was 71.0 mol%. According to the results of the phenotypic and chemotaxonomic phylogenetic analyses, strain 1.1416T represents a novel species of the genus Luteimonas, for which the name Luteimonas lumbrici sp. nov. is proposed, with strain 1.1416T (=KCTC 62979T=CCTCC AB 2018348T) as the type strain.

Asticcacaulis tiandongensis sp. nov., a new member of the genus Asticcacaulis, isolated from a cave soil sample.

A Gram-stain negative, aerobic, motile and rod-shaped bacterium, designated strain 3.1105T, was isolated from a karst district soil sample collected from Tiandong cave, Guizhou province, south-west PR China. The isolate grew at 10-40 °C and pH 5.0-8.0 and tolerated up to 1 % NaCl (w/v) on R2A medium, with optimal growth at 25-30 °C, pH 7.0 and 0 % NaCl (w/v). Cells showed oxidase-positive and catalase-positive reactions. The respiratory quinone was Q-10. The predominant cellular fatty acids contained C18 : 1ω7c 11-methyl, summed feature 8 (C18 : 1ω7c or C18 : 1ω6c), C16 : 0 and C17 : 0. The major polar lipids were phosphatidylglycerol and monoglycosyldiglycerides. The genomic DNA G+C content was 56.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that 3.1105T should be affiliated to the genus Asticcacaulis and showed highest 16S rRNA gene sequence similarity values with Asticcacaulis excentricus CB 48T (96.0 %), Asticcacaulis endophyticus ZFGT-14T (95.3 %) and lower than 95.3 % similarity to other species of the genus Asticcacaulis. The polyphasic taxonomic characteristics indicated that strain 3.1105T represents a novel species of the genus Asticcacaulis, for which the name Asticcacaulis tiandongensis sp. nov., (type strain 3.1105T=KCTC 62978T=CCTCC AB 2018268T) is proposed.