Construction of a miRNA Signature Using Support Vector Machine to Identify Microsatellite Instability Status and Prognosis in Gastric Cancer.

Background: The specific role and prognostic value of DNA repair and replication-associated miRNAs in gastric cancer (GC) have not been clearly elucidated. Therefore, comprehensive analysis of miRNAs in GC is crucial for proposing therapeutic strategies and survival prediction. Methods: Firstly, clinical information and transcriptome data of TCGA-GC were downloaded from the database. In the entire cohort, we performed differential analysis in all miRNAs and support vector machine (SVM) was used to eliminate redundant miRNAs. Subsequently, we combined survival data and cox regression analysis to construct a miRNA signature in the training cohort. In addition, we used PCA, Kaplan-Meier, and ROC analysis to explore the prognosis value of risk score in the training and testing cohort. It is worth noting that multiple algorithms were used to evaluate difference of immune microenvironment (TME), microsatellite instability (MSI), tumor mutational burden (TMB), and immunotherapy in different risk groups. Finally, we investigated the potential mechanism about miRNA signature. Results: We constructed miRNA signature based on the following 4 miRNAs: hsa-miR-139-5p, hsa-miR-139-3p, hsa-miR-146b-5p, and hsa-miR-181a-3p. Univariate and multivariate Cox regression analyses suggested that risk score is a risk factor and an independent prognostic factor in GC patients. The AUC value of ROC analysis showed a robust prediction accuracy in each cohort. Moreover, significant differences in immune functions, immune cell content, immune checkpoint, MSI status, and TMB score were excavated in different groups distinguished by risk score. Finally, based on the above four miRNA target genes, we revealed that the signature was enriched in DNA repair and replication. Conclusion: We have developed a robust risk-formula based on 4 miRNAs that provides accurate risk stratification and prognostic prediction for GC patients. In addition, different risk subgroups may potentially guide the choice of targeted therapy.

Paracoccus shandongensis sp. nov., Isolated from Activated Sludge.

A novel strain, wg2T, was isolated from activated sludge obtained from wastewater treatment plant in Shandong province, China. The bacterium was Gram-strain-negative, aerobic, rod-shaped, non-flagellated and non-gliding. This bacterium was characterized to determine its taxonomic position using the polyphasic approach. Strain wg2T grew at 25-45 °C (optimum, 30 °C), at salinities of 0-7.0% (w/v) NaCl (optimum, 0-2.0%) and at pH 7-9 (optimum, pH 7.0). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain wg2T clustered with species of genus Paracoccus and shares high similarities with Paracoccus sediminis DSM 26170 T (98.1%) and Paracoccus fontiphilus MVW-1 T (97.7%), respectively. The genome size of strain wg2T was 3.93 Mbp and the DNA G + C content was 66.05%. The dDDH values and ANI between strain wg2T and each of reference strains P. sediminis DSM 26170 T, P. fontiphilus MVW-1 T and P. denitrificans DSM 413 T were 18.3, 12.5, 24.5% and 85.3, 87.0, 78.4%, respectively. The major respiratory quinone was found to be Q-10 and the major fatty acid was C18:1 ω7c. The polar lipids consisted of aminoglycolipid (AGL), phosphatidylcholine (PC), glycolipid (GL), phosphatidylserine (PS), phosphatidylglycerol phosphate (PGP), aminophospholipids (APL). Combining above descriptions, strain wg2T should represent a novel species of genus Paracoccus, for which the name Paracoccus shandongensis sp. nov., is proposed. The type strain is wg2T (= KCTC 72862 T = CCTCC AB 2019401 T).

Mesorhizobium xinjiangense sp. nov., isolated from rhizosphere soil of Alhagi sparsifolia.

A beige-pigmented, Gram-strain-negative, aerobic, rod-shaped, non-flagellated and non-gliding bacterium, designated strain lm94T, was isolated from rhizosphere soil of Alhagi sparsifolia obtained from Alar city, located in Xinjiang province, China. Growth occurred at 20-45 °C (optimum, 37 °C), in the presence of 0-6% (w/v) NaCl (optimum, 0-1%) and at pH 6.0-9.5 (optimum, pH 7.0-7.5). Phylogenetic analysis based on 16S rRNA gene sequence showed that strain lm94T belonged to the genus Mesorhizobium, with highest sequence similarity to Mesorhizobium wenxiniae WYCCWR 10195T (96.6%). Genome sequencing revealed a genome size of 5 256 375 bp and a G + C content of 63.6 mol%. The average nucleotide identity value and the digital DNA-DNA hybridization value between strain lm94T and M. wenxiniae LMG 30254T were 75.0% and 20.0%, respectively. The major respiratory quinone was Q-10. The major fatty acids were C19:0 cyclo ω8c and Summed Feature 8 (C18:1 ω6c and/or C18:1 ω7c) and its polar lipids consisted of phosphatidylethanolamine (PE), phosphatidylglycerol (PG), unidentified phospholipid (PL), phosphatidylcholine (PC), diphosphatidylglycerol (DPG), unidentified aminolipid (AL), unknown glycolipid (GL), unidentified aminophospholipid (APL2) and unidentified polar lipid (L1 and L2). On the basis of these data, strain lm94T is considered to represent a novel species of the genus Mesorhizobium, for which the name Mesorhizobium xinjiangense sp. nov. is proposed. The type strain is lm94T (=KCTC 72863T=CCTCC AB2019377T).

Chelativorans alearense sp. nov., A Novel Bacterial Species Isolated From Soil in Alear, China.

A novel Gram-strain-negative, rod-shaped, non-flagellated, non-gliding, beige-pigmented and aerobic bacterium, designated strain UJN715T, was isolated from rhizosphere soil of Alhagi sparsifolia obtained from Alear city, located in Xinjiang province, PR China. Growth optimally occurred at 37 °C, pH 6.5-7.5, and 0-3% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain UJN715T belonged to the genus Chelativorans, with the highest sequence similarity to Chelativorans multitrophicus DSM 9103 T (97.7%). Genome sequencing revealed a genome size of 5 702 301 bp and a G + C content of 64.1 mol%. The ANI, POCP and the dDDH between strain UJN715T and C. multitrophicus DSM 9103 T were 76.2%, 49.3%, and 20.5%, respectively. The prediction result of secondary metabolites based on genome showed that the strain UJN715T contained one cluster of ectoine production, one cluster of non-ribosomal peptide synthetase (NRPS), one cluster of type I polyketide synthases (TIPKS), one cluster of bacteriocin, one cluster of TfuA-related, one cluster of N-acetylglutaminylglutamine amide (NAGGN) production, one cluster of terpene production, two clusters of homoserine lactone (Hserlactone) production. The major respiratory quinone was Q-10. The major fatty acids were iso-C17:0, C18:0 and C19:0 cyclo ω8c and its polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, phospholipids, unknown lipids, diphosphatidylglycerol, aminoglycolipid, unidentified aminophospholipids. On the basis of these data, strain UJN715T is considered to represent a novel species of the genus Chelativorans, for which the name Chelativorans alearense sp. nov. is proposed. The type strain is UJN715T (= KCTC 72856T = CCTCC AB2019378T).

Paracoccus binzhouensis sp. nov., isolated from activated sludge.

A gram-stain-negative, non-motile and rod-shaped strain, designated wg1T, was isolated from activated sludge obtained from wastewater treatment plant in Binzhou (Shandong province, PR China). Growth of strain wg1T occurred at 25-45 °C (optimum, 37 °C), at pH 7.0-9.0 (optimum growth at pH 8.0) and at a salinity range of 0-4% (optimum, 1%). The chemotaxonomic, phenotypic and genomic traits were investigated. The 16S rRNA gene sequence analysis showed that strain wg1T belonged to the genus Paracoccus. The species with highest similarity to strain wg1T was Paracoccus communis VKM B-2787T (98.27%), followed by Paracoccus kondratievae VKM B-2222T (98.25%). The isoprenoid quinone was Q-10. Major cellular fatty acids were summed feature 8, C16:0 and C18:0. The major polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), aminoglycolipid (AGL), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), one unidentified lipid (L) and one unidentified phospholipid (PL). The genome size was 4,834,448 bp with a G+C content of 67.67 mol%. The prediction result of secondary metabolites based on genome has shown that the strain wg1T contained 12 clusters, and the gene involved in primary metabolism showed differences in the comparison between wg1T and reference strains. The dDDH values of strain wg1T with P. communis VKM B-2787T, P. kondratievae VKM B-2222T and P. denitrificans DSM 413T were 45.30, 30.60 and 39.50%, respectively. Based on its physiological properties, chemotaxonomic characteristics and low ANI and dDDH results, strain wg1T is considered to represent a novel species for which the name Paracoccus binzhouensis sp. nov., is proposed. The type strain is wg1T (= KCTC 72861T = CCTCC AB 2019400T).

Propylenella binzhouense gen. nov., sp. nov. isolated from activated sludge, and proposal of Propylenellaceae fam. nov.

A Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped, and aerobic bacterial strain (designated L72T) was isolated from propylene oxide saponification wastewater activated sludge obtained from a wastewater treatment facility in Binzhou (Shandong Province, PR China). Strain L72T grew between 25 and 40 °C (optimum growth at 30 °C). The pH range for growth was between 6.0 and 8.0 (optimum growth at pH 7.0). The range of NaCl concentrations for the growth of strain L72T was 0-3.0 % (w/v), with optimum growth at 1.0-2.0 % (w/v). The major cellular fatty acids of strain L72T were C19:0cyclo ω8c, C18:1ω7c, iso-C15:0, and anteiso-C15:0. Strain L72T contained Q-10 as the predominant respiratory quinone. The polar lipid profile was composed of Phosphatidylcholine, Glycolipid, Aminophospholipid, Phosphatidylethanolamine, Phosphatidylserine, Phosphatidyldimethylethanolamine, one unknown lipid (L) and two unidentified Phospholipids (PL). Genome sequencing revealed a genome size of 4,703,686 bp and a G + C content of 69.0 mol%. The 16S rRNA gene sequence similarities of strain L72T with other species were less than 94%. Phylogenetic analyses based on 16S rRNA gene sequences and genome data, revealed that strain L72T formed a distinct phylogenetic lineage within the order Hyphomicrobiales, separating them from members of all families. Strain L72T showed 70.7% average nucleotide identity and 18.6% digital DNA-DNA hybridization identity with the closely related species Rhodoligotrophos defluvii. Based on the phenotypic, phylogenetic and chemotaxonomic data, a new family Propylenellaceae fam. nov. comprising the genus Propylenella gen. nov. and species Propylenella binzhouense sp. nov. is proposed. The type strain is L72T (=  CCTCC AB 2019081T  =  KCTC 72254T).

Chelativorans xinjiangense sp. nov., a novel bacterial species isolated from soil in Xinjiang, China.

A novel Gram-strain-negative, beige-pigmented, aerobic, rod-shaped, non-flagellated and non-gliding bacterium, designated strain lm93T, was isolated from rhizosphere soil of Alhagi sparsifolia obtained from Alar city, located in Xinjiang province, China. Growth optimally occurred at 30 °C, pH 6.5-7.5, and 0-2% (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain lm93T belonged to the genus Chelativorans, with highest sequence similarity to Chelativorans multitrophicus DSM 9103T (96.9%). Genome sequencing revealed a genome size of 5 689 708 bp and a G + C content of 64.3 mol%. The ANI, POCP and the dDDH between strain lm93T and C. multitrophicus DSM 9103T were 76.4%, 54.8% and 0.8%, respectively. The prediction result of secondary metabolites based on genome showed that the strain lm93T contained one cluster of bacteriocin, one cluster of terpene production, two clusters of ectoine production, one cluster of non-ribosomal peptide synthetase, one cluster of type I polyketide synthases, three clusters of homoserine lactone production, one cluster of N-acetylglutaminylglutamine amide production and one cluster of phosphonate production. The major respiratory quinone was Q-10. The major fatty acids were C19:0 cyclo ω8c, iso-C17:0 and summed feature 8 (C18:1 ω6c and/or C18:1 ω7c) and its polar lipids consisted of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified aminophospholipids, aminoglycolipid, three unknown lipids and diphosphatidylglycerol. On the basis of these data, strain lm93T is considered to represent a novel species of the genus Chelativorans, for which the name Chelativorans xinjiangense sp. nov. is proposed. The type strain is lm93T (= KCTC 72857T = CCTCC AB2019376T).

Chryseobacterium binzhouense sp. nov., isolated from activated sludge.

A golden-pigmented, Gram-strain-negative, aerobic, rod-shaped, non-flagellated and non-gliding bacterium, designated strain lm2T, was isolated from activated sludge obtained from a wastewater treatment plant in Binzhou (Shandong province, PR China). Growth occurred at 15-45°C (optimum, 30 °C), in the presence of 0-5.0 % (w/v) NaCl (optimum, 0-2.0 %) and at pH 6.5-8.0 (optimum, pH 7.0-7.5). The chemotaxonomic, phenotypic and genomic traits were investigated. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain lm2T belonged to the genus Chryseobacterium, with highest sequence similarity to Chryseobacterium echinoideorum CC-CZW010T (97.1 %). Genome sequencing revealed a genome size of 3 611 894 bp and a G+C content of 34.9 mol%. The average nucleotide identity value and the digital DNA-DNA hybridization (dDDH) value between strain lm2T and C. echinoideorum JCM 30470T were 87.8 and 34.7 %, respectively. The major respiratory quinone was Menaquinone-6 (MK-6). The major fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and iso-C17 : 1 ω9c and its polar lipids consisted of phosphatidylethanolamine (PE), unidentified lipids (L1-5) and unidentified aminolipids (AL1-4). On the basis of these data, strain lm2T is considered to represent a novel species of the genus Chryseobacterium, for which the name Chryseobacterium binzhouense sp. nov. is proposed. The type strain is lm2T (=KCTC 72529T=CCTCC AB2019126T).

Rhodoligotrophos defluvii sp. nov., isolated from activated sludge.

A Gram-stain-negative, non-spore-forming, non-motile, short-rod-shaped and aerobic bacterial strain (designated lm1T) was isolated from propylene oxide saponification wastewater activated sludge obtained from a wastewater treatment facility in Binzhou (Shandong province, PR China). Strain lm1T grew between 15 and 45 °C (optimum, 40 °C). The pH range for growth was at pH 4.0-10.0 (optimum growth at pH 8.0). The range of NaCl concentration for the growth of strain lm1T was 0-4.0 % (w/v), with optimum growth at 1.0-2.0 % (w/v). Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain lm1T belonged to the genus Rhodoligotrophos and was closely related to Rhodoligotrophos appendicifer JCM 16873T (96.7 % 16S rRNA gene sequence similarity) and Rhodoligotrophosjinshengii CCTCC AB2013083T (96.2 %). The average nucleotide identity value and the digital DNA-DNA hybridization value between strain lm1T and R. appendicifer JCM 16873T were 73.4 and 14.3 %, respectively. The major cellular fatty acids of strain lm1T were C19 : 0cyclo ω8c, C18 : 1ω7c and C16 : 0. Strain lm1T contained Q-10 as the predominant respiratory quinone. The polar lipid profile was composed of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, three unidentified aminolipids, one unidentified glycolipid and five unknown lipids. The G+C content of the genomic DNA was 64.4 mol%. Based on polyphasic taxonomic data, strain lm1T could be classified as a representative of a novel species of the genus Rhodoligotrophos, for which the name Rhodoligotrophosdefluvii sp. nov. is proposed. The type strain is lm1T (=CCTCC AB2019071T=KCTC 72156T).

[Overview of patents on targeted genome editing technologies and their implications for innovation and entrepreneurship education in universities].

Zinc finger nuclease, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats/Cas9 nuclease are important targeted genome editing technologies. They have great significance in scientific research and applications on aspects of functional genomics research, species improvement, disease prevention and gene therapy. There are past or ongoing disputes over ownership of the intellectual property behind every technology. In this review, we summarize the patents on these three targeted genome editing technologies in order to provide some reference for developing genome editing technologies with self-owned intellectual property rights and some implications for current innovation and entrepreneurship education in universities.

[Progression on genetic knockout tools in Mycobacterium].

Pathogenic mycobacteria were and remain a heavy burden to public health. Unfortunately, genetic manipulation including knockout technologies of Mycobacterium is difficult compared with other traditional model organisms. To overcome this obstacle, achievements in Mycobacterium knockout technologies were summarized, including delivery vector, sequence-specific recombination system, as well as the recently developed recombinogenic engineering and its application. The future for this tool innovation is also addressed.

[The progress of nanomedicine inspired by bacteriophage].

Nanomedicine offers great promise for early diagnosis and treatment of formidable diseases. The unique morphology and biology characteristics of bacteriophage provide unprecedented opportunity for such endeavor. The paper summarizes the application of bacteriophage in nanobiomaterials, nanomedicine, nanomedicine delivery and nanodiagnosis, especially the nano-imaging reagents and future direction concerning nanomedicine based on bacteriophage.