Erratum: Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform.

This corrects the article 10.3791/66058.

Multi-Gene Single Nucleotide Polymorphism Detection in Gastric Cancer Based on Ion Semiconductor Sequencing Platform.

Gastric cancer is a common heterogeneous tumor. Most patients have advanced gastric cancer at the time of diagnosis and often need chemotherapy. Although 5-fluorouracil (5-FU) is widely used for treatment, its therapeutic sensitivity and drug tolerance still need to be determined, which emphasizes the importance of individualized administration. Pharmacogenetics can guide the clinical implementation of individualized treatment. Single nucleotide polymorphisms (SNPs), as a genetic marker, contribute to the selection of appropriate chemotherapy regimens and dosages. Some SNPs are associated with folate metabolism, the therapeutic target of 5-FU. Methylenetetrahydrofolate reductase (MTHFR) rs1801131 and rs1801133, dihydrofolate reductase (DHFR) rs1650697 and rs442767, methionine synthase (MTR) rs1805087, gamma-glutamyl hydrolase (GGH) rs11545078 and solute carrier family 19 member 1 (SLC19A1) rs1051298 have been investigated in different kinds of cancers and antifolate antitumor drugs, which have potential forecasting and guiding significance for application of 5-FU. The ion torrent next-generation semiconductor sequencing technology can rapidly detect gastric cancer-related SNPs. Each time a base is extended in a DNA chain, an H+ will be released, causing local pH changes. The ionic sensor detects pH changes and converts chemical signals into digital signals, achieving sequencing by synthesis. This technique has low sample requirement, simple operation, low cost, and fast sequencing speed, which is beneficial for guiding individualized chemotherapy by SNPs.

Aerococcus agrisoli sp. nov., isolated from paddy soil.

A non-spore-forming, Gram-stain-positive, short rod-shaped strain, designated SJQ22T, was isolated from a paddy soil sample collected in Shanghai, PR China. A comparative analysis of 16S rRNA gene sequences showed that strain SJQ22T fell within the genus Aerococcus, forming a clear cluster with the type strains of Aerococcus viridans (98.6 % sequence similarity) and Aerococcus urinaeequi (98.5 % sequence similarity). Strain SJQ22T grew at 30-45 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0) and with a NaCl concentration of 0-4 % (optimum, 1 %). Cells were negative for oxidase and catalase activity. Chemotaxonomic analysis showed that strain SJQ22T possessed C16:0 and C18:1 ω9c as the predominant fatty acids. The DNA G + C content was 39.0 mol%. Strain SJQ22T exhibited DNA-DNA relatedness levels of 13±2 % with A. viridans ATCC 11563T and 9±2 % with A. urinaeequi IFO 12173T. Based on the data obtained, strain SJQ22T represents a novel species of the genus Aerococcus, for which the name Aerococcus agrisoli sp. nov. is proposed. The type strain is SJQ22T (=JCM 33111T=CCTCC AB 2018283T).

Clinical outcomes of conversion surgery following immune checkpoint inhibitors and chemotherapy in stage IV gastric cancer.

BACKGROUND: The clinical benefit of conversion surgery following immunochemotherapy in patients with stage IV gastric cancer (GC) remains uncertain. This study aims to clarify the clinical outcomes of conversion surgery for such patients. METHODS: This retrospective cohort study enroled consecutive patients with stage IV GC treated with a combination of immune checkpoint inhibitors and chemotherapy and/or anti-human epidermal growth factor receptor-2 targeted therapy as first-line therapy. Cumulative survival curves were estimated using Kaplan-Meier method. Logistic regression and Cox regression analyses were conducted to identify factors associated with conversion surgery and survival, respectively. RESULTS: Among the 136 patients included in the study. The disease control rate was 72.1% (98/136), with objective response rate in 58.8% (80/136) and complete response rate in 5.9% (8/136). Among 98 patients with disease control, 56 patients underwent palliative immunochemotherapy with median progression-free survival (PFS) and overall survival at 9.2 and 16.2 months, respectively; the remaining 42 patients underwent conversion surgery, yielding an unreached median PFS over a 19.0-month median follow-up, accompanied by 1-year overall survival and PFS rates of 96.6% and 89.1%, respectively. The R0 resection rate reached 90.5% (38/42). 7 out of 42 patients achieved pathological complete response, of whom three patients demonstrated human epidermal growth factor receptor-2 positivity. No serious complications leading to death were observed during the perioperative period. Multivariate analysis indicated that programmed death ligand 1 combined positive score greater than or equal to 5 (odds ratio, 0.22; 95% CI, 0.08-0.57; P =0.002) favored successful conversion surgery, while signet ring cell carcinoma (hazard ratio, 6.29; 95% CI, 1.56-25.36; P =0.010) was the poor prognostic factor associated with survival in patients who underwent conversion surgery. CONCLUSIONS: Conversion surgery holds the potential for significant survival benefits in stage IV GC patients who have achieved a favourable clinical response to immunochemotherapy. Individuals with signet ring cell carcinoma may experience increased post-conversion surgery recurrence.

Oxidation leaching of chromium from electroplating sludge: Ultrasonic enhancement and its mechanism.

The oxidation leaching of chromium from electroplating sludge was investigated, and ultrasonication was introduced for the enhancement of the leaching process. Two different types of Cr-bearing electroplating sludge were selected for the study, and the effects of the reagent dosage, temperature, and ultrasonic pulse ratio on the leaching efficiency were tested through oxidation leaching experiments. The experimental results show that hydrogen peroxide and sodium hypochlorite exhibit different leaching effects on different types of electroplating sludge. The control of reagent dosage is crucial for the oxidation leaching of Cr, while the effect of temperature turns out to be small. Hydrogen peroxide turns out to be a more effective oxidizer for chromium sludge, and the leaching efficiency of Cr could be promoted from 77.52% to 87.08% using ultrasonic enhancement under optimum conditions. Interestingly, sodium hypochlorite exhibited better leaching efficiency than hydrogen peroxide for the mixed sludge since the organic matter in the mixed sludge will lead to the rapid decomposition and consumption of hydrogen peroxide. The leaching efficiency of Cr from the mixed sludge could also be promoted from 56.82% to 67.10% using ultrasonic enhancement under optimum conditions. According to the scanning electron microscope imaging, ultrasonic enhancement can create voids and cracks on the surface of the sludge particles, hence promoting the contact between electroplating sludge and leaching agents, and promoting the oxidation leaching efficiency. In addition, ultrasound seems to be able to remove the coverings on the surface of the mixed sludge particles, which may facilitate the oxidation reaction.

Aquabacterium soli sp. nov., a novel bacterium isolated from soil under the long-term application of bifenthrin.

Strain SJQ9T, an aerobic bacterium isolated from a soil sample collected in Shanghai, PR China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, 30-35 °C and in the presence of 1 % (w/v) NaCl. A comparative analysis of 16S rRNA gene sequences showed that strain SJQ9T fell within the genus Aquabacterium. The closest phylogenetic relatives of strain SJQ9T were Aquabacterium citratiphilum DSM 11900T (98.6 % sequence similarity) and Aquabacterium commune DSM 11901T (96.4 %). Cells of the strain were Gram-stain-negative, motile, non-spore-forming, rod-shaped and positive for oxidase activity and negative for catalase. The chemotaxonomic properties of strain SJQ9T were consistent with those of the genus Aquabacterium: the major fatty acid was summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c). The isoprenoid quinone was Q-8. The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content was 65.7 mol%. Strain SH9T exhibited a DNA-DNA relatedness level of 34±2 % with A. citratiphilum DSM 11900T and 28±3 % with A. commune DSM 11901T. Based on the obtained data, strain SJQ9T represents a novel species of the genus Aquabacterium, for which the name Aquabacterium soli sp. nov. is proposed. The type strain is SJQ9T (=JCM 33106T=CCTCC AB 2018284T).

Characterization of the Propham Biodegradation Pathway in Starkeya sp. Strain YW6 and Cloning of a Novel Amidase Gene mmH.

We previously isolated a monocrotophos-degrading strain Starkeya sp. YW6, which could also degrade propham. Here, we show that strain YW6 metabolizes propham via a pathway in which propham is initially hydrolyzed to aniline and then converted to catechol, which is then oxidized via an ortho-cleavage pathway. The novel amidase gene mmH was cloned from strain YW6 and expressed in Escherichia coli BL21(DE3). MmH, which exhibits aryl acylamidase activity, was purified for enzymatic analysis. Bioinformatic analysis confirmed that MmH belongs to the amidase signature (AS) enzyme family and shares 26-50% identity with several AS family members. MmH (molecular mass of 53 kDa) was most active at 40 °C and pH 8.0 and showed high activity toward propham, with Kcat and Km values of 33.4 s-1 and 16.9 µM, respectively. These characteristics make MmH suitable for novel amide biosynthesis and environmental remediation.

Falsochrobactrum shanghaiense sp. nov., isolated from paddy soil and emended description of the genus Falsochrobactrum.

A non-spore-forming, motile, Gram-stain-negative, short rod-shaped strain, designated HN4T, was isolated from a paddy soil sample collected in Shanghai, China. A comparative analysis o-f 16S rRNA gene sequences showed that strain HN4T fell within the genus Falsochrobactrum, forming a clear cluster with the type strain of Falsochrobactrum ovis, with which it exhibited a 16S rRNA gene sequence similarity value of 98.2 %. Strain HN4T grew optimally at pH 7.0, 30-35 °C and in the presence of 1 % (w/v) NaCl. It was positive for oxidase activity. Chemotaxonomic analysis showed that strain HN4T contained ubiquinone-10 as the predominant respiratory quinone and possessed summed feature 8(C18 : 1ω7c and/or C18 : 1ω6c) and C19 : 0cyclo ω8c as predominant fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine. The DNA G+C content was 56.9 mol%. Strain HN4T exhibited a DNA-DNA relatedness level of 18±1 % with Falsochrobactrum ovis CCM 8460T. Based on the data obtained in this study, strain HN4T represents a novel species of the genus Falsochrobactrum, for which the name Falsochrobactrumshanghaiense sp. nov. is proposed. The type strain is HN4T (=JCM 32785T=CCTCC AB 2018063T).

Alsobacter soli sp. nov., a novel bacterium isolated from paddy soil, emended description of the genus Alsobacter and description of the family Alsobacteraceae fam. nov.

Strain SH9T, an aerobic bacterium isolated from a paddy soil sample collected in Shanghai, China, was characterized using a polyphasic approach. It grew optimally at pH 7.0, temperatures of 30-35 °C and in the presence of 1 % (w/v) NaCl. Comparative analysis of 16S rRNA gene sequences showed that strain SH9T fell within the genus Alsobacter, forming a clear cluster with the type strain of Alsobacter metallidurans, with which it exhibited a 16S rRNA gene sequence similarity value of 98.5 %. Cells of strain SH9T were Gram-stain-negative, motile, non-spore-forming, rod-shaped, positive for catalase and oxidase activity, and negative for atmospheric nitrogen fixation and nitrate reduction. The strain was a chemo-organotrophic bacterium, incapable of growth on C1 substrates. The chemotaxonomic properties of strain SH9T were consistent with those of the genus Alsobacter: the predominant ubiquinone was Q-10, and the major fatty acid was summed feature 8 (C18 : 1ω7c and/or C18 : 1ω6c). The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine and phosphatidylmonomethylethanolamine. The DNA G+C content was 68.5 mol%. Strain SH9T exhibited a DNA-DNA relatedness level of 20±2 % with A. metallidurans NBRC 107718T. Based on the data obtained, strain SH9T represents a novel species of the genus Alsobacter, for which the name Alsobactersoli sp. nov. is proposed. The type strain is SH9T (=JCM 32501T=CCTCC AB 2017284T). A new family, Alsobacteraceae fam. nov., is also proposed encompassing strain SH9T and Alsobacter metallidurans NBRC 107718T.

DGCR5 induces osteogenic differentiation by up-regulating Runx2 through miR-30d-5p.

BACKGROUND: Postmenopausal osteoporosis (PMOP) is a metabolic bone disease caused by unbalance between osteoblast bone formation and osteoclast bone resorption. In this study, the moderating effect of DGCR5 on osteogenic differentiation and its role in PMOP was assessed. METHODS: The expression levels of DGCR5, miR-30d-5p, and Runt-related transcription factor 2 (Runx2) mRNA and protein were determined by qRT-PCR and western blot, separately. The bone marrow human mesenchymal stem cells (hMSCs) were isolated from bone marrow of patients with PMOP or the healthy control. ALP activity and bone mineral density (BMD) were detected to reflect the osteogenic differentiation status. RIP and RNA pull-down assay were performed to explore the combination and interaction between DGCR5 and miR-30d-5p. RESULTS: Compared with the healthy control group (n = 20), DGCR5 was down-regulated in hMSCs from patients with PMOP (n = 20). Overexpression of DGCR5 induced osteogenic differentiation of hMSCs. DGCR5 up-regulated the expression of Runx2 through miR-30d-5p. DGCR5 up-regulated the expression of Runx2 through miR-30d-5p to induce osteogenic differentiation of hMSCs. CONCLUSION: DGCR5 negatively regulates miR-30d-5p, and it up-regulates Runx2 through miR-30d-5p, thereby inducing osteogenic differentiation of hMSCs, which may help to delay PMOP development.

Isolation of monocrotophos-degrading strain Sphingobiumsp. YW16 and cloning of its TnopdA.

The bacterial strain Sphingobium sp. YW16, which is capable of degrading monocrotophos, was isolated from paddy soil in China. Strain YW16 could hydrolyze monocrotophos to dimethylphosphate and N-methylacetoacetamide and utilize dimethylphosphate as the sole carbon source but could not utilize N-methylacetoacetamide. Strain YW16 also had the ability to hydrolyze other organophosphate pesticides. A fragment (7067 bp) that included the organophosphorus hydrolase gene, opdA, was acquired from strain YW16 using the shotgun technique combined with SEFA-PCR. Its sequence illustrated that opdA was included in TnopdA, which consisted of a transpose gene, a putative integrase gene, a putative ATP-binding protein gene, and opdA. Additionally, a conjugal transfer protein gene, traI, was located downstream of TnopdA. The juxtaposition of TnopdA with TraI suggests that opdA may be transferred from strain YW16 to other bacteria through conjugation. OpdA was able to hydrolyze a wide range of organophosphate pesticides, with the hydrolysis efficiency decreasing as follows: methyl parathion > fenitrothion > phoxim > dichlorvos > ethyl parathion > trichlorfon > triazophos > chlorpyrifos > monocrotophos > diazinon. This work provides the first report of opdA in the genus Sphingobium.

Deregulated AJAP1/ß-catenin/ZEB1 signaling promotes hepatocellular carcinoma carcinogenesis and metastasis.

Adherens junctions-associated protein 1 (AJAP1) is an integral membrane protein that is thought to function as a tumor suppressor in various malignancies. Downregulation of AJAP1 mRNA levels may predict recurrence in hepatocellular carcinoma (HCC) patients, but the underlying molecular mechanism is unknown. This was addressed in the present study by examining the role of AJAP1 in HCC cell proliferation, migration, and invasion in vitro as well as in human specimens and mouse xenograft model. We found that AJAP1 expression was reduced in HCC cells and human HCC tissue, which was associated with metastasis. AJAP1 overexpression inhibited HCC progression and metastasis, while its silencing had the opposite effect both in vitro and in vivo. Furthermore, AJAP1 blocked epithelial-to-mesenchymal transition by interacting with ß-catenin and inhibiting its nuclear translocation, which suppressed zinc finger E-box binding homeobox 1 (ZEB1) transcription. These results indicate that AJAP1 inhibits HCC metastasis, and is thus a potential therapeutic target for HCC treatment.