O ⁶-carboxymethyl guanine(O ⁶-CMG) is a highly mutagenic alkylation product of DNA that causes gastrointestinal cancer in organisms. Existing studies used mutant Mycobacterium smegmatis porin A (MspA) nanopore assisted by Phi29 DNA polymerase to localize it. Recently, machine learning technology has been widely used in the analysis of nanopore sequencing data. But the machine learning always need a large number of data labels that have brought extra work burden to researchers, which greatly affects its practicability. Accordingly, this paper proposes a nano-Unsupervised-Deep-Learning method (nano-UDL) based on an unsupervised clustering algorithm to identify methylation events in nanopore data automatically. Specially, nano-UDL first uses the deep AutoEncoder to extract features from the nanopore dataset and then applies the MeanShift clustering algorithm to classify data. Besides, nano-UDL can extract the optimal features for clustering by joint optimizing the clustering loss and reconstruction loss. Experimental results demonstrate that nano-UDL has relatively accurate recognition accuracy on the O ⁶-CMG dataset and can accurately identify all sequence segments containing O ⁶-CMG. In order to further verify the robustness of nano-UDL, hyperparameter sensitivity verification and ablation experiments were carried out in this paper. Using machine learning to analyze nanopore data can effectively reduce the additional cost of manual data analysis, which is significant for many biological studies, including genome sequencing.
Deep Learning ; Guanine ; Nanopore Sequencing ; Nanopores ; Porins/genetics*

In order to provide a rational research basis for clinical detection and genetic engineering vaccine, plasmid pET-28a (+) encoding both Porin gene PIA and PIB of Neisseria gonorrhoeae was constructed and a fusion protein in E. coli DE3 expressed. The fragments of PIA and PIB gene of Neisseria gonorrhoeae were amplified and cloned into prokaryotic expression plasmid pET-28a (+) with double restriction endonuclease cut to construct recombinant pET-PIB-PIA. The recombinant was verified with restriction endonuclease and sequenced and transformed into E. coli DE3 to express the fusion protein PIB-PIA after induced with IPTG. The results showed PIA-PIB fusion DNA fragment was proved correct through sequencing. A 67 kD (1 kD= 0.992 1 ku) fusion protein had been detected by SDS-PAGE. It was concluded that the fusion protein was successively expressed.
Cloning, Molecular ; Escherichia coli ; genetics ; metabolism ; Humans ; Neisseria gonorrhoeae ; genetics ; Plasmids ; biosynthesis ; genetics ; Porins ; biosynthesis ; genetics ; Prokaryotic Cells ; metabolism ; Recombinant Fusion Proteins ; biosynthesis ; genetics ; Transfection ; Vaccines, Synthetic

Objective: To study the polymorphism in P66 and its human B-cell epitopes of Methods: Polymerase chain reaction (PCR) and sequencing were used to obtain the P66 sequences of 59 Chinese Results: Results showed that genetic and amino acid diversity presented in the 66 kD protein of all 59 Chinese strains, especially in Conclusion In P66 of 59 Chinese strains, polymorphisms were widely distributed. More importantly, the P66 amino acid sequences of
Bacterial Proteins/genetics* ; Borrelia burgdorferi/genetics* ; China ; Cluster Analysis ; Epitopes, B-Lymphocyte/genetics* ; Genetic Markers ; Genotype ; Humans ; Mutation ; Polymerase Chain Reaction ; Polymorphism, Genetic ; Porins/genetics*

OBJECTIVETo construct a recombinant eukaryotic expression plasmid pcDNA3.1-Ct MOMP168 including Ct MOMP multi-epitopes gene, and evaluate the Ct MOMP-specific humoral and cellular immune response induced by pcDNA3.1-Ct MOMP168 in BALB/c mice.

METHODSRecombinant plasmid pcDNA3.1-Ct MOMP168 including Ct MOMP multi-epitopes gene was constructed. Then, BALB/c mice were randomly assigned to receive (intramuscular injection) either pcDNA3.1-Ct MOMP168 or pcDNA3.1 or PBS (n = 12, 100 microg/time per mouse), and the same immunization schedule was repeated for the third time at 2 week intervals. The titers of anti-Ct MOMP antibody and its antibody subtypes in sera, the cytotoxicity of Ct MOMP-specific cytotoxic T lymphocyte (CTL) in spleen, and the level of cytokine (IFN-gamma, IL-4, IL-10)-producing CD3(+) T cells in spleen were detected by ELISA, LDH release assays and intracellular cytokine staining-fluorescence activated cell sorter (ICS-FACS), respectively.

RESULTSThe recombinant plasmid pcDNA3.1-Ct MOMP168 was able to induce Ct-specific antibody response (A(490) = 0.973 +/- 0.136; serum titer was 1:1000) as compared with pcDNA3.1 (A(490) = 0.180 +/- 0.025) and PBS (A(490) = 0.110 +/- 0.015), and the major antibody subtype was IgG2a with statistical significance (F = 106.884, P < 0.05). When the ratio of effector cells and target cells reached to 50:1, the activity of cytotoxic T-lymphocyte in pcDNA3.1-Ct MOMP168 immunized mice (41.71% +/- 8.34%) was significantly higher (F = 22.315, P < 0.05) than that in pcDNA3.1 immunized mice (18.40% +/- 3.45%) and PBS immunized mice (14.50% +/- 2.42%). The levels of CD3(+) IFN-gamma(+) T cells in pcDNA3.1-Ct MOMP168 immunized mice (1.15% +/- 0.16%) were significantly higher (F = 99.638, P < 0.05) than that in pcDNA3.1 immunized mice (0.12% +/- 0.08%) and PBS immunized mice (0.09% +/- 0.03%), while the significant difference in the levels of IL-4(+) CD3(+) T cells and IL-10(+) CD3(+) T cells was not observed (F = 0.886 and 1.112, P > 0.05) between pcDNA3.1-Ct MOMP168 immunized mice (0.13% +/- 0.08% and 0.14% +/- 0.08%) and pcDNA3.1 (0.07% +/- 0.05% and 0.13% +/- 0.06%) or PBS immunized mice (0.08% +/- 0.04% and 0.07% +/- 0.04%).

CONCLUSIONIn BALB/c mice, the recombinant plasmid pcDNA3.1-Ct MOMP168 might induce not only the generation of Ct-specific antibody, but also the high level of Ct MOMP-specific CD3(+) IFN-gamma(+) T cells.

Animals ; Bacterial Outer Membrane Proteins ; genetics ; immunology ; Bacterial Vaccines ; immunology ; Chlamydia trachomatis ; genetics ; immunology ; Immunization ; Male ; Mice ; Mice, Inbred BALB C ; Porins ; genetics ; immunology ; T-Lymphocytes, Cytotoxic ; immunology

In this study, the ompS gene, a major outer membrane protein gene of Legionella pneumophila, was obtained from the DNA of Legionella pneumophila by PCR. The gene was cloned into prokaryotic expressional plasmid pUC18 to construct recombinant plasmid. The recombinant plasmid was transformed into E. coli strain BL21. The identification was made by means of restriction enzyme analysis, polymerase chain reaction, DNA sequencing analysis, SDS--polyacrylamine gel electrophoresis analysis and Western blot. The results showed that the ompS gene of 914 bp was amplified from Legionella pneumophila DNA, the recombinant plasmid pLPompS was constructed and its expression in prokaryotic cell was detected successfully.
Amino Acid Sequence ; Bacterial Proteins ; biosynthesis ; genetics ; Base Sequence ; Cloning, Molecular ; Humans ; Legionella pneumophila ; genetics ; Molecular Sequence Data ; Porins ; biosynthesis ; genetics ; Prokaryotic Cells ; metabolism

OBJECTIVETo construct a fused expression vector of the outer membrane protein gene PorB of Neisseria gonorrhoeae, express the fusion protein in the prokaryotic system, and obtain a gene recombination protein, for the purpose of preparing the ground for further research on the pathopoiesis and immune protective response of PorB.

METHODSA pair of primers were designed according to the known sequence of the PorB gene, and the PorB gene was amplified by PCR from the genome of Neisseria gonorrhoeae 29403 and cloned into the prokaryotic expression plasmid pGEX-4T-1 to generate pGEX-4T-PorB recombinants. The recombinant plasmid pGEX4T-PorB was transferred into competent cells E. coli BL21. After confirmed by restriction endonuclease digestion, PCR and DNA sequencing analysis, the recombinant protein was induced to express by isopropyl-beta-D-thiogalactoside (IPTG), and examined by SDS-PAGE and Western blotting.

RESULTSRestriction endonuclease digestion, PCR amplification and DNA sequencing analysis showed that the PorB gene of 1 047 bp was amplified from Neisseria gonorrhoeae DNA, and the recombinant plasmid pGEX-4T-PorB was successfully constructed and highly expressed in E. coli.

CONCLUSIONThe prokaryotic expression vector of pGEX-4T-PorB was successfully constructed and efficiently expressed in the prokaryotic system, which has provided a basis for further study on the biological activity of the PorB protein, as well as animal immune experiment and detection of Neisseria gonorrhoeae, and its application as a mucosal immune vaccine.

Bacterial Outer Membrane Proteins ; genetics ; metabolism ; Cloning, Molecular ; Escherichia coli ; metabolism ; Gene Expression ; Genetic Vectors ; Molecular Sequence Data ; Neisseria gonorrhoeae ; genetics ; metabolism ; Plasmids ; Porins ; genetics ; metabolism

Bacterial Outer Membrane Proteins ; chemistry ; genetics ; metabolism ; Escherichia coli Proteins ; chemistry ; genetics ; metabolism ; Glutamic Acid ; genetics ; metabolism ; Histidine ; genetics ; Hydrogen-Ion Concentration ; Ion Channel Gating ; genetics ; Lipid Bilayers ; metabolism ; Mutant Proteins ; chemistry ; genetics ; metabolism ; Mutation ; Porins ; chemistry ; genetics ; metabolism

In order to amplify pilA gene and ompC gene of avian pathogenic Escherichia coli (APEC) strain, two pairs of primers were designed according to the GenBank sequences, and a 549 bp pilA gene and a 1104 bp ompC gene were obtained by PCR separately. Sequence analysis indicated that the homology of the nucleotide sequence of AEPC strain to those other reference strains was 98.18% of the pilA gene and 97.28% of the ompC gene. Two expression plasmids pETpilA and pETompC were constructed by inserting pilA gene and ompC gene into the prokaryotic expression vector pET-28a. The two plasmids were transformated into E. coli BL21 separately and two recombinant strains BL21 (pETpilA) and BL21 (pETompC) were obtained. The type 1 fimbraie and the out membrane protein were highly expressed when the recombinant strain BL21 (pETpilA) and BL21 (pETompC) were induced by IPTG Two specific proteins were detected by SDS-PAGE and immunogenicity of the expressed protein was confirmed by Western blotting and ELISA. The expressed fimbraie and OmpC were transformed into vaccine. The protective immune response was proved after the mice were immunized with the two vaccines. The results showed that the recombinant strain BL21 (pETpilA) and BL21 (pETompC) could be as candidate vaccine to provide protective immune response against AEPC infection.
Animals ; Cloning, Molecular ; Escherichia coli ; genetics ; immunology ; metabolism ; Escherichia coli Proteins ; genetics ; immunology ; metabolism ; Escherichia coli Vaccines ; immunology ; Fimbriae Proteins ; genetics ; immunology ; metabolism ; Gene Expression Regulation, Bacterial ; Genes, Bacterial ; Mice ; Porins ; genetics ; immunology ; metabolism ; Recombinant Fusion Proteins ; genetics ; immunology ; metabolism

This study was conducted to potentiate the expression of outer membrane protein OmpL17 of the strong virulent L. interrogans serovar Lai and investigate its immunogenicity in rabbits. The OmpL17 was cloned into prokaryotic expression vector pGEX-1lambdaT. The recombination expression plasmid pGEX-OmpL17 was transformed into E. Coli JM109. The GST fused protein GST-OmpL17 was expressed after induction by IPTG, then GST-tag was by thrombin and purified using Bulk GST purification Modules. SDS-PAGE and Western blotting analysis indicated that the molecular weight of GST-OmpL17 and OmpL17 was about 54 KDa and 28 KDa respectively. The outer membrane protein OmpL17 was subcutaneously injected into rabbits and high titre anti-OmpL17 antibody was obtained (1:4896) which could conjugate specifical with OmpL17. In conclusion, OmpL17 and specifical anti-OmpL17 antibody were obtained, which provided an experimental basis for researching pathogenic effect and immunity functions of OmpL17.
Bacterial Outer Membrane Proteins ; biosynthesis ; genetics ; immunology ; Bacterial Proteins ; biosynthesis ; genetics ; immunology ; Cloning, Molecular ; Humans ; Leptospira interrogans ; genetics ; immunology ; Porins ; biosynthesis ; genetics ; immunology ; Recombinant Proteins ; biosynthesis ; genetics ; immunology ; Virulence

OBJECTIVETo explore the role of ompT gene in uropathogenic E. coli (UPEC) CFT073 strain in urinary tract infection (UTI).

METHODSAn ompT deletion mutant (COTD) was generated by λ Red recombineering in the UPEC CFT073 strain, which was characterized by PCR and sequencing. C57B/L6 mouse models of acute UTI with the mutant and wild-type strains were established to compare the colonization abilities of the two strains in the bladder. The adhesion of CFT073 mutant to human unthelial 5637 cells was also investigated in vitro.

RESULTSPCR and DNA sequencing confirmed the loss of ompT gene in the mutant COTD. The in vitro adhesion rate of the mutant strain COTD to 5637 cells was (6.7±2.2)%, significantly lower than that of (8.3±1.9)% of the wild-type strain (P<0.05). In the murine models of acute UTI, the mutant strain showed a mean colonization number of about (17±8)×10⁴ cfu, which was significantly lower than that of (7∓2)×10⁵ cfu of the wide-type CFT073 strain (P<0.05).

CONCLUSIONOmpT gene can be involved in the colonization of UPEC in the bladder tissue and plays an important role in the pathogenesis of UPEC-induced UTI.

Animals ; Bacterial Proteins ; genetics ; Cell Line ; Escherichia coli Infections ; microbiology ; Escherichia coli Proteins ; genetics ; Gene Knockout Techniques ; Humans ; Mice ; Mice, Inbred C57BL ; Porins ; genetics ; Urinary Tract Infections ; microbiology ; Uropathogenic Escherichia coli ; genetics