In order to develop a simple and efficient site-directed mutagenesis solution, the Gibson assembly technique was used to clone the cyclin dependent kinase 4 gene with single or double site mutations, with the aim to simplify the overlap extension PCR. The gene fragments containing site mutations were amplified using a strategy similar to overlap extension PCR. Meanwhile, an empty plasmid was digested by double restriction endonucleases to generate a linearized vector with a short adaptor overlapping with the targeted gene fragments. The gene fragments were directly spliced with the linearized vector by Gibson assembly in an isothermal, single-reaction, creating a recombinant plasmid. After the recombinant plasmids were transformed into competent Escherichia coli DH5α, several clones were screened from each group. Through restriction analysis and DNA sequencing, it was found that the randomly selected clones were 100% target mutants. Since there was neither tedious multiple-round PCR amplification nor frequent DNA extraction operation, and there was no need to digest the original plasmid, this protocol circumvents many factors that may interfere with the conventional site-directed mutagenesis. Hence, genes with single or multiple mutations could be cloned easily and efficiently. In summary, the major defects associated with overlap extension PCR and rolling circle amplification were circumvented in this protocol, making it a good solution for site-directed mutagenesis.
Clone Cells ; Mutagenesis, Site-Directed ; Mutation ; Plasmids/genetics* ; Polymerase Chain Reaction/methods*

OBJECTIVES: To study the association between paroxysmal nocturnal hemoglobinuria (PNH) clone and immunosuppressive therapy (IST) in children with severe aplastic anemia (SAA). METHODS: A retrospective analysis was performed on the medical data of 151 children with SAA who were admitted and received IST from January 2012 to May 2020. According to the status of PNH clone, these children were divided into a negative PNH clone group (n=135) and a positive PNH clone group (n=16). Propensity score matching was used to balance the confounding factors, and the impact of PNH clone on the therapeutic effect of IST was analyzed. RESULTS: The children with positive PNH clone accounted for 10.6% (16/151), and the median granulocyte clone size was 1.8%. The children with positive PNH clone had an older age and a higher reticulocyte count at diagnosis (P<0.05). After propensity score matching, there were no significant differences in baseline features between the negative PNH clone and positive PNH clone groups (P>0.05). The positive PNH clone group had a significantly lower overall response rate than the negative PNH clone group at 6, 12, and 24 months after IST (P<0.05). The evolution of PNH clone was heterogeneous after IST, and the children with PNH clone showed an increase in the 3-year cumulative incidence rate of aplastic anemia-PNH syndrome (P<0.05). CONCLUSIONS SAA children with positive PNH clone at diagnosis tend to have poor response to IST and are more likely to develop aplastic anemia-PNH syndrome.
Anemia, Aplastic/drug therapy* ; Child ; Clone Cells ; Hemoglobinuria, Paroxysmal/etiology* ; Humans ; Immunosuppression Therapy ; Retrospective Studies

In order to establish an infectious clone for CDV-3, a commercial vaccine strain of canine distemper virus for mink, to provide reference for the studies of pathogenesis and novel vaccine development of CDV. Thirteen pairs of primers were used to amplify the full-length genome of CDV-3 strain. Five long fragments were obtained based on single restriction site analysis of the whole genome of CDV-3 by RT-PCR. Five fragments were successively inserted into the multiple clone sites in the modified eukaryotic vector of pcDNA3.2 by restriction enzymes and splicing. Meanwhile, the hammerhead ribozyme and hepatitis delta virus ribozyme sequences were added to the beginning of F1 fragment and the ending of F5 fragment, respectively. Then, the full-length cDNA recombinant plasmid of CDV-3 was obtained and named as pcDNA3.2-CDV-3. In addition, three helper plasmids, expressing the N protein, P protein and L protein of the CDV-3 strain respectively, were constructed. The 293T cells were transfected with the full-length cDNA recombinant plasmid and three helper plasmids by Lipofectamine™ 2000. At 3 days post transfection, the supernatant was added to the monolayer of Vero cells to observe the typical syncytium of CDV. Indirect immunofluorescence and artificial label identification of recombinant virus rCDV-3 were conducted after the occurrence of lesions. Finally, the growth characteristics of wtCDV-3 and rCDV-3 were compared after passaging of rCDV-3. The identification of the full-length cDNA recombinant plasmid and three helper plasmids by restriction enzyme digestion and sequencing were consistent with expected. The Vero cells infected with the recombinant rCDV-3 showed typical syncytic. The identification of indirect immunofluorescence and labeled marker, and observation under electron microscope proved that the rCDV-3 was indeed rescued from the recombinant plasmid of pcDNA3.2-CDV-3. In comparison of the virus titers of wtCDV-3, rCDV-3 replicated massively and rapidly and reached the maximize virus titer of 10⁷·⁶⁶⁷ TCID₅₀/mL within 36 h post infection (p.i.) in Vero cells, while wtCDV-3 grew gradually to 10⁶·⁶⁶⁷ TCID₅₀/mL at 72 h p.i. in Vero cells. This reverse genetic system of CDV-3 strain has been established successfully, to provide reference for the studies of pathogenesis and novel vaccine development of CDV.
Animals ; Chlorocebus aethiops ; Clone Cells ; DNA, Complementary ; Distemper Virus, Canine/genetics* ; Plasmids/genetics* ; Vero Cells

Immunoglobulin G4 (IgG4)-related dacryoadenitis and sialoadenitis (IgG4-DS) are part of a multiorgan fibroinflammatory condition of unknown etiology termed IgG4-related disease (IgG4-RD), which has been recognized as a single diagnostic entity for less than 15 years. Histopathologic examination is critical for diagnosis of IgG4-RD. CD4+ T and B cells, including IgG4-expressing plasma cells, constitute the major inflammatory cell populations in IgG4-RD and are thought to cause organ damage and tissue fibrosis. Patients with IgG4-RD who have active, untreated disease exhibit significant increase of IgG4-secreting plasmablasts in the blood. Considerable insight into the immunologic mechanisms of IgG4-RD has been achieved in the last decade using novel molecular biology approaches, including next-generation and single-cell RNA sequencing. Exploring the interactions between CD4+ T cells and B lineage cells is critical for understanding the pathophysiology of IgG4-RD. Establishment of pathogenic T cell clones and identification of antigens specific to these clones constitutes the first steps in determining the pathogenesis of the disease. Herein, the clinical features and mechanistic insights regarding pathogenesis of IgG4-RD were reviewed.
B-Lymphocytes ; Clone Cells ; Dacryocystitis ; Diagnosis ; Fibrosis ; Humans ; Immunoglobulins ; Molecular Biology ; Plasma Cells ; Sequence Analysis, RNA ; Sialadenitis ; T-Lymphocytes

Sequence type (ST) 33 of Shiga toxin-producing Escherichia coli (STEC) strain O91:H14 has been proposed as a potential domestic clone of STEC in Korea because of its high prevalence among human patients with mild diarrhea or asymptomatic carriers. Herein, the clonal diversity of 17 STEC O91:H14 isolates of ST33 during 2003 to 2014 was analyzed by pulsed-field gel electrophoresis, including 14 isolates from human patients and 3 from retail meats. Their virulence characteristics, acid resistance, and antimicrobial susceptibility were also determined. Our results showed that all isolates were clustered mainly into three different pulsotypes and were likely low pathogenic without antimicrobial resistance.
Clone Cells ; Diarrhea ; Electrophoresis, Gel, Pulsed-Field ; Escherichia coli ; Humans ; Korea ; Meat ; Molecular Epidemiology ; Prevalence ; Shiga Toxin ; Shiga-Toxigenic Escherichia coli ; Virulence

Among various vaccines against Actinobacillus pleuropneumoniae, subunit vaccines using recombinant proteins of ApxI, ApxII, and ApxIII as vaccine antigens have shown good efficacy in terms of safety and protection. Therefore, subunit vaccines are being applied worldwide and the development of new subunit vaccines is actively being conducted. To evaluate the efficacy of the subunit vaccines, it is important to measure immune responses to each Apx toxin separately. However, the cross-reactivity of antibodies makes it difficult to measure specific immune reactivity to each toxin. In the present study, specific antigen regions among the toxins were identified and cloned to solve this problem. The antigenicity of each recombinant protein was demonstrated by Western blot. Using the recombinant proteins, we developed enzyme-linked immunosorbent assay (ELISA) methods that can detect specific immune responses to each Apx toxin in laboratory guinea pigs. We suggest that the ELISA method developed in this study can be an important tool in the evaluation of vaccine efficiency and vaccine development.
Actinobacillus pleuropneumoniae ; Actinobacillus ; Animals ; Antibodies ; Blotting, Western ; Clone Cells ; Enzyme-Linked Immunosorbent Assay ; Guinea Pigs ; Methods ; Recombinant Proteins ; Vaccines ; Vaccines, Subunit

This study examined the effects of a caffeine treatment to improve nuclear reprogramming in porcine cloned embryos. Embryonic development and the expression of genes related to pluripotency (POU5F1, SOX2, NANOG, and CDX2) were compared after caffeine supplementation during manipulation at different concentrations (0, 1.25, 2.5, and 5.0 mM) and after varying the delayed activation time (control, 1, 2, and 4 h) after fusion. Caffeine added to media during manipulation produced a higher rate of development to blastocysts in the 1.25 mM group than in the other concentration groups (22.8% vs. 16.1%, 16.2%, and 19.2%; p < 0.05). When caffeine was added during the 4 h delayed activation, the 1.25 mM caffeine concentration produced a significantly higher rate of development than those in the other 4 h-activation-delayed caffeine concentration groups (22.4% vs. 9.4%, 14.0%, and 11.1%; p < 0.05). On the other hand, no significant improvement over that in the control group was observed when caffeine was supplemented during both the manipulation period and delayed activation period (16.0% vs. 15.2%), respectively. The levels of POU5F1, SOX2, and NANOG expression in blastocysts were significantly higher in the delayed activation caffeine group (4 h, 1.25 mM) than in the control group (1 h, 0 mM; p < 0.05). In conclusion, a caffeine treatment at 1.25 mM during delayed activation for 4 h can improve the preimplantation development of porcine somatic cell nuclear transfer embryos by activating nuclear reprogramming.
Blastocyst ; Caffeine ; Cellular Reprogramming ; Clone Cells ; Embryonic Development ; Embryonic Structures ; Female ; Hand ; Pregnancy

BACKGROUND: The recent expansion of knowledge about various ABO alleles has led to the need for a comprehensive measure to cover the numerous polymorphisms dispersed in the ABO gene. A few studies have examined the diversity of the O allele compared to A or B subgroup alleles, resulting in antigenic changes. This study investigated the relationship between the serologic and molecular genetic characteristics of the O alleles in the Korean population. METHODS: One hundred and five samples from healthy blood group O subjects were selected randomly. The isoagglutinin titer was measured using a tube agglutination and gel microcolumn assay. The ABO alleles were analyzed by sequencing exons 6 and 7 of the ABO gene. When the origin of a heterozygous nucleotide sequence was ambiguous, it was separated into a single allele using mono-allele amplification or cloning. RESULTS: The median IgM isoagglutinin titer was eight. In contrast, the median IgG anti-A and anti-B isoagglutinin titers were 64 and 32, respectively. The IgG isoagglutinin titer showed a significant increase with age (P<0.0001). Six O alleles were observed in 105 blood group O populations by sequencing. The O01 and O02 alleles were common (0.57, 0.36). Three rare O alleles (O04, O05, and O06) and one novel non-deletional O allele were found. CONCLUSION: The distribution of isoagglutinin titers of blood group O and the genetic frequency of O alleles in this study would form the basis of the development and interpretation of ABO genotyping and serologic workup in the Korean population.
Agglutination ; Alleles ; Base Sequence ; Clone Cells ; Cloning, Organism ; Exons ; Immunoglobulin G ; Immunoglobulin M ; Molecular Biology ; Sequence Analysis

BACKGROUND: Flow cytometry analysis of paroxysmal nocturnal hemoglobinuria (PNH) is significantly affected by the methodology used. The lack of data on the effect of age and refrigeration on PNH clone stability motivated us to study these aspects using flow cytometry. METHODS: Peripheral blood was collected from six patients, of which two presented with PNH. All samples were tested immediately and stored at room temperature (RT, 20–25℃) and at 4℃ for re-analysis at 24, 48, 72 hr and 7 days. Anti-CD59-fluorescein isothiocyanate (Beckman Coulter, USA) and anti-CD235a-phycoerythrin (PE; Beckman Coulter) were used to stain red blood cells (RBCs). Fluorescein-labeled proaerolysin (Cedarlane, Canada), anti-CD15-PE (Beckman Coulter), anti-CD24-PE-cyanin 5 (Beckman Coulter), and anti-CD45-PE-cyanin 7 (Beckman Coulter) were used to stain granulocytes. Flow cytometry was performed using a FC500 flow cytometer (Beckman Coulter). The effects of time and temperature were analyzed using generalized estimating equations. RESULTS: No significant differences in the gated percentage of RBCs and PNH clone size of RBCs were observed between the RT and 4℃ groups up to 7 days of testing. The percentage of gated neutrophils decreased with specimen age (P<0.001) and a better correlation with baseline was obtained at 4℃ than at RT (P=0.014). Neutrophil PNH clones were stable until 48 hr and 72 hr at RT and 4℃, respectively, and could not be analyzed at 7 days. CONCLUSIONS: RBC analysis was successfully performed up to 7 days. For neutrophils, testing within 48 hr is recommended, because the number of gated cells decreases significantly with age.
Clone Cells ; Erythrocytes ; Flow Cytometry ; Granulocytes ; Hemoglobinuria, Paroxysmal ; Humans ; Neutrophils ; Refrigeration

A rapid diagnostic test (RDT) kit was developed to detect non-structural protein 1 (NS1) of yellow fever virus (YFV) using monoclonal antibody. NS1 protein was purified from the cultured YFV and used to immunize mice. Monoclonal antibody to NS1 was selected and conjugated with colloidal gold to produce the YFV NS1 RDT kit. The YFV RDTs were evaluated for sensitivity and specificity using positive and negative samples of monkeys from Brazil and negative human blood samples from Korea. Among monoclonal antibodies, clones 3A11 and 3B7 proved most sensitive, and used for YFV RDT kit. Diagnostic accuracy of YFV RDT was fairly high; Sensitivity was 0.0% and specificity was 100% against Dengue viruses type 2 and 3, Zika, Chikungunya and Mayaro viruses. This YFV RDT kit could be employed as a test of choice for point-of-care diagnosis and large scale surveys of YFV infection under clinical or field conditions in endemic areas and on the globe.
Animals ; Antibodies, Monoclonal ; Brazil ; Clone Cells ; Dengue Virus ; Diagnosis ; Diagnostic Tests, Routine ; Gold Colloid ; Haplorhini ; Humans ; Korea ; Mice ; Point-of-Care Systems ; Sensitivity and Specificity ; Yellow fever virus ; Yellow Fever