BACKGROUND: Carbapenemase-producing Enterobacteriaceae (CPE) has been increasingly reported worldwide in the past 10 years, which is an important infection control concern. Since the epidemiology and characteristics of these CPEs vary according to institutes, we aimed to characterize CPEs in a university hospital during the recent 4 years. METHODS: From October 2011 to September 2015, CPE isolates from clinical specimens and hospital surveillance cultures were collected. Carbapenem resistance was confirmed by disk diffusion method and Minimal Inhibitory Concentration (MIC) was determined by agar dilution method. Carbapenemase production was tested by double disk test using aminophenylboronic acid and dipicolic acid. PCR and sequence analysis were performed to detect bla(KPC), bla(IMP-1), bla(VIM-2), bla(NDM-1)-like genes and bla(OXA-48) gene. Pulsed-field gel electrophoresis (PFGE) and Multilocus sequence typing (MLST) were conducted for KPC-producing Klebsiella pneumoniae isolates. RESULTS: Twenty-five isolates (11%) of CPE were identified among 222 carbapenem-resistant Enterobacteriacae isolates during the study period. The most prevalent CPE was KPC-producing K. pneumonia and others were IMP-1, VIM-2, NDM-1 type and OXA-48 producing CPEs. Most of these CPEs showed resistance to carbapenems with variable MICs. The sequence types (STs) of KPC-producing K. pneumoniae were ST307 and ST11. The PFGE of ST11 and ST307 showed clonality in each group suggesting the possibility of in-hospital outbreak. CONCLUSION: The prevalence of CPE has been increasing. In our institute, KPC-producing K. pneumoniae was the most frequently isolated CPE in the recent 4 years. CPE including KPC producers can easily transfer their resistance. Therefore continuous monitoring and more intensified infection control for CPE should be considered.
Academies and Institutes ; Agar ; Carbapenems ; Diffusion ; Drug Resistance, Bacterial ; Electrophoresis, Gel, Pulsed-Field ; Enterobacteriaceae* ; Epidemiology ; Infection Control ; Klebsiella pneumoniae ; Korea* ; Methods ; Molecular Epidemiology* ; Multilocus Sequence Typing ; Pneumonia ; Polymerase Chain Reaction ; Prevalence ; Sequence Analysis

OBJECTIVETo study the effect of Tiantai No. 1 [symbol in text] on gene expression profile in hippocampus of Alzheimer's disease (AD) rat, molecular genetic target points of the effect of this drug were defined, its molecular genetic pharmacodynamic mechanism of anti-AD was further explored at molecular gene level, and a scientific basis was provided for its clinical availability and promotion.

METHODSThirty male Sprague-Dawley rats were divided into three groups with 10 rats per group: sham-operation group, model group and Tiantai No. 1 group. Sterile surgical procedure was applied, the model group with bilateral hippocampal injection of Aβ1-40 was established, and normal saline was used instead of Aβ1-40 in the sham-operation group. One week after the models was made, rats were administered by gastric lavage once every day for three consecutive weeks. The rats of the sham-operation group and the model group were daily fed with purified water by lavage; the rats of the Tiantai No.1 group treated group were administered with Tiantai No.1 by lavage. Total RNAs of hippocampus tissues were extracted with Trizol, the changes of hippocampus gene expression profiles in the above three groups were analyzed by using Affymetrix rat whole genome expression profile microarray.

RESULTSMicroarray analysis showed that, compared with the sham-operation group, the hippocampus of the model group had 50 up-regulated genes with significant difference (fold change >2), and 21 down-regulated genes with significant difference (fold change <0.5); compared with the hippocampus of the model group, the hippocampus of the Tiantai No. 1 group was found to have 5 up-regulated genes with significant difference (fold change >2) and 20 down-regulated genes with significant difference (fold change <0.5). The functions of differentially expressed genes of the groups were involved in nervous system's development, neuronic differentiation and function-regulation, cellular growth and differentiation and apoptosis, synaptic occurrence and plasticity, inflammation and immune response, ion channels/transporters, cellular signal transduction, cellular material/energy metabolism and so on.

CONCLUSIONTiantai No. 1 can regulate hippocampal function, and further regulate the brain function of animals in multiple gene target points by a number of ways.

Alzheimer Disease ; genetics ; pathology ; Animals ; Body Weight ; drug effects ; Computational Biology ; methods ; Drugs, Chinese Herbal ; pharmacology ; Electrophoresis, Agar Gel ; Gene Expression Profiling ; Gene Expression Regulation ; drug effects ; Hippocampus ; drug effects ; metabolism ; pathology ; Male ; Nucleic Acid Denaturation ; Organ Size ; drug effects ; RNA ; isolation & purification ; metabolism ; Rats, Sprague-Dawley

OBJECTIVE: To establish miniSTR fluorescent detection system with all detected fragments below 150 bp and to enhance the efficiency of detecting the degraded DNA samples. METHODS: All candidate primers were designed by Primer Premier 5 and screened by FastPCR 6.0. The miniSTR multiplex system was established by these selected loci labeling by four fluorescent dye. The parameters of PCR and primer concentrations were subsequently optimized. The electrophoresis was fulfilled under POP4 on 3100-Avant and the typing data was validated by standard DNA 9947A and 007. Fresh blood samples and difficult degraded DNA samples were tested to evaluate the usefulness of the system. RESULTS: All amplicons in the established miniSTR fluorescent detection system (D12ATA63, D2S1776, D1GATA113, D4S2408, D17S974, D20S482, D3S3053, Amelogenin, D6S474, D9S1122) were less than 150bp. The profile showed a balanced peak height without extra stutter by optimal protocol. Allele frequencies showed no deviations from Hardy-Weinberg equilibrium. The system showed accumulated probability of discrimination 0.999 999 983 and accumulated triplet excluding probability of paternity 0.996 8. It could detect corrupt muscle tissue, low copy number DNA samples and human tissues fixed by 40% formaldehyde solution for 12 days. CONCLUSION The miniSTR fluorescent detection system could be solely used for personal identification of degraded DNA samples or complementally used for paternity tests. And the system could enhance the ability of detecting the trace and degraded DNA.
DNA/chemistry* ; DNA Fingerprinting ; DNA Primers/genetics* ; Electrophoresis, Agar Gel ; Forensic Genetics ; Gene Frequency/genetics* ; Genetic Markers/genetics* ; Genetics, Population ; Humans ; Polymerase Chain Reaction/methods* ; Reference Standards ; Sequence Analysis, DNA/methods*

OBJECTIVETo establish a method for identifying Panax ginseng and P. quinquefolius with PCR-SSCP, on the basis of specific SNP identification sites of their ITS2 bar codes.

METHODITS2 sequences of P. ginseng and P. quinquefolius recorded in GenBank were searched to conduct a comparative analysis and screen out specific SNP identification sites of their ITS2 bar codes. Based on that, the Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method was adopted for analyzing 11 P. ginseng samples and 10 P. quinquefolius samples and verifying sequencing of their PCR products.

RESULTThe P. ginseng and P. quinquefolius samples had the same agarose mages of PCR-SSCP with the standard medicines. There were significant differences between the PCR-SSCP agarose mages of P. ginseng and P. quinquefolius, with identifical identification results between PCR-SSCP and sequencing.

CONCLUSIONCompared with the sequencing method, PCR-SSCP is so rapid and accurate that it can be used for identifying P. ginseng and P. quinquefolius medicines.

DNA Barcoding, Taxonomic ; methods ; DNA, Plant ; analysis ; genetics ; DNA, Ribosomal Spacer ; analysis ; genetics ; Electrophoresis, Agar Gel ; Panax ; classification ; genetics ; Polymerase Chain Reaction ; Polymorphism, Single Nucleotide ; Polymorphism, Single-Stranded Conformational ; Reproducibility of Results ; Species Specificity

OBJECTIVE: To compare effects of three different methods for mtDNA extraction from common sarcosaphagous insects including cetyl trimethyl ammonium bromide (CTAB) method, sodium dodecyl sulfate-potassium acetate (SDS-KAc) method and sodium dodecyl sulfate-proteinase K (SDS-PK) method. METHODS: Seventy-two insects from four species [Chrysomya megacephala (Fabricius, 1784), Eusilpha bicolor (Fairmaire, 1896), Paraeutrichopus pecoudi (Mateu, 1954), Vespa velutina (Lepeletier, 1836)] were collected from the corpses of the rabbits in Changsha district. The total DNA of above samples was extracted by CTAB, SDS-Kac and SDS-PK methods. The purity and concentration of DNA were examined by protein-nucleic acid spectrophotometry, and mtDNA were amplified by specific primers and PCR products were detected by agarose gel electrophoresis. Then PCR products were sequenced and subsequently up-loaded to GenBank. RESULTS: mtDNA was successfully extracted with three methods from most of the samples. The SDS-PK method was better in DNA purity compared to other methods and the CTAB method was superior in extracting DNA from old samples, while SDS-KAc method showed no significant difference for extraction effects of different samples. CONCLUSION The most appropriate method should be chosen depending on different situations. SDS-PK method is expected to obtain high-quality DNA, while CTAB method is preferred in extracting obsolete samples. SDS-KAc method is low cost and can be used in various kinds of preliminary experiments.
Animals ; Coleoptera/genetics* ; DNA Primers ; DNA, Mitochondrial/isolation & purification* ; Diptera/genetics* ; Electrophoresis, Agar Gel ; Entomology ; Forensic Medicine/methods* ; Gene Amplification ; Insecta/genetics* ; Polymerase Chain Reaction/methods* ; Quaternary Ammonium Compounds/chemistry* ; Rabbits ; Reproducibility of Results ; Sequence Analysis, DNA ; Sodium Dodecyl Sulfate/chemistry*

BACKGROUND: In addition to Klinefelter's syndrome, microdeletion of Yq is the most common genetic cause of male infertility; 15% of azoospermic or 5-10% of oligozoospermic males have Yq deletions. We evaluated a Yq microdeletion kit (LG Life Sciences, Korea) for identifying microdeletions in the azoospermic factor (AZF) regions of the Yq. METHODS: The kit was designed to amplify 3 regions of the AZF gene (AZFa, AZFb, and AZFc) using 15 sequence-tagged sites. We evaluated the preclinical performance of the kit. For clinical validation, 58 patients including 25 idiopathic azoospermic or oligozoospermic patients were examined. RESULTS: We observed clear bands on electrophoresis of DNA, up to a DNA concentration of 3.12 ng/microliter; the known microdeletion regions of all 6 reference cell-lines (Coriell, USA) were accurately detected and no false positive/negative results showed with normal female (n=11) and fertile male (n=15) specimens. This kit could identify the same microdeletions in the common regions, similar to another commercial kit. Among the 58 male infertile patients, 7 (12.1%) had microdeletions of the Yq. Among the idiopathic azoospermic (n=22) and oligozoospermic (n=3) patients, 3 (12.0%) had microdeletions. Further, 2 of 21 varicocele patients (9.5%), 1 of 4 patients with testicular failure, and 1 patient with a 45,X/46,XY mosaic had microdeletions. CONCLUSIONS: The kit was effective for detecting microdeletions of the Yq. We identified microdeletions in 12% of the infertile patients. This Y chromosome microdeletion detection kit is useful for screening Yq microdeletions in infertile patients.
Azoospermia/genetics ; *Chromosome Deletion ; *Chromosomes, Human, Y ; Electrophoresis, Agar Gel/methods ; Female ; Humans ; Infertility, Male/genetics ; Male ; Oligospermia/genetics ; Polymerase Chain Reaction/*methods ; Reagent Kits, Diagnostic ; Reproducibility of Results ; Seminal Plasma Proteins/*genetics ; Sensitivity and Specificity ; Varicocele/genetics

A simple, rapid and sensitive colorimetric Reverse Transcription Loop Mediated Isothermal Amplification (RT-LAMP) method was established to detect human influenza A H1N1 virus. The method employed a set of six specially designed primers that recognized eight distinct sequences of the HA gene for amplification of nucleic acid under isothermal conditions at 65 degrees C for one and half hour. The amplification process of RT-LAMP was monitored by the addition of HNB (Hydroxy naphthol blue) dye prior to amplification. A positive reaction was indicated by a color change from violet to sky blue and confirmed by agarose electrophoresis. The specificity of the RT-LAMP assay was validated by cross-reaction with different swine and human influenza virus including human seasonal influenza A /H1N1 A /H3N2, influenza B and swine A /H1N1. The sensitivity of this assay was evaluated by serial dilutions of RNA molecules from in vitro transcription of human influenza A H1N1 HA gene. The assay was further evaluated with 30 clinical specimens with suspected pandemic influenza A H1N1 virus infection in parallel with RT-PCR detection and 26 clinical specimens with seasonal influenza virus infection. Our results showed that the RT-LAMP was able to achieve a sensitivity of 60 RNA copies with high specificity, and detection rate was comparable to that of the RT-PCR with the clinical samples of pandemic influenza A H1N1 infection. The RT-LAMP reaction with HNB could also be measured at 650nm in a microplate reader for quantitative analysis. Thus, we concluded that this colorimetric RT-LAMP assay had potential for the rapid screening of the human influenza A H1N1 virus infection in National influenza monitoring network laboratories and sentinel hospitals of provincial and municipal region in China.
Animals ; Colorimetry ; methods ; DNA Primers ; genetics ; Electrophoresis, Agar Gel ; Hemagglutinin Glycoproteins, Influenza Virus ; genetics ; Humans ; Influenza A Virus, H1N1 Subtype ; genetics ; Influenza A Virus, H3N2 Subtype ; genetics ; Influenza, Human ; diagnosis ; virology ; Naphthalenesulfonates ; chemistry ; Nucleic Acid Amplification Techniques ; methods ; Orthomyxoviridae Infections ; diagnosis ; veterinary ; virology ; Reverse Transcriptase Polymerase Chain Reaction ; methods ; Sensitivity and Specificity ; Swine ; Swine Diseases ; diagnosis ; virology ; Temperature

OBJECTIVE: To explore mitochondrial DNA (mtDNA) extraction effects of different parts from sarcosaphagous insects using improved cetyltriethylammnonium bromide (CTAB) method. METHODS: Thirteen Lucilia sericata (Meigen) and 13 Nicrophorus fossor (Erichson) were collected from the corpses of rabbits placed on the outdoor lawn in Huhehot district. Four parts (head, chest muscle, legs and wings) of insect were collected, and the mtDNA of all samples were extracted using CTAB method. The purity and concentration were tested using protein and nucleic acid spectrophotometry. The integrity of the extracted mtDNA and PCR products were checked by agarose gel electrophoresis. The PCR products were sequenced and the obtained sequences were imputed into GenBank for comparison. RESULTS: mtDNA were successfully extracted from 10 head samples, 6 legs samples, 4 wing samples and 13 chest muscle samples of the Lucilia sericata (Meigen). Also, mtDNA were successfully extracted from 5 head samples, 8 legs samples, 3 wing samples and 13 chest muscle samples of the Nicrophorus fossor (Erichson). CONCLUSION mtDNA can be obtained from chest muscle and other parts of sarcosaphagous insects using the improved CTAB method.
Animals ; Coleoptera/genetics* ; DNA, Mitochondrial/isolation & purification* ; Diptera/genetics* ; Electron Transport Complex IV/genetics* ; Electrophoresis, Agar Gel ; Entomology ; Forensic Medicine/methods* ; Polymerase Chain Reaction/methods* ; Rabbits ; Sequence Analysis, DNA ; Species Specificity

OBJECTIVETo establish a simple, rapid and easy method for screening the gene mutation in hemophilia A, which was further applied to a direct diagnosis and carrier detection at gene level.

METHODSTwenty-four clinically diagnosed hemophilia pedigrees, including all the hemophilia patients and female members, were tested for the introns 22 and 1 in factor VIII gene by using inversion polymerase chain reaction (PCR) and regular PCR techniques. All the 26 exons of factor VIII gene were consecutively screened in the 17 patients manifesting non-inverted sequences in intron 22 by using PCR, subsequently all the 37 amplicons resulted from 26 exons were analyzed by conformation sensitive gel electrophoresis (CSGE), finally the mutated exons were subjected to sequencing verification. According to the mutation results, mothers and twin sisters of the hemophilia probands were tested by CSGE or subjected to nucleotide sequencing directly, to ascertain if those individuals had the same mutation or were the carriers of disease-causing gene.

RESULTSIntron 22 inversion was detected in 7 hemophilia probands out of 24 hemophilia pedigrees, intron 1 inversion was not detected in these pedigrees. Single-base mutations distributed in different exons of factor VIII gene were detected in 13 pedigrees with family history and 3 sporadic pedigrees, diagnosed as non-inverted 22 intron patients. By comprehensive usage of PCR-CSGE and nucleotide sequencing, the positive rate and the diagnosable rate of gene diagnosis or carrier detection in the 24 hemophilia pedigrees was 94.12% and 100% respectively.

CONCLUSIONPCR-CSGE is a highly sensitive and special assay for detecting single base mutation. By integrated utilization of introns 22 and 1 of factor VIII gene detection and PCR-CSGE genotyping, combining with nucleotide sequencing, a direct diagnosis of all hemophilia pedigrees be could nearly make at gene level, including the sporadic families. This method might be used to screen new mutation theoretically and ascertain the mutation type. It is a simple, rapid and low-cost method, possessing unique advantages in direct diagnosis of hemophilia A and carrier screening. It should have important application value in hemophilia diagnosis.

Electrophoresis, Agar Gel ; methods ; Exons ; Factor VIII ; genetics ; Female ; Hemophilia A ; diagnosis ; genetics ; Heterozygote ; Humans ; Introns ; Male ; Mutation ; Pedigree ; Polymerase Chain Reaction ; methods

INTRODUCTIONPolymerase chain reaction (PCR)-based molecular techniques are useful adjunctive tools in the diagnosis of cutaneous T-cell lymphomas (CTCL). This study compares the sensitivity of PCR analysis of the T-cell receptor-gamma (TCR-gamma) gene rearrangements using conventional polyacrylamide gel electrophoresis (PCR-PAGE) and fluorescent capillary electrophoresis (PCR-FCE).

MATERIALS AND METHODSA total of 22 paraffin blocks were analysed using PCR-PAGE and PCR-FCE. There were 17 cases of mycosis fungoides (MF), 4 cases of non-MF CTCL and 1 case of lymphoblastic leukaemia.

RESULTSComplete agreement was obtained between PCR-PAGE and PCR-FCE in 19 of the 22 cases, giving a concordance rate of 86.4%. PCR-FCE had a higher sensitivity of 77.3%, compared to 63.6% for PCR-PAGE, allowing the detection of 3 additional cases of clonal T-cell rearrangements, which had equivocal or polyclonal bands on PAGE. Two of these 3 cases were in erythrodermic MF patients. PCR-FCE also allowed the detection of matching clones in serial specimens taken from different sites and at different time intervals in patients with MF. However, matching clones from different specimens can be achieved qualitatively in PCR-PAGE by running and comparing these on the same polyacrylamide gel block.

CONCLUSIONSBoth PCR-PAGE and PCR-FCE are useful in detecting T-cell clones in CTCL, with both methods being comparable in sensitivity and showing a high concordance rate of 86.4%. PCR-FCE has the added advantage of exhibiting semiquantitative properties, which may be important in early or erythrodermic MF cases, but the requirement for sophisticated and costly machinery limits its availability to high-capacity laboratories. The well-established PCR-PAGE method is a suitable alternative in routine clinical applications.

Base Sequence ; Electrophoresis, Agar Gel ; Electrophoresis, Capillary ; methods ; Electrophoresis, Polyacrylamide Gel ; Fluorescence ; Gene Rearrangement, gamma-Chain T-Cell Antigen Receptor ; Humans ; Lymphoma, T-Cell ; diagnosis ; Mycosis Fungoides ; Polymerase Chain Reaction ; methods ; Sensitivity and Specificity