A new automatic selection approach of microorganism specific fragment combination is presented in this paper. Genetic algorithm is used to search optimal solution on the basis of classification ability of SNP combination, which is evaluated by the rough set theory. Other related experimental parameters are also been incorporated. Experimental results show that the method can find the best SNP combination pattern efficiently and accurately, which implies that it is a reliable approach to the genechip probe design.
Algorithms ; Microbiological Techniques ; methods ; Models, Genetic ; Oligonucleotide Array Sequence Analysis ; methods

Aptamers are a group of artificial oligonucleotides identified by exponential enrichment system evolution technology (Selective expansion of ligands by exponential enrichment, SELEX). Aptamers have been widely used in basic research, clinical diagnostics, and nano-technology. In this article we will introduce the technology of aptamer and summarize its applications in medical microbiology.
Aptamers, Nucleotide ; biosynthesis ; genetics ; Microbiological Techniques ; methods ; Microbiology ; SELEX Aptamer Technique ; methods ; trends

OBJECTIVEThis research was to establish a method for fast identification of mycobacteria in microtiter liquid culture and to evaluate its clinical value.

METHODS2-thiophenecarboxylic acid hydrazide (TCH) and paranitrobenzoic acid (PNB) at different concentrations were added into liquid culture in 96-well plate. Different mycobacterium standard strains were incubated in liquid culture with PNB and TCH for 7 to 10 days. According to the growth assay for 15 mycobacterium strains and 30 mycobacterium tuberculosis strains, the best PNB and TCH concentration were determined. A total of 424 clinical mycobacterium isolates were identified by microtiter liquid culture at the best PNB and TCH concentration. The results of microtiter liquid culture were compared with those of PCR and DNA sequencing.

RESULTSThe best concentration of PNB was 200 µg/ml in microtiter liquid culture. Compared with the results of PCR, the sensitivity and specificity for identification of mycobacterium tuberculosis complex in microtiter liquid culture were 97.8% (306/313) and 100.0% (107/107) respectively and those for non-tuberculosis mycobacteria in microtiter liquid culture were 100.0% (107/107) and 96.5% (306/317) respectively. The best concentration of TCH was 0.5 µg/ml. Compared with the results of PCR, the sensitivity of mycobacterium tuberculosis in microtiter liquid culture was 100.0% (305/305). The specificity remained under and more studies were needed.

CONCLUSIONIn microtiter liquid culture with PNB and TCH, mycobacteria can be identified in 7 to 10 days. The results were accurate and the process was simple without expensive equipments. This method meets clinical needs and can be used in all level hospitals in China.

Culture Media ; Microbiological Techniques ; methods ; Mycobacterium tuberculosis ; isolation & purification ; Sensitivity and Specificity

OBJECTIVETo compare the detection effect of Legionella pollution in spring water by three methods, namely traditional plating method, fluorescent quantitation PCR method and ethidium monoazide (EMA) fluorescent quantitation PCR method.

METHODSEvery month (except May), we collected 11 water samples from the 5 selected hot spring pools in one hot spring resort in Beijing in 2011. A total of 121 water samples were collected, and then were detected by the above three methods qualitatively and quantitatively.

RESULTSIn our study, the Legionella pollution rate was separately 74.4% (90/121), 100.0% (121/121) and 100.0% (121/121) by the above three methods. The quantitative value of Legionella in the 121 water samples detected by the three methods were around 0.10-216.00 colony-forming units (CFU)/ml, 1.47-1557.75 gene units (GU)/ml and 0.20-301.69 GU/ml, respectively. The median (25th and 75th percentiles) was 75.30 (32.51-192.10) GU/ml, 36.46 (16.08-91.21) GU/ml and 5.30 (0.00-33.70) CFU/ml, respectively. The difference in the quantitative value of Legionella detected by the three methods showed statistical significance (χ(2) = 187.900, P < 0.01). The quantitative value of Legionella detected by fluorescent quantitation PCR method was the highest, followed by the value Legionella detected by EMA-fluorescent quantitation PCR method and traditional plating method.

CONCLUSIONThe sensitivity of the PCR methods was higher than traditional plating method, in detecting Legionella pollution in spring water, especially the EMA- fluorescent quantitation PCR method, which was more suitable for detecting Legionella in water.

Environmental Monitoring ; methods ; Hot Springs ; microbiology ; Legionella ; classification ; isolation & purification ; Microbiological Techniques ; Water Microbiology

The essay introduces the study on the performance monitoring tests for the resistance to wet bacterial penetration about surgical gowns and surgical drapes in accordance with ISO 22610.
Microbiological Techniques ; instrumentation ; methods ; Operating Rooms ; Protective Clothing ; microbiology ; standards ; Surgical Attire ; microbiology ; standards

OBJECTIVETo develop a high-throughput diagnostic method with suspension array technique for detecting pathogenic microbes.

METHODSThe probes and positive controls of 56 kinds of pathogenic microbes were designed, synthesized, and used to detect pathogenic microbes with suspension array technique.

RESULTSFluorescence signals of 56 positive controls were higher than those of the negative controls, and there was no cross-reaction between the probes and positive controls of different microbes.

CONCLUSIONBased on suspension array technique, the high-throughput diagnostic method may be useful in clinical detection of pathogenic microbes.

Animals ; Communicable Diseases ; microbiology ; virology ; Enterovirus ; isolation & purification ; Humans ; Microbiological Techniques ; Mumps virus ; isolation & purification ; Oligonucleotide Array Sequence Analysis ; methods ; Pseudomonas aeruginosa ; isolation & purification

BACKGROUND/AIMS: The aim of this study was to evaluate the peritonitis-causing bacteria detected in peritoneal fluid using a blood culture bottle in patients undergoing continuous ambulatory peritoneal dialysis (CAPD). METHODS: One-hundred and eleven dialysates from 43 patients suspected of peritonitis related to CAPD were retrospectively evaluated between May 2000 and February 2008. In all cases, 5 to 10 mL of dialysate was inoculated into a pair of BacT/Alert blood culture bottles, and 50 mL of centrifuged dialysate was simultaneously inoculated into a solid culture media for conventional culture. The results were compared to those of the conventional culture method. Isolated microorganisms were compared between the two methods. RESULTS: The blood culture method was positive in 78.6% (88 / 112) of dialysate specimens and the conventional culture method in 50% (56 / 112, p < 0.001). CONCLUSIONS: The blood culture method using the BacT/Alert system is useful for culturing dialysates and improves the positive culture rate in patients with suspected peritonitis compared to the conventional culture method.
Culture Media ; Dialysis Solutions ; Gram-Negative Bacterial Infections/*diagnosis/microbiology ; Gram-Positive Bacterial Infections/*diagnosis/microbiology ; Humans ; Kidney Failure, Chronic/*therapy ; Microbiological Techniques/*methods ; Peritoneal Dialysis, Continuous Ambulatory/*adverse effects ; Peritonitis/*diagnosis/microbiology ; Sensitivity and Specificity

This study aims at trying to establish a novel method of sterility test for injections based on biothermodynamics, in order to overcome the deficiencies of routine sterility tests such as long detecting cycle, low sensitivity and prone to misjudgments. A biothermodynamics method was adopted to rapidly detect the microorganism contamination of injections by monitoring the heat metabolism during the growth of microbe. The growth rate equal to or greater than zero and the heat power difference of P(i) and P(0) with three folds higher than the noise of baseline were chosen as indexes to study the heat change rule of microbe. In this way, the effectiveness of the new method to detect strains required by conventional sterility test or in injection samples was also investigated. Results showed that the Gram-positive bacteria, Gram-negative bacteria and fungi demanded by sterility testing methodology could be detected by biothermodynamics method within 10 hours, with the sensitivity lower than 100 CFU x mL(-1). Meanwhile, this method was successfully applied to the sterility test of Compound Yinchen injection (FFYC), Shuanghuanglian powder injection (SHL) and Compound Triamcinolone injection (TAND) which were sterilized with different degrees. Therefore, the biothermodynamics method, with advantages of fast detection and high sensitivity, could be a complementary solution for conventional sterility tests.
Anti-Inflammatory Agents ; administration & dosage ; chemistry ; Drug Contamination ; Drugs, Chinese Herbal ; administration & dosage ; chemistry ; Fungi ; isolation & purification ; Gram-Negative Bacteria ; isolation & purification ; Gram-Positive Bacteria ; isolation & purification ; Hot Temperature ; Injections ; Microbiological Techniques ; methods ; Sensitivity and Specificity ; Sterilization ; Triamcinolone ; administration & dosage ; chemistry

The commonly used plant constitutive expression vector pBI121 was modified by insertion of two directly orientated lox sites each at one end of the selectable marker gene NPTII and by replacing the GUS gene with a sequence composed of multiple cloning sites (MCS). The resulting plant expression vector pBI121-lox-MCS is widely usable to accommodate various target genes through the MCS, and more importantly to allow the NPTII gene removed from transformed plants upon the action of the Cre recombinase. In addition, the CaMV 35S promoter located upstream of the MCS can be substituted with any other promoters to form plant vectors with expression features specified by the introduced promoters. Provided in this paper is an example that an enhanced phloem-specific promoter of the pumpkin PP2 gene (named dENP) was used to construct an NPTII-removable phloem-specific expression vector pBdENP-lox-MCS. Moreover, to facilitate screening of selectable marker-removed gene and the composite sequence is flanked by lox sites. Thus the selectable marker-free plants can be visually identified by loss of GFP fluorescence. The above newly created plant expression vectors can be used to develop selectable marker-removable transgenic plants for a variety of purposes.
Attachment Sites, Microbiological ; genetics ; Binding Sites ; genetics ; Cloning, Molecular ; Gene Knockout Techniques ; methods ; Genes, Plant ; genetics ; Genetic Markers ; genetics ; Genetic Vectors ; genetics ; Green Fluorescent Proteins ; genetics ; metabolism ; Integrases ; genetics ; metabolism ; Plants ; genetics ; Plants, Genetically Modified ; genetics ; Recombination, Genetic

OBJECTIVETo establish the DNA microarray to detect influenza viruses and avian influenza viruses, and identify their virulence.

METHODSHemagglutinin (HA), neuramidinase (NA) and nucleoprotein(NP) genes were chosen simultaneously as targets for designing a microarray used for detection of viruses and identification virulence. The nucleic acid were amplified by single primer amplication (SPA). And then its specificity,sensitivity and reproducibility were evaluated.

RESULTSThe microarray was able to specially detect H1N1, H3N2, B influenza viruses and H5N1, H9N2 avian influenza viruses. Their limits were 8HAU, 16HAU, 32HAU, and 8HAU, 8HAU respectively. The limit for virulence was 32HAU. When samples were analyzed by both RT-PCR and microarray in parallel, the results agreed in 83.9% (47/56).

CONCLUSIONThe microarray can detect and distinguish five tested viruses, and especially identify virulence. It not only supplies an assistant tool for clinical diagnosis and control of infectious disease, but also is valuable for controlling and preventing outbreak of avian influenza epidemic.

Animals ; Birds ; Humans ; Influenza A virus ; genetics ; isolation & purification ; pathogenicity ; Influenza in Birds ; virology ; Influenza, Human ; virology ; Microbiological Techniques ; Oligonucleotide Array Sequence Analysis ; methods ; Orthomyxoviridae ; genetics ; isolation & purification ; pathogenicity ; RNA, Viral ; analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Sensitivity and Specificity ; Virulence ; genetics