Nested real-time PCR for hepatitis A detection

Aims:  The hepatitis A virus (HAV) is one of the most important human foodborne pathogens causing a number of worldwide outbreaks each year. The detection of HAV in food samples remains a complex issue, because commonly used detection tools, such as conventional or even real-time PCR assays, are often unable to detect HAV with sufficient sensitivity. The aims of this study were to develop highly sensitive and specific nested real-time PCR (NRT-PCR)-based method for HAV detection in food and to compare it with currently available methods.
Methods and Results:  By combining conventional PCR, nested PCR and real-time PCR techniques, we have developed a specific NRT-PCR assay for the detection of HAV. The procedure involves two consecutive PCRs, the first of which is performed as a conventional RT-PCR using primers specific for HAV 5' noncoding region. The second reaction involves a real-time PCR using a nested primer pair specific for the first PCR product and a TaqMan probe.
Conclusions:  We have developed a novel NRT-PCR method capable of detecting as little as 0·2 PFU of HAV, which is significantly more sensitive than any other PCR technique tested in our system.
Significance and Impact of the Study:  NRT-PCR provides a potentially useful method for detecting HAV at extremely low levels, as frequently found in food samples, and can be potentially adopted as a regulatory method to ensure food safety.     

The development of rapid real-time PCR detection system for Vibrio parahaemolyticus in raw oyster

Aims:  To develop a new rapid real-time polymerase chain reaction (PCR) based detection system for Vibrio parahaemolyticus ( V. parahaemolyticus ) applicable to raw oyster samples.
Methods and Results:  V. parahaemolyticus cells were artificially inoculated to oysters. Samples were homogenized in 100 ml of sterile saline water and serially diluted to 1·5 CFU ml⁻¹ level. One millilitre of diluents was centrifuged and the pellet was resuspended with 100  μ l of de-ionized water. DNA was extracted by boiling for 20 min, and 0·5  μ l was used as a template for PCR reaction. Real-time PCR was performed with TMC-1000 system (1  μ l PCR system). The detection system was found to achieve detection limit of 1·5 CFU g⁻¹ for V. parahaemolyticus . Furthermore, the specificities of these assay systems were confirmed with more than 20 bacterial strains, including various Vibrio species.
Conclusions:  Rapid and sensitive food-borne pathogen detection techniques for V. parahaemolyticus is important to the food industry and consumers. The direct detection of V. parahaemolyticus from food is possible with micro real-time PCR system.
Significance and Impact of the Study:  This study shows that oyster samples can be tested for V. parahaemolyticus with a rapid, specific and simple procedure.     

Molecular Ecology of Pyrethroid Knockdown Resistance in Culex pipiens pallens Mosquitoes

Pyrethroid insecticides have been extensively used in China and worldwide for public health pest control. Accurate resistance monitoring is essential to guide the rational use of insecticides and resistance management. Here we examined the nucleotide diversity of the para-sodium channel gene, which confers knockdown resistance (kdr) in Culex pipiens pallens mosquitoes in China. The sequence analysis of the para-sodium channel gene identified L1014F and L1014S mutations. We developed and validated allele-specific PCR and the real-time TaqMan methods for resistance diagnosis. The real-time TaqMan method is more superior to the allele-specific PCR method as evidenced by higher amplification rate and better sensitivity and specificity. Significant positive correlation between kdr allele frequency and bioassay-based resistance phenotype demonstrates that the frequency of L1014F and L1014S mutations in the kdr gene can be used as a molecular marker for deltamethrin resistance monitoring in natural Cx. pipiens pallens populations in the East China region. The laboratory selection experiment found that L1014F mutation frequency, but not L1014S mutation, responded to deltamethrin selection, suggesting that the L1014F mutation is the key mutation conferring resistance to deltamethrin. High L1014F mutation frequency detected in six populations of Cx. pipens pallens suggests high prevalence of pyrethroid resistance in Eastern China, calling for further surveys to map the resistance in China and for investigating alternative mosquito control strategies.     

细菌群体感应信号分子的光电检测技术

群体感应（quorum sensing，QS）是一种依赖菌群密度的细菌交流系统。在探究细菌群体感应系统的调控机制中，对QS信号分子的鉴别和检测是不可或缺的环节，其对生命科学、药学等领域涉及细菌等微生物的相互作用、高效检测和作用机制解析等具有重要的参考意义。本文在总结不同类型细菌QS信号分子来源和结构的基础上，对QS信号分子的光电检测方法和技术进行了综述，重点对光电传感检测的敏感介质、传感界面、传感机制及测试效果进行探讨，同时关注了将微流控芯片分析技术应用于细菌QS信号分子原位监测的相关研究进展。     

细菌双杂交系统的优化及其应用

细菌双杂交系统是一种用于检测体内蛋白质互作的方法,该方法互补腺苷酸环化酶功能,通过检测细胞表达的β-半乳糖苷酶LacZ的活性,分析蛋白质互作能力.但在应用过程中,发现存在操作繁琐、灵敏度低、难实现高通量操作等缺陷.本研究目的是对原有细菌双杂交进行优化,建立一种操作方便、可批量操作、具有较高灵敏度和能够实现实时监测的细菌...     

Colony breeding system influences cuticular bacterial load of Formosan subterranean termite (Isoptera: Rhinotermitidae) workers

The goal of this study was to test whether the breeding system and/or the degree of inbreeding of field colonies of the Formosan subterranean termite, Coptotermes formosanus, Shiraki (Isoptera: Rhinotermitidae) influences bacterial load on the cuticle of foraging workers. We enumerated bacterial load on the cuticle of groups of workers foraging in 20 inground monitoring stations surrounding the French Market in New Orleans, LA, and identified bacteria species using 16S rRNA gene sequencing. We used microsatellite genotyping to assign the 20 worker groups to seven simple family colonies (headed by a single pair of reproductives) and four extended family colonies (headed by multiple inbreeding reproductives) with a wide range of degrees of inbreeding. Workers from extended family colonies had a higher bacterial load than those from simple family colonies; however, bacterial load was not significantly correlated to the degree of inbreeding, possibly because of confounding factors in colony life history, such as age and/or size of colonies. Colonies with high bacterial load did not have a higher proportion of entomopathogens, and thus, bacterial load is not necessarily an indicator for disease risk. The majority of bacteria cultured from the cuticle of termites were soil bacteria with no known pathology against termites.     

Intelligent real-time performance monitoring and quality prediction for batch/fed-batch cultivations

Supervision of batch bioprocess operations in real-time during the progress of a batch run offers many advantages over end-of-batch quality control. Multivariate statistical techniques such as multiway partial least squares (MPLS) provide an efficient modeling and supervision framework. A new type of MPLS modeling technique that is especially suitable for online real-time process monitoring and the multivariate monitoring charts are presented. This online process monitoring technique is also extended to include predictions of end-of-batch quality measurements during the progress of a batch run. Process monitoring, quality estimation and fault diagnosis activities are automated and supervised by embedding them into a real-time knowledge-based system (RTKBS). Interpretation of multivariate charts is also automated through a generic rule-base for efficient alarm handling. The integrated RTKBS and the implementation of MPLS-based process monitoring and quality control are illustrated using a fed-batch penicillin production benchmark process simulator.     

Characterization of rpoB mutations associated with rifampin resistance in Mycobacterium tuberculosis from eastern China

Aims:  The aim of this study was to investigate the features of rpoB gene mutations associated with Rifampin (RIF) resistance in Mycobacterium tuberculosis ( M. tuberculosis ) in eastern China.
Methods and Results:  The mutations of rpoB gene in 56 clinical isolates of M. tuberculosis resisted to one to four first-line drugs (rifampin, isonicotinyl hydrazide, ethambutol and streptomycin) were analysed by polymerase chain reaction single strand conformation polymorphism analysis (PCR-SSCP) and DNA sequencing. The results of PCR-SSCP showed 52 isolates were positive (existing rpoB mutation) including 47 isolates resisted to RIF. Subsequent results of DNA sequencing showed that 54 isolates had rpoB gene mutation including 49 isolates resisted to RIF. The most frequently mutated sites were at codons 526 (73·2%), 513 (10·7%) and 531 (3·5%).
Conclusions:  The rpoB codon 526 was the most frequently mutated site of RIF-resistant M. tuberculosis strains in eastern China and its frequency is significantly higher ( P  < 0·0001) compared with that in other areas of China and in other geographic regions worldwide.
Significance and Impact of the Study:  Our results reveal that geographic variation is responsible for rpoB mutations in M. tuberculosis and the resulting information will be helpful to improve a novel rapid molecular drug resistance screening approach for MDR TB.     

Assessment of the bacterial diversity of breast milk of healthy women by quantitative real-time PCR

Aims:  Breast milk has been described as a source of bacteria influencing the development of the infant gut microbiota. Up to the present, few studies have been focused on the application of culture-independent techniques to study bacterial diversity in breast milk. In this context, the aim of this study was to characterize the breast milk microbiota of healthy women by applying the quantitative real-time PCR technique (qRTi-PCR).
Methods and Results:  A total of 50 breast milk samples were analysed by qPCR to assess the presence of different bacterial genera or clusters, including the Bifidobacterium , Lactobacillus , Staphylococcus , Bacteroides , Enterococcus , Streptococcus , Clostridium cluster IV and Clostridium cluster XIVa–XIVb groups. Staphylococcus , Streptococcus , Bifidobacterium and Lactobacillus were the predominant groups and were detected in all the samples. Clostridium XIVa–XIVb and Enterococcus were detected in most of the samples in contrast to the Bacteroides and Clostridium cluster IV groups.
Conclusions:  Our results confirm the abundance of bacterial DNA in breast milk samples and suggest that the qRTi-PCR technique has a huge potential in the microbiological analysis of human milk.
Significance and Impact of the study:  qRTi-PCR allowed the detection of bacterial DNA of streptococci, staphylococci, lactic acid bacteria and bifidobacteria in the samples of human milk, which confirms that breast milk can be an important source of bacteria and bacterial DNA to the infant gut.     

Genome-wide detection of unknown subtle mutations in bacteria by combination of MutS and RDA

We propose a procedure for detecting unknown, subtle DNA changes throughout the entire bacterial genome by a combination of MutS and RDA. Current techniques detect subtle mutations after PCR amplification of the target regions, so the mutation detection is done between amplified PCR fragments. In this paper, genome-wide subtle mutation scanning in bacteria was performed by combining the MutS and RDA techniques. Our strategy for cloning a small mutation region is composed of two steps: an enrichment of fragments containing subtle mutations using MutS, followed by an RDA subtraction procedure for further enrichment. We successfully identified small mutations such as a four-base insertion, a two-base insertion, and transition mutations in bacteria.     

A dynamic real-time method for monitoring epithelial barrier function in vitro

The intestinal epithelium functions as a physical barrier against the harmful environment of the lumen, which usually becomes impaired in the presence of intestinal diseases. In this work, we introduce an electronic impedance-based analysis using a real-time xCELLigence system to record the dynamic processes of ethanol-induced intestinal barrier dysfunction. In terms of analyzing morphological alterations in the paracellular junction complex and the organization of pericellular F-actin, this novel, real-time, cell-based technology shows considerable correlations with the standard transepithelial electrical resistance endpoint assay. In addition, monitoring barrier functions in real time allows unbiased screening and characterization of biochemical agents in the lumen that affect epithelial integrity. This functional assay further identifies the in vitro roles of the inducible nitric oxide synthase inhibitor, epithelial growth factor, tyrosine kinases, and phosphatases in regulating epithelial barrier function in response to ethanol administration. Taken together, our findings suggest that this novel, real-time, high-throughput method offers a promising tool for monitoring epithelial barrier functions in situations with more physiological relevance.     

The tetracycline resistance gene tet39 is present in both Gram-negative and Gram-positive bacteria from a polluted river, Southwestern Nigeria

Aim:  Previous analysis of tet39 suggests it may be present in other bacterial species. Hence, we investigated the host range of tet39 among bacterial from a poultry waste polluted river in Southwestern Nigeria.
Methods and Results:  Thirteen resistant bacterial isolated from the water and sediment of the polluted river was investigated for the presence of tetracycline resistance genes tetA , tetB , tetC , tet39 and the transposon integrase gene of the Tn916/1545 family by PCR. While tetA , tetB , tetC and integrase genes cannot be detected in any of the organisms, tet39 was detected in eight of the tested organisms including three Gram-positive species. Sequence analysis showed the genes have high sequence identities (≥99%) with tet39 of Acinetobacter sp. LUH5605, the first and only bacterial genus from which the gene has been reported to date. This is a novel observation.
Conclusions:  This study shows that apart from Acinetobacter , tet39 is present in other bacterial species tested in this study.
Significance and Impact of the Study:  This study adds to available information on the occurrence and distribution of tet39 among environmental bacteria and suggests that the gene has a broader host range than previously reported.     

Real-time impedance analysis of host cell response to meningococcal infection

Measuring cell proliferation and cell death during bacterial infection involves performing end-point assays that represent the response at a single time point. A new technology from Roche Applied Science and ACEA Biosciences allows continuous monitoring of cells in real-time using specialized cell culture microplates containing micro-electrodes. The xCELLigence system enables continuous measurement and quantification of cell adhesion, proliferation, spreading, cell death and detachment, thus creating a picture of cell function during bacterial infection. Furthermore, lag and log phases can be determined to estimate optimal times to infect cells.In this study we used this system to provide valuable insights into cell function in response to several virulence factors of the meningitis causing pathogen Neisseria meningitidis, including the lipopolysaccharide (LPS), the polysaccharide capsule and the outer membrane protein Opc. We observed that prolonged time of infection with pathogenic Neisseria strains led to morphological changes including cell rounding and loss of cell-cell contact, thus resulting in changed electrical impedance as monitored in real-time. Furthermore, cell function in response to 14 strains of apathogenic Neisseria spp. (N. lactamica and N. mucosa) was analyzed. In contrast, infection with apathogenic N. lactamica isolates did not change electrical impedance monitored for 48 h. Together our data show that this system can be used as a rapid monitoring tool for cellular function in response to bacterial infection and combines high data acquisition rates with ease of handling.     

The allele-specific probe and primer amplification assay, a new real-time PCR method for fine quantification of single-nucleotide polymorphisms in pooled DNA

The evolution of fungicide resistance within populations of plant pathogens must be monitored to develop management strategies. Such monitoring often is based on microbiological tests, such as microtiter plate assays. Molecular monitoring methods can be considered if the mutations responsible for resistance have been identified. Allele-specific real-time PCR approaches, such as amplification refractory mutation system (ARMS) PCR and mismatch amplification mutation assay (MAMA) PCR, are, despite their moderate efficacy, among the most precise methods for refining SNP quantification. We describe here a new real-time PCR method, the allele-specific probe and primer amplification assay (ASPPAA PCR). This method makes use of mixtures of allele-specific minor groove binder (MGB) TaqMan probes and allele-specific primers for the fine quantification of SNPs from a pool of DNA extracted from a mixture of conidia. It was developed for a single-nucleotide polymorphism (SNP) that is responsible for resistance to the sterol biosynthesis inhibitor fungicide fenhexamid, resulting in the replacement of the phenylalanine residue (encoded by the TTC codon) in position 412 of the enzymatic target (3-ketoreductase) by a serine (TCC), valine (GTC), or isoleucine (ATC) residue. The levels of nonspecific amplification with the ASPPAA PCR were reduced at least four times below the level of currently available allele-specific real-time PCR approaches due to strong allele specificity in amplification cycles, including two allele selectors. This new method can be used to quantify a complex quadriallelic SNP in a DNA pool with a false discovery rate of less than 1%.     

A rapid and simple method for the determination of base substitution and frameshift specificity of mutagens

A rapid method for the determination of mutagenic specificity has been developed which makes use of the ochre mutation (TAA) in the his-4 gene of Escherichiacoli. Reversion to His⁺ may occur by suppressor mutation (Type I) or by mutation within the his-4 gene (Type II). The Type I mutations may be further subdivided with respect to the type of suppressor mutation by their ability to suppress nonsense mutants of bacteriophage T4, thus allowing the identification of the responsible base substitution (Kato et al., 1980). The system has the ability to identify mutagens which produce A:T → G:C transitions since only Type II mutants can arise through this base substitution; and in fact, the system confirms the A:T → G:C specificity of the mutagen, N⁴-hydroxycytidine (Janion and Glickman, 1980) since only Type II mutants were induced by treatment with this base analogue.When this system was further tested with several additional mutagens, the results indicate that ethyl methanesulphonate, methyl nitrosourea and ethyl nitrosourea produce primarily Type I revertants which were primarily G:C → A:T transitions. UV-light, γ-rays, 4NQO and methyl methanesulphonate produced all types of base substitutions. The tester strain was further improved by introducing a series of sequenced trp^? frameshift mutations, thus allowing the simultaneous monitoring of frameshift and base-substitution mutations.     

Dynamic Monitoring of Cellular Remodeling Induced by the Transforming Growth Factor-β1

The plasticity of differentiated adult cells could have a great therapeutic potential, but at the same time, it is characteristic of progression of serious pathological states such as cancer and fibrosis. In this study, we report on the application of a real-time noninvasive system for dynamic monitoring of cellular plasticity. Analysis of the cell impedance profile recorded as cell index using a real-time cell analyzer revealed its significant increase after the treatment of prostate epithelial cells with the transforming growth factor-β1. Changes in the cell index profile were paralleled with cytoskeleton rebuilding and induction of epithelial–mesenchymal transition and negatively correlated with cell proliferation. This novel application of such approach demonstrated a great potential of the impedance-based system for noninvasive and real-time monitoring of cellular fate.     

The structure of the outer membrane protein OmpX from Escherichia coli reveals possible mechanisms of virulence.

BACKGROUND: The integral outer membrane protein X (OmpX) from Escherichia coli belongs to a family of highly conserved bacterial proteins that promote bacterial adhesion to and entry into mammalian cells. Moreover, these proteins have a role in the resistance against attack by the human complement system. Here we present the first crystal structure of a member of this family. RESULTS: The crystal structure of OmpX from E. coli was determined at 1.9 A resolution using multiple isomorphous replacement. OmpX consists of an eight-stranded antiparallel all-next-neighbor beta barrel. The structure shows two girdles of aromatic amino acid residues and a ribbon of nonpolar residues that attach to the membrane interior. The core of the barrel consists of an extended hydrogen-bonding network of highly conserved residues. OmpX thus resembles an inverse micelle. The structure explains the dramatically improved crystal quality of OmpX containing the mutation His100-->Asn, which made the X-ray analysis possible. The coordination spheres of two bound platinum ions are described. CONCLUSIONS: The OmpX structure shows that within a family of virulence-related membrane proteins, the membrane-spanning part of the protein is much better conserved than the extracellular loops. Moreover, these loops form a protruding beta sheet, the edge of which presumably binds to external proteins. It is suggested that this type of binding promotes cell adhesion and invasion and helps defend against the complement system. Although OmpX has the same beta-sheet topology as the structurally related outer membrane protein A (OmpA), their barrels differ with respect to the shear numbers and internal hydrogen-bonding networks.     

Biological control of streptococcal infection in Nile tilapia Oreochromis niloticus (Linnaeus, 1758) using filter‐feeding bivalve mussel Pilsbryoconcha exilis (Lea, 1838)

Since bivalve mussels are able to graze heavily on bacteria, in this paper it is hypothesized that when mussels are cultured with fish, the filtering efficiency of the mussels will keep the bacterial population below a certain threshold and thus assist in reducing the risk of bacterial disease outbreaks. The ability of the filter‐feeding bivalve mussel Pilsbryoconcha exilis to control Streptococcus agalactiae was tested in a laboratory‐scale tilapia culture system. Juvenile Nile tilapia (Oreochromis niloticus), the bivalve mussel as well as the bacteria were cultured at different combinations using four treatments: treatment‐1: mussel and bacteria but no fish, treatment‐2: tilapia and mussel but no bacteria, treatment‐3: tilapia and bacteria but no mussel, and treatment‐4: tilapia, mussels, and bacteria. All treatments were run in three replicates; stocking rates were 10 tilapia juveniles; five mussels; and about 3.5 × 10⁵ colony forming units (CFU) ml^?1 of bacteria in 50‐L aquaria with 40‐L volume. The mussel reduced the bacterial population by 83.6–87.1% in a 3‐week period whereas in the absence of the mussel, the bacterial counts increased by 31.5%. Oresence of the mussel also resulted in significantly higher growth and lower mortality of tilapia juveniles than when the mussel was absent. The results of this experiment suggest that the freshwater mussel P. exilis could control the population of S. agalactiae in a laboratory‐scale tilapia culture system. Future studies should focus on the dynamic interactions among fish, mussels, and bacteria as well as on how input such as feed and other organic materials affect these interactions.