Microbial characterization of nitrification in a shallow, nitrogen-contaminated aquifer, Cape Cod, Massachusetts and detection of a novel cluster associated with nitrifying Betaproteobacteria

Groundwater nitrification is a poorly characterized process affecting the speciation and transport of nitrogen. Cores from two sites in a plume of contamination were examined using culture-based and molecular techniques targeting nitrification processes. The first site, located beneath a sewage effluent infiltration bed, received treated effluent containing O₂ (> 300 µM) and NH₄⁺ (51–800 µM). The second site was 2.5 km down-gradient near the leading edge of the ammonium zone within the contaminant plume and featured vertical gradients of O₂, NH₄⁺, and NO₃⁻ (0–300, 0–500, and 100–200 µM with depth, respectively). Ammonia- and nitrite-oxidizers enumerated by the culture-based MPN method were low in abundance at both sites (1.8 to 350 g^− 1 and 33 to 35,000 g^− 1, respectively). Potential nitrifying activity measured in core material in the laboratory was also very low, requiring several weeks for products to accumulate. Molecular analysis of aquifer DNA (nested PCR followed by cloning and 16S rDNA sequencing) detected primarily sequences associated with the Nitrosospira genus throughout the cores at the down-gradient site and a smaller proportion from the Nitrosomonas genus in the deeper anoxic, NH₄⁺ zone at the down-gradient site. Only a single Nitrosospira sequence was detected beneath the infiltration bed. Furthermore, the majority of Nitrosospira-associated sequences represent an unrecognized cluster. We conclude that an uncharacterized group associated with Nitrosospira dominate at the geochemically stable, down-gradient site, but found little evidence for Betaproteobacteria nitrifiers beneath the infiltration beds where geochemical conditions were more variable.     

PGD for monogenic disorders: aspects of molecular biology

Preimplantation genetic diagnosis (PGD) for monogenic diseases has known a considerable evolution since its first application in the early 1990s. Especially the technical aspects of the genetic diagnosis itself, the single-cell genetic analysis, has constantly evolved to reach levels of accuracy and efficiency nearing those of genetic diagnosis on regular DNA samples. In this review, we will focus on the molecular biological techniques that are currently in use in the most advanced centers for PGD for monogenic disorders, including multiplex polymerase chain reaction (PCR) and post-PCR diagnostic methods, whole genome amplification (WGA) and multiple displacement amplification (MDA). As it becomes more and more clear that when it comes to ethically difficult indications, PGD goes further than prenatal diagnosis (PND), we will also briefly discuss ethical issues. Copyright © 2008 John Wiley & Sons, Ltd.     

The StepOne real-time polymerase chain reaction detection of Salmonella sp., Salmonella enterica ser. typhimurium and enteritidis in milk and meat

The aim of this study was to follow contamination of ready to eat milk and meat products with Salmonella spp. by using the StepOne real-time polymerase chain reaction (PCR). Classical microbiological methods for detection of foodborne bacteria involve the use of pre-enrichment and/or specific enrichment, following isolation of bacteria in solid media and the final confirmation by biochemical and/or serological tests. We used the PrepSEQ Rapid Spin Sample Preparation Kit for isolation of DNA and MicroSEQ® Salmonella spp. Detection Kit for pursuance of the real-time PCR (Applied Biosystems). In samples without incubation we detected strain of Salmonella sp. in 5 out of 25 samples (swabs), as well as in the internal positive control (IPC), which was positive in all samples. This StepOne real-time PCR assay is extremely useful for any laboratory equipped by real-time PCR. It is a fast, reproducible, simple, specific and sensitive way to detect nucleic acids, which could be used in clinical diagnostic tests in the future. Our results indicated that real-time PCR assay developed in this study could sensitively detect Salmonella spp. in ready-to-eat food. This could prevent infection caused by Salmonella, and also could benefit food manufacturing companies by extending their product's shelf-life as well as saving the cost of warehousing their food products while awaiting pathogen testing results.     

Combining Flow Cytometry and Real-Time PCR Methodology to Demonstrate Consumption by Prymnesium parvum1

Bowers, Holly A., Andreas Brutemark, Wanderson F. Carvalho, and Edna Granéli, 2010. Combining Flow Cytometry and Real-Time PCR Methodology to Demonstrate Consumption by Prymnesium parvum. Journal of the American Water Resources Association (JAWRA) 46(1):133-143. DOI: 10.1111/j.1752-1688.2009.00397.x Abstract: Harmful algal bloom species can persist in the environment, impacting aquatic life and human health. One of the mechanisms by which some harmful algal bloom species are able to persist is by consumption of organic particles. Methods to demonstrate and measure consumption can yield insight into how populations thrive. Here, we combine flow cytometry and real-time PCR to demonstrate consumption of a cryptophyte species (Rhodomonas sp.) by a toxic mixotrophic haptophyte (Prymnesium parvum). Using flow cytometry, the feeding frequency of a population of P. parvum cells was calculated using the phycoerythrin (PE) fluorescence signal from Rhodomonas sp. and the fluorescence of an acidotropic probe labeling the food vacuoles. Feeding frequency increased in the beginning of the experiment and then began to decline, reaching a maximum of 47.5% of the whole P. parvum population after 212 min. The maximum number of consumed Rhodomonas sp. cells was 0.8 per P. parvum cell, and occurred after 114 min corresponding to an ingestion rate of 0.4 Rhodomonas sp. cells/P. parvum/h. Cells from the feeding P. parvum population were sorted, washed, and subjected to a real-time PCR assay targeting the cryptophyte 18S locus. There was a correlation between cycle threshold (Ct) values and number of consumed prey cells calculated by fluorescence. Overall, this study shows that flow cytometric analysis, of the acidotropic probe and prey pigments, is an efficient and rapid tool in enumerating food vacuoles and the number of prey cells consumed. Furthermore, we suggest that real-time PCR can be applied to cells sorted by flow cytometry, thus allowing for the detection and potential quantification of the targeted prey cells.     

TFM实时成像技术在缺陷检测中的应用

在压力容器的超声检测中,为解决传统相控阵（PA）二维成像存在缺陷图像畸变,难以准确定性等问题,采用1种基于全聚焦法（TFM）的实时超声成像技术,使用一维线阵和二维面阵分别对孔等典型实际缺陷进行扫查,获得缺陷的二维和三维图像,从定量角度对比分析2者的准确度。结果表明:该方法获得的三维图像测量误差在8%以内,具有更高的精确度和检出率,对于孔类缺陷的还原度更高,这对于缺陷检测与评估以及和特种设备的安全生产具有重要意义。     

Wildlife identified as major source of Escherichia coli in agriculturally dominated watersheds by BOX A1R-derived genetic fingerprints

The presence of Escherichia coli in recreational and potable waters is a major concern to the general public as elevated levels of E. coli suggest the presence of pathogenic bacteria and viruses. Unfortunately, traditional microbial techniques do not allow specific identification of the source of E. coli. This reduces the ability to target management practices that reduce bacterial contamination. In the Finger Lakes region of western New York, USA, wildlife resides in relatively high densities on watersheds dominated by people and dairy farms, and as a result, the sources of fecal degradation of potable and recreational waters are often unknown. In the Conesus Lake watershed, the sources of microbial contamination were assessed using Rep-PCR molecular tools, a method of amplifying repetitive DNA sequences found throughout the E. coli genome to produce distinct fingerprints for a given ecotype. Molecular fingerprints of E. coli isolated from regional populations of cattle, humans, geese and deer were compared to E. coli isolated from stream water samples. Canonical discriminant function analysis indicated that the DNA fingerprints of the original source group isolates were correctly predicted 90.2% of the time. Since land use in the sub-watersheds was dominated by dairy and cash crop farms, it was expected that the majority of E. coli isolated would be identified as cows; however, an unexpectedly high percentage of isolates were identified as wildlife (geese and deer). Geese were the dominant source of E. coli (44.7-73.7% of the total sources) in four sub-watersheds followed by cows (10.5-21.1%), deer (10.5-18.4%), humans (5.3-12.9%) and unidentifiable sources (0.0-11.8%). Management practices intended to decrease the number of cattle or the amount of manure spread in a sub-watershed were reflected in a decrease of E. coli ecotypes associated with dairy cows.