Design and use of group-specific primers and probes for real-time quantitative PCR

Real-time quantitative polymerase chain reaction (qPCR) has gained popularity as a technique to detect and quantify a specific group of target microorganisms from various environmental samples including soil, water, sediments, and sludge. Although qPCR is a very useful technique for nucleic acid quantification, accurately quantifying the target microbial group strongly depends on the quality of the primer and probe used. Many aspects of conducting qPCR assays have become increasingly routine and automated; however, one of the most important aspects, designing and selecting primer and probe sets, is often a somewhat arcane process. In many cases, failed or non-specific amplification can be attributed to improperly designed primer-probe sets. This paper is intended to provide guidelines and general principles for designing group-specific primers and probes for qPCR assays. We demonstrate the effectiveness of these guidelines by reviewing the use of qPCR to study anaerobic processes and biologic nutrient removal processes. qPCR assays using group-specific primers and probes designed with this method, have been used to successfully quantify 16S ribosomal Ribonucleic Acid (16S rRNA) gene copy numbers from target methanogenic and ammonia-oxidizing bacteria in various laboratory- and full-scale biologic processes. Researchers with a good command of primer and probe design can use qPCR as a valuable tool to study biodiversity and to develop more efficient control strategies for biologic processes.     

Identification of Sources Contributing to Mid-Atlantic Regional Aerosol

Abstract

Source types or source regions contributing to the concentration of atmospheric fine particles measured at Brigantine National Wildlife Refuge, NJ, were identified using a factor analysis model called Positive Matrix Factorization (PMF). Cluster analysis of backward air trajectories on days of high- and low-factor concentrations was used to link factors to potential source regions. Brigantine is a Class I visibility area with few local sources in the center of the eastern urban corridor and is therefore a good location to study Mid-Atlantic regional aerosol. Sulfate (expressed as ammonium sulfate) was the most abundant species, accounting for 49% of annual average fine mass. Organic compounds (22%; expressed as 1.4 × organic carbon) and ammonium nitrate (10%) were the next abundant species. Some evidence herein suggests that secondary organic aerosol formation is an important contributor to summertime regional aerosol.

Nine factors were identified that contributed to PM_2.5 mass concentrations: coal combustion factors (66%, summer and winter), sea salt factors (9%, fresh and aged), motor vehicle/mixed combustion (8%), diesel/Zn-Pb (6%), incinerator/industrial (5%), oil combustion (4%), and soil (2%). The aged sea salt concentrations were highest in springtime, when the land breeze-sea breeze cycle is strongest. Comparison of backward air trajectories of high- and low-concentration days suggests that Brigantine is surrounded by sources of oil combustion, motor vehicle/mixed combustion, and waste incinerator/industrial emissions that together account for 17% of PM_2.5 mass. The diesel/Zn-Pb factor was associated with sources north and west of Brigantine. Coal combustion factors were associated with coal-fired power plants west and southwest of the site. Particulate carbon was associated not only with oil combustion, motor vehicle/mixed combustion, waste incinerator/industrial, and diesel/Pb-Zn, but also with the coal combustion factors, perhaps through common transport.     

Distributions of heavy metals in the sediments of South Korean harbors

Bottom sediments of harbors in the South Korea have been long suspected for metal contamination due to ship-based and urban-based activities for the past several decades. A number of areas have been suspected to impair ecosystem services to the local residents and drawn complaints from main stakeholders. Twelve contamination suspected harbors were subject to evaluate the level of contamination of Cr, Ni, Cu, Zn, As, Cd, Pb and Hg. The level of sediment contamination for each metal was evaluated comparing the relative enrichment of a given metal to pollution-insensitive aluminum. Regional background concentration of a given metal was also determined based on its down core measurement and sediment texture. Ecological risk posed by the presence of heavy metals was evaluated using the sediment quality guidelines (SQGs) developed by United States National Ocean and Atmosphere Administration (US NOAA) as benchmarks for evaluating sediment chemistry to aquatic organisms. Cu, Zn, Cd, Pb and Hg in the surface sediment were found to be higher than a factor of 1.5 than background sediments, and the overall metal contaminations of surface sediment can be regarded as medium-high- to high-priority sites in the sense of SQGs.     

Receptor-mediated in vitro bioassay for characterization of Ah-R-active compounds and activities in sediment from Korea

Sediment extracts of stream sediments, collected from inland areas of Lake Shihwa (LSI) and Masan Bay (MBI), were screened for their abilities to induce aryl hydrocarbon receptor (Ah-R) mediated gene expression in vitro. Cell viability assay was also performed to examine cytotoxic effects on the Ah-R-mediated activities of sediment samples. Over 80% (30 out of 36) of sediment raw extracts (REs) induced significant Ah-R-mediated activities in the H4IIE-luc cell bioassays. Ah-R-mediated activities of sediment REs from LSI locations (mean=58%-TCDD-max; n=21) were greater than those of sediment REs from MBI locations (mean=35%-TCDD-max; n=15), in general. Seven (mean+/-SD=100+/-14%-TCDD-max) of 21 sediment REs from LSI showed Ah-R-mediated activities comparable to that (set to, 100%-TCDD-max) elicited by 1240 pM TCDD. Whereas, in MBI, only two REs from M1 (93%-TCDD-max) and M9 (82%-TCDD-max) showed significantly great responses that comparable to maximum response of TCDD standard curve. Sample potencies relative to the TCDD standard (TCDD-EQs) were estimated based on full dose-response characteristics of REs and TCDD-EQs were found to be 14-868 pg TCDD/g, dw and 17-275 pg TCDD/g, dw, in LSI and MBI, respectively. A range of TCDD-EQ20-80 of samples, based on multiple estimates of relative potency (REP20-80), did not vary greatly (2-4-fold) in the H4IIE-luc bioassays, which indicated relatively low degree of uncertainties in point estimates of REP for sediment REs examined. Acid-treatment of REs samples improved quantitative biological responses of samples followed by decreases in cytotoxicity identified by MTT cell viability assays.     

Identification of sources contributing to Mid-Atlantic regional aerosol

Source types or source regions contributing to the concentration of atmospheric fine particles measured at Brigantine National Wildlife Refuge, NJ, were identified using a factor analysis model called Positive Matrix Factorization (PMF). Cluster analysis of backward air trajectories on days of high- and low-factor concentrations was used to link factors to potential source regions. Brigantine is a Class I visibility area with few local sources in the center of the eastern urban corridor and is therefore a good location to study Mid-Atlantic regional aerosol. Sulfate (expressed as ammonium sulfate) was the most abundant species, accounting for 49% of annual average fine mass. Organic compounds (22%; expressed as 1.4 x organic carbon) and ammonium nitrate (10%) were the next abundant species. Some evidence herein suggests that secondary organic aerosol formation is an important contributor to summertime regional aerosol. Nine factors were identified that contributed to PM2.5 mass concentrations: coal combustion factors (66%, summer and winter), sea salt factors (9%, fresh and aged), motor vehicle/mixed combustion (8%), diesel/Zn-Pb (6%), incinerator/industrial (5%), oil combustion (4%), and soil (2%). The aged sea salt concentrations were highest in springtime, when the land breeze-sea breeze cycle is strongest. Comparison of backward air trajectories of high- and low-concentration days suggests that Brigantine is surrounded by sources of oil combustion, motor vehicle/mixed combustion, and waste incinerator/industrial emissions that together account for 17% of PM2.5 mass. The diesel/Zn-Pb factor was associated with sources north and west of Brigantine. Coal combustion factors were associated with coal-fired power plants west and southwest of the site. Particulate carbon was associated not only with oil combustion, motor vehicle/mixed combustion, waste incinerator/industrial, and diesel/Pb-Zn, but also with the coal combustion factors, perhaps through common transport.     

Identification of triploid trophoblast cells in peripheral blood of a woman with a partial hydatidiform molar pregnancy

In a woman with a partial hydatidiform molar pregnancy with 69,XXY karyotype, the presence of male fetal cells of trophoblastic origin was demonstrated in maternal blood by X/Y-chromosome specific PCR and by immunostaining combined with FISH on two cell populations isolated from maternal blood. Blood was obtained three weeks prior to the detection of fetal demise, at 13 weeks' gestation. Results were confirmed on formalin-fixed paraffin-embedded molar tissue, removed at 16 weeks' gestational age for therapeutic reasons. The results indicate that both plasma and cells from maternal peripheral blood might be useful for non-invasive prenatal diagnosis of fetal aneuploidies, as described in the current case with a partial molar pregnancy. Copyright © 2001 John Wiley & Sons, Ltd.     

Characterization and recovery of mercury from spent fluorescent lamps

Fluorescent lamps rely on mercury as the source of ultraviolet radiation for the production of visible light. Partitioning of mercury among vapor phase, loose phosphor powders produced during breaking and washing steps, glass matrices, phosphor powders attached on the glass and aluminum end caps was examined from simulated laboratory lamp recycling tests for different types of spent and new fluorescent lamps. Mercury concentrations in lamp glasses taken from commercial lamp recyclers were also analyzed for comparison with the simulated results of spent and new lamps of different types. The mercury content of the glass from spent lamps was highly variable depending on the lamp type and manufacturer; the median values of the mercury concentration in glasses for spent 26- (T8) and 38-mm (T12) diameter fluorescent lamps were approximately 30 and 45 microg/g, respectively. The average mercury concentration of samples taken from recycler A was 29.6 microg/g, which was about 64% of median value measured from the spent T12 lamps. Over 94% of total mercury in lamps remained either as a component of phosphor powders attached inside the lamp or in glass matrices. New T12 lamps had a higher partitioning percentage of elemental mercury in the vapor phase (0.17%) than spent T12 lamps (0.04%), while spent lamps had higher partitioning percentages of mercury resided on end-caps and phosphor powders detached from the breaking and washing steps. The TCLP values of simulated all lamp-glasses and samples obtained from recyclers were higher than the limit of LDR standard (0.025 mg/L). After investigating acid treatment and high temperature treatment as mercury reclamation techniques, it was found that heating provided the most effective mercury capture. Although the initial mercury concentrations of individual sample were different, the mercury concentrations after 1 h exposure at 100 degrees C were below 4 mug/g for all samples (i.e., <1% remaining). Therefore, it is recommended that heating be used for recovering mercury from spent fluorescent lamps.     

A DYNAMIC SYSTEM MODEL FOR SIMULATING SEDIMENT DISCHARGE1

ABSTRACT: A dynamic sediment discharge model was developed and proposed for the simulation of watershed systems. It war developed from an expansion of splash and flow erosion relationships under steady state conditions. It was described as a general erosion model that can be reduced to forms comparable to many conceptual soil erosion and sediment yield models. The model incorporates eight parameters such as rainfall intensities, runoff rates, and previous sediment discharges. The model was tested with two small watersheds with simulation results which were very satisfactory compared to the data.     

Quantifying and managing regional greenhouse gas emissions：Waste sector of Daejeon, Korea

A credible accounting of national and regional inventories for the greenhouse gas （GHG） reduction has emerged as one of the most significant current discussions. This article assessed the regional GHG emissions by three categories of the waste sector in Daejeon Metropolitan City （DMC）, Korea, examined the potential for DMC to reduce GHG emission, and discussed the methodology modified from Intergovernmental Panel on Climate Change and Korea national guidelines. During the last five years, DMC＇s overall GHG emissions were 239 thousand tons C02 eq./year from eleven public environmental infrastructure facilities, with a population of 1.52 million. Of the three categories, solid waste treatment/disposal contributes 68%, whilst wastewater treatment and others contribute 22% and 10% respectively. Among GHG unit emissions per ton of waste treatment, the biggest contributor was waste incineration of 694 kg CO2 eq./ton, followed by waste disposal of 483 kg CO2 eq./ton, biological treatment of solid waste of 209 kg CO2 eq./ton, wastewater treatment of 0.241 kg CO2 eq./m3, and public water supplies of 0.067 kg CO2 eq./m3. Furthermore, it is suggested that the potential in reducing GHG emissions from landfill process can be as high as 47.5% by increasing landfill gas recovery up to 50%. Therefore, it is apparent that reduction strategies for the main contributors of GHG emissions should take precedence over minor contributors and lead to the best practice for managing GHGs abatement.