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.     

Characteristics of fungal flora in onion farmlands with potential link to human mycotic keratitis

Acquisition of mycotic keratitis has been linked to agricultural activities. Although fungi were identified in injured eyes, data derived directly from farmlands are limited. Following five cases of fungal corneal ulcers in onion harvesters in the monsoon area of Taiwan, the present study further determined fungi genera and their concentrations in onion crops and surface soils of onion farmlands. In total, 52, 100 and 100 samples of soils, onion leaves and bulb scales, respectively, were collected from three monsoon and one non-monsoon farmlands. Fungal colonies were counted and microscopically examined after incubation at 25°C for 4–7 days on malt extract agar with 40?g?mL^?1 chloramphenicol. Results showed the peak fungi levels were mostly observed at harvest time. Among keratitis-related fungi, Aspergillus predominated in soils as well as in onion bulb scales, while Alternaria in onion leaves. Cladosporium was also prevalent in soils, onion leaves and scales. Other keratitis-related fungi included Acremonium, Curvalaria, Fusarium, Mycelia, Penicillium, Rhizoctonia and Rhizopus. The present study provides an exposure link between onion harvesters and presence of keratitis-related fungi from onion crops and soils, which may account for mycotic ocular infection via hand-to-eye contact and airborne transmission during the monsoon season.     

Evaluation of food waste disposal options by LCC analysis from the perspective of global warming: Jungnang case, South Korea

The costs associated with eight food waste disposal options, dry feeding, wet feeding, composting, anaerobic digestion, co-digestion with sewage sludge, food waste disposer, incineration, and landfilling, were evaluated in the perspective of global warming and energy and/or resource recovery. An expanded system boundary was employed to compare by-products. Life cycle cost was analyzed through the entire disposal process, which included discharge, separate collection, transportation, treatment, and final disposal stages, all of which were included in the system boundary. Costs and benefits were estimated by an avoided impact. Environmental benefits of each system per 1 tonne of food waste management were estimated using carbon prices resulting from CO(2) reduction by avoided impact, as well as the prices of by-products such as animal feed, compost, and electricity. We found that the cost of landfilling was the lowest, followed by co-digestion. The benefits of wet feeding systems were the highest and landfilling the lowest.     

Effects of sedimentation on the gorgonian <Emphasis Type="Italic">Subergorgia suberosa</Emphasis> (Pallas, 1766)

Effects of oceanic and terrestrial sediment suspensions on the behavioral traits activity, colony expansion, and mucus formation of the gorgonian octocoral Subergorgia suberosa (Pallas, 1766) were studied in the laboratory. Increased sediment concentration significantly changed the logits of activity indices (as colony expansion) and was correlated with decreased activity. For both sources of sediments, the activity index decreased as the concentration of sediment increased. The level of decrease was more significance for terrestrial sediments. The activity index showed no clear time pattern for the control group, but a decrease over time occurred in both sediment treatment groups. Activity change was linearly correlated with exposure time and concentration of terrestrial and ocean sediments. The activity indices of polyps were negatively correlated with the formation of mucus sheets (correlation = −0.536, p = 0.048). For both sources of sediments, the frequency of mucus sheet formation (MSF) increased with sediment concentration. Increases in terrestrial sediment loads resulted in more striking effects. The probability for MSF under different sediment groups at different concentrations over time was modeled by regressions. Frequency of polyp activity is suggested as a suitable biomarker to monitor the effects of sedimentation stress.     

Effects of fine particulate matter and its constituents on emergency room visits for asthma in southern Taiwan during 2008–2010: a population-based study

Environmental Science and Pollution Research - This population-based study evaluated the short-term association between fine particulate matter (PM2.5) concentrations and its constituents and...     

Effect of metal and glycol on mechanochemical dechlorination of polychlorinated biphenyls (PCBs)

This paper assesses the potential of mechanochemical method with fine metal powder, glycol and alkali for polychlorinated biphenyls (PCBs) removal from waste insulating oil. The effects of relevant parameters, such as kinds of chemicals, rate and time of milling were examined. After each run, the total PCBs content in waste insulating oil was measured. Polyethylene glycol 200, long chain-glycol was more effective than triethylene glycol and ethylene glycol, short chain-glycol as hydrogen donor in mechanochemical dechlorination of PCBs. A maximum of 99.9% PCBs removal (below 2ppm) and 94% total chlorine removal were achieved with the mechanochemical process for 2h.     

DIGITAL SIMULATION OF THE EFFECT OF THERMAL DISCHARGE ON STREAM WATER QUALITY1

A modified transient version of the Streeter-Phelps model along with the energy balance equation is employed to analyze the effects of waste heat discharge from power plants on stream water quality. Analysis is also made to examine the effects of the upstream water quality and stream velocity on the downstream DO concentration level. The resulting coupled nonlinear hyperbolic partial differential equations representing the energy, BOD and DO concentrations are solved by the method of characteristics and simulated on a digital computer. Final numerical results indicate that the allowable quantity of thermal discharge does heavily depend on the upstream quality.     

WATER QUALITY CONTROL BY ARTIFICIAL AERATION OF STREAM RECEIVING THERMAL AND ORGANIC WASTE DISCHARGES1

ABSTRACT: The purpose of this work is to study the installation of artificial aerators for water quality control of a stream which receives thermal and organic waste discharges. The location and numer of diffuser type aerators to be installed along the stream are determined so as to maintain the stream DO content above a certain minimum requirement (4 mg/l or 5 mg/l) for normal aquatic life. Effects of the stream velocity, upstream BOD concentration and rates of thermal and organic waste discharges to the stream are examined.