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.     

Relationship of firm attributes,ownership structure and business network on climate change efforts: evidence from Malaysia

This paper presents a case study of land-use/land-cover (LULC) changes from 1975 to 2014 in the central highlands of Ethiopia and traces out its impact on socioeconomic conditions of the local community in the study area. We used four time series Landsat satellite images, that is, Landsat MSS (1975), Landsat Thematic Mapper (1986), Enhanced Thematic Mapper (2000), and Landsat 8 OLI scenes (2014), to investigate the changes in LULC. In addition, individual interviews with 51 randomly selected households, discussions with focus group and key informants, and field observations were also incorporated for the study. The image classification indicated four categories of LULC classes: Natural forest, eucalyptus plantations, cropland/settlements, and grasslands. Between 1975 and 2014, cropland/settlements and eucalyptus plantations considerably increased, whereas grassland cover drastically decreased. According to the results, the area under cropland/settlements and eucalyptus plantations increased by 62 and 335%, respectively, with 74% concomitant decrease in the area of grasslands in the same period. Survey results showed that deterioration of soil fertility (41.2%) followed by shortage of land (35.3%) is the major constraint for crop production for poor farmers in the study area. However, better-off farmers ranked deterioration of soil fertility (64.7%) followed by lack of credit (17.6%) as priority constraints for crop production. Interviews mainly focused on selected women group revealed that the expansion of eucalyptus in the area greatly curbed the burdens of collecting fuel woods from long distances in the past. The availability of too many religious holidays (on average 16 days/month) directly or indirectly contributes to the current seasonal food shortages of the community. Generally, our results show that the community in the study area is beset with a host of social, economic, and institutional challenges. As a result, majority of the farming households are destitute, unable to make a livelihood from their small plot of land and live in absolute poverty. Therefore, in light of these finding, it is imperative that timely interventions by government and other development stakeholders are needed to come to grips with problems of soil fertility, land-use change, and food insecurity in the study area.     

The role of black carbon as a catalyst for environmental redox transformation

Black carbon (BC) is an important class of geosorbents that control the fate and transport of organic pollutants in soil and sediment. We previously demonstrated a new role of BC as an electron transfer mediator in the abiotic reduction of nitroaromatic and nitramine compounds by Oh and Chiu (Environ Sci Technol 43:6983-6988, 2009). We proposed that BC can catalyze the reduction of nitro compounds because it contains microscopic graphitic (graphene) domains, which facilitate both sorption and electron transfer. In this study, we assessed the ability of different types of BC--graphite, activated carbon, and diesel soot--to mediate the reduction of 2,4-dinitrotoluene (DNT) and 2,4-dibromophenol (DBP) by H(2)S. All three types of BC enhanced DNT and DBP reduction. H(2)S supported BC-mediated reduction, as was observed previously with a thiol reductant. The results suggest that BC may influence the fate of organic pollutants in reducing subsurface environments through redox transformation in addition to sorption.     

Tritium levels in Chinese cabbage and radish plants acutely exposed to HTO vapor at different growth stages

To simulate an acute exposure of Chinese cabbage and radish plants to airborne HTO, the potted plants were exposed to HTO vapor under semi-outdoor conditions for 1h at different times from the early to late growth stages. The plants were grown outdoors and the plant tritium was measured at the end of an exposure (h(0)) and at harvest. The leaf tissue free water tritium (TFWT) concentrations at h(0) were considerably lower than estimated equilibrium concentrations. In the leaves of Chinese cabbage, the exposure at the earlier growth stage generally ended with a higher TFWT concentration. Such a tendency was not apparent either in the leaves or roots of radish. On the other hand, the earlier stage exposure gave rise to lower TFWT concentrations at the harvest of both crops. For the OBT (organically bound tritium), however, the same occurred only in the Chinese cabbage leaves. During the period between the exposure and harvest, the TFWT concentrations reduced by factors of up to 1.1 x 10(6) for the Chinese cabbage leaves and 1.3 x 10(4) for the radish roots. Based on the activity ratios of OBT to TFWT at harvest, it is estimated that OBT mostly contributes much more to the ingestion dose than TFWT does.     

A multi-variate methodology for analyzing pre-existing lake water quality data

Environmental agencies are given the task of monitoring water quality in rivers, lakes, and other bodies of water, for the purpose of comparing the results with regulatory standards. Monitoring follows requirements set by regulations, and data are collected in a systematic way for the intended purpose. Monitoring enables agencies to determine whether water bodies are polluted. Much effort is spent per monitoring event, resulting in hundreds of data points typically used solely for comparison with regulatory standards and then stored for little further use. This paper devises a data analysis methodology that can make use of the pre-existing datasets to extract more useful information on water quality trends, without new sample collection and analysis. In this paper, measured lake water quality data are subjected to statistical analyses including Principal Component Analysis (PCA) to deduce changes in water quality spatially and temporally over several years. It was found that the lake as a whole changed temporally by season, rather than spatially. Storm events caused the greatest shifts in water quality, though the shifts were fairly consistent across sampling stations. This methodology can be applied to similar datasets, especially with the recent emphasis by the U.S. EPA on protection of lakes as water sources. Water quality managers using these techniques may be able to lower their monitoring costs by eliminating redundant water quality parameters found in this analysis.     

A statistical model to predict and analyze air surface temperature based on remotely sensed observations

Environmental Science and Pollution Research - Air surface temperature (AST) is a crucial importance element for many applications such as hydrology, agriculture, and climate change studies. The...