No abstract

rRNA accessibility is a major sensitivity issue limiting the design of working probes for fluorescence in situ hybridization (FISH). Previous studies empirically highlighted the accessibility of target sites on rRNA maps by grouping probes into six classes according to their brightness levels. In this study, a recently proposed mechanistic model of FISH, based on the thermodynamics of secondary nucleic acid interactions, was used to evaluate the accessibility of the 16S rRNA of Escherichia coli to fluorescein-labeled oligonucleotides when thermodynamic and kinetic barriers were eliminated. To cover the entire 16S rRNA, 109 probes were designed with an average thermodynamic affinity (⌬G o overall ) of ؊13.5 kcal/mol. Fluorescence intensity was measured by flow cytometry, and a brightness threshold between classes 3 and 4 was used as the requirement for proof of accessibility. While 46% of the probes were above this threshold with conventional 3-h hybridizations, extending the incubation period to 96 h dramatically increased the fraction of bright probes to 86%. Insufficient thermodynamic affinity and/or fluorophore quenching was demonstrated to cause the low fluorescence intensity of the remaining 14% of the probes. In the end, it was proven that every nucleotide in the 16S rRNA of E. coli could be targeted with a bright probe and, therefore, that there were no truly inaccessible target regions in the 16S rRNA. Based on our findings and mechanistic modeling, a rational design strategy involving ⌬G o overall , hybridization kinetics, and fluorophore quenching is recommended for the development of bright probes.

e Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as an integral part of the full-cycle rRNA approach. A major challenge in FISH is the design of oligonucleotide probes with high sensitivity and specificity to their target group. The rapidly expanding number of rRNA sequences has increased awareness of the number of potential nontargets for every FISH probe, making the design of new FISH probes challenging using traditional methods. In this study, we conducted a systematic analysis of published probes that revealed that many have insufficient coverage or specificity for their intended target group. Therefore, we developed an improved thermodynamic model of FISH that can be applied at any taxonomic level, used the model to systematically design probes for all recognized genera of bacteria and archaea, and identified potential cross-hybridizations for the selected probes. This analysis resulted in high-specificity probes for 35.6% of the genera when a single probe was used in the absence of competitor probes and for 60.9% when up to two competitor probes were used. Requiring the hybridization of two independent probes for positive identification further increased specificity. In this case, we could design highly specific probe sets for up to 68.5% of the genera without the use of competitor probes and 87.7% when up to two competitor probes were used. The probes designed in this study, as well as tools for designing new probes, are available online (http://DECIPHER.cee.wisc.edu).

Solid waste management was one of the most significant environmental issues encountered in developing countries. Quantity of produced waste as well as its composition was known to vary by general consumption patterns that were affected by socio‐economic status, household size, or even by seasons. Due to the dynamic nature of waste quantity and composition, the handling and disposal of waste in an economically and environmentally feasible way presented itself as a challenge. Therefore, in order to conduct a successful decision‐making process to determine the feasible and sustainable processes in the disposal of waste, priority should be given to the statement of the problem at hand. The aim of this study is to achieve a characterization of municipal solid waste of Istanbul, Turkey. Waste samples were collected from the transfer stations servicing certain zones of the city and consequently substance group, moisture content and calorific value analyses were performed over these samples. Results indicated that approximately 54% of the municipal solid waste composition was of organic nature. The paper/cardboard group was coming next in ranking with a proportion of 15.57%. Average moisture content of samples was calculated to be 62.41% and 1435 kcal kg−1 was calculated to represent the average calorific value. © 2012 American Institute of Chemical Engineers Environ Prog, 32: 734–739, 2013

Ozonation of chloride-rich textile wastewater is a common pretreatment practice in order to increase biodegradability and therefore meet the discharge limits. This study is the first to investigate ozone-chloride/bromide interactions and formation of hazardous adsorbable organic halogens (AOX) in real textile wastewater. Initially effect of ozonation on chloride-rich real textile wastewater samples were investigated for adsorbable organic halogens (AOX) formation, biodegradability and toxicity. After 15 min of ozonation, maximum levels of chlorine/bromine generation (0.3 mg/l) and AOX formation (399 mg/l) were reached. OUR and SOUR levels both increased by approximately 58%. Daphnia magna toxicity peaked at 100% for 10 min ozonated sample. Considering adverse effects of ozonation on chloride-rich textile industry effluents, we proposed replacement of NaCl with Na 2 SO 4 . Comparative ozonation experiments were carried out for both chloride and sulfate containing synthetic dyeing wastewater samples. Results showed that use of sulfate in reactive dyeing increased biodegradability and decreased acute toxicity. Although sulfate is preferred over chloride for more effective dyeing performance, the switch has been hampered due to sodium sulfate's higher unit cost. However, consideration of indirect costs such as contributions to biodegradability, toxicity, water and salt recovery shall facilitate textile industry's switch from chloride to sulfate. Recently, a hybrid approach of advanced oxidation prior to biodegradation is found to be the most environmentally friendly and