United States Environmental Protection Agency

About: United States Environmental Protection Agency is a government organization based out in Washington D.C., District of Columbia, United States. It is known for research contribution in the topics: Population & Environmental exposure. The organization has 13873 authors who have published 26902 publications receiving 1191729 citations. The organization is also known as: EPA & Environmental Protection Agency.

Fungal-specific PCR primers developed for analysis of the ITS region of environmental DNA extracts

Abstract: The Internal Transcribed Spacer (ITS) regions of fungal ribosomal DNA (rDNA) are highly variable sequences of great importance in distinguishing fungal species by PCR analysis. Previously published PCR primers available for amplifying these sequences from environmental samples provide varying degrees of success at discriminating against plant DNA while maintaining a broad range of compatibility. Typically, it has been necessary to use multiple primer sets to accommodate the range of fungi under study, potentially creating artificial distinctions for fungal sequences that amplify with more than one primer set. Numerous sequences for PCR primers were tested to develop PCR assays with a wide range of fungal compatibility and high discrimination from plant DNA. A nested set of 4 primers was developed that reflected these criteria and performed well amplifying ITS regions of fungal rDNA. Primers in the 5.8S sequence were also developed that would permit separate amplifications of ITS1 and ITS2. A range of basidiomycete fruiting bodies and ascomycete cultures were analyzed with the nested set of primers and Restriction Fragment Length Polymorphism (RFLP) fingerprinting to demonstrate the specificity of the assay. Single ectomycorrhizal root tips were similarly analyzed. These primers have also been successfully applied to Quantitative PCR (QPCR), Length Heterogeneity PCR (LH-PCR) and Terminal Restriction Fragment Length Polymorphism (T-RFLP) analyses of fungi. A set of wide-range plant-specific primers were developed at positions corresponding to one pair of the fungal primers. These were used to verify that the host plant DNA was not being amplified with the fungal primers. These plant primers have been successfully applied to PCR-RFLP analyses of forest plant tissues from above- and below-ground samples and work well at distinguishing a selection of plants to the species level. The complete set of primers was developed with an emphasis on discrimination between plant and fungal sequences and should be particularly useful for studies of fungi where samples also contain high levels of background plant DNA, such as verifying ectomycorrhizal morphotypes or characterizing phylosphere communities.

Microbial Population Changes during Bioremediation of an Experimental Oil Spill

Abstract: Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil spill. Four treatments (no oil control, oil alone, oil plus nutrients, and oil plus nutrients plus an indigenous inoculum) were applied. In situ microbial community structures were monitored by phospholipid fatty acid (PLFA) analysis and 16S rDNA PCR-denaturing gradient gel electrophoresis (DGGE) to (i) identify the bacterial community members responsible for the decontamination of the site and (ii) define an end point for the removal of the hydrocarbon substrate. The results of PLFA analysis demonstrated a community shift in all plots from primarily eukaryotic biomass to gram-negative bacterial biomass with time. PLFA profiles from the oiled plots suggested increased gram-negative biomass and adaptation to metabolic stress compared to unoiled controls. DGGE analysis of untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. This banding pattern disappeared in all oiled plots, indicating that the structure and diversity of the dominant bacterial community changed substantially. No consistent differences were detected between nutrient-amended and indigenous inoculum-treated plots, but both differed from the oil-only plots. Prominent bands were excised for sequence analysis and indicated that oil treatment encouraged the growth of gram-negative microorganisms within the α-proteobacteria and Flexibacter-Cytophaga-Bacteroides phylum. α-Proteobacteria were never detected in unoiled controls. PLFA analysis indicated that by week 14 the microbial community structures of the oiled plots were becoming similar to those of the unoiled controls from the same time point, but DGGE analysis suggested that major differences in the bacterial communities remained.

Microwave-assisted organic synthesis and transformations using benign reaction media.

Abstract: A nonclassical heating technique using microwaves, termed "Bunsen burner of the 21st century", is rapidly becoming popular and is dramatically reducing reaction times. The significant outcomes of microwave (MW)-assisted green chemistry endeavors, which have resulted in the development of synthetic protocols for drugs and fine chemicals synthesis that are relatively more sustainable, are summarized. The use of emerging microwave-assisted chemistry techniques in conjunction with greener reaction media is dramatically reducing chemical waste and reaction times in several organic syntheses and chemical transformations. A brief historic account of our own experiences in developing MW-assisted organic transformations, which involve various benign alternatives, such as solid-supported reagents, and greener reaction media, namely, aqueous, ionic liquid, and solvent-free, for the synthesis of various heterocycles, coupling reactions, oxidation-reduction reactions, and some name reactions are described. Synthesis of Heterocycles. The synthetic chemistry community has been under increased pressure to produce, in an environmentally benign fashion, the myriad of heterocyclic systems required by society in a short span of time, and one of the best options to accelerate these synthetic processes is to use MW technology. The efficient use of the MW heating approach for the synthesis of various heterocyclic compounds in aqueous and solvent-free medium is discussed. Organic Named Reactions. The application of MW chemistry for various named reaction such as the Prins reaction, the Suzuki reaction, the Heck reaction, the Aza-Michael reaction, Trost's gamma-addition, and the Cannizzaro reaction are summarized. Synthesis and Application of Ionic Liquids. Ionic liquids (ILs), being polar and ionic, in character couple with MW irradiation very efficiently and are, therefore, ideal MW-absorbing candidates for expediting chemical reactions. MW-assisted solvent-free synthesis and application of ILs are discussed. Oxidation-Reduction Reactions. MW protocols using mineral oxides such as alumina, silica, and clay to immobilize reagents on such solid supports have been extensively explored under "dry" media conditions. Various solvent-free examples of oxidation reactions are discussed that involve mixing of neat substrates with clay-supported iron(III) nitrate (clayfen) or iodobenzene diacetate (IBD) as an oxidant; some interesting MW reduction protocols using borohydrides are also discussed. Protection-Deprotection Reactions. The protection and deprotection of alcohols and amines are common events in multistep organic syntheses. Various protection and deprotection protocols under MW irradiation are discussed, including tetrahydropyranylation and (benzyloxycarbonyl) (Cbz)-protection, which are the most frequently employed methods.

The Ecological Risks and Benefits of Genetically Engineered Plants

Abstract: Discussions of the environmental risks and benefits of adopting genetically engineered organisms are highly polarized between pro- and anti-biotechnology groups, but the current state of our knowledge is frequently overlooked in this debate. A review of existing scientific literature reveals that key experiments on both the environmental risks and benefits are lacking. The complexity of ecological systems presents considerable challenges for experiments to assess the risks and benefits and inevitable uncertainties of genetically engineered plants. Collectively, existing studies emphasize that these can vary spatially, temporally, and according to the trait and cultivar modified.