Reference design and operations for deep borehole disposal of high-level radioactive waste.

A reference design and operational procedures for the disposal of high-level radioactive waste in deep boreholes have been developed and documented. The design and operations are feasible with currently available technology and meet existing safety and anticipated regulatory requirements. Objectives of the reference design include providing a baseline for more detailed technical analyses of system performance and serving as a basis for comparing design alternatives. Numerous factors suggest that deep borehole disposal of high-level radioactive waste is inherently safe. Several lines of evidence indicate that groundwater at depths of several kilometers in continental crystalline basement rocks has long residence times and low velocity. High salinity fluids have limited potential for vertical flow because of density stratification and prevent colloidal transport of radionuclides. Geochemically reducing conditions in the deep subsurface limit the solubility and enhance the retardation of key radionuclides. A non-technical advantage that the deep borehole concept may offer over a repository concept is that of facilitating incremental construction and loading at multiple perhaps regional locations. The disposal borehole would be drilled to a depth of 5,000 m using a telescoping design and would be logged and tested prior to waste emplacement. Waste canisters would be constructed of carbon steel, sealed by welds, and connected into canister strings with high-strength connections. Waste canister strings of about 200 m length would be emplaced in the lower 2,000 m of the fully cased borehole and be separated by bridge and cement plugs. Sealing of the upper part of the borehole would be done with a series of compacted bentonite seals, cement plugs, cement seals, cement plus crushed rock backfill, and bridge plugs. Elements of the reference design meet technical requirements defined in the study. Testing and operational safety assurance requirements are also defined. Overall, the results of the reference design development and the cost analysis support the technical feasibility of the deep borehole disposal concept for high-level radioactive waste

Enhanced Geothermal Systems (EGS) well construction technology evaluation report.

Electricity production from geothermal resources is currently based on the exploitation of hydrothermal reservoirs. Hydrothermal reservoirs possess three ingredients critical to present day commercial extraction of subsurface heat: high temperature, in-situ fluid and high permeability. Relative to the total subsurface heat resource available, hydrothermal resources are geographically and quantitatively limited. A 2006 DOE sponsored study led by MIT entitled 'The Future of Geothermal Energy' estimates the thermal resource underlying the United States at depths between 3 km and 10 km to be on the order of 14 million EJ. For comparison purposes, total U.S. energy consumption in 2005 was 100 EJ. The overwhelming majority of this resource is present in geological formations which lack either in-situ fluid, permeability or both. Economical extraction of the heat in non-hydrothermal situations is termed Enhanced or Engineered Geothermal Systems (EGS). The technologies and processes required for EGS are currently in a developmental stage. Accessing the vast thermal resource between 3 km and 10 km in particular requires a significant extension of current hydrothermal practice, where wells rarely reach 3 km in depth. This report provides an assessment of well construction technology for EGS with two primary objectives: (1) Determining the ability of existing technologies to develop EGS wells. (2) Identifying critical well construction research lines and development technologies that are likely to enhance prospects for EGS viability and improve overall economics. Towards these ends, a methodology is followed in which a case study is developed to systematically and quantitatively evaluate EGS well construction technology needs. A baseline EGS well specification is first formulated. The steps, tasks and tools involved in the construction of this prospective baseline EGS well are then explicitly defined by a geothermal drilling contractor in terms of sequence, time and cost. A task and cost based analysis of the exercise is subsequently conducted to develop a deeper understanding of the key technical and economic drivers of the well construction process. Finally, future research & development recommendations are provided and ranked based on their economic and technical significance

Advanced drilling systems study.

This report documents the results of a study of advanced drilling concepts conducted jointly for the Natural Gas Technology Branch and the Geothermal Division of the U.S. Department of Energy. A number of alternative rock cutting concepts and drilling systems are examined. The systems cover the range from current technology, through ongoing efforts in drilling research, to highly speculative concepts. Cutting mechanisms that induce stress mechanically, hydraulically, and thermally are included. All functions necessary to drill and case a well are considered. Capital and operating costs are estimated and performance requirements, based on comparisons of the costs for alternative systems to conventional drilling technology, are developed. A number of problems common to several alternatives and to current technology are identified and discussed

Development of a system to provide diagnostics-while-drilling.

This report describes development of a system that provides high-speed, real-time downhole data while drilling. Background of the project, its benefits, major technical challenges, test planning, and test results are covered by relatively brief descriptions in the body of the report, with some topics presented in more detail in the attached appendices

Reference design and operations for deep borehole disposal of high-level radioactive waste.

A reference design and operational procedures for the disposal of high-level radioactive waste in deep boreholes have been developed and documented. The design and operations are feasible with currently available technology and meet existing safety and anticipated regulatory requirements. Objectives of the reference design include providing a baseline for more detailed technical analyses of system performance and serving as a basis for comparing design alternatives. Numerous factors suggest that deep borehole disposal of high-level radioactive waste is inherently safe. Several lines of evidence indicate that groundwater at depths of several kilometers in continental crystalline basement rocks has long residence times and low velocity. High salinity fluids have limited potential for vertical flow because of density stratification and prevent colloidal transport of radionuclides. Geochemically reducing conditions in the deep subsurface limit the solubility and enhance the retardation of key radionuclides. A non-technical advantage that the deep borehole concept may offer over a repository concept is that of facilitating incremental construction and loading at multiple perhaps regional locations. The disposal borehole would be drilled to a depth of 5,000 m using a telescoping design and would be logged and tested prior to waste emplacement. Waste canisters would be constructed of carbon steel, sealed by welds, and connected into canister strings with high-strength connections. Waste canister strings of about 200 m length would be emplaced in the lower 2,000 m of the fully cased borehole and be separated by bridge and cement plugs. Sealing of the upper part of the borehole would be done with a series of compacted bentonite seals, cement plugs, cement seals, cement plus crushed rock backfill, and bridge plugs. Elements of the reference design meet technical requirements defined in the study. Testing and operational safety assurance requirements are also defined. Overall, the results of the reference design development and the cost analysis support the technical feasibility of the deep borehole disposal concept for high-level radioactive waste

Dietary Selenomethionine Administration and Its Effects on the American Alligator (Alligator mississippiensis): Oxidative Status and Corticosterone Levels

Selenium (Se) is an essential nutrient which in excess causes toxicity. The disposal of incompletely combusted coal, which often is rich in Se, into aquatic settling basins is increasing the risk of Se exposure worldwide. However, very few studies have looked at the physiological effects of Se exposure on long-lived, top trophic vertebrates, such as the American alligator (Alligator mississippiensis). During a 7-week period, alligators were fed one of three dietary treatments: mice injected with deionized water or mice injected with water containing 1000 or 2000 ppm selenomethionine (SeMet). One week after the last feeding alligators were bled within 3 min of capture for plasma corticosterone (CORT). A few days later, all alligators were euthanized and whole blood and tail tissue were harvested to measure oxidative damage, an antioxidant-associated transcription factor, and antioxidant enzymes [glutathione peroxidase-1 (GPX1), superoxide dismutase-1 (SOD1), and SOD2] by Western blotting. There was a dose-dependent increase in baseline CORT levels in alligators administered SeMet. Except for blood SOD2 levels, SeMet treatment had no effect (p \u3e 0.05 for all) on oxidative status: oxidative damage, GPX1, SOD1, and muscle SOD2 levels were similar among treatments. Our results illustrate that high levels of Se may act as a stressor to crocodilians. Future studies should investigate further the physiological effects of Se accumulation in long-lived, top-trophic vertebrates

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

Massively parallel DNA sequencing offers many benefits, but major inhibitory cost factors include: (1) start-up (i.e., purchasing initial reagents and equipment); (2) buy-in (i.e., getting the smallest possible amount of data from a run); and (3) sample preparation. Reducing sample preparation costs is commonly addressed, but start-up and buy-in costs are rarely addressed. We present dual-indexing systems to address all three of these issues. By breaking the library construction process into universal, re-usable, combinatorial components, we reduce all costs, while increasing the number of samples and the variety of library types that can be combined within runs. We accomplish this by extending the Illumina TruSeq dual-indexing approach to 768 (384 + 384) indexed primers that produce 384 unique dual-indexes or 147,456 (384 × 384) unique combinations. We maintain eight nucleotide indexes, with many that are compatible with Illumina index sequences. We synthesized these indexing primers, purifying them with only standard desalting and placing small aliquots in replicate plates. In qPCR validation tests, 206 of 208 primers tested passed (99% success). We then created hundreds of libraries in various scenarios. Our approach reduces start-up and per-sample costs by requiring only one universal adapter that works with indexed PCR primers to uniquely identify samples. Our approach reduces buy-in costs because: (1) relatively few oligonucleotides are needed to produce a large number of indexed libraries; and (2) the large number of possible primers allows researchers to use unique primer sets for different projects, which facilitates pooling of samples during sequencing. Our libraries make use of standard Illumina sequencing primers and index sequence length and are demultiplexed with standard Illumina software, thereby minimizing customization headaches. In subsequent papers, we use these same primers with different adapter stubs to construct amplicon and restriction-site associated DNA libraries, but their use can be expanded to any type of library sequenced on Illumina platforms

Adapterama III: Quadruple-indexed, double/triple-enzyme RADseq libraries (2RAD/3RAD)

Molecular ecologists frequently use genome reduction strategies that rely upon restriction enzyme digestion of genomic DNA to sample consistent portions of the genome from many individuals (e.g., RADseq, GBS). However, researchers often find the existing methods expensive to initiate and/or difficult to implement consistently, especially because it is difficult to multiplex sufficient numbers of samples to fill entire sequencing lanes. Here, we introduce a low-cost and highly robust approach for the construction of dual-digest RADseq libraries that build on adapters and primers designed in . Major features of our method include: (1) minimizing the number of processing steps; (2) focusing on a single strand of sample DNA for library construction, allowing the use of a non-phosphorylated adapter on one end; (3) ligating adapters in the presence of active restriction enzymes, thereby reducing chimeras; (4) including an optional third restriction enzyme to cut apart adapter-dimers formed by the phosphorylated adapter, thus increasing the efficiency of adapter ligation to sample DNA, which is particularly effective when only low quantity/quality DNA samples are available; (5) interchangeable adapter designs; (6) incorporating variable-length internal indexes within the adapters to increase the scope of sample indexing, facilitate pooling, and increase sequence diversity; (7) maintaining compatibility with universal dual-indexed primers and thus, Illumina sequencing reagents and libraries; and, (8) easy modification for the identification of PCR duplicates. We present eight adapter designs that work with 72 restriction enzyme combinations. We demonstrate the efficiency of our approach by comparing it with existing methods, and we validate its utility through the discovery of many variable loci in a variety of non-model organisms. Our 2RAD/3RAD method is easy to perform, has low startup costs, has increased utility with low-concentration input DNA, and produces libraries that can be highly-multiplexed and pooled with other Illumina libraries

Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix)

Next-generation sequencing (NGS) of amplicons is used in a wide variety of contexts. In many cases, NGS amplicon sequencing remains overly expensive and inflexible, with library preparation strategies relying upon the fusion of locus-specific primers to full-length adapter sequences with a single identifying sequence or ligating adapters onto PCR products. In , we presented universal stubs and primers to produce thousands of unique index combinations and a modifiable system for incorporating them into Illumina libraries. Here, we describe multiple ways to use the system and other approaches for amplicon sequencing on Illumina instruments. In the variant we use most frequently for large-scale projects, we fuse partial adapter sequences (TruSeq or Nextera) onto the 5\u27 end of locus-specific PCR primers with variable-length tag sequences between the adapter and locus-specific sequences. These fusion primers can be used combinatorially to amplify samples within a 96-well plate (8 forward primers + 12 reverse primers yield 8 × 12 = 96 combinations), and the resulting amplicons can be pooled. The initial PCR products then serve as template for a second round of PCR with dual-indexed iTru or iNext primers (also used combinatorially) to make full-length libraries. The resulting quadruple-indexed amplicons have diversity at most base positions and can be pooled with any standard Illumina library for sequencing. The number of sequencing reads from the amplicon pools can be adjusted, facilitating deep sequencing when required or reducing sequencing costs per sample to an economically trivial amount when deep coverage is not needed. We demonstrate the utility and versatility of our approaches with results from six projects using different implementations of our protocols. Thus, we show that these methods facilitate amplicon library construction for Illumina instruments at reduced cost with increased flexibility. A simple web page to design fusion primers compatible with iTru primers is available at: http://baddna.uga.edu/tools-taggi.html. A fast and easy to use program to demultiplex amplicon pools with internal indexes is available at: https://github.com/lefeverde/Mr_Demuxy

Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Summary Contaminants such as heavy metals may contribute to the dissemination of antimicrobial resistance (AMR) by enriching resistance gene determinants via co‐selection mechanisms. In the present study, a survey was performed on soils collected from four areas at the Savannah River Site (SRS), South Carolina, USA, with varying contaminant profiles: relatively pristine (Upper Three Runs), heavy metals (Ash Basins), radionuclides (Pond B) and heavy metal and radionuclides (Tim’s Branch). Using 16S rRNA gene amplicon sequencing, we explored the structure and diversity of soil bacterial communities. Sites with legacies of metal and/or radionuclide contamination displayed significantly lower bacterial diversity compared to the reference site. Metagenomic analysis indicated that multidrug and vancomycin antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) including those associated with copper, arsenic, iron, nickel and zinc were prominent in all soils including the reference site. However, significant differences were found in the relative abundance and diversity of certain ARGs and MRGs in soils with metal/radionuclide contaminated soils compared to the reference site. Co‐occurrence patterns revealed significant ARG/MRG subtypes in predominant soil taxa including Acidobacteriaceae, Bradyrhizobium, Mycobacterium, Streptomyces, Verrumicrobium, Actinomadura and Solirubacterales. Overall, the study emphasizes the potential risk of human activities on the dissemination of AMR in the environment