Stability of bulk Ba2YCu3O(7-x) in a variety of environments

Small bars of ceramic Ba2YCu3O(7-x) were fabricated and subjected to environments similar to those that might be encountered during some NASA missions. These conditions include ambient conditions, high humidity, vacuum, and high fluences of electrons and protrons. The normal state resistivity or critical current density (J sub c) were monitored during these tests to assess the stability of the material. When normal state resistivity is used as a criterion, the ambient stability of these samples was relatively good, exhibiting only a 2 percent degradation over a 3 month period. The humidity stability was shown to be very poor, and to be a steep function of temperature. Samples stored at 50 C for 40 min increased in normal state resistivity by four orders of magnitude. Kinetic analysis indicates that the degradation reaction is second order with water vapor concentration. It is suspected that humidity degradation also accounts for the ambient instability. The samples were stable to vacuum over a period of at least 3 months. Degradation of J sub c in a 1 MeV electron fluence of 9.7 x 10 to the 14th e(-)/sq cm was determined to be no more than about 2 percent. Degradation of J sub c in a 8.7 x 10 to the 14th p(+)/sq cm of 42 MeV protons was found to be grain size dependent. Samples with smaller grain size and initial J sub c of about 240 A/sq cm showed no degradation. while that with larger grain size and an initial J sub c of about 30 A/sq cm degraded to 37 percent of its original value

Molecular typing of mycobacterium tuberculosis by using nine novel variable-number tandem repeats across the Beijing family and low-copy-number IS6110 isolates

Molecular epidemiological tools for genotyping clinical isolates of Mycobacterium tuberculosis have been developed and used to help track and contain transmission of tuberculosis. We identified 87 short sequence repeat loci within the genome of the M. tuberculosis H37Rv strain. Nine tandem repeats were found to be variable (variable-number tandem repeats (VNTRs)) in a set of 91 isolates. Fifty-seven of the isolates had only four IS6110 bands. The other 34 isolates were members of the Beijing strain family. The number of alleles of each these nine VNTRs was determined by examining each isolate. Six of the loci (Mtb-v1, -v4, -v10, -v15, -v18, and -v20) were able to differentiate the Beijing spoligotype identical isolates into seven distinct genotypes. Five of the loci (Mtb-v3, -v5, -v6, -v10, and -v15) were informative in discriminating the four-band IS6110 restriction fragment length polymorphism isolates from each other. The Nei's diversity values of each marker ranged from 0.02 to 0.59, with the number of alleles ranging from two to eight across the entire strain set. These nine loci provide a useful, discriminatory extension of VNTR typing methods for application to molecular epidemiologic studies of M. tuberculosis

Resilience and Resistance of Sagebrush Ecosystems: Implications for State and Transition Models and Management Treatments

In sagebrush ecosystems invasion of annual exotics and expansion of piñon (Pinus monophylla Torr. and Frem.) and juniper (Juniperus occidentalis Hook., J. osteosperma [Torr.] Little) are altering fire regimes and resulting in large-scale ecosystem transformations. Management treatments aim to increase resilience to disturbance and enhance resistance to invasive species by reducing woody fuels and increasing native perennial herbaceous species. We used Sagebrush Steppe Treatment Evaluation Project data to test predictions on effects of fire vs. mechanical treatments on resilience and resistance for three site types exhibiting cheatgrass (Bromus tectorum L.) invasion and/or piñon and juniper expansion: 1) warm and dry Wyoming big sagebrush (WY shrub); 2) warm and moist Wyoming big sagebrush (WY PJ); and 3) cool and moist mountain big sagebrush (Mtn PJ). Warm and dry (mesic/aridic) WY shrub sites had lower resilience to fire (less shrub recruitment and native perennial herbaceous response) than cooler and moister (frigid/xeric) WY PJ and Mtn PJ sites. Warm (mesic) WY Shrub and WY PJ sites had lower resistance to annual exotics than cool (frigid to cool frigid) Mtn PJ sites. In WY shrub, fire and sagebrush mowing had similar effects on shrub cover and, thus, on perennial native herbaceous and exotic cover. In WY PJ and Mtn PJ, effects were greater for fire than cut-and-leave treatments and with high tree cover in general because most woody vegetation was removed increasing resources for other functional groups. In WY shrub, about 20% pretreatment perennial native herb cover was necessary to prevent increases in exotics after treatment. Cooler and moister WY PJ and especially Mtn PJ were more resistant to annual exotics, but perennial native herb cover was still required for site recovery. We use our results to develop state and transition models that illustrate how resilience and resistance influence vegetation dynamics and management options

Restoration Handbook for Sagebrush Steppe Ecosystems with Emphasis on Greater Sage-Grouse Habitat—Part 3. Site Level Restoration Decisions

Sagebrush steppe ecosystems in the United States currently (2016) occur on only about one-half of their historical land area because of changes in land use, urban growth, and degradation of land, including invasions of non-native plants. The existence of many animal species depends on the existence of sagebrush steppe habitat. The greater sage-grouse (Centrocercus urophasianus) depends on large landscapes of intact habitat of sagebrush and perennial grasses for their existence. In addition, other sagebrush-obligate animals have similar requirements and restoration of landscapes for greater sage-grouse also will benefit these animals. Once sagebrush lands are degraded, they may require restoration actions to make those lands viable habitat for supporting sagebrush-obligate animals, livestock, and wild horses, and to provide ecosystem services for humans now and for future generations. When a decision is made on where restoration treatments should be applied, there are a number of site-specific decisions managers face before selecting the appropriate type of restoration. This site-level decision tool for restoration of sagebrush steppe ecosystems is organized in nine steps. ●Step 1 describes the process of defining site-level restoration objectives. ●Step 2 describes the ecological site characteristics of the restoration site. This covers soil chemistry and texture, soil moisture and temperature regimes, and the vegetation communities the site is capable of supporting. ●Step 3 compares the current vegetation to the plant communities associated with the site State and Transition models. ●Step 4 takes the manager through the process of current land uses and past disturbances that may influence restoration success. ●Step 5 is a brief discussion of how weather before and after treatments may impact restoration success. ●Step 6 addresses restoration treatment types and their potential positive and negative impacts on the ecosystem and on habitats, especially for greater sage-grouse. We discuss when passive restoration options may be sufficient and when active restoration may be necessary to achieve restoration objectives. ●Step 7 addresses decisions regarding post-restoration livestock grazing management. ●Step 8 addresses monitoring of the restoration; we discuss important aspects associated with implementation monitoring as well as effectiveness monitoring. ●Step 9 takes the information learned from monitoring to determine how restoration actions in the future might be adapted to improve restoration success

Restoration Handbook for Sagebrush Steppe Ecosystems with Emphasis on Greater Sage-Grouse Habitat—Part 2. Landscape Level Restoration Decisions

Sagebrush steppe ecosystems in the United States currently (2015) occur on only about one-half of their historical land area because of changes in land use, urban growth, and degradation of land, including invasions of non-native plants. The existence of many animal species depends on the existence of sagebrush steppe habitat. The greater sage-grouse (Centrocercus urophasianus) is a landscape-dependent bird that requires intact habitat and combinations of sagebrush and perennial grasses to exist. In addition, other sagebrush-obligate animals also have similar requirements and restoration of landscapes for greater sage-grouse also will benefit these animals. Once sagebrush lands are degraded, they may require restoration actions to make those lands viable habitat for supporting sagebrush-obligate animals. Land managers do not have resources to restore all locations because of the extent of the restoration need and because some land uses are not likely to change, therefore, restoration decisions made at the landscape to regional scale may improve the effectiveness of restoration to achieve landscape and local restoration objectives. We present a landscape restoration decision tool intended to assist decision makers in determining landscape objectives, to identify and prioritize landscape areas where sites for priority restoration projects might be located, and to aid in ultimately selecting restoration sites guided by criteria used to define the landscape objectives. The landscape restoration decision tool is structured in five sections that should be addressed sequentially. Each section has a primary question or statement followed by related questions and statements to assist the user in addressing the primary question or statement. This handbook will guide decision makers through the important process steps of identifying appropriate questions, gathering appropriate data, developing landscape objectives, and prioritizing landscape patches where potential sites for restoration projects may be located. Once potential sites are selected, land managers can move to the site-specific decision tool to guide restoration decisions at the site level

Restoration Handbook for Sagebrush Steppe Ecosystems with Emphasis on Greater Sage-Grouse Habitat—Part 1. Concepts for Understanding and Applying Restoration

Sagebrush steppe ecosystems in the United States currently occur on only about one-half of their historical land area because of changes in land use, urban growth, and degradation of land, including invasions of non-native plants. The existence of many animal species depends on the existence of sagebrush steppe habitat. The greater sage-grouse (Centrocercus urophasianus) is a landscape-dependent bird that requires intact habitat and combinations of sagebrush and perennial grasses to exist. In addition, other sagebrush-obligate animals also have similar requirements and restoration of landscapes for greater sage-grouse also will benefit these animals. Once sagebrush lands are degraded, they may require restoration actions to make those lands viable habitat for supporting sagebrush-obligate animals. This restoration handbook is the first in a three-part series on restoration of sagebrush ecosystems. In Part 1, we discuss concepts surrounding landscape and restoration ecology of sagebrush ecosystems and greater sage-grouse that habitat managers and restoration practitioners need to know to make informed decisions regarding where and how to restore specific areas. We will describe the plant dynamics of sagebrush steppe ecosystems and their responses to major disturbances, fire, and defoliation. We will introduce the concepts of ecosystem resilience to disturbances and resistance to invasions of annual grasses within sagebrush steppe. An introduction to soils and ecological site information will provide insights into the specific plants that can be restored in a location. Soil temperature and moisture regimes are described as a tool for determining resilience and resistance and the potential for various restoration actions. Greater sage-grouse are considered landscape birds that require large areas of intact sagebrush steppe; therefore, we describe concepts of landscape ecology that aid our decisions regarding habitat restoration. We provide a brief overview of restoration techniques for sage-grouse habitat restoration. We conclude with a description of the critical nature of monitoring for adaptive management of sagebrush steppe restoration at landscape- and project-specific levels

Pre-columbian origins for North American anthrax

Disease introduction into the New World during colonial expansion is well documented and had a major impact on indigenous populations; however, few diseases have been associated with early human migrations into North America. During the late Pleistocene epoch, Asia and North America were joined by the Beringian Steppe ecosystem which allowed animals and humans to freely cross what would become a water barrier in the Holocene. Anthrax has clearly been shown to be dispersed by human commerce and trade in animal products contaminated with Bacillus anthracis spores. Humans appear to have brought B. anthracis to this area from Asia and then moved it further south as an ice-free corridor opened in central Canada ~13,000 ybp. In this study, we have defined the evolutionary history of Western North American (WNA) anthrax using 2,850 single nucleotide polymorphisms (SNPs) and 285 geographically diverse B. anthracis isolates. Phylogeography of the major WNA B. anthracis clone reveals ancestral populations in northern Canada with progressively derived populations to the south; the most recent ancestor of this clonal lineage is in Eurasia. Our phylogeographic patterns are consistent with B. anthracis arriving with humans via the Bering Land Bridge. This northern-origin hypothesis is highly consistent with our phylogeographic patterns and rates of SNP accumulation observed in current day B. anthracis isolates. Continent-wide dispersal of WNA B. anthracis likely required movement by later European colonizers, but the continent's first inhabitants may have seeded the initial North American populations

Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing

Background: In the event of biocrimes or infectious disease outbreaks, high-resolution genetic characterization for identifying the agent and attributing it to a specific source can be crucial for an effective response. Until recently, in-depth genetic characterization required expensive and time-consuming Sanger sequencing of a few strains, followed by genotyping of a small number of marker loci in a panel of isolates at or by gel-based approaches such as pulsed field gel electrophoresis, which by necessity ignores most of the genome. Next-generation, massively parallel sequencing (MPS) technology (specifically the Applied Biosystems sequencing by oligonucleotide ligation and detection (SOLiD™) system) is a powerful investigative tool for rapid, cost-effective and parallel microbial whole-genome characterization. Results: To demonstrate the utility of MPS for whole-genome typing of monomorphic pathogens, four Bacillus anthracis and four Yersinia pestis strains were sequenced in parallel. Reads were aligned to complete reference genomes, and genomic variations were identified. Resequencing of the B. anthracis Ames ancestor strain detected no false-positive single-nucleotide polymorphisms (SNPs), and mapping of reads to the Sterne strain correctly identified 98% of the 133 SNPs that are not clustered or associated with repeats. Three geographically distinct B. anthracis strains from the A branch lineage were found to have between 352 and 471 SNPs each, relative to the Ames genome, and one strain harbored a genomic amplification. Sequencing of four Y. pestis strains from the Orientalis lineage identified between 20 and 54 SNPs per strain relative to the CO92 genome, with the single Bolivian isolate having approximately twice as many SNPs as the three more closely related North American strains. Coverage plotting also revealed a common deletion in two strains and an amplification in the Bolivian strain that appear to be due to insertion element-mediated recombination events. Most private SNPs (that is, a, variant found in only one strain in this set) selected for validation by Sanger sequencing were confirmed, although rare falsepositive SNPs were associated with variable nucleotide tandem repeats. Conclusions: The high-throughput, multiplexing capability, and accuracy of this system make it suitable for rapid whole-genome typing of microbial pathogens during a forensic or epidemiological investigation. By interrogating nearly every base of the genome, rare polymorphisms can be reliably discovered, thus facilitating high-resolution strain tracking and strengthening forensic attribution

A Synopsis of Short-Term Response to Alternative Restoration Treatments in Sagebrush-Steppe: The SageSTEP Project

The Sagebrush Steppe Treatment Evaluation Project (SageSTEP) is an integrated long-term study that evaluates ecological effects of alternative treatments designed to reduce woody fuels and to stimulate the herbaceous understory of sagebrush steppe communities of the Intermountain West. This synopsis summarizes results through 3 yr posttreatment. Woody vegetation reduction by prescribed fire, mechanical treatments, or herbicides initiated a cascade of effects, beginning with increased availability of nitrogen and soil water, followed by increased growth of herbaceous vegetation. Response of butterflies and magnitudes of runoff and erosion closely followed herbaceous vegetation recovery. Effects on shrubs, biological soil crust, tree cover, surface woody fuel loads, and sagebrush-obligate bird communities will take longer to be fully expressed. In the short term, cool wet sites were more resilient than warm dry sites, and resistance was mostly dependent on pretreatment herbaceous cover. At least 10 yr of posttreatment time will likely be necessary to determine outcomes for most sites. Mechanical treatments did not serve as surrogates for prescribed fire in how each influenced the fuel bed, the soil, erosion, and sage-obligate bird communities. Woody vegetation reduction by any means resulted in increased availability of soil water, higher herbaceous cover, and greater butterfly numbers. We identified several trade-offs (desirable outcomes for some variables, undesirable for others), involving most components of the study system. Trade-offs are inevitable when managing complex natural systems, and they underline the importance of asking questions about the whole system when developing management objectives. Substantial spatial and temporal heterogeneity in sagebrush steppe ecosystems emphasizes the point that there will rarely be a “recipe” for choosing management actions on any specific area. Use of a consistent evaluation process linked to monitoring may be the best chance managers have for arresting woodland expansion and cheatgrass invasion that may accelerate in a future warming climate

Whole-genome analysis of Exserohilum rostratum from an outbreak of fungal meningitis and other infections

Exserohilum rostratum was the cause of most cases of fungal meningitis and other infections associated with the injection of contaminated methylprednisolone acetate produced by the New England Compounding Center (NECC). Until this outbreak, very few human cases of Exserohilum infection had been reported, and very little was known about this dematiaceous fungus, which usually infects plants. Here, we report using whole-genome sequencing (WGS) for the detection of single nucleotide polymorphisms (SNPs) and phylogenetic analysis to investigate the molecular origin of the outbreak using 22 isolates of E. rostratum retrieved from 19 case patients with meningitis or epidural/spinal abscesses, 6 isolates from contaminated NECC vials, and 7 isolates unrelated to the outbreak. Our analysis indicates that all 28 isolates associated with the outbreak had nearly identical genomes of 33.8 Mb. A total of 8 SNPs were detected among the outbreak genomes, with no more than 2 SNPs separating any 2 of the 28 genomes. The outbreak genomes were separated from the next most closely related control strain by ∼136,000 SNPs. We also observed significant genomic variability among strains unrelated to the outbreak, which may suggest the possibility of cryptic speciation in E. rostratum