[ 13 C 6 ]salicylate, [U-13 C]naphthalene, and [U-13 C]phenanthrene were synthesized and separately added to slurry from a bench-scale, aerobic bioreactor used to treat soil contaminated with polycyclic aromatic hydrocarbons. Incubations were performed for either 2 days (salicylate, naphthalene) or 7 days (naphthalene, phenanthrene). Total DNA was extracted from the incubations, the "heavy" and "light" DNA were separated, and the bacterial populations associated with the heavy fractions were examined by denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone libraries. Unlabeled DNA from Escherichia coli K-12 was added to each sample as an internal indicator of separation efficiency. While E. coli was not detected in most analyses of heavy DNA, a low number of E. coli sequences was recovered in the clone libraries associated with the heavy DNA fraction of [ 13 C]phenanthrene incubations. The number of E. coli clones recovered proved useful in determining the relative amount of light DNA contamination of the heavy fraction in that sample. Salicylate-and naphthalene-degrading communities displayed similar DGGE profiles and their clone libraries were composed primarily of sequences belonging to the Pseudomonas and Ralstonia genera. In contrast, heavy DNA from the phenanthrene incubations displayed a markedly different DGGE profile and was composed primarily of sequences related to the Acidovorax genus. There was little difference in the DGGE profiles and types of sequences recovered from 2-and 7-day incubations with naphthalene, so secondary utilization of the 13 C during the incubation did not appear to be an issue in this experiment.
To determine whether the diversity of pyrene-degrading bacteria in an aged polycyclic aromatic hydrocarbon-contaminated soil is affected by the addition of inorganic nutrients or by slurrying the soil, various incubation conditions (all including phosphate buffer) were examined by mineralization studies and stable-isotope probing (SIP). The addition of nitrogen to either continuously mixed slurry or static field-wet soil incubations increased the rate and extent of mineralization of [(14)C]pyrene, with the most rapid mineralization observed in slurried, nitrogen-amended soil. Microcosms of slurry and static field-wet soil amended with nitrogen were also examined by SIP with [U-(13)C]pyrene. Recovered (13)C-enriched deoxyribonucleic acid (DNA) was analyzed by denaturing-gradient gel electrophoresis (DGGE) and 16S ribosomal ribonucleic acid (rRNA) gene clone libraries. DGGE profiles of (13)C-enriched DNA fractions from both incubation conditions were similar, suggesting that pyrene-degrading bacterial community diversity may be independent of treatment method. The vast majority (67 of 71) of the partial sequences recovered from clone libraries were greater than or equal to 97% similar to one another, 98% similar to sequences of pyrene-degrading bacteria previously detected by SIP with pyrene in different soil, and only 89% similar to the closest cultivated genus. All of the sequences recovered from the field-wet incubation and most of the sequences recovered from the slurry incubation were in this clade. Of the four sequences from slurry incubations not within this clade, three possessed greater than 99% similarity to the 16S rRNA gene sequences of phylogenetically dissimilar Caulobacter spp.
Purpose: Advances in clinical genomic sequencing capabilities, including reduced costs and knowledge gains, have bolstered the consideration of genomic screening in healthy adult populations. Yet, little is known about the existing landscape of genomic screening programs in the United States. It can be difficult to find information on current implementation efforts and best practices, particularly in light of critical questions about equity, cost, and benefit. Methods: In 2020, we searched publicly available information on the Internet and the scientific literature to identify programs and collect information, including: setting, program funding, targeted population, test offered, and patient cost. Program representatives were contacted throughout 2020 and 2021 to clarify, update, and supplement the publicly available information. Results: Twelve programs were identified. Information was available on key program features, such as setting, genes tested, and target populations. Data on costs, outcomes, or long-term sustainability plans were not always available. Most programs offered testing at no or significantly reduced cost due to generous pilot funding, although the sustainability of these programs remains unknown. Gene testing lists were diverse, ranging from 11 genes (CDC tier 1 genes) to 59 genes (ACMG secondary findings list v.2) to broad exome and genome sequencing. This diversity presents challenges for harmonized data collection and assessment of program outcomes. Conclusions: Early programs are exploring the logistics and utility of population genomic screening in various settings. Coordinated efforts are needed to take advantage of data collected about uptake, infrastructure, and intervention outcomes to inform future research, evaluation, and program development.
We investigated enrichment with salicylate as a method to stimulate the degradation of polycyclic aromatic hydrocarbons (PAHs) by a microbial communityfrom a bioreactortreating PAH-contaminated soil. DNA-based stable isotope probing (SIP) was used to compare the effect of alternate methods of salicylate addition (spike vs slow, continuous addition) on the diversity of the enriched microbial community. After identification of salicylate degraders by SIP, real-time quantitative PCR (qPCR) primers were developed to quantify the abundances of three groups containing salicylate-utilizing organisms in the bioreactor community before and after enrichment. The different methods of salicylate addition were found to select for different microbial communities. Two groups containing salicylate-degrading bacteria increased in abundance substantially after enrichment by continuous addition of salicylate but did not increase in abundance in response to the spike addition, whereas a third group increased in abundance in response to both methods of salicylate addition. The initial rate of naphthalene mineralization increased significantly after enrichment by spike addition of salicylate, but neither phenanthrene nor benzo[a] pyrene mineralization rates were enhanced. Continuous addition of salicylate did not enhance the mineralization rate for any of the PAHs. These results suggest that enrichment with salicylate can select for naphthalene-degrading bacteria, but does not select for organisms responsible for degrading PAHs of higher molecular weight. Differences in microbial selection observed in this study that resulted from different rates of carbon source addition also have implications for the design of SIP experiments with water-soluble carbon sources.
An emerging role for DNA sequencing is to identify people at risk for an inherited cancer syndrome in order to prevent or ameliorate the manifestation of symptoms. Two cancer syndromes, Hereditary Breast and Ovarian Cancer and Lynch Syndrome meet the “Tier 1” evidence threshold established by the Centers for Disease Control and Prevention (CDC) for routine testing of patients with a personal or family history of cancer. Advancements in genomic medicine have accelerated public health pilot programs for these highly medically actionable conditions. In this brief report, we provide descriptive statistics from a survey of 746 US respondents from a Qualtrics panel about the public’s awareness of genetic testing, interest in learning about their cancer risk, and likelihood of participating in a population genetic screening (PGS) test. Approximately of half the respondents were aware of genetic testing for inherited cancer risk (n = 377/745, 50.6%) and would choose to learn about their cancer risk (n-309/635, 48.7%). Characteristics of those interested in learning about their cancer risk differed by educational attainment, age, income, insurance status, having a primary care doctor, being aware of genetic testing, and likelihood of sharing information with family (p < 0.05). A sizeable majority of the respondents who were interested in about learning their cancer risk also said that they were likely to participate in a PGS test that involved a clinical appointment and blood draw, but no out-of-pocket cost (n = 255/309, 82.5%). Reasons for not wanting to participate included not finding test results interesting or important, concerns about costs, and feeling afraid to know the results. Overall, our results suggest that engaging and educating the general population about the benefits of learning about an inherited cancer predisposition may be an important strategy to address recruitment barriers to PGS.
Recent advances in genomic sequencing and genomic medicine are reshaping the landscape of clinical care. As a screening modality, genetic sequencing has the potential to dramatically expand the clinical utility of newborn screening (NBS), though significant barriers remain regarding ethical, legal, and social implications (ELSI) and technical and evidentiary challenges. Stakeholder-informed implementation research is poised to grapple with many of these barriers, and parents are crucial stakeholders in this process. We describe the formation and activities of a Community Research Board (CRB) composed of parents with diverse backgrounds assembled to participate in an ongoing research partnership with genomic and public health researchers at the University of North Carolina. The mission of the CRB is to provide insight into parental perspectives regarding the prospect of adding genomic sequencing to NBS and collaboratively develop strategies to ensure its equitable uptake. We describe how these contributions can improve the accessibility of research and recruitment methods and promote trust and inclusivity within diverse communities to maximize the societal benefit of population genomic screening in healthy children.
The USACE-Norfolk District (NAO) and the City of Petersburg, VA are working toward restoring the former Appomattox River Federal Navigation Channel. In this effort, ~350,000 cubic yards of deposited sediment will be removed from-14 feet MLLW up to + 6 feet MLLW over a ~1 mile reach of the Appomattox River. Historical industrial uses have resulted in PAH contamination exceeding 500 mg/kg on average, with hotspots detected in excess of 5,000 mg/kg based on USACE 2004 analytical data. To support the NAO with its assessment of contaminant distribution, upland source control measures, dredge sequencing, sediment capping requirements to address residual contaminants and beneficial reuse options for the dredged material have been evaluated. In support of beneficial reuse as agricultural soil, a lab treatability study has been completed to assess biodegradation potential. Total PAH concentrations in three laboratory test pans after 46 weeks of treatment indicated an overall 80% contaminant reduction using an enhanced bioremediation process. The results of this bench-scale study were used as the basis for the design of a pilot field-scale landfarm study demonstration undertaken during July 2007. After five months of treatment, LMW PAHs in landfarm material appear to have degraded first while HMW PAHs are degrading more slowly, a process which generally mimics the results of the laboratory investigation. Conclusions based on the laboratory and landfarm activities as well as the technical and regulatory issues that must be resolved to allow eventual placement of the material at a mine reclamation site for revegetation purposes will be presented.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.