Metagenomic Analysis of the Bioremediation of Diesel-Contaminated Canadian High Arctic Soils

As human activity in the Arctic increases, so does the risk of hydrocarbon pollution events. On site bioremediation of contaminated soil is the only feasible clean up solution in these remote areas, but degradation rates vary widely between bioremediation treatments. Most previous studies have focused on the feasibility of on site clean-up and very little attention has been given to the microbial and functional communities involved and their ecology. Here, we ask the question: which microorganisms and functional genes are abundant and active during hydrocarbon degradation at cold temperature? To answer this question, we sequenced the soil metagenome of an ongoing bioremediation project in Alert, Canada through a time course. We also used reverse-transcriptase real-time PCR (RT-qPCR) to quantify the expression of several hydrocarbon-degrading genes. Pseudomonas species appeared as the most abundant organisms in Alert soils right after contamination with diesel and excavation (t = 0) and one month after the start of the bioremediation treatment (t = 1m), when degradation rates were at their highest, but decreased after one year (t = 1y), when residual soil hydrocarbons were almost depleted. This trend was also reflected in hydrocarbon degrading genes, which were mainly affiliated with Gammaproteobacteria at t = 0 and t = 1m and with Alphaproteobacteria and Actinobacteria at t = 1y. RT-qPCR assays confirmed that Pseudomonas and Rhodococcus species actively expressed hydrocarbon degradation genes in Arctic biopile soils. Taken together, these results indicated that biopile treatment leads to major shifts in soil microbial communities, favoring aerobic bacteria that can degrade hydrocarbons

High Quality Care and Ethical Pay-for-Performance: A Society of General Internal Medicine Policy Analysis

BACKGROUND: Pay-for-performance is proliferating, yet its impact on key stakeholders remains uncertain. OBJECTIVE: The Society of General Internal Medicine systematically evaluated ethical issues raised by performance-based physician compensation. RESULTS: We conclude that current arrangements are based on fundamentally acceptable ethical principles, but are guided by an incomplete understanding of health-care quality. Furthermore, their implementation without evidence of safety and efficacy is ethically precarious because of potential risks to stakeholders, especially vulnerable patients. CONCLUSION: We propose four major strategies to transition from risky pay-for-performance systems to ethical performance-based physician compensation and high quality care. These include implementing safeguards within current pay-for-performance systems, reaching consensus regarding the obligations of key stakeholders in improving health-care quality, developing valid and comprehensive measures of health-care quality, and utilizing a cautious evaluative approach in creating the next generation of compensation systems that reward genuine quality

Multiple Organ System Defects and Transcriptional Dysregulation in the Nipbl+/− Mouse, a Model of Cornelia de Lange Syndrome

Cornelia de Lange Syndrome (CdLS) is a multi-organ system birth defects disorder linked, in at least half of cases, to heterozygous mutations in the NIPBL gene. In animals and fungi, orthologs of NIPBL regulate cohesin, a complex of proteins that is essential for chromosome cohesion and is also implicated in DNA repair and transcriptional regulation. Mice heterozygous for a gene-trap mutation in Nipbl were produced and exhibited defects characteristic of CdLS, including small size, craniofacial anomalies, microbrachycephaly, heart defects, hearing abnormalities, delayed bone maturation, reduced body fat, behavioral disturbances, and high mortality (75–80%) during the first weeks of life. These phenotypes arose despite a decrease in Nipbl transcript levels of only ∼30%, implying extreme sensitivity of development to small changes in Nipbl activity. Gene expression profiling demonstrated that Nipbl deficiency leads to modest but significant transcriptional dysregulation of many genes. Expression changes at the protocadherin beta (Pcdhb) locus, as well as at other loci, support the view that NIPBL influences long-range chromosomal regulatory interactions. In addition, evidence is presented that reduced expression of genes involved in adipogenic differentiation may underlie the low amounts of body fat observed both in Nipbl+/− mice and in individuals with CdLS

Comparative mesocosm study of biostimulation efficiency in two different oil-amended sub-antarctic soils

Biological treatment has become increasingly popular as a remediation method for soils and groundwater contaminated with petroleum hydrocarbon, chlorinated solvents, and pesticides. Bioremediation has been considered for application in cold regions such as Arctic and sub-Arctic climates and Antarctica. Studies to date suggest that indigenous microbes suitable for bioremediation exist in soils in these regions. This paper reports on two case studies at the sub-Antarctic Kerguelen Island, in which indigenous bacteria were found that were capable of mineralizing petroleum hydrocarbons in soil contaminated with crude oil and diesel fuel. All results demonstrate a serious influence of the soil properties on the biostimulation efficiency. Both temperature elevation and fertilizer addition have a more significant impact on the microbial assemblages in the mineral soil than in the organic one. Analysis of the hydrocarbons remaining at the end of the experiments confirmed the bacterial observations. Optimum temperature seems to be around 10°C in organic soil while it was higher in mineral soil. The benefit of adding nutrient was much stronger in mineral than in the organic soil. Overall, this study suggests on the basis of microbiological and physicochemical parameters, that biostimulation treatments were driven by soil properties and that ex-situ bioremediation for treatment of cold contaminated soils will allow greater control over soil temperature, a limiting factor in cold climates.French Polar Institute (IPEV) and EU project FaceiT (Fast Advanced Cellular and Ecosystems Information Technologies [STREP grant no 018391 (COGE)

How Doctors and Patients Discuss Routine Clinical Decisions: Informed Decision Making in the Outpatient Setting

OBJECTIVE: To characterize the informed consent process in routine, primary care office practice. DESIGN: Cross-sectional, descriptive evaluation of audiotaped encounters. SETTING: Offices of primary care physicians in Portland, Oregon. PARTICIPANTS: Internists (54%) and family physicians (46%), and their patients. MEASUREMENTS AND MAIN RESULTS: Audiotapes of primary care office visits from a previous study of doctor-patient communication were coded for the number and type of clinical decisions made. The discussion between doctor and patient was scored according to six criteria for informed decision making: description of the nature of the decision, discussion of alternatives, discussion of risks and benefits, discussion of related uncertainties, assessment of the patient’s understanding and elicitation of the patient’s preference. Discussions leading to decisions included fewer than two of the six described elements of informed decision making (mean 1.23, median 1.0), most frequent of these was description of the nature of the decision (83% of discussion). Discussion of risks and benefits was less frequent (9%), and assessment of understanding was rare (2%). Discussions of management decisions were generally more substantive than discussions of diagnostic decisions (p = .05). CONCLUSIONS: Discussions leading to clinical decisions in these primary care settings did not fulfill the criteria considered integral to informed decision making. Physicians frequently described the nature of the decision, less frequently discussed risks and benefits, and rarely assessed the patient’s understanding of the decision