New Arsenate Reductase Gene (arrA) PCR Primers for Diversity Assessment and Quantification in Environmental Samples.

The extent of arsenic contamination in drinking water and its potential threat to human health have resulted in considerable research interest in the microbial species responsible for arsenic reduction. The arsenate reductase gene (arrA), an important component of the microbial arsenate reduction system, has been widely used as a biomarker to study arsenate-reducing microorganisms. A new primer pair was designed and evaluated for quantitative PCR (qPCR) and high-throughput sequencing of the arrA gene, because currently available PCR primers are not suitable for these applications. The primers were evaluated in silico and empirically tested for amplification of arrA genes in clones and for amplification and high-throughput sequencing of arrA genes from soil and groundwater samples. In silico, this primer pair matched (≥90% DNA identity) 86% of arrA gene sequences from GenBank. Empirical evaluation showed successful amplification of arrA gene clones of diverse phylogenetic groups, as well as amplification and high-throughput sequencing of independent soil and groundwater samples without preenrichment, suggesting that these primers are highly specific and can amplify a broad diversity of arrA genes. The arrA gene diversity from soil and groundwater samples from the Cache Valley Basin (CVB) in Utah was greater than anticipated. We observed a significant correlation between arrA gene abundance, quantified through qPCR, and reduced arsenic (AsIII) concentrations in the groundwater samples. Furthermore, we demonstrated that these primers can be useful for studying the diversity of arsenate-reducing microbial communities and the ways in which their relative abundance in groundwater may be associated with different groundwater quality parameters. IMPORTANCE: Arsenic is a major drinking water contaminant that threatens the health of millions of people worldwide. The extent of arsenic contamination and its potential threat to human health have resulted in considerable interest in the study of microbial species responsible for the reduction of arsenic, i.e., the conversion of AsV to AsIII In this study, we developed a new primer pair to evaluate the diversity and abundance of arsenate-reducing microorganisms in soil and groundwater samples from the CVB in Utah. We observed significant arrA gene diversity in the CVB soil and groundwater samples, and arrA gene abundance was significantly correlated with the reduced arsenic (AsIII) concentrations in the groundwater samples. We think that these primers are useful for studying the ecology of arsenate-reducing microorganisms in different environments.

Dehalococcoides and general bacterial ecology of differentially trichloroethene dechlorinating flow-through columns.

The diversity of Dehalococcoides mccartyi (Dhc) and/or other organohalide respiring or associated microorganisms in parallel, partial, or complete trichloroethene (TCE) dehalogenating systems has not been well described. The composition of Dhc populations and the associated bacterial community that developed over 7.5 years in the top layer (0-10 cm) of eight TCE-fed columns were examined using pyrosequencing. Columns biostimulated with one of three carbon sources, along with non-stimulated controls, developed into complete (ethene production, whey amended), partial (cis-dichloroethene (DCE) and VC, an emulsified oil with nonionic surfactant), limited (<5 % cis-DCE and 95 % TCE, an emulsified oil), and non- (controls) TCE dehalogenating systems. Bioaugmentation of one column of each treatment with Bachman Road enrichment culture did not change Dhc populations nor the eventual degree of TCE dehalogenation. Pyrosequencing revealed high diversity among Dhc strains. There were 13 OTUs that were represented by more than 1000 sequences each. Cornell group-related populations dominated in complete TCE dehalogenating columns, while Pinellas group related Dhc dominated in all other treatments. General microbial communities varied with biostimulation, and three distinct microbial communities were established: one each for whey, oils, and control treatments. Bacterial genera, including Dehalobacter, Desulfitobacterium, Sulfurospirillum, Desulfuromonas, and Geobacter, all capable of partial TCE dehalogenation, were abundant in the limited and partial TCE dehalogenating systems. Dhc strain diversity was wider than previously reported and their composition within the community varied significantly depending on the nature of the carbon source applied and/or changes in the Dhc associated partners that fostered different biogeochemical conditions across the columns.

Dehalococcoides abundance and alternate electron acceptor effects on large, flow-through trichloroethene dechlorinating columns.

Trichloroethene (TCE) in groundwater is a major health concern and biostimulation/bioaugmentation-based strategies have been evaluated to achieve complete reductive dechlorination with varying success. Different carbon sources were hypothesized to stimulate different extents of TCE reductive dechlorination. Ecological conditions that developed different dechlorination stages were investigated by quantitating Dehalococcoides 16S rRNA (Dhc) and reductive dehalogenase gene abundance, and by describing biogeochemical properties of laboratory columns in response to this biostimulation. Eight large columns (183 cm × 15.2 cm), packed with aquifer material from Hill AFB, Utah, that were continuously fed TCE for 7.5 years. Duplicate columns were biostimulated with whey or one of two different Newman Zone® emulsified oil formulations containing either nonionic surfactant (EOLN) or standard surfactant (EOL). Two columns were non-stimulated controls. Complete (whey amended), partial (EOLN amended), limited (EOL), and non-TCE dehalogenating systems (controls) developed over the course of the study. Bioaugmentation of half of the columns with Bachman Road culture 3 years prior to dismantling did not influence the extent of TCE dehalogenation. Multivariate analysis clustered samples by biostimulation treatments and extent of TCE dehalogenation. Dhc, tceA, and bvcA gene concentrations did not show a consistent relationship with TCE dehalogenation but the vcrA gene was more abundant in completely dehalogenating, whey-treated columns. The whey columns developed strongly reducing conditions producing Fe(II), sulfide, and methane. Biostimulation with different carbon and energy sources can support high concentrations of diverse Dhc, but carbon addition has a major influence on biogeochemical processes effecting the extent of TCE dehalogenation.

Enabling Science Support for Better Decision-Making when Responding to Chemical Spills.

Chemical spills and accidents contaminate the environment and disrupt societies and economies around the globe. In the United States there were approximately 172,000 chemical spills that affected US waterbodies from 2004 to 2014. More than 8000 of these spills involved non-petroleum-related chemicals. Traditional emergency responses or incident command structures (ICSs) that respond to chemical spills require coordinated efforts by predominantly government personnel from multiple disciplines, including disaster management, public health, and environmental protection. However, the requirements of emergency response teams for science support might not be met within the traditional ICS. We describe the US ICS as an example of emergency-response approaches to chemical spills and provide examples in which external scientific support from research personnel benefitted the ICS emergency response, focusing primarily on nonpetroleum chemical spills. We then propose immediate, near-term, and long-term activities to support the response to chemical spills, focusing on nonpetroleum chemical spills. Further, we call for science support for spill prevention and near-term spill-incident response and identify longer-term research needs. The development of a formal mechanism for external science support of ICS from governmental and nongovernmental scientists would benefit rapid responders, advance incident- and crisis-response science, and aid society in coping with and recovering from chemical spills.

Bioaccumulation of copper, lead, and zinc in six macrophyte species grown in simulated stormwater bioretention systems.

Stormwater bioretention (BR) systems collect runoff containing heavy metals, which can concentrate in soil environments and potentially leach into groundwater. This greenhouse experiment evaluated differences among six plant species undergoing three varying hydraulic and pollutant loads in their bioaccumulation potential when subjected to continual application of low metal concentrations as a means of preventing copper, lead, and zinc accumulation in the BR soil. Results show that >92% of metal mass applied to the treatments via synthetic stormwater was removed from the exfiltrate within 27 cm of soil depth. Compacted soil conditions of unplanted controls retained significantly more Cu, Pb, and Zn than Carex praegracilis, and Carex microptera treatments. Differences in above and below ground plant tissue concentrations differed among species, resulting in significant differences in mass accumulation. In the above ground tissue, from highest to lowest, Phragmites australis accumulated 8 times more Cu than Scirpus acutus, and C. microptera accumulated 18 times more Pb, and 6 times more Zn than Scirpus validus. These results, and differences among species in mass distribution of the metals recovered at the end of the study, reveal various metal accumulation mechanisms.

Arsenic(V) reduction in relation to Iron(III) transformation and molecular characterization of the structural and functional microbial community in sediments of a basin-fill aquifer in Northern Utah.

Basin-fill aquifers of the Southwestern United States are associated with elevated concentrations of arsenic (As) in groundwater. Many private domestic wells in the Cache Valley Basin, UT, have As concentrations in excess of the U.S. EPA drinking water limit. Thirteen sediment cores were collected from the center of the valley at the depth of the shallow groundwater and were sectioned into layers based on redoxmorphic features. Three of the layers, two from redox transition zones and one from a depletion zone, were used to establish microcosms. Microcosms were treated with groundwater (GW) or groundwater plus glucose (GW+G) to investigate the extent of As reduction in relation to iron (Fe) transformation and characterize the microbial community structure and function by sequencing 16S rRNA and arsenate dissimilatory reductase (arrA) genes. Under the carbon-limited conditions of the GW treatment, As reduction was independent of Fe reduction, despite the abundance of sequences related to Geobacter and Shewanella, genera that include a variety of dissimilatory iron-reducing bacteria. The addition of glucose, an electron donor and carbon source, caused substantial shifts toward domination of the bacterial community by Clostridium-related organisms, and As reduction was correlated with Fe reduction for the sediments from the redox transition zone. The arrA gene sequencing from microcosms at day 54 of incubation showed the presence of 14 unique phylotypes, none of which were related to any previously described arrA gene sequence, suggesting a unique community of dissimilatory arsenate-respiring bacteria in the Cache Valley Basin.

The prognostic impact of immune-related adverse events during anti-PD1 treatment in melanoma and non-small-cell lung cancer: a real-life retrospective study.

Background: Nivolumab and pembrolizumab, two PD1 inhibitors, trigger immune-related adverse events in approximately 50% of patients. Our objective was to determine whether these immune-related adverse events are associated with patient outcomes. Patients and Methods: Retrospective cohort study, realized at the Institut Universitaire du Cancer de Toulouse, of all the patients treated with nivolumab or pembrolizumab off clinical trials. We included patients (i) diagnosed with unresectable stage III or stage IV melanoma or with recurrent stage IIIB or stage IV non-small cell lung cancer (ii) on nivolumab 3mg/kg or pembrolizumab 2mg/kg every 2 or 3 weeks respectively. Results: Of the 311 patients included (of 641 eligible subjects), 120 (38.6%) had melanoma and 191 (61.4%) had non-small cell lung cancer; 241 (77.5%) were treated with nivolumab with a median follow-up of 24 months (20-29). We observed 166 immune-related adverse events in 116 (37.3%) patients, categorized as "early" (onset before 12 weeks in melanoma and before 8 weeks in lung cancer) in 63 (54.3%) patients. Early and late adverse events were significantly associated with an increase in overall survival: adjusted hazard ratio 0.58 [0.41-0.84] (p = .003) and 0.28 [0.16-0.50] (p < .001) respectively. The overall response rate was significantly increased in patients with an immune-related adverse event (53.9% vs 12.9%, p < .001) Conclusions: This study validates the association between immune-related adverse events and anti-PD1 efficacy in real-life, especially if these events are delayed. Our results, along with further studies on the place of immunosuppressive drugs in the therapeutic strategy, could improve the management of these adverse events.

Genome-wide linkage scan for nicotine dependence in European Americans and its converging results with African Americans in the Mid-South Tobacco Family sample.

Previously, we reported a genome-wide scan for nicotine dependence (ND) in the African American (AA) sample of the Mid-South Tobacco Family (MSTF) cohort. In this study, we conducted a genome-wide scan in 629 individuals representing 200 nuclear families of European American (EA) origin of the MSTF cohort with the goals of identifying vulnerability loci for ND in the EAs and determining converging regions across the ethnic groups. We examined 385 autosomal microsatellite markers for ND, which was assessed by smoking quantity (SQ), the Heaviness of Smoking Index (HSI) and the Fagerström test for ND (FTND). After performing linkage analyses using various methods implemented in the GENEHUNTER and SAGE programs, we found eight regions on chromosomes 2, 4, 9-12, 17 and 18 that met the criteria for suggestive linkage to at least one ND measure in the EA sample. Of these, the region on chromosome 4 at 43 cM showed suggestive linkage to indexed SQ, the HSI and the FTND, and the region on chromosome 9 at 24 cM showed suggestive linkage to the HSI and the FTND. To increase detection power, we analyzed a combined AA and EA sample using age, gender and ethnicity as covariates and found that the region on chromosome 12 near marker D12S372 showed significant linkage to SQ. Additionally, we found six regions on chromosomes 9-11, 13 and 18 that showed suggestive linkage to at least one ND measure in the combined sample. When we compared the linkage peaks detected for ND among the two samples and a combined sample, we found that four regions on chromosomes 9 (two regions), 11 and 18 overlapped. On the other hand, we identified five regions on chromosomes 2, 4, 10, 12 and 17 that showed linkage to ND only in the EA sample, and two regions on chromosomes 10 and 13 that showed linkage to ND only in the AA sample. For those linkages identified in only one sample, we found that the combined analysis of AA plus EA samples actually decreased the linkage signal. This indicates that some chromosomal regions may be more homogenous than others across the ethnic samples. All regions except for the one on chromosome 12 have been detected at nominally significant levels in other studies, providing independent replication of ND loci in different populations.

Iron and arsenic release from aquifer solids in response to biostimulation.

Biostimulation has been used at various contaminated sites to promote the reductive dechlorination of trichloroethylene (TCE), but the addition of carbon and energy donor also stimulates bacteria that use Fe(III) as the terminal electron acceptor (TEA) in potential competition with dechlorination processes. Microcosm studies were conducted to determine the influence of various carbon donors on the extent of reductive dissolution of aquifer solids containing Fe(III) and arsenic. Glucose, a fermentable and respirable carbon donor, led to the production of 1500 mg Fe(II) kg(-1), or 24% of the total Fe in the aquifer sediment being reduced to Fe(II), whereas the same concentration of carbon as acetate resulted in only 300 mg Fe(II) kg(-1) being produced. The biogenic Fe(II) produced with acetate was exclusively associated with the solid phase whereas with fermentable carbon donors as whey and glucose, 22 and 54% of the Fe(II) was in solution. With fermentation, some of the metabolites appear to be electron shuttling chemicals and chelating agents that facilitate the reductive dissolution of even crystalline Fe(III) oxides. Without the presence of electron shuttling chemicals, only surficial Fe in direct contact with the bacteria was bioavailable, as illustrated when acetate was used. Regardless of carbon donor type and concentration, As concentrations in the water exceeded drinking water standards. The As dissolution appears to have been the result of the direct use of As as an electron acceptor by dissimilatory arsenic reducing bacteria. Our findings indicate that selection of the carbon and energy donor for biostimulation for remediation of chlorinated solvent impacted aquifers may greatly influence the extent of the reductive dissolution of iron minerals in direct competition with dechlorination processes. Biostimulation may also result in a significant release of As to the solution phase, contributing to further contamination of the aquifer.

Controlling the abuse of illicit methadone in Washington, DC.

Methadone hydrochloride has been found to be medically safe when administered in the setting of a well-organized heroin addition treatment program. The abuse of illicit methadone, outside the therapeutic setting, has aroused considerable controversy, particularly with regard to the public health hazards of primary methadone addiction, overdose, abuse, and childhood poisoning. We attempted to document the nature and extent of these negative aspects of the diversion of methadone into the illicit drug market, using data collected between 1969 and 1974 in the District of Columbia. The data illustrate the severe problems created by the widespread availability of illicit methadone, and document that, with the appropriate controls, the large-scale use of methadone in addiction treatment is feasible with minimum risk of methadone addiction and overdose in the community.

Alprazolam in panic disorder and agoraphobia: results from a multicenter trial. I. Efficacy in short-term treatment.

Following promising preliminary evidence, the benzodiazepine-derivative alprazolam was studied in a large, placebo-controlled, eight-week, flexible-dose trial in patients with agoraphobia with panic attacks and panic disorder. Of 526 patients, 481 completed three weeks of treatment; however, significantly more placebo (102/234) than alprazolam (21/247) recipients subsequently dropped out of the trial, primarily citing ineffectiveness (of placebo) as the reason. Alprazolam was found to be effective and well tolerated. There were significant alprazolam-placebo differences in improvement for (1) spontaneous and situational panic attacks, (2) phobic fears, (3) avoidance behavior, (4) anxiety, and (5) secondary disability, all significant by the end of week 1. At the primary comparison point (week 4), 82% of the patients receiving alprazolam were rated moderately improved or better vs 43% of the placebo group. At that point, 50% of the alprazolam recipients vs 28% of placebo recipients were free of panic attacks.

Secondary depression in panic disorder and agoraphobia. I. Frequency, severity, and response to treatment.

Depressive symptomatology in 481 subjects with panic disorder and phobic avoidance was studied as part of an investigation of the efficacy of alprazolam in panic disorder. Subjects who had a major depressive episode (MDE) before the onset of their panic disorder were not included in the trial. With this exclusion criterion, 31% of subjects had a secondary MDE occurring after the onset of the panic disorder. The occurrence of secondary MDE was related to the length of time subjects were ill with panic disorder. Compared with the subjects without depression, those subjects with current MDE had higher scores on measures of anxiety and depression but not on the number of panic attacks per week. The presence of depression and the degree of phobic avoidance contributed independently to measures of the severity of the panic illness. Alprazolam was effective in reducing panic and depressive symptomatology in both depressed and nondepressed subjects with panic disorder. The presence of an MDE was not predictive of the outcome of treatment for the panic and phobic symptoms. Subjects with or without depression responded similarly to alprazolam.

Alprazolam in panic disorder and agoraphobia: results from a multicenter trial. II. Patient acceptance, side effects, and safety.

In a multicenter placebo-controlled study, the safety, side effects, and patient acceptance of alprazolam for the treatment of panic disorder and agoraphobia were examined. A total of 525 patients meeting DSM-III criteria for agoraphobia with panic attacks or panic disorder were randomly assigned to receive alprazolam or placebo, which they took for eight weeks. The mean daily dose at the end of the study was 5.7 mg of alprazolam or 7.5 capsules of placebo daily. Potentially serious reactions to alprazolam occurred in ten of 263 subjects who received the drug. These included acute intoxication (three), hepatitis (two), mania (two), amnesia (one), aggressive behavior (one), and depression (one). Treatment-related side effects that were worse in patients taking alprazolam than in those taking placebo included sedation, fatigue, ataxia, slurred speech, and amnesia. Sedation was the most frequent but tended to subside with dose reduction or continued administration of the drug. Patient acceptance of alprazolam, as measured by the rate of completion for study participants, was high. Eighty-four percent of patients receiving active drug completed the study compared with 50% receiving placebo.

Subcortical abnormalities detected in bipolar affective disorder using magnetic resonance imaging. Clinical and neuropsychological significance.

Magnetic resonance imaging was utilized to determine the nature and rate of subcortical abnormalities in bipolar affective disorder. Nine of 19 bipolar patients and no controls demonstrated subcortical signal hyperintensities on blind evaluation of the images. There was no apparent change in the appearance of the hyperintensities in 7 of 7 subjects with abnormal magnetic resonance images who underwent repeated imaging at 1 year. Bipolar patients with abnormalities had a history of more hospitalizations and appeared more impaired on tests of fluency and recall when compared with bipolar patients without abnormalities or with controls. The possible etiology and significance of signal hyperintensities in bipolar affective disorder is discussed.

The cholinergic rapid eye movement induction test with arecoline in depression.

The cholinergic rapid eye movement (REM) induction test using arecoline hydrobromide, a cholinergic muscarinic receptor agonist, was studied in patients with affective disorder and in normal controls to determine whether or not depression is associated with enhanced induction of REM sleep by muscarinic agonists. Arecoline induced REM sleep in a dose-dependent fashion in both patients and controls compared with placebo infusions. Compared with normal controls, patients entered REM sleep significantly more rapidly following intravenous administration of 1.0 mg of arecoline hydrobromide than they did following administration of 0.5 mg of arecoline hydrobromide or placebo. These results, as well as those of previous studies, support the hypothesis that patients with affective disorder show a functional supersensitive induction of REM sleep in response to muscarinic receptor agonists and may be consistent with the hypothesis that functional muscarinic receptor "up regulation" is associated with depression.

Magnetic resonance imaging and mood disorders. Localization of white matter and other subcortical abnormalities.

BACKGROUND: Recent reports in the literature document an association between focal white matter abnormalities in bipolar as well as unipolar mood disorder. The importance of this finding and other associated anatomic differences is uncertain. METHODS: We examined the volume of abnormal white matter and other brain volumes using quantitative magnetic resonance imaging analysis. We explored the relationship of these variables with diagnosis, cognitive function, and clinical variables in 36 patients with bipolar disorder, 30 patients with unipolar disorder, and 26 control subjects who were free from significant medical and neurologic illness. RESULTS: Younger patients with bipolar disorder (but not similarly aged patients with unipolar disorder or controls) have an increased volume of abnormal white matter. Data also indicate that the total volume of abnormal white matter may be associated with increased cognitive impairment, increased rate of psychiatric illness in the family, and onset after adolescence. CONCLUSION: Patients with bipolar disorder demonstrate a pattern of subcortical brain morphologic abnormalities and cognitive impairment.

Impairment in pure and comorbid generalized anxiety disorder and major depression at 12 months in two national surveys.

OBJECTIVE: Generalized anxiety disorder might be better conceptualized as a prodrome, residual, or severity marker of major depression or other comorbid disorders than as an independent diagnosis. The authors questioned whether generalized anxiety disorder itself is associated with role impairment or whether the impairment of patients with generalized anxiety disorder is due to depression or other comorbid disorders. METHOD: The authors assessed data from the National Comorbidity Survey and the Midlife Development in the United States Survey for generalized anxiety disorder and major depression at 12 months by using the DSM-III-R criteria with modified versions of the Composite International Diagnostic Interview. RESULTS: The prevalences of generalized anxiety disorder at 12 months were 3.1% and 3.3%, respectively, in the National Comorbidity Survey and the Midlife Development in the United States Survey; the prevalences of major depression at 12 months were 10.3% and 14.1%. The majority of respondents with generalized anxiety disorder at 12 months in the National Comorbidity Survey (58.1%) and the Midlife Development in the United States Survey (69.7%) also met the criteria for major depression at 12 months. Comparisons of respondents with one versus neither disorder showed that both disorders had statistically significant independent associations with impairment that were roughly equal in magnitude. These associations could not be explained by the other comorbid DSM-III-R disorders or by sociodemographic variables. CONCLUSIONS: These results show that a substantial amount of generalized anxiety disorder occurs independently of major depression and that the role impairment of generalized anxiety disorder is comparable to that of major depression.

Alprazolam plasma concentrations and treatment response in panic disorder and agoraphobia.

OBJECTIVE: The authors' goal was to evaluate the relationship between plasma concentrations of alprazolam and both treatment response and side effects in patients with panic disorder and agoraphobia. METHOD: Ninety-six patients with panic disorder and agoraphobia were treated at three sites in a 6-week, fixed-dose, double-blind, placebo-controlled, dose-response study of 2 mg/day or 6 mg/day of alprazolam. Assessments were made of panic attacks, avoidance behavior, generalized anxiety, and global response. Blood samples were collected throughout the study and analyzed for alprazolam and other benzodiazepines. RESULTS: Patient compliance with the protocol was judged to be good on the basis of plasma concentrations. According to logistic regression analysis, the relationships between plasma alprazolam concentration and response, as reflected by number of panic attacks reported, phobia ratings, physicians' and patients' ratings of global improvement, and the emergence of side effects, were significant. However, there was no significant relationship between plasma alprazolam concentration and the degree of generalized anxiety symptoms. CONCLUSIONS: The authors conclude that plasma concentration of alprazolam is related to treatment response, particularly in panic attacks. The alprazolam concentration associated with treatment response or with emergence of a given side effect varied widely among individuals, highlighting the necessity for individualized dose adjustment to obtain optimal treatment response while minimizing side effects.

"CORT-EX:" a program for quantitative analysis of brain SPECT data.

A program was developed to extract from brain SPECT data global as well as regional concentrations of a radiopharmaceutical while allowing for improved subjective evaluation of its distribution. This program was used to process the data obtained from 17 normal subjects, 20 min, 2 hr, and 4 hr after the injection of iodine-labeled iodoamphetamines. The mean absolute cortical uptake at these three time periods was 0.921 (+/- 0.185), 0.803 (+/- 0.107), and 0.748 (+/- 0.103) in arbitrary units (+/- s.d.), respectively. The regional distribution of the tracer became more uniform with time due to an uneven washout rate. The cerebellum was noted to have a very high variability in its uptake and a high washout rate, making it unsuitable as an internal standard for relative quantification. Finally, a repeat study was performed on 10 subjects. No significant difference could be demonstrated in the mean uptake of the group at 2 and 4 hr, however the difference observed in the 20 min uptake values was significant at the p = 0.05 level.