Proceed With Caution Shaw, George B.; Shaw, Alan T.; Holdeman, Timothy G. ...
Water environment & technology,
01/1993, Volume:
5, Issue:
11
Magazine Article
During construction of a major trunk sewer in Greene County, Ohio, an aquifer contaminated with volatile organic compounds (VOC) was discovered in the area where the sewer was to be laid, and it was ...feared that the construction work could result in contaminated groundwater reaching surface waters and wells. Studies were carried out to estimate the highest VOC concentrations along the path of the sewer and to determine the requirements for treatment of groundwater removed during dewatering. Models of groundwater flow were used to evaluate alternative configurations for the dewatering wells and assess the possible effects of dewatering on the contaminant plume. The special requirements needed for construction of the sewer to prevent spread of the pollution are outlined.
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α-Helical transmembrane proteins termed membrane transporters mediate the passage of small hydrophilic substrate molecules across biological lipid bilayer membranes. Annotating the specific ...substrates of the dozens to hundreds of individual transporters of an organism is an important task. In the past, machine learning classifiers have been successfully trained on pan-organism data sets to predict putative substrates of transporters. Here, we critically examine the selection of an optimal data set of protein sequence features for the classification task. We focus on membrane transporters of the three model organisms Escherichia coli, Arabidopsis thaliana, and Saccharomyces cerevisiae, as well as human. We show that organism-specific classifiers can be robustly trained if at least 20 samples are available for each substrate class. If information from position-specific scoring matrices is included, such classifiers have F1 scores between 0.85 and 1.00. For the largest data set (A. thaliana), a 4-class classifier yielded an F-score of 0.97. On a pan-organism data set composed of transporters of all four organisms, amino acid and sugar transporters were predicted with an F1 score of 0.91.
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IJS, KILJ, NUK, PNG, UL, UM
Responses of the microbiota to diet are highly personalized but mechanistically not well understood because many metabolic capabilities and interactions of human gut microorganisms are unknown. Here ...we show that sulfoquinovose (SQ), a sulfonated monosaccharide omnipresent in green vegetables, is a selective yet relevant substrate for few but ubiquitous bacteria in the human gut. In human feces and in defined co-culture, Eubacterium rectale and Bilophila wadsworthia used recently identified pathways to cooperatively catabolize SQ with 2,3-dihydroxypropane-1-sulfonate as a transient intermediate to hydrogen sulfide (H
S), a key intestinal metabolite with disparate effects on host health. SQ-degradation capability is encoded in almost half of E. rectale genomes but otherwise sparsely distributed among microbial species in the human intestine. However, re-analysis of fecal metatranscriptome datasets of four human cohorts showed that SQ degradation (mostly from E. rectale and Faecalibacterium prausnitzii) and H
S production (mostly from B. wadsworthia) pathways were expressed abundantly across various health states, demonstrating that these microbial functions are core attributes of the human gut. The discovery of green-diet-derived SQ as an exclusive microbial nutrient and an additional source of H
S in the human gut highlights the role of individual dietary compounds and organosulfur metabolism on microbial activity and has implications for precision editing of the gut microbiota by dietary and prebiotic interventions.
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Hydrogen sulfide (H₂S) production in the intestinal microbiota has many contributions to human health and disease. An important source of H₂S in the human gut is anaerobic respiration of sulfite ...released from the abundant dietary and host-derived organic sulfonate substrate in the gut, taurine (2-aminoethanesulfonate). However, the enzymes that allow intestinal bacteria to access sulfite from taurine have not yet been identified. Here we decipher the complete taurine desulfonation pathway in Bilophila wadsworthia 3.1.6 using differential proteomics, in vitro reconstruction with heterologously produced enzymes, and identification of critical intermediates. An initial deamination of taurine to sulfoacetaldehyde by a known taurine: pyruvate aminotransferase is followed, unexpectedly, by reduction of sulfoacetaldehyde to isethionate (2-hydroxyethanesulfonate) by an NADH-dependent reductase. Isethionate is then cleaved to sulfite and acetaldehyde by a previously uncharacterized glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslA). The acetaldehyde produced is oxidized to acetyl-CoA by a dehydrogenase, and the sulfite is reduced to H₂S by dissimilatory sulfite reductase. This unique GRE is also found in Desulfovibrio desulfuricans DSM642 and Desulfovibrio alaskensis G20, which use isethionate but not taurine; corresponding knockout mutants of D. alaskensis G20 did not grow with isethionate as the terminal electron acceptor. In conclusion, the novel radical-based C-S bond-cleavage reaction catalyzed by IslA diversifies the known repertoire of GRE superfamily enzymes and enables the energy metabolism of B. wadsworthia. This GRE is widely distributed in gut bacterial genomes and may represent a novel target for control of intestinal H₂S production.
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Sulfoquinovose (SQ, 6-deoxy-6-sulfoglucose) is produced by plants and other phototrophs and its biodegradation is a relevant component of the biogeochemical carbon and sulfur cycles. SQ is known to ...be degraded by aerobic bacterial consortia in two tiers via C
3
-organosulfonates as transient intermediates to CO
2
, water and sulfate. In this study, we present a first laboratory model for anaerobic degradation of SQ by bacterial consortia in two tiers to acetate and hydrogen sulfide (H
2
S). For the first tier, SQ-degrading
Escherichia coli
K-12 was used. It catalyzes the fermentation of SQ to 2,3-dihydroxypropane-1-sulfonate (DHPS), succinate, acetate and formate, thus, a novel type of mixed-acid fermentation. It employs the characterized SQ Embden-Meyerhof-Parnas pathway, as confirmed by mutational and proteomic analyses. For the second tier, a DHPS-degrading
Desulfovibrio
sp. isolate from anaerobic sewage sludge was used, strain DF1. It catalyzes another novel fermentation, of the DHPS to acetate and H
2
S. Its DHPS desulfonation pathway was identified by differential proteomics and demonstrated by heterologously produced enzymes: DHPS is oxidized via 3-sulfolactaldehyde to 3-sulfolactate (SL) by two NAD
+
-dependent dehydrogenases (DhpA, SlaB); the SL is cleaved by an SL sulfite-lyase known from aerobic bacteria (SuyAB) to pyruvate and sulfite. The pyruvate is oxidized to acetate, while the sulfite is used as electron acceptor in respiration and reduced to H
2
S. In conclusion, anaerobic sulfidogenic SQ degradation was demonstrated as a novel link in the biogeochemical sulfur cycle. SQ is also a constituent of the green-vegetable diet of herbivores and omnivores and H
2
S production in the intestinal microbiome has many recognized and potential contributions to human health and disease. Hence, it is important to examine bacterial SQ degradation also in the human intestinal microbiome, in relation to H
2
S production, dietary conditions and human health.
Valproate (VPA) and trichostatin A (TSA), inhibitors of zinc-dependent deacetylase activity, induce reduction in the levels of mRNA encoding oestrogen receptor-alpha (ERalpha), resulting in ...subsequent clearance of ERalpha protein from breast and ovarian cell lines. Inhibition of oestrogen signalling may account for the endocrine disorders, menstrual abnormalities, osteoporosis and weight gain that occur in a proportion of women treated with VPA for epilepsy or for bipolar mood disorder. Transcriptome profiling revealed that VPA and TSA also modulate the expression of, among others, key regulatory components of the cell cycle. Meta-analysis of genes directly responsive to oestrogen indicates that VPA and TSA have a generally antioestrogenic profile in ERalpha positive cells. Concomitant treatment with cycloheximide prevented most of these changes in gene expression, including downregulation of ERalpha mRNA, indicating that a limited number of genes signal a hyperacetylated state within cells. Three members of the NAD-dependent deacetylases, the sirtuins, are upregulated by VPA and by TSA and sirtuin activity contributes to loss of ERalpha expression. However, prolonged inhibition of the sirtuins by sirtinol also induces loss of ERalpha from cells. Mechanistically, we show that VPA invokes reversible promoter shutoff of the ERalpha, pS2 and cyclin D1 promoters, by inducing recruitment of methyl cytosine binding protein 2 (MeCP2) with concomitant exclusion of the maintenance methylase DNMT1. Furthermore, we demonstrate that, in the presence of VPA, local DNA methylation, deacetylation and demethylation of activated histones and recruitment of inhibitory complexes occurs on the pS2 promoter.
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DOBA, EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, IZUM, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UILJ, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Clinical care guidelines are typically developed by clinicians and researchers. Including patient and caregiver voices in guideline development may help create guidelines that are more useful for ...patients and consequently improve their guideline adherence. Although there is substantial research on the factors the affect providers' adherence to guidelines, there is less research on the factors that affect patients' compliance with guideline recommendations, especially among those with rare disorders. The purpose of this study is to explore factors that are likely to affect patient/caregiver adherence to endocrine and bone health recommendations for Duchenne Muscular Dystrophy (DMD). To do so, we used qualitative data collected as part of the study designed to develop, implement, and evaluate a new online, modified-Delphi approach to engaging patients with rare diseases and their caregivers in guideline development, using care guidelines for DMD as a case study.
We thematically analyzed qualitative data collected from 95 adults with DMD and their caregivers who participated in at least one round of our online Modified-Delphi panel process. Participants rated and commented on the patient-centeredness of 19 recommendations about vertical growth, weight management, bone health, and delayed puberty included in the 2018 DMD care considerations. Patient-centeredness was operationalized as the importance and acceptability of care recommendations.
Thematic analyses revealed six factors that affect guideline adherence from the patient/caregiver perspective: content and format of recommendations, patient and provider characteristics, and social and financial factors.
This study used a novel approach to exploring patient and caregiver perspectives on factors that may affect guideline adherence. The six factors identified by DMD patients and caregivers are similar to the factors affecting provider adherence and are not limited to DMD. Understanding consistency between provider- and patient/caregiver-identified barriers to following guideline recommendations can lead to developing more successful interventions for increasing guideline adherence.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Patients and caregivers are increasingly recognized as key stakeholders in developing clinical practice guidelines (CPGs). Online engagement approaches offer the promise of a rigorous, scalable, and ...convenient engagement method. This paper illustrates how an online modified-Delphi approach could be used to engage patients, caregivers, and other stakeholder in CPG development. It provides practical guidance for conducting online modified-Delphi panels that covers (1) joint development of the engagement approach with relevant stakeholders, (2) adaptation of methods used by experts in guideline development, (3) pilot testing, (4) participant recruitment, (5) determining panel size and composition, (6) building participant capacity, (7) facilitation of two-way interaction, (8) continuous engagement and retention of participants, (9) rigorous data analysis, (10) evaluation of engagement activities, and (11) result dissemination. The paper is based on a recently completed study about engaging individuals with Duchenne muscular dystrophy (DMD) and their caregivers in determining the patient-centeredness of DMD care guidelines.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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