Genome analysis and physiological comparison of Alicycliphilus denitrificans strains BC and K601T

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601T. Genes involved in cyclohexanol degradation were only found in strain K601T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.This research was supported by the Technology Foundation, the Applied Science Division (STW) of the Netherlands Organization for Scientific Research (NWO), project number 08053, the graduate school WIMEK (Wageningen Institute for Environment and Climate Research, which is part of SENSE Research School for Socio-Economic and Natural Sciences of the Environment, www.wimek-new.wur.nl and www.sense.nl), SKB (Dutch Centre for Soil Quality Management and Knowledge Transfer, www.skbodem.nl) and the Consolider project CSD-2007-00055. The research was incorporated in the TRIAS (TRIpartite Approaches 469 toward Soil systems processes) program (http://www.nwo.nl/en/research-and-results/programmes/alw/trias-tripartite-approach-to-soil-system-processes/index. html). Flávia Talarico Saia was supported by a FAPESP (the State of São Paulo Research Foundation) scholarship (2006-01997/5). The work conducted by the DOE JGI is supported by the Office of Science of the United States Department of Energy under contract number DE-AC02-05CH11231. Alfons Stams acknowledges support by an ERC (European Research Counsil) advanced grant (project 323009). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Ameliorating effects of Ascorbic acid and Ammi Visnaga seeds on cigarette and water- pipe smoking Cytotoxicity in the lung and heart ventricle

Abstract A current study investigated the effects of smoking (Cigarettes and Water-pipes) on the lung and cardiac ventricles by comparing the cytotoxic effects of smoking with certain natural antioxidants. 56 male albino rats were randomly assigned to 7 groups (N = 8 per group). Group 1 was a negative control that was exposed to fresh air; Group 2 was a positive group exposed to the most popular cigarette brands in the Jordanian market (red LM cigarettes) for 30 consecutive days, one cigarette per rat. Groups 3 and 4 were exposed to a cigarette smoking treatment with one of the natural antioxidants (vitamin C, Ammi Visnagia seed extract, respectively). Rats in group 5 were exposed to flavored water-pipe smoke resulting from the complete burning of 20 g from one coastal for 30 days, one session a day, and groups 6–7 were exposed to cigarette smoking with treatment with one of the selected natural antioxidants (Ascorbic acid vitamin C, Ammi Visnagia seed extract). According to immunohistochemistry investigations, smoking exposure has been linked to negative tissue consequences. Both types of smoking models induced the expression of the p53 protein in heart and lung tissues. However, p53 was mildly expressed in the heart and considerably in the lung. In conclusion, investigations were conducted on the impact of smoking on different levels, such as histological changes in the trachea, lung, and heart ventricle, as well as its influence on the expression of the p53 protein. The administration of Ammi Visnaga seed extract and Ascorbic acid exhibited protective effects against the detrimental effects of smoking through all the aforementioned methods

A multinational study of treatment failures in asthma management

EmSetting: Emergency rooms. Objective: To assess quality of care and its determinants for asthma patients before emergency room treatment. Design: Consecutive patients with acute severe asthma attending emergency rooms were questioned about the severity of their disease and treatment in the previous 4 weeks. Prescriptions of inhaled corticosteroids were recorded. Other outcomes included self-reported adherence to treatment and loss of work. Results: Thirteen centres in 11 countries recruited 1156 patients. Only 36% of patients with persistent asthma had been prescribed an adequate dose of inhaled corticosteroids. This percentage improved in those receiving regular care from the same doctor (OR 2.86, 95%CI 1.38-5.96), and was at least as good for the 10% of patients receiving 'private' health care (OR 3.08, 95%CI 1.69-5.62). Forty-four per cent of patients had health insurance covering some asthma medications. These patients were more likely to be receiving adequate inhaled corticosteroids (OR 1.74, 95%CI 1.17-2.58), and reported better adherence than those without insurance (OR 3.00, 95%CI 1.64-5.50). Of those on adequate inhaled corticosteroids, 18% had lost work in each of the 4 previous weeks compared with 59% among those more than one treatment step below the recommended dose.ergency rooms. Conclusions: Access to adequate treatment is critical for better management of asthma

A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways

All sequence data from this study were deposited at the European Bioinformatics Institute under the accession numbers ERS1670018 to ERS1670023. Further, all assigned genes, taxonomy, function, sequences of contigs, genes and proteins can be found in Table S3.In this study, we report transcription of genes involved in aerobic and anaerobic benzene degradation pathways in a benzene-degrading denitrifying continuous culture. Transcripts associated with the family Peptococcaceae dominated all samples (2136% relative abundance) indicating their key role in the community. We found a highly transcribed gene cluster encoding a presumed anaerobic benzene carboxylase (AbcA and AbcD) and a benzoate-coenzyme A ligase (BzlA). Predicted gene products showed >96% amino acid identity and similar gene order to the corresponding benzene degradation gene cluster described previously, providing further evidence for anaerobic benzene activation via carboxylation. For subsequent benzoyl-CoA dearomatization, bam-like genes analogous to the ones found in other strict anaerobes were transcribed, whereas gene transcripts involved in downstream benzoyl-CoA degradation were mostly analogous to the ones described in facultative anaerobes. The concurrent transcription of genes encoding enzymes involved in oxygenase-mediated aerobic benzene degradation suggested oxygen presence in the culture, possibly formed via a recently identified nitric oxide dismutase (Nod). Although we were unable to detect transcription of Nod-encoding genes, addition of nitrite and formate to the continuous culture showed indication for oxygen production. Such an oxygen production would enable aerobic microbes to thrive in oxygen-depleted and nitrate-containing subsurface environments contaminated with hydrocarbons.This study was supported by a grant of BE-Basic-FES funds from the Dutch Ministry of Economic Affairs. The research of A.J.M. Stams is supported by an ERC grant (project 323009) and the gravitation grant “Microbes for Health and Environment” (project 024.002.002) of the Netherlands Ministry of Education, Culture and Science. F. Hugenholtz was supported by the same gravitation grant (project 024.002.002). B. Hornung is supported by Wageningen University and the Wageningen Institute for Environment and Climate Research (WIMEK) through the IP/OP program Systems Biology (project KB-17-003.02-023).info:eu-repo/semantics/publishedVersio

Effects of pre-operative isolation on postoperative pulmonary complications after elective surgery: an international prospective cohort study

We aimed to determine the impact of pre-operative isolation on postoperative pulmonary complications after elective surgery during the global SARS-CoV-2 pandemic. We performed an international prospective cohort study including patients undergoing elective surgery in October 2020. Isolation was defined as the period before surgery during which patients did not leave their house or receive visitors from outside their household. The primary outcome was postoperative pulmonary complications, adjusted in multivariable models for measured confounders. Pre-defined sub-group analyses were performed for the primary outcome. A total of 96,454 patients from 114 countries were included and overall, 26,948 (27.9%) patients isolated before surgery. Postoperative pulmonary complications were recorded in 1947 (2.0%) patients of which 227 (11.7%) were associated with SARS-CoV-2 infection. Patients who isolated pre-operatively were older, had more respiratory comorbidities and were more commonly from areas of high SARS-CoV-2 incidence and high-income countries. Although the overall rates of postoperative pulmonary complications were similar in those that isolated and those that did not (2.1% vs 2.0%, respectively), isolation was associated with higher rates of postoperative pulmonary complications after adjustment (adjusted OR 1.20, 95%CI 1.05-1.36, p = 0.005). Sensitivity analyses revealed no further differences when patients were categorised by: pre-operative testing; use of COVID-19-free pathways; or community SARS-CoV-2 prevalence. The rate of postoperative pulmonary complications increased with periods of isolation longer than 3 days, with an OR (95%CI) at 4-7 days or ≥ 8 days of 1.25 (1.04-1.48), p = 0.015 and 1.31 (1.11-1.55), p = 0.001, respectively. Isolation before elective surgery might be associated with a small but clinically important increased risk of postoperative pulmonary complications. Longer periods of isolation showed no reduction in the risk of postoperative pulmonary complications. These findings have significant implications for global provision of elective surgical care

Technology as a disruptive agent: Intergenerational perspectives

YesThis study explores how British South Asian parents perceive their children’s technology consumption through their collectivist lenses and interdependent values. The findings for this qualitative study indicate that second and third generation South Asian parents acknowledge the benefits of children’s technology use; but largely perceive technology as a disruptive agent, whereby children are becoming isolated and increasingly independent within the household. The analysis aims to understand how parents view their children’s relationship with others as a result of technology consumption. Accordingly, this paper proposes an extension of the Construal of self conceptualisation and contributes a Techno-construal matrix that establishes a dyadic connection between technology consumption and cultural values. Overall, the study reveals that children display less inter-reliance and conformance typically associated with collectivist cultures, resulting from their technology use. Consequently, parents interpret their children’s shift from interdependence to more independence as a disruptive and unsettling phenomenon within the household

Identification of enzymes involved in anaerobic benzene degradation by a strictly anaerobic iron-reducing enrichment culture.

Summary Anaerobic benzene degradation was studied with a highly enriched iron-reducing culture (BF) composed of mainly Peptococcaceae-related Gram-positive microorganisms. The proteomes of benzene-, phenol- and benzoate-grown cells of culture BF were compared by SDS-PAGE. A specific benzene-expressed protein band of 60 kDa, which could not be observed during growth on phenol or benzoate, was subjected to N-terminal sequence analysis. The first 31 amino acids revealed that the protein was encoded by ORF 138 in the shotgun sequenced metagenome of culture BF. ORF 138 showed 43% sequence identity to phenylphosphate carboxylase subunit PpcA of Aromatoleum aromaticum strain EbN1. A LC/ESI-MS/MS-based shotgun proteomic analysis revealed other specifically benzene-expressed proteins with encoding genes located adjacent to ORF 138 on the metagenome. The protein products of ORF 137, ORF 139 and ORF 140 showed sequence identities of 37% to phenylphosphate carboxylase PpcD of A. aromaticum strain EbN1, 56% to benzoate-CoA ligase (BamY) of Geobacter metallireducens and 67% to 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD/UbiX) of A. aromaticum strain EbN1 respectively. These genes are proposed as constituents of a putative benzene degradation gene cluster ( approximately 17 kb) composed of carboxylase-related genes. The identified gene sequences suggest that the initial activation reaction in anaerobic benzene degradation is probably a direct carboxylation of benzene to benzoate catalysed by putative anaerobic benzene carboxylase (Abc). The putative Abc probably consists of several subunits, two of which are encoded by ORFs 137 and 138, and belongs to a family of carboxylases including phenylphosphate carboxylase (Ppc) and 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD/UbiX)