Expanding the set of rhodococcal Baeyer–Villiger monooxygenases by high-throughput cloning, expression and substrate screening

To expand the available set of Baeyer–Villiger monooxygenases (BVMOs), we have created expression constructs for producing 22 Type I BVMOs that are present in the genome of Rhodococcus jostii RHA1. Each BVMO has been probed with a large panel of potential substrates. Except for testing their substrate acceptance, also the enantioselectivity of some selected BVMOs was studied. The results provide insight into the biocatalytic potential of this collection of BVMOs and expand the biocatalytic repertoire known for BVMOs. This study also sheds light on the catalytic capacity of this large set of BVMOs that is present in this specific actinomycete. Furthermore, a comparative sequence analysis revealed a new BVMO-typifying sequence motif. This motif represents a useful tool for effective future genome mining efforts.

Distinct routes of lineage development reshape the human blood hierarchy across ontogeny.

In a classical view of hematopoiesis, the various blood cell lineages arise via a hierarchical scheme starting with multipotent stem cells that become increasingly restricted in their differentiation potential through oligopotent and then unipotent progenitors. We developed a cell-sorting scheme to resolve myeloid (My), erythroid (Er), and megakaryocytic (Mk) fates from single CD34(+) cells and then mapped the progenitor hierarchy across human development. Fetal liver contained large numbers of distinct oligopotent progenitors with intermingled My, Er, and Mk fates. However, few oligopotent progenitor intermediates were present in the adult bone marrow. Instead, only two progenitor classes predominate, multipotent and unipotent, with Er-Mk lineages emerging from multipotent cells. The developmental shift to an adult "two-tier" hierarchy challenges current dogma and provides a revised framework to understand normal and disease states of human hematopoiesis.This work was supported by Postdoctoral Fellowship Awards from Canadian Institute of Health Research (CIHR) to FN and SZ. SZ is supported by (Aplastic Anemia). FN is a recipient of a scholar’s research award from the Ontario Institute of Cancer Research (OICR), through generous support from the Ontario Ministry of Research and Innovation. Research in EL laboratory is supported by a Wellcome Trust Sir Henry Dale Fellowship and core support grant from the Wellcome Trust and MRC to the Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute. Work in the Dick laboratory is supported by grants from the CIHR, Canadian Cancer Society, Terry Fox Foundation, Genome Canada through the Ontario Genomics Institute, OICR with funds from the province of Ontario, a Canada Research Chair and the Ontario Ministry of Health and Long Term Care (OMOHLTC).This is the author accepted manuscript. The final version is available from AAAS via http://dx.doi.org/10.1126/science.aab211

PubChem3D: Similar conformers

<p>Abstract</p> <p>Background</p> <p>PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.</p> <p>Results</p> <p>The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST) of 0.8 or greater and a color Tanimoto (CT) of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds") for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs), despite limited PubChem 2-D similarity.</p> <p>In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average count of conformer neighbors per conformer increases rather slowly as a function of diverse conformers considered, with only a 70% increase for a ten times growth in conformers per compound (a 68-fold increase in the conformer pairs considered).</p> <p>Neighboring 3-D conformers on the scale performed, if implemented naively, is an intractable problem using a modest sized compute cluster. Methodology developed in this work relies on a series of filters to prevent performing 3-D superposition optimization, when it can be determined that two conformers cannot possibly be a neighbor. Most filters are based on Tanimoto equation volume constraints, avoiding incompatible conformers; however, others consider preliminary superposition between conformers using reference shapes.</p> <p>Conclusion</p> <p>The "Similar Conformers" 3-D neighboring relationship locates similar small molecules of biological interest that may go unnoticed when using traditional 2-D chemical structure graph-based methods, making it complementary to such methodologies. The computational cost of 3-D similarity methodology on a wide scale, such as PubChem contents, is a considerable issue to overcome. Using a series of efficient filters, an effective throughput rate of more than 150,000 conformers per second per processor core was achieved, more than two orders of magnitude faster than without filtering.</p

Night-time measurements of HO<inf>x</inf> during the RONOCO project and analysis of the sources of HO<inf>2</inf>

Abstract. Measurements of the radical species OH and HO2 were made using the fluorescence assay by gas expansion (FAGE) technique during a series of night-time and daytime flights over the UK in summer 2010 and winter 2011. OH was not detected above the instrument's 1σ limit of detection during any of the night-time flights or during the winter daytime flights, placing upper limits on [OH] of 1.8 × 106 molecule cm−3 and 6.4 × 105 molecule cm−3 for the summer and winter flights, respectively. HO2 reached a maximum concentration of 3.2 × 108 molecule cm−3 (13.6 pptv) during a night-time flight on 20 July 2010, when the highest concentrations of NO3 and O3 were also recorded. An analysis of the rates of reaction of OH, O3, and the NO3 radical with measured alkenes indicates that the summer night-time troposphere can be as important for the processing of volatile organic compounds (VOCs) as the winter daytime troposphere. An analysis of the instantaneous rate of production of HO2 from the reactions of O3 and NO3 with alkenes has shown that, on average, reactions of NO3 dominated the night-time production of HO2 during summer and reactions of O3 dominated the night-time HO2 production during winter. This work was funded by the UK Natural Environment Research Council (NE/F004664/1). The authors would like to thank ground staff, engineers, scientists, and pilots involved in RONOCO for making this project a success. Airborne data were obtained using the BAe 146-301 Atmospheric Research Aircraft (ARA) flown by Directflight Ltd. and managed by the Facility for Airborne Atmospheric Measurements (FAAM), which is a joint entity of the Natural Environment Research Council (NERC) and the Met Office.This is the final version of the article. It first appeared from Copernicus Publications via http://dx.doi.org/10.5194/acp-15-8179-201

Night-time measurements of HOx during the RONOCO project and analysis of the sources of HO2

Measurements of the radical species OH and HO2 were made using the fluorescence assay by gas expansion (FAGE) technique during a series of night-time and daytime flights over the UK in summer 2010 and winter 2011. OH was not detected above the instrument's 1σ limit of detection during any of the night-time flights or during the winter daytime flights, placing upper limits on [OH] of 1.8 × 106 molecule cm−3 and 6.4 × 105 molecule cm−3 for the summer and winter flights, respectively. HO2 reached a maximum concentration of 3.2 × 108 molecule cm−3 (13.6 pptv) during a night-time flight on 20 July 2010, when the highest concentrations of NO3 and O3 were also recorded. An analysis of the rates of reaction of OH, O3, and the NO3 radical with measured alkenes indicates that the summer night-time troposphere can be as important for the processing of volatile organic compounds (VOCs) as the winter daytime troposphere. An analysis of the instantaneous rate of production of HO2 from the reactions of O3 and NO3 with alkenes has shown that, on average, reactions of NO3 dominated the night-time production of HO2 during summer and reactions of O3 dominated the night-time HO2 production during winter

Bioassay studies support the potential for latrogenic transmission of variant Creutzfeldt Jakob disease through dental procedures

Background: Evidence is required to quantify the potential risks of transmission of variant Creutzfeldt Jakob (vCJD) through dental procedures. Studies, using animal models relevant to vCJD, were performed to address two questions. Firstly, whether oral tissues could become infectious following dietary exposure to BSE? Secondly, would a vCJD-contaminated dental instrument be able to transmit disease to another patient? Methods: BSE-301V was used as a clinically relevant model for vCJD. VM-mice were challenged by injection of infected brain homogenate into the small intestine (Q1) or by five minute contact between a deliberately-contaminated dental file and the gingival margin (Q2). Ten tissues were collected from groups of challenged mice at three or four weekly intervals, respectively. Each tissue was pooled, homogenised and bioassayed in indicator mice. Findings: Challenge via the small intestine gave a transmission rate of 100% (mean incubation 157±17 days). Infectivity was found in both dental pulp and the gingival margin within 3 weeks of challenge and was observed in all tissues tested within the oral cavity before the appearance of clinical symptoms. Following exposure to deliberately contaminated dental files, 97% of mice developed clinical disease (mean incubation 234±33 days). Interpretation: Infectivity was higher than expected, in a wider range of oral tissues, than was allowed for in previous risk assessments. Disease was transmitted following transient exposure of the gingiva to a contaminated dental file. These observations provide evidence that dental procedures could be a route of cross-infection for vCJD and support the enforcement of single-use for certain dental instruments

Learners' decisions for attending Pediatric Grand Rounds: a qualitative and quantitative study

BACKGROUND: Although grand rounds plays a major educational role at academic medical centers, there has been little investigation into the factors influencing the learners' decision to attend. Greater awareness of attendees' expectations may allow grand rounds planners to better accommodate the learners' perspective, potentially making continuing education activities more attractive and inviting. METHODS: We used both qualitative (part A) and quantitative (part B) techniques to investigate the motivators and barriers to grand rounds attendance. Part A investigated contextual factors influencing attendance as expressed through attendee interviews. Transcripts of the interviews were analyzed using grounded theory techniques. We created a concept map linking key factors and their relationships. In part B we quantified the motivators and barriers identified during the initial interviews through a survey of the grand rounds audience. RESULTS: Sixteen persons voluntarily took part in the qualitative study (part A) by participating in one of seven group interview sessions. Of the 14 themes that emerged from these sessions, the most frequent factors motivating attendance involved competent practice and the need to know. All sessions discussed intellectual stimulation, social interaction, time constraints and convenience, licensure, content and format, and absence of cost for attending sessions. The 59 respondents to the survey (part B) identified clinically-useful topics (85%), continuing education credit (46%), cutting-edge research (27%), networking (22%), and refreshments (8%) as motivators and non-relevant topics (44%) and too busy to attend (56%) as barriers. CONCLUSION: Greater understanding of the consumers' perspective can allow planners to tailor the style, content, and logistics to make grand rounds more attractive and inviting

Valuing biodiversity and ecosystem services: a useful way to manage and conserve marine resources?

Valuation of biodiversity and ecosystem services (ES) is widely recognized as a useful, though often controversial, approach to conservation and management. However, its use in the marine environment, hence evidence of its efficacy, lags behind that in terrestrial ecosystems. This largely reflects key challenges to marine conservation and management such as the practical difficulties in studying the ocean, complex governance issues and the historically-rooted separation of biodiversity conservation and resource management. Given these challenges together with the accelerating loss of marine biodiversity (and threats to the ES that this biodiversity supports), we ask whether valuation efforts for marine ecosystems are appropriate and effective. We compare three contrasting systems: the tropical Pacific, Southern Ocean and UK coastal seas. In doing so, we reveal a diversity in valuation approaches with different rates of progress and success. We also find a tendency to focus on specific ES (often the harvested species) rather than biodiversity. In light of our findings, we present a new conceptual view of valuation that should ideally be considered in decision-making. Accounting for the critical relationships between biodiversity and ES, together with an understanding of ecosystem structure and functioning, will enable the wider implications of marine conservation and management decisions to be evaluated. We recommend embedding valuation within existing management structures, rather than treating it as an alternative or additional mechanism. However, we caution that its uptake and efficacy will be compromised without the ability to develop and share best practice across regions

Evaluation of the activity of CYP2C19 in Gujrati and Marwadi subjects living in Mumbai (Bombay)

BACKGROUND: Inherited differences in the metabolism and disposition of drugs, and genetic polymorphisms in the targets of drug therapy (e.g., receptors), can greatly influence efficacy and toxicity of medications. Marked interethnic differences in CYP2C19 (a member of the cytochrome P-450 enzyme superfamily catalyzing phase I drug metabolism) which affects the metabolism of a number of clinically important drugs have been documented. The present study evaluated the activity of CYP2C19 in normal, healthy Gujrati and Marwadi subjects by phenotyping (a western Indian population). METHODS: All subjects received 20 mg of omeprazole, which was followed by blood collection at 3 hrs to estimate the metabolic ratio of omeprazole to 5-hydroxyomeprazole. The analysis was done by HPLC. RESULTS: It was seen that 10.36% of this population were poor metabolizers(PM) whereas 89.63% were extensive metabolizers(EM). CONCLUSION: A genotyping evaluation would better help in identifying population specific genotypes and thus help individualize drug therapy