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An integrated workflow for phenazine-modifying enzyme characterization

Coates, R Cameron ; Bowen, Benjamin P ; Oberortner, Ernst ; [et al.]

Oxford University Press (OUP) ; 2018

In: Journal of Industrial Microbiology and Biotechnology Vol. 45, No. 7 ( 2018-07-01), p. 567-577

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In: Journal of Industrial Microbiology and Biotechnology, Oxford University Press (OUP), Vol. 45, No. 7 ( 2018-07-01), p. 567-577

Abstract: Increasing availability of new genomes and putative biosynthetic gene clusters (BGCs) has extended the opportunity to access novel chemical diversity for agriculture, medicine, environmental and industrial purposes. However, functional characterization of BGCs through heterologous expression is limited because expression may require complex regulatory mechanisms, specific folding or activation. We developed an integrated workflow for BGC characterization that integrates pathway identification, modular design, DNA synthesis, assembly and characterization. This workflow was applied to characterize multiple phenazine-modifying enzymes. Phenazine pathways are useful for this workflow because all phenazines are derived from a core scaffold for modification by diverse modifying enzymes (PhzM, PhzS, PhzH, and PhzO) that produce characterized compounds. We expressed refactored synthetic modules of previously uncharacterized phenazine BGCs heterologously in Escherichia coli and were able to identify metabolic intermediates they produced, including a previously unidentified metabolite. These results demonstrate how this approach can accelerate functional characterization of BGCs.

Type of Medium: Online Resource

ISSN: 1476-5535 , 1367-5435

URL: Article

DOI: 10.1007/s10295-018-2025-5

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2018

detail.hit.zdb_id: 1482484-X

SSG: 12

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Biosynthetic origin of natural products isolated from marine microorganism–invertebrate assemblages

Simmons, T. Luke ; Coates, R. Cameron ; Clark, Benjamin R. ; [et al.]

Proceedings of the National Academy of Sciences ; 2008

In: Proceedings of the National Academy of Sciences Vol. 105, No. 12 ( 2008-03-25), p. 4587-4594

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 105, No. 12 ( 2008-03-25), p. 4587-4594

Abstract: In all probability, natural selection began as ancient marine microorganisms were required to compete for limited resources. These pressures resulted in the evolution of diverse genetically encoded small molecules with a variety of ecological and metabolic roles. Remarkably, many of these same biologically active molecules have potential utility in modern medicine and biomedical research. The most promising of these natural products often derive from organisms richly populated by associated microorganisms (e.g., marine sponges and ascidians), and often there is great uncertainty about which organism in these assemblages is making these intriguing metabolites. To use the molecular machinery responsible for the biosynthesis of potential drug-lead natural products, new tools must be applied to delineate their genetic and enzymatic origins. The aim of this perspective is to highlight both traditional and emerging techniques for the localization of metabolic pathways within complex marine environments. Examples are given from the literature as well as recent proof-of-concept experiments from the authors' laboratories.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.0709851105

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2008

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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Minimum Information about a Biosynthetic Gene cluster

Medema, Marnix H ; Kottmann, Renzo ; Yilmaz, Pelin ; [et al.]

Springer Science and Business Media LLC ; 2015

In: Nature Chemical Biology Vol. 11, No. 9 ( 2015-9), p. 625-631

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In: Nature Chemical Biology, Springer Science and Business Media LLC, Vol. 11, No. 9 ( 2015-9), p. 625-631

Type of Medium: Online Resource

ISSN: 1552-4450 , 1552-4469

URL: Article

DOI: 10.1038/nchembio.1890

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2015

detail.hit.zdb_id: 2190276-8

SSG: 12

SSG: 15,3

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Single Cell Genome Amplification Accelerates Identification of the Apratoxin Biosynthetic Pathway from a Complex Microbial Assemblage

Grindberg, Rashel V. ; Ishoey, Thomas ; Brinza, Dumitru ; [et al.]

Public Library of Science (PLoS) ; 2011

In: PLoS ONE Vol. 6, No. 4 ( 2011-4-12), p. e18565-

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In: PLoS ONE, Public Library of Science (PLoS), Vol. 6, No. 4 ( 2011-4-12), p. e18565-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0018565

DOI: 10.1371/journal.pone.0018565.g001

DOI: 10.1371/journal.pone.0018565.g002

DOI: 10.1371/journal.pone.0018565.g003

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DOI: 10.1371/journal.pone.0018565.t001

DOI: 10.1371/journal.pone.0018565.s001

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DOI: 10.1371/journal.pone.0018565.s003

DOI: 10.1371/journal.pone.0018565.s004

DOI: 10.1371/journal.pone.0018565.s005

DOI: 10.1371/journal.pone.0018565.s006

DOI: 10.1371/journal.pone.0018565.s007

DOI: 10.1371/journal.pone.0018565.s008

DOI: 10.1371/journal.pone.0018565.s009

DOI: 10.1371/journal.pone.0018565.s010

DOI: 10.1371/journal.pone.0018565.s011

DOI: 10.1371/journal.pone.0018565.s012

DOI: 10.1371/journal.pone.0018565.s013

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2011

detail.hit.zdb_id: 2267670-3

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Characterization of Cyanobacterial Hydrocarbon Composition and Distribution of Biosynthetic Pathways

Coates, R. Cameron ; Podell, Sheila ; Korobeynikov, Anton ; [et al.]

Public Library of Science (PLoS) ; 2014

In: PLoS ONE Vol. 9, No. 1 ( 2014-1-27), p. e85140-

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In: PLoS ONE, Public Library of Science (PLoS), Vol. 9, No. 1 ( 2014-1-27), p. e85140-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0085140

DOI: 10.1371/journal.pone.0085140.g001

DOI: 10.1371/journal.pone.0085140.g002

DOI: 10.1371/journal.pone.0085140.g003

DOI: 10.1371/journal.pone.0085140.g004

DOI: 10.1371/journal.pone.0085140.g005

DOI: 10.1371/journal.pone.0085140.s001

DOI: 10.1371/journal.pone.0085140.s002

DOI: 10.1371/journal.pone.0085140.s003

DOI: 10.1371/journal.pone.0085140.s004

DOI: 10.1371/journal.pone.0085140.s005

DOI: 10.1371/journal.pone.0085140.s006

DOI: 10.1371/journal.pone.0085140.s007

DOI: 10.1371/journal.pone.0085140.s008

DOI: 10.1371/journal.pone.0085140.s009

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2014

detail.hit.zdb_id: 2267670-3

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1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Mukherjee, Supratim ; Seshadri, Rekha ; Varghese, Neha J ; [et al.]

Springer Science and Business Media LLC ; 2017

In: Nature Biotechnology Vol. 35, No. 7 ( 2017-07), p. 676-683

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In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 35, No. 7 ( 2017-07), p. 676-683

Abstract: We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic diversity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic diversity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 samples, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a divergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.

Type of Medium: Online Resource

ISSN: 1087-0156 , 1546-1696

URL: Article

DOI: 10.1038/nbt.3886

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2017

detail.hit.zdb_id: 1494943-X

detail.hit.zdb_id: 1311932-1

SSG: 12

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Erratum: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life

Mukherjee, Supratim ; Seshadri, Rekha ; Varghese, Neha J ; [et al.]

Springer Science and Business Media LLC ; 2018

In: Nature Biotechnology Vol. 36, No. 4 ( 2018-4), p. 368-368

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In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 36, No. 4 ( 2018-4), p. 368-368

Type of Medium: Online Resource

ISSN: 1087-0156 , 1546-1696

URL: Article

DOI: 10.1038/nbt0418-368c

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2018

detail.hit.zdb_id: 1494943-X

detail.hit.zdb_id: 1311932-1

SSG: 12

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Giant Marine Cyanobacteria Produce Exciting Potential Pharmaceuticals

Gerwick, William H. ; Grindberg, Rashel V. ; Coates, R. Cameron ; [et al.]

American Society for Microbiology ; 2008

In: Microbe Magazine Vol. 3, No. 6 ( 2008-06-01), p. 277-284

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In: Microbe Magazine, American Society for Microbiology, Vol. 3, No. 6 ( 2008-06-01), p. 277-284

Type of Medium: Online Resource

ISSN: 1558-7452 , 1558-7460

URL: Article

DOI: 10.1128/microbe.3.277.1

Language: English

Publisher: American Society for Microbiology

Publication Date: 2008

detail.hit.zdb_id: 2232608-X

SSG: 12

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Trauma Association of Canada (TAC) Annual Scientific Meeting. The Westin Whistler Resort & Spa, Whistler, BC, Thursday, Apr. 11 to Saturday, Apr. 13, 2013Testing the reliability of tools for pediatric trauma teamwork evaluation in a North American high-resource simulation settingThe association of etomidate with mortality in trauma patientsDefinition of isolated hip fractures as an exclusion criterion in trauma centre performance evaluations: a systematic reviewEstimation of acute care hospitalization costs for trauma hospital performance evaluation: a systematic reviewHospital length of stay following admission for traumatic injury in Canada: a multicentre cohort studyPredictors of hospital length of stay following traumatic injury: a multicentre cohort studyInfluence of the heterogeneity in definitions of an isolated hip fracture used as an exclusion criterion in trauma centre performance evaluations: a multicentre cohort studyPediatric trauma, advocacy skills and medical studentsCompliance with the prescribed packed red blood cell, fresh frozen plasma and platelet ratio for the trauma transfusion pathway at a level 1 trauma centreEarly fixed-wing aircraft activation for major trauma in remote areasDevelopment of a national, multi-disciplinary trauma crisis resource management curriculum: results from the pilot courseThe management of blunt hepatic trauma in the age of angioembolization: a single centre experienceEarly predictors of in-hospital mortality in adult trauma patientsThe impact of open tibial fracture on health service utilization in the year preceding and following injuryA systematic review and meta-analysis of the efficacy of red blood cell transfusion in the trauma populationSources of support for paramedics managing work-related stress in a Canadian EMS service responding to multisystem trauma patientsAnalysis of prehospital treatment of pain in the multisystem trauma patient at a community level 2 trauma centreIncreased mortality associated with placement of central lines during trauma resuscitationChronic pain after serious injury — identifying high risk patientsEpidemiology of in-hospital trauma deaths in a Brazilian university teaching hospitalIncreased suicidality following major trauma: a population-based studyDevelopment of a population-wide record linkage system to support trauma researchInduction of hmgb1 by increased gut permeability mediates acute lung injury in a hemorrhagic shock and resuscitation mouse modelPatients who sustain gunshot pelvic fractures are at increased risk for deep abscess formation: aggravated by rectal injuryAre we transfusing more with conservative management of isolated blunt splenic injury? A retrospective studyMotorcycle clothesline injury prevention: Experimental test of a protective deviceA prospective analysis of compliance with a massive transfusion protocol - activation alone is not enoughAn evaluation of diagnostic modalities in penetrating injuries to the cardiac box: Is there a role for routine echocardiography in the setting of negative pericardial FAST?Achievement of pediatric national quality indicators — an institutional report cardProcess mapping trauma care in 2 regional health authorities in British Columbia: a tool to assist trauma sys tem design and evaluationPatient safety checklist for emergency intubation: a systematic reviewA standardized flow sheet improves pediatric trauma documentationMassive transfusion in pediatric trauma: a 5-year retrospective reviewIs more better: Does a more intensive physiotherapy program result in accelerated recovery for trauma patients?Trauma care: not just for surgeons. Initial impact of implementing a dedicated multidisciplinary trauma team on severely injured patientsThe role of postmortem autopsy in modern trauma care: Do we still need them?Prototype cervical spine traction device for reduction stabilization and transport of nondistraction type cervical spine injuriesGoing beyond organ preservation: a 12-year review of the beneficial effects of a nonoperative management algorithm for splenic traumaAssessing the construct validity of a global disability measure in adult trauma registry patientsThe mactrauma TTL assessment tool: developing a novel tool for assessing performance of trauma traineesA quality improvement approach to developing a standardized reporting format of ct findings in blunt splenic injuriesOutcomes in geriatric trauma: what really mattersFresh whole blood is not better than component therapy (FFP:RBC) in hemorrhagic shock: a thromboelastometric study in a small animal modelFactors affecting mortality of chest trauma patients: a prospective studyLong-term pain prevalence and health related quality of life outcomes for patients enrolled in a ketamine versus morphine for prehospital traumatic pain randomized controlled trialDescribing pain following trauma: predictors of persistent pain and pain prevalenceManagement strategies for hemorrhage due to pelvic trauma: a survey of Canadian general surgeonsMajor trauma follow-up clinic: Patient perception of recovery following severe traumaLost opportunities to enhance trauma practice: culture of interprofessional education and sharing among emergency staffPrehospital airway management in major trauma and traumatic brain injury by critical care paramedicsImproving patient selection for angiography and identifying risk of rebleeding after angioembolization in the nonoperative management of high grade splenic injuriesFactors predicting the need for angioembolization in solid organ injuryProthrombin complex concentrates use in traumatic brain injury patients on oral anticoagulants is effective despite underutilizationThe right treatment at the right time in the right place: early results and associations from the introduction of an all-inclusive provincial trauma care systemA multicentre study of patient experiences with acute and postacute injury carePopulation burden of major trauma: Has introduction of an organized trauma system made a difference?Long-term functional and return to work outcomes following blunt major trauma in Victoria, AustraliaSurgical dilemma in major burns victim: heterotopic ossification of the tempromandibular jointWhich radiological modality to choose in a unique penetrating neck injury: a differing opinionThe Advanced Trauma Life Support (ATLS) program in CanadaThe Rural Trauma Team Development Course (RTTDC) in Pakistan: Is there a role?Novel deployment of BC mobile medical unit for coverage of BMX world cup sporting eventIncidence and prevalence of intra-abdominal hypertension and abdominal compartment syndrome in critically ill adults: a systematic review and meta-analysisRisk factors for intra-abdominal hypertension and abdominal compartment syndrome in critically ill or injured adults: a systematic review and meta-analysisA comparison of quality improvement practices at adult and pediatric trauma centresInternational trauma centre survey to evaluate content validity, usability and feasibility of quality indicatorsLong-term functional recovery following decompressive craniectomy for severe traumatic brain injuryMorbidity and mortality associated with free falls from a height among teenage patients: a 5-year review from a level 1 trauma centreA comparison of adverse events between trauma patients and general surgery patients in a level 1 trauma centreProcoagulation, anticoagulation and fibrinolysis in severely bleeding trauma patients: a laboratorial characterization of the early trauma coagulopathyThe use of mobile technology to facilitate surveillance and improve injury outcome in sport and physical activityIntegrated knowledge translation for injury quality improvement: a partnership between researchers and knowledge usersThe impact of a prevention project in trauma with young and their learningIntraosseus vascular access in adult trauma patients: a systematic reviewThematic analysis of patient reported experiences with acute and post-acute injury

Hoit, G. ; Hinkewich, C. ; Tiao, J. ; [et al.]

CMA Impact Inc. ; 2013

In: Canadian Journal of Surgery Vol. 56, No. 2 Suppl ( 2013-04), p. S1-S42

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In: Canadian Journal of Surgery, CMA Impact Inc., Vol. 56, No. 2 Suppl ( 2013-04), p. S1-S42

Type of Medium: Online Resource

ISSN: 0008-428X , 1488-2310

URL: Article

DOI: 10.1503/cjs.005813

Language: English

Publisher: CMA Impact Inc.

Publication Date: 2013

detail.hit.zdb_id: 2026595-5

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BNT162b2 mRNA Vaccination Against Coronavirus Disease 2019 is Associated With a Decreased Likelihood of Multisystem Inflammatory Syndrome in Children Aged 5–18 Years—United States, July 2021 – April 2022

Zambrano, Laura D ; Newhams, Margaret M ; Olson, Samantha M ; [et al.]

Oxford University Press (OUP) ; 2023

In: Clinical Infectious Diseases Vol. 76, No. 3 ( 2023-02-08), p. e90-e100

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In: Clinical Infectious Diseases, Oxford University Press (OUP), Vol. 76, No. 3 ( 2023-02-08), p. e90-e100

Abstract: Multisystem inflammatory syndrome in children (MIS-C), linked to antecedent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, is associated with considerable morbidity. Prevention of SARS-CoV-2 infection or coronavirus disease 2019 (COVID-19) by vaccination might also decrease MIS-C likelihood. Methods In a multicenter, case-control, public health investigation of children ages 5–18 years hospitalized from 1 July 2021 to 7 April 2022, we compared the odds of being fully vaccinated (2 doses of BNT162b2 vaccine ≥28 days before hospital admission) between MIS-C case-patients and hospital-based controls who tested negative for SARS-CoV-2. These associations were examined by age group, timing of vaccination, and periods of Delta and Omicron variant predominance using multivariable logistic regression. Results We compared 304 MIS-C case-patients (280 [92%] unvaccinated) with 502 controls (346 [69%] unvaccinated). MIS-C was associated with decreased likelihood of vaccination (adjusted OR [aOR]: .16; 95% CI: .10–.26), including among children ages 5–11 years (aOR: .22; 95% CI: .10–.52), ages 12–18 years (aOR: .10; 95% CI: .05–.19), and during the Delta (aOR: .06; 95% CI: .02–.15) and Omicron (aOR: .22; 95% CI: .11–.42) variant-predominant periods. This association persisted beyond 120 days after the second dose (aOR: .08; 95% CI: .03–.22) in 12–18-year-olds. Among all MIS-C case-patients, 187 (62%) required intensive care unit admission and 280 (92%) vaccine-eligible case-patients were unvaccinated. Conclusions Vaccination with 2 doses of BNT162b2 is associated with reduced likelihood of MIS-C in children ages 5–18 years. Most vaccine-eligible hospitalized patients with MIS-C were unvaccinated.

Type of Medium: Online Resource

ISSN: 1058-4838 , 1537-6591

URL: Article

DOI: 10.1093/cid/ciac637

RVK:

XA 10000

Language: English

Publisher: Oxford University Press (OUP)

Publication Date: 2023

detail.hit.zdb_id: 2002229-3

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