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Rationally designed mariner vectors for functional genomic analysis of Actinobacillus pleuropneumoniae and other Pasteurellaceae species by transposon-directed insertion-site sequencing (TraDIS)

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Animal Diseases 2021年第4期1卷 249-261页

作者： Janine T.Bossé Yanwen Li Leon G.Leanse Liqing Zhou Roy R.Chaudhuri Sarah E.Peters Jinhong wang Gareth A.Maglennon Matthew T.G.Holden Duncan J.Maskell Alexander w.Tucker brendan w.wren Andrew N.Rycroft Paul R.Langford on behalf of the BRaDPT consortium Section of Paediatric Infectious Disease Department of Infectious DiseaseImperial College LondonSt.Mary’s CampusLondonUK wellman Center for Photomedicine Harvard Medical SchoolBostonUSA The Applied Diagnostic Research and Evaluation Unit St George’s University of LondonLondonUK Department of Veterinary Medicine University of CambridgeCambridgeUK Department of Molecular Biology and Biotechnology University of SheffieldSheffieldUK Department of Pathology and Pathogen Biology The Royal Veterinary CollegeHatfieldUK The wellcome Trust Sanger Institute CambridgeUK School of Medicine University of St AndrewsSt AndrewsUK The University of Melbourne ParkvilleVictoriaAustralia s Faculty of Infectious&Tropical Diseases London School of Hygiene&Tropical MedicineLondonUK

Comprehensive identification of conditionally essential genes requires efficient tools for generating high-density transposon libraries that, ideally, can be analysed using next-generation sequencing methods such as Transposon Directed Insertion-site Sequencing (TraDIS). The Himar1 (mariner) transposon is ideal for generating near-saturating mutant libraries, especially in AT-rich chromosomes, as the requirement for integration is a TA dinucleotide, and this transposon has been used for mutagenesis of a wide variety of bacteria. However, plasmids for mariner delivery do not necessarily work well in all bacteria. In particular, there are limited tools for functional genomic analysis of Pasteurellaceae species of major veterinary importance, such as swine and cattle pathogens, Actinobacillus pleuropneumoniae and Pasteurella multocida, respectively. Here, we developed plasmids, pTsodCPC9 and pTlacPC9 (differing only in the promoter driving expression of the transposase gene), that allow delivery of mariner into both these pathogens, but which should also be applicable to a wider range of bacteria. Using the pTlacPC9 vector, we have generated, for the first time, saturating mariner mutant libraries in both A. pleuropneumoniae and P. multocida that showed a near random distribution of insertions around the respective chromosomes as detected by TraDIS. A preliminary screen of 5000 mutants each identified 8 and 14 genes, respectively, that are required for growth under anaerobic conditions. Future high-throughput screening of the generated libraries will facilitate identification of mutants required for growth under different conditions, including in vivo, highlighting key virulence factors and pathways that can be exploited for development of novel therapeutics and vaccines.

关键词： Mariner Transposon TraDIS Pasteurellaceae Actinobacillus pleuropneumoniae Pasteurella multocida

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Sticking together:Mechanisms of quartz synneusis in high-silica magma

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Geoscience Frontiers 2023年第2期14卷 40-46页

作者： brendan Dyck Department of Earth Environmental and Geographic SciencesThe University of British Columbia4237 University WayKelownaBC V1V 1V7Canada

The formation of crystal clusters by synneusis(magmatic sintering)affects a wide range of magmatic systems from olivine clusters in komatiite to quartz clusters in high-silica granite.A common feature of synneusis in any mineral phase is the alignment of neighbouring crystals in certain lower-energy orientation ***,the underlying mechanisms involved with both the alignment of crystals in lower-energy orientations and the binding of crystal clusters are not well *** the absence of mechanisms that bind crystals together upon contact,the same hydrodynamic forces that may bring crystals together can in theory also serve to disaggregate *** I use cathodoluminescence imaging and crystal orientation data from quartz clusters in high-silica granite to show that i)rapid crystalline neck growth along attachment surfaces and ii)grain rotation are two mechanisms that reduce the grain boundary energy of crystal clusters while increasing clusters’shear *** continued crystallization of sintered phases as the magmatic body cools further cements crystal pairs and resists cluster *** these mechanisms underpin both the formation and preservation of large crystal clusters in dynamic magmatic environments.

关键词： Synneusis Granite Magmatic behaviour EBSD Cathodoluminescence Quartz

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Influence of towing speed on effectiveness of rolling dynamic compaction

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Journal of Rock Mechanics and Geotechnical Engineering 2020年第1期12卷 126-134页

作者： brendan T.Scott Mark B.Jaksa Peter w.Mitchell School of Civil Environmental and Mining EngineeringThe University of AdelaideSouth Australia5005Australia Aurecon AdelaideSouth Australia5000Australia

The influence of towing speed on the effectiveness of the 4-sided impact roller using earth pressure cells(EPCs)is *** field trials were undertaken;the first trial used three EPCs placed at varying depths between 0.5 m and 1.5 m with towing speeds of 9-12 km/*** second used three EPCs placed at a uniform depth of 0.8 m,with towing speeds of 5-15 km/*** findings from the two trials confirmed that towing speed influences the pressure imparted to the ground and hence compactive *** paper proposes that the energy imparted to the ground is best described in terms of work done,which is the sum of the change in both potential and kinetic *** practice of using either kinetic energy or gravitational potential energy should be avoided as neither can accurately quantify rolling dynamic compaction(RDC)when towing speed is varied.

关键词： Rolling dynamic compaction(RDC) Optimum towing speed Ground improvement

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Incidence Category of the Young Lattice,Injections Between Finite Sets,and Koszulity

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Algebra Colloquium 2021年第2期28卷 195-212页

作者： brendan Dubsky Jie Xiao Department of Mathematics Uppsala UniversityUppsalaSweden 不详

we study the quadratic quotients of the incidence category of the Young lattice defined by the zero relations corresponding to adding two boxes to the same row,or to the same column,or *** show that the last quotient corresponds to the Koszul dual of the original incidence category,while the first two quotients axe,in a natural way,Koszul duals of each other and hence they axe in particular Koszul *** of these two quotients are known to be basic representatives in the Morita equivalence class of the category of injections between finite *** also present a new,rather direct,argument establishing this Morita equivalence.

关键词： Young lattice Koszulity category of injections Koszul duality

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Exploring the metamorphic consequences of secular change in the siliciclastic compositions of continental margins

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Geoscience Frontiers 2018年第4期9卷 967-975页

作者： Gautier Nicoli brendan Dyck Department of Earth Sciences University of Cambridge Department of Earth Sciences Simon Fraser University

Shale and greywacke compositions from the Archean to Phanerozoic record a secular change in the siliciclastic material that comprises much of Earth＇s continental margins, past and present. This study explores the metamorphic consequence of these compositional changes, by comparing phase equilibrium models constructed for average Archean, Proterozoic, and Phanerozoic shale and greywacke compositions equilibrated along two Barrovian-type geotherms： 1330℃/GPa（A） and 800 ℃/GPa（B）. Our models show that Archean siliciclastic rocks can retain up to 4 vol.% water at middle to lower crustal conditions, nearly twice that of Proterozoic and Phanerozoic compositions. The increased ferromagnesium content of Archean siliciclastic rocks stabilizes chlorite to higher temperatures and results in a biotite-rich assemblage at solidus temperatures. Accordingly, water-absent biotite dehydration melting is predicted to play a greater role in the generation of melt in the metamorphism of Archean aged units,and water-absent muscovite dehydration melting is of increasing importance through the Proterozoic and Phanerozoic. This secular variation in predicted mineral assemblages demonstrates the care with which metamorphic facies diagrams should be applied to Archean compositions. Moreover, secular changes in the composition of shale and greywacke is reflected in the evolution of anatectic melt towards an increasingly less viscous, Ca-rich, and Mg-poor monzogranite.

关键词： Secular change Shale Greywacke Dehydration melting Thermodynamic modelling Perple_X

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Gene Duplication and the Evolution of Plant MADS-box Transcription Factors

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Journal of Genetics and Genomics 2012年第4期39卷 157-165页

作者： Chiara A.Airoldi brendan Davies Centre for Plant Sciences University of Leeds

Since the first MADS-box transcription factor genes were implicated in the establishment of floral organ identity in a couple of model plants, the size and scope of this gene family has begun to be appreciated in a much wider range of species. Over the course of millions of years the number of MADS-box genes in plants has increased to the point that the Arabidopsis genome contains more than 100. The understanding gained from studying the evolution, regulation and function of multiple MADS-box genes in an increasing set of species, makes this large plant transcription factor gene family an ideal subject to study the processes that lead to an increase in gene number and the selective birth, death and repurposing of its component members. Here we will use examples taken from the MADS-box gene family to review what is known about the factors that influence the loss and retention of genes duplicated in different ways and examine the varied fates of the retained genes and their associated biological outcomes.

关键词： Flower development MADS-box transcription factor Gene duplication Evolution

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Testosterone treatment in older men： glass half empty or half full？

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Asian Journal of Andrology 2017年第5期19卷 512-514页

作者： brendan J Nolan Mathis Grossmann Department of Endocrinology Austin HealthHeidelberg Victoria 3084 Australia Department of Medicine University of Melbourne Austin HealthHeidelberg Victoria 3084 Australia

In a series of randomized controlled trials published in JAMA and JAMA Intern Med,US researchers have examined the effect of testosterone treatment in older men with testosterone levels 〈275 ng dl^-1 on coronary arte... 详细信息

关键词： randomized controlled trials bone density cognitive function coronary artery

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Metamorphic consequences of secular changes in oceanic crust composition and implications for uniformitarianism in the geological record

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Geoscience Frontiers 2018年第4期9卷 1009-1019页

作者： Richard M.Palin brendan Dyck Department of Geology and Geological Engineering Colorado School of Mines Department of Earth Sciences Simon Fraser University

Cooling of the Earth＇s mantle since the Meso-Archean is predicted by thermal and petrological models to have induced a secular change in the composition of primary mantle-derived magmas-and thus bulk oceanic crust; in particular, suggesting a decrease in maficity over time. This hypothesis underpins several recent studies that have addressed key geological questions concerning evolving plate tectonic styles, the rates and timing of continental crust formation, comparative planetology, and the emergence of complex life on Earth. Major, minor, and trace element geochemical analyses of（meta）mafic rocks preserved in the geological record allows exploration of this theory, although no consensus currently exists about the magnitude of this change and what compositions-if anything-constitute representative examples of Paleo-, Meso-, or Neo-Archean primitive oceanic crust. In this work, we review the current state of understanding of this issue, and use phase equilibria to examine the different mineral assemblages and rock types that would form during metamorphism of basalt of varying maficity in subduction zone environments. The presence（or absence） of such metamorphic products in the geological record is often used as evidence for（or against） the operation of modern-day subductiondriven plate tectonics on Earth at particular time periods; however, the control that secular changes in composition have on the stability of mineral assemblages diagnostic of subduction-zone metamorphism weakens such uniformitarianistic approaches. Geodynamic interpretations of the Archean metamorphic rock record must therefore employ a different set of petrological criteria for determining tectonothermal histories than those applied to Proterozoic or Phanerozoic equivalents.

关键词： Archean Mantle cooling Oceanic crust Basalt Metamorphism Uniformitarianism

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Mitochondrial inorganic polyphosphate(polyP):the missing link of mammalian bioenergetics

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Neural Regeneration Research 2021年第11期16卷 2227-2228页

作者： brendan McIntyre Maria E.Solesio Department of Biology Rutgers UniversityCamdenNJUSA

Bioenergetics imbalance is a deleterious feature,which is present in the etiopathology of many human diseases,including in diabetes,cancer,and ***,targeting the components of mammalian bioenergetics,as well as the mechanisms that regulate the relationship between these components,could be a promising pharmacological strategy against a wide variety of *** for many years mammalian bioenergetics has been exclusively circumscribed to the mitochondrial oxidative phosphorylation(OXPHOS),which is the main mechanism to obtain adenosine triphosphate(ATP)in mammals,and to the cytoplasmic glycolysis and the closely related pentose phosphate pathway,in the last few decades many authors have advocated for expanding this term to include all the mechanisms that are involved in matching the cellular demands and production of energy to meet the needs of the cell under different states,including physiological and pathological *** broader definition will include other key energy metabolites,such as the ubiquitous inorganic polyphosphate(polyP).

关键词： inorganic diseases pathology

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Factors that mediate colonization of the human stomach by Helicobacter pylori

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world Journal of Gastroenterology 2014年第19期20卷 5610-5624页

作者： Ciara Dunne brendan Dolan Marguerite Clyne School of Medicine and Medical Science and Conway Institute of Biomedical and Biomolecular Science University College DublinBelfieldDublin 4Ireland

Helicobacter pylori(***)colonizes the stomach of humans and causes chronic *** majority of bacteria live in the mucus layer overlying the gastric epithelial cells and only a small proportion of bacteria are found interacting with the epithelial *** bacteria living in the gastric mucus may act as a reservoir of infection for the underlying cells which is essential for the development of *** of gastric mucus is likely to be key to the establishment of chronic *** *** manages to colonise and survive in the hostile environment of the human stomach and avoid removal by mucus flow and killing by gastric acid is the subject of this *** also discuss how bacterial and host factors may together go some way to explaining the susceptibility to colonization and the outcome of infection in different *** infection of the gastric mucosa has become a paradigm for chronic *** of why *** is such a successful pathogen may help us understand how other bacterial species colonise mucosal surfaces and cause disease.

关键词： Helicobacter pylori Colonization Infection Gastric mucosa Urease Flagella Polymorphisms Adhesins CagA Type IV secretion system

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