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Ranking higher taxa using divergence times:a case study in dothideomycetes

Fungal diversity 2017年第3期84卷 75-99页

作者： Jian-Kui Liu Kevin d.Hyde Rajesh Jeewon Alan J.L.phillips Sajeewa S.N.Maharachchikumbura Martin Ryberg Zuo-Yi Liu Qi Zhao Key Laboratory for Plant diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunming 650201People’s Republic of China Guizhou Institute of Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand departmental of Health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius University of Lisbon Faculty of SciencesBiosystems and Integrative Sciences InstituteCampo Grande1749-016 LisbonPortugal department of Crop Sciences College of Agricultural and Marine SciencesSultan Qaboos UniversityPO Box 8123 Al KhoudOman department of Organismal Biology Uppsala UniversityNorbyvägen 18D75236 UppsalaSweden

The current classification system for the recognition of taxonomic ranks among fungi,especially at highranking level,is *** the development of molecular approaches and the availability of fossil calibration data,the use of divergence times as a universally standardized criterion for ranking taxa has now become *** can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of *** chose dothideomycetes,the largest class of the phylum Ascomycota,which contains 32 orders,to establish ages at which points orders have split;and Pleosporales,the largest order of dothideomycetes with 55 families,to establish family divergence *** have assembled a multi-gene data set(LSU,SSU,TEF1 and RPB2)from 391 taxa representing most family groups of dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of dothideomycetes *** separated datasets were analysed:(i)272 taxa representing 32 orders of dothideomycetes were included for the order level analysis,and(ii)191 taxa representing 55 families of Pleosporales were included for the family level *** results indicate that divergence times(crown age)for most orders(20 out of 32,or 63%)are between 100 and 220 Mya,while divergence times for most families(39 out of 55,or 71%)are between 20 and 100 *** believe that divergence times can provide additional evidence to support establishment of higher level taxa,such as families,orders and *** advantage of this added approach,we can strive towards establishing a standardized taxonomic system both within and outside *** this study we found that molecular dating coupled with phylogenetic inferences provides no support for the taxonomic status of two currently recognized orders,namely Bezerromycetales and Wiesneriomycetales and these are treated as sy

关键词： BEAST Clade age Classification Calibration Family Order Phylogeny Pleosporales

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水催化脱卤反应:构建每次一个水分子的纳米化学反应体系(英文)

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光散射学报 2005年第3期 63-65页

作者： d.L.phillips,W.M.Kwok department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong S.A.R. China department of Chemistry The University of Hong Kong Pokfulam Road Hong Kong S.A.R. China

A combined experimental and theoretical study of the photochemistry of CHBr3in pure water and in acetonitrile/water mixed solvents is reported that elucidates the reactions and mechanisms responsible for the photochemical conversion of the halogen atoms in CHBr3into three bromide ions in water *** is the most abundant source of organic bromine in the ocean and atmosphere and this makes it an attractive polyhalomethane to study [1]. Ultraviolet excitation with 253.7 nm light （from a Hg lamp） of low concentrations （d CHCl2Br in aqueous solution led to complete conversion of the halogens into halide ions （bromide and/or chloride） with similar photo-quantum yields of about 0.43 [2]. C-Br bond cleavage for the CHBr3molecule and the CHBr2radical in the gas phase have been estimated to require 63.8 and 73.6 kcal/mol of energy respectively [3]. The 253.7 nm photon has about 113 kcal/mol of energy and is thus only likely to break one carbon-halogen bond in the CHBr3, CHBr2Cl and CHCl2Br molecules following 253.7 nm excitation. How does the 253.7 nm photolysis of low concentrations of CHBr3, CHBr2Cl, and CHCl2Br in water lead to complete conversion of the halogen atoms into bromide and/or chloride ion products and where does the energy come from to break all three carbon-halogen bonds?

关键词： HBr Cl CO

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Arabidopsis thaliana T-dNA Mutants Implicate GAUT Genes in the Biosynthesis of Pectin and Xylan in Cell Walls and Seed Testa

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Molecular Plant 2009年第5期2卷 1000-1014页

作者： Kerry H. Caffall Sivakumar Pattathil Sarah E. phillips Michael G. Hahn debra Mohnen department of Biochemistry and Molecular Biology University of Georgia Athens GA 30602 USA Complex Carbohydrate Research Center BioEnergy Science Center 315 Riverbend Road University of Georgia Athens GA 30602 USA department of Plant Biology University of Georgia Athens GA 30602 USA

Galacturonosyltransferase 1 （GAUT1） is an α1,4-d-galacturonosyltransferase that transfers galacturonic acid from uridine 5＇-diphosphogalacturonic acid onto the pectic polysaccharide homogalacturonan （Sterling et al., 2006）. The 25-member Arabidopsis thaliana GAUT1-related gene family encodes 15 GAUT and 10 GAUT-like （GATL） proteins with, respectively, 56-84 and 42-53% amino acid sequence similarity to GAUT1. Previous phylogenetic analyses of AtGAUTs indicated three clades： A through C. A comparative phylogenetic analysis of the Arabidopsis, poplar and rice GAUT families has sub-classified the GAUTs into seven clades： clade A-1 （GAUTs 1 to 3）; A-2 （GAUT4）; A-3 （GAUTs 5 and 6）; A-4 （GAUT7）; B-1 （GAUTs 8 and 9）; B-2 （GAUTs 10 and 11）; and clade C （GAUTs 12 to 15）. The Arabidopsis GAUTs have a distribution comparable to the poplar orthologs, with the exception of GAUT2, which is absent in poplar. Rice, however, has no orthologs of GAUTs 2 and 12 and has multiple apparent orthologs of GAUTs 1, 4, and 7 compared with eitherArabidopsis or poplar. The cell wall glycosyl residue compositions of 26 homozygous T-dNA insertion mutants for 13 of 15 Arabidopsis GAUTgenes reveal significantly and reproducibly different cell walls in specific tissues of gaut mutants 6, 8, 9, 10, 11, 12, 13, and 14 from that of wild-type Arabidopsis walls. Pectin and xylan polysaccharides are affected by the loss of GAUT function, as demonstrated by the altered galacturonic acid, xylose, rhamnose, galactose, and arabinose composition of distinct gaut mutant walls. The wall glycosyl residue compositional phenotypes observed among the gaut mutants suggest that at least six different biosynthetic linkages in pectins and/or xylans are affected by the lesions in these GAUTgenes. Evidence is also presented to support a role for GAUT11 in seed mucilage expansion and in seed wall and mucilage composition.

关键词： Carbohydrate metabolism cell walls Arabidopsis biosynthesis mutant pectin mucilage

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霉菌毒素对动物生产及动物产品的危害及控制

霉菌毒素对动物生产及动物产品的危害及控制

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食品、饲料安全与风险评估学术会议

作者： Sun anquan T.d.phillips 奥格生物技术(上海)有限公司 Texas A&M University

霉菌毒素研究自上世纪60年代以来一直是个热门课题,世界霉菌毒素研讨会及美国霉菌毒素委员会为我们提供了丰富的资料。在中国由于实验条件的限制,在霉菌毒素研究领域比较落后,而中国饲料业及养殖业对霉菌毒素的了解严重不足,这种认识上... 详细信息

霉菌毒素研究自上世纪60年代以来一直是个热门课题,世界霉菌毒素研讨会及美国霉菌毒素委员会为我们提供了丰富的资料。在中国由于实验条件的限制,在霉菌毒素研究领域比较落后,而中国饲料业及养殖业对霉菌毒素的了解严重不足,这种认识上不足导致中国市场出现许多低效或无效产品。消费者使用后达不到脱除毒素的目的,有可能继发免疫系统抑

关键词：霉菌毒素吸附能力玉米赤霉烯酮霉菌毒素吸附剂动物产品呕吐毒素黄曲霉毒素

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Secreted frizzled related-protein 2(Sfrp2)deficiency decreases adult skeletal stem cell function in mice

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Bone Research 2021年第4期9卷 606-617页

作者： Luis Fernandez de Castro Brian丄Sworder Byron Mui Kathryn Futrega Agnes Berendsen Matthew d.phillips Nathan J.Burbach Natasha Cherman Sergei Kuznetsov Yankel Gabet Kenn Holmbeck Pamela G.Robey Skeletal Biology Section National Institute of Dental and Craniofacial ResearchNational Institutes of HealthDepartment of Health and Human ServicesNational Institutes of HealthBethesdaMDUSA department of Molecular Medicine Boston UniversityBostonMAUSA School of dentistry University of Minnesota-Twin CitiesMinneapolisMNUSA department of Anatomy and Anthropology Sackler Faculty of MedicineTel Aviv UniversityTel Aviv-YafoIsrael

In a previous transcriptomic study of human bone marrow stromal cells(BMSCs,also known as bone marrow-derived^mesenchymal stem cells#,)/SFRP2 was highly over-represented in a subset of multipotent BMSCs(skeletal stem cells,SSCs),which recreate a bone/marrow organ in an in vivo ectopic bone formation *** modulate WNT signaling,which is essential to maintain skeletal homeostasis,but the specific role of SFRP2 in BMSCs/SSCs is ***,we evaluated Sfrp2 deficiency on BMSC/SSC function in models of skeletal organogenesis and *** skeleton of Sfrp2-def\c\ent(KO)mice is overtly normal;but their BMSCs/SSCs exhibit reduced colony-forming efficiency,reflecting low SSC self-renewal/***2 KO BMSCs/SSCs formed less trabecular bone than those from WT littermates in the ectopic bone formation ***,regeneration of a cortical drilled hole defect was dramatically impaired in Sfrp2 KO ***2-deficient BMSCs/SSCs exhibited poor in vitro osteogenic differentiation as measured by Runx2 and Osterix expression and calcium ***,activation of the Wnt co-receptor;Lrp6,and expression of Wnt target genes,Axin2,C-myc and Cyclin dl,were reduced in Sfrp2-deficient BMSCs/*** of recombinant Sfrp2 restored most of these activities,suggesting that Sfrp2 acts as a Wnt *** demonstrate that Sfrp2 plays a role in self-renewal of SSCs and in the recruitment and differentiation of adult SSCs during bone ***2 is also a useful marker of BMSC/SSC multipotency,and a factor to potentially improve the quality of ex vivo expanded BMSC/SSC products.

关键词： skeletal impaired healing

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Microfungi on Tamarix

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Fungal diversity 2017年第1期82卷 239-306页

作者： Kasun M.Thambugala dinushani A.daranagama Alan J.L.phillips Timur S.Bulgakov darbhe J.Bhat Erio Camporesi Ali H.Bahkali Prapassorn d.Eungwanichayapant Zuo-Yi Liu Kevin d.Hyde Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouPeople’s Republic of China Centre of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesNo 31st West Beichen RoadChaoyang DistrictBeijing 100101People’s Republic of China Faculty of Sciences Biosystems and Integrative Sciences Institute(BioISI)University of LisbonCampo Grande1749-016 LisbonPortugal Academy of Biology and Biotechnology Southern Federal UniversityRostov-on-Don344090 Rostov RegionRussia Formerly department of Botany Goa UniversityGoaIndia Curca No.128/1–JAzad Housing SocietyGoa VelhaIndia A.M.B.Gruppo Micologico ForliveseBAntonio Cicognani^ Via Roma 18ForlìItaly A.M.B.Circolo Micologico BGiovanni Carini^ C.P.314BresciaItaly department of Botany and Microbiology College of ScienceKing Saud UniversityP.O.Box:2455Riyadh 1145Saudi Arabia

Tamarix species are small trees that grow in various natural habitats and have a wide geographic *** species previously found on Tamarix and recently collected in Italy and Russia were identified based on morphological characters and analyses of gene sequence *** sexual morph of the coelomycetous genus Homortomyces was collected for the first time and is described and illustrated.A new family,Homortomycetaceae(dothideomycetes,families incertae sedis)is introduced to accommodate *** new genera Neomicrosphaeropsis(didymellaceae)and Tamaricicola(Pleosporaceae)are introduced in this *** tamaricicola was recollected and is placed in Neomicrosphaeropsis based on morphology and molecular *** new species,Cytospora italica,***,diaporthe ravennica,Eutypella tamaricis,Neomicrosphaeropsis italica,***,***,Keissleriella tamaricicola,Paracamarosporium tamaricis and Tamaricicola muriformis are introduced,while Alternaria tenuissima,dothiorella sarmentorum,Neofusicoccum luteum,Paraepicoccum amazonense,Pleospora herbarum and Pseudocamarosporium propinquum are reported for the first time on Tamarix *** descriptions and ***-gene analyses show that Paraepicoccum amazonense should be placed in Pleosporineae,Pleosporales,where it is closely related to Camarosporium sensu *** herbarium specimens were studied to illustrate other fungal species recorded on Tamarix species.A comprehensive account of microfungi on Tamarix is provided,which includes a list with data from the literature,as well as those identified in the present *** taxonomic placement of most taxa discussed in this study is based on a modern taxonomic framework based on analysis of multi-gene sequence data.

关键词： dothideomycetes Homortomycetaceae Incertae sedis New species Phylogeny Pleosporales Sordariomycetes Tamaricaceae Taxonomy

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人类在地球表面系统中的地位与作用——人与环境系统某些理论问题的探讨

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中国人口·资源与环境 1993年第2期3卷 77-81页

作者： Jonathan d.phillips 李荣升赵善伦

在研究人类对环境的影响时,若把人类因素作为地球表面系统的一个组成部分,该系统是不稳定的,在干扰破坏后不能恢复平衡;若把人类因素当做系统外的成分,则系统对人类的影响是稳定的,在非灾难性干扰破坏后,系统能恢复到接近原来存在的状态... 详细信息

在研究人类对环境的影响时,若把人类因素作为地球表面系统的一个组成部分,该系统是不稳定的,在干扰破坏后不能恢复平衡;若把人类因素当做系统外的成分,则系统对人类的影响是稳定的,在非灾难性干扰破坏后,系统能恢复到接近原来存在的状态,此结论由对系统物质流和能量流的计算来证明。

关键词：地球环境人类

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A field guide for aging passerine nestlings using growth data and predictive modeling

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Avian Research 2021年第2期12卷 141-149页

作者： Audrey A.Sanchez Andrew W.Bartlow Allison M.Chan Jeanne M.Fair Aaron A.Skinner Kelly Hutchins Maria A.Musgrave Emily M.phillips Brent E.Thompson Charles d.Hathcock Environmental Stewardship Los Alamos National LaboratoryLos AlamosNMUSA Biosecurity and Public Health Los Alamos National LaboratoryLos AlamosNMUSA Water Program N3BLos AlamosNMUSA

Background:Accurate nestling age is valuable for studies on nesting strategies,productivity,and impacts on repro-ductive *** aging guides consist of descriptions and photographs that are time consuming to read and subjective to *** Western Bluebird(Sialia mexicana)is a secondary cavity-nesting passerine that nests in coniferous and open deciduous *** box programs for cavity-nesting species have provided suitable nesting locations and opportunities for data collection on nestling growth and ***:We developed models for predicting the age of Western Bluebird nestlings from morphometric meas-urements using model training and *** were developed for mass,tarsus,and two different culmen ***:Our models were accurate to within less than a day,and each model worked best for a specific age *** mass and tarsus models can be used to estimate the ages of Western Bluebird nestlings 0-10 days old and were accurate to within 0.5 days for mass and 0.7 days for *** culmen models can be used to estimate ages of nest-lings 0-15 days old and were also accurate to within less than a *** daily mean,minimum,and maximum values of each morphometric measurement are provided and can be used in the field for accurate nestling age estimations in real ***:The model training and validation procedures used here demonstrate that this method can create aging models that are highly *** methods can be applied to any passerine species provided sufficient nest-ling morphometric data are available.

关键词： Cavity-nesting Nest boxes Nestling development Predictive models Western Bluebird

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Performance and calibration of quark/gluon-jet taggers using 140 fb^(-1) of pp collisions at √s=13 TeV with the ATLAS detector

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Chinese Physics C 2024年第2期48卷 1-25页

作者： G. Aad B. Abbott K. Abeling N.J. Abicht S.H. Abidi A. Aboulhorma H. Abramowicz H. Abreu Y. Abulaiti B.S. Acharya C. Adam Bourdarios L. Adamczyk S.V. Addepalli M.J. Addison J. Adelman A. Adiguzel T. Adye A.A. Affolder Y. Afik M.N. Agaras J. Agarwala A. Aggarwal C. Agheorghiesei A. Ahmad F. Ahmadov W.S. Ahmed S. Ahuja X. Ai G. Aielli A. Aikot M. Ait Tamlihat B. Aitbenchikh I. Aizenberg M. Akbiyik T.P.A. Åkesson A.V. Akimov d. Akiyama N.N. Akolkar K. Al Khoury G.L. Alberghi J. Albert P. Albicocco G.L. Albouy S. Alderweireldt M. Aleksa I.N. Aleksandrov C. Alexa T. Alexopoulos F. Alfonsi M. Algren M. Alhroob B. Ali H.M.J. Ali S. Ali S.W. Alibocus M. Aliev G. Alimonti W. Alkakhi C. Allaire B.M.M. Allbrooke J.F. Allen C.A. Allendes Flores P.P. Allport A. Aloisio F. Alonso C. Alpigiani M. Alvarez Estevez A. Alvarez Fernandez M. Alves Cardoso M.G. Alviggi M. Aly Y. Amaral Coutinho A. Ambler C. Amelung M. Amerl C.G. Ames d. Amidei S.P. Amor dos Santos K.R. Amos V. Ananiev C. Anastopoulos T. Andeen J.K. Anders S.Y. Andrean A. Andreazza S. Angelidakis A. Angerami A.V. Anisenkov A. Annovi C. Antel M.T. Anthony E. Antipov M. Antonelli F. Anulli M. Aoki T. Aoki J.A. Aparisi Pozo M.A. Aparo L. Aperio Bella C. Appelt A. Apyan N. Aranzabal S.J. Arbiol Val C. Arcangeletti A.T.H. Arce E. Arena J-F. Arguin S. Argyropoulos J.-H. Arling O. Arnaez H. Arnold G. Artoni H. Asada K. Asai S. Asai N.A. Asbah J. Assahsah K. Assamagan R. Astalos S. Atashi R.J. Atkin M. Atkinson H. Atmani P.A. Atmasiddha K. Augsten S. Auricchio A.d. Auriol V.A. Austrup G. Avolio K. Axiotis G. Azuelos d. Babal H. Bachacou K. Bachas A. Bachiu F. Backman A. Badea P. Bagnaia M. Bahmani A.J. Bailey V.R. Bailey J.T. Baines L. Baines O.K. Baker E. Bakos d. Bakshi Gupta V. Balakrishnan R. Balasubramanian E.M. Baldin P. Balek E. Ballabene F. Balli L.M. Baltes W.K. Balunas J. Balz E. Banas M. Bandieramonte A. Bandyopadhyay S. Bansal L. Barak M. Barakat E.L. Barberio d. Barberis M. Barbero M.Z. Barel K.N. Barends T. Barillari M-S. Barisits T. Barklow P. Baron d.A. Baron Mo The ATLAS Collaboration

The identification of jets originating from quarks and gluons,often referred to as quark/gluon tagging,plays an important role in various analyses performed at the Large Hadron Collider,as Standard Model measurements and searches for new particles decaying to quarks often rely on suppressing a large gluon-induced *** paper describes the measurement of the efficiencies of quark/gluon taggers developed within the ATLAS Collaboration,using √s=13 TeV proton–proton collision data with an integrated luminosity of 140 fb^(-1) collected by the ATLAS *** taggers with high performances in rejecting jets from gluon over jets from quarks are studied:one tagger is based on requirements on the number of inner-detector tracks associated with the jet,and the other combines several jet substructure observables using a boosted decision tree.A method is established to determine the quark/gluon fraction in data,by using quark/gluon-enriched subsamples defined by the jet *** in tagging efficiency between data and simulation are provided for jets with transverse momentum between 500 GeV and 2 TeV and for multiple tagger working points.

关键词： ATLAS JET QUARK GLUON TAGGING

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霉菌毒素研究新进展

霉菌毒素研究新进展

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第五届全国饲料营养学术研讨会

作者：孙安全 Karo Mikaelian T．d．phillips 美国创实营养有限公司美国创实营养有限公司 Taxas A ＆ M University

＜正＞霉菌毒素研究自20世纪60年代以来一直是个热门课题,世界霉菌毒素研讨会及美国霉菌毒素委员会为我们提供了丰富的资料。在中国由于实验条件的限制,在霉菌毒素研究领域比较落后,而中国饲料业及养殖业对霉菌毒素的了解严重不足,这种... 详细信息

＜正＞霉菌毒素研究自20世纪60年代以来一直是个热门课题,世界霉菌毒素研讨会及美国霉菌毒素委员会为我们提供了丰富的资料。在中国由于实验条件的限制,在霉菌毒素研究领域比较落后,而中国饲料业及养殖业对霉菌毒素的了解严重不足,这种认识上不足导致中国市场出现许多低效或无效产品。消费者使用后达不到脱除毒素的目的,有可能继发免疫系统抑制,导致传染病的暴发。如在发达国家及世界卫生组织公认黄曲霉毒素是危害最严重的毒素,在中国却有许多公司利用毒素自然存在的浓度差异,片面夸大次要毒素如呕吐毒素,T2毒素的危害,从而误导客户;反观目前市

关键词：霉菌毒素吸附剂市场养猪生产

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