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Resolving the Mortierellaceae phylogeny through synthesis of multi-gene phylogenetics and phylogenomics

Fungal Diversity 2020年第5期104卷 267-289页

作者： Natalie vandepol Julian Liber Alessandro Desirò Hyunsoo Na Megan Kennedy Kerrie Barry igor v.grigoriev Andrew N.Miller Kerry O’Donnell Jason E.Stajich Gregory Bonito Department of Microbiology and Molecular Genetics Michigan State UniversityEast LansingMI 48824USA Department of Plant Biology Michigan State UniversityEast LansingMI 48824USA Department of Plant Soil and Microbial Sciences Michigan State UniversityEast LansingMI 48824USA Joint Genome Institute BerkeleyCA 94720USA Illinois Natural History Survey University of Illinois Urbana-ChampaignChampaignIL 61820USA United States Department of Agriculture Agricultural Research ServicePeoriaIL 61604USA Department of Microbiology and Plant Pathology&Institute for Integrative Genome Biology University of California-RiversideRiversideCA 92521USA

Early efforts to classify Mortierellaceae were based on macro-and micromorphology,but sequencing and phylogenetic studies with ribosomal DNA(rDNA)markers have demonstrated conflicting taxonomic groupings and polyphyletic *** some taxonomic confusion in the family has been clarified,rDNA data alone is unable to resolve higher level phylogenetic relationships within *** this study,we applied two parallel approaches to resolve the Mortierel-laceae phylogeny:low coverage genome(LCG)sequencing and high-throughput,multiplexed targeted amplicon sequenc-ing to generate sequence data for multi-gene *** then combined our datasets to provide a well-supported genome-based phylogeny having broad sampling depth from the amplicon *** the Mortierellaceae phylogeny into monophyletic genera resulted in 13 genera,7 of which are newly ***-coverage genome sequencing proved to be a relatively cost-effective means of generating a high-confidence *** multi-gene phylogenetics approach enabled much greater sampling depth and breadth than the LCG approach,but has limitations *** present this work to resolve some of the taxonomic confusion and provide a genus-level framework to empower future studies on Mortierellaceae diversity and evolution.

关键词： Mortierellaceae Phylogenomics Molecular systematics Taxonomy Multi-locus sequence typing

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基于羊肚菌属类群线粒体基因组的比较分析揭示其结构与进化

基于羊肚菌属类群线粒体基因组的比较分析揭示其结构与进化

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中国菌物学会2024年学术年会

作者：陶刚 Steven Ahrendt Shingo Miyauchi 竺筱洁彭浩 Kurt Labutti Alicia Clum Richard Hayes Philippe Clowez Greg Bonito igor v.grigoriev Francis M.Martin 贵州民族大学生态环境工程学院 Université de Lorraine INRAEUnité Mixte de Recherche Interactions Arbres/MicroorganismesCentre INRAE Grand Est Nancy U.S.Department of Energy Joint Genome Institute Lawrence Berkeley National Laboratory Okinawa Institute of Science and Technology Graduate University Plant Soil and Microbial Sciences Michigan State University Department of Plant and Microbial Biology University of California Berkeley

羊肚菌属物种在陆地生态系统中具有重要意义,展现出从腐生到共生的一系列生态生活方式。然而,这些子囊菌的线粒体基因组尚未得到彻底研究,从而阻碍了对其遗传组成和生态角色的全面理解。在本研究中,我们分析了包括黄色羊肚菌、黑色羊肚... 详细信息

羊肚菌属物种在陆地生态系统中具有重要意义,展现出从腐生到共生的一系列生态生活方式。然而,这些子囊菌的线粒体基因组尚未得到彻底研究,从而阻碍了对其遗传组成和生态角色的全面理解。在本研究中,我们分析了包括黄色羊肚菌、黑色羊肚菌、红色羊肚菌和假羊肚菌在内的30个羊肚菌科物种的线粒体基因组。这些线粒体基因组是圆形或线性DNA分子,长度范围为150到565 kbp,GC含量范围为38%到48%。在这些羊肚菌科的线粒体基因组中,鉴定出15个核心蛋白编码基因、28–33个tRNA基因和两个rRNA基因。基因顺序显示出高度的保守性,其中cox1基因始终位于rnS基因旁边,cob基因被apt基因夹在两侧。然而,也观察到一些例外情况,如梯棱羊肚菌Morchella importuna中的atp6和rps3的基因重排,以及某些羊肚菌线粒体基因组中atp6和atp8的逆序排列。然而,tRNA基因的排列仍然是保守的。我们还调查了LAGLIDADG (LAGs)和GIY-YIG (GIYs)家族的归巢内切酶基因(HEGs)的分布和系统发育。总共检测到925个LAG和GIY序列,单个物种包含19–44个HEGs。这些HEGs主要位于cox1、cob、cox2和nad5内含子中,其存在和分布在羊肚菌物种间显示出显著的多样性。这一发现支持进化的"Aenaon模型",该模型提出内含子和HEGs的共同进化有助于真菌线粒体基因组的多样性。本研究为羊肚菌科的系统发育和进化提供了新的见解。

关键词：羊肚菌属线粒体基因组基因组共线性蛋白编码基因归巢内切酶基因

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Cortical hem signaling center: functions, development, and potential implications for evolution and brain disorders

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Neural Regeneration Research 2025年第4期20卷 1079-1080页

作者： victor v.Chizhikov igor Y.Iskusnykh Department of Anatomy and Neurobiology University of Tennessee Health Science CenterMemphisTNUSA

Development of the telencephalon relies upon several signaling centers-localized cellular populations that supply secreted factors to pattern the cortical *** such signaling center is the cortical hem,which arises during embryonic development at the telencephalic dorsal midline,adjacent to the choroid plexus and hippocampal primordium(Figure 1A).While the cortical hem has also been described in reptiles and birds,most of our knowledge about the developmental roles of the cortical hem is derived from the analysis in *** cortical hem produces several types of secreted molecules,including wingless-related integration site(Wnt)and bone morphogenetic(Bmp)*** cortical hem is particularly important for the development of the hippocampus,which is involved in learning and memory,and the neocortex,which is the most complex brain region that mediates multiple types of behavior and higher cognitive functions(Mangale et al.,2008;Dal-valle-Anton and Borrell,2022).

关键词： epithelium Figure center

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Elucidating elusive quaternary selenide EuCeCuSe3:Synthesis,crystal structure,properties and theoretical studies

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Journal of Rare Earths 2024年第1期42卷 163-171,I0006页

作者： Maxim v.grigoriev Anna v.Ruseikina Maxim S.Molokeev vladimir A.Chernyshev Aleksandr S.Aleksandrovsky Alexander S.Krylov Svetlana N.Krylova Nikolai P.Shestakov Dmitriy A.velikanov Alexander A.Garmonov Alexey v.Matigorov Evgeny A.Ostapchuk Thomas Schleid Damir A.Safin Laboratory of Theory and Optimization of Chemical and Technological Processes University of TyumenVolodarskogo Str.6625003TyumenRussian Federation Kirensky Institute of Physics Federal Research Center KSC SB RASAkademgorodok 50 Bld.38660036KrasnoyarskRussian Federation Department of Physics Far Eastern State Transport UniversitySerysheva Str.47680021KrasnoyarskRussian Federation Institute of Natural Sciences and Mathematics Ural Federal University Named After the First President of Russia B.N.YeltsinMira Str.19620002EkaterinburgRussian Federation Department of Photonics and Laser Technology Siberian Federal UniversitySvobodnii Ave.79660079KrasnoyarskRussian Federation Institute of Physics and Technology University of TyumenVolodarskogo Str.6625003 TyumenRussian Federation Institute for Inorganic Chemistry University of StuttgartPfaffenwaldring 55D-70569StuttgartGermany Scientific and Educational and Innovation Center for Chemical and Pharmaceutical Technologies Ural Federal University named after the First President of Russia B.N.YeltsinMira Str.19620002 EkaterinburgRussian Federation University of Tyumen Volodarskogo Str.6625003TyumenRussian Federation

We report on the novel heterometallic quaternary selenide EuCeCuSe3,the fabrication of which has been a challenge until this *** structure of the reported selenide was elucidated from the powder X-ray diffraction data,which revealed the formation of EuCeCuSe3with excellent yield(96.7%)accompanied with a minor fraction of CeSe2(3.3%),and was best solved in orthorhombic space group Pnma with the BaLaCuS3structural ***,the crystal structure of the title compound completes the row of the heterometallic quaternary selenides EuRECuSe3(RE=La,Pr,Nd,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu,Y),of which the cerium-based derivative exclusively belongs to the BaLaCuS3structural *** distortion of the CuSe4polyhedron was compared for the whole series of EuRECuSe3compounds using theτ4-descriptor for four coordinated ions,which revealed the highest degree of distortion for the Ce3+-containing selenide,followed by the La3+-based ***,the crystallographic and geometrical parameters of the reported selenide were discussed in comparison to the Ce3+-based sulfides SrCeCuS3and *** initio calculations of the crystal structure,a phonon spectrum and elastic constants for the crystal of EuCeCuSe3were also *** types and wavenumbers of fundame ntal modes were determined and the involvement of ions participating in the phonon modes was *** experimental IR spectrum of the reported selenide was interpreted and found to be in agreement with the calculated *** experimental direct band gap of EuCeCuSe3was measured to be 1.36 ev that is consistent with the concept of its origin due to interband transitions between orbitals emerging mainly from 4f(valence band)and 5d(conduction band)levels of the Eu2+*** dependence of the Young’s modulus on the direction demonstrates the anisotropy of the elastic properties,while the vickers hardness for EuCeCuSe3was calculated to be 5.2 ***,the title compound is paramagnetic above 4 K.

关键词： Quaternary selenide Synthesis Crystal structure Ab initio calculations Magnetic measurements Spectroscopy

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Microheterogeneity of the Koupol Deposit Fahlores as a Reflection of Changing of Physicochemical Parameters of the Ore-Forming Solution

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Journal of Earth Science 2013年第2期24卷 179-187页

作者： igor'v Kemkin Raisa A Kemkina Far East Geological Institute Far Eastern Branch of the Russian Academy of Sciences Far East Federal University

New data on a zonal structure of the Koupol deposit fahlores grains are given, and features of their chemism are shown. The fahlores chemical composition within the zones evolves from essentially arsenious （Fe-tennantite and Zn-tennantite）, through mixed fahlores （Zn-tennantitetetrahedrite arsenious and Zn-tennantite-tetrahedrite antimonous）, to essential antimonous （Ag-bearing Zn-tetrahedrite）. varying chemical composition manifested as mineralogical-geochemical zonation of the fahlores grains is caused by changes of physicochemical conditions of the ore forming process during the time.

关键词： fahlore mineralogical-geochemical zonation physicochemical condition Koupol deposit.

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Influence of Small-Size Contaminations on Thin Film Structural Properties

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Chinese Physics Letters 2019年第3期36卷 82-85页

作者： F.v.grigoriev v.B.Sulimov Jinlong Zhang Xinbin Cheng Zhanshan Wang A.v.Tikhonravov Research Computing Center M.V.Lomonosov Moscow State University MOE Key Laboratory of Advanced Micro-Structured Materials Institute of Precision Optical Engineering School of Physics Science and EngineeringTongji University IFSA Collaborative Innovation Center Shanghai Jiao Tong University

An approach for studying the influence of nano-particles on the structural properties of deposited thin films is proposed. It is based on the molecular dynamic modeling of the deposition process in the presence of contaminating nano-particles. The nano-particle is assumed to be immobile and its interaction with film atoms is described by a spherically symmetric potential. The approach is applied to the investigation of properties of silicon dioxide films. visualization tools are used to investigate the porosity associated with nano-particles. The structure of the film near the nano-particle is studied using the radial distribution function. It is found that fluctuations of film density near the nano-particles are essentially different in the cases of low-energy and high-energy deposition processes.

关键词： Influence Small-Size Properties

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Comparative geochemical study of the cherty rocks of the Taukha terrane(Sikhote-Alin)and its paleogeodynamic significance

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Acta Geochimica 2020年第4期39卷 539-560页

作者： igor v.Kemkin Raisa A.Kemkina Far East Geological Institute Far Eastern Branch of Russian Academy of SciencesProspect 100-Letiya Vladivostoka159VladivostokRussia 690022 Far Eastern Federal University Soukhanova Street8VladivostokRussia 690950

The article presents the results of a comparative geochemical study of cherts and siliceous-clayey rocks composing the tectono-sedimentary complexes of various structural levels of the Taukha terrain of the Sikhote-Alin Late Jurassic-Early Cretaceous accretionary *** data obtained show that the same-aged parts of the crosssections of the cherty-terrigenous sequences of the terrane lower and middle structural levels are characterized by significantly different contents and distribution patterns of major petrogenic oxides,trace,and rare-earth elements due to their accumulation in various facies of oceanic *** set of geochemical data indicates that the formation of both tectono-sedimentary complexes was carried out differently,gradually replacing each others’facies oceanic zones,and started in the near-spreading ridge area,then in the pelagial,and completed in the continental-margin deposition *** on the time interval of the facies conditions changing for each complex(i.e.,time of transition from one facies zone to another),the speeds of a paleo-oceanic plate motion(and,correspondingly,the speeds of spreading)for individual intervals of the Jurassic were *** in the spreading speeds at various sites of a paleorift zone caused the turning of a paleocontinent margin contour and spreading ridge axis at the perpendicular position,which in turn caused change of the geodynamic mode on the eastern margin of the PaleoAsian continent at the Jurassic-Cretaceous transition.

关键词： Geochemistry Radiolarian cherts Deposition environment Paleo-Pacific plate Sikhote-Alin

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Influence of Pt/Pd state on ceria-based support in CO oxidation

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Journal of Rare Earths 2023年第12期41卷 1963-1968,I0005页

作者： igor v.Zagaynov Elena Yu.Liberman Alexander v.Naumkin A.A.Baikov Institute of Metallurgy and Materials Science MoscowRussia D.I.Mendeleev University of Chemical Technology of Russia MoscowRussia A.N.Nesmeyanov Institute of Organoelement Compounds MoscowRussia

Noble metal(M:Pt,Pd,PtPd) supported on ceria system catalysts were *** oxidized and reduced forms of the active component were examined in CO *** catalysts become more active after a reduction pretreatment,which shifts the temperature of CO *** of the data obtained from characterization techniques indicates that the strong interaction of metal ions with the support prevent the reduction of the initial MO_(x)to metallic *** formation of M-ceria interfaces efficiently boosts the oxygen activation during CO oxidation,leading to the formation of chemisorbed O on M and the regeneration of the ceria lattice oxygen,thus greatly improving the catalytic performance.

关键词： Ceria Platinum Palladium CO oxidation Rare earths

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Heat Transfer and Fluid Flow over a Single Disk in a Fluid Rotating as a Rigid Body

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Journal of Thermal Science 2004年第3期13卷 279-282页

作者： igor v. SHEvCHUK Matthias H. BUSCHMANN Institute of Engineering Thermophysics Ukrainian National Academy of Sciences 2a Zhelyabov St. Kiev 03057 UkraineInstitute of Fluid Mechanics Dresden University of Technology 01062 Dresden Germany

Laminar heat transfer problem is analyzed for a disk rotating with the angular speed ωin a co-rotating fluid (with the angular speed Ω). The fluid is swirled in accordance with a forced-vortex law, it rotates as a solid body at β= Ω/ω= const. Radial variation of the disk’s surface temperature follows a power law. An exact numerical solution of the problem is obtained basing on the self-similar profiles of the local temperature of fluid, its static pressure and velocity components. Numerical computations were done at the Prandtl numbers Pr = 1(?)0.71. It is shown that with increasing βboth radial and tangential components of shear stresses decrease, and to zero value at β= 1. Nusselt number is practically constant at β= 0(?) 0.3 (and even has a point of a maximum in this region); Nu decrease noticeably for larger βvalues.

关键词： rotating disk heat transfer fluid flow Nusselt number swirl.

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On the possible orbital motion of Sgr A* in the smooth potential of the Milky Way

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Research in Astronomy and Astrophysics 2020年第12期20卷 383-390页

作者： igor’I.Nikiforov Angelina v.veselova St.Petersburg State University Universitetskij Prospekt 28Staryj PeterhofSt.Petersburg 198504Russia

The modern accuracy of measurements allows the residual/peculiar(Galactocentric) velocity of the supermassive black hole(SMBH) in our Galaxy, Sgr A*, on the order of several kilometers per *** integrate possible orbits of the SMBH along with the surrounding nuclear stellar cluster(NSC) for a barred model of the Galaxy using modern constraints on the components of the SMBH Galactocentric velocity. Is is shown that the range of oscillations of the SMBH + NSC in a regular Galactic field in the plane of the Galaxy allowed by these constraints strongly depends on the set of central components of the Galactic potential. If the central components are represented only by a bulge/bar, for a point estimate of the SMBH Galactocentric velocity, the oscillation amplitude does not exceed 7 pc in the case that a classical bulge is present and reaches 25 pc if there is no bulge;with SMBH velocity components within the 2σ significance level, the amplitude can reach 15 and 50 pc, respectively. However, when taking into account the nuclear stellar disk(NSD), even in the absence of a bulge, the oscillation amplitude is only 5 pc for the point estimate of the SMBH velocity, and 10 pc for the 2σ significance level. Thus, the possible oscillations of the SMBH + NSC complex from the confirmed components of the Galaxy’s potential are mostly limited by the NSD, and even taking into account the uncertainty of the mass of the latter, the oscillation amplitude can hardly exceed 13 pc = 6′.

关键词： Galaxy:center Galaxy:fundamental parameters Galaxy:kinematics and dynamics

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