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The Expansion and Diversification of Pentatricopeptide Repeat RNA-Editing Factors in Plants

Molecular Plant 2020年第2期13卷 215-230页

作者： Bernard Gutmann Santana Royan mareike schallenberg-rudinger Henning Lenz Ian R.Castleden Rose McDowell Michael AVacher Julian Tonti-Filippini Charles SBond Volker Knoop Ian D.Small Australian Research Council Centre of Excellence in Plant Energy Biology The University of Western AustraliaCrawleyPerth 6009WAAustralia School of Molecular Sciences The University of Western AustraliaCrawleyPerth 6009WAAustralia IZMB-Institut fur Zellulare und Molekulare Botanik Abteilung Molekulare EvolutionUniversitat BonnKirschallee 153115 BonnGermany Present address:EditForce Inc. West zone#429Kyushu University744 MotookaNishi-KuFukuokaJapan Present address:IBG-2:Plant Sciences Forschungszentrum Jiilich GmbH52425 JulichGermany Present address:Australian eHealth Research Centre Commonwealth Scientific and Industrial Research OrganisationFloreatPerth 6014WAAustralia

The RNA-binding pentatricopeptide repeat(PPR)family comprises hundreds to thousands of genes in most plants,but only a few dozen in algae,indicating massive gene expansions during land plant *** nature and timing of these expansions has not been well defined due to the sparse sequence data available from early-diverging land plant *** this study,we exploit the comprehensive OneKP datasets of over 1000 transcriptomes from diverse plants and algae toward establishing a clear picture of the evolution of this massive gene family,focusing on the proteins typically associated with RNA editing,which show the most spectacular variation in numbers and domain composition across the plant *** characterize over 2250000 PPR motifs in over 400000 *** lycophytes,polypod ferns,and hornworts,nearly 10%of expressed protein-coding genes encode putative PPR editing factors,whereas they are absent from algae and complex-thalloid *** show that rather than a single expansion,most land plant lineages with high numbers of editing factors have continued to generate novel sequence *** identify sequence variations that imply functional differences between PPR proteins in seed plants versus non-seed plants and variations we propose to be linked to seed-plant-specific editing ***,using the sequence variations across the datasets,we develop a structural model of the catalytic DYW domain associated with C-to-U editing and identify a clade of unique DYW variants that are strong candidates as U-to-C RNA-editing factors,given their phylogenetic distribution and sequence characteristics.

关键词： RNA editing RNA-binding protein organelles

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Influence of smoke, heat and fire on germination of woody species occurring in the dry valleys of southwest China

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Journal of Plant Ecology 2019年第6期12卷 931-940页

作者： mareike Roeder Weidong Yang Kyle W.Tomlinson Center for Integrative Conservation Xishuangbanna Tropical Botanical GardenChinese Academy of SciencesMenglunMenglaYunnan 666303China Institute of Floodplain Ecology Karlsruhe Institute of TechnologyJosefstraße 1D–76437 RastattGermany

Aims Savannahs depend on fire for their *** influences regeneration from seeds in several ways:it converts the environment into a more open space which can benefit the establishment of seedlings,and fire itself can also enhance germination by chemical and physical cues,such as smoke and *** is limited information as to how seed of Asian savannah species respond to fire,even though Asia has several dry vegetation types that are associated with *** main question was whether fire enhances or triggers the germination of woody species occurring in southwest Chinese dry valleys,which have savannah *** We conducted tests with heat(80°C)and smoke solution treatments,and tests with real fire by burning grass on top of sand trays containing *** tested 35 species,including savannah species,and gully and forest *** on seed availability,not all species were tested for all ***-six species had total germination>4%and these were used for *** Findings Heat increased germination of three species(strongest reaction:Dodonaea viscosa),smoke increased germination of five species(strongest reaction:Calotropis gigantea).Both treatments decreased germination for five and seven species,*** fire was detrimental for most species,except for ***,which is known to respond positively to heat *** though fire-related cues were not a trigger for germination for most species in our study,fire could still be crucial for regeneration by competition release.

关键词： smoke water burning biomass germination time Dodonaea viscosa Calotropis gigantea seed mass water content dark germination

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Classes of tree-based networks

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Visual Computing for Industry,Biomedicine,and Art 2020年第1期3卷 104-129页

作者： mareike Fischer Michelle Galla Lina Herbst Yangjing Long Kristina Wicke Institute of Mathematics and Computer Science University of GreifswaldWalther-Rathenau-Straße 4717489 GreifswaldGermany School of Mathematics and Statistics Central China Normal University800 Dongchuan RoadShanghai 200240China

Recently,so-called tree-based phylogenetic networks have attracted considerable *** networks can be constructed from a phylogenetic tree,called the base tree,by adding additional *** primary aim of this study is to provide sufficient criteria for tree-basedness by reducing phylogenetic networks to related graph *** though it is generally known that determining whether a network is tree-based is an NP-complete problem,one of these criteria,namely edge-basedness,can be verified in linear ***,the class of edgebased networks is closely related to a well-known family of graphs,namely,the class of generalized series-parallel graphs,and we explore this relationship in full ***,we introduce further classes of tree-based networks and analyze their relationships.

关键词： Phylogenetic tree Phylogenetic network Tree-based network Edge-based network Chordal network Hamilton connected Hamiltonian path Generalized series-parallel graphs Series-parallel graphs

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Do alternative stable states exist in large shallow Taihu Lake,China?

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Journal of Oceanology and Limnology 2023年第3期41卷 959-971页

作者： Yan LI Yu MA Haijun WANG Hongzhu WANG Yongde CUI Shijun BIAN Miao ZHANG Mengmei LIU Yexin YU Marc schallenberg State Key Laboratory of Freshwater Ecology and Biotechnology Institute of HydrobiologyChinese Academy of SciencesWuhan 430072China Institute for Ecological Research and Pollution Control of Plateau Lakes School of Ecology and Environmental ScienceYunnan UniversityKunming 650504China University of Chinese Academy of Sciences Beijing 100049China Department of Zoology University of OtagoPO Box 56Dunedin 9054New Zealand

Regime shifts from submersed macrophyte dominance to phytoplankton dominance have been widely reported in small-to medium-sized shallow ***,alternative stable states in large shallow lakes(surface area>500 km^(2))remain *** understand the alternative stable states and the main influencing factors of submersed macrophytes in large lakes,the ecosystem states from monitoring data from 1959 to 2019 in large shallow Taihu Lake(2338 km^(2)in average depth of 2.12 m)in China were *** in submersed macrophyte coverage(C_(Mac))and phytoplankton chlorophyll a(Chl a)in the time series and their relationships with environmental factors were *** the field investigation from August 2018 to May 2019,nutrients and Chl a showed obvious heterogeneity across the lake,being generally higher in the western and northern areas and lower in the southeast area,while C_(Mac)was only observed in the eastern areas,e.g.,East Taihu Lake,Xukou Bay,and Gonghu *** the long-term monitoring from 1959 to 2019 in the Central Region,Meiliang Bay,and East Taihu Lake,Chl a increased significantly in the time series.C_(Mac)varied slightly among different subareas,always at low levels(<10%)in the Central Region and Meiliang Bay but at relatively high levels in East Taihu Lake(10%–90%).Frequency distributions of response variables had no multimodality except for C_(Mac)in East Taihu Lake,with two peaks between 15%and 20%and between 55%and 60%.A dual relationship was found between Chl a and total phosphorus(TP)in the areas with and without macrophytes,while C_(Mac)showed no relationship with TP,and submersed macrophytes did not flourish in the Central Region and Meiliang Bay even when TP was at very low levels(≈10 mg/m3).Taihu Lake had similar algal turbidity(TurbAlg)as small-to mediumsized lakes but generally presented with higher values of nonalgal turbidity(TurbNonAlg),as did their contribution to total turbidity as a *** study suggested that

关键词： alternative stable state submersed macrophyte phytoplankton Taihu Lake large shallow lake

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Multiplexed detection and differentiation of bacterial enzymes and bacteria by color-encoded sensor hydrogels

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Bioactive Materials 2021年第12期6卷 4286-4300页

作者： Zhiyuan Jia mareike Müller Tony Le Gall Martijn Riool Max Müller Sebastian A.J.Zaat Tristan Montier Holger Schönherr Physical Chemistry I&Research Center of Micro and Nanochemistry and Engineering(Cμ) Department of Chemistry and BiologyUniversity of SiegenAdolf-Reichwein-Straße 257076SiegenGermany Univ Brest INSERMEFSUMR 1078 GGFBF-29200BrestFrance Department of Medical Microbiology and Infection Prevention Amsterdam institute for Infection and ImmunityAmsterdam UMCUniversity of AmsterdamMeibergdreef 91105AZAmsterdamthe Netherlands CHRU de Brest Service degenetique medicale et de biologie de la reproductionCentre de Réference des Maladies Rares《Maladies neuromusculaires》F-29200BrestFrance

We report on the fabrication and characterization of color-encoded chitosan hydrogels for the rapid,sensitive and specific detection of bacterial enzymes as well as the selective detection of a set of tested bacteria through characteristic enzyme *** patterned sensor hydrogels are functionalized with three different colorimetric enzyme substrates affording the multiplexed detection and differentiation ofα-glucosidase,β-galactosidase andβ-*** limits of detection of the hydrogels for an observation time of 60 min using a conventional microplate reader correspond to concentrations of 0.2,3.4 and 4.5 nM of these enzymes,*** on their different enzyme expression patterns,Staphylococcus aureus strain RN4220,methicillin-resistant ***(MRSA)strain N315,both producingα-glucosidase,but notβ-glucuronidase andβ-galactosidase,Escherichia coli strain DH5α,producingβ-glucuronidase andα-glucosidase,but notβ-galactosidase,and the enterohemorrhagic ***(EHEC)strain E32511,producingβ-galactosidase,but none of the other two enzymes,can be reliably and rapidly distinguished from each *** results confirm the applicability of enzyme sensing hydrogels for the detection and discrimination of specific enzymes to facilitate differentiation of bacterial *** hydrogels thus possess the potential to be further refined as detection units of a multiplexed format to identify certain bacteria for future application in point-of-care microbiological diagnostics in food safety and medical settings.

关键词： Multiplexed biosensors Bacteria detection Bacterial enzyme Reporter hydrogels Colorimetric substrates

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Correction to: Classes of tree-based networks

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Visual Computing for Industry,Biomedicine,and Art 2021年第1期4卷 7-8页

作者： mareike Fischer Lina Herbst Michelle Galla Yangjing Long Kristina Wicke Institute of Mathematics and Computer Science University of GreifswaldGreifswaldGermany School of Mathematics and Statistics Central China Normal UniversityWuhanHubeiChina

Following publication of the original article[1],in the description of the leaf shrinking procedure as well as in Algorithm 1 and the definition of edge-based graphs in[1],the condition that G contains at least two le... 详细信息

关键词： networks condition tree

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N-酰化内酰胺在肽類合成中的應用

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高分子学报 1957年第3期 153-158页

作者： J. rudinger,楊承淑捷克斯洛伐克科學院博士

肽類合成中的主要問題是酰胺键的形成。除此以外,還要把組成的氨基酸中不参加反應的氨基或羧基,適當地保護起來。對多官能的氨基酸,更需要封住某些其他官能團。這個問題,對一氨二羧酸(谷氨酸,天門冬氨酸),或二氨一羧酸(賴氨酸,鳥氨酸等)... 详细信息

肽類合成中的主要問題是酰胺键的形成。除此以外,還要把組成的氨基酸中不参加反應的氨基或羧基,適當地保護起來。對多官能的氨基酸,更需要封住某些其他官能團。這個問題,對一氨二羧酸(谷氨酸,天門冬氨酸),或二氨一羧酸(賴氨酸,鳥氨酸等),更为複雜。因為這里要封住的基團和要參加組成肽鍵的基團屬於同一類型,活潑度相差很少。

关键词：谷氨酸 CHC NH 衍生物 α-氨基戊二酸神经递体酮酸氨基丁酸

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充满流体的膨胀管中的激波

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力学进展 1984年第4期 514-520页

作者： G.rudinger 何卓烈

引言不可压缩流体流过膨胀管,在某种程度上,与气体流过刚性管相似。在这两种系统中都可能建立波,只是前者是由于管子的膨胀所致,而后者则是由于气体的压缩所致。膨胀管的波的传播过程主要发生在生物系统中,例如,大动脉、大静脉或泌尿管中,

关键词：激波分离流动面积比橡皮管粘性流动方程边界层分离流体风洞膨胀管

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In Vivo Function of Tic22, a Protein Import Component of the Intermembrane Space of Chloroplasts

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Molecular Plant 2013年第3期6卷 817-829页

作者： mareike Rudolf Anu B. Machettira Lucia E. Groβ Katrin L. Weber Kathrin Bolte Tihana Bionda Maik S. Sommer Uwe G. Maier Andreas RM. Weber Enrico Schleiff Joanna Tripp Department of Biosciences Molecular Cell Biology of Plants Center of Membrane Proteomics and Cluster of Excellence Frankfurt Goethe University Max-von-Laue Str. 9 D-60438 Frankfurt Germany Institute of Plant Biochemistry Heinrich-Heine-University Universitatsstr. 1 D-40225 Dusseldorf Germany Cell Biology Philipps University Marburg Karl-von-Frisch-Str. 8 D-35032 Marburg Germany LOEWE Center for Synthetic Microbiology (SYNMIKRO) Hans-Meerwein-Str. D-35032 Marburg Germany

Preprotein import into chloroplasts depends on macromolecular machineries in the outer and inner chloroplast envelope membrane （TOC and TIC）. It was suggested that both machineries are interconnected by components of the intermembrane space （IMS）. That is, amongst others, Tic22, of which two closely related isoforms exist in Arabidopsis thaliana, namely atTic22-III and atTic22-IV. We investigated the function of Tic22 in vivo by analyzing T-DNA insertion lines of the corresponding genes. While the T-DNA insertion in the individual genes caused only slight defects, a double mutant of both isoforms showed retarded growth, a pale phenotype under high-light conditions, a reduced import rate, and a reduction in the photosynthetic performance of the plants. The latter is supported by changes in the metabolite content of mutant plants when compared to wild-type. Thus, our results support the notion that Tic22 is directly involved in chloroplast preprotein import and might point to a particular importance of Tic22 in chloroplast biogenesis at times of high import rates.

关键词： protein translocation TOC and TIC intermembrane space translocon chloroplast biogenesis metabolitecontent.

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Structural insight into the binding mechanism of macrodomain protein TARG1 with poly-ADP-ribose chains

Structural insight into the binding mechanism of macrodomain...

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2019中国化学会第十五届全国计算（机）化学学术会议

作者：傅薇 mareike Bütepage Bernhard Lüscher Jinyu Li 福州大学 Institute of Biochemistry and Molecular Biology Medical School RWTH Aachen University National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies College of Chemistry Fuzhou University

Macrodomains constitute a protein motif family present in all kingdoms of life1. Emerging evidence indicates that specific macrodomain proteins interact with mono-ADP-ribosylation（MARylation） on target proteins to ‘read’ and ‘erase’ this modification2. Therefore, macrodomains are implicated in many MARylation-dependent cellular activities that include DNA repair processes, gene transcription, and intracellular signaling. Very recently, we found that terminal ADP-ribose glycohydrolase 1（TARG1）, a macrodomain-containing protein is also capable to form complexes with poly-ADP-ribose（PAR） chains in vitro and in cell3. However, the structural basis of the binding of TARG1 to PAR and its biological relevant cross-talk with MARylation are still unknown. Here, an integrated in silico strategy combining docking and molecular dynamics（MD） simulation was applied to predict the structural models of TARG1 bound to both branched and linear forms of pentameric PAR chains. Our 1000 ns-long MD simulations showed that each PAR chain may stably bind at the lip region of the enzymatic site of TARG1 with one terminal ADP-ribose unit inserted into the ADP-ribose binding pocket. Specifically, the binding mode of the former well resembled the one of ADP-ribose alone with TARG1 as observed in NMR structure4. Additionally, the key residues selectively engaged with branched and linear PAR chains were identified. The mutagenesis assays on these residues are ongoing to validate the complex models predicted here. Our work will substantially promote and accelerate the investigations of the role of TARG1 in the cross-talk between mono-and poly-ADP-ribosylations for cell physiology and disease-related processes.

关键词： ADP-ribosylation PAR chain TARG1 molecular dynamics

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