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Incidence of human papilloma virus in esophageal squamous cell carcinoma in patients from the Lublin region

World Journal of Gastroenterology 2012年第40期18卷 5739-5744页

作者： Andrzej Dabrowski Wojciech Kwasniewski Tomasz Skoczylas wiesawa bednarek Dorota Kuzma Anna Gozdzicka-Józefiak Second Department of General and Gastrointestinal Surgery Oncological Surgery of the Alimentary TractMedical University of Lublin Department of Gynecological Oncology and Gynecology Medical University of Lublin Department of Molecular Virology Institute of Experimental BiologyAdam Mickiewicz University

AIM:To assess the prevalence of human papilloma virus(HPV) in esophageal squamous cell carcinoma(ESCC) in the south-eastern region of Poland.METHODS:The study population consisted of 56 ESCC patients and 35 controls.The controls were patients referred to our department due to other nonesophageal and non-oncological disorders with no gross or microscopic esophageal pathology as confirmed by endoscopy and histopathology.In the ESCC patients,samples were taken from normal mucosa(56 mucosa samples) and from the tumor(56 tumor samples).Tissue samples from the controls were taken from normal mucosa of the middle esophagus(35 control samples).Quantitative determination of DNA was carried out using a spectrophotometric method.Genomic DNA was isolated using the QIAamp DNA Midi Kit.HPV infection was identified following PCR amplification of the HPV gene sequence,using primers MY09 and MY11 complementary to the genome sequence of at least 33 types of HPV.The sequencing results were computationally analyzed using the basic local alignment search tool database.RESULTS:In tumor samples,HPV DNA was identified in 28 of 56 patients(50%).High risk HPV phenotypes(16 or/and 18) were found in 5 of 56 patients(8.9%),low risk in 19 of 56 patients(33.9%) and other types of HPV(37,81,97,CP6108) in 4 of 56 patients(7.1%).In mucosa samples,HPV DNA was isolated in 21 of 56 patients(37.5%).High risk HPV DNA was confirmed in 3 of 56 patients(5.3%),low risk HPV DNA in 12 of 56 patients(21.4%),and other types of HPV in 6 of 56 patients(10.7%).In control samples,HPV DNA was identified in 4 of 35 patients(11.4%) with no high risk HPV.The occurrence of HPV in ESCC patients was significantly higher than in the controls [28 of 56(50%) vs 4 of 35(11.4%),P < 0.001].In esophageal cancer patients,both in tumor and mucosa samples,the predominant HPV phenotypes were low risk HPV,isolated 4 times more frequently than high risk phenotypes [19 of 56(33.9%) vs 5 of 56(8.9%),P < 0.001].A higher prevalence of HPV was identified in female patients(71.4% vs 46.9%

关键词：乳头状瘤病毒鳞状细胞癌食管癌发病率患者基因组DNA 肿瘤性疾病 DNA分离

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Specialized metabolites as versatile tools in shaping plant-microbe associations

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Molecular Plant 2023年第1期16卷 122-144页

作者： Gopal Singh Himani Agrawal Paweł bednarek Institute of Bioorganic Chemistry Polish Academy of SciencesNoskowskiego 12/1461-704 PoznańPoland

Plants are rich repository of a large number of chemical compounds collectively referred to as specialized metabolites.These compounds are of importance for adaptive processes including responses against changing abiotic conditions and interactions with various co-existing organisms.One of the strikingly affirmed functions of these specialized metabolites is their involvement in plants’life-long interactions with complex multi-kingdom microbiomes including both beneficial and harmful microorganisms.Recent developments in genomic and molecular biology tools not only help to generate well-curated information about regulatory and structural components of biosynthetic pathways of plant specialized metabolites but also to create and screen mutant lines defective in their synthesis.In this review,we have comprehensively surveyed the function of these specialized metabolites and discussed recent research findings demonstrating the responses of various microbes on tested mutant lines having defective biosynthesis of particular metabolites.In addition,we attempt to provide key clues about the impact of these metabolites on the assembly of the plant microbiome by summarizing the major findings of recent comparative metagenomic analyses of available mutant lines under customized and natural microbial niches.Subsequently,we delineate benchmark initiatives that aim to engineer or manipulate the biosynthetic pathways to produce specialized metabolites in heterologous systems but also to diversify their immune function.While denoting the function of these metabolites,we also discuss the critical bottlenecks associated with understanding and exploiting their function in improving plant adaptation to the environment.

关键词： microbiome nitrogen/sulfur-containing compounds phenylpropanoids plant immunity symbiosis terpenoids

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Three-dimensional visualization of planta clathrin-coated vesicles at ultrastructural resolution

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Molecular Plant 2022年第10期15卷 1533-1542页

作者： Alexander Johnson Walter A.Kaufmann Christoph Sommer Tommaso Costanzo Dana A.Dahhan Sebastian Y.bednarek Jiri Friml Institute of Science and Technology Austria(ISTA) 3400KlosterneuburgAustria UW-Madison Department of Biochemistry433 Babcock Dr.MadisonWI 53706USA

Biological systems are the sum of their dynamic three-dimensional(3D)parts.Therefore,it is critical to study biological structures in 3D and at high resolution to gain insights into their physiological functions.Electron microscopy of metal replicas of unroofed cells and isolated organelles has been a key technique to visualize intracellular structures at nanometer resolution.However,many of these methods require specialized equipment and personnel to complete them.Here,we present novel accessible methods to analyze biological structures in unroofed cells and biochemically isolated organelles in 3D and at nanometer resolution,focusing on Arabidopsis clathrin-coated vesicles(CCVs).While CCVs are essential trafficking organelles,their detailed structural information is lacking due to their poor preservation when observed via classical electron microscopy protocols experiments.First,we establish a method to visualize CCVs in unroofed cells using scanning transmission electron microscopy tomography,providing sufficient resolution to define the clathrin coat arrangements.Critically,the samples are prepared directly on electron microscopy grids,removing the requirement to use extremely corrosive acids,thereby enabling the use of this method in any electron microscopy lab.Secondly,we demonstrate that this standardized sample preparation allows the direct comparison of isolated CCV samples with those visualized in cells.Finally,to facilitate the high-throughput and robust screening of metal replicated samples,we provide a deep learning analysis method to screen the“pseudo 3D”morphologies of CCVs imaged with 2D modalities.Collectively,our work establishes accessible ways to examine the 3D structure of biological samples and provide novel insights into the structure of plant CCVs.

关键词： Arabidopsis thaliana clathrin-coated vesicles STEM tomography electron microscopy clathrin-mediated endocytosis

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Delineating the glioblastoma stemness by genes involved in cytoskeletal rearrangements and metabolic alterations

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World Journal of Stem Cells 2023年第5期15卷 302-322页

作者： Żaneta Kałuzińska-Kołat Damian Kołat Katarzyna Kośla Elżbieta Płuciennik Andrzej K bednarek Department of Experimental Surgery Medical University of LodzLodz 90-136LodzkiePoland Department of Molecular Carcinogenesis Medical University of LodzLodz 90-752LodzkiePoland Department of Functional Genomics Medical University of LodzLodz 90-752LodzkiePoland

Literature data on glioblastoma ongoingly underline the link between metabolism and cancer stemness,the latter is one responsible for potentiating the resistance to treatment,inter alia due to increased invasiveness.In recent years,glioblastoma stemness research has bashfully introduced a key aspect of cytoskeletal rearrangements,whereas the impact of the cytoskeleton on invasiveness is well known.Although non-stem glioblastoma cells are less invasive than glioblastoma stem cells(GSCs),these cells also acquire stemness with greater ease if characterized as invasive cells and not tumor core cells.This suggests that glioblastoma stemness should be further investigated for any phenomena related to the cytoskeleton and metabolism,as they may provide new invasion-related insights.Previously,we proved that interplay between metabolism and cytoskeleton existed in glioblastoma.Despite searching for cytoskeleton-related processes in which the investigated genes might have been involved,not only did we stumble across the relation to metabolism but also reported genes that were found to be implicated in stemness.Thus,dedicated research on these genes in GSCs seems justifiable and might reveal novel directions and/or biomarkers that could be utilized in the future.Herein,we review the previously identified cytoskeleton/metabolism-related genes through the prism of glioblastoma stemness.

关键词： Glioblastoma Stemness Cytoskeleton Metabolism Biomarkers Therapy

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UGT76B1 controls the growth-immunity trade-off during systemic acquired resistance

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Molecular Plant 2021年第4期14卷 544-546页

作者： Marta Pastorczyk-Szlenkier Pawei bednarek Institute of Bioorganic Chemistry Polish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland

Higher plants evolved multiple innate immune systems to combat pathogens present in their living environment.However,activation of the complex immune responses allocates nutrient resources into biosynthesis of various defense molecules,and this in turn often represses growth and development of the entire plant.Over the years,the significance of the effective coregulation of growth and immunity has been demonstrated with dwarf phenotypes of autoimmune mutant lines of model plants displaying constitutive defense responses(van Wersch et al.,2016).This tightly regulated balance,termed the growthimmunity trade-off,is an important objective in plant breeding,which ultimately aims at plant cultivars that are both highly resistant and efficient in terms of growth and yield(Ning et al.,2017).

关键词： breeding cultivar dwarf

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Regulation of Pathogen-Triggered Tryptophan Metabolism in Arabidopsis thaliana by MYB Transcription Factors and Indole Glucosinolate Conversion Products

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Molecular Plant 2016年第5期9卷 682-695页

作者： Henning Frerigmann Mariola Pislewska-bednarek Andrea Sanchez-Vallet Antonio Molina Erich Glawischnig Tamara Gigolashvili Pawel bednarek Botanical Institute and Cluster of Excellence on Plant Sciences(CEPLAS) University of Cologne BioCenter Zulpicher Straβe 47b 50674 Cologne Germany Institute of Bioorganic Chemistry Polish Academy of Sciences Noskowskiego12/14 61-704 Pozna(n) Poland Centro de Biotecnologiay Genomica de Plantas Unlversidad Politecnica de Madrid Campus Montegancedo Pozuelo de Alarcon 28223 Madrid Spain Lehrstuhl for Genetik Technische Universitat Munchen Emil-Ramann-Str. 8 85354 Freising Germany ETH Zurich Department of Environmental Systems Science GHN H41 Universitatsstrasse 16 8092 Zurich Switzerland

MYB34, MYB51, and MYB122 transcription factors are known as decisive regulators of indolic glucosinolate （IG） biosynthesis with a strong impact on expression of genes encoding CYP79B2 and CYP79B3 enzymes that redundantly convert tryptophan to indole-3-acetaldoxime （IAOx）. This intermediate represents a branching point for IG biosynthesis, and pathways leading to camalexin and indole-carboxylic acids （ICA）. Here we investigate how these MYBs affect the pathogen-triggered Trp metabolism. Our experiments indicated that these three MYBs affect not only IG production but also constitutive biosynthesis of other IAOx- derived metabolites. Strikingly, the PENETRATION 2 （PEN2）-dependent IG-metabolism products, which are absent in myb34/51/122 and pen2 mutants, were indispensable for full flg22-mediated induction of other IAOx-dedved compounds. However, germ induction and accumulation of ICAs and camalexin upon path- ogen infection was not compromised in myb34/51/122 plants, despite strongly reduced IG levels. Hence, in comparison with cyp79B2/B3, which lacks all IAOx-derived metabolites, we found myb34/51/122 an ideal tool to analyze IG contribution to resistance against the necrotrophic fungal pathogen Plectosphaerella cucumerina. The susceptibility of myb34/51/122 was similar to that of pen2, but much lower than susceptibility of cyp79B2/B3, indicating that MYB34/51/122 contribute to resistance toward P. cucumerina exclu- sively through IG biosynthesis, and that PEN2 is the main leaf myrosinase activating IGs in response to microbial pathogens.

关键词： indolic glucosinate P/ectosphaere//a cucumerina MAMP-triggered immunity Trp metabolism indole-3-carboxylic acids camalexin

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Coupling of the Magnetostriction and Hall Effect in the Porous Magnetorheological Composite

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Journal of Electromagnetic Analysis and Applications 2010年第1期2卷 1-6页

作者： Stanislaw bednarek 不详

The first part of this paper is presents a method for producing the composite which shows ferromagnetic, highly-elastic and electrically-conducting properties. This composite consists of ferromagnetic particles of the size 0.15-0.25 mm made of the chemically pure iron. The mentioned particles were dispersed in the elastic porous silicone the matrix with pores of the size 0.15-0.25 mm. Colloidal graphite particles of the size not exceeding 0.5 μm were added to the matrix to increase electrical conductivity. The production method consist in mixing particles of iron, graphite and sodium chloride with non-polymerized silicone and rinsing salt particles by water after the matrix polymerization. In its second part the paper provides a description of the measurement system for longitudinal magnetostriction and the Hall voltage. The magnetic field with the induction of ± 8 T produced by the Bitter type magnet was applied to the composite samples. The supplying voltage was applied to these samples and the Hall voltage was measured at the electrodes glued to them. The longitudinal magnetostriction was measured by means of the capacitor with a variable capacity placed at the upper surface of these samples. The linear magnetostriction exceeding ± 6 % and the Hall voltage reaching ± 5.5 nV were detected by the conducted measurements. Both the longitudinal magnetostriction and the Hall voltage show nonlinear changes and hysteresis lopes during the magnetic field application and the supplying current flow. The coupling of these changes and other regularities observed in the investigated composites and especially their non-linearity and hysteresis, are discussed in the final part of the paper.

关键词： Hall Effect Magnetostriction Non-linearity Hysteresis Composite Porous Elastic Ferromagnetic

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评价系统研究中的关键原则

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外语研究 2018年第1期35卷 39-45页

作者： Monika bednarek 郇昌鹏澳大利亚悉尼大学语言学系上海交通大学外国语学院上海200240

评价系统(Martin&White 2005)是一个人际语义系统,现有研究大多应用评价系统进行话语分析,较少涉及评价分析中的方法论问题。仅有的少数探讨评价分析方法论的研究主要关注双重标注问题,而非评价分析的系统方法和原则。本文试图弥补这一... 详细信息

评价系统(Martin&White 2005)是一个人际语义系统,现有研究大多应用评价系统进行话语分析,较少涉及评价分析中的方法论问题。仅有的少数探讨评价分析方法论的研究主要关注双重标注问题,而非评价分析的系统方法和原则。本文试图弥补这一不足,促使学界关注评价研究中的方法论问题,对此开展更深层次的探讨。本文重点探讨应用评价系统进行话语分析时需要考虑的方法论问题以及解决办法。具体分三个主题进行论述:第一,文本选取;第二,文本的评价分析(透明度、一致性、简约法则,以及语料之间和语料内部的差异);第三,评价分析结果的阐释。

关键词：评价系统方法论基于语料库的话语分析

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Arabidopsis Heterotrimeric G-protein Regulates Cell Wall Defense and Resistance to Necrotrophic Fungi

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Molecular Plant 2012年第1期5卷 98-114页

作者： Magdalena Delgado-Cerezo Clara Sanchez-Rodriguez Viviana Escudero Eva Miedes Paula Virginia Fernandez Lucia Jorda Camilo Hernandez-Blanco Andrea Sanchez-Vallet Pawel bednarek Paul Schulze-Lefert Shauna Somervilleg Jose Manuel Estevez Staffan Persson Antonio Molina Centro de Biotecnologia y Genomica de Plantas （UPM-INIA） Universidad Politecnica de Madrid Campus de Montegancedo E-28223-Pozuelo de Alarcbn （Madrid） Spain Max-Planck-lnstitute fLir Molekulare Pflanzenphysiologie Am MQhlenberg 2 14476 Potsdam Germany Laboratorio de Fisiologia y Biologia Molecular IFIByNE （CONICET） FCEyN-Universidad de Buenos Aires Pab. II Intendente Guiraldes 2160 Buenos Aires C1428EGA Argentina Present address： Laboratory of Phytopathology Wageningen University Droevendaalsesteeg 1 6708 PB Wageningen The Netherlands Max Planck Institut for Zuchtungsforschung Department of Plant Microbe Interactions Carl-von-Linne-Weg 10 D-50829 Koln Germany Institute of Bioorganic Chemistry Polish Academy of Sciences Noskowskiego 12/14 61-704 Poznan Poland Energy Biosciences Institute 130 Calvin Hall University of California at Berkeley Berkeley CA 94720 USA

The Arabidopsis heterotrimeric G-protein controls defense responses to necrotrophic and vascular fungi. The agbl mutant impaired in the Gβ subunit displays enhanced susceptibility to these pathogens. Gβ/AGB1 forms an obligate dimer with either one of the Arabidopsis Gγsubunits （γ1/AGG1 and γ2/AGG2）. Accordingly, we now demonstrate that the aggl agg2 double mutant is as susceptible as agbl plants to the necrotrophic fungus Plectosphaerella cucumerina. To elucidate the molecular basis of heterotrimeric G-protein-mediated resistance, we performed a comparative transcriptomic analysis of agbl-1 mutant and wild-type plants upon inoculation with P cucumerina. This analysis, together with metab- olomic studies, demonstrated that G-protein-mediated resistance was independent of defensive pathways required for resistance to necrotrophic fungi, such as the salicylic acid, jasmonic acid, ethylene, abscisic acid, and tryptophan-derived metabolites signaling, as these pathways were not impaired in agbl and aggl agg2 mutants. Notably, many mis-reguiated genes in agbl plants were related with cell wall functions, which was also the case in aggl agg2 mutant. Biochemical analyses and Fourier Transform InfraRed （FTIR） spectroscopy of cell walls from G-protein mutants revealed that the xylose content was lower in agbl and aggl agg2 mutants than in wild-type plants, and that mutant walls had similar FTIR spec-tratypes, which differed from that of wild-type plants. The data presented here suggest a canonical functionality of the Gβ and Gγ1/γ2 subunits in the control of Arabidopsis immune responses and the regulation of cell wall composition.

关键词： Plant immunity cell wall indole glucosinolates xylose necrotropic fungi G-protein.

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Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple(Malus×domestica)

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Horticulture Research 2019年第1期6卷 1116-1128页

作者： Katchen Julliany Pereira Silva Jugpreet Singh Ryland bednarek Zhangjun Fei awais Khan Plant Pathology and Plant-Microbe Biology Section Cornell UniversityGenevaNY 14456USA Boyce Thompson Institute Cornell UniversityIthacaNY 14853USA

Apple cultivars with durable resistance are needed for sustainable management of fire blight,the most destructive bacterial disease of apples.Although studies have identified genetic resistance to fire blight in both wild species and cultivated apples,more research is needed to understand the molecular mechanisms underlying host–pathogen interaction and differential genotypic responses to fire blight infection.We have analyzed phenotypic and transcriptional responses of‘Empire’and‘Gala’apple cultivars to fire blight by infecting them with a highly aggressive E.amylovora strain.Disease progress,based on the percentage of visual shoot necrosis,started showing significant(p<0.001)differences between‘Empire’and‘Gala’4 days after infection(dai).‘Empire’seems to slow down bacterial progress more rapidly after this point.We further compared transcriptome profiles of‘Empire’and‘Gala’at three different time points after fire blight infection.More genes showed differential expression in‘Gala’at earlier stages,but the number of differentially expressed genes increased in‘Empire’at 3 dai.Functional classes related to defense,cell cycle,response to stress,and biotic stress were identified and a few co-expression gene networks showed particular enrichment for plant defense and abiotic stress response genes.Several of these genes also co-localized in previously identified quantitative trait locus regions for fire blight resistance on linkage groups 7 and 12,and can serve as functional candidates for future research.These results highlight different molecular mechanisms for pathogen perception and control in two apple cultivars and will contribute toward better understanding of E.amylovora-Malus pathosystem.

关键词： blight cultivar networks

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