MicrobiologyOpen

Cover image for Vol. 5 Issue 2

Early View (Online Version of Record published before inclusion in an issue)

Edited by Pierre Cornelis, Microbial Interactions, VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium

Impact Factor: 2.213

ISI Journal Citation Reports © Ranking: 2014: 75/119 (Microbiology)

Online ISSN: 2045-8827

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  1. 1 - 28
  1. Original Research

    1. You have full text access to this OnlineOpen article
      Effects of dietary Lactobacillus plantarum and AHL lactonase on the control of Aeromonas hydrophila infection in tilapia

      Wenshu Liu, Chao Ran, Zhi Liu, Qian Gao, Shude Xu, Einar Ringø, Reidar Myklebust, Zemao Gu and Zhigang Zhou

      Article first published online: 20 APR 2016 | DOI: 10.1002/mbo3.362

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      Lactobacillus plantarum JCM1149 and acylated homoserine lactonase AIO6 enhanced the resistance against Aeromonas hydrophila. Density of tilapia fed AIO6 was significantly lower than those of the control. Lb. plantarum JCM1149 is recommended to control the A. hydrophila infection in tilapia.

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      Spatial and temporal variability of bacterial communities within a combined sewer system

      Henriette Stokbro Jensen, Raju Sekar, Will J. Shepherd, Andrew M. Osborn, Simon Tait and Catherine A. Biggs

      Article first published online: 10 APR 2016 | DOI: 10.1002/mbo3.356

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      Microbial communities in sewers influence the sewer environment and cause problems such as odor generation. Little is known about the long-term variations in these communities. In this work, it was found that the bacterial communities in the wastewater and biofilms are distinctly different and see variations in very different length and timescales.

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      RNA-seq transcriptome analysis of a Pseudomonas strain with diversified catalytic properties growth under different culture medium

      Jia-Wei Yang, Dai-Jun Zheng, Bao-Dong Cui, Min Yang and Yong-Zheng Chen

      Article first published online: 6 APR 2016 | DOI: 10.1002/mbo3.357

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      In this study, a Pseudomonas strain exhibit versatile oxidation activity to synthesize chiral sulfoxides and reduction activity to synthesize chiral alcohols growth under different culture mediums, respectively. Further comparative transcriptome analysis provides insights into the mechanism of diversity in catalytic properties, as well as candidate enzymes for application of enantiomerically pure molecules and pharmaceuticals biocatalysis.

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      Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis

      Qassim Esmaeel, Maude Pupin, Nam Phuong Kieu, Gabrielle Chataigné, Max Béchet, Jovana Deravel, François Krier, Monica Höfte, Philippe Jacques and Valérie Leclère

      Article first published online: 5 APR 2016 | DOI: 10.1002/mbo3.347

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      A genome mining was carried out on 48 Burkholderia strains. A bioinformatics screening for nonribosomal peptide synthetases (NRPSs) led to the identification of new secondary metabolites, especially siderophores and lipopeptides.

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      Molecular and proteome analyses highlight the importance of the Cpx envelope stress system for acid stress and cell wall stability in Escherichia coli

      Kristin Surmann, Emina Ćudić, Elke Hammer and Sabine Hunke

      Article first published online: 2 APR 2016 | DOI: 10.1002/mbo3.353

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      Here, we asked how the absolute molecular amounts and stoichiometry of the envelope stress proteins CpxA, CpxR, and CpxP are affected to better understand the functionality and dynamics of the Cpx envelope stress two-component system in Escherichia coli and how activation of the Cpx system impacts on the global proteome. Using selected reaction monitoring, we report that the amounts of CpxA and CpxR and their stoichiometry are only marginally affected by Cpx activation, but a 10-fold excess of CpxP is required to turn off the Cpx response. Global proteome analysis identifies a previously unknown role for Cpx system in downregulating the acid stress response and assigns the Cpx system a general role in cell wall stability.

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      Identification of inhibitors of the transmembrane protease FlaK of Methanococcus maripaludis

      Ina Coburger, Yvonne Schaub, Dirk Roeser, Kornelia Hardes, Patrick Maeder, Nina Klee, Torsten Steinmetzer, Diana Imhof, Wibke E. Diederich and Manuel E. Than

      Article first published online: 1 APR 2016 | DOI: 10.1002/mbo3.358

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      FlaK represents a GxGD-type intramembrane cleaving proteases (I-CLiP) with homology to the Alzheimer protein gamma-secretase. We developed an optimized gel-shift activity assay for FlaK, analyzed its inhibition, and identified the nonpeptidic compound 9 as its first inhibitor. In this way, we provided the needed tools to further study its enzymatic cycle and also to enable further studies toward a functional understanding of other GxGD-type intramembrane cleaving proteases (I-CLiPs).

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      Identification of ABCC2 as a binding protein of Cry1Ac on brush border membrane vesicles from Helicoverpa armigera by an improved pull-down assay

      Zishan Zhou, Zeyu Wang, Yuxiao Liu, Gemei Liang, Changlong Shu, Fuping Song, Xueping Zhou, Alejandra Bravo, Mario Soberón and Jie Zhang

      Article first published online: 1 APR 2016 | DOI: 10.1002/mbo3.360

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      Cry1Ac toxin could bound to six classes of aminopeptidase-N, alkaline phosphatase, cadherin-like protein, ABCC2, actin, ATPase, polycalin, and some other proteins not previously characterized as Cry toxin-binding molecules such as dipeptidyl peptidase or carboxyl/choline esterase and some serine proteases. This is the first report that provides evidence of direct binding of Cry1Ac toxin to ABCC2 in Helicoverpa armigera.

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      Adaptive responses of outer membrane porin balance of Yersinia ruckeri under different incubation temperature, osmolarity, and oxygen availability

      Evgeniya Bystritskaya, Anna Stenkova, Dmitriy Chistuylin, Nadezhda Chernysheva, Valentina Khomenko, Stanislav Anastyuk, Olga Novikova, Alexander Rakin and Marina Isaeva

      Article first published online: 1 APR 2016 | DOI: 10.1002/mbo3.354

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      The capability of Yersinia ruckeri to survive in the aquatic systems reflects its adaptation to the unfavorable environments. The nonspecific porins are a key factor contributing to the permeability. We studied the influence of the stimuli, such as temperature, osmolarity, and oxygen availability on regulation of Y. ruckeri porins.

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      Autophagy is dispensable to overcome ER stress in the filamentous fungus Aspergillus niger

      Anne-Marie Burggraaf and Arthur F. J. Ram

      Article first published online: 29 MAR 2016 | DOI: 10.1002/mbo3.359

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      The prevention of protein accumulations in the endoplasmic reticulum (ER) by efficient clearance of misfolded proteins is important for cellular function. This study investigates whether improperly folded proteins are removed via the autophagy pathway as an alternative to proteasomal degradation via ER-associated degradation. The results show that the degradation of misfolded proteins from the ER is independent of autophagy in the filamentous fungus Aspergillus niger.

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      Response of enzyme activities and microbial communities to soil amendment with sugar alcohols

      Huili Yu, Peng Si, Wei Shao, Xiansheng Qiao, Xiaojing Yang, Dengtao Gao and Zhiqiang Wang

      Article first published online: 23 MAR 2016 | DOI: 10.1002/mbo3.355

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      Our analysis of changes in microbial functional diversity and soil enzyme activities identified different susceptibilities to sorbitol and mannitol, revealing selective pressure on the function of the soil microbial community during the cultivable period.

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      Constitutive aneuploidy and genomic instability in the single-celled eukaryote Giardia intestinalis

      Pavla Tůmová, Magdalena Uzlíková, Tomáš Jurczyk and Eva Nohýnková

      Article first published online: 23 MAR 2016 | DOI: 10.1002/mbo3.351

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      The Giardia cells are constitutively aneuploid with a large inter- and intrapopulational karyotype heterogeneity. Aneuploidy is likely tolerated and propagated due to absence of p53-mediated cell cycle arrest and might serve as a mechanism for generating genetic diversity of this human parasite. A proliferative disadvantage was detected in Giardia cell lines with chromosomal instability

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      CRISPR1 analysis of naturalized surface water and fecal Escherichia coli suggests common origin

      Lisa D. Tymensen

      Article first published online: 22 MAR 2016 | DOI: 10.1002/mbo3.348

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      Phylogenetic relationships of naturalized and fecal E. coli phylogroup B1 strains based on multilocus sequence typing (MLST). Strain ID's are followed by a symbol representing the source of isolation (naturalized, circle; fecal, square), and the CRISPR relatedness group (G6, red; G7, green; G8, purple; G9, teal; ungrouped, black; Touchon et al. ).

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      Estimation of Mycobacterium avium subsp. paratuberculosis load in raw bulk tank milk in Emilia-Romagna Region (Italy) by qPCR

      Matteo Ricchi, Roberto Savi, Luca Bolzoni, Stefano Pongolini, Irene R Grant, Caterina De Cicco, Giulia Cerutti, Giuliana Cammi, Chiara A. Garbarino and Norma Arrigoni

      Article first published online: 17 MAR 2016 | DOI: 10.1002/mbo3.350

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      The bulk tank milk from Emilia-Romagna region (2934 samples) has been screened for the presence of Mycobacterium avium subsp. paratuberculosis by two qPCRs. Positive samples were also quantified by qPCR, indicating low potential exposure for consumers if the milk subsequently undergoes pasteurization.

    14. You have full text access to this OnlineOpen article
      Refactoring the λ phage lytic/lysogenic decision with a synthetic regulator

      Gonzalo Durante-Rodríguez, José Miguel Mancheño, Eduardo Díaz and Manuel Carmona

      Article first published online: 14 MAR 2016 | DOI: 10.1002/mbo3.352

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      We construct a new synthetic regulator that allows us to reprogram crucial molecular cell decision with the orthogonal inducers. The construction of artificial regulators paves the way for a novel experimental approach to create new à la carte regulatory proteins to reprogram crucial cell functions.

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      Anaerobic microbial community response to methanogenic inhibitors 2-bromoethanesulfonate and propynoic acid

      Tara M. Webster, Adam L. Smith, Raghav R. Reddy, Ameet J. Pinto, Kim F. Hayes and Lutgarde Raskin

      Article first published online: 14 MAR 2016 | DOI: 10.1002/mbo3.349

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      This manuscript reports a comprehensive approach to characterizing the effects of commonly used methanogenesis inhibitors on an anaerobic microbial community. We use mock and environmental communities and target two genes using DNA- and RNA-based methods. Results from Illumina sequencing of the 16S rRNA gene, 16S rRNA cDNA, mcrA gene, and mcrA transcript cDNA highlight shifts in both methanogenic archaeal activity and syntrophic bacterial activity.

    16. You have full text access to this OnlineOpen article
      The HigB/HigA toxin/antitoxin system of Pseudomonas aeruginosa influences the virulence factors pyochelin, pyocyanin, and biofilm formation

      Thammajun L. Wood and Thomas K. Wood

      Article first published online: 14 MAR 2016 | DOI: 10.1002/mbo3.346

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      The previously uncharacterized proteins HigB (unannotated) and HigA (PA4674) of Pseudomonas aeruginosa PA14 form a type II TA system in which antitoxin HigA masks the RNase activity of toxin HigB through direct binding. Furthermore, toxin HigB reduces production of the virulence factors pyochelin, pyocyanin, swarming, and biofilm formation; hence, this system affects the pathogencity of this strain in a manner that has not been demonstrated previously for TA systems.

    17. You have full text access to this OnlineOpen article
      Microcin determinants are associated with B2 phylogroup of human fecal Escherichia coli isolates

      Lenka Micenková, Juraj Bosák, Barbora Štaudová, Darina Kohoutová, Darina Čejková, Vladana Woznicová, Martin Vrba, Alena Ševčíková, Jan Bureš and David Šmajs

      Article first published online: 14 MAR 2016 | DOI: 10.1002/mbo3.345

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      This study tested whether human fecal E. coli isolates belonging to different phylogroups differ in prevalence of bacteriocinogenic strains and prevalence of individual bacteriocinogenic determinants. A set of 1283 E. coli isolates was tested for the presence of DNA regions allowing classification into E. coli phylogroups and for the ability to produce bacteriocins (23 colicins and 7 microcins). The highest prevalence of bacteriocinogeny was found in phylogroup B2, suggesting that bacteriocinogeny and especially the synthesis of microcins was associated with virulent and resident E. coli isolates.

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      Decomposition of plant-sourced carbon compounds by heterotrophic betaproteobacteria isolated from a tropical Costa Rican bromeliad

      Jane Klann, Alexandra McHenry, Carin Montelongo and Shana K. Goffredi

      Article first published online: 25 FEB 2016 | DOI: 10.1002/mbo3.344

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      Betaproteobacteria isolated from a bromeliad tank displayed high temperature and comparatively low pH optima, and metabolism of plant-sourced material, reflecting the tropical, acidic nature of the novel habitat.

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      The Caenorhabditis elegans p38 MAPK Gene plays a key role in protection from mycobacteria

      Thushara Galbadage, Tonya F. Shepherd, Suat L. G. Cirillo, Tina L. Gumienny and Jeffrey D. Cirillo

      Article first published online: 25 FEB 2016 | DOI: 10.1002/mbo3.341

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      Mycobacterial infections currently afflict more than one-third of the world's population. We have developed a nematode model for mycobacterial infections that has a number of advantages and is likely to speed progress toward development of interventions in the field. We demonstrate that this model can differentiate pathogenic from nonpathogenic strains, and can be used to analyze the genes involved in disease processes. Colonization of nematodes can be used to dissect a number of the cellular signaling and cytoskeletal interaction pathways. We utilized this model to identify the key signaling pathways involved in productive infections and a new mechanism that pathogens use to prevent protection from disease in the host.

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      Role of bacteria in the production and degradation of Microcystis cyanopeptides

      Enora Briand, Jean-François Humbert, Kevin Tambosco, Myriam Bormans and William H. Gerwick

      Article first published online: 25 FEB 2016 | DOI: 10.1002/mbo3.343

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      This work reports a cyanopeptides-degradation capability of a natural bacterial community associated to Microcystis aeruginosa

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      Two parallel pathways for ferric and ferrous iron acquisition support growth and virulence of the intracellular pathogen Francisella tularensis Schu S4

      Natalie Pérez, Richard Johnson, Bhaswati Sen and Girija Ramakrishnan

      Article first published online: 25 FEB 2016 | DOI: 10.1002/mbo3.342

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      We have examined the mechanisms that mediate iron acquisition in the Gram-negative Francisella tularensis strain SchuS4 and demonstrate that it possesses only two parallel pathways of siderophore-mediated ferric iron acquisition and ferrous iron transport. These specialized mechanisms involving high-affinity outer-membrane transporters adequately support growth and full virulence of this intracellular pathogen.

    22. You have full text access to this OnlineOpen article
      FliH and FliI ensure efficient energy coupling of flagellar type III protein export in Salmonella

      Tohru Minamino, Miki Kinoshita, Yumi Inoue, Yusuke V. Morimoto, Kunio Ihara, Satomi Koya, Noritaka Hara, Noriko Nishioka, Seiji Kojima, Michio Homma and Keiichi Namba

      Article first published online: 25 FEB 2016 | DOI: 10.1002/mbo3.340

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      FlhA requires the support of FliH and FliI to efficiently and properly interact with FliJ and the flagellar type III secretion chaperone–substrate complexes.

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      Identification and functional analysis of a bacteriocin, pyocin S6, with ribonuclease activity from a Pseudomonas aeruginosa cystic fibrosis clinical isolate

      Jozef Dingemans, Maarten G. K. Ghequire, Michael Craggs, René De Mot and Pierre Cornelis

      Article first published online: 9 FEB 2016 | DOI: 10.1002/mbo3.339

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      Soluble pyocins are bacterial toxins produced by Pseudomonas aeruginosa to kill relatives. Here, we describe a new pyocin, S6, with the same receptor-binding and translocation domain as S1, but a 16S ribonuclease domain similar to colicin E3. The S6 gene and the immunity protein coding gene are present in few isolates, but has been partially deleted from strain PAO1. The immunity gene is highly expressed, showing an uncoupling with the toxin gene. Both the strain immunity gene and the one from PAO1 confer protection.

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      Toxin MqsR cleaves single-stranded mRNA with various 5' ends

      Nityananda Chowdhury, Brian W. Kwan, Louise C. McGibbon, Paul Babitzke and Thomas K. Wood

      Article first published online: 5 FEB 2016 | DOI: 10.1002/mbo3.335

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      Using RNA that is single-stranded, double-stranded, or folds into a stem loop or pseudoknot, we found that toxin MqsR of the MqsR/MqsA TA system cleaves primarily single-stranded RNA. Furthermore, we found that 5′ processing is not required for the RNA to be a substrate since MqsR has activity on RNA with 5′-ppp, 5′-p and 5′-OH ends. Hence, MqsR cleavage of mRNA does not depend on preprocessing by RNA pyrophosphohydrolase (RppH) to remove pyrophosphate like RNase E, the primary enzyme for mRNA turnover, which implies that once activated by stress, toxin MqsR can rapidly degrade nearly all the mRNA (all but 14 Escherichia coli transcripts have 5′-GCU sites) as well as possibly tRNA and rRNA.

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      New insights into FtsZ rearrangements during the cell division of Escherichia coli from single-molecule localization microscopy of fixed cells

      Alexey D. Vedyaykin, Innokentii E. Vishnyakov, Vasilisa S. Polinovskaya, Mikhail A. Khodorkovskii and Anton V. Sabantsev

      Article first published online: 3 FEB 2016 | DOI: 10.1002/mbo3.336

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      Single-molecule localization microscopy (SMLM) combined with IF was used to visualize FtsZ in fixed Esherichia coli cells. This approach allowed us to obtain images of FtsZ structures at different stages of cell division and measure dimensions of Z-ring.

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      Effects of norspermidine on Pseudomonas aeruginosa biofilm formation and eradication

      Lin Qu, Pengfei She, Yangxia Wang, Fengxia Liu, Di Zhang, Lihua Chen, Zhen Luo, Huan Xu, Yong Qi and Yong Wu

      Article first published online: 27 JAN 2016 | DOI: 10.1002/mbo3.338

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      Norspermidine could inhibit biofi lm formation and eradicate 24- h mature biofi lm in Pseudomonas aeruginosa , prevent cell- surface attachment, and downregulate QS- related gene expression.

    27. You have full text access to this OnlineOpen article
      Oscillating behavior of Clostridium difficile Min proteins in Bacillus subtilis

      Jana Makroczyová, Ján Jamroškovič, Eva Krascsenitsová, Nad'a Labajová and Imrich Barák

      Article first published online: 27 JAN 2016 | DOI: 10.1002/mbo3.337

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      The placement of the bacterial division septum at the midcell site is very precise and it is partially controlled by Min system in many rod-shaped bacteria. Escherichia coli Min system oscillates from pole to pole in contrast with less dynamic Bacillus subtilis Min system. Interestingly, many Clostridia species contain homologs proteins from both Min systems. Because of C.difficile anaerobic life style and its confined genetic toolbox, we investigated the mechanism of action of the C.difficile Min proteins in B.subtilis and we showed that this system exhibits oscillatory behavior in the host.

    28. You have full text access to this OnlineOpen article
      Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis

      Peng Deng, Xiaoqiang Wang, Sonya M. Baird, Kurt C. Showmaker, Leif Smith, Daniel G. Peterson and Shien Lu

      Article first published online: 14 JAN 2016 | DOI: 10.1002/mbo3.333

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      Burkholderia contaminans MS14 shows significant antimicrobial activities against plant and animal pathogenic fungi and bacteria. The MS14 whole genome was sequenced. The genome analysis revealed MS14 harbored multiple antimicrobial-related gene loci. In addition, MS14 genome lacks key virulence-related genes by comparison to the pathogenic Burkholderia species.

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