Browsing by Subject "1183 Plant biology, microbiology, virology"

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  • Sennikov, Alexander Nikolaevich (2015)
  • Lai, Jeffrey K. F.; Sam, I-Ching; Verlhac, Pauline; Baguet, Joel; Eskelinen, Eeva-Liisa; Faure, Mathias; Chan, Yoke Fun (2017)
    Viruses have evolved unique strategies to evade or subvert autophagy machinery. Enterovirus A71 (EV-A71) induces autophagy during infection in vitro and in vivo. In this study, we report that EV-A71 triggers autolysosome formation during infection in human rhabdomyosarcoma (RD) cells to facilitate its replication. Blocking autophagosome-lysosome fusion with chloroquine inhibited virus RNA replication, resulting in lower viral titres, viral RNA copies and viral proteins. Overexpression of the non-structural protein 2BC of EV-A71 induced autolysosome formation. Yeast 2-hybrid and co-affinity purification assays showed that 2BC physically and specifically interacted with a N-ethylmaleimide-sensitive factor attachment receptor (SNARE) protein, syntaxin-17 (STX17). Co-immunoprecipitation assay further showed that 2BC binds to SNARE proteins, STX17 and synaptosome associated protein 29 (SNAP29). Transient knockdown of STX17, SNAP29, and microtubule-associated protein 1 light chain 3B (LC3B), crucial proteins in the fusion between autophagosomes and lysosomes) as well as the lysosomal-associated membrane protein 1 (LAMP1) impaired production of infectious EV-A71 in RD cells. Collectively, these results demonstrate that the generation of autolysosomes triggered by the 2BC non-structural protein is important for EV-A71 replication, revealing a potential molecular pathway targeted by the virus to exploit autophagy. This study opens the possibility for the development of novel antivirals that specifically target 2BC to inhibit formation of autolysosomes during EV-A71 infection.
  • Domanska, Ausra; Flatt, Justin Wayne; Jukonen, Joonas; Geraets, James; Butcher, Sarah Jane (2019)
    Human parechovirus 3 (HPeV3) infection is associated with sepsis characterized by significant immune activation and subsequent tissue damage in neonates. Strategies to limit infection have been unsuccessful due to inadequate molecular diagnostic tools for early detection and the lack of a vaccine or specific antiviral therapy. Toward the latter, we present a 2.8-angstrom-resolution structure of HPeV3 in complex with fragments from a neutralizing human monoclonal antibody, AT12-015, using cryo-electron microscopy (cryo-EM) and image reconstruction. Modeling revealed that the epitope extends across neighboring asymmetric units with contributions from capsid proteins VP0, VP1, and VP3. Antibody decoration was found to block binding of HPeV3 to cultured cells. Additionally, at high resolution, it was possible to model a stretch of RNA inside the virion and, from this, identify the key features that drive and stabilize protein-RNA association during assembly. IMPORTANCE Human parechovirus 3 (HPeV3) is receiving increasing attention as a prevalent cause of sepsis-like symptoms in neonates, for which, despite the severity of disease, there are no effective treatments available. Structural and molecular insights into virus neutralization are urgently needed, especially as clinical cases are on the rise. Toward this goal, we present the first structure of HPeV3 in complex with fragments from a neutralizing monoclonal antibody. At high resolution, it was possible to precisely define the epitope that, when targeted, prevents virions from binding to cells. Such an atomic-level description is useful for understanding host-pathogen interactions and viral pathogenesis mechanisms and for finding potential cures for infection and disease.
  • Kaasalainen, Ulla Susanna; Heinrichs, Jochen; Renner, Matthew; Hedenäs, Lars; Schäfer-Verwimp, Alfons; Lee, Gaik; Ignatov, Michael; Rikkinen, Jouko; Schmidt, Alexander (2018)
    Fossil tree resins preserve a wide range of animals, plants, fungi and microorganisms in microscopic fidelity. Fossil organisms preserved in an individual piece of amber lived at the same time in Earth history and mostly even in the same habitat, but they were not necessarily parts of the same interacting community. Here, we report on an in situ preserved corticolous community from a piece of Miocene Dominican amber which is composed of a lichen, a moss and three species of leafy liverworts. The lichen is assigned to the extant genus Phyllopsora (Ramalinaceae, Lecanoromycetes) and is described as P. magna Kaasalainen, Rikkinen & A. R. Schmidt sp. nov. The moss, Aptychellites fossilis Schaf.-Verw., Hedenas, Ignatov & Heinrichs gen. & sp. nov., closely resembles the extant genus Aptychella of the family Pylaisiadelphaceae. The three leafy liverworts comprise the extinct Lejeuneaceae species Cheilolejeunea antiqua (Grolle) Ye & Zhu, 2010 and Lejeunea miocenica Heinrichs, Schaf.-Verw., M. A. M. Renner & G. E. Lee sp. nov. and the extinct Radulaceae species Radula intecta M. A. M. Renner, Schaf.-Verw. & Heinrichs sp. nov. The presence of five associated extinct cryptogam species, four of which belong to extant genera, further substantiates the notion of a stasis in morphotype diversity, but a certain turnover of species, in the Caribbean since the early Miocene.
  • Yu, Xia; Åvall-Jääskeläinen, Silja; Koort, Joanna; Lindholm, Agneta; Rintahaka, Johanna; von Ossowski, Ingemar; Palva, Airi; Hynönen, Ulla (2017)
    Lactobacillus ruminis, an autochthonous member of the gastrointestinal microbiota of humans and many animals, is a less characterized but interesting species for many reasons, including its intestinal prevalence and possible positive roles in host-microbe crosstalk. In this study, we isolated a novel L. ruminis strain (GRL 1172) from porcine feces and analyzed its functional characteristics and niche adaptation factors in parallel with those of three other L. ruminis strains (a human isolate, ATCC 25644, and two bovine isolates, ATCC 27780 and ATCC 27781). All the strains adhered to fibronectin, type I collagen, and human colorectal adenocarcinoma cells (HT-29), but poorly to type IV collagen, porcine intestinal epithelial cells (IPEC-1), and human colon adenocarcinoma cells (Caco-2). In competition assays, all the strains were able to inhibit the adhesion of Yersinia enterocolitica and enterotoxigenic Escherichia coli (ETEC, F4(+)) to fibronectin, type I; collagen, IPEC-1, and Caco-2 cells, and the inhibition rates tended to be higher than in exclusion assays. The culture supernatants of the tested strains inhibited the growth of six selected pathogens to varying extents. The inhibition was solely based on the low pH resulting from acid production during growth. All four L. ruminis strains supported the barrier function maintenance of Caco-2 cells, as shown by the modest increase in trans-epithelial electrical resistance and the prevention of dextran diffusion during co-incubation. However, the strains could not prevent the barrier damage caused by ETEC in the Caco-2 cell model. All the tested strains and their culture supernatants were able to provoke Toll-like receptor (TLR) 2-mediated NF-kappa B activation and IL-8 production in vitro to varying degrees. The induction of TLR5 signaling revealed that flagella were expressed by all the tested strains, but to different extents. Flagella and pili were observed by electron microscopy on the newly isolated strain GRL 1172.
  • Lubbers, Ronnie J. M.; Dilokpimol, Adiphol; Visser, Jaap; Makela, Miia R.; Hilden, Kristiina S.; de Vries, Ronald P. (2019)
    Aromatic compounds derived from lignin are of great interest for renewable biotechnical applications. They can serve in many industries e.g. as biochemical building blocks for bioplastics or biofuels, or as antioxidants, flavor agents or food preservatives. In nature, lignin is degraded by microorganisms, which results in the release of homocyclic aromatic compounds. Homocyclic aromatic compounds can also be linked to polysaccharides, tannins and even found freely in plant biomass. As these compounds are often toxic to microbes already at low concentrations, they need to be degraded or converted to less toxic forms. Prior to ring cleavage, the plant- and lignin-derived aromatic compounds are converted to seven central ring-fission intermediates, i.e. catechol, protocatechuic acid, hydroxyquinol, hydroquinone, gentisic acid, gallic acid and pyrogallol through complex aromatic metabolic pathways and used as energy source in the tricarboxylic acid cycle. Over the decades, bacterial aromatic metabolism has been described in great detail. However, the studies on fungal aromatic pathways are scattered over different pathways and species, complicating a comprehensive view of fungal aromatic metabolism. In this review, we depicted the similarities and differences of the reported aromatic metabolic pathways in fungi and bacteria. Although both microorganisms share the main conversion routes, many alternative pathways are observed in fungi. Understanding the microbial aromatic metabolic pathways could lead to metabolic engineering for strain improvement and promote valorization of lignin and related aromatic compounds.
  • Mellor, Nathan; Vaughan-Hirsch, John; Kumpers, Britta M. C.; Help-Rinta-Rahko, Hanna; Miyashima, Shunsuke; Mahonen, Ari Pekka; Campilho, Ana; Kings, John R.; Bishopp, Anthony (2019)
    Pattern formation is typically controlled through the interaction between molecular signals within a given tissue. During early embryonic development, roots of the model plant Arabidopsis thatiana have a radially symmetric pattern, but a heterogeneous input of the hormone auxin from the two cotyledons forces the vascular cylinder to develop a diarch pattern with two xylem poles. Molecular analyses and mathematical approaches have uncovered the regulatory circuit that propagates this initial auxin signal into a stable cellular pattern. The diarch pattern seen in Arabidopsis is relatively uncommon among flowering plants, with most species having between three and eight xylem poles. Here, we have used multiscale mathematical modelling to demonstrate that this regulatory module does not require a heterogeneous auxin input to specify the vascular pattern. Instead, the pattern can emerge dynamically, with its final form dependent upon spatial constraints and growth. The predictions of our simulations compare to experimental observations of xylem pole number across a range of species, as well as in transgenic systems in Arabidopsis in which we manipulate the size of the vascular cylinder. By considering the spatial constraints, our model is able to explain much of the diversity seen in different flowering plant species.
  • Mollerup, Filip; Aumala, Ville; Parikka, Kirsti Maria; Mathieu, Yan; Brumer, Harry; Tenkanen, Tiina Maija; Master, Emma (2019)
    Copper radical alcohol oxidases belonging to auxiliary activity family 5, subfamily 2 (AA5_2) catalyze the oxidation of galactose and galactosides, as well as aliphatic alcohols. Despite their broad applied potential, so far very few AA5_2 members have been biochemically characterized. We report the recombinant production and biochemical characterization of an AA5_2 oxidase from Penicillium rubens Wisconsin 54-1255 (PruAA5_2A), which groups within an unmapped clade phylogenetically distant from those comprising AA5_2 members characterized to date. PruAA5_2 preferentially oxidized raffinose over galactose; however, its catalytic efficiency was 6.5 times higher on glycolaldehyde dimer compared to raffinose. Deep sequence analysis of characterized AA5_2 members highlighted amino acid pairs correlated to substrate range and conserved within the family. Moreover, PruAA5_2 activity spans substrate preferences previously reported for AA5 subfamily 1 and 2 members, identifying possible functional overlap across the AA5 family.
  • Massart, Sebastien; Candresse, Thierry; Gil, Jose; Lacomme, Christophe; Predajna, Lukas; Ravnikar, Maja; Reynard, Jean-Sebastien; Rumbou, Artemis; Saldarelli, Pasquale; Skoric, Dijana; Vainio, Eeva J.; Valkonen, Jari P. T.; Vanderschuren, Herve; Varveri, Christina; Wetzel, Thierry (2017)
    Recent advances in high-throughput sequencing technologies and bioinformatics have generated huge new opportunities for discovering and diagnosing plant viruses and viroids. Plant virology has undoubtedly benefited from these new methodologies, but at the same time, faces now substantial bottlenecks, namely the biological characterization of the newly discovered viruses and the analysis of their impact at the biosecurity, commercial, regulatory, and scientific levels. This paper proposes a scaled and progressive scientific framework for efficient biological characterization and risk assessment when a previously known or a new plant virus is detected by next generation sequencing (NGS) technologies. Four case studies are also presented to illustrate the need for such a framework, and to discuss the scenarios.
  • Jaber, Emad; Kovalchuk, Andriy; Raffaello, Tommaso; Keriö, Susanna; Teeri, Teemu; Asiegbu, Fred O. (2018)
    Both the establishment of sustainable forestry practices and the improvement of commercially grown trees require better understanding of mechanisms used by forest trees to combat microbial pathogens. We investigated the contribution of a gene encoding Scots pine (Pinus sylvestris L.) antimicrobial protein Sp-AMP2 (PR-19) to the host defenses to evaluate the potential of Sp-AMP genes as molecular markers for resistance breeding. We developed transgenic tobacco plants expressing the Sp-AMP2 gene. Transgenic plants showed a reduction in the size of lesions caused by the necrotrophic pathogen Botrytis cinerea. In order to investigate Sp-AMP2 gene expression level, four transgenic lines were tested in comparison to control and non-transgenic plants. No Sp-AMP2 transcripts were observed in any of the control and non-transgenic plants tested. The transcript of Sp-AMP2 was abundantly present in all transgenic lines. Sp-AMP2 was induced highly in response to the B. cinerea infection at 3 d.p.i. This study provides an insight into the role of Sp-AMP2 and its functional and ecological significance in the regulation of plant–pathogen interactions.
  • Kaurilind, Eve; Xu, Enjun; Brosche, Mikael (2015)
    Background: To survive in a changing environment plants constantly monitor their surroundings. In response to several stresses and during photorespiration plants use reactive oxygen species as signaling molecules. The Arabidopsis thaliana catalase2 (cat2) mutant lacks a peroxisomal catalase and under photorespiratory conditions accumulates H2O2, which leads to activation of cell death. Methods: A cat2 double mutant collection was generated through crossing and scored for cell death in different assays. Selected double mutants were further analyzed for photosynthetic performance and H2O2 accumulation. Results: We used a targeted mutant analysis with more than 50 cat2 double mutants to investigate the role of stress hormones and other defense regulators in H2O2 -mediated cell death. Several transcription factors (AS1, MYB30, MYC2, WRKY70), cell death regulators (RCD1, DND1) and hormone regulators (AXR1, ERA1, SID2, EDS1, SGT1b) were essential for execution of cell death in cat2. Genetic loci required for cell death in cat2 was compared with regulators of cell death in spontaneous lesion mimic mutants and led to the identification of a core set of plant cell death regulators. Analysis of gene expression data from cat2 and plants undergoing cell death revealed similar gene expression profiles, further supporting the existence of a common program for regulation of plant cell death. Conclusions: Our results provide a genetic framework for further study on the role of H2O2 in regulation of cell death. The hormones salicylic acid, jasmonic acid and auxin, as well as their interaction, are crucial determinants of cell death regulation.
  • Zappa, Emilio; Dykeman, Eric C.; Geraets, James A.; Twarock, Reidun (2016)
    In this paper we describe a group theoretical approach to the study of structural transitions of icosahedral quasicrystals and point arrays. We apply the concept of Schur rotations, originally proposed by Kramer, to the case of aperiodic structures with icosahedral symmetry; these rotations induce a rotation of the physical and orthogonal spaces invariant under the icosahedral group, and hence, via the cut-and-project method, a continuous transformation of the corresponding model sets. We prove that this approach allows for a characterisation of such transitions in a purely group theoretical framework, and provide explicit computations and specific examples. Moreover, we prove that this approach can be used in the case of finite point sets with icosahedral symmetry, which have a wide range of applications in carbon chemistry (fullerenes) and biology (viral capsids).
  • Kneis, David; Hiltunen, Teppo; Hess, Stefanie (2019)
    Horizontal gene transfer is an essential component of bacterial evolution. Quantitative information on transfer rates is particularly useful to better understand and possibly predict the spread of antimicrobial resistance. A variety of methods has been proposed to estimate the rates of plasmid-mediated gene transfer all of which require substantial labor input or financial resources. A cheap but reliable method with high-throughput capabilities is yet to be developed in order to better capture the variability of plasmid transfer rates, e.g. among strains or in response to environmental cues. We explored a new approach to the culture-based estimation of plasmid transfer rates in liquid media allowing for a large number of parallel experiments. It deviates from established approaches in the fact that it exploits data on the absence/presence of transconjugant cells in the wells of a well plate observed over time. Specifically, the binary observations are compared to the probability of transconjugant detection as predicted by a dynamic model. The bulk transfer rate is found as the best-fit value of a designated model parameter. The feasibility of the approach is demonstrated on mating experiments where the RP4 plasmid is transfered from Serratia marcescens to several Escherichia coil recipients. The methods uncertainty is explored via split sampling and virtual experiments.
  • Christenhusz, Maarten; Zhang, Xian-Chun; Schneider, Harald (2011)
    Throughout the history of the classification of extant ferns (monilophytes) and lycophytes, familial and generic concepts have been in great flux. For the organisation of lycophytes and ferns in herbaria, books, checklists, indices and spore banks and on the internet, this poses a problem, and a standardized linear sequence of these plants is therefore in great need. We provide here a linear classification to the extant lycophytes and ferns based on current phylogenetic knowledge; this provides a standardized guide for organisation of fern collections into a more natural sequence. Two new families, Diplaziopsidaceae and Rhachidosoraceae, are here introduced.
  • Sabouri, Salehe; Sepehrizadeh, Zargham; Amirpour-Rostami, Sahar; Skurnik, Mikael (2017)
    Phage therapy is an old method of combating bacterial pathogens that has recently been taken into consideration due to the alarming spread of antibiotic resistance. Escherichia coli 0157:H7 is a foodborne pathogen that causes hemorrhagic colitis and life-threatening Hemolytic Uremic Syndrome (HUS). There are several studies on isolation of specific phages against E. coli 0157:H7 and more than 60 specific phase have been published so far. Although in vitro experiments have been successful in elimination or reduction of E. coli 0157:H7numbers, in vivo experiments have not been as promising. This may be due to escape of bacteria to locations where phages have difficulties to enter or due to the adverse conditions in the gastrointestinal tract that affect phage viability and proliferation. To get around the latter obstacle, an alternative phage delivery method such as polymer microen-capsulation should be tried. While the present time results are not very encouraging the work should be continued as more efficient phage treatment regimens might be found in future. (C)2016 Elsevier B.V. All rights reserved.
  • Khazaei, Hamid; Stoddard, Frederick L.; Purves, Randy W.; Vandenberg, Albert (2018)
    Faba bean (Viciafaba L.) is a valuable grain legume and a staple protein crop in many countries. Its large and complex genome requires novel approaches for its genetic dissection. Here we introduce a multi-parent population developed from four founders (ILB 938/2, Disco/2, IG 114476 and IG 132238). The selection of parental lines was based on geographic (Colombia, France, Bangladesh and China), genetic and phenotypic diversity. The parental lines were inbred and then genotyped using 875 single nucleotide polymorphism (SNP) markers. Based on molecular data, the parents had high homozygosity and high genetic distance among them. The population segregates for several important traits such as seed morphology, seed chemistry, phenology, plant architecture, drought response, yield and its components, and resistance to Botrytis fabae. The population was checked for unbiased segregation in each generation by observing simply inherited Mendelian traits such as stipule spot pigmentation (SSP) and flower colour at different generations. All 1200 four-way cross Fl plants had pigmented flowers and stipule spots. The segregation ratios for white flower colour (single gene, zt2) fit 7:1, 13:3 and 25:7 at F2, F3 and F4 generations, respectively, and the segregation ratio of SSP (two recessive unlinked genes, ssp1 and ssp2) fit 49:15 and 169:87 at the F2 and F3 generations, respectively, demonstrating unbiased generation advance. We will subject the F5 generation of this population to a high-throughput SNP array and make it available for further phenotyping and genotyping.
  • Christenhusz, Maarten; Reveal, James; Farjon, Aljos; Gardner, Martin F.; Mill, Robert R.; Chase, Mark W. (2011)
    A new classification and linear sequence of the gymnosperms based on previous molecular and morphological phylogenetic and other studies is presented. Currently accepted genera are listed for each family and arranged according to their (probable) phylogenetic position. A full synonymy is provided, and types are listed for accepted genera. An index to genera assists in easy access to synonymy and family placement of genera.
  • Miettinen, Otto; Niemelä, Tuomo; Ryvarden, Leif (2007)
    Irpex cremicolor, a poroid basidiomycete, is described as new based on collections from old-growth forests in northern Finland and Norway. It is characterised by a resupinate habit, lacerate pores, and a dimitic hyphal system. Most of the septa are simple, but scattered clamps are present. The species reminds of the North American Oxyporus similis, which is re-described and compared to the closely reminiscent O. obducens. These two are often considered synonyms, but they are kept separate here on account of minor differences in their hyphal and spore characteristics.