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  • 51.
    Armstrong, Ellie E.
    et al.
    Stanford Univ, Dept Biol, Stanford, CA 94305 USA.
    Prost, Stefan
    Stanford Univ, Dept Biol, Stanford, CA 94305 USA;Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA.
    Ertz, Damien
    Bot Garden Meise, Dept Res, Meise, Belgium;Federat Wallonie Bruxelles, Direct Gen Enseignement Non Obligatoire & Rech Sc, Brussels, Belgium.
    Westberg, Martin
    Uppsala Univ, Museum Evolut, Uppsala, Sweden.
    Frisch, Andreas
    Norwegian Univ Sci & Technol, NTNU Univ Museum, Trondheim, Norway.
    Bendiksby, Mika
    Norwegian Univ Sci & Technol, NTNU Univ Museum, Trondheim, Norway.
    Draft Genome Sequence and Annotation of the Lichen-Forming Fungus Arthonia radiata2018Ingår i: MICROBIOLOGY RESOURCE ANNOUNCEMENTS, ISSN 2576-098X, Vol. 6, nr 14, artikel-id e00281-18Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report here the draft de novo genome assembly, transcriptome assembly, and annotation of the lichen-forming fungus Arthonia radiata (Pers.) Ach., the type species for Arthoniomycetes, a class of lichen-forming, lichenicolous, and saprobic Ascomycota. The genome was assembled using overlapping paired-end and mate pair libraries and sequenced on an Illumina HiSeq 2500 instrument.

  • 52.
    Asghar, Naveed
    et al.
    Sodertorn Univ, Sch Nat Sci Technol & Environm Studies, Huddinge, Sweden.;Orebro Univ, Sch Med Sci, Orebro, Sweden.;Orebro Univ, Fac Med & Hlth, iRiSC, Orebro, Sweden..
    Pettersson, John H.-O.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Norwegian Inst Publ Hlth, Dept Infect Dis Epidemiol & Modelling, Oslo, Norway.;Natl Vet Inst, Dept Microbiol, Uppsala, Sweden..
    Dinnetz, Patrik
    Sodertorn Univ, Sch Nat Sci Technol & Environm Studies, Huddinge, Sweden..
    Andreassen, Ashild
    Norwegian Inst Publ Hlth, Div Infect Dis Control, Dept Virol, Oslo, Norway..
    Johansson, Magnus
    Orebro Univ, Sch Med Sci, Orebro, Sweden.;Orebro Univ, Fac Med & Hlth, iRiSC, Orebro, Sweden..
    Deep sequencing analysis of tick-borne encephalitis virus from questing ticks at natural foci reveals similarities between quasispecies pools of the virus2017Ingår i: Journal of General Virology, ISSN 0022-1317, E-ISSN 1465-2099, Vol. 98, nr 3, s. 413-421Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Every year, tick-borne encephalitis virus (TBEV) causes severe central nervous system infection in 10 000 to 15 000 people in Europe and Asia. TBEV is maintained in the environment by an enzootic cycle that requires a tick vector and a vertebrate host, and the adaptation of TBEV to vertebrate and invertebrate environments is essential for TBEV persistence in nature. This adaptation is facilitated by the error-prone nature of the virus's RNA-dependent RNA polymerase, which generates genetically distinct virus variants called quasispecies. TBEV shows a focal geographical distribution pattern where each focus represents a TBEV hotspot. Here, we sequenced and characterized two TBEV genomes, JP-296 and JP-554, from questing Ixodes ricinus ticks at a TBEV focus in central Sweden. Phylogenetic analysis showed geographical clustering among the newly sequenced strains and three previously sequenced Scandinavian strains, Toro-2003, Saringe-2009 and Mandal-2009, which originated from the same ancestor. Among these five Scandinavian TBEV strains, only Mandal-2009 showed a large deletion within the 3' non-coding region (NCR), similar to the highly virulent TBEV strain Hypr. Deep sequencing of JP-296, JP-554 and Mandal-2009 revealed significantly high quasispecies diversity for JP-296 and JP-554, with intact 3' NCRs, compared to the low diversity in Mandal-2009, with a truncated 3' NCR. Single-nucleotide polymorphism analysis showed that 40% of the single-nucleotide polymorphisms were common between quasispecies populations of JP-296 and JP-554, indicating a putative mechanism for how TBEV persists and is maintained within its natural foci.

  • 53.
    Ast, Jennifer C
    et al.
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Dunlap, Paul V
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Phylogenetic analysis of the lux operon distinguishes two evolutionarily distinct clades of Photobacterium leiognathi.2004Ingår i: Archives of Microbiology, ISSN 0302-8933, E-ISSN 1432-072X, Vol. 181, nr 5, s. 352-61Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The luminous marine bacterium Photobacterium mandapamensis was synonymized several years ago with Photobacterium leiognathi based on a high degree of phenotypic and genetic similarity. To test the possibility that P. leiognathi as now formulated, however, actually contains two distinct bacterial groups reflecting the earlier identification of P. mandapamensis and P. leiognathi as separate species, we compared P. leiognathi strains isolated from light-organ symbiosis with leiognathid fishes (i.e., ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1) with strains from seawater originally described as P. mandapamensis and later synonymized as P. leiognathi (i.e., ATCC 27561(T) and ATCC 33981) and certain strains initially identified as P. leiognathi (i.e., PL-721, PL-741, 554). Analysis of the 16S rRNA and gyrB genes did not resolve distinct clades, affirming a close relationship among these strains. However, strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 were found to bear a luxF gene in the lux operon ( luxABFE), whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 lack this gene ( luxABE). Phylogenetic analysis of the luxAB(F)E region confirmed this distinction. Furthermore, ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554 all produced a higher level of luminescence on high-salt medium, as previously described for PL-721, whereas ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1 all produced a higher level of luminescence on low-salt medium, a characteristic of P. leiognathi from leiognathid fish light organs. These results demonstrate that P. leiognathi contains two evolutionarily and phenotypically distinct clades, P. leiognathi subsp. leiognathi (strains ATCC 25521(T), ATCC 25587, lequu.1.1 and lleuc.1.1), and P. leiognathi subsp. mandapamensis (strains ATCC 27561(T), ATCC 33981, PL-721, PL-741 and 554).

  • 54.
    Ast, Jennifer C
    et al.
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Dunlap, Paul V
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Phylogenetic resolution and habitat specificity of members of the Photobacterium phosphoreum species group.2005Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 7, nr 10, s. 1641-54Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Substantial ambiguity exists regarding the phylogenetic status of facultatively psychrophilic luminous bacteria identified as Photobacterium phosphoreum, a species thought to be widely distributed in the world's oceans and believed to be the specific bioluminescent light-organ symbiont of several deep-sea fishes. Members of the P. phosphoreum species group include luminous and non-luminous strains identified phenotypically from a variety of different habitats as well as phylogenetically defined lineages that appear to be evolutionarily distinct. To resolve this ambiguity and to begin developing a meaningful knowledge of the geographic distributions, habitats and symbiotic relationships of bacteria in the P. phosphoreum species group, we carried out a multilocus, fine-scale phylogenetic analysis based on sequences of the 16S rRNA, gyrB and luxABFE genes of many newly isolated luminous strains from symbiotic and saprophytic habitats, together with previously isolated luminous and non-luminous strains identified as P. phosphoreum from these and other habitats. Parsimony analysis unambiguously resolved three evolutionarily distinct clades, phosphoreum, iliopiscarium and kishitanii. The tight phylogenetic clustering within these clades and the distinct separation between them indicates they are different species, P. phosphoreum, Photobacterium iliopiscarium and the newly recognized 'Photobacterium kishitanii'. Previously reported non-luminous strains, which had been identified phenotypically as P. phosphoreum, resolved unambiguously as P. iliopiscarium, and all examined deep-sea fishes (specimens of families Chlorophthalmidae, Macrouridae, Moridae, Trachichthyidae and Acropomatidae) were found to harbour 'P. kishitanii', not P. phosphoreum, in their light organs. This resolution revealed also that 'P. kishitanii' is cosmopolitan in its geographic distribution. Furthermore, the lack of phylogenetic variation within 'P. kishitanii' indicates that this facultatively symbiotic bacterium is not cospeciating with its phylogenetically divergent host fishes. The results of this fine-scale phylogenetic analysis support the emerging view that bacterial species names should designate singular historical entities, i.e. discrete lineages diagnosed by a significant divergence of shared derived nucleotide characters.

  • 55.
    Ast, Jennifer C
    et al.
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Urbanczyk, Henryk
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Dunlap, Paul V
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Natural merodiploidy of the lux-rib operon of Photobacterium leiognathi from coastal waters of Honshu, Japan.2007Ingår i: Journal of Bacteriology, ISSN 0021-9193, E-ISSN 1098-5530, Vol. 189, nr 17, s. 6148-58Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Sequence analysis of the bacterial luminescence (lux) genes has proven effective in helping resolve evolutionary relationships among luminous bacteria. Phylogenetic analysis using lux genes, however, is based on the assumptions that the lux genes are present as single copies on the bacterial chromosome and are vertically inherited. We report here that certain strains of Photobacterium leiognathi carry multiple phylogenetically distinct copies of the entire operon that codes for luminescence and riboflavin synthesis genes, luxCDABEG-ribEBHA. Merodiploid lux-rib strains of P. leiognathi were detected during sequence analysis of luxA. To define the gene content, organization, and sequence of each lux-rib operon, we constructed a fosmid library of genomic DNA from a representative merodiploid strain, lnuch.13.1. Sequence analysis of fosmid clones and genomic analysis of lnuch.13.1 defined two complete, physically separate, and apparently functional operons, designated lux-rib1 and lux-rib2. P. leiognathi strains lelon.2.1 and lnuch.21.1 were also found to carry lux-rib1 and lux-rib2, whereas ATCC 25521T apparently carries only lux-rib1. In lnuch.13.1, lelon.2.1, lnuch.21.1, and ATCC 25521T, lux-rib1 is flanked upstream by lumQ and putA and downstream by a gene for a hypothetical multidrug efflux pump. In contrast, transposase genes flank lux-rib2 of lnuch.13.1, and the chromosomal location of lux-rib2 apparently differs in lnuch.13.1, lelon.2.1, and lnuch.21.1. Phylogenetic analysis demonstrated that lux-rib1 and lux-rib2 are more closely related to each other than either one is to the lux and rib genes of other bacterial species, which rules out interspecies lateral gene transfer as the origin of lux-rib2 in P. leiognathi; lux-rib2 apparently arose within a previously unsampled or extinct P. leiognathi lineage. Analysis of 170 additional strains of P. leiognathi, for a total of 174 strains examined from coastal waters of Japan, Taiwan, the Philippine Islands, and Thailand, identified 106 strains that carry only a single lux-rib operon and 68 that carry multiple lux-rib operons. Strains bearing a single lux-rib operon were obtained throughout the geographic sampling range, whereas lux-rib merodiploid strains were found only in coastal waters of central Honshu. This is the first report of merodiploidy of lux or rib genes in a luminous bacterium and the first indication that a natural merodiploid state in bacteria can correlate with geography.

  • 56.
    Atterby, Clara
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Mourkas, Evangelos
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Univ Bath, Dept Biol & Biochem, Milner Ctr Evolut, Bath, Avon, England.
    Meric, Guillaume
    Univ Bath, Dept Biol & Biochem, Milner Ctr Evolut, Bath, Avon, England.
    Pascoe, Ben
    Univ Bath, Dept Biol & Biochem, Milner Ctr Evolut, Bath, Avon, England;MRC CLIMB Consortium, Bath, Avon, England.
    Wang, Helen
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Waldenström, Jonas
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, Kalmar, Sweden.
    Sheppard, Samuel K.
    Univ Bath, Dept Biol & Biochem, Milner Ctr Evolut, Bath, Avon, England;MRC CLIMB Consortium, Bath, Avon, England.
    Olsen, Björn
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Järhult, Josef D.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    Ellström, Patrik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Infektionsmedicin.
    The Potential of Isolation Source to Predict Colonization in Avian Hosts: A Case Study in Campylobacter jejuni Strains From Three Bird Species2018Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 9, artikel-id 591Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Campylobacter jejuni is the primary cause of bacterial gastroenteritis worldwide, infecting humans mostly through consumption of contaminated poultry. C. jejuni is common in the gut of wild birds, and shows distinct strain-specific association to particular bird species. This contrasts with farm animals, in which several genotypes co-exist. It is unclear if the barriers restricting transmission between host species of such specialist strains are related to environmental factors such as contact between host species, bacterial survival in the environment, etc., or rather to strain specific adaptation to the intestinal environment of specific hosts. We compared colonization dynamics in vivo between two host-specific C. jejuni from a song thrush (ST-1304 complex) and a mallard (ST-995), and a generalist strain from chicken (ST-21 complex) in a wild host, the mallard (Anas platyrhynchos). In 18-days infection experiments, the song thrush strain showed only weak colonization and was cleared from all birds after 10 days, whereas both mallard and chicken strains remained stable. When the chicken strain was given 4 days prior to co-infection of the same birds with a mallard strain, it was rapidly outcompeted by the latter. In contrast, when the mallard strain was given 4 days prior to co-infection with the chicken strain, the mallard strain remained and expansion of the chicken strain was delayed. Our results suggest strain-specific differences in the ability of C. jejuni to colonize mallards, likely associated with host origin. This difference might explain observed host association patterns in C. jejuni from wild birds.

  • 57. Babina, Arianne M
    et al.
    Lea, Nicholas E
    Meyer, Michelle M
    In Vivo Behavior of the Tandem Glycine Riboswitch in Bacillus subtilis.2017Ingår i: mBio, ISSN 2161-2129, E-ISSN 2150-7511, Vol. 8, nr 5, artikel-id e01602-17Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In many bacterial species, the glycine riboswitch is composed of two homologous ligand-binding domains (aptamers) that each bind glycine and act together to regulate the expression of glycine metabolic and transport genes. While the structure and molecular dynamics of the tandem glycine riboswitch have been the subject of numerous in vitro studies, the in vivo behavior of the riboswitch remains largely uncharacterized. To examine the proposed models of tandem glycine riboswitch function in a biologically relevant context, we characterized the regulatory activity of mutations to the riboswitch structure in Bacillus subtilis using β-galactosidase assays. To assess the impact disruptions to riboswitch function have on cell fitness, we introduced these mutations into the native locus of the tandem glycine riboswitch within the B. subtilis genome. Our results indicate that glycine does not need to bind both aptamers for regulation in vivo and mutations perturbing riboswitch tertiary structure have the most severe effect on riboswitch function and gene expression. We also find that in B. subtilis, the glycine riboswitch-regulated gcvT operon is important for glycine detoxification.IMPORTANCE The glycine riboswitch is a unique cis-acting mRNA element that contains two tandem homologous glycine-binding domains that act on a single expression platform to regulate gene expression in response to glycine. While many in vitro experiments have characterized the tandem architecture of the glycine riboswitch, little work has investigated the behavior of this riboswitch in vivo In this study, we analyzed the proposed models of tandem glycine riboswitch regulation in the context of its native locus within the Bacillus subtilis genome and examined how disruptions to glycine riboswitch function impact organismal fitness. Our work offers new insights into riboswitch function in vivo and reinforces the potential of riboswitches as novel antimicrobial targets.

  • 58.
    Babina, Arianne M.
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Boston Coll, Dept Biol, Chestnut Hill, MA 02467 USA.
    Parker, Darren J.
    MIT, Dept Biol, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
    Li, Gene-Wei
    MIT, Dept Biol, 77 Massachusetts Ave, Cambridge, MA 02139 USA.
    Meyer, Michelle M.
    Boston Coll, Dept Biol, Chestnut Hill, MA 02467 USA.
    Fitness advantages conferred by the L20-interacting RNA cis-regulator of ribosomal protein synthesis in Bacillus subtilis2018Ingår i: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 24, nr 9, s. 1133-1143Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In many bacteria, ribosomal proteins autogenously repress their own expression by interacting with RNA structures typically located in the 5'-UTRs of their mRNA transcripts. This regulation is necessary to maintain a balance between ribosomal proteins and rRNA to ensure proper ribosome production. Despite advances in noncoding RNA discovery and validation of RNA-protein regulatory interactions, the selective pressures that govern the formation and maintenance of such RNA cis-regulators in the context of an organism remain largely undetermined. To examine the impact disruptions to this regulation have on bacterial fitness, we introduced point mutations that abolish ribosomal protein binding and regulation into the RNA structure that controls expression of ribosomal proteins L20 and L35 within the Bacillus subtilis genome. Our studies indicate that removing this regulation results in reduced log phase growth, improper rRNA maturation, and the accumulation of a kinetically trapped or misassembled ribosomal particle at low temperatures, suggesting defects in ribosome synthesis. Such work emphasizes the important role regulatory RNAs play in the stoichiometric production of ribosomal components for proper ribosome composition and overall organism viability and reinforces the potential of targeting ribosomal protein production and ribosome assembly with novel antimicrobials.

  • 59. Babina, Arianne M
    et al.
    Soo, Mark W
    Fu, Yang
    Meyer, Michelle M
    An S6: S18 complex inhibits translation of E. coli rpsF.2015Ingår i: RNA: A publication of the RNA Society, ISSN 1355-8382, E-ISSN 1469-9001, Vol. 21, nr 12, s. 2039-46Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    More than half of the ribosomal protein operons in Escherichia coli are regulated by structures within the mRNA transcripts that interact with specific ribosomal proteins to inhibit further protein expression. This regulation is accomplished using a variety of mechanisms and the RNA structures responsible for regulation are often not conserved across bacterial phyla. A widely conserved mRNA structure preceding the ribosomal protein operon containing rpsF and rpsR (encoding S6 and S18) was recently identified through comparative genomics. Examples of this RNA from both E. coli and Bacillus subtilis were shown to interact in vitro with an S6:S18 complex. In this work, we demonstrate that in E. coli, this RNA structure regulates gene expression in response to the S6:S18 complex. β-galactosidase activity from a lacZ reporter translationally fused to the 5' UTR and first nine codons of E. coli rpsF is reduced fourfold by overexpression of a genomic fragment encoding both S6 and S18 but not by overexpression of either protein individually. Mutations to the mRNA structure, as well as to the RNA-binding site of S18 and the S6-S18 interaction surfaces of S6 and S18, are sufficient to derepress β-galactosidase activity, indicating that the S6:S18 complex is the biologically active effector. Measurement of transcript levels shows that although reporter levels do not change upon protein overexpression, levels of the native transcript are reduced fourfold, suggesting that the mRNA regulator prevents translation and this effect is amplified on the native transcript by other mechanisms.

  • 60.
    Badary, Amr
    et al.
    Tokyo Univ Agr & Technol, Grad Sch Engn, Dept Biotechnol & Life Sci, 2-24-16 Naka Cho, Koganei, Tokyo 1848588, Japan.;JST, CREST, 2-24-16 Naka Cho, Koganei, Tokyo 1848588, Japan..
    Takamatsu, Shouhei
    Tokyo Univ Agr & Technol, Grad Sch Engn, Dept Biotechnol & Life Sci, 2-24-16 Naka Cho, Koganei, Tokyo 1848588, Japan.;JST, CREST, 2-24-16 Naka Cho, Koganei, Tokyo 1848588, Japan..
    Nakajima, Mitsuharu
    JST, CREST, 2-24-16 Naka Cho, Koganei, Tokyo 1848588, Japan.;Tokyo Univ Agr & Technol, Inst Global Innovat Res, 3-8-1 Harumi Cho, Fuchu, Tokyo 1838538, Japan..
    Ferri, Stefano
    JST, CREST, 2-24-16 Naka Cho, Koganei, Tokyo 1848588, Japan.;Shizuoka Univ, Dept Appl Chem & Biochem Engn, Naka Ku, 3-5-1 Johoku, Hamamatsu, Shizuoka 4328561, Japan..
    Lindblad, Peter
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Sode, Koji
    Tokyo Univ Agr & Technol, Grad Sch Engn, Dept Biotechnol & Life Sci, 2-24-16 Naka Cho, Koganei, Tokyo 1848588, Japan.;JST, CREST, 2-24-16 Naka Cho, Koganei, Tokyo 1848588, Japan.;Tokyo Univ Agr & Technol, Inst Global Innovat Res, 3-8-1 Harumi Cho, Fuchu, Tokyo 1838538, Japan..
    Glycogen Production in Marine Cyanobacterial Strain Synechococcus sp NKBG 15041c2018Ingår i: Marine Biotechnology, ISSN 1436-2228, E-ISSN 1436-2236, Vol. 20, nr 2, s. 109-117Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An important feature offered by marine cyanobacterial strains over freshwater strains is the capacity to grow in seawater, replacing the need for often-limited freshwater. However, there are only limited numbers of marine cyanobacteria that are available for genetic manipulation and bioprocess applications. The marine unicellular cyanobacteria Synechococcus sp. strain NKBG 15041c (NKBG15041c) has been extensively studied. Recombinant DNA technologies are available for this strain, and its genomic information has been elucidated. However, an investigation of carbohydrate production, such as glycogen production, would provide information for inevitable biofuel-related compound production, but it has not been conducted. In this study, glycogen production by marine cyanobacterium NKBG15041c was investigated under different cultivation conditions. NKBG15041c yielded up to 399 mu g/ml/OD730 when cells were cultivated for 168 h in nitrogen-depleted medium (marine BG11(Delta N)) after medium replacement (336 h after inoculation). Cultivation under nitrogen-limited conditions also yielded an accumulation of glycogen in NKBG15041c cells (1 mM NaNO3, 301 mu g/ml/OD730; 3 mM NaNO3, 393 mu g/ml/OD730; and 5 mM NaNO3, 328 mu g/ml/OD730) under ambient conditions. Transcriptional analyses were carried out for 13 putative genes responsible for glycogen synthesis and catabolism that were predicted based on homology analyses with Synechocystis sp. PCC 6803 (PCC6803) and Synechococcus sp. PCC7002 (PCC7002). The transcriptional analyses revealed that glycogen production in NKBG15041c under nitrogen-depleted conditions can be explained by the contribution of both increased carbon flux towards glycogen synthesis, similar to PCC6803 and PCC7002, and increased transcriptional levels of genes responsible for glycogen synthesis, which is different from the conventionally reported phenomenon, resulting in a relatively high amount of glycogen under ambient conditions compared to PCC6803 and PCC7002.

  • 61.
    Bagge, Joakim
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Hedman, Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Smedsrud, Sabina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Svärdström, Cornelia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Söderberg, Elisabeth
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Valdés, Fernando
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Utveckling av metodik för påvisning och typning av Listeria i livsmedelskedjan2017Självständigt arbete på grundnivå (kandidatexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
  • 62.
    Baho, Didier
    et al.
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Peter, Hannes
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Tranvik, Lars J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Resistance and resilience of microbial communities: temporal and spatial insurance against perturbations2012Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 14, nr 9, s. 2283-2292Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Bacteria play fundamental roles for many ecosystem processes; however, little empirical evidence is available on how environmental perturbations affect their composition and function. We investigated how spatial and temporal refuges affect the resistance and resilience of a freshwater bacterioplankton community upon a salinity pulse perturbation in continuous cultures. Attachment to a surface avoided the flushing out of cells and enabled re-colonization of the liquid phase after the perturbation, hence serving as a temporal refuge. A spatial refuge was established by introduction of bacteria from an undisturbed reservoir upstream of the continuous culture vessel, acting analogous to a regional species pool in a metacommunity. The salinity pulse affected bacterial community composition and the rates of respiration and the pattern of potential substrate utilization as well as the correlation between composition and function. Compared with the no-refuge treatment, the temporal refuge shortened return to pre-perturbation conditions, indicating enhanced community resilience. Composition and function were less disturbed in the treatment providing a spatial refuge, suggesting higher resistance. Our results highlight that spatial and temporal dynamics in general and refuges in particular need to be considered for conceptual progress in how microbial metacommunities are shaped by perturbations.

  • 63.
    Bahram, Mohammad
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Ulls Vag 16, S-75651 Uppsala, Sweden.
    Anslan, Sten
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, Tartu, Estonia;Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
    Hildebrand, Falk
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
    Bork, Peer
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany;Max Delbruck Ctr Mol Med, Berlin, Germany;Univ Wurzburg, Bioctr, Dept Bioinformat, Wurzburg, Germany.
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14A Ravila, EE-50411 Tartu, Estonia.
    Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment2019Ingår i: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 11, nr 4, s. 487-494Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    High-throughput studies of microbial communities suggest that Archaea are a widespread component of microbial diversity in various ecosystems. However, proper quantification of archaeal diversity and community ecology remains limited, as sequence coverage of Archaea is usually low owing to the inability of available prokaryotic primers to efficiently amplify archaeal compared to bacterial rRNA genes. To improve identification and quantification of Archaea, we designed and validated the utility of several primer pairs to efficiently amplify archaeal 16S rRNA genes based on up-to-date reference genes. We demonstrate that several of these primer pairs amplify phylogenetically diverse Archaea with high sequencing coverage, outperforming commonly used primers. Based on comparing the resulting long 16S rRNA gene fragments with public databases from all habitats, we found several novel family- to phylum-level archaeal taxa from topsoil and surface water. Our results suggest that archaeal diversity has been largely overlooked due to the limitations of available primers, and that improved primer pairs enable to estimate archaeal diversity more accurately.

  • 64.
    Bahram, Mohammad
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Hildebrand, Falk
    Forslund, Sofia K
    Anderson, Jennifer L
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Soudzilovskaia, Nadejda A
    Bodegom, Peter M
    Bengtsson-Palme, Johan
    Anslan, Sten
    Coelho, Luis Pedro
    Harend, Helery
    Huerta-Cepas, Jaime
    Medema, Marnix H
    Maltz, Mia R
    Mundra, Sunil
    Olsson, Pål Axel
    Pent, Mari
    Põlme, Sergei
    Sunagawa, Shinichi
    Ryberg, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Tedersoo, Leho
    Bork, Peer
    Structure and function of the global topsoil microbiome.2018Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 560, nr 7717, s. 233-237Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

  • 65.
    Bahram, Mohammad
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden.
    Vanderpool, Dan
    Univ Montana, Div Biol Sci, 32 Campus Dr, Missoula, MT 59812 USA.
    Pent, Mari
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Hiltunen, Markus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Ryberg, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics2018Ingår i: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, nr 2, s. 155-166Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.

  • 66.
    Balaban, Nathalie Q.
    et al.
    Hebrew Univ Jerusalem, Racah Inst Phys, Jerusalem, Israel.
    Helaine, Sophie
    Imperial Coll London, MRC Ctr Mol Bacteriol & Infect, London, England.
    Lewis, Kim
    Northeastern Univ, Dept Biol, Boston, MA 02115 USA.
    Ackermann, Martin
    Swiss Fed Inst Technol, Inst Biogeochem & Pollutant Dynam, Zurich, Switzerland;Eawag, Dept Environm Microbiol, Dubendorf, Switzerland.
    Aldridge, Bree
    Tufts Univ, Sch Med, Dept Mol Biol & Microbiol, Boston, MA 02111 USA.
    Andersson, Dan I
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Brynildsen, Mark P.
    Princeton Univ, Dept Chem & Biol Engn, Princeton, NJ 08544 USA.
    Bumann, Dirk
    Univ Basel, Biozentrum, Focal Area Infect Biol, Basel, Switzerland.
    Camilli, Andrew
    Tufts Univ, Sch Med, Dept Mol Biol & Microbiol, Boston, MA 02111 USA.
    Collins, James J.
    MIT, Dept Biol Engn, Inst Med Engn & Sci, 77 Massachusetts Ave, Cambridge, MA 02139 USA;MIT, Synthet Biol Ctr, 77 Massachusetts Ave, Cambridge, MA 02139 USA;Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02115 USA;Broad Inst MIT & Harvard, Cambridge, MA USA.
    Dehio, Christoph
    Univ Basel, Biozentrum, Focal Area Infect Biol, Basel, Switzerland.
    Fortune, Sarah
    Harvard TH Chan Sch Publ Hlth, Dept Immunol & Infect Dis, Boston, MA USA.
    Ghigo, Jean-Marc
    Inst Pasteur, Genet Biofilms Lab, Paris, France.
    Hardt, Wolf-Dietrich
    Swiss Fed Inst Technol, Inst Microbiol, Zurich, Switzerland.
    Harms, Alexander
    Univ Basel, Biozentrum, Focal Area Infect Biol, Basel, Switzerland.
    Heinemann, Matthias
    Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Mol Syst Biol, Groningen, Netherlands.
    Hung, Deborah T.
    Broad Inst MIT & Harvard, Cambridge, MA USA.
    Jenal, Urs
    Univ Basel, Biozentrum, Focal Area Infect Biol, Basel, Switzerland.
    Levin, Bruce R.
    Emory Univ, Dept Biol, Atlanta, GA 30322 USA.
    Michiels, Jan
    Univ Leuven, KU Leuven, Ctr Microbiol, Leuven, Belgium.
    Storz, Gisela
    Eunice Kennedy Shriver Natl Inst Child Hlth & Hum, Div Mol & Cellular Biol, Bethesda, MD USA.
    Tan, Man-Wah
    Genentech Inc, Infect Dis Dept, San Francisco, CA USA.
    Tenson, Tanel
    Univ Tartu, Inst Technol, Tartu, Estonia.
    Van Melderen, Laurence
    Univ Libre Bruxelles, Fac Sci, Brussels, Belgium.
    Zinkernagel, Annelies
    Univ Zurich, Univ Hosp Zurich, Div Infect Dis, Zurich, Switzerland.
    Definitions and guidelines for research on antibiotic persistence2019Ingår i: Nature Reviews Microbiology, ISSN 1740-1526, E-ISSN 1740-1534, Vol. 17, nr 7, s. 441-448Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Increasing concerns about the rising rates of antibiotic therapy failure and advances in single-cell analyses have inspired a surge of research into antibiotic persistence. Bacterial persister cells represent a subpopulation of cells that can survive intensive antibiotic treatment without being resistant. Several approaches have emerged to define and measure persistence, and it is now time to agree on the basic definition of persistence and its relation to the other mechanisms by which bacteria survive exposure to bactericidal antibiotic treatments, such as antibiotic resistance, heteroresistance or tolerance. In this Consensus Statement, we provide definitions of persistence phenomena, distinguish between triggered and spontaneous persistence and provide a guide to measuring persistence. Antibiotic persistence is not only an interesting example of non-genetic single-cell heterogeneity, it may also have a role in the failure of antibiotic treatments. Therefore, it is our hope that the guidelines outlined in this article will pave the way for better characterization of antibiotic persistence and for understanding its relevance to clinical outcomes.

  • 67.
    Balmonte, John Paul
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Buckley, Andrew
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Hoarfrost, Adrienne
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Ghobrial, Sherif
    Univ New Hampshire, Inst Study Earth Oceans & Space, Durham, NH 03824 USA.
    Ziervogel, Kai
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Teske, Andreas
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Arnosti, Carol
    Univ N Carolina, Dept Marine Sci, Chapel Hill, NC 27599 USA.
    Community structural differences shape microbial responses to high molecular weight organic matter2019Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, nr 2, s. 557-571Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The extent to which differences in microbial community structure result in variations in organic matter (OM) degradation is not well understood. Here, we tested the hypothesis that distinct marine microbial communities from North Atlantic surface and bottom waters would exhibit varying compositional succession and functional shifts in response to the same pool of complex high molecular weight (HMW-OM). We also hypothesized that microbial communities would produce a broader spectrum of enzymes upon exposure to HMW-OM, indicating a greater potential to degrade these compounds than reflected by initial enzymatic activities. Our results show that community succession in amended mesocosms was congruent with cell growth, increased bacterial production and most notably, with substantial shifts in enzymatic activities. In all amended mesocosms, closely related taxa that were initially rare became dominant at time frames during which a broader spectrum of active enzymes were detected compared to initial timepoints, indicating a similar response among different communities. However, succession on the whole-community level, and the rates, spectra and progression of enzymatic activities, reveal robust differences among distinct communities from discrete water masses. These results underscore the crucial role of rare bacterial taxa in ocean carbon cycling and the importance of bacterial community structure for HMW-OM degradation.

  • 68. Bambou, Jean-Christophe
    et al.
    Giraud, Antoine
    Menard, Sandrine
    Begue, Bernadette
    Rakotobe, Sabine
    Heyman, Martine
    Taddei, François
    Cerf-Bensussan, Nadine
    Gaboriau-Routhiau, Valérie
    In vitro and ex vivo activation of the TLR5 signaling pathway in intestinal epithelial cells by a commensal Escherichia coli strain.2004Ingår i: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 279, nr 41, s. 42984-92Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The capacity of non-pathogenic enteric bacteria to induce a pro-inflammatory response is under debate in terms of its effect on the symbiosis between the mammalian host and its commensal gut microflora. Activation of NF-kappaB and induction of interleukin-8 (IL-8) and CCL-20 by the commensal Escherichia coli strain MG1655 were first studied in vitro in the human intestinal epithelial cell (IECs) lines HT29-19A and Caco-2, transfected or not with plasmids encoding dominant negative Toll-like receptor (TLR) 5 and myeloid differentiation factor-88 (MyD88) adaptor protein. The response of enterocytes in situ was then assessed using murine ileal biopsies mounted in Ussing chambers. Commensal E. coli induced NF-kappaB DNA binding, NF-kappaB transcriptional activity, CCL-20 expression, and IL-8 secretion in the human IEC lines. E. coli MG1655 flagellin was necessary and sufficient to trigger this pro-inflammatory pathway via its interaction with TLR5 and the subsequent recruitment of the adaptor protein MyD88. Following epithelial cell polarization, signaling could be induced by live E. coli and flagellin on the apical side of HT29-19A. The in vivo relevance of our findings was confirmed, because immunohistochemical staining of murine ileum demonstrated expression of TLR5 in the apical part of enterocytes in situ. Furthermore, flagellin added on the mucosal side of murine ileal biopsies mounted in Ussing chambers induced a basolateral production of KC, a functional murine homolog of human IL-8. These findings provide strong evidence that flagellin released by flagellated commensal bacteria in the intestinal lumen can induce a pro-inflammatory response in enterocytes in vivo.

  • 69.
    Banin, Ehud
    et al.
    Bar Ilan Univ, Fac Life Sci, IL-82900 Ramat Gan, Israel..
    Hughes, Diarmaid
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Kuipers, Oscar P.
    Univ Groningen, Mol Genet, NL-9747 AG Groningen, Netherlands..
    Bacterial pathogens, antibiotics and antibiotic resistance: Editorial2017Ingår i: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 41, nr 3, s. 450-452, artikel-id fux016Artikel i tidskrift (Övrigt vetenskapligt)
  • 70.
    Barrenäs, Fredrik
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräkningsbiologi och bioinformatik. Univ Washington, Dept Microbiol, Seattle, WA 98195 USA.
    Raehtz, Kevin
    Univ Pittsburgh, Dept Med, Div Infect Dis, Pittsburgh, PA USA;Univ Pittsburgh, Sch Med, Dept Microbiol & Mol Genet, Pittsburgh, PA USA.
    Xu, Cuiling
    Univ Pittsburgh, Sch Med, Dept Pathol, Pittsburgh, PA USA.
    Law, Lynn
    Univ Washington, Dept Immunol, Seattle, WA 98195 USA;Univ Washington, Ctr Innate Immun & Immune Dis, Seattle, WA 98195 USA.
    Green, Richard R.
    Univ Washington, Dept Immunol, Seattle, WA 98195 USA;Univ Washington, Ctr Innate Immun & Immune Dis, Seattle, WA 98195 USA.
    Silvestri, Guido
    Emory Univ, Dept Pathol & Lab Med, Atlanta, GA 30322 USA;Emory Univ, Yerkes Natl Primate Res Ctr, Div Microbiol & Immunol, Atlanta, GA 30322 USA.
    Bosinger, Steven E.
    Emory Univ, Dept Pathol & Lab Med, Atlanta, GA 30322 USA;Emory Univ, Yerkes Natl Primate Res Ctr, Div Microbiol & Immunol, Atlanta, GA 30322 USA.
    Nishida, Andrew
    Univ Washington, Dept Microbiol, Seattle, WA 98195 USA.
    Li, Qingsheng
    Univ Nebraska, Sch Biol Sci, Nebraska Ctr Virol, Lincoln, NE USA.
    Lu, Wuxun
    Univ Nebraska, Sch Biol Sci, Nebraska Ctr Virol, Lincoln, NE USA.
    Zhang, Jianshui
    Univ Nebraska, Sch Biol Sci, Nebraska Ctr Virol, Lincoln, NE USA.
    Thomas, Matthew J.
    Univ Washington, Dept Immunol, Seattle, WA 98195 USA;Univ Washington, Washington Natl Primate Res Ctr, Seattle, WA 98195 USA.
    Chang, Jean
    Univ Washington, Dept Immunol, Seattle, WA 98195 USA;Univ Washington, Ctr Innate Immun & Immune Dis, Seattle, WA 98195 USA.
    Smith, Elise
    Univ Washington, Dept Immunol, Seattle, WA 98195 USA;Univ Washington, Ctr Innate Immun & Immune Dis, Seattle, WA 98195 USA.
    Weiss, Jeffrey M.
    Univ Washington, Dept Microbiol, Seattle, WA 98195 USA.
    Dawoud, Reem A.
    Emory Univ, Dept Pathol & Lab Med, Atlanta, GA 30322 USA.
    Richter, George H.
    Univ Pittsburgh, Sch Med, Dept Pathol, Pittsburgh, PA USA.
    Trichel, Anita
    Univ Pittsburgh, Div Lab Anim Resources, Pittsburgh, PA USA.
    Ma, Dongzhu
    Univ Pittsburgh, Dept Orthoped Surg, Pittsburgh, PA USA.
    Peng, Xinxia
    North Carolina State Univ, Dept Mol Biomed Sci, Raleigh, NC 27695 USA.
    Komorowski, Jan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräkningsbiologi och bioinformatik.
    Apetrei, Cristian
    Univ Pittsburgh, Dept Med, Div Infect Dis, Pittsburgh, PA USA;Univ Pittsburgh, Sch Med, Dept Microbiol & Mol Genet, Pittsburgh, PA USA.
    Pandrea, Ivona
    Univ Pittsburgh, Sch Med, Dept Microbiol & Mol Genet, Pittsburgh, PA USA;Univ Pittsburgh, Sch Med, Dept Pathol, Pittsburgh, PA USA.
    Gale, Michael, Jr.
    Univ Washington, Dept Immunol, Seattle, WA 98195 USA;Univ Washington, Ctr Innate Immun & Immune Dis, Seattle, WA 98195 USA;Univ Washington, Washington Natl Primate Res Ctr, Seattle, WA 98195 USA.
    Macrophage-associated wound healing contributes to African green monkey SIV pathogenesis control2019Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, artikel-id 5101Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Natural hosts of simian immunodeficiency virus (SIV) avoid AIDS despite lifelong infection. Here, we examined how this outcome is achieved by comparing a natural SIV host, African green monkey (AGM) to an AIDS susceptible species, rhesus macaque (RM). To asses gene expression profiles from acutely SIV infected AGMs and RMs, we developed a systems biology approach termed Conserved Gene Signature Analysis (CGSA), which compared RNA sequencing data from rectal AGM and RM tissues to various other species. We found that AGMs rapidly activate, and then maintain, evolutionarily conserved regenerative wound healing mechanisms in mucosal tissue. The wound healing protein fibronectin shows distinct tissue distribution and abundance kinetics in AGMs. Furthermore, AGM monocytes exhibit an embryonic development and repair/regeneration signature featuring TGF-beta and concomitant reduced expression of inflammatory genes compared to RMs. This regenerative wound healing process likely preserves mucosal integrity and prevents inflammatory insults that underlie immune exhaustion in RMs.

  • 71.
    Bartke, Katrin
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Recombinant mosaic genomes and the evolution of novel antibiotic-resistant bacteria.2017Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The frequency of antibiotic resistance and its spread are increasing rapidly. One of the main mechanisms responsible for this is conjugation, a means of horizontal gene transfer (HGT) evolved by many plasmids. Conjugative plasmids can occasionally integrate into a bacterial chromosome and in this way mediate the transfer of small or large regions of chromosomal DNA from one bacterium to another within and across bacterial species. Integration of the foreign chromosomal DNA into the recipient bacterium creates a recombinant mosaic chromosome. The creation of mosaic chromosomes is associated with bacterial speciation and with the success of some globally successful antibiotic resistant strains. However, very little is known about the genetic constraints of these events, in particular how the creation of a mosaic chromosome effects bacterial fitness, and whether compensatory evolution can restore relative fitness. The aims of this study were: (I) to create a number of such recombinants from an hfr E. coli donor and a restriction-negative S. typhimurium recipient with integration of E. coli DNA at different chromosomal locations in S. typhimurium; (II) to analyse recombinant genome architecture by whole genome sequencing (WGS) and relate this to relative growth fitness; and (III) to conduct an evolution experiment with conjugants that had reduced growth fitness compared to the parental strains, to assess their ability to ameliorate these fitness costs by compensatory evolution. Findings from the WGS and growth rate assays suggested a strong correlation between the genetic architecture of a recombinant and its respective relative fitness. It could be seen that specific chromosomal positions are unfavourable for integration and come with a high fitness cost for the recombinant bacterium, while in other positions integrations did not reduce or even improved fitness in comparison to the parental strains. The evolution experiment revealed, that while compensation of high fitness costs is possible, it is a long process that requires the accumulation of multiple changes and mutations. Moreover, no universal way of solving the relative fitness problems associated with the mosaic chromosomes presented itself.

  • 72.
    Beier, Sara
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Bacterial chitin degradation: mechanisms and ecophysiological strategies2013Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 4, s. 149-Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities.

  • 73. Bendall, Matthew L
    et al.
    Stevens, Sarah LR
    Chan, Leong-Keat
    Malfatti, Stephanie
    Schwientek, Patrick
    Tremblay, Julien
    Schackwitz, Wendy
    Martin, Joel
    Pati, Amrita
    Bushnell, Brian
    Froula, Jeff
    Kang, Dongwan
    Tringe, Susannah G
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Moran, Mary A
    Shade, Ashley
    Newton, Ryan J
    McMahon, Katherine D
    Malmstrom, Rex R
    Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations2016Ingår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, nr 7, s. 1589-1601Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Here, from a 9-year metagenomic study of a freshwater lake (2005-2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. These patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the /`ecotype model/' of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.

  • 74.
    Bennke, Christin M.
    et al.
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Reintjes, Greta
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Schattenhofer, Martha
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Ellrott, Andreas
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Wulf, Jörg
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Zeder, Michael
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany.;Technobiol GmbH, Buchrain, Switzerland..
    Fuchs, Bernhard M.
    Max Planck Inst Marine Microbiol, Dept Mol Ecol, Bremen, Germany..
    Modification of a High-Throughput Automatic Microbial Cell Enumeration System for Shipboard Analyses2016Ingår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 82, nr 11, s. 3289-3296Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the age of ever-increasing "-omics" studies, the accurate and statistically robust determination of microbial cell numbers within often-complex samples remains a key task in microbial ecology. Microscopic quantification is still the only method to enumerate specific subgroups of microbial clades within complex communities by, for example, fluorescence in situ hybridization (FISH). In this study, we improved an existing automatic image acquisition and cell enumeration system and adapted it for usage at high seas on board an oceanographic research ship. The system was evaluated by testing settings such as minimal pixel area and image exposure times ashore under stable laboratory conditions before being brought on board and tested under various wind and wave conditions. The system was robust enough to produce high-quality images even with ship heaves of up to 3m and pitch and roll angles of up to 6.3 degrees. On board the research ship, on average, 25% of the images acquired from plankton samples on filter membranes could be used for cell enumeration. Automated enumeration was highly correlated with manual counts (r(2)>0.9). Even the smallest of microbial cells in the open ocean, members of the alphaproteobacterial SAR11 clade, could be confidently detected and enumerated. The automated image acquisition and cell enumeration system developed here enables an accurate and reproducible determination of microbial cell counts in planktonic samples and allows insight into the abundance and distribution of specific microorganisms already on board within a few hours.

    IMPORTANCE In this research article, we report on a new system and software pipeline, which allows for an easy and quick image acquisition and the subsequent enumeration of cells in the acquired images. We put this pipeline through vigorous testing and compared it to manual microscopy counts of microbial cells on membrane filters. Furthermore, we tested this system at sea on board a marine research vessel and counted bacteria on board within a few hours after the retrieval of water samples. The imaging and counting system described here has been successfully applied to a number of laboratory-based studies and allowed the quantification of thousands of samples and FISH preparations (see, e.g., H. Teeling, B. M. Fuchs, D. Becher, C. Klockow, A. Gardebrecht, C. M. Bennke, M. Kassabgy, S. Huang, A. J. Mann, J. Waldmann, M. Weber, A. Klindworth, A. Otto, J. Lange, J. Bernhardt, C. Reinsch, M. Hecker, J. Peplies, F. D. Bockelmann, U. Callies, G. Gerdts, A. Wichels, K. H. Wiltshire, F. O. Glockner, T. Schweder, and R. Amann, Science 336:608-611, 2012, http://dx.doi.org/10.1126/science.1218344). We adjusted the standard image acquisition software to withstand ship movements. This system will allow for more targeted sampling of the microbial community, leading to a better understanding of the role of microorganisms in the global oceans.

  • 75.
    Berenjian, Saideh
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Construction of Adenovirus Vectors for Studies of Protein Function and RNA Interference2006Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    During an adenovirus infection the accumulation of alternatively spliced mRNAs is subjected to a tight temporal regulation. The IIIa protein is a structural protein expressed exclusively late after infection. To study the significance of the restricted IIIa protein expression we used a Tet-ON regulated adenoviral vector to overexpress the IIIa protein during the early phase of infection. The results show that unregulated IIIa protein expression caused a reduction in late viral protein accumulation and a slight block of viral DNA replication. Further, the results indicate that IIIa splicing might be subjected to a regulation via a feed back loop stimulating its own expression.

    To improve the efficacy of vectors for regulated transgene expression, we constructed binary adenoviral vectors based on the Tet-ON and Tet-OFF systems. These vectors encode both the transcriptional activator and the tetracycline-regulated expression cassette from the same viral unit, ensuring that each infected cell will express both the activator and the reporter gene. In model experiments this system was shown to result in a tight control of gene expression with no detectable background expression of the transgene and induction levels reaching 500-600 fold.

    Introduction of dsRNA into a cell will induce a sequence specific degradation of the homologous mRNA via a mechanism named RNA interference (RNAi). The adenovirus VA RNAs are short highly structured RNAs that are expressed in large amounts late during an adenovirus infection. Here we showed that both VA RNAI and VA RNAII functions as virus-encoded suppressors of RNAi, by interfering with the activity of Dicer, the enzyme that cleaves the initial dsRNA to short-interfering RNAs (siRNAs) that mediate RNAi. Further, the VA RNAs themselves are substrates for Dicer and are cleaved into siRNAs in vivo that are incorporated into active RNA-induced silencing complexes.

    There is a great interest in developing novel therapeutic strategies based on RNAi. We constructed adenoviral vectors that express short hairpin RNAs, which in vivo will be cleaved to siRNAs that induce sequence-specific RNAi. We compared the efficiency of RNAi induced by vectors based on the viral VA RNAI and the human U6 promoters. Our results suggest that under conditions where the recombinant virus does not replicate, the VA RNA promoter is more effective in down regulating target gene expression, whereas the U6 promoter was more effective under replicative conditions.

    Delarbeten
    1. Unscheduled expression of capsid protein IIIa results in defects in adenovirus major late mRNA and protein expression
    Öppna denna publikation i ny flik eller fönster >>Unscheduled expression of capsid protein IIIa results in defects in adenovirus major late mRNA and protein expression
    2002 (Engelska)Ingår i: Virus research, Vol. 83, s. 197-206Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-93995 (URN)
    Tillgänglig från: 2006-02-09 Skapad: 2006-02-09 Senast uppdaterad: 2011-01-11Bibliografiskt granskad
    2. Binary AdEasy Vector systems designed for Tet-ON or Tet-OFF regulated control of transgene expression
    Öppna denna publikation i ny flik eller fönster >>Binary AdEasy Vector systems designed for Tet-ON or Tet-OFF regulated control of transgene expression
    2006 (Engelska)Ingår i: Virus research, Vol. 115, s. 16-23Artikel i tidskrift (Refereegranskat) Published
    Identifikatorer
    urn:nbn:se:uu:diva-93996 (URN)
    Tillgänglig från: 2006-02-09 Skapad: 2006-02-09 Senast uppdaterad: 2011-06-28Bibliografiskt granskad
    3. Suppression of RNA interference by adenovirus virus-associated RNA
    Öppna denna publikation i ny flik eller fönster >>Suppression of RNA interference by adenovirus virus-associated RNA
    Visa övriga...
    2005 (Engelska)Ingår i: Journal of Virology, ISSN 0022-538X, E-ISSN 1098-5514, Vol. 79, nr 15, s. 9556-65Artikel i tidskrift (Refereegranskat) Published
    Nyckelord
    Adenoviruses; Human/*genetics, Base Sequence, Cell Line, Humans, Molecular Sequence Data, Mutation, RNA Interference, RNA; Small Interfering/genetics, RNA; Viral/chemistry/genetics/*metabolism/*physiology, Research Support; Non-U.S. Gov't, Ribonuclease III/antagonists & inhibitors/metabolism, Virus Integration, eIF-2 Kinase/antagonists & inhibitors/metabolism
    Identifikatorer
    urn:nbn:se:uu:diva-80238 (URN)10.1128/JVI.79.15.9556-9565.2005 (DOI)16014917 (PubMedID)
    Tillgänglig från: 2006-05-04 Skapad: 2006-05-04 Senast uppdaterad: 2017-12-14Bibliografiskt granskad
    4. Construction of adenovirus vector systems based on the viral VA RNAI and the human U6 promoters for short hairpin RNA expression in mammalian cells
    Öppna denna publikation i ny flik eller fönster >>Construction of adenovirus vector systems based on the viral VA RNAI and the human U6 promoters for short hairpin RNA expression in mammalian cells
    (Engelska)Manuskript (Övrigt vetenskapligt)
    Identifikatorer
    urn:nbn:se:uu:diva-93998 (URN)
    Tillgänglig från: 2006-02-09 Skapad: 2006-02-09 Senast uppdaterad: 2011-06-28
  • 76.
    Berga, Mercè
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Yinghua, Zha
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Székely, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Langenheder, Silke
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Testing responses of bacterial communities to environmental change using whole ecosystem manipulation experimentsManuskript (preprint) (Övrigt vetenskapligt)
  • 77.
    Berga, Mercè
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Germany.
    Zha, Yinghua
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Székely, Anna J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Langenheder, Silke
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes2017Ingår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, artikel-id 948Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Disturbances and environmental change are important factors determining the diversity,composition, and functioning of communities. However, knowledge about how naturalbacterial communities are affected by such perturbations is still sparse. We performeda whole ecosystem manipulation experiment with freshwater rock pools where weapplied salinity disturbances of different intensities. The aim was to test how thecompositional and functional resistance and resilience of bacterial communities,alpha- and beta-diversity and the relative importance of stochastic and deterministiccommunity assembly processes changed along a disturbance intensity gradient.We found that bacterial communities were functionally resistant to all salinity levels (3, 6, and 12 psu) and compositionally resistant to a salinity increase to 3 psu andresilient to increases of 6 and 12 psu. Increasing salinities had no effect on local richnessand evenness, beta-diversity and the proportion of deterministically vs. stochasticallyassembled communities. Our results show a high functional and compositional stabilityof bacterial communities to salinity changes of different intensities both at localand regional scales, which possibly reflects long-term adaptation to environmentalconditions in the study system.

  • 78.
    Berga, Mercè
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Östman, Örjan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Lindström, Eva
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Langenheder, Silke
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Effects of predation and dispersal on the diversity an functioning of bacterial metacommunitiesManuskript (preprint) (Övrigt vetenskapligt)
  • 79.
    Berga Quintana, Mercè
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Assembly Mechanisms in Aquatic Bacterial Communities: The Role of Disturbances, Dispersal and History2013Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Environmental conditions, biotic interactions, dispersal and history have been suggested to be important processes influencing the spatial distribution of organisms and thus to affect community assembly. Understanding how these processes influence community assembly is important, particularly because community diversity and composition are suggested to be relevant for ecosystem functioning. Moreover, bacteria are strongly contributing to nutrient and carbon cycle. Bacteria are highly abundant and ubiquitous, and thus it is relevant to study how they are assembled. This thesis aims to gain insight on the role of these processes on aquatic bacterial community assembly, diversity and functioning. The studies included in this thesis involve transplant and microcosm experiments performed in the lab as well as manipulation experiments and field surveys in a natural rock pool systems. Bacterial community composition was addressed by analysis of 16S rRNA gene and community functioning by measuring bacterial production, community respiration and the ability to use different carbon substrates. This thesis highlights that species sorting is a very important assembly mechanism for bacterial communities, but also finds that other processes such as dispersal and history contribute to the patterns observed. Dispersal caused rescuing effects compensating for losses of diversity; at the same time it increased the similarity between communities. Moreover, bacteria have shown a high level of functional plasticity when colonizing a new locality. Interestingly, past environmental conditions explained the structure of bacterial communities better than present-day environmental conditions. Disturbances and biotic interactions are also important in the assembly of communities. Disturbance caused temporary shifts in bacterial function and changes in composition, the magnitude of which depended on the intensity and the frequency of the disturbance. However, natural aquatic bacterial communities showed quite high resilience capacities. Competition can shift the proportion of generalists and specialists species whereas predation or trophic interactions have been found to decrease diversity and to modify the importance of stochasticity. Both caused alterations of community functioning. Finally, this thesis shows that the diversity-functioning relationship is context dependent. Further research should be directed to understanding the intensity and direction of changes in composition and how this affects the functionality of bacterial communities

    Delarbeten
    1. Effects of Disturbance Intensity and Frequency on Bacterial Community Composition and Function
    Öppna denna publikation i ny flik eller fönster >>Effects of Disturbance Intensity and Frequency on Bacterial Community Composition and Function
    2012 (Engelska)Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, nr 5, s. e36959-Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Disturbances influence community structure and ecosystem functioning. Bacteria are key players in ecosystems and it is therefore crucial to understand the effect of disturbances on bacterial communities and how they respond to them, both compositionally and functionally. The main aim of this study was to test the effect of differences in disturbance strength on bacterial communities. For this, we implemented two independent short-term experiments with dialysis bags containing natural bacterial communities, which were transplanted between ambient and 'disturbed' incubation tanks, manipulating either the intensity or the frequency of a salinity disturbance. We followed changes in community composition by terminal restriction fragment analysis (T-RFLP) and measured various community functions (bacterial production, carbon substrate utilization profiles and rates) directly after and after a short period of recovery under ambient conditions. Increases in disturbance strength resulted in gradually stronger changes in bacterial community composition and functions. In the disturbance intensity experiment, the sensitivity to the disturbance and the ability of recovery differed between different functions. In the disturbance frequency experiment, effects on the different functions were more consistent and recovery was not observed. Moreover, in case of the intensity experiment, there was also a time lag in the responses of community composition and functions, with functional responses being faster than compositional ones. To summarize, our study shows that disturbance strength has the potential to change the functional performance and composition of bacterial communities. It further highlights that the overall effects, rates of recovery and the degree of congruence in the response patterns of community composition and functioning along disturbance gradients depend on the type of function and the character of the disturbance.

    Nationell ämneskategori
    Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-177625 (URN)10.1371/journal.pone.0036959 (DOI)000305339400046 ()
    Tillgänglig från: 2012-07-18 Skapad: 2012-07-17 Senast uppdaterad: 2017-12-07Bibliografiskt granskad
    2. Testing responses of bacterial communities to environmental change using whole ecosystem manipulation experiments
    Öppna denna publikation i ny flik eller fönster >>Testing responses of bacterial communities to environmental change using whole ecosystem manipulation experiments
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Ekologi Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-207179 (URN)
    Tillgänglig från: 2013-09-10 Skapad: 2013-09-10 Senast uppdaterad: 2014-05-08
    3. Mechanisms determining the fate of dispersed bacterial communities in new environments
    Öppna denna publikation i ny flik eller fönster >>Mechanisms determining the fate of dispersed bacterial communities in new environments
    2013 (Engelska)Ingår i: ISME Journal, ISSN 1751-7362, Vol. 7, nr 1, s. 61-71Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Recent work has shown that dispersal has an important role in shaping microbial communities. However, little is known about how dispersed bacteria cope with new environmental conditions and how they compete with local resident communities. To test this, we implemented two full-factorial transplant experiments with bacterial communities originating from two sources (freshwater or saline water), which were incubated, separately or in mixes, under both environmental conditions. Thus, we were able to separately test for the effects of the new environment with and without interactions with local communities. We determined community composition using 454-pyrosequencing of bacterial 16S rRNA to specifically target the active fraction of the communities, and measured several functional parameters. In absence of a local resident community, the net functional response was mainly affected by the environmental conditions, suggesting successful functional adaptation to the new environmental conditions. Community composition was influenced both by the source and the incubation environment, suggesting simultaneous effects of species sorting and functional plasticity. In presence of a local resident community, functional parameters were higher compared with those expected from proportional mixes of the unmixed communities in three out of four cases. This was accompanied by an increase in the relative abundance of generalists, suggesting that competitive interactions among local and immigrant taxa could explain the observed functional overachievement. In summary, our results suggest that environmental filtering, functional plasticity and competition are all important mechanisms influencing the fate of dispersed communities.

    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-192014 (URN)10.1038/ismej.2012.80 (DOI)000313236000006 ()
    Tillgänglig från: 2013-01-24 Skapad: 2013-01-15 Senast uppdaterad: 2014-01-23Bibliografiskt granskad
    4. The spatial structure of bacterial communities is influenced by historical environmental conditions
    Öppna denna publikation i ny flik eller fönster >>The spatial structure of bacterial communities is influenced by historical environmental conditions
    2014 (Engelska)Ingår i: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 95, nr 5, s. 1134-1140Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    The spatial structure of ecological communities, including that of bacteria, is often influenced by species sorting by contemporary environmental conditions. Moreover, historical processes, i.e., ecological and evolutionary events that have occurred at some point in the past, such as dispersal limitation, drift, priority effects, or selection by past environmental conditions, can be important, but are generally investigated much less. Here, we conducted a field study using 16 rock pools, where we specifically compared the importance of past vs. contemporary environmental conditions for bacterial community structure by correlating present differences in bacterial community composition among pools to environmental conditions measured on the same day, as well as to those measured 2, 4, 6, and 8 d earlier. The results prove that selection by past environmental conditions exists, since we were able to show that bacterial communities are, to a greater extent, an imprint of past compared to contemporary environmental conditions. We suggest that this is the result of a combination of different mechanisms, including priority effects that cause rapid adaptation to new environmental conditions of taxa that have been initially selected by past environmental conditions, and slower rates of turnover in community composition compared to environmental conditions.

    Nationell ämneskategori
    Ekologi Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-207181 (URN)10.1890/13-1300.1 (DOI)000336740500003 ()
    Tillgänglig från: 2013-09-10 Skapad: 2013-09-10 Senast uppdaterad: 2017-12-06Bibliografiskt granskad
    5. Effects of predation and dispersal on the diversity an functioning of bacterial metacommunities
    Öppna denna publikation i ny flik eller fönster >>Effects of predation and dispersal on the diversity an functioning of bacterial metacommunities
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Ekologi Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-207177 (URN)
    Tillgänglig från: 2013-09-10 Skapad: 2013-09-10 Senast uppdaterad: 2014-01-23
  • 80. Bergenholtz, Sa Schoug
    et al.
    Wessman, Per
    Wuttke, Anne
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk cellbiologi.
    Håkansson, Sebastian
    A case study on stress preconditioning of a Lactobacillus strain prior to freeze-drying2012Ingår i: Cryobiology, ISSN 0011-2240, E-ISSN 1090-2392, Vol. 64, nr 3, s. 152-159Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Freeze-drying of bacterial cells with retained viability and activity after storage requires appropriate formulation, i.e. mixing of physiologically adapted cell populations with suitable protective agents, and control of the freeze-drying process. Product manufacturing may alter the clinical effects of probiotics and it is essential to identify and understand possible factor co-dependencies during manufacturing. The physical solid-state behavior of the formulation and the freeze-drying parameters are critical for bacterial survival and thus process optimization is important, independent of strain. However, the maximum yield achievable is also strain-specific and strain survival is governed by e.g. medium, cell type, physiological state, excipients used, and process. The use of preferred compatible solutes for cross-protection of Lactobacilli during industrial manufacturing may be a natural step to introduce robustness, but knowledge is lacking on how compatible solutes, such as betaine, influence formulation properties and cell survival. This study characterized betaine formulations, with and without sucrose, and tested these with the model lactic acid bacteria Lactobacillus coryniformis Si3. Betaine alone did not act as a lyo-protectant and thus betaine import prior to freeze-drying should be avoided. Differences in protective agents were analyzed by calorimetry, which proved to be a suitable tool for evaluating the characteristics of the freeze-dried end products.

  • 81.
    Berghoff, Bork A.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi. Justus Liebig Univ, Inst Mikrobiol & Mol Biol, D-35392 Giessen, Germany..
    Hoekzema, Mirthe
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Aulbach, Lena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Wagner, Gerhart E. H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Two regulatory RNA elements affect TisB-dependent depolarization and persister formation2017Ingår i: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 103, nr 6, s. 1020-1033Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Bacterial survival strategies involve phenotypic diversity which is generated by regulatory factors and noisy expression of effector proteins. The question of how bacteria exploit regulatory RNAs to make decisions between phenotypes is central to a general understanding of these universal regulators. We investigated the TisB/IstR-1 toxin-antitoxin system of Escherichia coli to appreciate the role of the RNA antitoxin IstR-1 in TisB-dependent depolarization of the inner membrane and persister formation. Persisters are phenotypic variants that have become transiently drug-tolerant by arresting growth. The RNA antitoxin IstR-1 sets a threshold for TisB-dependent depolarization under DNA-damaging conditions, resulting in two sub-populations: polarized and depolarized cells. Furthermore, our data indicate that an inhibitory 5 UTR structure in the tisB mRNA serves as a regulatory RNA element that delays TisB translation to avoid inappropriate depolarization when DNA damage is low. Investigation of the persister sub-population further revealed that both regulatory RNA elements affect persister levels as well as persistence time. This work provides an intriguing example of how bacteria exploit regulatory RNAs to control phenotypic heterogeneity.

  • 82.
    Berghoff, Bork A.
    et al.
    Justus Liebig Univ, Inst Mikrobiol & Mol Biol, Giessen, Germany..
    Karlsson, Torgny
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Medicinsk genetik och genomik.
    Kallman, Thomas
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Wagner, Gerhart E. H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Grabherr, Manfred G.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study2017Ingår i: BioData Mining, ISSN 1756-0381, E-ISSN 1756-0381, Vol. 10, artikel-id 30Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess global gene expression changes on the RNA level (transcriptome). While advances in high-throughput RNA-sequencing (RNA-seq) technologies allow for inexpensive data generation, accurate post-processing and normalization across samples is required to eliminate any systematic noise introduced by the biochemical and/or technical processes. Existing methods thus either normalize on selected known reference genes that are invariant in expression across the experiment, assume that the majority of genes are invariant, or that the effects of up-and down-regulated genes cancel each other out during the normalization.

    Results: Here, we present a novel method, moose(2), which predicts invariant genes in silico through a dynamic programming (DP) scheme and applies a quadratic normalization based on this subset. The method allows for specifying a set of known or experimentally validated invariant genes, which guides the DP. We experimentally verified the predictions of this method in the bacterium Escherichia coli, and show how moose(2) is able to (i) estimate the expression value distances between RNA-seq samples, (ii) reduce the variation of expression values across all samples, and (iii) to subsequently reveal new functional groups of genes during the late stages of DNA damage. We further applied the method to three eukaryotic data sets, on which its performance compares favourably to other methods. The software is implemented in C++ and is publicly available from http://grabherr.github.io/moose2/.

    Conclusions: The proposed RNA-seq normalization method, moose(2), is a valuable alternative to existing methods, with two major advantages: (i) in silico prediction of invariant genes provides a list of potential reference genes for downstream analyses, and (ii) non-linear artefacts in RNA-seq data are handled adequately to minimize variations between replicates.

  • 83.
    Bergin, Claudia
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Max Planck Inst Marine Mikrobiol, Bremen, Germany.
    Wentrup, C.
    Max Planck Inst Marine Mikrobiol, Bremen, Germany.;Univ Vienna, Div Microbial Ecol, Dept Microbiol & Ecosyst Sci, Vienna, Austria..
    Brewig, N.
    Max Planck Inst Marine Mikrobiol, Bremen, Germany..
    Blazejak, A.
    Max Planck Inst Marine Mikrobiol, Bremen, Germany..
    Erseus, C.
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden..
    Giere, O.
    Univ Hamburg, Biozentrum Grindel, Zool Inst, Hamburg, Germany.;Univ Hamburg, Zool Museum, Hamburg, Germany..
    Schmid, M.
    Univ Vienna, Div Microbial Ecol, Dept Microbiol & Ecosyst Sci, Vienna, Austria..
    De Wit, P.
    Univ Gothenburg, Tjarmo Marine Lab, Dept Marine Sci, Stromstad, Sweden..
    Dubilier, N.
    Max Planck Inst Marine Mikrobiol, Bremen, Germany..
    Acquisition of a Novel Sulfur-Oxidizing Symbiont in the Gutless Marine Worm Inanidrilus exumae2018Ingår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 84, nr 7, artikel-id e02267-17Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Gutless phallodrilines are marine annelid worms without a mouth or gut, which live in an obligate association with multiple bacterial endosymbionts that supply them with nutrition. In this study, we discovered an unusual symbiont community in the gutless phallodriline Inanidrilus exumae that differs markedly from the microbiomes of all 22 of the other host species examined. Comparative 16S rRNA gene sequence analysis and fluorescence in situ hybridization revealed that I. exumae harbors cooccurring gamma-, alpha-, and deltaproteobacterial symbionts, while all other known host species harbor gamma-and either alpha-or deltaproteobacterial symbionts. Surprisingly, the primary chemoautotrophic sulfur oxidizer "Candidatus Thiosymbion" that occurs in all other gutless phallodriline hosts does not appear to be present in I. exumae. Instead, I. exumae harbors a bacterial endosymbiont that resembles "Ca. Thiosymbion" morphologically and metabolically but originates from a novel lineage within the class Gammaproteo-bacteria. This endosymbiont, named Gamma 4 symbiont here, had a 16S rRNA gene sequence that differed by at least 7% from those of other free-living and symbiotic bacteria and by 10% from that of "Ca. Thiosymbion." Sulfur globules in the Gamma 4 symbiont cells, as well as the presence of genes characteristic for autotrophy (cbbL) and sulfur oxidation (aprA), indicate that this symbiont is a chemoautotrophic sulfur oxidizer. Our results suggest that a novel lineage of free-living bacteria was able to establish a stable and specific association with I. exumae and appears to have displaced the "Ca. Thiosymbion" symbionts originally associated with these hosts. IMPORTANCE All 22 gutless marine phallodriline species examined to date live in a highly specific association with endosymbiotic, chemoautotrophic sulfur oxidizers called "Ca. Thiosymbion." These symbionts evolved from a single common ancestor and represent the ancestral trait for this host group. They are transmitted vertically and assumed to be in transition to becoming obligate endosymbionts. It is therefore surprising that despite this ancient, evolutionary relationship between phallodriline hosts and "Ca. Thiosymbion," these symbionts are apparently no longer present in Inanidrilus exumae. They appear to have been displaced by a novel lineage of sulfur-oxidizing bacteria only very distantly related to "Ca. Thiosymbion." Thus, this study highlights the remarkable plasticity of both animals and bacteria in establishing beneficial associations: the phallodriline hosts were able to acquire and maintain symbionts from two very different lineages of bacteria, while sulfur-oxidizing bacteria from two very distantly related lineages were able to independently establish symbiotic relationships with phallodriline hosts.

  • 84.
    Berglin, Lennart
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC.
    Kjellander, Marcus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    Johansson, Gunnar
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Biokemi.
    In situ generation of iminodiacetic acid groups on nanoporous alumina for the reversible immobilization of enzymes and other biomolecules2014Ingår i: Biotechnology letters, ISSN 0141-5492, E-ISSN 1573-6776, Vol. 36, nr 9, s. 1819-1825Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Nanoporous alumina membranes were silanized with aminopropylsilane and iminodiacetic acid (IDA) groups were generated in situ by reaction with iodoacetate. The membranes were mounted in standard filter holders, connected to a HPLC system and saturated with selected metal ions. Cu(II) allowed the capture of chicken muscle lactate dehydrogenase with such stability, repeatability and reproducibility that Michaelis-Menten kinetics could be studied. The IDA surface was stable for months and could be depleted and regenerated with metal ions multiple times without appreciable loss of capacity. The binding of lactate dehydrogenase influenced the backpressure to the extent that could be expected for a monolayer according to Poiseuilles law.

  • 85. Bergman, Birgitta
    et al.
    Sandh, Gustaf
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - Ångström, Molekylär biomimetik.
    Lin, Senjie
    Larsson, John
    Carpenter, Edward J
    Trichodesmium: a widespread marine cyanobacterium with unusual nitrogen fixation properties2013Ingår i: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 37, nr 3, s. 286-302Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    The last several decades have witnessed dramatic advances in unfolding the diversity and commonality of oceanic diazotrophs and their N(2) -fixing potential. More recently substantial progress in diazotrophic cell biology has provided a wealth of information on processes and mechanisms involved. The substantial contribution by the diazotrophic cyanobacterial genus Trichodesmium to the nitrogen influx of the global marine ecosystem is by now undisputable and of paramount ecological importance, while the underlying cellular and molecular regulatory physiology has only recently started to unfold. Here we explore and summarize current knowledge, related to optimization of its diazotrophic capacity, from genomics to ecophysiological processes, via eg. cellular differentiation (diazocytes) and temporal regulations, and suggest cellular research avenues that now ought to be explored. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  • 86.
    Bergman, Jessica
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Hammarlöf, Disa L
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Hughes, Diarmaid
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Reducing ppGpp Level Rescues an Extreme Growth Defect Caused by Mutant EF-Tu2014Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, nr 2, s. e90486-Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    Salmonella enterica grows extremely slowly when it depends on tufA499 (encoding the Gln125Arg mutant form of EF-Tu) to drive protein synthesis. We screened a plasmid library for multi-copy suppressors of the slow growth phenotype and identified spoT as a candidate. The spoT gene encodes a dual function enzyme with both ppGpp synthetase and hydrolase activities. When spoT was cloned behind an arabinose-inducible promoter the growth rate of the mutant strain increased in response to arabinose addition. We found that the slow-growing mutant strain had a relatively high basal level of ppGpp during exponential growth in rich medium. Overexpression of spoT significantly reduced this level of ppGpp suggesting that inappropriately high ppGpp levels might cause the slow growth rate associated with tufA499. We tested this hypothesis by inactivating relA (codes for RelA, a ribosome-associated ppGpp synthetase) in the mutant strain. This inactivation decreased the level of ppGpp in the mutant strain and increased its growth rate. Based on these data we propose that ribosomes depending on tufA499 for their supply of ternary complex (EF-Tu•GTP•aa-tRNA) experience amino acid starvation and that RelA on these starving ribosomes produces an excess of the alarmone ppGpp. This results in a suboptimal partitioning of transcription activity between genes important for fast growth in rich medium and genes important for growth in a poor medium. Accordingly, mutant bacteria growing in a rich medium act physiologically as though they were growing in a nutrient-poor environment. We propose that this generates a vicious circle and contributes to the extreme slow-growth phenotype associated with mutant EF-Tu. Reducing the level of ppGpp increases the growth rate of the mutant because it breaks this circle and reduces the wasteful misdirection of resources in the cell.

  • 87. Bergström, Sven
    et al.
    Olsen, Björn
    Burman, Nils
    Gothefors, Leif
    Jaenson, Thomas G.T.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för evolution, genomik och systematik.
    Jonsson, Maria
    Mejlon, Hans
    Uppsala universitet, Enheten för musik och museer, Evolutionsmuseet.
    Molecular characterization of Borrelia burgdorferi isolated from Ixodes ricinus in northern Sweden.1992Ingår i: Scandinavian Journal of Infectious Diseases, ISSN 0036-5548, E-ISSN 1651-1980, Vol. 24, nr 2, s. 181-188Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ixodes ricinus ticks, harbouring Borrelia burgdorferi, were found in an area in northern Sweden, not thought to be endemic for Lyme borreliosis. This investigation took place at Norrbyskär, an island situated in the Bothnian Gulf, 63 degrees 33'N/19 degrees 52'E. One of 42 nymphal and 8/43 adult I. ricinus ticks collected carried spirochetes as seen by phase contrast microscopy. Pure bacterial cultures were obtained from 2 of the ticks. Western blot analysis using species-specific monoclonal antibodies showed that the isolated spirochetes were B. burgdorferi. The identity of the isolated spirochetes was confirmed by DNA amplification using B. burgdorferi OspA and flagellin gene specific oligonucleotides as well as partial DNA sequencing of the respective OspA and flagellin genes. The 2 isolated spirochaete populations were different as shown by their protein profiles in sodium dodecyl sulphate polyacrylamide gels. Moreover, the demonstration of Lyme borreliosis in a patient from the island of Norrbyskär indicates the need for clinical consideration of this disease in northern Sweden.

  • 88.
    Berruga Fernández, Talía
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. European Centre for Disease Prevention and Control.
    Risk Assessment for the Transmission of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) on Aircraft: A Systematic Review2019Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Introduction: MERS-CoV causes a respiratory disease that can be fatal. Although it is most common in countries in the Arabian Peninsula, through travel it has been exported to 17 countries outside Middle East. Most of these exportations have occurred by people travelling by air. The Risk Assessment Guidelines for Infectious Disease transmitted on Aircraft (RAGIDA) produced by the European Centre of Disease Prevention and Control, advises European countries on the measures to take when an infected individual travels by air.

    Aim: To gather all available information on the MERS-CoV cases that have travelled by air and produce an update of the RAGIDA project.

    Methods: A systematic review was conducted. The online health databases used were PubMed, Embase, Scopus and Global Index Medicus. As additional information sources, Google was searched for grey literature and hand searching was performed on the Early Warning and Response System of the EU, as well as the Disease Outbreak News page of WHO.

    Results: A total of 48 records were identified, describing 22 cases of MERS that travelled on board a total of 31 flights. No cases of in-flight transmission were observed in any of the flights. Contact tracing (CT) was performed for 18 of the 22 cases. Most countries defined “contacts” as the passengers sitting in the same row and the two rows in front and behind the case. Only one country decided to trace all passengers and crew on board the aircraft. 

    Conclusion: A conservative approach might be more adequate when performing CT of an aircraft where a case of MERS has travelled, because of the lack of in-flight transmission observed and the great amount of resources needed for a CT investigation.

    Publikationen är tillgänglig i fulltext från 2020-04-01 00:00
  • 89.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    How to see more: double hybridization to reveal ecological differentiation among close bacterial relatives2017Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, nr 6, s. 2110-2111Artikel i tidskrift (Övrigt vetenskapligt)
  • 90.
    Bier, Raven L.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Field and chemistry data from 2016 Fluctuations Project2016Dataset
  • 91.
    Björklund, Viktor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    ProQ-dependent phenotypes in Escherichia coli and Salmonella Typhimurium2017Självständigt arbete på avancerad nivå (yrkesexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    RNA-binding proteins (RBPs) regulate gene expression at the posttranscriptional

    level by interacting with mRNAs and sRNAs. Recently,

    ProQ has been discovered to be a global RBP with extensive RNA

    targets in

    Escherichia coli and Salmonella enterica. However, many

    aspects of the function of ProQ, including mechanisms of RNA-binding,

    regulated pathways, and ProQ-dependent phenotypes are yet to be

    understood. In this study, it is shown that ProQ can affect both persister

    cell

    􀀀formation and motility. A proQ deletion reduces the number of

    persister cells independent of both SOS-response and the persisterrelated

    type I toxin/antitoxin system

    tisB/istR-1. Furthermore, ProQ

    overexpression also reduces persister cell formation, indicating an

    intricate regulation by ProQ on persister-related pathways. Finally,

    it is confirmed that deletion of

    proQ leads to down-regulation of

    motility-related genes.

  • 92.
    Blieck, Alain
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Clement, Gael
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Leliévre, Herve
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Luksevics, Ervins
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Streel, Maurice
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Thorez, Jaques
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Young, Gavin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    The biostratigraphic and Palaeogeographic framework of the earliest diversification of tetrapods (Late Devonian) - a critical review2007Ingår i: Terrestrialization influenses on the Palaeozoic geosphere-biospere (Workshop ECLIPSE II, Paris, 8-9 october), 2007Konferensbidrag (Övrig (populärvetenskap, debatt, mm))
    Abstract [en]

    Ichthyostega was the first Devonian tetrapod to be subject to a whole-body reconstruction and remains, together with Acanthostega one of only two Devonian tetrapods for which near-complete postcranial material is available. It is thus crucially important for our understanding of the earliest stages of tetrapod evolution and terrestrialization. Based on extensive re-examination of original material, augmented by recently collected specimens, we present a new reconstruction of Ichthyostega that differs substantially from those previously published and reveals hitherto unrecognised regionalization in the vertebral column. Ichthyostega is the earliest vertebrate to show obvious adaptations for non-swimming locomotion. Uniquely among early tetrapods, the presacral vertebral column shows pronounced regionalization of neural arch morphology, suggesting that it was adapted for dorsoventral rather than lateral flexion.

  • 93.
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Interrelationships and evolutionary history of the anaspid fishes.2005Ingår i: Journal of Vertebrate Paleontology, ISSN 0272-4634, Vol. 25, nr 3, s. 28A-Artikel i tidskrift (Refereegranskat)
  • 94.
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Taxonomic revision of the Late Devonian tetrapod Ichthyostega from East Greenland.2005Ingår i: Palaeontology, ISSN 0031-0239, Vol. 48, nr 1, s. 111-134Artikel i tidskrift (Refereegranskat)
  • 95.
    Blom, Henning
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Clack, Jennifer
    The postcranial skeleton of the Devonian tetrapod Ichthyostega from East Greenland.2005Ingår i: GFF, ISSN 1103-5897, Vol. 127, s. 45-Artikel i tidskrift (Övrigt vetenskapligt)
  • 96. Bohus, Veronika
    et al.
    Tóth, Erika M.
    Székely, Anna J.
    Makk, Judit
    Baranyi, Krisztián
    Patek, Gábor
    Schunk, János
    Márialigeti, Károly
    Microbiological investigation of an industrial ultra pure supply water plant using cultivation-based and cultivation-independent methods2010Ingår i: Water Research, ISSN 0043-1354, E-ISSN 1879-2448, Vol. 44, nr 20, s. 6124-6132Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Ultra pure waters (UPW), characterized by extremely low salt and nutrient concentrations, can suffer from microbial contamination which causes biofouling and biocorrosion, possibly leading to reduced lifetime and increased operational costs. Samples were taken from an ultra pure supply water producing plant of a power plant. Scanning electron microscopic examination was carried out on the biofilms formed in the system. Biofilm, ion exchange resin, and water samples were characterized by culture-based methods and molecular fingerprinting (terminal restriction fragment length polymorphism [T-RFLP] analysis and molecular cloning). Identification of bacteria was based on 16S rDNA sequence comparison. A complex microbial community structure was revealed. Nearly 46% of the clones were related to as yet uncultured bacteria. The community profiles of the water samples were the most diverse and most of bacteria were recruited from bacterial communities of tube surface and ion exchange resin biofilms. Microbiota of different layers of the mixed bed ion exchange resin showed the highest similarity. Most of the identified taxa (dominated by β-Proteobacteria) could take part in microbially influenced corrosion. © 2010 Elsevier Ltd.

  • 97.
    Boisvert, Catherine
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    A lobe-finned fish sheds new light on the origin of the tetrapod pelvic girdle.2005Ingår i: Journal of Vertebrate Paleontology, ISSN 0272-4634, Vol. 25, nr 3, s. 38A-Artikel i tidskrift (Övrigt vetenskapligt)
  • 98.
    Boisvert, Catherine
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Pelvic girdle transformations from lobe-finned fish to tetrapods.2005Ingår i: PaleoBios, ISSN 0031-0298, Vol. 25, nr 2 (supplement), s. 20-Artikel i tidskrift (Övrigt vetenskapligt)
  • 99.
    Boisvert, Catherine
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Pelvic morphology in sarcopterygians and tetrapods: novelties at the fish-tetrapod boundary.2005Ingår i: GFF, ISSN 1103-5897, Vol. 127, s. 45-Artikel i tidskrift (Övrig (populärvetenskap, debatt, mm))
  • 100.
    Boisvert, Catherine
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    The pelvic fin and girdle of Panderichthys and the origin of tetrapod locomotion.2005Ingår i: Nature, ISSN 0028-0836, Vol. 438, nr 7071, s. 1145-1147Artikel i tidskrift (Refereegranskat)
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