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  • 551.
    Volkov, Ivan
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär systembiologi.
    Seefeldt, A. Carolin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär systembiologi.
    Johansson, Magnus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär systembiologi.
    Tracking of single tRNAs for translation kinetics measurements in chloramphenicol treated bacteria2019Ingår i: Methods, ISSN 1046-2023, E-ISSN 1095-9130, Vol. 162-163, s. 23-30Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Chloramphenicol is a broad-spectrum antibiotic targeting the protein synthesis machinery by binding to the bacterial ribosome. Chloramphenicol has been considered a classic general inhibitor of translation, blocking the accommodation of aa-tRNA into the A site of the large ribosomal subunit. However, recent studies suggest that this proposed mechanism is a simplification and that the effect of chloramphenicol on mRNA translation is much more dynamic. By tracking single dye-labelled elongator and initiator tRNAs in Escherichia coli cells treated with chloramphenicol, we observe the direct effect of chloramphenicol on translation kinetics. We find clear indications of slow but significant mRNA translation on drug bound ribosomes.

  • 552.
    Vongsombath, Chanda
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Botanical Repellents and Pesticides Traditionally Used Against Haematophagous Invertebrates in Lao PDR2011Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Haematophagous parasites and disease vectors such as leeches, ticks, mites, lice, bed bugs, mosquitoes, and myiasis-causing fly larvae are common health problems in Lao Peoples Democratic Republic (Lao PDR). A main aim of my field work in Lao PDR in 2006-2010 was to document traditional knowledge among different ethnic groups about plants that people use to repel or to kill blood-feeding invertebrates. We carried out structured interviews in 66 villages comprising 17 ethnic groups, covering a range of ethnic group, throughout Lao PDR and recorded a total of 92 plant species - in 123 different plant-ectoparasite combinations - that are used as traditional repellents and/or as “pesticides” to kill "pest" invertebrates. Traditional use was confirmed in the scientific literature for 74 of these plant species, and for an additional 13 species based on literature on closely related species. We concluded that repellents and pesticides from many plant species are commonly used in the Lao countryside.

    We also investigated traditionally used Lao plants for their activity to repel or to kill certain disease vectors and parasites. Target organisms were mosquitoes (Diptera, Culicidae), fly larvae (Diptera, Cyclorrhapha) in fermented fish production, and terrestrial blood-sucking leeches (Hirudinea, Haemadipsidae). The potential mosquito repellent activities of essential oils of Croton roxburghii (Euphorbiaceae), Hyptis suaveolens (Lamiaceae), and Litsea cubeba (Lauraceae) were evaluated in the field near Vientiane. Oils at concentrations of 1.7-6.7 µg/cm2 were significantly repellent to Aedes, Armigeres and Culex attracted to human baits. The activities against fly larvae, infesting fermenting fish, of three plant species, Tadehagi triquetrum (Fabaceae), Uraria crinita (Fabaceae) and Bambusa multiplex (Poaceae) were investigated: When fresh material of the plants was added on top of fermenting fish infested with fly larvae significant proportions of the larvae were repelled or killed. The total protective effect, i.e., repellent and killing effect combined, of T. triquetrum, U. crinita, and B. multiplex was 60-83 %, 77-90 %, and 60-93 %, respectively.

    Field evaluation of the potential leech repellent activities of water extracts of Sapindus rarak (Sapindaceae), Catunaregam spathulifolia (Rubiaceae) and Vernonia elaeagnifolia, (Asteraceae) impregnated on stockings and worn by persons in two leech-infested biotopes revealed leech repellent activities of 82.6%, 62.6% and 63.0%, respectively. The corresponding repellencies of deltamethrin and diethyl-3-methyl-benzamide (DEET) were 73.1% and 88.4%, respectively. Identification of the active components in certain of the plants with the ultimate aim to develop more optimal, less costly repellents, insecticides, acaricides, and anti-leech compounds as alternatives to synthetic repellents and pesticides against blood-feeding insects, ticks, mites, and leeches is in progress.

    Delarbeten
    1. Botanical Repellents and Pesticides Traditionally Used Against Hematophagous Invertebrates in Lao People's Democratic Republic: A Comparative Study of Plants Used in 66 Villages
    Öppna denna publikation i ny flik eller fönster >>Botanical Repellents and Pesticides Traditionally Used Against Hematophagous Invertebrates in Lao People's Democratic Republic: A Comparative Study of Plants Used in 66 Villages
    Visa övriga...
    2010 (Engelska)Ingår i: Journal of medical entomology, ISSN 0022-2585, E-ISSN 1938-2928, Vol. 47, nr 3, s. 400-414Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Hematophagous parasites such as leeches, ticks, mites, lice, bedbugs, mosquitoes, and myiasis-producing fly larvae are common health problems in Lao People's Democratic Republic. Several arthropod-borne infections, e.g., malaria, dengue fever, and Japanese encephalitis, are endemic there. Effective vector control methods including the use of pesticides, insecticide-treated bed nets, and synthetic and plant-based repellents are important means of control against such invertebrates and the pathogens they may transmit or directly cause. In this study, we documented traditional knowledge on plants that are used to repel or kill hematophagous arthropods, including mosquitoes, bedbugs, human lice, mites and ticks, fly larvae, and blood-sucking leeches. Structured interviews were carried out in 66 villages comprising 17 ethnic groups, covering a range of cultures, throughout Lao People's Democratic Republic. A total of 92 plant species was recorded as traditional repellents (including plants for pesticidal usages) in 123 different plant-ectoparasite combinations. The number and species of plants, and animal taxa repelled (or killed) per plant species differed per region, village, and ethnic group. Traditional use was confirmed in the scientific literature for 74 of these plant species, and for an additional 13 species using literature on closely related species. The use of botanical repellents and pesticides from many plant species is common and widespread in the Lao countryside. In the future, the identification of the active components in certain plants to develop more optimal, inexpensive repellents, insecticides, acaricides, or antileech compounds as alternatives to synthetic repellents/pesticides against blood-feeding insects, ticks, mites, and leeches is warranted.

    Nyckelord
    botanical repellents, ethnobotany, leeches, mosquitoes, myiasis
    Nationell ämneskategori
    Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-136563 (URN)10.1603/ME09273 (DOI)000277597000015 ()20496588 (PubMedID)
    Tillgänglig från: 2010-12-14 Skapad: 2010-12-13 Senast uppdaterad: 2017-12-11
    2. Efficacy of essential oils of traditionally used plant species to repel mosquitoes in Vientiane capital Lao PDR:
    Öppna denna publikation i ny flik eller fönster >>Efficacy of essential oils of traditionally used plant species to repel mosquitoes in Vientiane capital Lao PDR:
    Visa övriga...
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]
    Identifikatorer
    urn:nbn:se:uu:diva-149989 (URN)
    Tillgänglig från: 2011-03-24 Skapad: 2011-03-24 Senast uppdaterad: 2011-04-27
    3. A Fly in the Ointment: Evaluation of Traditional Use of Plants to Repel and Kill Blowfly Larvae in Fermented Fish
    Öppna denna publikation i ny flik eller fönster >>A Fly in the Ointment: Evaluation of Traditional Use of Plants to Repel and Kill Blowfly Larvae in Fermented Fish
    2011 (Engelska)Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, nr 12, artikel-id e29521Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Introduction: In rural areas in Laos, fly larvae infestations are common in fermenting fish. Blowflies (Chrysomyamegacephala, Diptera: Calliphoridae) are attracted to oviposit (and/or larviposit) onto fermenting fish which results ininfestations with fly larvae. Knowledge of traditional use of plants to repel larvae during the production of fermented fish iscommon and widespread in Lao PDR.

    Research Questions: How effective are the most salient species in repelling, and killing fly larvae in fermenting fish?

    Material and Methods: The three plant species most frequently reported to repel fly larvae during an ethnobotanical surveythroughout Lao PDR were tested for repellence and larvicidal activity of fly larvae infesting fermented fish. The lethality andrepellence of Tadehagi triquetrum (L.) H. Ohashi (Fabaceae), Uraria crinita (L.) Desv. ex DC. (Fabaceae) and Bambusa multiplex(Lour.) Raeusch. ex Schult. & Schult. f. (Poaceae) were tested in an experimental design using fermenting fish in Vientiane,Lao PDR.

    Results: The repellent effect of fresh material of T. triquetrum and U. crinita, and the larvicidal effect of fresh B. multiplex, issignificantly more effective than that of dried material of the same species, and the total effect (repellence and larvicidaleffect combined) for each of the three species was significantly more effective for fresh than for dry material. Fresh materialof T. triquetrum, U. crinita, or B. multiplex added on top of the fermenting fish repelled 50%, 54%, 37%, and killed 22%, 28%,and 40% of fly larvae. The total effect was not significantly different per species at 72%, 82%, and 77%, respectively.

    Discussion and Conclusions: The three most salient species are effective in repelling and killing fly larvae in the productionof fermented fish, and may be essential to augment food safety during traditional fermentation in open jars.

    Nationell ämneskategori
    Lantbruksvetenskaper Botanik
    Identifikatorer
    urn:nbn:se:uu:diva-149968 (URN)10.1371/journal.pone.0029521 (DOI)000298665600041 ()
    Tillgänglig från: 2011-03-24 Skapad: 2011-03-24 Senast uppdaterad: 2017-12-11Bibliografiskt granskad
    4. Keeping Leeches at Bay: Field Evaluation of Plant-Derived Extracts against Terrestrial Blood-Sucking Leeches (Haemadipsidae) in Lao PDR
    Öppna denna publikation i ny flik eller fönster >>Keeping Leeches at Bay: Field Evaluation of Plant-Derived Extracts against Terrestrial Blood-Sucking Leeches (Haemadipsidae) in Lao PDR
    2011 (Engelska)Ingår i: Acta Tropica, ISSN 0001-706X, E-ISSN 1873-6254, Vol. 119, nr 2-3, s. 178-182Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Terrestrial blood-sucking leeches (Haemadipsidae) are common in the damp forests of the subtropicaland tropical Indo-Pacific region. Members of the genus Haemadipsa are abundant in Laos and adjacentcountries of Southeast Asia, and discomfort to people and livestock. Plant-derived repellents againstarthropods and leeches are common in Lao PDR, and have been used by Lao ethnic groups for generations.Numerous studies have been conducted on the efficacy of traditional plant-derived repellents againstmosquitoes but only a few on repellents against terrestrial blood-sucking leeches. Field experimentswere conducted to evaluate the leech repellent activities of aqueous extracts of three traditionally usedplant species, Sapindus rarak DC., Catunaregam spathulifolia Tirv. and Vernonia elaeagnifolia DC. Stockingsimpregnated with aqueous extracts exhibited moderate to high leech repellent activity, C. spathulifolia(62.6%), V. elaeagnifolia (63.0%), and S. rarak (82.6%). The corresponding repellencies of deltamethrin andDEET were 73.1% and 88.4%, respectively. An aqueous extract of S. rarak applied on cloth at a concentrationof 1.9 mg/cm2 is an effective and practical prevention method significantly reducing the number of bloodfeedingleeches recorded on stockings worn by humans. This plant species is common in Southeast Asiaand can be obtained at limited or no cost.

    Nyckelord
    Plant repellents, Leeches, Traditional Knowledge, Parasites
    Nationell ämneskategori
    Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-149973 (URN)10.1016/j.actatropica.2011.05.014 (DOI)000293717200018 ()
    Tillgänglig från: 2011-03-24 Skapad: 2011-03-24 Senast uppdaterad: 2017-12-11Bibliografiskt granskad
  • 553.
    Vongsombath, Chanda
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    De Boer, Hugo J.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Pålsson, Katinka
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Keeping Leeches at Bay: Field Evaluation of Plant-Derived Extracts against Terrestrial Blood-Sucking Leeches (Haemadipsidae) in Lao PDR2011Ingår i: Acta Tropica, ISSN 0001-706X, E-ISSN 1873-6254, Vol. 119, nr 2-3, s. 178-182Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Terrestrial blood-sucking leeches (Haemadipsidae) are common in the damp forests of the subtropicaland tropical Indo-Pacific region. Members of the genus Haemadipsa are abundant in Laos and adjacentcountries of Southeast Asia, and discomfort to people and livestock. Plant-derived repellents againstarthropods and leeches are common in Lao PDR, and have been used by Lao ethnic groups for generations.Numerous studies have been conducted on the efficacy of traditional plant-derived repellents againstmosquitoes but only a few on repellents against terrestrial blood-sucking leeches. Field experimentswere conducted to evaluate the leech repellent activities of aqueous extracts of three traditionally usedplant species, Sapindus rarak DC., Catunaregam spathulifolia Tirv. and Vernonia elaeagnifolia DC. Stockingsimpregnated with aqueous extracts exhibited moderate to high leech repellent activity, C. spathulifolia(62.6%), V. elaeagnifolia (63.0%), and S. rarak (82.6%). The corresponding repellencies of deltamethrin andDEET were 73.1% and 88.4%, respectively. An aqueous extract of S. rarak applied on cloth at a concentrationof 1.9 mg/cm2 is an effective and practical prevention method significantly reducing the number of bloodfeedingleeches recorded on stockings worn by humans. This plant species is common in Southeast Asiaand can be obtained at limited or no cost.

  • 554.
    Vosseberg, Julian
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. Univ Utrecht, Dept Biol, Theoret Biol & Bioinformat, Utrecht, Netherlands.
    Martijn, Joran
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J. G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Draft Genome Sequence of "Candidatus Moanabacter tarae," Representing a Novel Marine Verrucomicrobial Lineage2018Ingår i: MICROBIOLOGY RESOURCE ANNOUNCEMENTS, ISSN 2576-098X, Vol. 7, nr 15, artikel-id UNSP e00951-18Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Tara Oceans Consortium has published various metagenomes of marine environmental samples. Here, we report a contig of 2.6 Mbp from the assembly of a sample collected near the Marquesas Islands in the Pacific Ocean, covering a nearly complete novel verrucomicrobial genome. We propose the name "Candidates Moanabacter tarae" for the corresponding bacterium.

  • 555.
    Waege, J.
    et al.
    Leibniz Inst Balt Sea Res, Seestr 15, D-18119 Rostock, Germany.
    Strassert, Jürgen F. H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Systematisk biologi.
    Landsberger, A.
    Transgen Technol Charite, Berlin, Germany.
    Loick-Wilde, N.
    Leibniz Inst Balt Sea Res, Seestr 15, D-18119 Rostock, Germany.
    Schmale, O.
    Leibniz Inst Balt Sea Res, Seestr 15, D-18119 Rostock, Germany.
    Stawiarski, B.
    Leibniz Inst Balt Sea Res, Seestr 15, D-18119 Rostock, Germany.
    Kreikemeyer, B.
    Univ Hosp Rostock, Dept Med Microbiol & Hosp Hyg, Rostock, Germany.
    Michel, G.
    Transgen Technol Charite, Berlin, Germany.
    Labrenz, M.
    Leibniz Inst Balt Sea Res, Seestr 15, D-18119 Rostock, Germany.
    Microcapillary sampling of Baltic Sea copepod gut microbiomes indicates high variability among individuals and the potential for methane production2019Ingår i: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 95, nr 4, artikel-id fiz024Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The paradox of methane oversaturation in oxygenated surface water has been described in many pelagic systems and still raises the question of the source. Temora sp. and Acartia sp. commonly dominate the surface and subsurface waters of the central Baltic Sea. It is hypothesised that their gut microbiome at least partly contributes to the methane anomaly in this ecosystem. However, the potential pathway for this methane production remains unclear. Using a microcapillary technique, we successfully overcame the challenge of sampling the gut microbiome of copepods <1 mm. 16S rRNA gene amplicon sequencing revealed differences among the dominant bacterial communities associated with Temora sp. (Actinobacteria, Betaproteobacteria and Flavobacteriia) and Acartia sp. (Actinobacteria, Alphaproteobacteria and Betaproteobacteria) and the surrounding water (Proteobacteria, Cyanobacteria and Verrucomicrobia), but also intraspecific variability. In both copepods, gut-specific prokaryotic taxa and indicative species for methane production pathways (methanogenesis, dimethylsulfoniopropionate or methylphosphonate) were present. The relative abundance of archaea and methanogens was investigated using droplet digital polymerase chain reaction and showed a high variability among copepod individuals, underlining intra- and interspecific differences in copepod-associated prokaryotic communities. Overall, this work highlights that the guts of Temora sp. and Acartia sp. have the potential for methane production but are probably no hotspot.

  • 556.
    Wahab, Tara
    et al.
    Public Health Agency of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Ferrari, Sevinc
    National Veterinary Institute, Swedish Forum for Biopreparedness Diagnostics.
    Lindberg, Martina
    National Food Agency, Swedish Forum for Biopreparedness Diagnostics.
    Bäckman, Stina
    Swedish Defence Research Institute, Swedish Forum for Biopreparedness Diagnostics.
    Kaden, Rene
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Klinisk mikrobiologi och infektionsmedicin, Klinisk bakteriologi. National Veterinary Institute of Sweden, Swedish Forum for Biopreparedness Diagnostics.
    Draft Genome Sequences of Brucella suis Biovar 4 Strain NCTC 10385, Brucella ceti Strain NCTC 12891T, Brucella inopinata Strain CAMP 6436T, and Brucella neotomae Strain ATCC 23459T2014Ingår i: Genome Announcements, ISSN 2169-8287, E-ISSN 2169-8287, Vol. 2, nr 5, s. e00783-14-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    With the aim of developing quantitative PCR methods for the detection and differentiation of Brucella species, the genomes of Brucella ceti, Brucella inopinata, Brucella netotomae, and Brucella suis biovar 4 were sequenced and analyzed.

  • 557. Walker, Thomas
    et al.
    Klasson, Lisa
    Sebaihia, Mohammed
    Sanders, Mandy J
    Thomson, Nicholas R
    Parkhill, Julian
    Sinkins, Steven P
    Ankyrin repeat domain-encoding genes in the wPip strain of Wolbachia from the Culex pipiens group.2007Ingår i: BMC biology, ISSN 1741-7007, Vol. 5, s. 39-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    BACKGROUND: Wolbachia are obligate endosymbiotic bacteria maternally transmitted through the egg cytoplasm that are responsible for several reproductive disorders in their insect hosts, such as cytoplasmic incompatibility (CI) in infected mosquitoes. Species in the Culex pipiens complex display an unusually high number of Wolbachia-induced crossing types, and based on present data, only the wPip strain is present.

    RESULTS: The sequencing of the wPip strain of Wolbachia revealed the presence of 60 ankyrin repeat domain (ANK) encoding genes and expression studies of these genes were carried out in adult mosquitoes. One of these ANK genes, pk2, is shown to be part of an operon of three prophage-associated genes with sex-specific expression, and is present in two identical copies in the genome. Another homolog of pk2 is also present that is differentially expressed in different Cx. pipiens group strains. A further two ANK genes showed sex-specific regulation in wPip-infected Cx. pipiens group adults.

    CONCLUSION: The high number, variability and differential expression of ANK genes in wPip suggest an important role in Wolbachia biology, and the gene family provides both markers and promising candidates for the study of reproductive manipulation.

  • 558.
    Wang, Daoyong
    et al.
    Southeast Univ, Minist Educ Dev Genes & Human Dis, Key Lab, Dept Biochem,Sch Med, Nanjing 210009, Jiangsu, Peoples R China..
    Xu, Shihui
    Southeast Univ, Minist Educ Dev Genes & Human Dis, Key Lab, Dept Biochem,Sch Med, Nanjing 210009, Jiangsu, Peoples R China..
    Song, Dan
    Southeast Univ, Minist Educ Dev Genes & Human Dis, Key Lab, Dept Biochem,Sch Med, Nanjing 210009, Jiangsu, Peoples R China..
    Knight, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Struktur- och molekylärbiologi.
    Mao, Xiaohua
    Southeast Univ, Minist Educ Dev Genes & Human Dis, Key Lab, Dept Biochem,Sch Med, Nanjing 210009, Jiangsu, Peoples R China..
    A gene encoding a potential adenosine 5 '-phosphosulphate kinase is necessary for timely development of Myxococcus xanthus2016Ingår i: Microbiology, ISSN 1350-0872, E-ISSN 1465-2080, Vol. 162, s. 672-683Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A Myxococcus xanthus gene, MXAN3487, was identified by transposon mutagenesis to be required for the expression of mcuABC, an operon coding for part of the chaperone-usher (CU) system in this bacterium. The MXAN3487 protein displays sequence and structural homology to adenosine 5'-phosphosulphate (APS) kinase family members and contains putative motifs for ATP and APS binding. Although the MXAN3487 locus is not linked to other sulphate assimilation genes, its protein product may have APS kinase activity in vivo and the importance of the ATP-binding site for activity was demonstrated. Expression of MXAN3487 was not affected by sulphate availability, suggesting that MXAN3487 may not function in a reductive sulphate assimilation pathway. Deletion of MXAN3487 significantly delayed fruiting body formation and the production of McuA, a spore coat protein secreted by the M. xanthus Mcu CU system. Based on these observations and data from our previous studies, we propose that MXAN3487 may phosphorylate molecules structurally related to APS, generating metabolites necessary for M. xanthus development, and that MXAN3487 exerts a positive effect on the mcuABC operon whose expression is morphogenesis dependent.

  • 559.
    Wang, Helen
    et al.
    Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, Stockholm, Sweden.
    Franke, CC
    Nordlund, Stefan
    Noren, Agneta
    Reversible membrane association of dinitrogenase reductase activating glycohydrolase in the regulation of nitrogenase activity in Rhodospirillum rubrum; dependence on GlnJ and AmtB12005Ingår i: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 253, nr 2, s. 273-279Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the photosynthetic bacterium Rhodospirillum rubrum nitrogenase activity is regulated by reversible ADP-ribosylation of dinitrogenase reductase in response to external so called "switch-off" effectors. Activation of the modified, inactive form is catalyzed by dinitrogenase reductase activating glycohydrolase (DRAG) which removes the ADP-ribose moiety. This study addresses the signal transduction between external effectors and DRAG. R. rubrum, wild-type and P(II) mutant strains, were studied with respect to DRAG localization. We conclude that GlnJ clearly has an effect on the association of DRAG to the membrane in agreement with the effect on regulation of nitrogenase activity. Furthermore, we have generated a R. rubrum mutant lacking the putative ammonium transporter AmtB1 which was shown not to respond to "switch-off" effectors; no loss of nitrogenase activity and no ADP-ribosylation. Interestingly, DRAG was mainly localized to the cytosol in this mutant. Overall the results support our model in which association to the membrane is part of the mechanism regulating DRAG activity.

  • 560.
    Wang, Helen
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Noren, Agneta
    Metabolic regulation of nitrogen fixation in Rhodospirillum rubrum2006Ingår i: Biochem Soc Trans., Vol. 34, nr 1, s. 160-161Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    Nitrogenase activity in Rhodospirillum rubrum is post-translationally regulated by DRAG (dinitrogenase reductase glycohydrolase) and DRAT (dinitrogenase reductase ADP-ribosylation transferase). When a sudden increase in fixed nitrogen concentration or energy depletion is sensed by the cells, DRAG is inactivated and DRAT activated. We propose that the regulation of DRAG is dependent on its location in the cell and the presence of an ammonium-sensing protein.

  • 561.
    Wang, Kun
    et al.
    Stockholm Univ, Dept Mol Biosci, Wenner Gren Inst, Svante Arrhenius V 20C, SE-10691 Stockholm, Sweden.
    Sybers, David
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium.
    Maklad, Hassan Ramadan
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium.
    Lemmens, Liesbeth
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium.
    Lewyllie, Charlotte
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium;Vrije Univ Brussel, Dept Biol, Lab Cell Genet, Pl Laan 2, B-1050 Brussels, Belgium.
    Zhou, Xiaoxiao
    Univ Duisburg Essen, Mol Enzymtechnol & Biochem, Biofilm Ctr, ZWU,Fak Chem, Univ Str 2, D-45117 Essen, Germany.
    Schult, Frank
    Univ Duisburg Essen, Mol Enzymtechnol & Biochem, Biofilm Ctr, ZWU,Fak Chem, Univ Str 2, D-45117 Essen, Germany.
    Bräsen, Christopher
    Univ Duisburg Essen, Mol Enzymtechnol & Biochem, Biofilm Ctr, ZWU,Fak Chem, Univ Str 2, D-45117 Essen, Germany.
    Siebers, Bettina
    Univ Duisburg Essen, Mol Enzymtechnol & Biochem, Biofilm Ctr, ZWU,Fak Chem, Univ Str 2, D-45117 Essen, Germany.
    Valegård, Karin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär biofysik.
    Lindås, Ann-Christin
    Stockholm Univ, Dept Mol Biosci, Wenner Gren Inst, Svante Arrhenius V 20C, SE-10691 Stockholm, Sweden.
    Peeters, Eveline
    Vrije Univ Brussel, Dept Bioengn Sci, Res Grp Microbiol, Pl Laan 2, B-1050 Brussels, Belgium.
    A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius2019Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, artikel-id 1542Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Fatty acid metabolism and its regulation are known to play important roles in bacteria and eukaryotes. By contrast, although certain archaea appear to metabolize fatty acids, the regulation of the underlying pathways in these organisms remains unclear. Here, we show that a TetR-family transcriptional regulator (FadR(sa)) is involved in regulation of fatty acid metabolism in the crenarchaeon Sulfolobus acidocaldarius. Functional and structural analyses show that FadR(sa) binds to DNA at semi-palindromic recognition sites in two distinct stoichiometric binding modes depending on the operator sequence. Genome-wide transcriptomic and chromatin immunoprecipitation analyses demonstrate that the protein binds to only four genomic sites, acting as a repressor of a 30-kb gene cluster comprising 23 open reading frames encoding lipases and beta-oxidation enzymes. Fatty acyl-CoA molecules cause dissociation of FadR(sa) binding by inducing conformational changes in the protein. Our results indicate that, despite its similarity in overall structure to bacterial TetR-family FadR regulators, FadR(sa) displays a different acyl-CoA binding mode and a distinct regulatory mechanism.

  • 562. Wang, Nancy
    et al.
    Söderbom, Fredrik
    Center for Molecular Genetics, Department of Biology, University of California—San Diego, La Jolla, California .
    Anjard, Christophe
    Shaulsky, Gad
    Loomis, William F
    SDF-2 induction of terminal differentiation in Dictyostelium discoideum is mediated by the membrane-spanning sensor kinase DhkA.1999Ingår i: Molecular and Cellular Biology, ISSN 0270-7306, E-ISSN 1098-5549, Vol. 19, nr 7, s. 4750-4756Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    SDF-2 is a peptide released by prestalk cells during culmination that stimulates prespore cells to encapsulate. Genetic evidence indicates that the response is dependent on the dhkA gene. This gene encodes a member of the histidine kinase family of genes that functions in two-component signal transduction pathways. The sequence of the N-terminal half of DhkA predicts two hydrophobic domains separated by a 310-amino-acid loop that could bind a ligand. By inserting MYC6 epitopes into DhkA, we were able to show that the loop is extracellular while the catalytic domain is cytoplasmic. Cells expressing the MYC epitope in the extracellular domain of DhkA were found to respond only if induced with 100-fold-higher levels of SDF-2 than required to induce dhkA+ cells; however, they could be induced to sporulate by addition of antibodies specific to the MYC epitope. To examine the enzymatic activity of DhkA, we purified the catalytic domain following expression in bacteria and observed incorporation of labelled phosphate from ATP consistent with histidine autophosphorylation. Site-directed mutagenesis of histidine1395 to glutamine in the catalytic domain blocked autophosphorylation. Furthermore, genetic analyses showed that histidine1395 and the relay aspartate2075 of DhkA are both critical to its function but that another histidine kinase, DhkB, can partially compensate for the lack of DhkA activity. Sporulation is drastically reduced in double mutants lacking both DhkA and DhkB. Suppressor studies indicate that the cyclic AMP (cAMP) phosphodiesterase RegA and the cAMP-dependent protein kinase PKA act downstream of DhkA.

  • 563.
    Warsi, Omar M.
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Lundin, Erik
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Lustig, Ulrika
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Näsvall, Joakim
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Andersson, Dan I
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Selection for novel metabolic capabilities in Salmonella enterica2019Ingår i: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 73, nr 5, s. 990-1000Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Bacteria are known to display extensive metabolic diversity and many studies have shown that they can use an extensive repertoire of small molecules as carbon‐ and energy sources. However, it is less clear to what extent a bacterium can expand its existing metabolic capabilities by acquiring mutations that, for example, rewire its metabolic pathways. To investigate this capability and potential for evolution of novel phenotypes, we sampled large populations of mutagenized Salmonella enterica to select very rare mutants that can grow on minimal media containing 124 low molecular weight compounds as sole carbon sources. We found mutants growing on 18 of these novel carbon sources, and identified the causal mutations that allowed growth for four of them. Mutations that relieve physiological constraints or increase expression of existing pathways were found to be important contributors to the novel phenotypes. For the remaining 14 novel phenotypes, whole genome sequencing of independent mutants and genetic analysis suggested that these novel metabolic phenotypes result from a combination of multiple mutations. This work, by virtue of identifying the genetic and mechanistic basis for new metabolic capabilities, sheds light on the properties of adaptive landscapes underlying the evolution of novel phenotypes.

  • 564.
    Wille, Michelle
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, SE-39182 Kalmar, Sweden;Peter Doherty Inst Infect & Immun, WHO Collaborating Ctr Reference & Res Influenza, 792 Elizabeth St, Melbourne, Vic 3000, Australia.
    Latorre-Margalef, Neus
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, SE-39182 Kalmar, Sweden;Lund Univ, Dept Biol, Ecol Bldg, S-22362 Lund, Sweden.
    Tolf, Conny
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, SE-39182 Kalmar, Sweden.
    Halpin, Rebecca
    J Craig Venter Inst, Dept Infect Dis, Rockville, MD USA.
    Wentworth, David
    J Craig Venter Inst, Dept Infect Dis, Rockville, MD USA.
    Fouchier, Ron A. M.
    Erasmus MC, Dept Virol, Rotterdam, Netherlands.
    Raghwani, Jayna
    Univ Oxford, Dept Zool, Oxford OX1 3SY, England.
    Pybus, Oliver G.
    Univ Oxford, Dept Zool, Oxford OX1 3SY, England.
    Olsen, Björn
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Waldenström, Jonas
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst, SE-39182 Kalmar, Sweden.
    Where do all the subtypes go?: Temporal dynamics of H8-H12 influenza A viruses in waterfowl2018Ingår i: Virus Evolution, ISSN 0042-725X, E-ISSN 2281-1605, Vol. 4, nr 2, artikel-id vey025Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Influenza A virus (IAV) is ubiquitous in waterfowl. In the northern hemisphere IAV prevalence is highest during the autumn and coincides with a peak in viral subtype diversity. Although haemagglutinin subtypes H1-H12 are associated with waterfowl hosts, subtypes H8-H12 are detected very infrequently. To better understand the role of waterfowl in the maintenance of these rare subtypes, we sequenced H8-H12 viruses isolated from Mallards (Anas platyrhynchos) from 2002 to 2009. These rare viruses exhibited varying ecological and phylodynamic features. The Eurasian clades of H8 and H12 phylogenies were dominated by waterfowl sequences; mostly viruses sequenced in this study. H11, once believed to be a subtype that infected charadriiformes (shorebirds), exhibited patterns more typical of common virus subtypes. Finally, subtypes H9 and H10, which have maintained lineages in poultry, showed markedly different patterns: H10 was associated with all possible NA subtypes and this drove HA lineage diversity within years. Rare viruses belonging to subtypes H8-H12 were highly reassorted, indicating that these rare subtypes are part of the broader IAV pool. Our results suggest that waterfowl play a role in the maintenance of these rare subtypes, but we recommend additional sampling of non-traditional hosts to better understand the reservoirs of these rare viruses.

  • 565.
    Wistrand-Yuen, Erik
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Knopp, Michael
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Hjort, Karin
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Koskiniemi, Sanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Berg, Otto G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär systembiologi.
    Andersson, Dan I.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Evolution of high-level resistance during low-level antibiotic exposure2018Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, nr 1, artikel-id 1599Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    It has become increasingly clear that low levels of antibiotics present in many environments can select for resistant bacteria, yet the evolutionary pathways for resistance development during exposure to low amounts of antibiotics remain poorly defined. Here we show that Salmonella enterica exposed to sub-MIC levels of streptomycin evolved high-level resistance via novel mechanisms that are different from those observed during lethal selections. During lethal selection only rpsL mutations are found, whereas at sub-MIC selection resistance is generated by several small-effect resistance mutations that combined confer high-level resistance via three different mechanisms: (i) alteration of the ribosomal RNA target (gidB mutations), (ii) reduction in aminoglycoside uptake (cyoB, nuoG, and trkH mutations), and (iii) induction of the aminoglycoside-modifying enzyme AadA (znuA mutations). These results demonstrate how the strength of the selective pressure influences evolutionary trajectories and that even weak selective pressures can cause evolution of high-level resistance.

  • 566. Wiweger, M
    et al.
    Farbos, I
    Ingouff, M
    Lagercrantz, U
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Institutionen för evolution, genomik och systematik, Evolutionär funktionsgenomik. evolutionär funktionsgenomik.
    Von Arnold, S
    Expression of Chia4-Pa chitinase genes during somatic and zygotic embryo development in Norway spruce (Picea abies): similarities and differences between gymnosperm and angiosperm class IV chitinases.2003Ingår i: J Exp Bot, ISSN 0022-0957, Vol. 54, nr 393, s. 2691-9Artikel i tidskrift (Refereegranskat)
  • 567. Wu, Xiaofen
    et al.
    Holmfeldt, Karin
    Hubalek, Valerie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Lundin, Daniel
    Åström, Mats
    Bertilsson, Stefan
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Dopson, Mark
    Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations2016Ingår i: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, nr 5, s. 1192-1203Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from <20 to several thousand years) and depth (171 to 448 m) revealed phylogenetically distinct microbial community subsets that either passed or were retained by a 0.22 mu m filter. Such cells of <0.22 mu m would have been overlooked in previous studies relying on membrane capture. Metagenomes from the three water types were used for reconstruction of 69 distinct microbial genomes, each with >86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the <0.22 mu m populations were generally smaller than their phylogenetically closest relatives, suggesting that small dimensions along with a reduced genome size may be adaptations to oligotrophy. Shallow 'modern marine' water showed community members with a predominantly heterotrophic lifestyle. In contrast, the deeper, 'old saline' water adhered more closely to the current paradigm of a hydrogen-driven deep biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

  • 568.
    Wu, Xiaofen
    et al.
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMIS, S-39182 Kalmar, Sweden..
    Pedersen, Karsten
    Microbial Analyt Sweden AB, Molnlycke, Sweden..
    Edlund, Johanna
    Microbial Analyt Sweden AB, Molnlycke, Sweden..
    Eriksson, Lena
    Microbial Analyt Sweden AB, Molnlycke, Sweden..
    Astrom, Mats
    Linnaeus Univ, Dept Biol & Environm Sci, Kalmar, Sweden..
    Andersson, Anders F.
    KTH Royal Inst Technol, Sch Biotechnol, Sci Life Lab, Stockholm, Sweden..
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Dopson, Mark
    Linnaeus Univ, Ctr Ecol & Evolut Microbial Model Syst EEMIS, S-39182 Kalmar, Sweden..
    Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters2017Ingår i: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, artikel-id 37Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. Results: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth. Using 16S rRNA gene sequencing, we showed that planktonic and attached populations were dissimilar while gene frequencies in the metagenomes suggested that hydrogen-fed, carbon dioxide-and nitrogen-fixing populations were responsible for biofilm formation across the two aquifers. Metagenome analyses further suggested that only a subset of the populations were able to attach and produce an extracellular polysaccharide matrix. Initial biofilm formation is thus likely to be mediated by a few bacterial populations which were similar to Epsilonproteobacteria, Deltaproteobacteria, Betaproteobacteria, Verrucomicrobia, and unclassified bacteria. Conclusions: Populations potentially capable of attaching to a surface and to produce extracellular polysaccharide matrix for attachment were identified in the terrestrial deep biosphere. Our results suggest that the biofilm populations were taxonomically distinct from the planktonic community and were enriched in populations with a chemolithoautotrophic and diazotrophic metabolism coupling hydrogen oxidation to energy conservation under oligotrophic conditions.

  • 569. Wurzbacher, Christian
    et al.
    Attermeyer, Katrin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany.
    Kettner, Maria Therese
    Flintrop, Clara
    Warthmann, Norman
    Hilt, Sabine
    Grossart, Hans-Peter
    Monaghan, Michael T.
    DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom2017Ingår i: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 9, nr 4, s. 383-388Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. We tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. We found significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a three-month period in spring. Patterns followed the same trend as plankton estimates measured using traditional microscopic methods. We characterized the bloom of a conditionally rare bacterial taxon belonging to Arcicella, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. Our data demonstrate the potential of universal DNA metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.

  • 570.
    Wurzbacher, Christian
    et al.
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Germany; Berlin Center for Genomics in Biodiversity Research, Germany; Department of Biological and Environmental Sciences, University of Gothenburg, Sweden.
    Fuchs, Andrea
    Carl-von-Ossietzky University Oldenburg, Germany; Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Germany.
    Attermeyer, Katrin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Leibniz-InsLeibniz-Institute of Freshwater Ecology and Inland Fisheries, Germanytitute of Freshwater Ecology and Inland Fisheries, Alte Fischerhütte 2, 16775 Stechlin, Germany.
    Frindte, Katharina
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany; Institute of Crop Science and Resource Conservation – Molecular Biology of the Rhizosphere, Bonn University, Germany.
    Grossart, Hans-Peter
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Germany; Institute for Biochemistry and Biology, Potsdam University, Germany.
    Hupfer, Michael
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Germany.
    Casper, Peter
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Germany.
    Monaghan, Michael T.
    Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Germany; Berlin Center for Genomics in Biodiversity Research, Germany.
    Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment2017Ingår i: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 5, artikel-id 41Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments.

    Methods: We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1–4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota.

    Results: Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5–14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions.

    Conclusions: By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper “replacement horizon” is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower “depauperate horizon” is characterized by low taxonomic richness, more stable “low-energy” conditions, and a dominance of enigmatic Archaea.

  • 571.
    Xie, Hao
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Metabolic engineering for optimizing isobutanol production in Synechocystis PCC 68032018Självständigt arbete på avancerad nivå (masterexamen), 30 poäng / 45 hpStudentuppsats (Examensarbete)
    Abstract [en]

    The diminishing of fossil fuels and growing concerns towards climate change have intensified biofuel production from renewable resources. Recently, progresses are made in microbial production of biofuels. Among various biofuels, isobutanol is gaining an increasing attention due to its high energy content and suitable chemical and physical properties, enabling it to be a suitable substitution of fossil fuel. In this study, instead of using heterotrophic microorganisms, we performed metabolic engineering of Synechocystis PCC 6803 (Synechocystis) for isobutanol production under autotrophic condition. After introduced 2-keto acid pathway, Synechocystis is able to produce isobutanol when provided with water, carbon dioxide and solar energy. When cultivated in an optimal condition (50 μmol photons m-1s-2 and adjusted pH to 7-8 with HCl), the engineered strain pEEK2-ST was able to produce 425 mg L-1 in-flask isobutanol titer and 911 mg L-1 cumulative isobutanol titer, respectively, in 46 days. There should be bottlenecks existing in 2-keto acid pathway based on the similar isobutanol production of strain pEEK2-ST with and without pyruvate addition. However, the attempt to identify potential bottlenecks of upstream genes by overexpressing ST and one of the three upstream genes failed, instead what we conclude is that the isobutanol production is tightly correlated to Kivd (ST) expression level. Thus, more strategies will be employed for identifying bottlenecks successfully and further improvement of isobutanol production in the future. In conclusion, this study demonstrates the importance of cultivation condition on isobutanol production in Synechocystis.

    Publikationen är tillgänglig i fulltext från 2020-06-11 15:29
  • 572.
    Xu, Feifei
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Comparative Genomics in Diplomonads: Lifestyle Variations Revealed at Genetic Level2015Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    As sequencing technologies advance genome studies are becoming a basic tool for studying an organism, and with more genomes available comparative genomics is maturing into a powerful tool for biological research. This thesis demonstrates the strength of a comparative genomics approach on a group of understudied eukaryotes, the diplomonads.

    Diplomonads are a group of single cell eukaryotic flagellates living in oxygen-poor environments. Most diplomonads are intestinal parasites, like the well-studied human parasite Giardia intestinalis. There are seven different G. intestinalis assemblages (genotypes) affecting different hosts, and it’s under debate whether these are one species. A genome-wide study of three G. intestinalis genomes from different assemblages reveals little inter-assemblage sexual recombination, supporting that the different G. intestinalis assemblages are genetically isolated and thus different species.

    A genomic comparison between the fish parasite S. salmonicida and G. intestinalis reveals genetic differences reflecting differences in their parasitic lifestyles. There is a tighter transcriptional regulation and a larger metabolic reservoir in S. salmonicida, likely adaptations to the fluctuating environments it encounters during its systemic infection compared to G. intestinalis which is a strict intestinal parasite.

    The S. salmonicida genome analysis also discovers genes involved in energy metabolism. Some of these are experimentally shown to localize to mitochondrion-related organelles in S. salmonicida, indicating that they possess energy-producing organelles that should be classified as hydrogenosomes, as opposed to the mitosomes in G. intestinalis.

    A transcriptome analysis of the free-living Trepomonas is compared with genomic data from the two parasitic diplomonads. The majority of the genes associated with a free-living lifestyle, like phagocytosis and a larger metabolic capacity, are of prokaryotic origin. This suggests that the ancestor of the free-living diplomonad was likely host-associated and that the free-living lifestyle is a secondary adaptation acquired through horizontal gene transfers. 

    In conclusion, this thesis uses different comparative genomics approaches to broaden the knowledge on diplomonad diversity and to provide more insight into how the lifestyle differences are reflected on the genetic level. The bioinformatics pipelines and expertise gained in these studies will be useful in other projects in diplomonads and other organismal groups.

    Delarbeten
    1. Genome-Wide Analyses of Recombination Suggest That Giardia intestinalis Assemblages Represent Different Species
    Öppna denna publikation i ny flik eller fönster >>Genome-Wide Analyses of Recombination Suggest That Giardia intestinalis Assemblages Represent Different Species
    2012 (Engelska)Ingår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, nr 10, s. 2895-2898Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Giardia intestinalis is a major cause of waterborne enteric disease in humans. The species is divided into eight assemblages suggested to represent separate Giardia species based on host specificities and the genetic divergence of marker genes. We have investigated whether genome-wide recombination occurs between assemblages using the three available G. intestinalis genomes. First, the relative nonsynonymous substitution rates of the homologs were compared for 4,009 positional homologs. The vast majority of these comparisons indicate genetic isolation without interassemblage recombinations. Only a region of 6 kbp suggests genetic exchange between assemblages A and E, followed by gene conversion events. Second, recombination-detecting software fails to identify within-gene recombination between the different assemblages for most of the homologs. Our results indicate very low frequency of recombination between the syntenic core genes, suggesting that G. intestinalis assemblages are genetically isolated lineages and thus should be viewed as separated Giardia species.

    Nationell ämneskategori
    Naturvetenskap Medicin och hälsovetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-175947 (URN)10.1093/molbev/mss107 (DOI)000309927900003 ()22474166 (PubMedID)
    Tillgänglig från: 2012-06-14 Skapad: 2012-06-14 Senast uppdaterad: 2017-12-07Bibliografiskt granskad
    2. Hydrogenosomes in the diplomonad Spironucleus salmonicida
    Öppna denna publikation i ny flik eller fönster >>Hydrogenosomes in the diplomonad Spironucleus salmonicida
    Visa övriga...
    2013 (Engelska)Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 4, s. 2493-Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Acquisition of the mitochondrion is a key event in the evolution of the eukaryotic cell, but diversification of the organelle has occurred during eukaryotic evolution. One example of such mitochondria-related organelles (MROs) are hydrogenosomes, which produce ATP by substrate- level phosphorylation with hydrogen as a byproduct. The diplomonad parasite Giardia intestinalis harbours mitosomes, another type of MRO. Here we identify MROs in the salmon parasite Spironucleus salmonicida with similar protein import and Fe-S cluster assembly machineries as in Giardia mitosomes. We find that hydrogen production is prevalent in the diplomonad genus Spironucleus, and that S. salmonicida MROs contain enzymes characteristic of hydrogenosomes. Evolutionary analyses of known hydrogenosomal components indicate their presence in the diplomonad ancestor, and subsequent loss in Giardia. Our results suggest that hydrogenosomes are metabolic adaptations predating the split between parabasalids and diplomonads, which is deeper than the split between animals and fungi in the eukaryotic tree.

    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-210741 (URN)10.1038/ncomms3493 (DOI)000325534300002 ()
    Tillgänglig från: 2013-11-14 Skapad: 2013-11-14 Senast uppdaterad: 2017-12-06Bibliografiskt granskad
    3. The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments
    Öppna denna publikation i ny flik eller fönster >>The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments
    Visa övriga...
    2014 (Engelska)Ingår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, nr 2, s. e1004053-Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Spironucleus salmonicida causes systemic infections in salmonid fish. It belongs to the group diplomonads, binucleated heterotrophic flagellates adapted to micro-aerobic environments. Recently we identified energy-producing hydrogenosomes in S. salmonicida. Here we present a genome analysis of the fish parasite with a focus on the comparison to the more studied diplomonad Giardia intestinalis. We annotated 8067 protein coding genes in the ∼12.9 Mbp S. salmonicida genome. Unlike G. intestinalis, promoter-like motifs were found upstream of genes which are correlated with gene expression, suggesting a more elaborate transcriptional regulation. S. salmonicida can utilise more carbohydrates as energy sources, has an extended amino acid and sulfur metabolism, and more enzymes involved in scavenging of reactive oxygen species compared to G. intestinalis. Both genomes have large families of cysteine-rich membrane proteins. A cluster analysis indicated large divergence of these families in the two diplomonads. Nevertheless, one of S. salmonicida cysteine-rich proteins was localised to the plasma membrane similar to G. intestinalis variant-surface proteins. We identified S. salmonicida homologs to cyst wall proteins and showed that one of these is functional when expressed in Giardia. This suggests that the fish parasite is transmitted as a cyst between hosts. The extended metabolic repertoire and more extensive gene regulation compared to G. intestinalis suggest that the fish parasite is more adapted to cope with environmental fluctuations. Our genome analyses indicate that S. salmonicida is a well-adapted pathogen that can colonize different sites in the host.

    Nationell ämneskategori
    Mikrobiologi Genetik
    Identifikatorer
    urn:nbn:se:uu:diva-224545 (URN)10.1371/journal.pgen.1004053 (DOI)000332021500041 ()24516394 (PubMedID)
    Tillgänglig från: 2014-05-14 Skapad: 2014-05-14 Senast uppdaterad: 2019-03-19Bibliografiskt granskad
    4. On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp PC1
    Öppna denna publikation i ny flik eller fönster >>On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp PC1
    Visa övriga...
    2016 (Engelska)Ingår i: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 14, artikel-id 62Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Background: It is generally thought that the evolutionary transition to parasitism is irreversible because it is associated with the loss of functions needed for a free-living lifestyle. Nevertheless, free-living taxa are sometimes nested within parasite clades in phylogenetic trees, which could indicate that they are secondarily free-living. Herein, we test this hypothesis by studying the genomic basis for evolutionary transitions between lifestyles in diplomonads, a group of anaerobic eukaryotes. Most described diplomonads are intestinal parasites or commensals of various animals, but there are also free-living diplomonads found in oxygen-poor environments such as marine and freshwater sediments. All these nest well within groups of parasitic diplomonads in phylogenetic trees, suggesting that they could be secondarily free-living. Results: We present a transcriptome study of Trepomonas sp. PC1, a diplomonad isolated from marine sediment. Analysis of the metabolic genes revealed a number of proteins involved in degradation of the bacterial membrane and cell wall, as well as an extended set of enzymes involved in carbohydrate degradation and nucleotide metabolism. Phylogenetic analyses showed that most of the differences in metabolic capacity between free-living Trepomonas and the parasitic diplomonads are due to recent acquisitions of bacterial genes via gene transfer. Interestingly, one of the acquired genes encodes a ribonucleotide reductase, which frees Trepomonas from the need to scavenge deoxyribonucleosides. The transcriptome included a gene encoding squalene-tetrahymanol cyclase. This enzyme synthesizes the sterol substitute tetrahymanol in the absence of oxygen, potentially allowing Trepomonas to thrive under anaerobic conditions as a free-living bacterivore, without depending on sterols from other eukaryotes. Conclusions: Our findings are consistent with the phylogenetic evidence that the last common ancestor of diplomonads was dependent on a host and that Trepomonas has adapted secondarily to a free-living lifestyle. We believe that similar studies of other groups where free-living taxa are nested within parasites could reveal more examples of secondarily free-living eukaryotes.

    Nyckelord
    Free-living; Parasite; Diplomonad; Dollo's law; Reversibility; Trepomonas; Horizontal gene transfer; Ribonucleotide reductase
    Nationell ämneskategori
    Evolutionsbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-251638 (URN)10.1186/s12915-016-0284-z (DOI)000381184600002 ()27480115 (PubMedID)
    Forskningsfinansiär
    Forskningsrådet Formas, 2010-899Science for Life Laboratory - a national resource center for high-throughput molecular bioscienceVetenskapsrådet
    Anmärkning

    Correction in: BMC Biology, vol. 14, article number 77

    DOI: 10.1186/s12915-016-0302-1

    Tillgänglig från: 2015-04-23 Skapad: 2015-04-22 Senast uppdaterad: 2017-12-04Bibliografiskt granskad
  • 573.
    Xu, Feifei
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Jerlström-Hultqvist, Jon
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi.
    Einarsson, Elin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Astvaldsson, Asgeir
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Svärd, Staffan G
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Andersson, Jan O
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments2014Ingår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, nr 2, s. e1004053-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Spironucleus salmonicida causes systemic infections in salmonid fish. It belongs to the group diplomonads, binucleated heterotrophic flagellates adapted to micro-aerobic environments. Recently we identified energy-producing hydrogenosomes in S. salmonicida. Here we present a genome analysis of the fish parasite with a focus on the comparison to the more studied diplomonad Giardia intestinalis. We annotated 8067 protein coding genes in the ∼12.9 Mbp S. salmonicida genome. Unlike G. intestinalis, promoter-like motifs were found upstream of genes which are correlated with gene expression, suggesting a more elaborate transcriptional regulation. S. salmonicida can utilise more carbohydrates as energy sources, has an extended amino acid and sulfur metabolism, and more enzymes involved in scavenging of reactive oxygen species compared to G. intestinalis. Both genomes have large families of cysteine-rich membrane proteins. A cluster analysis indicated large divergence of these families in the two diplomonads. Nevertheless, one of S. salmonicida cysteine-rich proteins was localised to the plasma membrane similar to G. intestinalis variant-surface proteins. We identified S. salmonicida homologs to cyst wall proteins and showed that one of these is functional when expressed in Giardia. This suggests that the fish parasite is transmitted as a cyst between hosts. The extended metabolic repertoire and more extensive gene regulation compared to G. intestinalis suggest that the fish parasite is more adapted to cope with environmental fluctuations. Our genome analyses indicate that S. salmonicida is a well-adapted pathogen that can colonize different sites in the host.

  • 574.
    Yang, Yang
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    Stenger-Kovacs, Csilla
    Univ Pannonia, Dept Limnol, Egyet U 10, H-8200 Veszprem, Hungary..
    Padisak, Judit
    Univ Pannonia, Dept Limnol, Egyet U 10, H-8200 Veszprem, Hungary.;MTA PE Limnoecol Res Grp, Egyet U 10, H-8200 Veszprem, Hungary..
    Pettersson, Kurt
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik.
    Effects of winter severity on spring phytoplankton development in a temperate lake (Lake Erken, Sweden)2016Ingår i: Hydrobiologia, ISSN 0018-8158, E-ISSN 1573-5117, Vol. 780, nr 1, s. 47-57Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Phytoplankton seasonal succession has been linked to a variety of serial environmental changes, especially weather- and climate-induced physical forcing. This study compared spring phytoplankton dynamics after winters of different severity (cold, normal, and warm) in Lake Erken, Sweden. The spring diatom bloom was dominated by different functional groups: group A (centric diatoms 5-10 mu m) after cold winters, B (centric diatoms > 15 mu m) after normal winters, and P (Aulacoseira granulata, Fragilaria crotonensis) after warm winters. Our results suggest that weather-related processes were the primary external drivers accounting for differences in spring phytoplankton dynamics in Lake Erken. Spring phytoplankton are influenced by overwintering species from the last autumn that can initiate the following spring bloom. Average taxonomic distinctness of the spring community was assessed using a new biodiversity measurement that incorporates taxonomic relatedness information. This value was lower than expected after warm and cold winters, which had winter air temperature 1A degrees C deviation from an average value calculated over 21 years. Such winters increased the level of disturbance or stress to the lake, resulting in a spring with less diverse phytoplankton by narrowing the niche for species with various ecological requirements.

  • 575.
    Yeo, Sara K.
    et al.
    University of Hawaii.
    Huggett, Megan J.
    University of Hawaii.
    Eiler, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Rappé, Michael S.
    University of Hawaii.
    Coastal Bacterioplankton Community Dynamics in Response to a Natural Disturbance2013Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 2, s. e56207-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In order to characterize how disturbances to microbial communities are propagated over temporal and spatial scales in aquatic environments, the dynamics of bacterial assemblages throughout a subtropical coastal embayment were investigated via SSU rRNA gene analyses over an 8-month period, which encompassed a large storm event. During non-perturbed conditions, sampling sites clustered into three groups based on their microbial community composition: an offshore oceanic group, a freshwater group, and a distinct and persistent coastal group. Significant differences in measured environmental parameters or in the bacterial community due to the storm event were found only within the coastal cluster of sampling sites, and only at 5 of 12 locations; three of these sites showed a significant response in both environmental and bacterial community characteristics. These responses were most pronounced at sites close to the shoreline. During the storm event, otherwise common bacterioplankton community members such as marine Synechococcus sp. and members of the SAR11 clade of Alphaproteobacteria decreased in relative abundance in the affected coastal zone, whereas several lineages of GammaproteobacteriaBetaproteobacteria, and members of the Roseobacter clade of Alphaproteobacteria increased. The complex spatial patterns in both environmental conditions and microbial community structure related to freshwater runoff and wind convection during the perturbation event leads us to conclude that spatial heterogeneity was an important factor influencing both the dynamics and the resistance of the bacterioplankton communities to disturbances throughout this complex subtropical coastal system. This heterogeneity may play a role in facilitating a rapid rebound of regions harboring distinctly coastal bacterioplankton communities to their pre-disturbed taxonomic composition.

  • 576.
    Yutin, Natalya
    et al.
    NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA..
    Bäckstrom, Disa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Ettema, Thijs J G
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Krupovic, Mart
    Inst Pasteur, Dept Microbiol, Unite Biol Mol Gene Chez Extremophiles, Paris, France..
    Koonin, Eugene V.
    NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bethesda, MD 20894 USA..
    Vast diversity of prokaryotic virus genomes encoding double jelly-roll major capsid proteins uncovered by genomic and metagenomic sequence analysis2018Ingår i: Virology Journal, ISSN 1743-422X, E-ISSN 1743-422X, Vol. 15, artikel-id 67Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Analysis of metagenomic sequences has become the principal approach for the study of the diversity of viruses. Many recent, extensive metagenomic studies on several classes of viruses have dramatically expanded the visible part of the virosphere, showing that previously undetected viruses, or those that have been considered rare, actually are important components of the global virome.

    Results: We investigated the provenance of viruses related to tail-less bacteriophages of the family Tectiviridae by searching genomic and metagenomics sequence databases for distant homologs of the tectivirus-like Double JellyRoll major capsid proteins (DJR MCP). These searches resulted in the identification of numerous genomes of viruslike elements that are similar in size to tectiviruses (10-15 kilobases) and have diverse gene compositions. By comparison of the gene repertoires, the DJR MCP-encoding genomes were classified into 6 distinct groups that can be predicted to differ in reproduction strategies and host ranges. Only the DJR MCP gene that is present by design is shared by all these genomes, and most also encode a predicted DNA-packaging ATPase; the rest of the genes are present only in subgroups of this unexpectedly diverse collection of DJR MCP-encoding genomes. Only a minority encode a DNA polymerase which is a hallmark of the family Tectiviridae and the putative family "Autolykiviridae". Notably, one of the identified putative DJR MCP viruses encodes a homolog of Cas1 endonuclease, the integrase involved in CRISPR-Cas adaptation and integration of transposon-like elements called casposons. This is the first detected occurrence of Cas1 in a virus. Many of the identified elements are individual contigs flanked by inverted or direct repeats and appear to represent complete, extrachromosomal viral genomes, whereas others are flanked by bacterial genes and thus can be considered as proviruses. These contigs come from metagenomes of widely different environments, some dominated by archaea and others by bacteria, suggesting that collectively, the DJR MCP-encoding elements have a broad host range among prokaryotes.

    Conclusions: The findings reported here greatly expand the known host range of (putative) viruses of bacteria and archaea that encode a DJR MCP. They also demonstrate the extreme diversity of genome architectures in these viruses that encode no universal proteins other than the capsid protein that was used as the marker for their identification. From a supposedly minor group of bacterial and archaeal viruses, these viruses are emerging as a substantial component of the prokaryotic virome.

  • 577.
    Zanaty, Ali M.
    et al.
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Erfan, Ahmed M.
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Mady, Wessam H.
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Amer, Fatma
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Nour, Ahmed A.
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Rabie, Neveen
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Samy, Mohamed
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Selim, Abdullah A.
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Hassan, Wafaa M. M.
    Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Naguib, Mahmoud
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Anim Hlth Res Inst, Natl Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt.
    Avian influenza virus surveillance in migratory birds in Egypt revealed a novel reassortant H6N2 subtype2019Ingår i: Avian Research, ISSN 0005-2175, E-ISSN 2053-7166, Vol. 10, nr 1, artikel-id 41Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background

    Avian influenza viruses (AIVs) have been identified from more than 100 different species of wild birds around the globe. Wild migratory birds can act as potential spreaders for AIVs to domestic birds between different countries. Egypt is situated on important migratory flyways for wild birds between different continents. While much is known about circulation of zoonotic potential H5N1 and H9N2 AIVs in domestic poultry in Egypt, little is known about the pivotal role of migratory birds in the maintenance and transmission of the viruses in Egypt.

    Methods

    Targeted AIV surveillance has been conducted in 2017 in different wetlands areas in Northern and Eastern Egypt.

    Results

    AIV of subtype H5 was detected in two bird species. In addition, a novel reassortant strain of the H6N2 subtype was identified which reveals the continuous risk of new influenza virus(es) introduction into Egypt. This novel virus possesses a reassortant pattern originating from different AIV gene pools.

    Conclusions

    Intervention control strategies should be performed to minimize the possible contact of domestic birds with wild birds to lower the risk of virus transmission at this interface. In addition, constant monitoring of AIVs in migratory birds is essential in the early detection of influenza virus introduction into Egypt.

  • 578.
    Zaremba-Niedzwiedzka, Katarzyna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Viklund, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Zhao, Weizhou
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Ast, Jennifer
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Språkvetenskapliga fakulteten, Institutionen för nordiska språk.
    Sczyrba, Alexander
    Woyke, Tanja
    McMahon, Katherina
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Stepanauskas, Ramunas
    Andersson, Siv
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade2013Ingår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, nr 11, artikel-id R130Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.

  • 579.
    Zaremba-Niedźwiedzka, Katarzyna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Microbial Metagenomics: A Tale of the Dead and the Living2013Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    It is a microbial world we live in: microbes outnumber other organisms by several orders of magnitude, and they have great importance for the environment. However, environmental microbes are notoriously difficult to grow in the laboratory, and using culture independent techniques is necessary to expand our view. In this thesis, I apply metagenomics and single-cell genomics to environmental samples from ancient human remains and lakes.

    First, I used metagenomics to learn about bacteria from a Neanderthal’s bone and the gut of Ötzi, a frozen natural mummy. Both were exploratory studies where the main question was what kind of bacteria are present. I found out that Streptomyces dominated this particular Neanderthal fossil, and the DNA lacked the damage that is often seen in ancient samples. Ötzi's gut sample was dominated by Clostridia and fungi belonging to Basidiomycota.

    Second, ten single-cell amplified genomes of freshwater Alphaproteobacterium LD12 and three metagenomes from Swedish lakes were sequenced. Comparative metagenomics allowed hypothesizing about which functions are important for microbe proliferation in freshwater, pointing to osmoregulation and transport proteins and, possibly, to different strategies of metabolizing sugars. I also focused on SAR11 sister-groups in oceans and lakes. Phylogenies and sequence evolutionary distance estimates indicated the existence of microclusters within LD12, showing variation in abundance between lakes. The most striking difference was the relative amount of recombination compared to mutation, the estimated r/m ratio. SAR11 marine and their freshwater cousins are found at the opposite extremes of the r/m range, lowest and highest, respectively. The genetic background or sequence diversity did not explain the observed dramatic difference, so it is possibly connected to environmental adaptation or population dynamics.

    In addition, I have spent a substantial amount of effort benchmarking available metagenomic methods, for example fragment recruitment of metagenomes to reference genomes.

    In conclusion, my exploratory metagenomic studies have shed some light on the bacteria present in ancient human remains; comparative metagenomics has suggested the importance of substrate preference on functional differences between lakes and oceans; finally, single-cell genomes have allowed some insight into molecular evolutionary processes taking place in the freshwater LD12 bacterium. 

    Delarbeten
    1. No Ancient DNA Damage in Actinobacteria from the Neanderthal Bone
    Öppna denna publikation i ny flik eller fönster >>No Ancient DNA Damage in Actinobacteria from the Neanderthal Bone
    2013 (Engelska)Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 5, s. e62799-Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Background: The Neanderthal genome was recently sequenced using DNA extracted from a 38,000-year-old fossil. At the start of the project, the fraction of mammalian and bacterial DNA in the sample was estimated to be <6% and 9%, respectively. Treatment with restriction enzymes prior to sequencing increased the relative proportion of mammalian DNA to 15%, but the large majority of sequences remain uncharacterized. Principal Findings: Our taxonomic profiling of 3.95 Gb of Neanderthal DNA isolated from the Vindija Neanderthal Vi33.16 fossil showed that 90% of about 50,000 rRNA gene sequence reads were of bacterial origin, of which Actinobacteria accounted for more than 75%. Actinobacteria also represented more than 80% of the PCR-amplified 16S rRNA gene sequences from a cave sediment sample taken from the same G layer as the Neanderthal bone. However, phylogenetic analyses did not identify any sediment clones that were closely related to the bone-derived sequences. We analysed the patterns of nucleotide differences in the individual sequence reads compared to the assembled consensus sequences of the rRNA gene sequences. The typical ancient nucleotide substitution pattern with a majority of C to T changes indicative of DNA damage was observed for the Neanderthal rRNA gene sequences, but not for the Streptomyces-like rRNA gene sequences. Conclusions/Significance: Our analyses suggest that the Actinobacteria, and especially members of the Streptomycetales, contribute the majority of sequences in the DNA extracted from the Neanderthal fossil Vi33.16. The bacterial DNA showed no signs of damage, and we hypothesize that it was derived from bacteria that have been enriched inside the bone. The bioinformatic approach used here paves the way for future studies of microbial compositions and patterns of DNA damage in bacteria from archaeological bones. Such studies can help identify targeted measures to increase the relative amount of endogenous DNA in the sample.

    Nationell ämneskategori
    Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-205391 (URN)10.1371/journal.pone.0062799 (DOI)000321202100042 ()
    Tillgänglig från: 2013-08-29 Skapad: 2013-08-16 Senast uppdaterad: 2017-12-06Bibliografiskt granskad
    2. Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
    Öppna denna publikation i ny flik eller fönster >>Single cell genomics reveals low recombination frequencies in freshwater bacteria of the SAR11 clade
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    2013 (Engelska)Ingår i: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 14, nr 11, artikel-id R130Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Background: The SAR11 group of Alphaproteobacteria is highly abundant in the oceans. It contains a recently diverged freshwater clade, which offers the opportunity to compare adaptations to salt-and freshwaters in a monophyletic bacterial group. However, there are no cultivated members of the freshwater SAR11 group and no genomes have been sequenced yet. Results: We isolated ten single SAR11 cells from three freshwater lakes and sequenced and assembled their genomes. A phylogeny based on 57 proteins indicates that the cells are organized into distinct microclusters. We show that the freshwater genomes have evolved primarily by the accumulation of nucleotide substitutions and that they have among the lowest ratio of recombination to mutation estimated for bacteria. In contrast, members of the marine SAR11 clade have one of the highest ratios. Additional metagenome reads from six lakes confirm low recombination frequencies for the genome overall and reveal lake-specific variations in microcluster abundances. We identify hypervariable regions with gene contents broadly similar to those in the hypervariable regions of the marine isolates, containing genes putatively coding for cell surface molecules. Conclusions: We conclude that recombination rates differ dramatically in phylogenetic sister groups of the SAR11 clade adapted to freshwater and marine ecosystems. The results suggest that the transition from marine to freshwater systems has purged diversity and resulted in reduced opportunities for recombination with divergent members of the clade. The low recombination frequencies of the LD12 clade resemble the low genetic divergence of host-restricted pathogens that have recently shifted to a new host.

    Nationell ämneskategori
    Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-206203 (URN)10.1186/gb-2013-14-11-r130 (DOI)000330616200009 ()24286338 (PubMedID)
    Forskningsfinansiär
    Vetenskapsrådet, 349-2007-831 621-2008-3259 621-2011-4669-4669 2009-3784 2008-1923 2012-3892EU, Europeiska forskningsrådetGöran Gustafssons Stiftelse för främjande av vetenskaplig forskning vid Uppsala universitet och Kungl tekniska högskolan (UU/KTH)Knut och Alice Wallenbergs Stiftelse, KAW-2011.0148 KAW-2012.0075Swedish National Infrastructure for Computing (SNIC), p2006019 p2009043
    Tillgänglig från: 2013-09-03 Skapad: 2013-08-29 Senast uppdaterad: 2019-09-20Bibliografiskt granskad
    3. Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
    Öppna denna publikation i ny flik eller fönster >>Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics
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    2014 (Engelska)Ingår i: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 16, nr 9, s. 2682-2698Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Little is known about the diversity and structuring of freshwater microbial communities beyond the patterns revealed by tracing their distribution in the landscape with common taxonomic markers such as the ribosomal RNA. To address this gap in knowledge, metagenomes from temperate lakes were compared to selected marine metagenomes. Taxonomic analyses of rRNA genes in these freshwater metagenomes confirm the previously reported dominance of a limited subset of uncultured lineages of freshwater bacteria, whereas Archaea were rare. Diversification into marine and freshwater microbial lineages was also reflected in phylogenies of functional genes and there were also significant differences in functional beta-diversity. The pathways and functions that accounted for these differences are involved in osmoregulation, active transport, carbohydrate and amino acid metabolism. Moreover, predicted genes orthologous to active transporters and recalcitrant organic matter degradation were more common in microbial genomes from oligotrophic versus eutrophic lakes. This comparative metagenomic analysis allowed us to formulate a general hypothesis that oceanic- compared to freshwater-dwelling microorganisms, invest more in metabolism of amino acids and that strategies of carbohydrate metabolism differ significantly between marine and freshwater microbial communities.

    Nationell ämneskategori
    Mikrobiologi Naturvetenskap
    Identifikatorer
    urn:nbn:se:uu:diva-206205 (URN)10.1111/1462-2920.12301 (DOI)000341579700006 ()24118837 (PubMedID)
    Anmärkning

    Published in 2013 as Epub ahead of print

    Tillgänglig från: 2013-09-03 Skapad: 2013-08-29 Senast uppdaterad: 2017-12-06Bibliografiskt granskad
    4. Metagenomic analysis of a distal gut sample from the Tyrolean Iceman
    Öppna denna publikation i ny flik eller fönster >>Metagenomic analysis of a distal gut sample from the Tyrolean Iceman
    Visa övriga...
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-206206 (URN)
    Tillgänglig från: 2013-09-03 Skapad: 2013-08-29 Senast uppdaterad: 2014-01-23
    5. Testing fragment recruitment methods by simulating environmental communities of different complexities
    Öppna denna publikation i ny flik eller fönster >>Testing fragment recruitment methods by simulating environmental communities of different complexities
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Bioinformatik och systembiologi
    Identifikatorer
    urn:nbn:se:uu:diva-206208 (URN)
    Tillgänglig från: 2013-09-03 Skapad: 2013-08-29 Senast uppdaterad: 2014-01-23
  • 580.
    Zaremba-Niedźwiedzka, Katarzyna
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Zheng, Zongli
    Arvén-Norling, Jenny
    Maixner, Frank
    Zink, Albert
    Engstrand, Lars
    Andersson, Siv
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Metagenomic analysis of a distal gut sample from the Tyrolean IcemanManuskript (preprint) (Övrigt vetenskapligt)
  • 581.
    Zepeda, Vanessa K.
    et al.
    Univ Hawaii Manoa, Dept Microbiol, Honolulu, HI 96822 USA..
    Busse, Hans-Juergen
    Vet Med Univ Wien, Inst Mikrobiol, A-1210 Vienna, Austria..
    Golke, Jan
    Vet Med Univ Wien, Inst Mikrobiol, A-1210 Vienna, Austria..
    Saw, Jimmy H. W.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Alam, Maqsudul
    Univ Hawaii Manoa, Dept Microbiol, Honolulu, HI 96822 USA..
    Donachie, Stuart P.
    Univ Hawaii Manoa, Dept Microbiol, Honolulu, HI 96822 USA..
    Terasakiispira papahanaumokuakeensis gen. nov., sp nov., a gammaproteobacterium from Pearl and Hermes Atoll, Northwestern Hawaiian Islands2015Ingår i: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 65, s. 3609-3617Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A Gram-negative, helical bacterium designated PH27A(T) was cultivated from an anchialine pool on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The obligately halophilic strain was motile by bipolar tufts of flagella and grew optimally at pH 7, and microaerobically or aerobically. Closest neighbours based on 16S rRNA gene nucleotide sequence identity are Marinospirillum celere v1c_Sn-red(T) (93.31 %) and M. alkaliphilum Z4(T) (92.10 %) in the family Oceanospirillaceae, class Gammaproteobacteria. PH27A(T) is distinguished phenotypically from members of the genus Marinospirillum by its hydrolysis of gelatin, the absence of growth in media containing <= 1 % (w/v) NaCl and the ranges of temperature (12-40 degrees C) and pH (5-8) for growth. The major compound ubiquinone Q-9 distinguishes the quinone system of strain PH27A(T) from those in members of the genus Marinospirillum and other members of the Oceanospirillaceae, in which the major quinone is Q-8. Major polar lipids in PH27A(T) were phosphatidylethanolamine and phosphatidylglycerol, with moderate amounts of diphosphatidylglycerol and phosphatidylserine. Spermidine and cadaverine dominated the polyamine pattern; large proportions of cadaverine have not been reported in members of the genus Marinospirillum. Genotypic and chemotaxonomic data show that PH27A(T) does not belong in the genus Marinospirillum or other genera of the family Oceanospirillaceae or the Halomonadaceae. We propose a new genus, Terasakiispira gen. nov., be created to accommodate Terasakiispira papahanaumokuakeensis gen. nov., sp. nov. as the type species, with PH27A(T) (=ATCC BAA-995(T)=DSM 16455(T)=DSM 23961(T)) as the type strain.

  • 582.
    Zha, Yinghua
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Assembly of Gut Microbial Communities in Freshwater Fish and Their Roles in Fish Condition2017Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Animal hosts provide associated microorganisms with suitable ecological niches in their intestines. Microbes help their hosts to digest food, protect against pathogens, and influence the host’s metabolisms. Compositional variation of gut microbial communities is common among hosts, and may affect the health status of hosts. Diet and genetic factors are well known to influence the assembly of gut microbial communities. This thesis focuses on disentangling the contributions of factors including host genetics (sex), diet, environment, and other ecological processes to the assembly of gut microbial communities in freshwater fish. The association between gut microbial communities and fish condition is also evaluated in this thesis.

    Applying metacommunity theory, we found environmental factors including fish habitat, fish species, their diet, dispersal factors including microbes from fish diet, and ecological drift contributed to the assembly of fish gut microbial communities. The proportion of their contribution varied between fish species, where ecological drift explained more in perch than in roach.

    Under natural conditions fish populations face the risk of predation, which can induce competition and impose predation stress within prey individuals. This can therefore lead to changes in their diet qualities and quantities. In this thesis, it was shown that fish diet in terms of qualities and quantities significantly influenced the overall gut microbial composition, and this influence was dependent on fish sex, a host genetic factor. Predation stress was also suggested to significantly decrease the species richness. Furthermore, when fish were experiencing a diet shift, we showed that different bacterial phyla from novel food had different colonization success in the intestine, and this colonization success was positively influenced by predation stress. Fish condition was suggested in this thesis to be affected by gut microbial composition, especially by the contributions of the bacterial phyla Tenericutes and Actinobacteria.

    Delarbeten
    1. Contributions of environment and ecological processes to gut microbial communities in freshwater fish
    Öppna denna publikation i ny flik eller fönster >>Contributions of environment and ecological processes to gut microbial communities in freshwater fish
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Ekologi Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-314231 (URN)
    Tillgänglig från: 2017-01-31 Skapad: 2017-01-31 Senast uppdaterad: 2017-02-01
    2. Stress responses in intestinal microbiota and host condition depend on gender and diet in a vertebrate
    Öppna denna publikation i ny flik eller fönster >>Stress responses in intestinal microbiota and host condition depend on gender and diet in a vertebrate
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Ekologi Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-314232 (URN)
    Tillgänglig från: 2017-01-31 Skapad: 2017-01-31 Senast uppdaterad: 2017-01-31
    3. Effects of food ration and predation stress on perch gut microbial communities
    Öppna denna publikation i ny flik eller fönster >>Effects of food ration and predation stress on perch gut microbial communities
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Ekologi Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-314233 (URN)
    Tillgänglig från: 2017-01-31 Skapad: 2017-01-31 Senast uppdaterad: 2017-01-31
    4. Colonization and extinction probabilities in fish gut microbial communities under diet switch and predation stress
    Öppna denna publikation i ny flik eller fönster >>Colonization and extinction probabilities in fish gut microbial communities under diet switch and predation stress
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Ekologi Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-314234 (URN)
    Tillgänglig från: 2017-01-31 Skapad: 2017-01-31 Senast uppdaterad: 2017-01-31
  • 583.
    Zha, Yinghua
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Alexander, Eiler
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.; eDNA Solut Ltd, Molndal, Sweden..
    Johansson, Frank
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Svanbäck, Richard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Effects of predation stress and food ration on perch gut microbiota2018Ingår i: Microbiome, ISSN 0026-2633, E-ISSN 2049-2618, Vol. 6, artikel-id 28Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Gut microbiota provide functions of importance to influence hosts' food digestion, metabolism, and protection against pathogens. Factors that affect the composition and functions of gut microbial communities are well studied in humans and other animals; however, we have limited knowledge of how natural food web factors such as stress from predators and food resource rations could affect hosts' gut microbiota and how it interacts with host sex. In this study, we designed a two-factorial experiment exposing perch (Perca fluviatilis) to a predator (pike, Esox lucius), and different food ratios, to examine the compositional and functional changes of perch gut microbiota based on 16S rRNA amplicon sequencing. We also investigated if those changes are host sex dependent.

    Results: We showed that overall gut microbiota composition among individual perch significantly responded to food ration and predator presence. We found that species richness decreased with predator presence, and we identified 23 taxa from a diverse set of phyla that were over-represented when a predator was present. For example, Fusobacteria increased both at the lowest food ration and at predation stress conditions, suggesting that Fusobacteria are favored by stressful situations for the host. In concordance, both food ration and predation stress seemed to influence the metabolic repertoire of the gut microbiota, such as biosynthesis of other secondary metabolites, metabolism of cofactors, and vitamins. In addition, the identified interaction between food ration and sex emphasizes sex-specific responses to diet quantity in gut microbiota.

    Conclusions: Collectively, our findings emphasize an alternative state in gut microbiota with responses to changes in natural food webs depending on host sex. The obtained knowledge from this study provided us with an important perspective on gut microbiota in a food web context.

  • 584.
    Zha, Yinghua
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Berga, Mercè
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Comte, Jérôme
    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 Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities2016Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, nr 5, artikel-id e0155239Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Natural communities are open systems and consequently dispersal can play an important role for the diversity, composition and functioning of communities at the local scale. It is, however, still unclear how effects of dispersal differ depending on the initial diversity of local communities. Here we implemented an experiment where we manipulated the initial diversity of natural freshwater bacterioplankton communities using a dilution-to-extinction approach as well as dispersal from a regional species pool. The aim was further to test whether dispersal effects on bacterial abundance and functional parameters (average community growth rates, respiration rates, substrate utilisation ability) differ in dependence of the initial diversity of the communities. First of all, we found that both initial diversity and dispersal rates had an effect on the recruitment of taxa from a regional source, which was higher in communities with low initial diversity and at higher rates of dispersal. Higher initial diversity and dispersal also promoted higher levels of richness and evenness in local communities and affected, both, separately or interactively, the functional performance of communities. Our study therefore suggests that dispersal can influence the diversity, composition and functioning of bacterial communities and that this effect may be enhanced if the initial diversity of communities is depleted.

  • 585.
    Zha, Yinghua
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Eiler, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Johansson, Frank
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Svanbäck, Richard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Colonization and extinction probabilities in fish gut microbial communities under diet switch and predation stressManuskript (preprint) (Övrigt vetenskapligt)
  • 586.
    Zha, Yinghua
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Eiler, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Johansson, Frank
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Svanbäck, Richard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Effects of food ration and predation stress on perch gut microbial communitiesManuskript (preprint) (Övrigt vetenskapligt)
  • 587.
    Zha, Yinghua
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Lindström, Eva S.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Eiler, Alexander
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi.
    Svanbäck, Richard
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Contributions of environment and ecological processes to gut microbial communities in freshwater fishManuskript (preprint) (Övrigt vetenskapligt)
  • 588.
    Zhang, Jiazhuo
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Isolation and Characterization of Uncultured Freshwater Bacterioplankton from Lake Ekoln and Lake Erken through Dilution-to-Extinction Approach and Molecular Analysis Tools2012Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Not many of the abundant freshwater bacterial groups have a representative cultured isolate. In this master thesis project, some abundant bacterioplankton from two lakes (Lake Ekoln and Lake Erken) could be isolated by a dilution-to-extinction approach. Sterilized lake water which was obtained through an ultrafiltration system was used resembling a natural medium. Specific fragments of 16s rRNA of the isolates were amplified by universal bacterial primers (27f and 1492r, 341f and 805r.) for genotyping against a freshwater sequence database and RDP training set (Version 7). A total of 33 isolates from the two lakes were taxonomically classified and revealed the isolation of typical and abundant freshwater bacteria. Original bacterial community of Lake Ekoln was also analyzed by 16S rRNA clone library construction for diversity study. Phylogenetic trees were built through neighbor-joining method by Mega (Version 5) to reveal the evolutionary relationships among database entries, obtained isolates and clones. 

  • 589.
    Zhao, Hongxing
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Molekylära verktyg.
    Chen, Maoshan
    Monash Univ, Cent Clin Sch, Australian Ctr Blood Dis, Clayton, Vic, Australia.
    Valdes, Alberto
    Univ Alcala De Henares, Dept Analyt Chem Phys Chem & Chem Engn, Madrid, Spain.
    Lind, Sara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Kemiska sektionen, Institutionen för kemi - BMC, Analytisk kemi.
    Pettersson, Ulf
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Medicinsk genetik och genomik.
    Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during adenovirus type 2 infection2019Ingår i: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 19, artikel-id 15Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Human adenovirus (Ad) infection leads to the changes of host cell gene expression and biosynthetic processes. Transcriptomics in adenovirus type 2 (Ad2)-infected lung fibroblasts (IMR-90) cells has previously been studied using RNA sequencing. However, this study included only two time points (12 and 24 hpi) using constrained 76bp long sequencing reads. Therefore, a more detailed study of transcription at different phases of infection using an up-graded sequencing technique is recalled. Furthermore, the correlation between transcription and protein expression needs to be addressed.

    Results: In total, 3556 unique cellular genes were identified as differentially expressed at the transcriptional level with more than 2-fold changes in Ad2-infected cells as compared to non-infected cells by using paired-end sequencing. Based on the kinetics of the gene expression changes at different times after infection, these RNAs fell into 20 clusters. Among them, cellular genes involved in immune response were highly up-regulated in the early phase before becoming down-regulated in the late phase. Comparison of differentially expressed genes at transcriptional and posttranscriptional levels revealed low correlation. Particularly genes involved in cellular immune pathways showed a negative correlation. Here, we highlight the genes which expose inconsistent expression profiles with an emphasis on key factors in cellular immune pathways including NFB, JAK/STAT, caspases and MAVS. Different from their transcriptional profiles with up- and down-regulation in the early and late phase, respectively, these proteins were up-regulated in the early phase and were sustained in the late phase. A surprising finding was that the target genes of the sustained activators failed to show response.

    Conclusion: There were features common to genes which play important roles in cellular immune pathways. Their expression was stimulated at both RNA and protein levels during the early phase. In the late phase however, their transcription was suppressed while protein levels remained stable. These results indicate that Ad2 and the host cell use different strategies to regulate cellular immune pathways. A control mechanism at the post-translational level must thus exist which is under the control of Ad2.

  • 590.
    Zhao, Weizhou
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Andersson, Siv G. E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Molekylär evolution.
    Single cell genomics of deep ocean bacteria2014Ingår i: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 22, nr 5, s. 233-234Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    SAR11 is one of the most abundant bacterioplanktons in the upper surface waters of the oceans. In a recent issue of The ISME Journal, Thrash and colleagues present the genomes of four single SAR11 cells isolated from the deep oceans that are enriched in genes for membrane biosynthetic functions.

  • 591.
    Zhao, Yani
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Systemic RNAi Relies on the Endomembrane System in Caenorhabditis elegans2017Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    The membrane system of a eukaryotic cell is a large and complex system handling the transport, exchange and degradation of many kinds of material. Recent research shows that double-stranded RNA (dsRNA) mediated gene silencing (RNA interference) is a membrane related process. After long dsRNA is processed to small interfering RNA (siRNA) by Dicer, the guide strand and passenger strand are separated in the RNA induced silencing complex (RISC) by Argonaute. The process of loading siRNA into RISC has been suggested to occur at the rough Endoplasmic Reticulum (rER).The components of RISC also associate with late endosomes/multivesicular bodies (MVBs). Furthermore, disturbing the balance between late endosomes/MVBs and lysosomes has been shown to affect the efficiency of silencing.

    We use the nematode Caenorhabditis elegans as our model organism to study two questions: how does membrane transport affect RNAi and spreading of RNAi from the recipient cells to other tissues (systemic RNAi); and how does RNA transport contribute to the multigenerational silencing induced by dsRNA (RNAi inheritance)? Using SID-5, a protein required for efficient systemic RNAi, as bait in a yeast two-hybrid (Y2H) screen, we got 32 SID-5 interacting candidate proteins. Two of these are the SNARE protein SEC-22 and the putative RNA binding protein C12D8.1. In two additional Y2H screens, we found that SID-5 interacts with multiple syntaxin SNAREs, including SYX-6, whereas SEC-22 only interacts with SYX-6. SNAREs usually function in vesicle fusion processes. We found the two SNARE proteins SEC-22 and SYX-6 to be negative regulators of RNAi and to localize to late endosomes/MVBs. In addition, loss of sid-5 leads to an endosome maturation defect. Finally, we found that the putative RNA binding protein C12D8.1 negatively regulates RNAi inheritance and that C12D8.1 mutant animals show impaired RNAi upon targeting a new gene. Taken together, the results presented in this thesis provide us with more evidence for the connection of the membrane transport system and RNAi. The identification of a putative negative regulator of RNAi inheritance further enriches this research field.

    Delarbeten
    1. The conserved SNARE SEC-22 localizes to late endosomes and negatively regulates RNA interference in Caenorhabditis elegans
    Öppna denna publikation i ny flik eller fönster >>The conserved SNARE SEC-22 localizes to late endosomes and negatively regulates RNA interference in Caenorhabditis elegans
    2017 (Engelska)Ingår i: RNA, ISSN 1355-8382, Vol. 23, nr 3, s. 297-307Artikel i tidskrift (Refereegranskat) Published
    Nationell ämneskategori
    Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-321388 (URN)10.1261/rna.058438.116 (DOI)
    Tillgänglig från: 2017-05-04 Skapad: 2017-05-04 Senast uppdaterad: 2017-10-13
    2. RNA Transport Protein SID-5 Interacts with Multiple SNAREs and Affects Membrane Trafficking in C. elegans Intestinal Cells
    Öppna denna publikation i ny flik eller fönster >>RNA Transport Protein SID-5 Interacts with Multiple SNAREs and Affects Membrane Trafficking in C. elegans Intestinal Cells
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-320894 (URN)
    Tillgänglig från: 2017-04-26 Skapad: 2017-04-26 Senast uppdaterad: 2017-10-13
    3. Putative RNA-Binding Protein C12D8.1 Negatively Regulates Inheritance of RNAi in Caenorhabditis elegans
    Öppna denna publikation i ny flik eller fönster >>Putative RNA-Binding Protein C12D8.1 Negatively Regulates Inheritance of RNAi in Caenorhabditis elegans
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Biologiska vetenskaper
    Identifikatorer
    urn:nbn:se:uu:diva-320895 (URN)
    Tillgänglig från: 2017-04-26 Skapad: 2017-04-26 Senast uppdaterad: 2017-10-13
  • 592.
    Zubair, Saima
    et al.
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Fischer, Anne
    Int Livestock Res Inst, Nairobi, Kenya.;Int Ctr Insect Physiol & Ecol, Nairobi, Kenya..
    Liljander, Anne
    Int Livestock Res Inst, Nairobi, Kenya..
    Meens, Jochen
    Univ Vet Med Hannover, Inst Microbiol, Dept Infect Dis, Hannover, Germany..
    Hegerman, Jan
    Hannover Med Sch, Inst Funct & Appl Anat, Hannover, Germany.;Biomed Res Endstage & Obstruct Lung Dis Hannover, Hannover, Germany.;REBIRTH Cluster Excellence, Hannover, Germany..
    Gourle, Hadrien
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Bishop, Richard P.
    Int Livestock Res Inst, Nairobi, Kenya..
    Roebbelen, Ina
    Int Livestock Res Inst, Nairobi, Kenya..
    Younan, Mario
    Vet Sans Frontieres Germany, Nairobi, Kenya..
    Mustafa, Mudassir Imran
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Samhällsvetenskapliga fakulteten, Institutionen för informatik och media. Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för folkhälso- och vårdvetenskap, Klinisk psykologi i hälso- och sjukvård.
    Mushtaq, Mamoona
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Bongcam-Rudloff, Erik
    Swedish Univ Agr Sci, SLU Global Bioinformat Ctr, Dept Anim Breeding & Genet, SE-75007 Uppsala, Sweden..
    Jores, Joerg
    Int Livestock Res Inst, Nairobi, Kenya..
    Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel2015Ingår i: Standards in Genomic Sciences, ISSN 1944-3277, E-ISSN 1944-3277, Vol. 10, artikel-id 109Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79 % of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), similar to 18 % were within the variable genome (shared among multiple but not all isolates) and similar to 3 % were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.

  • 593.
    Ástvaldsson, Ásgeir
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Pathogenesis and Cell Biology of the Salmon Parasite Spironucleus salmonicida2019Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [en]

    Spironucleus species are classified as diplomonad organisms, diverse eukaryotic flagellates found in oxygen-deprived environments. Members of Spironucleus are parasitic and can infect a variety of hosts, such as mice and birds, while the majority are found to infect fish. Massive outbreaks of severe systemic infection caused by a Spironucleus member, Spironucleus salmonicida (salmonicida = salmon killer), have been reported in farmed salmonids resulting in large economic impacts for aquaculture.

    In this thesis, the S. salmonicida genome was sequenced and compared to the genome of its diplomonad relative, the mammalian pathogen G. intestinalis (Paper I). Our analyses revealed large genomic differences between the two parasites that collectively suggests that S. salmonicida is more capable of adapting to different environments. As S. salmonicida can infiltrate different host tissues, we provide molecular evidence for how the parasite can tolerate oxygenated environments and suggest oxygen as a potential regulator of virulence factors (Paper III). To further investigate the molecular responses of the parasite and in addition, its host, during infection we set up an interaction system of S. salmonicida and ASK (Atlantic salmon kidney) cells (Paper VI).

    To study the cell biology in S. salmonicida we optimized an enzymatic proximity labeling method using ascorbate peroxidase (APEX) as a reporter for transmission electron microscopy (TEM) (Paper IV). As the system is robust and versatile, we showed the localization and performed ultrastructural characterization of numerous proteins in S. salmonicida and G. intestinalis. We furthermore utilized the APEX system to study the annexin protein family in S. salmonicida (Paper II). Super resolution microscopy and TEM were applied to show that the annexins are mostly associated with cytoskeletal and membranous structures. In addition, we performed phylogenetic analyses concluding that the annexin gene family is expanded in diplomonads.

    We performed experimental infection in Atlantic salmon and derived a potential model for the route of infection (Paper V). The results suggested multiple routes of transmission between hosts for the parasite.

    To conclude, the comprehensive work in this thesis has provided valuable insights into the pathogenesis and cell biology of the highly adaptable diplomonad parasite S. salmonicida.      

    Delarbeten
    1. The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments
    Öppna denna publikation i ny flik eller fönster >>The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments
    Visa övriga...
    2014 (Engelska)Ingår i: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 10, nr 2, s. e1004053-Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Spironucleus salmonicida causes systemic infections in salmonid fish. It belongs to the group diplomonads, binucleated heterotrophic flagellates adapted to micro-aerobic environments. Recently we identified energy-producing hydrogenosomes in S. salmonicida. Here we present a genome analysis of the fish parasite with a focus on the comparison to the more studied diplomonad Giardia intestinalis. We annotated 8067 protein coding genes in the ∼12.9 Mbp S. salmonicida genome. Unlike G. intestinalis, promoter-like motifs were found upstream of genes which are correlated with gene expression, suggesting a more elaborate transcriptional regulation. S. salmonicida can utilise more carbohydrates as energy sources, has an extended amino acid and sulfur metabolism, and more enzymes involved in scavenging of reactive oxygen species compared to G. intestinalis. Both genomes have large families of cysteine-rich membrane proteins. A cluster analysis indicated large divergence of these families in the two diplomonads. Nevertheless, one of S. salmonicida cysteine-rich proteins was localised to the plasma membrane similar to G. intestinalis variant-surface proteins. We identified S. salmonicida homologs to cyst wall proteins and showed that one of these is functional when expressed in Giardia. This suggests that the fish parasite is transmitted as a cyst between hosts. The extended metabolic repertoire and more extensive gene regulation compared to G. intestinalis suggest that the fish parasite is more adapted to cope with environmental fluctuations. Our genome analyses indicate that S. salmonicida is a well-adapted pathogen that can colonize different sites in the host.

    Nationell ämneskategori
    Mikrobiologi Genetik
    Identifikatorer
    urn:nbn:se:uu:diva-224545 (URN)10.1371/journal.pgen.1004053 (DOI)000332021500041 ()24516394 (PubMedID)
    Tillgänglig från: 2014-05-14 Skapad: 2014-05-14 Senast uppdaterad: 2019-03-19Bibliografiskt granskad
    2. Comparative cell biology and evolution of Annexins in Diplomonads
    Öppna denna publikation i ny flik eller fönster >>Comparative cell biology and evolution of Annexins in Diplomonads
    Visa övriga...
    2016 (Engelska)Ingår i: MSphere, ISSN 2379-5042, Vol. 1, nr 2, artikel-id e00032-15Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Annexins are multifunctional, calcium-binding proteins found in organisms across all kingdoms. Most studies of annexins from single-celled eukaryotes have focused on the alpha-giardins, proteins assigned to the group E annexins, expressed by the diplomonad Giardia intestinalis. We have characterized the annexin gene family in another diplomonad parasite, Spironucleus salmonicida, by phylogenetic and experimental approaches. We constructed a comprehensive phylogeny of the diplomonad group E annexins and found that they are abundant across the group with frequent gene duplications and losses. The annexins of S. salmonicida were found to be related to alpha-giardins but with better-preserved type II Ca2+ coordination sites. Two annexins were confirmed to bind phospholipids in a Ca2+-dependent fashion but with different specificities. Superresolution and confocal microscopy of epitope-tagged S. salmonicida annexins revealed localization to distinct parts of the cytoskeleton and membrane. The ultrastructural details of the localization of several annexins were determined by proximity labeling and transmission electron microscopy. Two annexins localize to a novel cytoskeletal structure in the anterior of the cell. Our results show that the annexin gene family is expanded in diplomonads and that these group E annexins are associated mostly with cytoskeletal and membrane structures. IMPORTANCE Annexins are proteins that associate with phospholipids in a Ca2+-dependent fashion. These proteins have been intensely studied in animals and plants because of their importance in diverse cellular processes, yet very little is known about annexins in single-celled eukaryotes, which represent the largest diversity of organisms. The human intestinal parasite Giardia intestinalis is known to have more annexins than humans, and they contribute to its pathogenic potential. In this study, we investigated the annexin complement in the salmon pathogen Spironucleus salmonicida, a relative of G. intestinalis. We found that S. salmonicida has a large repertoire of annexins and that the gene family has expanded separately across diplomonads, with members showing sequence diversity similar to that seen across kingdom-level groups such as plants and animals. S. salmonicida annexins are prominent components of the cytoskeleton and membrane. Two annexins are associated with a previously unrecognized structure in the anterior of the cell.

    Ort, förlag, år, upplaga, sidor
    Uppsala: , 2016
    Nyckelord
    intestinal parasite, annexins, diplomonad, Spironucleus salmonicida, Giardia, proximity labeling, APEX
    Nationell ämneskategori
    Cellbiologi Mikrobiologi Evolutionsbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-264537 (URN)10.1128/mSphere.00032-15 (DOI)000392584700008 ()
    Forskningsfinansiär
    Vetenskapsrådet, 2012-3364Forskningsrådet Formas, 2013-910
    Tillgänglig från: 2015-10-14 Skapad: 2015-10-14 Senast uppdaterad: 2019-03-19Bibliografiskt granskad
    3. Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida
    Öppna denna publikation i ny flik eller fönster >>Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida
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    2019 (Engelska)Ingår i: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 17, nr 1, artikel-id 19Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    Background: Spironucleus salmonicida is an anaerobic parasite that can cause systemic infections in Atlantic salmon. Unlike other diplomonad parasites, such as the human pathogen Giardia intestinalis, Spironucleus species can infiltrate the blood stream of their hosts eventually colonizing organs, skin and gills. How this presumed anaerobe can persist and invade oxygenated tissues, despite having a strictly anaerobic metabolism, remains elusive.

    Results: To investigate how S. salmonicida response to oxygen stress, we performed RNAseq transcriptomic analyses of cells grown in the presence of oxygen or antioxidant-free medium. We found that over 20% of the transcriptome is differentially regulated in oxygen (1705 genes) and antioxidant-depleted (2280 genes) conditions. These differentially regulated transcripts encode proteins related to anaerobic metabolism, cysteine and Fe-S cluster biosynthesis, as well as a large number of proteins of unknown function. S. salmonicida does not encode genes involved in the classical elements of oxygen metabolism (e.g., catalases, superoxide dismutase, glutathione biosynthesis, oxidative phosphorylation). Instead, we found that genes encoding bacterial-like oxidoreductases were upregulated in response to oxygen stress. Phylogenetic analysis revealed some of these oxygen-responsive genes (e.g., nadh oxidase, rubrerythrin, superoxide reductase) are rare in eukaryotes and likely derived from lateral gene transfer (LGT) events into diplomonads from prokaryotes. Unexpectedly, we observed that many host evasion- and invasion-related genes were also upregulated under oxidative stress suggesting that oxygen might be an important signal for pathogenesis.

    Conclusion: While oxygen is toxic for related organisms, such as G. intestinalis, we find that oxygen is likely a gene induction signal for host invasion- and evasion-related pathways in S. salmonicida. These data provide the first molecular evidence for how S. salmonicida could tolerate oxic host environments and demonstrate how LGT can have a profound impact on the biology of anaerobic parasites.

    Nyckelord
    Anaerobiosis, Diplomonads, Giardia, Lateral gene transfer, Oxygen stress, Parasitology, Protist, RNAseq, Spironucleosis, Spironucleus
    Nationell ämneskategori
    Biokemi och molekylärbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-378917 (URN)10.1186/s12915-019-0634-8 (DOI)000459961200001 ()
    Forskningsfinansiär
    EU, Europeiska forskningsrådet, 310039-PUZZLE_CELLStiftelsen för strategisk forskning (SSF)Vetenskapsrådet, 2015-04959Forskningsrådet Formas, 2016-00539
    Tillgänglig från: 2019-03-12 Skapad: 2019-03-12 Senast uppdaterad: 2019-03-22Bibliografiskt granskad
    4. Proximity Staining using Enzymatic Protein Tagging in Diplomonads
    Öppna denna publikation i ny flik eller fönster >>Proximity Staining using Enzymatic Protein Tagging in Diplomonads
    2019 (Engelska)Ingår i: mSphere, E-ISSN 2379-5042, Vol. 4, nr 2, artikel-id e00153-19Artikel i tidskrift (Refereegranskat) Published
    Abstract [en]

    The diplomonads are a group of understudied eukaryotic flagellates whose most prominent member is the human pathogen Giardia intestinalis. Methods commonly used in other eukaryotic model systems often require special optimization in diplomonads due to the highly derived character of their cell biology. We have optimized a proximity labeling protocol using pea ascorbate peroxidase (APEX) as a reporter for transmission electron microscopy (TEM), to enable study of ultrastructural cellular details in diplomonads. Currently available TEM-compatible tags requires light-induced activation (1, 2) or are inactive in many cellular compartments (3) while ascorbate peroxidase has not been shown to have those limitations. Here we have optimized the in vivo activity of two versions of pea ascorbate peroxidase (APXW41F and APEX) using the diplomonad fish parasite Spironucleus salmonicida, a relative of G. intestinalis. We exploited the well-known peroxidase substrates, Amplex UltraRed and 3,3’-diaminobenzidine (DAB), to validate the activity of the two tags and argue that APEX is the most stable version to use in Spironucleus salmonicida. Next, we fused APEX to proteins with established localization to evaluate the activity of APEX in different cellular compartments of the diplomonad cell and used Amplex UltraRed as well as antibodies along with super-resolution microscopy to confirm the protein-APEX localization. The ultrastructural details of protein-APEX fusions were determined by TEM and we observed marker activity in all cellular compartments tested when using the DAB substrate. Finally, we show that the optimized conditions established for S. salmonicida can be used in the related diplomonad G. intestinalis.

    Nationell ämneskategori
    Cellbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-379669 (URN)
    Forskningsfinansiär
    Forskningsrådet Formas, 2016-00539
    Tillgänglig från: 2019-03-19 Skapad: 2019-03-19 Senast uppdaterad: 2019-03-20
    5. Experimental challenge of Atlantic salmon (Salmo salar) with the diplomonad parasite Spironucleus salmonicida to characterize the infection cycle
    Öppna denna publikation i ny flik eller fönster >>Experimental challenge of Atlantic salmon (Salmo salar) with the diplomonad parasite Spironucleus salmonicida to characterize the infection cycle
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    Experimental infections were performed of Atlantic salmon (Salmo salar) from the Baltic Sea region with the Diplomonad fish parasite Spironucleus salmonicida in order to define the infection cycle, specifically the time-line and putative routes of transmission. An oral infection protocol using axenic parasites was developed, as were new diagnostic tools using PCR and specific antibodies. We also produced firefly luciferase expressing S. salmonicida parasites that could be identified in the infected fish using in vivo and ex vivo imaging. The new tools made it possible to follow the S. salmonicida infection cycle in detail. Three different stages of the infection were identified: one initial intestinal stage, followed by a blood stage and a final tissue stage. Parasites intubated into the intestine attached to the intestinal surface and were identified in the blood after 1-3 weeks. Skin lesions and infections of the muscles, internal organs and eyes were seen 4-10 weeks after initiation of infection. Several morphologically different forms of S. salmonicida cells were detected in ex vivo cell-cultures of biopsies from skin lesions. By this infection trial we have been able to show that S. salmonicida may use several alternative routes of transmission. One alternative is the fecal-oral route, similar to other Diplomonad parasites but the parasites can also be excreted directly into the surrounding water from the mucous layer of the skin or from an ulcerated skin lesion. This information can be used to prevent the transmission of the parasite in fish farms.

    Nyckelord
    Diplomonads, Spironucleus salmonis, Salmo salar, fish infection, pathology
    Nationell ämneskategori
    Mikrobiologi
    Identifikatorer
    urn:nbn:se:uu:diva-378925 (URN)
    Forskningsfinansiär
    Forskningsrådet Formas, 2016-00539
    Tillgänglig från: 2019-03-09 Skapad: 2019-03-09 Senast uppdaterad: 2019-03-19
    6. Dual transcriptomic analysis of Spironucleus salmonicida-infected salmon cells identifies putative virulence factors and host responses
    Öppna denna publikation i ny flik eller fönster >>Dual transcriptomic analysis of Spironucleus salmonicida-infected salmon cells identifies putative virulence factors and host responses
    Visa övriga...
    (Engelska)Manuskript (preprint) (Övrigt vetenskapligt)
    Nationell ämneskategori
    Biokemi och molekylärbiologi
    Identifikatorer
    urn:nbn:se:uu:diva-379666 (URN)
    Tillgänglig från: 2019-03-19 Skapad: 2019-03-19 Senast uppdaterad: 2019-03-19
  • 594.
    Åminne, Ann
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för kvinnors och barns hälsa.
    Evaluation of preanalytic methods in order to shorten the processing time before identification of fungal microorganisms by the MALDI-TOF MS2015Självständigt arbete på grundnivå (högskoleexamen), 10 poäng / 15 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Identification of fungi is based on macroscopic observations of morphology and microscopic characteristics. These conventional methods are time-consuming and requires expert knowledge. For the past years Matrix-assisted laser desorption ionization-time of flight mass spectrometry has been used for routine bacterial identification in clinical laboratories but not yet in the same extension for fungi. In this study three preanalytic preparation methods for fungi were evaluated in order to shorten the processing time in routine laboratory performance.

    Clinically relevant strains (n=18) of molds and dermatophytes were cultivated on agar plates and prepared according to the different preparation methods for protein extraction. Each strain was analyzed in quadruplicate by the MALDI Biotyper and the database Filamentous Fungi Library 1.0.

    The results showed that the genus and species identification rates of the least time-consuming direct extraction method were 33% and 11% respectively. Using the formic acid extraction method, the genus and species identification rates were 83% and 44%, respectively. For the longest sample preparation method, liquid media culturing before formic acid extraction, successfully identified all strains except one, which resulted in an identification rate of 94% and 78% respectively.

    This study shows that preparing samples in cultured liquid media MADLI-TOF MS effectively identified fungal strains to both genus- and species-level. This method was however too time-consuming and cumbersome to be recommended as a replacement to the conventional method. Future studies should be aimed at expanding the reference library and making the direct extraction method more reproducible in terms of obtaining more reliable identification rates.

9101112 551 - 594 av 594
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