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  • 1.
    Abbott, Jessica K.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Zooekologi.
    Bedhomme, Stéphanie
    Evolutionary Systems Virology Group, University of Valencia.
    Chippindale, Adam K.
    Biology Department, Queen's University.
    Sexual conflict in wing size and shape in Drosophila melanogaster2010Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 23, nr 9, 1989-1997 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Intralocus sexual conflict occurs when opposing selection pressures operate on loci expressed in both sexes, constraining the evolution of sexual dimorphism and displacing one or both sexes from their optimum. We eliminated intralocus conflict in Drosophila melanogaster by limiting transmission of all major chromosomes to males, thereby allowing them to win the intersexual tug-of-war. Here, we show that this male-limited (ML) evolution treatment led to the evolution (in both sexes) of masculinized wing morphology, body size, growth rate, wing loading, and allometry. In addition to more male-like size and shape, ML evolution resulted in an increase in developmental stability for males. However, females expressing ML chromosomes were less developmentally stable, suggesting that being ontogenetically more male-like was disruptive to development. We suggest that sexual selection over size and shape of the imago may therefore explain the persistence of substantial genetic variation in these characters and the ontogenetic processes underlying them.

  • 2.
    Abbott, Jessica K.
    et al.
    Queen's University.
    Gosden, Thomas P.
    Lund University.
    Correlated morphological and colour differences among females of the damselfly Ischnura elegans2009Inngår i: Ecological Entomology, ISSN 0307-6946, E-ISSN 1365-2311, Vol. 34, nr 3, 378-386 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    1. The female-limited colour polymorphic damselfly Ischnura elegans has proven to be an interesting study organism both as an example of female sexual polymorphism, and in the context of the evolution of colour polymorphism. The study of colour polymorphism can also have broader applications as a model of speciation processes.

    2. Previous research suggests that there exist correlations between colour morph and other phenotypic traits, and that the different female morphs in I. elegans may be pursuing alternative phenotypically integrated strategies. However, previous research on morphological differences in southern Swedish individuals of this species was only carried out on laboratory-raised offspring from a single population, leaving open the question of how widespread such differences are.

    3. We therefore analysed multi-generational data from 12 populations, investigating morphological differences between the female morphs in the field, differences in the pattern of phenotypic integration between morphs, and quantified selection on morphological traits.

    4. We found that consistent morphological differences did indeed exist between the morphs across all study populations, confirming that the previously observed differences were not simply a laboratory artefact.  We also found, somewhat surprisingly, that despite the existence of sexual dimorphism in body size and shape, patterns of phenotypic integration differed most between the morphs and not between the sexes. Finally, linear selection gradients showed that female morphology affected fecundity differently between the morphs.

    5. We discuss the relevance of these results to the male mimicry hypothesis and to the existence of potential ecological differences between the morphs.

  • 3.
    Abbott, Jessica K.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och evolution, Zooekologi.
    Svensson, Erik I.
    Lund University.
    Morph-specific variation in intersexual genetic correlations in an intra-specific mimicry system2010Inngår i: Evolutionary Ecology Research, ISSN 1522-0613, Vol. 12, nr 1, 105-118 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Positive intersexual genetic correlations are typically viewed as constraining the evolution of sexual dimorphism, when traits are subject to sexually antagonistic selection. Our study species, the damselfly Ischnura elegans, has a female-limited colour polymorphism with three female colour morphs (males are monomorphic), one of which is considered a male mimic.

    Question: Are there morph-specific differences in the magnitude of intersexual genetic correlations in I. elegans? Specifically, do male-mimic (Androchrome) females have higher intersexual genetic correlations for morphological traits than non-mimic (Infuscans) females?

    Methods: We collected copulating pairs in the field and raised offspring from these pairs in the laboratory. We measured five morphological traits in both parent and offspring generations and investigated their heritabilities and genetic correlations.

    Results: We found a negative overall relationship between the degree of sexual dimorphism for a trait and its intersexual genetic correlation. But the magnitude and direction of intersexual genetic correlations depended on the female morph. As expected, male mimic (Androchrome) females had higher intersexual genetic correlations. In addition, the genetic correlations between the morphs were in all cases significantly lower than unity. Male mimic (Androchrome) females had higher mother-son covariances than the non-mimic (Infuscans) morph, and this difference is the proximate explanation for the difference in intersexual genetic correlations between the morphs.

  • 4.
    Abbott, Jessica K.
    et al.
    Lund University.
    Svensson, Erik I.
    Lund University.
    Ontogeny of sexual dimorphism and phenotypic integration in heritable morphs2008Inngår i: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 22, nr 1, 103-121 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    In this study we investigated the developmental basis of adult phenotypes in a non-model organism, a polymorphic damselfly (Ischnura elegans) with three female colour morphs. This polymorphic species presents an ideal opportunity to study intraspecific variation in growth trajectories, morphological variation in size and shape during the course of ontogeny, and to relate these juvenile differences to the phenotypic differences of the discrete adult phenotypes; the two sexes and the three female morphs. We raised larvae of different families in individual enclosures in the laboratory, and traced morphological changes during the course of ontogeny. We used principal components analysis to examine the effects of Sex, Maternal morph, and Own morph on body size and body shape. We also investigated the larval fitness consequences of variation in size and shape by relating these factors to emergence success. Females grew faster than males and were larger as adults, and there was sexual dimorphism in body shape in both larval and adult stages. There were also significant effects of both maternal morph and own morph on growth rate and body shape in the larval stage. There were significant differences in body shape, but not body size, between the adult female morphs, indicating phenotypic integration between colour, melanin patterning, and body shape. Individuals that emerged successfully grew faster and had different body shape in the larval stage, indicating internal (non-ecological) selection on larval morphology. Overall, morphological differences between individuals at the larval stage carried over to the adult stage. Thus, selection in the larval stage can potentially result in correlated responses in adult phenotypes and vice versa.

  • 5.
    Abbott, Jessica K.
    et al.
    Lund University.
    Svensson, Erik I.
    Lund University.
    Phenotypic and genetic variation in emergence and development time of a trimorphic damselfly2005Inngår i: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 18, nr 6, 1464-1470 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although colour polymorphisms in adult organisms of many taxa are often adaptive in the context of sexual selection or predation, genetic correlations between colour and other phenotypic traits expressed early in ontogeny could also play an important role in polymorphic systems. We studied phenotypic and genetic variation in development time among female colour morphs in the polymorphic damselfly Ischnura elegans in the field and by raising larvae in a common laboratory environment. In the field, the three different female morphs emerged at different times. Among laboratory-raised families, we found evidence of a significant correlation between maternal morph and larval development time in both sexes. This suggests that the phenotypic correlation between morph and emergence time in the field has a parallel in a genetic correlation between maternal colour and offspring development time. Maternal colour morph frequencies could thus potentially change as correlated responses to selection on larval emergence dates. The similar genetic correlation in male offspring suggests that sex-limitation in this system is incomplete, which may lead to an ontogenetic sexual conflict between selection for early male emergence (protandry) and emergence times associated with maternal morph.

  • 6.
    Abuabaid, Hanan
    et al.
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Karlsson, Mattias
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Scherbak, Nikolai
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Olsson, Per-Erik
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Jass, Jana
    Örebro universitet, Institutionen för naturvetenskap och teknik.
    Probiotic Lactobacillus rhamnosus alters inflammatory responses of bladder epithelial and macrophage-like cells in co-cultureManuskript (preprint) (Annet vitenskapelig)
  • 7. Achouiti, Ahmed
    et al.
    Vogl, Thomas
    Urban, Constantin F
    Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Klinisk bakteriologi. Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    Röhm, Marc
    Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS). Umeå universitet, Medicinska fakulteten, Institutionen för klinisk mikrobiologi, Klinisk bakteriologi.
    Hommes, Tijmen J
    van Zoelen, Marieke AD
    Florquin, Sandrine
    Roth, Johannes
    van't Veer, Cornelis
    de Vos, Alex F
    van der Poll, Tom
    Myeloid-related protein-14 contributes to protective immunity in gram-negative pneumonia derived sepsis2012Inngår i: PLoS Pathogens, ISSN 1553-7374, Vol. 8, nr 10, e1002987- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Klebsiella (K.) pneumoniae is a common cause of pneumonia-derived sepsis. Myeloid related protein 8 (MRP8, S100A8) and MRP14 (S100A9) are the most abundant cytoplasmic proteins in neutrophils. They can form MRP8/14 heterodimers that are released upon cell stress stimuli. MRP8/14 reportedly exerts antimicrobial activity, but in acute fulminant sepsis models MRP8/14 has been found to contribute to organ damage and death. We here determined the role of MRP8/14 in K. pneumoniae sepsis originating from the lungs, using an established model characterized by gradual growth of bacteria with subsequent dissemination. Infection resulted in gradually increasing MRP8/14 levels in lungs and plasma. Mrp14 deficient (mrp14(-/-)) mice, unable to form MRP8/14 heterodimers, showed enhanced bacterial dissemination accompanied by increased organ damage and a reduced survival. Mrp14(-/-) macrophages were reduced in their capacity to phagocytose Klebsiella. In addition, recombinant MRP8/14 heterodimers, but not MRP8 or MRP14 alone, prevented growth of Klebsiella in vitro through chelation of divalent cations. Neutrophil extracellular traps (NETs) prepared from wildtype but not from mrp14(-/-) neutrophils inhibited Klebsiella growth; in accordance, the capacity of human NETs to kill Klebsiella was strongly impaired by an anti-MRP14 antibody or the addition of zinc. These results identify MRP8/14 as key player in protective innate immunity during Klebsiella pneumonia.

  • 8.
    Acuna, Lillian G.
    et al.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Pablo Cardenas, Juan
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Covarrubias, Paulo C.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Jose Haristoy, Juan
    Fundación Ciencia & Vida, Chile.
    Flores, Rodrigo
    Fundación Ciencia & Vida, Chile.
    Nuñez, Harold
    Fundación Ciencia & Vida, Chile.
    Riadi, Gonzalo
    Universidad de Talca, Chile.
    Shmaryahu, Amir
    Fundación Ciencia & Vida, Chile.
    Valdes, Jorge
    Center for Systems Biotechnology, Chile.
    Dopson, Mark
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    Rawlings, Douglas E.
    University of Stellenbosch, South Africa.
    Banfield, Jillian F.
    University of California, USA.
    Holmes, David S.
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Quatrini, Raquel
    Fundación Ciencia & Vida, Chile ; Universidad Andres Bello, Chile.
    Architecture and Gene Repertoire of the Flexible Genome of the Extreme Acidophile Acidithiobacillus caldus2013Inngår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 11, e78237Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. Principal Findings: Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions. Significance: For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.

  • 9. Adamsson, I
    et al.
    Edlund, Charlotta
    Södertörns högskola, Avdelning Naturvetenskap.
    Seensalu, R
    Engstrand, L
    The use of AP-PCR and flaA-RFLP typing to investigate treatment failure in Helicobacter pylori infection2000Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 6, nr 5, 265-267 s.Artikkel i tidsskrift (Fagfellevurdert)
  • 10.
    Adler, Lennart
    et al.
    Göteborgs universitet.
    Wadskog, Ingrid
    Högskolan i Jönköping, Tekniska Högskolan, JTH, Kemiteknik.
    Ion homeostasis in Saccharomyces cerevisiae under NaCl stress2003Inngår i: Yeast stress responses / [ed] Stefan Hohmann, Willem H. Mager, Berlin: Springer , 2003, 201-239 s.Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 11.
    Adler, Marlen
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Mechanisms and Dynamics of Carbapenem Resistance in Escherichia coli2014Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    The emergence of extended spectrum β-lactamase (ESBL) producing Enterobacteriaceae worldwide has led to an increased use of carbapenems and may drive the development of carbapenem resistance. Existing mechanisms are mainly due to acquired carbapenemases or the combination of ESBL-production and reduced outer membrane permeability. The focus of this thesis was to study the development of carbapenem resistance in Escherichia coli in the presence and absence of acquired β-lactamases. To this end we used the resistance plasmid pUUH239.2 that caused the first major outbreak of ESBL-producing Enterobacteriaceae in Scandinavia.

    Spontaneous carbapenem resistance was strongly favoured by the presence of the ESBL-encoding plasmid and different mutational spectra and resistance levels arose for different carbapenems. Mainly, loss of function mutations in the regulators of porin expression caused reduced influx of antibiotic into the cell and in combination with amplification of β-lactamase genes on the plasmid this led to high resistance levels. We further used a pharmacokinetic model, mimicking antibiotic concentrations found in patients during treatment, to test whether ertapenem resistant populations could be selected even at these concentrations. We found that resistant mutants only arose for the ESBL-producing strain and that an increased dosage of ertapenem could not prevent selection of these resistant subpopulations. In another study we saw that carbapenem resistance can even develop in the absence of ESBL-production. We found mutants in export pumps and the antibiotic targets to give high level resistance albeit with high fitness costs in the absence of antibiotics. In the last study, we used selective amplification of β-lactamases on the pUUH239.2 plasmid by carbapenems to determine the cost and stability of gene amplifications. Using mathematical modelling we determined the likelihood of evolution of new gene functions in this region. The high cost and instability of the amplified state makes de novo evolution very improbable, but constant selection of the amplified state may balance these factors until rare mutations can establish a new function.

    In my studies I observed the influence of β-lactamases on carbapenem resistance and saw that amplification of these genes would further contribute to resistance. The rapid disappearance of amplified arrays of resistance genes in the absence of antibiotic selection may lead to the underestimation of gene amplification as clinical resistance mechanism. Amplification of β-lactamase genes is an important stepping-stone and might lead to the evolution of new resistance genes.

  • 12.
    Adler, Marlen
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Anjum, Mehreen
    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.
    Sandegren, Linus
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Combinations of mutations in envZ, ftsI, mrdA, acrB and acrR can cause high-level carbapenem resistance in Escherichia coli2016Inngår i: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 71, nr 5, 1188-1198 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The worldwide spread of ESBL-producing Enterobacteriaceae has led to an increased use of carbapenems, the group of beta-lactams with the broadest spectrum of activity. Bacterial resistance to carbapenems is mainly due to acquired carbapenemases or a combination of ESBL production and reduced drug influx via loss of outer-membrane porins. Here, we have studied the development of carbapenem resistance in Escherichia coli in the absence of beta-lactamases. We selected mutants with high-level carbapenem resistance through repeated serial passage in the presence of increasing concentrations of meropenem or ertapenem for similar to 60 generations. Isolated clones were whole-genome sequenced, and the order in which the identified mutations arose was determined in the passaged populations. Key mutations were reconstructed, and bacterial growth rates of populations and isolated clones and resistance levels to 23 antibiotics were measured. High-level resistance to carbapenems resulted from a combination of downstream effects of envZ mutation and target mutations in AcrAB-TolC-mediated drug export, together with PBP genes [mrdA (PBP2) after meropenem exposure or ftsI (PBP3) after ertapenem exposure]. Our results show that antibiotic resistance evolution can occur via several parallel pathways and that new mechanisms may appear after the most common pathways (i.e. beta-lactamases and loss of porins) have been eliminated. These findings suggest that strategies to target the most commonly observed resistance mechanisms might be hampered by the appearance of previously unknown parallel pathways to resistance.

  • 13.
    Adler, Marlen
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Anjum, Mehreen
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Berg, Otto, G.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Beräknings- och systembiologi.
    Andersson, Dan I.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    Sandegren, Linus
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    High Fitness Costs and Instability of Gene Duplications Reduce Rates of Evolution of New Genes by Duplication-Divergence Mechanisms2014Inngår i: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, nr 6, 1526-1535 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [sv]

    An important mechanism for generation of new genes is by duplication-divergence of existing genes. Duplication-divergence includes several different sub-models, such as subfunctionalization where after accumulation of neutral mutations the original function is distributed between two partially functional and complementary genes, and neofunctionalization where a new function evolves in one of the duplicated copies while the old function is maintained in another copy. The likelihood of these mechanisms depends on the longevity of the duplicated state, which in turn depends on the fitness cost and genetic stability of the duplications. Here, we determined the fitness cost and stability of defined gene duplications/amplifications on a low copy number plasmid. Our experimental results show that the costs of carrying extra gene copies are substantial and that each additional kbp of DNA reduces fitness by approximately 0.15%. Furthermore, gene amplifications are highly unstable and rapidly segregate to lower copy numbers in absence of selection. Mathematical modelling shows that the fitness costs and instability strongly reduces the likelihood of both sub- and neofunctionalization, but that these effects can be off-set by positive selection for novel beneficial functions.

  • 14. Agvald-Öhman, C
    et al.
    Wernerman, J
    Nord, C E
    Edlund, Charlotta
    Södertörns högskola, Avdelning Naturvetenskap.
    Anaerobic bacteria commonly colonize the lower airways of intubated ICU patients2003Inngår i: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 9, nr 5, 397-405 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Objectives To investigate respiratory tract colonization by aerobic and anaerobic bacteria in mechanically ventilated patients. Methods Bacterial colonization of the stomach and the respiratory tract was qualitatively and quantitatively analyzed over time in 41 consecutive mechanically ventilated patients in a Swedish intensive care unit (ICU), with special emphasis on elucidation of the role of anaerobic bacteria in the lower respiratory tract. Samples were taken from the oropharynx, gastric juice, subglottic space and trachea within 24 h (median 14 h) of intubation, and then every third day until day 18 and every fifth day until day 33. Results The patients were often heavily colonized with microorganisms not considered to belong to a healthy normal oropharyngeal and gastric flora on admission to the ICU. A majority harbored enterococci, coagulase-negative staphylococci and Candida spp. in at least one site on day 1. Anaerobic bacteria, mainly peptostreptococci and Prevotella spp., were isolated from subglottic and/or tracheal secretions in 59% of the patients. Different routes of tracheal colonization for different groups of microorganisms were found. Primary or concomitant colonization of the oropharynx with staphylococci, enterococci, enterobacteria and Candida was often seen, while Pseudomonas spp., other non-fermenting Gram-negative rods and several anaerobic species often primarily colonized the trachea, indicating exogenous or direct gastrointestinal routes of colonization. Conclusions Mechanically ventilated patients were heavily colonized in their lower airways by potential pathogenic microorganisms, including a high load of anaerobic bacteria. Different routes of colonization were shown for different species.

  • 15.
    Ah-King, Malin
    et al.
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Centrum för genusvetenskap.
    Barron, Andrew B.
    Herberstein, Marie E.
    Genital Evolution: Why Are Females Still Understudied?2014Inngår i: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 12, nr 5, e1001851- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The diversity, variability, and apparent rapid evolution of animal genitalia are a vivid focus of research in evolutionary biology, and studies exploring genitalia have dramatically increased over the past decade. These studies, however, exhibit a strong male bias, which has worsened since 2000, despite the fact that this bias has been explicitly pointed out in the past. Early critics argued that previous investigators too often considered only males and their genitalia, while overlooking female genitalia or physiology. Our analysis of the literature shows that overall this male bias has worsened with time. The degree of bias is not consistent between subdisciplines: studies of the lock-and-key hypothesis have been the most male focused, while studies of cryptic female choice usually consider both sexes. The degree of bias also differed across taxonomic groups, but did not associate with the ease of study of male and female genital characteristics. We argue that the persisting male bias in this field cannot solely be explained by anatomical sex differences influencing accessibility. Rather the bias reflects enduring assumptions about the dominant role of males in sex, and invariant female genitalia. New research highlights how rapidly female genital traits can evolve, and how complex coevolutionary dynamics between males and females can shape genital structures. We argue that understanding genital evolution is hampered by an outdated single-sex bias.

  • 16.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Can fossils illuminate the evolution of gnathostome head development?2006Inngår i: European Society for Evolutionary Developmental Biology: The First and Founding Meeting, August 2006, Prague, 2006, 363- s.Konferansepaper (Annet (populærvitenskap, debatt, mm))
  • 17.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    CT scanning the nose of Eusthenopteron.2006Inngår i: Journal of Vertebrate Paleontology, ISSN 0272-4634, Vol. 26, nr 3(supplement), 35A- s.Artikkel i tidsskrift (Annet vitenskapelig)
  • 18.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Fossils, developmental patterning and the origin of tetrapods.2003Inngår i: The new panorama of animal evolution, Pensoft Publishers, Sofia, Bulgaria , 2003, 45-54 s.Kapittel i bok, del av antologi (Fagfellevurdert)
  • 19.
    Ahlberg, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Clack, Jennifer
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    The axial skeleton of the Devonian tetrapod Ichthyostega.2005Inngår i: Nature, ISSN 0028-0836, Vol. 437, nr 7055, 137-140 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

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

  • 20.
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Fossils, developmental patterning and the origin of tetrapods2003Inngår i: The new panorama of animal evolution: Proceedings of the 18th international congress of zoology, Sofia and Moscow: Pensoft Publishers , 2003, 44-54 s.Kapittel i bok, del av antologi (Annet vitenskapelig)
  • 21.
    Ahlberg, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Friedman, Matt
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    New light on the earliest known tetrapod jaw.2005Inngår i: Journal of Vertebrate Paleontology, ISSN 0272-4634, Vol. 25, nr 3, 720-724 s.Artikkel i tidsskrift (Fagfellevurdert)
  • 22.
    Ahlberg, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi. Evolutionär organismbiologi.
    Köntges, Georgy
    Homologies and cell populations: a response to Sánchez-Villagra and Maier.2006Inngår i: Evolution and Development, ISSN 1520-541X, Vol. 8, 116-118 s.Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
  • 23.
    Ahlberg, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för fysiologi och utvecklingsbiologi, Evolutionär organismbiologi.
    Smith, Moya
    MRC Centre for Developmental Neurobiology, King's College London, London SE1 1UL, UK.
    Johanson, Zerina
    Department of Biological Sciences and MUCEP, Department of Earth and Planetary Sciences, Macquarie University, Sydney 2010, Australia.
    Developmental plasticity and disparity in early dipnoan (lungfish) dentitions.2006Inngår i: Evolution & Development, ISSN 1520-541X, E-ISSN 1525-142X, Vol. 8, nr 4, 331-349 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although the lungfish (Dipnoi) belong within the Osteichthyes, their dentitions are radically different from other osteichthyans. Lungfish dentitions also show a uniquely high structural disparity during the early evolution of the group, partly owing to the independent variation of odontogenic and odontoclastic processes that are tightly and stereotypically coordinated in other osteichthyans. We present a phylogenetic analysis of early lungfishes incorporating a novel approach to coding these process characters in preference to the resultant adult dental morphology. The results only partially resolve the interrelationships of Devonian dipnoans, but show that the widely discussed hypothesis of separate tooth-plated, dentine-plated, and denticulated lineages is unlikely to be true. The dipnoan status of Diabolepis is corroborated. Lungfish dentitions seem to have undergone extensive and nonparsimonious evolution during the early history of the group, but much of the resulting disparity can be explained by a modest number of evolutionary steps in the underlying developmental processes, those for dental formation (odontogenic) and those for the remodeling of dentine tissue (odontoclastic). Later in lungfish evolution, this disparity was lost as the group settled to a pattern of dental development that is just as stereotypic as, but completely different from, that of other osteichthyans.

  • 24.
    Ahlström, Anna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Testing the specificity of the pBAD arabinose reporter2017Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    The project highlights Salmonella enterica subspecies enterica serovar Typhimurium (S. Tm)'s ability to metabolize simple sugars released from dead commensal bacteria, by using the pBAD (araBAD promoter) system as a reporter of L-arabinose availability. Using bioinformatics and homology of conserved L-arabinose transporter genes shared in Escherichia coli K12 (E. coli) and S. Tm, we aimed to create a S. Tm mutant strain unable to obtain L-arabinose from it environment. During the projects course of time it was discovered that L-arabinose transporters are not a shared gene trait between E. coli and S. Tm, and that putative L-arabinose transporter orthologues may exists in the S. Tm genome.

    Fulltekst tilgjengelig fra 2018-06-30 15:30
  • 25.
    Ahmad, Irfan
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
    Rouf, Syed Fazle
    Sun, Lei
    Cimdins, Annika
    Shafeeq, Sulman
    Le Guyon, Soazig
    Schottkowski, Marco
    Rhen, Mikael
    Romling, Ute
    BcsZ inhibits biofilm phenotypes and promotes virulence by blocking cellulose production in Salmonella enterica serovar Typhimurium2016Inngår i: Microbial Cell Factories, ISSN 1475-2859, E-ISSN 1475-2859, Vol. 15, 177Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Background: Cellulose, a 1,4 beta-glucan polysaccharide, is produced by a variety of organisms including bacteria. Although the production of cellulose has a high biological, ecological and economical impact, regulatory mechanisms of cellulose biosynthesis are mostly unknown. Family eight cellulases are regularly associated with cellulose biosynthesis operons in bacteria; however, their function is poorly characterized. In this study, we analysed the role of the cellulase BcsZ encoded by the bcsABZC cellulose biosynthesis operon of Salmonella enterica serovar Typhimurium (S. Typhimurium) in biofilm related behavior. We also investigated the involvement of BcsZ in pathogenesis of S. Typhimurium including a murine typhoid fever infection model. Result: In S. Typhimurium, cellulase BcsZ with a putative periplasmic location negatively regulates cellulose biosynthesis. Moreover, as assessed with a non-polar mutant, BcsZ affects cellulose-associated phenotypes such as the rdar biofilm morphotype, cell clumping, biofilm formation, pellicle formation and flagella-dependent motility. Strikingly, although upregulation of cellulose biosynthesis was not observed on agar plate medium at 37 degrees C, BcsZ is required for efficient pathogen-host interaction. Key virulence phenotypes of S. Typhimurium such as invasion of epithelial cells and proliferation in macrophages were positively regulated by BcsZ. Further on, a bcsZ mutant was outcompeted by the wild type in organ colonization in the murine typhoid fever infection model. Selected phenotypes were relieved upon deletion of the cellulose synthase BcsA and/or the central biofilm activator CsgD. Conclusion: Although the protein scaffold has an additional physiological role, our findings indicate that the catalytic activity of BcsZ effectively downregulates CsgD activated cellulose biosynthesis. Repression of cellulose production by BcsZ subsequently enables Salmonella to efficiently colonize the host.

  • 26.
    Ahmed, Engy
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Holmström, Sara
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Soil Microorganisms and Mineral Weathering: Mechanics of Biotite Dissolution2012Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Soil microorganisms play an important role in the environment by contributing to leach and release of essential elements from soil minerals that are required not only for their own nutrition but also for plants growth. This study aims to compare between the mechanisms of different fungal and bacterial species isolated from podzol soil in biotite dissolution. Microplate devices with 6 wells were used for the biological weathering experiments. All of the sterilized microplate wells were filled with 4g/l of biotite followed by 12 ml of an iron free diluted mineral liquid medium. In these conditions, biotite particles are the only source of the essential elements for the microorganisms. To characterize the mechanisms of biotite dissolution, we monitored siderophores production, microbial biomass, pH, exchangeable cations concentration and SEM analysis for mineral surface. There was a significant difference between the behavior of the fungal and bacterial species in dissolution of biotite. This difference may be due to the variation of these microorganisms in their mechanics of interaction with mineral surface. It was observed also that these microorganisms directly and indirectly induce biotite dissolution. Defining soil as a system driven by biological mechanisms rather than chemical processes has major implications for our understanding of how the system functions and how it will respond to changing conditions.

  • 27.
    Ahmed, Engy
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Holmström, Sara
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    THE MICROBE-MINERAL INTERACTIONS IN THE ACIDIC PODZOL SOIL2013Inngår i: Mineralogical magazine, ISSN 0026-461X, E-ISSN 1471-8022, Vol. 77, nr 5, 564- s.Artikkel i tidsskrift (Annet (populærvitenskap, debatt, mm))
    Abstract [en]

    Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies, like siderophores, which are operationally defined as low-molecular-mass biogenic Fe(III)-binding compounds, that can increase iron’s bioavailability by promoting the dissolution of iron-bearing minerals. In the present study, we aimed to investigate the composition of hydroxamate siderophores in the soil horizons of the acidic podzol, and study how they are affected by the presence of specific mineral types and microbial communities.

     Three different minerals (apatite, biotite and oligioclase) were inserted in the soil horizons (O (organic), E (eluvial), B (upper illuvial), and C (mineral)). After two years, soil samples were collected from both the bulk soil (next to the minerals) and from the soil attached to the mineral surfaces. The concentration of ten different fungal tri-hydroxamates and five bacterial ones were determined by high-performance liquid chromatography coupled to electrospray ionization mass spectrometry (HPLC-ESI-MS). In addition, total microbial composition and diversity were studied.

    Our field experiment succeeded in describing the relationship between the presence of siderophores, soil horizon and mineral type, in addition to understanding the interaction between mineral type and soil microbial composition. A wide range of fungal and bacterial hydroxamates were detected throughout the soil profile. On the other hand, the presence of the minerals completely altered the diversity of siderophores. In addition, each mineral had a unique interaction with hydroxamates in the different soil horizons. There were also a good relationship between the microbial diversity and the siderophore distribution. 

  • 28.
    Ahmed, Engy
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Holmström, Sara
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    The Roles and Applications of Siderophores in Natural Environments2013Konferansepaper (Annet vitenskapelig)
    Abstract [en]

    Siderophores are organic compounds with low molecular mass that are produced by microorganisms growing under conditions of low iron. The primary function of these compounds is to chelate ferric iron from different terrestrial and aquatic habitats and thereby make it available for microbial cells.

    Siderophores have received much attention in recent years because of their potential roles and applications in various areas of environmental research. For instance, the production of siderophores can provide a quick identification of microbes to the species level that called “siderotyping”. On the other hand, siderophores could also function as biocontrol, biosensor, and bioremediation agents, in addition to their important role in mineral weathering and enhancing plant growth. In the present study, we aimed to investigate the composition of trihydroxamate siderophores in soil samples from different horizons (O (organic), E (eluvial), B (upper illuvial), and C (parent material)) of a podzol soil in Sweden, and study how they are affected by the presence of specific mineral types (apatite, biotite and oligioclase) that were inserted in the soil for two years in a field experiment.

    Our field experiment succeeded in describing the relationship between the presence of siderophores, soil horizons and mineral types. A wide range of fungal and bacterial hydroxamates were detected throughout the soil profile. On the other hand, the presence of the minerals completely altered the diversity of siderophores. In addition, each mineral had a unique interaction with hydroxamates in the different soil horizons. Our next step is to gain greater insight into the siderotyping to illustrate the relationship between the siderophore types that was found throughout the soil profile and on the different mineral surfaces and the microbial diversity by using metagenomic applications.

  • 29.
    Ahmed, Engy
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Holmström, Sara
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Brüchert, Volker
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    Holm, Nils G.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för geologiska vetenskaper.
    The Role of Microorganisms in the diversity and distribution of siderophores in Podzolic Forest Soil2013Inngår i: Mineralogical magazine, ISSN 0026-461X, E-ISSN 1471-8022, Vol. 77, nr 2, 161--208(48) s.Artikkel i tidsskrift (Annet vitenskapelig)
    Abstract [en]

    Iron is a key component of the chemical architecture of the biosphere. Due to the low bioavailability of iron in the environment, microorganisms have developed specific uptake strategies. The most important one is the production of siderophores, which are operationally defined as low-molecular-mass biogenic Fe (III)-binding compounds which may greatly increase bioavailability of Fe [1]. One of the primary biogeochemical functions of siderophores is therefore to increase Fe bioavailability by promoting the dissolution of iron-bearing minerals [2]. This study aims to understand the role of microorganisms in the chemical diversity and distribution of siderophores in podzol soil and how this diversity can contribute to the bioavailability of Fe in forest soil.Soil samples were collected from an experimental site in the area of Bispgården in central Sweden (63°07′N, 16°70′E) from the O (organic), E (eluvial), B1 (upper illuvial), and C (mineral) horizons. Concentration and chemical composition of dissolved and adsorbed siderophores in the soil samples were determined using colorimetric assays and high-performance liquid chromatography.The highest siderophore concentrations were found in the O layer and thereafter decreased by depth. Concentrations of dissolved hydroxamate, catecholate and carboxylate siderophores were up to 84, 17 and 0.2 nmol/ g soil, respectively. In contrast, concentrations of adsorbed hydroxamates, catecholates and carboxylates were only up to 1.8, 3 and 0.2 nmol/ g soil, respectively.Siderophore-producing microorganisms were isolated from the same soil samples. Viable fungi, bacteria and actinomycete counts ranged from 7 to 300, from 300 to 1800, and from 0 to 5 cfu/gm, respectively. The highest counts were found in the O and E layers. Only the E layer contained the three types of siderophore-producing microorganisms investigated in this study. Siderophores were extracted from culture filtrates of the isolated microorganisms when grown under iron-limited conditions. These extracts varied considerably in siderophore composition. Fungal isolates produced up to 183 μM of hydroxamates, especially those isolated from the O layer, whereas bacteria and actinomycete isolated from the O and E layers of the soil produced high amounts of carboxylate, catecholate and hydroxamate siderophores. Actinomycete produced up to 93 μM of hydroxamates and 47 μM of catecholates, while bacteria produced up to 34 μM of carboxylates and up to 14 μM of catecholates.The depth variability in concentration and chemical composition and the good correlation between abundance of siderophore-producing microorganisms and siderophore soil concentrations strongly suggest that these siderophore-producing microorganisms play an important role in the mobilization of iron in the podzol soil that may be important in iron availability to plants in forest environment.

    [1] Clay et al. (1981) Biochemistry 20, 2432-2436. [2] Duckworth et al. (2009) ChemGeol 260, 149-158.

  • 30.
    Ahmed Osman, Omneya
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Beier, Sara
    Leibniz Inst Balt Sea Res, Warnemunde, Germany..
    Grabherr, Manfred
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Bertilsson, Stefan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Interactions of Freshwater Cyanobacteria with Bacterial Antagonists2017Inngår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 83, nr 7, UNSP e02634Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Cyanobacterial and algal mass development, or blooms, have severe effects on freshwater and marine systems around the world. Many of these phototrophs produce a variety of potent toxins, contribute to oxygen depletion, and affect water quality in several ways. Coexisting antagonists, such as cyanolytic bacteria, hold the potential to suppress, or even terminate, such blooms, yet the nature of this interaction is not well studied. We isolated 31 cyanolytic bacteria affiliated with the genera Pseudomonas, Stenotrophomonas, Acinetobacter, and Delftia from three eutrophic freshwater lakes in Sweden and selected four phylogenetically diverse bacterial strains with strong-to-moderate lytic activity. To characterize their functional responses to the presence of cyanobacteria, we performed RNA sequencing (RNA-Seq) experiments on coculture incubations, with an initial predator-prey ratio of 1: 1. Genes involved in central cellular pathways, stress-related heat or cold shock proteins, and antitoxin genes were highly expressed in both heterotrophs and cyanobacteria. Heterotrophs in coculture expressed genes involved in cell motility, signal transduction, and putative lytic activity. L, D-Transpeptidase was the only significantly upregulated lytic gene in Stenotrophomonas rhizophila EK20. Heterotrophs also shifted their central metabolism from the tricarboxylic acid cycle to the glyoxylate shunt. Concurrently, cyanobacteria clearly show contrasting antagonistic interactions with the four tested heterotrophic strains, which is also reflected in the physical attachment to their cells. In conclusion, antagonistic interactions with cyanobacteria were initiated within 24 h, and expression profiles suggest varied responses for the different cyanobacteria and studied cyanolytes. IMPORTANCE Here, we present how gene expression profiles can be used to reveal interactions between bloom-forming freshwater cyanobacteria and antagonistic heterotrophic bacteria. Species-specific responses in both heterotrophs and cyanobacteria were identified. The study contributes to a better understanding of the interspecies cellular interactions underpinning the persistence and collapse of cyanobacterial blooms.

  • 31.
    Ainhoa, Moliner Morro
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi. Microbiology, Tumour and Cell Biology Department, Karolinska Institutet.
    Depicting the role of CD2AP during Old World alphavirus infection2017Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Fulltekst tilgjengelig fra 2018-01-01 16:00
  • 32.
    Akram, Neelam
    Linnéuniversitetet, Fakulteten för Hälso- och livsvetenskap (FHL), Institutionen för biologi och miljö (BOM).
    From genes to ecological function in marine bacteria2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Bacteria in the sea are constantly exposed to environmental challenges (e.g. variations in nutrient concentrations, temperature and light conditions), and therefore appropriate gene expression response strategies to cope with them efficiently are evolved. This thesis investigates some interconnected questions regarding such adaptive strategies employed by marine bacteria.

    The recently discovered ability of bacteria to use the membrane protein proteorhodopsin (PR) to harvest light energy for cell metabolism were investigated in Vibrio sp. AND4 and Dokdonia sp. MED134. PR phototrophy in AND4 promoted survival during starvation, the molecular basis for which were the upregulation of the PR gene by nutrient limitation rather than light. MED134, in contrast, uses PR phototrophy to grow better, and we discovered that the light-stimulated growth was stronger in seawater with the single carbon compound alanine compared to a mixture of complex organic matter. Thus, differences between bacteria in PR gene expression regulation in response to light, nutrients or organic matter quality critically determine the ecological role of PR phototrophy in the sea.

    Current observations that membrane transporters (including PR) are highly expressed in seawater inspired a comparative analysis of transporter distributions in marine bacteria. Totally, 192 transporter families were found in 290 genome-sequenced strains. Consistent differences, but also similarities, in the number of transporters were found between major bacterial groups. Interestingly, sodium transporters were found to be more abundant in PR-containing SAR11. These findings suggest that bacteria have inherently distinctive potentials to adapt to resource variations in the sea.

    To examine links between transcriptional responses and growth of bacteria under controlled environmental settings, a mesocosm phytoplankton bloom experiment was performed. Transcriptional analysis of the microbial community (i.e. metatranscriptomics) revealed 2800 categories of functional genes (SEED functions), of which around 10% were overrepresented in either the bloom mesocosms or the controls. Importantly, these functions indicated potential metabolic mechanisms (e.g. TonB mediated nutrient transport) by which bacteria took advantage of the bloom conditions.

    This thesis combines analyses of model organisms with community analysis and highlights the possibilities to identify important mechanisms that underlie the ecological success of different bacteria in the marine environment. 

  • 33.
    Akram, Neelam
    Linnéuniversitetet, Institutionen för biologi och miljö (BOM).
    From genes to ecological function in marine bacteria2013Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    Bacteria in the sea are constantly exposed to environmental challenges (e.g. variations in nutrient concentrations, temperature and light conditions), and therefore appropriate gene expression response strategies to cope with them efficiently are evolved. This thesis investigates some interconnected questions regarding such adaptive strategies employed by marine bacteria.

    The recently discovered ability of bacteria to use the membrane protein proteorhodopsin (PR) to harvest light energy for cell metabolism were investigated in Vibrio sp. AND4 and Dokdonia sp. MED134. PR phototrophy in AND4 promoted survival during starvation, the molecular basis for which were the upregulation of the PR gene by nutrient limitation rather than light. MED134, in contrast, uses PR phototrophy to grow better, and we discovered that the light-stimulated growth was stronger in seawater with the single carbon compound alanine compared to a mixture of complex organic matter. Thus, differences between bacteria in PR gene expression regulation in response to light, nutrients or organic matter quality critically determine the ecological role of PR phototrophy in the sea.

    Current observations that membrane transporters (including PR) are highly expressed in seawater inspired a comparative analysis of transporter distributions in marine bacteria. Totally, 192 transporter families were found in 290 genome-sequenced strains. Consistent differences, but also similarities, in the number of transporters were found between major bacterial groups. Interestingly, sodium transporters were found to be more abundant in PR-containing SAR11. These findings suggest that bacteria have inherently distinctive potentials to adapt to resource variations in the sea.

    To examine links between transcriptional responses and growth of bacteria under controlled environmental settings, a mesocosm phytoplankton bloom experiment was performed. Transcriptional analysis of the microbial community (i.e. metatranscriptomics) revealed 2800 categories of functional genes (SEED functions), of which around 10% were overrepresented in either the bloom mesocosms or the controls. Importantly, these functions indicated potential metabolic mechanisms (e.g. TonB mediated nutrient transport) by which bacteria took advantage of the bloom conditions.

    This thesis combines analyses of model organisms with community analysis and highlights the possibilities to identify important mechanisms that underlie the ecological success of different bacteria in the marine environment. 

  • 34.
    Alexeyev, O. A.
    et al.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi.
    Jahns, A. C.
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk biovetenskap, Patologi.
    Sampling and detection of skin Propionibacterium acnes: Current status2012Inngår i: Anaerobe, ISSN 1075-9964, E-ISSN 1095-8274, Vol. 18, nr 5, 479-483 s.Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    A connection between acne vulgaris and Propionibacterium acnes has long been suggested. Over the years, several human skin microbiota sampling methods have been evolved and applied, e.g. swab, scrape, extraction techniques including cyanoacrylate gel sampling as well as punch biopsy. Collected samples have been processed following various methodologies ranging from culture studies to probe labelling and molecular analysis. Direct visualization techniques have recently shown the existence of anatomically distinct skin P acnes populations: epidermal and follicular. P. acnes biofilms appear to be a common phenomenon. Current sampling approaches target different skin populations of P. acnes and the presence of microbial biofilms can influence the retrieval of P. acnes. The anatomical considerations must be taken into account while interpreting microbiological data. (C) 2012 Elsevier Ltd. All rights reserved.

  • 35.
    Allkja, Jontana
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinsk biokemi och mikrobiologi.
    The influence of copper on mast cell during bacterial infections2017Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
    Abstract [en]

    Mast cells are innate immune cells generally known for their harmful effects, particularly their role in asthma and autoimmune diseases. However, they can also recognize pathogens and mount a response to them. Copper is essential for proper cell function and homeostasis. Research has shown that changes in copper levels can affect mast cell morphology and gene expression of many of its immune mediators. It has also been shown that the copper transporter Ctr2 plays an important role in mast cell physiology. In this project, we investigated whether the same effects can be seen when mast cells are stimulated with bacteria, namely Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli). For this purpose, wild type and Ctr2 knockout mast cells were treated with different concentrations of copper for 72 hours and later co-cultured with either S. aureus or E. coli. Wild type cells were also treated with a copper chelator to investigate the effect of copper starvation. Release of IL-6 and CCL2, two common mediators released in response to bacteria, were measured by ELISA, while their gene expression was measured by qPCR. Results showed that either copper starvation or, 10 μM copper cause an increase in IL-6 and CCL2 protein levels, but have no effect on gene expression. The 10 μM copper effect was not observed in the Ctr2 knockout cells. In conclusion, not much is known about the mechanisms involved in the mast cell response to bacteria. However, it appears that copper can affect either different stages of the same pathway, or different pathways in a similar manner.

  • 36.
    Almeida, Rafael M.
    et al.
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Nobrega, Gabriel N.
    Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Ciencia Solo, Piracicaba, Brazil..
    Junger, Pedro C.
    Univ Fed Rio de Janeiro, Lab Limnol, Rio De Janeiro, Brazil..
    Figueiredo, Aline V.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Andrade, Anizio S.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    de Moura, Caroline G. B.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Tonetta, Denise
    Univ Fed Santa Catarina, Lab Freshwater Ecol, Florianopolis, SC, Brazil..
    Oliveira, Ernandes S., Jr.
    Radboud Univ Nijmegen, Dept Aquat Ecol & Environm Biol, Inst Water & Wetland Res, NL-6525 ED Nijmegen, Netherlands..
    Araujo, Fabiana
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Rust, Felipe
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Pineiro-Guerra, Juan M.
    Univ Republica, Dept Ecol Teor & Aplicada, Ctr Univ Reg Este, Montevideo, Uruguay.;Univ Republica, Fac Ciencias, Montevideo, Uruguay..
    Mendonca, Jurandir R., Jr.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Medeiros, Leonardo R.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Pinheiro, Lorena
    Univ Fed Estado Rio de Janeiro, Dept Ciencias Nat, Rio De Janeiro, Brazil..
    Miranda, Marcela
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Costa, Mariana R. A.
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Melo, Michaela L.
    Univ Fed Sao Carlos, Lab Microbial Proc & Biodivers, BR-13560 Sao Carlos, SP, Brazil..
    Nobre, Regina L. G.
    Univ Fed Rio Grande do Norte, Lab Limnol, BR-59072970 Natal, RN, Brazil..
    Benevides, Thiago
    Univ Fed Rio de Janeiro, Lab Limnol, Rio De Janeiro, Brazil..
    Roland, Fabio
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    de Klein, Jeroen
    Wageningen Univ, Aquat Ecol & Environm Sci, NL-6700 AP Wageningen, Netherlands..
    Barros, Nathan O.
    Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil..
    Mendonca, Raquel
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Limnologi. Univ Fed Juiz de Fora, Inst Ciencias Biol, Dept Biol, Aquat Ecol Lab, Juiz De Fora, Brazil.
    Becker, Vanessa
    Univ Fed Rio Grande do Norte, Lab Water Resources & Environm Sanitat, BR-59072970 Natal, RN, Brazil..
    Huszar, Veral. M.
    Univ Fed Rio de Janeiro, Museu Nacl, Lab Ficol, Rio De Janeiro, Brazil..
    Kosten, Sarian
    Radboud Univ Nijmegen, Dept Aquat Ecol & Environm Biol, Inst Water & Wetland Res, NL-6525 ED Nijmegen, Netherlands..
    High Primary Production Contrasts with Intense Carbon Emission in a Eutrophic Tropical Reservoir2016Inngår i: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, 717Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Recent studies from temperate lakes indicate that eutrophic systems tend to emit less carbon dioxide (Co-2) and bury more organic carbon (OC) than oligotrophic ones, rendering them CO2 sinks in some cases. However, the scarcity of data from tropical systems is critical for a complete understanding of the interplay between eutrophication and aquatic carbon (C) fluxes in warm waters. We test the hypothesis that a warm eutrophic system is a source of both CO2 and CH4 to the atmosphere, and that atmospheric emissions are larger than the burial of OC in sediments. This hypothesis was based on the following assumptions: (i) OC mineralization rates are high in warm water systems, so that water column CO2 production overrides the high C uptake by primary producers, and (ii) increasing trophic status creates favorable conditions for CH4 production. We measured water-air and sediment-water CO2 fluxes, CH4 diffusion, ebullition and oxidation, net ecosystem production (NEP) and sediment OC burial during the dry season in a eutrophic reservoir in the semiarid northeastern Brazil. The reservoir was stratified during daytime and mixed during nighttime. In spite of the high rates of primary production (4858 +/- 934 mg C m(-2) d(-1)), net heterotrophy was prevalent due to high ecosystem respiration (5209 +/- 992 mg C m(-2) d(-1)). Consequently, the reservoir was a source of atmospheric CO2 (518 +/- 182 mg C m(-2) d(-1)). In addition, the reservoir was a source of ebullitive (17 +/- 10 mg C m(-2) d(-1)) and diffusive CH4 (11 +/- 6 mg C m(-2) d(-1)). OC sedimentation was high (1162 mg C m(-2) d(-1)), but our results suggest that the majority of it is mineralized to CO2 (722 +/- 182 mg C m(-2) d(-1)) rather than buried as OC (440 mg C m(-2) d(-1)). Although temporally resolved data would render our findings more conclusive, our results suggest that despite being a primary production and OC burial hotspot, the tropical eutrophic system studied here was a stronger CO2 and CH4 source than a C sink, mainly because of high rates of OC mineralization in the water column and sediments.

  • 37. Alonso-Saez, L.
    et al.
    Vazquez-Dominguez, E.
    Cardelus, C.
    Pinhassi, Jarone
    Högskolan i Kalmar, Naturvetenskapliga institutionen.
    Sala, M. M.
    Lekunberri, I.
    Balague, V.
    Vila-Costa, M.
    Unrein, F.
    Massana, R.
    Simo, R.
    Gasol, J. M.
    Factors controlling the year-round variability in carbon flux through bacteria in a coastal marine system2008Inngår i: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 11, nr 3, 397-409 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Data from several years of monthly samplings are combined with a 1-year detailed study of carbon flux through bacteria at a NW Mediterranean coastal site to delineate the bacterial role in carbon use and to assess whether environmental factors or bacterial assemblage composition affected the in situ rates of bacterial carbon processing. Leucine (Leu) uptake rates [as an estimate of bacterial heterotrophic production (BHP)] showed high interannual variability but, on average, lower values were found in winter (around 50 pM Leu(-1) h(-1)) as compared to summer (around 150 pM Leu(-1) h(-1)). Leu-to-carbon conversion factors ranged from 0.9 to 3.6 kgC mol Leu(-1), with generally higher values in winter. Leu uptake was only weakly correlated to temperature, and over a full-year cycle (in 2003), Leu uptake peaked concomitantly with winter chlorophyll a (Chl a) maxima, and in periods of high ectoenzyme activities in spring and summer. This suggests that both low molecular weight dissolved organic matter (DOM) released by phytoplankton, and high molecular weight DOM in periods of low Chl a, can enhance BHP. Bacterial respiration (BR, range 7-48 mu g C l(-1) d(-1)) was not correlated to BHP or temperature, but was significantly correlated to DOC concentration. Total bacterial carbon demand (BHP plus BR) was only met by dissolved organic carbon produced by phytoplankton during the winter period. We measured bacterial growth efficiencies by the short-term and the long-term methods and they ranged from 3 to 42%, increasing during the phytoplankton blooms in winter (during the Chl a peaks), and in spring. Changes in bacterioplankton assemblage structure (as depicted by denaturing gradient gel electrophoresis fingerprinting) were not coupled to changes in ecosystem functioning, at least in bacterial carbon use.

  • 38. Alonso-Saéz, Laura
    et al.
    Waller, Allison S
    Mende, Daniel R
    Bakker, Kevin
    Farnelid, Hanna
    Linnéuniversitetet, Fakultetsnämnden för naturvetenskap och teknik, Institutionen för naturvetenskap, NV.
    Yager, Patricia L
    Lovejoy, Connie
    Tremblay, Jean-Eric
    Potvin, Marianne
    Heinrich, Friederike
    Estrada, Marta
    Riemann, Lasse
    Marine Biological Section, University of Copenhagen, 3000 Helsingør, Denmark .
    Bork, Peer
    Pedros-Alio, Carlos
    Bertilsson, Stefan
    Role for urea in nitrification by polar marine Archaea2012Inngår i: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, nr 44, 17989-17994 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Despite the high abundance of Archaea in the global ocean, their metabolism and biogeochemical roles remain largely unresolved. We investigated the population dynamics and metabolic activity of Thaumarchaeota in polar environments, where these microorganisms are particularly abundant and exhibit seasonal growth. Thaumarchaeota were more abundant in deep Arctic and Antarctic waters and grew throughout the winter at surface and deeper Arctic halocline waters. However, in situ single-cell activity measurements revealed a low activity of this group in the uptake of both leucine and bicarbonate (<5% Thaumarchaeota cells active), which is inconsistent with known heterotrophic and autotrophic thaumarchaeal lifestyles. These results suggested the existence of alternative sources of carbon and energy. Our analysis of an environmental metagenome from the Arctic winter revealed that Thaumarchaeota had pathways for ammonia oxidation and, unexpectedly, an abundance of genes involved in urea transport and degradation. Quantitative PCR analysis confirmed that most polar Thaumarchaeota had the potential to oxidize ammonia, and a large fraction of them had urease genes, enabling the use of urea to fuel nitrification. Thaumarchaeota from Arctic deep waters had a higher abundance of urease genes than those near the surface suggesting genetic differences between closely related archaeal populations. In situ measurements of urea uptake and concentration in Arctic waters showed that small-sized prokaryotes incorporated the carbon from urea, and the availability of urea was often higher than that of ammonium. Therefore, the degradation of urea may be a relevant pathway for Thaumarchaeota and other microorganisms exposed to the low-energy conditions of dark polar waters.

  • 39. Alriksson, B.
    et al.
    Rose, S. H.
    Van Zyl, W. H.
    Sjöde, A.
    Nilvebrant, N. -O
    RISE., STFI-Packforsk.
    Jönsson, L. J.
    Cellulase production from spent lignocellulose hydrolysates by recombinant aspergillus niger2009Inngår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 75, nr 8, 2366-2374 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A recombinant Aspergillus niger strain expressing the Hypocrea jecorina endoglucanase Cel7B was grown on spent hydrolysates (stillage) from sugarcane bagasse and spruce wood. The spent hydrolysates served as excellent growth media for the Cel7B-producing strain, A. niger D15[egI], which displayed higher endoglucanase activities in the spent hydrolysates than in standard medium with a comparable monosaccharide content (e.g., 2,100 nkat/ml in spent bagasse hydrolysate compared to 480 nkat/ml in standard glucose-based medium). In addition, A. niger D15[egI] was also able to consume or convert other lignocellulose-derived compounds, such as acetic acid, furan aldehydes, and phenolic compounds, which are recognized as inhibitors of yeast during ethanolic fermentation. The results indicate that enzymes can be produced from the stillage stream as a high-value coproduct in secondgeneration bioethanol plants in a way that also facilitates recirculation of process water.

  • 40.
    Alström, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Teknisk-naturvetenskapliga fakulteten, Biologiska sektionen, Institutionen för evolutionsbiologi, Systematisk zoologi.
    Species Limits and Systematics in Some Passerine Birds2002Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    I use morphological, vocal, molecular, behavioural, ecological and distributional data to re-evaluate the systematics of three passerine bird groups, the Mirafraassamica complex (bush-larks), the genus Seicercus ("spectacled-warblers"; with emphasis on the the S. burkii complex) and the genus Motacilla (wagtails). Two new species are described: Seicercus soror and Motacilla samveasnae. I propose that the polytypic species M. assamica should be treated as four separate species: M. assamica, M. affinis, M. microptera and M. marionae (it is also remarked that the proper name of the latter is M. erythrocephala). That is primarily supported by vocalisations and mitochondrial DNA. The latter data set also suggests that M. assamica sensu lato is paraphyletic, since M. erythroptera, which is always treated as a separate species, is nested within the M. assamica complex. I propose that the polytypic species S. burkii comprises six sibling species. Some of these are found to breed sympatrically, although mainly or entirely segregated altitudinally. Mitochondrial DNA suggests that the S. burkii complex is non-monophyletic, and also that the divergence of the different taxa is much older than indicated by morphological and vocal data. According to the molecular phylogeny, both the genera Seicercus and its assumed sister genus Phylloscopus are paraphyletic. That is corroborated by independent data. The phylogenetic study of the genus Motacilla reveals incongruence between mitochondrial DNA, nuclear DNA and non-molecular data. I conclude that the nuclear gene tree reflects the organismal phylogeny more faithfully than the mitochondrial gene tree. The latter is likely to have been affected by introgressive hybridisation, possibly also stochastic lineage sorting. The most remarkable result that is strongly supported by both mitochondrial and nuclear DNA is that M. flava is non-monophyletic.

  • 41.
    Altgård, Sofia
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Berggren, Sofia
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Björklund, Viktor
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Lundsten, Sara
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Olafsson, Thorsteinn
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Pettersson, Lovisa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Ett nytt multiplext PCR-protokoll för identifiering och detektion av Shigella och enteroinvasiv E. coli (EIEC) från livsmedel2014Independent thesis Basic level (degree of Bachelor), 10 poäng / 15 hpOppgave
    Abstract [en]

    This report is the result of a project in the course Independent Projekt in Molecular Biotechnology at Uppsala University during the spring of 2014. The foremost purpose of the course is to give students the opportunity to carry through exstensive work in a project environment. This project was formed based on a comission from the biotechnology company SweTree Technologies, and the goal has been to compose a summary of the different techniques and methods that exist in the field of mass propagation of trees through the method of somatic embryogenesis.

    The project group has obtained information about the area mainly throgh reading patents, trying to find key components and bottlenecks in other companies’ somatic embryogenesis technologies. This paper is divided into different sections, containing the patents of the automation of different steps in the process. This is to make it easier for readers to find information about the area they are interested in, as well as to illustrate the main parts of the process as percieved by the project group.

    Currently, there are several automated solutions for almost every step in the process, some of which are already in use. All the information obtained shows that the cost and labour has decreased with the development of this technology. While there is still room for significant devolopment in order to produce a complete automated process, there is no doubt that this method is becoming an ever more important asset in the area of forestry. Our hope is that this report may be a useful tool for companies or laymen to geta grasp of the field of automated mass production of trees.

  • 42. Alvarez, Beatriz
    et al.
    Krogh-Andersen, Kasper
    Tellgren-Roth, Christian
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi.
    Martinez, Noelia
    Guenaydin, Goekce
    Lin, Yin
    Cruz Martin, M.
    Alvarez, Miguel A.
    Hammarstroem, Lennart
    Marcotte, Harold
    An Exopolysaccharide-Deficient Mutant of Lactobacillus rhamnosus GG Efficiently Displays a Protective Llama Antibody Fragment against Rotavirus on Its Surface2015Inngår i: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 81, nr 17, 5784-5793 s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Rotavirus is the leading cause of infantile diarrhea in developing countries, where it causes a high number of deaths among infants. Two vaccines are available, being highly effective in developed countries although markedly less efficient in developing countries. As a complementary treatment to the vaccines, a Lactobacillus strain producing an anti-rotavirus antibody fragment in the gastrointestinal tract could potentially be used. In order to develop such an alternative therapy, the effectiveness of Lactobacillus rhamnosus GG to produce and display a VHH antibody fragment (referred to as anti-rotavirus protein 1 [ARP1]) on the surface was investigated. L. rhamnosus GG is one of the best-characterized probiotic bacteria and has intrinsic antirotavirus activity. Among four L. rhamnosus GG strains [GG (CMC), GG (ATCC 53103), GG (NCC 3003), and GG (UT)] originating from different sources, only GG (UT) was able to display ARP1 on the bacterial surface. The genomic analysis of strain GG (UT) showed that the genes welE and welF of the EPS cluster are inactivated, which causes a defect in exopolysaccharide (EPS) production, allowing efficient display of ARP1 on its surface. Finally, GG (UT) seemed to confer a level of protection against rotavirus-induced diarrhea similar to that of wild-type GG (NCC 3003) in a mouse pup model, indicating that the EPS may not be involved in the intrinsic antirotavirus activity. Most important, GG (EM233), a derivative of GG (UT) producing ARP1, was significantly more protective than the control strain L. casei BL23.

  • 43.
    Alvarez, Laura
    et al.
    Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS). Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Hernandez, Sara B
    Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS). Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    de Pedro, Miguel A
    Cava, Felipe
    Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS). Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Ultra-Sensitive, High-Resolution Liquid Chromatography Methods for the High-Throughput Quantitative Analysis of Bacterial Cell Wall Chemistry and Structure2016Inngår i: Bacterial Cell Wall Homeostasis: Methods and Protocols / [ed] Hee-Jeon Hong, New York: Springer Science+Business Media B.V., 2016, Vol. 1440, 11-27 s.Kapittel i bok, del av antologi (Fagfellevurdert)
    Abstract [en]

    High-performance liquid chromatography (HPLC) analysis has been critical for determining the structural and chemical complexity of the cell wall. However this method is very time consuming in terms of sample preparation and chromatographic separation. Here we describe (1) optimized methods for peptidoglycan isolation from both Gram-negative and Gram-positive bacteria that dramatically reduce the sample preparation time, and (2) the application of the fast and highly efficient ultra-performance liquid chromatography (UPLC) technology to muropeptide separation and quantification. The advances in both analytical instrumentation and stationary-phase chemistry have allowed for evolved protocols which cut run time from hours (2-3 h) to minutes (10-20 min), and sample demands by at least one order of magnitude. Furthermore, development of methods based on organic solvents permits in-line mass spectrometry (MS) of the UPLC-resolved muropeptides. Application of these technologies to high-throughput analysis will expedite the better understanding of the cell wall biology.

  • 44.
    Amer, Ayad
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Costa, Tiago
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Farag, Salah
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet).
    Avican, Ummehan
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    Forsberg, Åke
    Umeå universitet, Medicinska fakulteten, Institutionen för molekylärbiologi (Medicinska fakulteten). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR). Umeå universitet, Medicinska fakulteten, Molekylär Infektionsmedicin, Sverige (MIMS).
    Francis, Matthew
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet). Umeå universitet, Medicinska fakulteten, Umeå Centre for Microbial Research (UCMR).
    Genetically engineered frameshifted YopN-TyeA chimeras influence type III secretion system function in Yersinia pseudotuberculosis2013Inngår i: PLoS ONE, ISSN 1932-6203, Vol. 8, nr 10, e77767- s.Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Type III secretion is a tightly controlled virulence mechanism utilized by many gram negative bacteria to colonize their eukaryotic hosts. To infect their host, human pathogenic Yersinia spp. translocate protein toxins into the host cell cytosol through a preassembled Ysc-Yop type III secretion device. Several of the Ysc-Yop components are known for their roles in controlling substrate secretion and translocation. Particularly important in this role is the YopN and TyeA heterodimer. In this study, we confirm that Y. pseudotuberculosis naturally produce a 42 kDa YopN-TyeA hybrid protein as a result of a +1 frame shift near the 3 prime of yopN mRNA, as has been previously reported for the closely related Y. pestis. To assess the biological role of this YopN-TyeA hybrid in T3SS by Y. pseudotuberculosis, we used in cis site-directed mutagenesis to engineer bacteria to either produce predominately the YopN-TyeA hybrid by introducing +1 frame shifts to yopN after codon 278 or 287, or to produce only singular YopN and TyeA polypeptides by introducing yopN sequence from Y. enterocolitica, which is known not to produce the hybrid. Significantly, the engineered 42 kDa YopN-TyeA fusions were abundantly produced, stable, and were efficiently secreted by bacteria in vitro. Moreover, these bacteria could all maintain functionally competent needle structures and controlled Yops secretion in vitro. In the presence of host cells however, bacteria producing the most genetically altered hybrids (+1 frameshift after 278 codon) had diminished control of polarized Yop translocation. This corresponded to significant attenuation in competitive survival assays in orally infected mice, although not at all to the same extent as Yersinia lacking both YopN and TyeA proteins. Based on these studies with engineered polypeptides, most likely a naturally occurring YopN-TyeA hybrid protein has the potential to influence T3S control and activity when produced during Yersinia-host cell contact.

  • 45.
    Amlinger, Lina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    The type I-E CRISPR-Cas system: Biology and applications of an adaptive immune system in bacteria2017Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    CRISPR-Cas systems are adaptive immune systems in bacteria and archaea, consisting of a clustered regularly interspaced short palindromic repeats (CRISPR) array and CRISPR associated (Cas) proteins. In this work, the type I-E CRISPR-Cas system of Escherichia coli was studied.

    CRISPR-Cas immunity is divided into three stages. In the first stage, adaptation, Cas1 and Cas2 store memory of invaders in the CRISPR array as short intervening sequences, called spacers. During the expression stage, the array is transcribed, and subsequently processed into small CRISPR RNAs (crRNA), each consisting of one spacer and one repeat. The crRNAs are bound by the Cascade multi-protein complex. During the interference step, Cascade searches for DNA molecules complementary to the crRNA spacer. When a match is found, the target DNA is degraded by the recruited Cas3 nuclease.

    Host factors required for integration of new spacers into the CRISPR array were first investigated. Deleting recD, involved in DNA repair, abolished memory formation by reducing the concentration of the Cas1-Cas2 expression plasmid, leading to decreased amounts of Cas1 to levels likely insufficient for spacer integration. Deletion of RecD has an indirect effect on adaptation. To facilitate detection of adaptation, a sensitive fluorescent reporter was developed where an out-of-frame yfp reporter gene is moved into frame when a new spacer is integrated, enabling fluorescent detection of adaptation. Integration can be detected in single cells by a variety of fluorescence-based methods. A second aspect of this thesis aimed at investigating spacer elements affecting target interference. Spacers with predicted secondary structures in the crRNA impaired the ability of the CRISPR-Cas system to prevent transformation of targeted plasmids. Lastly, in absence of Cas3, Cascade was successfully used to inhibit transcription of specific genes by preventing RNA polymerase access to the promoter.

    The CRISPR-Cas field has seen rapid development since the first demonstration of immunity almost ten years ago. However, much research remains to fully understand these interesting adaptive immune systems and the research presented here increases our understanding of the type I-E CRISPR-Cas system. 

  • 46.
    Amlinger, Lina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Hoekzema, Mirthe
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Wagner, E. Gerhart H.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Koskiniemi, Sanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Lundgren, Magnus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Quantification of CRISPR-Cas spacer integration using a fluorescent reporterManuskript (preprint) (Annet vitenskapelig)
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Larsson, Martin
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Koskiniemi, Sanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Lundgren, Magnus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Deletion of recD indirectly reduce adaptation in the type I-E CRISPR-Cas systemManuskript (preprint) (Annet vitenskapelig)
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    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Saunders, Sita J.
    Lundgren, Magnus
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för cell- och molekylärbiologi, Mikrobiologi.
    Backofen, Rolf
    Effect of spacer sequence on efficiency of Type I-E CRISPR-Cas systemsManuskript (preprint) (Annet vitenskapelig)
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    Fuhrman, J.A.
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    Högskolan i Kalmar, Naturvetenskapliga institutionen.
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    Bacterioplankton growth in seawater: I.Growth kinetics and cellular characteristics in seawater cultures1984Inngår i: Marine Ecology Progress Series, ISSN 0171-8630, E-ISSN 1616-1599, Vol. 18, 31-39 s.Artikkel i tidsskrift (Fagfellevurdert)
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    Host range, symbiotic effectiveness and nodulation competitiveness of some indigenous cowpea bradyrhizobia isolates from the transitional savannah zone of Ghana2008Inngår i: African Journal of Biotechnology, ISSN 1684-5315, Vol. 7, nr 8, 988-996 s.Artikkel i tidsskrift (Fagfellevurdert)
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