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  • 1.
    Abafogi, Abdurhaman Teyib
    et al.
    Sungkyunkwan Univ, South Korea.
    Kim, Jaewon
    Sungkyunkwan Univ, South Korea.
    Lee, Jinyeop
    Sungkyunkwan Univ, South Korea.
    Mohammed, Merem Omer
    Sungkyunkwan Univ, South Korea.
    van Noort, Danny
    Linköping University, Department of Physics, Chemistry and Biology, Biotechnology. Linköping University, Faculty of Science & Engineering. Univ Ljubljana, Slovenia; Univ Ingn and Tecnol UTEC, Peru.
    Park, Sungsu
    Sungkyunkwan Univ, South Korea; Sungkyunkwan Univ, South Korea; Sungkyunkwan Univ, South Korea.
    3D-Printed Modular Microfluidic Device Enabling Preconcentrating Bacteria and Purifying Bacterial DNA in Blood for Improving the Sensitivity of Molecular Diagnostics2020In: Sensors, E-ISSN 1424-8220, SENSORS, Vol. 20, no 4, article id 1202Article in journal (Refereed)
    Abstract [en]

    Molecular diagnostics for sepsis is still a challenge due to the presence of compounds that interfere with gene amplification and bacteria at concentrations lower than the limit of detection (LOD). Here, we report on the development of a 3D printed modular microfluidic device (3Dpm mu FD) that preconcentrates bacteria of interest in whole blood and purifies their genomic DNA (gDNA). It is composed of a W-shaped microchannel and a conical microchamber. Bacteria of interest are magnetically captured from blood in the device with antibody conjugated magnetic nanoparticles (Ab-MNPs) at 5 mL/min in the W-shaped microchannel, while purified gDNA of the preconcentrated bacteria is obtained with magnetic silica beads (MSBs) at 2 mL/min in the conical microchamber. The conical microchamber was designed to be connected to the microchannel after the capturing process using a 3D-printed rotary valve to minimize the exposure of the MSBs to interfering compounds in blood. The pretreatment process of spiked blood (2.5 mL) can be effectively completed within about 50 min. With the 3Dpm mu FD, the LOD for the target microorganism Escherichia coli O157:H7 measured by both polymerase chain reaction (PCR) with electrophoresis and quantitative PCR was 10 colony forming unit (CFU) per mL of whole blood. The results suggest that our method lowers the LOD of molecular diagnostics for pathogens in blood by providing bacterial gDNA at high purity and concentration.

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  • 2.
    Abbott, Jessica K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    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 melanogaster2010In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 23, no 9, p. 1989-1997Article in journal (Refereed)
    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.

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  • 3.
    Abbott, Jessica K.
    et al.
    Queen's University.
    Gosden, Thomas P.
    Lund University.
    Correlated morphological and colour differences among females of the damselfly Ischnura elegans2009In: Ecological Entomology, ISSN 0307-6946, E-ISSN 1365-2311, Vol. 34, no 3, p. 378-386Article in journal (Refereed)
    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.

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  • 4.
    Abbott, Jessica K.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Svensson, Erik I.
    Lund University.
    Morph-specific variation in intersexual genetic correlations in an intra-specific mimicry system2010In: Evolutionary Ecology Research, ISSN 1522-0613, E-ISSN 1937-3791, Vol. 12, no 1, p. 105-118Article in journal (Refereed)
    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.

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  • 5.
    Abbott, Jessica K.
    et al.
    Lund University.
    Svensson, Erik I.
    Lund University.
    Ontogeny of sexual dimorphism and phenotypic integration in heritable morphs2008In: Evolutionary Ecology, ISSN 0269-7653, E-ISSN 1573-8477, Vol. 22, no 1, p. 103-121Article in journal (Refereed)
    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.

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  • 6.
    Abbott, Jessica K.
    et al.
    Lund University.
    Svensson, Erik I.
    Lund University.
    Phenotypic and genetic variation in emergence and development time of a trimorphic damselfly2005In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 18, no 6, p. 1464-1470Article in journal (Refereed)
    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.

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  • 7.
    Abdalaal, Hind
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pundir, Shreya
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Ge, Xueliang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Sanyal, Suparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Näsvall, Joakim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Collateral toxicity limits the evolution of bacterial Release Factor 2 towards total omnipotence2020In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 37, no 10, p. 2918-2930Article in journal (Refereed)
    Abstract [en]

    When new genes evolve through modification of existing genes, there are often trade-offs between the new and original functions, making gene duplication and amplification necessary to buffer deleterious effects on the original function. We have used experimental evolution of a bacterial strain lacking peptide release factor 1 (RF1) in order to study how peptide release factor 2 (RF2) evolves to compensate the loss of RF1. As expected, amplification of the RF2-encoding gene prfB to high copy number was a rapid initial response, followed by the appearance of mutations in RF2 and other components of the translation machinery. Characterization of the evolved RF2 variants by their effects on bacterial growth rate, reporter gene expression, and in vitro translation termination reveals a complex picture of reduced discrimination between the cognate and near cognate stop codons and highlight a functional trade-off that we term “collateral toxicity”. We suggest that this type of trade-off may be a more serious obstacle in new gene evolution than the more commonly discussed evolutionary trade-offs between “old” and “new” functions of a gene, as it cannot be overcome by gene copy number changes. Further, we suggest a model for how RF2 autoregulation responds not only to alterations in the demand for RF2 activity, but also for RF1 activity.

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  • 8.
    Abdelfattah, Ahmed
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Germany; Graz University of Technology, Austria .
    Tack, Ayco J. M.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Lobato, Carolina
    Wassermann, Birgit
    Berg, Gabriele
    From seed to seed: the role of microbial inheritance in the assembly of the plant microbiome2023In: Trends in Microbiology, ISSN 0966-842X, E-ISSN 1878-4380, Vol. 31, no 4, p. 346-355Article, review/survey (Refereed)
    Abstract [en]

    Despite evidence that the microbiome extends host genetic and phenotypic traits, information on how the microbiome is transmitted and maintained across generations remains fragmented. For seed-bearing plants, seeds harbor a distinct microbiome and play a unique role by linking one generation to the next. Studies on microbial inheritance, a process we suggest including both vertical transmission and the subsequent migration of seed microorganisms to the new plant, thus become essential for our understanding of host evolutionary potential and host–microbiome coevolution. We propose dividing the inheritance process into three stages: (i) plant to seed, (ii) seed dormancy, and (iii) seed to seedling. We discuss the factors affecting the assembly of the microbiome during the three stages, highlight future research directions, and emphasize the implications of microbial inheritance for fundamental science and society.

  • 9.
    Abozeid, Hassanein H.
    et al.
    Cairo Univ, Fac Vet Med, Dept Poultry Dis, Giza 12211, Egypt..
    Naguib, Mahmoud
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Infectious Bronchitis Virus in Egypt: Genetic Diversity and Vaccination Strategies2020In: Veterinary Sciences, E-ISSN 2306-7381, Vol. 7, no 4, article id 204Article, review/survey (Refereed)
    Abstract [en]

    Infectious bronchitis virus (IBV) is a highly evolving avian pathogen that has increasingly imposed a negative impact on poultry industry worldwide. In the last 20 years, IBV has been continuously circulating among chicken flocks in Egypt causing huge economic losses to poultry production. Multiple IBV genotypes, namely, GI-1, GI-13, GI-16, and GI-23 have been reported in Egypt possessing different genetic and pathogenic features. Different vaccine programs are being used to control the spread of the disease in Egypt. However, the virus continues to spread and evolve where multiple IBV variants and several recombination evidence have been described. In this review, we highlight the current knowledge concerning IBV circulation, genesis, and vaccination strategies in Egypt. In addition, we analyze representative Egyptian IBV strains from an evolutionary perspective based on available data of their S1 gene. We also provide insight into the importance of surveillance programs and share our perspectives for better control of IBV circulating in Egypt.

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  • 10.
    Abreu, Clare I.
    et al.
    Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Stanford University, Stanford, CA, USA.
    Bello, Martina Dal
    Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
    Bunse, Carina
    Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden.
    Pinhassi, Jarone
    Centre for Ecology and Evolution of Microbial Model Systems, Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.
    Gore, Jeff
    Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
    Warmer temperatures favor slower-growing bacteria in natural marine communities2023In: Science Advances, E-ISSN 2375-2548, Vol. 9, no 19, article id eade8352Article in journal (Refereed)
    Abstract [en]

    Earth’s life-sustaining oceans harbor diverse bacterial communities that display varying composition across time and space. While particular patterns of variation have been linked to a range of factors, unifying rules are lacking, preventing the prediction of future changes. Here, analyzing the distribution of fast- and slow-growing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperature-dependent growth rates differentially modulate the impact of mortality on species abundances. Changes in bacterial community structure promoted by temperature are independent of variations in nutrients along spatial and temporal gradients. Our results help explain why slow growers dominate at the ocean surface, during summer, and near the tropics and provide a framework to understand how bacterial communities will change in a warmer world.

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  • 11.
    Abreu, Clare I.
    et al.
    MIT, USA;Stanford Univ, USA.
    Dal Bello, Martina
    MIT, USA.
    Bunse, Carina
    University of Gothenburg, Sweden.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gore, Jeff
    MIT, USA.
    Warmer temperatures favor slower-growing bacteria in natural marine communities2023In: Science Advances, E-ISSN 2375-2548, Vol. 9, no 19, article id 26eade8352Article in journal (Refereed)
    Abstract [en]

    Earth's life-sustaining oceans harbor diverse bacterial communities that display varying composition across time and space. While particular patterns of variation have been linked to a range of factors, unifying rules are lacking, preventing the prediction of future changes. Here, analyzing the distribution of fast- and slowgrowing bacteria in ocean datasets spanning seasons, latitude, and depth, we show that higher seawater temperatures universally favor slower-growing taxa, in agreement with theoretical predictions of how temperaturedependent growth rates differentially modulate the impact of mortality on species abundances. Changes in bacterial community structure promoted by temperature are independent of variations in nutrients along spatial and temporal gradients. Our results help explain why slow growers dominate at the ocean surface, during summer, and near the tropics and provide a framework to understand how bacterial communities will change in a warmer world.

  • 12.
    Abuabaid, Hanan
    et al.
    Örebro University, School of Science and Technology.
    Karlsson, Mattias
    Örebro University, School of Science and Technology.
    Scherbak, Nikolai
    Örebro University, School of Science and Technology.
    Olsson, Per-Erik
    Örebro University, School of Science and Technology.
    Jass, Jana
    Örebro University, School of Science and Technology.
    Probiotic Lactobacillus rhamnosus alters inflammatory responses of bladder epithelial and macrophage-like cells in co-cultureManuscript (preprint) (Other academic)
  • 13. Achouiti, Ahmed
    et al.
    Vogl, Thomas
    Urban, Constantin F
    Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology. Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS).
    Röhm, Marc
    Umeå University, Faculty of Medicine, Molecular Infection Medicine Sweden (MIMS). Umeå University, Faculty of Medicine, Department of Clinical Microbiology, Clinical Bacteriology.
    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 sepsis2012In: PLoS Pathogens, ISSN 1553-7374, Vol. 8, no 10, p. e1002987-Article in journal (Refereed)
    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.

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  • 14.
    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
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    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 caldus2013In: PLOS ONE, E-ISSN 1932-6203, Vol. 8, no 11, article id e78237Article in journal (Refereed)
    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.

  • 15. Adamsson, I
    et al.
    Edlund, Charlotta
    Södertörn University, Avdelning Naturvetenskap.
    Seensalu, R
    Engstrand, L
    The use of AP-PCR and flaA-RFLP typing to investigate treatment failure in Helicobacter pylori infection2000In: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 6, no 5, p. 265-267Article in journal (Refereed)
  • 16.
    Adel, Amany
    et al.
    Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Abdelmagid, Marwa A.
    Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Mohamed, Ahmed Abd-Elhalem
    Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Wasberg, Anishia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Mosaad, Zienab
    Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Selim, Karim
    Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Shaaban, Asmaa
    Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Tarek, Mohamed
    Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Hagag, Naglaa M.
    Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Lundkvist, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ellström, Patrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences.
    Naguib, Mahmoud
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Anim Hlth Res Inst, Agr Res Ctr, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Genetic Variations among Different Variants of G1-like Avian Influenza H9N2 Viruses and Their Pathogenicity in Chickens2022In: Viruses, E-ISSN 1999-4915, Vol. 14, no 5, article id 1030Article in journal (Refereed)
    Abstract [en]

    Since it was first discovered, the low pathogenic avian influenza (LPAI) H9N2 subtype has established linages infecting the poultry population globally and has become one of the most prevalent influenza subtypes in domestic poultry. Several different variants and genotypes of LPAI H9N2 viruses have been reported in Egypt, but little is known about their pathogenicity and how they have evolved. In this study, four different Egyptian LPAI H9N2 viruses were genetically and antigenically characterized and compared to representative H9N2 viruses from G1 lineage. Furthermore, the pathogenicity of three genetically distinct Egyptian LPAI H9N2 viruses was assessed by experimental infection in chickens. Whole-genome sequencing revealed that the H9N2 virus of the Egy-2 G1-B lineage (pigeon-like) has become the dominant circulating H9N2 genotype in Egypt since 2016. Considerable variation in virus shedding at day 7 post-infections was detected in infected chickens, but no significant difference in pathogenicity was found between the infected groups. The rapid spread and emergence of new genotypes of the influenza viruses pinpoint the importance of continuous surveillance for the detection of novel reassortant viruses, as well as monitoring the viral evolution.

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  • 17.
    Adel, Amany
    et al.
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Mohamed, Ahmed Abd Elhalem
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Samir, Mahmoud
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Hagag, Naglaa M.
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Erfan, Ahmed
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Said, Mahmoud
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Arafa, Abd El Satar
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Hassan, Wafaa M. M.
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    El Zowalaty, Mohamed E.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Shahien, Momtaz A.
    Agr Res Ctr, Anim Hlth Res Inst, Reference Lab Vet Qual Control Poultry Prod, Giza 12618, Egypt..
    Epidemiological and molecular analysis of circulating fowl adenoviruses and emerging of serotypes 1, 3, and 8b in Egypt2021In: Heliyon, E-ISSN 2405-8440, Vol. 7, no 12, article id e08366Article in journal (Refereed)
    Abstract [en]

    Fowl adenoviruses (FAdVs) are a large group of viruses of different serotypes. They are responsible for inclusion body hepatitis, adenoviral gizzard erosion, and hepatitis hydropericardium syndrome. The present study presents a comprehensive overview of FAdVs in Egypt, with a focus on the epidemiological features of virus serotypes across the country. We conducted molecular investigation of multiple FAdV species based on the genetic signature of hypervariable regions 1-4 in the loop1 (L1) region of the hexon gene. Epidemiologically, the Nile Delta governorates showed high positivity of FAdVs, which were more commonly found in broilers than in layers. Genetically, species D and serotype 8a/E dominated, and the findings also revealed the emergence of new FAdV serotypes 1, 3, and 8b. The comparative analysis of hypervariable regions in the L1 region of the hexon gene revealed variables specific to each virus serotype. In silico predictions of L1 region revealed variations in the molecular structure and predicted the antigenic epitopes which may affect the cross-antigenicity between the different FAdV species and serotypes.

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  • 18.
    Adler, Lennart
    et al.
    Göteborgs universitet.
    Wadskog, Ingrid
    Jönköping University, School of Engineering, JTH, Chemical Engineering.
    Ion homeostasis in Saccharomyces cerevisiae under NaCl stress2003In: Yeast stress responses / [ed] Stefan Hohmann, Willem H. Mager, Berlin: Springer , 2003, p. 201-239Chapter in book (Other academic)
  • 19.
    Adler, Marlen
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Mechanisms and Dynamics of Carbapenem Resistance in Escherichia coli2014Doctoral thesis, comprehensive summary (Other academic)
    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.

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  • 20.
    Adler, Marlen
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Anjum, Mehreen
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Dan I.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Sandegren, Linus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Combinations of mutations in envZ, ftsI, mrdA, acrB and acrR can cause high-level carbapenem resistance in Escherichia coli2016In: Journal of Antimicrobial Chemotherapy, ISSN 0305-7453, E-ISSN 1460-2091, Vol. 71, no 5, p. 1188-1198Article in journal (Refereed)
    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.

  • 21.
    Adler, Marlen
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Anjum, Mehreen
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Berg, Otto, G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Andersson, Dan I.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Sandegren, Linus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    High Fitness Costs and Instability of Gene Duplications Reduce Rates of Evolution of New Genes by Duplication-Divergence Mechanisms2014In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 31, no 6, p. 1526-1535Article in journal (Refereed)
    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.

  • 22.
    af Klercker, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    The impact of the ribosomal 16S rRNA modifications on the antibiotic susceptibility and fitness in Escherichia coli  2024Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The rRNA molecules which make up the two subunits of the Escherichia coli ribosome are extensively post-transcriptionally modified. The specific purpose of each modification is still unknown. It is proposed that they provide a structure for the ribosomal assembly, which would indicate that they are essential. However, previous literature in this area using E. coli shows that when the modification enzymes are removed individually the effects on growth fitness and antibiotic sensitivity are limited. This makes their role in ribosomal assembly unclear. The effect of removing multiple ribosomal modification enzymes is largely unexplored. The position of many of the modifications are found in clusters, usually in the catalytic domains of the ribosome, which are often targeted by antibiotics, indicating that removing the modification enzymes could affect antibiotic sensitivity. Most of the previous studies on strains with these modification enzymes removed were performed with traditional lambda-red that leaves behind FRT scars, which can cause unwanted spontaneous excisions via recombination between the FRT scars. Here, DIRex lambda-red was used to create clean deletions, which does not produce FRT scars and therefore, allows for more reliable analysis of the ribosomal modification enzymes’ role. The results show that there is a fitness cost and change in antibiotic sensitivity due to multiple of the deletions of the ribosomal modification enzymes. For some of the modifications, this is true when that particular site alone is left unmodified, while for other positions, these effects are only observed when multiple sites are modified simultaneously. For example, the methyltransferase RsmG knockout has a big effect on streptomycin resistance but no fitness cost, while the methyltransferase RsmA and RsmF knockouts causes a fitness cost in combination and causes tetracycline and gentamycin resistance respectively. This indicates that the ribosomal modifications significantly affect the interaction with antibiotics and fitness, and therefore, have a significant part in ribosomal function. 

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  • 23.
    Affonso, Igor de Paiva
    et al.
    Universidade Estadual de Maringá, Maringá, Brazil; Universidade Tecnológica Federal do Paraná, Campus Ponta Grossa, Brazil.
    Karling, Leticia Cucolo
    Universidade Estadual de Maringá, Maringá, Brazil.
    Takemoto, Ricardo Massato
    Núcleo de Pesquisas em Limnologia Ictiologia e Aqüicultura – Nupélia, Maringá, Brazil.
    Gomes, Luiz Carlos
    Universidade Estadual de Maringá, Maringá, Brazil; Núcleo de Pesquisas em Limnologia Ictiologia e Aqüicultura – Nupélia, Maringá, Brazil.
    Nilsson, Per Anders
    Karlstad University, Faculty of Health, Science and Technology (starting 2013), Department of Environmental and Life Sciences (from 2013). Department of Biology, Lund University, Lund, Sweden.
    Light-induced eye-fluke behavior enhances parasite life cycle2017In: Frontiers in Ecology and the Environment, ISSN 1540-9295, E-ISSN 1540-9309, Vol. 15, no 6, p. 340-341Article in journal (Refereed)
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  • 24.
    Afonina, Irina
    et al.
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; Singapore–MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, 1 Create Way, Singapore, Singapore.
    Tien, Brenda
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Nair, Zeus
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; Interdisciplinary Graduate School, Nanyang Technological University, 61 Nanyang Drive, Singapore, Singapore.
    Matysik, Artur
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Lam, Ling Ning
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Veleba, Mark
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Jie, Augustine Koh Jing
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    Rashid, Rafi
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; Graduate School for Integrative Sciences & Engineering, National University of Singapore, 21 Lower Kent Ridge Rd, Singapore, Singapore.
    Cazenave-Gassiot, Amaury
    Singapore Lipidomics Incubator, National University of Singapore, 28 Medical Dr, Singapore, Singapore; Department of Biochemistry, National University of Singapore, 8 Medical Drive, Block MD7, Singapore, Singapore.
    Wenk, Marcus
    Singapore Lipidomics Incubator, National University of Singapore, 28 Medical Dr, Singapore, Singapore; Department of Biochemistry, National University of Singapore, 8 Medical Drive, Block MD7, Singapore, Singapore; Department of Biological Sciences, Faculty of Science, National University of Singapore, 16 Science Drive 4, Singapore, Singapore.
    Wai, Sun Nyunt
    Umeå University, Faculty of Medicine, Umeå Centre for Microbial Research (UCMR). Umeå University, Faculty of Medicine, Department of Molecular Biology (Faculty of Medicine).
    Kline, Kimberly A.
    Singapore Centre for Environmental Life Science Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, Singapore.
    The composition and function of Enterococcus faecalis membrane vesicles2021In: MicroLife, E-ISSN 2633-6693, Vol. 2, article id uqab002Article in journal (Refereed)
    Abstract [en]

    Membrane vesicles (MVs) contribute to various biological processes in bacteria, including virulence factor delivery, antimicrobial resistance, host immune evasion and cross-species communication. MVs are frequently released from the surface of both Gram-negative and Gram-positive bacteria during growth. In some Gram-positive bacteria, genes affecting MV biogenesis have been identified, but the mechanism of MV formation is unknown. In Enterococcus faecalis, a causative agent of life-threatening bacteraemia and endocarditis, neither mechanisms of MV formation nor their role in virulence has been examined. Since MVs of many bacterial species are implicated in host–pathogen interactions, biofilm formation, horizontal gene transfer, and virulence factor secretion in other species, we sought to identify, describe and functionally characterize MVs from E. faecalis. Here, we show that E. faecalis releases MVs that possess unique lipid and protein profiles, distinct from the intact cell membrane and are enriched in lipoproteins. MVs of E. faecalis are specifically enriched in unsaturated lipids that might provide membrane flexibility to enable MV formation, providing the first insights into the mechanism of MV formation in this Gram-positive organism.

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  • 25.
    Agongo, Hassanat
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Characterization of DNA Methylation in Giardia intestinalis2021Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Abstract

    G. intestinalis is an intestinal protozoan parasite that causes 180 million symptomatic diarrheacases (giardiasis) and more than 0.5 billion asymptomatic infections per year. Symptomaticinfections are usually treated with metronidazole (Flagyl). However, resistance is emerging, andan alternative treatment is required. The mechanism to which the parasite causes the disease is notunderstood and, neither is the regulation of encystation (a process where trophozoites differentiateto cyst) However, preliminary data suggest that an epigenetic mechanism is involved. DNAmethylation is an important epigenetic regulator in many organisms, but it is not known if theDNA is methylated in Giardia. The main goal of this project was to characterize DNA methylationin G. intestinalis and, if it exists, study if it is linked to cell differentiation and use it as a target fordrug treatment. We found out using the dot blot technique complemented withimmunofluorescence assays, that 6mA and 5mC DNA methylation exists on the genomic DNA ofthe assemblage A G. intestinalis isolate WB. 6mA methylation was also found on RNA. However,no major differences were detected between trophozoites and cysts. Assemblage B Giardia isolates(GS and H3) also have methylated genomic DNA, but we detected lower levels of methylation. Abioinformatic search was performed in the G. intestinalis WB genome in an attempt to identifyDNA methylases. Expression levels through-out the life cycle, sequence similarities and structuralmodelling using iTASSER identified six putative DNA methylases in the WB genome. The sixDNA methylases were over-expressed in Giardia, three were lethal and three localized to thenucleus. 5-azacytidine and 5-aza-2’-deoxycytidine nucleoside analog drugs prevent methylationand are incorporated into RNA and DNA, respectively. We tested these two drugs on Giardiatrophozoites, and both have effects on the trophozoite stage (IC50 1.46±0.46 μM for 5-aza-2’-deoxycytidine and 111±24 μM for 5-Azacytidine). The 5-aza-2’-deoxycytidine drug is actuallymore effective than metronidazole, showing that nucleoside analogs affecting DNA methylationcould be alternative drugs for treatment of giardiasis.

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  • 26. Agostinelli, Marta
    et al.
    Cleary, Michelle
    Martin, Juan A.
    Albrectsen, Benedicte R.
    Umeå University, Faculty of Science and Technology, Department of Plant Physiology. Umeå University, Faculty of Science and Technology, Umeå Plant Science Centre (UPSC).
    Witzell, Johanna
    Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity2018In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 9, article id 1758Article in journal (Refereed)
    Abstract [en]

    Ecological significance of trees growing in urban and peri-urban settings is likely to increase in future land-use regimes, calling for better understanding of their role as potential reservoirs or stepping stones for associated biodiversity. We studied the diversity of fungal endophytes in woody tissues of asymptomatic even aged pedunculate oak trees, growing as amenity trees in a peri-urban setting. The trees were classified into three groups according to their phenotypic vitality (high, medium, and low). Endophytes were cultured on potato dextrose media from surface sterilized twigs and DNA sequencing was performed to reveal the taxonomic identity of the morphotypes. In xylem tissues, the frequency and diversity of endophytes was highest in oak trees showing reduced vitality. This difference was not found for bark samples, in which the endophyte infections were more frequent and communities more diverse than in xylem. In general, most taxa were shared across the samples with few morphotypes being recovered in unique samples. Leaf phenolic profiles were found to accurately classify the trees according to their phenotypic vitality. Our results confirm that xylem is more selective substrate for endophytes than bark and that endophyte assemblages in xylem are correlated to the degree of host vitality. Thus, high vitality of trees may be associated with reduced habitat quality to wood-associated endophytes.

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  • 27.
    Agostinelli, Marta
    et al.
    Swedish University of Agricultural Sciences, Sweden.
    Cleary, Michelle
    Swedish University of Agricultural Sciences, Sweden.
    Martín, Juan A
    Technical University of Madrid, Spain.
    Albrectsen, Benedicte R
    Umeå University, Sweden.
    Witzell, Johanna
    Swedish University of Agricultural Sciences, Sweden.
    Pedunculate Oaks (Quercus robur L.) Differing in Vitality as Reservoirs for Fungal Biodiversity2018In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 9, article id 1758Article in journal (Refereed)
    Abstract [en]

    Ecological significance of trees growing in urban and peri-urban settings is likely to increase in future land-use regimes, calling for better understanding of their role as potential reservoirs or stepping stones for associated biodiversity. We studied the diversity of fungal endophytes in woody tissues of asymptomatic even aged pedunculate oak trees, growing as amenity trees in a peri-urban setting. The trees were classified into three groups according to their phenotypic vitality (high, medium, and low). Endophytes were cultured on potato dextrose media from surface sterilized twigs and DNA sequencing was performed to reveal the taxonomic identity of the morphotypes. In xylem tissues, the frequency and diversity of endophytes was highest in oak trees showing reduced vitality. This difference was not found for bark samples, in which the endophyte infections were more frequent and communities more diverse than in xylem. In general, most taxa were shared across the samples with few morphotypes being recovered in unique samples. Leaf phenolic profiles were found to accurately classify the trees according to their phenotypic vitality. Our results confirm that xylem is more selective substrate for endophytes than bark and that endophyte assemblages in xylem are correlated to the degree of host vitality. Thus, high vitality of trees may be associated with reduced habitat quality to wood-associated endophytes.

  • 28.
    Aguilera, Anabella
    et al.
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Alegria Zufia, Javier
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Bas Conn, Laura
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Gurlit, Leandra
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Śliwińska-Wilczewska, Sylwia
    Mount Allison University, Sackville, New Brunswick, Canada; Laboratory of Marine Plant Ecophysiology, Institute of Oceanography, University of Gdansk, Gdynia, Poland.
    Budzałek, Gracjana
    Laboratory of Marine Plant Ecophysiology, Institute of Oceanography, University of Gdansk, Gdynia, Poland.
    Lundin, Daniel
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Pinhassi, Jarone
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Legrand, Catherine
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden; School of Business, Innovation and Sustainability, Halmstad University, Halmstad, Sweden.
    Farnelid, Hanna
    Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden.
    Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria2023In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920Article in journal (Refereed)
    Abstract [en]

    Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcB and cpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10–30°C), light (10–190 μmol photons m−2 s−1), and salinity (2–14 PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.

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  • 29.
    Aguilera, Anabella
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Alegria Zufia, Javier
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bas Conn, Laura
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Gurlit, Leandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Śliwińska‐Wilczewska, Sylwia
    Mount Allison University, Canada;University of Gdansk, Poland.
    Budzałek, Gracjana
    University of Gdansk, Poland.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Halmstad University, Sweden.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ecophysiological analysis reveals distinct environmental preferences in closely related Baltic Sea picocyanobacteria2023In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 25, no 9, p. 1674-1695Article in journal (Refereed)
    Abstract [en]

    Cluster 5 picocyanobacteria significantly contribute to primary productivity in aquatic ecosystems. Estuarine populations are highly diverse and consist of many co-occurring strains, but their physiology remains largely understudied. In this study, we characterized 17 novel estuarine picocyanobacterial strains. Phylogenetic analysis of the 16S rRNA and pigment genes (cpcBandcpeBA) uncovered multiple estuarine and freshwater-related clusters and pigment types. Assays with five representative strains (three phycocyanin rich and two phycoerythrin rich) under temperature (10–30°C), light(10–190 μmol  photons  m-2s-1), and salinity (2–14  PSU) gradients revealed distinct growth optima and tolerance, indicating that genetic variability was accompanied by physiological diversity. Adaptability to environmental conditions was associated with differential pigment content and photosynthetic performance. Amplicon sequence variants at a coastal and an offshore station linked population dynamics with phylogenetic clusters, supporting that strains isolated in this study represent key ecotypes within the Baltic Sea picocyanobacterial community. The functional diversity found within strains with the same pigment type suggests that understanding estuarine picocyanobacterial ecology requires analysis beyond the phycocyanin and phycoerythrin divide. This new knowledge of the environmental preferences in estuarine picocyanobacteria is important for understanding and evaluating productivity in current and future ecosystems.

  • 30.
    Aguilera, Anabella
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Klemencic, Marina
    University of Ljubljana, Slovenia.
    Sueldo, Daniela J.
    University of Warwick, UK.
    Rzymski, Piotr
    Poznan University of Medical Sciences, Poland;Universal Scientific Education and Research Network (USERN), Poland.
    Giannuzzi, Leda
    National University of La Plata, Argentina.
    Martin, Maria Victoria
    CONICET Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC), Argentina;Fundación para Investigaciones Biológicas Aplicadas (FIBA), Argentina.
    Cell death in Cyanobacteria: current understanding and recommendations for a consensus on its nomenclature2021In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 12, p. 1-15, article id 631654Article, review/survey (Refereed)
    Abstract [en]

    Cyanobacteria are globally widespread photosynthetic prokaryotes and are major contributors to global biogeochemical cycles. One of the most critical processes determining cyanobacterial eco-physiology is cellular death. Evidence supports the existence of controlled cellular demise in cyanobacteria, and various forms of cell death have been described as a response to biotic and abiotic stresses. However, cell death research in this phylogenetic group is a relatively young field and understanding of the underlying mechanisms and molecular machinery underpinning this fundamental process remains largely elusive. Furthermore, no systematic classification of modes of cell death has yet been established for cyanobacteria. In this work, we analyzed the state of knowledge in the field of cyanobacterial cell death. Based on that, we propose unified criterion for the definition of accidental, regulated, and programmed forms of cell death in cyanobacteria based on molecular, biochemical, and morphologic aspects following the directions of Nomenclature Committee on Cell Death (NCCD). With this, we aim to provide a guide to standardize the nomenclature related to this topic in a precise and consistent manner, which will facilitate further ecological, evolutionary and applied research in the field of cyanobacterial cell death

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  • 31.
    Aguilera, Anabella
    et al.
    Fdn Invest Biol Aplicadas CIB FIBA, Argentina.
    Steelheart, Charlotte
    Univ Nacl La Plata, Argentina.
    Alegre, Matias
    Univ Nacl La Plata, Argentina.
    Berdun, Federico
    Fdn Invest Biol Aplicadas CIB FIBA, Argentina.
    Salerno, Graciela
    Fdn Invest Biol Aplicadas CIB FIBA, Argentina.
    Bartoli, Carlos
    Univ Nacl La Plata, Argentina.
    Pagnussat, Gabriela
    Univ Nacl Mar del Plata, Argentina.
    Victoria Martin, Maria
    Fdn Invest Biol Aplicadas CIB FIBA, Argentina.
    Measurement of Ascorbic Acid and Glutathione Content in Cyanobacterium Synechocystis sp. PCC 68032020In: Bio-protocol, E-ISSN 2331-8325, Vol. 10, no 20, p. 1-7, article id e3800Article in journal (Refereed)
    Abstract [en]

    Ascorbic acid (AsA) and gluthathione (GSH) are two key components of the antioxidant machinery of eukaryotic and prokaryotic cells. The cyanobacterium Synechocystis sp. PCC 6803 presents both compounds in different concentrations (AsA, 20-100 mu M and GSH, 2-5 mM). Therefore, it is important to have precise and sensitive methods to determine the redox status in the cell and to detect variations in this antioxidants. In this protocol, we describe an improved method to estimate the content of both antioxidants (in their reduced and oxidized forms) from the same sample obtained from liquid cultures of Synechocystis sp. PCC 6803.

  • 32. Agvald-Öhman, C
    et al.
    Wernerman, J
    Nord, C E
    Edlund, Charlotta
    Södertörn University, Avdelning Naturvetenskap.
    Anaerobic bacteria commonly colonize the lower airways of intubated ICU patients2003In: Clinical Microbiology and Infection, ISSN 1198-743X, E-ISSN 1469-0691, Vol. 9, no 5, p. 397-405Article in journal (Refereed)
    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.

  • 33.
    Ah-King, Malin
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Centre for Gender Research.
    Barron, Andrew B.
    Herberstein, Marie E.
    Genital Evolution: Why Are Females Still Understudied?2014In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 12, no 5, p. e1001851-Article in journal (Refereed)
    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.

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  • 34.
    Ahlberg, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Can fossils illuminate the evolution of gnathostome head development?2006In: European Society for Evolutionary Developmental Biology: The First and Founding Meeting, August 2006, Prague, 2006, p. 363-Conference paper (Other (popular scientific, debate etc.))
  • 35.
    Ahlberg, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology. Evolutionär organismbiologi.
    CT scanning the nose of Eusthenopteron.2006In: Journal of Vertebrate Paleontology, ISSN 0272-4634, Vol. 26, no 3(supplement), p. 35A-Article in journal (Other scientific)
  • 36.
    Ahlberg, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology. Evolutionär organismbiologi.
    Fossils, developmental patterning and the origin of tetrapods.2003In: The new panorama of animal evolution, Pensoft Publishers, Sofia, Bulgaria , 2003, p. 45-54Chapter in book (Refereed)
  • 37.
    Ahlberg, Per
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology. Evolutionär organismbiologi.
    Clack, Jennifer
    Blom, Henning
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    The axial skeleton of the Devonian tetrapod Ichthyostega.2005In: Nature, ISSN 0028-0836, Vol. 437, no 7055, p. 137-140Article in journal (Refereed)
    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.

  • 38.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    Fossils, developmental patterning and the origin of tetrapods2003In: The new panorama of animal evolution: Proceedings of the 18th international congress of zoology, Sofia and Moscow: Pensoft Publishers , 2003, p. 44-54Chapter in book (Other academic)
  • 39.
    Ahlberg, Per
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology. Evolutionär organismbiologi.
    Friedman, Matt
    Blom, Henning
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    New light on the earliest known tetrapod jaw.2005In: Journal of Vertebrate Paleontology, ISSN 0272-4634, Vol. 25, no 3, p. 720-724Article in journal (Refereed)
  • 40.
    Ahlberg, Per
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology. Evolutionär organismbiologi.
    Köntges, Georgy
    Homologies and cell populations: a response to Sánchez-Villagra and Maier.2006In: Evolution and Development, ISSN 1520-541X, Vol. 8, p. 116-118Article in journal (Other (popular scientific, debate etc.))
  • 41.
    Ahlberg, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Physiology and Developmental Biology, Evolutionary Organism Biology.
    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.2006In: Evolution & Development, ISSN 1520-541X, E-ISSN 1525-142X, Vol. 8, no 4, p. 331-349Article in journal (Refereed)
    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.

  • 42.
    Ahle, Charlotte M.
    et al.
    Beiersdorf AG, Research & Development, Front End Innovation, Hamburg, Germany; Department of Microbiology and Biotechnology, University of Hamburg, Hamburg, Germany.
    Stødkilde, Kristian
    Department of Biomedicine, Aarhus University, Aarhus, Denmark.
    Afshar, Mastaneh
    Department of Biomedicine, Aarhus University, Aarhus, Denmark.
    Poehlein, Anja
    Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, University of Göttingen, Göttingen, Germany.
    Ogilvie, Lesley A.
    Max Planck Institute for Molecular Genetics, Berlin, Germany.
    Söderquist, Bo
    Örebro University, School of Medical Sciences. Department of Laboratory Medicine, Clinical Microbiology.
    Hüpeden, Jennifer
    Beiersdorf AG, Research & Development, Front End Innovation, Hamburg, Germany.
    Brüggemann, Holger
    Department of Biomedicine, Aarhus University, Aarhus, Denmark.
    Staphylococcus saccharolyticus: An Overlooked Human Skin Colonizer2020In: Microorganisms, E-ISSN 2076-2607, Vol. 8, no 8, article id E1105Article in journal (Refereed)
    Abstract [en]

    Coagulase-negative staphylococcal species constitute an important part of the human skin microbiota. In particular, facultative anaerobic species such as Staphylococcus epidermidis and Staphylococcus capitis can be found on the skin of virtually every human being. Here, we applied a culture-independent amplicon sequencing approach to identify staphylococcal species on the skin of healthy human individuals. While S. epidermidis and S. capitis were found as primary residents of back skin, surprisingly, the third most abundant member was Staphylococcus saccharolyticus, a relatively unstudied species. A search of skin metagenomic datasets detected sequences identical to the genome of S. saccharolyticus in diverse skin sites, including the back, forehead, and elbow pit. Although described as a slow-growing anaerobic species, a re-evaluation of its growth behavior showed that S. saccharolyticus can grow under oxic conditions, and, in particular, in a CO2-rich atmosphere. We argue here that S. saccharolyticus was largely overlooked in previous culture-dependent and -independent studies, due to its requirement for fastidious growth conditions and the lack of reference genome sequences, respectively. Future studies are needed to unravel the microbiology and host-interacting properties of S. saccharolyticus and its role as a prevalent skin colonizer.

  • 43.
    Ahlstrom, Christina A. A.
    et al.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA..
    Woksepp, Hanna
    Kalmar Cty Reg, Dept Res, Kalmar, Sweden.;Linnaeus Univ, Dept Chem & Biomed Sci, Kalmar, Sweden..
    Sandegren, Linus
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ramey, Andrew M. M.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA..
    Bonnedahl, Jonas
    Linköping Univ, Dept Biomed & Clin Sci, Linköping, Sweden.;Kalmar Cty Reg, Dept Infect Dis, Kalmar, Sweden..
    Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches2023In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 89, no 6Article in journal (Refereed)
    Abstract [en]

    Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted.

    IMPORTANCE Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene blaOXA-48. This is the most frequently reported carbapenem-resistant clone in wild birds, though it was unclear if it circulated within wild bird populations or was exchanged among other niches. The results from this study suggest that E. coli ST38 strains, including those resistant to carbapenems, are frequently exchanged among wild birds, humans, and the environment. Carbapenem-resistant E. coli ST38 clones in wild birds are likely acquired from the local environment and do not constitute an independent dissemination pathway within wild bird populations. Management actions aimed at preventing the environmental dissemination and acquisition of antimicrobial resistance by wild birds may be warranted.

  • 44.
    Ahlstrom, Christina A. A.
    et al.
    US Geol Survey, USA.
    Woksepp, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Kalmar County Region, Sweden.
    Sandegren, Linus
    Uppsala University, Sweden.
    Ramey, Andrew M. M.
    US Geol Survey, USA.
    Bonnedahl, Jonas
    Linköping University, Sweden;Kalmar County Region, Sweden.
    Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches2023In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 89, no 6, article id e0031923Article in journal (Refereed)
    Abstract [en]

    Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene bla(OXA-48). Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted.IMPORTANCE Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene bla(OXA-48). This is the most frequently reported carbapenem-resistant clone in wild birds, though it was unclear if it circulated within wild bird populations or was exchanged among other niches. The results from this study suggest that E. coli ST38 strains, including those resistant to carbapenems, are frequently exchanged among wild birds, humans, and the environment. Carbapenem-resistant E. coli ST38 clones in wild birds are likely acquired from the local environment and do not constitute an independent dissemination pathway within wild bird populations. Management actions aimed at preventing the environmental dissemination and acquisition of antimicrobial resistance by wild birds may be warranted.

  • 45.
    Ahlstrom, Christina A. A.
    et al.
    US Geol Survey, AK 99508 USA.
    Woksepp, Hanna
    Kalmar Cty Reg, Sweden; Linnaeus Univ, Sweden.
    Sandegren, Linus
    Uppsala Univ, Sweden.
    Ramey, Andrew M. M.
    US Geol Survey, AK 99508 USA.
    Bonnedahl, Jonas
    Linköping University, Department of Biomedical and Clinical Sciences, Division of Inflammation and Infection. Linköping University, Faculty of Medicine and Health Sciences. Kalmar Cty Reg, Sweden.
    Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches2023In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 89, no 6, article id e0031923Article in journal (Refereed)
    Abstract [en]

    Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene bla(OXA-48). Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted.IMPORTANCE Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic. Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene bla(OXA-48). This is the most frequently reported carbapenem-resistant clone in wild birds, though it was unclear if it circulated within wild bird populations or was exchanged among other niches. The results from this study suggest that E. coli ST38 strains, including those resistant to carbapenems, are frequently exchanged among wild birds, humans, and the environment. Carbapenem-resistant E. coli ST38 clones in wild birds are likely acquired from the local environment and do not constitute an independent dissemination pathway within wild bird populations. Management actions aimed at preventing the environmental dissemination and acquisition of antimicrobial resistance by wild birds may be warranted.

  • 46.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA.
    Bonnedahl, Jonas
    Linkoping Univ, Dept Clin & Expt Med, SE-58183 Linkoping, Sweden;Kalmar Cty Hosp, Dept Infect Dis, SE-39185 Kalmar, Sweden.
    Woksepp, Hanna
    Kalmar Cty Hosp, Dept Clin Microbiol, SE-39185 Kalmar, Sweden.
    Hernandez, Jorge
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Ramey, Andrew M.
    US Geol Survey, Alaska Sci Ctr, Anchorage, AK 99508 USA.
    Acquisition and dissemination of cephalosporin-resistant E.coli in migratory birds sampled at an Alaska landfill as inferred through genomic analysis2018In: Scientific Reports, E-ISSN 2045-2322, Vol. 8, article id 7361Article in journal (Refereed)
    Abstract [en]

    Antimicrobial resistance (AMR) in bacterial pathogens threatens global health, though the spread of AMR bacteria and AMR genes between humans, animals, and the environment is still largely unknown. Here, we investigated the role of wild birds in the epidemiology of AMR Escherichia coli. Using next-generation sequencing, we characterized cephalosporin-resistant E. coli cultured from sympatric gulls and bald eagles inhabiting a landfill habitat in Alaska to identify genetic determinants conferring AMR, explore potential transmission pathways of AMR bacteria and genes at this site, and investigate how their genetic diversity compares to isolates reported in other taxa. We found genetically diverse E. coli isolates with sequence types previously associated with human infections and resistance genes of clinical importance, including blaCTX-M and blaCMY. Identical resistance profiles were observed in genetically unrelated E. coli isolates from both gulls and bald eagles. Conversely, isolates with indistinguishable core-genomes were found to have different resistance profiles. Our findings support complex epidemiological interactions including bacterial strain sharing between gulls and bald eagles and horizontal gene transfer among E. coli harboured by birds. Results suggest that landfills may serve as a source for AMR acquisition and/or maintenance, including bacterial sequence types and AMR genes relevant to human health.

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  • 47.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, AK 99508 USA.
    Bonnedahl, Jonas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences. Kalmar Cty Council, Sweden.
    Woksepp, Hanna
    Kalmar Cty Hosp, Sweden.
    Hernandez, Jorge
    Kalmar Cty Hosp, Sweden.
    Reed, John A.
    US Geol Survey, AK 99508 USA.
    Tibbitts, Lee
    US Geol Survey, AK 99508 USA.
    Olsen, Bjoern
    Uppsala Univ, Sweden.
    Douglas, David C.
    US Geol Survey, AK USA.
    Ramey, Andrew M.
    US Geol Survey, AK 99508 USA.
    Satellite tracking of gulls and genomic characterization of faecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial-resistant Escherichia coli on the Kenai Peninsula, Alaska2019In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 28, no 10, p. 2531-2545Article in journal (Refereed)
    Abstract [en]

    Gulls (Larus spp.) have frequently been reported to carry Escherichia coli exhibiting antimicrobial resistance (AMR E. coli); however, the pathways governing the acquisition and dispersal of such bacteria are not well described. We equipped 17 landfill-foraging gulls with satellite transmitters and collected gull faecal samples longitudinally from four locations on the Kenai Peninsula, Alaska to assess: (a) gull attendance and transitions between sites, (b) spatiotemporal prevalence of faecally shed AMR E. coli, and (c) genomic relatedness of AMR E. coli isolates among sites. We also sampled Pacific salmon (Oncorhynchus spp.) harvested as part of personal-use dipnet fisheries at two sites to assess potential contamination with AMR E. coli. Among our study sites, marked gulls most commonly occupied the lower Kenai River (61% of site locations) followed by the Soldotna landfill (11%), lower Kasilof River (5%) and upper Kenai River (amp;lt;1%). Gulls primarily moved between the Soldotna landfill and the lower Kenai River (94% of transitions among sites), which were also the two locations with the highest prevalence of AMR E. coli. There was relatively high spatial and temporal variability in AMR E. coli prevalence in gull faeces and there was no evidence of contamination on salmon harvested in personal-use fisheries. We identified E. coli sequence types and AMR genes of clinical importance, with some isolates possessing genes associated with resistance to as many as eight antibiotic classes. Our findings suggest that gulls acquire AMR E. coli at habitats with anthropogenic inputs and subsequent movements may represent pathways through which AMR is dispersed.

  • 48.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, AK 99508 USA.
    Ramey, Andrew M.
    US Geol Survey, AK 99508 USA.
    Woksepp, Hanna
    Kalmar Council, Sweden.
    Bonnedahl, Jonas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences. Kalmar Council, Sweden.
    Early emergence of mcr-1-positive Enterobacteriaceae in gulls from Spain and Portugal2019In: Environmental Microbiology Reports, E-ISSN 1758-2229, Vol. 11, no 5, p. 669-671Article in journal (Refereed)
    Abstract [en]

    We tested extended-spectrum beta-lactamase producing bacteria from wild gulls (Larus spp.) sampled in 2009 for the presence of mcr-1. We report the detection of mcr-1 and describe genome characteristics of four Escherichia coli and one Klebsiella pneumoniae isolate from Spain and Portugal that also exhibited colistin resistance. Results represent the earliest evidence for colistin-resistant bacteria in European wildlife.

  • 49.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, AK 99508 USA.
    Ramey, Andrew M.
    US Geol Survey, AK 99508 USA.
    Woksepp, Hanna
    Dept Dev and Publ and Hlth, Sweden.
    Bonnedahl, Jonas
    Linköping University, Department of Clinical and Experimental Medicine, Division of Microbiology, Infection and Inflammation. Linköping University, Faculty of Medicine and Health Sciences. Dept Infect Dis, Sweden.
    Repeated Detection of Carbapenemase-Producing Escherichia coil in Gulls Inhabiting Alaska2019In: Antimicrobial Agents and Chemotherapy, ISSN 0066-4804, E-ISSN 1098-6596, Vol. 63, no 8, article id e00758-19Article in journal (Refereed)
    Abstract [en]

    Here, we report the first detection of carbapenemase-producing Escherichia coli in Alaska and in wildlife in the United States. Wild bird (gull) feces sampled at three locations in Southcentral Alaska yielded isolates that harbored plasmidencoded bla(kpc-2), or chromosomally encoded bla(OXA-48) and genes associated with antimicrobial resistance to up to eight antibiotic classes.

  • 50.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, USA.
    Scott, Laura C.
    US Geol Survey, USA.
    Woksepp, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Region Kalmar County, Sweden.
    Bonnedahl, Jonas
    Linköping University, Sweden;Region Kalmar County, Sweden.
    Ramey, Andrew M.
    US Geol Survey, USA.
    Environmental antimicrobial resistance gene detection from wild bird habitats using two methods: A commercially available culture-independent qPCR assay and culture of indicator bacteria followed by whole-genome sequencing2023In: Journal of Global Antimicrobial Resistance, ISSN 2213-7165, E-ISSN 2213-7173, Vol. 33, p. 186-193Article in journal (Refereed)
    Abstract [en]

    Objectives: A variety of methods have been developed to detect antimicrobial resistance (AMR) in differ-ent environments to better understand the evolution and dissemination of this public health threat. Com-parisons of results generated using different AMR detection methods, such as quantitative PCR (qPCR) and whole-genome sequencing (WGS), are often imperfect, and few studies have analysed samples in parallel to evaluate differences. In this study, we compared bacterial culture and WGS to a culture-independent commercially available qPCR assay to evaluate the concordance between methods and the utility of each in answering research questions regarding the presence and epidemiology of AMR in wild bird habitats.Methods: We first assessed AMR gene detection using qPCR in 45 bacterial isolates from which we had existing WGS data. We then analysed 52 wild bird faecal samples and 9 spatiotemporally collected water samples using culture-independent qPCR and WGS of phenotypically resistant indicator bacterial isolates.Results: Overall concordance was strong between qPCR and WGS of bacterial isolates, although concor-dance differed among antibiotic classes. Analysis of wild bird faecal and water samples revealed that more samples were determined to be positive for AMR via qPCR than via culture and WGS of bacterial isolates, although qPCR did not detect AMR genes in two samples from which phenotypically resistant isolates were found.Conclusions: Both qPCR and culture followed by sequencing may be effective approaches for characteris-ing AMR genes harboured by wild birds, although data streams produced using these different tools may have advantages and disadvantages that should be considered given the application and sample matrix.Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )

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