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  • 1.
    Abellan-Flos, Marta
    et al.
    Univ Namur, Belgium;PSL Univ, France.
    Timmer, Brian J. J.
    KTH Royal Institute of Technology, Sweden.
    Altun, Samuel
    Attana AB, Sweden.
    Aastrup, Teodor
    Attana AB, Sweden.
    Vincent, Stephane P.
    Univ Namur, Belgium.
    Ramström, Olof
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. KTH Royal Institute of Technology, Sweden;Univ Massachusetts, USA.
    QCM sensing of multivalent interactions between lectins and well-defined glycosylated nanoplatforms2019In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 139, article id 111328Article in journal (Refereed)
    Abstract [en]

    Quartz crystal microbalance (QCM) methodology has been adopted to unravel important factors contributing to the "cluster glycoside effect" observed in carbohydrate-lectin interactions. Well-defined, glycosylated nanostructures of precise sizes, geometries and functionalization patterns were designed and synthesized, and applied to analysis of the interaction kinetics and thermodynamics with immobilized lectins. The nanostructures were based on Borromean rings, dodecaamine cages, and fullerenes, each of which carrying a defined number of carbohydrate ligands at precise locations. The synthesis of the Borromeates and dodecaamine cages was easily adjustable due to the modular assembly of the structures, resulting in variations in presentation mode. The binding properties of the glycosylated nanoplatforms were evaluated using flow-through QCM technology, as well as hemagglutination inhibition assays, and compared with dodecaglycosylated fullerenes and a monovalent reference. With the QCM setup, the association and dissociation rate constants and the associated equilibrium constants of the interactions could be estimated, and the results used to delineate the multivalency effects of the lectin-nanostructure interactions.

  • 2.
    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.

  • 3.
    Abromaitis, V.
    et al.
    Kaunas Univ Technol, Lithuania ; Wetsus, European Ctr Excellence Sustainable Water Technol, Netherlands.
    Racys, V.
    Kaunas Univ Technol, Lithuania.
    van der Marel, P.
    WLN, Netherlands.
    Ni, Gaofeng
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wolthuizen, A. L.
    Wageningen Univ, Netherlands.
    Meulepas, R. J. W.
    Wetsus, European Ctr Excellence Sustainable Water Technol, Netherlands.
    Effect of shear stress and carbon surface roughness on bioregeneration and performance of suspended versus attached biomass in metoprolol-loaded biological activated carbon systems2017In: Chemical Engineering Journal, ISSN 1385-8947, E-ISSN 1873-3212, Vol. 317, p. 503-511Article in journal (Refereed)
    Abstract [en]

    The bioregeneration of activated carbon (AC) in biological activated carbon (BAC) systems is limited by sorption-desorption hysteresis and transport between the adsorbent and biomass. In this study, we investigated these limitations and whether a biofilm covering the AC surface is required. Consequently, BAC reactors were operated at different shear stress and AC surface smoothness, since this may affect biofilm formation. The experiments were carried out in BAC and blank reactors treating synthetic wastewater containing the pharmaceutical metoprolol. After start-up, all reactors removed metoprolol completely; however, after 840 h the removal dropped due to saturation of the AC. In the blank reactors, the removal dropped to 0% while in the BAC reactors removal recovered to >99%, due to increased biological activity. During the initial phase, the metoprolol was adsorbed, rather than biodegraded. At the end, the AC from the BAC reactors had higher pore volume and sorption capacity than from the blank reactors, showing that the AC had been bioregenerated. At high shear (G = 25 s(-1)), the rough AC granules (R-a = 13 mu m) were covered with a 50-400 gm thick biofilm and the total protein content of the biofilm was 2.6 mg/gAC, while at lower shear (G = 8.8 s(-1)) the rough AC granules were only partly covered. The biofilm formation at lower shear (G = 8.8 s(-1)) on smooth AC granules (R-a = 1.6 mu m) was negligible. However, due to the presence of suspended biomass the reactor performance or bioregeneration were not reduced. This showed that direct contact between the AC and biomass was not essential in mixed BAC systems. The microbial analyses of the suspended biomass and the biofilm on AC surface indicated that metoprolol was mainly biodegraded in suspension. (C) 2017 Elsevier B.V. All rights reserved.

  • 4.
    Abudaya, Mohammed
    et al.
    Natl Res Ctr, Palestine.
    Ulman, Aylin
    Univ British Columbia, Canada.
    Salah, Jehad
    Minist Agr, Palestine.
    Fernando, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Manta Trust, UK;Blue Resources Trust, Sri Lanka.
    Wor, Catarina
    Univ British Columbia, Canada.
    di Sciara, Giuseppe Notarbartolo
    Tethys Res Inst, Italy.
    Speak of the devil ray (Mobula mobular) fishery in Gaza2018In: Reviews in Fish Biology and Fisheries, ISSN 0960-3166, E-ISSN 1573-5184, Vol. 28, no 1, p. 229-239Article in journal (Refereed)
    Abstract [en]

    Little is known about the giant devil ray (Mobula mobular), an endangered species endemic to the Mediterranean. Gaza is the only region where this species is targeted, hence, this fishery was studied to address the knowledge gap on fishery interactions, species behavior, and life-history traits. Devil rays have been frequenting this maritime area for at least the past 50 years for a short window from February to April. Landings are reported from 2005 to 2016, along with disc-width (DW) measurements for recent years. A total of 304 M. mobular (over 90% males) were landed in Gaza from 2014 to 2016, most which were mature and appeared to be mating (over 90% of males had sperm-filled claspers), providing critical insight that this area may serve as a mating ground. Yearly landings are shown here to closely match the allowed fishing distance from shore, which changes regularly, indicating that the rays are normally caught between 6 and 12 n.m. offshore. Width-weight conversion parameters are calculated for the first time for this species: a = 2.68 x 10(-6) and b = 4.39. Fresh protein drives this local fishery, as food security is a major issue. An export market for gill plates was reported intermittently, and is no longer possible due to strict trade restrictions. We highlight the lack of awareness of fishers regarding the IUCN's Red List 'Endangered' status of devil rays, and stress the urgent need for national protection of this species, particularly due to the species' very slow life-history traits and probable usage of this area as a mating ground.

  • 5.
    Ackerfors, Viktoria
    Linnaeus University, Faculty of Technology, Department of Forestry and Wood Technology.
    Vilken inställning har Länsstyrelserna till naturvårdsbränningar i områden med fornlämningar och övriga kulturhistoriska lämningar?2020Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Skogsbränderna har en stor betydelse för den biologiska mångfalden. Det brandpåverkade landskapet och dess dynamik skapar viktiga substrat och livsmiljöer för många pyrofila arter. På grund av att skogsbränderna har minskat i antal sedan 1800-talet, har kontrollerade naturvårdsbränningar utförts som ett komplement för dessa sedan 1980-talet. De kontrollerade naturvårdsbränningarna skapar de miljöer och substrat som många arter är beroende av. Eftersom tidigare mänsklig verksamhet satt prägel på skogarna återfinns idag ett stort antal fornlämningar och övriga kulturhistoriska lämningar i skogsmarkerna. Det är en utmaning att utföra naturvårdsbränningarna så att dessa lämningar inte skadas. Det råder också en brist på tydliga riktlinjer om hur Länsstyrelserna ska förhålla sig till naturvårdsbränningar i områden med lämningar. Denna studies syfte var att undersöka vilken inställning Länsstyrelserna har till naturvårdsbränningar i områden med fornlämningar eller övriga kulturhistoriska lämningar.

    Nyckelord: Naturvårdsbränningar, fornlämningar, övriga kulturhistoriska lämningar, Länsstyrelsen

    Keyword: Prescribed burnings, ancient remains, other cultural-historical remains, County Administrative Boards

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  • 6.
    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.

  • 7.
    Acuña, Ulyana Muñoz
    et al.
    Ohio State University, USA.
    Curley, Robert W
    Ohio State University, USA.
    Fatima, Nighat
    Quaid-i-Azam University, Pakistan;University of Hawaii at Hilo, USA.
    Ahmed, Safia
    Quaid-i-Azam University, Pakistan.
    Chang, Leng Chee
    University of Hawaii at Hilo, USA.
    De Blanco, Esperanza J Carcache
    Ohio State University, USA.
    Differential Effect of Wortmannolone Derivatives on MDA-MB-231 Breast Cancer Cells.2017In: Anticancer Research, ISSN 0250-7005, E-ISSN 1791-7530, Vol. 37, no 4, p. 1617-1623Article in journal (Refereed)
    Abstract [en]

    BACKGROUND/AIM: The survival rate of women diagnosed with triple-negative breast-cancer (TNBC) remains low. Hence, this study aimed at the chemical and biological optimization of furanosteroid derivatives for the treatment of this type of malignancy using TNBC cells.

    MATERIALS AND METHODS: Semi-synthetic analogs of wortmannolone (1-6) that negatively affected the aberrant pathways in tumor cells were evaluated in hormone-independent breast cancer cells using western blot and cell-cycle analysis.

    RESULTS: Wortmannolone derivatization generated NF-ĸB inhibitors as new lead structures for further development. Compound (3) was found to be the most significantly active lead.

    CONCLUSION: Structure-activity analysis in the present study showed that acetylation of the hydroxyl groups and substitution on C3 and C17 of wortmannolone enhanced biological activity. Alpha-substitution of the acetyl group in C3 on ring A (compound 3) resulted in ROS inducing effect; however, presence of an acetyl group in β-position of C3 displayed the highest NF-ĸB p65 inhibitory activity (0.60 μM).

  • 8.
    Adler, Anna
    et al.
    Uppsala University, Sweden.
    Fritsch, Marlene
    Uppsala University, Sweden.
    Fromell, Karin
    Uppsala University, Sweden.
    Leneweit, Gero
    ABNOBA GmbH, Germany;Assoc Promot Canc Therapy, Germany.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala University, Sweden.
    Nilsson, Bo
    Uppsala University, Sweden.
    Teramura, Yuji
    Uppsala University, Sweden;Cellular & Mol Biotechnol Res Inst CMB, Japan;Univ Tsukuba, Japan.
    Regulation of the innate immune system by fragmented heparin-conjugated lipids on lipid bilayered membranes in vitro2023In: Journal of materials chemistry. B, ISSN 2050-750X, E-ISSN 2050-7518, Vol. 11, no 46, p. 11121-11134Article in journal (Refereed)
    Abstract [en]

    Surface modification with heparin is a powerful biomaterial coating strategy that protects against innate immunity activation since heparin is a part of the proteoglycan heparan sulfate on cell surfaces in the body. We studied the heparinization of cellular and material surfaces via lipid conjugation to a heparin-binding peptide. In the present study, we synthesized fragmented heparin (fHep)-conjugated phospholipids and studied their regulation of the innate immune system on a lipid bilayered surface using liposomes. Liposomes have versatile applications, such as drug-delivery systems, due to their ability to carry a wide range of molecules. Owing to their morphological similarity to cell membranes, they can also be used to mimic a simple cell-membrane to study protein-lipid interactions. We investigated the interaction of complement-regulators, factor H and C4b-binding protein (C4BP), as well as the coagulation inhibitor antithrombin (AT), with fHep-lipids on the liposomal surface. Herein, we studied the ability of fHep-lipids to recruit factor H, C4BP, and AT using a quartz crystal microbalance with dissipation monitoring. With dynamic light scattering, we demonstrated that liposomes could be modified with fHep-lipids and were stable up to 60 days at 4 degree celsius. Using a capillary western blot-based method (Wes), we showed that fHep-liposomes could recruit factor H in a model system using purified proteins and assist in the degradation of the active complement protein C3b to iC3b. Furthermore, we found that fHep-liposomes could recruit factor H and AT from human plasma. Therefore, the use of fHep-lipids could be a potential coating for liposomes and cell surfaces to regulate the immune system on the lipid surface.

  • 9.
    Adler, Anna
    et al.
    Uppsala University, Sweden.
    Inoue, Yuuki
    The University of Tokyo, Japan.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Baba, Teruhiko
    National Institute of Advanced Industrial Science and Technology, Japan.
    Ishihara, Kazuhiko
    The University of Tokyo, Japan.
    Nilsson, Bo
    Uppsala University, Sweden.
    Teramura, Yuji
    Uppsala University, Sweden;National Institute of Advanced Industrial Science and Technology, Japan.
    Effect of liposome surface modification with water-soluble phospholipid polymer chain-conjugated lipids on interaction with human plasma proteins2022In: Journal of materials chemistry. B, ISSN 2050-750X, E-ISSN 2050-7518, Vol. 10, no 14, p. 2512-2522Article in journal (Refereed)
    Abstract [en]

    Alternative liposome surface coatings for PEGylation to evade the immune system, particularly the complement system, have garnered significant interest. We previously reported poly(2-methacryloyloxyethyl phosphorylcholine) (MPC)-based lipids (PMPC-lipids) and investigated the surface modification of liposomes. In this study, we synthesize PMPC-lipids with polymerization degrees of 10 (MPC10-lipid), 20 (MPC20-lipid), 50 (MPC50-lipid), and 100 (MPC100-lipid), and coated liposomes with 1, 5, or 10 mol% PMPC-lipids (PMPC-liposomes). Non-modified and PEGylated liposomes are used as controls. We investigate the liposome size, surface charge, polydispersity index, and adsorption of plasma proteins to the liposomes post incubation in human plasma containing N,N,N′,N′-ethylenediamine tetraacetic acid (EDTA) or lepirudin by some methods such as sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE), western blotting, and automated capillary western blot, with emphasis on the binding of complement protein C3. It is shown that the coating of liposome PMPC-lipids can suppress protein adsorption more effectively with an increase in the molecular weight and molar ratio (1-10 mol%). Apolipoprotein A-I is detected on PMPC-liposomes with a higher molecular weight and higher molar ratio of PMPC-lipids, whereas α2-macroglobulin is detected on non-modified, PEGylated, and PMPC-liposomes with a shorter polymer chain. In addition, a correlation is shown among the PMPC molecular weight, molar ratio, and C3 binding. The MPC10-lipid cannot inhibit C3 binding efficiently, whereas surface modifications with 10 mol% MPC20-lipid and 5 mol% and 10 mol% MPC50-lipid suppress both total protein and C3 binding. Hence, liposome modification with PMPC-lipids can be a possible strategy for avoiding complement activation.

  • 10.
    Adler, Anna
    et al.
    Uppsala University, Sweden.
    Inoue, Yuuki
    Univ Tokyo, Japan.
    Sato, Yuya
    Univ Tokyo, Japan.
    Ishihara, Kazuhiko
    Univ Tokyo, Japan.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Linnaeus University, Linnaeus Knowledge Environments, Advanced Materials. Uppsala University, Sweden.
    Nilsson, Bo
    Uppsala University, Sweden.
    Teramura, Yuji
    Uppsala University, Sweden;Univ Tokyo, Japan;Natl Inst Adv Ind Sci & Technol, Japan.
    Synthesis of poly(2-methacryloyloxyethyl phosphorylcholine)-conjugated lipids and their characterization and surface properties of modified liposomes for protein interactions2021In: Biomaterials Science, ISSN 2047-4830, E-ISSN 2047-4849, Vol. 9, no 17, p. 5854-5867Article in journal (Refereed)
    Abstract [en]

    Poly(ethylene glycol) (PEG) is frequently used for liposomal surface modification. However, as PEGylated liposomes are cleared rapidly from circulation upon repeated injections, substitutes of PEG are being sought. We focused on a water-soluble polymer composed of 2-methacryloyloxyethyl phosphorylcholine (MPC) units, and synthesized poly(MPC) (PMPC)-conjugated lipid (PMPC-lipid) with degrees of MPC polymerization ranging from 10 to 100 (calculated molecular weight: 3 to 30 kDa). In addition, lipids with three different alkyl chains, myristoyl, palmitoyl, and stearoyl, were applied for liposomal surface coating. We studied the interactions of PMPC-lipids with plasma albumin, human complement protein C3 and fibrinogen using a quartz crystal microbalance with energy dissipation, and found that adsorption of albumin, C3 and fibrinogen could be suppressed by coating with PMPC-lipids. In particular, the effect was more pronounced for PMPC chains with higher molecular weight. We evaluated the size, polydispersity index, surface charge, and membrane fluidity of the PMPC-lipid-modified liposomes. We found that the effect of the coating on the dispersion stability was maintained over a long period (98 days). Furthermore, we also demonstrated that the anti-PEG antibody did not interact with PMPC-lipids. Thus, our findings suggest that PMPC-lipids can be used for liposomal coating.

  • 11.
    Adler, Anna
    et al.
    Uppsala University, Sweden.
    Manivel, Vivek Anand
    Uppsala University, Sweden.
    Fromell, Karin
    Uppsala University, Sweden.
    Teramura, Yuji
    Uppsala University, Sweden;Cellular & Mol Biotechnol Res Inst CMB, Japan.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala University, Sweden.
    Nilsson, Bo
    Uppsala University, Sweden.
    A Robust Method to Store Complement C3 With Superior Ability to Maintain the Native Structure and Function of the Protein2022In: Frontiers in Immunology, E-ISSN 1664-3224, Vol. 13, article id 891994Article in journal (Refereed)
    Abstract [en]

    Complement components have a reputation to be very labile. One of the reasons for this is the spontaneous hydrolysis of the internal thioester that is found in both C3 and C4 (but not in C5). Despite the fact that approximate to 20,000 papers have been published on human C3 there is still no reliable method to store the protein without generating C3(H2O), a fact that may have affected studies of the conformation and function of C3, including recent studies on intracellular C3(H2O). The aim of this work was to define the conditions for storage of native C3 and to introduce a robust method that makes C3 almost resistant to the generation of C3(H2O). Here, we precipitated native C3 at the isoelectric point in low ionic strength buffer before freezing the protein at -80 degrees C. The formation of C3(H2O) was determined using cation exchange chromatography and the hemolytic activity of the different C3 preparations was determined using a hemolytic assay for the classical pathway. We show that freezing native C3 in the precipitated form is the best method to avoid loss of function and generation of C3(H2O). By contrast, the most efficient way to consistently generate C3(H2O) was to incubate native C3 in a buffer at pH 11.0. We conclude that we have defined the optimal storage conditions for storing and maintaining the function of native C3 without generating C3(H2O) and also the conditions for consistently generating C3(H2O).

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  • 12.
    Adolfsson Jörby, Sofie
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Local Agenda 21 in practice: a Swedish example2000In: Sustainable Development, ISSN 0968-0802, Vol. 8, no 4, p. 201-214Article in journal (Refereed)
  • 13.
    Adolfsson, Oscar
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Consequences on population dynamics following regained connectivity in pike (Esox lucius) spawning location2020Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Distributional movements of subpopulations may act as a buffer to prevent the loss of a species in a certain area. However, within subpopulations adaptations may evolve that makes the inhabitants of a certain habitat to better cope with prevailing environmental conditions. If such traits are related to reproduction, they may reduce the opportunity of gene exchange between other subpopulations. Also, a lack of adaptations to a specific habitat may be what prevents a group of individuals, arriving from an adjacent habitat, to successfully colonize an area where a previous subpopulation has been lost.This is the report from a field study conducted in the wetland Lake Långsjön, that in 2018 was restored in order to promote the recruitment of anadromous pike (Esox lucius) to the Baltic Sea. Commonly, wetlands that are restored to promote anadromous pike recruitment, are constructed so that they enable spawning migration from the sea towards the wetland and juvenile emigration towards the sea only. In that sense Lake Långsjön is different, from other wetlands restored for the same purpose, due to that it is connected to both the Baltic Sea and an upstream located freshwater lake. By quantifying the migration of pike (spawners and juveniles) in both directions I explore the consequences that the regained connectivity between the Lake Långsjön and the coast may have on the population dynamics within this wetland; (i) whether it is potentially influenced by allowing mixture between pike with different migratory strategies for spawning (anadromous and potamodromous), (ii) what drivers there are of pike fry emigration and how they may influence the pike fry emigration route and (iii) whether or not the pike of potamodromous origin, resident in the upstream located lake, may work as a source, providing the Baltic Sea with pike juveniles. Pike spawners arriving in the wetland were caught in traps between March - April. Pike fry were caught withing the wetland with fyke nets and by netting. Emigrating pike fry were caught in fyke nets. Findings suggest that spawning migration patterns do not differ between anadromous and potamodromous pike. However, the spawners arriving from the Baltic Sea I suggested are to be composed by offspring of potamodromous origin, possibly hatched during the previous season, and that they as juveniles swam downstream. This, in turn, indicates that the potamodromous stock can help establish an anadromous stock in the Baltic Sea. Still, due to the observation of pike fry displaying an emigration behaviour upstream, origin is identified as a factor that may influence the pike fry emigration route. Also, this emigration pattern seems to indicate a heritable trait that has not been described before among pike, that of downstream spawning. The restoration of the wetland and the regained connectivity is key, both for the ability to restock the Baltic Sea with pike juveniles but also to ensure the conservation of a fascinating stock of pike exhibiting a unique spawning strategy

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  • 14.
    Aeinehband, Shahin
    et al.
    Karolinska Institutet.
    Lindblom, Rickard P. F.
    Karolinska Institutet.
    Al Nimer, Faiez
    Karolinska Institutet.
    Vijayaraghavan, Swetha
    Karolinska Institutet.
    Sandholm, Kerstin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Khademi, Mohsen
    Karolinska Institutet.
    Olsson, Tomas
    Karolinska Institutet.
    Nilsson, Bo
    Uppsala University.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala University.
    Darreh-Shori, Taher
    Karolinska Institutet.
    Piehl, Fredrik
    Karolinska Institutet.
    Complement Component C3 and Butyrylcholinesterase Activity Are Associated with Neurodegeneration and Clinical Disability in Multiple Sclerosis2015In: PLOS ONE, E-ISSN 1932-6203, Vol. 10, no 4, article id e0122048Article in journal (Refereed)
    Abstract [en]

    Dysregulation of the complement system is evident in many CNS diseases but mechanisms regulating complement activation in the CNS remain unclear. In a recent large rat genomewide expression profiling and linkage analysis we found co-regulation of complement C3 immediately downstream of butyrylcholinesterase (BuChE), an enzyme hydrolyzing acetylcholine (ACh), a classical neurotransmitter with immunoregulatory effects. We here determined levels of neurofilament-light (NFL), a marker for ongoing nerve injury, C3 and activity of the two main ACh hydrolyzing enzymes, acetylcholinesterase (AChE) and BuChE, in cerebrospinal fluid (CSF) from patients with MS (n = 48) and non-inflammatory controls (n = 18). C3 levels were elevated in MS patients compared to controls and correlated both to disability and NFL. C3 levels were not induced by relapses, but were increased in patients with >= 9 cerebral lesions on magnetic resonance imaging and in patients with progressive disease. BuChE activity did not differ at the group level, but was correlated to both C3 and NFL levels in individual samples. In conclusion, we show that CSF C3 correlates both to a marker for ongoing nerve injury and degree of disease disability. Moreover, our results also suggest a potential link between intrathecal cholinergic activity and complement activation. These results motivate further efforts directed at elucidating the regulation and effector functions of the complement system in MS, and its relation to cholinergic tone.

  • 15.
    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.

  • 16.
    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.

  • 17.
    Aguilera, Anabella
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Almanza, Viviana
    Univ Concepcion, Chile.
    Haakonsson, Signe
    Univ Republica, Uruguay.
    Palacio, Hilda
    Univ CES, Colombia.
    Rodas, Gilberto A. Benitez
    Univ Nacl Asuncion, Paraguay.
    Barros, Mario U. G.
    Univ Fed Ceara, Brazil;Water Resources Management Co Ceara, Brazil.
    Capelo-Neto, Jose
    Univ Fed Ceara, Brazil.
    Urrutia, Roberto
    Univ Concepcion, Chile.
    Aubriot, Luis
    Univ Republica, Uruguay.
    Bonilla, Sylvia
    Univ Republica, Uruguay.
    Cyanobacterial bloom monitoring and assessment in Latin America2023In: Harmful Algae, ISSN 1568-9883, E-ISSN 1878-1470, Vol. 125, article id 102429Article in journal (Refereed)
    Abstract [en]

    Cyanobacterial blooms have serious adverse effects on human and environmental health. In Latin America, one of the main world's freshwater reserves, information on this phenomenon remains sparse. To assess the current situation, we gathered reports of cyanobacterial blooms and associated cyanotoxins in freshwater bodies from South America and the Caribbean (Latitude 22 degrees N to 45 degrees S) and compiled the regulation and monitoring procedures implemented in each country. As the operational definition of what is a cyanobacterial bloom remains controversial, we also analyzed the criteria used to determine the phenomena in the region. From 2000 to 2019, blooms were reported in 295 water bodies distributed in 14 countries, including shallow and deep lakes, reservoirs, and rivers. Cyanotoxins were found in nine countries and high concentrations of microcystins were reported in all types of water bodies. Blooms were defined according to different, and sometimes arbitrary criteria including qualitative (changes in water color, scum presence), quantitative (abundance), or both. We found 13 different cell abundance thresholds defining bloom events, from 2 x 10(3) to 1 x 10(7) cells mL(-1). The use of different criteria hampers the estimation of bloom occurrence, and consequently the associated risks and economic impacts. The large differences between countries in terms of number of studies, monitoring efforts, public access to the data and regulations regarding cyanobacteria and cyanotoxins highlights the need to rethink cyanobacterial bloom monitoring, seeking common criteria. General policies leading to solid frameworks based on defined criteria are needed to improve the assessment of cyanobacterial blooms in Latin America. This review represents a starting point toward common approaches for cyanobacterial monitoring and risk assessment, needed to improve regional environmental policies.

  • 18.
    Aguilera, Anabella
    et al.
    Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Argentina.
    Berdun, Federico
    Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Argentina.
    Bartoli, Carlos
    Universidad Nacional de La Plata, Argentina.
    Steelheart, Charlotte
    Universidad Nacional de La Plata, Argentina.
    Alegre, Matías
    Universidad Nacional de La Plata, Argentina.
    Bayir, Hülya
    University of Pittsburgh, USA.
    Tyurina, Yulia Y.
    University of Pittsburgh, USA.
    Kagan, Valerian E.
    University of Pittsburgh, USA;IM Sechenov Moscow State Medical University, Russia.
    Salerno, Graciela
    Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Argentina.
    Pagnussat, Gabriela
    Universidad Nacional de Mar del Plata, Argentina.
    Martin, María Victoria
    Fundación para Investigaciones Biológicas Aplicadas (CIB-FIBA), Argentina.
    C-ferroptosis is an iron-dependent form of regulated cell death in cyanobacteria2021In: Journal of Cell Biology, ISSN 0021-9525, E-ISSN 1540-8140, Vol. 221, no 2, article id e201911005Article in journal (Refereed)
    Abstract [en]

    Ferroptosis is an oxidative and iron-dependent form of regulated cell death (RCD) recently described in eukaryotic organisms like animals, plants, and parasites. Here, we report that a similar process takes place in the photosynthetic prokaryote Synechocystis sp. PCC 6803 in response to heat stress. After a heat shock, Synechocystis sp. PCC 6803 cells undergo a cell death pathway that can be suppressed by the canonical ferroptosis inhibitors, CPX, vitamin E, Fer-1, liproxstatin-1, glutathione (GSH), or ascorbic acid (AsA). Moreover, as described for eukaryotic ferroptosis, this pathway is characterized by an early depletion of the antioxidants GSH and AsA, and by lipid peroxidation. These results indicate that all of the hallmarks described for eukaryotic ferroptosis are conserved in photosynthetic prokaryotes and suggest that ferroptosis might be an ancient cell death program.

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  • 19.
    Aguilera, Anabella
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Distéfano, Ayelén
    Universidad Nacional de Mar del Plata, Argentina.
    Jauzein, Cécile
    Ifremer, France.
    Correa-Aragunde, Natalia
    Universidad Nacional de Mar del Plata, Argentina.
    Martinez, Dana
    Universidad Nacional de La Plata, Argentina.
    Martin, María Victoria
    Fundación para InveUniversidad Nacional de Mar del Plata, Argentina.
    Sueldo, Daniela J
    Norwegian University of Science and Technology, Norway.
    Do photosynthetic cells communicate with each other during cell death? From cyanobacteria to vascular plants2022In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 73, no 22, p. 7219-7242Article, review/survey (Refereed)
    Abstract [en]

    As in metazoans, life in oxygenic photosynthetic organisms relies on the accurate regulation of cell death. During development and in response to the environment, photosynthetic cells activate and execute cell death pathways that culminate in the death of a specific group of cells, a process known as regulated cell death (RCD). RCD control is instrumental, as its misregulation can lead to growth penalties and even the death of the entire organism. Intracellular molecules released during cell demise may act as ‘survival’ or ‘death’ signals and control the propagation of cell death to surrounding cells, even in unicellular organisms. This review explores different signals involved in cell-cell communication and systemic signalling in photosynthetic organisms, in particular Ca2+, reactive oxygen species, lipid derivates, nitric oxide, and eATP. We discuss their possible mode-of-action as either ‘survival’ or ‘death’ molecules and their potential role in determining cell fate in neighbouring cells. By comparing the knowledge available across the taxonomic spectrum of this coherent phylogenetic group, from cyanobacteria to vascular plants, we aim at contributing to the identification of conserved mechanisms that control cell death propagation in oxygenic photosynthetic organisms 

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  • 20.
    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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  • 21.
    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.

  • 22.
    Aguirre-Gutierrez, Jesus
    et al.
    Naturalis Biodivers Ctr, Netherlands;Univ Oxford, UK;Univ Amsterdam, Netherlands.
    WallisDeVries, Michiel F.
    De Vlinderstichting, Netherlands;Wageningen Univ, Netherlands.
    Marshall, Leon
    Naturalis Biodivers Ctr, Netherlands;Univ Namur, Belgium.
    van't Zelfde, Maarten
    Naturalis Biodivers Ctr, Netherlands;Leiden Univ, Netherlands.
    Villalobos-Arambula, Alma R.
    Univ Guadalajara, Mexico.
    Boekelo, Bastiaen
    Wageningen Univ & Res, Netherlands.
    Bartholomeus, Harm
    Wageningen Univ & Res, Netherlands.
    Franzén, Markus
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. UFZ, Helmholtz Ctr Environm Res, Germany.
    Biesmeijer, Jacobus C.
    Naturalis Biodivers Ctr, Netherlands;Leiden Univ, Netherlands.
    Butterflies show different functional and species diversity in relationship to vegetation structure and land use2017In: Global Ecology and Biogeography, ISSN 1466-822X, E-ISSN 1466-8238, Vol. 26, no 10, p. 1126-1137Article in journal (Refereed)
    Abstract [en]

    AimBiodiversity is rapidly disappearing at local and global scales also affecting the functional diversity of ecosystems. We aimed to assess whether functional diversity was correlated with species diversity and whether both were affected by similar land use and vegetation structure drivers. Better understanding of these relationships will allow us to improve our predictions regarding the effects of future changes in land use on ecosystem functions and services. LocationThe Netherlands. MethodsWe compiled a dataset of c.3 million observations of 66 out of 106 known Dutch butterfly species collected across 6,075 sampling locations during a period of 7 years, together with very high-resolution maps of land use and countrywide vegetation structure data. Using a mixed-effects modelling framework, we investigated the relationship between functional and species diversity and their main land use and vegetation structure drivers. ResultsWe found that high species diversity does not translate into high functional diversity, as shown by their different spatial distribution patterns in the landscape. Functional and species diversity are mainly driven by different sets of structural and land use parameters (especially average vegetation height, amount of vegetation between 0.5 and 2m, natural grassland, sandy soils vegetation, marsh vegetation and urban areas). We showed that it is a combination of both vegetation structural characteristics and land use variables that defines functional and species diversity. Main conclusionsFunctional diversity and species diversity of butterflies are not consistently correlated and must therefore be treated separately. High functional diversity levels occurred even in areas with low species diversity. Thus, conservation actions may differ depending on whether the focus is on conservation of high functional diversity or high species diversity. A more integrative analysis of biodiversity at both species and trait levels is needed to infer the full effects of environmental change on ecosystem functioning.

  • 23.
    Aguirre-Gutiérrez, Jesús
    et al.
    Naturalis Biodiversity Center, The Netherlands ; University of Amsterdam, The Netherlands.
    Kissling, W. Daniel
    University of Amsterdam, The Netherlands.
    Carvalheiro, Luísa G.
    Universidade de Brasília, Brazil ; University of Lisbon, Portugal.
    WallisDeVries, Michiel F.
    Wageningen University, The Netherlands.
    Franzén, Markus
    Helmholtz-Centre for Environmental Research - UFZ, Germany.
    Biesmeijer, Jacobus C.
    Naturalis Biodiversity Center, The Netherlands ; University of Amsterdam, The Netherlands.
    Functional traits help to explain half-century long shifts in pollinator distributions2016In: Scientific Reports, E-ISSN 2045-2322, Vol. 6, article id 24451Article in journal (Refereed)
    Abstract [en]

    Changes in climate and land use can have important impacts on biodiversity. Species respond to such environmental modifications by adapting to new conditions or by shifting their geographic distributions towards more suitable areas. The latter might be constrained by species’ functional traits that influence their ability to move, reproduce or establish. Here, we show that functional traits related to dispersal, reproduction, habitat use and diet have influenced how three pollinator groups (bees, butterflies and hoverflies) responded to changes in climate and land-use in the Netherlands since 1950. Across the three pollinator groups, we found pronounced areal range expansions (>53%) and modelled range shifts towards the north (all taxa: 17–22 km), west (bees: 14 km) and east (butterflies: 11 km). The importance of specific functional traits for explaining distributional changes varied among pollinator groups. Larval diet preferences (i.e. carnivorous vs. herbivorous/detritivorous and nitrogen values of host plants, respectively) were important for hoverflies and butterflies, adult body size for hoverflies, and flight period length for all groups. Moreover, interactions among multiple traits were important to explain species’ geographic range shifts, suggesting that taxon-specific multi-trait analyses are needed to predict how global change will affect biodiversity and ecosystem services.

  • 24.
    Ahlberg, Louise
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Molecular sexing and species determination of the Sylvia cantillans complex.2022Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Abstract

    The Sylvia cantillans complex is a collection of closely related passerine birds including three species (S. cantillans, S. subalpina and S. inornata) that are further subdivided into four subspecies (S. c. cantillans, S. c. albistriata, S. i. inornata, S. i. iberiae). All taxa in the complex are morphologically similar and difficult to discern from each other based on plumage. Furthermore, sexing birds is also difficult as females and males without breeding plumage are almost identical. In this study I used molecular methods to identify S. cantillans complex birds in order to compare field-based and molecular observations. DNA was extracted from a set of feathers collected from S. cantillans complex birds from Italy to determine species, based on mitochondrial gene cytochrome b sequences. The sex was determined using PCR amplicon profiles of CHD1W and CHD1Z genes that differ in size between males and females. The cytochrome b amplification was successful in all feathers and CHD1W and CHD1Z in all but two. The molecular work was compared with the results of phenotypic identification made by ringers and expert ornithologists. The experts on average, identified the correct species in 51% of the warblers, and sex 66% and 64% for females and males respectively. This highlights that molecular methods are highly effective to determine species and sex and that they are more reliable than identification by plumage alone. This is important to keep in mind in studies of diversity and conservation to avoid underestimating the number of species and the sex of individuals involved, which might cause more harm than good.

  • 25.
    Ahlstrand, Emma
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Metal ions in life: towards accurate computer-aided studies ofprotein-ion interactions2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The importance of ions in life sciences can not be overstated. The interaction betweenmetal ions and proteins is vital because it is involved in a variety of biological processes.The ions contribute to stability and function of proteins. Moreover, they are relevant indisease progression.Realistic computer simulations pave the way for drug development, through providingdetailed insights into the dynamics of proteins and various biological processes thatoccur in the body. Such information can be impossible to achieve through experimentsof living subjects in vivo or from test tube experiments in vitro alone. However,theoretical methods have to result in accurate predictions. In my thesis, I studieddifferent ways to handle the ions in simulations. Since the systems contain thousands ofatoms the calculations are demanding. Despite the availability of computer clusters, thecom putational capacity is not sufficient. I have examined the simplified models used insimulations of larger systems (e.g., whole proteins) to pave the way for improvements ofthe simulation models.Different ions have different effects on biochemical systems and it is important to beable to distinguish between them. Thus, from a biochemical point of view, it is centralto be able to describe their unique characteristics. Their difference can be from vital totoxic to the body. Zinc is essential and present in more than 3000 proteins in our bodyand has a very flexible interaction with proteins. This property has proved to be hard toreproduce in computer simulations. Cadmium can replace zinc, but is toxic because itdoes not have the same catalytic ability. From a modelling perspective do these ions havesimilar characteristics as they have the same ionic charge. Inclusion of more realisticelectron effects may be necessary to be able to simulate the difference.With my studies, I have contributed towards a better understanding of the interactionsbetween metal ions and proteins. I have pointed out a direction for further improvementof methods for simulations of large systems.For the same purpose, I have also studied the frequently occurring ions sodium andpotassium found as salts in all body fluids, but also lithium belonging to the same groupin the periodic table and used in therapeutic purposes. The results show that potassiumand sodium can be simulated by a commonly used computational approach, whereasmore advanced methods are required to study lithium ions accurately.Overall, the work within this thesis has explored ion-protein interactions and providedinformation about methods for energy calculations and models for molecular dynamicssimulations for some of the most important ions within biochemistry.

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  • 26.
    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.

  • 27.
    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/ )

  • 28.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, USA.
    van Toor, Mariëlle L.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Woksepp, Hanna
    Kalmar County Hospital, Sweden.
    Chandler, Jeffrey C.
    USDA APHIS WS, USA.
    Reed, John A.
    US Geol Survey, USA.
    Reeves, Andrew B.
    US Geol Survey, USA.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Franklin, Alan B.
    USDA APHIS WS, USA.
    Douglas, David C.
    US Geol Survey, USA.
    Bonnedahl, Jonas
    Linköping University, Sweden;Region Kalmar county, Sweden.
    Ramey, Andrew M.
    US Geol Survey, USA.
    Evidence for continental-scale dispersal of antimicrobial resistant bacteria by landfill-foraging gulls2021In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 764, p. 1-10, article id 144551Article, review/survey (Refereed)
    Abstract [en]

    Anthropogenic inputs into the environment may serve as sources of antimicrobial resistant bacteria and alter the ecology and population dynamics of synanthropic wild animals by providing supplemental forage. In this study, we used a combination of phenotypic and genomic approaches to characterize antimicrobial resistant indicator bacteria, animal telemetry to describe host movement patterns, and a novel modeling approach to combine information from these diverse data streams to investigate the acquisition and long-distance dispersal of antimicrobial resistant bacteria by landfill-foraging gulls. Our results provide evidence that gulls acquire antimicrobial resistant bacteria from anthropogenic sources, which they may subsequently disperse across and between continents via migratory movements. Furthermore, we introduce a flexible modeling framework to estimate the relative dispersal risk of antimicrobial resistant bacteria in western North America and adjacent areas within East Asia, which may be adapted to provide information on the risk of dissemination of other organisms and pathogens maintained by wildlife through space and time. Published by Elsevier B.V.

  • 29.
    Ahlstrom, Christina A.
    et al.
    US Geol Survey, USA.
    Woksepp, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Medicine and Optometry. Kalmar County Hospital, Sweden.
    Sandegren, Linus
    Uppsala University, Sweden.
    Mohsin, Mashkoor
    Univ Agr Faisalabad, Pakistan.
    Hasan, Badrul
    Uppsala University, Sweden;Anim Bacteriol Sect, Australia.
    Muzyka, Denys
    Inst Expt & Clin Vet Med, Ukraine.
    Hernandez, Jorge
    Kalmar County Hospital, Sweden.
    Aguirre, Filip
    Kalmar County Hospital, Sweden.
    Tok, Atalay
    Uppsala University, Sweden.
    Söderman, Jan
    Linköping University, Sweden.
    Olsen, Björn
    Uppsala University, Sweden.
    Ramey, Andrew M.
    US Geol Survey, USA.
    Bonnedahl, Jonas
    Linköping University, Sweden;Region Kalmar County, Sweden.
    Genomically diverse carbapenem resistant Enterobacteriaceae from wild birds provide insight into global patterns of spatiotemporal dissemination2022In: Science of the Total Environment, ISSN 0048-9697, E-ISSN 1879-1026, Vol. 824, article id 153632Article in journal (Refereed)
    Abstract [en]

    Carbapenem resistant Enterobacteriaceae (CRE) are a threat to public health globally, yet the role of the environment in the epidemiology of CRE remains elusive. Given that wild birds can acquire CRE, likely from foraging in anthropogenically impacted areas, and may aid in the maintenance and dissemination of CRE in the environment, a spatiotemporal comparison of isolates from different regions and timepoints may be useful for elucidating epidemiological information. Thus, we characterized the genomic diversity of CRE from fecal samples opportunistically collected from gulls (Larus spp.) inhabiting Alaska (USA), Chile, Spain, Turkey, and Ukraine and from black kites (Milvus migrans) sampled in Pakistan and assessed evidence for spatiotemporal patterns of dissemination. Within and among sampling locations, a high diversity of carbapenemases was found, including Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-beta-lactamase (NDM), oxacillinase (OXA), and Verona integron Metallo beta-lactamase (VIM). Although the majority of genomic comparisons among samples did not provide evidence for spatial dissemination, we did find strong evidence for dissemination among Alaska, Spain, and Turkey. We also found strong evidence for temporal dissemination among samples collected in Alaska and Pakistan, though the majority of CRE clones were transitory and were not repeatedly detected among locations where samples were collected longitudinally. Carbapenemase-producing hypervirulent K. pneumoniae was isolated from gulls in Spain and Ukraine and some isolates harbored antimicrobial resistance genes conferring resistance to up to 10 different antibiotic classes, including colistin. Our results are consistent with local acquisition of CRE by wild birds with spatial dissemination influenced by intermediary transmission routes, likely involving humans. Furthermore, our results support the premise that anthropogenicallyassociated wild birds may be good sentinels for understanding the burden of clinically-relevant antimicrobial resistance in the local human population.

  • 30.
    Akram, Neelam
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    From genes to ecological function in marine bacteria2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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

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  • 31.
    Akram, Neelam
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Palovaara, Joakim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Forsberg, Jeremy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Milton, Debra L.
    Luo, Haiwei
    Gonzalez, Jose M.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp AND42013In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 15, no 5, p. 1400-1415Article in journal (Refereed)
    Abstract [en]

    Proteorhodopsin (PR), a ubiquitous membrane photoprotein in marine environments, acts as a light-driven proton pump and can provide energy for bacterial cellular metabolism. However, knowledge of factors that regulate PR gene expression in different bacteria remains strongly limited. Here, experiments with Vibrio sp. AND4 showed that PR phototrophy promoted survival only in cells from stationary phase and not in actively growing cells. PR gene expression was tightly regulated, with very low values in exponential phase, a pronounced peak at the exponential/stationary phase intersection, and a marked decline in stationary phase. Thus, PR gene expression at the entry into stationary phase preceded, and could therefore largely explain, the stationary phase light-induced survival response in AND4. Further experiments revealed nutrient limitation, not light exposure, regulated this differential PR expression. Screening of available marine vibrios showed that the PR gene, and thus the potential for PR phototrophy, is found in at least three different clusters in the genus Vibrio. In an ecological context, our findings suggest that some PR-containing bacteria adapted to the exploitation of nutrient-rich micro-environments rely on a phase of relatively slowly declining resources to mount a cellular response preparing them for adverse conditions dispersed in the water column.

  • 32.
    Alam, A. B. M. Sarowar
    et al.
    IUCN Bangladesh, Dhaka, Bangladesh..
    Ahmed, Sakib
    IUCN Bangladesh, Bangladesh.
    Azmiri, Kazi Zenifar
    IUCN Bangladesh, Bangladesh.
    Amin, Raquibul
    IUCN Bangladesh, Bangladesh.
    van Toor, Mariëlle L.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Datta, Ashis Kumar
    Jahangirnagar Univ, Bangladesh.
    Waldenström, Jonas
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ul Haque, Enam
    Bangladesh Bird Club, Bangladesh.
    Chowdhury, Sayam U.
    Univ Cambridge, UK.
    Population trends and effects of local environmental factors on waterbirds at Tanguar Haor freshwater wetland complex in northeast Bangladesh2023In: Avian Conservation and Ecology - Écologie et conservation des oiseaux, ISSN 1712-6568, E-ISSN 1712-6568, Vol. 18, no 1, article id 18Article in journal (Refereed)
    Abstract [en]

    Analysis of long-term datasets on bird populations can be used to answer ecological and management questions that are useful for conservation. Tanguar Haor (9500 ha) is one of the major freshwater wetlands in Bangladesh and supports a large number of migratory and resident waterbirds. Because of its unique ecological and economic values, it is arguably the most notable wetland in the floodplains of northeast Bangladesh and in the region. This Ramsar site supports globally important populations of threatened waterbirds, such as the Baer's Pochard Aythya baeri, Common Pochard Aythya ferina, Falcated Duck Mareca falcata, Ferruginous Duck Aythya nyroca, Oriental Darter Anhinga melanogaster, and Black-tailed Godwit Limosa limosa. Considering the international significance of this site, knowledge gaps on waterbird population trends, and key ecological factors, we conducted waterbird census between 2008 and 2021 to identify priority sites for conservation, population trends of resident and migratory waterbirds, and environmental factors that influence their abundances. We recorded a total of 69 species of waterbirds (maximum count of 166,788 individuals in 2013) and assessed population trends of 47 species. Of these, peak counts of 15 species exceeded the 1% threshold of their Asian-Australian Flyway population estimates. Most species (59%) showed a declining trend, including the critically endangered Baer's Pochard and the vulnerable Common Pochard, and 16 species (41%) showed an increasing trend. Based on the abundance and species diversity, we have identified Chotainna beel and Lechuamara beel as conservation priority sites within the Haor complex and discuss key threats to these areas. We also offer evidence that adjusting water-level management to annual rainfall patterns could be a useful intervention for waterbird management. Involving local communities in conservation efforts by creating bird sanctuaries within the Haor complex will strengthen waterbird conservation in the country and along the East Asian-Australian Flyway.

  • 33.
    Alatalo, Rauno V.
    et al.
    University of Jyväskylä, Finland.
    Eriksson, Dag
    Uppsala University, Sweden.
    Gustafsson, Lars
    Uppsala University, Sweden.
    Larsson, Kjell
    Uppsala University, Sweden.
    Exploitation competition influences the use of foraging sites by tits: Experimental evidence1987In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 68, no 2, p. 284-290Article in journal (Refereed)
    Abstract [en]

    In coniferous forests of central Sweden, tits (Paridae) and the Goldcrest, Regulus regulus, exploit nonrenewable resources in their group territories during winter. The smaller and socially subordinate species, the Goldcrest and the Coal Tit, Parus ater, forage on the outermost tree parts, while the larger and dominant Willow Tit, Parus montanus, and Crested Tit, Parus cristatus, forage on the inner tree parts. We removed Coal Tits and Goldcrests in three flocks in early winter to see if their absence would cause changes in the foraging patterns of the two dominant species. In late winter, Crested Tits foraged farther outward on branches of spruce in experimental flocks than they did in the control flocks. In spruce, Willow Tits foraged nearer the trunk than Crested Tits, and they did not respond to the experiment. In pine, Willow Tits, however, did move from branches to twigs in the absence of Coal Tits and Goldcrests. The experiment indicates that exploitation competition directly based on food depletion, without any interference, may influence the use of foraging sites by tits in coniferous forests.

  • 34.
    Albet-Torres, Nuria
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Månsson, Alf
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Long-Term Storage of Surface-Adsorbed Protein Machines2011In: Langmuir, ISSN 0743-7463, E-ISSN 1520-5827, Vol. 27, no 11, p. 7108-7112Article in journal (Refereed)
    Abstract [en]

    The effective and simple long-term storage of complex functional proteins is critical in achieving commercially viable biosensors. This issue is particularly challenging in recently proposed types of nanobiosensors, where molecular-motor-driven transportation substitutes microfluidics and forms the basis for novel detection schemes. Importantly, therefore, we here describe that delicate heavy meromyosin (HMM)-based nanodevices (HMM motor fragments adsorbed to silanized surfaces and actin bound to HMM) fully maintain their function when stored at -20 degrees C for more than a month. The mechanisms for the excellent preservation of acto-HMM motor function upon repeated freeze thaw cycles are discussed. The results are important to the future commercial implementation of motor-based nanodevices and are of more general value to the long-term storage of any protein-based bionanodevice.

  • 35. Alder, V A
    et al.
    Cuzin-Roudy, J
    Fransz, G
    Granéli, Edna
    Department of Marine Ecology, University of Lund .
    Larsen, J
    Rabbani, M M
    Thomsen, H
    Macro- and micrograzing effects on phytoplankton communities1989In: The expedition Antarktis VII/3 (EPOS LEG 2) of RV "Polarstern" in 1988/89 / [ed] I. Hempel, P.H. Schalk and V. Smetacek, Bremerhaven: Alfred- Wegener-Institut für Polar Meeresforschung , 1989, p. 123-130Chapter in book (Other academic)
  • 36.
    Alegria Zufia, Javier
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Linnaeus University, Linnaeus Knowledge Environments, Water.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Linnaeus University, Linnaeus Knowledge Environments, Water. Halmstad University, Sweden.
    Seasonality of Coastal Picophytoplankton Growth, Nutrient Limitation, and Biomass Contribution2021In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 12, article id 786590Article in journal (Refereed)
    Abstract [en]

    Picophytoplankton in the Baltic Sea includes the simplest unicellular cyanoprokaryotes (Synechococcus/Cyanobium) and photosynthetic picoeukaryotes (PPE). Picophytoplankton are thought to be a key component of the phytoplankton community, but their seasonal dynamics and relationships with nutrients and temperature are largely unknown. We monitored pico- and larger phytoplankton at a coastal site in Kalmar Sound (K-Station) weekly during 2018. Among the cyanoprokaryotes, phycoerythrin-rich picocyanobacteria (PE-rich) dominated in spring and summer while phycocyanin-rich picocyanobacteria (PC-rich) dominated during autumn. PE-rich and PC-rich abundances peaked during summer (1.1 x 10(5) and 2.0 x 10(5) cells mL(-1)) while PPE reached highest abundances in spring (1.1 x 10(5) cells mL(-1)). PPE was the main contributor to the total phytoplankton biomass (up to 73%). To assess nutrient limitation, bioassays with combinations of nitrogen (NO3 or NH4) and phosphorus additions were performed. PE-rich and PC-rich growth was mainly limited by nitrogen, with a preference for NH4 at >15 degrees C. The three groups had distinct seasonal dynamics and different temperature ranges: 10 degrees C and 17-19 degrees C for PE-rich, 13-16 degrees C for PC-rich and 11-15 degrees C for PPE. We conclude that picophytoplankton contribute significantly to the carbon cycle in the coastal Baltic Sea and underscore the importance of investigating populations to assess the consequences of the combination of high temperature and NH4 in a future climate.

  • 37.
    Alegria Zufia, Javier
    et al.
    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. Linnaeus University, Linnaeus Knowledge Environments, Water. Halmstad University, Sweden.
    Farnelid, Hanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Linnaeus University, Linnaeus Knowledge Environments, Water.
    Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea2022In: Scientific Reports, E-ISSN 2045-2322, Vol. 12, no 1, article id 14330Article in journal (Refereed)
    Abstract [en]

    Picocyanobacteria (< 2 mu m in diameter) are significant contributors to total phytoplankton biomass. Due to the high diversity within this group, their seasonal dynamics and relationship with environmental parameters, especially in brackish waters, are largely unknown. In this study, the abundance and community composition of phycoerythrin rich picocyanobacteria (PE-SYN) and phycocyanin rich picocyanobacteria (PC-SYN) were monitored at a coastal (K-station) and at an offshore station (LMO; similar to 10 km from land) in the Baltic Sea over three years (2018-2020). Cell abundances of picocyanobacteria correlated positively to temperature and negatively to nitrate (NO3) concentration. While PE-SYN abundance correlated to the presence of nitrogen fixers, PC-SYN abundance was linked to stratification/shallow waters. The picocyanobacterial targeted amplicon sequencing revealed an unprecedented diversity of 2169 picocyanobacterial amplicons sequence variants (ASVs). A unique assemblage of distinct picocyanobacterial clades across seasons was identified. Clade A/B dominated the picocyanobacterial community, except during summer when low NO3, high phosphate (PO4) concentrations and warm temperatures promoted S5.2 dominance. This study, providing multiyear data, links picocyanobacterial populations to environmental parameters. The difference in the response of the two functional groups and clades underscore the need for further high-resolution studies to understand their role in the ecosystem.

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  • 38.
    Alegria Zufía, Javier
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Picophytoplankton seasonal dynamics in the Baltic Sea2022Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Picophytoplankton (<2 μm diameter) is a diverse group of picocyanobacterial and photosynthetic picoeukaryotes (PPE).Picophytoplankton contribute significantly to total phytoplankton biomassand can dominate primary production in oceans, lakes and estuaries. In the estuarine Baltic Sea, the composition of picophytoplankton is linked to the north to south salinity gradient but knowledge of the seasonal dynamics interms of abundance, biomass and diversity is largely unknown. This thesis investigated the in situ dynamics, bottom up and top down controls of picocyanobacteria (SYN; consisting of primarily Synechococcus and Cyanobium among other genuses) and PPE at two sampling stations, one coastal and one offshore. Monitoring data over three years (2018-2020) showed high biomass contribution across all seasons. Picocyanobacterial peak abundances occurred from spring to summer at the coastal station and in late-summer to autumn at the offshore station (up to 4.7 × 105 cells mL-1).Differentiation of pigment populations showed that phycoerythrin rich(PE)-SYN was the main contributor to SYN abundances except at the coastalstation during summer, when PE-SYN and phycocyanin rich (PC)-SYN had equal contributions. PPE peak abundances occurred during late summer to autumn (up to 1.1 × 105 cells mL-1 cells ml-1). Temperature was linked topicophytoplankton growth and abundance, with PE-SYN, PCSYN and PPEadapted to different temperature ranges. Temperature also affected SYNnitrogen preference: SYN was nitrogen limited during early summer and at>15°C there was a preference for ammonium over nitrate. Clade A/B dominated the SYN community, except during summer at the coastal station when low nitrate and warm temperatures promoted S5.2 dominance. Grazing was observed to control SYN and PPE abundances and had an effect on the SYN community structure. Identification and laboratory experiments of key Synechococcus strains using a range of salinity, temperature and light conditions provided important insights into the physiological diversity of co-occurring ecotypes and links to the SYN dynamics that were observed in the field. In summary, this thesis provided novel information of picophytoplankton dynamics and community structure in the Baltic Sea. The results show that picophytoplankton play a relevant role in Baltic Sea and shows the importance of monitoring programs to understand picophytoplankton dynamics.

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  • 39.
    Alfredsson, Hanna
    University of Kalmar, School of Pure and Applied Natural Sciences. University of Kalmar, School of Pure and Applied Natural Sciences.
    Prey selection of European eel (Anguilla anguilla) larvae in the Sargasso Sea: a molecular approach.2009Independent thesis Advanced level (degree of Master (Two Years)), 40 credits / 60 HE creditsStudent thesis
    Abstract [en]

    Abstract

    The European eel (Anguilla anguilla) migrates to the Sargasso Sea to spawn. Even though the biology of A. anguilla leptocephali in the Sargasso Sea has been studied for several decades, information regarding their diet has remained unknown until now. Previous dietary studies concerning other species of leptocephali in the Pacific Ocean have been limited to the recognition of identifiable prey remains amongst gut contents. Hence, in this study a molecular approach relying on the detection of prey DNA amongst gut contents was used to study dietary profiles of A. anguilla leptocephali in the Sargasso Sea.

     

    Leptocephali were collected during the circumglobal Galathea 3 expedition in spring 2007 to the Sargasso Sea. DNA extracted from gut contents were PCR amplified using universal primers targeting the nuclear 18S rRNA gene. In order to separate eel amplicons from prey amplicons, PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE). Furthermore, clone libraries were constructed using universal primers targeting a portion of the 18S rRNA and mitochondrial COI gene, respectively. In total, the gut contents of 78 leptocephali were screened by DGGE.

     

    A diverse array of eukaryotic taxa was identified, hence demonstrating the applicability of a universal PCR- DGGE approach to study gut contents of leptocephali. The results presented here show, for the first time, that young stages of A. anguilla leptocephali feed on a large variety of zooplankton of which many were gelatinous (e.g. Hydrozoa, Thaliacea and Ctenophora). Several of the identified taxa also constitute important parts of the Sargasso Sea zooplankton community and are of size ranges (adult or larval stages) that made them reasonable as leptocephali prey.

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  • 40.
    Almeida, Juan Pablo
    et al.
    Lund University, Sweden.
    Rosenstock, Nicholas P.
    Lund University, Sweden.
    Forsmark, Benjamin
    Swedish University of Agricultural Sciences, Sweden.
    Bergh, Johan
    Linnaeus University, Faculty of Technology, Department of Forestry and Wood Technology.
    Wallander, Håkan
    Lund University, Sweden.
    Ectomycorrhizal community composition and function in a spruce forest transitioning between nitrogen and phosphorus limitation2019In: Fungal ecology, ISSN 1754-5048, E-ISSN 1878-0083, Vol. 40, p. 20-31Article in journal (Refereed)
    Abstract [en]

    Nitrogen is the main limiting nutrient in boreal ecosystems, but studies in southwest Sweden suggest that certain forests approach phosphorus (P) limitation driven by nitrogen (N) deposition. We added N, P or N + P to a Norway spruce forest in this region, to push the system to N or P limitation. Tree growth and needle nutrient concentrations indicated that the trees are P limited. EMF biomass was reduced only by N + P additions. Soil EMF communities responded more strongly to P than to N. Addition of apatite to ingrowth meshbags altered EMF community composition and enhanced the abundance of Imleria badia in the control and N plots, but not when P was added. The ecological significance of this species is discussed. Effects on tree growth, needle chemistry, and EMF communities indicate a dynamic interaction between EMF fungi and the nutrient status of trees and soils. (C) 2018 Elsevier Ltd and British Mycological Society. All rights reserved.

  • 41.
    Almqvist, Maria
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vanvårdens inverkan på nötkreaturs välfärd och hälsa2013Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Farmers are required to make sure that cattles basic needs are met, but still every year cases of neglect occur where the farmer has not complied within the animal welfare law and regulations. The aim of this study was to investigate how cattle are affected physically and behaviourally by neglect in the form of underfeeding, starvation and lack of sanitation, which animals are most vulnerable to the impact and what prospects they have to recover. The study was conducted as a literature study and the results show that these types of neglect have a large impact on the cattle welfare. Underfeeding and starvation causes physical changes leading to reduced milk production, reduced muscle mass, impaired immune function, poor reproductive performance and changes in rumen microflora leading to decreased number of microbes and pH change. Physical changes due to the lack of sanitation consist of increased vulnerability to hoof diseases and mastitis, burns, and increased sensitivity to temperature. The behaviourally changes that occur because of underfeeding and starvation include changes in eating habits, reduced lying time and reduced sleeping time. Insufficient sanitation cause behavioural changes including changes in laying time, increased agression, and slower movement. Pregnant cows and cows at peak lactation are sensitive to underfeeding and starvation, but also calves. Cattle kept in groups are most at risk for being contaminated. If the neglect is not too severe or prolonged, recovery can take place but in more serious cases of neglect, there is danger of the cattle’s life.

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  • 42.
    Alneberg, Johannes
    et al.
    KTH Royal instute of technology, Sweden.
    Bennke, Christin
    Leibniz Inst Balt Sea Res, Germany.
    Beier, Sara
    Leibniz Inst Balt Sea Res, Germany;Sorbonne Univ, France.
    Bunse, Carina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Carl von Ossietzky Univ Oldenburg, Germany;Alfred Wegener Institut, Germany.
    Quince, Christopher
    Univ Warwick, UK.
    Ininbergs, Karolina
    Stockholm University, Sweden;Karolinska Institutet, Sweden.
    Riemann, Lasse
    Univ Copenhagen, Denmark.
    Ekman, Martin
    Stockholm University, Sweden.
    Juergens, Klaus
    Leibniz Inst Balt Sea Res, Germany.
    Labrenz, Matthias
    Leibniz Inst Balt Sea Res, Germany.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Linnaeus University, Linnaeus Knowledge Environments, Water.
    Andersson, Anders F.
    KTH Royal instute of technology, Sweden.
    Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes2020In: Communications Biology, E-ISSN 2399-3642, Vol. 3, no 1, p. 1-10, article id 119Article in journal (Refereed)
    Abstract [en]

    Alneberg et al. conduct metagenomics binning of water samples collected over major environmental gradients in the Baltic Sea. They use machine-learning to predict the placement of genome clusters along niche gradients based on the content of functional genes. The genome encodes the metabolic and functional capabilities of an organism and should be a major determinant of its ecological niche. Yet, it is unknown if the niche can be predicted directly from the genome. Here, we conduct metagenomic binning on 123 water samples spanning major environmental gradients of the Baltic Sea. The resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 of the metagenome sequences of the prokaryotic size-fraction. By using machine-learning, the placement of a genome cluster along various niche gradients (salinity level, depth, size-fraction) could be predicted based solely on its functional genes. The same approach predicted the genomes' placement in a virtual niche-space that captures the highest variation in distribution patterns. The predictions generally outperformed those inferred from phylogenetic information. Our study demonstrates a strong link between genome and ecological niche and provides a conceptual framework for predictive ecology based on genomic data.

  • 43.
    Alneberg, Johannes
    et al.
    KTH Royal Institute of Technology, Sweden.
    Karlsson, Christofer M. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Divne, Anna-Maria
    Uppsala University, Sweden.
    Bergin, Claudia
    Uppsala University, Sweden.
    Homa, Felix
    Uppsala University, Sweden.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University, Sweden.
    Hugerth, Luisa W.
    KTH Royal Institute of Technology, Sweden;Karolinska Institutet, Sweden.
    Ettema, Thijs J. G.
    Uppsala University, Sweden.
    Bertilsson, Stefan
    Uppsala University, Sweden.
    Andersson, Anders F.
    KTH Royal Institute of Technology, Sweden.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes2018In: Microbiome, E-ISSN 2049-2618, Vol. 6, article id 173Article in journal (Refereed)
    Abstract [en]

    Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.

  • 44.
    Alneberg, Johannes
    et al.
    KTH Royal Institute of Technology, Sweden.
    Sundh, John
    Stockholm University, Sweden.
    Bennke, Christin
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Beier, Sara
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Hugerth, Luisa W.
    KTH Royal Institute of Technology, Sweden.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Kisand, Veljo
    Univ Tartu, Estonia.
    Riemann, Lasse
    Univ Copenhagen, Denmark.
    Juergens, Klaus
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Labrenz, Matthias
    Leibniz Inst Balt Sea Res Warnemunde, Germany.
    Andersson, Anders F.
    KTH Royal Institute of Technology, Sweden.
    BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea2018In: Scientific Data, E-ISSN 2052-4463, Vol. 5, article id 180146Article in journal (Refereed)
    Abstract [en]

    The Baltic Sea is one of the world's largest brackish water bodies and is characterised by pronounced physicochemical gradients where microbes are the main biogeochemical catalysts. Meta-omic methods provide rich information on the composition of, and activities within, microbial ecosystems, but are computationally heavy to perform. We here present the Baltic Sea Reference Metagenome (BARM), complete with annotated genes to facilitate further studies with much less computational effort. The assembly is constructed using 2.6 billion metagenomic reads from 81 water samples, spanning both spatial and temporal dimensions, and contains 6.8 million genes that have been annotated for function and taxonomy. The assembly is useful as a reference, facilitating taxonomic and functional annotation of additional samples by simply mapping their reads against the assembly. This capability is demonstrated by the successful mapping and annotation of 24 external samples. In addition, we present a public web interface, BalticMicrobeDB, for interactive exploratory analysis of the dataset. [GRAPHICS] .

  • 45. Alonso-Saez, L.
    et al.
    Vazquez-Dominguez, E.
    Cardelus, C.
    Pinhassi, Jarone
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Sala, M. M.
    Lekunberri, I.
    Balague, V.
    Vila-Costa, M.
    Unrein, F.
    Massana, R.
    Simo, R.
    Gasol, J. M.
    Factors controlling the year-round variability in carbon flux through bacteria in a coastal marine system2008In: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 11, no 3, p. 397-409Article in journal (Refereed)
    Abstract [en]

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

  • 46. Alonso-Saez, Laura
    et al.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Pernthaler, Jakob
    Gasol, Josep M.
    Leucine-to-carbon empirical conversion factor experiments: does bacterial community structure have an influence?2010In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 12, no 11, p. 2988-2997Article in journal (Refereed)
    Abstract [en]

    The suitability of applying empirical conversion factors (eCFs) to determine bacterial biomass production remains unclear because seawater cultures are usually overtaken by phylotypes that are not abundant in situ. While eCFs vary across environments, it has not been tested whether differences in eCFs are driven by changes in bacterial community composition or by in situ environmental conditions. We carried out seawater cultures throughout a year to analyse the correlation between eCFs and bacterial community structure, analysed by catalysed reporter deposition fluorescence in situ hybridization. Gammaproteobacteria usually dominated seawater cultures, but their abundance exhibited a wide range (25–73% of cell counts) and significantly increased with inorganic nutrient enrichment. Flavobacteria were less abundant but increased up to 40% of cells counts in winter seawater cultures, when in situ chlorophyll a was high. The correlations between eCFs and the abundance of the main broad phylogenetic groups (Gamma-, Alphaproteobacteria and Flavobacteria) were significant, albeit weak, while more specific groups (Alteromonadaceae and Rhodobacteraceae) were not significantly correlated. Our results show that the frequent development of the fast-growing group Alteromonadaceae in seawater cultures does not strongly drive the observed variations in eCFs. Rather, the results imply that environmental conditions and the growth of specific phylotypes interact to determine eCFs.

  • 47. Alonso-Saéz, Laura
    et al.
    Waller, Allison S
    Mende, Daniel R
    Bakker, Kevin
    Farnelid, Hanna
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Yager, Patricia L
    Lovejoy, Connie
    Tremblay, Jean-Eric
    Potvin, Marianne
    Heinrich, Friederike
    Estrada, Marta
    Riemann, Lasse
    Marine Biological Section, University of Copenhagen, 3000 Helsingør, Denmark .
    Bork, Peer
    Pedros-Alio, Carlos
    Bertilsson, Stefan
    Role for urea in nitrification by polar marine Archaea2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 44, p. 17989-17994Article in journal (Refereed)
    Abstract [en]

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

  • 48.
    Alriksson, Claes-Göran
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Texturvariationer i skogsmark - effekter på tillväxt och gödslingsrespons?: Studie i ett försök med behovsanpassad gödsling i Ebbegärde2019Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    En mängd olika ståndortsfaktorer påverkar trädens tillväxt. Några av dessa kan påverkas genom olika skogsskötselmetoder, t ex näringstillförsel. I ett flertal försök de senaste decennierna har skogsgödsling visat sig kunna öka tillväxten markant. Faktorer som inte är påverkbara, som t ex markens textur och markens jorddjup kan då bli begränsande för tillväxten eftersom en finkornig textur oftast är gynnsam ur tillväxtsynpunkt. Föreliggande undersökning syftar till att se om det finns en texturvariation inom en begränsad yta och dess effekter på tillväxten. Texturen undersöktes genom torrsiktning. Resultaten visar att det förelåg en stor variation av texturen på beståndsnivå och att det kan påverka tillväxten i kombination med andra begränsande faktorer såsom vattentillgång.

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  • 49.
    Alstermark, Mirjam
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Fluorescens in situ hybridisering: Optimering och vidareutveckling av en kurslaboration på Biomedicinska analytikerprogrammet2019Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Fluorescens in situ hybridization (FISH) is used to detect cytogenetic aberrations and abnormalities of Deoxyribonucleic acid (DNA) and Ribonucleic Acid (RNA). The FISH begins with chromosome extraction of the desired cell preparation then a direct or indirect fluorescently labeled probe (15-30 base pair long) is hybridized to its genetic target sequence. The preparation can thereafter be analyzed in fluorescence microscope to see bound probe at chromosome level. In the course “Advanced laboratory methodology” for the Biomedical Scientist program, Linnaeus University, a FISH laboratory experiment is conducted where results have not been clear nor reproducible.

    The aim of this study was to improve the laboratory experiment FISH.

    Human Cardiac Microvascular Endothelial Cells (HCMEC) was grown to 60 % and 80 % confluence, to an estimated number of ≥ 3 x106, and analyzed by G-band staining and DNA-FISH. G-band staining showed many cells in interphase and few free chromosomes of cells with 60 % confluence. G-band staining and DNA-FISH showed that cells grown to 80 % confluence showed more free chromosomes from metaphase. The cancer cell lines VMM1 and H1915 were therefore grown to 80 % confluence and ≥ 3 x106. Multicolor-FISH on VMM1 and H1915 showed results from all painting probes blue/aqua, red and green. The conclusion is that in chromosomal extraction from cultured adherent cells should be 80 % confluent to give clear and reproducible probe staining of chromosomes in metaphase when assayed with Multicolor FISH. Analysis of 80 % confluent cells and the use of Multicolor FISH technology is a clear improvement to the “Advanced laboratory methodology” course.

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  • 50.
    Alvunger, David
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Variation in number of vertebrae in populations of pike (Esox lucius) in the south-east of Sweden2016Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Vertebral number (VN) is known to vary greatly across different taxa, but also within species orpopulations. Extensive research has shown that VN in fish is the result of interactions between geneticstructure and plastic responses to environmental cues during ontogeny. A frequently reported pattern is the tendency for VN to vary with body shape and/or length of the fish. The pike (Esox lucius) of the Baltic Sea has a complex population structure, with genetically distinct subpopulations consisting of homing anadromous individuals. Individuals belonging to these subpopulations are sympatric for most of their lives and become allopatric briefly during spawning each year. This study examined the distribution of VN in three anadromous sympatric subpopulations of pike in the Baltic. Significant differences in VN were found between juveniles and adults belonging to different subpopulations, but also across life-stageswithin all three subpopulations. Results from a common-garden experiment indicated that differences in VN among subpopulations were in part the result of genetic differences, indicative of evolutionary change. Furthermore, a quadratic regression revealed a curvilinear relationship between VN and bodylength of juveniles. Taken together, these results suggest that the combined effects of stabilizing and divergent selection might have played a role in shaping the distribution of VN in pike of the Baltic. The distribution of VN within subpopulations seems to be under the influence of stabilizing selection. Differences among subpopulations might instead reflect local adaptations driven by divergent selection. These findings signal the need for conservationists to view these subpopulations as unique units of management.

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