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  • 1. 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.

  • 2.
    Cinner, Joshua E.
    et al.
    James Cook Univ, Australia.
    McClanahan, Tim R.
    Wildlife Conservat Soc, USA.
    MacNeil, M. Aaron
    Australian Inst Marine Sci, Australia.
    Graham, Nicholas A. J.
    James Cook Univ, Australia.
    Daw, Tim M.
    Univ E Anglia, UK;Stockholm University.
    Mukminin, Ahmad
    Wildlife Conservat Soc, Indonesia.
    Feary, David A.
    Univ Technol Sydney, Australia.
    Rabearisoa, Ando L.
    Conservat Int, Madagascar.
    Wamukota, Andrew
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences. Coral Reef Conservat Program, Kenya.
    Jiddawi, Narriman
    Univ Dar Es Salaam, Tanzania.
    Campbell, Stuart J.
    Wildlife Conservat Soc, Indonesia.
    Baird, Andrew H.
    James Cook Univ, Australia.
    Januchowski-Hartley, Fraser A.
    James Cook Univ, Australia.
    Hamed, Salum
    Lahari, Rachael
    Wildlife Conservat Soc Papua New Guinea Program, Papua N Guinea.
    Morove, Tau
    Wildlife Conservat Soc Papua New Guinea Program, Papua N Guinea.
    Kuange, John
    Wildlife Conservat Soc Papua New Guinea Program, Papua N Guinea.
    Comanagement of coral reef social-ecological systems2012In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 14, p. 5219-5222Article in journal (Refereed)
    Abstract [en]

    In an effort to deliver better outcomes for people and the ecosystems they depend on, many governments and civil society groups are engaging natural resource users in collaborative management arrangements (frequently called comanagement). However, there are few empirical studies demonstrating the social and institutional conditions conducive to successful comanagement outcomes, especially in small-scale fisheries. Here, we evaluate 42 comanagement arrangements across five countries and show that: (i) comanagement is largely successful at meeting social and ecological goals; (ii) comanagement tends to benefit wealthier resource users; (iii) resource overexploitation is most strongly influenced by market access and users' dependence on resources; and (iv) institutional characteristics strongly influence livelihood and compliance outcomes, yet have little effect on ecological conditions.

  • 3. Clark, Richard
    et al.
    Fisher, Harold
    Dempster, Louise
    Daly, Norelle
    Rosengren, Johan
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Nevin, Simon
    Meunier, Fred
    Adams, David
    Craik, David
    Engineering stable peptide toxins by means of backbone cyclization: Stabilization of the alpha-conotoxin MII2005In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 102, no 39, p. 13767-72Article in journal (Refereed)
  • 4.
    Durante, Federica
    et al.
    University of Milano-Bicocca, Italy.
    Fiske, Susan T.
    Princeton University, USA.
    Gelfand, Michele
    University of Maryland, USA.
    Crippa, Franca
    University of Milano-Bicocca, Italy.
    Suttora, Chiara
    University of Milano-Bicocca, Italy.
    Stillwell, Amelia
    Stanford University, USA.
    Asbrock, Frank
    Chemnitz University of Technology, Germany.
    Aycan, Zeynep
    Koc University, Turkey.
    Bye, Hege
    University of Bergen, Norway.
    Carlsson, Rickard
    Linnaeus University, Faculty of Health and Life Sciences, Department of Psychology.
    Björklund, Fredrik
    Lund University.
    Dagher, Munqith
    Independent Institute for Administration and Civil Society Studies, Jordan.
    Geller, Armando
    Scensei, Switzerland.
    Larsen, Christian Albrekt
    Aalborg University, Denmark.
    Latif, Abdel-Hamid Abdel
    The Egyptian Research and Training Center, Egypt.
    Mähönen, Tuuli Anna
    University of Helsinki, Finland.
    Jasinskaja-Lahti, Inga
    University of Helsinki, Finland.
    Teymoori, Ali
    University of Bordeaux, France.
    Ambivalent stereotypes link to peace, conflict, and inequality across 38 nations2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 4, p. 669-674Article in journal (Refereed)
    Abstract [en]

    A cross-national study, 49 samples in 38 nations (n = 4,344), inves- tigates whether national peace and conflict reflect ambivalent warmth and competence stereotypes: High-conflict societies (Pakistan) may need clearcut, unambivalent group images distinguishing friends from foes. Highly peaceful countries (Denmark) also may need less ambivalence because most groups occupy the shared national identity, with only a few outcasts. Finally, nations with interme- diate conflict (United States) may need ambivalence to justify more complex intergroup-system stability. Using the Global Peace Index to measure conflict, a curvilinear (quadratic) relationship be- tween ambivalence and conflict highlights how both extremely peaceful and extremely conflictual countries display lower stereo- type ambivalence, whereas countries intermediate on peace-conflict present higher ambivalence. These data also replicated a linear inequality–ambivalence relationship. 

  • 5.
    Forsman, Anders
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Effects of genotypic and phenotypic variation on establishment are important for conservation, invasion and infection biology.2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 1, p. 302-307Article in journal (Refereed)
    Abstract [en]

    There is abundant evidence that the probability of successful establishment in novel environments increases with number of individuals in founder groups and with number of repeated introductions. Theory posits that the genotypic and phenotypic variation among individuals should also be important, but few studies have examined whether founder diversity influences establishment independent of propagule pressure, nor whether the effect is model or context dependent. I summarize the results of 18 experimental studies and report on a metaanalysis that provides strong evidence that higher levels of genotypic and phenotypic diversity in founder groups increase establishment success in plants and animals. The effect of diversity is stronger in experiments carried out under natural conditions in the wild than under seminatural or standardized laboratory conditions. The realization that genetic and phenotypic variation is key to successful establishment may improve the outcome of reintroduction and translocation programs used to vitalize or restore declining and extinct populations. Founder diversity may also improve the ability of invasive species to establish and subsequently spread in environments outside of their native community, and enhance the ability of pathogens and parasites to colonize and invade the environment constituted by their hosts. It is argued that exchange of ideas, methodological approaches, and insights of the role of diversity for establishment in different contexts may further our knowledge, vitalize future research, and improve management plans in different disciplines.

  • 6. Gonzalez, J. M.
    et al.
    Fernandez-Gomez, B.
    Fernandez-Guerra, A.
    Gomez-Consarnau, Laura
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Sanchez, O.
    Coll-Llado, M.
    del Campo, J.
    Escudero, L.
    Rodriguez-Martinez, R.
    Alonso-Saez, L.
    Latasa, M.
    Paulsen, I.
    Nedashkovskaya, O. I.
    Lekunberri, I.
    Pinhassi, Jarone
    University of Kalmar, School of Pure and Applied Natural Sciences.
    Pedros-Alio, C.
    Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria)2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 25, p. 8724-8729Article in journal (Refereed)
    Abstract [en]

    Analysis of marine cyanobacteria and proteobacteria genomes has provided a profound understanding of the life strategies of these organisms and their ecotype differentiation and metabolisms. However, a comparable analysis of the Bacteroidetes, the third major bacterioplankton group, is still lacking. In the present paper, we report on the genome of Polaribacter sp. strain MED152. On the one hand, MED152 contains a substantial number of genes for attachment to surfaces or particles, gliding motility, and polymer degradation. This agrees with the currently assumed life strategy of marine Bacteroidetes. On the other hand, it contains the proteorhoclopsin gene, together with a remarkable suite of genes to sense and respond to light, which may provide a survival advantage in the nutrient-poor sun-lit ocean surface when in search of fresh particles to colonize. Furthermore, an increase in CO2 fixation in the light suggests that the limited central metabolism is complemented by anaplerotic inorganic carbon fixation. This is mediated by a unique combination of membrane transporters and carboxylases. This suggests a dual life strategy that, if confirmed experimentally, would be notably different from what is known of the two other main bacterial groups (the autotrophic cyanobacteria and the heterotrophic proteobacteria) in the surface oceans. The Polaribacter genome provides insights into the physiological capabilities of proteorhodopsin-containing bacteria. The genome will serve as a model to study the cellular and molecular processes in bacteria that express proteorhoclopsin, their adaptation to the oceanic environment, and their role in carbon-cycling.

  • 7.
    Harboe, Morten
    et al.
    Oslo University Hospital, Norway.
    Johnson, Christina
    Oslo University Hospital, Norway.
    Nymo, Stig
    Nordland Hospital, Norway.
    Ekholt, Karin
    Oslo University Hospital, Norway.
    Schjalm, Camilla
    Oslo University Hospital, Norway.
    Lindstad, Julie K.
    Oslo University Hospital, Norway.
    Pharo, Anne
    Oslo University Hospital, Norway.
    Hellerud, Bernt Christian
    Oslo University Hospital, Norway.
    Nilsson Ekdahl, Kristina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Uppsala University.
    Mollnes, Tom Eirik
    Oslo University Hospital, Norway ; Nordland Hospital, Norway ; University of Oslo, Norway ; University of Tromsø, Norway ; Norwegian University of Science and Technology, Norway.
    Nilsson, Per H.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. Oslo University Hospital, Norway ; University of Oslo, Norway.
    Properdin binding to complement activating surfaces depends on initial C3b deposition2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 4, p. E534-E539Article in journal (Refereed)
    Abstract [en]

    Two functions have been assigned to properdin; stabilization of the alternative convertase, C3bBb, is well accepted, whereas the role of properdin as pattern recognition molecule is controversial. The presence of nonphysiological aggregates in purified properdin preparations and experimental models that do not allow discrimination between the initial binding of properdin and binding secondary to C3b deposition is a critical factor contributing to this controversy. In previous work, by inhibiting C3, we showed that properdin binding to zymosan and Escherichia coli is not a primary event, but rather is solely dependent on initial C3 deposition. In the present study, we found that properdin in human serum bound dose-dependently to solid-phase myeloperoxidase. This binding was dependent on C3 activation, as demonstrated by the lack of binding in human serum with the C3-inhibitor compstatin Cp40, in C3-depleted human serum, or when purified properdin is applied in buffer. Similarly, binding of properdin to the surface of human umbilical vein endothelial cells or Neisseria meningitidis after incubation with human serum was completely C3-dependent, as detected by flow cytometry. Properdin, which lacks the structural homology shared by other complement pattern recognition molecules and has its major function in stabilizing the C3bBb convertase, was found to bind both exogenous and endogenous molecular patterns in a completely C3-dependent manner. We therefore challenge the view of properdin as a pattern recognition molecule, and argue that the experimental conditions used to test this hypothesis should be carefully considered, with emphasis on controlling initial C3 activation under physiological conditions.

  • 8.
    Holmfeldt, Karin
    et al.
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721.
    Solonenko, Natalie
    Shah, Manesh
    Corrier, Kristen
    Riemann, Lasse
    Department of Biology, University of Copenhagen, 3000 Helsingor, Denmark.
    VerBerkmoes, Nathan C.
    Sullivan, Matthew B.
    Twelve previously unknown phage genera are ubiquitous in global oceans2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 31, p. 12798-12803Article in journal (Refereed)
    Abstract [en]

    Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an under-represented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four well-known viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing.

  • 9. Leuzinger, Sebastian
    et al.
    Bigler, Christof
    Wolf, Annett
    Linnaeus University, The University Administration.
    Koerner, Christian
    Poor methodology for predicting large-scale tree die-off2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 38Article in journal (Refereed)
  • 10.
    Liu, Yu
    et al.
    The Scripps Research Institute, USA.
    Tan, Yun Lei
    The Scripps Research Institute, USA.
    Zhang, Xin
    The Scripps Research Institute, USA.
    Bhabha, Gira
    University of California, USA.
    Ekiert, Damian C
    University of California, USA.
    Genereux, Joseph C
    The Scripps Research Institute, USA.
    Cho, Younhee
    The Scripps Research Institute, USA.
    Kipnis, Yakov
    University of Washington, USA.
    Bjelic, Sinisa
    University of Washington, USA.
    Baker, David
    University of Washington, USA.
    Kelly, Jeffery W
    The Scripps Research Institute, USA.
    Small molecule probes to quantify the functional fraction of a specific protein in a cell with minimal folding equilibrium shifts.2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 12, p. 4449-4454Article in journal (Refereed)
    Abstract [en]

    Although much is known about protein folding in buffers, it remains unclear how the cellular protein homeostasis network functions as a system to partition client proteins between folded and functional, soluble and misfolded, and aggregated conformations. Herein, we develop small molecule folding probes that specifically react with the folded and functional fraction of the protein of interest, enabling fluorescence-based quantification of this fraction in cell lysate at a time point of interest. Importantly, these probes minimally perturb a protein's folding equilibria within cells during and after cell lysis, because sufficient cellular chaperone/chaperonin holdase activity is created by rapid ATP depletion during cell lysis. The folding probe strategy and the faithful quantification of a particular protein's functional fraction are exemplified with retroaldolase, a de novo designed enzyme, and transthyretin, a nonenzyme protein. Our findings challenge the often invoked assumption that the soluble fraction of a client protein is fully folded in the cell. Moreover, our results reveal that the partitioning of destabilized retroaldolase and transthyretin mutants between the aforementioned conformational states is strongly influenced by cytosolic proteostasis network perturbations. Overall, our results suggest that applying a chemical folding probe strategy to other client proteins offers opportunities to reveal how the proteostasis network functions as a system to regulate the folding and function of individual client proteins in vivo.

  • 11.
    Matusovsky, Oleg S.
    et al.
    McGill Univ, Canada.
    Månsson, Alf
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Persson, Malin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences. McGill Univ, Canada.
    Cheng, Yu-Shu
    McGill Univ, Canada.
    Rassier, Dilson E.
    McGill Univ, Canada.
    High-speed AFM reveals subsecond dynamics of cardiac thin filaments upon Ca2+ activation and heavy meromyosin binding2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 33, p. 16384-16393Article in journal (Refereed)
    Abstract [en]

    High-speed atomic force microscopy (HS-AFM) can be used to study dynamic processes with real-time imaging of molecules within 1- to 5-nm spatial resolution. In the current study, we evaluated the 3-state model of activation of cardiac thin filaments (cTFs) isolated as a complex and deposited on a mica-supported lipid bilayer. We studied this complex for dynamic conformational changes 1) at low and high [Ca2+] (pCa 9.0 and 4.5), and 2) upon myosin binding to the cTF in the nucleotide-free state or in the presence of ATP. HS-AFM was used to directly visualize the tropo-myosin-troponin complex and Ca2+-induced tropomyosin movements accompanied by structural transitions of actin monomers within cTFs. Our data show that cTFs at relaxing or activating conditions are not ultimately in a blocked or activated state, respectively, but rather the combination of states with a prevalence that is dependent on the [Ca2+] and the presence of weakly or strongly bound myosin. The weakly and strongly bound myosin induce similar changes in the structure of cTFs as confirmed by the local dynamical displacement of individual tropomyosin strands in the center of a regulatory unit of cTF at the relaxed and activation conditions. The displacement of tropomyosin at the relaxed conditions had never been visualized directly and explains the ability of myosin binding to TF at the relaxed conditions. Based on the ratios of nonactivated and activated segments within cTFs, we proposed a mechanism of tropomyosin switching from different states that includes both weakly and strongly bound myosin.

  • 12.
    Nicolau, Dan V., Jr.
    et al.
    Univ Calif Berkeley,USA ; Mol Sense Ltd, UK.
    Lard, Mercy
    Lund University.
    Korten, Till
    Tech Univ Dresden, Germany ; Max Planck Inst Mol Cell Biol & Genet, Germany.
    van Delft, Falco C. M. J. M.
    Philips Res MiPlaza & Philips Innovat Serv, Netherlands.
    Persson, Malin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Bengtsson, Elina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Månsson, Alf
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Diez, Stefan
    Tech Univ Dresden, Germany ; Max Planck Inst Mol Cell Biol & Genet, Germany.
    Linke, Heiner
    Lund University.
    Nicolau, Dan V.
    Univ Liverpool, UK ; McGill Univ, Canada.
    REPLY TO EINARSSON: The computational power of parallel network exploration with many bioagents2016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 23, p. E3188-E3188Article in journal (Refereed)
  • 13.
    Nicolau, Dan V., Jr.
    et al.
    University of California, USA ; Molecular Sense, Ltd., UK.
    Lard, Mercy
    Lund University.
    Korten, Till
    Technische Universität Dresden, Germany ; Max Planck Institute of Molecular Cell Biology and Genetics, Germany.
    van Delftf, Falco C. M. J. M.
    Philips Research MiPlaza, The Netherlands ; Philips Innovation Services, The Netherlands.
    Persson, Malin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Bengtsson, Elina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Månsson, Alf
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Diez, Stefan
    Technische Universität Dresden, Germany ; Max Planck Institute of Molecular Cell Biology and Genetics, Germany.
    Linke, Heiner
    Lund University.
    Nicolau, Dan V.
    University of Liverpool, UK ; McGill University, Canada.
    Parallel computation with molecular-motor-propelled agents in nanofabricated networks2016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 10, p. 2591-2596Article in journal (Refereed)
    Abstract [en]

    The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular-motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.

  • 14.
    Okabayashi, Norio
    et al.
    Univ Regensburg, Germany;Kanazawa Univ, Japan.
    Peronio, Angelo
    Univ Regensburg, Germany.
    Paulsson, Magnus
    Linnaeus University, Faculty of Technology, Department of Physics and Electrical Engineering.
    Arai, Toyoko
    Kanazawa Univ, Japan.
    Giessibl, Franz J.
    Univ Regensburg, Germany.
    Vibrations of a molecule in an external force field2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 18, p. 4571-4576Article in journal (Refereed)
    Abstract [en]

    The vibration of a molecule adsorbed on a surface contains essential information on the molecule–surface bond, which is important to understand the surface reactions that occur, e.g., in catalytic reactions. Accessing the vibrational energies of a single molecule is possible by combining scanning tunneling microscopy with inelastic electron spectroscopy. However, the tip of a microscope exerts a force on a nearby molecule, and possibly even induces slight structural changes. To study this problem, we have further incorporated atomic force microscopy. The relationship between the exerted forces and vibrational energies is well reproduced by a classical mechanical model. This combined technique opens the possibility to study the atomic-scale interaction of a molecule on a surface with unprecedented precision.The oscillation frequencies of a molecule on a surface are determined by the mass distribution in the molecule and the restoring forces that occur when the molecule bends. The restoring force originates from the atomic-scale interaction within the molecule and with the surface, which plays an essential role in the dynamics and reactivity of the molecule. In 1998, a combination of scanning tunneling microscopy with inelastic tunneling spectroscopy revealed the vibrational frequencies of single molecules adsorbed on a surface. However, the probe tip itself exerts forces on the molecule, changing its oscillation frequencies. Here, we combine atomic force microscopy with inelastic tunneling spectroscopy and measure the influence of the forces exerted by the tip on the lateral vibrational modes of a carbon monoxide molecule on a copper surface. Comparing the experimental data to a mechanical model of the vibrating molecule shows that the bonds within the molecule and with the surface are weakened by the proximity of the tip. This combination of techniques can be applied to analyze complex molecular vibrations and the mechanics of forming and loosening chemical bonds, as well as to study the mechanics of bond breaking in chemical reactions and atomic manipulation.

  • 15.
    Paerl, Ryan W.
    et al.
    University of Copenhagen, Denmark;North Carolina State University, USA.
    Sundh, John
    Stockholm University;Royal Institute of Technology.
    Tan, Demeng
    University of Copenhagen, Denmark.
    Svenningsen, Sine L.
    University of Copenhagen, Denmark.
    Hylander, Samuel
    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.
    Andersson, Anders F.
    Royal Institute of Technology.
    Riemann, Lasse
    University of Copenhagen, Denmark.
    Prevalent reliance of bacterioplankton on exogenous vitamin B1 and precursor availability2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 44, p. E10447-E10456Article in journal (Refereed)
    Abstract [en]

    Vitamin B1 (B1 herein) is a vital enzyme cofactor required by virtually all cells, including bacterioplankton, which strongly influence aquatic biogeochemistry and productivity and modulate climate on Earth. Intriguingly, bacterioplankton can be de novo B1 synthesizers or B1 auxotrophs, which cannot synthesize B1 de novo and require exogenous B1 or B1 precursors to survive. Recent isolate-based work suggests select abundant bacterioplankton are B1 auxotrophs, but direct evidence of B1 auxotrophy among natural communities is scant. In addition, it is entirely unknown if bulk bacterioplankton growth is ever B1-limited. We show by surveying for B1-related genes in estuarine, marine, and freshwater metagenomes and metagenome-assembled genomes (MAGs) that most naturally occurring bacterioplankton are B1 auxotrophs. Pyrimidine B1-auxotrophic bacterioplankton numerically dominated metagenomes, but multiple other B1-auxotrophic types and distinct uptake and B1-salvaging strategies were also identified, including dual (pyrimidine and thiazole) and intact B1 auxotrophs that have received little prior consideration. Time-series metagenomes from the Baltic Sea revealed pronounced shifts in the prevalence of multiple B1-auxotrophic types and in the B1-uptake and B1-salvaging strategies over time. Complementarily, we documented B1/precursor limitation of bacterioplankton production in three of five nutrient-amendment experiments at the same time-series station, specifically when intact B1 concentrations were ≤3.7 pM, based on bioassays with a genetically engineered Vibrio anguillarum B1-auxotrophic strain. Collectively, the data presented highlight the prevalent reliance of bacterioplankton on exogenous B1/precursors and on the bioavailability of the micronutrients as an overlooked factor that could influence bacterioplankton growth and succession and thereby the cycling of nutrients and energy in aquatic systems.

  • 16.
    Palovaara, Joakim
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Akram, Neelam
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bunse, Carina
    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.
    Pedrós-Alió, Carlos
    CSIC, Inst Ciencies Mar, Spain.
    González, José M.
    Univ La Laguna, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 35, p. E3650-E3658Article in journal (Refereed)
    Abstract [en]

    Proteorhodopsin (PR) is present in half of surface ocean bacterioplankton, where its light-driven proton pumping provides energy to cells. Indeed, PR promotes growth or survival in different bacteria. However, the metabolic pathways mediating the light responses remain unknown. We analyzed growth of the PR-containing Dokdonia sp. MED134 (where light-stimulated growth had been found) in seawater with low concentrations of mixed [yeast extract and peptone (YEP)] or single (alanine, Ala) carbon compounds as models for rich and poor environments. We discovered changes in gene expression revealing a tightly regulated shift in central metabolic pathways between light and dark conditions. Bacteria showed relatively stronger light responses in Ala compared with YEP. Notably, carbon acquisition pathways shifted toward anaplerotic CO2 fixation in the light, contributing 31 +/- 8% and 24 +/- 6% of the carbon incorporated into biomass in Ala and YEP, respectively. Thus, MED134 was a facultative double mixotroph, i.e., photo- and chemotrophic for its energy source and using both bicarbonate and organic matter as carbon sources. Unexpectedly, relative expression of the glyoxylate shunt genes (isocitrate lyase and malate synthase) was >300-fold higher in the light-but only in Ala-contributing a more efficient use of carbon from organic compounds. We explored these findings in metagenomes and metatranscriptomes and observed similar prevalence of the glyoxylate shunt compared with PR genes and highest expression of the isocitrate lyase gene coinciding with highest solar irradiance. Thus, regulatory interactions between dissolved organic carbon quality and central metabolic pathways critically determine the fitness of surface ocean bacteria engaging in PR phototrophy.

  • 17.
    Tamas, Ivica
    et al.
    Uppsala University ; Stockholm University.
    Wernegreen, Jennifer J
    Marine Biological Laboratory, USA.
    Nystedt, Björn
    Uppsala University.
    Kauppinen, Seth N
    Marine Biological Laboratory, USA.
    Darby, Alistair C
    Uppsala University.
    Gomez-Valero, Laura
    Uppsala University.
    Lundin, Daniel
    Stockholm University.
    Poole, Anthony M
    Stockholm University.
    Andersson, Siv G E
    Uppsala University.
    Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 39, p. 14934-9Article in journal (Refereed)
    Abstract [en]

    Among host-dependent bacteria that have evolved by extreme reductive genome evolution, long-term bacterial endosymbionts of insects have the smallest (160-790 kb) and most A + T-rich (>70%) bacterial genomes known to date. These genomes are riddled with poly(A) tracts, and 5-50% of genes contain tracts of 10 As or more. Here, we demonstrate transcriptional slippage at poly(A) tracts within genes of Buchnera aphidicola associated with aphids and Blochmannia pennsylvanicus associated with ants. Several tracts contain single frameshift deletions; these apparent pseudogenes showed patterns of constraint consistent with purifying selection on the encoded proteins. Transcriptional slippage yielded a heterogeneous population of transcripts with variable numbers of As in the tract. Across several frameshifted genes, including B. aphidicola cell wall biosynthesis genes and a B. pennsylvanicus histidine biosynthesis gene, 12-50% of transcripts contained corrected reading frames that could potentially yield full-length proteins. In situ immunostaining confirmed the production of the cell wall biosynthetic enzyme UDP-N-acetylmuramyl pentapeptide synthase encoded by the frameshifted murF gene. Simulation studies indicated an overrepresentation of poly(A) tracts in endosymbiont genomes relative to other A + T-rich bacterial genomes. Polymerase infidelity at poly(A) tracts rescues the functionality of genes with frameshift mutations and, conversely, reduces the efficiency of expression for in-frame genes carrying poly(A) regions. These features of homopolymeric tracts could be exploited to manipulate gene expression in small synthetic genomes.

  • 18. Wang, C. L.
    et al.
    Chen, S.
    Vergin, K. L.
    Giovannoni, S. J.
    Chan, S.
    DeMott, W. M. S.
    Taghizadeh, K.
    Cordero, O.
    Cutler, M.
    Timberlake, S.
    Alm, E. J.
    Polz, M. F.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Deng, Z.
    Dedon, P. C.
    DNA phosphorothioation is widespread and quantized in bacterial genomes2011In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 108, p. 2963-2968Article in journal (Refereed)
    Abstract [en]

     Phosphorothioate (PT) modification of DNA, with sulfur replacing a nonbridging phosphate oxygen, was recently discovered as a product of the dnd genes found in bacteria and archaea. Given our limited understanding of the biological function of PT modifications, including sequence context, genomic frequencies, and relationships to the diversity of dnd gene clusters, we under-took a quantitative study of PT modifications in prokaryotic genomes using a liquid chromatography-coupled tandem quadrupole mass spectrometry approach. The results revealed a diversity of unique PT sequence contexts and three discrete genomic frequencies in a wide range of bacteria. Metagenomic analyses of PT modifications revealed unique ecological distributions, and a phylogenetic comparison of dnd genes and PT sequence contexts strongly supports the horizontal transfer of dnd genes. These results are consistent with the involvement of PT modifications in a type of restriction-modification system with wide distribution in prokaryotes.

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