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  • 1.
    Bravo, Giangiacomo
    et al.
    Linnaeus University, Faculty of Social Sciences, Department of Social Studies.
    Grimaldo, Francisco
    Univ Valencia, Spain.
    Lopez-Inesta, Emilia
    Univ Valencia, Spain.
    Mehmani, Bahar
    Elsevier,Netherlands.
    Squazzoni, Flaminio
    Univ Milan, Italy.
    The effect of publishing peer review reports on referee behavior in five scholarly journals2019In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 10, article id 322Article, review/survey (Refereed)
    Abstract [en]

    To increase transparency in science, some scholarly journals are publishing peer review reports. But it is unclear how this practice affects the peer review process. Here, we examine the effect of publishing peer review reports on referee behavior in five scholarly journals involved in a pilot study at Elsevier. By considering 9,220 submissions and 18,525 reviews from 2010 to 2017, we measured changes both before and during the pilot and found that publishing reports did not significantly compromise referees' willingness to review, recommendations, or turn-around times. Younger and non-academic scholars were more willing to accept to review and provided more positive and objective recommendations. Male referees tended to write more constructive reports during the pilot. Only 8.1% of referees agreed to reveal their identity in the published report. These findings suggest that open peer review does not compromise the process, at least when referees are able to protect their anonymity.

  • 2.
    Chieh, Hsu
    et al.
    University of Basel, Switzerland.
    Scherrer, S
    University of Basel, Switzerland.
    Buetti-Dinh, Antoine
    University of Basel, Switzerland.
    Ratna, P
    University of Basel, Switzerland.
    Pizzolato, J
    University of Basel, Switzerland.
    Jaquet, V
    University of Basel, Switzerland.
    Becskei, A
    University of Basel, Switzerland.
    Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution.2012In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 3, p. Article ID: 682-Article in journal (Refereed)
    Abstract [en]

    During evolution, genetic networks are rewired through strengthening or weakening their interactions to develop new regulatory schemes. In the galactose network, the GAL1/GAL3paralogues and the GAL2 gene enhance their own expression mediated by the Gal4p transcriptional activator. The wiring strength in these feedback loops is set by the number of Gal4p binding sites. Here we show using synthetic circuits that multiplying the binding sites increases the expression of a gene under the direct control of an activator, but this enhancement is not fed back in the circuit. The feedback loops are rather activated by genes that have frequent stochastic bursts and fast RNA decay rates. In this way, rapid adaptation to galactose can be triggered even by weakly expressed genes. Our results indicate that nonlinear stochastic transcriptional responses enable feedback loops to function autonomously, or contrary to what is dictated by the strength of interactions enclosing the circuit.

  • 3.
    Drake, Henrik
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Ivarsson, Magnus
    Swedish Museum of Natural History.
    Bengtson, Stefan
    Swedish Museum of Natural History.
    Heim, Christine
    Georg-August University, Germany.
    Siljeström, Sandra
    SP Technical Research Institute of Sweden.
    Whitehouse, Martin J.
    Swedish Museum of Natural History.
    Broman, Curt
    Stockholm University.
    Belivanova, Veneta
    Swedish Museum of Natural History.
    Åström, Mats E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, p. 1-9, article id 55Article in journal (Refereed)
    Abstract [en]

    The deep biosphere is one of the least understood ecosystems on Earth. Although most microbiological studies in this system have focused on prokaryotes and neglected microeukaryotes, recent discoveries have revealed existence of fossil and active fungi in marine sediments and sub-seafloor basalts, with proposed importance for the subsurface energy cycle. However, studies of fungi in deep continental crystalline rocks are surprisingly few. Consequently, the characteristics and processes of fungi and fungus-prokaryote interactions in this vast environment remain enigmatic. Here we report the first findings of partly organically preserved and partly mineralized fungi at great depth in fractured crystalline rock (−740 m). Based on environmental parameters and mineralogy the fungi are interpreted as anaerobic. Synchrotron-based techniques and stable isotope microanalysis confirm a coupling between the fungi and sulfate reducing bacteria. The cryptoendolithic fungi have significantly weathered neighboring zeolite crystals and thus have implications for storage of toxic wastes using zeolite barriers.

  • 4.
    Drake, Henrik
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Åström, Mats E.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Heim, Christine
    Univ Göttingen, Germany.
    Broman, Curt
    Stockholm University.
    Åstrom, Jan
    CSC IT Ctr Sci, Finland.
    Whitehouse, Martin
    Swedish Museum of Natural History.
    Ivarsson, Magnus
    Swedish Museum of Natural History.
    Siljeström, Sandra
    SP Tech Res Inst Sweden.
    Sjövall, Peter
    SP Tech Res Inst Sweden.
    Extreme C-13 depletion of carbonates formed during oxidation of biogenic methane in fractured granite2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 7020Article in journal (Refereed)
    Abstract [en]

    Precipitation of exceptionally C-13-depleted authigenic carbonate is a result of, and thus a tracer for, sulphate-dependent anaerobic methane oxidation, particularly in marine sediments. Although these carbonates typically are less depleted in C-13 than in the source methane, because of incorporation of C also from other sources, they are far more depleted in C-13 (delta C-13 as light as - 69% V-PDB) than in carbonates formed where no methane is involved. Here we show that oxidation of biogenic methane in carbon-poor deep groundwater in fractured granitoid rocks has resulted in fracture-wall precipitation of the most extremely C-13-depleted carbonates ever reported, delta C-13 down to - 125% V-PDB. A microbial consortium of sulphate reducers and methane oxidizers has been involved, as revealed by biomarker signatures in the carbonates and S-isotope compositions of co-genetic sulphide. Methane formed at shallow depths has been oxidized at several hundred metres depth at the transition to a deep-seated sulphate-rich saline water. This process is so far an unrecognized terrestrial sink of methane.

  • 5.
    Ejsmond, Maciej J.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Jagiellonian University, Poland.
    Phillips, Karl P.
    University College Cork, Ireland;Marine Institute, Ireland.
    Babik, Wiesław
    Jagiellonian University, Poland.
    Radwan, Jacek
    Adam Mickiewicz University, Poland.
    The role of MHC supertypes in promoting trans-species polymorphism remains an open question2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, no 1, p. 1-4, article id 4362Article in journal (Refereed)
  • 6.
    Zhang, Sicai
    et al.
    Harvard Med Sch, USA.
    Masuyer, Geoffrey
    Stockholm University.
    Zhang, Jie
    Harvard Med Sch, USA.
    Shen, Yi
    Harvard Med Sch, USA.
    Lundin, Daniel
    Stockholm University.
    Henriksson, Linda
    Stockholm University.
    Miyashita, Shin-Ichiro
    Harvard Med Sch, USA.
    Martinez-Carranza, Markel
    Stockholm University.
    Dong, Min
    Harvard Med Sch, USA.
    Stenmark, Pål
    Stockholm University.
    Identification and characterization of a novel botulinum neurotoxin2017In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 8, article id 14130Article in journal (Refereed)
    Abstract [en]

    Botulinum neurotoxins are known to have seven serotypes (BoNT/A-G). Here we report a new BoNT serotype, tentatively named BoNT/X, which has the lowest sequence identity with other BoNTs and is not recognized by antisera against known BoNTs. Similar to BoNT/B/D/F/G, BoNT/X cleaves vesicle-associated membrane proteins (VAMP) 1, 2 and 3, but at a novel site (Arg66-Ala67 in VAMP2). Remarkably, BoNT/X is the only toxin that also cleaves non-canonical substrates VAMP4, VAMP5 and Ykt6. To validate its activity, a small amount of full-length BoNT/X was assembled by linking two non-toxic fragments using a transpeptidase (sortase). Assembled BoNT/X cleaves VAMP2 and VAMP4 in cultured neurons and causes flaccid paralysis in mice. Thus, BoNT/X is a novel BoNT with a unique substrate profile. Its discovery posts a challenge to develop effective countermeasures, provides a novel tool for studying intracellular membrane trafficking, and presents a new potential therapeutic toxin for modulating secretions in cells.

  • 7.
    Zhu, Ling
    et al.
    University of Oxford, UK ; The Pirbright Institute, UK.
    Wang, Xiangxi
    Chinese Academy of Science, China.
    Ren, Jingshan
    University of Oxford, UK.
    Porta, Claudine
    University of Oxford, UK ; The Pirbright Institute, UK.
    Wenham, Hannah
    The Pirbright Institute, UK.
    Ekström, Jens-Ola
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Panjwani, Anusha
    The Pirbright Institute, UK.
    Knowles, Nick J.
    The Pirbright Institute, UK.
    Kotecha, Abhay
    University of Oxford, UK.
    Siebert, C. Alistair
    University of Oxford, UK.
    Lindberg, A. Michael
    Linnaeus University, Faculty of Health and Life Sciences, Department of Chemistry and Biomedical Sciences.
    Fry, Elizabeth E.
    University of Oxford, UK.
    Rao, Zihe
    Chinese Academy of Science, China ; Tsinghua University, China.
    Tuthill, Tobias J.
    The Pirbright Institute, UK.
    Stuart, David I.
    University of Oxford, UK ; Harwell Science and Innovation Campus, UK.
    Structure of Ljungan virus provides insight into genome packaging of this picornavirus2015In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 6, article id 8316Article in journal (Refereed)
    Abstract [en]

    Picornaviruses are responsible for a range of human and animal diseases, but how their RNA genome is packaged remains poorly understood. A particularly poorly studied group within this family are those that lack the internal coat protein, VP4. Here we report the atomic structure of one such virus, Ljungan virus, the type member of the genus Parechovirus B, which has been linked to diabetes and myocarditis in humans. The 3.78-angstrom resolution cryo-electron microscopy structure shows remarkable features, including an extended VP1 C terminus, forming a major protuberance on the outer surface of the virus, and a basic motif at the N terminus of VP3, binding to which orders some 12% of the viral genome. This apparently charge-driven RNA attachment suggests that this branch of the picornaviruses uses a different mechanism of genome encapsidation, perhaps explored early in the evolution of picornaviruses.

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