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  • 1. Alonso-Blanco, Carlos
    et al.
    Andrade, Jorge
    Becker, Claude
    Bemm, Felix
    Bergelson, Joy
    Borgwardt, Karsten M.
    Cao, Jun
    Chae, Eunyoung
    Dezwaan, Todd M.
    Ding, Wei
    Ecker, Joseph R.
    Exposito-Alonso, Moises
    Farlow, Ashley
    Fitz, Joffrey
    Gan, Xiangchao
    Grimm, Dominik G.
    Hancock, Angela M.
    Henz, Stefan R.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Horton, Matthew
    Jarsulic, Mike
    Kerstetter, Randall A.
    Korte, Arthur
    Korte, Pamela
    Lanz, Christa
    Lee, Cheng-Ruei
    Meng, Dazhe
    Michael, Todd P.
    Mott, Richard
    Muliyati, Ni Wayan
    Nägele, Thomas
    Nagler, Matthias
    Nizhynska, Viktoria
    Nordborg, Magnus
    Novikova, Polina Yu.
    Picó, F. Xavier
    Platzer, Alexander
    Rabanal, Fernando A.
    Rodriguez, Alex
    Rowan, Beth A.
    Salomé, Patrice A.
    Schmid, Karl J.
    Schmitz, Robert J.
    Seren, Ümit
    Sperone, Felice Gianluca
    Sudkamp, Mitchell
    Svardal, Hannes
    Tanzer, Matt M.
    Todd, Donald
    Volchenboum, Samuel L.
    Wang, Congmao
    Wang, George
    Wang, Xi
    Weckwerth, Wolfram
    Weigel, Detlef
    Zhou, Xuefeng
    1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana2016In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 166, no 2, p. 481-491Article in journal (Refereed)
    Abstract [en]

    Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.

  • 2.
    Antoniou-Kourounioti, Rea L.
    et al.
    Norwich Research Park, Norwich, United Kingdom.
    Hepworth, Jo
    Norwich Research Park, Norwich, United Kingdom.
    Heckmann, Amélie
    Norwich Research Park, Norwich, United Kingdom.
    Duncan, Susan
    Norwich Research Park, Norwich, United Kingdom.
    Qüesta, Julia
    Norwich Research Park, Norwich, United Kingdom.
    Rosa, Stefanie
    Norwich Research Park, Norwich, United Kingdom.
    Säll, Torbjörn
    Lund University, Lund.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Dean, Caroline
    Norwich Research Park, Norwich, United Kingdom.
    Howard, Martin
    Norwich Research Park, Norwich, United Kingdom.
    Temperature Sensing Is Distributed throughout the Regulatory Network that Controls FLC Epigenetic Silencing in Vernalization2018In: Cell systems, ISSN 2405-4712, Vol. 7, no 6, p. 643-655Article in journal (Refereed)
    Abstract [en]

    Many organisms need to respond to complex, noisy environmental signals for developmental decision making. Here, we dissect how Arabidopsis plants integrate widely fluctuating field temperatures over month-long timescales to progressively upregulate VERNALIZATION INSENSITIVE3 (VIN3) and silence FLOWERING LOCUS C (FLC), aligning flowering with spring. We develop a mathematical model for vernalization that operates on multiple timescales-long term (month), short term (day), and current (hour)-and is constrained by experimental data. Our analysis demonstrates that temperature sensing is not localized to specific nodes within the FLC network. Instead, temperature sensing is broadly distributed, with each thermosensory process responding to specific features of the plants' history of exposure to warm and cold. The model accurately predicts FLC silencing in new field data, allowing us to forecast FLC expression in changing climates. We suggest that distributed thermosensing may be a general property of thermoresponsive regulatory networks in complex natural environments. 

  • 3. Barsoum, N
    et al.
    Nilsson, Christer
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Lakes as potential barriers to gene flow in the hydrochorus plant species Angelica archangelica L. subsp. archangelicaManuscript (Other academic)
  • 4.
    Bång, Åsa
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Nilsson, Christer
    Control of plant species diversity in riparian corridors: Konferens OIKOS 20022002Conference paper (Other academic)
    Abstract [en]

    previous study has shown that plant communities differ floristically between impoundments but remain similar within impoundments in a regulated river. The same pattern did not occur among plant species in a free-flowing river which instead showed a continuous change in species composition from the headwaters to the coast. This strongly suggests that the dispersal of plants is obstructed when dams are built on rivers. The present project will specifically study whether dams also affect the genetic diversity among and between populations of plant species. Filipendula ulmaria will be used as a first test species. A second question is whether tributaries have any impact on the distribution of genetic diversity of plant species within impoundments. A third question deals with the impact of seed and pollen dispersal on the genetic diversity among and between plant species populations. The project combines field sampling, field experiments and laboratory methods such as isoenzymes, microsatellites and other DNA-methods.

  • 5.
    Bång, Åsa
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Jonsson, Bengt Gunnar
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Effects of pollination distance on reproductive success in Filipendula ulmariaManuscript (preprint) (Other academic)
  • 6.
    Bång, Åsa
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Jonsson, Bengt Gunnar
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Equal seed set and germination rate over distance and indication of self incompatibility in artificial crosses of Filipendula ulmariaManuscript (Other academic)
  • 7.
    Bång, Åsa
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Jägbrant, Veronica
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Spatial genetic structure of a common riparian plant species, Meadowsweet (Filipendula ulmaria) in northern SwedenManuscript (Other academic)
  • 8.
    Bång, Åsa
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Jägbrant, Veronica
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Nilsson, Christer
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Differences in spatial genetic structure of riparian Filipendula ulmaria between an within river catchments in northern SwedenManuscript (preprint) (Other academic)
  • 9.
    Bång, Åsa
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Nilsson, Christer
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    The potential role of tributaries as seed sources to an impoundment in northern Sweden: a field experiment with seed mimics2007In: Rivers Research and Applications: an international journal devoted to river research and management, ISSN 1535-1459, E-ISSN 1535-1467, Vol. 23, no 10, p. 1049-1057Article in journal (Refereed)
    Abstract [en]

    Fragmentation and flow regulation of rivers by large dams are known to obstruct the longitudinal dispersal of waterborne plant propagules between impoundments, and to affect plant community composition. However, even several decades after a dam has been built, impoundments may still have a relatively species-rich riparian flora. We hypothesized that free-flowing tributaries act as the major gene pools for such impoundments, thus alleviating the fragmenting effect large dams have on the main channel. The importance of tributaries as seed sources was tested by releasing wooden seed mimics in three different-sized (0.22-6.93 m3 s-1) tributaries of an impoundment in the Ume River in northern Sweden. In each tributary seed mimics were released, during the spring flood peak, from three points approximately 1, 2 and 3 km upstream the outlet in the impoundment. The importance of a tributary as a seed source increased with tributary size. Of the 9000 released seed mimics 1.5 % reached the impoundment; 1.2 % of the 9000 originated from the largest tributary and 0.3 % from the middle-sized one. The smallest tributary retained all its mimics.

  • 10.
    Bång, Åsa
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Nilsson, Christer
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    What is the role of tributaries as seed sources for a run-of-river impoundment: a field experiment: Konferens SISORL 20042004Conference paper (Other academic)
    Abstract [en]

    The reservoirs in impounded rivers are blocked by dams, implying that plant seeds, especially waterborne ones, have trouble dispersing between reservoirs. We examined whether the tributaries have an important role in the dispersal of seeds to a specific reservoir. We did this by releasing small, coloured wooden cubes in three tributaries of the Stensele reservoir in northern Sweden, one small, one middle-sized and one large-sized. This work was carried out in spring during major flood. At the day of cube release, we counted the number of cubes that dispersed from the tributaries out into the reservoir. In summer, we collected the cubes that had stranded on the banks of the tributaries to learn how far they had spread within each stream. Our examinations showed that a big stream disperses most seeds the longest distance. The smaller the stream, the shorter the distance the seeds were spread, and the fewer the seeds that reached the reservoir. We concluded that large tributaries have an important role in dispersing plants to reservoirs of impounded rivers.

  • 11.
    Carlsson, Fredrik
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of applied science and design.
    Edman, Mattias
    Mid Sweden University, Faculty of Science, Technology and Media, Department of applied science and design.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of applied science and design.
    Eriksson, Anna-Maria
    Mid Sweden University, Faculty of Science, Technology and Media, Department of applied science and design.
    Jonsson, Bengt Gunnar
    Mid Sweden University, Faculty of Science, Technology and Media, Department of applied science and design.
    Increased heat resistance in mycelia from wood fungi prevalent in forests characterized by fire: a possible adaptation to forest fire.2012In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 116, no 10, p. 1025-1031Article in journal (Refereed)
    Abstract [en]

    Abstract

    Forest fire has for a long time been the major stand replacing/modifying disturbance in boreal forests. For organisms to adopt to this phenomenon different strategies for protective measurements has evolved. This study focuses on the organism group of wood fungi, and one of several possibilities for adaptation to forest fire - increased heat resistance in the mycelia. 16 species of wood fungi where selected and sorted a priori according to their prevalence for fire affected substrate. These were isolated and re-inoculated on pine wood before testing. Experiments where done in a series where the mycelia was exposed to 100, 140, 180, 220°C for 5, 10, 15, 20, 15 min. A very clear difference was found, the group containing species with a prevalence for a fire affected substrate had a much higher survival rate over all combinations of time and temperature compared to species with a more general ecology. This data suggests that increased heat resistance in mycelia could be a possible adaptation to forest fire. This in turn has major impacts on the ecology and population dynamics of wood fungi. An increase in temperature could shift the population structure in a log, allowing minor non fruiting mycelia content to expand on the expense of earlier dominant colonizers. Furthermore this study has implications on how to control prescribed restoration burning events. When burning areas where the dead wood content is dominated by early decay stages, loss of species can be avoided by proper management.

  • 12.
    Carlsson, Fredrik
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Edman, Mattias
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Jonsson, Bengt Gunnar
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Effect of heat on interspecific competition in saprotrophic wood fungi2014In: Fungal ecology, ISSN 1754-5048, E-ISSN 1878-0083, Vol. 11, p. 100-106Article in journal (Refereed)
    Abstract [en]

    Some boreal wood fungi that are associated with forest fire or open dry habitats have an increased resistance to heat in comparison to species associated with a less specific distribution or species found in mesic forests. We hypothesize that extreme temperature-stress experienced during fires will favor species adapted to heat and, ultimately, the composition of species inhabiting logs in such habitats will change. Competitiveness after temperature stress was examined in three fire-associated species – Dichomitus squalens, Gloeophyllum sepiarium and Phlebiopsis gigantea – and three non fire-associated species – Ischnoderma benzoinum, Phellinus pini and Fomitopsis pinicola. There was a difference between the fire-associated species and the non fire-associated species with respect to competitive strength after heat stress. All fire-associated species had an advantage after heat treatment, colonizing a larger volume of wood than any non-fire-associated competitor. Our findings suggest that increased heat tolerance of mycelia can exert a competitive balance shift after forest fire. It shows that a system governed by forest fire will be dominance controlled under certain conditions. Furthermore, from a management perspective, during a prescribed burning, certain species already present in the ecosystem will be favored if the fire is not allowed to totally consume the substrates.

  • 13. Carlsson, Fredrik
    et al.
    Holm, Svante
    SNP development for P. gigantea; Method and resources. Primer noteManuscript (preprint) (Other academic)
    Abstract [en]

    Phlebiopsis gigantea is an interesting species from many perspectives. It is common in many forests and can often be seen as an early colonizer on fresh wood after a clear cutting. After a forest fire it has been found to be abundant in newly burned forests, in some cases being the dominating species on the majority of logs and stumps (Olsson and Jonsson 2009; Eriksson et al. in prep.). In a study to test heat tolerance in species possibly favored by forest fire P. gigantea showed a remarkable resistance, allowing it not only to survive the forest fire but also to thrive in the microclimatic situation created by the event (Carlsson et al. in press). 

    It is used by forest agencies as a bio controller against Root rot (Rotstop©) from Heterobasidium annosum in parts of boreal fennoscandia, applied at 47 000 ha annually. The practice is that a solution of fungal spores is sprayed on to stumps of already logged trees to prevent the spread of the protagonist fungi. Spores from only one strain of P. gigantea have been used for preparation until the year of 2005 (Rishbeth 1959, Tohr 2003). The spread of genetic material from one individual could have consequences on the population structure of the species as well as other species present in the ecosystem. Stenlid et al. 2009 investigated the population structure in strains from 11 populations spread across the boreal zone from Finland to North America, using microsatellite markers.  And found that, so far very little effect from the use of the fungicide was detectable outside of the plots where Rotstop© was applied (Stenlid et al 2009).

    We aim to develop a set of snp markers for further use in a population study, looking at the effectors mentioned above. We will try to exclude the influence of fungicide usage to detect structures possibly created by forest fire.

  • 14.
    Carlsson, Fredrik
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Koch, Christin
    Edman, Mattias
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Testing the probability of finding major decomposing basidiomycetes in logs with T-RFLP - implications for field samplingManuscript (preprint) (Other academic)
    Abstract [en]

    In this article we examine the limitations and potential of T-RFLP for the accurate detection of fungal species in dead wood. We collected cross-sections of decayed logs to evaluate the number of fungal species domains that are likely to be hit when drilling a sawdust sample from a log. We used these estimates to simulate the number of species that would be found using a certain number of samples. We found that in 99% of the simulations, 4 or fewer species would be contained in a sample. Based on these results we tested the probability of detecting two species of wood-decaying basidiomycetes at three different DNA concentration ratios: 1:1, 1:5 and 1:20. An additional experiment was done with 3-5 species. It was possible to detect all species at ratios higher than 1:20 but lower than 1:5; in this range all peaks were easily detected. We were able to detect all species in the mixtures of 3-5 species, with extracts from both pure cultures and wood.

  • 15.
    Carlsson, Fredrik
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Olsson, Jörgen
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Strong clustering in a SNP study of Phlebiopsis gigantea in swedenManuscript (preprint) (Other academic)
    Abstract [en]

    The population structures of wood decaying basidomycetes depend on several factors; one is dispersal pattern of spores, another is age structure including lifespan and also environmental impacts like forest fires. Phlebiopsis gigantea has been shown to be in the group of basidomycetes that have a well developed tolerance to heat, is long-distance wind dispersed and whose fruit body show up early in succession on fallen logs. In a study of 132 individuals from 3 pairs of locations, 350 km apart, in middle to northern Sweden we used 26 SNP-markers in 6 loci to make a genetic clustering study using STRUCTURE (v. 2.3.4.). The hypothesis; first, clustering should follow the geographic sampling locations with more gene flow between geographically close locations, second; that genetic distance between different clusters should be low due to the long distance dispersal of spores, third; as markers are random we don’t expect to find a correlation between locations affected by forest fires and locations not affected by forest fires. In the study we found 5 clusters (Pr[K= 1]) with moderate to high Fst values (0,0697-03939). Clusters had a poor geographical correlation to sampled populations indicating a complicated population structure. Out of 132 individuals 119 had a private genotype showing a large genetic variation over the total area and a low level of clones in the field.         

  • 16.
    Duncan, S.
    et al.
    John Innes Centre, Norwich, United Kingdom .
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Questa, J.
    John Innes Centre, Norwich, United Kingdom .
    Irwin, J.
    John Innes Centre, Norwich, United Kingdom .
    Grant, A.
    Department of Environmental Sciences, University of East Anglia, Norwich, United Kingdom .
    Dean, C.
    John Innes Centre, Norwich, United Kingdom .
    Seasonal shift in timing of vernalization as an adaptation to extreme winter2015In: eLIFE, ISSN 2050-084X, Vol. 4, no JULYArticle in journal (Refereed)
    Abstract [en]

    The requirement for vernalization, a need for prolonged cold to trigger flowering, aligns reproductive development with favorable spring conditions. In Arabidopsis thaliana vernalization depends on the cold-induced epigenetic silencing of the floral repressor locus FLC. Extensive natural variation in vernalization response is associated with A. thaliana accessions collected from different geographical regions. Here, we analyse natural variation for vernalization temperature requirement in accessions, including those from the northern limit of the A. thaliana range. Vernalization required temperatures above 0°C and was still relatively effective at 14°C in all the accessions. The different accessions had characteristic vernalization temperature profiles. One Northern Swedish accession showed maximum vernalization at 8°C, both at the level of flowering time and FLC chromatin silencing. Historical temperature records predicted all accessions would vernalize in autumn in N. Sweden, a prediction we validated in field transplantation experiments. The vernalization response of the different accessions was monitored over three intervals in the field and found to match that when the average field temperature was given as a constant condition. The vernalization temperature range of 0–14°C meant all accessions fully vernalized before snowfall in N. Sweden. These findings have important implications for understanding the molecular basis of adaptation and for predicting the consequences of climate change on flowering time.

  • 17.
    Hepworth, Jo
    et al.
    Norwich Research Park, Norwich, UK.
    Antoniou-Kourounioti, Rea L.
    Norwich Research Park, Norwich, UK.
    Bloomer, Rebecca H.
    Norwich Research Park, Norwich, UK.
    Selga, Catja
    Lund University.
    Berggren, Kristina
    Mid Sweden University, Faculty of Science, Technology and Media.
    Cox, Deborah
    Norwich Research Park, Norwich, UK.
    Collier Harris, Barley R.
    Norwich Research Park, Norwich, UK.
    Irwin, Judith A.
    Norwich Research Park, Norwich, UK.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Säll, Torbjörn
    Lund University.
    Howard, Martin
    Norwich Research Park, Norwich, UK.
    Dean, Caroline
    Norwich Research Park, Norwich, UK.
    Absence of warmth permits epigenetic memory of winter in Arabidopsis2018In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, no 1, article id 639Article in journal (Refereed)
    Abstract [en]

    Plants integrate widely fluctuating temperatures to monitor seasonal progression. Here, we investigate the temperature signals in field conditions that result in vernalisation, the mechanism by which flowering is aligned with spring. We find that multiple, distinct aspects of the temperature profile contribute to vernalisation. In autumn, transient cold temperatures promote transcriptional shutdown of Arabidopsis FLOWERING LOCUS C (FLC), independently of factors conferring epigenetic memory. As winter continues, expression of VERNALIZATION INSENSITIVE3 (VIN3), a factor needed for epigenetic silencing, is upregulated by at least two independent thermosensory processes. One integrates long-term cold temperatures, while the other requires the absence of daily temperatures above 15 °C. The lack of spikes of high temperature, not just prolonged cold, is thus the major driver for vernalisation. Monitoring of peak daily temperature is an effective mechanism to judge seasonal progression, but is likely to have deleterious consequences for vernalisation as the climate becomes more variable. 

  • 18.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences, Engineering and Mathematics.
    Changing ploidy levels in artificial crossings in Potentilla argenteaManuscript (Other academic)
  • 19.
    Holm, Svante
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Bång, Åsa
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    High gene flow and differences in pollination pattern in a paternity analysis of a small riparian population of Filipendula ulmariaManuscript (preprint) (Other academic)
  • 20.
    Holm, Svante
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Bång, Åsa
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Jonsson, Bengt Gunnar
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Paternity analysis in Filipendula ulmaria indicates high level of gene flow between populations, using AFLPManuscript (Other academic)
  • 21.
    Holm, Svante
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Forsberg, D
    Nordstrand, A
    The gentic structure of Fresh water pearl mussel (Margaritifera margaritifera); influenced by recent human activity?Manuscript (Other (popular science, discussion, etc.))
  • 22.
    Högberg, Björn
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering, Physics and Mathematics.
    Helmersson, J.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering, Physics and Mathematics.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Olin, Håkan
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering, Physics and Mathematics.
    DNA Coated Nanoparticle eight-mers as Programmable Self-Assembly Building Blocks2005In: Foundations of nanoscience (FNANO05): Self-assembled architectures and devices, 2005, p. 219-226Conference paper (Other academic)
  • 23.
    Högberg, Björn
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering, Physics and Mathematics.
    Helmersson, Jing
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Olin, Håkan
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Engineering, Physics and Mathematics.
    Study of DNA-Coated Nanoparticles as Possible Programmable Self-Assembly Building-Blocks2006In: Applied Surface Science, ISSN 0169-4332, E-ISSN 1873-5584, Vol. 252, no 15, p. 5538-5541Article in journal (Refereed)
    Abstract [en]

    Nanoparticles coated with single stranded DNA have been shown to efficiently hybridize to targets of complementary DNA. This property might be used to implement programmable (or algorithmic) self-assembly to build nanoparticle structures. However, we argue that a DNA coated nanoparticle by itself cannot be used as a programmable self-assembly building block since it does not have directed bonds. A general scheme for assembling and purifying nanoparticle eight-mers with eight geometrically well-directed bonds is presented together with some preliminary experimental work.

     

     

  • 24. Kawakatsu, Taiji
    et al.
    Huang, Shao-shan Carol
    Jupe, Florian
    Sasaki, Eriko
    Schmitz, Robert J.
    Urich, Mark A.
    Castanon, Rosa
    Nery, Joseph R.
    Barragan, Cesar
    He, Yupeng
    Chen, Huaming
    Dubin, Manu
    Lee, Cheng-Ruei
    Wang, Congmao
    Bemm, Felix
    Becker, Claude
    O’Neil, Ryan
    O’Malley, Ronan C.
    Quarless, Danjuma X.
    Alonso-Blanco, Carlos
    Andrade, Jorge
    Bergelson, Joy
    Borgwardt, Karsten
    Chae, Eunyoung
    Dezwaan, Todd
    Ding, Wei
    Ecker, Joseph R.
    Expósito-Alonso, Moisés
    Farlow, Ashley
    Fitz, Joffrey
    Gan, Xiangchao
    Grimm, Dominik G.
    Hancock, Angela
    Henz, Stefan R.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Horton, Matthew
    Jarsulic, Mike
    Kerstetter, Randall A.
    Korte, Arthur
    Korte, Pamela
    Lanz, Christa
    Lee, Chen-Ruei
    Meng, Dazhe
    Michael, Todd P.
    Mott, Richard
    Muliyati, Ni Wayan
    Nägele, Thomas
    Nagler, Matthias
    Nizhynska, Viktoria
    Nordborg, Magnus
    Novikova, Polina
    Picó, F. Xavier
    Platzer, Alexander
    Rabanal, Fernando A.
    Rodriguez, Alex
    Rowan, Beth A.
    Salomé, Patrice A.
    Schmid, Karl
    Seren, Ümit
    Sperone, Felice Gianluca
    Sudkamp, Mitchell
    Svardal, Hannes
    Tanzer, Matt M.
    Todd, Donald
    Volchenboum, Samuel L.
    Wang, George
    Wang, Xi
    Weckwerth, Wolfram
    Weigel, Detlef
    Zhou, Xuefeng
    Schork, Nicholas J.
    Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions2016In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 166, no 2, p. 492-505Article in journal (Refereed)
    Abstract [en]

    The epigenome orchestrates genome accessibility, functionality, and three-dimensional structure. Because epigenetic variation can impact transcription and thus phenotypes, it may contribute to adaptation. Here, we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Genomes collection of Arabidopsis thaliana. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. Comparison to cistrome and epicistrome datasets identifies associations between transcription factor binding sites, methylation, nucleotide variation, and co-expression modules. Physical maps for nine of the most diverse genomes reveal how transposons and other structural variants shape the epigenome, with dramatic effects on immunity genes. The 1001 Epigenomes Project provides a comprehensive resource for understanding how variation in DNA methylation contributes to molecular and non-molecular phenotypes in natural populations of the most studied model plant.

  • 25.
    Nilsson, Christer
    et al.
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Bång, Åsa
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Control of plant species diversity in riparian corridors: Konferens ESEB 20032003Conference paper (Other academic)
    Abstract [en]

    previous study has shown that plant communities differ floristically between impoundments but remain similar within impoundments in a regulated river. The same pattern did not occur among plant species in a free-flowing river which instead showed a continuous change in species composition from the headwaters to the coast. This strongly suggests that the dispersal of plants is obstructed when dams are built on rivers. The present project will specifically study whether dams also affect the genetic diversity among and between populations of plant species. Filipendula ulmaria will be used as a first test species. A second question is whether tributaries have any impact on the distribution of genetic diversity of plant species within impoundments. A third question deals with the impact of seed and pollen dispersal on the genetic diversity among and between plant species populations. The project combines field sampling, field experiments and laboratory methods such as isoenzymes, microsatellites and other DNA-methods.

  • 26.
    Novikova, P. Y.
    et al.
    Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
    Hohmann, N.
    Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany .
    Nizhynska, V.
    Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
    Tsuchimatsu, T.
    Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
    Ali, J.
    Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany.
    Muir, G.
    Vienna Graduate School of Population Genetics, Institut für Populationsgenetik, Vetmeduni, Vienna, Austria .
    Guggisberg, A.
    Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland .
    Paape, T.
    Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland .
    Schmid, K.
    Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany .
    Fedorenko, O. M.
    Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Petrozavodsk, Russian Federation .
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Säll, T.
    Department of Biology, Lund University, Lund, Sweden .
    Schlötterer, C.
    Institut für Populationsgenetik, Vetmeduni, Vienna, Austria .
    Marhold, K.
    Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic .
    Widmer, A.
    Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany .
    Sese, J.
    Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan .
    Shimizu, K. K.
    Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland .
    Weigel, D.
    Max Planck Institute for Developmental Biology, Tübingen, Germany .
    Krämer, U.
    Department of Plant Physiology, Ruhr-Universität Bochum, Bochum, Germany .
    Koch, M. A.
    Centre for Organismal Studies Heidelberg, University of Heidelberg, Heidelberg, Germany .
    Nordborg, M.
    Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria .
    Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism2016In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 48, no 9, p. 1077-1082Article in journal (Refereed)
    Abstract [en]

    The notion of species as reproductively isolated units related through a bifurcating tree implies that gene trees should generally agree with the species tree and that sister taxa should not share polymorphisms unless they diverged recently and should be equally closely related to outgroups. It is now possible to evaluate this model systematically. We sequenced multiple individuals from 27 described taxa representing the entire Arabidopsis genus. Cluster analysis identified seven groups, corresponding to described species that capture the structure of the genus. However, at the level of gene trees, only the separation of Arabidopsis thaliana from the remaining species was universally supported, and, overall, the amount of shared polymorphism demonstrated that reproductive isolation was considerably more recent than the estimated divergence times. We uncovered multiple cases of past gene flow that contradict a bifurcating species tree. Finally, we showed that the pattern of divergence differs between gene ontologies, suggesting a role for selection. © 2016 Nature America, Inc. All rights reserved.

  • 27.
    Novikova, Polina Yu
    et al.
    Gregor Mendel Inst, Vienna, Austria; Vienna Grad Sch Populat Genet, Vienna, Austria.
    Tsuchimatsu, Takashi
    Gregor Mendel Inst, Vienna, Austria.
    Simon, Samson
    Université de Lille, France.
    Nizhynska, Viktoria
    Gregor Mendel Inst, Vienna, Austria.
    Voronin, Viktor
    Gregor Mendel Inst, Vienna, Austria.
    Burns, Robin
    Gregor Mendel Inst, Vienna, Austria.
    Fedorenko, Olga M.
    Russian Acad Sci, Petrozavodsk, Russia.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Saell, Torbjoern
    Lund Univ, Dept Biol, Lund.
    Prat, Elisa
    INRA CNRGV, Castanet Tolosan, France.
    Marande, William
    INRA CNRGV, Castanet Tolosan, France.
    Castric, Vincent
    Univ Lille, France.
    Nordborg, Magnus
    Gregor Mendel Inst, Vienna, Austria.
    Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica2017In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 4, p. 957-968Article in journal (Refereed)
    Abstract [en]

    Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual-a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-offunction allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.

  • 28.
    Plötner, Björn
    et al.
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Nurmi, Markus
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Fischer, Axel
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Watanabe, Mutsumi
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Schneeberger, Korbinian
    Max Planck Institute for Plant Breeding, Cologne, Germany.
    Holm, Svante
    Mid Sweden University, Faculty of Science, Technology and Media, Department of Natural Sciences.
    Vaid, Neha
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Schöttler, Mark Aurel
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Walther, Dirk
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Hoefgen, Rainer
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Weigel, Detlef
    Max Planck Institute for Developmental Biology, Tübingen, Germany.
    Laitinen, Roosa A. E.
    Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
    Chlorosis caused by two recessively interacting genes reveals a role of RNA helicase in hybrid breakdown in Arabidopsis thaliana2017In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 91, no 2, p. 251-262Article in journal (Refereed)
    Abstract [en]

    Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden). In addition to chlorosis, a fraction of the F2 plants have defects in leaf and embryo development, and reduced photosynthetic efficiency. Hybrid chlorosis is due to two major-effect loci, of which one, originating from Lov-5, appears to encode an RNA helicase (AtRH18). To examine the role of the chlorosis allele in the Lövvik area, in addition to eight accessions collected in 2009, we collected another 240 accessions from 15 collections sites, including Lövvik, from Northern Sweden in 2015. Genotyping revealed that Lövvik collection site is separated from the rest. Crosses between 109 accessions from this area and Sha revealed 85 cases of hybrid chlorosis, indicating that the chlorosis-causing allele is common in this area. These results suggest that hybrid breakdown alleles not only occur at rapidly evolving loci, but also at genes that code for conserved processes.

1 - 28 of 28
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