Publications

@article{kohorn2021effects,

title = {Effects of Arabidopsis wall associated kinase mutations on ESMERALDA1 and elicitor induced ROS},

author = {Bruce D Kohorn and Bridgid E Greed and Gregory Mouille and Stéphane Verger and Susan L Kohorn},

year  = {2021},

date = {2021-01-01},

journal = {Plos one},

volume = {16},

number = {5},

pages = {e0251922},

publisher = {Public Library of Science San Francisco, CA USA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{malivert2021feronia,

title = {FERONIA and microtubules independently contribute to mechanical integrity in the Arabidopsis shoot},

author = {Alice Malivert and Özer Erguvan and Antoine Chevallier and Antoine Dehem and Rodrigue Friaud and Mengying Liu and Marjolaine Martin and Théophile Peyraud and Olivier Hamant and Stéphane Verger},

year  = {2021},

date = {2021-01-01},

journal = {PLoS biology},

volume = {19},

number = {11},

pages = {e3001454},

publisher = {Public Library of Science San Francisco, CA USA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Johan_Henriksson_94038920,

title = {Mapping Rora expression in resting and activated CD4+ T cells},

author = {Johan Henriksson and Liora Haim-Vilmovsky and Scott N. Mueller and Johan Henriksson and Jennifer A. Walker and Zhichao Miao and Eviatar Natan and Gozde Kar and Simon Clare and Jillian L. Barlow and Evelina Charidemou and Lira Mamanova and Xi Chen and Valentina Proserpio and Jhuma Pramanik and Steven Woodhouse and Anna V. Protasio and Mirjana Efremova and Julian L. Griffin and Matt Berriman and Gordon Dougan and Jasmin Fisher and John C. Marioni and Andrew N. J. McKenzie and Sarah A. Teichmann},

url = {http://doi.org/10.1371/journal.pone.0251233},

doi = {10.1371/journal.pone.0251233},

year  = {2021},

date = {2021-01-01},

journal = {PLOS ONE},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jafari_2021b,

title = {Activity and stress during a critical period regulate olfactory sensory neuron differentiation},

author = {Shadi Jafari and Johan Henriksson and Hua Yan and Mattias Alenius},

url = {https://doi.org/10.1101%2F2021.01.13.426514},

doi = {10.1101/2021.01.13.426514},

year  = {2021},

date = {2021-01-01},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ma2021antibiotic,

title = {Antibiotic resistance in shiga toxigenic Escherichia coli isolates from surface waters and sediments in a mixed use urban agricultural landscape},

author = {Yvonne Ma and Jessica Chen and Karen Fong and Stephanie Nadya and Kevin Allen and Chad Laing and Kim Ziebell and Ed Topp and Laura M Carroll and Martin Wiedmann and others},

year  = {2021},

date = {2021-01-01},

journal = {Antibiotics},

volume = {10},

number = {3},

pages = {237},

publisher = {MDPI},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2021accurate,

title = {Accurate de novo identification of biosynthetic gene clusters with GECCO},

author = {Laura M Carroll and Martin Larralde and Jonas Simon Fleck and Ruby Ponnudurai and Alessio Milanese and Elisa Cappio and Georg Zeller},

year  = {2021},

date = {2021-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Abreu2020,

title = {A metabolite roadmap of the wood-forming tissue in Populus tremula},

author = {Ilka N. Abreu and Annika I. Johansson and Katarzyna Sokołowska and Totte Niittylä and Björn Sundberg and Torgeir R. Hvidsten and Nathaniel R. Street and Thomas Moritz},

url = {https://onlinelibrary.wiley.com/doi/10.1111/nph.16799},

doi = {10.1111/nph.16799},

issn = {14698137},

year  = {2020},

date = {2020-12-01},

journal = {New Phytologist},

volume = {228},

number = {5},

pages = {1559--1572},

publisher = {Blackwell Publishing Ltd},

abstract = {Wood, or secondary xylem, is the product of xylogenesis, a developmental process that begins with the proliferation of cambial derivatives and ends with mature xylem fibers and vessels with lignified secondary cell walls. Fully mature xylem has undergone a series of cellular processes, including cell division, cell expansion, secondary wall formation, lignification and programmed cell death. A complex network of interactions between transcriptional regulators and signal transduction pathways controls wood formation. However, the role of metabolites during this developmental process has not been comprehensively characterized. To evaluate the role of metabolites during wood formation, we performed a high spatial resolution metabolomics study of the wood-forming zone of Populus tremula, including laser dissected aspen ray and fiber cells. We show that metabolites show specific patterns within the wood-forming zone, following the differentiation process from cell division to cell death. The data from profiled laser dissected aspen ray and fiber cells suggests that these two cell types host distinctly different metabolic processes. Furthermore, by integrating previously published transcriptomic and proteomic profiles generated from the same trees, we provide an integrative picture of molecular processes, for example, deamination of phenylalanine during lignification is of critical importance for nitrogen metabolism during wood formation.},

keywords = {cambium, crysectioning, laser capture microdissection, metabolomics, Populus, wood},

pubstate = {published},

tppubtype = {article}

}

@article{Mahler2020,

title = {Leaf shape in Populus tremula is a complex, omnigenic trait},

author = {Niklas Mähler and Bastian Schiffthaler and Kathryn M. Robinson and Barbara K. Terebieniec and Matej Vučak and Chanaka Mannapperuma and Mark E. S. S. Bailey and Stefan Jansson and Torgeir R. Hvidsten and Nathaniel R. Street},

url = {https://onlinelibrary.wiley.com/doi/full/10.1002/ece3.6691 https://onlinelibrary.wiley.com/doi/abs/10.1002/ece3.6691 https://onlinelibrary.wiley.com/doi/10.1002/ece3.6691},

doi = {10.1002/ece3.6691},

issn = {2045-7758},

year  = {2020},

date = {2020-11-01},

journal = {Ecology and Evolution},

volume = {10},

number = {21},

pages = {11922--11940},

publisher = {John Wiley and Sons Ltd},

keywords = {complex trait, GWAS, leaf shape, natural variation, omnigenic, Populus tremula},

pubstate = {published},

tppubtype = {article}

}

@article{PhysRevE.102.012302,

title = {Mapping flows on sparse networks with missing links},

author = {Jelena Smiljanic and Daniel Edler and Martin Rosvall},

url = {https://link.aps.org/doi/10.1103/PhysRevE.102.012302},

doi = {10.1103/PhysRevE.102.012302},

year  = {2020},

date = {2020-07-01},

journal = {Phys. Rev. E},

volume = {102},

pages = {012302},

publisher = {American Physical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32634386,

title = {How geographic productivity patterns affect food-web evolution},

author = {Jonas Wickman and Ulf Dieckmann and Cang Hui and Åke Brännström},

year  = {2020},

date = {2020-07-01},

journal = {J. Theor. Biol.},

volume = {506},

pages = {110374},

note = {[DOI:hrefhttps://dx.doi.org/10.1016/j.jtbi.2020.11037410.1016/j.jtbi.2020.110374] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/3263438632634386]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Muller2020,

title = {A single gene underlies the dynamic evolution of poplar sex determination},

author = {Niels A. Müller and Birgit Kersten and Ana P. Leite Montalvão and Niklas Mähler and Carolina Bernhardsson and Katharina Bräutigam and Zulema Carracedo Lorenzo and Hans Hoenicka and Vikash Kumar and Malte Mader and Birte Pakull and Kathryn M. Robinson and Maurizio Sabatti and Cristina Vettori and Pär K. Ingvarsson and Quentin Cronk and Nathaniel R. Street and Matthias Fladung},

url = {http://www.nature.com/articles/s41477-020-0672-9},

doi = {10.1038/s41477-020-0672-9},

issn = {2055-0278},

year  = {2020},

date = {2020-06-01},

journal = {Nature Plants},

pages = {1--8},

publisher = {Nature Publishing Group},

abstract = {Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive1. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes. Populus has young sex chromosomes despite ancient dioecy. This study shows that the ARR17 gene functions as a sex switch, triggering female development when on and male development when off. This single-gene system enables dynamic evolution of poplar sex chromosomes.},

keywords = {evolution, Genomics, Natural variation in plants, Plant evolution, Plant genetics},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32547784,

title = {Ecological speciation in European whitefish is driven by a large-gaped predator},

author = {Gunnar Öhlund and Mats Bodin and Karin A. Nilsson and Sven‐Ola Öhlund and Kenyon B. Mobley and Alan G. Hudson and Mikael Peedu and Åke Brännström and Pia Bartels and Kim Præbel and Catherine L. Hein and Petter Johansson and Göran Englund},

year  = {2020},

date = {2020-06-01},

journal = {Evol Lett},

volume = {4},

number = {3},

pages = {243--256},

note = {[PubMed Central:hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293097PMC7293097] [DOI:hrefhttps://dx.doi.org/10.1002/evl3.16710.1002/evl3.167] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/2665578226655782]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Enevold2020,

title = {Tunable Two-Dimensional Patterning of a Semiconducting and Nanometer-Thin C 60 Fullerene Film Using a Spatial Light Modulator},

author = {Jenny Enevold and Tobias Dahlberg and Tim Stangner and Shi Tang and E. Mattias Lindh and Eduardo Gracia-Espino and Magnus Andersson and Ludvig Edman},

url = {https://pubs.acs.org/doi/10.1021/acsanm.0c00793},

doi = {10.1021/acsanm.0c00793},

issn = {2574-0970},

year  = {2020},

date = {2020-05-01},

journal = {ACS Applied Nano Materials},

pages = {acsanm.0c00793},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Escamez2020,

title = {Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis},

author = {Sacha Escamez and Domenique André and Bernadette Sztojka and Benjamin Bollhöner and Hardy Hall and Béatrice Berthet and Ute Voß and Amnon Lers and Alexis Maizel and Magnus Andersson and Malcolm Bennett and Hannele Tuominen},

url = {https://linkinghub.elsevier.com/retrieve/pii/S0960982219315805},

doi = {10.1016/j.cub.2019.11.078},

issn = {09609822},

year  = {2020},

date = {2020-02-01},

journal = {Current Biology},

volume = {30},

number = {3},

pages = {455--464.e7},

abstract = {Unlike animal development, plant organ growth is widely accepted to be determined by cell division without any contribution of cell elimination. We investigated this paradigm during Arabidopsis lateral root formation when growth of the new primordia (LRP) from pericycle-derived stem cells deep inside the root is reportedly facilitated by remodeling of the walls of overlying cells without apparent cell death. However, we observed the induction of marker genes for cell types undergoing developmental cell death in several cells overlying the growing LRP. Transmission electron microscopy, time-lapse confocal and light sheet microscopy techniques were used to establish that cell death occurred at least in a subset of endodermal LRP-overlying cells during organ emergence. Significantly, organ emergence was retarded in mutants lacking a positive cell death regulator, and restored by inducing cell death in cells overlying LRP. Hence, we conclude that in the case of LRP, cell elimination contributes to organ growth.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Haas2020,

title = {Candidate regulators and target genes of drought stress in needles and roots of Norway spruce. },

author = {Julia C. Haas and Alexander Vergara and Vaughan Hurry and Nathaniel R. Street.},

doi = {10.1101/517151},

year  = {2020},

date = {2020-01-20},

journal = {Biorxiv},

keywords = {vergara},

pubstate = {published},

tppubtype = {article}

}

@article{Vergara2020,

title = { Norway spruce deploys tissue specific canonical responses to acclimate to cold.  },

author = {Alexander Vergara and Julia Christa Haas and Paulina Stachula and Nathaniel R. Street and Vaughan Hurry},

doi = {10.1101/2020.01.13.904805},

year  = {2020},

date = {2020-01-17},

journal = {Biorxiv},

keywords = {vergara},

pubstate = {published},

tppubtype = {article}

}

@article{mendez2020novel,

title = {Novel effective Bacillus cereus group species “Bacillus clarus” is represented by antibiotic-producing strain ATCC 21929 isolated from soil},

author = {Marysabel Méndez Acevedo and Laura M Carroll and Manjari Mukherjee and Emma Mills and Lingzi Xiaoli and Edward G Dudley and Jasna Kovac},

year  = {2020},

date = {2020-01-01},

journal = {mSphere},

volume = {5},

number = {6},

pages = {e00882--20},

publisher = {American Society for Microbiology 1752 N St., NW, Washington, DC},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN784,

title = {Timeline of autumn phenology in temperate deciduous trees},

author = {I. Dox and J. Gricar and L. J. Marchand and S. Leys and P. Zuccarini and C. Geron and P. Prislan and B. Marien and P. Fonti and H. Lange and J. Penuelas and J. Van den Bulcke and M. Campioli},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32348497},

doi = {10.1093/treephys/tpaa058},

issn = {1758-4469 (Electronic) 

0829-318X (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Tree Physiology},

volume = {40},

number = {8},

pages = {1001-1013},

abstract = {Cessation of xylem formation or wood growth (CWG) and onset of foliar senescence (OFS) are key autumn phenological events in temperate deciduous trees. Their timing is fundamental for the development and survival of trees, ecosystem nutrient cycling and the seasonal exchange of matter and energy between the biosphere and atmosphere, and affects the impact and feedback of forests to global change. A large-scale experimental effort and improved observational methods have allowed us to compare the timing of CWG and OFS for different deciduous tree species in Western Europe, particularly in silver birch, a pioneer species, and European beech, a late-succession species, at stands of different latitudes, of different levels of site fertility, for 2 years with contrasting meteorological and drought conditions, i.e., the low moderately dry 2017 and the extremely dry 2018. Specifically, we tested whether foliar senescence started before, after or concurrently with CWG. Onset of foliar senescence and CWG occurred generally between late September and early November, with larger differences across species and sites for OFS. Foliar senescence started concurrently with CWG in most cases, except for the drier 2018 and, for beech, at the coldest site, where OFS occurred significantly later than CWG. The behavior of beech in Spain, the southern edge of its European distribution, was unclear, with no CWG, but very low wood growth at the time of OFS. Our study suggests that OFS is generally triggered by the same drivers of CWG or when wood growth decreases in late summer, indicating an overarching mechanism of sink limitation as a possible regulator of the timing of foliar senescence.},

note = {Dox, Inge 

Gricar, Jozica 

Marchand, Lorene J 

Leys, Sebastien 

Zuccarini, Paolo 

Geron, Charly 

Prislan, Peter 

Marien, Bertold 

Fonti, Patrick 

Lange, Holger 

Penuelas, Josep 

Van den Bulcke, Jan 

Campioli, Matteo 

eng 

Research Support, Non-U.S. Gov't 

Canada 

Tree Physiol. 2020 Jul 30;40(8):1001-1013. doi: 10.1093/treephys/tpaa058.},

keywords = {*Ecosystem  Europe  Plant Leaves  Seasons  Spain  Temperature  *Trees  *autumn phenology  *chlorophyll  *foliar senescence  *sink limitation  *wood growth  *xylem formation},

pubstate = {published},

tppubtype = {article}

}

@article{mahmud2020prokseq,

title = {ProkSeq for complete analysis of RNA-seq data from prokaryotes},

author = {AKM Firoj Mahmud and Soumyadeep Nandi and Maria Fallman},

year  = {2020},

date = {2020-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Mahmude01006-20,

title = {Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis},

author = {Firoj A K M Mahmud and Kristina Nilsson and Anna Fahlgren and Roberto Navais and Rajdeep Choudhury and Kemal Avican and Maria Fällman},

editor = {Ryan McClure},

url = {https://msystems.asm.org/content/5/6/e01006-20},

doi = {10.1128/mSystems.01006-20},

year  = {2020},

date = {2020-01-01},

journal = {mSystems},

volume = {5},

number = {6},

publisher = {American Society for Microbiology Journals},

abstract = {RpoN, an alternative sigma factor commonly known as σ54, is implicated in persistent stages of Yersinia pseudotuberculosis infections in which genes associated with this regulator are upregulated. We here combined phenotypic and genomic assays to provide insight into its role and function in this pathogen. RpoN was found essential for Y. pseudotuberculosis virulence in mice, and in vitro functional assays showed that it controls biofilm formation and motility. Mapping genome-wide associations of Y. pseudotuberculosis RpoN using chromatin immunoprecipitation coupled with next-generation sequencing identified an RpoN binding motif located at 103 inter- and intragenic sites on both sense and antisense strands. Deletion of rpoN had a large impact on gene expression, including downregulation of genes encoding proteins involved in flagellar assembly, chemotaxis, and quorum sensing. There were also clear indications of cross talk with other sigma factors, together with indirect effects due to altered expression of other regulators. Matching differential gene expression with locations of the binding sites implicated around 130 genes or operons potentially activated or repressed by RpoN. Mutagenesis of selected intergenic binding sites confirmed both positive and negative regulatory effects of RpoN binding. Corresponding mutations of intragenic sense sites had less impact on associated gene expression. Surprisingly, mutating intragenic sites on the antisense strand commonly reduced expression of genes carried by the corresponding sense strand.IMPORTANCE The alternative sigma factor RpoN (σ54), which is widely distributed in eubacteria, has been implicated in controlling gene expression of importance for numerous functions including virulence. Proper responses to host environments are crucial for bacteria to establish infection, and regulatory mechanisms involved are therefore of high interest for development of future therapeutics. Little is known about the function of RpoN in the intestinal pathogen Y. pseudotuberculosis, and we therefore investigated its regulatory role in this pathogen. This regulator was indeed found to be critical for establishment of infection in mice, likely involving its requirement for motility and biofilm formation. The RpoN regulon involved both activating and suppressive effects on gene expression which could be confirmed with mutagenesis of identified binding sites. This is the first study of its kind of RpoN in Y. pseudotuberculosis, revealing complex regulation of gene expression involving both productive and silent effects of its binding to DNA, providing important information about RpoN regulation in enterobacteria.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}