Publications

@article{RN979,

title = {When things get MESI: The Manipulation Experiments Synthesis Initiative—A coordinated effort to synthesize terrestrial global change experiments},

author = {Kevin Van Sundert and Sebastian Leuzinger and Martin K. -F. Bader and Scott X. Chang and Martin G. De Kauwe and Jeffrey S. Dukes and J. Adam Langley and Zilong Ma and Bertold Mariën and Simon Reynaert and Jingyi Ru and Jian Song and Benjamin Stocker and César Terrer and Joshua Thoresen and Eline Vanuytrecht and Shiqiang Wan and Kai Yue and Sara Vicca},

url = {https://doi.org/10.1111/gcb.16585},

doi = {https://doi.org/10.1111/gcb.16585},

issn = {1354-1013},

year  = {2023},

date = {2023-01-01},

journal = {Global Change Biology},

volume = {n/a},

number = {n/a},

abstract = {Abstract Responses of the terrestrial biosphere to rapidly changing environmental conditions are a major source of uncertainty in climate projections. In an effort to reduce this uncertainty, a wide range of global change experiments have been conducted that mimic future conditions in terrestrial ecosystems, manipulating CO2, temperature, and nutrient and water availability. Syntheses of results across experiments provide a more general sense of ecosystem responses to global change, and help to discern the influence of background conditions such as climate and vegetation type in determining global change responses. Several independent syntheses of published data have yielded distinct databases for specific objectives. Such parallel, uncoordinated initiatives carry the risk of producing redundant data collection efforts and have led to contrasting outcomes without clarifying the underlying reason for divergence. These problems could be avoided by creating a publicly available, updatable, curated database. Here, we report on a global effort to collect and curate 57,089 treatment responses across 3644 manipulation experiments at 1145 sites, simulating elevated CO2, warming, nutrient addition, and precipitation changes. In the resulting Manipulation Experiments Synthesis Initiative (MESI) database, effects of experimental global change drivers on carbon and nutrient cycles are included, as well as ancillary data such as background climate, vegetation type, treatment magnitude, duration, and, unique to our database, measured soil properties. Our analysis of the database indicates that most experiments are short term (one or few growing seasons), conducted in the USA, Europe, or China, and that the most abundantly reported variable is aboveground biomass. We provide the most comprehensive multifactor global change database to date, enabling the research community to tackle open research questions, vital to global policymaking. The MESI database, freely accessible at doi.org/10.5281/zenodo.7153253, opens new avenues for model evaluation and synthesis-based understanding of how global change affects terrestrial biomes. We welcome contributions to the database on GitHub.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Hernández-Verdeja2022,

title = {GENOMES UNCOUPLED1 plays a key role during the de-etiolation process in Arabidopsis},

author = {Tamara Hernández-Verdeja; Linda Vuorijoki; Xu Jin; Alexander Vergara; Carole Dubreuil; Åsa Strand},

doi = {https://doi.org/10.1111/nph.18115},

year  = {2022},

date = {2022-07-01},

urldate = {2022-07-01},

journal = {New Phytologist},

volume = {235},

issue = {1},

pages = {188-203},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Malyshev2022a,

title = {pH-induced changes in Raman, UV–vis absorbance, and fluorescence spectra of dipicolinic acid (DPA)},

author = {Dmitry Malyshev and Rasmus Öberg and Lars Landström and Per Ola Andersson and Tobias Dahlberg and Magnus Andersson},

url = {https://linkinghub.elsevier.com/retrieve/pii/S1386142522000178},

doi = {10.1016/j.saa.2022.120869},

issn = {13861425},

year  = {2022},

date = {2022-04-01},

journal = {Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy},

volume = {271},

pages = {120869},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN440,

title = {Timing leaf senescence: A generalized additive models for location, scale and shape approach},

author = {Bertold Mariën and Dimitri Papadimitriou and Titta Kotilainen and Paolo Zuccarini and Inge Dox and Melanie Verlinden and Thilo Heinecke and Joachim Mariën and Patrick Willems and Mieke Decoster and Aina Gascó and Holger Lange and Josep Peñuelas and Matteo Campioli},

doi = {10.1016/j.agrformet.2022.108823},

issn = {01681923},

year  = {2022},

date = {2022-01-01},

journal = {Agricultural and Forest Meteorology},

volume = {315},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cohn2022salmonella,

title = {Salmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle},

author = {Alexa R Cohn and Renato H Orsi and Laura M Carroll and Jingqiu Liao and Martin Wiedmann and Rachel A Cheng},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Microbiology},

volume = {13},

pages = {4725},

publisher = {Frontiers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gaballa2022more,

title = {More than mcr: Canonical Plasmid-and Transposon-Encoded Mobilized Colistin Resistance (mcr) Genes Represent a Subset of Phosphoethanolamine Transferases},

author = {Ahmed Gaballa and Martin Wiedmann and Laura M Carroll},

year  = {2022},

date = {2022-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022laboratory,

title = {Laboratory Misidentifications Resulting from Taxonomic Changes to Bacillus cereus Group Species, 2018--2022},

author = {Laura M Carroll and Itumeleng Matle and Jasna Kovac and Rachel A Cheng and Martin Wiedmann},

year  = {2022},

date = {2022-01-01},

journal = {Europe},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022strains,

title = {Strains Associated with Two 2020 Welder Anthrax Cases in the United States Belong to Separate Lineages within Bacillus cereus sensu lato},

author = {Laura M Carroll and Chung K Marston and Cari B Kolton and Christopher A Gulvik and Jay E Gee and Zachary P Weiner and Jasna Kovac},

year  = {2022},

date = {2022-01-01},

journal = {Pathogens},

volume = {11},

number = {8},

pages = {856},

publisher = {MDPI},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{paoli2022biosynthetic,

title = {Biosynthetic potential of the global ocean microbiome},

author = {Lucas Paoli and Hans-Joachim Ruscheweyh and Clarissa C Forneris and Florian Hubrich and Satria Kautsar and Agneya Bhushan and Alessandro Lotti and Quentin Clayssen and Guillem Salazar and Alessio Milanese and others},

year  = {2022},

date = {2022-01-01},

journal = {Nature},

volume = {607},

number = {7917},

pages = {111--118},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022genomic,

title = {Genomic Sequencing of Bacillus cereus Sensu Lato Strains Isolated from Meat and Poultry Products in South Africa Enables Inter-and Intranational Surveillance and Source Tracking},

author = {Laura M Carroll and Rian Pierneef and Aletta Mathole and Abimbola Atanda and Itumeleng Matle},

year  = {2022},

date = {2022-01-01},

journal = {Microbiology Spectrum},

pages = {e00700--22},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022multidrug,

title = {A multidrug-resistant Salmonella enterica serotype Typhimurium DT104 lineage circulating among humans and cattle in the United States lost the ability to produce pertussis-like toxin ArtAB in close temporal proximity to the global DT104 epidemic},

author = {Laura M Carroll and Nicolo Piacenza and Rachel A Cheng and Martin Wiedmann and Claudia Guldimann},

year  = {2022},

date = {2022-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mahoney2022associations,

title = {Associations between Listeria monocytogenes genomic characteristics and adhesion to polystyrene at 8° C},

author = {David Burke James Mahoney and Justin Falardeau and Patricia Hingston and Cora Chmielowska and Laura M Carroll and Martin Wiedmann and Sung Sik Jang and Siyun Wang},

year  = {2022},

date = {2022-01-01},

journal = {Food Microbiology},

volume = {102},

pages = {103915},

publisher = {Academic Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022keeping,

title = {Keeping up with the Bacillus cereus group: taxonomy through the genomics era and beyond},

author = {Laura M Carroll and Rachel A Cheng and Martin Wiedmann and Jasna Kovac},

year  = {2022},

date = {2022-01-01},

journal = {Critical reviews in food science and nutrition},

volume = {62},

number = {28},

pages = {7677--7702},

publisher = {Taylor & Francis},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Solowiej-Wedderburn2022.09.16.508225,

title = {Cell strain energy costs of active control of contractility},

author = {Josephine Solowiej-Wedderburn and Carina M. Dunlop},

url = {https://www.biorxiv.org/content/early/2022/09/16/2022.09.16.508225},

doi = {10.1101/2022.09.16.508225},

year  = {2022},

date = {2022-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Cell mechanosensing is implicated in the control of a broad range of cell behaviours, with cytoskeletal contractility a key component. Experimentally, it is observed that the contractility of the cell responds to increasing substrate stiffness, showing increased contractile force and changing the distribution of cytoskeletal elements. Here we show using a theoretical model of active cell contractility that upregulation of contractility need not be energetically expensive, especially when combined with changes in adhesion and contractile distribution. Indeed, we show that a feedback mechanism based on maintenance of strain energy would require an upregulation in contractile pressure on all but the softest substrates. We consider both the commonly reported substrate strain energy and active work done. We demonstrate substrate strain energy would select for the observed clustering of cell adhesions on stiffer substrates which also enable an upregulation of total contractile pressure; while localisation of contractility has the greatest impact on the internal work.Competing Interest StatementThe authors have declared no competing interest.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articlej,

title = {Sticking around: Cell adhesion patterning for energy minimization and substrate mechanosensing},

author = {Josephine Solowiej-Wedderburn and Carina Dunlop},

doi = {10.1016/j.bpj.2022.03.017},

year  = {2022},

date = {2022-01-01},

journal = {Biophysical Journal},

volume = {121},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Malyshev2022,

title = {Laser induced degradation of bacterial spores during micro-Raman spectroscopy},

author = {Dmitry Malyshev and Rasmus Öberg and Tobias Dahlberg and Krister Wiklund and Lars Landström and Per Ola Andersson and Magnus Andersson},

url = {https://doi.org/10.1016/j.saa.2021.120381 https://linkinghub.elsevier.com/retrieve/pii/S1386142521009586},

doi = {10.1016/j.saa.2021.120381},

issn = {13861425},

year  = {2022},

date = {2022-01-01},

journal = {Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy},

volume = {265},

pages = {120381},

publisher = {The Author(s)},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vergara2021,

title = {Norway spruce deploys tissue-specific responses during acclimation to cold},

author = {Alexander Vergara and Julia Christa Haas and Tuuli Aro and Paulina Stachula and Nathaniel Robert Street and Vaughan Hurry},

url = {https://onlinelibrary.wiley.com/doi/full/10.1111/pce.14241 https://onlinelibrary.wiley.com/doi/abs/10.1111/pce.14241 https://onlinelibrary.wiley.com/doi/10.1111/pce.14241},

doi = {10.1111/pce.14241},

issn = {13653040},

year  = {2021},

date = {2021-12-01},

journal = {Plant Cell and Environment},

publisher = {John Wiley & Sons, Ltd},

abstract = {Climate change in the conifer-dominated boreal forest is expected to lead to warmer but more dynamic winter air temperatures, reducing the depth and duration of snow cover and lowering winter soil temperatures. To gain insight into the mechanisms that have enabled conifers to dominate extreme cold environments, we performed genome-wide RNA-Seq analysis from needles and roots of non-dormant two-year Norway spruce (Picea abies (L.) H. Karst), and contrasted these response to herbaceous model Arabidopsis We show that the main transcriptional response of Norway spruce needles exposed to cold was delayed relative to Arabidopsis, and this delay was associated with slower development of freezing tolerance. Despite this difference in timing, Norway spruce principally utilizes early response transcription factors (TFs) belonging to the same gene families as Arabidopsis, indicating broad evolutionary conservation of cold response networks. In keeping with their different metabolic and developmental states, needles and root of Norway spruce showed contrasting results. Regulatory network analysis identified both conserved TFs with known roles in cold acclimation (e.g. homologs of ICE1, AKS3, and of the NAC and AP2/ERF superfamilies), but also a root-specific bHLH101 homolog, providing functional insights into cold stress response strategies in Norway spruce.},

keywords = {cold, Norway spruce, transcriptome},

pubstate = {published},

tppubtype = {article}

}

@article{Christie2021,

title = {qtlXplorer: an online systems genetics browser in the Eucalyptus Genome Integrative Explorer (EucGenIE)},

author = {Nanette Christie and Chanaka Mannapperuma and Raphael Ployet and Karen Merwe and Niklas Mähler and Nicolas Delhomme and Sanushka Naidoo and Eshchar Mizrachi and Nathaniel R. Street and Alexander A. Myburg},

url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04514-9},

doi = {10.1186/S12859-021-04514-9},

issn = {1471-2105},

year  = {2021},

date = {2021-12-01},

journal = {BMC Bioinformatics 2021 22:1},

volume = {22},

number = {1},

pages = {1--21},

publisher = {BioMed Central},

abstract = {Affordable high-throughput DNA and RNA sequencing technologies are allowing genomic analysis of plant and animal populations and as a result empowering new systems genetics approaches to study complex traits. The availability of intuitive tools to browse and analyze the resulting large-scale genetic and genomic datasets remain a significant challenge. Furthermore, these integrative genomics approaches require innovative methods to dissect the flow and interconnectedness of biological information underlying complex trait variation. The Plant Genome Integrative Explorer (PlantGenIE.org) is a multi-species database and domain that houses online tools for model and woody plant species including Eucalyptus. Since the Eucalyptus Genome Integrative Explorer (EucGenIE) is integrated within PlantGenIE, it shares genome and expression analysis tools previously implemented within the various subdomains (ConGenIE, PopGenIE and AtGenIE). Despite the success in setting up integrative genomics databases, online tools for systems genetics modelling and high-resolution dissection of complex trait variation in plant populations have been lacking. We have developed qtlXplorer ( 

 https://eucgenie.org/QTLXplorer 

 

 ) for visualizing and exploring systems genetics data from genome-wide association studies including quantitative trait loci (QTLs) and expression-based QTL (eQTL) associations. This module allows users to, for example, find co-located QTLs and eQTLs using an interactive version of Circos, or explore underlying genes using JBrowse. It provides users with a means to build systems genetics models and generate hypotheses from large-scale population genomics data. We also substantially upgraded the EucGenIE resource and show how it enables users to combine genomics and systems genetics approaches to discover candidate genes involved in biotic stress responses and wood formation by focusing on two multigene families, laccases and peroxidases. qtlXplorer adds a new dimension, population genomics, to the EucGenIE and PlantGenIE environment. The resource will be of interest to researchers and molecular breeders working in Eucalyptus and other woody plant species. It provides an example of how systems genetics data can be integrated with functional genetics data to provide biological insight and formulate hypotheses. Importantly, integration within PlantGenIE enables novel comparative genomics analyses to be performed from population-scale data.},

keywords = {Algorithms, Bioinformatics, Computational Biology/Bioinformatics, Computer Appl. in Life Sciences, Microarrays},

pubstate = {published},

tppubtype = {article}

}

@article{Panadeiro2021,

title = {A review of 28 free animal-tracking software applications: current features and limitations},

author = {Veronica Panadeiro and Alvaro Rodriguez and Jason Henry and Donald Wlodkowic and Magnus Andersson},

url = {http://dx.doi.org/10.1038/s41684-021-00811-1 https://www.nature.com/articles/s41684-021-00811-1},

doi = {10.1038/s41684-021-00811-1},

issn = {0093-7355},

year  = {2021},

date = {2021-09-01},

journal = {Lab Animal},

volume = {50},

number = {9},

pages = {246--254},

publisher = {Springer US},

abstract = {Well-quantified laboratory studies can provide a fundamental understanding of animal behavior in ecology, ethology and ecotoxicology research. These types of studies require observation and tracking of each animal in well-controlled and defined arenas, often for long timescales. Thus, these experiments produce long time series and a vast amount of data that require the use of software applications to automate the analysis and reduce manual annotation. In this review, we examine 28 free software applications for animal tracking to guide researchers in selecting the software that might best suit a particular experiment. We also review the algorithms in the tracking pipeline of the applications, explain how specific techniques can fit different experiments, and finally, expose each approach's weaknesses and strengths. Our in-depth review includes last update, type of platform, user-friendliness, off- or online video acquisition, calibration method, background subtraction and segmentation method, species, multiple arenas, multiple animals, identity preservation, manual identity correction, data analysis and extra features. We found, for example, that out of 28 programs, only 3 include a calibration algorithm to reduce image distortion and perspective problems that affect accuracy and can result in substantial errors when analyzing trajectories and extracting mobility or explored distance. In addition, only 4 programs can directly export in-depth tracking and analysis metrics, only 5 are suited for tracking multiple unmarked animals for more than a few seconds and only 11 have been updated in the period 2019–2021.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nasstrom2021,

title = {Synthetic NAC 71-82 Peptides Designed to Produce Fibrils with Different Protofilament Interface Contacts},

author = {Thomas Näsström and Tobias Dahlberg and Dmitry Malyshev and Jörgen Ådén and Per Ola Andersson and Magnus Andersson and Björn C G Karlsson},

url = {https://www.mdpi.com/1422-0067/22/17/9334},

doi = {10.3390/ijms22179334},

issn = {1422-0067},

year  = {2021},

date = {2021-08-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {17},

pages = {9334},

abstract = {Alpha-synucleinopathies are featured by fibrillar inclusions in brain cells. Although $alpha$-synuclein fibrils display structural diversity, the origin of this diversity is not fully understood. We used molecular dynamics simulations to design synthetic peptides, based on the NAC 71-82 amino acid fragment of $alpha$-synuclein, that govern protofilament contacts and generation of twisted fibrillar polymorphs. Four peptides with structures based on either single or double fragments and capped or non-capped ends were selected for further analysis. We determined the fibrillar yield and the structures from these peptides found in the solution after fibrillisation using protein concentration determination assay and circular dichroism spectroscopy. In addition, we characterised secondary structures formed by individual fibrillar complexes using laser-tweezers Raman spectroscopy. Results suggest less mature fibrils, based on the lower relative $beta$-sheet content for double- than single-fragment peptide fibrils. We confirmed this structural difference by TEM analysis which revealed, in addition to short protofibrils, more elongated, twisted and rod-like fibril structures in non-capped and capped double-fragment peptide systems, respectively. Finally, time-correlated single-photon counting demonstrated a difference in the Thioflavin T fluorescence lifetime profiles upon fibril binding. It could be proposed that this difference originated from morphological differences in the fibril samples. Altogether, these results highlight the potential of using peptide models for the generation of fibrils that share morphological features relevant for disease, e.g., twisted and rod-like polymorphs.},

keywords = {$alpha$ -synuclein, fibril polymorphs, nac 71-82 peptides},

pubstate = {published},

tppubtype = {article}

}