Saqib Qamar

@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{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{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 = {},

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 = {},

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 = {},

pubstate = {published},

tppubtype = {article}

}

@article{Dahlberg2021,

title = {Optical design for laser tweezers Raman spectroscopy setups for increased sensitivity and flexible spatial detection},

author = {Tobias Dahlberg and Magnus Andersson},

url = {https://www.osapublishing.org/abstract.cfm?URI=ao-60-16-4519},

doi = {10.1364/AO.424595},

issn = {1559-128X},

year  = {2021},

date = {2021-06-01},

journal = {Applied Optics},

volume = {60},

number = {16},

pages = {4519},

abstract = {We demonstrate a method to double the collection efficiency in Laser Tweezers Raman Spectroscopy (LTRS) by collecting both the forward and back-scattered light in a single-shot multitrack measurement. Our method can collect signals at different sample volumes, granting both the pinpoint spatial selectivity of confocal Raman and the bulk sensitivity of non-confocal Raman simultaneously. Further, we display that our approach allows for reduced detector integration time and laser power. Thus, our method will enable the monitoring of biological samples sensitive to high intensities for longer times. Additionally, we demonstrate that by a simple modification, we can add polarization sensitivity and retrieve extra biochemical information.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Nilsson2021,

title = {Step-by-step guide to 3D print motorized rotation mounts for optical applications},

author = {Daniel P. G. Nilsson and Tobias Dahlberg and Magnus Andersson},

url = {https://www.osapublishing.org/abstract.cfm?URI=ao-60-13-3764},

doi = {10.1364/AO.422695},

issn = {1559-128X},

year  = {2021},

date = {2021-05-01},

journal = {Applied Optics},

volume = {60},

number = {13},

pages = {3764},

abstract = {Motorized rotation mounts and stages are versatile instruments that introduce computer control to optical systems, enabling automation and scanning actions. They can be used for intensity control and position adjustments, etc. However, these rotation mounts come with a hefty price tag, and this limits their use. This work shows how to build two different types of motorized rotation mounts for 1" optics, using a 3D printer and off-the-shelf components. The first is intended for reflective elements, like mirrors and gratings, and the second for transmissive elements, like polarizers and retarders. We evaluate and compare their performance to commercial systems based on velocity, resolution, accuracy, backlash, and axis wobble. Also, we investigate the angular stability using Allan variance analysis. The results show that our mounts perform similar to systems costing more than 2000 Euro, while also being quick to build and costing less than 200 Euro. As a proof of concept, we show how to control lasers used in an optical tweezers and Raman spectroscopy setup. When used for this, the 3D printed motorized rotational mounts provide intensity control with a resolution of $0.03$ percentage points or better.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Baker2021,

title = {Impact of an alpha helix and a cysteine–cysteine disulfide bond on the resistance of bacterial adhesion pili to stress},

author = {Joseph L Baker and Tobias Dahlberg and Esther Bullitt and Magnus Andersson},

url = {http://biorxiv.org/content/early/2021/01/19/2021.01.18.427124.abstract http://www.pnas.org/lookup/doi/10.1073/pnas.2023595118},

doi = {10.1073/pnas.2023595118},

issn = {0027-8424},

year  = {2021},

date = {2021-05-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {118},

number = {21},

pages = {e2023595118},

abstract = {Escherichia coli express adhesion pili that mediate attachment to host cell surfaces and are exposed to body fluids in the urinary and gastrointestinal tracts. Pilin subunits are organized into helical polymers, with a tip adhesin for specific host binding. Pili can elastically unwind when exposed to fluid flow forces, reducing the adhesin load, thereby facilitating sustained attachment. Here we investigate biophysical and structural differences of pili commonly expressed on bacteria that inhabit the urinary and intestinal tracts. Optical tweezers measurements reveal that class 1a pili of uropathogenic E. coli (UPEC), as well as class 1b of enterotoxigenic E. coli (ETEC), undergo an additional conformational change beyond pilus unwinding, providing significantly more elasticity to their structure than ETEC class 5 pili. Examining structural and steered molecular dynamics simulation data, we find that this difference in class 1 pili subunit behavior originates from an $alpha$-helical motif that can unfold when exposed to force. A disulfide bond cross-linking $beta$-strands in class 1 pili stabilizes subunits, allowing them to tolerate higher forces than class 5 pili that lack this covalent bond. We suggest that these extra contributions to pilus resiliency are relevant for the UPEC niche, since resident bacteria are exposed to stronger, more transient drag forces compared to those experienced by ETEC bacteria in the mucosa of the intestinal tract. Interestingly, class 1b ETEC pili include the same structural features seen in UPEC pili, while requiring lower unwinding forces that are more similar to those of class 5 ETEC pili.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10.7554/eLife.60607,

title = {BipA exerts temperature-dependent translational control of biofilm-associated colony morphology in textitVibrio cholerae},

author = {Teresa del Peso Santos and Laura Alvarez and Brandon Sit and Oihane Irazoki and Jonathon Blake and Benjamin R Warner and Alyson R Warr and Anju Bala and Vladimir Benes and Matthew K Waldor and Kurt Fredrick and Felipe Cava},

editor = {Wendy S Garrett and Tâm Mignot and Jay Zhu},

url = {https://doi.org/10.7554/eLife.60607},

doi = {10.7554/eLife.60607},

issn = {2050-084X},

year  = {2021},

date = {2021-02-01},

journal = {eLife},

volume = {10},

pages = {e60607},

publisher = {eLife Sciences Publications, Ltd},

abstract = {Adaptation to shifting temperatures is crucial for the survival of the bacterial pathogen textitVibrio cholerae. Here, we show that colony rugosity, a biofilm-associated phenotype, is regulated by temperature in textitV. cholerae strains that naturally lack the master biofilm transcriptional regulator HapR. Using transposon-insertion mutagenesis, we found the textitV. cholerae ortholog of BipA, a conserved ribosome-associated GTPase, is critical for this temperature-dependent phenomenon. Proteomic analyses revealed that loss of BipA alters the synthesis of >300 proteins in textitV. cholerae at 22°C, increasing the production of biofilm-related proteins including the key transcriptional activators VpsR and VpsT, as well as proteins important for diverse cellular processes. At low temperatures, BipA protein levels increase and are required for optimal ribosome assembly in textitV. cholerae, suggesting that control of BipA abundance is a mechanism by which bacteria can remodel their proteomes. Our study reveals a remarkable new facet of textitV. cholerae’s complex biofilm regulatory network.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schneider2021,

title = {Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce},

author = {Andreas N. Schneider and John Sundh and Görel Sundström and Kerstin Richau and Nicolas Delhomme and Manfred Grabherr and Vaughan Hurry and Nathaniel R. Street},

url = {https://journals.asm.org/doi/abs/10.1128/mSystems.00884-20},

doi = {10.1128/MSYSTEMS.00884-20/SUPPL_FILE/MSYSTEMS.00884-20-SF006.EPS},

issn = {2379-5077},

year  = {2021},

date = {2021-02-01},

journal = {mSystems},

volume = {6},

number = {1},

publisher = {American Society for Microbiology},

abstract = {A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius . IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Malyshev2021,

title = {Mode of Action of Disinfection Chemicals on the Bacterial Spore Structure and Their Raman Spectra},

author = {Dmitry Malyshev and Tobias Dahlberg and Krister Wiklund and Per Ola Andersson and Sara Henriksson and Magnus Andersson},

url = {https://pubs.acs.org/doi/10.1021/acs.analchem.0c04519},

doi = {10.1021/acs.analchem.0c04519},

issn = {0003-2700},

year  = {2021},

date = {2021-02-01},

journal = {Analytical Chemistry},

volume = {93},

number = {6},

pages = {3146--3153},

publisher = {American Chemical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{PhysRevResearch.3.013055,

title = {Modeling protein target search in human chromosomes},

author = {Markus Nyberg and Tobias Ambjörnsson and Per Stenberg and Ludvig Lizana},

url = {https://link.aps.org/doi/10.1103/PhysRevResearch.3.013055},

doi = {10.1103/PhysRevResearch.3.013055},

year  = {2021},

date = {2021-01-01},

journal = {Phys. Rev. Research},

volume = {3},

pages = {013055},

publisher = {American Physical Society},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1111/gcb.15448,

title = {Integrating carbon emission, accumulation and transport in inland waters to understand their role in the global carbon cycle},

author = {Dominic Vachon and Ryan A Sponseller and Jan Karlsson},

url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/gcb.15448},

doi = {https://doi.org/10.1111/gcb.15448},

year  = {2021},

date = {2021-01-01},

journal = {Global Change Biology},

volume = {27},

number = {4},

pages = {719-727},

abstract = {Abstract Inland waters receive a significant quantity of carbon (C) from land. The fate of this C during transit, whether it is emitted to the atmosphere, accumulated in sediments or transported to the ocean, can considerably reshape the landscape C balance. However, these different fates of terrestrial C are not independent but are instead linked via several catchment and aquatic processes. Thus, according to mass conservation, any environmental change inducing a shift in a particular C fate should come at the expense of at least one other fate. Nonetheless, studies that have investigated C emission, accumulation and transport concertedly are scarce, resulting in fragmented knowledge of the role of inland waters in the global C cycle. Here, we propose a framework to understand how different C fates in aquatic systems are interlinked and covary under environmental changes. First, to explore how C fates are currently distributed in streams, rivers, reservoirs and lakes, we compiled data from the literature and show that ‘C fate allocation’ varies widely both within and among inland water systems types. Secondly, we developed a framework that integrates C fates in any inland water system by identifying the key processes underlying their linkages. Our framework places the partitioning between the different C forms, and how this is controlled by export from land, internal transformations and hydrology, as central to understanding C fate allocation. We argue that, by focusing on a single fate, studies could risk drawing misleading conclusions regarding how environmental changes will alter the role of inland waters in the global C cycle. Our framework thus allows us to holistically assess the consequences of such changes on coupled C fluxes, setting a foundation for understanding the contemporary and future fate of land-derived C in inland water systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{baral2021external,

title = {External Mechanical Cues Reveal a Katanin-Independent Mechanism behind Auxin-Mediated Tissue Bending in Plants},

author = {Anirban Baral and Bibek Aryal and Kristoffer Jonsson and Emily Morris and Elsa Demes and Shogo Takatani and Stéphane Verger and Tongda Xu and Malcolm Bennett and Olivier Hamant and others},

year  = {2021},

date = {2021-01-01},

journal = {Developmental Cell},

volume = {56},

number = {1},

pages = {67--80},

publisher = {Elsevier},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{malivert2021turning,

title = {Turning plants from passive to active material: FERONIA and microtubules independently contribute to mechanical feedback},

author = {Alice Malivert and Ozer Erguvan and Antoine Chevallier and Antoine Dehem and Rodrique Friaud and Mengying Liu and Marjolaine Martin and Theophile Peyraud and Olivier Hamant and Stephane Verger},

year  = {2021},

date = {2021-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@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{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 = {},

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 = {},

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 = {},

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 = {},

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 = {},

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}

}

@article{Avican2020.06.29.177147,

title = {RNA Atlas of Human Bacterial Pathogens Uncovers Stress Dynamics Linked to Infection},

author = {Kemal Avican and Jehad Aldahdooh and Matteo Togninalli and Jing Tang and Karsten M Borgwardt and Mikael Rhen and Maria Fällman},

url = {https://www.biorxiv.org/content/early/2020/06/29/2020.06.29.177147},

doi = {10.1101/2020.06.29.177147},

year  = {2020},

date = {2020-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Despite being genetically diverse, bacterial pathogens can adapt to similar stressful environments in human host, but how this diversity allows them to achive this is yet not fully understood. Knowledge gained through comparative genomics is insufficient as it lacks the level of gene expression reflecting gene usage. To fill this gap, we investigated the transcriptome of 32 diverse bacterial pathogens under 11 host related stress conditions. We revealed that diverse bacterial pathogens have common responses to similar stresses to a certain extent but mostly employ their unique repertoire with intersections between different stress responses. We also identified universal stress responders which shed light on the nature of antimicrobial targets. In addition, we found that known and unknown putative novel ncRNAs comprised a significant proportion of the responses. All the data is collected in PATHOgenex atlas, providing ample opportunities to discover novel players critical for virulence and maintenance of infection.Competing Interest StatementThe authors have declared no competing interest.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Schneiders2020.11.04.369199,

title = {Spatiotemporal Variations in Growth Rate and Virulence Plasmid Copy Number during Yersinia pseudotuberculosis Infection},

author = {Stephan Schneiders and Tifaine Hechard and Tomas Edgren and Kemal Avican and Maria Fällman and Anna Fahlgren and Helen Wang},

url = {https://www.biorxiv.org/content/early/2020/11/06/2020.11.04.369199},

doi = {10.1101/2020.11.04.369199},

year  = {2020},

date = {2020-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Pathogenic Yersinia spp. depend on the activity of a potent virulence plasmid-encoded ysc/yop type 3 secretion system (T3SS) to colonize hosts and cause disease. It was recently shown that Y. pseudotuberculosis up-regulates the virulence plasmid copy number (PCN) during infection and the resulting elevated gene dose of plasmid-encoded T3SS genes is essential for virulence. When and how this novel regulatory mechanism is deployed and regulates the replication of the virulence plasmid during infection is unknown. In the current study, we applied droplet digital PCR (ddPCR) to investigate the dynamics of Y. pseudotuberculosis virulence PCN variations and growth rates in infected mouse organs. We demonstrated that both PCN and growth varied in different tissues and over time throughout the course of infection, indicating that the bacteria adapted to discrete microenvironments during infection. The PCN was highest in Peyertextquoterights Patches and caecum during the clonal invasive phase of the infection, while the fastest growth rates were found in the draining mesenteric lymph nodes. In deeper, systemic organs, the PCN was lower and more modest growth rates were recorded. Our study indicates that increased gene dosage of the plasmid-encoded T3SS genes is most important early in the infection during invasion of the host. The described ddPCR approach will greatly simplify analyses of PCN, growth dynamics, and bacterial loads in infected tissues, and will be readily applicable to other infection models.Importance Studying pathogenic bacteria proliferating inside infected hosts is challenging using traditional methods, especially the transit and reversible genetic events. The bacteria are effectively diluted by the overwhelming number of host cells present in infected tissues. Using an innovative droplet digital PCR (ddPCR) approach, we have determined the virulence plasmid copy number (PCN) variations and growth rates of Yersinia during the course of infection in a mouse model. Here, we show that both the virulence plasmid copy number and bacterial growth rates display spatiotemporal variations in mice during infection. We demonstrate that the peak-to-trough ratio can be used as a proxy for determining the growth rate of invasive bacterial pathogen during infection, and ddPCR as the method of choice for quantifying DNA in host-pathogen interaction context. This proof-of-concept ddPCR approach can be easily applied for any bacterial pathogens and any infection models, for analysis of PCN, growth dynamics and bacterial loads.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fernandez2020non,

title = {Non-cyanobacterial diazotrophs dominate nitrogen-fixing communities in permafrost thaw ponds},

author = {Leyden Fernandez and Stefan Bertilsson and Sari Peura},

year  = {2020},

date = {2020-01-01},

journal = {Limnology and Oceanography},

volume = {65},

pages = {S180--S193},

publisher = {John Wiley & Sons, Inc. Hoboken, USA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{fernandez2020diazotroph,

title = {Diazotroph genomes and their seasonal dynamics in a stratified humic bog lake},

author = {Leyden Fernandez and Sari Peura and Alexander Eiler and Alexandra M Linz and Katherine D McMahon and Stefan Bertilsson},

year  = {2020},

date = {2020-01-01},

journal = {Frontiers in microbiology},

volume = {11},

pages = {1500},

publisher = {Frontiers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{buck2020comprehensive,

title = {Comprehensive dataset of shotgun metagenomes from stratified freshwater lakes and ponds},

author = {Moritz Buck and Sarahi L Garcia and Leyden Fernandez Vidal and Gaetan Martin and Gustavo Martinez A Rodriguez and Jatta Saarenheimo and Jakob Zopfi and Stefan Bertilsson and Sari Peura},

year  = {2020},

date = {2020-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/lol2.10161,

title = {Methane emission offsets carbon dioxide uptake in a small productive lake},

author = {Dominic Vachon and Timon Langenegger and Daphne Donis and Stan E Beaubien and Daniel F McGinnis},

url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10161},

doi = {https://doi.org/10.1002/lol2.10161},

year  = {2020},

date = {2020-01-01},

journal = {Limnology and Oceanography Letters},

volume = {5},

number = {6},

pages = {384-392},

abstract = {Abstract Here, we investigate the importance of net CH4 production and emissions in the carbon (C) budget of a small productive lake by monitoring CH4, CO2, and O2 for two consecutive years. During the study period, the lake was mostly a net emitter of both CH4 and CO2, while showing positive net ecosystem production. The analyses suggest that during the whole study period, 32% ± 26% of C produced by net ecosystem production was ultimately converted to CH4 and emitted to the atmosphere. When converted to global warming potential, CH4 emission (in CO2 equivalents) was about 3–10 times higher than CO2 removal from in-lake net ecosystem production over 100-yr and 20-yr time frames, respectively. Although more work in similar systems is needed to generalize these findings, our results provide evidence of the important greenhouse gas imbalance in human-impacted aquatic systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{https://doi.org/10.1002/lol2.10135,

title = {Paired O2–CO2 measurements provide emergent insights into aquatic ecosystem function},

author = {Dominic Vachon and Steven Sadro and Matthew J Bogard and Jean-François Lapierre and Helen M Baulch and James A Rusak and Blaize A Denfeld and Alo Laas and Marcus Klaus and Jan Karlsson and Gesa A Weyhenmeyer and Paul A del Giorgio},

url = {https://aslopubs.onlinelibrary.wiley.com/doi/abs/10.1002/lol2.10135},

doi = {https://doi.org/10.1002/lol2.10135},

year  = {2020},

date = {2020-01-01},

journal = {Limnology and Oceanography Letters},

volume = {5},

number = {4},

pages = {287-294},

abstract = {Scientific Significance Statement Metabolic stoichiometry predicts that dissolved oxygen (O2) and carbon dioxide (CO2) in aquatic ecosystems should covary inversely; however, field observations often diverge from theoretical expectations. Here, we propose a suite of metrics describing this O2 and CO2 decoupling and introduce a conceptual framework for interpreting these metrics within aquatic ecosystems. Within this framework, we interpret cross-system patterns of high-frequency O2 and CO2 measurements in 11 northern lakes and extract emergent insights into the metabolic behavior and the simultaneous roles of chemical and physical forcing in shaping ecosystem processes. This approach leverages the power of high-frequency paired O2–CO2 measurements, and yields a novel, integrative aquatic system typology which can also be applicable more broadly to streams and rivers, wetlands and marine systems.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kostylenko_2020,

title = {Parametric Identification of the Dynamics of Inter-Sectoral Balance: Modelling and Forecasting},

author = {Olena Kostylenko and Helena Sofia Rodrigues and Delfim F M Torres},

url = {http://dx.doi.org/10.1007/978-3-030-26149-8_11},

doi = {10.1007/978-3-030-26149-8_11},

issn = {2198-4190},

year  = {2020},

date = {2020-01-01},

journal = {Studies in Systems, Decision and Control},

pages = {133--143},

publisher = {Springer International Publishing},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{HERNANDEZ2020107578,

title = {Modulation of Peptidoglycan Synthesis by Recycled Cell Wall Tetrapeptides},

author = {Sara B Hernández and Tobias Dörr and Matthew K Waldor and Felipe Cava},

url = {https://www.sciencedirect.com/science/article/pii/S2211124720305271},

doi = {https://doi.org/10.1016/j.celrep.2020.107578},

issn = {2211-1247},

year  = {2020},

date = {2020-01-01},

journal = {Cell Reports},

volume = {31},

number = {4},

pages = {107578},

abstract = {Summary 

The bacterial cell wall is made of peptidoglycan (PG), a polymer that is essential for the maintenance of cell shape and survival. During growth, bacteria remodel their PG, releasing fragments that are predominantly re-internalized and recycled. Here, we show that Vibrio cholerae recycles PG fragments modified with non-canonical d-amino acids (NCDAA), which lead to the accumulation of cytosolic PG tetrapeptides. We demonstrate that the accumulation of recycled tetrapeptides has two regulatory consequences for the cell wall: reduction of d,d-cross-linkage and reduction of PG synthesis. We further demonstrate that l,d-carboxypeptidases from five different species show a preferential activity for substrates containing canonical (d-alanine) versus non-canonical (d-methionine) d-amino acids, suggesting that the accumulation of intracellular tetrapeptides in NCDAA-rich environments is widespread. Collectively, this work reveals a regulatory role of NCDAA linking PG recycling and synthesis to promote optimal cell wall assembly and composition in the stationary phase.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{articleb,

title = {Chemically Induced Cell Wall Stapling in Bacteria},

author = {Sylvia Rivera and Akbar Espaillat and Arjun Aditham and Peyton Shieh and Chris Muriel-Mundo and Justin Kim and Felipe Cava and Sloan M Siegrist},

doi = {10.1016/j.chembiol.2020.11.006},

year  = {2020},

date = {2020-01-01},

journal = {Cell Chemical Biology},

volume = {28},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{raggi2020polar,

title = {Polar expedition: mechanisms for protein polar localization},

author = {Sara Raggi and Elsa Demes and Sijia Liu and Stéphane Verger and Stéphanie Robert},

year  = {2020},

date = {2020-01-01},

journal = {Current Opinion in Plant Biology},

volume = {53},

pages = {134--140},

publisher = {Elsevier Current Trends},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{baral2020external,

title = {External mechanical cues reveal core molecular pathway behind tissue bending in plants},

author = {Anirban Baral and Emily Morris and Bibek Aryal and Kristoffer Jonsson and Stephane Verger and Tongda Xu and Malcolm J Bennett and Olivier Hamant and Rishikesh P Bhalerao},

year  = {2020},

date = {2020-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{takatani2020microtubule,

title = {Microtubule response to tensile stress is curbed by NEK6 to buffer growth variation in the Arabidopsis hypocotyl},

author = {Shogo Takatani and Stéphane Verger and Takashi Okamoto and Taku Takahashi and Olivier Hamant and Hiroyasu Motose},

year  = {2020},

date = {2020-01-01},

journal = {Current Biology},

volume = {30},

number = {8},

pages = {1491--1503},

publisher = {Cell Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{verger2020tension,

title = {A tension-adhesion feedback loop in plant epidermis (vol 7, e34460, 2018)},

author = {Stephane Verger and Yuchen Long and Arezki Boudaoud and Olivier Hamant},

year  = {2020},

date = {2020-01-01},

journal = {ELIFE},

volume = {9},

publisher = {ELIFE SCIENCES PUBLICATIONS LTD SHERATON HOUSE, CASTLE PARK, CAMBRIDGE, CB3~…},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{doi:10.1002/ecs2.3051,

title = {Fitting functional response surfaces to data: a best practice guide},

author = {Wojciech Uszko and Sebastian Diehl and Jonas Wickman},

url = {https://esajournals.onlinelibrary.wiley.com/doi/abs/10.1002/ecs2.3051},

doi = {10.1002/ecs2.3051},

year  = {2020},

date = {2020-01-01},

journal = {Ecosphere},

volume = {11},

number = {4},

pages = {e03051},

abstract = {Abstract Describing how resource consumption rates depend on resource density, conventionally termed “functional responses,” is crucial to understanding the population dynamics of trophically interacting organisms. Yet, accurately determining the functional response for any given pair of predator and prey remains a challenge. Moreover, functional responses are potentially complex surfaces in multidimensional space, where resource density is only one of several factors determining consumption rates. We explored how three sources of error can be addressed in the design and statistical analysis of functional response experiments: ill-chosen spacing of prey densities, heteroscedastic variance in consumption rates, and non-independence of parameters of the function describing prey consumption in relation to prey density and additional environmental factors. We generated extensive, virtual data sets that simulated feeding experiments in which both prey density and environmental temperature were varied, and for which the true, deterministic functional response surface was known and realistic variance had been added. We compared eight different methods of functional response fitting, one of which stood out as best performing. We subsequently tested several conclusions from the simulation study against experimental data of zooplankton feeding on algae across a broad range of temperatures. We summarize our main findings in three best practice guidelines for the experimental estimation of functional response surfaces, of which the second is the most important: (1) space prey densities logarithmically, starting from very low densities; (2) log-transform prey consumption data prior to fitting; and (3) fit a multivariate functional response surface to all data (including all prey densities and other factors, in our case temperature) in a single step. We also observed that functional response surfaces were fitted more accurately and precisely than their component parameters. The latter occurred because parameter estimates were non-independent, which is an inevitable feature of fitting complex nonlinear functions to data: A given response surface can often be described with near-equal accuracy by multiple parameter combinations. We therefore conclude that fitted functional response models perform better at optimizing the fit of the overall response surface than at determining how component parameters, such as the attack rate or handling time, depend on environmental factors such as temperature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bota2020.03.18.20038349,

title = {Socio-economic and environmental patterns behind H1N1 spreading in Sweden},

author = {Andras Bota and Martin Holmberg and Lauren Gardner and Martin Rosvall},

url = {https://www.medrxiv.org/content/early/2020/04/24/2020.03.18.20038349},

doi = {10.1101/2020.03.18.20038349},

year  = {2020},

date = {2020-01-01},

journal = {medRxiv},

publisher = {Cold Spring Harbor Laboratory Press},

abstract = {The first influenza pandemic in our century started in 2009, spreading from Mexico to the rest of the world, infecting a noticeable fraction of the world population. The outbreak reached Europe in late April, and eventually, almost all countries had confirmed H1N1 cases. On 6 May, Swedish authorities reported the first confirmed influenza case. By the time the pandemic ended, more than 10 thousand people were infected in the country. In this paper, we aim to discover critical socio-economic, travel, and environmental factors contributing to the spreading of H1N1 in Sweden covering six years between 2009 and 2015, focusing on the onset and 2. the peak of the epidemic phase in each municipality. We apply the Generalized Inverse Infection Method (GIIM) to identify these factors. GIIM represents an epidemic spreading process on a network of nodes corresponding to geographical objects, connected by links indicating travel routes, and transmission probabilities assigned to the links guiding the infection process. The GIIM method uses observations on a real-life outbreak as a training dataset to estimate these probabilities and construct a simulated outbreak matching the training data as close as possible. Our results show that the influenza outbreaks considered in this study are mainly driven by the largest population centers in the country. Also, changes in temperature have a noticeable effect. Other socio-economic factors contribute only moderately to the epidemic peak and have a negligible effect on the epidemic onset. We also demonstrate that by training our model on the 2009 outbreak, we can predict the timing of the epidemic onset in the following five seasons with good accuracy. The model proposed in this paper provides a real-time decision support tool advising on resource allocation and surveillance. Furthermore, while this study only considers H1N1 outbreaks, the model can be adapted to other influenza strains or diseases with a similar transmission mechanism.Competing Interest StatementThe authors have declared no competing interest.Funding StatementAndras Bota was supported by the Olle Engkvist Byggmästare Foundation. Martin Rosvall was supported by the Swedish Research Council, grant 2016-00796.Author DeclarationsAll relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript.YesAll necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesData available on request from the authors},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid32393882,

title = {Organizing principles for vegetation dynamics},

author = {O Franklin and S P Harrison and R Dewar and C E Farrior and Åke Brännström and U Dieckmann and S Pietsch and D Falster and W Cramer and M Loreau and H Wang and A Mäkelä and K T Rebel and E Meron and S J Schymanski and E Rovenskaya and B D Stocker and S Zaehle and S Manzoni and M van Oijen and I J Wright and P Ciais and P M van Bodegom and J Peñuelas and F Hofhansl and C Terrer and N A Soudzilovskaia and G Midgley and I C Prentice},

year  = {2020},

date = {2020-01-01},

journal = {Nat Plants},

volume = {6},

number = {5},

pages = {444--453},

note = {[DOI:hrefhttps://dx.doi.org/10.1038/s41477-020-0655-x10.1038/s41477-020-0655-x] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/3239388232393882]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid31914166,

title = {Emergence of social inequality in the spatial harvesting of renewable public goods},

author = {J Joshi and Åke Brännström and U Dieckmann},

year  = {2020},

date = {2020-01-01},

journal = {PLoS Comput. Biol.},

volume = {16},

number = {1},

pages = {e1007483},

note = {[PubMed Central:hrefhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6974303PMC6974303] [DOI:hrefhttps://dx.doi.org/10.1371/journal.pcbi.100748310.1371/journal.pcbi.1007483] [PubMed:hrefhttps://www.ncbi.nlm.nih.gov/pubmed/1822176118221761]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN1,

title = {COVID-19 healthcare demand and mortality in Sweden in response to non-pharmaceutical mitigation and suppression scenarios},

author = {H Sjodin and A F Johansson and A Brannstrom and Z Farooq and H K Kriit and A Wilder-Smith and C Astrom and J Thunberg and M Soderquist and J Rocklov},

url = {https://www.ncbi.nlm.nih.gov/pubmed/32954400},

doi = {10.1093/ije/dyaa121},

issn = {1464-3685 (Electronic) 

0300-5771 (Linking)},

year  = {2020},

date = {2020-01-01},

journal = {Int J Epidemiol},

keywords = {},

pubstate = {published},

tppubtype = {article}

}