Publications

@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{Jafari_2021,

title = {Stress and odorant receptor feedback during a critical period after hatching regulates olfactory sensory neuron differentiation in Drosophila},

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

editor = {Bassem A. Hassan},

url = {https://doi.org/10.1371%2Fjournal.pbio.3001101},

doi = {10.1371/journal.pbio.3001101},

year  = {2021},

date = {2021-04-01},

journal = {PLOS Biology},

volume = {19},

number = {4},

pages = {e3001101},

publisher = {Public Library of Science (PLoS)},

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 = {biofilm, BipA, HapR, temperature, textit{Vibrio cholerae}, translation},

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 = {ectomycorrhiza, fungi, ITS amplicon sequencing, metatranscriptomics, Norway spruce, nutrient enrichment, phyllosphere, phyllosphere-inhabiting microbes, tree roots},

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{Mihai_2021,

title = {Meta-Analysis of Gene Popularity: Less Than Half of Gene Citations Stem from Gene Regulatory Networks},

author = {Ionut Sebastian Mihai and Debojyoti Das and Gabija Maršalkaite and Johan Henriksson},

url = {https://doi.org/10.3390%2Fgenes12020319},

doi = {10.3390/genes12020319},

year  = {2021},

date = {2021-02-01},

journal = {Genes},

volume = {12},

number = {2},

pages = {319},

publisher = {MDPI AG},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{kipper2021recent,

title = {Recent Evolution and Genomic Profile of Salmonella enterica Serovar Heidelberg Isolates from Poultry Flocks in Brazil},

author = {Diéssy Kipper and Renato H Orsi and Laura M Carroll and Andrea K Mascitti and André F Streck and André SK Fonseca and Nilo Ikuta and Eduardo C Tondo and Martin Wiedmann and Vagner R Lunge},

year  = {2021},

date = {2021-01-01},

journal = {Applied and environmental microbiology},

volume = {87},

number = {21},

pages = {e01036--21},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cohn2021characterization,

title = {Characterization of basal transcriptomes identifies potential metabolic and virulence-associated adaptations among diverse nontyphoidal Salmonella enterica serovars},

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

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in microbiology},

volume = {12},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2021genomic,

title = {Genomic characterization of endemic and ecdemic non-typhoidal Salmonella enterica lineages circulating among animals and animal products in South Africa},

author = {Laura M Carroll and Rian Pierneef and Masenyabu Mathole and Itumeleng Matle},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in microbiology},

volume = {12},

publisher = {Frontiers Media SA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2021monitoring,

title = {Monitoring the Microevolution of Salmonella enterica in Healthy Dairy Cattle Populations at the Individual Farm Level Using Whole-Genome Sequencing},

author = {Laura M Carroll and Ariel J Buehler and Ahmed Gaballa and Julie D Siler and Kevin J Cummings and Rachel A Cheng and Martin Wiedmann},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in microbiology},

pages = {3166},

publisher = {Frontiers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN783,

title = {Drought elicits contrasting responses on the autumn dynamics of wood formation in late successional deciduous tree species},

author = {I. Dox and P. Prislan and J. Gricar and B. Mariën and N. Delpierre and O. Flores and S. Leys and C. B. K. Rathgeber and P. Fonti and M. Campioli},

url = {https://www.ncbi.nlm.nih.gov/pubmed/33616191},

doi = {10.1093/treephys/tpaa175},

issn = {1758-4469 (Electronic) 

0829-318X (Linking)},

year  = {2021},

date = {2021-01-01},

journal = {Tree Physiology},

abstract = {Research on wood phenology has mainly focused on reactivation of the cambium in spring. In this study we investigated if summer drought advances cessation of wood formation and if it has any influence on wood structure in late successional forest trees of the temperate zone. The end of xylogenesis was monitored between August and November in stands of European beech and pedunculate oak in Belgium for two consecutive years, 2017 and 2018, with the latter year having experienced an exceptional summer drought. Wood formation in oak was affected by the drought, with oak trees ceasing cambial activity and wood maturation about three weeks earlier in 2018 compared to 2017. Beech ceased wood formation before oak, but its wood phenology did not differ between years. Furthermore, between the two years, no significant difference was found in ring width, percentage of mature fibers in the late season, vessel size and density. In 2018, beech did show thinner fiber walls, while oak showed thicker walls. In this paper, we showed that summer drought can have an important impact on late season wood phenology xylem development. This will help to better understand forest ecosystems and improve forest models.},

note = {Dox, Inge 

Prislan, Peter 

Gricar, Jozica 

Marien, Bertold 

Delpierre, Nicolas 

Flores, Omar 

Leys, Sebastien 

Rathgeber, Cyrille B K 

Fonti, Patrick 

Campioli, Matteo 

eng 

Canada 

Tree Physiol. 2021 Feb 22. pii: 6056328. doi: 10.1093/treephys/tpaa175.},

keywords = {beech  cessation of wood formation  drought  oak  xylogenesis},

pubstate = {published},

tppubtype = {article}

}

@article{RN497,

title = {High-Resolution X-Ray Computed Tomography: A New Workflow for the Analysis of Xylogenesis and Intra-Seasonal Wood Biomass Production},

author = {Romain Lehnebach and Matteo Campioli and Jozica Gričar and Peter Prislan and Bertold Mariën and Hans Beeckman and Jan Van den Bulcke},

url = {https://www.frontiersin.org/article/10.3389/fpls.2021.698640},

doi = {10.3389/fpls.2021.698640},

issn = {1664-462X},

year  = {2021},

date = {2021-01-01},

journal = {Frontiers in Plant Science},

volume = {12},

number = {1495},

abstract = {Understanding tree growth and carbon sequestration are of crucial interest to forecast the feedback of forests to climate change. To have a global understanding of the wood formation, it is necessary to develop new methodologies for xylogenesis measurements, valid across diverse wood structures and applicable to both angiosperms and gymnosperms. In this study, the authors present a new workflow to study xylogenesis using high-resolution X-ray computed tomography (HRXCT), which is generic and offers high potential for automatization. The HXRCT-based approach was benchmarked with the current classical approach (microtomy) on three tree species with contrasted wood anatomy (Pinus nigra, Fagus sylvatica, and Quercus robur). HRXCT proved to estimate the relevant xylogenesis parameters (timing, duration, and growth rates) across species with high accuracy. HRXCT showed to be an efficient avenue to investigate tree xylogenesis for a wide range of wood anatomies, structures, and species. HRXCT also showed its potential to provide quantification of intra-annual dynamics of biomass production through high-resolution 3D mapping of wood biomass within the forming growth ring.},

keywords = {High-Resolution X-Ray Computed Tomography (HRXCT), Microtomy, Secondary growth phenology, tree growth, Xylogenesis},

pubstate = {published},

tppubtype = {article}

}

@article{RN443,

title = {Does drought advance the onset of autumn leaf senescence in temperate deciduous forest trees?},

author = {B. Mariën and I. Dox and H. J. De Boeck and P. Willems and S. Leys and D. Papadimitriou and M. Campioli},

doi = {10.5194/bg-18-3309-2021},

issn = {1726-4189},

year  = {2021},

date = {2021-01-01},

journal = {Biogeosciences},

volume = {18},

number = {11},

pages = {3309-3330},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{RN441,

title = {On the Below- and Aboveground Phenology in Deciduous Trees: Observing the Fine-Root Lifespan, Turnover Rate, and Phenology of Fagus sylvatica L., Quercus robur L., and Betula pendula Roth for Two Growing Seasons},

author = {Bertold Mariën and Ivika Ostonen and Alice Penanhoat and Chao Fang and Hòa Xuan Nguyen and Tomáš Ghisi and Páll Sigurðsson and Patrick Willems and Matteo Campioli},

url = {https://www.mdpi.com/1999-4907/12/12/1680},

doi = {10.3390/f12121680},

issn = {1999-4907},

year  = {2021},

date = {2021-01-01},

journal = {Forests},

volume = {12},

number = {12},

pages = {1680},

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 = {carbon cycle, conceptual framework, coupled fluxes, global change, inland waters, terrestrial carbon fate},

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}

}