Publications

@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{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}

}

@article{kohorn2021effects,

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

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

year  = {2021},

date = {2021-01-01},

journal = {Plos one},

volume = {16},

number = {5},

pages = {e0251922},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{malivert2021feronia,

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

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

year  = {2021},

date = {2021-01-01},

journal = {PLoS biology},

volume = {19},

number = {11},

pages = {e3001454},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Johan_Henriksson_94038920,

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

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

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

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

year  = {2021},

date = {2021-01-01},

journal = {PLOS ONE},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Jafari_2021b,

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

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

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

doi = {10.1101/2021.01.13.426514},

year  = {2021},

date = {2021-01-01},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{ma2021antibiotic,

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

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

year  = {2021},

date = {2021-01-01},

journal = {Antibiotics},

volume = {10},

number = {3},

pages = {237},

publisher = {MDPI},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2021accurate,

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

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

year  = {2021},

date = {2021-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}