Publications

@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{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{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{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{Haas2020,

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

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

doi = {10.1101/517151},

year  = {2020},

date = {2020-01-20},

journal = {Biorxiv},

keywords = {vergara},

pubstate = {published},

tppubtype = {article}

}

@article{Vergara2020,

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

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

doi = {10.1101/2020.01.13.904805},

year  = {2020},

date = {2020-01-17},

journal = {Biorxiv},

keywords = {vergara},

pubstate = {published},

tppubtype = {article}

}

@article{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 = {-amino acids, -carboxypeptidase, -transpeptidase, cell wall, NCDAA, peptidoglycan recycling, Tn-seq},

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}

}