Saqib Qamar

@article{Hernández-Verdeja2022,

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

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

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

year  = {2022},

date = {2022-07-01},

urldate = {2022-07-01},

journal = {New Phytologist},

volume = {235},

issue = {1},

pages = {188-203},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Malyshev2022a,

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

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

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

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

issn = {13861425},

year  = {2022},

date = {2022-04-01},

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

volume = {271},

pages = {120869},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022keeping,

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

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

year  = {2022},

date = {2022-01-01},

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

volume = {62},

number = {28},

pages = {7677--7702},

publisher = {Taylor & Francis},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{mahoney2022associations,

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

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

year  = {2022},

date = {2022-01-01},

journal = {Food Microbiology},

volume = {102},

pages = {103915},

publisher = {Academic Press},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022multidrug,

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

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

year  = {2022},

date = {2022-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022genomic,

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

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

year  = {2022},

date = {2022-01-01},

journal = {Microbiology Spectrum},

pages = {e00700--22},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{paoli2022biosynthetic,

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

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

year  = {2022},

date = {2022-01-01},

journal = {Nature},

volume = {607},

number = {7917},

pages = {111--118},

publisher = {Nature Publishing Group},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022strains,

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

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

year  = {2022},

date = {2022-01-01},

journal = {Pathogens},

volume = {11},

number = {8},

pages = {856},

publisher = {MDPI},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{carroll2022laboratory,

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

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

year  = {2022},

date = {2022-01-01},

journal = {Europe},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{gaballa2022more,

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

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

year  = {2022},

date = {2022-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{cohn2022salmonella,

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

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

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Microbiology},

volume = {13},

pages = {4725},

publisher = {Frontiers},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{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{articlej,

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

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

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

year  = {2022},

date = {2022-01-01},

journal = {Biophysical Journal},

volume = {121},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Solowiej-Wedderburn2022.09.16.508225,

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

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

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

doi = {10.1101/2022.09.16.508225},

year  = {2022},

date = {2022-01-01},

journal = {bioRxiv},

publisher = {Cold Spring Harbor Laboratory},

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

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{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{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 = {},

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{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 = {},

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}

}

@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}

}