1
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Puente-Sánchez F, Hoetzinger M, Buck M, Bertilsson S. Exploring environmental intra-species diversity through non-redundant pangenome assemblies. Mol Ecol Resour 2023; 23:1724-1736. [PMID: 37382302 DOI: 10.1111/1755-0998.13826] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/24/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023]
Abstract
At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined "species", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.
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Affiliation(s)
- Fernando Puente-Sánchez
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Matthias Hoetzinger
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
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2
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Rodríguez-Gijón A, Buck M, Andersson AF, Izabel-Shen D, Nascimento FJA, Garcia SL. Linking prokaryotic genome size variation to metabolic potential and environment. ISME Commun 2023; 3:25. [PMID: 36973336 PMCID: PMC10042847 DOI: 10.1038/s43705-023-00231-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/02/2023] [Accepted: 03/14/2023] [Indexed: 03/29/2023]
Abstract
While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dandan Izabel-Shen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
| | - Francisco J A Nascimento
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden
- Baltic Sea Centre, Stockholm University, Stockholm, Sweden
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, 106 91, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
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3
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Wang B, Hu H, Bishop K, Buck M, Björn E, Skyllberg U, Nilsson MB, Bertilsson S, Bravo AG. Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence. J Hazard Mater 2023; 442:130057. [PMID: 36179622 DOI: 10.1016/j.jhazmat.2022.130057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 09/05/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
Peatlands are generally important sources of methylmercury (MeHg) to adjacent aquatic ecosystems, increasing the risk of human and wildlife exposure to this highly toxic compound. While microorganisms play important roles in mercury (Hg) geochemical cycles where they directly and indirectly affect MeHg formation in peatlands, potential linkages between net MeHg formation and microbial communities involving these microorganisms remain unclear. To address this gap, microbial community composition and specific marker gene transcripts were investigated along a trophic gradient in a geographically constrained peatland chronosequence. Our results showed a clear spatial pattern in microbial community composition along the gradient that was highly driven by peat soil properties and significantly associated with net MeHg formation as approximated by MeHg concentration and %MeHg of total Hg concentration. Known fermentative, syntrophic, methanogenic and iron-reducing metabolic guilds had the strong positive correlations to net MeHg formation, while methanotrophic and methylotrophic microorganisms were negatively correlated. Our results indicated that sulfate reducers did not have a key role in net MeHg formation. Microbial activity as interpreted from 16S rRNA sequences was significantly correlated with MeHg and %MeHg. Our findings shed new light on the role of microbial community in net MeHg formation of peatlands that undergo ontogenetic change.
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Affiliation(s)
- Baolin Wang
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 550081 Guiyang, China; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Haiyan Hu
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 550081 Guiyang, China.
| | - Kevin Bishop
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
| | - Ulf Skyllberg
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden
| | - Mats B Nilsson
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-90183 Umeå, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Andrea G Bravo
- Department of Marine Biology and Oceanography, Institut de Ciències del Mar (ICM-CSIC), Pg Marítim de la Barceloneta 37-49, E08003 Barcelona, Catalunya, Spain
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4
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Capo E, Feng C, Bravo AG, Bertilsson S, Soerensen AL, Pinhassi J, Buck M, Karlsson C, Hawkes J, Björn E. Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters. Environ Sci Technol 2022; 56:13119-13130. [PMID: 36069707 PMCID: PMC9494745 DOI: 10.1021/acs.est.2c03784] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (HgII) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved HgII-sulfide species were strong predictors of both the HgII methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc+ microorganisms by reconstructing their genomes from metagenomes (i.e., hgc+ MAGs), which highlighted the versatility of putative HgII methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the HgII methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.
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Affiliation(s)
- Eric Capo
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
- Department
of Aquatic Sciences and Assessment, Swedish
University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Caiyan Feng
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
| | - Andrea G. Bravo
- Department
of Marine Biology and Oceanography, Institute of Marine Sciences, Spanish National Research Council (CSIC), Barcelona 08003, Spain
| | - Stefan Bertilsson
- Department
of Aquatic Sciences and Assessment, Swedish
University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Anne L. Soerensen
- Department
of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm 104 05, Sweden
| | - Jarone Pinhassi
- Centre
for Ecology and Evolution in Microbial Model Systems—EEMiS, Linnaeus University, Kalmar 391 82, Sweden
| | - Moritz Buck
- Department
of Aquatic Sciences and Assessment, Swedish
University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Camilla Karlsson
- Centre
for Ecology and Evolution in Microbial Model Systems—EEMiS, Linnaeus University, Kalmar 391 82, Sweden
| | - Jeffrey Hawkes
- Department
of Chemistry, Uppsala University, Uppsala 751 23, Sweden
| | - Erik Björn
- Department
of Chemistry, Umeå University, Umeå 901 87, Sweden
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5
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Capo E, Peterson BD, Kim M, Jones DS, Acinas SG, Amyot M, Bertilsson S, Björn E, Buck M, Cosio C, Elias DA, Gilmour C, Goñi Urriza MS, Gu B, Lin H, Liu YR, McMahon K, Moreau JW, Pinhassi J, Podar M, Puente-Sánchez F, Sánchez P, Storck V, Tada Y, Vigneron A, Walsh D, Vandewalle-Capo M, Bravo AG, Gionfriddo C. A consensus protocol for the recovery of mercury methylation genes from metagenomes. Mol Ecol Resour 2022; 23:190-204. [PMID: 35839241 PMCID: PMC10087281 DOI: 10.1111/1755-0998.13687] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/24/2022] [Accepted: 07/08/2022] [Indexed: 11/27/2022]
Abstract
Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-MATE (Hg-cycling Microorganisms in Aquatic and Terrestrial Ecosystems) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on co-assembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a co-assembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.
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Affiliation(s)
- Eric Capo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain.,Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Benjamin D Peterson
- Department of Bacteriology, University of Wisconsin at Madison, 53706, Madison, WI, USA
| | - Minjae Kim
- Natural Resource Ecology Laboratory, Colorado State University, 80523, Fort Collins, CO, USA
| | - Daniel S Jones
- Department of Earth and Environmental Science, New Mexico Institute of Mining and Technology, 87801, Socorro, NM, USA.,National Cave and Karst Research Institute, 88220, Carlsbad, NM, USA
| | - Silvia G Acinas
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
| | - Marc Amyot
- Department of Biological Sciences, University of Montréal, Montréal, QC, H3C 5J9, Canada
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, 90736, Umeå, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Claudia Cosio
- University of Reims Champagne-Ardenne, 51100, Reims, France
| | | | - Cynthia Gilmour
- Smithsonian Environmental Research Center, 21037, Edgewater, MD, USA
| | | | - Baohua Gu
- Oak Ridge National Lab, 37830, Oak Ridge, TN, USA
| | - Heyu Lin
- School of Geography, Earth and Atmospheric Sciences, The University of Melbourne, 3010, Parkville, VIC, Australia
| | - Yu-Rong Liu
- College of Resources and Environment, Huazhong Agricultural University, 430070, Wuhan, China
| | - Katherine McMahon
- Department of Bacteriology, University of Wisconsin at Madison, 53706, Madison, WI, USA
| | - John W Moreau
- School of Geographical and Earth Sciences, University of Glasgow, G12 8RZ, Glasgow, UK
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, 39231, Kalmar, Sweden
| | - Mircea Podar
- Oak Ridge National Lab, 37830, Oak Ridge, TN, USA
| | - Fernando Puente-Sánchez
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Pablo Sánchez
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
| | - Veronika Storck
- Department of Biological Sciences, University of Montréal, Montréal, QC, H3C 5J9, Canada
| | - Yuya Tada
- National Institute for Minamata Disease, Department of Environment and Public Health, Kumamoto, 867-0008, Japan
| | - Adrien Vigneron
- University of Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, 64000, France
| | - David Walsh
- Department of Biology, Concordia University, Montreal, Quebec H4BIR6, Canada
| | - Marine Vandewalle-Capo
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Andrea G Bravo
- Department of Marine Biology and Oceanography, Institute of Marine Sciences, CSIC, Barcelona, 08003, Spain
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6
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Buck M, Mehrshad M, Bertilsson S. mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation. NAR Genom Bioinform 2022; 4:lqac060. [PMID: 35979445 PMCID: PMC9376867 DOI: 10.1093/nargab/lqac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/25/2022] [Accepted: 07/28/2022] [Indexed: 12/02/2022] Open
Abstract
Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled genomes or through single-cell genomes. While this expanded diversity can provide novel insights into microbial population structure, most tools available for core-genome estimation are sensitive to genome completeness. Consequently, a major portion of the huge phylogenetic diversity uncovered by environmental genomic approaches remains excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core genome for sets of genomes of highly diverse completeness range. The likelihood for each gene cluster to belong to core or accessory genome is estimated by computing the probability of its presence/absence pattern in the target genome set. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates to state-of-the-art tools Roary and PPanGGOLiN for high-quality genomes and is capable of using genomes at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.
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Affiliation(s)
- Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences , Lennart Hjelms väg 9, 75651 Uppsala, Sweden
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7
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Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, Garcia SL. A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy. Front Microbiol 2022; 12:761869. [PMID: 35069467 PMCID: PMC8767057 DOI: 10.3389/fmicb.2021.761869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/15/2021] [Indexed: 01/09/2023] Open
Abstract
Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.
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Affiliation(s)
- Alejandro Rodríguez-Gijón
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Julia K. Nuy
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Tanja Woyke
- DOE Joint Genome Institute, Berkeley, CA, United States
| | - Sarahi L. Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
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8
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Hartmann L, Hecker J, Rothenberg-Thurley M, Rivière J, Ksienzyk B, Buck M, Van Der Garde M, Fischer L, Winter S, Rauner M, Tsourdi E, Sockel K, Schneider M, Kubasch A, Nolde M, Hausmann D, Lützner J, Roth A, Bassermann F, Spiekermann K, Hofbauer L, Platzbecker U, Götze K, Metzeler K. Topic: AS04-MDS Biology and Pathogenesis/AS04b-Clonal diversity & evolution. Leuk Res 2021. [DOI: 10.1016/j.leukres.2021.106681.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Martin G, Rissanen AJ, Garcia SL, Mehrshad M, Buck M, Peura S. Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes. Front Microbiol 2021; 12:669937. [PMID: 34456882 PMCID: PMC8397446 DOI: 10.3389/fmicb.2021.669937] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/30/2021] [Indexed: 11/21/2022] Open
Abstract
Boreal lakes and ponds produce two-thirds of the total natural methane emissions above the latitude of 50° North. These lake emissions are regulated by methanotrophs which can oxidize up to 99% of the methane produced in the sediments and the water column. Despite their importance, the diversity and distribution of the methanotrophs in lakes are still poorly understood. Here, we used shotgun metagenomic data to explore the diversity and distribution of methanotrophs in 40 oxygen-stratified water bodies in boreal and subarctic areas in Europe and North America. In our data, gammaproteobacterial methanotrophs (order Methylococcales) generally dominated the methanotrophic communities throughout the water columns. A recently discovered lineage of Methylococcales, Candidatus Methylumidiphilus, was present in all the studied water bodies and dominated the methanotrophic community in lakes with a high relative abundance of methanotrophs. Alphaproteobacterial methanotrophs were the second most abundant group of methanotrophs. In the top layer of the lakes, characterized by low CH4 concentration, their abundance could surpass that of the gammaproteobacterial methanotrophs. These results support the theory that the alphaproteobacterial methanotrophs have a high affinity for CH4 and can be considered stress-tolerant strategists. In contrast, the gammaproteobacterial methanotrophs are competitive strategists. In addition, relative abundances of anaerobic methanotrophs, Candidatus Methanoperedenaceae and Candidatus Methylomirabilis, were strongly correlated, suggesting possible co-metabolism. Our data also suggest that these anaerobic methanotrophs could be active even in the oxic layers. In non-metric multidimensional scaling, alpha- and gammaproteobacterial methanotrophs formed separate clusters based on their abundances in the samples, except for the gammaproteobacterial Candidatus Methylumidiphilus, which was separated from these two clusters. This may reflect similarities in the niche and environmental requirements of the different genera within alpha- and gammaproteobacterial methanotrophs. Our study confirms the importance of O2 and CH4 in shaping the methanotrophic communities and suggests that one variable cannot explain the diversity and distribution of the methanotrophs across lakes. Instead, we suggest that the diversity and distribution of freshwater methanotrophs are regulated by lake-specific factors.
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Affiliation(s)
- Gaëtan Martin
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Antti J. Rissanen
- Faculty of Engineering and Natural Sciences, Tampere University, Tampere, Finland
| | - Sarahi L. Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Sweden
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10
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Mehrshad M, Lopez-Fernandez M, Sundh J, Bell E, Simone D, Buck M, Bernier-Latmani R, Bertilsson S, Dopson M. Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater. Nat Commun 2021; 12:4253. [PMID: 34253732 PMCID: PMC8275790 DOI: 10.1038/s41467-021-24549-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
While oligotrophic deep groundwaters host active microbes attuned to the low-end of the bioenergetics spectrum, the ecological constraints on microbial niches in these ecosystems and their consequences for microbiome convergence are unknown. Here, we provide a genome-resolved, integrated omics analysis comparing archaeal and bacterial communities in disconnected fracture fluids of the Fennoscandian Shield in Europe. Leveraging a dataset that combines metagenomes, single cell genomes, and metatranscriptomes, we show that groundwaters flowing in similar lithologies offer fixed niches that are occupied by a common core microbiome. Functional expression analysis highlights that these deep groundwater ecosystems foster diverse, yet cooperative communities adapted to this setting. We suggest that these communities stimulate cooperation by expression of functions related to ecological traits, such as aggregate or biofilm formation, while alleviating the burden on microorganisms producing compounds or functions that provide a collective benefit by facilitating reciprocal promiscuous metabolic partnerships with other members of the community. We hypothesize that an episodic lifestyle enabled by reversible bacteriostatic functions ensures the subsistence of the oligotrophic deep groundwater microbiome.
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Affiliation(s)
- Maliheh Mehrshad
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Margarita Lopez-Fernandez
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden ,grid.4489.10000000121678994Present Address: Department of Microbiology, University of Granada, Granada, Spain
| | - John Sundh
- grid.10548.380000 0004 1936 9377Dept of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Emma Bell
- grid.5333.60000000121839049Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland ,grid.22072.350000 0004 1936 7697Present Address: Department of Biological Sciences, University of Calgary, Calgary, Alberta Canada
| | - Domenico Simone
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden ,grid.6341.00000 0000 8578 2742SLU Bioinformatics Infrastructure, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Moritz Buck
- grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rizlan Bernier-Latmani
- grid.5333.60000000121839049Environmental Microbiology Laboratory, Environmental Engineering Institute, School of Architecture, Civil and Environmental Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stefan Bertilsson
- grid.8993.b0000 0004 1936 9457Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.6341.00000 0000 8578 2742Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Mark Dopson
- grid.8148.50000 0001 2174 3522Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, Kalmar, Sweden
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11
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Garcia SL, Mehrshad M, Buck M, Tsuji JM, Neufeld JD, McMahon KD, Bertilsson S, Greening C, Peura S. Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations. mSystems 2021; 6:e01196-20. [PMID: 33975970 PMCID: PMC8125076 DOI: 10.1128/msystems.01196-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/09/2021] [Indexed: 01/15/2023] Open
Abstract
Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or "species"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.
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Affiliation(s)
- Sarahi L Garcia
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Maliheh Mehrshad
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Moritz Buck
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Jackson M Tsuji
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Josh D Neufeld
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Katherine D McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin, Madison, Madison, Wisconsin, USA
- Department of Bacteriology, University of Wisconsin, Madison, Madison, Wisconsin, USA
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology, Uppsala University, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Uppsala, Uppsala, Sweden
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12
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Rissanen AJ, Saarela T, Jäntti H, Buck M, Peura S, Aalto SL, Ojala A, Pumpanen J, Tiirola M, Elvert M, Nykänen H. Vertical stratification patterns of methanotrophs and their genetic controllers in water columns of oxygen-stratified boreal lakes. FEMS Microbiol Ecol 2021; 97:fiaa252. [PMID: 33316049 PMCID: PMC7840105 DOI: 10.1093/femsec/fiaa252] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 12/10/2020] [Indexed: 11/20/2022] Open
Abstract
The vertical structuring of methanotrophic communities and its genetic controllers remain understudied in the water columns of oxygen-stratified lakes. Therefore, we used 16S rRNA gene sequencing to study the vertical stratification patterns of methanotrophs in two boreal lakes, Lake Kuivajärvi and Lake Lovojärvi. Furthermore, metagenomic analyses were performed to assess the genomic characteristics of methanotrophs in Lovojärvi and the previously studied Lake Alinen Mustajärvi. The methanotroph communities were vertically structured along the oxygen gradient. Alphaproteobacterial methanotrophs preferred oxic water layers, while Methylococcales methanotrophs, consisting of putative novel genera and species, thrived, especially at and below the oxic-anoxic interface and showed distinct depth variation patterns, which were not completely predictable by their taxonomic classification. Instead, genomic differences among Methylococcales methanotrophs explained their variable vertical depth patterns. Genes in clusters of orthologous groups (COG) categories L (replication, recombination and repair) and S (function unknown) were relatively high in metagenome-assembled genomes representing Methylococcales clearly thriving below the oxic-anoxic interface, suggesting genetic adaptations for increased stress tolerance enabling living in the hypoxic/anoxic conditions. By contrast, genes in COG category N (cell motility) were relatively high in metagenome-assembled genomes of Methylococcales thriving at the oxic-anoxic interface, which suggests genetic adaptations for increased motility at the vertically fluctuating oxic-anoxic interface.
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Affiliation(s)
- Antti J Rissanen
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 6, FI-33720, Tampere, Finland
| | - Taija Saarela
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, FI-70210, Kuopio, Finland
| | - Helena Jäntti
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, FI-70210, Kuopio, Finland
| | - Moritz Buck
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, box 7050, SE-75007, Uppsala, Sweden
| | - Sari Peura
- Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Almas allé 5, SE-75651, Uppsala, Sweden
| | - Sanni L Aalto
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, FI-70210, Kuopio, Finland
- Department of Biological and Environmental Sciences, University of Jyväskylä, Survontie 9 C, FI-40014, Jyväskylä, Finland
| | - Anne Ojala
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 1, FI-00014, Helsinki, Finland
- Institute of Atmospheric and Earth System Research (INAR)/Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Viikinkaari 1, FI-00014, Helsinki, Finland
| | - Jukka Pumpanen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, FI-70210, Kuopio, Finland
| | - Marja Tiirola
- Department of Biological and Environmental Sciences, University of Jyväskylä, Survontie 9 C, FI-40014, Jyväskylä, Finland
| | - Marcus Elvert
- MARUM - Center for Marine Environmental Sciences & Faculty of Geosciences, University of Bremen, Leobener Str. 8, D-28359, Bremen, Germany
| | - Hannu Nykänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Yliopistonranta 1 E, FI-70210, Kuopio, Finland
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13
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Capo E, Bravo AG, Soerensen AL, Bertilsson S, Pinhassi J, Feng C, Andersson AF, Buck M, Björn E. Deltaproteobacteria and Spirochaetes-Like Bacteria Are Abundant Putative Mercury Methylators in Oxygen-Deficient Water and Marine Particles in the Baltic Sea. Front Microbiol 2020; 11:574080. [PMID: 33072037 PMCID: PMC7536318 DOI: 10.3389/fmicb.2020.574080] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 08/25/2020] [Indexed: 11/13/2022] Open
Abstract
Methylmercury (MeHg), a neurotoxic compound biomagnifying in aquatic food webs, can be a threat to human health via fish consumption. However, the composition and distribution of the microbial communities mediating the methylation of mercury (Hg) to MeHg in marine systems remain largely unknown. In order to fill this knowledge gap, we used the Baltic Sea Reference Metagenome (BARM) dataset to study the abundance and distribution of the genes involved in Hg methylation (the hgcAB gene cluster). We determined the relative abundance of the hgcAB genes and their taxonomic identity in 81 brackish metagenomes that cover spatial, seasonal and redox variability in the Baltic Sea water column. The hgcAB genes were predominantly detected in anoxic water, but some hgcAB genes were also detected in hypoxic and normoxic waters. Phylogenetic analysis identified putative Hg methylators within Deltaproteobacteria, in oxygen-deficient water layers, but also Spirochaetes-like and Kiritimatiellaeota-like bacteria. Higher relative quantities of hgcAB genes were found in metagenomes from marine particles compared to free-living communities in anoxic water, suggesting that such particles are hotspot habitats for Hg methylators in oxygen-depleted seawater. Altogether, our work unveils the diversity of the microorganisms with the potential to mediate MeHg production in the Baltic Sea and pinpoint the important ecological niches for these microorganisms within the marine water column.
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Affiliation(s)
- Eric Capo
- Department of Chemistry, Umeå University, Umeå, Sweden.,Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Andrea G Bravo
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Anne L Soerensen
- Department of Environmental Research and Monitoring, Swedish Museum of Natural History, Stockholm, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Kalmar, Sweden
| | - Caiyan Feng
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Anders F Andersson
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, Umeå, Sweden
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14
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Abstract
AbstractThe Fukushima accident reveals the need for additional safety systems for nuclear power plants. One promising option is the supercritical carbon-dioxide (sCO2) heat removal system, which consists of a simple Brayton cycle. This study provides an overview of the extensions and validation of the thermal-hydraulic system code ATHLET for the simulation of sCO2 power cycles, especially with regard to the sCO2 heat removal system. The properties of CO2, heat transfer and pressure drop correlations, as well as compact heat exchanger and turbomachinery modelling are considered.
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Affiliation(s)
- M. Hofer
- 1University of Stuttgart, Institute of Nuclear Technology and Energy Systems, E-mail: , Tel.: 004971168560855
| | - M. Buck
- 2University of Stuttgart, Institute of Nuclear Technology and Energy Systems, E-mail:
| | - J. Starflinger
- 3University of Stuttgart, Institute of Nuclear Technology and Energy Systems, E-mail:
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15
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Freiría López M, Buck M, Starflinger J. Neutronic modeling of debris beds for a criticality evaluation. ANN NUCL ENERGY 2019. [DOI: 10.1016/j.anucene.2019.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Perez-Martin S, Pfrang W, Girault N, Cloarec L, Laborde L, Buck M, Matuzas V, Flores y Flores A, Raison P, Smith A, Mozzani N, Feria F, Herranz L, Farges B. Development and assessment of ASTEC-Na fuel pin thermo-mechanical models performed in the European JASMIN project. ANN NUCL ENERGY 2018. [DOI: 10.1016/j.anucene.2017.12.061] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Mantzouki E, Lürling M, Fastner J, de Senerpont Domis L, Wilk-Woźniak E, Koreivienė J, Seelen L, Teurlincx S, Verstijnen Y, Krztoń W, Walusiak E, Karosienė J, Kasperovičienė J, Savadova K, Vitonytė I, Cillero-Castro C, Budzyńska A, Goldyn R, Kozak A, Rosińska J, Szeląg-Wasielewska E, Domek P, Jakubowska-Krepska N, Kwasizur K, Messyasz B, Pełechaty A, Pełechaty M, Kokocinski M, García-Murcia A, Real M, Romans E, Noguero-Ribes J, Duque DP, Fernández-Morán E, Karakaya N, Häggqvist K, Demir N, Beklioğlu M, Filiz N, Levi EE, Iskin U, Bezirci G, Tavşanoğlu ÜN, Özhan K, Gkelis S, Panou M, Fakioglu Ö, Avagianos C, Kaloudis T, Çelik K, Yilmaz M, Marcé R, Catalán N, Bravo AG, Buck M, Colom-Montero W, Mustonen K, Pierson D, Yang Y, Raposeiro PM, Gonçalves V, Antoniou MG, Tsiarta N, McCarthy V, Perello VC, Feldmann T, Laas A, Panksep K, Tuvikene L, Gagala I, Mankiewicz-Boczek J, Yağcı MA, Çınar Ş, Çapkın K, Yağcı A, Cesur M, Bilgin F, Bulut C, Uysal R, Obertegger U, Boscaini A, Flaim G, Salmaso N, Cerasino L, Richardson J, Visser PM, Verspagen JMH, Karan T, Soylu EN, Maraşlıoğlu F, Napiórkowska-Krzebietke A, Ochocka A, Pasztaleniec A, Antão-Geraldes AM, Vasconcelos V, Morais J, Vale M, Köker L, Akçaalan R, Albay M, Špoljarić Maronić D, Stević F, Žuna Pfeiffer T, Fonvielle J, Straile D, Rothhaupt KO, Hansson LA, Urrutia-Cordero P, Bláha L, Geriš R, Fránková M, Koçer MAT, Alp MT, Remec-Rekar S, Elersek T, Triantis T, Zervou SK, Hiskia A, Haande S, Skjelbred B, Madrecka B, Nemova H, Drastichova I, Chomova L, Edwards C, Sevindik TO, Tunca H, Önem B, Aleksovski B, Krstić S, Vucelić IB, Nawrocka L, Salmi P, Machado-Vieira D, de Oliveira AG, Delgado-Martín J, García D, Cereijo JL, Gomà J, Trapote MC, Vegas-Vilarrúbia T, Obrador B, Grabowska M, Karpowicz M, Chmura D, Úbeda B, Gálvez JÁ, Özen A, Christoffersen KS, Warming TP, Kobos J, Mazur-Marzec H, Pérez-Martínez C, Ramos-Rodríguez E, Arvola L, Alcaraz-Párraga P, Toporowska M, Pawlik-Skowronska B, Niedźwiecki M, Pęczuła W, Leira M, Hernández A, Moreno-Ostos E, Blanco JM, Rodríguez V, Montes-Pérez JJ, Palomino RL, Rodríguez-Pérez E, Carballeira R, Camacho A, Picazo A, Rochera C, Santamans AC, Ferriol C, Romo S, Soria JM, Dunalska J, Sieńska J, Szymański D, Kruk M, Kostrzewska-Szlakowska I, Jasser I, Žutinić P, Gligora Udovič M, Plenković-Moraj A, Frąk M, Bańkowska-Sobczak A, Wasilewicz M, Özkan K, Maliaka V, Kangro K, Grossart HP, Paerl HW, Carey CC, Ibelings BW. Temperature Effects Explain Continental Scale Distribution of Cyanobacterial Toxins. Toxins (Basel) 2018; 10:toxins10040156. [PMID: 29652856 PMCID: PMC5923322 DOI: 10.3390/toxins10040156] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/27/2018] [Accepted: 03/29/2018] [Indexed: 11/29/2022] Open
Abstract
Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.
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Affiliation(s)
- Evanthia Mantzouki
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, 1205 Geneva, Switzerland.
| | - Miquel Lürling
- Department of Environmental Sciences, Wageningen University & Research, 6700 Wageningen, The Netherlands.
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 Wageningen, The Netherlands.
| | - Jutta Fastner
- German Environment Agency, Unit Drinking Water Resources and Water Treatment, Corrensplatz 1, 14195 Berlin, Germany.
| | - Lisette de Senerpont Domis
- Department of Environmental Sciences, Wageningen University & Research, 6700 Wageningen, The Netherlands.
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 Wageningen, The Netherlands.
| | - Elżbieta Wilk-Woźniak
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Krakow, Poland.
| | - Judita Koreivienė
- Institute of Botany, Nature Research Centre, Vilnius 08412, Lithuania.
| | - Laura Seelen
- Department of Environmental Sciences, Wageningen University & Research, 6700 Wageningen, The Netherlands.
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 Wageningen, The Netherlands.
| | - Sven Teurlincx
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), 6700 Wageningen, The Netherlands.
| | - Yvon Verstijnen
- Department of Environmental Sciences, Wageningen University & Research, 6700 Wageningen, The Netherlands.
| | - Wojciech Krztoń
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Krakow, Poland.
| | - Edward Walusiak
- Institute of Nature Conservation, Polish Academy of Sciences, 31-120 Krakow, Poland.
| | - Jūratė Karosienė
- Institute of Botany, Nature Research Centre, Vilnius 08412, Lithuania.
| | | | - Ksenija Savadova
- Institute of Botany, Nature Research Centre, Vilnius 08412, Lithuania.
| | - Irma Vitonytė
- Institute of Botany, Nature Research Centre, Vilnius 08412, Lithuania.
| | | | - Agnieszka Budzyńska
- Department ofWater Protection, Adam Mickiewicz University, 61614 Poznan, Poland.
| | - Ryszard Goldyn
- Department ofWater Protection, Adam Mickiewicz University, 61614 Poznan, Poland.
| | - Anna Kozak
- Department ofWater Protection, Adam Mickiewicz University, 61614 Poznan, Poland.
| | - Joanna Rosińska
- Department ofWater Protection, Adam Mickiewicz University, 61614 Poznan, Poland.
| | | | - Piotr Domek
- Department ofWater Protection, Adam Mickiewicz University, 61614 Poznan, Poland.
| | | | - Kinga Kwasizur
- Department of Hydrobiology, Adam Mickiewicz University, 61614 Poznan, Poland.
| | - Beata Messyasz
- Department of Hydrobiology, Adam Mickiewicz University, 61614 Poznan, Poland.
| | | | - Mariusz Pełechaty
- Department of Hydrobiology, Adam Mickiewicz University, 61614 Poznan, Poland.
| | - Mikolaj Kokocinski
- Department of Hydrobiology, Adam Mickiewicz University, 61614 Poznan, Poland.
| | - Ana García-Murcia
- Department of Limnology and Water Quality, AECOM U.R.S, 08036 Barcelona, Spain.
| | - Monserrat Real
- Department of Limnology and Water Quality, AECOM U.R.S, 08036 Barcelona, Spain.
| | - Elvira Romans
- Department of Limnology and Water Quality, AECOM U.R.S, 08036 Barcelona, Spain.
| | - Jordi Noguero-Ribes
- Department of Limnology and Water Quality, AECOM U.R.S, 08036 Barcelona, Spain.
| | - David Parreño Duque
- Department of Limnology and Water Quality, AECOM U.R.S, 08036 Barcelona, Spain.
| | | | - Nusret Karakaya
- Department of Environmental Engineering, Abant Izzet Baysal University, 14280 Bolu, Turkey.
| | - Kerstin Häggqvist
- Department of Science and Engineering, Åbo Akademi University, 20520 Åbo, Finland.
| | - Nilsun Demir
- Department of Fisheries and Aquaculture, Ankara University, 6100 Ankara, Turkey.
| | - Meryem Beklioğlu
- Department of biology, Middle East Technical University, 6800 Ankara, Turkey.
| | - Nur Filiz
- Department of biology, Middle East Technical University, 6800 Ankara, Turkey.
| | - Eti E. Levi
- Department of biology, Middle East Technical University, 6800 Ankara, Turkey.
| | - Uğur Iskin
- Department of biology, Middle East Technical University, 6800 Ankara, Turkey.
| | - Gizem Bezirci
- Department of biology, Middle East Technical University, 6800 Ankara, Turkey.
| | | | - Koray Özhan
- Institute of Marine Sciences, Department of Oceanography, Middle East Technical University, 06800 Ankara, Turkey.
| | - Spyros Gkelis
- Department of Botany, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Manthos Panou
- Department of Botany, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.
| | - Özden Fakioglu
- Department of Basic Science, Ataturk University, 25240 Erzurum, Turkey.
| | - Christos Avagianos
- Water Quality Department, Athens Water Supply and Sewerage Company, 11146 Athens, Greece.
| | - Triantafyllos Kaloudis
- Water Quality Department, Athens Water Supply and Sewerage Company, 11146 Athens, Greece.
| | - Kemal Çelik
- Department of Biology, Balikesir University, 10145 Balikesir, Turkey.
| | - Mete Yilmaz
- Department of Bioengineering, Bursa Technical University, 16310 Bursa, Turkey.
| | - Rafael Marcé
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain.
| | - Nuria Catalán
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain.
- Department of Ecology and Genetics, Limnology, Uppsala University, 75236 Uppsala, Sweden.
| | - Andrea G. Bravo
- Department of Ecology and Genetics, Limnology, Uppsala University, 75236 Uppsala, Sweden.
| | - Moritz Buck
- Department of Ecology and Genetics, Limnology, Uppsala University, 75236 Uppsala, Sweden.
| | - William Colom-Montero
- Department of Ecology and Genetics, Erken Laboratory, Uppsala University, 76173 Norrtalje, Sweden.
| | - Kristiina Mustonen
- Department of Ecology and Genetics, Erken Laboratory, Uppsala University, 76173 Norrtalje, Sweden.
| | - Don Pierson
- Department of Ecology and Genetics, Erken Laboratory, Uppsala University, 76173 Norrtalje, Sweden.
| | - Yang Yang
- Department of Ecology and Genetics, Erken Laboratory, Uppsala University, 76173 Norrtalje, Sweden.
| | - Pedro M. Raposeiro
- Research Center in Biodiversity and Genetic Resources (CIBIO-Azores), InBIO Associated Laboratory, Faculty of Sciences and Technology, University of the Azores, 9501-801 Ponta Delgada, Portugal.
| | - Vítor Gonçalves
- Research Center in Biodiversity and Genetic Resources (CIBIO-Azores), InBIO Associated Laboratory, Faculty of Sciences and Technology, University of the Azores, 9501-801 Ponta Delgada, Portugal.
| | - Maria G. Antoniou
- Department of Environmental Science and Technology, Cyprus University of Technology, 3036 Lemesos, Cyprus.
| | - Nikoletta Tsiarta
- Department of Environmental Science and Technology, Cyprus University of Technology, 3036 Lemesos, Cyprus.
| | - Valerie McCarthy
- Centre for Freshwater and Environmental Studies, Dundalk Institute of Technology, A91 K584 Dundalk, Ireland.
| | - Victor C. Perello
- Centre for Freshwater and Environmental Studies, Dundalk Institute of Technology, A91 K584 Dundalk, Ireland.
| | - Tõnu Feldmann
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51014 Tartu, Estonia.
| | - Alo Laas
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51014 Tartu, Estonia.
| | - Kristel Panksep
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51014 Tartu, Estonia.
| | - Lea Tuvikene
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51014 Tartu, Estonia.
| | - Ilona Gagala
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, 90364 Lodz, Poland.
| | - Joana Mankiewicz-Boczek
- European Regional Centre for Ecohydrology of the Polish Academy of Sciences, 90364 Lodz, Poland.
| | - Meral Apaydın Yağcı
- Republic of Turkey Ministry of Food Agriculture, Fisheries Research Institute, 32500 Eğirdir, Isparta, Turkey.
| | - Şakir Çınar
- Republic of Turkey Ministry of Food Agriculture, Fisheries Research Institute, 32500 Eğirdir, Isparta, Turkey.
| | - Kadir Çapkın
- Republic of Turkey Ministry of Food Agriculture, Fisheries Research Institute, 32500 Eğirdir, Isparta, Turkey.
| | - Abdulkadir Yağcı
- Republic of Turkey Ministry of Food Agriculture, Fisheries Research Institute, 32500 Eğirdir, Isparta, Turkey.
| | - Mehmet Cesur
- Republic of Turkey Ministry of Food Agriculture, Fisheries Research Institute, 32500 Eğirdir, Isparta, Turkey.
| | - Fuat Bilgin
- Republic of Turkey Ministry of Food Agriculture, Fisheries Research Institute, 32500 Eğirdir, Isparta, Turkey.
| | - Cafer Bulut
- Republic of Turkey Ministry of Food Agriculture, Fisheries Research Institute, 32500 Eğirdir, Isparta, Turkey.
| | - Rahmi Uysal
- Republic of Turkey Ministry of Food Agriculture, Fisheries Research Institute, 32500 Eğirdir, Isparta, Turkey.
| | - Ulrike Obertegger
- Department of Sustainable Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy.
| | - Adriano Boscaini
- Department of Sustainable Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy.
| | - Giovanna Flaim
- Department of Sustainable Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy.
| | - Nico Salmaso
- Department of Sustainable Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy.
| | - Leonardo Cerasino
- Department of Sustainable Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy.
| | - Jessica Richardson
- Department of Biological and Environmental Sciences, University of Stirling, Stirling FK9 4LA, UK.
| | - Petra M. Visser
- Department of Freshwater and Marine Ecology, University of Amsterdam, 1090 GE Amsterdam, The Netherlands.
| | - Jolanda M. H. Verspagen
- Department of Freshwater and Marine Ecology, University of Amsterdam, 1090 GE Amsterdam, The Netherlands.
| | - Tünay Karan
- Department of Molecular Biology and Genetics, Gaziosmanpasa University, 60250 Merkez, Turkey.
| | | | | | | | - Agnieszka Ochocka
- Department of Freshwater Protection, Institute of Environmental Protection- National Research Institute, 01-692 Warsaw, Poland.
| | - Agnieszka Pasztaleniec
- Department of Freshwater Protection, Institute of Environmental Protection- National Research Institute, 01-692 Warsaw, Poland.
| | - Ana M. Antão-Geraldes
- Centro de Investigação da Montanha, Instituto Politécnico de Bragança, Campus de Santa Apolónia, 5300-253 Bragança, Portugal;
| | - Vitor Vasconcelos
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) and University of Porto, 4450-208 Matosinhos, Portugal.
| | - João Morais
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) and University of Porto, 4450-208 Matosinhos, Portugal.
| | - Micaela Vale
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) and University of Porto, 4450-208 Matosinhos, Portugal.
| | - Latife Köker
- Department of Freshwater Resource and Management, Faculty of Aquatic Sciences, Istanbul University, 34134 Istanbul, Turkey.
| | - Reyhan Akçaalan
- Department of Freshwater Resource and Management, Faculty of Aquatic Sciences, Istanbul University, 34134 Istanbul, Turkey.
| | - Meriç Albay
- Department of Freshwater Resource and Management, Faculty of Aquatic Sciences, Istanbul University, 34134 Istanbul, Turkey.
| | | | - Filip Stević
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia.
| | - Tanja Žuna Pfeiffer
- Department of Biology, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia.
| | - Jeremy Fonvielle
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany.
| | - Dietmar Straile
- Department of Biology, Limnological Institute, University of Konstanz, 78464 Konstanz, Germany.
| | - Karl-Otto Rothhaupt
- Department of Biology, Limnological Institute, University of Konstanz, 78464 Konstanz, Germany.
| | | | - Pablo Urrutia-Cordero
- Department of Ecology and Genetics, Limnology, Uppsala University, 75236 Uppsala, Sweden.
- Department of Biology, Lund University, 22362 Lund, Sweden.
| | - Luděk Bláha
- RECETOX, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic.
| | - Rodan Geriš
- Department of Hydrobiology, Morava Board Authority, 60200 Brno, Czech Republic.
| | - Markéta Fránková
- Laboratory of Paleoecology, Institute of Botany, The Czech Academy of Sciences, 60200 Brno, Czech Republic.
| | - Mehmet Ali Turan Koçer
- Department of Environment and Resource Management, Mediterranean Fisheries Research Production and Training Institute, 7090 Antalya, Turkey.
| | - Mehmet Tahir Alp
- Faculty of Aquaculture, Mersin University, 33160 Mersin, Turkey.
| | - Spela Remec-Rekar
- Department ofWater Quality, Slovenian Environmental Agency, 1000 Ljubljana, Slovenia.
| | - Tina Elersek
- Department of Genetic Toxicology and Cancer Biology, National Institute of Biology, 1000 Ljubljana, Slovenia.
| | - Theodoros Triantis
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research «DEMOKRITOS», 15341 Attiki, Greece.
| | - Sevasti-Kiriaki Zervou
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research «DEMOKRITOS», 15341 Attiki, Greece.
| | - Anastasia Hiskia
- Institute of Nanoscience and Nanotechnology, National Center for Scientific Research «DEMOKRITOS», 15341 Attiki, Greece.
| | - Sigrid Haande
- Department of Freshwater Ecology, Norwegian Institute for Water Research, 0349 Oslo, Norway.
| | - Birger Skjelbred
- Department of Freshwater Ecology, Norwegian Institute for Water Research, 0349 Oslo, Norway.
| | - Beata Madrecka
- Institute of Environmental Engineering, Poznan University of Technology, 60965 Poznan, Poland.
| | - Hana Nemova
- National Reference Center for Hydrobiology, Public Health Authority of the Slovak Republic, 82645 Bratislava, Slovakia.
| | - Iveta Drastichova
- National Reference Center for Hydrobiology, Public Health Authority of the Slovak Republic, 82645 Bratislava, Slovakia.
| | - Lucia Chomova
- National Reference Center for Hydrobiology, Public Health Authority of the Slovak Republic, 82645 Bratislava, Slovakia.
| | - Christine Edwards
- School of Pharmacy and Life Sciences, Robert Gordon University, Aberdeen AB10 7GJ, UK.
| | | | - Hatice Tunca
- Department of Biology, Sakarya University, 54187 Sakarya, Turkey.
| | - Burçin Önem
- Department of Biology, Sakarya University, 54187 Sakarya, Turkey.
| | - Boris Aleksovski
- Faculty of Natural Sciences and Mathematics, SS Cyril and Methodius University, 1000 Skopje, Macedonia.
| | - Svetislav Krstić
- Faculty of Natural Sciences and Mathematics, SS Cyril and Methodius University, 1000 Skopje, Macedonia.
| | - Itana Bokan Vucelić
- Department for Ecotoxicology, Teaching Institute of Public Health of Primorje-Gorski Kotar County, 51000 Rijeka, Croatia.
| | - Lidia Nawrocka
- Institute of Technology, The State University of Applied Sciences, 82300 Elblag, Poland.
| | - Pauliina Salmi
- Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland.
| | - Danielle Machado-Vieira
- Departamento de Sistemática e Ecologia, Universidade Federal da Paraíba, 58059-970 Paraíba, Brasil.
| | | | | | - David García
- Department of Civil Engineering, University of A Coruña, 15192 A Coruña, Spain.
| | - Jose Luís Cereijo
- Department of Civil Engineering, University of A Coruña, 15192 A Coruña, Spain.
| | - Joan Gomà
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain.
| | - Mari Carmen Trapote
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain.
| | - Teresa Vegas-Vilarrúbia
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain.
| | - Biel Obrador
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, University of Barcelona, 08028 Barcelona, Spain.
| | - Magdalena Grabowska
- Department of Hydrobiology, University of Bialystok, 15245 Bialystok, Poland.
| | - Maciej Karpowicz
- Department of Hydrobiology, University of Bialystok, 15245 Bialystok, Poland.
| | - Damian Chmura
- Institute of Environmental Protection and Engineering, University of Bielsko-Biala, 43309 Bielsko-Biala, Poland.
| | - Bárbara Úbeda
- Department of Biology, University of Cádiz, 11510 Puerto Real, Cádiz, Spain.
| | - José Ángel Gálvez
- Department of Biology, University of Cádiz, 11510 Puerto Real, Cádiz, Spain.
| | - Arda Özen
- Department of Forest Engineering, University of Cankiri Karatekin, 18200 Cankiri, Turkey.
| | | | - Trine Perlt Warming
- Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.
| | - Justyna Kobos
- Department of Marine Biotechnology, University of Gdansk, 81378 Gdynia, Poland.
| | - Hanna Mazur-Marzec
- Department of Marine Biotechnology, University of Gdansk, 81378 Gdynia, Poland.
| | | | | | - Lauri Arvola
- Lammi Biological Station, University of Helsinki, 16900 Lammi, Finland.
| | - Pablo Alcaraz-Párraga
- Department of Animal Biology, Plant Biology and Ecology, University of Jaen, 23701 Jaen, Spain.
| | - Magdalena Toporowska
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, 20262 Lublin, Poland.
| | - Barbara Pawlik-Skowronska
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, 20262 Lublin, Poland.
| | - Michał Niedźwiecki
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, 20262 Lublin, Poland.
| | - Wojciech Pęczuła
- Department of Hydrobiology and Protection of Ecosystems, University of Life Sciences in Lublin, 20262 Lublin, Poland.
| | - Manel Leira
- Instituto Dom Luiz, University of Lisbon, 1749016 Lisbon, Portugal.
| | - Armand Hernández
- Institute of Earth Sciences Jaume Almera, ICTJA, CSIC, 08028 Barcelona, Spain.
| | | | | | | | | | | | | | - Rafael Carballeira
- Centro de Investigacións Cientificas Avanzadas (CICA), Facultade de Ciencias, Universidade da Coruña, 15071 A Coruña, Spain.
| | - Antonio Camacho
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 46980 Paterna Valencia, Spain.
| | - Antonio Picazo
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 46980 Paterna Valencia, Spain.
| | - Carlos Rochera
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 46980 Paterna Valencia, Spain.
| | - Anna C. Santamans
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 46980 Paterna Valencia, Spain.
| | - Carmen Ferriol
- Cavanilles Institute of Biodiversity and Evolutionary Biology, University of Valencia, 46980 Paterna Valencia, Spain.
| | - Susana Romo
- Department of Microbiology and Ecology, University of Valencia, 46100 Burjassot, Spain.
| | - Juan Miguel Soria
- Department of Microbiology and Ecology, University of Valencia, 46100 Burjassot, Spain. (J.M.S.)
| | - Julita Dunalska
- Department ofWater Protection Engineering, University ofWarmia and Mazury, 10-720 Olsztyn, Poland.
| | - Justyna Sieńska
- Department ofWater Protection Engineering, University ofWarmia and Mazury, 10-720 Olsztyn, Poland.
| | - Daniel Szymański
- Department ofWater Protection Engineering, University ofWarmia and Mazury, 10-720 Olsztyn, Poland.
| | - Marek Kruk
- Department of Tourism, Recreation and Ecology, University of Warmia and Mazury, 10-720 Olsztyn, Poland.
| | | | - Iwona Jasser
- Department of Plant Ecology and Environmental Conservation, Faculty of Biology, University ofWarsaw, 02-089 Warsaw, Poland.
| | - Petar Žutinić
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia.
| | - Marija Gligora Udovič
- Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia.
| | | | - Magdalena Frąk
- Department of Environmental Improvement, Faculty of Civil and Environmental Engineering, Warsaw University of Life Sciences—SGGW, 02-787Warsaw, Poland.
| | - Agnieszka Bańkowska-Sobczak
- Department of Hydraulic Engineering, Faculty of Civil and Environmental Engineering, Warsaw University of Life Sciences—SGGW, 02-787Warsaw, Poland.
| | - Michał Wasilewicz
- Department of Hydraulic Engineering, Faculty of Civil and Environmental Engineering, Warsaw University of Life Sciences—SGGW, 02-787Warsaw, Poland.
| | - Korhan Özkan
- Institute of Marine Sciences, Marine Biology and Fisheries, Middle East Technical University, 06800 Ankara, Turkey.
| | - Valentini Maliaka
- Society for the Protection of Prespa, 53077 Agios Germanos, Greece.
- Institute for Water and Wetland Research, Department of Aquatic Ecology and Environmental Biology, Radboud University Nijmegen, 6525 AJ Nijmegen, The Netherlands.
- Department of Environmental Sciences, Wageningen University & Research, 6700 Wageningen, The Netherlands.
| | - Kersti Kangro
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, 51014 Tartu, Estonia.
- Tartu Observatory, Faculty of Science and Technology, University of Tartu, 61602 Tartu, Estonia.
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany.
- Institute of Biochemistry and Biology, Potsdam University, 14469 Potsdam, Germany.
| | - Hans W. Paerl
- Institute of Marine Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 28557, USA.
| | - Cayelan C. Carey
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA 24061, USA.
| | - Bas W. Ibelings
- Department F.-A. Forel for Environmental and Aquatic Sciences, University of Geneva, 1205 Geneva, Switzerland.
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18
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Friedlander M, Rau J, Lee C, Meier W, Lesoin A, Kim JW, Poveda A, Buck M, Scambia G, Shimada M, Hilpert F, King M, Debruyne P, Bologna A, Malander S, Monk B, Petru E, Calvert P, Herzog T, Barrett C, du Bois A. Quality of life in patients with advanced epithelial ovarian cancer (EOC) randomized to maintenance pazopanib or placebo after first-line chemotherapy in the AGO-OVAR 16 trial. Measuring what matters—patient-centered end points in trials of maintenance therapy. Ann Oncol 2018; 29:737-743. [DOI: 10.1093/annonc/mdx796] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Eklöf K, Bishop K, Bertilsson S, Björn E, Buck M, Skyllberg U, Osman OA, Kronberg RM, Bravo AG. Formation of mercury methylation hotspots as a consequence of forestry operations. Sci Total Environ 2018; 613-614:1069-1078. [PMID: 28950669 DOI: 10.1016/j.scitotenv.2017.09.151] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 09/13/2017] [Accepted: 09/15/2017] [Indexed: 05/16/2023]
Abstract
Earlier studies have shown that boreal forest logging can increase the concentration and export of methylmercury (MeHg) in stream runoff. Here we test whether forestry operations create soil environments of high MeHg net formation associated with distinct microbial communities. Furthermore, we test the hypothesis that Hg methylation hotspots are more prone to form after stump harvest than stem-only harvest, because of more severe soil compaction and soil disturbance. Concentrations of MeHg, percent MeHg of total Hg (THg), and bacterial community composition were determined at 200 soil sampling positions distributed across eight catchments. Each catchment was either stem-only harvested (n=3), stem- and stump-harvested (n=2) or left undisturbed (n=3). In support of our hypothesis, higher MeHg to THg ratios was observed in one of the stump-harvested catchments. While the effects of natural variation could not be ruled out, we noted that most of the highest % MeHg was observed in water-filled cavities created by stump removal or driving damage. This catchment also featured the highest bacterial diversity and highest relative abundance of bacterial families known to include Hg methylators. We propose that water-logged and disturbed soil environments associated with stump harvest can favor methylating microorganisms, which also enhance MeHg formation.
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Affiliation(s)
- Karin Eklöf
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden.
| | - Kevin Bishop
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE-75007 Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, SE-75236 Uppsala, Sweden
| | - Erik Björn
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden
| | - Moritz Buck
- Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden; National Bioinformatics Infrastructure Sweden, Uppsala SE-75236, Sweden
| | - Ulf Skyllberg
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Omneya A Osman
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, SE-75236 Uppsala, Sweden
| | - Rose-Marie Kronberg
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden
| | - Andrea G Bravo
- Department of Ecology and Genetics, Limnology and Science for Life Laboratory, Uppsala University, SE-75236 Uppsala, Sweden
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20
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Bravo AG, Zopfi J, Buck M, Xu J, Bertilsson S, Schaefer JK, Poté J, Cosio C. Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases. ISME J 2018; 12:802-812. [PMID: 29321692 PMCID: PMC5864163 DOI: 10.1038/s41396-017-0007-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 09/29/2017] [Accepted: 10/18/2017] [Indexed: 11/16/2022]
Abstract
Microbial mercury (Hg) methylation in sediments can result in bioaccumulation of the neurotoxin methylmercury (MMHg) in aquatic food webs. Recently, the discovery of the gene hgcA, required for Hg methylation, revealed that the diversity of Hg methylators is much broader than previously thought. However, little is known about the identity of Hg-methylating microbial organisms and the environmental factors controlling their activity and distribution in lakes. Here, we combined high-throughput sequencing of 16S rRNA and hgcA genes with the chemical characterization of sediments impacted by a waste water treatment plant that releases significant amounts of organic matter and iron. Our results highlight that the ferruginous geochemical conditions prevailing at 1–2 cm depth are conducive to MMHg formation and that the Hg-methylating guild is composed of iron and sulfur-transforming bacteria, syntrophs, and methanogens. Deltaproteobacteria, notably Geobacteraceae, dominated the hgcA carrying communities, while sulfate reducers constituted only a minor component, despite being considered the main Hg methylators in many anoxic aquatic environments. Because iron is widely applied in waste water treatment, the importance of Geobacteraceae for Hg methylation and the complexity of Hg-methylating communities reported here are likely to occur worldwide in sediments impacted by waste water treatment plant discharges and in iron-rich sediments in general.
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Affiliation(s)
- Andrea G Bravo
- Limnology and Science for Life Laboratory, Uppsala University, Uppsala, SE-75236, Sweden
| | - Jakob Zopfi
- Aquatic and Stable Isotope Biogeochemistry, University of Basel, Basel, CH-4056, Switzerland
| | - Moritz Buck
- Limnology and Science for Life Laboratory, Uppsala University, Uppsala, SE-75236, Sweden
| | - Jingying Xu
- Limnology and Science for Life Laboratory, Uppsala University, Uppsala, SE-75236, Sweden
| | - Stefan Bertilsson
- Limnology and Science for Life Laboratory, Uppsala University, Uppsala, SE-75236, Sweden
| | - Jeffra K Schaefer
- Environmental Sciences, Rutgers University, New Brunswick, NJ, 08901, USA
| | - John Poté
- Environmental Biogeochemistry and Ecotoxicology, University of Geneva, Geneva, CH-1205, Switzerland
| | - Claudia Cosio
- Environmental Biogeochemistry and Ecotoxicology, University of Geneva, Geneva, CH-1205, Switzerland. .,Unité Stress Environnementaux et BIOSurveillance des Milieux Aquatiques UMR-I 02 (SEBIO), Université de Reims Champagne Ardenne, Reims, F-51687, France.
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21
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Anderson AE, Swan DJ, Wong OY, Buck M, Eltherington O, Harry RA, Patterson AM, Pratt AG, Reynolds G, Doran JP, Kirby JA, Isaacs JD, Hilkens CMU. Tolerogenic dendritic cells generated with dexamethasone and vitamin D3 regulate rheumatoid arthritis CD4 + T cells partly via transforming growth factor-β1. Clin Exp Immunol 2016; 187:113-123. [PMID: 27667787 DOI: 10.1111/cei.12870] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 09/09/2016] [Accepted: 09/21/2016] [Indexed: 12/28/2022] Open
Abstract
Tolerogenic dendritic cells (tolDC) are a new immunotherapeutic tool for the treatment of rheumatoid arthritis (RA) and other autoimmune disorders. We have established a method to generate stable tolDC by pharmacological modulation of human monocyte-derived DC. These tolDC exert potent pro-tolerogenic actions on CD4+ T cells. Lack of interleukin (IL)-12p70 production is a key immunoregulatory attribute of tolDC but does not explain their action fully. Here we show that tolDC express transforming growth factor (TGF)-β1 at both mRNA and protein levels, and that expression of this immunoregulatory cytokine is significantly higher in tolDC than in mature monocyte-derived DC. By inhibiting TGF-β1 signalling we demonstrate that tolDC regulate CD4+ T cell responses in a manner that is at least partly dependent upon this cytokine. Crucially, we also show that while there is no significant difference in expression of TGF-βRII on CD4+ T cells from RA patients and healthy controls, RA patient CD4+ T cells are measurably less responsive to TGF-β1 than healthy control CD4+ T cells [reduced TGF-β-induced mothers against decapentaplegic homologue (Smad)2/3 phosphorylation, forkhead box protein 3 (FoxP3) expression and suppression of (IFN)-γ secretion]. However, CD4+ T cells from RA patients can, nonetheless, be regulated efficiently by tolDC in a TGF-β1-dependent manner. This work is important for the design and development of future studies investigating the potential use of tolDC as a novel immunotherapy for the treatment of RA.
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Affiliation(s)
- A E Anderson
- Musculoskeletal Research Group.,Arthritis Research UK Rheumatoid Arthritis Centre of Excellence (RACE)
| | | | | | - M Buck
- Musculoskeletal Research Group
| | - O Eltherington
- Musculoskeletal Research Group.,Arthritis Research UK Rheumatoid Arthritis Centre of Excellence (RACE)
| | - R A Harry
- Musculoskeletal Research Group.,Arthritis Research UK Rheumatoid Arthritis Centre of Excellence (RACE)
| | | | - A G Pratt
- Musculoskeletal Research Group.,Arthritis Research UK Rheumatoid Arthritis Centre of Excellence (RACE)
| | - G Reynolds
- Musculoskeletal Research Group.,Arthritis Research UK Rheumatoid Arthritis Centre of Excellence (RACE)
| | | | - J A Kirby
- Applied Immunobiology and Transplantation Research Group, Institute of Cellular Medicine at the Newcastle NIHR Biomedical Research Centre, Newcastle University and Newcastle upon Tyne NHS Trust, Newcastle upon Tyne, UK
| | - J D Isaacs
- Musculoskeletal Research Group.,Arthritis Research UK Rheumatoid Arthritis Centre of Excellence (RACE)
| | - C M U Hilkens
- Musculoskeletal Research Group.,Arthritis Research UK Rheumatoid Arthritis Centre of Excellence (RACE)
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22
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Hubalek V, Wu X, Eiler A, Buck M, Heim C, Dopson M, Bertilsson S, Ionescu D. Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield. ISME J 2016; 10:2556. [PMID: 27645891 DOI: 10.1038/ismej.2016.94] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Scherer U, Buck M, Schuett W. Lateralisation in agonistic encounters: do mirror tests reflect aggressive behaviour? A study on a West African cichlid. J Fish Biol 2016; 89:1866-1872. [PMID: 27329496 DOI: 10.1111/jfb.13069] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 05/23/2016] [Indexed: 06/06/2023]
Abstract
In this study, population level lateralisation and the suitability of mirror tests as a test of natural aggressive behaviour in male rainbow kribs Pelvicachromis pulcher was investigated. Aggressive behaviour in live agonistic trials correlated positively with behaviours towards a mirror image and no visual lateralisation was detected.
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Affiliation(s)
- U Scherer
- Zoological Institute, Biocentre Grindel, University of Hamburg, Martin-Luther-King Platz 3, 20146, Hamburg, Germany
| | - M Buck
- Zoological Institute, Biocentre Grindel, University of Hamburg, Martin-Luther-King Platz 3, 20146, Hamburg, Germany
| | - W Schuett
- Zoological Institute, Biocentre Grindel, University of Hamburg, Martin-Luther-King Platz 3, 20146, Hamburg, Germany
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24
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Buck M, Nilsson LKJ, Brunius C, Dabiré RK, Hopkins R, Terenius O. Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes. Sci Rep 2016; 6:22806. [PMID: 26960555 PMCID: PMC4785398 DOI: 10.1038/srep22806] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 02/19/2016] [Indexed: 02/04/2023] Open
Abstract
The intolerable burden of malaria has for too long plagued humanity and the prospect of eradicating malaria is an optimistic, but reachable, target in the 21(st) century. However, extensive knowledge is needed about the spatial structure of mosquito populations in order to develop effective interventions against malaria transmission. We hypothesized that the microbiota associated with a mosquito reflects acquisition of bacteria in different environments. By analyzing the whole-body bacterial flora of An. gambiae mosquitoes from Burkina Faso by 16 S amplicon sequencing, we found that the different environments gave each mosquito a specific bacterial profile. In addition, the bacterial profiles provided precise and predicting information on the spatial dynamics of the mosquito population as a whole and showed that the mosquitoes formed clear local populations within a meta-population network. We believe that using microbiotas as proxies for population structures will greatly aid improving the performance of vector interventions around the world.
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Affiliation(s)
- Moritz Buck
- Evolutionary Biology Center and Bioinformatics Infrastructure for Life Sciences, Uppsala University, Norbyvägen 18D, 752 36 Uppsala Sweden
| | - Louise K J Nilsson
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden
| | - Carl Brunius
- Department of Food Science, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden
| | - Roch K Dabiré
- Institut de Recherche en Sciences de la Santé/Centre Muraz, O1 BP 390 Bobo-Dioulasso 01, Burkina Faso
| | - Richard Hopkins
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden.,Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent, ME4 4TB, United Kingdom
| | - Olle Terenius
- Department of Ecology, Swedish University of Agricultural Sciences (SLU), 750 07 Uppsala, Sweden
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Christel S, Fridlund J, Buetti-Dinh A, Buck M, Watkin EL, Dopson M. RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans. FEMS Microbiol Lett 2016; 363:fnw057. [PMID: 26956550 DOI: 10.1093/femsle/fnw057] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 01/08/2023] Open
Abstract
Acidithiobacillus ferrivorans is an acidophile implicated in low-temperature biomining for the recovery of metals from sulfide minerals. Acidithiobacillus ferrivorans obtains its energy from the oxidation of inorganic sulfur compounds, and genes encoding several alternative pathways have been identified. Next-generation sequencing of At. ferrivorans RNA transcripts identified the genes coding for metabolic and electron transport proteins for energy conservation from tetrathionate as electron donor. RNA transcripts suggested that tetrathionate was hydrolyzed by the tetH1 gene product to form thiosulfate, elemental sulfur and sulfate. Despite two of the genes being truncated, RNA transcripts for the SoxXYZAB complex had higher levels than for thiosulfate quinone oxidoreductase (doxDAgenes). However, a lack of heme-binding sites in soxX suggested that DoxDA was responsible for thiosulfate metabolism. Higher RNA transcript counts also suggested that elemental sulfur was metabolized by heterodisulfide reductase (hdrgenes) rather than sulfur oxygenase reductase (sor). The sulfite produced as a product of heterodisulfide reductase was suggested to be oxidized by a pathway involving the sat gene product or abiotically react with elemental sulfur to form thiosulfate. Finally, several electron transport complexes were involved in energy conservation. This study has elucidated the previously unknown At. ferrivorans tetrathionate metabolic pathway that is important in biomining.
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Affiliation(s)
- Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Jimmy Fridlund
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Antoine Buetti-Dinh
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
| | - Moritz Buck
- National Bioinformatics Infrastructure Sweden and Evolutionary Biology Center, Uppsala University, 751 05 Uppsala, Sweden
| | - Elizabeth L Watkin
- CHIRI Biosciences, School of Biomedical Sciences, Curtin University, Perth 6845, Australia
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, 391 82 Kalmar, Sweden
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Starflinger J, Buck M, Hartmann A, Kulenovic R, Leininger S, Rahman S, Rashid M. Recent numerical simulations and experiments on coolability of debris beds during severe accidents of light water reactors. Nuclear Engineering and Design 2015. [DOI: 10.1016/j.nucengdes.2015.09.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Garcia SL, Buck M, McMahon KD, Grossart HP, Eiler A, Warnecke F. Auxotrophy and intrapopulation complementary in the ‘interactome’ of a cultivated freshwater model community. Mol Ecol 2015; 24:4449-59. [DOI: 10.1111/mec.13319] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/09/2015] [Accepted: 07/10/2015] [Indexed: 01/05/2023]
Affiliation(s)
- Sarahi L. Garcia
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
| | - Moritz Buck
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
- BILS; Swedish Bioinformatics Infrastructure for Life Sciences; Husargatan 3 751 23 Uppsala Sweden
| | - Katherine D. McMahon
- Department of Bacteriology and Department of Civil and Environmental Engineering; University of Wisconsin-Madison; 5552 Microbial Sciences Building 1550 Linden Drive Madison WI 53706 USA
| | - Hans-Peter Grossart
- Department Experimental Limnology; Leibniz-Institute for Freshwater Ecology and Inland Fisheries; Alte Fischerhütte 2 OT Neuglobsow 16775 Stechlin Germany
- Institute for Biochemistry and Biology; Potsdam University; Karl-Liebknecht-Straße 24-25 Haus 25 14476 Potsdam Germany
| | - Alexander Eiler
- Department of Ecology and Genetics; Limnology and Science for Life Laboratory; Uppsala University; Norbyvägen 18D 752 36 Uppsala Sweden
| | - Falk Warnecke
- Jena School for Microbial Communication at Friedrich Schiller University Jena; Philosophenweg 12 07743 Jena Germany
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Buck M, Böckelmann I, Thielmann B. Zusammenhänge von Persönlichkeitsmerkmalen und arbeitsbezogenen Verhaltens- und Erlebensmustern. Gesundheitswesen 2014. [DOI: 10.1055/s-0034-1386870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Egelhaaf A, Cölln K, Schmitz B, Buck M, Wink M, Schneider D. Organ Specific Storage of Dietary Pyrrolizidine Alkaloids in the Arctiid Moth Creatonotos transiens. ACTA ACUST UNITED AC 2014. [DOI: 10.1515/znc-1990-1-220] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Larvae of the arctiid moth Creatonotos transiens obtained each 5 mg of heliotrine, a pyrrolizidine alkaloid, via an artificial diet. 7 S-H eliotrine is converted into its enantiomer, 7 R1-heliotrine, and some minor metabolites, such as callimorphine. 7 S- and 7 R-heliotrine are present in the insect predominantly (more than 97%) as their N-oxides. The distribution of heliotrine in the organs and tissues of larvae, prepupae, pupae and imagines was analyzed by capillary gas-liquid chromatography. A large proportion of the alkaloid is stored in the integument of all developmental stages, where it probably serves as a chemical defence compound against predators. Female imagines had transferred substantial amounts of heliotrine to their ovaries and subsequently to their eggs; males partly directed it to their pheromone biosynthesis.
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Affiliation(s)
- A. Egelhaaf
- Zoologisches Institut der Universität, Im Weyertal 119, D-5000 Köln 41, Bundesrepublik Deutschland
| | - K. Cölln
- Zoologisches Institut der Universität, Im Weyertal 119, D-5000 Köln 41, Bundesrepublik Deutschland
| | - B. Schmitz
- Zoologisches Institut der Universität, Im Weyertal 119, D-5000 Köln 41, Bundesrepublik Deutschland
| | - M. Buck
- Zoologisches Institut der Universität, Im Weyertal 119, D-5000 Köln 41, Bundesrepublik Deutschland
| | - M. Wink
- Pharmazeutisches Institut der Universität, Saarstraße 21, D-6500 Mainz, Bundesrepublik Deutschland
- Institut für Pharmazeutische Biologie, Universität Heidelberg, Im Neuenheimer Feld 364, D-6900 Heidelberg, Bundesrepublik Deutschland
| | - D. Schneider
- Max-Planck-Institut für Verhaltensphysiologie, D-8130 Seewiesen/Starnberg, Bundesrepublik Deutschland
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Mugnaini V, Tsotsalas M, Bebensee F, Grosjean S, Shahnas A, Bräse S, Lahann J, Buck M, Wöll C. Electrochemical investigation of covalently post-synthetic modified SURGEL coatings. Chem Commun (Camb) 2014; 50:11129-31. [DOI: 10.1039/c4cc03521f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Thiol–yne click chemistry post synthesis modification (PSM) is used to further functionalize a fully organic porous polymer coating (SURGEL). By cyclic voltammetry the resulting electrochemical properties are addressed. The Nernstian diffusion limited process observed in the presence of ferrocene as electrolyte is explained in terms of a high permeability of the SURGELs for ferrocene after PSM.
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Affiliation(s)
- V. Mugnaini
- Institute of Functional Interfaces (IFG)
- Karlsruhe Institute of Technology
- Eggenstein-Leopoldshafen, Germany
| | - M. Tsotsalas
- Institute of Functional Interfaces (IFG)
- Karlsruhe Institute of Technology
- Eggenstein-Leopoldshafen, Germany
| | - F. Bebensee
- Institute of Functional Interfaces (IFG)
- Karlsruhe Institute of Technology
- Eggenstein-Leopoldshafen, Germany
| | - S. Grosjean
- Institute for Organic Chemistry (IOC)
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe, Germany
- Institute of Toxicology and Genetics (ITG)
- Karlsruhe Institute of Technology (KIT)
| | - A. Shahnas
- Institute of Functional Interfaces (IFG)
- Karlsruhe Institute of Technology
- Eggenstein-Leopoldshafen, Germany
| | - S. Bräse
- Institute for Organic Chemistry (IOC)
- Karlsruhe Institute of Technology (KIT)
- 76131 Karlsruhe, Germany
- Institute of Toxicology and Genetics (ITG)
- Karlsruhe Institute of Technology (KIT)
| | - J. Lahann
- Institute of Functional Interfaces (IFG)
- Karlsruhe Institute of Technology
- Eggenstein-Leopoldshafen, Germany
| | - M. Buck
- EaStCHEM School of Chemistry
- University of St Andrews
- , UK
| | - C. Wöll
- Institute of Functional Interfaces (IFG)
- Karlsruhe Institute of Technology
- Eggenstein-Leopoldshafen, Germany
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Boerries M, Grahammer F, Eiselein S, Buck M, Meyer C, Goedel M, Bechtel W, Zschiedrich S, Pfeifer D, Laloë D, Arrondel C, Gonçalves S, Krüger M, Harvey SJ, Busch H, Dengjel J, Huber TB. Molecular fingerprinting of the podocyte reveals novel gene and protein regulatory networks. Kidney Int 2013; 83:1052-64. [PMID: 23364521 DOI: 10.1038/ki.2012.487] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A thorough characterization of the transcriptome and proteome of endogenous podocytes has been hampered by low cell yields during isolation. Here we describe a double fluorescent reporter mouse model combined with an optimized bead perfusion protocol and efficient single cell dissociation to yield more than 500,000 podocytes per mouse allowing for global, unbiased downstream applications. Combining mRNA and miRNA transcriptional profiling with quantitative proteomic analyses revealed programs of highly specific gene regulation tightly controlling cytoskeleton, cell differentiation, endosomal transport, and peroxisome function in podocytes. Strikingly, the analyses further predict that these podocyte-specific gene regulatory networks are accompanied by alternative splicing of respective genes. Thus, our 'omics' approach will facilitate the discovery and integration of novel gene, protein, and organelle regulatory networks that deepen our systematic understanding of podocyte biology.
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Affiliation(s)
- Melanie Boerries
- Freiburg Institute for Advanced Studies-LifeNet, Albert-Ludwigs-University Freiburg, Freiburg, Germany
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Galvão CW, Souza EM, Etto RM, Pedrosa FO, Chubatsu LS, Yates MG, Schumacher J, Buck M, Steffens MBR. The RecX protein interacts with the RecA protein and modulates its activity in Herbaspirillum seropedicae. Braz J Med Biol Res 2012; 45:1127-34. [PMID: 23044625 PMCID: PMC3854219 DOI: 10.1590/s0100-879x2012007500160] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Accepted: 08/14/2012] [Indexed: 11/22/2022] Open
Abstract
DNA repair is crucial to the survival of all organisms. The bacterial RecA protein is a central component in the SOS response and in recombinational and SOS DNA repairs. The RecX protein has been characterized as a negative modulator of RecA activity in many bacteria. The recA and recX genes of Herbaspirillum seropedicae constitute a single operon, and evidence suggests that RecX participates in SOS repair. In the present study, we show that the H. seropedicae RecX protein (RecX Hs) can interact with the H. seropedicaeRecA protein (RecA Hs) and that RecA Hs possesses ATP binding, ATP hydrolyzing and DNA strand exchange activities. RecX Hs inhibited 90% of the RecA Hs DNA strand exchange activity even when present in a 50-fold lower molar concentration than RecA Hs. RecA Hs ATP binding was not affected by the addition of RecX, but the ATPase activity was reduced. When RecX Hs was present before the formation of RecA filaments (RecA-ssDNA), inhibition of ATPase activity was substantially reduced and excess ssDNA also partially suppressed this inhibition. The results suggest that the RecX Hs protein negatively modulates the RecA Hs activities by protein-protein interactions and also by DNA-protein interactions.
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Affiliation(s)
- C W Galvão
- Departamento de Biologia Estrutural, Molecular e Genética, Universidade Estadual de Ponta Grossa, Ponta Grossa, PR, Brasil.
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Seubert A, Sureda A, Bader J, Lapins J, Buck M, Laurien E. The 3-D time-dependent transport code TORT-TD and its coupling with the 3D thermal-hydraulic code ATTICA3D for HTGR applications. Nuclear Engineering and Design 2012. [DOI: 10.1016/j.nucengdes.2011.09.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Kurtz J, Kaminsky M, Floquet A, Veillard A, Kimmig R, Dorum A, Elit L, Buck M, Petru E, Reed N, Scambia G, Varsellona N, Brown C, Pujade-Lauraine E. Ovarian cancer in elderly patients: carboplatin and pegylated liposomal doxorubicin versus carboplatin and paclitaxel in late relapse: a Gynecologic Cancer Intergroup (GCIG) CALYPSO sub-study. Ann Oncol 2011; 22:2417-2423. [DOI: 10.1093/annonc/mdr001] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
With mounting evidence that hypothermia is neuroprotective in newborns with hypoxic-ischemic encephalopathy (HIE), an increasing number of centers are offering this therapy. Hypothermia is associated with a wide range of physiologic changes affecting every organ system, and awareness of these effects is essential for optimum patient management. Lowering the core temperature also alters pharmacokinetic and pharmacodynamic properties of medications commonly used in asphyxiated neonates, necessitating close attention to drug efficacy and side effects. Rewarming introduces additional risks and challenges as the hypothermia-associated physiologic and pharmacologic changes are reversed. In this review we provide an organ system-based assessment of physiologic changes associated with hypothermia. We also summarize evidence from randomized controlled trials showing lack of serious adverse effects of moderate hypothermia therapy in term and near-term newborns with moderate-to-severe HIE. Finally, we review the effects of hypothermia on drug metabolism and clearance based on studies in animal models and human adults, and limited data from neonates.
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Affiliation(s)
- S Zanelli
- Department of Pediatrics, University of Virginia, Charlottesville, USA.
| | - M Buck
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA,Department of Pharmacy, University of Virginia, Charlottesville, VA, USA
| | - K Fairchild
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
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Huvet M, Toni T, Sheng X, Thorne T, Jovanovic G, Engl C, Buck M, Pinney JW, Stumpf MPH. The evolution of the phage shock protein response system: interplay between protein function, genomic organization, and system function. Mol Biol Evol 2010; 28:1141-55. [PMID: 21059793 PMCID: PMC3041696 DOI: 10.1093/molbev/msq301] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Sensing the environment and responding appropriately to it are key capabilities for the survival of an organism. All extant organisms must have evolved suitable sensors, signaling systems, and response mechanisms allowing them to survive under the conditions they are likely to encounter. Here, we investigate in detail the evolutionary history of one such system: The phage shock protein (Psp) stress response system is an important part of the stress response machinery in many bacteria, including Escherichia coli K12. Here, we use a systematic analysis of the genes that make up and regulate the Psp system in E. coli in order to elucidate the evolutionary history of the system. We compare gene sharing, sequence evolution, and conservation of protein-coding as well as noncoding DNA sequences and link these to comparative analyses of genome/operon organization across 698 bacterial genomes. Finally, we evaluate experimentally the biological advantage/disadvantage of a simplified version of the Psp system under different oxygen-related environments. Our results suggest that the Psp system evolved around a core response mechanism by gradually co-opting genes into the system to provide more nuanced sensory, signaling, and effector functionalities. We find that recruitment of new genes into the response machinery is closely linked to incorporation of these genes into a psp operon as is seen in E. coli, which contains the bulk of genes involved in the response. The organization of this operon allows for surprising levels of additional transcriptional control and flexibility. The results discussed here suggest that the components of such signaling systems will only be evolutionarily conserved if the overall functionality of the system can be maintained.
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Affiliation(s)
- M Huvet
- Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College London, London, United Kingdom.
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Simonsen KW, Steentoft A, Buck M, Hansen L, Linnet K. Screening and Quantitative Determination of Twelve Acidic and Neutral Pharmaceuticals in Whole Blood by Liquid-Liquid Extraction and Liquid Chromatography-Tandem Mass Spectrometry. J Anal Toxicol 2010; 34:367-73. [DOI: 10.1093/jat/34.7.367] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Elit L, Konner JA, Armstrong DK, Buck M, Dean A, Finkler NJ, Hulstine A, Schweizer C, Phillips M, Weil S. A randomized, double-blind, placebo-controlled phase II study of the efficacy and safety of farletuzumab (MORAb-003) in combination with weekly paclitaxel in subjects with platinum-resistant or refractory relapsed ovarian cancer. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.tps255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Kurtz J, Hilpert F, Dorum A, Veillard A, Elit L, Buck M, Petru E, Reed N, Scambia G, Varsellona N. Can elderly patients with recurrent ovarian cancer (ROC) be treated with a platinum-based doublet? Results from the CALYPSO trial. J Clin Oncol 2010. [DOI: 10.1200/jco.2010.28.15_suppl.5031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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41
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Buck M, Eisert F, Grunze M, Träger F. Wavelength Dependent Second Harmonic Generation: A New Spectroscopic Tool for the Study of Interfaces. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19930970326] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Bürger M, Buck M, Pohlner G, Rahman S, Kulenovic R, Fichot F, Ma W, Miettinen J, Lindholm I, Atkhen K. Coolability of particulate beds in severe accidents: Status and remaining uncertainties. Progress in Nuclear Energy 2010. [DOI: 10.1016/j.pnucene.2009.09.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Popp S, Stope M, Buck M, Joffroy C, Fritz P, Knabbe C. YB-1 Mediates a Crosstalk between ERα and TGFβ Signaling in Breast Cancer Cells. Cancer Res 2009. [DOI: 10.1158/0008-5472.sabcs-09-4172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The multifunctional Y-box binding protein-1 (YB-1) belongs to the highly conserved family of cold shock proteins being involved in transcriptional/translational regulation, DNA repair as well as stress response. Additionally, it is highly expressed in many malignant tissues which seems to correlate with a high proliferation level, drug resistance and a poor prognosis in a variety of tumors including breast cancer.Using quantitative immunohistochemistry we now confirm the previously described negative prognostic impact of YB-1 on survival in a clinical study with tumor samples from 199 breast cancer patients (p=0.0146; median follow up 79 months).Treatment of the estrogen receptor α (ERα) positive human breast cancer cell line MCF-7 with antiestrogens (4-hydroxytamoxifen, faslodex) resulted in a time and dose dependent decrease of YB-1 expression on the RNA- as well as on the protein level. In contrast, antiestrogen treatment of the ERα negative cell line MDA-MB-231 does not have any effect indicating that the antiestrogen effect on YB-1 is mediated by ERα. We have already demonstrated that the action of all antiestrogens is at least partially mediated by transforming growth factor β (TGFβ) (e.g. Breast Cancer Res. Treat. 107: 15-24, 2008). Using TGFβ-responsive reporter gene assays we now show that overexpression of YB-1 in MCF-7 cells enhances the induction of p3TPlux activity by TGFβ suggesting a crosstalk between YB-1 and TGFβ signaling pathways. Moreover, YB-1 also increases the antiestrogen induction of the TGFβ2-mRNA level coming along with a YB-1 regulated enhancement of the antiestrogen effect on cell growth.Very recent findings of our group point towards a ligand-independent influence of ERα on TGFβ signaling (Breast Cancer Res. Treat., in press). Due to the antiestrogen regulation of YB-1 via ERα and its crosstalk with the TGFβ pathway, the potential role of YB-1 as a mediator of the interaction between ERα and TGFβ signaling was analyzed. Performing pull-down assays with recombinant GST-ERα and whole cell lysates of MCF-7 cells confirms a protein-protein interaction between YB-1 and ERα. The physiological relevance of this interaction could be demonstrated, as the TGFβ-induced p3TPlux activity is clearly modulated by both, YB-1 and ERα.In conclusion, we present evidence that YB-1 and TGFβ signaling are functionally linked in MCF-7 cells. Combined with the detection of a physical interaction between YB-1 and ERα, our findings shed new light on a potential role of YB-1 as a part of the mechanism responsible for switching TGFβ from its anti-proliferative role in early tumor stages to tumor promoting effects in late-stage disease, most likely via a YB-1 regulated shift of TGFβ-signaling to pro-invasive pathways. This would also explain why high levels of YB-1 correlate with a poor prognosis in breast cancer patients.
Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4172.
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Affiliation(s)
- S. Popp
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Germany
| | - M. Stope
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Germany
| | - M. Buck
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Germany
| | - C. Joffroy
- 1Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Germany
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Mills D, Tuohy K, Booth J, Buck M, Crabbe M, Gibson G, Ames J. Dietary glycated protein modulates the colonic microbiota towards a more detrimental composition in ulcerative colitis patients and non-ulcerative colitis subjects. J Appl Microbiol 2008; 105:706-14. [DOI: 10.1111/j.1365-2672.2008.03783.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Landers KA, Samaratunga H, Teng L, Buck M, Burger MJ, Scells B, Lavin MF, Gardiner RA. Identification of claudin-4 as a marker highly overexpressed in both primary and metastatic prostate cancer. Br J Cancer 2008; 99:491-501. [PMID: 18648369 PMCID: PMC2527792 DOI: 10.1038/sj.bjc.6604486] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In the quest for markers of expression and progression for prostate cancer (PCa), the majority of studies have focussed on molecular data exclusively from primary tumours. Although expression in metastases is inferred, a lack of correlation with secondary tumours potentially limits their applicability diagnostically and therapeutically. Molecular targets were identified by examining expression profiles of prostate cell lines using cDNA microarrays. Those genes identified were verified on PCa cell lines and tumour samples from both primary and secondary tumours using real-time RT–PCR, western blotting and immunohistochemistry. Claudin-4, coding for an integral membrane cell-junction protein, was the most significantly (P<0.00001) upregulated marker in both primary and metastatic tumour specimens compared with benign prostatic hyperplasia at both RNA and protein levels. In primary tumours, claudin-4 was more highly expressed in lower grade (Gleason 6) lesions than in higher grade (Gleason ⩾7) cancers. Expression was prominent throughout metastases from a variety of secondary sites in fresh-frozen and formalin-fixed specimens from both androgen-intact and androgen-suppressed patients. As a result of its prominent expression in both primary and secondary PCas, together with its established role as a receptor for Clostridium perfringens enterotoxin, claudin-4 may be useful as a potential marker and therapeutic target for PCa metastases.
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Affiliation(s)
- K A Landers
- Department of Surgery, University of Queensland, Herston, Qld, Australia
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Buck M, Nehaniv CL. Communication and complexity in a GRN-based multicellular system for graph colouring. Biosystems 2008; 94:28-33. [PMID: 18606206 DOI: 10.1016/j.biosystems.2008.06.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2007] [Revised: 11/14/2007] [Accepted: 05/23/2008] [Indexed: 10/21/2022]
Abstract
Artificial Genetic Regulatory Networks (GRNs) are interesting control models through their simplicity and versatility. They can be easily implemented, evolved and modified, and their similarity to their biological counterparts makes them interesting for simulations of life-like systems as well. These aspects suggest they may be perfect control systems for distributed computing in diverse situations, but to be usable for such applications the computational power and evolvability of GRNs need to be studied. In this research we propose a simple distributed system implementing GRNs to solve the well known NP-complete graph colouring problem. Every node (cell) of the graph to be coloured is controlled by an instance of the same GRN. All the cells communicate directly with their immediate neighbours in the graph so as to set up a good colouring. The quality of this colouring directs the evolution of the GRNs using a genetic algorithm. We then observe the quality of the colouring for two different graphs according to different communication protocols and the number of different proteins in the cell (a measure for the possible complexity of a GRN). Those two points, being the main scalability issues that any computational paradigm raises, will then be discussed.
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Affiliation(s)
- Moritz Buck
- Centre for Computer Science & Informatics Research, University of Hertfordshire, Hatfield, Hertfordshire, United Kingdom.
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Bouguet-Bonnet S, Buck M. Compensatory and long-range changes in picosecond-nanosecond main-chain dynamics upon complex formation: 15N relaxation analysis of the free and bound states of the ubiquitin-like domain of human plexin-B1 and the small GTPase Rac1. J Mol Biol 2008; 377:1474-87. [PMID: 18321527 DOI: 10.1016/j.jmb.2008.01.081] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 01/21/2008] [Accepted: 01/25/2008] [Indexed: 11/28/2022]
Abstract
The formation of a complex between Rac1 and the cytoplasmic domain of plexin-B1 is one of the first documented cases of a direct interaction between a small guanosine 5'-triphosphatase (GTPase) and a transmembrane receptor. Structural studies have begun to elucidate the role of this interaction for the signal transduction mechanism of plexins. Mapping of the Rac1 GTPase surface that contacts the Rho GTPase binding domain of plexin-B1 by solution NMR spectroscopy confirms the plexin domain as a GTPase effector protein. Regions neighboring the GTPase switch I and II regions are also involved in the interaction and there is considerable interest to examine the changes in protein dynamics that take place upon complex formation. Here we present main-chain nitrogen-15 relaxation measurements for the unbound proteins as well as for the Rho GTPase binding domain and Rac1 proteins in their complexed state. Derived order parameters, S2, show that considerable motions are maintained in the bound state of plexin. In fact, some of the changes in S2 on binding appear compensatory, exhibiting decreased as well as increased dynamics. Fluctuations in Rac1, already a largely rigid protein on the picosecond-nanosecond timescale, are overall diminished, but isomerization dynamics in the switch I and II regions of the GTPase are retained in the complex and appear to be propagated to the bound plexin domain. Remarkably, fluctuations in the GTPase are attenuated at sites, including helices alpha6 (the Rho-specific insert helix), alpha7 and alpha8, that are spatially distant from the interaction region with plexin. This effect of binding on long-range dynamics appears to be communicated by hinge sites and by subtle conformational changes in the protein. Similar to recent studies on other systems, we suggest that dynamical protein features are affected by allosteric mechanisms. Altered protein fluctuations are likely to prime the Rho GTPase-plexin complex for interactions with additional binding partners.
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Affiliation(s)
- S Bouguet-Bonnet
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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Abstract
Self-assembled monolayers (SAMs) formed from bis(biphenyl-4-yl) diselenide (BBPDSe) on Au(111) and Ag(111) substrates have been characterized by high-resolution X-ray photoelectron spectroscopy, near-edge X-ray absorption fine structure spectroscopy, infrared reflection absorption spectroscopy, water contact angle measurements, and scanning tunneling microscopy (STM). BBPDSe was found to form contamination-free, densely packed, and well-ordered biphenyl selenolate (BPSe) SAMs on both Au and Ag. Spectroscopic data suggest very similar packing density, orientational order, and molecular inclination in BPSe/Au and BPSe/Ag. STM data give a similar intermolecular spacing of 5.3 +/- 0.4 A on both Au and Ag but exhibit differences in the exact arrangement of the BPSe molecules on these two substrates, with the (2 square root[3] x square root[3])R30 degrees and (square root[3] x square root[3])R30 degrees unit cells on Au and Ag, respectively. There is strong evidence for adsorbate-mediated substrate restructuring in the case of Au, whereas no clear statement on this issue can be made in the case of Ag. The film quality of the BPSe SAMs is superior to their thiol analogues, which is presumably related to a better ability of the selenolates to adjust the surface lattice of the substrate to the most favorable 2D arrangement of the adsorbate molecules. This suggests that aromatic selenolates represent an attractive alternative to the respective thiols.
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Affiliation(s)
- A Shaporenko
- Angewandte Physikalische Chemie, Universität Heidelberg, Im Neuenheimer Feld 253, 69120 Heidelberg, Germany
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Harnett P, Buck M, Beale P, Goldrick A, Allan S, Fitzharris B, De Souza P, Links M, Kalimi G, Davies T, Stuart-Harris R. Phase II study of gemcitabine and oxaliplatin in patients with recurrent ovarian cancer: an Australian and New Zealand Gynaecological Oncology Group study. Int J Gynecol Cancer 2007; 17:359-66. [PMID: 17362313 DOI: 10.1111/j.1525-1438.2007.00763.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Gemcitabine and oxaliplatin have shown single-agent activity in relapsed ovarian cancer. This combination was used to determine response rates, time-to-event efficacy measures, and toxicity in patients with recurrent ovarian cancer. Patients with prior platinum-based chemotherapy who had measurable lesions and/or elevated CA-125 levels were identified as group A (platinum-refractory/platinum-resistant patients) and group B (platinum-sensitive patients). All patients received gemcitabine 1000 mg/m(2) on days 1 and 8 and oxaliplatin 130 mg/m(2) on day 8 every 21 days for up to eight cycles. Seventy-five patients (21 in group A and 54 in group B), with a median age of 58 years (range, 37-78), were enrolled. A median of six cycles (range, 1-8) was administered. By intent-to-treat analysis, 15 patients with measurable disease achieved partial response for an overall best response rate of 20.0% (9.5% in group A and 24.1% in group B). CA-125 response was observed in 48.4% patients (30.0% in group A and 57.1% in group B). Median time to progressive disease was 7.1 months (95% CI, 5.6-9.0 months) with 5.0 months in group A and 8.3 months in group B. Median overall survival was 17.8 months (95% CI, 12.9-21.3 months) with 9.2 months for group A and 20.0 months for group B. Major grade 3/4 toxicities were neutropenia (61.3%), leukopenia (24.0%), nausea (16.0%), and vomiting (22.7%). We conclude that the combination of oxaliplatin and gemcitabine is active in patients with recurrent ovarian cancer, but the regimen is unsatisfactory for further study due to modest response and relatively high toxicity.
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Affiliation(s)
- P Harnett
- Department of Medical Oncology, Westmead Hospital, Westmead, New South Wales, Australia.
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Friedlander M, Buck M, Wyld D, Findlay M, Fitzharris B, De Souza P, Davies T, Kalimi G, Allan S, Perez D, Harnett P. Phase II study of carboplatin followed by sequential gemcitabine and paclitaxel as first-line treatment for advanced ovarian cancer. Int J Gynecol Cancer 2007; 17:350-8. [PMID: 17362312 DOI: 10.1111/j.1525-1438.2007.00795.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The aim of this exploratory phase II study was to evaluate sequential chemotherapy with carboplatin followed by gemcitabine-paclitaxel combination in chemonaive patients with advanced ovarian cancer. The primary objective was to evaluate time to progressive disease (TTPD); secondary objectives included the evaluation of 1- and 3-year survival, response rates, and toxicity. Following initial debulking surgery or biopsy, patients with FIGO stage IIC-IV disease received four cycles of carboplatin area under the curve (AUC) 6 (day 1) every 21 days, followed by four cycles of gemcitabine 1000 mg/m(2) (days 1 and 8) and paclitaxel 175 mg/m(2) (day 8) every 21 days. A total of 47 patients enrolled, 44 (93.6%) completed the initial four cycles, and 39 patients (82.9%) completed the planned eight cycles. The median and maximum lengths of follow-up were 31.2 and 43.7 months, respectively. Median TTPD was 13.8 months (95% CI, 11.6-21.0 months), and median survival time was 31.2 months (95% CI, 25.2-39.6 months). Survival at 1 and 3 years was 95.7% and 44.2%, respectively. Of the 43 evaluable patients, most (95.3%) of them achieved a CA-125 marker response based on Gynecologic Cancer Intergroup (GCIG) definition. The partial response rate in the seven patients with measurable disease was 46.4%. Myelosuppression was the major toxicity, with grade 3 and 4 neutropenia observed in 76.6% patients and thrombocytopenia in 12.8% patients. The sequential approach of carboplatin followed by gemcitabine-paclitaxel as first-line treatment for patients with ovarian cancer is feasible and well tolerated, and depending upon the findings from other major trials, it may merit further evaluation.
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Affiliation(s)
- M Friedlander
- Prince of Wales Hospital, Randwick, New South Wales, Australia.
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