| 1. |
- Janzon, Anders, 1978, et al.
(författare)
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Exploring the microbial resistome in river sediments exposed to extraordinary high levels of antibiotics
- 2010
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Ingår i: 35th FEBS Congress: Molecules of Life.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The rapid development and propagation of antibiotic resistance in pathogenic and opportunistic bacteria is a major threat to public health worldwide. The phenomenon has been widely studied in the clinical setting, but comparatively little is known about the prevalence and diversity of antibiotic resistance in communities of environmental bacteria, often referred to as the environmental resistome. As the external environment may function as a reservoir of resistance genes to human pathogens, we are interested in how environmental bacteria are affected by antibiotic pollution. We have previously isolated microbial DNA from river sediments taken up- and downstream from a water treatment plant that processes waste water from several pharmaceutical plants producing antibiotics. In a previous study, we used deep sequencing to identify unprecedented frequencies of known resistance genes to several classes of antibiotics in these samples. In this study, we aim to functionally characterize the resistome in a more open and exploratory way by screening genomic DNA libraries transformed into sensitive hosts. To generate the libraries, several experimental strategies were explored, including mechanical shearing and enzymatic digestion of the isolated DNA followed by blunt- or sticky end cloning into different plasmids, subsequently transformed into sensitive E. coli. Pros and cons of the different strategies will be discussed along with preliminary results of the screening against selected antibiotics.
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| 2. |
- Mukherjee, Vaskar, 1986, et al.
(författare)
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Phenomics, transcriptomics and metabolomics for identifying concentration-dependent chemical interactions and understanding the mechanistic basis of the mixture toxicity
- 2019
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The prevalence of mixtures of synthetic and natural chemicals in the environment is a growing concern for public health and environmental effects. Currently, most chemical legislations are based on the risk assessments carried out on individual substances and theoretical estimates of combination effect. However, exposure to multi-component mixtures may stimulate unpredicted overall toxic responses due to interactions, where interactions were scored as deviations from the independent action model. In our project, we investigated the frequency and magnitude of interactions in mixtures of five compounds - NaCl, HgCl2, paraquat, rapamycin, clotrimazole - with relatively known specific mode of action. Growth effects by all-combination pair-wise mixtures spanning a wide concentration range were investigated by employing high-resolution yeast phenomics. The baker’s/brewer’s yeast Saccharomyces cerevisiae and the marine yeast Debaryomyces hansenii are used in this study to identify evolutionary conserved mixture effects, with the aim to identify generic responses of relevance to a vast array of organisms. Our results clearly show that both synergistic and antagonistic relationships exist among the tested chemicals and some of these relationships are concentration-dependent. Evolutionary conserved interactions on the level of rate of growth were found for salt and rapamycin (synergy) as well as for salt and paraquat (antagonism). The mechanistic basis of the chemical interactions identified in our study was investigated by transcriptomics and metabolomics. As one example, we observed that several genes with symporter activity and with cation transmembrane transporter activity is downregulated in salt plus paraquat mixtures, while the expression of genes that are related to cofactor-dependent metabolic pathways is stimulated. We believe that the repression of symporter and ion transmembrane transport activity reduces paraquat entry to the yeast cells and thereby reduces its toxic response when combined with salt. On the other hand, upregulation of several of the genes (such as PGI1, PFK1, FBA1, and CDC19) related to cofactor-dependent metabolic pathways boost yeast fermentative activity. Since paraquat induces the production of reactive oxygen species (ROS) via respiration, a shift from aerobic respiration to anaerobic fermentation can reduce formation of ROS, thus reduces oxidative stress by paraquat.
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| 3. |
- Kolseth, Anna-Karin, et al.
(författare)
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Population Genetics on Ambrosia genus: Past, present and future
- 2014
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Konferensbidrag (refereegranskat)abstract
- A new Task Force within the COST-SMARTER has recently been created. This group is composed of population genetics experts from five European countries in charge of focusing on “Genetics on Ambrosia” (Austria, France, Germany, Hungary, Sweden). Their mission was to review molecular methods used in published genetics studies on common ragweed and to discuss about future projects. Two different types of molecular markers are generally used in the literature to investigate the genetic structure within and between introduced and/or native populations of common ragweed: microsatellite markers and amplified fragment length polymorphism (AFLP). These methods permit the researchers to trace-back the common ragweed invasion history and its worldwide spread as well as to identify certain evolutionary processes like selection, adaptation or genetic bottleneck due to different modes and adtes of introduction. One common conclusion is the presence of two main genetic clusters within Europe coming from two different regions of the native range. However, this conclusion is based on a limited number of microsatellite markers used (12 nuclear + 4 plastid). New methods using haplotype analysis or selected markers present on functional parts of the genome (i.e., related to herbicide-resistance) should be more investigated in order to increase the knowledge on common ragweed. Transcriptomic analyses are starting to be employed in USA to observe gene expression related to adaptations and identify the genes of the “invasiveness”. These new methods will now be promoted within the different European projects in order to open the way of whole-genome sequencing of Ambrosia artemisiifolia in the future.
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| 4. |
- Kvarnemo, Charlotta, et al.
(författare)
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Fish ART & sperm performance
- 2023
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Konferensbidrag (refereegranskat)abstract
- In species with alternative reproductive tactics (ART), parasitically spawning males have larger testes and greater sperm numbers as an evolved response to a higher degree of sperm competition. But do they also have higher sperm performance? We used sand gobies to test if it differs between breeding-coloured and sneaker-morph males. We compared sperm motility, velocity, longevity, morphometrics and gene expression of testes between the two morphs. We found 109 transcripts differentially expressed between the morphs. Notably, several mucin genes were upregulated in breeding-coloured males and two ATP-related genes were upregulated in sneaker-morph males. There was partial evidence of higher sperm velocity in sneaker-morph males, but no difference in sperm motility. Sand gobies have remarkably long-lived sperm, with almost no decline in motility and velocity over 22 hours, but again, this was equally true for both morphs. Sperm length did not differ between morphs and did not correlate with sperm velocity for either morph. Thus, other than a clear difference in testes gene expression, we found only modest differences between the two male morphs, confirming previous findings that increased sperm performance as an adaptation to sperm competition does not appear to be a primary target of evolution.
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| 5. |
- Rönkä, N., et al.
(författare)
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Panmixia at a distribution-wide scale but indications of genetic differentiation in isolated populations of the Terek Sandpiper (Xenus cinereus)
- 2016
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Ingår i: International Wader Study Group Conference 2016, 9-12 September 2016, Trabolgan, Cork, Ireland.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Populations at different parts of the species range may vary in their population dynamics and in their genetic structure and variation. Geographically separated populations or those located at the edge of the range may differ from the populations located at the core, or even be independent of them. The peripheral populations may hold genetic variation that is important for the adaptive potential of the species and therefore be of special conservation value. We studied the distribution-wide population genetic structure of the Terek Sandpiper (Xenus cinereus) using 13 microsatellite loci and two mitochondrial DNA markers: the control region and cytochrome oxidase I (COI). We evaluated the difference in genetic variation between the peripheral and core populations. Specifically, we sought signs of changes in population sizes and evaluated the management need of the populations. Distribution-wide differentiation was negligible, but geographically isolated populations in Finland and Dnieper River basin in Eastern Europe were differentiated from the main range. Edge populations had lower genetic variation than populations at the core when estimated with microsatellites and the COI, supporting the hypotheses where the core area of the distribution preserves the most variation. However, no such trend was observed with the control region data, which follows the model of no change throughout the distribution. The differences between the markers may reflect their different mutation rates, or be linked to the species’ dispersal behaviour. Our results revealed low overall nucleotide diversity and signs of past population contractions followed by expansion. Although the estimated current effective population size is large and therefore global conservation measures are not needed, the Finnish and Dnieper River basin populations nevertheless warrant management actions – not only because they may possess variation not present anywhere else, but also due to their smallness and large distances to the main range.
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| 6. |
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| 7. |
- Svensson, Ola, 1971-, et al.
(författare)
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Behavioural and genomic analyses of locally adapted sand goby populations over a steep salinity gradient
- 2023
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Konferensbidrag (refereegranskat)abstract
- Studies of colonization of new habitats appearing from rapidly changing environments increase our understanding of populations’ potential to cope with environmental changes. Here, we analyse behavioural, phenotypic and genetic variation involved in the successful establishment of the sand goby, Pomatoschistus minutus, over a steep salinity drop from 35 PSU in the North Sea (NE Atlantic) to two PSU in the inner parts of the post-glacial Baltic Sea. We show e.g. that populations are adapted to local salinity in a key reproductive trait, the proportion of motile sperm, which in itself may result in reproductive isolation caused by natural selection on immigrants. Genome variation shows strong differentiation among populations along the gradient. Sand gobies in the current Baltic Sea lineage is adapted to the low salinity in traits related to osmoregulation and reproduction, but also to both abiotic and biotic environmental factors correlated to salinity evident in traits such as vision and immune function. The salinity-biotic factors correlation is omnipresent in behavioral studies. Many loci also appear to be involved in these traits, but the specific functional mechanism (e.g., coding sequence, regulatory loci) remains to be clarified. We conclude that the first steps on the speciation continuum trajectory have been taken.
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| 8. |
- Svensson, Ola, 1971-, et al.
(författare)
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Post-glacial establishment of locally adapted sand goby populations over a steep salinity gradient
- 2023
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Konferensbidrag (refereegranskat)abstract
- Studies of colonization of new habitats that appear from rapidly changing environments are interesting and highly relevant to our understanding of divergence and speciation. Here, we analyse phenotypic and genetic variation involved in the successful establishment of a marine fish (sand goby, Pomatoschistus minutus) over a steep salinity drop from 35 PSU in the North Sea (NE Atlantic) to two PSU in the inner parts of the post-glacial Baltic Sea. We first show that populations are adapted to local salinity in a key reproductive trait, the proportion of motile sperm, which in itself may result in reproductive isolation caused by natural selection on immigrants. Thereafter, we show that genome variation at 22,190 single nucleotide polymorphisms (SNPs) shows strong differentiation among populations along the gradient. Sequences containing outlier SNPs and transcriptome sequences, mapped to a draft genome, reveal associations with genes with relevant functions for adaptation in this environment.
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| 9. |
- Buckland, Philip I., 1973-, et al.
(författare)
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The Strategic Environmental Archaeology Database : a resource for international, multiproxy and transdisciplinary studies of environmental and climatic change
- 2015
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Konferensbidrag (refereegranskat)abstract
- Climate and environmental change are global challenges which require global data and infrastructure to investigate. These challenges also require a multi-proxy approach, integrating evidence from Quaternary science and archaeology with information from studies on modern ecology and physical processes among other disciplines. The Strategic Environmental Archaeology Database (SEAD http://www.sead.se) is a Swedish based international research e-infrastructure for storing, managing, analysing and disseminating palaeoenvironmental data from an almost unlimited number of analysis methods. The system currently makes available raw data from over 1500 sites (>5300 datasets) and the analysis of Quaternary fossil insects, plant macrofossils, pollen, geochemistry and sediment physical properties, dendrochronology and wood anatomy, ceramic geochemistry and bones, along with numerous dating methods. This capacity will be expanded in the near future to include isotopes, multi-spectral and archaeo-metalurgical data. SEAD also includes expandable climate and environment calibration datasets, a complete bibliography and extensive metadata and services for linking these data to other resources. All data is available as Open Access through http://qsead.sead.se and downloadable software. SEAD is maintained and managed at the Environmental Archaeology Lab and HUMlab at Umea University, Sweden. Development and data ingestion is progressing in cooperation with The Laboratory for Ceramic Research and the National Laboratory for Wood Anatomy and Dendrochronology at Lund University, Sweden, the Archaeological Research Laboratory, Stockholm University, the Geoarchaeological Laboratory, Swedish National Historical Museums Agency and several international partners and research projects. Current plans include expanding its capacity to serve as a data source for any system and integration with the Swedish National Heritage Board's information systems. SEAD is partnered with the Neotoma palaeoecology database (http://www.neotomadb.org) and a new initiative for building cyberinfrastructure for transdisciplinary research and visualization of the long-term human ecodynamics of the North Atlantic funded by the National Science Foundation (NSF).
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| 10. |
- Da Silva Faria Oliveira, Fábio Luis, 1985, et al.
(författare)
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Genomic and transcriptomic analysis of Candida intermedia reveals genes for utilization of biotechnologically important carbon sources
- 2019
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- A future biobased society relies on efficient industrial microorganisms that can convert all sugars from agricultural, forestry and industrial waste streams into fuels, chemicals and materials. To be able to tailor-make such potent cell factories, we need a far better understanding of the proteins responsible for the assimilation of biotechnologically important carbon sources including pentoses, disaccharides and oligomers. The yeast Candida intermedia, known for its superior growth on xylose owing to its efficient uptake and conversion systems, can also utilize a range of other important carbon sources such as cellobiose, galactose and lactose. The aim of this project was to identify the genomic determinants for the utilization of these mono- and disaccharides in our in-house isolated C. intermedia strain CBS 141442. Genome sequencing and transcriptional (RNA seq) data analysis during growth in defined medium supplemented with glucose, xylose, galactose, lactose or cellobiose, revealed numerous distinct clusters of coregulated genes. By scanning the CBS 141442 genome for genes encoding Major Facilitator Superfamily (MFS) sugar transporters, and the RNA-seq dataset for the corresponding transcriptional profiles, we identified several novel genes encoding putative xylose transporters and multiple Lac12-like transporters likely involved in the uptake of disaccharides in C. intermedia. We also found that the yeast possesses no less than three genes encoding aldose reductases with different transcriptional profiles, and heterologous expression of the genes in Saccharomyces cerevisiae showed that the aldose reductases have different substrate and co-factor specificities, suggesting diverse physiological roles. Taken together, the results of this study provide insights into the mechanisms underlying carbohydrate metabolism in C. intermedia, and reveals several genes with potential future applications in cell factory development.
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