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R. Henrik Nilsson,
Leho Tedersoo,
Kessy Abarenkov,
Martin Ryberg, Erik Kristiansson,
Martin Hartmann,
Conrad L. Schoch,
Johan A. A. Nylander,
Johannes Bergsten,
Teresita M. Porter,
Ari Jumpponen,
Parag Vaishampayan,
Otso Ovaskainen,
Nils Hallenberg,
Johan Bengtsson-Palme,
K. Martin Eriksson,
Karl-Henrik Larsson,
Ellen Larsson,
Urmas Koeljalg
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R. Henrik Nilsson,
Leho Tedersoo,
Kessy Abarenkov,
Martin Ryberg, Erik Kristiansson,
Martin Hartmann,
Conrad L. Schoch,
Johan A. A. Nylander,
Johannes Bergsten,
Teresita M. Porter,
Ari Jumpponen,
Parag Vaishampayan,
Otso Ovaskainen,
Nils Hallenberg,
Johan Bengtsson-Palme,
K. Martin Eriksson,
Karl-Henrik Larsson,
Ellen Larsson,
Urmas Koeljalg
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ABSTRACT: Background Analysis of gene expression from different species is a powerfulway to identify evolutionarily conserved transcriptional responses. However,due to evolutionary events such as gene duplication, there is no one-to-onecorrespondence between genes from different species which makes comparisonof their expression profiles complex.Results In this paper we describe a new methodfor cross-species meta-analysis of gene expression. The method takes thehomology structure between compared speciesinto account and can therefore compare expression data from genes with anynumber of orthologs and paralogs. A simulation study shows that the proposedmethod results in a substantial increase in statistical power compared to previously suggestedprocedures. As a proof of concept, we analyzed microarray data from heatstress experiments performed in eight species and identified several well-knownevolutionarily conserved transcriptional responses. The method was alsoapplied to gene expression profiles from five studies of estrogen exposedfish and both known and potentially novel responses were identified.Conclusions The method described in this paper will further increasethe potential and reliability of meta-analysis of gene expression profilesfrom evolutionarily distant species. The method has been implemented in R andis freely available at http://bioinformatics.math.chalmers.se/Xspecies/.
BMC Bioinformatics 02/2013; 14(1):70. · 2.75 Impact Factor
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Kevin D. Hyde,
Dhanushka Udayanga,
Dimuthu S. Manamgoda,
Leho Tedersoo,
Ellen Larsson,
Kessy Abarenkov,
Yann J. K. Bertrand,
Bengt Oxelman,
Martin Hartmann,
Håvard Kauserud,
Martin Ryberg, Erik Kristiansson,
Henrik R. Nilsson
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ABSTRACT: The last twenty years have witnessed molecular data emerge as a primary
research instrument in most branches of mycology. Fungal systematics, taxonomy,
and ecology have all seen tremendous progress and have undergone rapid,
far-reaching changes as disciplines in the wake of continual improvement in DNA
sequencing technology. A taxonomic study that draws from molecular data
involves a long series of steps, ranging from taxon sampling through the
various laboratory procedures and data analysis to the publication process. All
steps are important and influence the results and the way they are perceived by
the scientific community. The present paper provides a reflective overview of
all major steps in such a project with the purpose to assist research students
about to begin their first study using DNA-based methods. We also take the
opportunity to discuss the role of taxonomy in biology and the life sciences in
general in the light of molecular data. While the best way to learn molecular
methods is to work side by side with someone experienced, we hope that the
present paper will serve to lower the learning threshold for the reader.
02/2013;
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ABSTRACT: The physiology and reproductive performance of eelpout (Zoarces viviparus) have been monitored along the Swedish coast for more than three decades. In this study, transcriptomic profiling was applied for the first time as an exploratory tool to search for new potential candidate biomarkers and to investigate possible stress responses in fish collected from a chronically polluted area. An oligonucleotide microarray with more than 15,000 sequences was used to assess differentially expressed hepatic mRNA levels in female eelpout collected from the contaminated area at Göteborg harbor compared to fish from a national reference site, Fjällbacka. Genes involved in apoptosis and DNA damage (e.g., SMAC/diablo homolog and DDIT4/DNA-damage-inducible protein transcript 4) had higher mRNA expression levels in eelpout from the harbor compared to the reference site, whereas mRNA expression of genes involved in the innate immune system (e.g., complement components and hepcidin) and protein transport/folding (e.g., signal recognition particle and protein disulfide-isomerase) were expressed at lower levels. Gene Ontology enrichment analysis revealed that genes involved biological processes associated with protein folding, immune responses and complement activation were differentially expressed in the harbor eelpout compared to the reference site. The differential mRNA expression of selected genes involved in apoptosis/DNA damage and in the innate immune system was verified by quantitative PCR, using the same fish in addition to eelpout captured four years later. Thus, our approach has identified new potential biomarkers of pollutant exposure and has generated hypotheses on disturbed physiological processes in eelpout. Despite a higher mRNA expression of genes related to apoptosis (e.g., diablo homolog) in eelpout captured in the harbor there were no significant differences in the number of TUNEL-positive apoptotic cells between sites. The mRNA level of genes involved in apoptosis/DNA damage and the status of the innate immune system in fish species captured in polluted environments should be studied in more detail to lay the groundwork for future biomonitoring studies.
Aquatic toxicology (Amsterdam, Netherlands) 12/2012; 130-131C:58-67. · 3.12 Impact Factor
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ABSTRACT: The Patancheru area near Hyderabad in India is recognized as a key link in the global supply chain for many bulk drugs. A central treatment plant receives wastewater from approximately 90 different manufacturers, and the resulting complex effluent has contaminated surface, ground, and drinking water in the region. Ecotoxicological testing of the effluent has shown adverse effects for several organisms, including aquatic vertebrates, at high dilutions. In addition, a recent study of microbial communities in river sediment indicated that the contamination of antibiotic substances might contribute to the emergence and spread of antibiotic resistance genes. In an attempt to start investigating how exposure to effluent-contaminated water may directly affect humans and other terrestrial vertebrates, rats were tube-fed effluent. Several pharmaceuticals present in the effluent could be detected in rat blood serum at low concentrations. However, results from exploratory microarray and quantitative polymerase chain reaction assays indicated no marked effects on hepatic gene transcription after 5 d of exposure. Neither did clinical analysis of blood serum constituents, used as biomarkers for human disease, reveal any significant changes, nor was there any weight gain. Taken together, the authors could not find evidence for any acute toxicity in the rat; however, the authors cannot rule out that higher doses of effluent or a longer exposure time may still be associated with risks for terrestrial vertebrates. Environ. Toxicol. Chem. © 2012 SETAC.
Environmental Toxicology and Chemistry 12/2012; · 2.81 Impact Factor
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ABSTRACT: Background. Gastrointestinal stromal tumors (GISTs) can be effectively treated with tyrosine kinase inhibitors (TKIs). However, some patients with GIST develop drug resistance, and alternative treatment strategies are therefore needed. The aim of this study was to analyze the expression of somatostatin receptors (SSTR) in GIST as a target for peptide receptor-mediated radiotherapy (PRRT). Material and methods. Expression profiling of SSTR1-5 was performed on biopsies from 34 GISTs (16 gastric tumors, 15 small intestinal tumors, and three rectal tumors). SSTR scintigraphy ((111)In-octreotide) and measurement of (111)In activity in tumor specimens was performed in seven patients. Uptake and internalization of (177)Lu- octreotate was studied in primary cell cultures from two patients. Results. Quantitative PCR analysis showed expression of SSTR1 and SSTR2 in the majority of tumors, while SSTR3-5 were expressed at low levels. Immunohistochemical analysis confirmed the presence of SSTR1 and SSTR2 proteins in all GISTs, and SSTR3-5 in a subset of tumors. Diagnostic imaging by SSTR scintigraphy, using (111)In-octreotide, demonstrated tumor uptake of (111)In in three of six GIST patients. Measurement of (111)In activity in excised tumor specimens from five patients gave tumor-to-blood (T/B) activity ratios of between eight and 96. Tumor cells in primary culture (gastric and small intestinal GIST) specifically bound and internalized (177)Lu when incubated with the therapeutic compound (177)Lu-octreotate for 4-48 hours (p < 0.05). Conclusion. Peptide receptor-mediated radiotherapy via SSTR may provide a novel treatment strategy in carefully selected GIST patients with TKI-resistant tumors.
Acta oncologica (Stockholm, Sweden) 11/2012; · 2.27 Impact Factor
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ABSTRACT: Ketoprofen and diclofenac are non-steroidal anti-inflammatory drugs (NSAIDs) often used for similar indications, and both are frequently found in surface waters. Diclofenac affects organ histology and gene expression in fish at around 1 μg/L. Here, we exposed rainbow trout to ketoprofen (1, 10 and 100 μg/L) to investigate if this alternative causes less risk for pharmacological responses in fish. The bioconcentration factor from water to fish blood plasma was <0.05 (4 for diclofenac based on previous studies). Ketoprofen only reached up to 0.6 ‰ of the human therapeutic plasma concentration, thus the probability of target-related effects was estimated to be fairly low. Accordingly, a comprehensive analysis of hepatic gene expression revealed no consistent responses. In some contrast, trout exposed to undiluted, treated sewage effluents bioconcentrated ketoprofen and other NSAIDs much more efficiently, according to a meta-analysis of recent studies. Neither of the setups is however an ideal representation of the field situation. If a controlled exposure system with a single chemical in pure water is a reasonable representation of the environment, then the use of ketoprofen is likely to pose a lower risk for wild fish than diclofenac, but if bioconcentration factors from effluent-exposed fish are applied, the risks may be more similar.
Journal of hazardous materials 05/2012; 229-230:100-6. · 4.14 Impact Factor
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ABSTRACT: Effluents from sewage treatment plants contain a mixture of micropollutants with the potential of harming aquatic organisms. Thus, addition of advanced treatment techniques to complement existing conventional methods has been proposed. Some of the advanced techniques could, however, potentially produce additional compounds affecting exposed organisms by unknown modes of action. In the present study the aim was to improve our understanding of how exposure to different sewage effluents affects fish. This was achieved by explorative microarray and quantitative PCR analyses of hepatic gene expression, as well as relative organ sizes of rainbow trout exposed to different sewage effluents (conventionally treated, granular activated carbon, ozonation (5 or 15 mg/L), 5 mg/L ozone plus a moving bed biofilm reactor, or UV-light treatment in combination with hydrogen peroxide). Exposure to the conventionally treated effluent caused a significant increase in liver and heart somatic indexes, an effect removed by all other treatments. Genes connected to xenobiotic metabolism, including cytochrome p450 1A, were differentially expressed in the fish exposed to the conventionally treated effluents, though only effluent treatment with granular activated carbon or ozone at 15 mg/L completely removed this response. The mRNA expression of heat shock protein 70 kDa was induced in all three groups exposed to ozone-treated effluents, suggesting some form of added stress in these fish. The induction of estrogen-responsive genes in the fish exposed to the conventionally treated effluent was effectively reduced by all investigated advanced treatment technologies, although the moving bed biofilm reactor was least efficient. Taken together, granular activated carbon showed the highest potential of reducing responses in fish induced by exposure to sewage effluents.
Science of The Total Environment 05/2012; 427-428:106-14. · 3.29 Impact Factor
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R. Henrik Nilsson,
Leho Tedersoo,
Kessy Abarenkov,
Martin Ryberg, Erik Kristiansson,
Martin Hartmann,
Conrad L. Schoch,
Johan A. A. Nylander,
Johannes Bergsten,
Teresita M. Porter,
Ari Jumpponen,
Parag Vaishampayan,
Otso Ovaskainen,
Nils Hallenberg,
Johan Bengtsson-Palme,
K. Martin Eriksson,
Karl-Henrik Larsson,
Ellen Larsson,
Urmas Koeljalg
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ABSTRACT: Molecular data form an important research tool in most branches of mycology. A non-trivial proportion of the public fungal DNA sequences are, however, compromised in terms of quality and reliability, contributing noise and bias to sequence-borne inferences such as phylogenetic analysis, diversity assessment, and barcoding. In this paper we discuss various aspects and pitfalls of sequence quality assessment. Based on our observations, we provide a set of guidelines to assist in manual quality management of newly generated, near-full-length (Sanger-derived) fungal ITS sequences and to some extent also sequences of shorter read lengths, other genes or markers, and groups of organisms. The guidelines are intentionally non-technical and do not require substantial bioinformatics skills or significant computational power. Despite their simple nature, we feel they would have caught the vast majority of the severely compromised ITS sequences in the public corpus. Our guidelines are nevertheless not infallible, and common sense and intuition remain important elements in the pursuit of compromised sequence data. The guidelines focus on basic sequence authenticity and reliability of the newly generated sequences, and the user may want to consider additional resources and steps to accomplish the best possible quality control. A discussion on the technical resources for further sequence quality management is therefore provided in the supplementary material.
MycoKeys. 01/2012; 4:37-63.
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ABSTRACT: Diclofenac is a nonsteroidal anti-inflammatory drug frequently found in the aquatic environment. Previous studies have reported histological changes in the liver, kidney, and gills of fish at concentrations similar to those measured in treated sewage effluents (approximately 1 µg/L). Analyses or predictions of blood plasma levels in fish allow a direct comparison with human therapeutic plasma levels and may therefore be used to indicate a risk for pharmacological effects in fish. To relate internal exposure to a pharmacological interaction, we investigated global hepatic gene expression together with bioconcentration in blood plasma and liver of rainbow trout (Oncorhynchus mykiss) exposed to waterborne diclofenac. At the highest exposure concentration (81.5 µg/L), the fish plasma concentration reached approximately 88% of the human therapeutic levels (C(max) ) after two weeks. Using an oligonucleotide microarray followed by quantitative PCR, we found extensive effects on hepatic gene expression at this concentration, and some genes were found to be regulated down to the lowest exposure concentration tested (1.6 µg/L), corresponding to a plasma concentration approximately 1.5% of the human C(max) . Thus, at concentrations detected in European surface waters, diclofenac can affect the expression of multiple genes in exposed fish. Functional analysis of differentially expressed genes revealed effects on biological processes such as inflammation and the immune response, in agreement with the mode of action of diclofenac in mammals. In contrast to some previously reported results, the bioconcentration factor was found to be stable (4.02 ± 0.75 for blood plasma and 2.54 ± 0.36 for liver) regardless of the water concentration.
Environmental Toxicology and Chemistry 06/2011; 30(9):2126-34. · 2.81 Impact Factor
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ABSTRACT: Medetomidine is under evaluation for use as an antifouling agent, and its effects on non-target aquatic organisms are therefore of interest. In this study, rainbow trout was exposed to low (0.5 and 5.0nM) concentrations of medetomidine for up to 54 days. Recently we have reported on effects on paleness and melanophore aggregation of medetomidine in these fish. Here, specific growth rates were investigated together with a broad set of physiological parameters including plasma levels of growth hormone (GH), insulin-like growth factor-I (IGF-I) and leptin, glucose and haemoglobin (Hb), hematocrit (Ht), condition factor, liver and heart somatic indexes (LSI, HSI). Hepatic enzyme activities of CYP1A (EROD activity), glutathione S-transferases (GST) and glutathione reductase (GR) were also measured. Additionally, hepatic mRNA expression was analysed through microarray and quantitative PCR in fish sampled after 31 days of exposure. Medetomidine at both concentrations significantly lowered blood glucose levels and the higher concentration significantly reduced the LSI. The mRNA expression analysis revealed few differentially expressed genes in the liver and the false discovery rate was high. Taken together, the results suggest that medetomidine at investigated concentrations could interfere with carbohydrate metabolism of exposed fish but without any clear consequences for growth.
Comparative Biochemistry and Physiology Part C Toxicology & Pharmacology 06/2011; 154(3):234-41. · 2.62 Impact Factor
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ABSTRACT: The high and sometimes inappropriate use of antibiotics has accelerated the development of antibiotic resistance, creating a major challenge for the sustainable treatment of infections world-wide. Bacterial communities often respond to antibiotic selection pressure by acquiring resistance genes, i.e. mobile genetic elements that can be shared horizontally between species. Environmental microbial communities maintain diverse collections of resistance genes, which can be mobilized into pathogenic bacteria. Recently, exceptional environmental releases of antibiotics have been documented, but the effects on the promotion of resistance genes and the potential for horizontal gene transfer have yet received limited attention. In this study, we have used culture-independent shotgun metagenomics to investigate microbial communities in river sediments exposed to waste water from the production of antibiotics in India. Our analysis identified very high levels of several classes of resistance genes as well as elements for horizontal gene transfer, including integrons, transposons and plasmids. In addition, two abundant previously uncharacterized resistance plasmids were identified. The results suggest that antibiotic contamination plays a role in the promotion of resistance genes and their mobilization from environmental microbes to other species and eventually to human pathogens. The entire life-cycle of antibiotic substances, both before, under and after usage, should therefore be considered to fully evaluate their role in the promotion of resistance.
PLoS ONE 01/2011; 6(2):e17038. · 4.09 Impact Factor
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ABSTRACT: The internal transcribed spacer (ITS) region of the nuclear ribosomal repeat unit holds a central position in the pursuit of the taxonomic affiliation of fungi recovered through environmental sampling. Newly generated fungal ITS sequences are typically compared against the International Nucleotide Sequence Databases for a species or genus name using the sequence similarity software suite blast. Such searches are not without complications however, and one of them is the presence of chimeric entries among the query or reference sequences. Chimeras are artificial sequences, generated unintentionally during the polymerase chain reaction step, that feature sequence data from two (or possibly more) distinct species. Available software solutions for chimera control do not readily target the fungal ITS region, but the present study introduces a blast-based open source software package (available at http://www.emerencia.org/chimerachecker.html) to examine newly generated fungal ITS sequences for the presence of potentially chimeric elements in batch mode. We used the software package on a random set of 12 300 environmental fungal ITS sequences in the public sequence databases and found 1.5% of the entries to be chimeric at the ordinal level after manual verification of the results. The proportion of chimeras in the sequence databases can be hypothesized to increase as emerging sequencing technologies drawing from pooled DNA samples are becoming important tools in molecular ecology research.
Molecular Ecology Resources 11/2010; 10(6):1076-1081. · 3.06 Impact Factor
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ABSTRACT: In gastrointestinal stromal tumors (GISTs), KIT exon 11 deletions are associated with poor prognosis. The aim of this study was to determine the gene expression profiles of GISTs carrying KIT exon 11 deletions and to identify genes associated with poor prognosis. Expression profiling was performed on nine tumors with KIT exon 11 deletions and 7 without KIT exon 11 mutations using oligonucleotide microarrays. In addition, gene expression profiles for 35 GISTs were analyzed by meta-analysis. Expression of CD133 (prominin-1) protein was examined by tissue microarray (TMA) analysis of 204 GISTs from a population-based study in western Sweden. Survival analysis was performed on patients subjected to R0 resection (n=180) using the Cox proportional hazards model. Gene expression profiling, meta-analysis, and qPCR showed up regulation of CD133 in GISTs carrying KIT exon 11 deletions. Immunohistochemical analysis on TMA confirmed CD133 expression in 28% of all tumors. CD133 positivity was more frequent in gastric GISTs (48%) than in small intestinal GISTs (4%). CD133 positivity was also more frequent in GISTs with KIT exon 11 mutations (41%) than in tumors with mutations in KIT exon 9, platelet-derived growth factor receptor α (PDGFRA), or wild-type tumors (0-17%). Univariate survival analysis showed a significant correlation between the presence of CD133 protein and shorter overall survival (hazard ratio=2.23, p=0.027). Multivariate analysis showed that CD133 provided additional information on patient survival compared to age, sex, National Institutes of Health (NIH) risk group and mutational status. CD133 is expressed in a subset of predominantly gastric GISTs with KIT exon 11 mutations and poor prognosis.
International Journal of Cancer 11/2010; 129(5):1149-61. · 5.44 Impact Factor
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ABSTRACT: Medetomidine is a new antifouling agent, and its effects in non-target aquatic organisms have been investigated. Earlier short-term studies in fish have shown a skin lightening response to medetomidine, but effects after chronic exposure have not been studied. In fish, the dark pigment melanin is contained within specialized cells, melanophores. Medetomidine binds to the melanophore alpha2-adrenoceptor, which stimulates pigment aggregation resulting in the light appearance. In the present study, rainbow trout (Oncorhynchus mykiss) was long-term exposed to 0.5 and 5.0 nM of medetomidine via water for 54 d. The fish were then photographed for paleness quantification and the images were analyzed using ImageJ analysis software. Additionally, scales were removed and used for in vitro function studies of the melanophores, monitoring the response to melanophore stimulating hormone (MSH) and subsequent medetomidine addition. The number of melanophores was also investigated. As a result of the medetomidine exposure, fish from the 5 nM treatment were significantly paler than control fish and the melanophores from these fishes were also more aggregated. Melanophores from all the treatments were functional, responding to MSH by dispersion and to subsequent medetomidine by aggregation. However, the results indicate a difference in sensitivity among treatments. The number of melanophores in the scales did not change significantly after long term exposure to medetomidine. These results suggest that the observed paleness may be reversible, even after chronic exposure.
Chemosphere 08/2010; 80(9):1050-5. · 3.21 Impact Factor
