uu.seUppsala University Publications
Change search
Link to record
Permanent link

Direct link
BETA
Källman, Thomas
Publications (10 of 17) Show all publications
Leal, L., Talla, V., Källman, T., Friberg, M., Wiklund, C., Dinca, V., . . . Backström, N. (2018). Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation. Molecular Ecology, 27(4), 935-948
Open this publication in new window or tab >>Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation
Show others...
2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 4, p. 935-948Article in journal (Refereed) Published
Abstract [en]

In temperate latitudes, many insects enter diapause (dormancy) during the cold season, a period during which developmental processes come to a standstill. The wood white (Leptidea sinapis) is a butterfly species distributed across western Eurasia that shows photoperiod-induced diapause with variation in critical day-length across populations at different latitudes. We assembled transcriptomes and estimated gene expression levels at different developmental stages in experimentally induced directly developing and diapausing cohorts of a single Swedish population of L. sinapis to investigate the regulatory mechanisms underpinning diapause initiation. Different day lengths resulted in expression changes of developmental genes and affected the rate of accumulation of signal molecules, suggesting that diapause induction might be controlled by increased activity of monoamine neurotransmitters in larvae reared under short-day light conditions. Expression differences between light treatment groups of two monoamine regulator genes (DDC and ST) were observed already in instar III larvae. Once developmental pathways were irreversibly set at instar V, a handful of genes related to dopamine production were differentially expressed leading to a significant decrease in expression of global metabolic genes and increase in expression of genes related to fatty acid synthesis and sequestration. This is in line with a time-dependent (hour-glass) model of diapause regulation where a gradual shift in the concentration of monoamine neurotransmitters and their metabolites during development of larvae under short-day conditions leads to increased storage of fat, decreased energy expenditures, and ultimately developmental stasis at the pupal stage.

Place, publisher, year, edition, pages
WILEY, 2018
Keywords
developmental plasticity, diapause, gene expression, hour-glass model, Lepidoptera, monoamine neurotransmitter
National Category
Developmental Biology
Identifiers
urn:nbn:se:uu:diva-351766 (URN)10.1111/mec.14501 (DOI)000428797100010 ()29411442 (PubMedID)
Funder
Swedish Research Council, 2013-4508]Science for Life Laboratory - a national resource center for high-throughput molecular bioscience, Backstrom_2014Knut and Alice Wallenberg Foundation
Available from: 2018-06-04 Created: 2018-06-04 Last updated: 2018-08-28Bibliographically approved
Jordan-Pla, A., Yu, S., Waldholm, J., Källman, T., Farrants, A.-K. O. & Visa, N. (2018). SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma. BMC Genomics, 19, Article ID 367.
Open this publication in new window or tab >>SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma
Show others...
2018 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 19, article id 367Article in journal (Refereed) Published
Abstract [en]

Background: Brahma (BRM) is the only catalytic subunit of the SVVI/SNF chromatin-remodeling complex of Drosophila melanogaster. The function of SWI/SNF in transcription has long been attributed to its ability to remodel nucleosomes, which requires the ATPase activity of BRM. However, recent studies have provided evidence for a non-catalytic function of BRM in the transcriptional regulation of a few specific genes. Results: Here we have used RNA-seq and ChIP-seq to identify the BRM target genes in 52 cells, and we have used a catalytically inactive BRM mutant (K804R) that is unable to hydrolyze ATP to investigate the magnitude of the non-catalytic function of BRM in transcription regulation. We show that 49% of the BRM target genes in 52 cells are regulated through mechanisms that do not require BRM to have an ATPase activity. We also show that the catalytic and non-catalytic mechanisms of SVVI/SNF regulation operate on two subsets of genes that differ in promoter architecture and are linked to different biological processes. Conclusions: This study shows that the non-catalytic role of SWI/SNF in transcription regulation is far more prevalent than previously anticipated and that the genes that are regulated by SVVI/SNF through ATPase-dependent and ATPase-independent mechanisms have specialized roles in different cellular and developmental processes.

Place, publisher, year, edition, pages
BIOMED CENTRAL LTD, 2018
Keywords
SWI/SNF, Gene expression, Transcription regulation, Drosophila melanogaster
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-357281 (URN)10.1186/s12864-018-4746-2 (DOI)000432702400002 ()29776334 (PubMedID)
Funder
Swedish Research Council
Available from: 2018-08-17 Created: 2018-08-17 Last updated: 2018-08-17Bibliographically approved
Gliga, A. R., Edoff, K., Caputo, F., Källman, T., Blom, H., Karlsson, H. L., . . . Fadeel, B. (2017). Cerium oxide nanoparticles inhibit differentiation of neural stem cells. Scientific Reports, 7, Article ID 9284.
Open this publication in new window or tab >>Cerium oxide nanoparticles inhibit differentiation of neural stem cells
Show others...
2017 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 9284Article in journal (Refereed) Published
Abstract [en]

Cerium oxide nanoparticles (nanoceria) display antioxidant properties and have shown cytoprotective effects both in vitro and in vivo. Here, we explored the effects of nanoceria on neural progenitor cells using the C17.2 murine cell line as a model. First, we assessed the effects of nanoceria versus samarium (Sm) doped nanoceria on cell viability in the presence of the prooxidant, DMNQ. Both particles were taken up by cells and nanoceria, but not Sm-doped nanoceria, elicited a temporary cytoprotective effect upon exposure to DMNQ. Next, we employed RNA sequencing to explore the transcriptional responses induced by nanoceria or Sm-doped nanoceria during neuronal differentiation. Detailed computational analyses showed that nanoceria altered pathways and networks relevant for neuronal development, leading us to hypothesize that nanoceria inhibits neuronal differentiation, and that nanoceria and Sm-doped nanoceria both interfere with cytoskeletal organization. We confirmed that nanoceria reduced neuron specific beta 3-tubulin expression, a marker of neuronal differentiation, and GFAP, a neuroglial marker. Furthermore, using super-resolution microscopy approaches, we could show that both particles interfered with cytoskeletal organization and altered the structure of neural growth cones. Taken together, these results reveal that nanoceria may impact on neuronal differentiation, suggesting that nanoceria could pose a developmental neurotoxicity hazard.

Place, publisher, year, edition, pages
Nature Publishing Group, 2017
National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-335234 (URN)10.1038/s41598-017-09430-8 (DOI)000408441600008 ()28839176 (PubMedID)
Available from: 2017-12-05 Created: 2017-12-05 Last updated: 2018-01-13Bibliographically approved
Porseryd, T., Volkova, K., Caspillo, N. R., Källman, T., Dinnetz, P. & Hallstrom, I. P. (2017). Persistent Effects of Developmental Exposure to 17 alpha-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior. Frontiers in Behavioral Neuroscience, 11, Article ID 69.
Open this publication in new window or tab >>Persistent Effects of Developmental Exposure to 17 alpha-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior
Show others...
2017 (English)In: Frontiers in Behavioral Neuroscience, ISSN 1662-5153, E-ISSN 1662-5153, Vol. 11, article id 69Article in journal (Refereed) Published
Abstract [en]

The synthetic estrogen 17 alpha-ethinylestradiol (EE2) is an endocrine disrupting compound of concern due to its persistence and widespread presence in the aquatic environment. Effects of developmental exposure to low concentrations of EE2 in fish on reproduction and behavior not only persisted to adulthood, but have also been observed to be transmitted to several generations of unexposed progeny. To investigate the possible biological mechanisms of the persistent anxiogenic phenotype, we exposed zebrafish embryos for 80 days post fertilization to 0, 3, and 10 ng/L EE2 (measured concentrations 2.14 and 7.34 ng/L). After discontinued exposure, the animals were allowed to recover for 120 days in clean water. Adult males and females were later tested for changes in stress response and shoal cohesion, and whole-brain gene expression was analyzed with RNA sequencing. The results show increased anxiety in the novel tank and scototaxis tests, and increased shoal cohesion in fish exposed during development to EE2. RNA sequencing revealed 34 coding genes differentially expressed in male brains and 62 in female brains as a result of EE2 exposure. Several differences were observed between males and females in differential gene expression, with only one gene, sv2b, coding for a synaptic vesicle protein, that was affected by EE2 in both sexes. Functional analyses showed that in female brains, EE2 had significant effects on pathways connected to the circadian rhythm, cytoskeleton and motor proteins and synaptic proteins. A large number of non-coding sequences including 19 novel miRNAs were also differentially expressed in the female brain. The largest treatment effect in male brains was observed in pathways related to cholesterol biosynthesis and synaptic proteins. Circadian rhythm and cholesterol biosynthesis, previously implicated in anxiety behavior, might represent possible candidate pathways connecting the transcriptome changes to the alterations to behavior. Further the observed alteration in expression of genes involved in synaptogenesis and synaptic function may be important for the developmental modulations resulting in an anxiety phenotype. This study represents an initial survey of the fish brain transcriptome by RNA sequencing after long-term recovery from developmental exposure to an estrogenic compound.

Keywords
stress behavior, brain transcriptome, 17 alpha-ethinylestradiol, RNA sequencing, developmental exposure, zebrafish, endocrine disrupting compounds, persistent effects
National Category
Neurosciences
Identifiers
urn:nbn:se:uu:diva-322799 (URN)10.3389/fnbeh.2017.00069 (DOI)000400103600001 ()28473760 (PubMedID)
Available from: 2017-06-20 Created: 2017-06-20 Last updated: 2018-01-13Bibliographically approved
Chen, J., Källman, T., Ma, X.-F., Zaina, G., Morgante, M. & Lascoux, M. (2016). Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies. G3: Genes, Genomes, Genetics, 6(7), 1979-1989
Open this publication in new window or tab >>Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies
Show others...
2016 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 7, p. 1979-1989Article in journal (Refereed) Published
Abstract [en]

The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower F-ST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both F-ST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.

Keywords
pooled sequencing, F-ST, allele frequencies, local adaptation
National Category
Genetics
Identifiers
urn:nbn:se:uu:diva-300546 (URN)10.1534/g3.116.028753 (DOI)000379590200018 ()27172202 (PubMedID)
Funder
EU, European Research CouncilSwedish Research Council Formas
Available from: 2016-08-10 Created: 2016-08-09 Last updated: 2017-11-28Bibliographically approved
Brousseau, L., Postolache, D., Lascoux, M., Drouzas, A. D., Källman, T., Leonarduzzi, C., . . . Vendramin, G. G. (2016). Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe. PLoS ONE, 11(7), Article ID e0158216.
Open this publication in new window or tab >>Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe
Show others...
2016 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 7, article id e0158216Article in journal (Refereed) Published
Abstract [en]

Background Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. Methods A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). Results HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. Conclusion Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.

National Category
Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-301423 (URN)10.1371/journal.pone.0158216 (DOI)000380005400037 ()
Available from: 2016-08-23 Created: 2016-08-23 Last updated: 2017-11-28Bibliographically approved
Tsuda, Y., Chen, J., Stocks, M., Källman, T., Sonstebo, J. H., Parducci, L., . . . Lascoux, M. (2016). The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?. Molecular Ecology, 25(12), 2773-2789
Open this publication in new window or tab >>The extent and meaning of hybridization and introgression between Siberian spruce (Picea obovata) and Norway spruce (Picea abies): cryptic refugia as stepping stones to the west?
Show others...
2016 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 12, p. 2773-2789Article in journal (Refereed) Published
Abstract [en]

Boreal species were repeatedly exposed to ice ages and went through cycles of contraction and expansion while sister species alternated periods of contact and isolation. The resulting genetic structure is consequently complex, and demographic inferences are intrinsically challenging. The range of Norway spruce (Picea abies) and Siberian spruce (Picea obovata) covers most of northern Eurasia; yet their geographical limits and histories remain poorly understood. To delineate the hybrid zone between the two species and reconstruct their joint demographic history, we analysed variation at nuclear SSR and mitochondrial DNA in 102 and 88 populations, respectively. The dynamics of the hybrid zone was analysed with approximate Bayesian computation (ABC) followed by posterior predictive STRUCTURE plot reconstruction and the presence of barriers across the range tested with estimated effective migration surfaces. To estimate the divergence time between the two species, nuclear sequences from two well-separated populations of each species were analysed with ABC. Two main barriers divide the range of the two species: one corresponds to the hybrid zone between them, and the other separates the southern and northern domains of Norway spruce. The hybrid zone is centred on the Urals, but the genetic impact of Siberian spruce extends further west. The joint distribution of mitochondrial and nuclear variation indicates an introgression of mitochondrial DNA from Norway spruce into Siberian spruce. Overall, our data reveal a demographic history where the two species interacted frequently and where migrants originating from the Urals and the West Siberian Plain recolonized northern Russia and Scandinavia using scattered refugial populations of Norway spruce as stepping stones towards the west.

Keywords
divergence, Eurasia, introgression, phylogeography, spruce
National Category
Botany Evolutionary Biology
Identifiers
urn:nbn:se:uu:diva-300075 (URN)10.1111/mec.13654 (DOI)000378941800010 ()27087633 (PubMedID)
Funder
Swedish Research Council FormasEU, European Research Council, KBBE-289119
Available from: 2016-08-02 Created: 2016-08-02 Last updated: 2017-11-28Bibliographically approved
Gyllenstrand, N., Karlgren, A., Clapham, D., Holm, K., Hall, A., Gould, P. D., . . . Lagercrantz, U. (2014). No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst). Plant and Cell Physiology, 55(3), 535-550
Open this publication in new window or tab >>No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst)
Show others...
2014 (English)In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 55, no 3, p. 535-550Article in journal (Refereed) Published
Keywords
Picea abies, circadian clock, diurnal cycling, phylogeny, gene expression, delayed fluorescence
National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-192178 (URN)10.1093/pcp/pct199 (DOI)000333096200007 ()
Available from: 2013-01-16 Created: 2013-01-16 Last updated: 2017-12-06Bibliographically approved
Källman, T., De Mita, S., Larsson, H., Gyllenstrand, N., Heuertz, M., Parducci, L., . . . Lascoux, M. (2014). Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]. PLoS ONE, 9(5), e95306
Open this publication in new window or tab >>Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]
Show others...
2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 5, p. e95306-Article in journal (Refereed) Published
Abstract [en]

The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce

National Category
Natural Sciences Genetics Biological Sciences
Identifiers
urn:nbn:se:uu:diva-180367 (URN)10.1371/journal.pone.0095306 (DOI)000338213300010 ()
Available from: 2012-09-05 Created: 2012-09-05 Last updated: 2017-12-07Bibliographically approved
Wang, J., Källman, T., Liu, J., Guo, Q., Wu, Y., Lin, K. & Lascoux, M. (2014). Speciation of two desert poplar species triggered by Pleistocene climatic oscillations. Heredity, 112(2), 156-164
Open this publication in new window or tab >>Speciation of two desert poplar species triggered by Pleistocene climatic oscillations
Show others...
2014 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 112, no 2, p. 156-164Article in journal (Refereed) Published
Abstract [en]

Despite the evidence that the Pleistocene climatic fluctuations have seriously affected the distribution of intraspecific diversity, less is known on its impact on interspecific divergence. In this study, we aimed to test the hypothesis that the divergence of two desert poplar species Populus euphratica Oliv. and P. pruinosa Schrenk. occurred during the Pleistocene. We sequenced 11 nuclear loci in 60 individuals from the two species to estimate the divergence time between them and to test whether gene flow occurred after species separation. Divergence time between the two species was estimated to be 0.66-1.37 million years ago (Ma), a time at which glaciation was at its maximum in China and deserts developed widely in central Asia. Isolation-with-Migration model also indicated that the two species had diverged in the presence of gene flow. We also detected evidence of selection at GO in P. euphratica and to a lesser extent at PhyB2. Together, these results underscore the importance of Pleistocene climate oscillations in triggering plant speciation as a result of habitats divergence.

Keywords
Pleistocene climate changes, speciation, desert poplar, selection signature
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-221004 (URN)10.1038/hdy.2013.87 (DOI)000331625800009 ()
Available from: 2014-03-25 Created: 2014-03-24 Last updated: 2017-12-05Bibliographically approved
Organisations

Search in DiVA

Show all publications