| 1. |
- Byström, Pär, et al.
(författare)
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Declining coastal piscivore populations in the Baltic Sea : where and when do sticklebacks matter?
- 2015
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Ingår i: Ambio. - : Springer Science and Business Media LLC. - 0044-7447 .- 1654-7209. ; 44:Suppl 3, s. S462-S471
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Tidskriftsartikel (refereegranskat)abstract
- Intraguild predation interactions make fish communities prone to exhibit alternative stable states with either piscivore or prey fish dominance. In the Baltic Sea, local declines of coastal piscivores like perch (Perca fluviatilis) have been observed to coincide with high densities of sticklebacks (Gasterosteus aculeatus). Mechanisms behind this shift between piscivore and stickleback dominance were studied both experimentally and in field. Results showed that predation by sticklebacks has a strong negative effect on perch larvae survival, but this effect rapidly decreases with increasing perch size, likely due to gape limitations and digestion constraints in sticklebacks. Large spatial and temporal variations in patterns of stickleback migration into perch spawning sites were observed. Whether or not high density of sticklebacks will cause declines in coastal piscivore populations is suggested to depend on the availability of spawning sites in which sticklebacks do not migrate into or arrive late in the reproduction season of coastal piscivores.
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| 2. |
- Hoffman, Daniel E., et al.
(författare)
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Changes in diurnal patterns within the Populus transcriptome and metabolome in response to photoperiod variation
- 2010
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Ingår i: Plant, Cell and Environment. - : Wiley. - 0140-7791 .- 1365-3040. ; 33:8, s. 1298-1313
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Tidskriftsartikel (refereegranskat)abstract
- Changes in seasonal photoperiod provides an important environmental signal that affects the timing of winter dormancy in perennial, deciduous, temperate tree species, such as hybrid aspen (Populus tremula x Populus tremuloides). In this species, growth cessation, cold acclimation and dormancy are induced in the autumn by the detection of day-length shortening that occurs at a given critical day length. Important components in the detection of such day-length changes are photoreceptors and the circadian clock, and many plant responses at both the gene regulation and metabolite levels are expected to be diurnal. To directly examine this expectation and study components in these events, here we report transcriptomic and metabolomic responses to a change in photoperiod from long to short days in hybrid aspen. We found about 16% of genes represented on the arrays to be diurnally regulated, as assessed by our pre-defined criteria. Furthermore, several of these genes were involved in circadian-associated processes, including photosynthesis and primary and secondary metabolism. Metabolites affected by the change in photoperiod were mostly involved in carbon metabolism. Taken together, we have thus established a molecular catalog of events that precede a response to winter.
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| 3. |
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| 4. |
- Jeppsson, Tobias, et al.
(författare)
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Oh, how we pick and choose: on theoretical constructs in subfields of ecology
- 2016
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Ecology consists of a large number of theoretical constructs, empirical patterns and methods; a pool from which applied ecology can draw ideas when exploring practical problems. Subfields of applied ecology - including pest control, conservation, and wildlife management - deal with the management of biological populations, and should therefore rest on the same ecological foundations. But is this really the case? We study this issue by analyzing recent citation rates (2010-2014) to more than 130 highly cited, classic publications, covering a wide range of topics. Using ordination methods, we find a clear clustering of journals, where conservation occupies another part of the ordination space than pest control. Classifying papers into broad topics reveals that the ordination patterns are driven by striking differences in how often ecological concepts are used in different subfields. While some patterns are easy to understand, e.g. the use of biodiversity concepts in conservation, others are left unexplained. For instance, the lack of spatial concepts and competition in pest control, predation in conservation journals, and foodweb ideas in wildlife journals are harder to understand. Microbial ecology also appears devoid of large parts of ecological theory. These patterns imply distinct divides within ecology, where subfields selectively use certain parts of ecological theory. Therefore, we argue that work in applied ecology would benefit from broader theoretical perspectives. Collaboration and inspiration across sub-disciplines could be one way to achieve this, perhaps inspiring novel research directions.
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| 5. |
- Karlsson, Jan, et al.
(författare)
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Response to Comment: Terrestrial support of pelagic consumers in unproductive lakes : uncertainty and potential in assessments using stable isotopes
- 2014
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Ingår i: Limnology and Oceanography. - : Wiley. - 1939-5590 .- 0024-3590. ; 59:5, s. 1800-1803
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Tidskriftsartikel (refereegranskat)abstract
- The use of stable carbon isotopes (d13C) has played a key role in estimation of the proportion of aquatic consumer biomass derived from terrestrial organic matter (OM; i.e., allochthony; Meili et al. 1996; Grey et al. 2001; Pace et al. 2004). However, the use of d13C for assessing allochthony has shortcomings because of the small natural separation between terrestrial and aquatic isotopic end members and the difficulty in physically separating autotrophic phytoplankton for d13C analysis from other components of particulate organic carbon (POC). These shortcomings are especially problematic in unproductive lakes where the phytoplankton are dominated by small and mixotrophic species, and where the internal photosynthesis is low compared to the input of terrestrial OM (Algesten et al. 2004; Jansson et al. 2008). Several alternative analyses and approaches have been tested to overcome these methodological limitations, including compound-specific analyses of phytoplankton biomarkers (Pace et al. 2007; Van Den Meersche et al. 2009; Berggren et al. 2014), manipulation of phytoplankton d13C by addition of 13C-labeled dissolved inorganic carbon (Pace et al. 2004; Taipale et al. 2008), addition of 13C-enriched OM (Karlsson et al. 2007; Bartels et al. 2012), and various mass balance and modeling approaches (Marty and Planas 2008; Mohamed and Taylor 2009; Berggren et al. 2010). Still, a generally applicable method is lacking, implying that the problems with assessing d13C of phytoplankton is a major limitation in the use of d13C for estimating allochthony with the accuracy needed for detailed understanding of food web dynamics.
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| 6. |
- Karlsson, Jan, et al.
(författare)
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Terrestrial organic matter support of lake food webs : Evidence from lake metabolism and stable hydrogen isotopes of consumers
- 2012
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Ingår i: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 57:4, s. 1042-1048
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Tidskriftsartikel (refereegranskat)abstract
- We quantified the utilization of terrestrial organic matter (OM) in the food web of a humic lake by analyzing the metabolism and the consumers' stable isotopic (C, H, N) composition in benthic and pelagic habitats. Terrestrial OM inputs (3 g C m(-2) d(-1)) to the lake greatly exceeded autochthonous OM production (3 mg C m(-2) d(-1)) in the lake. Heterotrophic bacterial growth (19 mg C m(-2) d(-1)) and community respiration (115 mg C m(-2) d(-1)) were high relative to algal photosynthesis and were predominantly (> 85%) supported by terrestrial OM in both habitats. Consequently, terrestrial OM fueled most (85%) of the total production at the base of the lake's food web (i.e., the sum of primary and bacterial production). Despite the uncertainties of quantitatively estimating resource use based on stable isotopes, terrestrial OM clearly also supported around half the zooplankton (47%), macrozoobenthos (63%), and fish (57%) biomass. These results indicate that, although rates of terrestrial OM inputs were around three orders of magnitude greater than that of autochthonous OM production, the use of the two resources by higher trophic levels was roughly equal. The disproportionally low reliance on terrestrial OM at higher trophic levels, compared with its high rates of input and high support of basic biomass production in the lake, suggests that autochthonous resources could not be completely replaced by terrestrial resources and indicates an upper limit to terrestrial support of lake food webs.
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| 7. |
- Kusano, Miyako, et al.
(författare)
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Metabolite signature during short-day induced growth cessation in populus
- 2011
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 2
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Tidskriftsartikel (refereegranskat)abstract
- The photoperiod is an important environmental signal for plants, and influences a wide range of physiological processes. For woody species in northern latitudes, cessation of growth is induced by short photoperiods. In many plant species, short photoperiods stop elongational growth after a few weeks. It is known that plant daylength detection is mediated by Phytochrome A (PHYA) in the woody hybrid aspen species. However, the mechanism of dormancy involving primary metabolism remains unclear. We studied changes in metabolite profiles in hybrid aspen leaves (young, middle, and mature leaves) during short-day-induced growth cessation, using a combination of gas chromatography–time-of-flight mass spectrometry, and multivariate projection methods. Our results indicate that the metabolite profiles in mature source leaves rapidly change when the photoperiod changes. In contrast, the differences in young sink leaves grown under long and short-day conditions are less distinct. We found short daylength induced growth cessation in aspen was associated with rapid changes in the distribution and levels of diverse primary metabolites. In addition, we conducted metabolite profiling of leaves of PHYA overexpressor (PHYAOX) and those of the control to find the discriminative metabolites between PHYAOX and the control under the short-day conditions. The metabolite changes observed in PHYAOX leaves, together with those in the source leaves, identified possible candidates for the metabolite signature (e.g., 2-oxo-glutarate, spermidine, putrescine, 4-amino-butyrate, and tryptophan) during short-day-induced growth cessation in aspen leaves.
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| 8. |
- Srivastava, Vaibhav, et al.
(författare)
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OnPLS integration of transcriptomic, proteomic and metabolomic data shows multi-level oxidative stress responses in the cambium of transgenic hipI- superoxide dismutase Populus plants
- 2013
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Ingår i: BMC Genomics. - : BioMed Central. - 1471-2164. ; 14
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Reactive oxygen species (ROS) are involved in the regulation of diverse physiological processes in plants, including various biotic and abiotic stress responses. Thus, oxidative stress tolerance mechanisms in plants are complex, and diverse responses at multiple levels need to be characterized in order to understand them. Here we present system responses to oxidative stress in Populus by integrating data from analyses of the cambial region of wild-type controls and plants expressing high-isoelectric-point superoxide dismutase (hipI-SOD) transcripts in antisense orientation showing a higher production of superoxide. The cambium, a thin cell layer, generates cells that differentiate to form either phloem or xylem and is hypothesized to be a major reason for phenotypic perturbations in the transgenic plants. Data from multiple platforms including transcriptomics (microarray analysis), proteomics (UPLC/QTOF-MS), and metabolomics (GC-TOF/MS, UPLC/MS, and UHPLC-LTQ/MS) were integrated using the most recent development of orthogonal projections to latent structures called OnPLS. OnPLS is a symmetrical multi-block method that does not depend on the order of analysis when more than two blocks are analysed. Significantly affected genes, proteins and metabolites were then visualized in painted pathway diagrams.RESULTS: The main categories that appear to be significantly influenced in the transgenic plants were pathways related to redox regulation, carbon metabolism and protein degradation, e.g. the glycolysis and pentose phosphate pathways (PPP). The results provide system-level information on ROS metabolism and responses to oxidative stress, and indicate that some initial responses to oxidative stress may share common pathways.CONCLUSION: The proposed data evaluation strategy shows an efficient way of compiling complex, multi-platform datasets to obtain significant biological information.
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| 9. |
- Trupp, Miles, et al.
(författare)
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Metabolite and peptide levels in plasma and CSF differentiating healthy controls from patients with newly diagnosed Parkinson's disease
- 2014
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Ingår i: Journal of Parkinson's Disease. - : Taylor & Francis. - 1877-7171 .- 1877-718X. ; 4:3, s. 549-560
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Tidskriftsartikel (refereegranskat)abstract
- Background: Parkinson's disease (PD) is a progressive, multi-focal neurodegenerative disease for which there is no effective disease modifying treatment. A critical requirement for designing successful clinical trials is the development of robust and reproducible biomarkers identifying PD in preclinical stages. Objective: To investigate the potential for a cluster of biomarkers visualized with multiple analytical platforms to provide a clinically useful tool. Methods: Gas Chromatography-Mass Spectrometry (GC-TOFMS) based metabolomics and immunoassay-based protein/peptide analyses on samples from patients with PD diagnosed in Northern Sweden. Low molecular weight compounds from both plasma and cerebrospinal fluid (CSF) from 20 healthy subjects (controls) and 20 PD patients at the time of diagnosis (baseline) were analyzed. Results: In plasma, we found a significant increase in several amino acids and a decrease in C16-C18 saturated and unsaturated fatty acids in patients as compared to control subjects. We also observed an increase in plasma levels of pyroglutamate and 2-oxoisocaproate (ketoleucine) that may be indicative of increased metabolic stress in patients. In CSF, there was a generally lower level of metabolites in PD as compared to controls, with a specific decrease in 3-hydroxyisovaleric acid, tryptophan and creatinine. Multivariate analysis and modeling of metabolites indicates that while the PD samples can be separated from control samples, the list of detected compounds will need to be expanded in order to define a robust predictive model. CSF biomarker immunoassays of candidate peptide/protein biomarkers revealed a significant decrease in the levels of A beta-38 and A beta-42, and an increase in soluble APP alpha in CSF of patients. Furthermore, these peptides showed significant correlations to each other, and positive correlations to the CSF levels of several 5- and 6-carbon sugars. However, combining these metabolites and proteins/peptides into a single model did not significantly improve the statistical analysis. Conclusions: Together, this metabolomics study has detected significant alterations in plasma and CSF levels of a cluster of amino acids, fatty acids and sugars based on clinical diagnosis and levels of known protein and peptide biomarkers.
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| 10. |
- Wuolikainen, Anna, et al.
(författare)
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Multi-platform mass spectrometry analysis of the CSF and plasma metabolomes of rigorously matched amyotrophic lateral sclerosis, Parkinson's disease and control subjects
- 2016
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Ingår i: Molecular Biosystems. - : Royal Society of Chemistry (RSC). - 1742-206X .- 1742-2051. ; 12:4, s. 1287-1298
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Tidskriftsartikel (refereegranskat)abstract
- Amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) are protein-aggregation diseases that lack clear molecular etiologies. Biomarkers could aid in diagnosis, prognosis, planning of care, drug target identification and stratification of patients into clinical trials. We sought to characterize shared and unique metabolite perturbations between ALS and PD and matched controls selected from patients with other diagnoses, including differential diagnoses to ALS or PD that visited our clinic for a lumbar puncture. Cerebrospinal fluid (CSF) and plasma from rigorously age-, sex- and sampling-date matched patients were analyzed on multiple platforms using gas chromatography (GC) and liquid chromatography (LC)-mass spectrometry (MS). We applied constrained randomization of run orders and orthogonal partial least squares projection to latent structure-effect projections (OPLS-EP) to capitalize upon the study design. The combined platforms identified 144 CSF and 196 plasma metabolites with diverse molecular properties. Creatine was found to be increased and creatinine decreased in CSF of ALS patients compared to matched controls. Glucose was increased in CSF of ALS patients and alpha-hydroxybutyrate was increased in CSF and plasma of ALS patients compared to matched controls. Leucine, isoleucine and ketoleucine were increased in CSF of both ALS and PD. Together, these studies, in conjunction with earlier studies, suggest alterations in energy utilization pathways and have identified and further validated perturbed metabolites to be used in panels of biomarkers for the diagnosis of ALS and PD.
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