| 1. |
- Ferrari, Raffaele, et al.
(författare)
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Frontotemporal dementia and its subtypes: a genome-wide association study.
- 2014
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Ingår i: Lancet Neurology. - 1474-4465. ; 13:7, s. 686-699
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Tidskriftsartikel (refereegranskat)abstract
- Frontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes-MAPT, GRN, and C9orf72-have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder.
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| 2. |
- Mareschal, Sylvain, et al.
(författare)
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Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML
- 2021
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Ingår i: Blood Advances. - : American Society of Hematology. - 2473-9529 .- 2473-9537. ; 5:4, s. 1003-1016
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Tidskriftsartikel (refereegranskat)abstract
- Although copy number alterations (CNAs) and translocations constitute the backbone of the diagnosis and prognostication of acute myeloid leukemia (AML), techniques used for their assessment in routine diagnostics have not been reconsidered for decades. We used a combination of 2 next-generation sequencing-based techniques to challenge the currently recommended conventional cytogenetic analysis (CCA), comparing the approaches in a series of 281 intensively treated patients with AML. Shallow whole-genome sequencing (sWGS) outperformed CCA in detecting European Leukemia Net (ELN)-defining CNAs and showed that CCA overestimated monosomies and suboptimally reported karyotype complexity. Still, the concordance between CCA and sWGS for all ELN CNA-related criteria was 94%. Moreover, using in silico dilution, we showed that 1 million reads per patient would be enough to accurately assess ELN-defining CNAs. Total genomic loss, defined as a total loss 200 Mb by sWGS, was found to be a better marker for genetic complexity and poor prognosis compared with the CCA-based definition of complex karyotype. For fusion detection, the concordance between CCA and whole-transcriptome sequencing (WTS) was 99%. WTS had better sensitivity in identifying inv(16) and KMT2A rearrangements while showing limitations in detecting lowly expressed PML-RARA fusions. Ligation-dependent reverse transcription polymerase chain reaction was used for validation and was shown to be a fast and reliable method for fusion detection. We conclude that a next-generation sequencing-based approach can replace conventional CCA for karyotyping, provided that efforts are made to cover lowly expressed fusion transcripts.
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| 3. |
- De Frenne, Pieter, et al.
(författare)
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Temperature effects on forest herbs assessed by warming and transplant experiments along a latitudinal gradient
- 2011
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Ingår i: Global Change Biology. - : Wiley. - 1354-1013 .- 1365-2486. ; 17:10, s. 3240-3253
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Tidskriftsartikel (refereegranskat)abstract
- Slow-colonizing forest understorey plants are probably not able to rapidly adjust their distribution range following large-scale climate change. Therefore, the acclimation potential to climate change within their actual occupied habitats will likely be key for their short-and long-term persistence. We combined transplant experiments along a latitudinal gradient with open-top chambers to assess the effects of temperature on phenology, growth and reproductive performance of multiple populations of slow-colonizing understorey plants, using the spring flowering geophytic forb Anemone nemorosa and the early summer flowering grass Milium effusum as study species. In both species, emergence time and start of flowering clearly advanced with increasing temperatures. Vegetative growth (plant height, aboveground biomass) and reproductive success (seed mass, seed germination and germinable seed output) of A. nemorosa benefited from higher temperatures. Climate warming may thus increase future competitive ability and colonization rates of this species. Apart from the effects on phenology, growth and reproductive performance of M. effusum generally decreased when transplanted southwards (e. g., plant size and number of individuals decreased towards the south) and was probably more limited by light availability in the south. Specific leaf area of both species increased when transplanted southwards, but decreased with open-top chamber installation in A. nemorosa. In general, individuals of both species transplanted at the home site performed best, suggesting local adaptation. We conclude that contrasting understorey plants may display divergent plasticity in response to changing temperatures which may alter future understorey community dynamics.
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| 4. |
- De Frenne, Pieter, et al.
(författare)
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The response of forest plant regeneration to temperature variation along a latitudinal gradient
- 2012
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Ingår i: Annals of Botany. - : Oxford University Press (OUP). - 0305-7364 .- 1095-8290. ; 109:5, s. 1037-1046
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Tidskriftsartikel (refereegranskat)abstract
- The response of forest herb regeneration from seed to temperature variations across latitudes was experimentally assessed in order to forecast the likely response of understorey community dynamics to climate warming. Seeds of two characteristic forest plants (Anemone nemorosa and Milium effusum) were collected in natural populations along a latitudinal gradient from northern France to northern Sweden and exposed to three temperature regimes in growth chambers (first experiment). To test the importance of local adaptation, reciprocal transplants were also made of adult individuals that originated from the same populations in three common gardens located in southern, central and northern sites along the same gradient, and the resulting seeds were germinated (second experiment). Seedling establishment was quantified by measuring the timing and percentage of seedling emergence, and seedling biomass in both experiments. Spring warming increased emergence rates and seedling growth in the early-flowering forb A. nemorosa. Seedlings of the summer-flowering grass M. effusum originating from northern populations responded more strongly in terms of biomass growth to temperature than southern populations. The above-ground biomass of the seedlings of both species decreased with increasing latitude of origin, irrespective of whether seeds were collected from natural populations or from the common gardens. The emergence percentage decreased with increasing home-away distance in seeds from the transplant experiment, suggesting that the maternal plants were locally adapted. Decreasing seedling emergence and growth were found from the centre to the northern edge of the distribution range for both species. Stronger responses to temperature variation in seedling growth of the grass M. effusum in the north may offer a way to cope with environmental change. The results further suggest that climate warming might differentially affect seedling establishment of understorey plants across their distribution range and thus alter future understorey plant dynamics.
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| 5. |
- Dietrich, Anna, 1979-, et al.
(författare)
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A long-term phytometer study to evaluate stream restoration along climate and discharge gradients
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Simplified channel morphology caused by the channelization of rivers to facilitatetimber floating resulted in a less variable flow regime with faster flows in the mainchannel. Restoration measures aiming to counteract these impacts, such as the returnof boulders to the channel and the reconnection of the riparian zone with instreamhabitats, are expected to create a higher, more natural hydrological variability andenhance riparian site quality. In this study, we analysed the number and duration offlooding events at channelized and restored river reaches with an indirect methodusing diurnal temperature oscillation. In a long-term field experiment, we evaluatedthe effect of flooding regime on riparian plant performance by measuring survival andbiomass increment of two transplanted phytometer species, a grass (Molinia caerulea)and a forb (Filipendula ulmaria). We found that flow variability was significantlyhigher at restored compared to channelized sites in medium-sized and large streams,particularly during summer months. Phytometer performance was better at restoredsites and positively correlated with summer flooding, indicating that a more variableflow after restoration improved site conditions for phytometer growth. This may notonly result from the higher heterogeneity in channel morphology caused by thereturned boulders, but can probably also be attributed to a lower flow velocity atrestored sites. Flood variables were more often correlated with other abiotic variablesat restored than at channelized sites, which points to an increased land-waterconnectivity as a result of restoration.
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| 6. |
- Dietrich, Anna L., et al.
(författare)
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A phytometer study evaluating the effects of stream restoration on riparian vegetation
- 2016
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Ingår i: Ecohydrology. - : Wiley. - 1936-0584 .- 1936-0592. ; 9:4, s. 646-658
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Tidskriftsartikel (refereegranskat)abstract
- Channelization of streams and rivers to facilitate timber floating has cut off riparian zones from the channel, covered them with coarse sediment and resulted in less flooding. Restoration measures aiming to counteract these impacts are expected to create a higher, more natural hydrological variability and enhance site quality for riparian plants. In a long-term field experiment, we evaluated the effect of flooding regime on riparian plant performance by measuring survival and biomass increment of two transplanted phytometer species, a grass (Molinia caerulea) and a forb (Filipendula ulmaria). We also analysed the number and duration of flooding events in channelized and restored stream and river reaches with an indirect method using diurnal temperature oscillation. We found that flow duration was higher, with significantly more flood events at restored compared with channelized sites in medium-sized and large watercourses, particularly during the summer months. Phytometer performance was better at restored sites, and it was positively correlated with duration and frequency of summer flooding, indicating that more but less intense floods after restoration improved site conditions for phytometer growth. This may not only result from an increased heterogeneity in channel morphology caused by the return of boulders but can probably also be attributed to a reduced current velocity at restored sites. Flood variables were more often correlated with other abiotic variables at restored than at channelized sites, which points to an increased land-water connectivity as a result of restoration.
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| 7. |
- Dietrich, Anna L., et al.
(författare)
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Restoration effects on germination and survival of plants in the riparian zone : a phytometer study
- 2015
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Ingår i: Plant Ecology. - : Springer Science and Business Media LLC. - 1385-0237 .- 1573-5052. ; 216:3, s. 465-477
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Tidskriftsartikel (refereegranskat)abstract
- Many streams that were channelized to facilitate timber floating in northern Sweden, have in recent years been restored by returning coarse sediment (cobbles and boulders) to the channel and reconnecting riparian with instream habitats. We asked if such restoration measures affect germination and survival of plants in the riparian zone, and if such potential effects depend on location in the catchment. We used a paired site approach, comparing the performance of Helianthus annuus (sunflower) phytometers (seeds and seedlings) in the riparian zone in channelized versus restored river reaches along climate and stream size gradients in the Vindel River catchment in northern Sweden. Phytometer survival, substrate availability, and soil nutrient content in large streams were enhanced by restoration, but overall, phytometer performance was negatively related to the length of the growing season, i.e. phytometers grew best at high altitudes and short growing seasons. This result may have been caused by less competition from the shorter and sparser neighbouring vegetation at these sites or to more frequent flooding events, enhancing retention of organic matter. Soil nutrient levels were lowest close to the coast and in large streams, probably due to deposition of mineral sediment. The higher availability of riparian habitat at restored than at channelized sites suggests that plant species richness and abundance may potentially increase after restoration. Seedling transplantation seems to be a preferable revegetation measure, because phytometer seedlings established better than seeds and survival was significantly higher at restored sites. The good plant performance at sites with short growing seasons and high altitudes suggests that, with limited resources, restoration measures should first be located to such sites.
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| 8. |
- Dietrich, Anna L., 1979-
(författare)
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Use of phytometers for evaluating ecological restoration
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The increase in ecological restoration can be attributed to valuation of healthyecosystems and concerns for future climate changes. Freshwaters belong among theglobally most altered ecosystems and are restored to counteract human impacts.Many Swedish streams that were channelized to facilitate timber floating have beenrestored by returning boulders and reconnecting riparian with instream habitats.Evaluation of restoration lacks reliable indicators of organism performance, possiblydue to the complexity of ecosystem responses. Phytometers, i.e. standardized plantstransplanted to different environments, are important indicators of restorationsuccess. Phytometers integrate multiple environmental factors and measureecosystem functions directly. This thesis combines a literature review with threeexperiments and focuses on phytometer use for evaluating ecological restoration. Werecommend using different phytometer species, life-forms and life-stages and longexperiments (>1 year) to obtain high resolution and generality (I). In greenhouse andfield experiments we investigated the effect of restoring channelized rivers onphytometers and abiotic variables in the riparian zone. We hypothesized thatphytometer performance varies with stream size and climate. In the greenhouse, weanalysed differences in fertility between channelized and restored reaches by growingphytometers on soils from experimental sites (II). Phytometers grew better on soilsfrom restored sites in small streams, indicating a positive effect of restoration on soil.We detected this effect already 3-7 years after restoration, suggesting a fasterrecovery than predicted. In a short-term field experiment focusing on germinationand establishment of sunflowers, seedling survival, substrate availability, and soilnutrient content in large streams were enhanced by restoration (III). Overall,phytometers performed best at high altitudes and short growing seasons. The use ofMolinia caerulea and Filipendula ulmaria as phytometers in a long-term fieldexperiment (IV) revealed a better performance at restored sites. One reason was thatsummer flow-variability was higher, particularly in medium-sized streams. Sincephytometers allocated more biomass to belowground parts at restored compared tochannelized sites, it seems important to separate above- and belowground biomass inrestoration evaluation. Restoration outcomes vary with location in the catchment.Knowing such potentially different responses could guide restorationists in where tolocate restoration to be effective or successful. We suggest that small streams reactparticularly fast to restoration. Given that the proportion of small streams is high andthat restoration success in headwaters may favour downstream reaches, werecommend restoration to begin in tributaries to larger rivers. It is not always knownwhy phytometers react the way they do. Greenhouse experiments can disentangle thecauses of phytometer responses in the field by focusing on single environmentalfactors. We demonstrate that phytometers integrate ecosystem responses torestoration by reflecting how environmental factors affect plants under fieldconditions. Further studies are needed to better understand the underlyingmechanisms.
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| 9. |
- Dietrich, Anna, 1979-, et al.
(författare)
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Phytometers are underutilised for evaluating ecological restoration
- 2013
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Ingår i: Basic and Applied Ecology. - Jena : Elsevier. - 1439-1791 .- 1618-0089. ; 14:5, s. 369-377
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Tidskriftsartikel (refereegranskat)abstract
- Ecological restoration increases, but evaluation of restoration efforts is inadequate because reliable performance indicators are lacking. As plants are important actors in ecological restoration, we suggest that they be used as meters, i.e. phytometers, of restoration success. Phytometer plants are transplanted to different conditions to integrate measures of the prevailing conditions. We analysed 100 studies for the use of phytometers and especially their applicability to evaluate ecological restoration. Most studies employed single species and life-stages and focused on habitat conditions and environmental impacts. Most experiments were conducted on grasslands in wet temperate regions. Growth was the dominant response variable, in long-term studies often combined with reproductive output and plant survival. Only five studies specifically evaluated ecological restoration, implying that its potential is not yet realised. We found phytometers promising in evaluating restoration outcomes given that they are easy to measure, can provide rapid results, and serve as integrative indicators of environmental conditions with the ability of covering many aspects of plant life and ecosystem processes. To evaluate restoration success with high resolution and generality, we suggest a combination of different phytometer species, life-forms and life-stages, and experimental periods >1 year to reduce effects of transplantation and between-year variation and to account for time lags in ecological processes and changes after restoration.
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| 10. |
- Dietrich, Anna, 1979-, et al.
(författare)
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The Use of Phytometers for Evaluating Restoration Effects on Riparian Soil Fertility
- 2014
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Ingår i: Journal of Environmental Quality. - : American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.. - 0047-2425 .- 1537-2537. ; 43:6, s. 1916-1925
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Tidskriftsartikel (refereegranskat)abstract
- The ecological restoration of streams in Sweden has become increasingly important to counteract effects of past timber floating. In this study, we focused on the effect on riparian soil properties after returning coarse sediment (cobbles and boulders) to the channel and reconnecting riparian with instream habitats. Restoration increases habitat availability for riparian plants, but its effects on soil quality are unknown. We also analyzed whether the restoration effect differs with variation in climate and stream size. We used standardized plant species to measure the performance of a grass (Phleum pratense L.) and a forb (Centaurea cyanus L.) in soils sampled in the riparian zones of channelized and restored streams and rivers. Furthermore, we analyzed the mass fractions of carbon (C) and nitrogen (N) along with the proportions of the stable isotopes C-13 and N-15 in the soil, as well as its grain size composition. We found a positive effect of restoration on biomass of phytometers grown in riparian soils from small streams, indicating that restoration enhanced the soil properties favoring plant performance. We suggest that changed flooding with more frequent but less severe floods and slower flows, enhancing retention, could explain the observed patterns. This positive effect suggests that it may be advantageous to initiate restoration efforts in small streams, which make up the highest proportion of the stream network in a catchment. Restoration responses in headwater streams may then be transmitted downstream to facilitate recovery of restored larger rivers. If the larger rivers were restored first, a slower reaction would be expected.
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