Research questions to facilitate the future development of European long-term ecosystem research infrastructures: A horizon scanning exercise.

Distributed environmental research infrastructures are important to support assessments of the effects of global change on landscapes, ecosystems and society. These infrastructures need to provide continuity to address long-term change, yet be flexible enough to respond to rapid societal and technological developments that modify research priorities. We used a horizon scanning exercise to identify and prioritize emerging research questions for the future development of ecosystem and socio-ecological research infrastructures in Europe. Twenty research questions covered topics related to (i) ecosystem structures and processes, (ii) the impacts of anthropogenic drivers on ecosystems, (iii) ecosystem services and socio-ecological systems and (iv), methods and research infrastructures. Several key priorities for the development of research infrastructures emerged. Addressing complex environmental issues requires the adoption of a whole-system approach, achieved through integration of biotic, abiotic and socio-economic measurements. Interoperability among different research infrastructures needs to be improved by developing standard measurements, harmonizing methods, and establishing capacities and tools for data integration, processing, storage and analysis. Future research infrastructures should support a range of methodological approaches including observation, experiments and modelling. They should also have flexibility to respond to new requirements, for example by adjusting the spatio-temporal design of measurements. When new methods are introduced, compatibility with important long-term data series must be ensured. Finally, indicators, tools, and transdisciplinary approaches to identify, quantify and value ecosystem services across spatial scales and domains need to be advanced.

Long-term changes (1990-2015) in the atmospheric deposition and runoff water chemistry of sulphate, inorganic nitrogen and acidity for forested catchments in Europe in relation to changes in emissions and hydrometeorological conditions.

The international Long-Term Ecological Research Network (ILTER) encompasses hundreds of long-term research/monitoring sites located in a wide array of ecosystems that can help us understand environmental change across the globe. We evaluated long-term trends (1990-2015) for bulk deposition, throughfall and runoff water chemistry and fluxes, and climatic variables in 25 forested catchments in Europe belonging to the UNECE International Cooperative Programme on Integrated Monitoring of Air Pollution Effects on Ecosystems (ICP IM). Many of the IM sites form part of the monitoring infrastructures of this larger ILTER network. Trends were evaluated for monthly concentrations of non-marine (anthropogenic fraction, denoted as x) sulphate (xSO4) and base cations x(Ca+Mg), hydrogen ion (H+), inorganic N (NO3 and NH4) and ANC (Acid Neutralising Capacity) and their respective fluxes into and out of the catchments and for monthly precipitation, runoff and air temperature. A significant decrease of xSO4 deposition resulted in decreases in concentrations and fluxes of xSO4 in runoff, being significant at 90% and 60% of the sites, respectively. Bulk deposition of NO3 and NH4 decreased significantly at 60-80% (concentrations) and 40-60% (fluxes) of the sites. Concentrations and fluxes of NO3 in runoff decreased at 73% and 63% of the sites, respectively, and NO3 concentrations decreased significantly at 50% of the sites. Thus, the LTER/ICP IM network confirms the positive effects of the emission reductions in Europe. Air temperature increased significantly at 61% of the sites, while trends for precipitation and runoff were rarely significant. The site-specific variation of xSO4 concentrations in runoff was most strongly explained by deposition. Climatic variables and deposition explained the variation of inorganic N concentrations in runoff at single sites poorly, and as yet there are no clear signs of a consistent deposition-driven or climate-driven increase in inorganic N exports in the catchments.

Prospective observational study of 177Lu-DOTA-octreotate therapy in 200 patients with advanced metastasized neuroendocrine tumours (NETs): feasibility and impact of a dosimetry-guided study protocol on outcome and toxicity.

PURPOSE: Peptide receptor radionuclide therapy in patients with neuroendocrine tumours has yielded promising results. This prospective study investigated the feasibility of dosimetry of the kidneys and bone marrow during therapy and its impact on efficacy and outcome. METHODS: The study group comprised 200 consecutive patients with metastasized somatostatin receptor-positive neuroendocrine tumours progressing on standard therapy or not suitable for other therapeutic options. A treatment cycle consisted of 7.4 GBq 177Lu-DOTA-octreotate with co-infusion of a mixed amino acid solution, and cycles were repeated until the absorbed dose to the kidneys reached 23 Gy or there were other reasons for stopping therapy. The Ki-67 index was ≤2% in 47 patients (23.5%), 3-20% in 121 (60.5%) and >20% in 16 (8%). RESULTS: In 123 patients (61.5%) the absorbed dose to the kidneys reached 23 Gy with three to nine cycles during first-line therapy; in no patient was a dose to the bone marrow of 2 Gy reached. The best responses (according to RECIST 1.1) were a complete response (CR) in 1 patient (0.5%), a partial response (PR) in 47 (23.5%), stable disease (SD) in 135 (67.5%) and progressive disease (PD) in 7 (3.5%). Median progression-free survival was 27 months (95% CI 22-30 months) in all patients, 33 months in those in whom the absorbed dose to the kidneys reached 23 Gy and 15 months in those in whom it did not. Median overall survival (OS) was 43 months (95% CI 39-53 months) in all patients, 54 months in those in whom the absorbed dose to the kidneys reached 23 Gy and 25 months in those in whom it did not. Median OS was 60 months in patients with a best response of PR or CR, 42 months in those with SD and 16 months in those with PD. Three patients (1.5%) developed acute leukaemia, 1 patient (0.5%) chronic leukaemia (unconfirmed) and 30 patients (15%) grade 3 or 4 bone marrow toxicity. Eight patients (4%) developed grade 2 kidney toxicity and one patient (0.5%) grade 4 kidney toxicity. CONCLUSIONS: Dosimetry-based therapy with 177Lu-DOTA-octreotate is feasible. Patients in whom the absorbed dose to the kidneys reached 23 Gy had a longer OS than those in whom it did not. Patients with CR/PR had a longer OS than those with SD. Bone marrow dosimetry did not predict toxicity.

SoilTrEC: a global initiative on critical zone research and integration.

Soil is a complex natural resource that is considered non-renewable in policy frameworks, and it plays a key role in maintaining a variety of ecosystem services (ES) and life-sustaining material cycles within the Earth's Critical Zone (CZ). However, currently, the ability of soil to deliver these services is being drastically reduced in many locations, and global loss of soil ecosystem services is estimated to increase each year as a result of many different threats, such as erosion and soil carbon loss. The European Union Thematic Strategy for Soil Protection alerts policy makers of the need to protect soil and proposes measures to mitigate soil degradation. In this context, the European Commission-funded research project on Soil Transformations in European Catchments (SoilTrEC) aims to quantify the processes that deliver soil ecosystem services in the Earth's Critical Zone and to quantify the impacts of environmental change on key soil functions. This is achieved by integrating the research results into decision-support tools and applying methods of economic valuation to soil ecosystem services. In this paper, we provide an overview of the SoilTrEC project, its organization, partnerships and implementation.

Forest floor vegetation response to nitrogen deposition in Europe.

Chronic nitrogen (N) deposition is a threat to biodiversity that results from the eutrophication of ecosystems. We studied long-term monitoring data from 28 forest sites with a total of 1,335 permanent forest floor vegetation plots from northern Fennoscandia to southern Italy to analyse temporal trends in vascular plant species cover and diversity. We found that the cover of plant species which prefer nutrient-poor soils (oligotrophic species) decreased the more the measured N deposition exceeded the empirical critical load (CL) for eutrophication effects (P = 0.002). Although species preferring nutrient-rich sites (eutrophic species) did not experience a significantly increase in cover (P = 0.440), in comparison to oligotrophic species they had a marginally higher proportion among new occurring species (P = 0.091). The observed gradual replacement of oligotrophic species by eutrophic species as a response to N deposition seems to be a general pattern, as it was consistent on the European scale. Contrary to species cover changes, neither the decrease in species richness nor of homogeneity correlated with nitrogen CL exceedance (ExCLemp N). We assume that the lack of diversity changes resulted from the restricted time period of our observations. Although existing habitat-specific empirical CL still hold some uncertainty, we exemplify that they are useful indicators for the sensitivity of forest floor vegetation to N deposition.

Adapting forest health assessments to changing perspectives on threats--a case example from Sweden.

A revised Swedish forest health assessment system is presented. The assessment system is composed of several interacting components which target information needs for strategic and operational decision making and accommodate a continuously expanding knowledge base. The main motivation for separating information for strategic and operational decision making is that major damage outbreaks are often scattered throughout the landscape. Generally, large-scale inventories (such as national forest inventories) cannot provide adequate information for mitigation measures. In addition to broad monitoring programs that provide time-series information on known damaging agents and their effects, there is also a need for local and regional inventories adapted to specific damage events. While information for decision making is the major focus of the health assessment system, the system also contributes to expanding the knowledge base of forest conditions. For example, the integrated monitoring programs provide a better understanding of ecological processes linked to forest health. The new health assessment system should be able to respond to the need for quick and reliable information and thus will be an important part of the future monitoring of Swedish forests.

Recovery of soil water, groundwater, and streamwater from acidification at the Swedish integrated monitoring catchments.

Recovery from anthropogenic acidification in streams and lakes is well documented across the northern hemisphere. In this study, we use 1996-2009 data from the four Swedish Integrated Monitoring catchments to evaluate how the declining sulfur deposition has affected sulfate, pH, acid neutralizing capacity, ionic strength, aluminum, and dissolved organic carbon in soil water, groundwater and runoff. Differences in recovery rates between catchments, between recharge and discharge areas and between soil water and groundwater are assessed. At the IM sites, atmospheric deposition is the main human impact. The chemical trends were weakly correlated to the sulfur deposition decline. Other factors, such as marine influence and catchment features, seem to be as important. Except for pH and DOC, soil water and groundwater showed similar trends. Discharge areas acted as buffers, dampening the trends in streamwater. Further monitoring and modeling of these hydraulically active sites should be encouraged.

Assessing the risk of N leaching from forest soils across a steep N deposition gradient in Sweden.

Nitrogen leaching from boreal and temporal forests, where normally most of the nitrogen is retained, has the potential to increase acidification of soil and water and eutrophication of the Baltic Sea. In parts of Sweden, where the nitrogen deposition has been intermediate to high during recent decades, there are indications that the soils are close to nitrogen saturation. In this study, four different approaches were used to assess the risk of nitrogen leaching from forest soils in different parts of Sweden. Nitrate concentrations in soil water and C:N ratios in the humus layer where interpreted, together with model results from mass balance calculations and detailed dynamic modelling. All four approaches pointed at a risk of nitrogen leaching from forest soils in southern Sweden. However, there was a substantial variation on a local scale. Basing the assessment on four different approaches makes the assessment robust.

p21-activated kinase 4 phosphorylation of integrin beta5 Ser-759 and Ser-762 regulates cell migration.

Modulation of integrin alphavbeta5 regulates vascular permeability, angiogenesis, and tumor dissemination. In addition, we previously found a role for p21-activated kinase 4 (PAK4) in selective regulation of integrin alphavbeta5-mediated cell motility (Zhang, H., Li, Z., Viklund, E. K., and Strömblad, S. (2002) J. Cell Biol. 158, 1287-1297). This report focuses on the molecular mechanisms of this regulation. We here identified a unique PAK4-binding membrane-proximal integrin beta5-SERS-motif involved in controlling cell attachment and migration. We also mapped the integrin beta5-binding site within PAK4. We found that PAK4 binding to integrin beta5 was not sufficient to promote cell migration, but that PAK4 kinase activity was required for PAK4 promotion of cell motility. Importantly, PAK4 specifically phosphorylated the integrin beta5 subunit at Ser-759 and Ser-762 within the beta5-SERS-motif. Point mutation of these two serine residues abolished the PAK4-induced cell migration, indicating a functional role for these phosphorylations in migration. Our results may give important leads to the functional regulation of integrin alphavbeta5, with implications for vascular permeability, angiogenesis, and cancer dissemination.

Biodiversity differences between managed and unmanaged forests: meta-analysis of species richness in Europe.

Past and present pressures on forest resources have led to a drastic decrease in the surface area of unmanaged forests in Europe. Changes in forest structure, composition, and dynamics inevitably lead to changes in the biodiversity of forest-dwelling species. The possible biodiversity gains and losses due to forest management (i.e., anthropogenic pressures related to direct forest resource use), however, have never been assessed at a pan-European scale. We used meta-analysis to review 49 published papers containing 120 individual comparisons of species richness between unmanaged and managed forests throughout Europe. We explored the response of different taxonomic groups and the variability of their response with respect to time since abandonment and intensity of forest management. Species richness was slightly higher in unmanaged than in managed forests. Species dependent on forest cover continuity, deadwood, and large trees (bryophytes, lichens, fungi, saproxylic beetles) and carabids were negatively affected by forest management. In contrast, vascular plant species were favored. The response for birds was heterogeneous and probably depended more on factors such as landscape patterns. The global difference in species richness between unmanaged and managed forests increased with time since abandonment and indicated a gradual recovery of biodiversity. Clearcut forests in which the composition of tree species changed had the strongest effect on species richness, but the effects of different types of management on taxa could not be assessed in a robust way because of low numbers of replications in the management-intensity classes. Our results show that some taxa are more affected by forestry than others, but there is a need for research into poorly studied species groups in Europe and in particular locations. Our meta-analysis supports the need for a coordinated European research network to study and monitor the biodiversity of different taxa in managed and unmanaged forests.

Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regions.

BACKGROUND: One of the many gene families that expanded in early vertebrate evolution is the neuropeptide (NPY) receptor family of G-protein coupled receptors. Earlier work by our lab suggested that several of the NPY receptor genes found in extant vertebrates resulted from two genome duplications before the origin of jawed vertebrates (gnathostomes) and one additional genome duplication in the actinopterygian lineage, based on their location on chromosomes sharing several gene families. In this study we have investigated, in five vertebrate genomes, 45 gene families with members close to the NPY receptor genes in the compact genomes of the teleost fishes Tetraodon nigroviridis and Takifugu rubripes. These correspond to Homo sapiens chromosomes 4, 5, 8 and 10. RESULTS: Chromosome regions with conserved synteny were identified and confirmed by phylogenetic analyses in H. sapiens, M. musculus, D. rerio, T. rubripes and T. nigroviridis. 26 gene families, including the NPY receptor genes, (plus 3 described recently by other labs) showed a tree topology consistent with duplications in early vertebrate evolution and in the actinopterygian lineage, thereby supporting expansion through block duplications. Eight gene families had complications that precluded analysis (such as short sequence length or variable number of repeated domains) and another eight families did not support block duplications (because the paralogs in these families seem to have originated in another time window than the proposed genome duplication events). RT-PCR carried out with several tissues in T. rubripes revealed that all five NPY receptors were expressed in the brain and subtypes Y2, Y4 and Y8 were also expressed in peripheral organs. CONCLUSION: We conclude that the phylogenetic analyses and chromosomal locations of these gene families support duplications of large blocks of genes or even entire chromosomes. Thus, these results are consistent with two early vertebrate tetraploidizations forming a paralogon comprising human chromosomes 4, 5, 8 and 10 and one teleost tetraploidization. The combination of positional and phylogenetic data further strengthens the identification of orthologs and paralogs in the NPY receptor family.

Heparan sulfate in trans potentiates VEGFR-mediated angiogenesis.

Several receptor tyrosine kinases require heparan sulfate proteoglycans (HSPGs) as coreceptors for efficient signal transduction. We have studied the role of HSPGs in the development of blood capillary structures from embryonic stem cells, a process strictly dependent on signaling via vascular endothelial growth factor receptor-2 (VEGFR-2). We show, by using chimeric cultures of embryonic stem cells defective in either HS production or VEGFR-2 synthesis, that VEGF signaling in endothelial cells is fully supported by HS expressed in trans by adjacent perivascular smooth muscle cells. Transactivation of VEGFR-2 leads to prolonged and enhanced signal transduction due to HS-dependent trapping of the active VEGFR-2 signaling complex. Our data imply that direct signaling via HSPG core proteins is dispensable for a functional VEGF response in endothelial cells. We propose that transactivation of tyrosine kinase receptors by HSPGs constitutes a mechanism for crosstalk between adjacent cells.

Conserved synteny between the Ciona genome and human paralogons identifies large duplication events in the molecular evolution of the insulin-relaxin gene family.

The aims of the study were to outline the sequence of events that gave rise to the vertebrate insulin-relaxin gene family and the chromosomal regions in which they reside. We analyzed the gene content surrounding the human insulin/relaxin genes with respect to what family they belonged to and if the duplication history of investigated families parallels the evolution of the insulin-relaxin family members. Markov Clustering and phylogenetic analysis were used to determine family identity. More than 15% of the genes belonged to families that have paralogs in the regions, defining two sets of quadruplicate paralogy regions. Thereby, the localization of insulin/relaxin genes in humans is in accordance with those regions on human chromosomes 1, 11, 12, 19q (insulin/insulin-like growth factors) and 1, 6p/15q, 9/5, 19p (insulin-like factors/relaxins) were formed during two genome duplications. We compared the human genome with that of Ciona intestinalis, a species that split from the vertebrate lineage before the two suggested genome duplications. Two insulin-like orthologs were discovered in addition to the already described Ci-insulin gene. Conserved synteny between the Ciona regions hosting the insulin-like genes and the two sets of human paralogons implies their common origin. Linkage of the two human paralogons, as seen in human chromosome 1, as well as the two regions hosting the Ciona insulin-like genes suggests that a segmental duplication gave rise to the region prior to the genome doublings. Thus, preserved gene content provides support that genome duplication(s) in addition to segmental and single-gene duplications shaped the genomes of extant vertebrates.

Origin of the prolactin-releasing hormone (PRLH) receptors: evidence of coevolution between PRLH and a redundant neuropeptide Y receptor during vertebrate evolution.

We present seven new vertebrate homologs of the prolactin-releasing hormone receptor (PRLHR) and show that these are found as two separate subtypes, PRLHR1 and PRLHR2. Analysis of a number of vertebrate sequences using phylogeny, pharmacology, and paralogon analysis indicates that the PRLHRs are likely to share a common ancestry with the neuropeptide Y (NPY) receptors. Moreover, a micromolar level of NPY was able to bind and inhibit completely the PRLH-evoked response in PRLHR1-expressing cells. We suggest that an ancestral PRLH peptide started coevolving with a redundant NPY binding receptor, which then became PRLHR, approximately 500 million years ago. The PRLHR1 subtype was shown to have a relatively high evolutionary rate compared to receptors with fixed peptide preference, which could indicate a drastic change in binding preference, thus supporting this hypothesis. This report suggests how gene duplication events can lead to novel peptide ligand/receptor interactions and hence spur the evolution of new physiological functions.

Genome duplication-driven evolution of gene families: insights from the formation of the insulin family.

The aim of this study was to outline the sequence of events that gave rise to the members of the insulin gene family in chordates. As part of our research, we looked for the chromosomal localization of insulin family members in the human genome.

Numerous groups of chromosomal regional paralogies strongly indicate two genome doublings at the root of the vertebrates.

The appearance of the vertebrates demarcates some of the most far-reaching changes of structure and function seen during the evolution of the metazoans. These drastic changes of body plan and expansion of the central nervous system among other organs coincide with increased gene numbers. The presence of several groups of paralogous chromosomal regions in the human genome is a reflection of this increase. The simplest explanation for the existence of these paralogies would be two genome doublings with subsequent silencing of many genes. It is argued that gene localization data and the delineation of paralogous chromosomal regions give more reliable information about these types of events than dendrograms of gene families as gene relationships are often obscured by uneven replacement rates as well as other factors. Furthermore, the topographical relations of some paralogy groups are discussed.

Nature of distribution of mercury in the sediments of the river Yamuna (tributary of the Ganges), India.

Suspended Particulate Matter (SPM), surface (bed sediments) and short length cores of sediments collected from the largest tributary of the river Ganges, namely the river Yamuna, were analysed for total mercury as well as its fractionation in various size and chemical sites in the sediments following standard procedures. Also, attempts were made to determine the vertical distribution in sediments in relation to the recent timescale of a few decades. Our observations indicate that the SPM in general showed higher levels of total mercury compared to the surface sediments while at places the enhancement could be by a factor of 10, say around 25 microg g(-1) in the downstream region that integrates the industrial midstream and agricultural downstream terrain near its confluence with the Ganges. Surface sediments in the upstream direction near the Himalayan foothills and SPM in the lower reaches showed significant high Index of Geoaccumulation (Igeo) as defined by Müller. Size fractionation studies indicate that the finer fraction preferentially showed higher levels of mercury while in the lower reaches of the river, the total mercury is equitably distributed among all size fractions. The proportion of the residual fraction of mercury in relation to mobile fractions, in general decreases downstream towards its confluence with the Ganges river. In sediment cores, the vertical distribution show systematic peaks of mercury indicating that addition of this toxic metal to the aquatic system is in direct proportion to the increase in various types of human activities such as thermal power plants, land use changes (urbanisation) in the midstream region and intensive fertiliser application in lower reaches of this vast river basin.

Differential tyrosine phosphorylation of fibroblast growth factor (FGF) receptor-1 and receptor proximal signal transduction in response to FGF-2 and heparin.

The sulfated regions in heparan sulfate and heparin are known to affect fibroblast growth factor (FGF) function. We have studied the mechanism whereby heparin directs FGF-2-induced FGF receptor-1 (FGFR-1) signal transduction. FGF-2 alone stimulated maximal phosphorylation of Src homology domain 2 tyrosine phosphatase (SHP-2) and the adaptor molecule Crk, in heparan sulfate-deficient Chinese hamster ovary (CHO) 677 cells expressing FGFR-1. In contrast, for phospholipase Cgamma(1) (PLCgamma(1)) and the adaptor molecule Shb to be maximally tyrosine-phosphorylated, cells had to be stimulated with both FGF-2 and heparin (100 ng/ml). Tyrosine residues 463 in the juxtamembrane domain and 766 in the C-terminal tail in FGFR-1 are known to bind Crk and PLCgamma(1), respectively. Analysis of tryptic phosphopeptide maps of FGFR-1 from cells stimulated with FGF-2 alone and FGF-2 together with heparin showed that FGF-2 alone stimulated a several-fold increase in tyrosine 463 in the juxtamembrane domain. In contrast, heparin had to be included in order for tyrosine 766 to be phosphorylated to the same fold level. Our data imply that tyrosine 463 is phosphorylated and able to transduce signals in response to FGF-2 treatment alone; furthermore, we suggest that FGFR-1 dimerization/kinase activation is stabilized by heparin.

The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints.

The superfamily of G-protein-coupled receptors (GPCRs) is very diverse in structure and function and its members are among the most pursued targets for drug development. We identified more than 800 human GPCR sequences and simultaneously analyzed 342 unique functional nonolfactory human GPCR sequences with phylogenetic analyses. Our results show, with high bootstrap support, five main families, named glutamate, rhodopsin, adhesion, frizzled/taste2, and secretin, forming the GRAFS classification system. The rhodopsin family is the largest and forms four main groups with 13 sub-branches. Positions of the GPCRs in chromosomal paralogons regions indicate the importance of tetraploidizations or local gene duplication events for their creation. We also searched for "fingerprint" motifs using Hidden Markov Models delineating the putative inter-relationship of the GRAFS families. We show several common structural features indicating that the human GPCRs in the GRAFS families share a common ancestor. This study represents the first overall map of the GPCRs in a single mammalian genome. Our novel approach of analyzing such large and diverse sequence sets may be useful for studies on GPCRs in other genomes and divergent protein families.