| 1. |
- Bruneau, Anne, et al.
(författare)
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Advances in Legume Systematics 14. Classification of Caesalpinioideae. Part 2: Higher-level classification
- 2024
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Ingår i: PhytoKeys. - Sofia : Pensoft Publishers. - 1314-2011 .- 1314-2003. ; 240, s. 1-552
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Tidskriftsartikel (refereegranskat)abstract
- Caesalpinioideae is the second largest subfamily of legumes (Leguminosae) with ca. 4680 species and 163 genera. It is an ecologically and economically important group formed of mostly woody perennials that range from large canopy emergent trees to functionally herbaceous geoxyles, lianas and shrubs, and which has a global distribution, occurring on every continent except Antarctica. Following the recent re-circumscription of 15 Caesalpinioideae genera as presented in Advances in Legume Systematics 14, Part 1, and using as a basis a phylogenomic analysis of 997 nuclear gene sequences for 420 species and all but five of the genera currently recognised in the subfamily, we present a new higher-level classification for the subfamily. The new classification of Caesalpinioideae comprises eleven tribes, all of which are either new, reinstated or re-circumscribed at this rank: Caesalpinieae Rchb. (27 genera / ca. 223 species), Campsiandreae LPWG (2 / 5-22), Cassieae Bronn (7 / 695), Cera-tonieae Rchb. (4 / 6), Dimorphandreae Benth. (4 / 35), Erythrophleeae LPWG (2 /13), Gleditsieae Nakai (3 / 20), Mimoseae Bronn (100 / ca. 3510), Pterogyneae LPWG (1 / 1), Schizolobieae Nakai (8 / 42-43), Sclerolobieae Benth. & Hook. f. (5 / ca. 113). Although many of these lineages have been recognised and named in the past, either as tribes or informal generic groups, their circumscriptions have varied widely and changed over the past decades, such that all the tribes described here differ in generic membership from those previously recognised. Importantly, the approximately 3500 species and 100 genera of the former subfamily Mimosoideae are now placed in the reinstated, but newly circumscribed, tribe Mimoseae. Because of the large size and ecological importance of the tribe, we also provide a clade-based classification system for Mimoseae that includes 17 named lower-level clades. Fourteen of the 100 Mimoseae genera remain unplaced in these lower-level clades: eight are resolved in two grades and six are phylogenetically isolated monogeneric lineages. In addition to the new classification, we provide a key to genera, morphological descriptions and notes for all 163 genera, all tribes, and all named clades. The diversity of growth forms, foliage, flowers and fruits are illustrated for all genera, and for each genus we also provide a distribution map, based on quality-controlled herbarium specimen localities. A glossary for specialised terms used in legume morphology is provided. This new phylogenetically based classification of Caesalpinioideae provides a solid system for communication and a framework for downstream analyses of biogeography, trait evolution and diversification, as well as for taxonomic revision of still understudied genera.
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| 2. |
- Kehoe, Laura, et al.
(författare)
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Make EU trade with Brazil sustainable
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 364:6438, s. 341-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 3. |
- Marques, Joana F, et al.
(författare)
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Genetic diversity of Pomatoschistus microps (Perciformes: Gobiidae) in ecologically differentiated estuarine systems
- 2012
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Ingår i: Folia Zoologica. - 0139-7893. ; 61:2, s. 106-117
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Tidskriftsartikel (refereegranskat)abstract
- A landscape genetics approach was applied to common goby (Pomatoschistus microps) sampled from three estuaries (six sites) of the Portuguese coast. Individuals of each site were genotyped for eight microsatellite loci and levels of genetic diversity and differentiation were correlated to present-day estuarine characteristics and historical events. A general ecological state for each sampling site was obtained from a principal component analysis (PCA) applied to estuarine geomorphologic characteristics and levels of heavy metals and total polycyclic aromatic hydrocarbons contamination. Genetic diversity was higher than that previously reported for common goby in the Atlantic and Mediterranean. F-ST were generally very low (0.000-0.049), as well as Nei's genetic distances (0.000-0.167), although the later were statistically significant. Estuarine geomorphology and heavy metal contamination contributed the most to estuarine ecological differentiation but no trend was detected in the relationship between these characteristics and samples' genetic diversity. Mantel tests also revealed no significant relationships between geographic, genetic and ecological distances. Null alleles only contributed to explain significant Hardy-Weinberg departures in two of the eight loci scored, although disequilibria were detected in at least two loci per sample. Notwithstanding its exploratory character, results suggest an important role for historical factors in the timing and direction of P. microps colonization of the Portuguese estuaries. Environmental variation and P. microps ability to cope with it are also structuring factors in establishing and maintaining the patchy genetic diversity detected in the studied estuaries.
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| 4. |
- Bossini-Castillo, Lara, et al.
(författare)
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A replication study confirms the association of TNFSF4 (OX40L) polymorphisms with systemic sclerosis in a large European cohort
- 2011
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Ingår i: Annals of the Rheumatic Diseases. - : BMJ. - 1468-2060 .- 0003-4967. ; 70:4, s. 638-641
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Tidskriftsartikel (refereegranskat)abstract
- Objectives The aim of this study was to confirm the influence of TNFSF4 polymorphisms on systemic sclerosis (SSc) susceptibility and phenotypic features. Methods A total of 8 European populations of Caucasian ancestry were included, comprising 3014 patients with SSc and 3125 healthy controls. Four genetic variants of TNFSF4 gene promoter (rs1234314, rs844644, rs844648 and rs12039904) were selected as genetic markers. Results A pooled analysis revealed the association of rs1234314 and rs12039904 polymorphisms with SSc (OR 1.15, 95% CI 1.02 to 1.31; OR 1.18, 95% CI 1.08 to 1.29, respectively). Significant association of the four tested variants with patients with limited cutaneous SSc (lcSSc) was revealed (rs1234314 OR 1.22, 95% CI 1.07 to 1.38; rs844644 OR 0.91, 95% CI 0.83 to 0.99; rs844648 OR 1.10, 95% CI 1.01 to 1.20 and rs12039904 OR 1.20, 95% CI 1.09 to 1.33). Association of rs1234314, rs844648 and rs12039904 minor alleles with patients positive for anti-centromere antibodies (ACA) remained significant (OR 1.23, 95% CI 1.10 to 1.37; OR 1.12, 95% CI 1.01 to 1.25; OR 1.22, 95% CI 1.07 to 1.38, respectively). Haplotype analysis confirmed a protective haplotype associated with SSc, lcSSc and ACA positive subgroups (OR 0.88, 95% CI 0.82 to 0.96; OR 0.88, 95% CI 0.80 to 0.96; OR 0.86, 95% CI 0.77 to 0.97, respectively) and revealed a new risk haplotype associated with the same groups of patients (OR 1.14, 95% CI 1.03 to 1.26; OR 1.20, 95% CI 1.08 to 1.35; OR 1.23, 95% CI 1.07 to 1.42, respectively). Conclusions The data confirm the influence of TNFSF4 polymorphisms in SSc genetic susceptibility, especially in subsets of patients positive for lcSSc and ACA.
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| 5. |
- Duarte, Irina A., et al.
(författare)
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Bioconcentration of neuroactive pharmaceuticals in fish: Relation to lipophilicity, experimental design and toxicity in the aquatic environment
- 2022
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Ingår i: Science of the Total Environment. - : Elsevier. - 0048-9697 .- 1879-1026. ; 812
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Tidskriftsartikel (refereegranskat)abstract
- Uptake of contaminants is linked to their toxicity and is usually estimated through their lipophilicity (logKow). Here, we review current literature regarding bioconcentration, i.e. uptake of contaminants from the external environment only, and the effects of exposure to neuroactive pharmaceuticals in fish. We aim to determine if lipophilicity is a suitable predictor of bioconcentration of these compounds in fish, to identify major drivers of bioconcentration and explore the link between bioconcentration potential and toxicity, focusing on survival, growth, condition, behaviour and reproduction endpoints. Additionally, we compare concentrations known to elicit significant effects in fish with current environmental concentrations, identifying exposure risk in ecosystems. The majority of studies have focused on antidepressants, mainly fluoxetine, and encompasses mostly freshwater species. Few studies determined pharmaceuticals bioconcentration, and even a smaller portion combined bioconcentration with other toxicity endpoints. Results show that lipophilicity isn't a good predictor of neuroactive pharmaceuticals' bioconcentration in fish, which in turn is highly influenced by experimental parameters, including abiotic conditions, species and life-stage. The need for increased standardization of experimental settings is key towards improving accuracy of environmental risk assessments and application in future regulatory schemes. Still, increased fish lethality was linked to increased bioconcentration, yet no other correlations were observed when considering effects on growth, condition, behaviour or reproduction, likely as a result of insufficient and variable data. In the context of current environmental concentrations, several neuroactive pharmaceuticals were found to be potentially threatening, while data on occurrence is lacking for some compounds, particularly in brackish/marine systems. Specifically, nine compounds (fluoxetine, citalopram, sertraline, amitriptyline, venlafaxine, clozapine, carbamazepine, metamfetamine and oxazepam) were found at concentrations either above or critically close to minimum response concentrations, thus likely to affect fish in freshwater and brackish or marine environments, which supports further exploration in risk management strategies and monitoring programs in aquatic environments.
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| 6. |
- Duarte, Irina A., et al.
(författare)
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Neuroactive pharmaceuticals in estuaries : occurrence and tissue-specific bioaccumulation in multiple fish species
- 2023
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Ingår i: Environmental Pollution. - : Elsevier. - 0269-7491 .- 1873-6424. ; 316:Part 1
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Tidskriftsartikel (refereegranskat)abstract
- Contamination of surface waters by pharmaceuticals is an emerging problem globally. This is because the increased access and use of pharmaceuticals by a growing world population lead to environmental contamination, threatening non-target species in their natural environment. Of particular concern are neuroactive pharmaceuticals, which are known to bioaccumulate in fish and impact a variety of individual processes such as fish reproduction or behaviour, which can have ecological impacts and compromise fish populations. In this work, we investigate the occurrence and bioaccumulation of 33 neuroactive pharmaceuticals in brain, muscle and liver tissues of multiple fish species collected in four different estuaries (Douro, Tejo, Sado and Mira). In total, 28 neuroactive pharmaceuticals were detected in water and 13 in fish tissues, with individual pharmaceuticals reaching maximum concentrations of 1590 ng/L and 207 ng/g ww, respectively. The neuroactive pharmaceuticals with the highest levels and highest frequency of detection in the water samples were psychostimulants, antidepressants, opioids and anxiolytics, whereas in fish tissues, antiepileptics, psychostimulants, anxiolytics and antidepressants showed highest concentrations. Bioaccumulation was ubiquitous, occurring in all seven estuarine and marine fish species. Notably, neuroactive compounds were detected in every water and fish brain samples, and in 95% of fish liver and muscle tissues. Despite variations in pharmaceutical occurrence among estuaries, bioaccumulation patterns were consistent among estuarine systems, with generally higher bioaccumulation in fish brain followed by liver and muscle. Moreover, no link between bioaccumulation and compounds' lipophilicity, species habitat use patterns or trophic levels was observed. Overall, this work highlights the occurrence of a highly diverse suite of neuroactive pharmaceuticals and their pervasiveness in waters and fish from estuarine systems with contrasting hydromorphology and urban development and emphasizes the urgent need for toxicity assessment of these compounds in natural ecosystems, linked to internalized body concentration in non-target species.
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| 7. |
- Gorlova, Olga, et al.
(författare)
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Identification of Novel Genetic Markers Associated with Clinical Phenotypes of Systemic Sclerosis through a Genome-Wide Association Strategy
- 2011
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7404. ; 7:7
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this study was to determine, through a genome-wide association study (GWAS), the genetic components contributing to different clinical sub-phenotypes of systemic sclerosis (SSc). We considered limited (IcSSc) and diffuse (dcSSc) cutaneous involvement, and the relationships with presence of the SSc-specific auto-antibodies, anti-centromere (ACA), and anti-topoisomerase I (ATA). Four GWAS cohorts, comprising 2,296 SSc patients and 5,171 healthy controls, were meta-analyzed looking for associations in the selected subgroups. Eighteen polymorphisms were further tested in nine independent cohorts comprising an additional 3,175 SSc patients and 4,971 controls. Conditional analysis for associated SNPs in the HLA region was performed to explore their independent association in antibody subgroups. Overall analysis showed that non-HLA polymorphism rs11642873 in IRF8 gene to be associated at GWAS level with lcSSc (P = 2.32x10(-12), OR = 0.75). Also, rs12540874 in GRB10 gene (P = 1.27 x 10(-6), OR = 1.15) and rs11047102 in SOX5 gene (P = 1.39x10(-7), OR = 1.36) showed a suggestive association with lcSSc and ACA subgroups respectively. In the HLA region, we observed highly associated allelic combinations in the HLA-DQB1 locus with ACA (P = 1.79x10(-61), OR = 2.48), in the HLA-DPA1/B1 loci with ATA (P = 4.57x10(-76), OR = 8.84), and in NOTCH4 with ACA P = 8.84x10(-21), OR = 0.55) and ATA (P = 1.14x10(-8), OR = 0.54). We have identified three new non-HLA genes (IRF8, GRB10, and SOX5) associated with SSc clinical and autoantibody subgroups. Within the HLA region, HLA-DQB1, HLA-DPA1/B1, and NOTCH4 associations with SSc are likely confined to specific auto-antibodies. These data emphasize the differential genetic components of subphenotypes of SSc.
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