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| 2. |
- Ferreira, Daniela, et al.
(författare)
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Transcription and regulation of the hydrogenase(s) accessory genes, hypFCDEAB, in the cyanobacterium Lyngbya majuscula CCAP 1446/4
- 2007
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Ingår i: Archives of Microbiology. - : Springer Science and Business Media LLC. - 0302-8933 .- 1432-072X. ; 188:6, s. 609-617
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Tidskriftsartikel (refereegranskat)abstract
- Lyngbya majuscula CCAP 1446/4 is a filamentous cyanobacterium possessing both an uptake and a bi-directional hydrogenase. The presence of a single copy of the hyp operon in the cyanobacterial genomes suggests that these accessory genes might be responsible for the maturation of both hydrogenases. We investigated the concomitant transcription of hypFCDEAB with the hydrogenases structural genes-hup and hox. RT-PCRs performed with L. majuscula cells grown under different physiological conditions showed a substantial decrease in the relative amount of hupL transcript under non-N-2-fixing conditions. In contrast, no significant differences were observed for the transcript levels of hypFCDEAB in all conditions tested, while minor fluctuations could be discerned for hoxH. Previously, it was demonstrated that the transcriptional regulators NtcA and LexA interact with the promoter regions of hup and hox, respectively, and that putative binding sites for both proteins are present in the hyp promoter of L. majuscula. Therefore, a putative involvement of NtcA and LexA in the regulation of the hyp transcription was investigated. Electrophoretic mobility shift assays resulted in NtcA or LexA-bound retarded fragments, suggesting the involvement of these proteins in the transcriptional regulation of hypFCDEAB.
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| 3. |
- Ferreira, Mafalda S., et al.
(författare)
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The evolution of white-tailed jackrabbit camouflage
- 2023
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 379:6638, s. 1238-1242
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Tidskriftsartikel (refereegranskat)abstract
- The genetic basis of adaptive traits has rarely been used to predict future vulnerability of populations to climate change. We show that light versus dark seasonal pelage in white-tailed jackrabbits (Lepus townsendii) tracks snow cover and is primarily determined by genetic variation at endothelin receptor type B (EDNRB), corin serine peptidase (CORIN), and agouti signaling protein (ASIP). Winter color variation was associated with deeply divergent alleles at these genes, reflecting selection on both ancestral and introgressed variation. Forecasted reductions in snow cover are likely to induce widespread camouflage mismatch. However, simulated populations with variation for darker winter pelage are predicted to adapt rapidly, providing a trait-based genetic framework to facilitate evolutionary rescue. These discoveries demonstrate how the genetic basis of climate change adaptation can inform conservation.
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| 4. |
- Ferreira, Mafalda S, et al.
(författare)
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The Legacy of Recurrent Introgression during the Radiation of Hares
- 2020
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Ingår i: Systematic Biology. - : Oxford University Press (OUP). - 1063-5157 .- 1076-836X. ; 70:3, s. 593-607
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Tidskriftsartikel (refereegranskat)abstract
- Hybridization may often be an important source of adaptive variation, but the extent and long-term impacts of introgression have seldom been evaluated in the phylogenetic context of a radiation. Hares (Lepus) represent a widespread mammalian radiation of 32 extant species characterized by striking ecological adaptations and recurrent admixture. To understand the relevance of introgressive hybridization during the diversification of Lepus, we analyzed whole exome sequences (61.7 Mb) from 15 species of hares (1–4 individuals per species), spanning the global distribution of the genus, and two outgroups. We used a coalescent framework to infer species relationships and divergence times, despite extensive genealogical discordance. We found high levels of allele sharing among species and show that this reflects extensive incomplete lineage sorting and temporally layered hybridization. Our results revealed recurrent introgression at all stages along the Lepus radiation, including recent gene flow between extant species since the last glacial maximum but also pervasive ancient introgression occurring since near the origin of the hare lineages. We show that ancient hybridization between northern hemisphere species has resulted in shared variation of potential adaptive relevance to highly seasonal environments, including genes involved in circadian rhythm regulation, pigmentation, and thermoregulation. Our results illustrate how the genetic legacy of ancestral hybridization may persist across a radiation, leaving a long-lasting signature of shared genetic variation that may contribute to adaptation.
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| 5. |
- Ferreira, Mafalda S., et al.
(författare)
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The transcriptional landscape of seasonal coat colour moult in the snowshoe hare
- 2017
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Ingår i: Molecular Ecology. - : Wiley. - 0962-1083 .- 1365-294X. ; 26:16, s. 4173-4185
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Tidskriftsartikel (refereegranskat)abstract
- Seasonal coat colour change is an important adaptation to seasonally changing environments but the evolution of this and other circannual traits remains poorly understood. In this study, we use gene expression to understand seasonal coat colour moulting in wild snowshoe hares (Lepus americanus). We used hair colour to follow the progression of the moult, simultaneously sampling skin from three moulting stages in hares collected during the peak of the spring moult from white winter to brown summer pelage. Using RNA sequencing, we tested whether patterns of expression were consistent with predictions based on the established phases of the hair growth cycle. We found functionally consistent clustering across skin types, with 766 genes differentially expressed between moult stages. “White” pelage showed more differentially expressed genes that were upregulated relative to other skin types, involved in the transition between late telogen (quiescent stage) and the onset of anagen (proliferative stage). Skin samples from transitional “intermediate” and “brown” pelage were transcriptionally similar and resembled the regressive transition to catagen (regressive stage). We also detected differential expression of several key circadian clock and pigmentation genes, providing important means to dissect the bases of alternate seasonal colour morphs. Our results reveal that pelage colour is a useful biomarker for seasonal change but that there is a consistent lag between the main gene expression waves and change in visible coat colour. These experiments establish that developmental sampling from natural populations of nonmodel organisms can provide a crucial resource to dissect the genetic basis and evolution of complex seasonally changing traits.
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| 6. |
- Marques, João P., et al.
(författare)
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Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares
- 2017
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Ingår i: Scientific Data. - : Springer Science and Business Media LLC. - 2052-4463. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- We report the first mountain hare (Lepus timidus) transcriptome, produced by de novo assembly of RNA-sequencing reads. Data were obtained from eight specimens sampled in two localities, Alps and Ireland. The mountain hare tends to be replaced by the invading European hare (Lepus europaeus) in their numerous contact zones where the species hybridize, which affects their gene pool to a yet unquantified degree. We characterize and annotate the mountain hare transcriptome, detect polymorphism in the two analysed populations and use previously published data on the European hare (three specimens, representing the European lineage of the species) to identify 4 672 putative diagnostic sites between the species. A subset of 85 random independent SNPs was successfully validated using PCR and Sanger sequencing. These valuable genomic resources can be used to design tools to assess population status and monitor hybridization between species.
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| 7. |
- Muscarella, Robert, et al.
(författare)
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The global abundance of tree palms
- 2020
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 29:9, s. 1495-1514
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Tidskriftsartikel (refereegranskat)abstract
- AimPalms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change.LocationTropical and subtropical moist forests.Time periodCurrent.Major taxa studiedPalms (Arecaceae).MethodsWe assembled a pantropical dataset of 2,548 forest plots (covering 1,191 ha) and quantified tree palm (i.e., ≥10 cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure.ResultsOn average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work.ConclusionsTree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.
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| 8. |
- Nguyen, Thanh N, et al.
(författare)
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Global Impact of the COVID-19 Pandemic on Stroke Volumes and Cerebrovascular Events: A 1-Year Follow-up.
- 2023
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Ingår i: Neurology. - 1526-632X. ; 100:4
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Tidskriftsartikel (refereegranskat)abstract
- Declines in stroke admission, IV thrombolysis (IVT), and mechanical thrombectomy volumes were reported during the first wave of the COVID-19 pandemic. There is a paucity of data on the longer-term effect of the pandemic on stroke volumes over the course of a year and through the second wave of the pandemic. We sought to measure the effect of the COVID-19 pandemic on the volumes of stroke admissions, intracranial hemorrhage (ICH), IVT, and mechanical thrombectomy over a 1-year period at the onset of the pandemic (March 1, 2020, to February 28, 2021) compared with the immediately preceding year (March 1, 2019, to February 29, 2020).We conducted a longitudinal retrospective study across 6 continents, 56 countries, and 275 stroke centers. We collected volume data for COVID-19 admissions and 4 stroke metrics: ischemic stroke admissions, ICH admissions, IVT treatments, and mechanical thrombectomy procedures. Diagnoses were identified by their ICD-10 codes or classifications in stroke databases.There were 148,895 stroke admissions in the 1 year immediately before compared with 138,453 admissions during the 1-year pandemic, representing a 7% decline (95% CI [95% CI 7.1-6.9]; p < 0.0001). ICH volumes declined from 29,585 to 28,156 (4.8% [5.1-4.6]; p < 0.0001) and IVT volume from 24,584 to 23,077 (6.1% [6.4-5.8]; p < 0.0001). Larger declines were observed at high-volume compared with low-volume centers (all p < 0.0001). There was no significant change in mechanical thrombectomy volumes (0.7% [0.6-0.9]; p = 0.49). Stroke was diagnosed in 1.3% [1.31-1.38] of 406,792 COVID-19 hospitalizations. SARS-CoV-2 infection was present in 2.9% ([2.82-2.97], 5,656/195,539) of all stroke hospitalizations.There was a global decline and shift to lower-volume centers of stroke admission volumes, ICH volumes, and IVT volumes during the 1st year of the COVID-19 pandemic compared with the prior year. Mechanical thrombectomy volumes were preserved. These results suggest preservation in the stroke care of higher severity of disease through the first pandemic year.This study is registered under NCT04934020.
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| 9. |
- Pinto, Luís Valença, et al.
(författare)
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Assessment of NBS Impact on Pluvial Flood Regulation Within Urban Areas : A Case Study in Coimbra, Portugal
- 2022
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Ingår i: Nature-Based Solutions for Flood Mitigation. - Cham : Springer Science and Business Media Deutschland GmbH. - 9783030775056 ; , s. 289-312
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Bokkapitel (refereegranskat)abstract
- The majority of the world population is living in urban areas. As cities expand, soil sealing increases the vulnerability of urban areas to pluvial floods, and the consequent impacts on social and economic domains. Flood mitigation typically relies on grey infrastructures, but the implementation of Nature-Based Solutions (NBS) can be critical to cope with increasing flood hazard driven by urbanization and climate change. By mimicking natural hydrological processes, NBS enhance water retention, infiltration and evapotranspiration through greening, leading to lower runoff and flood hazard. The effectiveness of NBS on flood mitigation is affected by several factors including the type of NBS and the biophysical characteristics of the area. Nevertheless, a relatively limited number of studies have monitored the impact of NBS, and thus the lack of knowledge is still a barrier to the widespread implementation of this approach. This chapter assesses the impact of a Green Infrastructure (GI) located in Coimbra (Portugal), which performs as a NBS for runoff management and flood hazard mitigation. The study applies the widely used Curve Number method to estimate runoff within the Quinta de São Jerónimo study site, driven by rainfall events of 2-, 5-, 10- and 20-years recurrence, based on Intensity–Duration–Frequency precipitation curves. The results show that the implemented NBS can retain runoff produced by 20-years flood, decreasing the flood peak and flood hazard in downstream urban areas. This efficiency is achieved by combining blue, green and grey elements, and proved useful to enhance urban resilience. Furthermore, the green and blue elements of the NBS provide additional ecosystem services, including environmental, social and economic benefits (co-benefits), relevant for human well-being in urban areas.
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| 10. |
- Pinto, Luís Valença, et al.
(författare)
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Ecosystem services and well-being dimensions related to urban green spaces - A systematic review
- 2022
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Ingår i: Sustainable cities and society. - : Elsevier BV. - 2210-6707. ; 85
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Forskningsöversikt (refereegranskat)abstract
- Urban green spaces (UGS) supply several ecosystem services (ES) key to human wellbeing. In this article, we conducted a systematic review focused on identifying UGS's ES and wellbeing dimensions. From the 3626 articles screened, 218 were used in this review. Most studies were conducted in Europe, China, the United States of America (USA) and South Africa. Among all UGS, parks and gardens were the most investigated, with less of a focus on urban trees, forests, coastal mangroves, golf courses, roadside vegetation, and brownfields/unmanaged urban greenery. Cultural ES were the most studied, although it is well known that UGS also supply many provisioning and regulating ES. Health (mental and physical) and good social relations were the most investigated wellbeing dimensions, and food security received the least attention. Regarding the methodologies used to investigate the UGS contribution to human wellbeing, surveys, indicators, and surveys combined with statistical methods were the most common. Only a few works focusing on spatial modelling were validated, which is critical to ensure the reliability of the spatial models applied to UGS ES studies. Overall, this work identified the research gaps and future perspectives in ES and wellbeing dimensions provided by UGS, key to improving further research.
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