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| 2. |
- Leebens-Mack, James H., et al.
(författare)
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One thousand plant transcriptomes and the phylogenomics of green plants
- 2019
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Ingår i: Nature. - : Nature Publishing Group. - 0028-0836 .- 1476-4687. ; 574:7780, s. 679-
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Tidskriftsartikel (refereegranskat)abstract
- Green plants (Viridiplantae) include around 450,000-500,000 species(1,2) of great diversity and have important roles in terrestrial and aquatic ecosystems. Here, as part of the One Thousand Plant Transcriptomes Initiative, we sequenced the vegetative transcriptomes of 1,124 species that span the diversity of plants in a broad sense (Archaeplastida), including green plants (Viridiplantae), glaucophytes (Glaucophyta) and red algae (Rhodophyta). Our analysis provides a robust phylogenomic framework for examining the evolution of green plants. Most inferred species relationships are well supported across multiple species tree and supermatrix analyses, but discordance among plastid and nuclear gene trees at a few important nodes highlights the complexity of plant genome evolution, including polyploidy, periods of rapid speciation, and extinction. Incomplete sorting of ancestral variation, polyploidization and massive expansions of gene families punctuate the evolutionary history of green plants. Notably, we find that large expansions of gene families preceded the origins of green plants, land plants and vascular plants, whereas whole-genome duplications are inferred to have occurred repeatedly throughout the evolution of flowering plants and ferns. The increasing availability of high-quality plant genome sequences and advances in functional genomics are enabling research on genome evolution across the green tree of life.
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| 3. |
- Halbach, Laura, et al.
(författare)
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Tidewater Glaciers and Bedrock Characteristics Control the Phytoplankton Growth Environment in a Fjord in the Arctic
- 2019
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Ingår i: Frontiers in Marine Science. - : Frontiers Media SA. - 2296-7745. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- Meltwater discharge from tidewater glaciers impacts the adjacent marine environment. Due to the global warming, tidewater glaciers are retreating and will eventually terminate on land. Yet, the mechanisms through which meltwater runoff and subglacial discharge from tidewater glaciers influence marine primary production remain poorly understood, as data in close proximity to glacier fronts are scarce. Here, we show that subglacial meltwater discharge and bedrock characteristics of the catchments control the phytoplankton growth environment inside the fjord, based on data collected in close proximity to tidewater glacier fronts in Kongsfjorden, Svalbard from 26 to 31 July 2017. In the southern part of the inner fjord, glacial meltwater from subglacial discharge was rich in fine sediments derived from erosion of Devonian Old Red Sandstone and carbonate rock deposits, limiting light availability for phytoplankton (0.6 mg m(-3) Chl a on average, range 0.2-1.9 mg m(-3)). In contrast, coarser sediments derived from gneiss and granite bedrock and lower subglacial discharge rates were associated with more favourable light conditions facilitating a local phytoplankton bloom in the northern part of the inner fjord with mean Chl a concentration of 2.8 mg m(-3) (range 1.3-7.4 mg m(-3)). In the northern part, glacier meltwater was a direct source of silicic acid through weathering of the silica-rich gneiss and granite bedrock. Upwelling of the subglacial freshwater discharge plume at the Kronebreen glacier front in the southern part entrained large volumes of ambient, nutrient-rich bottom waters which led to elevated surface concentrations of ammonium, nitrate, and partly silicic acid. Total dissolved inorganic nitrogen transported to the surface with the upwelling of the subglacial discharge plume has a significant potential to enhance summer primary production in Kongsfjorden, with ammonium released from the seafloor being of particular importance. The transition from tidewater to land-terminating glaciers may, thus, reduce the input of nutrients to the surface layer with negative consequences for summer productivity.
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| 14. |
- Gusarova, Viktoria, et al.
(författare)
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Genetic inactivation of ANGPTL4 improves glucose homeostasis and is associated with reduced risk of diabetes
- 2018
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 9, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Angiopoietin-like 4 (ANGPTL4) is an endogenous inhibitor of lipoprotein lipase that modulates lipid levels, coronary atherosclerosis risk, and nutrient partitioning. We hypothesize that loss of ANGPTL4 function might improve glucose homeostasis and decrease risk of type 2 diabetes (T2D). We investigate protein-altering variants in ANGPTL4 among 58,124 participants in the DiscovEHR human genetics study, with follow-up studies in 82,766 T2D cases and 498,761 controls. Carriers of p.E40K, a variant that abolishes ANGPTL4 ability to inhibit lipoprotein lipase, have lower odds of T2D (odds ratio 0.89, 95% confidence interval 0.85-0.92, p = 6.3 × 10-10), lower fasting glucose, and greater insulin sensitivity. Predicted loss-of-function variants are associated with lower odds of T2D among 32,015 cases and 84,006 controls (odds ratio 0.71, 95% confidence interval 0.49-0.99, p = 0.041). Functional studies in Angptl4-deficient mice confirm improved insulin sensitivity and glucose homeostasis. In conclusion, genetic inactivation of ANGPTL4 is associated with improved glucose homeostasis and reduced risk of T2D.
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| 15. |
- Allocca, Giancarlo, et al.
(författare)
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Validation of 'Somnivore', a Machine Learning Algorithm for Automated Scoring and Analysis of Polysomnography Data
- 2019
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Ingår i: Frontiers in Neuroscience. - : Frontiers Media S.A.. - 1662-4548 .- 1662-453X. ; 13
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Tidskriftsartikel (refereegranskat)abstract
- Manual scoring of polysomnography data is labor-intensive and time-consuming, and most existing software does not account for subjective differences and user variability. Therefore, we evaluated a supervised machine learning algorithm, Somnivore (TM), for automated wake-sleep stage classification. We designed an algorithm that extracts features from various input channels, following a brief session of manual scoring, and provides automated wake-sleep stage classification for each recording. For algorithm validation, polysomnography data was obtained from independent laboratories, and include normal, cognitively-impaired, and alcohol-treated human subjects (total n = 52), narcoleptic mice and drug-treated rats (total n = 56), and pigeons (n = 5). Training and testing sets for validation were previously scored manually by 1-2 trained sleep technologists from each laboratory. F-measure was used to assess precision and sensitivity for statistical analysis of classifier output and human scorer agreement. The algorithm gave high concordance with manual visual scoring across all human data (wake 0.91 +/- 0.01; N1 0.57 +/- 0.01; N2 0.81 +/- 0.01; N3 0.86 +/- 0.01; REM 0.87 +/- 0.01), which was comparable to manual inter-scorer agreement on all stages. Similarly, high concordance was observed across all rodent (wake 0.95 +/- 0.01; NREM 0.94 +/- 0.01; REM 0.91 +/- 0.01) and pigeon (wake 0.96 +/- 0.006; NREM 0.97 +/- 0.01; REM 0.86 +/- 0.02) data. Effects of classifier learning from single signal inputs, simple stage reclassification, automated removal of transition epochs, and training set size were also examined. In summary, we have developed a polysomnography analysis program for automated sleep-stage classification of data from diverse species. Somnivore enables flexible, accurate, and high-throughput analysis of experimental and clinical sleep studies.
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| 16. |
- Björling, Alexander, 1983, et al.
(författare)
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Structural photoactivation of a full-length bacterial phytochrome
- 2016
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 2:8
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Tidskriftsartikel (refereegranskat)abstract
- Phytochromes are light sensor proteins found in plants, bacteria, and fungi. They function by converting a photon absorption event into a conformational signal that propagates from the chromophore through the entire protein. However, the structure of the photoactivated state and the conformational changes that lead to it are not known. We report time-resolved x-ray scattering of the full-length phytochrome from Deinococcus radiodurans on micro-and millisecond time scales. We identify a twist of the histidine kinase output domains with respect to the chromophore-binding domains as the dominant change between the photoactivated and resting states. The time-resolved data further show that the structural changes up to the microsecond time scales are small and localized in the chromophore-binding domains. The global structural change occurs within a few milliseconds, coinciding with the formation of the spectroscopic meta-Rc state. Our findings establish key elements of the signaling mechanism of full-length bacterial phytochromes.
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| 17. |
- Takala, Heikki, et al.
(författare)
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Light-induced structural changes in a monomeric bacteriophytochrome
- 2016
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 3:5
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Tidskriftsartikel (refereegranskat)abstract
- Phytochromes sense red light in plants and various microorganism. Light absorption causes structural changes within the protein, which alter its biochemical activity. Bacterial phytochromes are dimeric proteins, but the functional relevance of this arrangement remains unclear. Here, we use time-resolved X-ray scattering to reveal the solution structural change of a monomeric variant of the photosensory core module of the phytochrome from Deinococcus radiodurans. The data reveal two motions, a bend and a twist of the PHY domain with respect to the chromophore-binding domains. Infrared spectroscopy shows the refolding of the PHY tongue. We conclude that a monomer of the phytochrome photosensory core is sufficient to perform the light-induced structural changes. This implies that allosteric cooperation with the other monomer is not needed for structural activation. The dimeric arrangement may instead be intrinsic to the biochemical output domains of bacterial phytochromes. © Author(s) 2016.
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| 18. |
- Wang, Xiaocui, et al.
(författare)
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Generation of a large compressive strain wave in graphite by ultrashort-pulse laser irradiation
- 2019
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 6:2
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Tidskriftsartikel (refereegranskat)abstract
- We have studied strain wave generation in graphite induced by an intense ultrashort laser pulse. The study was performed in the intensity regime above the ablation threshold of graphite. The aim was to maximize the strain and, thus, also the internal pressure (stress). Laser pulses with a 1 ps temporal duration melt the surface of graphite resulting in a molten material which initially exists at the solid density. As the molten material expands, a compressive strain wave starts propagating into the crystal below the molten layer. The strain pulse was studied with time-resolved X-ray diffraction. At a temporal delay of 100 ps after laser excitation, we observed >10% compressive strain, which corresponds to a pressure of 7.2 GPa. This strain could be reproduced by hydrodynamic simulations, which also provided a temperature map as a function of time and depth.
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| 19. |
- Al-Handal, Adil Y, 1952, et al.
(författare)
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Observations on diatoms inhabiting natural and artificial substrates in Kongsfjorden, Svalbard, the Arctic
- 2016
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Ingår i: Polar Biology. - : Springer Science and Business Media LLC. - 0722-4060 .- 1432-2056. ; 39:11, s. 1913-1932
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Tidskriftsartikel (refereegranskat)abstract
- The most dramatic effects of global climate change are predicted for the Arctic, and there is a raising concern about the lack of baseline information on microalgal biodiversity. The present study was motivated by the general lack of information on species distribution of Arctic benthic diatoms and particularly studies providing photographs to facilitate morphological species identification. Diatoms were studied in samples collected from Ny lesund, Spitsbergen, Svalbard, during summer 2006 and spring 2008. Two types of samples were examined: diatoms scraped from ceramic tiles, immersed at 0.5 m depth (2006), and diatoms extracted from surface sediment, collected at 0.5 to 3 m depth (2008). A total number of 75 taxa belonging to 45 genera were encountered. Sixty-eight species were found in the sediment samples and 48 on the ceramic tiles, of which 41 species were found on both substrata. Common species of the tile assemblages were Fragilariopsis spp., Licmophora spp., Odontella aurita, Synedropsis hyperborea and Trachyneis aspera, while Thalassiosira spp., Diploneis spp. and Navicula spp. were common in the sediment samples. Twenty-five percent of the observed diatom species belonged to freshwater taxa brought to the fjord from surrounding meltwater and river discharges. ELMANN A, 1992, DEEP-SEA RESEARCH PART A-OCEANOGRAPHIC RESEARCH PAPERS, V39, PS525
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| 20. |
- Al-Handal, Adil Y, 1952, et al.
(författare)
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Two new marine species of Cocconeis (Bacillariophyceae) from the west coast of Sweden
- 2019
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Ingår i: European Journal of Taxonomy. - : Museum National D'Histoire Naturelle. - 2118-9773. ; 497, s. 1-16
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Tidskriftsartikel (refereegranskat)abstract
- This paper is part of a project of studying benthic diatom biodiversity on marine coastal regions of Sweden with focus on rare and less known species. Two new species of Cocconeis Ehrenb. are described from Vrango, a small island in the west coast of Sweden. Both species were found as epiphytic on the green alga Ulva intestinalis L. Cocconeis magnoareolata Al-Handal, Riaux-Gob., R.Jahn & A.K.Wulff sp. nov. is a small species not exceeding 9 mu m in length and characterized by having large subquadrangular areolae on the sternum valve. Cocconeis vrangoensis Al-Handal & Riaux-Gob. sp. nov. appears similar to some taxa of the 'Cocconeis scutellum complex', but differs by its stria density on both valves and variable features of the areola and valvocopula ultrastructure. Detailed descriptions based on light and electron microscopy examination, a comparison with closely related taxa, as well as a description of the habitat of both species are here presented.
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| 21. |
- Leshchev, Denis, et al.
(författare)
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Tracking the picosecond deactivation dynamics of a photoexcited iron carbene complex by time-resolved X-ray scattering
- 2018
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Ingår i: Chemical Science. - : Royal Society of Chemistry (RSC). - 2041-6520 .- 2041-6539. ; 9:2, s. 405-414
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Tidskriftsartikel (refereegranskat)abstract
- Recent years have seen the development of new iron-centered N-heterocyclic carbene (NHC) complexes for solar energy applications. Compared to typical ligand systems, the NHC ligands provide Fe complexes with longer-lived metal-to-ligand charge transfer (MLCT) states. This increased lifetime is ascribed to strong ligand field splitting provided by the NHC ligands that raises the energy levels of the metal centered (MC) states and therefore reduces the deactivation efficiency of MLCT states. Among currently known NHC systems, [Fe(btbip)2]2+ (btbip = 2,6-bis(3-tert-butyl-imidazol-1-ylidene)pyridine) is a unique complex as it exhibits a short-lived MC state with a lifetime on the scale of a few hundreds of picoseconds. Hence, this complex allows for a detailed investigation, using 100 ps X-ray pulses from a synchrotron, of strong ligand field effects on the intermediate MC state in an NHC complex. Here, we use time-resolved wide angle X-ray scattering (TRWAXS) aided by density functional theory (DFT) to investigate the molecular structure, energetics and lifetime of the high-energy MC state in the Fe-NHC complex [Fe(btbip)2]2+ after excitation to the MLCT manifold. We identify it as a 260 ps metal-centered quintet (5MC) state, and we refine the molecular structure of the excited-state complex verifying the DFT results. Using information about the hydrodynamic state of the solvent, we also determine, for the first time, the energy of the 5MC state as 0.75 ± 0.15 eV. Our results demonstrate that due to the increased ligand field strength caused by NHC ligands, upon transition from the ground state to the 5MC state, the metal to ligand bonds extend by unusually large values: by 0.29 Å in the axial and 0.21 Å in the equatorial direction. These results imply that the transition in the photochemical properties from typical Fe complexes to novel NHC compounds is manifested not only in the destabilization of the MC states, but also in structural distortion of these states.
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| 22. |
- Ohana, D., et al.
(författare)
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Identification of meat products by shotgun spectral matching
- 2016
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Ingår i: Food Chemistry. - : Elsevier BV. - 0308-8146 .- 1873-7072. ; 203, s. 28-34
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Tidskriftsartikel (refereegranskat)abstract
- A new method, based on shotgun spectral matching of peptide tandem mass spectra, was successfully applied to the identification of different food species. The method was demonstrated to work on raw as well as processed samples from 16 mammalian and 10 bird species by counting spectral matches to spectral libraries in a reference database with one spectral library per species. A phylogenetic tree could also be constructed directly from the spectra. Nearly all samples could be correctly identified at the species level, and 100% at the genus level. The method does not use any genomic information and unlike targeted methods, no prior knowledge of genetic variation within a genus or species is necessary.
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| 23. |
- Porcheret, Kate, et al.
(författare)
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Investigation of the impact of total sleep deprivation at home on the number of intrusive memories to an analogue trauma
- 2019
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Ingår i: Translational Psychiatry. - : Nature Publishing Group. - 2158-3188. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Sleep enhances the consolidation of memory; however, this property of sleep may be detrimental in situations where memories of an event can lead to psychopathology, such as following a traumatic event. Intrusive memories of trauma are emotional memories that spring to mind involuntarily and are a core feature of post-traumatic stress disorder. Total sleep deprivation in a hospital setting on the first night after an analogue trauma (a trauma film) led to fewer intrusive memories compared to sleep as usual in one study. The current study aimed to test an extension of these findings: sleep deprivation under more naturalistic conditions-at home. Polysomnographic recordings show inconsistent sleep deprivation was achieved at home. Fewer intrusive memories were reported on day 1 after the trauma film in the sleep-deprived condition. On day 2 the opposite was found: more intrusive memories in the sleep-deprived condition. However, no significant differences were found with the removal of two participants with extreme values and no difference was found in the total number of intrusive memories reported in the week following the trauma film. Voluntary memory of the trauma film was found to be slightly impaired in the sleep deprivation condition. In conclusion, compared to our eariler findings using total sleep deprivation in a hospital setting, in the current study the use of inconsistent sleep deprivation at home does not replicate the pattern of results on reducing the number of intrusive memories. Considering the conditions under which sleep deprivation (naturalistic versus hospital) was achieved requires further examination.
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| 24. |
- Porcheret, Kate, et al.
(författare)
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Psychological Effect of an Analogue Traumatic Event Reduced by Sleep Deprivation
- 2015
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Ingår i: Sleep. - : OXFORD UNIV PRESS INC. - 0161-8105 .- 1550-9109. ; 38:7, s. 1017-1025
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Tidskriftsartikel (refereegranskat)abstract
- Study Objective: To examine the effect of sleep deprivation compared to sleep, immediately after experimental trauma stimuli on the development of intrusive memories to that trauma stimuli. Design: Participants were exposed to a film with traumatic content (trauma film). The immediate response to the trauma film was assessed, followed by either total sleep deprivation (sleep deprived group, N = 20) or sleep as usual (sleep group, N = 22). Twelve hours after the film viewing the initial psychological effect of the trauma film was measured and for the subsequent 6 days intrusive emotional memories related to the trauma film were recorded in daily life. Setting: Academic sleep laboratory and participants' home environment. Participants: Healthy paid volunteers. Measurements and results: On the first day after the trauma film, the psychological effect as assessed by the Impact of Event Scale - Revised was lower in the sleep deprived group compared to the sleep group. In addition, the sleep deprived group reported fewer intrusive emotional memories (mean 2.28, standard deviation [SD] 2.91) compared to the sleep group (mean 3.76, SD 3.35). Because habitual sleep/circadian patterns, psychological health, and immediate effect of the trauma film were similar at baseline for participants of both groups, the results cannot be accounted for by pre-existing inequalities between groups. Conclusions: Our findings suggest that sleep deprivation on one night, rather than sleeping, reduces emotional effect and intrusive memories following exposure to experimental trauma.
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| 25. |
- Romanov, Roman A., et al.
(författare)
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Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes
- 2017
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Ingår i: Nature Neuroscience. - : Nature Publishing Group. - 1097-6256 .- 1546-1726. ; 20:2, s. 176-188
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Tidskriftsartikel (refereegranskat)abstract
- The hypothalamus contains the highest diversity of neurons in the brain. Many of these neurons can co-release neurotransmitters and neuropeptides in a use-dependent manner. Investigators have hitherto relied on candidate protein-based tools to correlate behavioral, endocrine and gender traits with hypothalamic neuron identity. Here we map neuronal identities in the hypothalamus by single-cell RNA sequencing. We distinguished 62 neuronal subtypes producing glutamatergic, dopaminergic or GABAergic markers for synaptic neurotransmission and harboring the ability to engage in task-dependent neurotransmitter switching. We identified dopamine neurons that uniquely coexpress the Onecut3 and Nmur2 genes, and placed these in the periventricular nucleus with many synaptic afferents arising from neuromedin S+ neurons of the suprachiasmatic nucleus. These neuroendocrine dopamine cells may contribute to the dopaminergic inhibition of prolactin secretion diurnally, as their neuromedin S+ inputs originate from neurons expressing Per2 and Per3 and their tyrosine hydroxylase phosphorylation is regulated in a circadian fashion. Overall, our catalog of neuronal subclasses provides new understanding of. hypothalamic organization and function.
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| 26. |
- Wells, M. L., et al.
(författare)
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Harmful algal blooms and climate change: Learning from the past and present to forecast the future
- 2015
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Ingår i: Harmful Algae. - : Elsevier BV. - 1568-9883. ; 49, s. 68-93
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Tidskriftsartikel (refereegranskat)abstract
- Climate change pressures will influence marine planktonic systems globally, and it is conceivable that harmful algal blooms may increase in frequency and severity. These pressures will be manifest as alterations in temperature, stratification, light, ocean acidification, precipitation-induced nutrient inputs, and grazing, but absence of fundamental knowledge of the mechanisms driving harmful algal blooms frustrates most hope of forecasting their future prevalence. Summarized here is the consensus of a recent workshop held to address what currently is known and not known about the environmental conditions that favor initiation and maintenance of harmful algal blooms. There is expectation that harmful algal bloom (HAB) geographical domains should expand in some cases, as will seasonal windows of opportunity for harmful algal blooms at higher latitudes. Nonetheless there is only basic information to speculate upon which regions or habitats HAB species may be the most resilient or susceptible. Moreover, current research strategies are not well suited to inform these fundamental linkages. There is a critical absence of tenable hypotheses for how climate pressures mechanistically affect HAB species, and the lack of uniform experimental protocols limits the quantitative cross-investigation comparisons essential to advancement. A HAB "best practices" manual would help foster more uniform research strategies and protocols, and selection of a small target list of model HAB species or isolates for study would greatly promote the accumulation of knowledge. Despite the need to focus on keystone species, more studies need to address strain variability within species, their responses under multifactorial conditions, and the retrospective analyses of long-term plankton and cyst core data; research topics that are departures from the norm. Examples of some fundamental unknowns include how larger and more frequent extreme weather events may break down natural biogeographic barriers, how stratification may enhance or diminish HAB events, how trace nutrients (metals, vitamins) influence cell toxicity, and how grazing pressures may leverage, or mitigate HAB development. There is an absence of high quality time-series data in most regions currently experiencing HAB outbreaks, and little if any data from regions expected to develop HAB events in the future. A subset of observer sites is recommended to help develop stronger linkages among global, national, and regional climate change and HAB observation programs, providing fundamental datasets for investigating global changes in the prevalence of harmful algal blooms. Forecasting changes in HAB patterns over the next few decades will depend critically upon considering harmful algal blooms within the competitive context of plankton communities, and linking these insights to ecosystem, oceanographic and climate models. From a broader perspective, the nexus of HAB science and the social sciences of harmful algal blooms is inadequate and prevents quantitative assessment of impacts of future HAB changes on human well-being. These and other fundamental changes in HAB research will be necessary if HAB science is to obtain compelling evidence that climate change has caused alterations in HAB distributions, prevalence or character, and to develop the theoretical, experimental, and empirical evidence explaining the mechanisms underpinning these ecological shifts. © 2015 Elsevier B.V.
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