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- Glasbey, JC, et al.
(författare)
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- 2021
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swepub:Mat__t
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| 6. |
- Tinker, N. A., et al.
(författare)
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New DArT markers for oat provide enhanced map coverage and global germplasm characterization
- 2009
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 10:39
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). Results: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' x 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. Conclusion: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity.
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- Fielding, J. James, et al.
(författare)
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Tracing lake pollution, eutrophication and partial recovery from the sediments of Windermere, UK, using geochemistry and sediment microfabrics
- 2020
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Ingår i: Science of the Total Environment. - : Elsevier BV. - 0048-9697 .- 1879-1026. ; 722
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Tidskriftsartikel (refereegranskat)abstract
- Many lakes undergo anthropogenically driven eutrophication and pollution leading to decreasedwater and sediment quality. These effects can enhance seasonally changing lake redox conditions that may concentrate potentially toxic elements. Here we report the results of a multi-method geochemical and sediment microfabric analysis applied to reconstruct the history of cultural eutrophication and pollution of the North and South Basins of Windermere, UK. Eutrophication developed from the mid-19th to the earliest 20th centuries. Enhanced lake productivity is indicated by increased sedimentary delta C-13, and increased pollution by a higher concentration of metals (Pb, Hg, and As) in the sediment, likely enhanced by incorporation and adsorption to settling diatom aggregates, preserved as sedimentary laminae. In the South Basin, increasing sediment delta N-15 values occur in step with Zn, Hg, and Cu, linking metal enrichment to isotopically heavy nitrate (N) from anthropogenic sources. From around 1930, decreases in Mn and Fe-rich laminae indicate reduced deep-water ventilation, whereas periods of sediment anoxia increased, being most severe in the deeper North Basin. Strongly reducing sediment conditions promoted Fe and Mn reduction and Pb-bearing barite formation, hitherto only described from toxic minewastes and contaminated soils. From 1980 there was an increase in indicators of bottomwater oxygenation, although not to before 1930. But in the South Basin, the continued impacts of sewage are indicated by elevated sediment delta N-15. Imaging and X-ray microanalysis using scanning electron microscopy has shown seasonal-scale redoxmineralisation of Mn, Fe, and Ba related to intermittent sediment anoxia. Elevated concentrations of these metals and As also occur in the surficial sediment and provide evidence for dynamic redox mobilisation of potentially toxic elements to the lake water. Concentrations of As (up to 80 ppm), exceed international Sediment Quality Standards. This process may become more prevalent in the future with climate change driving lengthened summer stratification.
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| 10. |
- Harding, P., et al.
(författare)
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Wind regime changes in the Euro-Atlantic region driven by Late-Holocene Grand Solar Minima
- 2022
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Ingår i: Climate Dynamics. - : Springer Science and Business Media LLC. - 0930-7575 .- 1432-0894.
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Tidskriftsartikel (refereegranskat)abstract
- Understanding atmospheric response to radiative forcing, including the intensity and distribution of wind patterns is critical as this might have important implications in the coming decades. Long-term episodes of reduced solar activity (i.e. Grand Solar Minima, GSM) have triggered rapid climate change in the past, recorded in proxy-based records, including varved sediments from Meerfelder Maar, Germany, where the Homeric GSM (~ 2800 years ago) was studied. This study reconstructs windy conditions during the same GSM from Diss Mere, another varved record in England, to support the solar-wind linkage in the North Atlantic-European region. We use diatoms as proxies for windiness and support the palaeolimnological and palaeoclimate interpretation with a multi-proxy approach, including sedimentological, geochemical, and biological (chironomids and pollen) evidence. The diatom assemblage documents a shift from Pantocsekiella ocellata dominance to Stephanodiscus parvus and Lindavia comta, indicating a shift to more turbulent waters from ~ 2767 ± 28, linked to increased windiness. This shift is synchronous with changes in 14C production, linked to solar activity changes during the GSM. Both proxy records reflect a rapid and synchronous atmospheric response (i.e. stronger winds) at the onset and during the GSM in the North Atlantic and continental Europe. In order to test whether this solar-wind linkage is consistent during other GSMs and to understand the underlying climate dynamics, we analyse the wind response to solar forcing at the two study sites during the Little Ice Age, a period that includes several GSMs. For this, we have used a reconstruction based on a 1200-year-long simulation with an isotope-enabled climate model. Our study suggests that wind anomalies in the North Atlantic-European sector may relate to an anomalous atmospheric circulation in response to long-term solar forcing leading to north-easterlies modulated by the East Atlantic pattern.
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| 11. |
- Holmes, Naomi, et al.
(författare)
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Climatic variability during the last millennium in Western Iceland from lake sediment records
- 2016
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Ingår i: The Holocene. - : SAGE Publications. - 0959-6836 .- 1477-0911. ; 26:5, s. 756-771
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Tidskriftsartikel (refereegranskat)abstract
- The aim of this research was to create a decadal-scale terrestrial quantitative palaeoclimate record for NW Iceland from lake sediments for the last millennium. Geochemical, stable isotope and chironomid reconstructions were obtained from a lake sequence constrained by tephra deposits on the Snaefellsnes peninsula, western Iceland. Obtaining a quantitative record proved problematic, but the qualitative chironomid record showed clear trends associated with past summer temperatures, and the sedimentological records provided evidence for past changes in precipitation, mediated through catchment soil in-wash. When the full range of chronological uncertainty is considered, four clear phases of climatic conditions were identified: (1) a relatively warm phase between AD 1020 and 1310; (2) a relatively stable period between AD 1310 and 1510, cooler than the preceding period but still notably warmer than the second half of the millennium; (3) a consistent reduction of temperatures between AD 1560 and 1810, with the coolest period between AD 1680 and 1810; and (4) AD 1840-2000 has temperatures mainly warmer than in the preceding two centuries, with a rising trend and increased variability from c. AD 1900 onwards. The reconstructions show clearly that the first half of the millennium experienced warmer climatic conditions than the second half, with a return to the warmer climate only occurring in the last c. 100 years. Much of the variability of the chironomid record can be linked to changes in the North Atlantic Oscillation (NAO). The reconstructions presented can track low-frequency and long-term trends effectively and consistently but high-resolution and calibrated quantitative records remain more of a challenge - not just in finding optimal sedimentary deposits but also in finding the most reliable proxy. It is this that presents the real challenge for Holocene climate reconstruction from this key area of the North Atlantic.
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| 12. |
- Menoni, C. S., et al.
(författare)
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Nanometer-scale imaging and ablation with Extreme Ultraviolet lasers
- 2007
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Ingår i: 2007 CONFERENCE ON LASERS & ELECTRO-OPTICS/QUANTUM ELECTRONICS AND LASER SCIENCE CONFERENCE (CLEO/QELS 2007), VOLS 1-5. - 9781424435906 ; , s. 1401-1402
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Konferensbidrag (refereegranskat)abstract
- The short wavelength and high brightness of compact extreme ultraviolet lasers is shown to enable the development of microscopes with spatial resolution of tens of nanometers and new types of nanoprobes.
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| 13. |
- Menoni, C. S., et al.
(författare)
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Nanoscale resolution microscopy and ablation with extreme ultraviolet lasers
- 2007
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Ingår i: 2007 IEEE LEOS ANNUAL MEETING CONFERENCE PROCEEDINGS, VOLS 1 AND 2. - 9781424409242 ; , s. 488-489
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Konferensbidrag (refereegranskat)abstract
- We obtain a spatial resolution down to 38 run with full field imaging and laser-ablation systems that exploit the short wavelength and high brightness output from compact extreme ultraviolet lasers in combination with zone plate optics.
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| 15. |
- Wilkins, Justin J., et al.
(författare)
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Variability in the population pharmacokinetics of isoniazid in South African tuberculosis patients
- 2011
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Ingår i: British Journal of Clinical Pharmacology. - : Wiley. - 0306-5251 .- 1365-2125. ; 72:1, s. 51-62
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Tidskriftsartikel (refereegranskat)abstract
- AIM This study was designed to characterize the population pharmacokinetics of isoniazid in South African pulmonary tuberculosis patients. METHODS Concentration-time measurements obtained from 235 patients receiving oral doses of isoniazid as part of routine tuberculosis chemotherapy in two clinical studies were pooled and subjected to nonlinear mixed-effects analysis. RESULTS A two-compartmental model, including first-order absorption and elimination with allometric scaling, was found to describe the observed dose-exposure relationship for oral isoniazid adequately. A mixture model was used to characterize dual rates of isoniazid elimination. Estimates of apparent clearance in slow and fast eliminators were 9.70 and 21.6 l h(-1), respectively. The proportion of fast eliminators in the population was estimated to be 13.2%. Central volume of distribution was estimated to be 10% smaller in female patients and clearance was found to be 17% lower in patients with HIV. Variability in absorption rate (90%) was completely interoccasional in nature, whereas in relative bioavailability, interoccasional variability (8.4%) was lower than interindividual variability (26%). Oral doses, given once daily according to dosing policies at the time, were sufficient to reach therapeutic concentrations in the majority of the studied population, regardless of eliminator phenotype. Simulations suggested that current treatment guidelines (5 mg kg(-1)) may be suboptimal in fast eliminators with low body weight. CONCLUSIONS A population pharmacokinetic model was developed to characterize the highly variable pharmacokinetics of isoniazid in a South African pulmonary tuberculosis patient population. Current treatment guidelines may lead to underexposure in rapid isoniazid eliminators.
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| 16. |
- Wilkins, Justin J., et al.
(författare)
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Variability in the population pharmacokinetics of pyrazinamide in South African tuberculosis patients
- 2006
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Ingår i: European Journal of Clinical Pharmacology. - : Springer Science and Business Media LLC. - 0031-6970 .- 1432-1041. ; 62:9, s. 727-735
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: This study was designed to characterize the population pharmacokinetics of pyrazinamide in South African pulmonary tuberculosis patients, with special reference to interindividual and interoccasional variability (IIV and IOV, respectively). METHODS: Concentration-time measurements obtained from 227 patients receiving oral doses of pyrazinamide were pooled to create a dataset containing 3,092 data points spanning multiple dosing occasions. The software program NONMEM was used to analyze the data. RESULTS: A one-compartment model with first-order absorption, including a zero-order component describing release from formulation, and first-order elimination best described the data. The absorption rate constant was estimated to be bimodally distributed between two distinct subgroups, fast and slow, in approximately even proportion. Absorption rate was threefold greater in fast absorbers (3.56 h(-1)) in comparison to slow absorbers (1.25 h(-1)). Typical values of oral clearance and apparent volume of distribution were estimated as 3.42 L h(-1) and 29.2 l, respectively. IOV was supported in oral clearance (0.0238, variance) and absorption rate (0.623, variance). The duration of zero-order absorption was estimated as 0.290 h, and was quite variable between patients (0.957, variance). CONCLUSION: The absorption of pyrazinamide in the studied population was highly variable and two separate subpopulations were identified. IOV accounted for a proportion of the variability in clearance and the absorption rate constant.
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| 22. |
- de Melo, C. M. R., et al.
(författare)
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Introduction and evaluation on the US West Coast of a new strain (Midori) of Pacific oyster (Crassostrea gigas) collected from the Ariake Sea, southern Japan
- 2021
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Ingår i: Aquaculture. - : Elsevier BV. - 0044-8486. ; 531
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Tidskriftsartikel (refereegranskat)abstract
- We describe the introduction, taxonomic identification and genetic parameters for farm traits of the Midori strain of the Pacific oyster Crassostrea gigas - a possible alternative to the widely farmed Miyagi strain on the US West Coast. Broodstock (G0) oysters collected from the mouth of the Midori river and near Iwajima Island, Ariake Bay, Japan were identified as C. gigas based on the nuclear internal transcribed spacer (ITS) region and 28S gene as well as a mitochondrial (COI) marker. G0 and G1 generations and G2 larvae and spat were maintained in quarantine conditions and subjected to numerous histological exams and PCR tests for detection of pathogens of concern. After the G1 generation and G2 early life stages were found to be free of detectable diseases, G2 spat were planted at farm test sites and adults were used to produce a G3 generation. This G3 generation was cultured under non-quarantine conditions and families were planted at sub-tidal and inter-tidal test sites, in Oregon and California, respectively. Field performance traits were measured to determine the potential for improvement through selection. Overall, Midori oysters showed significantly lower values for harvest yield, survival, individual average weight and dry meat weight compared with oysters from a selected stock of the Miyagi strain of Pacific oyster; however, shell shape index (a measure of shell depth) was significantly greater in Midori oysters. Heritability estimates for group traits at harvest (survival, yield and individual average harvest weight) were high, whereas heritability estimates for individual traits (individual weight, wet meat weight and dry meat weight) and for shell dimension measurements (shell length, shell width and shell depth) were moderate-to-high. Family-by-site (GxE) correlations were low-to-moderate for all measured traits. Genetic correlations were positive and moderate-to-high among group traits and shell dimensions. In contrast, correlations between shell shape and other traits had small-to-moderate negative values but these were not statistically significant. Estimated potential genetic gain for dry meat weight was high (46%) whereas estimated gains for yield, individual average weight, individual weight were high-to-moderate (approximately 10%). In contrast, shell shape showed very little potential for genetic gain through selection. Overall, the Midori strain of the Pacific oyster shows promise as a deep-cupped oyster for the half-shell trade. Statement of relevance: We describe the introduction of a new strain of Pacific oyster (Midori) collected from southern Japan to the US West Coast. Rigorous quarantine protocols and disease tests were applied to ensure that the risks of introducing diseases were minimized. The Midori strain was found to have a deeper cup than the commonly farmed Miyagi strain but the potential estimated gain for improving this trait through selection was small. © 2020 Elsevier B.V.
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| 23. |
- De Wit, Pierre, 1978, et al.
(författare)
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Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms
- 2018
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 19
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Tidskriftsartikel (refereegranskat)abstract
- Background: Despite recent work to characterize gene expression changes associated with larval development in oysters, the mechanism by which the larval shell is first formed is still largely unknown. In Crassostrea gigas, this shell forms within the first 24 h post fertilization, and it has been demonstrated that changes in water chemistry can cause delays in shell formation, shell deformations and higher mortality rates. In this study, we use the delay in shell formation associated with exposure to CO2-acidified seawater to identify genes correlated with initial shell deposition. Results: By fitting linear models to gene expression data in ambient and low aragonite saturation treatments, we are able to isolate 37 annotated genes correlated with initial larval shell formation, which can be categorized into 1) ion transporters, 2) shell matrix proteins and 3) protease inhibitors. Clustering of the gene expression data into co-expression networks further supports the result of the linear models, and also implies an important role of dynein motor proteins as transporters of cellular components during the initial shell formation process. Conclusions: Using an RNA-Seq approach with high temporal resolution allows us to identify a conceptual model for how oyster larval calcification is initiated. This work provides a foundation for further studies on how genetic variation in these identified genes could affect fitness of oyster populations subjected to future environmental changes, such as ocean acidification.
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| 24. |
- Dearing, John A., et al.
(författare)
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Safe and just operating spaces for regional social-ecological systems
- 2014
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Ingår i: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 28, s. 227-238
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Tidskriftsartikel (refereegranskat)abstract
- Humanity faces a major global challenge in achieving wellbeing for all, while simultaneously ensuring that the biophysical processes and ecosystem services that underpin wellbeing are exploited within scientifically informed boundaries of sustainability. We propose a framework for defining the safe and just operating space for humanity that integrates social wellbeing into the original planetary boundaries concept (Rockstrom et al., 2009a,b) for application at regional scales. We argue that such a framework can: (1) increase the policy impact of the boundaries concept as most governance takes place at the regional rather than planetary scale; (2) contribute to the understanding and dissemination of complexity thinking throughout governance and policy-making; (3) act as a powerful metaphor and communication tool for regional equity and sustainability. We demonstrate the approach in two rural Chinese localities where we define the safe and just operating space that lies between an environmental ceiling and a social foundation from analysis of time series drawn from monitored and palaeoecological data, and from social survey statistics respectively. Agricultural intensification has led to poverty reduction, though not eradicated it, but at the expense of environmental degradation. Currently, the environmental ceiling is exceeded for degraded water quality at both localities even though the least well-met social standards are for available piped water and sanitation. The conjunction of these social needs and environmental constraints around the issue of water access and quality illustrates the broader value of the safe and just operating space approach for sustainable development.
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| 25. |
- Dearing, JA, et al.
(författare)
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Social-ecological systems in the Anthropocene : The need for integrating social and biophysical records at regional scales.
- 2015
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Ingår i: The Anthropocene Review. - : SAGE Publications. - 2053-0196 .- 2053-020X. ; 2:3, s. 220-246
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Tidskriftsartikel (refereegranskat)abstract
- Understanding social-ecological system dynamics is a major research priority for sustainable management of landscapes, ecosystems and resources. But the lack of multi-decadal records represents an important gap in information that hinders the development of the research agenda. Without improved information on the long-term and complex interactions between causal factors and responses, it will be difficult to answer key questions about trends, rates of change, tipping points, safe operating spaces and pre-impact conditions. Where available long-term monitored records are too short or lacking, palaeoenvironmental sciences may provide continuous multi-decadal records for an array of ecosystem states, processes and services. Combining these records with conventional sources of historical information from instrumental monitoring records, official statistics and enumerations, remote sensing, archival documents, cartography and archaeology produces an evolutionary framework for reconstructing integrated regional histories. We demonstrate the integrated approach with published case studies from Australia, China, Europe and North America.
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