| 1. |
- Baker, Erin, et al.
(författare)
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Who is marginalized in energy justice? Amplifying community leader perspectives of energy transitions in Ghana
- 2021
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Ingår i: Energy Research & Social Science. - : Elsevier. - 2214-6296 .- 2214-6326. ; 73
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Tidskriftsartikel (refereegranskat)abstract
- There is a divide in energy access studies, between technologically-focused modeling papers in engineering and economics, and energy justice frameworks and principles grounded in social sciences. Quantitative computational models are necessary when analyzing energy, and more specifically electricity, systems, as they are technologically-complex systems that can diverge from intuitive patterns. To assure energy justice, these models must be reflective of, and informative to, a wide range of stakeholders, including households and communities alongside utilities, governments, and others. Yet, moving from a qualitative understanding of preferences to quantitative modeling is challenging. In this perspective piece, we pilot the use of the value-focused thinking framework to inform stakeholder engagement. The result is a strategic objective hierarchy that highlights the tradeoffs and the social, economic and technological factors that need to be measured in models. We apply the process in Ghana, using a survey, stakeholder workshops, and follow-up interviews to uncover key tradeoffs and stakeholder-derived objectives. We discuss three key areas that have been rarely, if ever, well-represented in energy models: (1) the relationship between the dynamics of electricity end-use and the technology and economic structure of the system; (2) explicit tradeoffs between electricity access, cost, and reliability as defined by stakeholders; and (3) the definition of new objectives, such as minimizing hazards related to theft. We conclude that this model of engagement provides an opportunity to tie together rigorous qualitative analysis and stakeholder engagement with crucial quantitative models of the electricity system.
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| 2. |
- Bredeweg, Erin L., et al.
(författare)
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A molecular genetic toolbox for Yarrowia lipolytica
- 2017
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Ingår i: Biotechnology for Biofuels. - : Springer Science and Business Media LLC. - 1754-6834 .- 1754-6834. ; 10:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain. Results: We have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. Conclusions: These molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products.
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| 3. |
- Combes, F., et al.
(författare)
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PKS 1830-211: OH and HI at z = 0.89 and the first MeerKAT UHF spectrum
- 2021
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Ingår i: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 648
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Tidskriftsartikel (refereegranskat)abstract
- The Large Survey Project (LSP) "MeerKAT Absorption Line Survey"(MALS) is a blind H I 21 cm and OH 18 cm absorption line survey in the L- and UHF-bands, primarily designed to better determine the occurrence of atomic and molecular gas in the circumgalactic and intergalactic medium, and its redshift evolution. Here we present the first results using the UHF band obtained towards the strongly lensed radio source PKS 1830-211, revealing the detection of absorption produced by the lensing galaxy. With merely 90 min of data acquired on-source for science verification and processed using the Automated Radio Telescope Imaging Pipeline (ARTIP), we detect in absorption the known H I 21 cm and OH 18 cm main lines at z = 0.89 at an unprecedented signal-to-noise ratio (4000 in the continuum, in each 6 km s-1 wide channel). For the first time we report the detection of OH satellite lines at z = 0.89, which until now have not been detected at z > 0.25. We decompose the OH lines into a thermal and a stimulated contribution, where the 1612 and 1720 MHz lines are conjugate. The total OH 1720 MHz emission line luminosity is 6100 L⊙. This is the most luminous known 1720 MHz maser line and is also among the most luminous of the OH main line megamasers. The absorption components of the different images of the background source sample different light paths in the lensing galaxy, and their weights in the total absorption spectrum are expected to vary in time on daily and monthly time scales. We compare our normalized spectra with those obtained more than 20 years ago, and find no variation. We interpret the absorption spectra with the help of a lens galaxy model derived from an N-body hydrodynamical simulation, with a morphology similar to its optical HST image. The resulting absorption lines depend mainly on the background continuum and the radial distribution of the gas surface density for each atomic and molecular species. We show that it is possible to reproduce the observations assuming a realistic spiral galaxy disk without invoking any central gas outflows. However, there are distinct and faint high-velocity features in the ALMA millimeter absorption spectra that most likely originate from high-velocity clouds or tidal features. These clouds may contribute to broaden the H I and OH spectra.
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| 4. |
- Duncan, Kyle D., et al.
(författare)
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In situ imaging reveals disparity between prostaglandin localization and abundance of prostaglandin synthases
- 2021
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Ingår i: Communications Biology. - : Springer Nature. - 2399-3642. ; 4:1
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Tidskriftsartikel (refereegranskat)abstract
- Duncan et al. use a mass spectrometry imaging method to assess the localization and concentration of prostaglandins (PGs) in mouse tissues during pregnancy. This study brings new biological insights into the spatial evaluation of PGs in tissues, which could reveal the functional significance of each PGs during different stages of embryo development/pregnancy. Prostaglandins are important lipids involved in mediating many physiological processes, such as allergic responses, inflammation, and pregnancy. However, technical limitations of in-situ prostaglandin detection in tissue have led researchers to infer prostaglandin tissue distributions from localization of regulatory synthases, such as COX1 and COX2. Herein, we apply a novel mass spectrometry imaging method for direct in situ tissue localization of prostaglandins, and combine it with techniques for protein expression and RNA localization. We report that prostaglandin D-2, its precursors, and downstream synthases co-localize with the highest expression of COX1, and not COX2. Further, we study tissue with a conditional deletion of transformation-related protein 53 where pregnancy success is low and confirm that PG levels are altered, although localization is conserved. Our studies reveal that the abundance of COX and prostaglandin D-2 synthases in cellular regions does not mirror the regional abundance of prostaglandins. Thus, we deduce that prostaglandins tissue localization and abundance may not be inferred by COX or prostaglandin synthases in uterine tissue, and must be resolved by an in situ prostaglandin imaging.
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| 5. |
- Holmfeldt, Linda, et al.
(författare)
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The genomic landscape of hypodiploid acute lymphoblastic leukemia
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1546-1718 .- 1061-4036. ; 45:3, s. 242-252
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Tidskriftsartikel (refereegranskat)abstract
- The genetic basis of hypodiploid acute lymphoblastic leukemia (ALL), a subtype of ALL characterized by aneuploidy and poor outcome, is unknown. Genomic profiling of 124 hypodiploid ALL cases, including whole-genome and exome sequencing of 40 cases, identified two subtypes that differ in the severity of aneuploidy, transcriptional profiles and submicroscopic genetic alterations. Near-haploid ALL with 24-31 chromosomes harbor alterations targeting receptor tyrosine kinase signaling and Ras signaling (71%) and the lymphoid transcription factor gene IKZF3 (encoding AIOLOS; 13%). In contrast, low-hypodiploid ALL with 32-39 chromosomes are characterized by alterations in TP53 (91.2%) that are commonly present in nontumor cells, IKZF2 (encoding HELIOS; 53%) and RB1 (41%). Both near-haploid and low-hypodiploid leukemic cells show activation of Ras-signaling and phosphoinositide 3-kinase (PI3K)-signaling pathways and are sensitive to PI3K inhibitors, indicating that these drugs should be explored as a new therapeutic strategy for this aggressive form of leukemia.
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| 6. |
- Hotchkiss, Erin, et al.
(författare)
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Modeling priming effects on microbial consumption of dissolved organic carbon in rivers
- 2014
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Ingår i: Journal of Geophysical Research - Biogeosciences. - 2169-8953 .- 2169-8961. ; 119:5, s. 982-995
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Tidskriftsartikel (refereegranskat)abstract
- Rivers receive and process large quantities of terrestrial dissolved organic carbon (DOC). Biologically available (unstable) DOC leached from primary producers may stimulate (i.e., prime) the consumption of more stable terrestrially derived DOC by heterotrophic microbes. We measured microbial DOC consumption (i.e., decay rates) from contrasting C sources in 10 rivers in the western and Midwestern United States using short-term bioassays of river water, soil and algal leachates, glucose, and commercial humate. We added inorganic nutrients (ammonium and phosphorus) to a subset of bioassays. We also amended a subset of river, soil, and commercial humate bioassays with glucose or algal leachates to test the hypothesis that unstable DOC primes consumption of more stable DOC. We used prior measurements of source-specific DOC bioavailability, linked with a Bayesian process model, to estimate means and posterior probability distributions for source-specific DOC decay rates in multisource bioassays. Modeled priming effects ranged from a -130 to +370% change in more stable DOC decay when incubated with unstable DOC. Glucose increased modeled river DOC decay by an average of 87% among all rivers. Glucose and algal leachates increased soil leachate and commercial humate decay by an average of 25% above background rates. Inorganic nutrient additions did not have consistent effects on DOC decay, likely because most of the study rivers had high ambient background nutrients. Our results demonstrate that the priming effect can augment DOC decay in rivers. In addition, Bayesian models can be used to estimate mechanisms driving aquatic ecosystem processes that are difficult to measure directly.
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| 7. |
- Phillips, Helen R. P., et al.
(författare)
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Global distribution of earthworm diversity
- 2019
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 0036-8075 .- 1095-9203. ; 366:6464, s. 480-
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Tidskriftsartikel (refereegranskat)abstract
- Soil organisms, including earthworms, are a key component of terrestrial ecosystems. However, little is known about their diversity, their distribution, and the threats affecting them. We compiled a global dataset of sampled earthworm communities from 6928 sites in 57 countries as a basis for predicting patterns in earthworm diversity, abundance, and biomass. We found that local species richness and abundance typically peaked at higher latitudes, displaying patterns opposite to those observed in aboveground organisms. However, high species dissimilarity across tropical locations may cause diversity across the entirety of the tropics to be higher than elsewhere. Climate variables were found to be more important in shaping earthworm communities than soil properties or habitat cover. These findings suggest that climate change may have serious implications for earthworm communities and for the functions they provide.
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| 8. |
- Pomraning, Kyle R., et al.
(författare)
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Regulation of yeast-to-hyphae transition in Yarrowia lipolytica
- 2018
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Ingår i: mSphere. - 2379-5042. ; 3:6
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Tidskriftsartikel (refereegranskat)abstract
- The yeast Yarrowia lipolytica undergoes a morphological transition from yeast-to-hyphal growth in response to environmental conditions. A forward genetic screen was used to identify mutants that reliably remain in the yeast phase, which were then assessed by whole-genome sequencing. All the smooth mutants identified, so named because of their colony morphology, exhibit independent loss of DNA at a repetitive locus made up of interspersed ribosomal DNA and short 10- to 40-mer telomere-like repeats. The loss of repetitive DNA is associated with downregulation of genes with stress response elements (5'-CCCCT-3') and upregulation of genes with cell cycle box (5'-ACGCG-3') motifs in their promoter region. The stress response element is bound by the transcription factor Msn2p in Saccharomyces cerevisiae. We confirmed that the Y. lipolytica msn2 (Ylmsn2) ortholog is required for hyphal growth and found that overexpression of Ylmsn2 enables hyphal growth in smooth strains. The cell cycle box is bound by the Mbp1p/Swi6p complex in S. cerevisiae to regulate G1-to-S phase progression. We found that overexpression of either the Ylmbp1 or Ylswi6 homologs decreased hyphal growth and that deletion of either Ylmbp1 or Ylswi6 promotes hyphal growth in smooth strains. A second forward genetic screen for reversion to hyphal growth was performed with the smooth-33 mutant to identify additional genetic factors regulating hyphal growth in Y. lipolytica. Thirteen of the mutants sequenced from this screen had coding mutations in five kinases, including the histidine kinases Ylchk1 and Ylnik1 and kinases of the high-osmolarity glycerol response (HOG) mitogen-activated protein (MAP) kinase cascade Ylssk2, Ylpbs2, and Ylhog1. Together, these results demonstrate that Y. lipolytica transitions to hyphal growth in response to stress through multiple signaling pathways.
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| 9. |
- Rutter, Nick, et al.
(författare)
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Evaluation of forest snow processes models (SnowMIP2)
- 2009
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Ingår i: Journal of Geophysical Research. - : American Geophysical Union (AGU). - 0148-0227 .- 2156-2202. ; 114:6
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Tidskriftsartikel (refereegranskat)abstract
- Thirty-three snowpack models of varying complexity and purpose were evaluated across a wide range of hydrometeorological and forest canopy conditions at five Northern Hemisphere locations, for up to two winter snow seasons. Modeled estimates of snow water equivalent (SWE) or depth were compared to observations at forest and open sites at each location. Precipitation phase and duration of above-freezing air temperatures are shown to be major influences on divergence and convergence of modeled estimates of the subcanopy snowpack. When models are considered collectively at all locations, comparisons with observations show that it is harder to model SWE at forested sites than open sites. There is no universal "best'' model for all sites or locations, but comparison of the consistency of individual model performances relative to one another at different sites shows that there is less consistency at forest sites than open sites, and even less consistency between forest and open sites in the same year. A good performance by a model at a forest site is therefore unlikely to mean a good model performance by the same model at an open site (and vice versa). Calibration of models at forest sites provides lower errors than uncalibrated models at three out of four locations. However, benefits of calibration do not translate to subsequent years, and benefits gained by models calibrated for forest snow processes are not translated to open conditions.
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| 10. |
- Senyard, Julienne M., et al.
(författare)
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Stop whining and make the best of it : a cross-national comparison of responses to regional disadvantage in the wine industry
- 2012
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Konferensbidrag (refereegranskat)abstract
- Our cross-national field study of wine entrepreneurship in the “wrong” places provides some redress to the focus of the “regional advantage” literature on places that have already won and on the firms that benefit from “clusters” and other centers of industry advantage. Regional “disadvantage” is at best a shadowy afterthought to this literature. By poking around in these shadows, we help to synthesize and extend the incipient yet burgeoning literature on entrepreneurial “resourcefulness” and we contribute to the developing body of insights and theory pertinent to the numerous but often ignored firms and startups that mostly need to worry about how they will compete at all now if they are ever to have of chance of “winning” in the future. The core of our findings suggests that understandable – though contested – processes of ingenuity underlie entrepreneurial responses to regional disadvantage. Because we study entrepreneurship that from many angles simply does not make sense, we are also able to proffer a novel perspective on entrepreneurial sensemaking.
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