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  • 1
    Online Resource
    Online Resource
    Copernicus GmbH ; 2020
    In:  Geoscientific Model Development Vol. 13, No. 1 ( 2020-01-10), p. 99-119
    In: Geoscientific Model Development, Copernicus GmbH, Vol. 13, No. 1 ( 2020-01-10), p. 99-119
    Abstract: Abstract. Sea ice is an important component of the global climate system. The presence of a snowpack covering sea ice can strongly modify the thermodynamic behavior of the sea ice, due to the low thermal conductivity and high albedo of snow. The snowpack can be stratified and change properties (density, water content, grain size and shape) throughout the seasons. Melting snow provides freshwater which can form melt ponds or cause flushing of salt out of the underlying sea ice, while flooding of the snow layer by saline ocean water can strongly impact both the ice mass balance and the freezing point of the snow. To capture the complex dynamics from the snowpack, we introduce modifications to the physics-based, multi-layer SNOWPACK model to simulate the snow–sea-ice system. Adaptations to the model thermodynamics and a description of water and salt transport through the snow–sea-ice system by coupling the transport equation to the Richards equation were added. These modifications allow the snow microstructure descriptions developed in the SNOWPACK model to be applied to sea ice conditions as well. Here, we drive the model with data from snow and ice mass-balance buoys installed in the Weddell Sea in Antarctica. The model is able to simulate the temporal evolution of snow density, grain size and shape, and snow wetness. The model simulations show abundant depth hoar layers and melt layers, as well as superimposed ice formation due to flooding and percolation. Gravity drainage of dense brine is underestimated as convective processes are so far neglected. Furthermore, with increasing model complexity, detailed forcing data for the simulations are required, which are difficult to acquire due to limited observations in polar regions.
    Type of Medium: Online Resource
    ISSN: 1991-9603
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2020
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  • 2
    In: Blood, American Society of Hematology, Vol. 124, No. 21 ( 2014-12-06), p. 764-764
    Abstract: Aberrant erythroid differentiation can give rise to anemias and leukemias. Regulated transcription elongation at erythroid loci is vital for specific differentiation steps during blood development. Transcriptional intermediary factor 1 gamma (TIF1γ), whose gene is mutated in the blood deficient zebrafish moonshine mutant, recruits positive elongation factors to erythroid genes, thus relieving paused Pol II. To elucidate the TIF1γ-mediated mechanisms in erythroid differentiation, we have performed a chemical suppressor screen in the bloodless moonshine mutant. Progeny of heterozygous moonshine mutants were treated at 50% epiboly with 4,000 individual chemical compounds with mostly known functional targets. A rescue in blood formation was assessed for by in situ hybridization for β-globin e3 expression in primitive erythrocytes at 22 hours post fertilization (hpf). Using this strategy we have identified peroxisome proliferator-activated receptor alpha (PPARα) agonists, most importantly, Clofibrate to rescue βe3 globin expression at 22 hpf in 70 - 90% of moonshine embryos in a dose-dependent manner. To address whether the rescue by Clofibrate is due to its activation of the PPARα receptor, we either knocked down PPARα using morpholinos or treated zebrafish embryos with the PPARα antagonist GW6471. In both cases we observed a significant reduction in Clofibrate-mediated rescue. To identify the PPARα-interacting proteome in an erythroid progenitor context, human K562 erythroleukemia cells expressing doxycyclin-inducible Flag-PPARα were generated. In these cells, PPARα target genes such as ANGPTL4 and PDK4 are activated starting four hours after doxycyclin addition and this activation is significantly reduced in the presence of the PPARα antagonist GW6471. Large-scale Flag-immunoprecipitation followed by mass spectrometric analysis identified the heterodimerization partner of PPARα, RXR, co-activators (NCOA1, NCOA6) and co-repressors (NCOR2), furthermore 24 subunits of the mediator complex, six subunits of the cohesin (loading) complex, seven RNA polymerase (Pol) II subunits as well as the Cyclin T1 subunit of P-TEFb and both subunits (SUPT5H, SUPT4H1) of DSIF, two proteins with a positive role in transcription elongation. In co-immunoprecipitation experiments using K562 cells, doxycyclin-induced PPARα activation leads to an enhanced interaction of Pol II with both, the Cyclin T1 and CDK9 subunits of P-TEFb. Morpholino-mediated knockdown of the mediator complex subunit med1 prevents Clofibrate-mediated rescue of βe3 globin expression in moonshine embryos. Together these data suggest that PPARα functionally interacts with the mediator complex in hematopoietic progenitors, leading to increased recruitment of the transcription elongation factors to lineage-specific genes. Our studies provide a basic understanding of the processes that regulate transcription elongation in the differentiation of hematopoietic cells, and could lead to novel therapeutic strategies for the treatment of blood diseases and leukemia. Disclosures Zon: FATE Therapeutics, Inc.: Consultancy, Equity Ownership, Founder Other, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties; Scholar Rock: Consultancy, Equity Ownership, Founder, Founder Other, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
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    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2014
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  • 3
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 80, No. 23_Supplement ( 2020-12-01), p. PR04-PR04
    Abstract: Understanding in-vivo mechanisms of erythropoiesis is critical for directed differentiation approaches to treat blood disorders such as leukemias. Zebrafish moonshine (mon) mutant embryos defective for the conserved transcriptional intermediary factor 1 gamma (tif1γ) do not specify enough erythroid progenitors due to a transcription elongation block characterized by aberrantly paused RNA polymerase II. To elucidate the TIF1γ-mediated mechanisms in erythroid differentiation, we performed a chemical suppressor screen using 3,100 compounds and identified inhibitors of the essential mitochondrial pyrimidine synthesis enzyme dihydroorotate dehydrogenase (DHODH). Leflunomide as well as the structurally unrelated DHODH inhibitor brequinar rescue the formation of erythroid progenitors in 61% (38/62) and 68% (50/74) of mon embryos, respectively. Beyond changes in nucleotide metabolism, in-vivo metabolic analyses revealed low levels of TCA cycle metabolites which were functionally linked to a reduced oxygen consumption rate. In addition, an increased 2HG/αKG ratio was associated with higher histone methylation states at H3K27, H3K36 and H4K20 as assessed by quantitative targeted mass spectrometry, which may contribute to the erythroid differentiation block upon tif1γ loss. DHODH is the only pyrimidine de novo synthesis enzyme located in mitochondria and its activity is coupled to that of the electron transport chain (ETC) via coenzyme Q (CoQ). Rotenone, a potent ETC complex I inhibitor reversed the rescue by DHODH inhibition in mon embryos. Through parallel genome-wide transcriptome and chromatin immunoprecipitation analyses, we found that genes encoding CoQ metabolic enzymes are direct TIF1γ targets. Treatment with the CoQ analog decylubiquinone rescued erythroid progenitors in 26% (33/126) of mon embryos. These results demonstrate a tight coordination of nucleotide and mitochondrial metabolism as a key function of tif1γ-dependent transcription and reveal that TIF1γ activity regulates a metabolic program that drives cell fate decisions in the early blood lineage. Our work highlights the importance of the plasticity achieved by transcription regulatory processes such as transcription elongation for metabolic processes during lineage differentiation and could have therapeutic potential for blood diseases. Citation Format: Marlies P. Rossmann, Karen Hoi, Victoria Chan, Brian J. Abraham, Song Yang, James Mullahoo, Malvina Papanastasiou, Ilaria Elia, Sejal Vyas, Partha P. Nag, Lucas B. Sullivan, Julie R. Perlin, Elliott J. Hagedorn, Sara Hetzel, Raha Weigert, Curtis R. Warren, Bilguujin Dorjsuren, Eugenia Custo Greig, Chad A. Cowan, Stuart L. Schreiber, Richard A. Young, Alexander Meissner, Marcia Haigis, Steven A. Carr, Leonard I. Zon. Transcriptional regulation of mitochondrial metabolism by TIF1γ drives erythroid progenitor differentiation [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PR04.
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
    RVK:
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2020
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  • 4
    In: Blood, American Society of Hematology, Vol. 134, No. Supplement_1 ( 2019-11-13), p. 152-152
    Abstract: Understanding the cell-autonomous as well as niche contributions governing erythropoiesis is critical for directed differentiation approaches of hematopoietic stem cells into differentiated red blood cells (RBCs) to treat blood disorders such as anemias and leukemias. Transcriptional intermediary factor 1 gamma (TIF1γ) is essential for erythropoiesis from zebrafish to mammals. Zebrafish moonshine mutant embryos defective for tif1γ do not make red blood cells (RBCs) due to a transcription elongation block characterized by aberrantly paused RNA polymerase II. Loss of factors involved in transcription elongation control, PAF1 and spt5, rescues the moonshine RBC defect. To elucidate the TIF1γ-mediated mechanisms in erythroid differentiation, we have performed a high-content chemical suppressor screen in the bloodless moonshine mutant using 3,500 compounds. Among the suppressors, we identified leflunomide, an inhibitor of dihydroorotate dehydrogenase (DHODH), an essential enzyme for de novo pyrimidine synthesis. Leflunomide as well as the structurally unrelated DHODH inhibitor brequinar both rescue the formation of primitive erythroid cells in 61% (38/62) and 68% (50/74) of moonshine embryos, respectively. Blastula transplant experiments revealed that tif1γ, in addition to its cell-autonomous role, plays a role in the hematopoietic niche for RBC development. Through in-vivo metabolomics analyses we have identified nucleotide metabolism as the most significantly altered process in moonshine mutants, including elevated levels of uridine monophosphate and low levels of nicotinamide adenine dinucleotide (NAD+). Low NAD+ levels are accompanied by a reduced oxygen consumption rate in tif1γ-depleted embryos by Seahorse analysis. In support, genome-wide transcriptome analysis coupled with chromatin immunoprecipitation studies revealed genes encoding coenzyme Q (CoQ) metabolic enzymes as direct TIF1γ targets. DHODH is the only enzyme of the pyrimidine de novo synthesis pathway located on the inner mitochondrial membrane and its activity is coupled to that of the electron transport chain (ETC). Rotenone, a potent ETC complex I inhibitor reverses the rescue of the blood defect by DHODH inhibition in moonshine embryos. Since DHODH function is linked to mitochondrial oxidative phosphorylation via CoQ activity, we asked whether alterations in mitochondrial metabolism might be causal for the RBC defect in moonshine mutants. Indeed, treatment with the CoQ analog decylubiquinone results in rescue of βe3 globin expression in 26% (33/126) of moonshine embryos. These results demonstrate a tight coordination of nucleotide and mitochondrial metabolism as a key function of tif1γ-dependent transcription and reveal that TIF1γ activity regulates a metabolic program that drives cell fate decisions in the early blood lineage. Our work highlights the importance of the plasticity achieved by transcription regulatory processes such as transcription elongation for metabolic processes during lineage differentiation and could have therapeutic potential for blood diseases and consequences for erythroid differentiation protocols. Disclosures Zon: Fate Therapeutics: Equity Ownership; Scholar Rock: Equity Ownership; CAMP4: Equity Ownership.
    Type of Medium: Online Resource
    ISSN: 0006-4971 , 1528-0020
    RVK:
    RVK:
    Language: English
    Publisher: American Society of Hematology
    Publication Date: 2019
    detail.hit.zdb_id: 1468538-3
    detail.hit.zdb_id: 80069-7
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  • 5
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 372, No. 6543 ( 2021-05-14), p. 716-721
    Abstract: Transcription and metabolism both influence cell function, but dedicated transcriptional control of metabolic pathways that regulate cell fate has rarely been defined. We discovered, using a chemical suppressor screen, that inhibition of the pyrimidine biosynthesis enzyme dihydroorotate dehydrogenase (DHODH) rescues erythroid differentiation in bloodless zebrafish moonshine (mon) mutant embryos defective for transcriptional intermediary factor 1 gamma ( tif1γ ). This rescue depends on the functional link of DHODH to mitochondrial respiration. The transcription elongation factor TIF1γ directly controls coenzyme Q (CoQ) synthesis gene expression. Upon tif1γ loss, CoQ levels are reduced, and a high succinate/α-ketoglutarate ratio leads to increased histone methylation. A CoQ analog rescues mon ’s bloodless phenotype. These results demonstrate that mitochondrial metabolism is a key output of a lineage transcription factor that drives cell fate decisions in the early blood lineage.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2021
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  • 6
    In: Cell, Elsevier BV, Vol. 184, No. 7 ( 2021-04), p. 1654-1656
    Type of Medium: Online Resource
    ISSN: 0092-8674
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    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2021
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    detail.hit.zdb_id: 2001951-8
    SSG: 12
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  • 7
    In: Immunity, Elsevier BV, Vol. 51, No. 1 ( 2019-07), p. 50-63.e5
    Type of Medium: Online Resource
    ISSN: 1074-7613
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2019
    detail.hit.zdb_id: 2001966-X
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  • 8
    Online Resource
    Online Resource
    Frontiers Media SA ; 2021
    In:  Frontiers in Marine Science Vol. 8 ( 2021-4-15)
    In: Frontiers in Marine Science, Frontiers Media SA, Vol. 8 ( 2021-4-15)
    Abstract: Snow depth on sea ice is an essential state variable of the polar climate system and yet one of the least known and most difficult to characterize parameters of the Arctic and Antarctic sea ice systems. Here, we present a new type of autonomous platform to measure snow depth, air temperature, and barometric pressure on drifting Arctic and Antarctic sea ice. “Snow Buoys” are designed to withstand the harshest environmental conditions and to deliver high and consistent data quality with minimal impact on the surface. Our current dataset consists of 79 time series (47 Arctic, 32 Antarctic) since 2013, many of which cover entire seasonal cycles and with individual observation periods of up to 3 years. In addition to a detailed introduction of the platform itself, we describe the processing of the publicly available (near real time) data and discuss limitations. First scientific results reveal characteristic regional differences in the annual cycle of snow depth: in the Weddell Sea, annual net snow accumulation ranged from 0.2 to 0.9 m (mean 0.34 m) with some regions accumulating snow in all months. On Arctic sea ice, the seasonal cycle was more pronounced, showing accumulation from synoptic events mostly between August and April and maxima in autumn. Strongest ablation was observed in June and July, and consistently the entire snow cover melted during summer. Arctic air temperature measurements revealed several above-freezing temperature events in winter that likely impacted snow stratigraphy and thus preconditioned the subsequent spring snow cover. The ongoing Snow Buoy program will be the basis of many future studies and is expected to significantly advance our understanding of snow on sea ice, also providing invaluable in situ validation data for numerical simulations and remote sensing techniques.
    Type of Medium: Online Resource
    ISSN: 2296-7745
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
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  • 9
    Online Resource
    Online Resource
    Elsevier BV ; 1972
    In:  Journal of Molecular Biology Vol. 64, No. 1 ( 1972-2), p. 237-245
    In: Journal of Molecular Biology, Elsevier BV, Vol. 64, No. 1 ( 1972-2), p. 237-245
    Type of Medium: Online Resource
    ISSN: 0022-2836
    Language: English
    Publisher: Elsevier BV
    Publication Date: 1972
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    SSG: 12
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  • 10
    Online Resource
    Online Resource
    The Company of Biologists ; 2021
    In:  Disease Models & Mechanisms Vol. 14, No. 6 ( 2021-06-01)
    In: Disease Models & Mechanisms, The Company of Biologists, Vol. 14, No. 6 ( 2021-06-01)
    Abstract: Mitochondria are organelles with vital functions in almost all eukaryotic cells. Often described as the cellular ‘powerhouses’ due to their essential role in aerobic oxidative phosphorylation, mitochondria perform many other essential functions beyond energy production. As signaling organelles, mitochondria communicate with the nucleus and other organelles to help maintain cellular homeostasis, allow cellular adaptation to diverse stresses, and help steer cell fate decisions during development. Mitochondria have taken center stage in the research of normal and pathological processes, including normal tissue homeostasis and metabolism, neurodegeneration, immunity and infectious diseases. The central role that mitochondria assume within cells is evidenced by the broad impact of mitochondrial diseases, caused by defects in either mitochondrial or nuclear genes encoding for mitochondrial proteins, on different organ systems. In this Review, we will provide the reader with a foundation of the mitochondrial ‘hardware’, the mitochondrion itself, with its specific dynamics, quality control mechanisms and cross-organelle communication, including its roles as a driver of an innate immune response, all with a focus on development, disease and aging. We will further discuss how mitochondrial DNA is inherited, how its mutation affects cell and organismal fitness, and current therapeutic approaches for mitochondrial diseases in both model organisms and humans.
    Type of Medium: Online Resource
    ISSN: 1754-8403 , 1754-8411
    Language: English
    Publisher: The Company of Biologists
    Publication Date: 2021
    detail.hit.zdb_id: 2451104-3
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