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- Sigmundsson, F., et al.
(författare)
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Segmented lateral dyke growth in a rifting event at Bardarbunga volcanic system, Iceland
- 2015
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 517:7533
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Tidskriftsartikel (refereegranskat)abstract
- Crust at many divergent plate boundaries forms primarily by the injection of vertical sheet-like dykes, some tens of kilometres long(1). Previous models of rifting events indicate either lateral dyke growth away from a feeding source, with propagation rates decreasing as the dyke lengthens(2-4), or magma flowing vertically into dykes from an underlying source(5,6), with the role of topography on the evolution of lateral dykes not clear. Here we show how a recent segmented dyke intrusion in the Bardarbunga volcanic system grew laterally for more than 45 kilometres at a variable rate, with topography influencing the direction of propagation. Barriers at the ends of each segment were overcome by the build-up of pressure in the dyke end; then a new segment formed and dyke lengthening temporarily peaked. The dyke evolution, which occurred primarily over 14 days, was revealed by propagating seismicity, ground deformation mapped by Global Positioning System(GPS), interferometric analysis of satellite radar images (InSAR), and graben formation. The strike of the dyke segments varies from an initially radial direction away from the Bardarbunga caldera, towards alignment with that expected from regional stress at the distal end. A model minimizing the combined strain and gravitational potential energy explains the propagation path. Dyke opening and seismicity focused at the most distal segment at any given time, and were simultaneous with magma source deflation and slow collapse at the Bardarbunga caldera, accompanied by a series of magnitude M > 5 earthquakes. Dyke growth was slowed down by an effusive fissure eruption near the end of the dyke. Lateral dyke growth with segment barrier breaking by pressure build-up in the dyke distal end explains how focused upwelling of magma under central volcanoes is effectively redistributed over long distances to create new upper crust at divergent plate boundaries.
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- Bowers, Robert M., et al.
(författare)
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Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
- 2017
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Ingår i: Nature Biotechnology. - : NATURE PUBLISHING GROUP. - 1087-0156 .- 1546-1696. ; 35:8, s. 725-731
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Tidskriftsartikel (refereegranskat)abstract
- We present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.
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- Prakash, Varsha, et al.
(författare)
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Ribosome biogenesis during cell cycle arrest fuels EMT in development and disease
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- Ribosome biogenesis is a canonical hallmark of cell growth and proliferation. Here we show that execution of Epithelial-to-Mesenchymal Transition (EMT), a migratory cellular program associated with development and tumor metastasis, is fueled by upregulation of ribosome biogenesis during G1/S arrest. This unexpected EMT feature is independent of species and initiating signal, and is accompanied by release of the repressive nucleolar chromatin remodeling complex (NoRC) from rDNA, together with recruitment of the EMT-driving transcription factor Snai1 (Snail1), RNA Polymerase I (Pol I) and the Upstream Binding Factor (UBF). EMT-associated ribosome biogenesis is also coincident with increased nucleolar recruitment of Rictor, an essential component of the EMT-promoting mammalian target of rapamycin complex 2 (mTORC2). Inhibition of rRNA synthesis in vivo differentiates primary tumors to a benign, Estrogen Receptor-alpha (ER alpha) positive, Rictor-negative phenotype and reduces metastasis. These findings implicate the EMT-associated ribosome biogenesis program with cellular plasticity, de-differentiation, cancer progression and metastatic disease.
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- Dass, Randall A., et al.
(författare)
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Wnt5a Signals through DVL1 to Repress Ribosomal DNA Transcription by RNA Polymerase I
- 2016
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Ingår i: PLoS Genetics. - : Public Library of Science (PLoS). - 1553-7390 .- 1553-7404. ; 12:8
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Tidskriftsartikel (refereegranskat)abstract
- Ribosome biogenesis is essential for cell growth and proliferation and is commonly elevated in cancer. Accordingly, numerous oncogene and tumor suppressor signaling pathways target rRNA synthesis. In breast cancer, non-canonical Wnt signaling by Wnt5a has been reported to antagonize tumor growth. Here, we show that Wnt5a rapidly represses rDNA gene transcription in breast cancer cells and generates a chromatin state with reduced transcription of rDNA by RNA polymerase I (Pol I). These effects were specifically dependent on Dishevelled1 (DVL1), which accumulates in nucleolar organizer regions (NORs) and binds to rDNA regions of the chromosome. Upon DVL1 binding, the Pol I transcription activator and deacetylase Sirtuin 7 (SIRT7) releases from rDNA loci, concomitant with disassembly of Pol I transcription machinery at the rDNA promoter. These findings reveal that Wnt5a signals through DVL1 to suppress rRNA transcription. This provides a novel mechanism for how Wnt5a exerts tumor suppressive effects and why disruption of Wnt5a signaling enhances mammary tumor growth in vivo.
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- Kurylo, Chad M., et al.
(författare)
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Endogenous rRNA Sequence Variation Can Regulate Stress Response Gene Expression and Phenotype
- 2018
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Ingår i: Cell Reports. - : CELL PRESS. - 2211-1247. ; 25:1, s. 236-248.e6
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Tidskriftsartikel (refereegranskat)abstract
- Prevailing dogma holds that ribosomes are uniform in composition and function. Here, we show that nutrient limitation-induced stress in E. coli changes the relative expression of rDNA operons to alter the rRNA composition within the actively translating ribosome pool. The most upregulated operon encodes the unique 16S rRNA, rrsH, distinguished by conserved sequence variation within the small ribosomal subunit. rrsH-bearing ribosomes affect the expression of functionally coherent gene sets and alter the levels of the RpoS sigma factor, the master regulator of the general stress response. These impacts are associated with phenotypic changes in antibiotic sensitivity, biofilm formation, and cell motility and are regulated by stress response proteins, ReIA and ReIE, as well as the metabolic enzyme and virulence-associated protein, AdhE. These findings establish that endogenously encoded, naturally occurring rRNA sequence variation can modulate ribosome function, central aspects of gene expression regulation, and cellular physiology.
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| 13. |
- Parks, Matthew M., et al.
(författare)
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Implications of sequence variation on the evolution of rRNA
- 2019
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Ingår i: Chromosome Research. - : Springer. - 0967-3849 .- 1573-6849. ; 27:1-2, s. 89-93
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Forskningsöversikt (refereegranskat)abstract
- The evolution of the multi-copy family of ribosomal RNA (rRNA) genes is unique in regard to its genetics and genome evolution. Paradoxically, rRNA genes are highly homogenized within and between individuals, yet they are globally distinct between species. Here, we discuss the implications for models of rRNA gene evolution in light of our recent discoveries that ribosomes bearing rRNA sequence variants can affect gene expression and physiology and that intra-individual rRNA alleles exhibit both context- and tissue-specific expression.
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| 14. |
- Parks, Matthew M., et al.
(författare)
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Variant ribosomal RNA alleles are conserved and exhibit tissue-specific expression
- 2018
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Ingår i: Science Advances. - : AMER ASSOC ADVANCEMENT SCIENCE. - 2375-2548. ; 4:2
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Tidskriftsartikel (refereegranskat)abstract
- The ribosome, the integration point for protein synthesis in the cell, is conventionally considered a homogeneous molecular assembly that only passively contributes to gene expression. Yet, epigenetic features of the ribosomal DNA (rDNA) operon and changes in the ribosomes molecular composition have been associated with disease phenotypes, suggesting that the ribosome itself may possess inherent regulatory capacity. Analyzing whole-genome sequencing data from the 1000 Genomes Project and the Mouse Genomes Project, we find that rDNA copy number varies widely across individuals, and we identify pervasive intra-and interindividual nucleotide variation in the 5S, 5.8S, 18S, and 28S ribosomal RNA (rRNA) genes of both human and mouse. Conserved rRNA sequence heterogeneities map to functional centers of the assembled ribosome, variant rRNA alleles exhibit tissue-specific expression, and ribosomes bearing variant rRNA alleles are present in the actively translating ribosome pool. These findings provide a critical framework for exploring the possibility that the expression of genomically encoded variant rRNA alleles gives rise to physically and functionally heterogeneous ribosomes that contribute to mammalian physiology and human disease.
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| 15. |
- Paz-Soldan, C., et al.
(författare)
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Recent DIII-D advances in runaway electron measurement and model validation
- 2019
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 59:6
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Tidskriftsartikel (refereegranskat)abstract
- Novel measurements and modeling of runaway electron (RE) dynamics in DIII-D have resolved experimental discrepancies and validated predictions for ITER, improving confidence that RE avoidance and mitigation can be predictably achieved. Considering RE formation, first experimental assessments of the RE seed current demonstrates that present hot-tail theories are not yet accurate and require improved treatment of the pellet dynamics. Novel measurements of kinetic instabilities in the MHz-range have been made in the RE formation phase, with the intensity of these modes correlated with previously unexplained empirical thresholds for RE generation. Controlled RE dissipation experiments in quiescent regimes have validated RE distribution function dependencies on collisional and synchrotron damping, both in terms of distribution function shape and dissipation rates. Measurements of RE bremsstrahlung and synchrotron emission are now used in tandem to resolve energy and pitch-angle effects. A resolution to long-standing dissipation anomalies in the quiescent regime is offered by taking into account kinetic instability effects on RE phase-space dynamics. Kinetic instabilities in the 100-200 MHz range are directly observed, though modeling finds the largest dissipation arises from GHz range instabilities that are beyond the reach of existing diagnostics. Kinetic instabilities are also observed in the mature post-disruption RE plateau phase, so long as the collisional damping rate is reduced with low-Z injection. Experiments with high-Z injection find that the dissipation rate saturates with injection quantity, likely due to neutral diffusion rates being slower than vertical instability rates in DIII-D. Considering the final loss, a 0D model for first-wall Joule heating is found to be in agreement with experiment, and controlled access to RE equilibria with edge safety factor of two identifies novel dynamics brought about by large-scale kink instabilities. These dynamics are typified by fast (tens of microseconds) RE loss rates without RE beam regeneration. The above measurements and comparison with theory represent significant advances in the understanding of RE dynamics and indicate possible new opportunities for RE avoidance or mitigation via kinetic instabilities.
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| 16. |
- Spake, Rebecca, et al.
(författare)
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Unpacking ecosystem service bundles : Towards predictive mapping of synergies and trade-offs between ecosystem services
- 2017
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Ingår i: Global Environmental Change. - : Elsevier BV. - 0959-3780 .- 1872-9495. ; 47, s. 37-50
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Tidskriftsartikel (refereegranskat)abstract
- Multiple ecosystem services (ES) can respond similarly to social and ecological factors to form bundles. Identifying key social-ecological variables and understanding how they co-vary to produce these consistent sets of ES may ultimately allow the prediction and modelling of ES bundles, and thus, help us understand critical synergies and trade-offs across landscapes. Such an understanding is essential for informing better management of multi-functional landscapes and minimising costly trade-offs. However, the relative importance of different social and biophysiCal drivers of ES bundles in different types of social-ecological systems remains unclear. As such, a bottom-up understanding of the determinants of ES bundles is a critical research gap in ES and sustainability science. Here, we evaluate the current methods used in ES bundle science and synthesize these into four steps that capture the plurality of methods used to examine predictors of ES bundles. We then apply these four steps to a cross-study comparison (North and South French Alps) of relationships between social-ecological variables and ES bundles, as it is widely advocated that cross-study comparisons are necessary for achieving a general understanding of predictors of ES associations. We use the results of this case study to assess the strengths and limitations of current approaches for understanding distributions of ES bundles. We conclude that inconsistency of spatial scale remains the primary barrier for understanding and predicting ES bundles. We suggest a hypothesis-driven approach is required to predict relationships between ES, and we outline the research required for such an understanding to emerge.
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| 22. |
- Venkateswaran, Ramkumar V, et al.
(författare)
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Anemia and its association with clinical outcome in heart failure patients undergoing cardiac resynchronization therapy.
- 2015
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Ingår i: Journal of Interventional Cardiac Electrophysiology. - : Springer Science and Business Media LLC. - 1572-8595 .- 1383-875X. ; 44:3, s. 297-304
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Tidskriftsartikel (refereegranskat)abstract
- Although a substantial proportion of patients with heart failure (HF) have anemia, there is a paucity of data evaluating the impact of anemia on clinical outcome in CRT patients. Our goal was to examine the ability of baseline hemoglobin (Hb) level and change in Hb level over time to predict clinical 2-year outcome and echocardiographic response to CRT.
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| 23. |
- Wan, Qun, et al.
(författare)
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Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography.
- 2015
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 112:40, s. 12384-12389
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Tidskriftsartikel (refereegranskat)abstract
- Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.
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