SwePub - search: WFRF:(Ivanova Natalia)

Enumeration	Reference	Cover	Find
1.	Alpizar, Francisco, 1974, et al. (author) Global Chemicals Outlook II. From Legacies to Innovative Solutions: Implementing the 2030 Agenda for Sustainable Development 2019 Reports (other academic/artistic)abstract 1. The size of the global chemical industry exceeded United States dollars 5 trillion in 2017. It is projected to double by 2030. Consumption and production are rapidly increasing in emerging economies. Global supply chains, and the trade of chemicals and products, are becoming increasingly complex. 2. Driven by global megatrends, growth in chemical-intensive industry sectors (e.g. construction, agriculture, electronics) creates risks, but also opportunities to advance sustainable consumption, production and product innovation. 3. Hazardous chemicals and other pollutants (e.g. plastic waste and pharmaceutical pollutants) continue to be released in large quantities. They are ubiquitous in humans and the environment and are accumulating in material stocks and products, highlighting the need to avoid future legacies through sustainable materials management and circular business models. 4. The benefits of action to minimize adverse impacts have been estimated in the high tens of billions of United States dollars annually. The World Health Organization estimated the burden of disease from selected chemicals at 1.6 million lives in 2016 (this is likely to be an underestimate). Chemical pollution also threatens a range of ecosystem services. 5. International treaties and voluntary instruments have reduced the risks of some chemicals and wastes, but progress has been uneven and implementation gaps remain. As of 2018, more than 120 countries had not implemented the Globally Harmonized System of Classification and Labelling of Chemicals. 6. Addressing legislation and capacity gaps in developing countries and emerging economies remains a priority. Also, resources have not matched needs. There are opportunities for new and innovative financing (e.g. through cost recovery and engagement of the financial sector). 7. Significant resources can be saved by sharing knowledge on chemical management instruments more widely, and by enhancing mutual acceptance of approaches in areas ranging from chemical hazard assessment to alternatives assessment. 8. Frontrunner companies – from chemical producers to retailers – are introducing sustainable supply chain management, full material disclosure, risk reduction beyond compliance, and human rights-based policies. However, widespread implementation of these initiatives has not yet been achieved. 9. Consumer demand, as well as green and sustainable chemistry education and innovation (e.g. though start-ups), are among the important drivers of change. They can be scaled up through enabling policies, reaping the potential benefits of chemistry innovations for sustainable development. 10. Global knowledge gaps can be filled. This can be achieved, for example, by taking steps to harmonize research protocols, considering health or environmental impact information and harm caused to set and address priorities (e.g. emerging issues), and strengthening the science-policy interface through enhanced collaboration of scientists and decision-makers.
2.	Angioni, C., et al. (author) The impact of poloidal asymmetries on tungsten transport in the core of JET H-mode plasmas 2015 In: Physics of Plasmas. - : AMER INST PHYSICS. - 1070-664X .- 1089-7674. ; 22:5 Journal article (peer-reviewed)abstract Recent progress in the understanding and prediction of the tungsten behaviour in the core of JET H-mode plasmas with ITER-like wall is presented. Particular emphasis is given to the impact of poloidal asymmetries of the impurity density. In particular, it is shown that the predicted reduction of temperature screening induced by the presence of low field side localization of the tungsten density produced by the centrifugal force is consistent with the observed tungsten behaviour in a JET discharge in H-mode baseline scenario. This provides first evidence of the role of poloidal asymmetries in reducing the strength of temperature screening. The main differences between plasma parameters in JET baseline and hybrid scenario discharges which affect the impact of poloidally asymmetric density on the tungsten radial transport are identified. This allows the conditions by which tungsten accumulation can be avoided to be more precisely defined.
3.	Arnichand, H., et al. (author) Discriminating the trapped electron modes contribution in density fluctuation spectra 2015 In: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 55:9 Journal article (peer-reviewed)abstract Quasi-coherent (QC) modes have been reported for more than 10 years in reflectometry fluctuations spectra in the core region of fusion plasmas. They have characteristics in-between coherent and broadband fluctuations as they oscillate at a marked frequency but have a wide spectrum. This work presents further evidences of the link recently established between QC modes and the trapped electron modes (TEM) instabilities (Arnichand et al 2014 Nucl. Fusion 54 123017). In electron cyclotron resonance heated discharges of Tore Supra, an enhancement of QC modes amplitude is observed in a region where TEM cause impurity transport and turbulence. In JET Ohmic plasmas, QC modes disappear during density ramp-up and current ramp-down. This is reminiscent of Tore Supra and TEXTOR observations during transitions from the linear Ohmic confinement (LOC) to the saturated Ohmic confinement (SOC) regimes. Evidencing TEM activity then becomes experimentally possible via analysis of fluctuation spectra.
4.	Baiocchi, B., et al. (author) Turbulent transport analysis of JET H-mode and hybrid plasmas using QuaLiKiz and Trapped Gyro Landau Fluid 2015 In: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 0741-3335 .- 1361-6587. ; 57:3 Journal article (peer-reviewed)abstract The physical transport processes at the basis of JET typical inductive H-mode scenarios and advanced hybrid regimes, with improved thermal confinement, are analyzed by means of some of the newest and more sophisticated quasi-linear transport models: trapped gyro Landau fluid (TGLF) and QuaLiKiz. The temporal evolution of JET pulses is modelled by CRONOS where the turbulent transport is modelled by either QuaLiKiz or TGLF. Both are first principle models with a more comprehensive physics than the models previously developed and therefore allow the analysis of the physics at the basis of the investigated scenarios. For H-modes, ion temperature gradient (ITG) modes are found to be dominant and the transport models are able to properly reproduce temperature profiles in self-consistent simulations. However, for hybrid regimes, in addition to ITG trapped electron modes (TEM) are also found to be important and different physical mechanisms for turbulence reduction play a decisive role. Whereas E x B flow shear and plasma geometry have a limited impact on turbulence, the presence of a large population of fast ions, quite important in low density regimes, can stabilize core turbulence mainly when the electromagnetic effects are taken into account. The TGLF transport model properly captures these mechanisms and correctly reproduces temperatures.
5.	Bolshakova, I., et al. (author) Experimental evaluation of stable long term operation of semiconductor magnetic sensors at ITER relevant environment 2015 In: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 55:8 Journal article (peer-reviewed)abstract The paper deals with radiation resistant sensors and their associated measuring instrumentation developed in the course of R and D activities carried out in the framework of an international collaboration. The first trial tests of three-dimensional (3D) probes with Hall sensors have been performed in European tokamaks TORE SUPRA (2004) and JET (2005). Later in 2009 six sets of 3D probes were installed in JET and now continue to operate. The statistical analysis performed in 2014 on the basis of the JET database have demonstrated stable long term operation of all 18 sensors of 3D probes. The results of measurements conducted at the neutron fluxes of nuclear reactors have demonstrated the operability of the sensors up to high neutron fluences of F > 10(18)n , cm(-2) that exceeds the maximum one for the locations of steady state sensors in ITER over its total lifetime.
6.	Bourdelle, C., et al. (author) L to H mode transition : parametric dependencies of the temperature threshold 2015 In: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 55:7 Journal article (peer-reviewed)abstract The L to H mode transition occurs at a critical power which depends on various parameters, such as the magnetic field, the density, etc. Experimental evidence on various tokamaks (JET, ASDEX-Upgrade, DIII-D, Alcator C-Mod) points towards the existence of a critical temperature characterizing the transition. This criterion for the L-H transition is local and is therefore easier to be compared to theoretical approaches. In order to shed light on the mechanisms of the transition, simple theoretical ideas are used to derive a temperature threshold (T-th). They are based on the stabilization of the underlying turbulence by a mean radial electric field shear. The nature of the turbulence varies as the collisionality decreases, from resistive ballooning modes to ion temperature gradient and trapped electron modes. The obtained parametric dependencies of the derived T-th are tested versus magnetic field, density, effective charge. Various robust experimental observations are reproduced, in particular T-th increases with magnetic field B and increases with density below the density roll-over observed on the power threshold.
7.	Bourdelle, C., et al. (author) WEST Physics Basis 2015 In: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 55:6 Journal article (peer-reviewed)abstract With WEST (Tungsten Environment in Steady State Tokamak) (Bucalossi et al 2014 Fusion Eng. Des. 89 907-12), the Tore Supra facility and team expertise (Dumont et al 2014 Plasma Phys. Control. Fusion 56 075020) is used to pave the way towards ITER divertor procurement and operation. It consists in implementing a divertor configuration and installing ITER-like actively cooled tungsten monoblocks in the Tore Supra tokamak, taking full benefit of its unique long-pulse capability. WEST is a user facility platform, open to all ITER partners. This paper describes the physics basis of WEST: the estimated heat flux on the divertor target, the planned heating schemes, the expected behaviour of the L-H threshold and of the pedestal and the potential W sources. A series of operating scenarios has been modelled, showing that ITER-relevant heat fluxes on the divertor can be achieved in WEST long pulse H-mode plasmas.
8.	Bowers, Robert M., et al. (author) Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea 2017 In: Nature Biotechnology. - : NATURE PUBLISHING GROUP. - 1087-0156 .- 1546-1696. ; 35:8, s. 725-731 Journal article (peer-reviewed)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.
9.	Chankin, A. V., et al. (author) Influence of the E X B drift in high recycling divertors on target asymmetries 2015 In: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 0741-3335 .- 1361-6587. ; 57:9 Journal article (peer-reviewed)abstract Detailed analysis of convective fluxes caused by E x B drifts is carried out in a realistic JET configuration, based on a series of EDGE2D-EIRENE runs. The EDGE2D-EIRENE code includes all guiding centre drifts, E x B as well as. B and centrifugal drifts. Particle sources created by divergences of radial and poloidal components of the E x B drift are separately calculated for each flux tube in the divertor. It is demonstrated that in high recycling divertor conditions radial E x B drift creates particle sources in the common flux region (CFR) consistent with experimentally measured divertor and target asymmetries, with the poloidal E x B drift creating sources of an opposite sign but smaller in absolute value. That is, the experimentally observed asymmetries in the CFR are the opposite to what poloidal E x B drift by itself would cause. In the private flux region (PFR), the situation is reversed, with poloidal E x B drift being dominant. In this region poloidal E x B drift by itself contributes to experimentally observed asymmetries. Thus, in each region, the dominant component of the E x B drift acts so as to create the density (and hence, also temperature) asymmetries that are observed both in experiment and in 2D edge fluid codes. Since the total number of charged particles is much greater in the CFR than in PFR, divertor asymmetries caused by the E x B drift should be attributed primarily to particle sources in the CFR caused by radial E x B drift.
10.	Cheng, Kimberley, et al. (author) Structural analysis of double translocated tmRNA on the 70S ribosome indicates flexibility of the tmRNA structure. Other publication (other academic/artistic)
11.	Cheng, Kimberley, et al. (author) tmRNA-SmpB complex mimics native aminoacyl-tRNAs in the A site of stalled ribosomes 2010 In: Journal of Structural Biology. - : Elsevier BV. - 1047-8477 .- 1095-8657. ; 169:3, s. 342-348 Journal article (peer-reviewed)abstract Bacterial ribosomes stalled on faulty, often truncated, mRNAs lacking stop codons are rescued by trans-translation. It relies on an RNA molecule (tmRNA) capable of replacing the faulty mRNA with its own open reading frame (ORF). Translation of tmRNA ORF results in the tagging of faulty protein for degradation and its release from the ribosome. We used single-particle cryo-electron microscopy to visualize tmRNA together with its helper protein SmpB on the 70S Escherichia coli ribosome in states subsequent to GTP hydrolysis on elongation factor Tu (EF-Tu). Three-dimensional reconstruction and heterogeneity analysis resulted in a 15 A resolution structure of the tmRNA-SmpB complex accommodated in the A site of the ribosome, which shows that SmpB mimics the anticodon- and D-stem of native tRNAs missing in the tRNA-like domain of tmRNA. We conclude that the tmRNA-SmpB complex accommodates in the ribosomal A site very much like an aminoacyl-tRNA during protein elongation.
12.	Conroy, Sean, et al. (author) The global build-up to intrinsic edge localized mode bursts seen in divertor full flux loops in JET 2015 In: Physics of Plasmas. - : AMER INST PHYSICS. - 1070-664X .- 1089-7674. ; 22:7 Journal article (peer-reviewed)abstract A global signature of the build-up to an intrinsic edge localized mode (ELM) is found in the temporal analytic phase of signals measured in full flux azimuthal loops in the divertor region of JET. Toroidally integrating, full flux loop signals provide a global measurement proportional to the voltage induced by changes in poloidal magnetic flux; they are electromagnetically induced by the dynamics of spatially integrated current density. We perform direct time-domain analysis of the high time-resolution full flux loop signals VLD2 and VLD3. We analyze plasmas where a steady H-mode is sustained over several seconds during which all the observed ELMs are intrinsic; there is no deliberate intent to pace the ELMing process by external means. ELM occurrence times are determined from the Be II emission at the divertor. We previously [ Chapman et al., Phys. Plasmas 21, 062302 (2014); Chapman et al., in 41st EPS Conference on Plasma Physics, Europhysics Conference Abstracts (European Physical Society, 2014), Vol. 38F, ISBN 2-914771-90-8] found that the occurrence times of intrinsic ELMs correlate with specific temporal analytic phases of the VLD2 and VLD3 signals. Here, we investigate how the VLD2 and VLD3 temporal analytic phases vary with time in advance of the ELM occurrence time. We identify a build-up to the ELM in which the VLD2 and VLD3 signals progressively align to the temporal analytic phase at which ELMs preferentially occur, on a similar to 2 - 5ms timescale. At the same time, the VLD2 and VLD3 signals become temporally phase synchronized with each other, consistent with the emergence of coherent global dynamics in the integrated current density. In a plasma that remains close to a global magnetic equilibrium, this can reflect bulk displacement or motion of the plasma. This build-up signature to an intrinsic ELM can be extracted from a time interval of data that does not extend beyond the ELM occurrence time, so that these full flux loop signals could assist in ELM prediction or mitigation.
13.	Cooper, W. A., et al. (author) Free boundary equilibrium in 3D tokamaks with toroidal rotation 2015 In: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 55:6 Journal article (peer-reviewed)abstract The three-dimensional VMEC equilibrium solver has been adapted to numerically investigate the approximate toroidal rotation model we have derived. We concentrate our applications on the simulation of JET snakes and MAST long-lived modes under free boundary conditions. Helical core solutions are triggered when exceeds a threshold value, typically 2.7% in JET-like plasmas. A large plasma current and edge bootstrap current can drive helical core formations at arbitrarily small in which the ideal saturated internal kink coexists with an ideal saturated external kink structure of opposite phase. The centrifugal force linked with the rotation has the effect of displacing the plasma column away from the major axis, but does not alter significantly the magnitude of the edge corrugation of the plasma. Error field correction coil currents in JET-like configurations increase the outer midplane distortions by 2 cm. The edge bootstrap current enhances the edge modulation of the plasma driven by the core snake deformations in MAST.
14.	Fil, A., et al. (author) Three-dimensional non-linear magnetohydrodynamic modeling of massive gas injection triggered disruptions in JET 2015 In: Physics of Plasmas. - : AMER INST PHYSICS. - 1070-664X .- 1089-7674. ; 22:6 Journal article (peer-reviewed)abstract JOREK 3D non-linear MHD simulations of a D-2 Massive Gas Injection (MGI) triggered disruption in JET are presented and compared in detail to experimental data. The MGI creates an overdensity that rapidly expands in the direction parallel to the magnetic field. It also causes the growth of magnetic islands (m/n = 2/1 and 3/2 mainly) and seeds the 1/1 internal kink mode. O-points of all island chains (including 1/1) are located in front of the MGI, consistently with experimental observations. A burst of MHD activity and a peak in plasma current take place at the same time as in the experiment. However, the magnitude of these two effects is much smaller than in the experiment. The simulated radiation is also much below the experimental level. As a consequence, the thermal quench is not fully reproduced. Directions for progress are identified. Radiation from impurities is a good candidate.
15.	Garcia, J., et al. (author) Key impact of finite-beta and fast ions in core and edge tokamak regions for the transition to advanced scenarios 2015 In: Nuclear Fusion. - : IOP PUBLISHING LTD. - 0029-5515 .- 1741-4326. ; 55:5 Journal article (peer-reviewed)abstract Extensive linear and non-linear gyrokinetic simulations and linear magnetohydrodynamic (MHD) analyses performed for JET hybrid discharges with improved confinement have shown that the large population of fast ions found in the plasma core under particular heating conditions has a strong impact on core microturbulence and edge MHD by reducing core ion heat fluxes and increasing pedestal pressure in a feedback mechanism. In the case of the ITER like wall, it is shown how this mechanism plays a decisive role for the transition to plasma regimes with improved confinement and it can explain the weak power degradation obtained in dedicated power scans. The mechanism is found to be highly dependent on plasma triangularity as it changes the balance between the improvement in the plasma core and the edge. The feedback mechanism can play a similar role in the ITER hybrid scenario as in the JET discharges analysed due to its high triangularity plasmas and the large amount of fast ions generated in the core by the heating systems and the alpha power.
16.	Giegerich, Thomas, et al. (author) Conceptual design of the mechanical tritium pumping system for jet DTE2 2015 In: Fusion science and technology. - : TAYLOR & FRANCIS INC. - 1536-1055 .- 1943-7641. ; 68:3, s. 630-634 Journal article (peer-reviewed)abstract This paper describes the conceptual design of the Mechanical Tritium Pumping System (MTPS) that shall be installed and tested at JET during the next Deuterium-Tritium-Experiment (DTE2). This pump train uses a two-stage liquid ring pump in combination with a booster pump to cover a pressure regime from 10(-1) Pa to 10(5) Pa. As working fluid for all pumps, mercury will be used for tritium compatibility reasons. Starting from the requirements to MTPS, the pumps and their arrangement will be described in this paper as well as the mercury containment strategy and safety- and control issues.
17.	Guillemaut, C., et al. (author) Ion target impact energy during Type I edge localized modes in JET ITER-like Wall 2015 In: Plasma Physics and Controlled Fusion. - : IOP PUBLISHING LTD. - 0741-3335 .- 1361-6587. ; 57:8 Journal article (peer-reviewed)abstract The ITER baseline scenario, with 500 MW of DT fusion power and Q = 10, will rely on a Type I ELMy H-mode, with Delta W = 0.7 MJ mitigated edge localized modes (ELMs). Tungsten (W) is the material now decided for the divertor plasma-facing components from the start of plasma operations. W atoms sputtered from divertor targets during ELMs are expected to be the dominant source under the partially detached divertor conditions required for safe ITER operation. W impurity concentration in the plasma core can dramatically degrade its performance and lead to potentially damaging disruptions. Understanding the physics of plasma-wall interaction during ELMs is important and a primary input for this is the energy of incoming ions during an ELM event. In this paper, coupled Infrared thermography and Langmuir Probe (LP) measurements in JET-ITER-Like-Wall unseeded H-mode experiments with ITER relevant ELM energy drop have been used to estimate the impact energy of deuterium ions (D+) on the divertor target. This analysis gives an ion energy of several keV during ELMs, which makes D+ responsible for most of the W sputtering in unseeded H-mode discharges. These LP measurements were possible because of the low electron temperature (T-e) during ELMs which allowed saturation of the ion current. Although at first sight surprising, the observation of low T-e at the divertor target during ELMs is consistent with the 'Free-Streaming' kinetic model which predicts a near-complete transfer of parallel energy from electrons to ions in order to maintain quasi-neutrality of the ELM filaments while they are transported to the divertor targets.
18.	Hallier, Marc, et al. (author) Pre-binding of small protein B to a stalled ribosome triggers trans-translation. 2004 In: J Biol Chem. - 0021-9258. ; 279, s. 25978-85 Journal article (other academic/artistic)
19.	He, Shaomei, et al. (author) Comparative Metagenomic and Metatranscriptomic Analysis of Hindgut Paunch Microbiota in Wood- and Dung-Feeding Higher Termites 2013 In: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 8:4, s. e61126- Journal article (peer-reviewed)abstract Termites effectively feed on many types of lignocellulose assisted by their gut microbial symbionts. To better understand the microbial decomposition of biomass with varied chemical profiles, it is important to determine whether termites harbor different microbial symbionts with specialized functionalities geared toward different feeding regimens. In this study, we compared the microbiota in the hindgut paunch of Amitermes wheeleri collected from cow dung and Nasutitermes corniger feeding on sound wood by 16S rRNA pyrotag, comparative metagenomic and metatranscriptomic analyses. We found that Firmicutes and Spirochaetes were the most abundant phyla in A. wheeleri, in contrast to N. corniger where Spirochaetes and Fibrobacteres dominated. Despite this community divergence, a convergence was observed for functions essential to termite biology including hydrolytic enzymes, homoacetogenesis and cell motility and chemotaxis. Overrepresented functions in A. wheeleri relative to N. corniger microbiota included hemicellulose breakdown and fixed-nitrogen utilization. By contrast, glycoside hydrolases attacking celluloses and nitrogen fixation genes were overrepresented in N. corniger microbiota. These observations are consistent with dietary differences in carbohydrate composition and nutrient contents, but may also reflect the phylogenetic difference between the hosts.
20.	Hernández-Alvarez, María Isabel, et al. (author) Deficient Endoplasmic Reticulum-Mitochondrial Phosphatidylserine Transfer Causes Liver Disease 2019 In: Cell. - : Cell Press. - 0092-8674 .- 1097-4172. ; 177:4, s. 881-895.e17 Journal article (peer-reviewed)abstract Non-alcoholic fatty liver is the most common liver disease worldwide. Here, we show that the mitochondrial protein mitofusin 2 (Mfn2) protects against liver disease. Reduced Mfn2 expression was detected in liver biopsies from patients with non-alcoholic steatohepatitis (NASH). Moreover, reduced Mfn2 levels were detected in mouse models of steatosis or NASH, and its re-expression in a NASH mouse model ameliorated the disease. Liver-specific ablation of Mfn2 in mice provoked inflammation, triglyceride accumulation, fibrosis, and liver cancer. We demonstrate that Mfn2 binds phosphatidylserine (PS) and can specifically extract PS into membrane domains, favoring PS transfer to mitochondria and mitochondrial phosphatidylethanolamine (PE) synthesis. Consequently, hepatic Mfn2 deficiency reduces PS transfer and phospholipid synthesis, leading to endoplasmic reticulum (ER) stress and the development of a NASH-like phenotype and liver cancer. Ablation of Mfn2 in liver reveals that disruption of ER-mitochondrial PS transfer is a new mechanism involved in the development of liver disease.
21.	Högfors-Rönnholm, Eva, et al. (author) Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials 2019 In: Scientific Data. - : Nature Publishing Group. - 2052-4463. ; 6, s. 1-6 Journal article (peer-reviewed)abstract Natural sulfide rich deposits are common in coastal areas worldwide, including along the Baltic Sea coast. When artificial drainage exposes these deposits to atmospheric oxygen, iron sulfide minerals in the soils are rapidly oxidized. This process turns the potential acid sulfate soils into actual acid sulfate soils and mobilizes large quantities of acidity and leachable toxic metals that cause severe environmental problems. It is known that acidophilic microorganisms living in acid sulfate soils catalyze iron sulfide mineral oxidation. However, only a few studies regarding these communities have been published. In this study, we sampled the oxidized actual acid sulfate soil, the transition zone where oxidation is actively taking place, and the deepest un-oxidized potential acid sulfate soil. Nucleic acids were extracted and 16S rRNA gene amplicons, metagenomes, and metatranscriptomes generated to gain a detailed insight into the communities and their activities. The project will be of great use to microbiologists, environmental biologists, geochemists, and geologists as there is hydrological and geochemical monitoring from the site stretching back for many years.
22.	Ivanova, Natalia, 1974- (author) Finding the unknowns in trans-translation 2005 Doctoral thesis (other academic/artistic)abstract Ribosomes stalled on problematic mRNAs can be rescued by a mechanism called trans-translation. This mechanism employs a dual transfer-messenger RNA molecule (tmRNA) together with a helper protein (SmpB). In this work we have used an in vitro translation system with pure components to further clarify the roles of tmRNA and SmpB in trans-translation. We found that SmpB binds ribosomes in vivo and in vitro independently of tmRNA presence and is essential for tmRNA binding and trans-peptidation. We show that two SmpB molecules can bind per ribosome, that SmpB does not leave the ribosome after trans-peptidation and that SmpB pre-bound to the ribosome can trigger trans-translation. We demonstrated that the rate of trans-transfer of a peptide from the P-site tRNA to Ala-tmRNA and the efficiency by which Ala-tmRNA competes with peptide release factors decrease with increasing the mRNA length downstream from the P site of the ribosome. We showed that trans-translation is strongly stimulated by RelE cleavage of A-site mRNA. We concluded that tmRNA action in vivo must always be preceded by mRNA truncation.We showed that rapid release of truncated mRNAs from the ribosome requires translocation of the peptidyl-tmRNA into the ribosomal P site, which is strictly EF-G dependent. mRNA release is slowed down by strong Shine and Dalgarno like sequences upstream the A site and by long 3’-extensions downstream from the P-site codon. Footprinting was used to monitor SmpB binding to tmRNA, ribosomes and subunits and to study tmRNA interactions with the ribosome at distinct trans-translation stages. We confirmed that two SmpB molecules bind per ribosome and interact with nucleotides below the L7/L12-stalk on the 50S subunit and near the subunit interface on the 30S. We showed that tmRNA is mostly in complex with SmpB in vivo and during trans-translation. Specific cleavage patterns of tmRNA were observed at different stages of trans-translation, but the overall tmRNA conformation seems to be maintained during the whole process.
23.	Ivanova, Natalia, et al. (author) Ihor R. Lemischka (1953-2017) 2018 In: Cell Stem Cell. - : Elsevier BV. - 1934-5909. ; 22:1, s. 16-17 Journal article (peer-reviewed)
24.	Ivanova, Natalia, et al. (author) Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA 2005 In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 33:11, s. 3529-3539 Journal article (peer-reviewed)abstract In trans-translation transfer messenger RNA (tmRNA) and small protein B (SmpB) rescue ribosomes stalled on truncated or in other ways problematic mRNAs. SmpB promotes the binding of tmRNA to the ribosome but there is uncertainty about the number of participating SmpB molecules as well as their ribosomal location. Here, the interaction of SmpB with ribosomal subunits and ribosomes was studied by isolation of SmpB containing complexes followed by chemical modification of ribosomal RNA with dimethyl sulfate, kethoxal and hydroxyl radicals. The results show that SmpB binds 30S and 50S subunits with 1:1 molar ratios and the 70S ribosome with 2:1 molar ratio. SmpB-footprints are similar on subunits and the ribosome. In the 30S subunit, SmpB footprints nucleotides that are in the vicinity of the P-site facing the E-site, and in the 50S subunit SmpB footprints nucleotides that are located below the L7/L12 stalk in the 3D structure of the ribosome. Based on these results, we suggest a mechanism where two molecules of SmpB interact with tmRNA and the ribosome during trans-translation. The first SmpB molecule binds near the factor-binding site on the 50S subunit helping tmRNA accommodation on the ribosome, whereas the second SmpB molecule may functionally substitute for a missing anticodon stem-loop in tmRNA during later steps of trans-translation.
25.	Ivanova, Natalia, et al. (author) Mapping the interaction of SmpB with ribosomes by footprinting of ribosomal RNA Other publication (other academic/artistic)

Skapa referenser, mejla, bekava och länka

Permalink

Träfflista för sökning "WFRF:(Ivanova Natalia) "

Refine your search

Year