| 1. |
- Al-Furoukh, Natalie, et al.
(författare)
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ClpX stimulates the mitochondrial unfolded protein response (UPRmt) in mammalian cells
- 2015
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Ingår i: Biochimica et Biophysica Acta. Molecular Cell Research. - : Elsevier BV. - 0167-4889 .- 1879-2596. ; 1853:10, s. 2580-2591
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Tidskriftsartikel (refereegranskat)abstract
- Proteostasis is crucial for life and maintained by cellular chaperones and proteases. One major mitochondrial protease is the ClpXP complex, which is comprised of a catalytic ClpX subunit and a proteolytic ClpP subunit. Based on two separate observations, we hypothesized that ClpX may play a leading role in the cellular function of ClpXP. Therefore, we analyzed the effect of ClpX overexpression on a myoblast proteome by quantitative proteomics. ClpX overexpression results in the upregulation of markers of the mitochondria( proteostasis pathway, known as the "mitochondrial unfolded protein response" (UPRmt). Although this pathway is described in detail in Caenorhabditis elegans, it is not clear whether it is conserved in mammals. Therefore, we compared features of the classical nematode UPRmt with our mammalian ClpX-triggered UPRmt dataset. We show that they share the same retrograde mitochondria-to-nucleus signaling pathway that involves the key UPRmt transcription factor CHOP (also known as Ddit3, CEBPZ or GADD153). In conclusion, our data confirm the existence of a mammalian UPRmt that has great similarity to the C elegans pathway. Furthermore, our results illustrate that ClpX overexpression is a good and simple model to study the underlying mechanisms of the UPRmt in mammalian cells.
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| 2. |
- Al-Furoukh, Natalie, et al.
(författare)
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NOA1, a novel ClpXP substrate, takes an unexpected nuclear detour prior to mitochondrial import.
- 2014
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:7
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Tidskriftsartikel (refereegranskat)abstract
- The mitochondrial matrix GTPase NOA1 is a nuclear encoded protein, essential for mitochondrial protein synthesis, oxidative phosphorylation and ATP production. Here, we demonstrate that newly translated NOA1 protein is imported into the nucleus, where it localizes to the nucleolus and interacts with UBF1 before nuclear export and import into mitochondria. Mutation of the nuclear localization signal (NLS) prevented both nuclear and mitochondrial import while deletion of the N-terminal mitochondrial targeting sequence (MTS) or the C-terminal RNA binding domain of NOA1 impaired mitochondrial import. Absence of the MTS resulted in accumulation of NOA1 in the nucleus and increased caspase-dependent apoptosis. We also found that export of NOA1 from the nucleus requires a leptomycin-B sensitive, Crm1-dependent nuclear export signal (NES). Finally, we show that NOA1 is a new substrate of the mitochondrial matrix protease complex ClpXP. Our results uncovered an unexpected, mandatory detour of NOA1 through the nucleolus before uptake into mitochondria. We propose that nucleo-mitochondrial translocation of proteins is more widespread than previously anticipated providing additional means to control protein bioavailability as well as cellular communication between both compartments.
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| 3. |
- Chen, Jing, et al.
(författare)
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Low-bias phosphopeptide enrichment from scarce samples using plastic antibodies
- 2015
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 5
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Tidskriftsartikel (refereegranskat)abstract
- Phosphospecific enrichment techniques and mass spectrometry (MS) are essential tools for comprehending the cellular phosphoproteome. Here, we report a fast and simple approach for low sequence-bias phosphoserine (pS) peptide capture and enrichment that is compatible with low biological or clinical sample input. The approach exploits molecularly imprinted polymers (MIPs, "plastic antibodies") featuring tight neutral binding sites for pS or pY that are capable of cross-reacting with phosphopeptides of protein proteolytic digests. The versatility of the resulting method was demonstrated with small samples of whole-cell lysate from human embryonic kidney (HEK) 293T cells, human neuroblastoma SH-SY5Y cells, mouse brain or human cerebrospinal fluid (CSF). Following pre-fractionation of trypsinized proteins by strong cation exchange (SCX) chromatography, pS-MIP enrichment led to the identification of 924 phosphopeptides in the HEK 293T whole-cell lysate, exceeding the number identified by TiO2-based enrichment (230). Moreover, the phosphopeptides were extracted with low sequence bias and showed no evidence for the characteristic preference of TiO2 for acidic amino acids (aspartic and glutamic acid). Applying the method to human CSF led to the discovery of 47 phosphopeptides belonging to 24 proteins and revealed three previously unknown phosphorylation sites.
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| 4. |
- de Groot, Frank M. F., et al.
(författare)
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2p x-ray absorption spectroscopy of 3d transition metal systems
- 2021
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Ingår i: Journal of Electron Spectroscopy and Related Phenomena. - : Elsevier BV. - 0368-2048 .- 1873-2526. ; 249
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Tidskriftsartikel (refereegranskat)abstract
- This review provides an overview of the different methods and computer codes that are used to interpret 2p x-ray absorption spectra of 3d transition metal ions. We first introduce the basic parameters and give an overview of the methods used. We start with the semi-empirical multiplet codes and compare the different codes that are available. A special chapter is devoted to the user friendly interfaces that have been written on the basis of these codes. Next we discuss the first principle codes based on band structure, including a chapter on Density Functional theory based approaches. We also give an overview of the first-principle multiplet codes that start from a cluster calculation and we discuss the wavefunction based methods, including multi-reference methods. We end the review with a discussion of the link between theory and experiment and discuss the open issues in the spectral analysis.
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| 5. |
- Heidler, Juliana, et al.
(författare)
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Nitric oxide-associated protein 1 (NOA1) is necessary for oxygen-dependent regulation of mitochondrial respiratory complexes.
- 2011
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 286:37
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Tidskriftsartikel (refereegranskat)abstract
- In eukaryotic cells, maintenance of cellular ATP stores depends mainly on mitochondrial oxidative phosphorylation (OXPHOS), which in turn requires sufficient cellular oxygenation. The crucial role of proper oxygenation for cellular viability is reflected by involvement of several mechanisms, which sense hypoxia and regulate activities of respiratory complexes according to available oxygen concentrations. Here, we focus on mouse nitric oxide-associated protein 1 (mNOA1), which has been identified as an important component of the machinery that adjusts OXPHOS activity to oxygen concentrations. mNOA1 is an evolutionary conserved GTP-binding protein that is involved in the regulation of mitochondrial protein translation and respiration. We found that mNOA1 is located mostly in the mitochondrial matrix from where it interacts with several high molecular mass complexes, most notably with the complex IV of the respiratory chain and the prohibitin complex. Knock-down of mNOA1 impaired enzyme activity I+III, resulting in oxidative stress and eventually cell death. mNOA1 is transcriptionally regulated in an oxygen-sensitive manner. We propose that oxygen-dependent regulation of mNOA1 is instrumental to adjusting OXPHOS activity to oxygen availability, thereby controlling mitochondrial metabolism.
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| 6. |
- Krüger, Kristin, et al.
(författare)
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Randomization as Mitigation of Directed Timing Inference Based Attacks on Time-Triggered Real-Time Systems with Task Replication
- 2021
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Ingår i: Leibniz Transactions on Embedded Systems. - 2199-2002.
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Tidskriftsartikel (refereegranskat)abstract
- Time-triggered real-time systems achieve deterministic behavior using schedules that are constructed offline, based on scheduling constraints. Their deterministic behavior makes time-triggered systems suitable for usage in safety-critical environments, like avionics. However, this determinism also allows attackers to fine-tune attacks that can be carried out after studying the behavior of the system through side channels, targeting safety-critical victim tasks. Replication -- i.e., the execution of task variants across different cores -- is inherently able to tolerate both accidental and malicious faults (i.e. attacks) as long as these faults are independent of one another. Yet, targeted attacks on the timing behavior of tasks which utilize information gained about the system behavior violate the fault independence assumption fault tolerance is based on. This violation may give attackers the opportunity to compromise all replicas simultaneously, in particular if they can mount the attack from already compromised components. In this paper, we analyze vulnerabilities of time-triggered systems, focusing on safety-certified multicore real-time systems. We introduce two runtime mitigation strategies to withstand directed timing inference based attacks: (i) schedule randomization at slot level, and (ii) randomization within a set of offline constructed schedules. We evaluate these mitigation strategies with synthetic experiments and a real case study to show their effectiveness and practicality.
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| 7. |
- Mast, Marcus, et al.
(författare)
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User-Centered Design of a Dynamic-Autonomy Remote Interaction Concept for Manipulation-Capable Robots to Assist Elderly People in the Home
- 2012
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Ingår i: Journal of Human-robot interaction. - 2163-0364. ; 1:1, s. 96-118
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we describe the development of a human-robot interaction concept for service robots to assist elderly people in the home with physical tasks. Our approach is based on the insight that robots are not yet able to handle all tasks autonomously with sufficient reliability in the complex and heterogeneous environments of private homes. We therefore employ remote human operators to assist on tasks a robot cannot handle completely autonomously. Our development methodology was user-centric and iterative, with six user studies carried out at various stages involving a total of 241 participants. The concept is under implementation on the Care-O-bot 3 robotic platform. The main contributions of this article are (1) the results of a survey in form of a ranking of the demands of elderly people and informal caregivers for a range of 25 robot services, (2) the results of an ethnography investigating the suitability of emergency teleassistance and telemedical centers for incorporating robotic teleassistance, and (3) a user-validated human-robot interaction concept with three user roles and corresponding three user interfaces designed as a solution to the problem of engineering reliable service robots for home environments.
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| 8. |
- Müller, Jens Daniel, et al.
(författare)
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Cyanobacteria net community production in the Baltic Sea as inferred from profiling pCO2 measurements
- 2021
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Ingår i: Biogeosciences. - : European Geosciences Union (EGU). - 1726-4170 .- 1726-4189. ; 18:17, s. 4889-4917
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Tidskriftsartikel (refereegranskat)abstract
- Organic matter production by cyanobacteria blooms is a major environmental concern for the Baltic Sea, as it promotes the spread of anoxic zones. Partial pressure of carbon dioxide (pCO2) measurements carried out on Ships of Opportunity (SOOP) since 2003 have proven to be a powerful tool to resolve the carbon dynamics of the blooms in space and time. However, SOOP measurements lack the possibility to directly constrain depth-integrated net community production (NCP) in moles of carbon per surface area due to their restriction to the sea surface. This study tackles the knowledge gap through (1) providing an NCP best guess for an individual cyanobacteria bloom based on repeated profiling measurements of pCO2 and (2) establishing an algorithm to accurately reconstruct depth-integrated NCP from surface pCO2 observations in combination with modelled temperature profiles.Goal (1) was achieved by deploying state-of-the-art sensor technology from a small-scale sailing vessel. The low-cost and flexible platform enabled observations covering an entire bloom event that occurred in July–August 2018 in the Eastern Gotland Sea. For the biogeochemical interpretation, recorded pCO2 profiles were converted to C∗T, which is the dissolved inorganic carbon concentration normalised to alkalinity. We found that the investigated bloom event was dominated by Nodularia and had many biogeochemical characteristics in common with blooms in previous years. In particular, it lasted for about 3 weeks, caused a C∗T drawdown of 90 µmol kg−1, and was accompanied by a sea surface temperature increase of 10 ∘C. The novel finding of this study is the vertical extension of the C∗T drawdown up to the compensation depth located at around 12 m. Integration of the C∗T drawdown across this depth and correction for vertical fluxes leads to an NCP best guess of ∼1.2 mol m−2 over the productive period.Addressing goal (2), we combined modelled hydrographical profiles with surface pCO2 observations recorded by SOOP Finnmaid within the study area. Introducing the temperature penetration depth (TPD) as a new parameter to integrate SOOP observations across depth, we achieve an NCP reconstruction that agrees to the best guess within 10 %, which is considerably better than the reconstruction based on a classical mixed-layer depth constraint.Applying the TPD approach to almost 2 decades of surface pCO2 observations available for the Baltic Sea bears the potential to provide new insights into the control and long-term trends of cyanobacteria NCP. This understanding is key for an effective design and monitoring of conservation measures aiming at a Good Environmental Status of the Baltic Sea.
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| 9. |
- Pohjoismäki, Jaakko L O, et al.
(författare)
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Postnatal cardiomyocyte growth and mitochondrial reorganization cause multiple changes in the proteome of human cardiomyocytes.
- 2013
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Ingår i: Molecular Biosystems. - : Royal Society of Chemistry (RSC). - 1742-206X .- 1742-2051. ; 9:6
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Tidskriftsartikel (refereegranskat)abstract
- Fetal (fCM) and adult cardiomyocytes (aCM) significantly differ from each other both by structure and biochemical properties. aCM own a higher mitochondrial mass compared to fCM due to increased energy demand and show a greater density and higher degree of structural organization of myofibrils. The energy metabolism in aCM relies virtually completely on β-oxidation of fatty acids while fCM use carbohydrates. Rewinding of the aCM phenotype (de-differentiation) arises frequently in diseased hearts spurring questions about its functional relevance and the extent of de-differentiation. Yet, surprisingly little is known about the changes in the human proteome occurring during maturation of fCM to aCM. Here, we examined differences between human fetal and adult hearts resulting in the quantification of 3500 proteins. Moreover, we analyzed mitochondrial proteomes from both stages to obtain more detailed insight into underlying biochemical differences. We found that the majority of changes between fCM and aCM were attributed to growth and maturation of cardiomyocytes. As expected, adult hearts showed higher mitochondrial mass and expressed increased levels of proteins involved in energy metabolism but relatively lower copy numbers of mitochondrial DNA (mtDNA) per total cell volume. We uncovered that the TFAM/mtDNA ratio was kept constant during postnatal development despite a significant increase of mitochondrial protein per mtDNA in adult mitochondria, which revises previous concepts.
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| 10. |
- Viotti, Corrado, et al.
(författare)
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The Endoplasmic Reticulum Is the Main Membrane Source for Biogenesis of the Lytic Vacuole in Arabidopsis
- 2013
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Ingår i: The Plant Cell. - : American Society of Plant Biologists. - 1040-4651 .- 1532-298X. ; 25:9, s. 3434-3449
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Tidskriftsartikel (refereegranskat)abstract
- Vacuoles are multifunctional organelles essential for the sessile lifestyle of plants. Despite their central functions in cell growth, storage, and detoxification, knowledge about mechanisms underlying their biogenesis and associated protein trafficking pathways remains limited. Here, we show that in meristematic cells of the Arabidopsis thaliana root, biogenesis of vacuoles as well as the trafficking of sterols and of two major tonoplast proteins, the vacuolar H+-pyrophosphatase and the vacuolar H+-adenosinetriphosphatase, occurs independently of endoplasmic reticulum (ER)-Golgi and post-Golgi trafficking. Instead, both pumps are found in provacuoles that structurally resemble autophagosomes but are not formed by the core autophagy machinery. Taken together, our results suggest that vacuole biogenesis and trafficking of tonoplast proteins and lipids can occur directly from the ER independent of Golgi function.
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