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- ItemIdentification of cleavage sites and substrate proteins for two mitochondrial intermediate peptidases in Arabidopsis thaliana(Oxford : Oxford University Press, 2015) Carrie, Chris; Venne, A. Saskia; Zahedi, René P.; Soll, JürgenMost mitochondrial proteins contain an N-terminal targeting signal that is removed by specific proteases following import. In plant mitochondria, only mitochondrial processing peptidase (MPP) has been characterized to date. Therefore, we sought to determine the substrates and cleavage sites of the Arabidopsis thaliana homologues to the yeast Icp55 and Oct1 proteins, using the newly developed ChaFRADIC method for N-terminal protein sequencing. We identified 88 and seven putative substrates for Arabidopsis ICP55 and OCT1, respectively. It was determined that the Arabidopsis ICP55 contains an almost identical cleavage site to that of Icp55 from yeast. However, it can also remove a far greater range of amino acids. The OCT1 substrates from Arabidopsis displayed no consensus cleavage motif, and do not contain the classical –10R motif identified in other eukaryotes. Arabidopsis OCT1 can also cleave presequences independently, without the prior cleavage of MPP. It was concluded that while both OCT1 and ICP55 were probably acquired early on in the evolution of mitochondria, their substrate profiles and cleavage sites have either remained very similar or diverged completely.
- ItemBenchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry(Oxford : Oxford University Press, 2015) Oetjen, Janina; Veselkov, Kirill; Watrous, Jeramie; McKenzie, James S.; Becker, Michael; Hauberg-Lotte, Lena; Kobarg, Jan Hendrik; Strittmatter, Nicole; Mróz, Anna K.; Hoffmann, Franziska; Trede, Dennis; Palmer, Andrew; Schiffler, Stefan; Steinhorst, Klaus; Aichler, Michaela; Goldin, Robert; Guntinas-Lichius, Orlando; von Eggeling, Ferdinand; Thiele, Herbert; Maedler, Kathrin; Walch, Axel; Maass, Peter; Dorrestein, Pieter C.; Takats, Zoltan; Alexandrov, TheodoreBackground: Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms. Findings: High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D desorption electrospray ionization (DESI) imaging MS data were collected from a human colorectal adenocarcinoma. Conclusions: With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets.
- ItemWhat the Phage: a scalable workflow for the identification and analysis of phage sequences(Oxford : Oxford University Press, 2022) Marquet, Mike; Hölzer, Martin; Pletz, Mathias W; Viehweger, Adrian; Makarewicz, Oliwia; Ehricht, Ralf; Brandt, ChristianPhages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed "What the Phage"(WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus supporting the user's decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage).
- ItemHigh-efficiency and reliable same-parent thermoelectric modules using Mg3Sb2-based compounds(Oxford : Oxford University Press, 2023) Jiang, Meng; Fu, Yuntian; Zhang, Qihao; Hu, Zhongliang; Huang, Aibin; Wang, Shuling; Wang, Lianjun; Jiang, WanThermoelectric modules can convert waste heat directly into useful electricity, providing a clean and sustainable way to use fossil energy more efficiently. Mg3Sb2-based alloys have recently attracted considerable interest from the thermoelectric community due to their nontoxic nature, abundance of constituent elements and excellent mechanical and thermoelectric properties. However, robust modules based on Mg3Sb2 have progressed less rapidly. Here, we develop multiple-pair thermoelectric modules consisting of both n-type and p-type Mg3Sb2-based alloys. Thermoelectric legs based on the same parent fit into each other in terms of thermomechanical properties, facilitating module fabrication and ensuring low thermal stress. By adopting a suitable diffusion barrier layer and developing a new joining technique, an integrated all-Mg3Sb2-based module demonstrates a high efficiency of 7.5% at a temperature difference of 380 K, exceeding the state-of-the-art same-parent thermoelectric modules. Moreover, the efficiency remains stable during 150 thermal cycling shocks (∼225 h), demonstrating excellent module reliability.
- ItemGeneral synthesis of 2D rare-earth oxide single crystals with tailorable facets(Oxford : Oxford University Press, 2021) Li, Linyang; Lu, Fangyun; Xiong, Wenqi; Ding, Yu; Lu, Yangyi; Xiao, Yao; Tong, Xin; Wang, Yao; Jia, Shuangfeng; Wang, Jianbo; Mendes, Rafael G.; Rümmeli, Mark H.; Yuan, Shengjun; Zeng, Mengqi; Fu, LeiTwo-dimensional (2D) rare-earth oxides (REOs) are a large family of materials with various intriguing applications and precise facet control is essential for investigating new properties in the 2D limit. However, a bottleneck remains with regard to obtaining their 2D single crystals with specific facets because of the intrinsic non-layered structure and disparate thermodynamic stability of different facets. Herein, for the first time, we achieve the synthesis of a wide variety of high-quality 2D REO single crystals with tailorable facets via designing a hard-soft-acid-base couple for controlling the 2D nucleation of the predetermined facets and adjusting the growth mode and direction of crystals. Also, the facet-related magnetic properties of 2D REO single crystals were revealed. Our approach provides a foundation for further exploring other facet-dependent properties and various applications of 2D REO, as well as inspiration for the precise growth of other non-layered 2D materials.
- ItemComparative Transcriptomics of Lowland Rice Varieties Uncovers Novel Candidate Genes for Adaptive Iron Excess Tolerance(Oxford : Oxford University Press, 2021) Kar, Saradia; Mai, Hans-Jörg; Khalouf, Hadeel; Abdallah, Heithem Ben; Flachbart, Samantha; Fink-Straube, Claudia; Bräutigam, Andrea; Xiong, Guosheng; Shang, Lianguang; Panda, Sanjib Kumar; Bauer, PetraIron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. The two lines differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation and Fe and metal contents. These responses were likely due to genetic origin as they were mirrored by differential gene expression patterns, obtained through RNA sequencing, and corresponding gene ontology term enrichment in tolerant vs. susceptible lines. Thirty-five genes of the metal homeostasis category, mainly root expressed, showed differential transcriptomic profiles suggestive of an induced tolerance mechanism. Twenty-two out of these 35 metal homeostasis genes were present in selection sweep genomic regions, in breeding signatures, and/or differentiated during rice domestication. These findings suggest that Fe excess tolerance is an important trait in the domestication of lowland rice, and the identified genes may further serve to design the targeted Fe tolerance breeding of rice crops.
- ItemSEC14-GOLD protein PATELLIN2 binds IRON-REGULATED TRANSPORTER1 linking root iron uptake to vitamin E(Oxford : Oxford University Press, 2023) Hornbergs, Jannik; Montag, Karolin; Loschwitz, Jennifer; Mohr, Inga; Poschmann, Gereon; Schnake, Anika; Gratz, Regina; Brumbarova, Tzvetina; Eutebach, Monique; Angrand, Kalina; Fink-Straube, Claudia; Stühler, Kai; Zeier, Jürgen; Hartmann, Laura; Strodel, Birgit; Ivanov, Rumen; Bauer, PetraOrganisms require micronutrients, and Arabidopsis (Arabidopsis thaliana) IRON-REGULATED TRANSPORTER1 (IRT1) is essential for iron (Fe2+) acquisition into root cells. Uptake of reactive Fe2+ exposes cells to the risk of membrane lipid peroxidation. Surprisingly little is known about how this is avoided. IRT1 activity is controlled by an intracellular variable region (IRT1vr) that acts as a regulatory protein interaction platform. Here, we describe that IRT1vr interacted with peripheral plasma membrane SEC14-Golgi dynamics (SEC14-GOLD) protein PATELLIN2 (PATL2). SEC14 proteins bind lipophilic substrates and transport or present them at the membrane. To date, no direct roles have been attributed to SEC14 proteins in Fe import. PATL2 affected root Fe acquisition responses, interacted with ROS response proteins in roots, and alleviated root lipid peroxidation. PATL2 had high affinity in vitro for the major lipophilic antioxidant vitamin E compound α-tocopherol. Molecular dynamics simulations provided insight into energetic constraints and the orientation and stability of the PATL2-ligand interaction in atomic detail. Hence, this work highlights a compelling mechanism connecting vitamin E with root metal ion transport at the plasma membrane with the participation of an IRT1-interacting and α-tocopherol-binding SEC14 protein.