Plant mitochondrial retrograde signaling: post-translational modifications enter the stage

Beside their central function in respiration plant mitochondria play important roles in diverse processes such as redox homeostasis, provision of precursor molecules for essential biosynthetic pathways, and programmed cell death. These different functions require the organelle to communicate with the rest of the cell by perceiving, transducing, and emitting signals. As the vast majority of mitochondrial proteins are encoded in the nuclear genome, changes in mitochondrial status must be fed back to the nucleus to coordinate gene expression accordingly, a process termed retrograde signaling. However, the nature of these signaling pathways in plants and their underlying signaling molecules - or indirect metabolite or redox signals are not completely resolved. We explore the potential of different post-translational modifications (PTMs) to contribute to mitochondrial retrograde signaling. Remarkably, the substrates used for modifying proteins in many major PTMs are either central metabolites or redox-active compounds, as for example ATP acetyl-CoA, NAD(+), and glutathione. This suggests that the metabolic status of organelles and of the cell in general could be indirectly gaged by the enzymes catalyzing the various PTMs. We examine the evidence supporting this hypothesis with regard to three major PTMs, namely phosphorylation, lysine acetylation, and glutathionylation and assess their potential to regulate not only organellar processes by modifying metabolic enzymes but also to influence nuclear gene expression

Ultrahigh resolution optical coherence tomography using a superluminescent light source

A superluminescent Ti:Al2O3 crystal is demonstrated as a light source for ultrahigh resolution optical coherence tomography (OCT). Single spatial mode, fiber coupled output powers of ~40 μW can be generated with 138 nm bandwidth using a 5 W frequency doubled, diode pumped laser, pumping a thin Ti:Al2O3 crystal. Ultrahigh resolution OCT imaging is demonstrated with 2.2 μm axial resolution in air, or 1.7 μm in tissue, with >86 dB sensitivity. This light source provides a simple and robust alternative to femtosecond lasers for ultrahigh resolution OCT imaging

MitoLoc: A method for the simultaneous quantification of mitochondrial network morphology and membrane potential in single cells.

Mitochondria assemble into flexible networks. Here we present a simple method for the simultaneous quantification of mitochondrial membrane potential and network morphology that is based on computational co-localisation analysis of differentially imported fluorescent marker proteins. Established in, but not restricted to, Saccharomyces cerevisiae, MitoLoc reproducibly measures changes in membrane potential induced by the uncoupling agent CCCP, by oxidative stress, in respiratory deficient cells, and in ∆fzo1, ∆ref2, and ∆dnm1 mutants that possess fission and fusion defects. In combination with super-resolution images, MitoLoc uses 3D reconstruction to calculate six geometrical classifiers which differentiate network morphologies in ∆fzo1, ∆ref2, and ∆dnm1 mutants, under oxidative stress and in cells lacking mtDNA, even when the network is fragmented to a similar extent. We find that mitochondrial fission and a decline in membrane potential do regularly, but not necessarily, co-occur. MitoLoc hence simplifies the measurement of mitochondrial membrane potential in parallel to detect morphological changes in mitochondrial networks. Marker plasmid open-source software as well as the mathematical procedures are made openly available.This work was supported by funding from the Wellcome Trust (RG 093735/Z/10/Z) and the ERC (Starting grant 260809). M.R. is a Wellcome Trust Research Career Development and Wellcome-Beit prize fellow.This is the final version. It was first published by Elsevier at http://www.sciencedirect.com/science/article/pii/S1567724915300088

Structural Investigation into Magnetic Spin Orders of a Manganese Phosphatic Oxyhydroxide, Mn5(PO4)2(PO3(OH))2(HOH)4

The ferri- and antiferromagnetic structures of a hureaulite-type synthetic compound, Mn2+5(PO4)2(PO3(OH))2(HOH)4, were elucidated by high-resolution neutron powder diffraction in combination with magnetic susceptibility and heat capacity measurements. At 6.17 K, the paramagnetic phase (space group: C2/c) transforms to inherit a ferrimagnetic order (magnetic space group: C2'/c'), followed at 1.86 K by an incommensurately modulated antiferromagnetic order (magnetic superspace group: P21/c.1'(α0γ)00s with the propagation vector k(0.523(2), 0, 0.055(1)). In the ferrimagnetic state, antiferromagnetic interactions are dominant for both intra and inter pentamers of Mn2+(O, HOH)6 octahedra. Differently aligned spin-canting sublattices seen in the ferrimagnetic models at 3.4, 4.5, and 6.1 K explain a weak ferromagnetism in the title compound. The observation of magnetic moments vigorously changing in a small temperature range of 6.1-1.5 K adumbrates a high complexity of interplaying structural and magnetic orders in this manganese phosphatic oxyhydroxide

Electron Detachment Dissociation for Top-Down Mass Spectrometry of Acidic Proteins

Electron detachment dissociation (EDD) is an emerging mass spectrometry (MS) technique for the primary structure analysis of peptides, carbohydrates, and oligonucleotides. Herein, we explore the potential of EDD for sequencing of proteins of up to 147 amino acid residues by using top-down MS. Sequence coverage ranged from 72 % for Melittin, which lacks carboxylic acid functionalities, to 19 % for an acidic 147-residue protein, to 12 % for Ferredoxin, which showed unusual backbone fragmentation next to cysteine residues. A limiting factor for protein sequencing by EDD is the facile loss of small molecules from amino acid side chains, in particular CO2. Based on the types of fragments observed and fragmentation patterns found, we propose detailed mechanisms for protein backbone cleavage and side chain dissociation in EDD. The insights from this study should further the development of EDD for top-down MS of acidic proteins

Mass spectrometry-based high-throughput proteomics and its role in biomedical studies and systems biology

There are multiple reasons why the next generation of biological and medical studies require increasing numbers of samples. Biological systems are dynamic, and the effect of a perturbation depends on the genetic background and environment. As a consequence, many conditions need to be considered to reach generalizable conclusions. Moreover, human population and clinical studies only reach sufficient statistical power if conducted at scale and with precise measurement methods. Finally, many proteins remain without sufficient functional annotations, because they have not been systematically studied under a broad range of conditions. In this review, we discuss the latest technical developments in mass spectrometry (MS)-based proteomics that facilitate large-scale studies by fast and efficient chromatography, fast scanning mass spectrometers, data-independent acquisition (DIA), and new software. We further highlight recent studies which demonstrate how high-throughput (HT) proteomics can be applied to capture biological diversity, to annotate gene functions or to generate predictive and prognostic models for human diseases. Keywords: biomarker discovery; data-independent acquisition; dynamic biological systems; gene annotation; precision medicine; proteomics

Real-time 6-DoF Pose Estimation by an Event-based Camera using Active LED Markers

Real-time applications for autonomous operations depend largely on fast and robust vision-based localization systems. Since image processing tasks require processing large amounts of data, the computational resources often limit the performance of other processes. To overcome this limitation, traditional marker-based localization systems are widely used since they are easy to integrate and achieve reliable accuracy. However, classical marker-based localization systems significantly depend on standard cameras with low frame rates, which often lack accuracy due to motion blur. In contrast, event-based cameras provide high temporal resolution and a high dynamic range, which can be utilized for fast localization tasks, even under challenging visual conditions. This paper proposes a simple but effective event-based pose estimation system using active LED markers (ALM) for fast and accurate pose estimation. The proposed algorithm is able to operate in real time with a latency below \SI{0.5}{\milli\second} while maintaining output rates of \SI{3}{\kilo \hertz}. Experimental results in static and dynamic scenarios are presented to demonstrate the performance of the proposed approach in terms of computational speed and absolute accuracy, using the OptiTrack system as the basis for measurement.Comment: 14 pages, 12 figures, this paper has been accepted to WACV 202

Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure

Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10% O2) and normal (21% O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure