Comparative quantitative proteomics to investigate the remodeling of bioenergetic pathways under iron deficiency in Chlamydomonas reinhardtii

The basic question addressed in this study is how energy metabolism is adjusted to cope with iron deficiency in Chlamydomonas reinhardtii. To investigate the impact of iron deficiency on bioenergetic pathways, comparative proteomics was combined with spectroscopic as well as voltametric oxygen measurements to assess protein dynamics linked to functional properties of respiratory and photosynthetic machineries. Although photosynthetic electron transfer is largely compromised under iron deficiency, our quantitative and spectroscopic data revealed that the functional antenna size of photosystem II (PSII) significantly increased. Concomitantly, stress-related chloroplast polypeptides, like 2-cys peroxiredoxin and a stress-inducible light-harvesting protein, LhcSR3, as well as a novel light-harvesting protein and several proteins of unknown function were induced under iron-deprivation. Respiratory oxygen consumption did not decrease and accordingly, polypeptides of respiratory complexes, harboring numerous iron-sulfur clusters, were only slightly diminished or even increased under low iron. Consequently, iron-deprivation induces a transition from photoheterotrophic to primarily heterotrophic metabolism, indicating that a hierarchy for iron allocations within organelles of a single cell exists that is closely linked with the metabolic state of the cell.     

Impact of Surface Active Compounds on Iron Catalyzed Oxidation of Methyl Linolenate in AOT–Water–Hexadecane Systems

Edible oils contain minor surface active components that form micro-heterogeneous environments, such as reverse micelles, which can alter the rate and direction of chemical reactions. However, little is known about the role of these micro-heterogeneous environments on lipid oxidation of bulk oil. Our objective was to evaluate the ability of water, cumene hydroperoxide, oleic acid, and phosphatidylcholine to influence the structure of reverse micelles in a model oil system: sodium bis(2-ethylhexyl) sulfosuccinate (aerosol-OT; AOT) in n-hexadecane. The influence of reverse micelle structure on iron catalyzed lipid oxidation was determined using methyl linolenate as an oxidizable substrate. The size and shape of the reverse micelle were investigated by small-angle x-ray scattering, and water contents was determined by Karl Fischer titrations. Lipid hydroperoxides and thiobarbituric acid reactive substances were used to follow lipid oxidation. Our results showed that AOT formed spherical reverse micelles in hexadecane. The size of the reverse micelles increased with increased water or phosphatidylcholine concentration, but decreased upon addition of cumene hydroperoxide or oleic acid. Iron catalyzed oxidation of methyl linolenate in the reverse micelle system decreased with increasing water concentration. Addition of phosphatidylcholine into the reverse micelle systems decreased methyl linolenate oxidation compared to control and reverse micelles with added oleic acid. These results indicate that water, cumene hydroperoxide, oleic acid, and phosphatidylcholine can alter reverse micelle size and lipid oxidation rates. Understanding how these compounds influence reverse micelle structure and lipid oxidation rates could provide information on how to modify bulk oil systems to increase oxidative stability.     

Proteomic analysis of peripheral blood mononuclear cells: selective protein processing observed in patients with rheumatoid arthritis

In a comparative proteome analysis of peripheral blood mononuclear cells (PBMCs), we analyzed 130 two-dimensional gels obtained from 33 healthy control individuals and 32 patients diagnosed with rheumatoid arthritis (RA). We found 16 protein spots that are deregulated in patients with RA and, using peptide mass fingerprinting and Western blot analyses, identified these spots as belonging to 9 distinct proteins. A hierarchical clustering procedure organizes the study subjects into two main clusters based on the expression of these 16 protein spots, one that contains mostly healthy control individuals and the other mostly RA patients. The majority of the proteins differentially expressed in RA patients when compared with healthy controls can be detected as protein fragments in PBMCs obtained from RA patients. This set of deregulated proteins includes several factors that have been shown to be autoantigens in autoimmune diseases.     

Land use intensification increasingly drives the spatiotemporal patterns of the global human appropriation of net primary production in the last century

Land use has greatly transformed Earth's surface. While spatial reconstructions of how the extent of land cover and land-use types have changed during the last century are available, much less information exists about changes in land-use intensity. In particular, global reconstructions that consistently cover land-use intensity across land-use types and ecosystems are missing. We, therefore, lack understanding of how changes in land-use intensity interfere with the natural processes in land systems. To address this research gap, we map land-cover and land-use intensity changes between 1910 and 2010 for 9 points in time. We rely on the indicator framework of human appropriation of net primary production (HANPP) to quantify and map land-use-induced alterations of the carbon flows in ecosystems. We find that, while at the global aggregate level HANPP growth slowed down during the century, the spatial dynamics of changes in HANPP were increasing, with the highest change rates observed in the most recent past. Across all biomes, the importance of changes in land-use areas has declined, with the exception of the tropical biomes. In contrast, increases in land-use intensity became the most important driver of HANPP across all biomes and settings. We conducted uncertainty analyses by modulating input data and assumptions, which indicate that the spatial patterns of land use and potential net primary production are the most critical factors, while spatial allocation rules and uncertainties in overall harvest values play a smaller role. Highlighting the increasing role of land-use intensity compared to changes in the areal extent of land uses, our study supports calls for better integration of the intensity dimension into global analyses and models. On top of that, we provide important empirical input for further analyses of the sustainability of the global land system.     

Folding of VemP into translation-arresting secondary structure is driven by the ribosome exit tunnel

The ribosome is a fundamental biomolecular complex that synthesizes proteins in cells. Nascent proteins emerge from the ribosome through a tunnel, where they may interact with the tunnel walls or small molecules such as antibiotics. These interactions can cause translational arrest with notable physiological consequences. Here, we studied the arrest caused by the regulatory peptide VemP, which is known to form α-helices inside the ribosome tunnel near the peptidyl transferase center under specific conditions. We used all-atom molecular dynamics simulations of the entire ribosome and circular dichroism spectroscopy to study the driving forces of helix formation and how VemP causes the translational arrest. To that aim, we compared VemP dynamics in the ribosome tunnel with its dynamics in solution. We show that the VemP peptide has a low helical propensity in water and that the propensity is higher in mixtures of water and trifluorethanol. We propose that helix formation within the ribosome is driven by the interactions of VemP with the tunnel and that a part of VemP acts as an anchor. This anchor might slow down VemP progression through the tunnel enabling α-helix formation, which causes the elongation arrest.     

Scaling up calcification,respiration, and photosynthesis rates of six prominent coral taxa

Coral reefs provide a range of important services to humanity, which are underpinned by community‐level ecological processes such as coral calcification. Estimating these processes relies on our knowledge of individual physiological rates and species‐specific abundances in the field. For colonial animals such as reef‐building corals, abundance is frequently expressed as the relative surface cover of coral colonies, a metric that does not account for demographic parameters such as coral size. This may be problematic because many physiological rates are directly related to organism size, and failure to account for linear scaling patterns may skew estimates of ecosystem functioning. In the present study, we characterize the scaling of three physiological rates — calcification, respiration, and photosynthesis — considering the colony size for six prominent, reef‐building coral taxa in Mo''orea, French Polynesia. After a seven‐day acclimation period in the laboratory, we quantified coral physiological rates for three hours during daylight (i.e., calcification and gross photosynthesis) and one hour during night light conditions (i.e., dark respiration). Our results indicate that area‐specific calcification rates are higher for smaller colonies across all taxa. However, photosynthesis and respiration rates remain constant over the colony‐size gradient. Furthermore, we revealed a correlation between the demographic dynamics of coral genera and the ratio between net primary production and calcification rates. Therefore, intraspecific scaling of reef‐building coral physiology not only improves our understanding of community‐level coral reef functioning but it may also explain species‐specific responses to disturbances.     

Molecular,Viral and Clinical Features of Alcohol- and Non-Alcohol-Induced Liver Injury

Hepatic cells are sensitive to internal and external signals. Ethanol is one of the oldest and most widely used drugs in the world. The focus on the mechanistic engine of the alcohol-induced injury has been in the liver, which is responsible for the pathways of alcohol metabolism. Ethanol undergoes a phase I type of reaction, mainly catalyzed by the cytoplasmic enzyme, alcohol dehydrogenase (ADH), and by the microsomal ethanol-oxidizing system (MEOS). Reactive oxygen species (ROS) generated by cytochrome (CYP) 2E1 activity and MEOS contribute to ethanol-induced toxicity. We aimed to: (1) Describe the cellular, pathophysiological and clinical effects of alcohol misuse on the liver; (2) Select the biomarkers and analytical methods utilized by the clinical laboratory to assess alcohol exposure; (3) Provide therapeutic ideas to prevent/reduce alcohol-induced liver injury; (4) Provide up-to-date knowledge regarding the Corona virus and its affect on the liver; (5) Link rare diseases with alcohol consumption. The current review contributes to risk identification of patients with alcoholic, as well as non-alcoholic, liver disease and metabolic syndrome. Additional prevalence of ethnic, genetic, and viral vulnerabilities are presented.     

Die Cuticula der Epidermis des Regenwurms (Lumbricus terrestris L.)

Zusammenfassung Die um 3–4 dicke Cuticula des Regenwurms (Lumbricus terrestris L.) besteht aus 20–30 sich annähernd rechtwinklig kreuzenden Lagen von Cuticulafibrillen. Senkrecht zu und zwischen den sich kreuzenden Fibrillen verlaufen röhrenförmige Zellfortsätze, Cuticulakanälchen von der Oberfläche der Epithelzelle zur Epicuticula. Die Epicuticula bildet eine kontinuierliche, mit feinen, dicht stehenden Exkreszenzen besetzte Schicht. Die zelluläre, respektive extrazelluläre Natur der Cuticulastrukturen und ihr funktionelles Verhalten werden besprochen. Anmerkung bei der Korrektur. Die Herren D. Peters (Hamburg) und W. J. Schmidt (Gießen) machten uns auf die Untersuchung der Cuticulastruktur des Regenwurms durch Reed und Rudall (1948) aufmerksam.Die von den englischen Autoren gewonnenen Abdruckpräparate aus verschieden tiefen Schichten der Cuticula stimmen mit den hier gezeigten Schnittpräparaten vorzüglich überein und ergänzen sie durch die Aufsicht auf die freie Oberfläche. Mit der Abdrucktechnik sind jedoch die Cuticula-Kanälchen zwischen den Fibrillen nicht erkannt worden. Einige der Vermutungen über die Bildung der Cuticulafibrulen (s. auch Rudall 1950) dürften deshalb hinfällig geworden sein. Über die chemische Zusammensetzung der Cuticula und ihre chemischen Unterschiede gegenüber Kollagen s. Watson und Smith (1956).Mit dankenswerter Unterstützung durch das Kultusministerium des Landes Nordrhein-Westfalen durchgeführte Untersuchung.     

Diazaborine treatment of yeast cells inhibits maturation of the 60S ribosomal subunit

Diazaborine treatment of yeast cells was shown previously to cause accumulation of aberrant, 3'-elongated mRNAs. Here we demonstrate that the drug inhibits maturation of rRNAs for the large ribosomal subunit. Pulse-chase analyses showed that the processing of the 27S pre-rRNA to consecutive species was blocked in the drug-treated wild-type strain. The steady-state level of the 7S pre-rRNA was clearly reduced after short-term treatment with the inhibitor. At the same time an increase of the 35S pre-rRNA was observed. Longer incubation with the inhibitor resulted in a decrease of the 27S precursor. Primer extension assays showed that an early step in 27S pre-rRNA processing is inhibited, which results in an accumulation of the 27SA2 pre-rRNA and a strong decrease of the 27SA3, 27SB1L, and 27SB1S precursors. The rRNA processing pattern observed after diazaborine treatment resembles that reported after depletion of the RNA binding protein Nop4p/Nop77p. This protein is essential for correct pre-27S rRNA processing. Using a green fluorescent protein-Nop4 fusion, we found that diazaborine treatment causes, within minutes, a rapid redistribution of the protein from the nucleolus to the periphery of the nucleus, which provides a possible explanation for the effect of diazaborine on rRNA processing.