Remotely sensed forest understory density and nest predator occurrence interact to predict suitable breeding habitat and the occurrence of a resident boreal bird species

Habitat suitability models (HSM) based on remotely sensed data are useful tools in conservation work. However, they typically use species occurrence data rather than robust demographic variables, and their predictive power is rarely evaluated. These shortcomings can result in misleading guidance for conservation. Here, we develop and evaluate a HSM based on correlates of long‐term breeding success of an open nest building boreal forest bird, the Siberian jay. In our study site in northern Sweden, nest failure of this permanent resident species is driven mainly by visually hunting corvids that are associated with human settlements. Parents rely on understory nesting cover as protection against these predators. Accordingly, our HSM includes a light detection and ranging (LiDAR) based metric of understory density around the nest and the distance of the nest to the closest human settlement to predict breeding success. It reveals that a high understory density 15–80 m around nests is associated with increased breeding success in territories close to settlements (<1.5 km). Farther away from human settlements breeding success is highest at nest sites with a more open understory providing a favorable warmer microclimate. We validated this HSM by comparing the predicted breeding success with landscape‐wide census data on Siberian jay occurrence. The correlation between breeding success and occurrence was strong up to 40 km around the study site. However, the HSM appears to overestimate breeding success in regions with a milder climate and therefore higher corvid numbers. Our findings suggest that maintaining patches of small diameter trees may provide a cost‐effective way to restore the breeding habitat for Siberian jays up to 1.5 km from human settlements. This distance is expected to increase in the warmer, southern, and coastal range of the Siberian jay where the presence of other corvids is to a lesser extent restricted to settlements

Oxidative modifications cross-talk in redox regulation of cellular physiology

1 p. OCC World Congress and Annual SFRR-E Conference 2017 Metabolic Stress and Redox Regulation Berlin, Germany 21-23 June 2017Redox balance plays an important role in the regulation of cellular physiology via orchestrated action of electron donors/acceptors, reactive oxygen and nitrogen species (RONS) and antioxidant defence mechanisms. Recently postulated hypothesis of "redox switches" via ROS-induced protein post-translational modifications (PTMs) acknowledge its importance in cellular signaling events. Importantly, impairment of redox homeostasis is a crucial factor in the development of numerous human pathologies including metabolic and cardiovascular diseases. However, the role of redox regulated modifications and PTM cross-talk is poorly investigated, mostly due to the analytical challenges in their high-throughput detection and quantification. Using state-of-the-art bioanalytical methods, a detailed investigation of different lipid and protein PTMs was performed using dynamic cardiomyocyte model of nitroxidative stress. Fluorescent microscopy revealed significant alterations in subcellular distribution of main cytoskeletal proteins – actin, vimentin and tubulin. Using in-depth proteomics approach over 35 different post-translational modifications were mapped and relatively quantified for cytoskeletal proteins. This allowed to identify “hot spots”, like the single cysteine residue of vimentin, which might play an important role in PTM cross-talk and thus take part in redox regulation.Funding was provided by SAF2015-68590-R from MINEICO (Spain) /FEDER and EU project 675132 (MASSTRPLAN) H2020-MSCA-ITN-2015Peer reviewe

Dynamic posttranslational modifications of cytoskeletal proteins unveil hot spots under nitroxidative stress

The cytoskeleton is a supramolecular structure consisting of interacting protein networks that support cell dynamics in essential processes such as migration and division, as well as in responses to stress. Fast cytoskeletal remodeling is achieved with the participation of regulatory proteins and posttranslational modifications (PTMs). Redox-related PTMs are emerging as critical players in cytoskeletal regulation. Here we used a cellular model of mild nitroxidative stress in which a peroxynitrite donor induced transient changes in the organization of three key cytoskeletal proteins, i.e., vimentin, actin and tubulin. Nitroxidative stress-induced reconfiguration of intermediate filaments, microtubules and actin structures were further correlated with their PTM profiles and dynamics of the PTM landscape. Using high-resolution mass spectrometry, 62 different PTMs were identified and relatively quantified in vimentin, actin and tubulin, including 12 enzymatic, 13 oxidative and 2 nitric oxide-derived modifications as well as 35 modifications by carbonylated lipid peroxidation products, thus evidencing the occurrence of a chain reaction with formation of numerous reactive species and activation of multiple signaling pathways. Our results unveil the presence of certain modifications under basal conditions and their modulation in response to stress in a target-, residue- and reactive species-dependent manner. Thus, some modifications accumulated during the experiment whereas others varied transiently. Moreover, we identified protein PTM “hot spots”, such as the single cysteine residue of vimentin, which was detected in seven modified forms, thus, supporting its role in PTM crosstalk and redox sensing. Finally, identification of novel PTMs in these proteins paves the way for unveiling new cytoskeleton regulatory mechanisms

Comparison of the acis-base properties of 5- and 6-uracilmethylphosphonate (5Umpa2- and 6Umpa2-) and some related compounds. Evidence for intramolecular hydrogen-bond formation in aqueous solution between (N1)H and the phosphonate group of 6Umpa2-

The acidity constants of 5-uracilmethylphosphonic acid, H2(5Umpa), and 6-uracilmethylphosphonic acid, H2(6Umpa), were determined by potentiometric pH titrations in aqueous solution (25 °C; I = 0.1 M, NaNO3). Comparison of these constants with those of related uracil derivatives (partly taken from the literature) allows the conclusion that an intramolecular hydrogen bond is formed between (N1)H and the phosphonate group of 6Umpa2−; the formation degree of this hydrogen-bonded isomer is estimated to be 86 ± 7%. The X-ray crystal structure analysis of H2(6Umpa) is reported but this solid state structure is dominated by intermolecular hydrogen bonds. In the context of the properties of 5Umpa2− and 6Umpa2− those of uracil are also discussed and from various comparisons of acidity constants it is concluded that deprotonation of uracil may occur at (N3)H as well as at (N1)H but that the (N3)-deprotonated species dominates with about 80% in aqueous solution at 25 °C and I = 0.1 M (Na+). The search for other examples of uracil derivatives which allow hydrogen-bond formation in aqueous solution has led to orotic acid (= 6-uracilcarboxylic acid; [H(6Urca)]) and 5-uracilcarboxylic acid [H(5Urca)]; based on acidity constant comparisons it is concluded that in aqueous solution (25 °C; I = 0.1 M, KCl) H(5Urca) exists to about 92 ± 10% as a species with a hydrogen bond between (C5)COOH and (C4)O, and 6Urca− to about 95 ± 5% as a species with a hydrogen bond between (C6)COO− and (N1)H. The importance of intramolecular hydrogen-bond formation to the acid–base properties of compounds in solution is briefly emphasized

Cross-talk between lipid and protein carbonylation in a dynamic cardiomyocyte model of mild nitroxidative stress

Reactive oxygen and nitrogen species (ROS/RNS) play an important role in the regulation of cardiac function. Increase in ROS/RNS concentration results in lipid and protein oxidation and is often associated with onset and/or progression of many cardiovascular disorders. However, interplay between lipid and protein modifications has not been simultaneously studied in detail so far. Biomolecule carbonylation is one of the most common biomarkers of oxidative stress. Using a dynamic model of nitroxidative stress we demonstrated rapid changes in biomolecule carbonylation in rat cardiomyocytes. Levels of carbonylated species increased as early as 15 min upon treatment with the peroxynitrite donor, 3-morpholinosydnonimine (SIN-1), and decreased to values close to control after 16 h. Total (lipids+proteins) vs. protein-specific carbonylation showed different dynamics, with a significant increase in protein-bound carbonyls at later time points. Treatment with SIN-1 in combination with inhibitors of proteasomal and autophagy/lysosomal degradation pathways allowed confirmation of a significant role of the proteasome in the degradation of carbonylated proteins, whereas lipid carbonylation increased in the presence of autophagy/lysosomal inhibitors. Electrophilic aldehydes and ketones formed by lipid peroxidation were identified and relatively quantified using LC-MS/MS. Molecular identity of reactive species was used for data-driven analysis of their protein targets. Combination of different enrichment strategies with LC-MS/MS analysis allowed identification of more than 167 unique proteins with 332 sites modified by electrophilic lipid peroxidation products. Gene ontology analysis of modified proteins demonstrated enrichment of several functional categories including proteins involved in cytoskeleton, extracellular matrix, ion channels and their regulation. Using calcium mobilization assays, the effect of nitroxidative stress on the activity of several ion channels was further confirmed. Keywords: Nitroxidative stress, Cardiomyocytes, Lipid oxidation, Protein oxidation, Lipid-protein adducts, Carbonylatio

Profiling and relative quantification of multiply nitrated and oxidized fatty acids

International audienceThe levels of nitro fatty acids (NO 2-FA), such as nitroarachidonic, nitrolinoleic, nitrooleic, and dinitrooleic acids, are elevated under various inflammatory conditions, and this results in different anti-inflammatory effects. However, other multiply nitrated and nitro-oxidized FAs have not been studied so far. Owing to the low concentrations in vivo, NO 2-FA analytics usually relies on targeted gas chromatography tandem mass spectrometry (MS/MS) or liquid chromatography-MS/MS, and thus require standard compounds for method development. To overcome this limitation and increase the number and diversity of analytes, we performed in-depth mass spectrometry (MS) profiling of nitration products formed in vitro by incubating fatty acids with NO 2 BF 4 , and ONOO-. The modified fatty acids were used to develop a highly specific and sensitive multiple reaction monitoring LC-MS method for relative quantification of 42 different nitrated and oxidized species representing three different groups: singly nitrated, multiply nitrated, and nitro-oxidized fatty acids. The method was validated in in vitro nitration kinetic studies and in a cellular model of nitrosative stress. NO 2-FA were quantified in lipid extracts from 3-morpholinosydnonimine-treated rat primary cardiomyocytes after 15, 30, and 70 min from stress onset. The relatively high levels of dinitrooleic, nitroarachidonic, hydroxynitrodocosapenataenoic, nitrodocosahexaenoic, hydroxynitrodocosahexaenoic, and dinitrodocosahexaenoic acids confirm the presence of multiply nitrated and nitro-oxidized fatty acids in biological systems for the first time. Thus, in vitro nitration was successfully used to establish a targeted LC-MS/MS method that was applied to complex biological samples for quantifying diverse NO 2-FA

Protein Carbonylation and Glycation in Legume Nodules

19 Pags.- 2 Tabls.- 11 Figs.- Supp. Data (15 Figs.- 5 Tabls.- 4 DataSets). Copyright © 2018 American Society of Plant Biologists. All rights reserved. Authors cannot archive post-print (ie final draft post-refereeing): Must link to publisher version, toll-free link provided.Nitrogen fixation is an agronomically and environmentally important process catalyzed by bacterial nitrogenase within legume root nodules. These unique symbiotic organs have high metabolic rates and produce large amounts of reactive oxygen species that may modify proteins irreversibly. Here, we examined two types of oxidative posttranslational modifications of nodule proteins: carbonylation, which occurs by direct oxidation of certain amino acids or by interaction with reactive aldehydes arising from cell membrane lipid peroxides; and glycation, which results from the reaction of lysine and arginine residues with reducing sugars or their autooxidation products. We used a strategy based on the enrichment of carbonylated peptides by affinity chromatography followed by liquid chromatography-tandem mass spectrometry to identify 369 oxidized proteins in bean (Phaseolus vulgaris) nodules. Of these, 238 corresponded to plant proteins and 131 to bacterial proteins. Lipid peroxidation products induced most carbonylation sites. This study also revealed that carbonylation has major effects on two key nodule proteins. Metal-catalyzed oxidation caused the inactivation of malate dehydrogenase and the aggregation of leghemoglobin. In addition, numerous glycated proteins were identified in vivo, including three key nodule proteins: sucrose synthase, glutamine synthetase, and glutamate synthase. Label-free quantification identified 10 plant proteins and 18 bacterial proteins as age-specifically glycated. Overall, our results suggest that the selective carbonylation or glycation of crucial proteins involved in nitrogen metabolism, transcriptional regulation, and signaling may constitute a mechanism to control cell metabolism and nodule senescence.This work was supported by the Ministerio de Economía y Competitividad-Fondos Europeos de Desarrollo Regional (grant AGL2014-53717-R to M.A.M. and M.B.), by the German Research Society (grant FR3117/2-1 to A.F. and A.K.), by the Russian Foundation for Basic Research (grant 18-016-00190 to A.F.), by the Deutsche Forschungsgemeinschaft (grant FE-1236/3-1 to M.F.), and by the European Regional Development Fund (European Union and Free State Saxony; grants 100146238 and 100121468 to M.F.).Peer reviewe

Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication

Summary: Chromatin organization must be maintained during cell proliferation to preserve cellular identity and genome integrity. However, DNA replication results in transient displacement of DNA-bound proteins, and it is unclear how they regain access to newly replicated DNA. Using quantitative proteomics coupled to Nascent Chromatin Capture or isolation of Proteins on Nascent DNA, we provide time-resolved binding kinetics for thousands of proteins behind replisomes within euchromatin and heterochromatin in human cells. This shows that most proteins regain access within minutes to newly replicated DNA. In contrast, 25% of the identified proteins do not, and this delay cannot be inferred from their known function or nuclear abundance. Instead, chromatin organization and G1 phase entry affect their reassociation. Finally, DNA replication not only disrupts but also promotes recruitment of transcription factors and chromatin remodelers, providing a significant advance in understanding how DNA replication could contribute to programmed changes of cell memory