Failure and moral distinction in a Ukrainian marketplace of ideas

This essay examines the generative effects of claiming moral failure within a Ukrainian liberal movement for media reform in post-Maidan, pre-invasion Ukraine. The reformers wished to reorganize news reporting around the ideals of autonomy, balanced objectivity, impartiality, and corrigibility, which they believed underpinned Western media. They decried most Ukrainian media as failing such standards, highlighting the individual moral failure of journalists bankrolled by oligarchs in return for favourable media representation. In turn, those from whom the reformers tried to distinguish themselves morally mocked them as ‘grant-eaters’ for their dependence on Western democracy promotion grants. This tussle pitted material success against yearnings for moral and professional probity. Developing Selka's idea of moral distinction, I argue that while the reformers’ pursuit of virtuous difference was sincere, their structural vulnerability vis-à-vis the mainstream media also made morality more salient as the basis for agonistic differentiation.     

Receptor association and tyrosine phosphorylation of S6 kinases

Ribosomal protein S6 kinase (S6K) is activated by an array of mitogenic stimuli and is a key player in the regulation of cell growth. The activation process of S6 kinase involves a complex and sequential series of multiple Ser/Thr phosphorylations and is mainly mediated via phosphatidylinositol 3-kinase (PI3K)-3-phosphoinositide-dependent protein kinase-1 (PDK1) and mTor-dependent pathways. Upstream regulators of S6K, such as PDK1 and protein kinase B (PKB/Akt), are recruited to the membrane via their pleckstrin homology (PH) or protein-protein interaction domains. However, the mechanism of integration of S6K into a multi-enzyme complex around activated receptor tyrosine kinases is not clear. In the present study, we describe a specific interaction between S6K with receptor tyrosine kinases, such as platelet-derived growth factor receptor (PDGFR). The interaction with PDGFR is mediated via the kinase or the kinase extension domain of S6K. Complex formation is inducible by growth factors and leads to S6K tyrosine phosphorylation. Using PDGFR mutants, we have shown that the phosphorylation is exerted via a PDGFR-src pathway. Furthermore, src kinase phosphorylates and coimmunoprecipitates with S6K in vivo. Inhibitors towards tyrosine kinases, such as genistein and PP1, or src-specific SU6656, but not PI3K and mTor inhibitors, lead to a reduction in tyrosine phosphorylation of S6K. In addition, we mapped the sites of tyrosine phosphorylation in S6K1 and S6K2 to Y39 and Y45, respectively. Mutational and immunofluorescent analysis indicated that phosphorylation of S6Ks at these sites does not affect their activity or subcellular localization. Our data indicate that S6 kinase is recruited into a complex with RTKs and src and becomes phosphorylated on tyrosine/s in response to PDGF or serum.     

Pexophagy is responsible for 65% of cases of peroxisome biogenesis disorders

Peroxisome biogenesis disorders (PBDs) is a group of diseases caused by mutations in one of the peroxins, proteins responsible for biogenesis of the peroxisomes. In recent years, it became clear that many peroxins (e.g., PEX3 and PEX14) play additional roles in peroxisome homeostasis (such as promoting autophagic degradation of peroxisomes or pexophagy), which are often opposite to their originally established functions in peroxisome formation and maintenance. Even more interesting, the peroxins that make up the peroxisomal AAA ATPase complex (AAA-complex) in yeast (Pex1, Pex6 and Pex15) or mammals (PEX1, PEX6, PEX26) are responsible for the downregulation of pexophagy. Moreover, this might be even their primary role in human: to prevent pexophagy by removing from the peroxisomal membrane the ubiquitinated peroxisomal matrix protein import receptor, Ub-PEX5, which is also a signal for the Ub-binding pexophagy receptor, NBR1. Remarkably, the peroxisomes rescued from pexophagy by autophagic inhibitors in PEX1^G843D (the most common PBD mutation) cells are able to import matrix proteins and improve their biochemical function suggesting that the AAA-complex per se is not essential for the protein import function in human. This paradigm-shifting discovery published in the current issue of Autophagy has raised hope for up to 65% of all PBD patients with various deficiencies in the AAA-complex. Recognizing PEX1, PEX6 and PEX26 as pexophagy suppressors will allow treating these patients with a new range of tools designed to target mammalian pexophagy.     

Application of docking methodologies to modeled proteins

Protein docking is essential for structural characterization of protein interactions. Besides providing the structure of protein complexes, modeling of proteins and their complexes is important for understanding the fundamental principles and specific aspects of protein interactions. The accuracy of protein modeling, in general, is still less than that of the experimental approaches. Thus, it is important to investigate the applicability of docking techniques to modeled proteins. We present new comprehensive benchmark sets of protein models for the development and validation of protein docking, as well as a systematic assessment of free and template-based docking techniques on these sets. As opposed to previous studies, the benchmark sets reflect the real case modeling/docking scenario where the accuracy of the models is assessed by the modeling procedure, without reference to the native structure (which would be unknown in practical applications). We also expanded the analysis to include docking of protein pairs where proteins have different structural accuracy. The results show that, in general, the template-based docking is less sensitive to the structural inaccuracies of the models than the free docking. The near-native docking poses generated by the template-based approach, typically, also have higher ranks than those produces by the free docking (although the free docking is indispensable in modeling the multiplicity of protein interactions in a crowded cellular environment). The results show that docking techniques are applicable to protein models in a broad range of modeling accuracy. The study provides clear guidelines for practical applications of docking to protein models.     

Chlorophyll fluorescence induction and relaxation system for the continuous monitoring of photosynthetic capacity in photobioreactors

The development of high‐performance photobioreactors equipped with automatic systems for non‐invasive real‐time monitoring of cultivation conditions and photosynthetic parameters is a challenge in algae biotechnology. Therefore, we developed a chlorophyll (Chl) fluorescence measuring system for the online recording of the light‐induced fluorescence rise and the dark relaxation of the flash‐induced fluorescence yield (Qa^? ? re‐oxidation kinetics) in photobioreactors. This system provides automatic measurements in a broad range of Chl concentrations at high frequency of gas‐tight sampling, and advanced data analysis. The performance of this new technique was tested on the green microalgae Chlamydomonas reinhardtii subjected to a sulfur deficiency stress and to long‐term dark anaerobic conditions. More than thousand fluorescence kinetic curves were recorded and analyzed during aerobic and anaerobic stages of incubation. Lifetime and amplitude values of kinetic components were determined, and their dynamics plotted on heatmaps. Out of these data, stress‐sensitive kinetic parameters were specified. This implemented apparatus can therefore be useful for the continuous real‐time monitoring of algal photosynthesis in photobioreactors.     

Young’s modulus of elasticity of Schlemm’s canal endothelial cells

Schlemm’s canal (SC) endothelial cells are likely important in the physiology and pathophysiology of the aqueous drainage system of the eye, particularly in glaucoma. The mechanical stiffness of these cells determines, in part, the extent to which they can support a pressure gradient and thus can be used to place limits on the flow resistance that this layer can generate in the eye. However, little is known about the biomechanical properties of SC endothelial cells. Our goal in this study was to estimate the effective Young’s modulus of elasticity of normal SC cells. To do so, we combined magnetic pulling cytometry of isolated cultured human SC cells with finite element modeling of the mechanical response of the cell to traction forces applied by adherent beads. Preliminary work showed that the immersion angles of beads attached to the SC cells had a major influence on bead response; therefore, we also measured bead immersion angle by confocal microscopy, using an empirical technique to correct for axial distortion of the confocal images. Our results showed that the upper bound for the effective Young’s modulus of elasticity of the cultured SC cells examined in this study, in central, non-nuclear regions, ranged between 1,007 and 3,053 Pa, which is similar to, although somewhat larger than values that have been measured for other endothelial cell types. We compared these values to estimates of the modulus of primate SC cells in vivo, based on images of these cells under pressure loading, and found good agreement at low intraocular pressure (8–15 mm Hg). However, increasing intraocular pressure (22–30 mm Hg) appeared to cause a significant increase in the modulus of these cells. These moduli can be used to estimate the extent to which SC cells deform in response to the pressure drop across the inner wall endothelium and thereby estimate the extent to which they can generate outflow resistance.     

Effect of the Earthworms Lumbricus terrestris and Aporrectodea caliginosa on Bacterial Diversity in Soil

Earthworms ingest large amounts of soil and have the potential to radically alter the biomass, activity, and structure of the soil microbial community. In this study, the diversity of eight bacterial groups from fresh soil, gut, and casts of the earthworms Lumbricus terrestris and Aporrectodea caliginosa were studied by single-strand conformation polymorphism (SSCP) analysis using both newly designed 16S rRNA gene-specific primer sets targeting Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, Bacteroidetes, Verrucomicrobia, Planctomycetes, and Firmicutes and a conventional universal primer set for SSCP, with RNA and DNA as templates. In parallel, the study of the relative abundance of these taxonomic groups in the same samples was performed using fluorescence in situ hybridization. Bacteroidetes, Alphaproteobacteria, and Betaproteobacteria were predominant in communities from the soil and worm cast samples. Representatives of classes Flavobacteria and Sphingobacteria (Bacteroidetes) and Pseudomonas spp. (low-abundant Gammaproteobacteria) were detected in soil and worm cast samples with conventional and taxon-targeting SSCP and through the sequence analysis of 16S rRNA clone libraries. Physiologically active unclassified Sphingomonadaceae (Alphaproteobacteria) and Alcaligenes spp. (Betaproteobacteria) also maintained their diversities during transit through the earthworm intestine and were found on taxon-targeting SSCP profiles from the soil and worm cast samples. In conclusion, our results suggest that some specific bacterial taxonomic groups maintain their diversity and even increase their relative numbers during transit through the gastrointestinal tract of earthworms.     

Acclimation of photosynthesis to nitrogen deficiency in Phaseolus vulgaris

Nitrogen deficiency diminishes consumption of photosynthates in anabolic metabolism. We studied adjustments of the photosynthetic machinery in nitrogen-deficient bean plants and found four phenomena. First, the number of chloroplasts per cell decreased. Chloroplasts of nitrogen starved leaves contained less pigments than those of control leaves, but the in vitro activities of light reactions did not change when measured on chlorophyll basis. Second, nitrogen deficiency induced cyclic electron transfer. The amounts of Rubisco and ferredoxin-NADP⁺ reductase decreased in nitrogen starved plants. Low activities of these enzymes are expected to lead to increase in reduction of oxygen by photosystem I. However, diaminobenzidine staining did not reveal hydrogen peroxide production in nitrogen starved plants. Measurements of far-red-light-induced redox changes of the primary donor of photosystem I suggested that instead of producing oxygen radicals, nitrogen starved plants develop a high activity of cyclic electron transport that competes with oxygen for electrons. Nitrogen starvation led to decrease in photochemical quenching and increase in non-photochemical quenching, indicating that cyclic electron transport reduces the plastoquinone pool and acidifies the lumen. A third effect is redistribution of excitation energy between the photosystems in favor of photosystem I. Thus, thylakoids of nitrogen starved plants appeared to be locked in state 2, which further protects photosystem II by decreasing its absorption cross-section. As a fourth response, the proportion of non-Q_B-reducing photosystem II reaction centers increased and the redox potential of the Q_B/Q_B⁻ pair decreased by 25 mV in a fraction of photosystem II centers of nitrogen starved plants.     

The role of karyopherins in the regulated sumoylation of septins

In the yeast Saccharomyces cerevisiae, several components of the septin ring are sumoylated during anaphase and then abruptly desumoylated at cytokinesis. We show that septin sumoylation is controlled by the interactions of two enzymes of the sumoylation pathway, Siz1p and Ulp1p, with the nuclear transport machinery. The E3 ligase Siz1p is imported into the nucleus by the karyopherin Kap95p during interphase. In M phase, Siz1p is exported from the nucleus by the karyopherin Kap142p/Msn5p and subsequently targeted to the septin ring, where it participates in septin sumoylation. We also show that the accumulation of sumoylated septins during mitosis is dependent on the interactions of the SUMO isopeptidase Ulp1p with Kap121p and Kap95p-Kap60p and the nuclear pore complex (NPC). In addition to sequestering Ulp1 at the NPC, Kap121p is required for targeting Ulp1p to the septin ring during mitosis. We present a model in which Ulp1p is maintained at the NPC during interphase and transiently interacts with the septin ring during mitosis.     

Influence of a Probiotic Strain of Enterococcus faecium on Salmonella enterica Serovar Typhimurium DT104 Infection in a Porcine Animal Infection Model

The beneficial effects of probiotic Enterococcus spp. in different hosts, such as mice and humans, have previously been reported in several studies. However, studies of large domestic animals, as well as challenge studies with pathogenic microorganisms, are very rare. Here, we investigated the influence of oral treatment of pigs with the probiotic bacterium Enterococcus faecium NCIMB 10415 on Salmonella enterica serovar Typhimurium DT104 infections in weaning piglets. Clinical symptoms, fecal excretion, the organ distribution of Salmonella, and the humoral immune response (immunoglobulin G [IgG], IgM, and IgA levels) in serum were examined. A pool of 89 piglets was randomly divided into probiotic and control groups. The probiotic group received a feed supplement containing E. faecium starting on day 14 postpartum prior to challenge with Salmonella serovar Typhimurium DT104 at 28 days postpartum. After challenge with Salmonella serovar Typhimurium DT104, piglets in both groups showed no severe clinical signs of salmonellosis. However, fecal excretion and colonization of Salmonella in organs were significantly greater in piglets fed E. faecium. Likewise, the humoral immune response against Salmonella (serum IgM and IgA levels) was significantly greater in the probiotic group animals than in control animals. The results of this study suggest that E. faecium NCIMB 10415 treatment enhanced the course of infection in weaning piglets challenged with Salmonella serovar Typhimurium DT104. However, the probiotic treatment also appeared to result in greater production of specific antibodies against Salmonella serovar Typhimurium DT104.The problem of increasing microbial resistance to antibiotics resulting from years of overuse and the resulting ban on the use of antibiotics in animal production have led to increased interest in alternatives to antibiotics in animal production. In recent years, probiotic bacteria have been considered as an alternative means of reducing pathogen loads in animal breeding and production units. However, while a number of studies have focused on the mode of action of probiotics, the mode of action these bacteria is not fully understood yet.A recent interdisciplinary research study of the modes of action of probiotics in swine showed that Enterococcus faecium NCIMB 10415 reduced the pathogenic bacterial load of healthy piglets (20, 26, 30, 36). In vitro studies further demonstrated that this E. faecium probiotic strain decreased the rate of invasion of a porcine intestinal epithelial cell line by Salmonella enterica serovar Typhimurium. To determine whether probiotics also provide a measure of protection during infections, experimental challenge studies with pathogenic bacteria at a defined infectious dose and under comparable conditions seem to be necessary. Field studies could be more representative of the real situation; however, the infection pressure is too low and difficult to define, and systematic sampling cannot be done.Studies of larger domestic and production animals are rare. Most such studies deal with the mode of action of probiotics in the healthy host, and only a few studies have investigated the mode of action in the context of infections with pathogenic bacteria, such as Salmonella.In a related study, weaned piglets were fed a mixture of five probiotic strains (one Pediococcus strain and four Lactobacillus strains) and challenged with Salmonella serovar Typhimurium (7). In that study, reduced incidence, severity, and duration of diarrhea and a reduced microbiological load of Salmonella were observed. Fedorka-Cray et al. (11) observed reduced numbers of Salmonella bacteria in cecal contents and at the ileocolic junction in S. enterica serovar Choleraesuis-challenged weaning piglets fed a competitive exclusion culture. In vitro investigations showed that Enterococcus strains have inhibitory effects on the growth of S. enterica serovar Enteritidis, and these effects were explained by both enterotoxin and nonenterotoxin factors (37). Other studies showed that E. faecium may be beneficial to the adhesion and colonization of Clostridium jejuni in the canine intestine (29) and reduced the rate of carryover infections with obligate intracellular pathogens from infected sows in piglets (26). E. faecium has also been shown to influence the composition of the bacterial community in the avian, swine, and canine gastrointestinal tracts (25, 29, 36).Infections with S. enterica are some of the most important sources of human gastroenteritis (39). In Germany, 52,563 human salmonellosis cases were reported in 2006 (http://www3.rki.de/SurvStat). The consumption of contaminated pork and pork products was found to be associated with 20% of human salmonellosis cases in Germany (33), indicating the importance of meat or meat products as a potential source of infection for consumers. Salmonella serovar Typhimurium, especially phage type DT104, is the Salmonella serotype most frequently isolated from pork (27), and it is of particular concern because of its acquisition of multiple antibiotic resistance (1, 38).In this study, we investigated the effect of E. faecium NCIMB 10415 on the infection dynamics of Salmonella serovar Typhimurium DT104, fecal shedding, and the patterns of Salmonella distribution in internal organs, as well as on the humoral immune response to Salmonella in weaning piglets. To the best of our knowledge, this is the first experimental study of the mode of action of a probiotic strain of E. faecium in which dissemination to different internal organs was investigated using weaned piglets experimentally infected with Salmonella.