Regulation of the action of early mitotic inhibitor 1 on the anaphase-promoting complex/cyclosome by cyclin-dependent kinases

Cell cycle regulation is characterized by alternating activities of cyclin-dependent kinases (CDKs) and of the ubiquitin ligase anaphase promoting complex/cyclosome (APC/C). During S-phase APC/C is inhibited by early mitotic inhibitor 1 (Emi1) to allow the accumulation of cyclins A and B and to prevent re-replication. Emi1 is degraded at prophase by a Plk1-dependent pathway. Recent studies in which the degradation pathway of Emi1 was disrupted have shown that APC/C is activated at mitotic entry despite stabilization of Emi1. These results suggested the possibility of additional mechanisms other than degradation of Emi1, which release APC/C from inhibition by Emi1 upon entry into mitosis. In this study we report one such mechanism, by which the ability of Emi1 to inhibit APC/C is negatively regulated by CDKs. We show that in Plk1-inhibited cells Emi1 is stabilized and phosphorylated, that Emi1 is phosphorylated by CDKs in mitotic but not S-phase cell extracts, and that Emi1 phosphorylation by mitotic cell extracts or purified CDKs markedly reduces the ability of Emi1 to bind and to inhibit APC/C. Finally, we show that the addition of extracts from S-phase cells to extracts from mitotic cells protects Emi1 from CDK-mediated inactivation.     

Gallocyanine as a Fluorogen for the Identification of NADPH-Dependent Production of Superoxide Anion Radical by Blood Cells

Russian Journal of Bioorganic Chemistry - The interaction of the oxazine dye gallocyanine with reactive oxygen ( $$^{\centerdot }{\text{O}}_{2}^{ - },$$ Н2О2) and halogen (HOCl) species...     

Fluorescent Probes for HOCl Detection in Living Cells

Russian Journal of Bioorganic Chemistry - Hypochlorous acid (HOCl) plays an important role in the immune system not only protecting the organism from pathogens, but also, due to its high...     

Value-complexity tradeoff explains mouse navigational learning

We introduce a novel methodology for describing animal behavior as a tradeoff between value and complexity, using the Morris Water Maze navigation task as a concrete example. We develop a dynamical system model of the Water Maze navigation task, solve its optimal control under varying complexity constraints, and analyze the learning process in terms of the value and complexity of swimming trajectories. The value of a trajectory is related to its energetic cost and is correlated with swimming time. Complexity is a novel learning metric which measures how unlikely is a trajectory to be generated by a naive animal. Our model is analytically tractable, provides good fit to observed behavior and reveals that the learning process is characterized by early value optimization followed by complexity reduction. Furthermore, complexity sensitively characterizes behavioral differences between mouse strains.     

Internalization of Salmonella enterica in Leaves Is Induced by Light and Involves Chemotaxis and Penetration through Open Stomata

Outbreaks of salmonellosis related to consumption of fresh produce have raised interest in Salmonella-plant interactions leading to plant colonization. Incubation of gfp-tagged Salmonella enterica with iceberg lettuce leaves in the light resulted in aggregation of bacteria near open stomata and invasion into the inner leaf tissue. In contrast, incubation in the dark resulted in a scattered attachment pattern and very poor stomatal internalization. Forcing stomatal opening in the dark by fusicoccin had no significant effect on Salmonella internalization. These results imply that the pathogen is attracted to nutrients produced de novo by photosynthetically active cells. Indeed, mutations affecting Salmonella motility and chemotaxis significantly inhibited bacterial internalization. These findings suggest a mechanistic account for entry of Salmonella into the plant''s apoplast and imply that either Salmonella antigens are not well recognized by the stoma-based innate immunity or that this pathogen has evolved means to evade it. Internalization of leaves may provide a partial explanation for the failure of sanitizers to efficiently eradicate food-borne pathogens in leafy greens.Salmonella enterica is a common cause of food-borne gastroenteritis, with an estimated number of 1 to 3 million human cases per year in the United States (15). Outbreaks related to consumption of fresh produce have been increasingly reported (28) and result in morbidity and high economic losses. For example, the recent produce-associated salmonellosis outbreak (5), the largest yet reported, has resulted in more than 1,400 persons infected with S. enterica serovar Saintpaul in 43 U.S. states and in Canada. Needless to say, such outbreaks are economically destructive to farmers and the fresh produce industry and damage consumer confidence in the safety of the food supply.Plants might become contaminated in the field through the use of contaminated irrigation water, such as raw sewage or partially treated recycled water, as well as through the use of animal manure for fertilization (2, 4, 16). Fresh produce can also become contaminated during harvest and at postharvest stages due to poor worker hygiene and low sanitation in the processing plant (2, 4). Enteropathogens can adapt to the phyllosphere environment, where they might interact with epiphytic bacteria and gain a foothold (3, 4, 14). It was suggested that transient occupants of the leaf, such as enteropathogens, may become incorporated into phylloplane biofilms and consequently gain protection from environmental stress (11). Studies of the interactions between Escherichia coli O157:H7 and cut lettuce leaves demonstrated attachment of bacteria to the surface, trichomes, stomata, and cut edges. Bacteria were also seen entrapped 20 to 100 μm below the surface in stomata and cut edges (27). Potential localization of human pathogens in the phyllosphere at sites inaccessible to sanitizers may lead to contamination of the food supply.The produce industry currently lacks an efficient control method to ensure complete removal or killing of food-borne pathogens in fresh or minimally processed fruits and vegetables. Therefore, understanding the contamination routes and the interplay between food-borne pathogens and plant tissues is essential in order to design new intervention strategies for ensuring the safety of fresh produce. Lettuce was associated with several outbreaks related to contamination with Salmonella (12, 16, 23, 32); therefore, interactions between this pathogen and lettuce leaves were investigated in this study.     

Multivalent human blood group ABH and Lewis glycotopes are key recognition factors for a lFuc>Man binding lectin from phytopathogenic Ralstonia solanacearum

Ralstonia solanacearum lectin (RSL), that might be involved in phytopathogenicity, has been defined as lFuc?Man specific. However, the effects of polyvalency of glycotopes and mammalian structural units on binding have not been established. In this study, recognition factors of RSL were comprehensively examined with natural multivalent glycotopes and monomeric ligands using enzyme linked lectin-sorbent and inhibition assays. Among the glycans tested, RSL reacted strongly with multivalent blood group A_h (GalNAcα1–3[Fucα1–2]Gal) and H (Fucα1–2Gal) active glycotopes, followed by B_h (Galα1–3[Fucα1–2]Gal), Le^a (Galβ1–3[Fucα1–4]GlcNAc) and Le^b (Fucα1–2Galβ1–3[Fucα1–4]GlcNAc) active glycotopes. But weak or negligible binding was observed for blood group precursors having Galβ1–3/4GlcNAcβ1- (I_β/II_β) residues or Galβ1–3GalNAcα1- (T_α), GalNAcα1-Ser/Thr (Tn) bearing glycoproteins. These results indicate that the density and degree of exposure of multivalent ligands of α1–2 linked lFuc to Gal at the non-reducing end is the most critical factor for binding. An inhibition study with monomeric ligands revealed that the combining site of RSL should be of a groove type to fit trisaccharide binding with highest complementarity to blood group H trisaccharide (H_L; Fucα1–2Galβ1–4Glc). The outstandingly broad RSL saccharide-binding profile might be related to the unusually wide spectrum of plants that suffer from R. solanacearum pathogenicity and provide ideas for protective antiadhesion strategies.     

Autoencoder based local T cell repertoire density can be used to classify samples and T cell receptors

Recent advances in T cell repertoire (TCR) sequencing allow for the characterization of repertoire properties, as well as the frequency and sharing of specific TCR. However, there is no efficient measure for the local density of a given TCR. TCRs are often described either through their Complementary Determining region 3 (CDR3) sequences, or theirV/J usage, or their clone size. We here show that the local repertoire density can be estimated using a combined representation of these components through distance conserving autoencoders and Kernel Density Estimates (KDE). We present ELATE–an Encoder-based LocAl Tcr dEnsity and show that the resulting density of a sample can be used as a novel measure to study repertoire properties. The cross-density between two samples can be used as a similarity matrix to fully characterize samples from the same host. Finally, the same projection in combination with machine learning algorithms can be used to predict TCR-peptide binding through the local density of known TCRs binding a specific target.