Cyclic Dinucleotides and the Innate Immune Response

Cyclic dinucleotides (CDNs) have been previously recognized as important secondary signaling molecules in bacteria and, more recently, in mammalian cells. In the former case, they represent secondary messengers affecting numerous responses of the prokaryotic cell, whereas in the latter, they act as agonists of the innate immune response. Remarkable new discoveries have linked these two patterns of utilization of CDNs as secondary messengers and have revealed unexpected influences they likely had on shaping human genetic variation. This Review summarizes these recent insights and provides a perspective on future unanswered questions in this exciting field

Android credit management application

Práce se zabývá návrhem a implementací Android aplikace pro správu úv¥r·. Základní poºadavky jsou dosáhnout zabezpe£eného p°ístupu uºivatel· k p°ehledu svých aktuálních úv¥r·. Pomocí aplikace mohou uºivatelé zjistit aktuální stav, p°ehled v²ech dokument· i oznámení d·leºitých termín·, coº zjednodu²í proces zaloºení a vedení úv¥r·. V práci je popsána analýza problém· a návrh jejich °e²ení na platform¥ opera£ního systému Android. P°i vývoji byl pouºit programovací jazyk Kotlin a vývojové prost°edí Android Studio.My work deals with the design and implementation of Android applications for loan management. The basic requirements for this application are to provide secure access to an overview of the user's current loans. Using the application, users can nd out the current status, an overview of all documents and announcements of important dates, which simplies the process of establishing and managing loans. The work describes the analysis of problems and the design of their solution on the Android platform. Kotlin programming language and Android Studio environment were used in the development

Reliability of Training Data Sets for ML Classifiers: a Lesson Learned from Mechanical Engineering

The popularity of learning and predictive technologies, across many problem domains, is unprecedented and it is often underpinned with the fact that we efficiently compute with vast amounts of data and data types, and thus should be able to resolve problems, which we could not in the past. This view is particularly common among scientists who believe that the excessive amount of data, we generate in real life, is ideal for performing predictions and training algorithms. However, the truth might be quite different. The paper illustrates the process of preparing a training data set for an ML classifier, which should predict certain conditions in mechanical engineering. It was not the case that it was difficult to define and choose classifiers, in order to secure safe predictions. It was our inability to create a safe, reliable and trustworthy training data set, from scientifically proven experiments, which created the problem. This places serious doubts on the way we use learning and predictive technologies today. It remains debatable what the next step should be. However, if in ML algorithms, and classifiers in particular, the semantic which is built-in data sets, influences classifier’s definition, it would be very difficult to evaluate and rely on them, before we understand data semantics fully. In other words, we still do not know how the semantic, sometimes hidden in a data set, can adversely affect algorithms trained by them

The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD.

Mycobacterium tuberculosis (Mtb) induces necrosis of infected cells to evade immune responses. Recently, we found that Mtb uses the protein CpnT to kill human macrophages by secreting its C-terminal domain, named tuberculosis necrotizing toxin (TNT), which induces necrosis by an unknown mechanism. Here we show that TNT gains access to the cytosol of Mtb-infected macrophages, where it hydrolyzes the essential coenzyme NAD(+). Expression or injection of a noncatalytic TNT mutant showed no cytotoxicity in macrophages or in zebrafish zygotes, respectively, thus demonstrating that the NAD(+) glycohydrolase activity is required for TNT-induced cell death. To prevent self-poisoning, Mtb produces an immunity factor for TNT (IFT) that binds TNT and inhibits its activity. The crystal structure of the TNT-IFT complex revealed a new NAD(+) glycohydrolase fold of TNT, the founding member of a toxin family widespread in pathogenic microorganisms

Reliability of Training Data Sets for ML Classifiers: A Lesson Learned from Mechanical Engineering

The popularity of learning and predictive technologies, across many problem domains, is unprecedented and it is often underpinned with the fact that we efficiently compute with vast amounts of data and data types, and thus should be able to resolve problems, which we could not in the past. This view is particularly common among scientists who believe that the excessive amount of data, we generate in real life, is ideal for performing predictions and training algorithms. However, the truth might be quite different. The paper illustrates the process of preparing a training data set for an ML classifier, which should predict certain conditions in mechanical engineering. It was not the case that it was difficult to define and choose classifiers, in order to secure safe predictions. It was our inability to create a safe, reliable and trustworthy training data set, from scientifically proven experiments, which created the problem. This places serious doubts on the way we use learning and predictive technologies today. It remains debatable what the next step should be. However, if in ML algorithms, and classifiers in particular, the semantic which is built-in data sets, influences classifier’s definition, it would be very difficult to evaluate and rely on them, before we understand data semantics fully. In other words, we still do not know how the semantic, sometimes hidden in a data set, can adversely affect algorithms trained by them

Role of Porins for Uptake of Antibiotics by Mycobacterium smegmatis▿ †

The outer membrane of mycobacteria presents an effective permeability barrier for many antibiotics. Transport pathways across this membrane are unknown for most drugs. Here, we examined which antibiotics utilize the porin pathway across the outer membrane of the model organism Mycobacterium smegmatis. Deletion of the porins MspA and MspC drastically increased the resistance of M. smegmatis ML10 to β-lactam antibiotics, while its β-lactamase activity remained unchanged. These results are consistent with the ninefold-reduced outer membrane permeability of the M. smegmatis porin mutants for cephaloridine and strongly indicate that β-lactam antibiotics rely on the porin pathway. The porin mutant ML10 accumulated less chloramphenicol and norfloxacin and was less susceptible to these antibiotics than wild-type M. smegmatis. These results demonstrated that small and hydrophilic antibiotics use the Msp porins for entering the cell. In contrast to norfloxacin, the hydrophobic moxifloxacin was 32-fold more effective in inhibiting the growth of M. smegmatis, presumably because it was able to diffuse through the lipid membrane. Structural models indicated that erythromycin, kanamycin, and vancomycin are too large to move through the MspA channel. This study presents the first experimental evidence that hydrophilic fluoroquinolones and chloramphenicol diffuse through porins in mycobacteria. Thus, mutations resulting in less efficient porins or lower porin expression levels are likely to represent a mechanism for the opportunistic pathogens M. avium, M. chelonae, and M. fortuitum, which have Msp-like porins, to acquire resistance to fluoroquinolones

Identification of a Novel Multidrug Efflux Pump of Mycobacterium tuberculosis▿ †

The impermeability of the outer membrane in combination with drug efflux are major determinants of the natural drug resistance of mycobacteria. β-Lactams are the most widely used antibiotics for treatment of bacterial infections. However, it is unknown how β-lactams enter Mycobacterium tuberculosis and whether efflux pumps exist that can export these drugs out of the cell. To identify the molecular mechanisms of M. tuberculosis resistance to β-lactams, a library of 7,500 transposon mutants was generated in the model organism Mycobacterium bovis BCG. Thirty-three unique insertion sites were determined that conferred medium or high-level (≥2,000 μg/ml) resistance to ampicillin. Three mutants in sulfolipid synthesis or transport were highly resistant to ampicillin, indicating an indirect effect of the lipid composition on the outer membrane permeability of M. bovis BCG to ampicillin. Mutants with insertions in genes encoding surface molecules such as PPE proteins or lipoarabinomannan were also completely resistant to ampicillin, thus suggesting a lack of transport across the outer membrane. Insertion of the transposon in front of bcg0231 increased transcription of the gene and concomitantly the resistance of M. bovis BCG to ampicillin, streptomycin, and chloramphenicol by 32- to 64-fold. Resistance to vancomycin and tetracycline was increased four- to eightfold. Bcg0231 and Rv0194 are almost identical ATP-binding cassette transporters. Expression of rv0194 significantly reduced accumulation of ethidium bromide and conferred multidrug resistance to Mycobacterium smegmatis. Both effects were abrogated in the presence of the efflux pump inhibitor reserpine. These results demonstrate that Rv0194 is a novel multidrug efflux pump of M. tuberculosis

The mycobacterium tuberculosis outer membrane channel protein CpnT confers susceptibility to toxic molecules

© 2015 American Society for Microbiology.Mycobacterium tuberculosis, the causative agent of tuberculosis, is protected from toxic solutes by an effective outer membrane permeability barrier. Recently, we showed that the outer membrane channel protein CpnT is required for efficient nutrient uptake by M. tuberculosis and Mycobacterium bovis BCG. In this study, we found that the cpnT mutant of M. bovis BCG is more resistant than the wild type to a large number of drugs and antibiotics, including rifampin, ethambutol, clarithromycin, tetracycline, and ampicillin, by 8- to 32-fold. Furthermore, the cpnT mutant of M. bovis BCG was 100-fold more resistant to nitric oxide, a major bactericidal agent required to control M. tuberculosis infections in mice. Thus, CpnT constitutes the first outer membrane susceptibility factor in slow-growing mycobacteria. The dual functions of CpnT in uptake of nutrients and mediating susceptibility to toxic molecules are reflected in macrophage infection experiments: while loss of CpnT was detrimental for M. bovis BCG in macrophages that enable bacterial replication, presumably due to inadequate nutrient uptake, it conferred a survival advantage in macrophages that mount a strong bactericidal response. Importantly, the cpnT gene showed a significantly higher density of nonsynonymous mutations in drug-resistant clinical M. tuberculosis strains, indicating that CpnT is under selective pressure in human tuberculosis and/or during chemotherapy. Our results indicate that the CpnT channel constitutes an outer membrane gateway controlling the influx of nutrients and toxic molecules into slow-growing mycobacteria. This study revealed that reducing protein-mediated outer membrane permeability might constitute a new drug resistance mechanism in slow-growing mycobacteria.This work was supported by a Senior Research Training Fellowship from the American Lung Association to O.D., by a fellowship (SFRH/BD/63747/2009) from the National Foundation for Science FCT to D.P. and grants PIC/IC/82859/2007, PTDC/BIA-BCM/102123/2008, and PTDC/SAU-MII/098024/2008 to E.A., and by National Institutes of Health grants AI63432, AI074805, and AI083632 to M.N.info:eu-repo/semantics/publishedVersio

Analysis of Innovation Development in the Economy with Exhaustible Resource Sector by First Order Dynamical Systems Application

This work analyzes innovation growth in the economy in condition of increase of natural resources extraction in a model framework. The main stylized fact for the model is that the economic growth in Russia in two last decades was not well balanced and a sufficient part of it was due to high prices of natural exhaustible resources (oil and gas). On the other side, there were also successful attempts to induce the growth based on the competency development. An endogenous growth model has been developed. It reflects both the growth of the resource extraction and the growth, connected with the increase in technological level of the economy. This model may be useful for a number of developing countries, which budget is in direct dependence on oil and gas exports. The model is discrete and multi-periodic one