41 research outputs found
ΠΠ»Π°ΡΡΠΈΡΠΈΠΊΠ°ΡΠΈΡ ΡΠ΄Π΅ΡΠΆΠ°Π½ΠΈΠΉ ΠΈΠ· Π·Π°ΡΠ°Π±ΠΎΡΠ½ΠΎΠΉ ΠΏΠ»Π°ΡΡ
Π Π΄Π°Π½Π½ΠΎΠΉ Π½Π°ΡΡΠ½ΠΎΠΉ ΡΡΠ°ΡΡΠ΅ ΠΏΠΎΡΡΠ°Π²Π»Π΅Π½Π° Π·Π°Π΄Π°ΡΠ° Π²ΡΡΡΠ½ΠΈΡΡ, ΠΊΠ°ΠΊ ΠΊΠ»Π°ΡΡΠΈΡΠΈΡΠΈΡΡΡΡΡΡ ΡΠ΄Π΅ΡΠΆΠ°Π½ΠΈΡ ΠΈΠ· Π·Π°ΡΠ°Π±ΠΎΡΠ½ΠΎΠΉ ΠΏΠ»Π°ΡΡ, ΠΎΡΠΌΠ΅ΡΠΈΡΡ ΠΎΡΠ½ΠΎΠ²Π½ΡΠ΅ ΠΌΠΎΠΌΠ΅Π½ΡΡ Π΄Π»Ρ ΡΠ΄Π΅ΡΠΆΠ°Π½ΠΈΡ. Π’Π°ΠΊΠΆΠ΅ Π² ΡΡΠ°ΡΡΠ΅ ΡΠ°ΡΡΠΌΠ°ΡΡΠΈΠ²Π°Π΅ΡΡΡ ΡΠΈΡΡΠ°ΡΠΈΡ, ΠΊΠΎΠ³Π΄Π° ΠΎΠ΄ΠΈΠ½ Π²ΠΈΠ΄ ΡΠ΄Π΅ΡΠΆΠ°Π½ΠΈΠΉ ΠΎΡΠ½ΠΎΡΠΈΡΡΡ ΠΊ ΡΠ°Π·Π½ΠΎΠΉ ΠΊΠ»Π°ΡΡΠΈΡΠΈΠΊΠ°ΡΠΈΠΈ, Π½Π° ΠΏΡΠΈΠΌΠ΅ΡΠ΅ Π°Π»ΠΈΠΌΠ΅Π½ΡΠΎΠ²
"ΠΠ΅Π³ΡΡΠ²ΠΎ ΠΎΡ ΡΠ²ΠΎΠ±ΠΎΠ΄Ρ" ΡΠΎΠ²Π΅ΡΡΠΊΠΈΡ Π±ΡΠ±ΠΈΠ±ΡΠΌΠ΅ΡΠΎΠ²: ΠΏΡΠ΅Π΄ΡΡΠ°Π²Π»Π΅Π½ΠΈΡ ΠΎ ΡΠΎΡΠΈΠ°Π»ΡΠ½ΠΎΠΌ ΠΈ ΡΠΊΠΎΠ½ΠΎΠΌΠΈΡΠ΅ΡΠΊΠΎΠΌ Π±Π»Π°Π³ΠΎΠΏΠΎΠ»ΡΡΠΈΠΈ ΠΏΠΎΡΠ»Π΅Π²ΠΎΠ΅Π½Π½ΠΎΠ³ΠΎ ΠΏΠΎΠΊΠΎΠ»Π΅Π½ΠΈΡ Π² Π‘Π‘Π‘Π
ΠΡΡΠΎΡΠΈΡΠ΅ΡΠΊΠΈΠ΅ ΠΈ ΡΠΎΡΠΈΠΎΠΊΡΠ»ΡΡΡΡΠ½ΡΠ΅ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ Π±ΡΠ±ΠΈΠ±ΡΠΌΠ΅ΡΠΎΠ² - ΠΏΠ΅ΡΠ²ΠΎΠ³ΠΎ ΠΏΠΎΡΠ»Π΅Π²ΠΎΠ΅Π½Π½ΠΎΠ³ΠΎ ΠΏΠΎΠΊΠΎΠ»Π΅Π½ΠΈΡ - Π½Π΅ ΡΠ΅ΡΡΡΡ ΡΠ²ΠΎΠ΅ΠΉ Π°ΠΊΡΡΠ°Π»ΡΠ½ΠΎΡΡΠΈ. Π ΡΡΠ°ΡΡΠ΅ Π°Π½Π°Π»ΠΈΠ·ΠΈΡΡΡΡΡΡ ΠΏΡΠ΅Π΄ΡΡΠ°Π²Π»Π΅Π½ΠΈΡ ΠΎ ΡΠΎΡΠΈΠ°Π»ΡΠ½ΠΎΠΌ ΠΈ ΡΠΊΠΎΠ½ΠΎΠΌΠΈΡΠ΅ΡΠΊΠΎΠΌ Π±Π»Π°Π³ΠΎΠΏΠΎΠ»ΡΡΠΈΠΈ ΠΏΠΎΡΠ»Π΅Π²ΠΎΠ΅Π½Π½ΠΎΠ³ΠΎ ΠΏΠΎΠΊΠΎΠ»Π΅Π½ΠΈΡ Π² Π‘Π‘Π‘Π ΡΠΊΠ²ΠΎΠ·Ρ ΠΏΡΠΈΠ·ΠΌΡ ΡΡΠ°Π½ΡΡΠΎΡΠΌΠ°ΡΠΈΠΉ ΠΏΠΎΡΡΠ΅Π±ΠΈΡΠ΅Π»ΡΡΠΊΠΈΡ
ΠΈΠ΄Π΅Π°Π»ΠΎΠ², ΡΠΎΡΠΈΠ°Π»ΠΈΡΡΠΈΡΠ΅ΡΠΊΠΈΡ
ΡΠ΅Π½Π½ΠΎΡΡΠ΅ΠΉ, ΠΏΡΠ΅Π΄ΡΡΠ°Π²Π»Π΅Π½ΠΈΠΉ ΠΎ ΠΏΡΠ΅ΡΡΠΈΠΆΠ½ΡΡ
Π²ΠΈΠ΄Π°Ρ
Π΄Π΅ΡΡΠ΅Π»ΡΠ½ΠΎΡΡΠΈ ΠΈ ΡΠΎΡΠΈΠ°Π»ΡΠ½ΠΎΠΌ ΡΡΠ°ΡΡΡΠ΅. ΠΡΡΠΎΡΠ½ΠΈΠΊΠΎΠ²ΡΡ Π±Π°Π·Ρ ΠΈΡΡΠ»Π΅Π΄ΠΎΠ²Π°Π½ΠΈΡ ΡΠΎΡΡΠ°Π²ΠΈΠ»ΠΈ ΠΌΠ°ΡΠ΅ΡΠΈΠ°Π»Ρ ΡΠΎΠ²Π΅ΡΡΠΊΠΎΠΉ Ρ
ΡΠ΄ΠΎΠΆΠ΅ΡΡΠ²Π΅Π½Π½ΠΎΠΉ ΠΊΠΈΠ½Π΅ΠΌΠ°ΡΠΎΠ³ΡΠ°ΡΠΈΠΈ, ΠΏΠΎΠ·Π²ΠΎΠ»ΡΡΡΠΈΠ΅ ΠΏΡΠΎΡΠ»Π΅Π΄ΠΈΡΡ ΠΈΡΡΠΎΡΠΈΡΠ΅ΡΠΊΠΈ ΠΎΠ±ΡΡΠ»ΠΎΠ²Π»Π΅Π½Π½ΡΠ΅ ΡΠ°Π·Π»ΠΈΡΠΈΡ ΡΠΎΡΠΈΠ°Π»ΡΠ½ΠΎΠ³ΠΎ ΠΏΡΠΎΡΠ΅ΡΡΠ° Π±ΡΠ±ΠΈΠ±ΡΠΌΠ΅ΡΠΎΠ² Π² Π·Π°ΠΏΠ°Π΄Π½ΠΎΠ΅Π²ΡΠΎΠΏΠ΅ΠΉΡΠΊΠΈΡ
ΡΡΡΠ°Π½Π°Ρ
ΠΈ Π² Π‘Π‘Π‘Π
Specific Recognition of Linear Ubiquitin Chains by NEMO Is Important for NF-ΞΊB Activation
Activation of nuclear factor-ΞΊB (NF-ΞΊB), a key mediator of inducible transcription in immunity, requires binding of NF-ΞΊB essential modulator (NEMO) to ubiquitinated substrates. Here, we report that the UBAN (ubiquitin binding in ABIN and NEMO) motif of NEMO selectively binds linear (head-to-tail) ubiquitin chains. Crystal structures of the UBAN motif revealed a parallel coiled-coil dimer that formed a heterotetrameric complex with two linear diubiquitin molecules. The UBAN dimer contacted all four ubiquitin moieties, and the integrity of each binding site was required for efficient NF-ΞΊB activation. Binding occurred via a surface on the proximal ubiquitin moiety and the canonical Ile44 surface on the distal one, thereby providing specificity for linear chain recognition. Residues of NEMO involved in binding linear ubiquitin chains are required for NF-ΞΊB activation by TNF-Ξ± and other agonists, providing an explanation for the detrimental effect of NEMO mutations in patients suffering from X-linked ectodermal dysplasia and immunodeficiency
The anti-inflammatory drug BAY 11-7082 suppresses the MyD88-dependent signalling network by targeting the ubiquitin system
The compound BAY 11-7082 inhibits IΞΊBΞ± [inhibitor of NF-ΞΊB (nuclear factor ΞΊB)Ξ±] phosphorylation in cells and has been used to implicate the canonical IKKs (IΞΊB kinases) and NF-ΞΊB in >350 publications. In the present study we report that BAY 11-7082 does not inhibit the IKKs, but suppresses their activation in LPS (lipopolysaccharide)-stimulated RAW macrophages and IL (interleukin)-1-stimulated IL-1R (IL-1 receptor) HEK (human embryonic kidney)-293 cells. BAY 11-7082 exerts these effects by inactivating the E2-conjugating enzymes Ubc (ubiquitin conjugating) 13 and UbcH7 and the E3 ligase LUBAC (linear ubiquitin assembly complex), thereby preventing the formation of Lys(63)-linked and linear polyubiquitin chains. BAY 11-7082 prevents ubiquitin conjugation to Ubc13 and UbcH7 by forming a covalent adduct with their reactive cysteine residues via Michael addition at the C(3) atom of BAY 11-7082, followed by the release of 4-methylbenzene-sulfinic acid. BAY 11-7082 stimulated Lys(48)-linked polyubiquitin chain formation in cells and protected HIF1Ξ± (hypoxia-inducible factor 1Ξ±) from proteasomal degradation, suggesting that it inhibits the proteasome. The results of the present study indicate that the anti-inflammatory effects of BAY 11-7082, its ability to induce B-cell lymphoma and leukaemic T-cell death and to prevent the recruitment of proteins to sites of DNA damage are exerted via inhibition of components of the ubiquitin system and not by inhibiting NF-ΞΊB
Detection of Biochemical Pathways by Probabilistic Matching of Phyletic Vectors
A phyletic vector, also known as a phyletic (or phylogenetic) pattern, is a binary representation of the presences and absences of orthologous genes in different genomes. Joint occurrence of two or more genes in many genomes results in closely similar binary vectors representing these genes, and this similarity between gene vectors may be used as a measure of functional association between genes. Better understanding of quantitative properties of gene co-occurrences is needed for systematic studies of gene function and evolution. We used the probabilistic iterative algorithm Psi-square to find groups of similar phyletic vectors. An extended Psi-square algorithm, in which pseudocounts are implemented, shows better sensitivity in identifying proteins with known functional links than our earlier hierarchical clustering approach. At the same time, the specificity of inferring functional associations between genes in prokaryotic genomes is strongly dependent on the pathway: phyletic vectors of the genes involved in energy metabolism and in de novo biosynthesis of the essential precursors tend to be lumped together, whereas cellular modules involved in secretion, motility, assembly of cell surfaces, biosynthesis of some coenzymes, and utilization of secondary carbon sources tend to be identified with much greater specificity. It appears that the network of gene coinheritance in prokaryotes contains a giant connected component that encompasses most biosynthetic subsystems, along with a series of more independent modules involved in cell interaction with the environment
Generic modeling and mapping languages for model management
Activities in management of schemas and schema mappings are usually solved by special-purpose solutions such as coding wrapper components or manually updating view definitions. The goal of model management is to raise the level of abstraction for metadata-intensive activities by providing a set of high-level operators that automate or semi-automate such tasks. The problems of model management are aggravated by the fact that usually heterogeneous modeling languages, such as the relational data model, XML Schema, or ontologies, are employed within the same organization. Therefore, model management aims at genericness by devising operations that are agnostic about the underlying native metamodels. Current solutions fail to be generic as they are restricted to certain combinations of modeling languages. Therefore, a generic solution for model management problems requires generic languages for modeling and mapping specification as well as algorithms operating on such generic representations. This work solves some of the problems in generic model management. In particular, the work makes the following contributions:1. A generic metamodel that allows the detailed representation of schemas imported from various native languages. This is required, for instance, by schema matching algorithms which use the knowledge about schemas to produce a mapping between them.2. The semantics of our generic metamodel serves as the foundation for a formal and generic schema mapping language which allows data exchange and query rewriting between schemas in different modeling languages. Unlike other languages, our mapping language at the same time supports powerful restructuring of data and is closed under composition.3. Our solutions for schema matching, mapping composition and other model management operations have been integrated into a holistic generic model management prototype system.4. Our schema mapping language has been used to develop an object-relational mapping tool and a federated data management system that is agnostic about the native metamodels employed by its data sources
Transformation of Models in(to) a Generic Metamodel
Model Management aims at developing new technologies and mechanisms to support the integration, evolution and matching of models. Such tasks are to be performed by means of a set of operators which work on models and their elements. Furthermore, model management performs these operations generically, that is, without being restricted to a particular metamodel (e.g. the relational or XML Schema metamodel). In order to allow this, a generic metamodel must be used for model representation. Operators manipulate exclusively models described in that generic language. Consequently, models represented in concrete metamodels have to be imported into the generic metamodel and vice versa. In this paper we describe how we implemented rule based Import and Export operators between concrete metamodels and our generic role based metamodel GeRoMe. In addition, the same rule based approach can be used to implement one of the main model management operators, namely ModelGen, in a generic way. This operator is used to transform models using certain constructs into models using other modeling constructs
MonA -- An Extensible Framework for Web Document Monitoring
This work presents an extensible architecture for fully-automated long-term monitoring of documents on the web. The framework enables easy coupling of existing search services of different kind, making the approach suitable for mixed environments (e.g. classic web and semantic web). The proposed architecture supports a process for repeated querying and classifying of documents based on a model of the domain of interest. In doing so, a well-organized version-controlled repository of documents is gradually built up
Matching of Ontologies with XML Schemas using a Generic Metamodel
Abstract. Schema matching is the task of automatically computing correspondences between schema elements. A multitude of schema matching approaches exists for various scenarios using syntactic, semantic, or instance information. The schema matching problem is aggravated by the fact that models to be matched are often represented in different modeling languages, e.g. OWL, XML Schema, or SQL DDL. Consequently, besides being able to match models in the same metamodel, a schema matching tool must be able to compute reasonable results when matching models in heterogeneous modeling languages. Therefore, we developed a matching component as a part of our model management system GeRoMeSuite which is based on our generic metamodel GeRoMe. As GeRoMe provides a unified representation of models, the matcher is able to match models represented in different languages with each other. In this paper, we will show in particular the results for matching XML Schemas with OWL ontologies as it is often required for the semantic annotation of existing XML data sources. GeRoMeSuite allows for flexible configuration of the matching system; various matching algorithms for element and structure level matching are provided and can be combined freely using different ways of aggregation and filtering in order to define new matching strategies. This makes the matcher highly configurable and extensible. We evaluated our system with several pairs of XML Schemas and OWL ontologies and compared the performance with results from other systems. The results are considerably better which shows that a matching system based on a generic metamodel is favorable for heterogeneous matching tasks.