Potassium Channels as a Potential Target Spot for Drugs

Aberrant function or expression of potassium channels can be underlying in pathologies such as cardiac arrhythmia, diabetes mellitus, hypertension, preterm birth, and various types of cancer. The expression of potassium channels is altered in many types of diseases. Also, we have previously shown that natural polyphenols, such as resveratrol, and selective synthetic modulators of potassium channels, like pinacidil, can alter their function and lead to the desired outcome. Therefore, targeting potassium channels with substance, which has an influence on their function, is promising access to cancer, diabetes mellitus, preterm birth, or hypertension therapy. In this chapter, we could discuss strategies for targeting different types of potassium channels as potential targets for synthetic and natural molecules therapy

PIBAS FedSPARQL: A web-based platform for integration and exploration of bioinformatics datasets

© 2017 The Author(s). Background: There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources. Results: PIBAS FedSPARQL is a web-based query builder and result set visualizer of bioinformatics data. As an advanced feature, our system can detect similar data items identified by different Uniform Resource Identifiers (URIs), using a text-mining algorithm based on the processing of named entities to be used in Vector Space Model and Cosine Similarity Measures. According to our knowledge, PIBAS FedSPARQL was unique among the systems that we found in that it allows detecting of similar data items. As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI, and one local initiative called CPCTAS, as well as additional user-specified data source. From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed. Based on the data obtained, end users have the ability to choose the most appropriate data sources in their area of interest and exploit their Resource Description Framework (RDF) structure, which allows users to select certain properties of data to enhance query results. Conclusions: The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics. Also, the novel similar data items detection algorithm can be particularly useful for suggesting new data sources and cost optimization for new experiments. PIBAS FedSPARQL can be expanded with new topics, subtopics and templates on demand, rendering information retrieval more robust

PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets

Abstract Background There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources. Results PIBAS FedSPARQL is a web-based query builder and result set visualizer of bioinformatics data. As an advanced feature, our system can detect similar data items identified by different Uniform Resource Identifiers (URIs), using a text-mining algorithm based on the processing of named entities to be used in Vector Space Model and Cosine Similarity Measures. According to our knowledge, PIBAS FedSPARQL was unique among the systems that we found in that it allows detecting of similar data items. As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI, and one local initiative called CPCTAS, as well as additional user-specified data source. From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed. Based on the data obtained, end users have the ability to choose the most appropriate data sources in their area of interest and exploit their Resource Description Framework (RDF) structure, which allows users to select certain properties of data to enhance query results. Conclusions The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics. Also, the novel “similar data items detection” algorithm can be particularly useful for suggesting new data sources and cost optimization for new experiments. PIBAS FedSPARQL can be expanded with new topics, subtopics and templates on demand, rendering information retrieval more robust

Imaging Spectrum of Intrahepatic Mass-Forming Cholangiocarcinoma and Its Mimickers: How to Differentiate Them Using MRI

Intrahepatic cholangiocarcinoma (ICC) is the second most common primary hepatic malignancy, with mass-forming growth pattern being the most common. The typical imaging appearance of mass-forming ICC (mICC) consists of irregular ring enhancement in the arterial phase followed by the progressive central enhancement on portal venous and delayed phases. However, atypical imaging presentation in the form of hypervascular mICC might also be seen, which can be attributed to distinct pathological characteristics. Ancillary imaging features such as lobular shape, capsular retraction, segmental biliary dilatation, and vascular encasement favor the diagnosis of mICC. Nevertheless, these radiological findings may also be present in certain benign conditions such as focal confluent fibrosis, sclerosing hemangioma, organizing hepatic abscess, or the pseudosolid form of hydatid disease. In addition, a few malignant lesions including primary liver lymphoma, hemangioendothelioma, solitary hypovascular liver metastases, and atypical forms of hepatocellular carcinoma (HCC), such as scirrhous HCC, infiltrative HCC, and poorly differentiated HCC, may also pose a diagnostic dilemma by simulating mICC in imaging studies. Diffusion-weighted imaging and the use of hepatobiliary contrast agents might be helpful for differential diagnosis in certain cases. The aim of this manuscript is to provide a comprehensive overview of mICC imaging features and to describe useful tips for differential diagnosis with its potential mimickers

The Association of Polymorphisms in Nrf2 and Genes Involved in Redox Homeostasis in the Development and Progression of Clear Cell Renal Cell Carcinoma

Deleterious effects of SNPs found in genes encoding transcriptional factors, as well as antioxidant and detoxification enzymes, are disputable; however, their functional significance seems to modify the risk for clear cell renal cell carcinoma (ccRCC) development and progression. We investigated the effect of specific Nrf2, SOD2, GPX1 gene variants and GSTP1ABCD haplotype on ccRCC risk and prognosis and evaluated the association between GSTP1 and regulatory (JNK1/2) and executor (caspase-3) apoptotic molecule expression in ccRCC tissue samples and the presence of GSTP1 : JNK1/2 protein : protein interactions. Genotyping was performed in 223 ccRCC patients and 336 matched controls by PCR-CTTP and qPCR. Protein expression was analyzed using immunoblot, while the existence of GSTP1 : JNK1 protein : protein interactions was investigated by immunoprecipitation experiments. An increased risk of ccRCC development was found among carriers of variant genotypes of both SOD2 rs4880 and GSTP1 rs1695 polymorphisms. Nrf2 rs6721961 genetic polymorphism in combination with both rs4880 and rs1695 showed higher ccRCC risk as well. Haplotype analysis revealed significant risk of ccRCC development in carriers of the GSTP1C haplotype. Furthermore, GSTP1 variant forms seem to affect the overall survival in ccRCC patients, and the proposed molecular mechanism underlying the GSTP1 prognostic role might be the presence of GSTP1 : JNK1/2 protein : protein interactions