Semantic Computational Models for Polypharmacology: Applications in Drug Repurposing

This paper proposes a computational model based on the first order logic reasoning, for managing discoveries in Polypharmacology for the purpose of efficient drug repositioning. The model uses computational reasoning upon advances documented in the published literature and thus is primarily based on the range of discoveries in biomedical science. The idea behind the model is to exploit drugs multiple intended and particularly unintended therapeutical and adverse targets and discover if they can lead us towards drug repurposing. Computational pharmacology is a very complex field, but reasoning upon its concept can bring us closer to the ideal poly pharmacological world of finding, developing and approving multitargeted drugs and use them in drug repurposing

INVESTIGATING THE ANTECEDENTS AND CONSEQUENCES OF SAUDIZATION IN THE CONSTRUCTION SECTOR

Over time, due to the increase in the numbers of foreign workers, both the Saudi population and the rate of unemployment among Saudi workers increased sharply so the Saudi government embarked on a process of replacing the foreign workers with Saudi workers. The government was concerned that there were many young people who remained jobless on leaving university whilst, at the same time in Saudi Arabia, there were many foreign nationals who, essentially, were taking jobs meant for the local population. This study aims to investigate, on the one hand, the factors affecting the adoption of Saudization and, on the other hand, to measure the effect of the adoption on the improvement of productivity and other benefits such as improving work opportunities and job security. Previous literature shows that there were four antecedents of the adoption of Saudization. These were: government policies and regulations to encourage adoption; facilitators and incentives of adoption; knowledge-sharing practices between Saudi and non-Saudi workers and the barriers to the adoption of Saudization. In the same line, the consequences of Saudization were increased productivity and other benefits of adoption. A model was developed to conceptualise the causal relationships between the constructs and the interactions amongst these constructs. This study employs mixed methods starting with a quantitative stage which was followed by a qualitative one. A questionnaire was used to collect data from 479 Saudi Arabian construction companies. Thereafter, 16 interviews were conducted with some of these IV companies’ managers. Structural equation modelling produced findings which revealed that, with the exception of barriers which had a negative effect on adoption, all the antecedents of the adoption of Saudization (policies and regulations, facilitators and incentives of adoption and knowledge-sharing practices) had a positive effect on the adoption of Saudization. Meanwhile, the adoption of Saudization had a positive effect on productivity and the other benefits of adoption. This study contributes to the theory since it has revealed a theoretical model which could be used in investigating the determinants and consequences of any localisation programme. It has also contributed to the practices used by the managers of construction companies and policy makers. Through identifying the antecedents and consequences of the adoption of Saudization and in parallel with preparing the required training needs to qualify Saudi’s young people, managers could deploy strategies to gradually replace foreign workers with Saudi workers. Also, this could encourage government bodies and policy makers to implement appropriate measures and incentives to encourage adoption and to reward the pioneer companies. In addition, it could help to finance training programmes and to restructure higher education to prepare qualified graduates who could fill the jobs previously taken by foreigners.Saudi Governmen

A Reference Computational Model to Manage the Semantics of Learning Environments using SWRL Enabled OWL Ontologies

This thesis proposes a reference model and its computational core to support the creation of software applications within educational environments, which address Differences In Learning (DiffInL) and are applicable to both learners and instructors. This work differs from others in that the strength of this model resides on the re-usable character of the reasoning mechanism enabled by the computational environment. The starting point is the definition of agreed learning goals that the learner needs to achieve. In turn, the reference model generates personalised, best-practice teaching and learning materials, suitable for achieving the individual’s learning goals. This reference model consists of MODEL and MANAGEMENT components. The MODEL components store the domain needed to create learners and instructional models, which are required for the creation of Learning Spaces (LeS). The MANAGEMENT compo- nent also manages the semantics stored in various model components in order to carry out the configuration of an LeS. The architecture of software applications generated from the reference model is illustrated and contains: Netbeans IDE 8.0.2, JavaServer Faces framework and OWL-API library. We tested this to generate teaching practices for Learning Difficulties (LDif) student. In order to prove the feasibility of creating a software application from the reference model, an example of a particular scenario in a specific educational setting for LDif Students has been shown. This proposed model has successfully proved its ability to address the needs of LDif Students through a corresponding novel and re-usable reasoning mechanism implemented in Web Ontology Language (OWL) and Semantic Web Rule Language (SWRL) computational environments. The reference model has shown its ability to integrate with different disciplines such as psychology, sociology and human-computer interactions. The main contribution to research is the creation of a novel reference computational model which addresses the needs of people with DiffInL. The strength of this model resides on the re-usable character of the reasoning mechanism enabled by the computational environment. The whole framework allows a unified implementation which takes into account classes, constraints, matching, and inference mechanisms for the complete configuration of an LeS. The suggested approach also differs from previous work in that it is personalised, and the applied reasoning rules are dynamic. Therefore this model can be constantly “tuned” according to the questions we may ask in such environments. Overall, the proposed reference model in this research offers a promising and feasible solution that can support current educational systems and benefit both learners and instructors. It also demonstrates the applicability of the latest technologies and would allow for future technologies to be incorporated, in order to enhance the model

Modulation of transglutaminase 2 activity in H9c2 cells by protein kinase A and protein kinase C signalling

Transglutaminase 2 (TG2; EC 2.3.2.13) has been shown to protect cardiomyocytes against ischaemia and reperfusion-induced cell death and to mediate cell survival in many cell types. Given the prominent role of PKA and PKC in cardioprotection, this study investigated whether TG2 was involved in the cytoprotection induced by activation of these two kinases in cardiomyocyte-like H9c2 cells. Cultured H9c2 cells were extracted following stimulation with activators of PKC (phorbol-12-myristate-13-acetate; PMA) and PKA (forskolin; FK). Transglutaminase 2 activity was determined using an amine incorporating (in vitro and in situ) and a protein crosslinking assays. Different protein kinase inhibitors were used to determine the involvement of PKC and PKA in the activation of TG2 in H9c2 cells. To confirm the involvement of TG2 activity via PKC and PKA, TG2 specific (Z-DON and R283) inhibitors were used. Western blot analysis revealed the presence of TG2 and TG1 (TG2 >> TG1) protein, but not TG3. Since the H2O2, a major contributor to reactive oxygen species following damage was used to induce oxidative stress. The role of TG2 in PMA- and forskolin-induced cytoprotection was investigated by monitoring H2O2-induced oxidative stress in H9c2 cells. The identification of TG2 substrates in H9c2 cells was investigated using pull down assay coupled with proteomic analysis techniques. The PMA and FK-induced time and concentration-dependent increases in TG2 catalysed biotin cadaverine incorporation in H9c2 cells. Forskolin but not PMA also increased TG2 catalysed protein crosslinking. The PKC (Ro-31 8220) and PKA (KT 5720 and Rp-8-Cl-cAMPS) inhibitors, blocked PMA and FK-induced TG2 activity. Immunocytochemistry using ExtrAvidin®-FITC revealed in situ TG2-mediated biotin cadaverine incorporation into protein substrates following stimulation of PMA, FK and their receptor agonists. The TG2 inhibitors Z-DON and R283 attenuated the PMA- and FK-induced increases in TG2 activity. Pre-treatment with PMA and FK reversed H2O2-induced cell death as judged by a MTT reduction assay and the release of cellular LDH. The TG2 inhibitors R283 and Z-DON blocked PMA and FK-induced cytoprotection. Proteomic analysis identified more than 25 proteins that serve as intracellular substrates for TG2 following PMA and FK stimulation. Some of these identified proteins have already been reported as TG2 substrates, but not in H9c2 cells e.g. tubulin while others e.g. α-actinin have not been identified before. In summary, these data have shown TG2 activity to be stimulated via PKA and PKC-dependent signalling pathways in H9c2 cells and suggest a role for TG2 in cytoprotection-induced via these two protein kinases

Comparative Outer Membrane Protein Analysis of High and Low-Invasive Strains of Cronobacter malonaticus

are an important group of foodborne pathogens that has been linked to life-threatening infections in both infants and adults. The major infections associated with species are neonatal meningitis, necrotizing enterocolitis, and septicaemia. There are seven species in the genus, of which only three are of clinical importance; , and . To date most studies have focussed on as it is the major species associated with neonatal infections. However, recently , in particular sequence type 7 (ST7), has been noted as being prevalent in adult infections and therefore warranting further investigation. In this study, eight strains of ST7, that had been isolated from a wide range of sources and varied in their virulence, were chosen for proteomic analysis of their outer membrane proteins (OMPs). One-dimensional gel analysis revealed a ~29 kDa size band that was only present in the highly invasive strains. Subsequent mass spectrometric analysis identified several peptides that matched the flagellin protein. The presence of flagellin protein was confirmed in 2D gel spot. Mass spectrometry analysis of total OMPs revealed that the four highly invasive strains expressed the main flagellum proteins that were absent from the four low invasive strains. These were the flagellar hook protein FlgE, flagellar hook-associated protein 1, flagellar hook-associated protein, flagellin, and flagellar hook-filament junction protein FlgL. This data indicates that flagellar proteins may have an important role in the organism's invasion properties

Neurite outgrowth inhibitory levels of organophosphates induce tissue transglutaminase activity in differentiating N2a cells: evidence for covalent adduct formation

Organophosphate compounds (OPs) induce both acute and delayed neurotoxic effects, the latter of which is believed to involve their interaction with proteins other than acetylcholinesterase. However, few OP-binding proteins have been identified that may have a direct role in OP-induced delayed neurotoxicity. Given their ability to disrupt Ca2+ homeostasis, a key aim of the current work was to investigate the effects of sub-lethal neurite outgrowth inhibitory levels of OPs on the Ca2+-dependent enzyme tissue transglutaminase (TG2). At 1–10 µM, the OPs phenyl saligenin phosphate (PSP) and chlorpyrifos oxon (CPO) had no effect cell viability but induced concentration-dependent decreases in neurite outgrowth in differentiating N2a neuroblastoma cells. The activity of TG2 increased in cell lysates of differentiating cells exposed for 24 h to PSP and chlorpyrifos oxon CPO (10 µM), as determined by biotin-cadaverine incorporation assays. Exposure to both OPs (3 and/or 10 µM) also enhanced in situ incorporation of the membrane permeable substrate biotin-X-cadaverine, as indicated by Western blot analysis of treated cell lysates probed with ExtrAvidin peroxidase and fluorescence microscopy of cell monolayers incubated with FITC-streptavidin. Both OPs (10 µM) stimulated the activity of human and mouse recombinant TG2 and covalent labelling of TG2 with dansylamine-labelled PSP was demonstrated by fluorescence imaging following SDS-PAGE. A number of TG2 substrates were tentatively identified by mass spectrometry, including cytoskeletal proteins, chaperones and proteins involved protein synthesis and gene regulation. We propose that the elevated TG2 activity observed is due to the formation of a novel covalent adduct between TG2 and OPs

ING3 promotes prostate cancer growth by activating the androgen receptor

Background The androgen receptor (AR) is a major driver of prostate cancer, and increased AR levels and co-activators of the receptor promote the development of prostate cancer. INhibitor of Growth (ING) proteins target lysine acetyltransferase or lysine deacetylase complexes to the histone H3K4Me3 mark of active transcription, to affect chromatin structure and gene expression. ING3 is a stoichiometric member of the TIP60 lysine acetyltransferase complex implicated in prostate cancer development. Methods Biopsies of 265 patients with prostate cancer were stained for ING3, pan-cytokeratin, and DNA. LNCaP and C4-2 androgen-responsive cells were used for in vitro assays including immunoprecipitation, western blotting, Luciferase reporter assay and quantitative polymerase chain reaction. Cell viability and migration assays were performed in prostate cancer cell lines using scrambled siRNA or siRNA targeting ING3. Results We find that ING3 levels and AR activity positively correlate in prostate cancer. ING3 potentiates androgen effects, increasing expression of androgen-regulated genes and androgen response element-driven reporters to promote growth and anchorage-independent growth. Conversely, ING3 knockdown inhibits prostate cancer cell growth and invasion. ING3 activates the AR by serving as a scaffold to increase interaction between TIP60 and the AR in the cytoplasm, enhancing receptor acetylation and translocation to the nucleus. Activation is independent of ING3's ability to target the TIP60 complex to H3K4Me3, identifying a previously unknown chromatin-independent cytoplasmic activity for ING3. In agreement with in vitro observations, analysis of The Cancer Genome Atlas (TCGA) data (n = 498) and a prostate cancer tissue microarray (n = 256) show that ING3 levels are higher in aggressive prostate cancers, with high levels of ING3 predicting shorter patient survival in a low AR subgroup. Including ING3 levels with currently used indicators such as the Gleason score provides more accurate prognosis in primary prostate cancer. Conclusions In contrast to the majority of previous reports suggesting tumor suppressive functions in other cancers, our observations identify a clear oncogenic role for ING3, which acts as a co-activator of AR in prostate cancer. Data from TCGA and our previous and current tissue microarrays suggest that ING3 levels correlate with AR levels and that in patients with low levels of the receptor, ING3 level could serve as a useful prognostic biomarker

β2-adrenoceptor-induced modulation of transglutaminase 2 transamidase activity in cardiomyoblasts

Tissue transglutaminase 2 (TG2) is modulated by protein kinase A (PKA) mediated phosphorylation: however, the precise mechanism(s) of its modulation by G-protein coupled receptors coupled to PKA activation are not fully understood. In the current study we investigated the potential regulation of TG2 activity by the β2-adrenoceptor in rat H9c2 cardiomyoblasts. Transglutaminase transamidation activity was assessed using amine-incorporating and protein cross-linking assays. TG2 phosphorylation was determined via immunoprecipitation and Western blotting. The long acting β2-adrenoceptor agonist formoterol induced time- and concentration-dependent increases in TG2 transamidation. Increases in TG2 activity were reduced by the TG2 inhibitors Z-DON (Benzyloxycarbonyl-(6-Diazo-5-oxonorleucinyl)-L-valinyl-L-prolinyl-L-leucinmethylester) and R283 (1,3,dimethyl-2[2-oxo-propyl]thio)imidazole chloride). Responses to formoterol were blocked by pharmacological inhibition of PKA, extracellular signal-regulated kinase 1 and 2 (ERK1/2), or phosphatidylinositol 3-kinase (PI-3K) signalling. Furthermore, the removal of extracellular Ca2+ also attenuated formoterol-induced TG2 activation. Fluorescence microscopy demonstrated TG2-induced biotin-X-cadaverine incorporation into proteins. Formoterol increased the levels of TG2-associated phosphoserine and phosphothreonine, which were blocked by inhibition of PKA, ERK1/2 or PI-3K signalling. Subsequent proteomic analysis identified known (e.g. lactate dehydrogenase A chain) and novel (e.g. Protein S100-A6) protein substrates for TG2. Taken together, the data obtained suggest that β2-adrenoceptor-induced modulation of TG2 represents a novel paradigm in β2-adrenoceptor cell signalling, expanding the repertoire of cellular functions responsive to catecholamine stimulation

β2-adrenoceptor-induced modulation of transglutaminase 2 transamidase activity in cardiomyoblasts

Tissue transglutaminase 2 (TG2) is modulated by protein kinase A (PKA) mediated phosphorylation: however, the precise mechanism(s) of its modulation by G-protein coupled receptors coupled to PKA activation are not fully understood. In the current study we investigated the potential regulation of TG2 activity by the β2-adrenoceptor in rat H9c2 cardiomyoblasts. Transglutaminase transamidation activity was assessed using amine-incorporating and protein cross-linking assays. TG2 phosphorylation was determined via immunoprecipitation and Western blotting. The long acting β2-adrenoceptor agonist formoterol induced time- and concentration-dependent increases in TG2 transamidation. Increases in TG2 activity were reduced by the TG2 inhibitors Z-DON (Benzyloxycarbonyl-(6-Diazo-5-oxonorleucinyl)-L-valinyl-L-prolinyl-L-leucinmethylester) and R283 (1,3,dimethyl-2[2-oxo-propyl]thio)imidazole chloride). Responses to formoterol were blocked by pharmacological inhibition of PKA, extracellular signal-regulated kinase 1 and 2 (ERK1/2), or phosphatidylinositol 3-kinase (PI-3K) signalling. Furthermore, the removal of extracellular Ca2+ also attenuated formoterol-induced TG2 activation. Fluorescence microscopy demonstrated TG2-induced biotin-X-cadaverine incorporation into proteins. Formoterol increased the levels of TG2-associated phosphoserine and phosphothreonine, which were blocked by inhibition of PKA, ERK1/2 or PI-3K signalling. Subsequent proteomic analysis identified known (e.g. lactate dehydrogenase A chain) and novel (e.g. Protein S100-A6) protein substrates for TG2. Taken together, the data obtained suggest that β2-adrenoceptor-induced modulation of TG2 represents a novel paradigm in β2-adrenoceptor cell signalling, expanding the repertoire of cellular functions responsive to catecholamine stimulation

A1 adenosine receptor-induced phosphorylation and modulation of transglutaminase 2 activity in H9c2 cells: a role in cell survival

The regulation of tissue transglutaminase (TG2) activity by the GPCR family is poorly understood. In this study, we investigated the modulation of TG2 activity by the A1 adenosine receptor in cardiomyocyte-like H9c2 cells.H9c2 cells were lysed following stimulation with the A1 adenosine receptor agonist N6-cyclopentyladenosine (CPA). Transglutaminase activity was determined using an amine incorporating and a protein cross linking assay. TG2 phosphorylation was assessed via immunoprecipitation and Western blotting. The role of TG2 in A1 adenosine receptor-induced cytoprotection was investigated by monitoring hypoxia-induced cell death. CPA induced time and concentration-dependent increases in amine incorporating and protein crosslinking activity of TG2. CPA-induced increases in TG2 activity were attenuated by the TG2 inhibitors Z-DON and R283. Responses to CPA were blocked by PKC (Ro 31-8220), MEK1/2 (PD 98059), p38 MAPK (SB 203580) and JNK1/2 (SP 600125) inhibitors and by removal of extracellular Ca2+. CPA triggered robust increases in the levels of TG2-associated phosphoserine and phosphothreonine, which were attenuated by PKC, MEK1/2 and JNK1/2 inhibitors. Fluorescence microscopy revealed TG2-mediated biotin-X-cadaverine incorporation into proteins and proteomic analysis identified known (Histone H4) and novel (Hexokinase 1) protein substrates for TG2. CPA pre-treatment reversed hypoxia-induced LDH release and decreases in MTT reduction. TG2 inhibitors R283 and Z-DON attenuated A1 adenosine receptor-induced cytoprotection. TG2 activity was stimulated by the A1 adenosine receptor in H9c2 cells via a multi protein kinase dependent pathway. These results suggest a role for TG2 in A1 adenosine receptor-induced cytoprotection