Month: October 2020

A small proportion of the available HIF1A was hydroxylated and the levels of both PHD1 and PHD2 increased. Despite binding to EBNA-3, HIF1A was able to transactivate its target genes, including those involved in the glycolytic pathway. PDK1 phosphorylates the mitochondrial pyruvate dehydrogenase complex responsible for oxidative decarboxylation of pyruvate. The higher level of PDK1 suggests that the oxidative decarboxylation of pyruvate may be slower in LCLs. The level of GLUT1, a glucose transporter responsible for glucose uptake, is high in thyroid and colorectal cancers. PGK1, a phosphoglycerate kinase, is secreted by fibrosarcoma cells at levels several-fold higher than for normal fibroblasts. PKLR catalyzes the conversion of phosphoenolpyruvate and ADP into pyruvate and ATP in the last step of glycolysis. Hexokinase phosphorylates glucose into glucose-6-phosphate, which is the first step of the glycolytic pathway. At high oxygen concentration, glucose is metabolized to CO2 and the cells produce ATP and precursors for amino acid synthesis, whereas only minimal amounts of lactate are generated from pyruvate. At low oxygen concentrations, the cells convert most of the pyruvate to lactate and much less ATP is generated, in a process referred to as anaerobic glycolysis. However, the rate of ATP production is higher and overall metabolism is more efficient during glycolysis. Schistosomiasis is an important helminth infection and mainly occurs in developing countries. Despite decades of control, there are still millions of people at risk of contracting this infection. Current schistosomiasis Life Science Reagents control strategies are mainly based on safe and effective drugs, such as praziquantel and oxamniquine, but these do not prevent reinfection and the number of infected people has remained constant. The best long-term strategy to control schistosomiasis is through immunization with an antischistosomiasis vaccine combined with drug treatment. A vaccine that induces even a partial reduction in worm burdens could considerably reduce pathology and limit parasitic transmission. Recently, novel potential vaccine antigens were evaluated, but the level of protection obtained by vaccination with these antigens rarely exceeded the 40% benchmark set by the The World Health Organization. Therefore, it is necessary to search for alternative highly protective vaccine candidates. In all organisms, galactose metabolism is catalyzed by three enzymes: galactokinase, galactose-1-phosphate uridyltransferase, and uridine diphosphate galactose 49-epimerase. GALE catalyzes the interconversion of UDP-galactose and UDP-glucose during normal galactose metabolism and it tightly binds the co-factor nicotinamide adenine dinucleotide required for catalytic activity. GALE also plays a pivotal role in the formation of extracellular polymeric substance, lipopolysaccharide, and capsular polysaccharide, which are related to biofilm formation. In humans, GALE deficiency results in an inborn error of metabolism, galactosemia. GALE also play an important role in the development of Drosophila melanogaster and Trypanosoma brucei. The gene encoding GALE also exists in Schistosoma japonicum; however, its specific function has not been elucidated. In the present study, we cloned and expressed full-length SjGALE cDNA and analyzed its expression level at different stages of schistosomal developmental and the localization of the protein. We also evaluated this protein as a vaccine candidate in vivo by examining the SjGALE-induced humoral and cellular immune protective mechanisms in a mouse model of schistosomal infection. An effective control strategy is to develop vaccines to prevent this disease.

In addition, as drugs can act on multiple targets, secondary targets can be utilized for novel drug indications as well. Several systematic approaches of finding new uses for old drugs have been proposed. These methods can be broadly classified into two categories: target discovery based on chemical compound similarity and literature-based discovery. Compound similarity has been a popular approach to identify drug targets for drug repurposing. The assumption is that similar drug compounds have similar targets so that targets that are not shared between a pair of similar compounds can be identified as novel targets to the other. By identifying new targets for existing compounds, new drug indications can then be proposed. On the other hand, typical text mining methods focus on the extraction of knowledge such as protein-protein interactions from biomedical literature. These text mining efforts including the BioCreAtIvE challenge, a community effort that aims to advance the development of biological knowledge extraction systems, focus on the extraction of biological knowledge that is explicitly stated in the literature. Literature-based discovery methods go a step further by identifying EX 527 relevant knowledge through text mining so that new knowledge can be inferred from existing knowledge. Swanson’s ABC Model is a popular literature-based discovery methodology that was proposed to link two concepts through a commonly shared concept. Scientific concepts A and C form a relationship when concept A cooccurs with concept B in one publication while concepts B and C cooccur in another publication. Variations of Swanson’s ABC models have been described in the literature for the identification of indirect relationships. However, approaches based on cooccurrences of concepts within abstracts tend to generate too many hypotheses. Another direction for network-based approaches aims to uncover knowledge through the creation of biological networks. STITCH and ChemProt are examples of network-based approaches that take interactions extracted from literature and integrates with data from biological knowledge bases to create chemical compound-protein interaction networks. This kind of approach in linking the concepts does not consider the inherent relationships between the pairs of concepts such as interaction type and directionality of interactions, thus leading to a large number of hypotheses. To handle large networks that are generated by means of literature mining and other data sources, visualization tools have been proposed to assist the discovery of novel drug indications. In this paper, we propose a new literature-based discovery approach for drug repurposing that integrates facts from various sources to infer novel indications by means of automated reasoning. Our approach captures the various effects of drugtarget interactions inside cells as well as the molecular mechanisms of diseases. Using cancer as an example, we utilized the wealth of knowledge about cancer and encoded oncogenes and tumor suppressors as well as cancer-related biological processes as the domain knowledge for our method. Together with the proteinprotein interactions and gene-disease associations acquired from the literature, our approach identified drugs that are potential candidates for the treatment of cancer. By considering the interaction types and their directionality and the domain knowledge involved in the mechanism of action of drugs, our approach aims to produce biologically meaningful hypotheses for novel drug indications and can significantly reduce the number of hypotheses as compared to previous text mining and literaturebased discovery approaches.

In contrast, the primary protein sequence is in many cases only a partial or no reliable predictor for protein structure. In this sense, the analyses presented here represent an opportunity where comprehensive subcellular localization data is available to assess the reliability of redundancies predicted by sequence homology. The 25 cell types and tissues used for our expression analysis are not representative or comprehensive, but chosen only for discernability in the binary analysis. Hence, a similarity score of 80% based on a score of ‘20’ cannot be compared as an absolute number, but only relative to the same criteria for other rabs. Neither cellular expression nor the subcellular localization criteria are sufficient to assess potential redundancy. For example, both rab3 and rabX4 are identically pan-neuronally expressed, but Rab3 marks synaptic vesicles whereas RabX4 marks Rab11-positive compartments. Conversely, rab21 and rabX4 have substantially different expression patterns, yet when they overlap in the nervous system they exhibit the identical subcellular localization profile. Hence, these two rab GTPases are potential candidates for similar or redundant functions in these cells only. More generally, in the pair-wise comparison a rab GTPase with restricted expression receives a low score when compared to a rab GTPase with broader expression, and hence will be categorized as less similar. However, this lower score does not correlate with the probability of redundancy in the cell types where the two rab GTPases are actually co-expressed. We therefore regard the combination of cellular and subcellular profile similarities as a means to restrict the number of potentially redundant rab GTPases. Importantly, all our rab-Gal4 lines represent targeting vectors for the generation of molecularly defined mutants through ends-out homologous recombination, as demonstrated in our original studies. Hence, the completed rab-Gal4 kit provides all ARRY-142886 MEK inhibitor necessary tools to experimentally test functional predictions from our analyses, as well as experiments using double and triple mutants to verify such functional relationships. The current model of drug discovery and development is perceived as a costly and time-consuming process. To reduce the cost and shorten the duration for drug development, drug repurposing, also known as drug repositioning, has become an attractive alternative to traditional drug development aiming to shorten the development process. Drug repurposing is the process of finding a new indication for existing drug compounds. In other words, it is a discovery process on how an existing drug compound can be used for the treatment of diseases other than its original indication. Reusing these drug compounds has the advantage of bypassing many of the expensive steps of drug development, such as in vitro and in vivo screening, chemical optimization, toxicology, bulk manufacturing, formulation development. This reduces cost and development risks, as well as shortens the typical 10–17 year process of drug development to 3–12 years. The best known success story of drug repositioning is the development of sildenafil, a compound that was developed by Pfizer and intended for the treatment of angina. Clinical trials of the drug showed unexpected side effects that led to the treatment of erectile dysfunction, and sildenafil became the blockbuster drug more commonly known as ViagraH. Further studies and repositioning of the drug compound showed yet another therapeutic indication for treating pulmonary arterial hypertension, marketed as RevatioH. This is due to the fact that sildenafil is an inhibitor of phosphodiesterase-5 proteins, and PDE-5 is known to be expressed in pulmonary hypertensive lungs.

Of note, previous studies had been done in preparation of peripheral blood mononuclear cells and thus could not attribute changes in cytokine production to individually polarized T cells. In line with these previous reports our study in CD4+ T cell Trichostatin A clones confirmed a conspicuous direct effect of ribavirin on TH1 cells, which may be linked to altered expression of interferon regulatory factors. On the other hand, our data suggest that changes in TH2 functions are unlikely to contribute much to the overall anti-HCV effect of ribavirin, because we observed only slightly reduced production of IL-10 in our TH2 clones. CD4+ Tregs are an alternative source of immunomodulatory cytokines such as IL-10. Thus far, however, frequencies of Tregs in liver and blood have not shown a clear pattern to treatment outcomes. In two recent studies numbers of Tregs remained unchanged in peripheral blood, whereas exposure to PEG-IFN/ribavirin resulted in increased frequencies of Tregs in the liver. None of the previous studies, however, has studied functions of single Tregs and specifically addressed the potential role of ribavirin. Here, our in vitro analysis of Treg clones revealed the novel finding that ribavirin markedly reduced production of IL-10 in Tregs, but did not affect their overall low proliferative capacity. Beyond that, our co-culture assays showed that ribavirinmediated inhibition of IL-10 production of Treg clones clearly resulted in improved proliferation of T effector cells irrespective from their antigen-specificity and functional polarization. Our data suggest that ribavirin specifically affects Tregs in patients with chronic hepatitis C, because we observed only negligible effects in Treg clones from patients with self-limited HCV infection and Tregs from healthy controls. Nevertheless we did not check explicitly antigen-specificity of the T cell clones in the current experiments. However, we have shown previously that our Treg clones recognize epitopes on HCV core in an antigenspecific, HLA-DR-restricted fasion. Thus, it is quite likely that the newly discovered action of ribavirin on Tregs holds also true for Tregs in patients with chronic hepatitis C. Moreover, we demonstrated inhibitory activity of ribavirin on Treg function at concentration levels which are typically achieved in vivo during ribavirin treatment. Moreover, the ribavirin effect could also be demonstrated at therapeutic concentrations of IFN-alpha suggesting that our in vitro findings might have relevance for the in vivo situation under interferon/ribavirin combination therapy. Overall, we did not find that ribavirin modulate transcription factors regulating TH1/TH2 cell responses. However, Brenndo¨rfer et al. recently demonstrated that ribavirin can reverse the HCV NS3/4A-mediated impairment of antiviral signalling pathways in vivo. In summary our analysis of T cell clones supports the concept of immune-mediated activity of ribavirin and suggests that this compound affects the T cell balance by two supplementary mechanisms: importantly also reverses Tregmediated inhibition of T effector cells by inhibiting IL-10 release of HCV-specific Tregs. Beyond that, in vivo reduced IL-10 production under ribavirin may also result in down-regulated expression of ICOS, altered costimulatory signalling and increased priming of T cells towards TH1 differentiation. Thus, in chronic hepatitis C ribavirin is likely to shift the functional balance in the immune system between Tregs and T effector cells towards more efficous effector responses, thus strengthening the antiviral activity of PEG-IFN/ribavirin combination therapy.

Over the past decade, carbapenem resistant Klebsiella pneumoniae is emerging as a major public health threat in many geographic areas. This type of resistance is mediated by plasmid-borne b-lactamases, mainly the serine-carbapenemase KPC and the metallo-b-lactamases VIM, IMP, and NDM. Once carbapenemase-producing K. pneumoniae are introduced into a health care facility with inadequate infection control practices, they may colonize a substantial number of patients and cause serious infections associated with adverse outcomes, prolonged hospital stay and increased costs. An important step towards controlling CPKP is to gain insight on the mechanisms by which these organisms disseminate within a healthcare facility and estimate the extent to which different infection control measures may contribute to CPKP containment. In the past few years, mathematical modeling has been used to assess the impact of measures to control the spread of pathogens – such as Methicillin-resistant Staphylococcus aureus and Vancomycin-resistant Enterococci – within the hospital setting and improve our ability to determine the quantitative effects of individual infection control measures. An important contribution of these models is their ability to estimate not only the effectiveness of each infection control measure, but also the effectiveness of combinations of measures, and determine those most suited for the particular setting and pathogen. In the present study we applied a mathematical model on microbiological surveillance data for CPKP colonization/infection collected during a non-interventional study that was conducted in a tertiary care hospital located in Athens, Greece, an area with high prevalence of CPKP infections. Our aims were to provide estimates of CPKP transmissibility as well as to assess the impact of various infection control interventions on CPKP containment. The present study provides important information on the estimates of CPKP transmissibility in a surgical unit and on the impact of various interventions for successful containment. By using data on the prevalence of CPKP on admission as well as on the occurrence of new acquisition within the unit, it was estimated that the basic reproduction number R0 of CPKP exceeded 1 and reached approximately 2 in the peak months. In time periods when the basic reproductive number was 2, admission of a single CPKP carrier would, on average, have generated 2 new cases. These findings indicate that CPKP has the potential to spread and trigger outbreaks in the healthcare setting. The R0 estimates for CPKP in the surgical unit were lower than the R0 predicted by similar modeling studies for VRE and MRSA that were conducted in ICUs. Variations in R0 for these pathogens may represent differences in the transmission dynamics of the organisms per se or they may reflect differences in the hospital settings where the studies were conducted; ICU, non-ICU, HCW to patient ratios and density of patient population. Indeed, the latter appears to play an important role in CYT387 cross-transmission of CPKP in our hospital. As was shown above, R0 estimates for this pathogen paralleled the fluctuations in bed occupancy, i.e. the higher the level of bed occupancy, the higher the R0. Similarly, Grundmann et al reported that clustered cases of MRSA within an ICU occurred more often during periods of staff deficit when the patient to nurse ratio was higher. Under the recorded infection control practices in the surgical unit, the effective reproductive number for CPKP exceeded unity for long periods of time. Apparently, the compliance level with hand hygiene was not adequate to contain cross-transmission within the unit.