Constraint-based Analysis of Substructures of Metabolic Networks

Constraint-based methods (CBMs) are promising tools for the analysis of metabolic networks, as they do not require detailed knowledge of the biochemical reactions. Some of these methods only need information about the stoichiometric coefficients of the reactions and their reversibility types, i.e., constraints for steady-state conditions. Nevertheless, CBMs have their own limitations. For example, these methods may be sensitive to missing information in the models. Additionally, they may be slow for the analysis of genome-scale metabolic models. As a result, some studies prefer to consider substructures of networks, instead of complete models. Some other studies have focused on better implementations of the CBMs. In Chapter 2, the sensitivity of flux coupling analysis (FCA) to missing reactions is studied. Genome-scale metabolic reconstructions are comprehensive, yet incomplete, models of real-world metabolic networks. While FCA has proved an appropriate method for analyzing metabolic relationships and for detecting functionally related reactions in such models, little is known about the impact of missing reactions on the accuracy of FCA. Note that having missing reactions is equivalent to deleting reactions, or to deleting columns from the stoichiometric matrix. Based on an alternative characterization of flux coupling relations using elementary flux modes, we study the changes that flux coupling relations may undergo due to missing reactions. In particular, we show that two uncoupled reactions in a metabolic network may be detected as directionally, partially or fully coupled in an incomplete version of the same network. Even a single missing reaction can cause significant changes in flux coupling relations. In case of two consecutive E. coli genome-scale networks, many fully-coupled reaction pairs in the incomplete network become directionally coupled or even uncoupled in the more complete reconstruction. In this context, we found gene expression correlation values being significantly higher for the pairs that remained fully coupled than for the uncoupled or directionally coupled pairs. Our study clearly suggests that FCA results are indeed sensitive to missing reactions. Since the currently available genome-scale metabolic models are incomplete, we advise to use FCA results with care. In Chapter 3, a different, but related problem is considered. Due to the large size of genome-scale metabolic networks, some studies suggest to analyze subsystems, instead of original genome-scale models. Note that analysis of a subsystem is equivalent to deletion of some rows from the stoichiometric matrix, or identically, assuming some internal metabolites to be external. We show mathematically that analysis of a subsystem instead of the original model can lead the flux coupling relations to undergo certain changes. In particular, a pair of (fully, partially or directionally) coupled reactions may be detected as uncoupled in the chosen subsystem. Interestingly, this behavior is the opposite of the flux coupling changes that may happen due to the existence of missing reactions, or equivalently, deletion of reactions. We also show that analysis of organelle subsystems has relatively little influence on the results of FCA, and therefore, many of these subsystems may be studied independent of the rest of the network. In Chapter 4, we introduce a rapid FCA method, which is appropriate for genome-scale networks. Previously, several approaches for FCA have been proposed in the literature, namely flux coupling finder algorithm, FCA based on minimal metabolic behaviors, and FCA based on elementary flux patterns. To the best of our knowledge none of these methods are available as a freely available software. Here, we introduce a new FCA algorithm FFCA (Feasibility-based Flux Coupling Analysis). This method is based on checking the feasibility of a system of linear inequalities. We show on a set of benchmarks that for genome-scale networks FFCA is faster than other existing FCA methods. Using FFCA, flux coupling analysis of genome-scale networks of S. cerevisiae and E. coli can be performed in a few hours on a normal PC. A corresponding software tool is freely available for non-commercial use. In Chapter 5, we introduce a new concept which can be useful in the analysis of fluxes in network substructures. Analysis of elementary modes (EMs) is proven to be a powerful CBM in the study of metabolic networks. However, enumeration of EMs is a hard computational task. Additionally, due to their large numbers, one cannot simply use them as an input for subsequent analyses. One possibility is to restrict the analysis to a subset of interesting reactions, rather than the whole network. However, analysis of an isolated subnetwork can result in finding incorrect EMs, i.e. the ones which are not part of any steady-state flux distribution in the original network. The ideal set of vectors to describe the usage of reactions in a subnetwork would be the set of all EMs projected onto the subset of interesting reactions. Recently, the concept of “elementary flux patterns” (EFPs) has been proposed. Each EFP is a subset of the support (i.e. non-zero elements) of at least one EM. In the present work, we introduce the concept of ProCEMs (Projected Cone Elementary Modes). The ProCEM set can be computed by projecting the flux cone onto the lower-dimensional subspace and enumerating the extreme rays of the projected cone. In contrast to EFPs, ProCEMs are not merely a set of reactions, but from the mathematical point of view they are projected EMs. We additionally prove that the set of EFPs is included in the set of ProCEM supports. Finally, ProCEMs and EFPs are compared in the study of substructures in biological networks

Effect of Supination Versus Pronation in the Non-Operative Treatment of Pediatric Supracondylar Humerus Fractures

Background: Supracondylar fracture of the humerus is the most common elbow injury that requires reduction and immobilization in the proper position to union. There are a few reports regarding the position of the forearm immobilization on elbow cosmetic outcome. Objectives: This study aimed to compare two modes of the forearm, supination and pronation in elbow deformity incidence after closed reduction and casting of this fracture. Patients and Methods: This prospective and descriptive study was carried out on children with supracondylar fracture of the humerus treated with closed reduction and cast immobilization in one of the two modes of either supination or pronation for a period of three weeks. Twenty-nine patients were immobilized in supination and 35 in pronation. Follow-up lasted for 8 months. Re-displacement was defined as the criteria and subsequent deformities of the elbow in patients, were assessed by clinical and radiographic examination. Results: A total of 64 patients, 50 boys and 14 girls, with the mean age of 4.8 years (3.1 to 8.5 years) participated. All fractures were closed and of the extension type. Forty-five cases had Gartland type II and 19 had type III fracture. Deformity of the elbow had occurred in seven cases (10.94%). Four cases of cubitus varus (CA 5 º - 16º) were observed in the supination group, of these, three patients had type III and one other had a type II fracture. In the pronation group, two cases of cubitus varus (CA 6 º - 14º) and one case of cubitus valgus (CA 17º) were observed, with type III initial fracture in all 3 cases. Conclusions: In regard to elbow malunion deformity, no obvious difference was observed between the two methods of supination and pronation in the closed treatment of supracondylar humerus fracture. However, as cubitus varus and valgus had occurred in both groups with unstable type III fractures, to prevent this complication, operative fixation is advised rather than closed reduction and position of the forearm immobilization

Novel heart valve prosthesis with self-endothelialization potential made of modified polyhedral oligomeric silsesquioxane-nanocomposite material

In the cardiovascular system, the endothelial layer provides a natural antithrombogenic surface on the inner portion of the heart and associated vessels. For a synthetic material therefore, the ability to attract and retain endothelial or endothelial progenitor cells (EPCs), ultimately creating a single endothelial layer on its surface, is of prime importance. The authors have developed a nanocomposite polymer, based on a combination of polyhedral oligomeric silsesquioxane nanoparticles and polycarbonate urea urethane (POSS-PCU), which is biocompatible and has been used in human for the world's first synthetic trachea, tear duct, and bypass graft. In this study, the authors modified the surface of this casted nanocomposite by grafting fibronectin derived bioactive peptides [glycine-arginine-glycine-aspartic acid-glycine (GRGDG) and lauric acid conjugated GRGDG (GRGDG-LA)] to enhance the endothelialization for using heart valves leaflets from circulating EPCs. Human peripheral blood mononuclear cells were separated using Ficoll-Paque centrifugation, with harvested EPCs purified using CD34 microbead labeling and magnetic-activated cell sorting. Cells were seeded onto 96 well plates coated with POSS-PCU, GRGDG/GRGDG-LA modified POSS-PCU and PCU polymers, for a period of 21 days. Cells were studied under light, confocal, and scanning electron microscope (SEM). Fluorescence-activated cell sorting was used to analyze cell surface markers. Cell attachment and proliferation was observed in all POSS-PCU samples, significantly higher than the activity seen within the control PCU polymers (p < 0.05). Microscopic examination revealed clonal expansion and morphological changes in cells seeded on POSS-PCU. The cells expressed increasing levels of mature endothelial cell markers over time with a concurrent reduction in hematopoietic stem cell marker expression. SEM showed a mixed population of morphologically differentiated endothelial cells and EPCs. These results support the use of heart valve made with the POSS-PCU polymer and demonstrate that suitable chemical modification of this nanocomposite could increase self-endothelialization potential and reduce associated thrombotic events

Rps27a might act as a controller of microglia activation in triggering neurodegenerative diseases

Neurodegenerative diseases (NDDs) are increasing serious menaces to human health in the recent years. Despite exhibiting different clinical phenotypes and selective neuronal loss, there are certain common features in these disorders, suggesting the presence of commonly dysregulated pathways. Identifying causal genes and dysregulated pathways can be helpful in providing effective treatment in these diseases. Interestingly, in spite of the considerable researches on NDDs, to the best of our knowledge, no dysregulated genes and/or pathways were reported in common across all the major NDDs so far. In this study, for the first time, we have applied the three-way interaction model, as an approach to unravel sophisticated gene interactions, to trace switch genes and significant pathways that are involved in six major NDDs. Subsequently, a gene regulatory network was constructed to investigate the regulatory communication of statistically significant triplets. Finally, KEGG pathway enrichment analysis was applied to find possible common pathways. Because of the central role of neuroinflammation and immune system responses in both pathogenic and protective mechanisms in the NDDs, we focused on immune genes in this study. Our results suggest that "cytokine-cytokine receptor interaction" pathway is enriched in all of the studied NDDs, while "osteoclast differentiation" and "natural killer cell mediated cytotoxicity" pathways are enriched in five of the NDDs each. The results of this study indicate that three pathways that include "osteoclast differentiation", "natural killer cell mediated cytotoxicity" and "cytokine-cytokine receptor interaction" are common in five, five and six NDDs, respectively. Additionally, our analysis showed that Rps27a as a switch gene, together with the gene pair Il-18, Cx3cl1 form a statistically significant and biologically relevant triplet in the major NDDs. More specifically, we suggested that Cx3cl1 might act as a potential upstream regulator of Il-18 in microglia activation, and in turn, might be controlled with Rps27a in triggering NDDs. © 2020 Khayer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Efficient inhibition of human immunodeficiency virus replication using novel modified microRNA-30a targeting 3'-untranslated region transcripts

RNA interference (RNAi)-based gene therapy is currently considered to be a combinatorial anti-human immunodeficiency virus-1 (HIV-1) therapy. Although arti­ficial polycistronic microRNAs (miRs) can reduce HIV-1 escape mutant variants, this approach may increase the risk of side effects. The present study aimed to optimize the efficiency of anti-HIV RNAi gene therapy in order to reduce the cell toxicity induced by multi-short hairpin RNA expression. An artificial miR-30a-3'-untranslated region (miR-3'-UTR) obtained from a single RNA polymerase II was used to simultaneously target all viral transcripts. The results of the present study demonstrated that HIV-1 replication was signifi­cantly inhibited in the cells with the miR-3'-UTR construct, suggesting that miR-3'-UTR may serve as a promising tool for RNAi-based gene therapy in the treatment of HIV-1. © 2016, Spandidos Publications. All Rights Reserved

How accessibility influences citation counts: The case of citations to the full text articles available from ResearchGate

It is generally believed that the number of citations to an article can positively be correlated to its free online availability. In the present study, we investigated the possible impact of academic social networks on the number of citations. We chose the social web service “ResearchGate” as a case. This website acts both as a social network to connect researchers, and at the same time, as an open access repository to publish post-print version of the accepted manuscripts and final versions of open access articles. We collected the data of 1823 articles published by the authors from four different universities. By analyzing these data, we showed that although different levels of full text availability are observed for the four universities, there is always a significant positive correlation between full text availability and the citation count. Moreover, we showed that both post-print version and publisher’s version (i.e., final published version) of the archived manuscripts receive more citations than non-OA articles, and the difference in the citation counts of post-print manuscripts and publisher’s version articles is nonsignificant

Phenotypic Identification and Genotypic Characterization of Plasmid‑Mediated AmpC β‑Lactamase‑Producing Escherichia coli and Klebsiella pneumoniae Isolates in Iran

One of the mechanisms of Klebsiella pneumoniae and Escherichia coli resistance to β-lactam antibiotics is the production of β-lactamase enzymes. Among these are the AmpC β-lactamases, which confer resistance to a class of antibiotics. However, little is known about the AmpC β-lactamases of K. pneumoniae and E. coli clinical isolates in Qazvin, Iran. This study was designed to assess the AmpC β-lactamases-producing strains and also identify the prevalence of AmpC β-lactamases genes. Antimicrobial susceptibility tests were performed on 435 K. pneumoniae and E. coli isolates using disk difusion technique. Plasmid-mediated AmpC genes were studied using a multiplex PCR assay. The AmpC β-lactamase-producer isolates were studied by employing cefoxitin disk difusion test, AmpC induction test, AmpC cefoxitin-EDTA test, and boronic acid disk test. Our results showed that of 46 (18.4%) cefoxitin-insensitive E. coli isolates, 10 (21.7%) were positive for AmpC β-lactamase genes, among them 4 (8.69%) isolates were positive for blaDHA genes and 6 (13%) for blaCIT genes. Of 57 (30.4%) cefoxitin-insensitive K. pneumoniae isolates, 10 (17.5%) were positive for AmpC gene with 4 (6.34%) and 6 (9.5%) isolates positive for blaDHA and blaCIT genes, respectively. However, no MOX, ACC, FOX, or EBC genes were detected in the isolates. Considering the results of diferent confrmatory phenotypic tests, the AmpC cefoxitin-EDTA test showed a higher discriminatory power for detecting AmpC β-lactamase-producing strains. The specifcity and sensitivity of AmpC cefoxitin-EDTA were 77%, 100% for K. pneumonia and 70%, 90% for E. coli higher than the other two tests, respectively. Also, the authors demonstrated high prevalence rate for resistance to certain antibiotics, such as cefuroxime, trimethoprim-sulfamethoxazole, ampicillin, and cefotaxime. In conclusion, our study provided valuable information regarding the plasmid-mediated AmpC β-lactamase gene content, antibiotic resistance, and confrmatory phenotypic tests for AmpC β-lactamases in E. coli and K. pneumoniae isolates from clinical sources

Formyl Peptide Receptor as a Novel Therapeutic Target for Anxiety-Related Disorders

Formyl peptide receptors (FPR) belong to a family of sensors of the immune system that detect microbe-associated molecules and inform various cellular and sensorial mechanisms to the presence of pathogens in the host. Here we demonstrate that Fpr2/3-deficient mice show a distinct profile of behaviour characterised by reduced anxiety in the marble burying and light-dark box paradigms, increased exploratory behaviour in an open-field, together with superior performance on a novel object recognition test. Pharmacological blockade with a formyl peptide receptor antagonist, Boc2, in wild type mice reproduced most of the behavioural changes observed in the Fpr2/3(-/-) mice, including a significant improvement in novel object discrimination and reduced anxiety in a light/dark shuttle test. These effects were associated with reduced FPR signalling in the gut as shown by the significant reduction in the levels of p-p38. Collectively, these findings suggest that homeostatic FPR signalling exerts a modulatory effect on anxiety-like behaviours. These findings thus suggest that therapies targeting FPRs may be a novel approach to ameliorate behavioural abnormalities present in neuropsychiatric disorders at the cognitive-emotional interface

Applying refinement to the use of mice and rats in rheumatoid arthritis research

Rheumatoid arthritis (RA) is a painful, chronic disorder and there is currently an unmet need for effective therapies that will benefit a wide range of patients. The research and development process for therapies and treatments currently involves in vivo studies, which have the potential to cause discomfort, pain or distress. This Working Group report focuses on identifying causes of suffering within commonly used mouse and rat ‘models’ of RA, describing practical refinements to help reduce suffering and improve welfare without compromising the scientific objectives. The report also discusses other, relevant topics including identifying and minimising sources of variation within in vivo RA studies, the potential to provide pain relief including analgesia, welfare assessment, humane endpoints, reporting standards and the potential to replace animals in RA research

Fast splice site detection using information content and feature reduction

Background: Accurate identification of splice sites in DNA sequences plays a key role in the prediction of gene structure in eukaryotes. Already many computational methods have been proposed for the detection of splice sites and some of them showed high prediction accuracy. However, most of these methods are limited in terms of their long computation time when applied to whole genome sequence data. Results: In this paper we propose a hybrid algorithm which combines several effective and informative input features with the state of the art support vector machine (SVM). To obtain the input features we employ information content method based on Shannon\u27s information theory, Shapiro\u27s score scheme, and Markovian probabilities. We also use a feature elimination scheme to reduce the less informative features from the input data. Conclusion: In this study we propose a new feature based splice site detection method that shows improved acceptor and donor splice site detection in DNA sequences when the performance is compared with various state of the art and well known method