A Survey on Graph Database Management Techniques for Huge Unstructured Data

Data analysis, data management, and big data play a major role in both social and business perspective, in the last decade. Nowadays, the graph database is the hottest and trending research topic. A graph database is preferred to deal with the dynamic and complex relationships in connected data and offer better results. Every data element is represented as a node. For example, in social media site, a person is represented as a node, and its properties name, age, likes, and dislikes, etc and the nodes are connected with the relationships via edges. Use of graph database is expected to be beneficial in business, and social networking sites that generate huge unstructured data as that Big Data requires proper and efficient computational techniques to handle with. This paper reviews the existing graph data computational techniques and the research work, to offer the future research line up in graph database management

CRISPRi screens reveal genes modulating yeast growth in lignocellulose hydrolysate.

BACKGROUND: Baker's yeast is a widely used eukaryotic cell factory, producing a diverse range of compounds including biofuels and fine chemicals. The use of lignocellulose as feedstock offers the opportunity to run these processes in an environmentally sustainable way. However, the required hydrolysis pretreatment of lignocellulosic material releases toxic compounds that hamper yeast growth and consequently productivity. RESULTS: Here, we employ CRISPR interference in S. cerevisiae to identify genes modulating fermentative growth in plant hydrolysate and in presence of lignocellulosic toxins. We find that at least one-third of hydrolysate-associated gene functions are explained by effects of known toxic compounds, such as the decreased growth of YAP1 or HAA1, or increased growth of DOT6 knock-down strains in hydrolysate. CONCLUSION: Our study confirms previously known genetic elements and uncovers new targets towards designing more robust yeast strains for the utilization of lignocellulose hydrolysate as sustainable feedstock, and, more broadly, paves the way for applying CRISPRi screens to improve industrial fermentation processes

Apigenin inhibits PMA-induced expression of pro-inflammatory cytokines and AP-1 factors in A549 cells

Acute and chronic alveolar or bronchial inflammation is thought to be central to the pathogenesis of many respiratory disorders. Cytokines and granulocyte macrophage colony-stimulating factors (GM-CSF) play an important role in chronic inflammation. Activator protein-1 (AP-1) the superfamily of transcription factors is involved in proliferation, differentiation, apoptosis, and transformation including inflammation. Understanding the function and regulation of proinflammatory factors involved in inflammation may provide the novel therapeutic strategies in the treatment of inflammatory diseases. Our aim of the present study is to investigate the pro-inflammatory cytokines and pattern of AP-1 factors expressed during activation of lung adenocarcinoma A549 cells by Phorbol-12-myristate-13-acetate (PMA) and to understand the anti-inflammatory effect of apigenin. A549 cells were treated with and without PMA or apigenin, and the cell viability was assessed by MTT assay. Expressions of inflammatory mediators and different AP-1 factors were analyzed by semi-quantitative RT-PCR. IL-6 protein secreted was analyzed by ELISA, and expressions of IL-1β, c-Jun, and c-Fos proteins were analyzed by Western blotting. Activation of A549 cells by PMA, induced the expression of pro-inflammatory cytokine (IL-1β, IL-2, IL-6, IL-8, and TNF-α) mRNAs and secretion of IL-6 and the expression of specific AP-1 factors (c-Jun, c-Fos, and Fra-1). Treatment of cells with apigenin, significantly inhibited PMA-stimulated mRNA expression of above pro-inflammatory cytokines, AP-1 factors, cyclooxygenase-2, and secretion of IL-6 protein. Results suggested that the AP-1 factors may be involved in inflammation and apigenin has anti-inflammatory effect, which may be useful for therapeutic management of lung inflammatory diseases. © 2015, Springer Science+Business Media New York

Aqueous areca nut extract induces oxidative stress in human lung epithelial A549 cells: Probable role of p21 in inducing cell death

Areca nut a well-known masticator used across globe. Habitual chewing of areca nut is associated with serious oral health effects. However, the role of areca nut in oxidative stress induction and cell death is less understood. Hence, in the present study we aimed to evaluate the toxic mechanism of areca nut extract on human lung epithelial A549 cells. Cells were treated with or without aqueous areca nut extract and cell viability was measured by MTT assay. Cells treated with areca nut extract show reduced viability in a dose dependent manner with the IC50 of 0.5 concentration. Areca nut extract induced the reactive oxygen species (ROS), lipid peroxidation followed by membrane damage with leakage of lactate dehydrogenase (LDH) enzyme. Cells with continuous exposure of areca nut extract depletes the free radical neutralizing anti-oxidant enzymes like superoxide dismutase (SOD), Glutathione peroxidase (GSH-Px) and Glutathione-S-transferase (GST). Further, the analysis of mRNA expression of apoptotic genes and cell cycle regulators show decreased expression of anti-apoptotic gene (Bcl-2), Cyclin E1, Cyclin D1, CDK4, Rb and p53 whereas induced expression of p21 and marginal increase of pro-apoptotic gene (Bax) confirms the toxic nature of areca nut. Thus, cell death due to areca nut exposure may be through different mechanism rather than the conventional apoptotic pathway, where p21 induction might be independent of p53 action, which possibly suggests that there may be a role of p21 in oxidative stress induced cell death. Further FACS analysis confirms cell death in areca nut treated cells. © 2016 Elsevier Inc

Cadmium induces oxidative stress and apoptosis in lung epithelial cells

Cadmium (Cd) is one of the well-known highly toxic environmental and industrial pollutants. Cd first accumulates in the nucleus and later interacts with zinc finger proteins of antiapoptotic genes and inhibit the binding of transcriptional factors and transcription. However, the role of Cd in oxidative stress and apoptosis is less understood. Hence, the present study was undertaken to unveil the mechanism of action. A549 cells were treated with or without Cd and cell viability was measured by MTT assay. Treatment of cells with Cd shows reduced viability in a dose-dependent manner with IC50 of 45 μM concentration. Cd significantly induces the reactive oxygen species (ROS), lipid peroxidation followed by membrane damage with the leakage of lactate dehydrogenase (LDH). Cells with continuous exposure of Cd deplete the antioxidant super oxide dismutase (SOD) and glutathione peroxidase (GSH-Px) enzymes. Further, analysis of the expression of genes involved in apoptosis show that both the extrinsic and intrinsic apoptotic pathways were involved. Death receptor marker tumor necrosis factor-α (TNF-α), executor caspase-8 and pro-apoptotic gene (Bax) were induced, while antiapoptotic gene (Bcl-2) was decreased in Cd-treated cells. Fluorescence-activated cell sorting (FACS) analysis further confirms the induction of apoptosis in Cd-treated A549 cells

2,3-Dibromo-1-(2,4-dichloro-5-fluoro­phen­yl)-3-phenyl­propan-1-one

In the title compound, C15H9Br2Cl2FO, the dihedral angle between the two aromatic rings is 6.0 (1)°. The dibromo­ethane fragment of the propan-1-one unit is disordered over two positions, with occupancies of ca 0.83 and 0.17. The crystal structure is stabilized by inter­molecular C—H⋯O hydrogen bonds, C—H⋯π inter­actions, and Br⋯Cl [3.505 (2) and 3.576 (6) Å] and Cl⋯F [3.176 (2) Å] short contacts

Nanopore Sequencing Accurately Identifies the Mutagenic DNA Lesion O; 6; -Carboxymethyl Guanine and Reveals Its Behavior in Replication

O; 6; -carboxymethylguanine (O; 6; -CMG) is a highly mutagenic alkylation product of DNA, triggering transition mutations relevant to gastrointestinal cancer. However, precise localization of a single O; 6; -CMG with conventional sequencing platforms is challenging. Here nanopore sequencing (NPS), which directly senses single DNA bases according to their physiochemical properties, was employed to detect O; 6; -CMG. A unique O; 6; -CMG signal was observed during NPS and a single-event call accuracy of >95 % was achieved. Moreover, O; 6; -CMG was found to be a replication obstacle for Phi29 DNA polymerase (Phi29 DNAP), suggesting this lesion could cause DNA sequencing biases in next generation sequencing (NGS) approaches

Stress activated p38 MAPK regulates cell cycle via AP-1 factors in areca extract exposed human lung epithelial cells

Abstract Areca nut chewing habits are associated with several oral manifestations like leukoplakia, submucous fibrosis and oral squamous cell carcinoma. Although numerous evidence on areca toxicity is known but the mechanistic pathway of disease causation is to be studied. Aqueous areca nut extract treated A549 cells showed reduced cell viability by 48 h with IC50 value of 0.50%. The toxic nature of areca nut induced the production of reactive oxygen species with decreased anti-oxidant glutathione S transferase levels lead to altered redox homeostasis. PCR studies showed decreased mRNA levels of Jun and Fos AP-1 subunits on extract treatment by 48 h. The protein levels of PCNA, CDK4, RB, p53, c-Jun and c-Fos were found to be downregulated with upregulated CDK inhibitor p21 on extract treatment as compared to control. Results of FACS analysis further confirm G1/S phase cell cycle arrest on areca nut extract exposure. The regulation of downstream AP-1 subunits by MAPKs was studied by using specific inhibitors of ERK, JNK and p38 along with areca nut extract. Results showed the redox activation of MAP kinases down regulated the mRNA levels of AP-1 subunits in aqueous areca nut extract treated cells. Hence the present study aids in elucidating the role of MAP kinases in regulating the AP-1 subunits and their implications on target genes that are involved regulation of various cellular processes. Further, it would help in understanding the mechanistic aspects of the diseased state which may facilitate in designing of new therapeutic modalities that could help in cancer management

OptFlux: an open-source software platform for in silico metabolic engineering

<p>Abstract</p> <p>Background</p> <p>Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications.</p> <p>Results</p> <p><it>OptFlux </it>is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes.</p> <p><it>OptFlux </it>also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms.</p> <p>The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. <it>OptFlux </it>has a visualization module that allows the analysis of the model structure that is compatible with the layout information of <it>Cell Designer</it>, allowing the superimposition of simulation results with the model graph.</p> <p>Conclusions</p> <p>The <it>OptFlux </it>software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization algorithms and the final users. It is a valuable platform for researchers in the field that have available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community.</p> <p>Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network topology analysis tools and the integration with Boolean network based regulatory models.</p