Comparative (computational) analysis of the DNA methylation status of trinucleotide repeat expansion diseases

Copyright © 2013 Mohammadmersad Ghorbani et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.This article has been made available through the Brunel Open Access Publishing Fund.Previous studies have examined DNA methylation in different trinucleotide repeat diseases. We have combined this data and used a pattern searching algorithm to identify motifs in the DNA surrounding aberrantly methylated CpGs found in the DNA of patients with one of the three trinucleotide repeat (TNR) expansion diseases: fragile X syndrome (FRAXA), myotonic dystrophy type I (DM1), or Friedreich’s ataxia (FRDA). We examined sequences surrounding both the variably methylated (VM) CpGs, which are hypermethylated in patients compared with unaffected controls, and the nonvariably methylated CpGs which remain either always methylated (AM) or never methylated (NM) in both patients and controls. Using the J48 algorithm of WEKA analysis, we identified that two patterns are all that is necessary to classify our three regions CCGG* which is found in VM and not in AM regions and AATT* which distinguished between NM and VM + AM using proportional frequency. Furthermore, comparing our software with MEME software, we have demonstrated that our software identifies more patterns than MEME in these short DNA sequences. Thus, we present evidence that the DNA sequence surrounding CpG can influence its susceptibility to be de novo methylated in a disease state associated with a trinucleotide repeat.European Union Seventh Framework Programme and The Brunel University Graduate Program

Effect of Extract of Aerial Parts of Urtica dioica (Urticaceae) on the Stability of Soybean Oil

Purpose: To evaluate the effectiveness of Urtica dioica (Urticaceae) extract as a natural antioxidant and compare with the most commonly used synthetic antioxidants, butylated hydroxyanisole (BHA) and butylated hydroxytoluene (BHT).Methods: Three different U. dioica extracts, viz, chloroform, methanol (80 %) and water extracts, were prepared. The antioxidant activity of the extracts were evaluated by 1,1-diphenyl-2-picryl hydrazyl (DPPH) radical scavenging and soybean oil models. Varying concentrations of the extracts (200, 500 and 800 ppm), BHA and BHT (100 and 200 ppm) were separately added to soybean oil and stored in the oven (60±1 °C) for 25 days. Peroxide and thiobarbituric acid (TBA) values were measured at various heating periods for the oil samples. Total phenolic and flavonoid contents of the extracts were determined using Folin–Ciocalteu and aluminium chloride methods, respectively, while the aerial parts of the plant were also phytochemically screened.Results: Analysis of the chemical composition of U. dioica aerial parts showed they contain crude proteins (21.78 %±0.11), crude lipids (1.66 %±0.03), total soluble carbohydrates (37.19 %±0.21), crude fibers (19.62 %±0.14) and ash (19.75 %±0.17). The aqueous extract contained the highest level of total phenolic contents (7.89 ±0.38, mg g-1 of powder) while the choroform extract contained the highest level of flavonoid contents (15.40 ±0.53 mg g-1 powder). The half-maximal concentration (IC50) values for chloroform, methanol (80 %) and aqueous extracts in respect of DPPH radical scavenging activity were 77.53±0.99, 199.71±1.02 and 159.88±1.57 μg ml-1, respectively. Mixing soybean oil with 200 - 800 ppm of extract decreased oil oxidation and formation rate of TBA reacting substances at a level that is almost equivalent to the synthetic antioxidant, BHT, at a concentration of 200 ppm.Conclusion: These findings demonstrate that mixing soybean oil with U. dioica extract can improve the quality of the oil during frying process.Keywords: Antioxidant activity; Soybean oil; DPPH; Peroxide value; Thiobarbituric acid value; Urtica dioic

Development of underground mine monitoring and communication system integrated ZigBee and GIS

An automated underground mine monitoring and communication system based on the integration of new technologies is introduced to promote safety and health, operational management and cost-effectiveness. The proposed system integration considering wireless sensor network (WSN) assisted geographic information system (GIS) enables to monitor and control underground mining applications from surface office. Based on the capabilities of WSNs, ZigBee network is adapted for near real-time monitoring, ventilation system control and emergency communication in underground mine. ZigBee nodes were developed to sense environmental attributes such as temperature, humidity and gases concentration; switching ON and OFF ventilation fans; and texting emergency messages. A trigger action plan for monitored attributes above normal and threshold value limits is programmed in the surface GIS management server. It is designed to turn the auxiliary fans on remotely or automatically in orange condition and sending evacuation messages for underground miners in unsafe (red) condition. Multi-users operation and 3D visualizations are other successful achievements of the proposed system for the underground monitoring and communication

Epoxy nanocomposites containing magnetite-carbon nanofibers aligned using a weak magnetic field

Novel magnetite-carbon nanofiber hybrids (denoted by "Fe3O4@CNFs") have been developed by coating carbon nanofibers (CNFs) with magnetite nanoparticles in order to align CNFs in epoxy using a relatively weak magnetic field. Experimental results have shown that a weak magnetic field (∼50 mT) can align these newly-developed nanofiber hybrids to form a chain-like structure in the epoxy resin. Upon curing, the epoxy nanocomposites containing the aligned Fe3O4@CNFs show (i) greatly improved electrical conductivity in the alignment direction and (ii) significantly higher fracture toughness when the Fe3O4@CNFs are aligned normal to the crack surface, compared to the nanocomposites containing randomly-oriented Fe3O4@CNFs. The mechanisms underpinning the significant improvements in the fracture toughness have been identified, including interfacial debonding, pull-out, crack bridging and rupture of the Fe3O4@CNFs, and plastic void growth in the polymer matrix

Relationships between symmetry-based graph measures

This paper addresses the problem of comparing different measures of graph symmetry. Two measures, each based on the number and respective sizes of the vertex orbits of the automorphism group or a graph, are compared. A real valued distance measure is used to compare the symmetry measures by establishing the limiting value of the distances for several well known classes of graphs.Peer reviewe

Cost-reliability analysis of hybrid pumped-battery storage for solar and wind energy integration in an island community

This paper presents a mathematical model for estimating the optimal sizing and assessing a standalone hybrid power system's performance entirely based on variable renewable energy sources and coupled with a hybrid energy storage system. This study evaluates how different levels of the main components' capital cost and the loss of power supply probability would affect the cost of energy and the power system's optimal sizing. The case study selected for this study was Ometepe Island in Nicaragua, where the crater lake of an extinct volcano was considered a feasible upper reservoir of a pumped storage hydropower plant, reducing the investments associated with this component. The mathematical formulation considers energy storage losses and gains, and the Pareto efficient solutions of the multi-objective optimization model simultaneously increase reliability, reduce the cost of energy, and minimize curtailment energy. By employing time-series with an hourly resolution, the model allows assessing the impact of the interannual variability of renewable energy sources on the system's performance. As for the case study, the cost of energy obtained from the model results ranges between €0.047/kWh and €0.095/kWh, based on international reference values, and these values match the information available in the literature and other databases

In vitro and In vivo antimycobacterial, hepatoprotective and immunomodulatory activity of Euclea natalensis and its mode of action

Ethnopharmacological relevance: The Natal gwarri or Natal ebony (Euclea natalensis A.DC.) is a deciduous tree found widespread throughout southern Africa, especially in Kwazulu-Natal and the southern cost. It has been widely used by indigenous communities such as the Zulus, Tsongas and Vendas for symptoms related to tuberculosis (TB). The decoctions made from the plant parts are administered for chest diseases to treat complications such as chest pains, bronchitis, pleurisy and asthma. TB is prevalent in immune-compromised patients and it is evident that TB-drugs cause hepatotoxicity. The objective of the present study was therefore to evaluate the antimycobacterial activity of the ethanolic extract of E. natalensis against TB and its hepatoprotective and immunomodulatory activities. Materials and methods: The antimycobacterial, antioxidant, hepatoprotective, immunomodulatory activity and cytotoxicity of the ethanolic extract of the shoots of E. natalensis were determined in vitro. The mechanism of action of the antituberculosis activity was determined by investigating the inhibitory effect on mycothiol disulfide reductase enzyme. Furthermore, the acute, sub-acute toxicity (50-2000 mg/kg) and antimycobacterial effect (300 mg/kg) of E. natalensis shoot extract were investigated in Balb/c mice. Hepatoprotective activity of the extract (50-150 mg/kg) was evaluated on isoniazid and rifampicin (50 mg/kg; i.p.) induced hepatic damage in a rat model. Results: The minimum inhibitory concentration of the extract was found to be 125 µg/ml against Mycobacterium tuberculosis. The extracts fifty percent inhibitory concentration (IC50) against 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radical was found to be 22.55 µg/ml. The plant showed a hepatoprotective effect (50% at 12.5 µg/ml) and the ability to increase T-helper 1 cell cytokines; Interleukin 12, Interleukin 2 and Interferon α by up to 12 fold and the ability to decrease the T-helper 2 cell cytokine Interleukin 10 4 fold when compared to baseline cytokine production. No cellular toxicity was observed in primary peripheral blood mononuclear cells (PBMC's) and two secondary cell lines; U937 monocytes and Chang liver cells (a derivative of the HepG2 cell line). During mechanistic studies, the extract showed a 50% inhibition of mycothiol reductase activity at 38.62 µg/ml. During the acute and sub-acute studies, E. natalensis exhibited no toxic effect and the fifty percent lethal dose (LD50) was established to be above 2000 mg/kg. The extract was able to reduce the mycobacterial load (1.5-fold reduction) in infected mice. Isoniazid and rifampicin caused significant hepatic damage in rats, and the extract was able to reduce the toxicity by 15% and 40% at 50 and 150 mg/kg respectively. Conclusion: The present study supports the traditional usage of the plant against tuberculosis symptoms. The study showed the ability of E. natalensis shoot extract to inhibit mycobacterial growth, stimulate an appropriate immune response and have a hepatic protective effect. Due to the extract's significant results for hepatoprotective, immunomodulatory effects and antimycobacterial activity, it may prove to be effective to serve as an adjuvant for TB-patients

Bacteriophage biodistribution and infectivity from honeybee to bee larvae using a T7 phage model

Bacteriophages (phages) or viruses that specifically infect bacteria have widely been studied as biocontrol agents against animal and plant bacterial diseases. They offer many advantages compared to antibiotics. The American Foulbrood (AFB) is a bacterial disease affecting honeybee larvae caused by Paenibacillus larvae. Phages can be very significant in fighting it mostly due to European restrictions to the use of antibiotics in beekeeping. New phages able to control P. larvae in hives have already been reported with satisfactory results. However, the efficacy and feasibility of administering phages indirectly to larvae through their adult workers only by providing phages in bees feeders has never been evaluated. This strategy is considered herein the most feasible as far as hive management is concerned. This in vivo study investigated the ability of a phage to reach larvae in an infective state after oral administration to honeybees. The screening (by direct PFU count) and quantification (by quantitative PCR) of the phage in bee organs and in larvae after ingestion allowed us to conclude that despite 104 phages reaching larvae only an average of 32 were available to control the spread of the disease. The fast inactivation of many phages in royal jelly could compromise this therapeutic approach. The protection of phages from hive-derived conditions should be thus considered in further developments for AFB treatment.This study was supported by the project APILYSE, PTDC/CVT-EPI/4008/2014 - POCI-01-0145-FEDER-016598, - funded by FEDER through COMPETE 2020 - Programa Operacional Competitividade e Internacionalização (POCI) and by national funds trough FCT - Fundação para a Ciência e a Tecnologia, I.P. The work was also supported by the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01-0145FEDER-006684) and BioTecNorte operation (NORTE-01-0145-FEDER-000004), funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte. HR was supported by FCT through the grant SFRH/BD/128859/2017. RC was founded by FCT and FEDER (POCI-010145-FEDER-007274).info:eu-repo/semantics/publishedVersio

Criticality and threat analysis on utility tunnels for planning security policies of utilities in urban underground space

A utility tunnel is defined as an underground structure containing one or more utilities, permitting the installation, maintenance and removal of the systems without the necessity of making street cuts or excavations. These underground facilities contain all essential utilities serving large urban areas collected together in a tunnel; therefore they are an inviting target for sabotage or vandalism. This paper proposes an expert system combining color-coded scales, Delphi and AHP methods to analyze criticality and threats on utility tunnels to support planning of security policies for utilities in urban subsurface.Cantó Perelló, J.; Curiel Esparza, J.; Calvo Peña, V. (2013). Criticality and threat analysis on utility tunnels for planning security policies of utilities in urban underground space. Expert Systems with Applications. 40(11):4707-4714. doi:10.1016/j.eswa.2013.02.031S47074714401

Structural and critical current properties in polycrystalline SmO1-xFxFeAs

A series of polycrystalline SmO1-xFxFeAs bulks (x=0.15, 0.2, 0.3 and 0.4) were prepared by the conventional solid state reaction. Resistivity, susceptibility, magnetic hysteresis, critical current density and microstructure of these samples have been investigated. It is found that critical transition temperature Tc increases steadily with increasing fluorine content, with the highest onset Tc=53 K at x=0.4. On the other hand, the superconductivity seems correlated with lattice constants; that is, Tc rises with the shrinkage of a-axis while resistivity increases with the enlargement of c-axis. A global critical current density of 1.1x10^4 A/cm^2 at 5 K in self field was achieved in the purest sample. A method of characterization of inter-grain current density is proposed. This method gives an inter-grain Jc of 3.6x10^3 A/cm^2 at 5 K in self field, in contrast to the intra-grain Jc of 10^6 A/cm^2. The effect of composition gradients on the inter-grain Jc in SmO1-xFxFeAs is also discussed.Comment: 18 pages, 7 figure