Search results for: tetracycline resistance genes.

Authors: Minsoo Lee, Yearn Jeong Kim, Yun-mi Kim, Sujeung Cheong, Sookyung Song

Abstract:

Bio-chips are used for experiments on genes and contain various information such as genes, samples and so on. The two-dimensional bio-chips, in which one axis represent genes and the other represent samples, are widely being used these days. Instead of experimenting with real genes which cost lots of money and much time to get the results, bio-chips are being used for biological experiments. And extracting data from the bio-chips with high accuracy and finding out the patterns or useful information from such data is very important. Bio-chip analysis systems extract data from various kinds of bio-chips and mine the data in order to get useful information. One of the commonly used methods to mine the data is classification. The algorithm that is used to classify the data can be various depending on the data types or number characteristics and so on. Considering that bio-chip data is extremely large, an algorithm that imitates the ecosystem such as the ant algorithm is suitable to use as an algorithm for classification. This paper focuses on finding the classification rules from the bio-chip data using the Ant Colony algorithm which imitates the ecosystem. The developed system takes in consideration the accuracy of the discovered rules when it applies it to the bio-chip data in order to predict the classes.

Keywords: Ant Colony System, DNA chip data, Classification.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1422

Authors: M. Anandhavalli Gauthaman

Abstract:

DNA microarrays allow the measurement of expression levels for a large number of genes, perhaps all genes of an organism, within a number of different experimental samples. It is very much important to extract biologically meaningful information from this huge amount of expression data to know the current state of the cell because most cellular processes are regulated by changes in gene expression. Association rule mining techniques are helpful to find association relationship between genes. Numerous association rule mining algorithms have been developed to analyze and associate this huge amount of gene expression data. This paper focuses on some of the popular association rule mining algorithms developed to analyze gene expression data.

Keywords: DNA microarray, gene expression, association rule mining.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2093

Authors: C. Gunavathi, K. Premalatha

Abstract:

Tumor classification is a key area of research in the field of bioinformatics. Microarray technology is commonly used in the study of disease diagnosis using gene expression levels. The main drawback of gene expression data is that it contains thousands of genes and a very few samples. Feature selection methods are used to select the informative genes from the microarray. These methods considerably improve the classification accuracy. In the proposed method, Genetic Algorithm (GA) is used for effective feature selection. Informative genes are identified based on the T-Statistics, Signal-to-Noise Ratio (SNR) and F-Test values. The initial candidate solutions of GA are obtained from top-m informative genes. The classification accuracy of k-Nearest Neighbor (kNN) method is used as the fitness function for GA. In this work, kNN and Support Vector Machine (SVM) are used as the classifiers. The experimental results show that the proposed work is suitable for effective feature selection. With the help of the selected genes, GA-kNN method achieves 100% accuracy in 4 datasets and GA-SVM method achieves in 5 out of 10 datasets. The GA with kNN and SVM methods are demonstrated to be an accurate method for microarray based tumor classification.

Keywords: F-Test, Gene Expression, Genetic Algorithm, k- Nearest-Neighbor, Microarray, Signal-to-Noise Ratio, Support Vector Machine, T-statistics, Tumor Classification.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 4487

Authors: Fatma N. Talkhan, H. H. Abo-Assy, K. A. Soliman, Marwa M. Azzam, A. Z. E. Abdelsalam, A. S. Abdel-Razek

Abstract:

The Egyptian Bacillus thuringiensis isolate (M5) produce crystal proteins that is toxic against insects was irradiated with UV light to induce mutants. Upon testing 10 of the resulting mutants for their toxicity against cotton leafworm larvae, the three mutants 62, 64 and 85 proved to be the most toxic ones. Upon testing these mutants along with their parental isolate by SDS-PAGE analysis of spores-crystals proteins as well as vegetative cells proteins, new induced bands appeared in the three mutants by UV radiation and also they showed disappearance of some other bands as compared with the wild type isolate. Multiplex PCR technique, with five sets of specific primers, was used to detect the three types of cryI genes cryIAa, cryIAb and cryIAc. Results showed that these three genes exist, as distinctive bands, in the wild type isolate (M5) as well as in mutants 62 and 85, while the mutant 64 had two distinctive bands of cryIAb and cryIAc genes, and a faint band of cryI Aa gene. Finally, these results revealed that mutant 62 is considered as the promising mutant since it is UV resistant, highly toxic against Spodoptera littoralis and active against a wide range of Lepidopteran insects.

Keywords: Bacillus thuringiensis, biological control, cry1 genes, multiplex PC, SDS- PAGE analysis.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1884

Authors: Khin May Win, Nan Sai Moon Kham

Abstract:

Identification of cancer genes that might anticipate the clinical behaviors from different types of cancer disease is challenging due to the huge number of genes and small number of patients samples. The new method is being proposed based on supervised learning of classification like support vector machines (SVMs).A new solution is described by the introduction of the Maximized Margin (MM) in the subset criterion, which permits to get near the least generalization error rate. In class prediction problem, gene selection is essential to improve the accuracy and to identify genes for cancer disease. The performance of the new method was evaluated with real-world data experiment. It can give the better accuracy for classification.

Keywords: Microarray data, feature selection, recursive featureelimination, support vector machines.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1502

Authors: Ahmad Ali Shahid, Muhammad Shakil Shaukat, Kamran Shehzad Bajwa, Abdul Qayyum Rao, Tayyab Husnain

Abstract:

Agriculture is the backbone of economy of Pakistan and cotton is the major agricultural export and supreme source of raw fiber for our textile industry. To combat severe problems of insect and weed, combination of three genes namely Cry1Ac, Cry2A and EPSPS genes was transferred in locally cultivated cotton variety MNH-786 with the use of Agrobacterium mediated genetic transformation. The present study focused on the molecular screening of transgenic cotton plants at T3 generation in order to confirm integration and expression of all three genes (Cry1Ac, Cry2A and EPSP synthase) into the cotton genome. Initially, glyphosate spray assay was used for screening of transgenic cotton plants containing EPSP synthase gene at T3 generation. Transgenic cotton plants which were healthy and showed no damage on leaves were selected after 07 days of spray. For molecular analysis of transgenic cotton plants in the laboratory, the genomic DNA of these transgenic cotton plants were isolated and subjected to amplification of the three genes. Thus, seventeen out of twenty (Cry1Ac gene), ten out of twenty (Cry2A gene) and all twenty (EPSP synthase gene) were produced positive amplification. On the base of PCR amplification, ten transgenic plant samples were subjected to protein expression analysis through ELISA. The results showed that eight out of ten plants were actively expressing the three transgenes. Real-time PCR was also done to quantify the mRNA expression levels of Cry1Ac and EPSP synthase gene. Finally, eight plants were confirmed for the presence and active expression of all three genes at T3 generation.

Keywords: Agriculture, Cotton, Transformation, Cry Genes, ELISA and PCR.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3074

Authors: Olga A. Berillo, Assel S. Issabekova, Anatoly T. Ivashchenko

Abstract:

MiRNAs participate in gene regulation of translation. Some studies have investigated the interactions between genes and intragenic miRNAs. It is important to study the miRNA binding sites of genes involved in carcinogenesis. RNAHybrid 2.1 and ERNAhybrid programmes were used to compute the hybridization free energy of miRNA binding sites. Of these 54 mRNAs, 22.6%, 37.7%, and 39.7% of miRNA binding sites were present in the 5'UTRs, CDSs, and 3'UTRs, respectively. The density of the binding sites for miRNAs in the 5'UTR ranged from 1.6 to 43.2 times and from 1.8 to 8.0 times greater than in the CDS and 3'UTR, respectively. Three types of miRNA interactions with mRNAs have been revealed: 5'- dominant canonical, 3'-compensatory, and complementary binding sites. MiRNAs regulate gene expression, and information on the interactions between miRNAs and mRNAs could be useful in molecular medicine. We recommend that newly described sites undergo validation by experimental investigation.

Keywords: Exon, intron, miRNA, oncogene.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1966

Authors: Patsaraporn Somboonsak, Mud-Armeen Munlin

Abstract:

In April 2009, a new variant of Influenza A virus subtype H1N1 emerged in Mexico and spread all over the world. The influenza has three subtypes in human (H1N1, H1N2 and H3N2) Types B and C influenza tend to be associated with local or regional epidemics. Preliminary genetic characterization of the influenza viruses has identified them as swine influenza A (H1N1) viruses. Nucleotide sequence analysis of the Haemagglutinin (HA) and Neuraminidase (NA) are similar to each other and the majority of their genes of swine influenza viruses, two genes coding for the neuraminidase (NA) and matrix (M) proteins are similar to corresponding genes of swine influenza. Sequence similarity between the 2009 A (H1N1) virus and its nearest relatives indicates that its gene segments have been circulating undetected for an extended period. Nucleic acid sequence Maximum Likelihood (MCL) and DNA Empirical base frequencies, Phylogenetic relationship amongst the HA genes of H1N1 virus isolated in Genbank having high nucleotide sequence homology. In this paper we used 16 HA nucleotide sequences from NCBI for computing sequence relationships similarity of swine influenza A virus using the following method MCL the result is 28%, 36.64% for Optimal tree with the sum of branch length, 35.62% for Interior branch phylogeny Neighber – Join Tree, 1.85% for the overall transition/transversion, and 8.28% for Overall mean distance.

Keywords: Sequence DNA, Relationship of swine, Swineinfluenza, Sequence Similarity

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2068

Authors: Amer A. Hasan, Mehri Igci, Ersin Borazan, Rozhgar A. Khailany, Emine Bayraktar, Ahmet Arslan

Abstract:

Gastric Cancer (GC) has high morbidity and fatality rate in various countries. It is still one of the most frequent and deadly diseases. Gastrokine1 (GKN1) and gastrokine2 (GKN2) genes are highly expressed in the normal stomach epithelium and play important roles in maintaining the integrity and homeostasis of stomach mucosal epithelial cells. In this study, 47 paired samples that were grouped according to the types of gastric cancer and the clinical characteristics of the patients, including gender and average of age. They were investigated with gene expression analysis and mutation screening by monitoring RT-PCR, SSCP and nucleotide sequencing techniques. Both GKN1 and GKN2 genes were observed significantly reduced found by (Wilcoxon signed rank test; p<0.05). As a result of gene screening, no mutation (no different genotype) was detected. It is considered that gene mutations are not the cause of gastrokines inactivation. In conclusion, the mRNA expression level of GKN1 and GKN2 genes statistically was decreased regardless the gender, age, or cancer type of patients. Reduced of gastrokine genes seem to occur at the initial steps of gastric cancer development.

Keywords: Diagnostic biomarker, gastric cancer, nucleotide sequencing, semi-quantitative RT-PCR.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1417

Authors: M. Farnush

Abstract:

This study is concerned with the microstructural analysis and improvement of wear resistance of 356 aluminum alloy by a high energy electron beam. Shock hardening on material by high energy electron beam improved wear resistance. Particularly, in the surface of material by shock hardening, the wear resistance was greatly enhanced to 29% higher than that of the 356 aluminum alloy substrate. These findings suggested that surface shock hardening using high energy electron beam irradiation was economical and useful for the development of surface shock hardening with improved wear resistance.

Keywords: Al356 alloy, HEEB, wear resistance, frictional characteristics.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1146

Authors: Frank Emmert Streib, Matthias Dehmer, Jing Liu, Max Mühlhauser

Abstract:

In this paper we present a method for gene ranking from DNA microarray data. More precisely, we calculate the correlation networks, which are unweighted and undirected graphs, from microarray data of cervical cancer whereas each network represents a tissue of a certain tumor stage and each node in the network represents a gene. From these networks we extract one tree for each gene by a local decomposition of the correlation network. The interpretation of a tree is that it represents the n-nearest neighbor genes on the n-th level of a tree, measured by the Dijkstra distance, and, hence, gives the local embedding of a gene within the correlation network. For the obtained trees we measure the pairwise similarity between trees rooted by the same gene from normal to cancerous tissues. This evaluates the modification of the tree topology due to progression of the tumor. Finally, we rank the obtained similarity values from all tissue comparisons and select the top ranked genes. For these genes the local neighborhood in the correlation networks changes most between normal and cancerous tissues. As a result we find that the top ranked genes are candidates suspected to be involved in tumor growth and, hence, indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, DNA microarray data, cancer.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1702

Authors: Alena Sicakova

Abstract:

Air-cooled Blast Furnace Slag Aggregate (BFSA) is usually referred to as a material providing for unique properties of concrete. On the other hand, negative influences are also presented in many aspects. The freeze-thaw resistance of concrete is dependent on many factors, including regional specifics and when a concrete mix is specified it is still difficult to tell its exact freeze-thaw resistance due to the different components affecting it. An important consideration in working with BFSA is the granularity and whether slag is sorted or not. The experimental part of the article represents a comparative testing of concrete using both the sorted and unsorted BFSA through the freeze-thaw resistance as an indicator of durability. Unsorted BFSA is able to be successfully used for concretes as they are specified for exposure class XF4 with providing that the type of cement is precisely selected.

Keywords: Blast furnace slag aggregate, concrete, freeze-thaw resistance.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2293

Authors: K. Kouzi

Abstract:

In order to have stable and high performance of direct torque and flux control (DTFC) of double star induction motor drive (DSIM), proper on-line adaptation of the stator resistance is very important. This is inevitably due to the variation of the stator resistance during operating conditions, which introduces error in estimated flux position and the magnitude of the stator flux. Error in the estimated stator flux deteriorates the performance of the DTFC drive. Also, the effect of error in estimation is very important especially at low speed. Due to this, our aim is to overcome the sensitivity of the DTFC to the stator resistance variation by proposing on-line fuzzy estimation stator resistance. The fuzzy estimation method is based on an on-line stator resistance correction through the variations of the stator current estimation error and its variations. The fuzzy logic controller gives the future stator resistance increment at the output. The main advantage of the suggested algorithm control is to avoid the drive instability that may occur in certain situations and ensure the tracking of the actual stator resistance. The validity of the technique and the improvement of the whole system performance are proved by the results.

Keywords: Direct torque control, dual stator induction motor, fuzzy logic estimation, stator resistance adaptation.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1116

Authors: Y. Li, K. Buddharaju, N. Singh, G. Q. Lo, S. J. Lee

Abstract:

Silicon nanowire (SiNW) based thermoelectric device (TED) has potential applications in areas such as chip level cooling/ energy harvesting. It is a great challenge however, to assemble an efficient device with these SiNW. The presence of parasitic in the form of interfacial electrical resistance will have a significant impact on the performance of the TED. In this work, we explore the effect of the electrical contact resistance on the performance of a TED. Numerical simulations are performed on SiNW to investigate such effects on its cooling performance. Intrinsically, SiNW individually without the unwanted parasitic effect has excellent cooling power density. However, the cooling effect is undermined with the contribution of the electrical contact resistance.

Keywords: Thermoelectric, silicon, nanowire, electrical contact resistance, parasitics.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2057

Authors: Marinka Baghdasaryan, Tigran Mnoyan

Abstract:

The pertinence of modeling the moment of resistance generated by the ore-grinding mill is substantiated. Based on the ranking of technological indices obtained in the result of the survey among the specialists of several beneficiating plants, the factors determining the level of the moment of resistance generated by the mill are revealed. A priori diagram of the ranks is obtained in which the factors are arranged in the descending order of the impact degree on the level of the moment. The obtained model of the moment of resistance shows the technological character of the operation modes of the ore-grinding mill and can be used for improving the operation modes of the system motor-mill and preventing the abnormal mode of the drive synchronous motor.

Keywords: Model, abnormal mode, mill, correlation, moment of resistance, rotational speed.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 935

Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

Abstract:

Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1968

Authors: Hsin-Ping Huang, Shyankay Jou

Abstract:

Resistive switching of aluminum nitride (AlN_x) thin film was demonstrated in a TaN/AlN_x/TiN memory cell that was prepared by sputter deposition techniques. The memory cell showed bipolar switching of resistance between +3.5 V and –3.5 V. The resistance ratio of high resistance state (HRS) to low resistance state (HRS), R_HRS/R_LRS, was about 2 over 100 cycles of endurance test. Both the LRS and HRS of the memory cell exhibited ohmic conduction at low voltages and Poole-Frenkel emission at high voltages. The electrical conduction in the TaN/AlN_x/TiN memory cell was possibly attributed to the interactions between charges and defects in the AlN_x film.

Keywords: Aluminum nitride, nonvolatile memory, resistive switching, thin films.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2642

Authors: S. A. Naeini, M. Ghorbani Tochaee

Abstract:

The aim of this study is to assess the influence of plastic fines content on sand-clay mixtures on maximum shear modulus and liquefaction resistance using a series of resonant column tests. A high plasticity clay called bentonite was added to 161 Firoozkooh sand at the percentages of 10, 15, 20, 25, 30 and 35 by dry weight. The resonant column tests were performed on the remolded specimens at constant confining pressure of 100 KPa and then the values of G_max and liquefaction resistance were investigated. The maximum shear modulus and cyclic resistance ratio (CRR) are examined in terms of fines content. Based on the results, the maximum shear modulus and liquefaction resistance tend to decrease within the increment of fine contents.

Keywords: Gmax, liquefaction, plastic fines, resonant column, sand-clay mixtures, bentonite.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 672

Authors: Mohd Shahriman B. Mohd Yunus, Mohd Hanif B. Jamaludin, Norain Bt. Bahror

Abstract:

The performance of an embedded grounding system is very important for the safe operation of electrical appliances and human beings. In principle, a safe grounding system has two objectives, which are to dissipate fault current without exceeding any operating and equipment limits and to ensure there is no risk of electric shock to humans in the vicinity of earthed facilities. The case studies in this paper present the calculating grounding resistance for multiple configurations of vertical and horizontally by using a simple and accurate formula. From the analytic calculated results, observed good/empirical relationship between the grounding resistance and length of the embedded grounding configurations. Moreover, the configurations of vertical and horizontal observed effectiveness of grounding resistance and good agreement on the reduction of grounding resistance values especially for vertical configuration.

Keywords: Grounding system, grounding resistance, soil resistivity, electrode geometry, configurations.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 424

Authors: Bo Meng, Wei Wang

Abstract:

Resistance of denial of service attacks is a key security requirement in voting protocols. Acquisti protocol plays an important role in development of internet voting protocols and claims its security without strong physical assumptions. In this study firstly Acquisti protocol is modeled in extended applied pi calculus, and then resistance of denial of service attacks is proved with ProVerif. The result is that it is not resistance of denial of service attacks because two denial of service attacks are found. Finally we give the method against the denial of service attacks.

Keywords: Applied pi calculus, protocol state, symbolic model, availability.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1212

Authors: Cheng-Hong Yang, Tsung-Mu Shih, Li-Yeh Chuang

Abstract:

Serial Analysis of Gene Expression is a powerful quantification technique for generating cell or tissue gene expression data. The profile of the gene expression of cell or tissue in several different states is difficult for biologists to analyze because of the large number of genes typically involved. However, feature selection in machine learning can successfully reduce this problem. The method allows reducing the features (genes) in specific SAGE data, and determines only relevant genes. In this study, we used a genetic algorithm to implement feature selection, and evaluate the classification accuracy of the selected features with the K-nearest neighbor method. In order to validate the proposed method, we used two SAGE data sets for testing. The results of this study conclusively prove that the number of features of the original SAGE data set can be significantly reduced and higher classification accuracy can be achieved.

Keywords: Serial Analysis of Gene Expression, Feature selection, Genetic Algorithm, K-nearest neighbor method.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1566

Authors: Helyane Bronoski Borges, Júlio Cesar Nievola

Abstract:

The most important subtype of non-Hodgkin-s lymphoma is the Diffuse Large B-Cell Lymphoma. Approximately 40% of the patients suffering from it respond well to therapy, whereas the remainder needs a more aggressive treatment, in order to better their chances of survival. Data Mining techniques have helped to identify the class of the lymphoma in an efficient manner. Despite that, thousands of genes should be processed to obtain the results. This paper presents a comparison of the use of various attribute selection methods aiming to reduce the number of genes to be searched, looking for a more effective procedure as a whole.

Keywords: Attribute selection, data mining.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1370

Authors: M. Marjaneh, M. Y. Narazah, H. Shahrul

Abstract:

Array-based gene expression analysis is a powerful tool to profile expression of genes and to generate information on therapeutic effects of new anti-cancer compounds. Anti-apoptotic effect of thymoquinone was studied in MCF7 breast cancer cell line using gene expression profiling with cDNA microarray. The purity and yield of RNA samples were determined using RNeasyPlus Mini kit. The Agilent RNA 6000 NanoLabChip kit evaluated the quantity of the RNA samples. AffinityScript RT oligo-dT promoter primer was used to generate cDNA strands. T7 RNA polymerase was used to convert cDNA to cRNA. The cRNA samples and human universal reference RNA were labelled with Cy-3-CTP and Cy-5-CTP, respectively. Feature Extraction and GeneSpring softwares analysed the data. The single experiment analysis revealed involvement of 64 pathways with up-regulated genes and 78 pathways with downregulated genes. The MAPK and p38-MAPK pathways were inhibited due to the up-regulation of PTPRR gene. The inhibition of p38-MAPK suggested up-regulation of TGF-ß pathway. Inhibition of p38-MAPK caused up-regulation of TP53 and down-regulation of Bcl2 genes indicating involvement of intrinsic apoptotic pathway. Down-regulation of CARD16 gene as an adaptor molecule regulated CASP1 and suggested necrosis-like programmed cell death and involvement of caspase in apoptosis. Furthermore, down-regulation of GPCR, EGF-EGFR signalling pathways suggested reduction of ER. Involvement of AhR pathway which control cytochrome P450 and glucuronidation pathways showed metabolism of Thymoquinone. The findings showed differential expression of several genes in apoptosis pathways with thymoquinone treatment in estrogen receptor-positive breast cancer cells.

Keywords: CARD16, CASP10, cDNA microarray, PTPRR, Thymoquinone.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2235

Authors: A. Nusrath Unissa, Sameer Hassan, Luke Elizabeth Hanna

Abstract:

Altered drug binding may be an important factor in isoniazid (INH) resistance, rather than major changes in the enzyme’s activity as a catalase or peroxidase (KatG). The identification of structural or functional defects in the mutant KatGs responsible for INH resistance remains as an area to be explored. In this connection, the differences in the binding affinity between wild-type (WT) and mutants of KatG were investigated, through the generation of three mutants of KatG, Ser315Thr [S315T], Ser315Asn [S315N], Ser315Arg [S315R] and a WT [S315]) with the help of software-MODELLER. The mutants were docked with INH using the software-GOLD. The affinity is lower for WT than mutant, suggesting the tight binding of INH with the mutant protein compared to WT type. These models provide the in silico evidence for the binding interaction of KatG with INH and implicate the basis for rationalization of INH resistance in naturally occurring KatG mutant strains of Mycobacterium tuberculosis.

Keywords: Mycobacterium tuberculosis, KatG, INH resistance, Mutants, Modeling, Docking.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2934

Authors: A. Ameur, B. Mokhtari, N. Essounbouli, L. Mokrani

Abstract:

This paper presents a speed sensorless direct torque control scheme using space vector modulation (DTC-SVM) for permanent magnet synchronous motor (PMSM) drive based a Model Reference Adaptive System (MRAS) algorithm and stator resistance estimator. The MRAS is utilized to estimate speed and stator resistance and compensate the effects of parameter variation on stator resistance, which makes flux and torque estimation more accurate and insensitive to parameter variation. In other hand the use of SVM method reduces the torque ripple while achieving a good dynamic response. Simulation results are presented and show the effectiveness of the proposed method.

Keywords: MRAS, PMSM, SVM, DTC, Speed and Resistance estimation, Sensorless drive

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3807

Authors: Delly C. Lestari, Linosefa, Ardiana Kusumaningrum, Andi Yasmon, Anis Karuniawati

Abstract:

The objective of this study is to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) harboring mecA genes from screening isolates among intensive care unit (ICU) patients. All MRSA screening isolates from ICU’s patients of Cipto Mangunkusumo Hospital during 2011 and 2014 were included in this study. Identification and susceptibility test was performed using Vitek2 system (Biomereux®). PCR was conducted to characterize the SCCmec of S. aureus harboring the mecA gene on each isolate. Patient’s history of illness was traced through medical record. 24 isolates from 327 screening isolates were MRSA positive (7.3%). From PCR, we found 17 (70.8%) isolates carrying SCCmec type I, 3 (12.5%) isolates carrying SCCmec type III, and 2 (8.3%) isolates carrying SCCmec type IV. In conclusion, SCCmec type I is the most prevalent MRSA colonization among ICU patients in Cipto Mangunkusumo Hospital.

Keywords: MRSA, mecA genes, ICU, colonization.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1132

Authors: Sergey M. Karabanov, Dmitry V. Suvorov

Abstract:

Magnetically controlled microelectromechanical system (MCMEMS) switches is one of the directions in the field of micropower switching technology. MCMEMS switches are a promising alternative to Hall sensors and reed switches. The most important parameter for MCMEMS is the contact resistance, which should have a minimum value and is to be stable for the entire duration of service life. The value and stability of the contact resistance is mainly determined by the contact coating material. This paper presents the research results of a contact coating based on nanoscale ruthenium films obtained by electrolytic deposition. As a result of the performed investigations, the deposition modes of ruthenium films are chosen, the regularities of the contact resistance change depending on the number of contact switching, and the coating roughness are established. It is shown that changing the coating roughness makes it possible to minimize the contact resistance.

Keywords: Contact resistance, electrode coating, electrolythic deposition, magnetically controlled MEMS.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 767

Authors: A. Shukla, A. Tarsauliya, R. Tiwari, S. Sharma

Abstract:

Cancer classification to their corresponding cohorts has been key area of research in bioinformatics aiming better prognosis of the disease. High dimensionality of gene data has been makes it a complex task and requires significance data identification technique in order to reducing the dimensionality and identification of significant information. In this paper, we have proposed a novel approach for classification of oral cancer into metastasis positive and negative patients. We have used significance analysis of microarrays (SAM) for identifying significant genes which constitutes gene signature. 3 different gene signatures were identified using SAM from 3 different combination of training datasets and their classification accuracy was calculated on corresponding testing datasets using k-Nearest Neighbour (kNN), Fuzzy C-Means Clustering (FCM), Support Vector Machine (SVM) and Backpropagation Neural Network (BPNN). A final gene signature of only 9 genes was obtained from above 3 individual gene signatures. 9 gene signature-s classification capability was compared using same classifiers on same testing datasets. Results obtained from experimentation shows that 9 gene signature classified all samples in testing dataset accurately while individual genes could not classify all accurately.

Keywords: Cancer, Gene Signature, SAM, Classification.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2028

Authors: G. B. Singh, S. Srivastava, N. Gupta

Abstract:

In the present work we report a gram negative bacterial isolate, from soil of a dye industry, with promising biorefining and bioremediation potential. This isolate (GBS.5) could utilize carbazole (nitrogen containing polycyclic aromatic hydrocarbon) as the sole source of nitrogen and carbon and utilize almost 98% of 3mM carbazole in 100 hours. The specific activity of our GBS.5 isolate for carbazole degradation at 30°C and pH 7.0 was found to be 11.36 μmol/min/g dry cell weight as compared to 10.4 μmol/min/g dry cell weight, the highest reported specific activity till date. The presence of car genes (the genes involved in denitrogenation of carbazole) was confirmed through PCR amplification.

Keywords: Biodenitrogenation, Biorefining, Carbazoledegradation, Crude oil.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1906

Authors: Jafar Ahmadi, Alireza Pour-Aboughadareh

Abstract:

Wheat is the first and the most important grain of the world and its bakery property is due to glutenin and gliadin qualities. Wheat seed proteins were divided into four groups according to solubility including albumin, globulin, glutenin and prolamin or gliadin. Gliadins are major components of the storage proteins in wheat endosperm. It seems that little information is available about gliadin genes in Iranian wild relatives of wheat. Thus, the aim of this study was the evaluation of the wheat wild relatives collected from different origins of Zagros Mountains in Iran, in terms of coding gliadin genes using specific primers. For this, forty accessions of Triticum boeoticum and Triticum urartu were selected for this study. For each accession, genomic DNA was extracted and PCRs were performed in total volumes of 15 μl. The amplification products were separated on 1.5% agarose gels. In results, for Gli-2A locus three allelic variants were detected by Gli-2As primer pairs. The sizes of PCR products for these alleles were 210, 490 and 700 bp. Only five (13%) and two accessions (5%) produced 700 and 490 bp fragments when their DNA was amplified with the Gli.As.2 primer pairs. However, 93% of the accessions carried allele 210 bp, and only 8% did not any product for this marker. Therefore, these germplasm could be used as rich gene pool to broaden the genetic base of bread wheat.

Keywords: Diploied wheat, gliadin, Triticum boeoticum, Triticum urartu.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1908