Search results for: gene frequency

Authors: Onur Potok, Deniz Deger, Kemal Ulutas, Sahin Yakut, Deniz Bozoglu

Abstract:

Thalium Selenide (TlSe) is used for optoelectronic devices, pressure sensitive detectors, and gamma-ray detectors. The TlSe samples were grown as large single crystals using the Stockbarger-Bridgman method. The thin films, in the form of Al/TlSe/Al, were deposited on the microscope slide in different thicknesses (300-3000 Å) using thermal evaporation technique at 10-5 Torr. The dielectric properties of (TlSe) thin films, capacitance (C) and dielectric loss factor (tanδ), were measured in a frequency range of 10-105 Hz, and temperatures between 213K and 393K via Broadband Dielectric Spectroscopy analyzer. The dielectric constant (ε’) and the dielectric loss (ε’’) of the thin films were derived from measured parameters (C and tanδ). These results showed that the dielectric properties of TlSe thin films are frequency and temperature dependent. The capacitance and the dielectric constant decrease with increasing frequency and decreasing temperature. The dielectric loss of TlSe thin films decreases with increasing frequency, on the other hand, they increase with increasing temperature and increasing thicknesses. There is two relaxation region in the investigated frequency and temperature interval. These regions can be called as low and high-frequency dispersion regions. Low-frequency dispersion region can be attributed to the polarization of the main part of the chain structure of TlSe while high-frequency dispersion region can be attributed to the polarization of side parts of the structure.

Keywords: thin films, thallium selenide, dielectric spectroscopy, binary compounds

Procedia PDF Downloads 139

Authors: Vinod Kumar Gupta, Narendrakumar M. Chaudhari, Suchismitha Iskepalli, Chitra Dutta

Abstract:

Background-The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference draft genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium. Results-The analysis reveals the exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from the human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. The pan-genome for Prevotella remains “open”. Distribution of various functional COG categories differs appreciably among the habitat-specific genes, within Prevotella pan-genome and between the GIT-derived Bacteroides and Prevotella. The skin and GIT isolates of Prevotella are enriched in singletons involved in Signal transduction mechanisms, while the UGT and oral isolates show higher representation of the Defense mechanisms category. No niche-specific variations could be observed in the distribution of KEGG pathways. Conclusion-Prevotella may have developed distinct genetic strategies for adaptation to different anatomical habitats through selective, niche-specific acquisition and elimination of suitable gene-families. In addition, individual microorganisms tend to develop their own distinctive adaptive stratagems through large repertoires of singletons. Such in situ, habitat-driven refurbishment of the genetic makeup can impart substantial intra-lineage genome diversity within the microbes without perturbing their general taxonomic heritage.

Keywords: body niche adaptation, human microbiome, pangenome, Prevotella

Procedia PDF Downloads 240

Authors: Yahia Massinissa, Yahia Mouloud

Abstract:

Cystic fibrosis (CF), the most common lethal genetic disease in the Europe population, is caused by mutations in the transmembrane conductance regulator gene (CFTR). It affects most organs including an epithelial tissue, base of hydroelectrolytic transepithelial transport, notably that aerial ways, the pancreas, the biliary ways, the intestine, sweat glands and the genital tractus. The gene whose anomalies are responsible of the cystic fibrosis codes for a protein Cl channel named CFTR (cystic fibrosis transmembrane conductance regulator) that exercises multiple functions in the cell, one of the most important in control of sodium and chlorine through epithelia. The deficient function translates itself notably by an abnormal production of viscous secretion that obstructs the execrator channels of this target organ: one observes then a dilatation, an inflammation and an atrophy of these organs. It also translates itself by an increase of the concentration in sodium and in chloride in sweat, to the basis of the sweat test. In order to do a phenotypical and genotypical diagnosis at a part of the Algerian population, our survey has been carried on 16 patients with evocative symptoms of the cystic fibrosis at that the clinical context has been confirmed by a sweat test. However, anomalies of the CFTR gene have been determined by electrophoresis in gel of polyacrylamide of the PCR products (polymerase chain reaction), after enzymatic digestion, then visualized to the ultraviolet (UV) after action of the ethidium bromide. All mutations detected at the time of our survey have already been identified at patients attained by this pathology in other populations of the world. However, the important number of found mutation with regard to the one of the studied patients testifies that the origin of this big clinical variability that characterizes the illness in the consequences of an enormous diversity of molecular defects of the CFTR gene.

Keywords: cystic fibrosis, CFTR gene, polymorphism, algerian population, sweat test, genotypical diagnosis

Procedia PDF Downloads 296

Authors: H. Nabaei, M. Joghataie

Abstract:

In this article, we study the design methods of matched filter with commercial software including CST Studio and ADS in specific frequency: 900 MHz. At first, we select two amounts of impedance for studying matching of them. Then, using by matched filter utility tool in ADS software, we simulate and deviate the elements of matched filters. In the following, we implement matched filter in CST STUDIO software. The simulated results show the great conformity in this field. Also, we peruse scattering and Impedance parameters in the Derivative structure. Finally, the layout of matched filter is obtained by the schematic tool of CST STUDIO. In fact, here, we present the design process of matched filters in the specific frequency.

Keywords: impedance matching, lumped element, transmission line, maximum power transmission, 3D layout

Procedia PDF Downloads 482

Authors: Maryam Monazzah, Ronak Samadpour, Mehdi Nasr-esfahani, Fatemeh Qalavand, Marziye Motamedi

Abstract:

Bipolaris sorokiniana, and Heterodera filipjevi, are important wheat diseases that lead to yield losses worldwide. Identifying novel resistant sources helps us combat these devastating diseases. In this study, we studied the role of Cre3 gene and antioxidant enzymes in the immune responses of wheat genotypes to H. filipjevi and B. sorokiniana. Therefore, real-time PCR analysis using Cre3 gene marker, a resistant gene to cereal cyst nematodes, was conducted on leaves and roots, along with changes ‎in the activity of antioxidant enzymes, peroxidase, and catalase. Enzyme activity assay was performed on roots attacked by nematode and in leaves infected with Bipolaris. Wheat accessions including “Bam” (resistant), “Parsi” (moderately-resistant), “Azar2”, “Ohadi”, “Homa” (highly-susceptible) were previously screened against both stresses under greenhouse and field conditions. Results showed that Cre3 expression against cyst nematodes was significantly higher in resistant cultivars compared to susceptible cultivars. Cre3 was used in marker-assisted selection programs to identify genotypes carrying resistant genes to cyst nematodes. Interestingly, Cre3 was also up-regulated in both tissues of resistant cultivars to B. sorokiniana. Therefore, Cre3 in wheat similarly modulates immunity against B. sorokiniana and might be one of the central components of the induced immune system in wheat. The activity of antioxidant enzymes also indicated the highest increase in resistant genotypes upon both stresses that subsequently neutralize oxidative stress in tissues and decrease damage. Further studies on these resistance components may help us gain insight into the molecular basis of resistance and shed new light on the interaction and overlap between different forms of stress.

Keywords: Bipolaris sorokiniana, Heterodera filipjevi, resistant gene expression, wheat

Procedia PDF Downloads 77

Authors: M. Abou Al-alaa, H. A. Elsadek, E. A. Abdallah, E. A. Hashish

Abstract:

A square patch antenna with both frequency and polarization reconfigurability is presented. The antenna consists of a square patch with coplanar feed on the ground plane. On the patch side, there is a parasitic square ring that is responsible for changing the antenna polarization. On the ground plane, there is a rectangular slot. By changing of length of this slot, the antenna resonance frequency can be changed. The antenna operates at 1.57 and 2.45 GHz that used in GPS and Bluetooth applications, respectively. The length of the slot in the proposed antenna is 40 mm, and the antenna operates at the lower frequency (1.57 GHz). By using switches in the ground plane the slot length can be adjust to 24 mm, so the antenna operates at upper frequency (2.45 GHz). Two switches are mounted on the parasitic ring at optimized positions. By switching between the different states of these two switches, the proposed antenna operates with linear polarization (LP) and circular polarization (CP) at each operating frequency. The antenna gain at 1.57 and 2.45 GHz are 5.9 and 7.64 dBi, respectively. The antenna is analyzed using the CST Microwave Studio. The proposed antenna was fabricated and measured. Results comparison shows good agreement. The antenna has applications in several wireless communication systems.

Keywords: microstrip patch antenna, reconfigurable antenna, frequency reconfigurability, polarization reconfigurability, parasitic square ring, linear polarization, circular polarization

Procedia PDF Downloads 514

Authors: Min Dai, Hong Liu, Shuaijie Qian

Abstract:

We study a portfolio selection problem of an investor who faces constraints on rebalancing frequency, which is common in pension fund investment. We formulate it as a multiple optimal stopping problem and utilize the dynamic programming principle. By numerically solving the corresponding Hamilton-Jacobi-Bellman (HJB) equation, we find a series of free boundaries characterizing optimal strategy, and the constraints significantly impact the optimal strategy. Even in the absence of transaction costs, there is a no-trading region, depending on the number of the remaining trading chances. We also find that the equivalent wealth loss caused by the constraints is large. In conclusion, our model clarifies the impact of the constraints on transaction frequency on the optimal strategy.

Keywords: portfolio selection, rebalancing frequency, optimal strategy, free boundary, optimal stopping

Procedia PDF Downloads 69

Authors: Yong Chen

Abstract:

To understand the detailed molecular mechanisms of memory formation in engram cells is one of the most fundamental questions in neuroscience. Recent single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) techniques have allowed us to explore the sparsely activated engram ensembles, enabling access to the molecular mechanisms that underlie experience-dependent memory formation and consolidation. However, the absence of specific and powerful computational methods to detect memory-related genes (modules) and their regulatory relationships in the sc/snRNA-seq datasets has strictly limited the analysis of underlying mechanisms and memory coding principles in mammalian brains. Here, we present a deep-learning method named SCENTBOX, to detect memory-related gene modules and causal regulatory relationships among themfromsc/snRNA-seq datasets. SCENTBOX first constructs codifferential expression gene network (CEGN) from case versus control sc/snRNA-seq datasets. It then detects the highly correlated modules of differential expression genes (DEGs) in CEGN. The deep network embedding and attention-based convolutional neural network strategies are employed to precisely detect regulatory relationships among DEG genes in a module. We applied them on scRNA-seq datasets of TRAP; Ai14 mouse neurons with fear memory and detected not only known memory-related genes, but also the modules and potential causal regulations. Our results provided novel regulations within an interesting module, including Arc, Bdnf, Creb, Dusp1, Rgs4, and Btg2. Overall, our methods provide a general computational tool for processing sc/snRNA-seq data from case versus control studie and a systematic investigation of fear-memory-related gene modules.

Keywords: sc/snRNA-seq, memory formation, deep learning, gene module, causal inference

Procedia PDF Downloads 110

Authors: Junaid Kameran Ahmed

Abstract:

A laminated plate composite of graphite/epoxy has been analyzed dynamically in the present work by using a quadratic element (8-node diso-parametric), and by depending on 1^st order shear deformation theory, every node in this element has 6-degrees of freedom (displacement in x, y, and z axis and twist about x, y, and z axis). The dynamic analysis in the present work covered parametric studies on a composite laminated plate (square plate) to determine its effect on the natural frequency of the plate. The parametric study is represented by set of changes (plate thickness, number of layers, support conditions, layer orientation), and the plates have been simulated by using ANSYS package 12. The boundary conditions considered in this study, at all four edges of the plate, are simply supported and fixed boundary condition. The results obtained from ANSYS program show that the natural frequency for both fixed and simply supported increases with increasing the number of layers, but this increase in the natural frequency for the first five modes will be neglected after 10 layers. And it is observed that the natural frequency of a composite laminated plate will change with the change of ply orientation, the natural frequency increases and it will be at maximum with angle 45 of ply for simply supported laminated plate, and maximum natural frequency will be with cross-ply (0/90) for fixed laminated composite plate. It is also observed that the natural frequency increase is approximately doubled when the thickness is doubled.

Keywords: laminated plate, orthotropic plate, square plate, natural frequency (free vibration), composite (graphite / epoxy)

Procedia PDF Downloads 329

Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

Abstract:

Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

Procedia PDF Downloads 466

Authors: Ahmad Ali Shahid, Mukhtar Ahmed

Abstract:

The demand for long staple fiber having better strength and length is increasing with the introduction of modern spinning and weaving industry in Pakistan. Work on gene discovery from developing cotton fibers has helped to identify dozens of genes that take part in cotton fiber development and several genes have been characterized for their role in fiber development. Sucrose synthase (SuS) is a key enzyme in the metabolism of sucrose in a plant cell, in cotton fiber it catalyzes a reversible reaction, but preferentially converts sucrose and UDP into fructose and UDP-glucose. UDP-glucose (UDPG) is a nucleotide sugar act as a donor for glucose residue in many glycosylation reactions and is essential for the cytosolic formation of sucrose and involved in the synthesis of cell wall cellulose. The study was focused on successful Agrobacterium-mediated stable transformation of SuS gene in pCAMBIA 1301 into cotton under a CaMV35S promoter. Integration and expression of the gene were confirmed by PCR, GUS assay, and real-time PCR. Young leaves of SuS overexpressing lines showed increased total soluble sugars and plant biomass as compared to non-transgenic control plants. Cellulose contents from fiber were significantly increased. SEM analysis revealed that fibers from transgenic cotton were highly spiral and fiber twist number increased per unit length when compared with control. Morphological data from field plants showed that transgenic plants performed better in field conditions. Incorporation of genes related to cotton fiber length and quality can provide new avenues for fiber improvement. The utilization of this technology would provide an efficient import substitution and sustained production of long-staple fiber in Pakistan to fulfill the industrial requirements.

Keywords: agrobacterium-mediated transformation, cotton fiber, sucrose synthase gene, staple length

Procedia PDF Downloads 219

Authors: J. H. Kim, J. H. Kwon, J. S. Park, K. J. Lim

Abstract:

This paper has investigated a technique that predicts the performance of a bar-type unimorph piezoelectric vibration actuator depending on the frequency. This paper has been proposed an equivalent circuit that can be easily analyzed for the bar-type unimorph piezoelectric vibration actuator. In the dynamic analysis, rigidity and resonance frequency, which are important mechanical elements, were derived using the basic beam theory. In the equivalent circuit analysis, the displacement and bandwidth of the piezoelectric vibration actuator depending on the frequency were predicted. Also, for the reliability of the derived equations, the predicted performance depending on the shape change was compared with the result of a finite element analysis program.

Keywords: actuator, piezoelectric, performance, unimorph

Procedia PDF Downloads 454

Authors: Islem Kedidi, Rihab Bedoui Bensalem, Faysal Manssouri

Abstract:

In traditional models of insurance data, the number and size of claims are assumed to be independent. Relaxing the independence assumption, this article explores the Vine copula to model dependence structure between multivariate frequency and average severity of insurance claim. To illustrate this approach, we use the Wisconsin local government property insurance fund which offers several insurance protections for motor vehicles, property and contractor’s equipment claims. Results show that the C-vine copula can better characterize the multivariate dependence structure between frequency and severity. Furthermore, we find significant dependencies especially between frequency and average severity among different coverage types.

Keywords: dependency modeling, government insurance, insurance claims, vine copula

Procedia PDF Downloads 191

Authors: Neda Menbari, Ramin Mehdiabadi

Abstract:

Background: breast cancer remains a critical global health issue, constituting a leading cause of cancer-related mortality in women. MicroRNAs (miRs) are natural RNA molecules that play an important role in cellular processes and regulate post-transcriptional gene expression. MiR-216b-5p is a miR that acts as a tumor suppressor. The expression levels of FoxM1 and miR-216b-5p in malignant and control cells have been evaluated by quantitative polymerase chain reaction (qPCR) technique and flow cytometry. Results: the results of this study revealed a significant downregulation of miR-216b-5p in cancerous cells compared to the control MCF-10A cells (P=0.0004). Interestingly, the expression of miR-216b-5p exhibited an inverse relationship with key clinical indicators such as tumor size, grade, and lymph node invasion. Conclusion: The study's findings showed the prognostic value of miR-216b-5p levels in breast cancer, and its reduced expression correlates with unfavorable tumor characteristics. This research recommends performing more studies on the role of FoxM1 and miR-216b-5p in breast cancer pathology which potentially paving the way for targeted therapeutic interventions.

Keywords: breast cancer, gene expression, FOXM1, microRNA

Procedia PDF Downloads 33

Authors: A. N. Dagang, E. I. Ismail, Z. Zakaria

Abstract:

This paper presents the analysis on the performance of monopole antenna with fluorescent tubes. In this research, the simulation and experimental approach is conducted. The fluorescent tube with different length and size is designed using Computer Simulation Technology (CST) software and the characteristics of antenna parameter are simulated throughout the software. CST was used to simulate antenna parameters such as return loss, resonant frequency, gain and directivity. Vector Network Analyzer (VNA) was used to measure the return loss of plasma antenna in order to validate the simulation results. In the simulation and experiment, the supply frequency is set starting from 1 GHz to 10 GHz. The results show that the return loss of plasma antenna changes when size of fluorescent tubes is varied, correspond to the different plasma properties. It shows that different values of plasma properties such as plasma frequency and collision frequency gives difference result of return loss, gain and directivity. For the gain, the values range from 2.14 dB to 2.36 dB. The return loss of plasma antenna offers higher value range from -22.187 dB to -32.903 dB. The higher the values of plasma frequency and collision frequency, the higher return loss can be obtained. The values obtained are comparative to the conventional type of metal antenna.

Keywords: plasma antenna, fluorescent tube, CST, plasma parameters

Procedia PDF Downloads 378

Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

Abstract:

Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

Procedia PDF Downloads 410

Authors: K. H. Reeta, Bhavana Prasher, Mitali Mukerji, Dhwani Dholakia, Sangeeta Khanna, Archana Vats, Shivam Pandey, Sandeep Seth, Subir Kumar Maulik

Abstract:

Introduction Research has demonstrated a connection between coronary artery disease (CAD) and genetics. We did a deep literature mining using both bioinformatics and manual efforts to identify the susceptible polymorphisms in coronary artery disease. Further, the study sought to validate these findings in an Asian population. Methodology In first phase, we used an automated pipeline which organizes and presents structured information on SNPs, Population and Diseases. The information was obtained by applying Natural Language Processing (NLP) techniques to approximately 28 million PubMed abstracts. To accomplish this, we utilized Python scripts to extract and curate disease-related data, filter out false positives, and categorize them into 24 hierarchical groups using named Entity Recognition (NER) algorithms. From the extensive research conducted, a total of 466 unique PubMed Identifiers (PMIDs) and 694 Single Nucleotide Polymorphisms (SNPs) related to coronary artery disease (CAD) were identified. To refine the selection process, a thorough manual examination of all the studies was carried out. Specifically, SNPs that demonstrated susceptibility to CAD and exhibited a positive Odds Ratio (OR) were selected, and a final pool of 324 SNPs was compiled. The next phase involved validating the identified SNPs in DNA samples of 96 CAD patients and 37 healthy controls from Indian population using Global Screening Array. ResultsThe results exhibited out of 324, only 108 SNPs were expressed, further 4 SNPs showed significant difference of minor allele frequency in cases and controls. These were rs187238 of IL-18 gene, rs731236 of VDR gene, rs11556218 of IL16 gene and rs5882 of CETP gene. Prior researches have reported association of these SNPs with various pathways like endothelial damage, susceptibility of vitamin D receptor (VDR) polymorphisms, and reduction of HDL-cholesterol levels, ultimately leading to the development of CAD. Among these, only rs731236 had been studied in Indian population and that too in diabetes and vitamin D deficiency. For the first time, these SNPs were reported to be associated with CAD in Indian population. Conclusion: This pool of 324 SNP s is a unique kind of resource that can help to uncover risk associations in CAD. Here, we validated in Indian population. Further, validation in different populations may offer valuable insights and contribute to the development of a screening tool and may help in enabling the implementation of primary prevention strategies targeted at the vulnerable population.

Keywords: coronary artery disease, single nucleotide polymorphism, susceptible SNP, bioinformatics

Procedia PDF Downloads 62

Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

Abstract:

Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max, and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, brassinosteroids, phylogenetic analysis, transcription factor

Procedia PDF Downloads 326

Authors: Ceyda Okudu, Secil Eroglu, Khandakar A. S. M. Saadat, Sibel O. Balci

Abstract:

Ring Finger Protein 2 (RNF2) is a member of polycomb repressive complex 1 (PRC1), which is one of the epigenetic regulators in the genome. When RNF2 combines with other PRC1 members, it mediates the mono-ubiquitination of Histon2A (H2A). In breast cancer, RNF2 is commonly overexpressed, and also it promotes metastasis and invasion in other aggressive tumors like melanoma, prostate, and hepatocarcinoma. The role of RNF2 in the metastasis and invasion of breast cancer has not yet been elucidated. Our aim is to observe the role of RNF2 in metastasis and invasion in this study by miRNA mediated RNF2 gene silencing in breast cancer cell lines. We selected miRNAs, targeting to RNF2 by searching online databases. miR-17-5p, miR20a-5p, and miR-106b-5p were transfected to breast cancer cell lines (MCF-7, MDA-MB-231, SK-BR-3, and ZR-75-1), and also we used normal breast epithelial cell line (hTERT-HME1) to compare RNF2 gene expression level. After 48-72 hours post-transfection, mRNAs were isolated from the cells, and gene expressions were measured by RT-qPCR after from cDNA syntheses. We observed that RNF2 was highly expressed in SK-BR-3 and MDA-MB-231 cell lines opposite to MCF-7 and ZR-75-1 cell lines. RNF2 was downregulated 5, 5 and 7 fold by miR17-5p, miR20a-5p and miR106b-5p respectively in MCF-7. However, in SK-BR-3 and ZR-75-1 cell lines, miRNAs did not affect significantly RNF2 gene expression level. miR20a-5p decreased RNF2 3 fold and miR17-5p and miR106b-5p did not affect MDA-MB-231. After gene expression analysis, we performed metastasis and invasion assay in MCF-7 cells. For metastasis, we used both wound healing assay and Transwell Cell Migration Assay, and we used Transwell Cell Invasion Assay for invasion. The data of this assay showed that miR17-5p and miR20a-5p decreased both invasion and metastasis level, but miR106b-5p has no effect. We would like to conclude that RNF2 can be targeted by miR17-5p, miR20a-5p and miR106b-5p in MCF-7 cells and also RNF2, which is one of the upregulated genes in aggressive tumor, can be decreased by using these miRNAs. In future, we would like to confirm these results at the protein level and also whether these miRNAs are direct target of RNF2 or not.

Keywords: breast cancer, epigenetic, microRNAs, RNF2

Procedia PDF Downloads 164

Authors: Ahmad H. Abdelgwad, Galal E. Nadim, Tarek M. Said, Amr M. Gody

Abstract:

The prime objective of this manuscript is to provide intensive review of the techniques used for permittivity measurements. The measurement techniques, relevant for any desired application, rely on the nature of the measured dielectric material, both electrically and physically, the degree of accuracy required, and the frequency of interest. Regardless of the way that distinctive sorts of instruments can be utilized, measuring devices that provide reliable determinations of the required electrical properties including the obscure material in the frequency range of interest can be considered. The challenge in making precise dielectric property or permittivity measurements is in designing of the material specimen holder for those measurements (RF and MW frequency ranges) and adequately modeling the circuit for reliable computation of the permittivity from the electrical measurements. If the RF circuit parameters such as the impedance or admittance are estimated appropriately at a certain frequency, the material’s permittivity at this frequency can be estimated by the equations which relate the way in which the dielectric properties of the material affect on the parameters of the circuit.

Keywords: dielectric permittivity, free space measurement, waveguide techniques, coaxial probe, cavity resonator

Procedia PDF Downloads 357

Authors: Yekta Ülgen, Fırat Matur

Abstract:

Cole-Cole parameters of 40 post-menopausal women are compared with their DEXA bone mineral density measurements. Impedance characteristics of four extremities are compared; left and right extremities are statistically same, but lower extremities are statistically different than upper ones due to their different fat content. The correlation of Cole-Cole impedance parameters to bone mineral density (BMD) is observed to be higher for a dominant arm. With the post menopausal population, ANOVA tests of the dominant arm characteristic frequency, as a predictor for DEXA classified osteopenic and osteoporotic population around the lumbar spine, is statistically very significant. When used for total lumbar spine osteoporosis diagnosis, the area under the Receiver Operating Curve of the characteristic frequency is 0.875, suggesting that the Cole-Cole plot characteristic frequency could be a useful diagnostic parameter when integrated into standard screening methods for osteoporosis. Moreover, the characteristic frequency can be directly measured by monitoring frequency driven the angular behavior of the dominant arm without performing any complex calculation.

Keywords: bioimpedance spectroscopy, bone mineral density, osteoporosis, characteristic frequency, receiver operating curve

Procedia PDF Downloads 511

Authors: S. Mohamed Rabeek, Mi Kyoung Park, M. Annamalai Arasu

Abstract:

This paper presents a design of a wireless read out system for tracking the frequency shift of the polymer coated piezoelectric micro electromechanical resonator due to gas absorption. The measure of this frequency shift indicates the percentage of a particular gas the sensor is exposed to. It is measured using an oscillator and an FPGA based frequency counter by employing the resonator as a frequency determining element in the oscillator. This system consists of a Gas Sensing Wireless Readout (GSWR) and an USB Wireless Transceiver (UWT). GSWR consists of an oscillator based on a trans-impedance sustaining amplifier, an FPGA based frequency readout, a sub 1GHz wireless transceiver and a micro controller. UWT can be plugged into the computer via USB port and function as a wireless module to transfer gas sensor data from GSWR to the computer through its USB port. GUI program running on the computer periodically polls for sensor data through UWT - GSWR wireless link, the response from GSWR is logged in a file for post processing as well as displayed on screen.

Keywords: gas sensor, GSWR, micromechanical system, UWT, volatile emissions

Procedia PDF Downloads 474

Authors: Dana Gabriková, Martin Mistrík, Jarmila Bernasovská, Iveta Tóthová, Jana Kisková

Abstract:

The Roma (Gypsies) is a transnational minority with a high degree of consanguineous marriages. Similar to other genetically isolated founder populations, the Roma harbor a number of unique or rare genetic disorders. This paper discusses about a rare form of Charcot-Marie-Tooth disease – type 4G (CMT4G), also called Hereditary Motor and Sensory Neuropathy type Russe, an autosomal recessive disease caused by mutation private to Roma characterized by abnormally increased density of non-myelinated axons. CMT4G was originally found in Bulgarian Roma and in 2009 two putative causative mutations in the HK1 gene were identified. Since then, several cases were reported in Roma families mainly from Bulgaria and Spain. Here we present a Slovak Roma family in which CMT4G was diagnosed on the basis of clinical examination and genetic testing. This case is a further proof of the role of the HK1 gene in pathogenesis of the disease. It confirms that mutation in the HK1 gene is a common cause of autosomal recessive CMT disease in Roma and should be considered as a common part of a diagnostic procedure.

Keywords: gypsies, HK1, HSMN-Russe, rare disease

Procedia PDF Downloads 375

Authors: Gail Louw, Helena Boshoff, Taeksun Song, Clifton Barry

Abstract:

Drug resistance in Mycobacterium tuberculosis is primarily attributed to mutations in target genes. These mutations incur a fitness cost and result in bacterial generations that are less fit, which subsequently acquire compensatory mutations to restore fitness. We hypothesize that mutations in specific drug target genes influence bacterial metabolism and cellular function, which affects its ability to develop subsequent resistance to additional agents. We aim to determine whether the sequential acquisition of drug resistance and specific mutations in a well-defined clinical M. tuberculosis strain promotes or limits the development of additional resistance. In vitro mutants resistant to pretomanid, linezolid, moxifloxacin, rifampicin and kanamycin were generated from a pan-susceptible clinical strain from the Beijing lineage. The resistant phenotypes to the anti-TB agents were confirmed by the broth microdilution assay and genetic mutations were identified by targeted gene sequencing. Growth of mono-resistant mutants was done in enriched medium for 14 days to assess in vitro fitness. Double resistant mutants were generated against anti-TB drug combinations at concentrations 5x and 10x the minimum inhibitory concentration. Subsequently, mutation frequencies for these anti-TB drugs in the different mono-resistant backgrounds were determined. The initial level of resistance and the mutation frequencies observed for the mono-resistant mutants were comparable to those previously reported. Targeted gene sequencing revealed the presence of known and clinically relevant mutations in the mutants resistant to linezolid, rifampicin, kanamycin and moxifloxacin. Significant growth defects were observed for mutants grown under in vitro conditions compared to the sensitive progenitor. Mutation frequencies determination in the mono-resistant mutants revealed a significant increase in mutation frequency against rifampicin and kanamycin, but a significant decrease in mutation frequency against linezolid and sutezolid. This suggests that these mono-resistant mutants are more prone to develop resistance to rifampicin and kanamycin, but less prone to develop resistance against linezolid and sutezolid. Even though kanamycin and linezolid both inhibit protein synthesis, these compounds target different subunits of the ribosome, thereby leading to different outcomes in terms of fitness in the mutants with impaired cellular function. These observations showed that oxazolidinone treatment is instrumental in limiting the development of multi-drug resistance in M. tuberculosis in vitro.

Keywords: oxazolidinones, mutations, resistance, tuberculosis

Procedia PDF Downloads 146

Authors: Xiaoping Su, Gabriel G. Malouf

Abstract:

Introduction: Breast cancer is a heterogeneous disease that can be classified in 4 subgroups using transcriptional profiling. The role of lncRNA expression in human breast cancer biology, prognosis, and molecular classification remains unknown. Methods and results: Using an integrative comprehensive analysis of lncRNA, mRNA and DNA methylation in 900 breast cancer patients from The Cancer Genome Atlas (TCGA) project, we unraveled the molecular portraits of 1,700 expressed lncRNA. Some of those lncRNAs (i.e, HOTAIR) are previously reported and others are novel (i.e, HOTAIRM1, MAPT-AS1). The lncRNA classification correlated well with the PAM50 classification for basal-like, Her-2 enriched and luminal B subgroups, in contrast to the luminal A subgroup which behaved differently. Importantly, estrogen receptor (ESR1) expression was associated with distinct lncRNA networks in lncRNA clusters III and IV. Gene set enrichment analysis for cis- and trans-acting lncRNA showed enrichment for breast cancer signatures driven by breast cancer master regulators. Almost two third of those lncRNA were marked by enhancer chromatin modifications (i.e., H3K27ac), suggesting that lncRNA expression may result in increased activity of neighboring genes. Differential analysis of gene expression profiling data showed that lncRNA HOTAIRM1 was significantly down-regulated in basal-like subtype, and DNA methylation profiling data showed that lncRNA HOTAIRM1 was highly methylated in basal-like subtype. Thus, our integrative analysis of gene expression and DNA methylation strongly suggested that lncRNA HOTAIRM1 should be a tumor suppressor in basal-like subtype. Conclusion and significance: Our study depicts the first lncRNA molecular portrait of breast cancer and shows that lncRNA HOTAIRM1 might be a novel tumor suppressor.

Keywords: lncRNA profiling, breast cancer, HOTAIRM1, tumor suppressor

Procedia PDF Downloads 93

Authors: Ankan Roy, Niharika, Samir Kumar Patra

Abstract:

Anomalous nexus of complex topological assemblies and spatiotemporal epigenetic choreography at chromosomal territory may forms the most sophisticated regulatory layer of gene expression in cancer. Colon cancer is one of the leading malignant neoplasms of the lower gastrointestinal tract worldwide. There is still a paucity of information about the complex molecular mechanisms of colonic cancerogenesis. Bioinformatics prediction and analysis helps to identify essential genes and significant pathways for monitoring and conquering this deadly disease. The present study investigates and explores potential hub genes as biomarkers and effective therapeutic targets for colon cancer treatment. Colon cancer patient sample containing gene expression profile datasets, such as GSE44076, GSE20916, and GSE37364 were downloaded from Gene Expression Omnibus (GEO) database and thoroughly screened using the GEO2R tool and Funrich software to find out common 2 differentially expressed genes (DEGs). Other approaches, including Gene Ontology (GO) and KEGG pathway analysis, Protein-Protein Interaction (PPI) network construction and hub gene investigation, Overall Survival (OS) analysis, gene correlation analysis, methylation pattern analysis, and hub gene-Transcription factors regulatory network construction, were performed and validated using various bioinformatics tool. Initially, we identified 166 DEGs, including 68 up-regulated and 98 down-regulated genes. Up-regulated genes are mainly associated with the Cytokine-cytokine receptor interaction, IL17 signaling pathway, ECM-receptor interaction, Focal adhesion and PI3K-Akt pathway. Downregulated genes are enriched in metabolic pathways, retinol metabolism, Steroid hormone biosynthesis, and bile secretion. From the protein-protein interaction network, thirty hub genes with high connectivity are selected using the MCODE and cytoHubba plugin. Survival analysis, expression validation, correlation analysis, and methylation pattern analysis were further verified using TCGA data. Finally, we predicted COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as potential master regulators in colonic cancerogenesis. Moreover, our experimental data highlights that disruption of lipid raft and RAS/MAPK signaling cascade affects this gene hub at mRNA level. We identified COL1A1, COL1A2, COL4A1, SPP1, SPARC, and THBS2 as determinant hub genes in colon cancer progression. They can be considered as biomarkers for diagnosis and promising therapeutic targets in colon cancer treatment. Additionally, our experimental data advertise that signaling pathway act as connecting link between membrane hub and gene hub.

Keywords: hub genes, colon cancer, DNA methylation, epigenetic engineering, bioinformatic predictions

Procedia PDF Downloads 116

Authors: Jagroop Singh Sidhu, Buta Singh

Abstract:

A low computational deblocking filter including three frequency related modes (smooth mode, intermediate mode, and non-smooth mode for low-frequency, mid-frequency, and high frequency regions, respectively) is proposed. The suggested approach requires zero additions, zero subtractions, zero multiplications (for intermediate region), no divisions (for non-smooth region) and no comparison. The suggested method thus keeps the computation lower and thus suitable for image coding systems based on blocks. Comparison of average number of operations for smooth, non-smooth, intermediate (per pixel vector for each block) using filter suggested by Chen and the proposed method filter suggests that the proposed filter keeps the computation lower and is thus suitable for fast processing algorithms.

Keywords: blocking artifacts, computational complexity, non-smooth, intermediate, smooth

Procedia PDF Downloads 450

Authors: Yun-Chin Chung, Nileema Divate, Gen-Hung Chen, Pei-Ru Huang, Rupesh Divate

Abstract:

Many environmental factors, such as glucose concentration, ethanol, temperature, osmotic pressure and pH, decrease the production rate of ethanol using yeast as a starter. Fermentation starters with high tolerance to various stresses are always demanded for brewing industry. Trehalose, a storage carbohydrate in cell wall of yeast, plays an important role in tolerance of environmental stress by preserving integrity of plasma membrane and stabilizing proteins. Furan aldehydes are toxic to yeast and the growth rate of yeast is significantly reduced if furan aldehydes were present in the fermentation medium. In yeast, aldehyde reductase is involved in the detoxification of reactive aldehydes and consequently the growth of yeast is improved. The aims of this study were to construct a genetic recombinant Saccharomyces cerevisiae or Pichia pastoris with furfural and HMF degrading and high ethanol tolerance capacities. Yeast strains were engineered by genetic recombination for overexpression of trehalose-6-phosphate synthase gene (tps1) and aldehyde reductase gene (ari1). TPS1 gene was cloned from S. cerevisiae by reverse transcription-polymerase chain reaction (RT-PCR) and then ligated with pGAPZαC vector. The constructed vector, pGAPZC-tps1, was transformed to recombinant yeasts strain with overexpression of ari1. The transformants with pGAPZC-tps1-ari1 were generated called STA (S. cerevisiae) and PTA (P. pastoris) with overexpression of tps1, ari1. PCR with tps1-specific primers and western blot with his-tag confirmed the gene insertion and protein expression of tps1 in the transformants, respectively. The neutral trehalase gene (nth1) of STA was successfully deleted and the novel strain STAΔN will be used for further study, including the measurement of trehalose concentration and ethanol, furfural tolerance assay.

Keywords: genetic recombinant, yeast, ethanol tolerance, trehalase, aldehyde reductase

Procedia PDF Downloads 408

Authors: Ali Bayram, Remzi Yiğiter

Abstract:

Objective: Alzheimer's disease (AD), the most common cause of dementia, is a progressive neurodegenerative disease. At present, diagnosis of AD is rather late in the disease. Therefore, we attempted to find peripheral biomarkers for the early diagnosis of AD. Herein, we conducted a study to investigate the unc-51 like autophagy activating kinase-1 (ULK1) mRNA expression levels in human peripheral blood mononuclear cells from patients with Alzheimer's disease. Method: To determine whether ULK1 gene expression are altered in AD patients, we measured their gene expression in human peripheral blood cell in 50 patients with AD and 50 age and gender matched healthy controls by quantitative real-time PCR technique. Results: We found that both ULK1 gene expression in peripheral blood cell were significantly decreased in patients with AD as compared with controls (p <0.05). Lower levels of ULK1 gene expression were significantly associated with the increased risk for AD. Conclusions: Serine/threonine-protein kinase involved in autophagy in response to starvation. Acts upstream of phosphatidylinositol 3-kinase PIK3C3 to regulate the formation of autophagophores, the precursors of autophagosomes. Part of regulatory feedback loops in autophagy: acts both as a downstream effector and negative regulator of mammalian target of rapamycin complex 1 (mTORC1) via interaction with RPTOR. Activated via phosphorylation by AMPK and also acts as a regulator of AMPK by mediating phosphorylation of AMPK subunits PRKAA1, PRKAB2, and PRKAG1, leading to negatively regulate AMPK activity. May phosphorylate ATG13/KIAA0652 and RPTOR; however such data need additional evidences. Plays a role early in neuronal differentiation and is required for granule cell axon formation. Alzheimer is the most common neurodegenerative disease. Our results provide useful information that the ULK1 gene expression is decreased in the neurodegeneration and AD patients with, indicating their possible systemic involvement in AD.

Keywords: Alzheimer’s sisease, ULK1, mRNA expression, RT-PCR

Procedia PDF Downloads 388

Authors: Jae Woong Sull, Sun Ha Jee

Abstract:

High-density lipoprotein (HDL) cholesterol levels are associated with decreased risk of coronary artery disease. Several genome-wide association studies (GWAS) for HDL cholesterol levels have implicated cholesterol ester transfer protein (CETP) as possibly causal. We tested for the association between single nucleotide polymorphisms (SNPs) in CETP gene and HDL cholesterol levels in Korean population. Subjects were selected from the Korean Metabolic Syndrome Research Initiative study in the Bundang-Gu area. A total of 2,304 individuals from Bundang-Gu were recruited in 2008. Other subjects were selected from the Severance Hospital (N=4,294). SNP rs6499861 in the CETP gene was associated with mean HDL cholesterol levels (effect per allele -2.044 mg/dL, p=7.23×10-7). Subjects with the CG/GG genotype had a 1.46 -fold (range 1.24–1.72-fold) higher risk of having abnormal HDL cholesterol levels (<40 mg/dL) than subjects with the CC genotype. When analyzed by gender, the association of CETP was stronger in women than in men. When analyzed by physical activity behavior, the association with CETP was much stronger in male subjects with low physical activity (OR=1.54, 95% CI: 1.23-1.92, P=0.0001) than in male subjects with high physical activity. This study clearly demonstrates that genetic variants in CETP influence HDL cholesterol levels in Korean adults.

Keywords: CETP, HDL cholesterol, physical activity, polymorphisms

Procedia PDF Downloads 277