Search results for: gene modules

Authors: Hung-Ming Lai, Andreas Albrecht, Kathleen Steinhöfel

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Cancers could normally be marked by a number of differentially expressed genes which show enormous potential as biomarkers for a certain disease. Recent years, cancer classification based on the investigation of gene expression profiles derived by high-throughput microarrays has widely been used. The selection of discriminative genes is, therefore, an essential preprocess step in carcinogenesis studies. In this paper, we have proposed a novel gene selector using information-theoretic measures for biological discovery. This multivariate filter is a four-stage framework through the analyses of feature relevance, feature interdependence, feature redundancy-dependence and subset rankings, and having been examined on the colon cancer data set. Our experimental result show that the proposed method outperformed other information theorem based filters in all aspect of classification errors and classification performance.

Keywords: Colon cancer, feature interdependence, feature subset selection, gene selection, microarray data analysis.

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Authors: S. Manzoor, A. Nadeem, M. Javed, ME. Babar

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A major goal in animal genetics is to understand the role of common genetic variants in diseases susceptibility and production traits. Sahiwal cattle can be considered as a global animal genetic resource due to its relatively high milk producing ability, resistance against tropical diseases and heat tolerant. CYP11B1 gene provides instructions for making a mitochondrial enzyme called steroid 11-beta-hydroxylase. It catalyzes the 11deoxy-cortisol to cortisol and 11deoxycorticosterone to corticosterone in cattle. The bovine CYP11B1 gene is positioned on BTA14q12 comprises of eight introns and nine exons and protein is associated with mitochondrial epithelium. The present study was aimed to identify the single-nucleotide polymorphisms in CYP11B1 gene in Sahiwal cattle breed of Pakistan. Four polymorphic sites were identified in exon one of CYP11B1 gene through sequencing approach. Significant finding was the incidence of the C→T polymorphism in 5'-UTR, causing amino acid substitution from alanine to valine (A30V) in Sahiwal cattle breed. That Ala/Val polymorphism may serve as a powerful genetic tool for the development of DNA markers that can be used for the particular traits for different local cattle breeds.

Keywords: CYP11B1, single nucleotide polymorphism, sahiwal cattle, Pakistan.

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Authors: N. J. Imu, N. Rabbani, Md E. Hossain

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Achieving national climate goals requires transforming the energy system and increasing the use of renewable energy in Bangladesh as renewable energy offers an environmentally friendly energy supply. In view of this, Bangladesh has set a goal of 100% renewable power generation by 2050. Among all the renewable energy, solar is the most effective and popular source of renewable energy in Bangladesh. In order to build up on-grid and off-grid solar systems to increase energy transformation, monocrystalline type (highly efficient) solar module, and the polycrystalline type (low-efficient) solar module are commonly used. Due to their low price and availability, polycrystalline-type solar modules dominated the local market in the past years. However, in recent times the use of monocrystalline types modules has increased considerably owing to the significant decrease in price difference that existed between these two modules. Despite the deployment of both mono- and poly-crystalline modules in the market, the proliferation of low-quality solar panels are dominating the market resulting in reduced generation of solar electricity than expected. This situation is further aggravated by insufficient information regarding the effect of solar irradiation on solar module performance in relation to the quality of the materials used for the production of the module. This research aims to evaluate the efficiency of monocrystalline and polycrystalline solar modules that are available in Bangladesh by considering seasonal variations. Both types of solar modules have been tested for three different capacities 45W, 60W, and 100W in Dhaka regions to evaluate their power generation capability under Standard Test Conditions (STC). Module testing data were recorded twelve months in a full year from January to December. Data for solar irradiation were collected using HT304N while HT I-V400 multifunction instrument was used for testing voltage and current of photovoltaic (PV) systems and complete power quality analyzer. Results obtained in this study indicated differences between the efficiencies of polycrystalline and monocrystalline solar modules under the country’s solar irradiation. The average efficiencies of 45W, 60W, and 100W monocrystalline solar panels were recorded as 11.73%, 13.41%, and 15.37% respectively while for polycrystalline panels were 8.66%, 9.37%, and 12.34%. Monocrystalline solar panels, which offer greater working output than polycrystalline ones, are also represented by the Pearson Correlation value. The output of polycrystalline solar panels fluctuated highly with the changes in irradiation and temperature whereas monocrystalline panels were much stable.

Keywords: Solar energy, solar irradiation, efficiency, polycrystalline solar module, monocrystalline solar module, SPSS analysis.

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Authors: Seo Young Kim, Jae Won Lee, Jong Sung Bae

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Microarray experiments are information rich; however, extensive data mining is required to identify the patterns that characterize the underlying mechanisms of action. For biologists, a key aim when analyzing microarray data is to group genes based on the temporal patterns of their expression levels. In this paper, we used an iterative clustering method to find temporal patterns of gene expression. We evaluated the performance of this method by applying it to real sporulation data and simulated data. The patterns obtained using the iterative clustering were found to be superior to those obtained using existing clustering algorithms.

Keywords: Clustering, microarray experiment, temporal pattern of gene expression data.

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Authors: Parvinder S. Sandhu, Sunil Khullar, Satpreet Singh, Simranjit K. Bains, Manpreet Kaur, Gurvinder Singh

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Fault-proneness of a software module is the probability that the module contains faults. To predict faultproneness of modules different techniques have been proposed which includes statistical methods, machine learning techniques, neural network techniques and clustering techniques. The aim of proposed study is to explore whether metrics available in the early lifecycle (i.e. requirement metrics), metrics available in the late lifecycle (i.e. code metrics) and metrics available in the early lifecycle (i.e. requirement metrics) combined with metrics available in the late lifecycle (i.e. code metrics) can be used to identify fault prone modules using Genetic Algorithm technique. This approach has been tested with real time defect C Programming language datasets of NASA software projects. The results show that the fusion of requirement and code metric is the best prediction model for detecting the faults as compared with commonly used code based model.

Keywords: Genetic Algorithm, Fault Proneness, Software Faultand Software Quality.

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Authors: Frank Emmert-Streib, Matthias Dehmer

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Inferring the network structure from time series data is a hard problem, especially if the time series is short and noisy. DNA microarray is a technology allowing to monitor the mRNA concentration of thousands of genes simultaneously that produces data of these characteristics. In this study we try to investigate the influence of the experimental design on the quality of the result. More precisely, we investigate the influence of two different types of random single gene perturbations on the inference of genetic networks from time series data. To obtain an objective quality measure for this influence we simulate gene expression values with a biologically plausible model of a known network structure. Within this framework we study the influence of single gene knock-outs in opposite to linearly controlled expression for single genes on the quality of the infered network structure.

Keywords: Dynamic Bayesian networks, microarray data, structure learning, Markov chain Monte Carlo.

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Authors: Parvinder S. Sandhu, Sandeep Khimta, Kiranpreet Kaur

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The prediction of Software quality during development life cycle of software project helps the development organization to make efficient use of available resource to produce the product of highest quality. “Whether a module is faulty or not" approach can be used to predict quality of a software module. There are numbers of software quality prediction models described in the literature based upon genetic algorithms, artificial neural network and other data mining algorithms. One of the promising aspects for quality prediction is based on clustering techniques. Most quality prediction models that are based on clustering techniques make use of K-means, Mixture-of-Guassians, Self-Organizing Map, Neural Gas and fuzzy K-means algorithm for prediction. In all these techniques a predefined structure is required that is number of neurons or clusters should be known before we start clustering process. But in case of Growing Neural Gas there is no need of predetermining the quantity of neurons and the topology of the structure to be used and it starts with a minimal neurons structure that is incremented during training until it reaches a maximum number user defined limits for clusters. Hence, in this work we have used Growing Neural Gas as underlying cluster algorithm that produces the initial set of labeled cluster from training data set and thereafter this set of clusters is used to predict the quality of test data set of software modules. The best testing results shows 80% accuracy in evaluating the quality of software modules. Hence, the proposed technique can be used by programmers in evaluating the quality of modules during software development.

Keywords: Growing Neural Gas, data clustering, fault prediction.

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Authors: U. Kairov, T. Karpenyuk, E. Ramanculov, A. Zinovyev

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The most common result of analysis of highthroughput data in molecular biology represents a global list of genes, ranked accordingly to a certain score. The score can be a measure of differential expression. Recent work proposed a new method for selecting a number of genes in a ranked gene list from microarray gene expression data such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. Here we present calculation results of relative connectivity of genes from META-OFTEN network and tentative biological interpretation of the most reproducible signal. The relative connectivity and inbetweenness values of genes from META-OFTEN network were estimated.

Keywords: Microarray, META-OFTEN, gene network.

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Authors: N. Reehana, A. Parveez Ahamed, D. Mubarak Ali, A. Suresh, R. Arvind Kumar, N. Thajuddin

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Cyanobacteria play a vital role in the production of phycobiliproteins that includes phycocyanin and phycoerythrin pigments. Phycocyanin and related phycobiliproteins have wide variety of application that is used in the food, biotechnology and cosmetic industry because of their color, fluorescent and antioxidant properties. The present study is focused to understand the pigment at molecular level in the Cyanobacteria Oscillatoria terebriformis NTRI05 and Oscillatoria foreaui NTRI06. After extraction of genomic DNA, the amplification of C-Phycocyanin gene was done with the suitable primer PCβF and PCαR and the sequencing was performed. Structural and Phylogenetic analysis was attained using the sequence to develop a molecular model.

Keywords: Cyanobacteria, C-Phycocyanin gene, Phylogenetic analysis, Structural analysis.

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Authors: C. Gunavathi, K. Premalatha

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Microarray technology is universally used in the study of disease diagnosis using gene expression levels. The main shortcoming of gene expression data is that it includes thousands of genes and a small number of samples. Abundant methods and techniques have been proposed for tumor classification using microarray gene expression data. Feature or gene selection methods can be used to mine the genes that directly involve in the classification and to eliminate irrelevant genes. In this paper statistical measures like T-Statistics, Signal-to-Noise Ratio (SNR) and F-Statistics are used to rank the genes. The ranked genes are used for further classification. Particle Swarm Optimization (PSO) algorithm and Shuffled Frog Leaping (SFL) algorithm are used to find the significant genes from the top-m ranked genes. The Naïve Bayes Classifier (NBC) is used to classify the samples based on the significant genes. The proposed work is applied on Lung and Ovarian datasets. The experimental results show that the proposed method achieves 100% accuracy in all the three datasets and the results are compared with previous works.

Keywords: Microarray, T-Statistics, Signal-to-Noise Ratio, FStatistics, Particle Swarm Optimization, Shuffled Frog Leaping, Naïve Bayes Classifier.

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

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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.

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Authors: Jiang Fan

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With growth of PV market in tropical region, it is necessary to investigate the performance of different types of PV technology under the tropical weather conditions. Singapore Polytechnic was funded by Economic Development Board (EDB) to set up a solar PV test-bed for the research on performance of different types of PV modules in the country. The PV test-bed installed the nine different types of PV systems that are integrated to power utility grid for monitoring and analyzing their operating performances. This paper presents the 12 months operational data of nine different PV systems and analyses on performances of installed PV systems using energy yield and performance ratio. The nine types of PV systems under test have shown their energy yields ranging from 2.67 to 3.36 kWh/kW_p and their performance ratios (PRs) ranging from 70% to 88%.

Keywords: Monocrystalline, Multicrystalline, Amorphous Silicon, Cadmium Telluride and thin film PV.

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Authors: Mohamed Hafez, Georg Hausner

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The full length mitochondrial small subunit ribosomal (mt-rns) gene has been characterized for Ophiostoma novo-ulmi subspecies americana. The gene was also characterized for Ophiostoma ulmi and a group II intron was noted in the mt-rns gene of O. ulmi. The insertion in the mt-rns gene is at position S952 and it is a group IIB1 intron that encodes a double motif LAGLIDADG homing endonuclease from an open reading frame located within a loop of domain III. Secondary structure models for the mt-rns RNA of O. novo-ulmi subsp. americana and O. ulmi were generated to place the intron within the context of the ribosomal RNA. The in vivo splicing of the O.ul-mS952 group II intron was confirmed with reverse transcription-PCR. A survey of 182 strains of Dutch Elm Diseases causing agents showed that the mS952 intron was absent in what is considered to be the more aggressive species O. novo-ulmi but present in strains of the less aggressive O. ulmi. This observation suggests that the O.ul-mS952 intron can be used as a PCR-based molecular marker to discriminate between O. ulmi and O. novo-ulmi subsp. americana.

Keywords: Dutch Elm Disease, group II introns, mtDNA, species identification

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Authors: Dae-ho Won, Jong-wook Hong, Yeon-Mo Yang, Jinung An

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To reduce accidents in the industry, WSNs(Wireless Sensor networks)- sensor data is used. WSNs- sensor data has the persistence and continuity. therefore, we design and exploit the buffer management system that has the persistence and continuity to avoid and delivery data conflicts. To develop modules, we use the multi buffers and design the buffer management modules that transfer sensor data through the context-aware methods.

Keywords: safe management system, buffer management, context-aware, input data stream

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Authors: Huong M. T. Nguyen, Hoa A. P. Nguyen, Mai P. T. Nguyen, Ngoc D. Ngo, Van T. Ta, Hai T. Le, Chi V. Phan

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Wilson’s disease (WD) is an autosomal recessive disorder of the copper metabolism, which is caused by a mutation in the copper-transporting P-type ATPase (ATP7B). The mechanism of this disease is the failure of hepatic excretion of copper to bile, and leads to copper deposits in the liver and other organs. The ATP7B gene is located on the long arm of chromosome 13 (13q14.3). This study aimed to investigate the gene mutation in the Vietnamese patients with WD, and make a presymptomatic diagnosis for their familial members. Forty-three WD patients and their 65 siblings were identified as having ATP7B gene mutations. Genomic DNA was extracted from peripheral blood samples; 21 exons and exon-intron boundaries of the ATP7B gene were analyzed by direct sequencing. We recognized four mutations ([R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G) in the sum of 20 detectable mutations, accounting for 87.2% of the total. Mutation S105* was determined to have a high rate (32.6%) in this study. The hotspot regions of ATP7B were found at exons 2, 16, and 8, and intron 14, in 39.6 %, 11.6 %, 9.3%, and 7 % of patients, respectively. Among nine homozygote/compound heterozygote siblings of the patients with WD, three individuals were determined as asymptomatic by screening mutations of the probands. They would begin treatment after diagnosis. In conclusion, 20 different mutations were detected in 43 WD patients. Of this number, four novel mutations were explored, including [R723=; H724Tfs*34], V1042Cfs*79, D1027H, and IVS6+3A>G. The mutation S105* is the most prevalent and has been considered as a biomarker that can be used in a rapid detection assay for diagnosis of WD patients. Exons 2, 8, and 16, and intron 14 should be screened initially for WD patients in Vietnam. Based on risk profile for WD, genetic testing for presymptomatic patients is also useful in diagnosis and treatment.

Keywords: ATP7B gene, mutation detection, presymptomatic diagnosis, Vietnamese Wilson’s disease.

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Authors: Umber Iqbal, Shaleeza Sohail, Muhammad Younas Javed

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True integration of multimedia services over wired or wireless networks increase the productivity and effectiveness in today-s networks. IP Multimedia Subsystems are Next Generation Network architecture to provide the multimedia services over fixed or mobile networks. This paper proposes an extended SIP-based QoS Management architecture for IMS services over underlying IP access networks. To guarantee the end-to-end QoS for IMS services in interconnection backbone, SIP based proxy Modules are introduced to support the QoS provisioning and to reduce the handoff disruption time over IP access networks. In our approach these SIP Modules implement the combination of Diffserv and MPLS QoS mechanisms to assure the guaranteed QoS for real-time multimedia services. To guarantee QoS over access networks, SIP Modules make QoS resource reservations in advance to provide best QoS to IMS users over heterogeneous networks. To obtain more reliable multimedia services, our approach allows the use of SCTP protocol over SIP instead of UDP due to its multi-streaming feature. This architecture enables QoS provisioning for IMS roaming users to differentiate IMS network from other common IP networks for transmission of realtime multimedia services. To validate our approach simulation models are developed on short scale basis. The results show that our approach yields comparable performance for efficient delivery of IMS services over heterogeneous IP access networks.

Keywords: SIP-Based QoS Management Architecture, IPMultimedia Subsystems, IP Access Networks

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Authors: Frank Emmert-Streib, Matthias Dehmer, Jing Liu, Max Muhlhauser

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The major objective of this paper is to introduce a new method to select genes from DNA microarray data. As criterion to select genes we suggest to measure the local changes in the correlation graph of each gene and to select those genes whose local changes are largest. More precisely, we calculate the correlation networks from DNA 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 tumor progression. 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. This indicates that our method captures essential information from the underlying DNA microarray data of cervical cancer.

Keywords: Graph similarity, generalized trees, graph alignment, DNA microarray data, cervical cancer.

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Authors: Zilya R. Vershinina, Andrei K. Baymiev, Aleksei K. Baymiev, Aleksei V. Chemeris

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This paper reports optimization of characteristics of bioballistic transformation of spring soft wheat (Triticum aestivum L. cultivar Raduga) and getting of transgenic plants, carrying pea lectin gene. This gene will let to create new associative wheat symbiosis with nodule bacteria of field pea, which has growth encouraging, fungistatic and other useful characteristics.

Keywords: transgenic wheat, pea lectin, rhizobia root colonization, symbiosis

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Authors: T. Taufik, R. Prasetyo, D. Dolan, D. Garinto

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Today-s Voltage Regulator Modules (VRMs) face increasing design challenges as the number of transistors in microprocessors increases per Moore-s Law. These challenges have recently become even more demanding as microprocessors operate at sub voltage range at significantly high current. This paper presents a new multiphase topology with cell configuration for improved performance in low voltage and high current applications. A lab scale hardware prototype of the new topology was design and constructed. Laboratory tests were performed on the proposed converter and compared with a commercially available VRM. Results from the proposed topology exhibit improved performance compared to the commercially available counterpart.

Keywords: Voltage Regulator Modules, dc-dc converters, powerelectronics.

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Authors: Muhammad Azam, Micheal Olaolu Arowolo, Fei He, Mihail Popescu, Dong Xu

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The number of biological papers is growing quickly, which means that the number of biological pathway figures in those papers is also increasing quickly. Each pathway figure shows extensive biological information, like the names of genes and how the genes are related. However, manually annotating pathway figures takes a lot of time and work. Even though using advanced image understanding models could speed up the process of curation, these models still need to be made more accurate. To improve gene name recognition from pathway figures, we applied a Siamese network to map image segments to a library of pictures containing known genes in a similar way to person recognition from photos in many photo applications. We used a triple loss function and a triplet spatial pyramid pooling network by combining the triplet convolution neural network and the spatial pyramid pooling (TSPP-Net). We compared VGG19 and VGG16 as the Siamese network model. VGG16 achieved better performance with an accuracy of 93%, which is much higher than Optical Character Recognition (OCR) results.

Keywords: Biological pathway, image understanding, gene name recognition, object detection, Siamese network, Visual Geometry Group.

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Authors: Reena Murali, David Peter S.

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The small interfering RNA (siRNA) alters the regulatory role of mRNA during gene expression by translational inhibition. Recent studies show that upregulation of mRNA because serious diseases like cancer. So designing effective siRNA with good knockdown effects plays an important role in gene silencing. Various siRNA design tools had been developed earlier. In this work, we are trying to analyze the existing good scoring second generation siRNA predicting tools and to optimize the efficiency of siRNA prediction by designing a computational model using Artificial Neural Network and whole stacking energy (%G), which may help in gene silencing and drug design in cancer therapy. Our model is trained and tested against a large data set of siRNA sequences. Validation of our results is done by finding correlation coefficient of experimental versus observed inhibition efficacy of siRNA. We achieved a correlation coefficient of 0.727 in our previous computational model and we could improve the correlation coefficient up to 0.753 when the threshold of whole tacking energy is greater than or equal to -32.5 kcal/mol.

Keywords: Artificial Neural Network, Double Stranded RNA, RNA Interference, Short Interfering RNA.

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Authors: Ahmad Zahran, Ahmed Herzallah, Ahmad Ahmad, Mahran Quraan

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Generation of high DC voltages is necessary for testing the insulation material of high voltage AC transmission lines with long lengths. The harmonic and ripple contents of the output DC voltage supplied by high voltage DC circuits require the use of costly capacitors to smooth the output voltage after rectification. This paper proposes a new modular multiplier high voltage DC generator with embedded Cockcroft-Walton circuits that achieve a negligible harmonic and ripple contents of the output DC voltage without the need for costly filters to produce a nearly constant output voltage. In this new topology, Cockcroft-Walton modules are connected in series to produce a high DC output voltage. The modules are supplied by low input AC voltage sources that have the same magnitude and frequency and shifted from each other by a certain angle to eliminate the harmonics from the output voltage. The small ripple factor is provided by the smoothing column capacitors and the phase shifted input voltages of the cascaded modules. The constituent harmonics within each module are determined using Fourier analysis. The viability of the proposed DC generator for testing purposes and the effectiveness of the cascaded connection are confirmed by numerical simulations using MATLAB/Simulink.

Keywords: Cockcroft-Walton circuit, Harmonics, Ripple factor, HVDC generator.

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Authors: Ali Baladi, Alireza Fallahi Arezoodar

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in dissimilar material joints, failure often occurs along the interface between two materials due to stress singularity. Stress distribution and its concentration depend on materials and geometry of the junction. Inhomogenity of stress distribution at the interface of junction of two materials with different elastic modules and stress concentration in this zone are the main factors resulting in rupture of the junction. Effect of joining angle in the interface of aluminum-polycarbonate will be discussed in this paper. Computer simulation and finite element analysis by ABAQUS showed that convex interfacial joint leads to stress reduction at junction corners in compare with straight joint. This finding is confirmed by photoelastic experimental results.

Keywords: Elastic Modules, Stress Concentration, JoiningAngle, Photoelastic.

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Authors: Aishwarya Ravichandra, Kirtana Kirtivasan, Adithi Mahesh, Ashwini S.Savanth

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A Non-Contact Digital Music System has been conceptualized and implemented to create a new era of digital music. This system replaces the strings of a traditional stringed instrument with laser beams to avoid bruising of the user’s hand. The system consists of seven laser modules, detector modules and distance sensors that form the basic hardware blocks of this instrument. Arduino ATmega2560 microcontroller is used as the primary interface between the hardware and the software. MIDI (Musical Instrument Digital Interface) is used as the protocol to establish communication between the instrument and the virtual synthesizer software.

Keywords: Arduino, Detector, Laser, MIDI, NOTE ON, NOTE OFF, PITCH BEND, Sharp IR distance sensor.

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Authors: Vishal Naranje, S. Kumar

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In this paper a low cost knowledge base system (KBS) framework is proposed for design of deep drawing die and procedure for developing system modules. The task of building the system is structured into different modules for major activities of design of deep drawing die. A manufacturability assessment module of the proposed framework is developed to check the manufacturability of deep drawn parts. The technological knowledge is represented by using IF- THEN rules and it is coded in AutoLISP language. The module is designed to be loaded into the prompt area of AutoCAD. The cost of implementation of proposed system makes it affordable for small and medium scale sheet metal industries.

Keywords: Knowledge base system, Deep drawing die, Manufacturability, Sheet metal.

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Authors: Roya Bakhtiar, Alireza Abdolmohammadi, Hadi Hajarian, Zahra Nikousefat, Davood, Kalantar-Neyestanaki

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The objective of the present study was to determine the polymorphism in the leptin (332G>A) and its association with biometric traits in Sanjabi sheep. For this purpose, blood samples from 96 rams were taken, and tail length, width tail, circumference tail, body length, body width, and height were simultaneously recorded. PCR was performed using specific primer to amplify 463 bp fragment including exon 3 of leptin gene, and PCR products were digested by Cail restriction enzymes. The 332G>A (at 332th nucleotide of exon 3 leptin gene) that caused an amino acid change from Arg to Gln was detected by Cail (CAGNNNCTG) endonuclease, as the endonuclease cannot cut this region if G nucleotide is located in this position. Three genotypes including GG (463), GA (463, 360and 103 bp) and GG (360 bp and 103 bp) were identified after digestion by enzyme. The estimated frequencies of three genotypes including GG, GA, and AA for 332G>A locus were 0.68, 0.29 and 0.03 and those were 0.18 and 0.82 for A and G alleles, respectively. In the current study, chi-square test indicated that 332G>A positions did not deviate from the Hardy–Weinberg (HW) equilibrium. The most important reason to show HW equation was that samples used in this study belong to three large local herds with a traditional breeding system having random mating and without selection. Shannon index amount was calculated which represent an average genetic variation in Sanjabi rams. Also, heterozygosity estimated by Nei index indicated that genetic diversity of mutation in the leptin gene is moderate. Leptin gene polymorphism in the 332G>A had significant effect on body length (P<0.05) trait, and individuals with GA genotype had significantly the higher body length compared to other individuals. Although animals with GA genotype had higher body width, this difference was not statistically significant (P>0.05). This non-synonymous SNP resulted in different amino acid changes at codon positions111(R/Q). As leptin activity is localized, at least in part, in domains between amino acid residues 106-1406, it is speculated that the detected SNP at position 332 may affect the activity of leptin and may lead to different biological functions. Based to our results, due to significant effect of leptin gene polymorphism on body size traits, this gene may be used a candidate gene for improving these traits.

Keywords: Body size, Leptin gene, PCR-RFLP, Sanjabi sheep.

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

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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.

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Authors: Rohayu Izanwati M. R., Muhamad Ridhwan M. R., Abbe Maleyki M. J., Ahmad Zubaidi A. L., Zahri M. K.

Abstract:

PPARs function as regulators of lipid and lipoprotein metabolism. The aim of the study was to compare the lipid profile between two phases of fasting and to examine the frequency and relationship of peroxisome proliferator-activated receptor, PPARα gene polymorphisms to lipid profile in fasting respondents. We conducted a case-control study protocol, which included 21 healthy volunteers without gender discrimination at the age of 18 years old. 3 ml of blood sample was drawn before the fasting phase and during the fasting phase (in Ramadhan month). 1ml of serum for the lipid profile was analyzed by using the automated chemistry analyser (Olympus, AU 400) and the data were analysed using the Paired T-Test (SPSS ver.20). DNA was extracted and PCR was conducted utilising 6 sets of primer. Primers were designed within 6 exons of interest in PPARα gene. Genetic and metabolic characteristics of fasting respondents and controls were estimated and compared. Fasting respondents were significantly have lowered the LDL levels (p=0.03). There were no polymorphisms detected except in exon 1 with 5% of this population study respectively. The polymorphisms in exon 1 of the PPARα gene were found in low frequency. Regarding the 1375G/T and 1386G/T polymorphisms in the exon 1 of the PPARα gene, the T-allele in fasting phase had no association with the decreased LDL levels (Fisher Exact Test). However this association is more promising when the sample size is larger in order to elucidate the precise impact of the polymorphisms on lipid profile in the population. In conclusion, the PPARα gene polymorphisms do not appear to affect the LDL of fasting respondents.

Keywords: Fasting, LDL, Peroxisome proliferator activated receptor alpha (PPAR-α), Polymorphisms.

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Authors: Farahnaz Amini, Woo Yun Kin, Lazwani Kolandaiveloo

Abstract:

Availability of different genetic tests after completion of Human Genome Project increases the physicians’ responsibility to keep themselves update on the potential implementation of these genetic tests in their daily practice. However, due to numbers of barriers, still many of physicians are not either aware of these tests or are not willing to offer or refer their patients for genetic tests. This study was conducted an anonymous, cross-sectional, mailed-based survey to develop a primary data of Malaysian physicians’ level of knowledge and perception of gene profiling. Questionnaire had 29 questions. Total scores on selected questions were used to assess the level of knowledge. The highest possible score was 11. Descriptive statistics, one way ANOVA and chi-squared test was used for statistical analysis. Sixty three completed questionnaires were returned by 27 general practitioners (GPs) and 36 medical specialists. Responders’ age ranges from 24 to 55 years old (mean 30.2 ± 6.4). About 40% of the participants rated themselves as having poor level of knowledge in genetics in general whilst 60% believed that they have fair level of knowledge; however, almost half (46%) of the respondents felt that they were not knowledgeable about available genetic tests. A majority (94%) of the responders were not aware of any lab or company which is offering gene profiling services in Malaysia. Only 4% of participants were aware of using gene profiling for detection of dosage of some drugs. Respondents perceived greater utility of gene profiling for breast cancer (38%) compared to the colorectal familial cancer (3%). The score of knowledge ranged from 2 to 8 (mean 4.38 ± 1.67). Non- significant differences between score of knowledge of GPs and specialists were observed, with score of 4.19 and 4.58 respectively. There was no significant association between any demographic factors and level of knowledge. However, those who graduated between years 2001 to 2005 had higher level of knowledge. Overall, 83% of participants showed relatively high level of perception on value of gene profiling to detect patient’s risk of disease. However, low perception was observed for both statements of using gene profiling for general population in order to alter their lifestyle (25%) as well as having the full sequence of a patient genome for the purpose of determining a patient’s best match for treatment (18%). The lack of clinical guidelines, limited provider knowledge and awareness, lack of time and resources to educate patients, lack of evidence-based clinical information and cost of tests were the most barriers of ordering gene profiling mentioned by physicians. In conclusion Malaysian physicians who participate in this study had mediocre level of knowledge and awareness in gene profiling. The low exposure to the genetic questions and problems might be a key predictor of lack of awareness and knowledge on available genetic tests. Educational and training workshop might be useful in helping Malaysian physicians incorporate genetic profiling into practice for eligible patients.

Keywords: Gene Profiling, Knowledge, Malaysia, Physician.

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Authors: Mohamed A. Mahfouz, M. A. Ismail

Abstract:

Biclustering is a very useful data mining technique for identifying patterns where different genes are co-related based on a subset of conditions in gene expression analysis. Association rules mining is an efficient approach to achieve biclustering as in BIMODULE algorithm but it is sensitive to the value given to its input parameters and the discretization procedure used in the preprocessing step, also when noise is present, classical association rules miners discover multiple small fragments of the true bicluster, but miss the true bicluster itself. This paper formally presents a generalized noise tolerant bicluster model, termed as μBicluster. An iterative algorithm termed as BIDENS based on the proposed model is introduced that can discover a set of k possibly overlapping biclusters simultaneously. Our model uses a more flexible method to partition the dimensions to preserve meaningful and significant biclusters. The proposed algorithm allows discovering biclusters that hard to be discovered by BIMODULE. Experimental study on yeast, human gene expression data and several artificial datasets shows that our algorithm offers substantial improvements over several previously proposed biclustering algorithms.

Keywords: Machine learning, biclustering, bi-dimensional clustering, gene expression analysis, data mining.

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