Search results for: Sense-antisense gene pair

Authors: Archana Panchapakesan Iyer, Taha Abdullah Kumosani

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Many high-risk pathogens that cause disease in humans are transmitted through various food items. Food-borne disease constitutes a major public health problem. Assessment of the quality and safety of foods is important in human health. Rapid and easy detection of pathogenic organisms will facilitate precautionary measures to maintain healthy food. The Polymerase Chain Reaction (PCR) is a handy tool for rapid detection of low numbers of bacteria. We have designed gene specific primers for most common food borne pathogens such as Staphylococci, Salmonella and E.coli. Bacteria were isolated from food samples of various food outlets and identified using gene specific PCRs. We identified Staphylococci, Salmonella and E.coli O157 using gene specific primers by rapid and direct PCR technique in various food samples. This study helps us in getting a complete picture of the various pathogens that threaten to cause and spread food borne diseases and it would also enable establishment of a routine procedure and methodology for rapid identification of food borne bacteria using the rapid technique of direct PCR. This study will also enable us to judge the efficiency of present food safety steps taken by food manufacturers and exporters.

Keywords: food borne pathogens, PCR, food safety, rapiddetection.

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Authors: Hao He, Shaoqian Li

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In this paper, we study the cooperative communications where multiple cognitive radio (CR) transmit-receive pairs competitive maximize their own throughputs. In CR networks, the influences of primary users and the spectrum availability are usually different among CR users. Due to the existence of multiple relay nodes and the different spectrum availability, each CR transmit-receive pair should not only select the relay node but also choose the appropriate channel. For this distributed problem, we propose a game theoretic framework to formulate this problem and we apply a regret-matching learning algorithm which is leading to correlated equilibrium. We further formulate a modified regret-matching learning algorithm which is fully distributed and only use the local information of each CR transmit-receive pair. This modified algorithm is more practical and suitable for the cooperative communications in CR network. Simulation results show the algorithm convergence and the modified learning algorithm can achieve comparable performance to the original regretmatching learning algorithm.

Keywords: cognitive radio, cooperative communication, relay selection, channel choice, regret-matching learning, correlated equilibrium.

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Authors: Fabian Horn, Reinhard Guthke

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In molecular biology, microarray technology is widely and successfully utilized to efficiently measure gene activity. If working with less studied organisms, methods to design custom-made microarray probes are available. One design criterion is to select probes with minimal melting temperature variances thus ensuring similar hybridization properties. If the microarray application focuses on the investigation of metabolic pathways, it is not necessary to cover the whole genome. It is more efficient to cover each metabolic pathway with a limited number of genes. Firstly, an approach is presented which minimizes the overall melting temperature variance of selected probes for all genes of interest. Secondly, the approach is extended to include the additional constraints of covering all pathways with a limited number of genes while minimizing the overall variance. The new optimization problem is solved by a bottom-up programming approach which reduces the complexity to make it computationally feasible. The new method is exemplary applied for the selection of microarray probes in order to cover all fungal secondary metabolite gene clusters for Aspergillus terreus.

Keywords: bottom-up approach, gene clusters, melting temperature, metabolic pathway, microarray probe design, probe selection

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Authors: Rosarin Rujananon, Poonsuk Prasertsan, Amornrat Phongdara, Tanate Panrat, Jibin Sun, Sugima Rappert, An-Ping Zeng

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In this study, a synthetic pathway was created by assembling genes from Clostridium butyricum and Escherichia coli in different combinations. Among the genes were dhaB1 and dhaB2 from C. butyricum VPI1718 coding for glycerol dehydratase (GDHt) and its activator (GDHtAc), respectively, involved in the conversion of glycerol to 3-hydroxypropionaldehyde (3-HPA). The yqhD gene from E.coli BL21 was also included which codes for an NADPHdependent 1,3-propanediol oxidoreductase isoenzyme (PDORI) reducing 3-HPA to 1,3-propanediol (1,3-PD). Molecular modeling analysis indicated that the conformation of fusion protein of YQHD and DHAB1 was favorable for direct molecular channeling of the intermediate 3-HPA. According to the simulation results, the yqhD and dhaB1 gene were assembled in the upstream of dhaB2 to express a fusion protein, yielding the recombinant strain E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP41Y3). Strain BP41Y3 gave 10-fold higher 1,3-PD concentration than E. coliBL21 (DE3)//pET22b+::yqhD-dhaB1_dhaB2 (strain BP31Y2) expressing the recombinant enzymes simultaneously but in a non-fusion mode. This is the first report using a gene fusion approach to enhance the biological conversion of glycerol to the value added compound 1,3- PD.

Keywords: Recombinant E.coli, 1, 3-propanediol, glycerol, fusion protein.

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Authors: Shaoyan Sun, Liwei Zhang, Chonghui Guo

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As the use of registration packages spreads, the number of the aligned image pairs in image databases (either by manual or automatic methods) increases dramatically. These image pairs can serve as a set of training data. Correspondingly, the images that are to be registered serve as testing data. In this paper, a novel medical image registration method is proposed which is based on the a priori knowledge of the expected joint intensity distribution estimated from pre-aligned training images. The goal of the registration is to find the optimal transformation such that the distance between the observed joint intensity distribution obtained from the testing image pair and the expected joint intensity distribution obtained from the corresponding training image pair is minimized. The distance is measured using the divergence measure based on Tsallis entropy. Experimental results show that, compared with the widely-used Shannon mutual information as well as Tsallis mutual information, the proposed method is computationally more efficient without sacrificing registration accuracy.

Keywords: Multimodality images, image registration, Shannonentropy, Tsallis entropy, mutual information, Powell optimization.

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Authors: T. Holden, G. Tremberger, Jr, E. Cheung, R. Subramaniam, R. Sullivan, N. Gadura, P. Schneider, P. Marchese, A. Flamholz, T. Cheung, D. Lieberman

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A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.

Keywords: Fractal dimension, archaea thermophiles, Shannon entropy, GC content

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Authors: Radomir Perzina, Jaroslav Ramik

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The Analytic Hierarchy Process is frequently used approach for solving decision making problems. There exists wide range of software programs utilizing that approach. Their main disadvantage is that they are relatively expensive and missing intermediate calculations. This work introduces a Microsoft Excel add-in called DAME – Decision Analysis Module for Excel. Comparing to other computer programs DAME is free, can work with scenarios or multiple decision makers and displays intermediate calculations. Users can structure their decision models into three levels – scenarios/users, criteria and variants. Items on all levels can be evaluated either by weights or pair-wise comparisons. There are provided three different methods for the evaluation of the weights of criteria, the variants as well as the scenarios – Saaty’s Method, Geometric Mean Method and Fuller’s Triangle Method. Multiplicative and additive syntheses are supported. The proposed software package is demonstrated on couple of illustrating examples of real life decision problems.

Keywords: Analytic hierarchy process, multi-criteria decision making, pair-wise comparisons, Microsoft Excel, Scenarios.

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Authors: Alexandra Oliveros, Miguel Sotaquirá

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DNA microarray technology is widely used by geneticists to diagnose or treat diseases through gene expression. This technology is based on the hybridization of a tissue-s DNA sequence into a substrate and the further analysis of the image formed by the thousands of genes in the DNA as green, red or yellow spots. The process of DNA microarray image analysis involves finding the location of the spots and the quantification of the expression level of these. In this paper, a tool to perform DNA microarray image analysis is presented, including a spot addressing method based on the image projections, the spot segmentation through contour based segmentation and the extraction of relevant information due to gene expression.

Keywords: Contour segmentation, DNA microarrays, edge detection, image processing, segmentation, spot addressing.

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

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

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

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Authors: Ahmed N. Shmroukh, Ahmed Hamza H. Ali, Ali K. Abel-Rahman

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This study is experimentally targeting to develop effective in heat and mass transfer processes for the adsorbate to obtain applicable adsorption capacity data. This is done by using fin and tube heat exchanger core and the adsorbate is adhesive over its surface and located as the core of the adsorber. The pairs are activated carbon powder/R-134a, activated carbon powder/R-407c, activated carbon powder/R-507A, activated carbon granules/R-507A, activated carbon granules/R-407c and activated carbon granules/R-134a, at different adsorption temperatures of 25, 30, 35 and 50°C. The following is results is obtained: at adsorption temperature of 25 °C the maximum adsorption capacity is found to be 0.8352kg/kg for activated carbon powder with R-134a and the minimum adsorption capacity found to be 0.1583kg/kg for activated carbon granules with R-407c. While, at adsorption temperature of 50°C the maximum adsorption capacity is found to be 0.3207kg/kg for activated carbon powder with R-134a and the minimum adsorption capacity found to be 0.0609kg/kg for activated carbon granules with R-407c. Therefore, the activated carbon powder/R-134a pair is highly recommended to be used as adsorption refrigeration working pair because of its higher maximum adsorption capacity than the other tested pairs, to produce a compact, efficient and reliable for long life performance adsorption refrigeration system.

Keywords: Adsorption, Adsorbent/Adsorbate Pairs, Adsorption Capacity, Refrigeration.

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Authors: C. Gunavathi, K. Premalatha

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

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

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: Begomovirus, AV1 gene, sequence, cloning, whitefly, okra, cotton, tomato, RAPD, phylogenetic tree and SDS-PAGE.

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Authors: Bezuidt O., Lima-Mendez G., Reva O. N.

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SeqWord Gene Island Sniffer, a new program for the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial genomes and further analyzed by sequence similarity and the functionality of encoded proteins. The results of this study are stored in an open database http://anjie.bi.up.ac.za/geidb/geidbhome. php). The developed computer program and the database provide the information valuable for further investigation of the distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.

Keywords: mobile genetic elements, virulence, bacterial genomes

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Authors: Yuan-Kang Shih, Shu-Li Chang, Shin-Shin Kao

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Qk n has been shown as an alternative to the hypercube family. For any even integer k ≥ 4 and any integer n ≥ 2, Qk n is a bipartite graph. In this paper, we will prove that given any pair of vertices, w and b, from different partite sets of Qk n, there exist 2n internally disjoint paths between w and b, denoted by {Pi | 0 ≤ i ≤ 2n-1}, such that 2n-1 i=0 Pi covers all vertices of Qk n. The result is optimal since each vertex of Qk n has exactly 2n neighbors.

Keywords: container, Hamiltonian, k-ary n-cube, m*-connected.

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Authors: Abtehal Y. Anaas, Mohd. Nazmi Bin Abd. Manap

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Meat Tenderness is one of the most important factors affecting consumers' assessment of meat quality. Variation in meat tenderness is genetically controlled and varies among breeds, and it is also influenced by environmental factors that can affect its creation during rigor mortis and postmortem. The final postmortem meat tenderization relies on the extent of proteolysis of myofibrillar proteins caused by the endogenous activity of the proteolytic calpain system. This calpain system includes different calcium-dependent cysteine proteases, and an inhibitor, calpastatin. It is widely accepted that in farm animals including chickens, the μ-calpain gene (CAPN1) is a physiological candidate gene for meat tenderness. This study aimed to identify the association of single nucleotide polymorphism (SNP) markers in the CAPN1 gene with the tenderness of chicken breast meat from two Malaysian native and commercial broiler breed crosses. Ten, five months old native chickens and ten, 42 days commercial broilers were collected from the local market and breast muscles were removed two hours after slaughter, packed separately in plastic bags and kept at -20ºC for 24 h. The tenderness phenotype for all chickens’ breast meats was determined by Warner-Bratzler Shear Force (WBSF). Thawing and cooking losses were also measured in the same breast samples before using in WBSF determination. Polymerase chain reaction (PCR) was used to identify the previously reported C7198A and G9950A SNPs in the CAPN1 gene and assess their associations with meat tenderness in the two breeds. The broiler breast meat showed lower shear force values and lower thawing loss rates than the native chickens (p<0.05), whereas there were similar in the rates of cooking loss. The study confirms some previous results that the markers CAPN1 C7198A and G9950A were not significantly associated with the variation in meat tenderness in chickens. Therefore, further study is needed to confirm the functional molecular mechanism of these SNPs and evaluate their associations in different chicken populations.

Keywords: CAPNl, chicken, meat tenderness, meat quality, SNPs.

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Authors: Amr A. El Hanafy, Muhammad Qureshi, Jamal Sabir, Mohamed Mutawakil, Mohamed M. Ahmed, Hassan El Ashmaoui, Hassan Ramadan, Mohamed Abou-Alsoud, Mahmoud Abdel Sadek

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Domestic goats (Capra hircus) are extremely diverse species and principal animal genetic resource of the developing world. These facilitate a persistent supply of meat, milk, fibre, and skin and are considered as important revenue generators in small pastoral environments. This study aimed to fingerprint β-LG gene at PCR-RFLP level in native Saudi goat breeds (Ardi, Habsi and Harri) in an attempt to have a preliminary image of β-LG genotypic patterns in Saudi breeds as compared to other foreign breeds such as Indian and Egyptian. Also, the Phylogenetic analysis was done to investigate evolutionary trends and similarities among the caprine β-LG gene with that of the other domestic specie, viz. cow, buffalo and sheep. Blood samples were collected from 300 animals (100 for each breed) and genomic DNA was extracted. A fragment of the β-LG gene (427bp) was amplified using specific primers. Subsequent digestion with Sac II restriction endonuclease revealed two alleles (A and B) and three different banding patterns or genotypes i.e. AA, AB and BB. The statistical analysis showed a general trend that β-LG AA genotype had higher milk yield than β-LG AB and β-LG BB genotypes. Nucleotide sequencing of the selected β-LG fragments was done and submitted to GenBank NCBI (Accession No. KJ544248, KJ588275, KJ588276, KJ783455, KJ783456 and KJ874959). Phylogenetic analysis on the basis of nucleotide sequences of native Saudi goats indicated evolutional similarity with the GenBank reference sequences of goat, Bubalus bubalis and Bos taurus. However, the origin of sheep which is the most closely related from the evolutionary point of view, was located some distance away.

Keywords: β-Lactoglobulin, Saudi goats, PCR-RFLP, Phylogenetic analysis.

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Authors: Sawangjit Sopid

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Atrazine, a herbicide widely used in sugarcane and corn production, is a frequently detected groundwater contaminant. An atrazine-degrading bacterium, strain KB02, was obtained from long-term atrazine-treated sugarcane field soils in Kanchanaburi province of Thailand. Strain KB02 had a rod-to-coccus morphological cycle during growth. Sequence analysis of the PCR product indicated that the 16S rRNA gene in strain KB02 was ranging from 97-98% identical to the same region in Klebsiella sp. Based on biochemical, physiological analysis and 16S rDNA sequence analysis of one representative isolate, strain KB02, the isolates belong to the genus Klebsiella in the family Enterobacteriaceae. Interestingly that the various primers for atzA, B and C failed to amplify genomic DNA of strain KB02. Whereas the expected PCR product of atzA, B and C were obtained from the reference strain, Arthrobacter sp. strain KU001.

Keywords: Atrazine, atz gene, Biodegradation, bioremediation, Klebsiella

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

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

Keywords: Exon, intron, miRNA, oncogene.

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Authors: Sitansu Kumar Verma, Soni Yadav, Jitendra Singh, Shraddha, Ajay Kumar

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MicroRNAs (miRNAs), a class of approximately 22 nucleotide long non coding RNAs which play critical role in different biological processes. The mature microRNA is usually 19–27 nucleotides long and is derived from a bigger precursor that folds into a flawed stem-loop structure. Mature micro RNAs are involved in many cellular processes that encompass development, proliferation, stress response, apoptosis, and fat metabolism by gene regulation. Resent finding reveals that certain viruses encode their own miRNA that processed by cellular RNAi machinery. In recent research indicate that cellular microRNA can target the genetic material of invading viruses. Cellular microRNA can be used in the virus life cycle; either to up regulate or down regulate viral gene expression Computational tools use in miRNA target prediction has been changing drastically in recent years. Many of the methods have been made available on the web and can be used by experimental researcher and scientist without expert knowledge of bioinformatics. With the development and ease of use of genomic technologies and computational tools in the field of microRNA biology has superior tremendously over the previous decade. This review attempts to give an overview over the genome wide approaches that have allow for the discovery of new miRNAs and development of new miRNA target prediction tools and databases.

Keywords: MicroRNAs, computational tools, gene regulation, databases, RNAi.

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Authors: Daniele Traversaro

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Problem: Senior citizens have been facing a challenging reality as a result of strict public health measures designed to protect people from the COVID-19 outbreak. These include the risk of social isolation due to the inability of the elderly to integrate with technology. Never before have Information and Communication Technology (ICT) skills become essential for their everyday life. Although third-age ICT education and lifelong learning are widely supported by universities and governments, there is a lack of literature on which teaching strategy/methodology to adopt in an entirely online ICT course aimed at third-age learners. This contribution aims to present an application of the Think-Pair-Share (TPS) learning method in an ICT third-age virtual classroom with an intergenerational approach to conducting online group labs and review activities. Research Question: Is collaborative learning suitable and effective, in terms of student engagement and learning outcomes, in an online ICT course for the elderly? Methods: In the TPS strategy a problem is posed by the teacher, students have time to think about it individually, and then they work in pairs (or small groups) to solve the problem and share their ideas with the entire class. We performed four experiments in the ICT course of the University of the Third Age of Genova (University of Genova, Italy) on the Microsoft Teams platform. The study cohort consisted of 26 students over the age of 45. Data were collected through online questionnaires. Two have been proposed, one at the end of the first activity and another at the end of the course. They consisted of five and three close-ended questions, respectively. The answers were on a Likert scale (from 1 to 4) except two questions (which asked the number of correct answers given individually and in groups) and the field for free comments/suggestions. Results: Groups achieve better results than individual students (with scores greater than one order of magnitude) and most students found TPS helpful to work in groups and interact with their peers. Insights: From these early results, it appears that TPS is suitable for an online third-age ICT classroom and useful for promoting discussion and active learning. Despite this, our work has several limitations. First of all, the results highlight the need for more data to be able to perform a statistical analysis in order to determine the effectiveness of this methodology in terms of student engagement and learning outcomes as future direction.

Keywords: Collaborative learning, information technology education, lifelong learning, older adult education, think-pair-share.

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Authors: Kobra Nalbandi, Bahram Baghban Kohnehrouz, Khalil Alami Saeed

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The low level of foreign genes expression in transgenic plants is a key factor that limits plant genetic engineering. Because of the critical regulatory activity of the promoters on gene transcription, they are studied extensively to improve the efficiency of the plant transgenic system. The strong constitutive promoters, such as CaMV 35S promoter and Ubiqutin 1 maize are usually used in plant biotechnology research. However the expression level of the foreign genes in all tissues is often undesirable. But using a strong seed-specific promoter to limit gene expression in the seed solves such problems. The purpose of this study is to isolate one of the seed specific promoters of Hordeum vulgare. So one of the common varieties of Hordeum vulgare in Iran was selected and their genomes extracted then the D-Hordein promoter amplified using the specific designed primers. Then the amplified fragment of the insert cloned in an appropriate vector and then transformed to E. coli. At last for the final admission of accuracy the cloned fragments sent for sequencing. Sequencing analysis showed that the cloned fragment DHPcontained motifs; like TATA box, CAAT-box, CCGTCC-box, AMYBOX1 and E-box etc., which constituted the seed-specific promoter activity. The results were compared with sequences existing in data banks. D-Hordein promoters of Alger has 99% similarity at 100 % coverage. The results also showed that D-Hordein promoter of barley and HMW promoter of wheat are too similar.

Keywords: Barley, Seed specific promoter, Hordein.

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Authors: Rostami F, Haj Hosseini R, Sharifi K, Daneshpour M, Azizi F, Hedayati M

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Expression and secretion of inflammation markers are disturbed in obesity. Interleukin-6 reduces body fat mass. The common G-174C polymorphism in the promoter of IL-6 gene has been reported that effects on transcriptional regulation. The objective was to investigate association of the common polymorphism G-174C with obesity in Iranian population. The present study is cross sectional association study that included 242 individuals (110 men and 132 women). Serum IL-6 levels, C-reactive protein, fasting blood glucose and blood lipids profile were measured .BMI and WHR were calculated. Genotyping is carried out by PCR and RFLP. The frequencies of G and C allele were 64.5% and 35.5%, respectively. The G-174C polymorphism was not associated with BMI and WHR. However in obese individual, fasting blood glucose was significantly higher in carrier of C allele compared with the noncarrier. The IL-6 G-174C polymorphism is not a risk factor for obesity in Iranian population.

Keywords: Interleukin 6, Polymorphism genetic, Obesity.

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Authors: Achraf El Allali, John R. Rose

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A number of competing methodologies have been developed to identify genes and classify DNA sequences into coding and non-coding sequences. This classification process is fundamental in gene finding and gene annotation tools and is one of the most challenging tasks in bioinformatics and computational biology. An information theory measure based on mutual information has shown good accuracy in classifying DNA sequences into coding and noncoding. In this paper we describe a species independent iterative approach that distinguishes coding from non-coding sequences using the mutual information measure (MIM). A set of sixty prokaryotes is used to extract universal training data. To facilitate comparisons with the published results of other researchers, a test set of 51 bacterial and archaeal genomes was used to evaluate MIM. These results demonstrate that MIM produces superior results while remaining species independent.

Keywords: Coding Non-coding Classification, Entropy, GeneRecognition, Mutual Information.

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Authors: R. K. Agrawal, Rajni Bala

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Developing an accurate classifier for high dimensional microarray datasets is a challenging task due to availability of small sample size. Therefore, it is important to determine a set of relevant genes that classify the data well. Traditionally, gene selection method often selects the top ranked genes according to their discriminatory power. Often these genes are correlated with each other resulting in redundancy. In this paper, we have proposed a hybrid method using feature ranking and wrapper method (Genetic Algorithm with multiclass SVM) to identify a set of relevant genes that classify the data more accurately. A new fitness function for genetic algorithm is defined that focuses on selecting the smallest set of genes that provides maximum accuracy. Experiments have been carried on four well-known datasets1. The proposed method provides better results in comparison to the results found in the literature in terms of both classification accuracy and number of genes selected.

Keywords: Gene selection, genetic algorithm, microarray datasets, multi-class SVM.

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Authors: J. Bernasovska, I. Boronova, J. Poracova, M. Mydlarova Blascakova, V. Szabadosova, P. Ruzbarsky, E. Petrejcikova, I. Bernasovsky

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The paper presents the results of the molecular genetics analysis in sports research, with special emphasis to use genetic information in diagnosing of motoric predispositions in Roma boys from East Slovakia. The ability and move are the basic characteristics of all living organisms. The phenotypes are influenced by a combination of genetic and environmental factors. Genetic tests differ in principle from the traditional motoric tests, because the DNA of an individual does not change during life. The aim of the presented study was to examine motion abilities and to determine the frequency of ACTN3 (R577X) gene in Roma children. Genotype data were obtained from 138 Roma and 155 Slovak boys from 7 to 15 years old. Children were investigated on physical performance level in association with their genotype. Biological material for genetic analyses comprised samples of buccal swabs. Genotypes were determined using Real Time High resolution melting PCR method (Rotor-Gene 6000 Corbett and Light Cycler 480 Roche). The software allows creating reports of any analysis, where information of the specific analysis, normalized and differential graphs and many information of the samples are shown. Roma children of analyzed group legged to non-Romany children at the same age in all the compared tests. The % distribution of R and X alleles in Roma children was different from controls. The frequency of XX genotype was 9.26%, RX 46.33% and RR was 44.41%. The frequency of XX genotype was 9.26% which is comparable to a frequency of an Indian population. Data were analyzed with the ANOVA test.

Keywords: ACTN3 gene, R577X polymorphism, Roma children, Slovakia, sports performance.

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Authors: Usha Chouhan, K. R. Pardasani

Abstract:

Phylogenies ; The evolutionary histories of groups of species are one of the most widely used tools throughout the life sciences, as well as objects of research with in systematic, evolutionary biology. In every phylogenetic analysis reconstruction produces trees. These trees represent the evolutionary histories of many groups of organisms, bacteria due to horizontal gene transfer and plants due to process of hybridization. The process of gene transfer in bacteria and hybridization in plants lead to reticulate networks, therefore, the methods of constructing trees fail in constructing reticulate networks. In this paper a model has been employed to reconstruct phylogenetic network in honey bee. This network represents reticulate evolution in honey bee. The maximum parsimony approach has been used to obtain this reticulate network.

Keywords: Hybridization, HGT, Reticulate networks, Recombination, Species, Parsimony.

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Authors: Mohamed El Morsy, Gabriela Achtenová

Abstract:

Research on damage of gears and gear pairs using vibration signals remains very attractive, because vibration signals from a gear pair are complex in nature and not easy to interpret. Predicting gear pair defects by analyzing changes in vibration signal of gears pairs in operation is a very reliable method. Therefore, a suitable vibration signal processing technique is necessary to extract defect information generally obscured by the noise from dynamic factors of other gear pairs.This article presents the value of cepstrum analysis in vehicle gearbox fault diagnosis. Cepstrum represents the overall power content of a whole family of harmonics and sidebands when more than one family of sidebands is present at the same time. The concept for the measurement and analysis involved in using the technique are briefly outlined. Cepstrum analysis is used for detection of an artificial pitting defect in a vehicle gearbox loaded with different speeds and torques. The test stand is equipped with three dynamometers; the input dynamometer serves asthe internal combustion engine, the output dynamometers introduce the load on the flanges of the output joint shafts. The pitting defect is manufactured on the tooth side of a gear of the fifth speed on the secondary shaft. Also, a method for fault diagnosis of gear faults is presented based on order Cepstrum. The procedure is illustrated with the experimental vibration data of the vehicle gearbox. The results show the effectiveness of Cepstrum analysis in detection and diagnosis of the gear condition.

Keywords: Cepstrum analysis, fault diagnosis, gearbox.

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Authors: Mai S. Mabrouk, Nahed H. Solouma, Abou-Bakr M. Youssef, Yasser M. Kadah

Abstract:

Many digital signal processing, techniques have been used to automatically distinguish protein coding regions (exons) from non-coding regions (introns) in DNA sequences. In this work, we have characterized these sequences according to their nonlinear dynamical features such as moment invariants, correlation dimension, and largest Lyapunov exponent estimates. We have applied our model to a number of real sequences encoded into a time series using EIIP sequence indicators. In order to discriminate between coding and non coding DNA regions, the phase space trajectory was first reconstructed for coding and non-coding regions. Nonlinear dynamical features are extracted from those regions and used to investigate a difference between them. Our results indicate that the nonlinear dynamical characteristics have yielded significant differences between coding (CR) and non-coding regions (NCR) in DNA sequences. Finally, the classifier is tested on real genes where coding and non-coding regions are well known.

Keywords: Gene prediction, nonlinear dynamics, correlation dimension, Lyapunov exponent.

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Authors: P. Ghasemi Dehkordi, A. Doosti, M. R. Hajimirzaei

Abstract:

TTV is an unenveloped circular single-stranded DNA virus with a diameter of 30-32 nm that first was described in 1997 in Japan. TTV was detected in various populations without proven pathology, including blood donors and in patients with chronic HBV and HCV hepatitis. The aim of this study was to determine the prevalence of TTV DNA in Iranian patients with chronic hepatitis B and C. Viral TTV-DNA was studied in 442 samples (202 with HBV, 138 with HCV and 102 controls) collected from west south of Iran. All extracted serum DNA was amplified by TTV ORF1 gene specific primers using the semi nested PCR technique. TTV DNA was detected in the serum of 8.9% and 10.8% patients with chronic hepatitis B and C, respectively. Prevalence of TTV-DNA in the serum of 102 controls was 2.9%. Results showed significant relation of TTV with HBV and HCV in patients by using T test examination (P<0.01). The prevalence of TTV-DNA in Iranian hepatitis B and C patients is rather high, and compare with other countries. To control and prevention of the distribution of TT-virus, examination of the blood and blood products it seems to be necessary.

Keywords: Transfusion-transmitted virus (TTV), Hepatitis Cvirus (HCV), Hepatitis B virus (HBV), ORF1 gene, Semi nested PCR, Iran.

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Authors: Yulia Irnidayanti, Win Darmanto, Agus Abadi

Abstract:

research goal was to determine the expression levels cDNA of brain embrio at gestation days 10 (GD-10). The Electroforesis DNA results showed that GAPDH, Fibronectin1, Ncam1, Tenascin, Vimentin, Neurofilament heavy, Neurofilament medium and Neurofilament low were 447 bp, 462 bp, 293 bp. 416 bp, 327 bp, 301 bp, 398 bp and 289 bp. Result of real-time RT-PCR on brain Embryo at gestation days 10 showed that the expression of copy gen Fibronectin 36 copies, Ncam 21,708 copies; Tenascin 24,505 copies; Vimentin 538,554 copies; Neurofilament heavy 2,419 copies; Neurofilament medium 92,928 copies; Neurofilament low 125,809 copies. Vimentin expressed gene copies is very high compared with other gene copies. This condition are caused by Vimentin, that contribute to proliferate of brain development. The vimentin role to cell proliferation of brain.

Keywords: GAPDH, Fibronectin, Ncam, Tenascin, vimentin, Neurofilamen heavy, Neurofilament medium, Neurofilamen low.

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