Search results for: gene pool

Authors: Neelima Gupta, Seema Aggarwal

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Most of the biclustering/projected clustering algorithms are based either on the Euclidean distance or correlation coefficient which capture only linear relationships. However, in many applications, like gene expression data and word-document data, non linear relationships may exist between the objects. Mutual Information between two variables provides a more general criterion to investigate dependencies amongst variables. In this paper, we improve upon our previous algorithm that uses mutual information for biclustering in terms of computation time and also the type of clusters identified. The algorithm is able to find biclusters with mixed relationships and is faster than the previous one. To the best of our knowledge, none of the other existing algorithms for biclustering have used mutual information as a similarity measure. We present the experimental results on synthetic data as well as on the yeast expression data. Biclusters on the yeast data were found to be biologically and statistically significant using GO Tool Box and FuncAssociate.

Keywords: Biclustering, mutual information.

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Authors: Laura Lukmanto, Harya Widiputra, Lukas

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Studies in economics domain tried to reveal the correlation between stock markets. Since the globalization era, interdependence between stock markets becomes more obvious. The Dynamic Interaction Network (DIN) algorithm, which was inspired by a Gene Regulatory Network (GRN) extraction method in the bioinformatics field, is applied to reveal important and complex dynamic relationship between stock markets. We use the data of the stock market indices from eight countries around the world in this study. Our results conclude that DIN is able to reveal and model patterns of dynamic interaction from the observed variables (i.e. stock market indices). Furthermore, it is also found that the extracted network models can be utilized to predict movement of the stock market indices with a considerably good accuracy.

Keywords: complex dynamic relationship, dynamic interaction network, interactive stock markets, stock market interdependence.

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Authors: Fuad M. Alkoot

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DNA data have been used in forensics for decades. However, current research looks at using the DNA as a biometric identity verification modality. The goal is to improve the speed of identification. We aim at using gene data that was initially used for autism detection to find if and how accurate is this data for identification applications. Mainly our goal is to find if our data preprocessing technique yields data useful as a biometric identification tool. We experiment with using the nearest neighbor classifier to identify subjects. Results show that optimal classification rate is achieved when the test set is corrupted by normally distributed noise with zero mean and standard deviation of 1. The classification rate is close to optimal at higher noise standard deviation reaching 3. This shows that the data can be used for identity verification with high accuracy using a simple classifier such as the k-nearest neighbor (k-NN). 

Keywords: Biometrics, identity verification, genetic data, k-nearest neighbor.

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Authors: J. Dutta, Narendranath S.

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In this research article a comprehensive investigation has been carried out to determine the effect of thermal cycle on temperature dependent process parameters developed during gas tungsten arc (GTA) welding of high carbon (AISI 1090) steel butt joints. An experiment based thermal analysis has been performed to obtain the thermal history. We have focused on different thermophysical properties such as thermal conductivity, heat transfer coefficient and cooling rate. Angular torch model has been utilized to find out the surface heat flux and its variation along the fusion zone as well as along the longitudinal direction from fusion boundary. After welding and formation of weld pool, heat transfer coefficient varies rapidly in the vicinity of molten weld bead and heat affected zone. To evaluate the heat transfer coefficient near the fusion line and near the rear end of the plate (low temperature region), established correlation has been implemented and has been compared with empirical correlation which is noted as coupled convective and radiation heat transfer coefficient. Change in thermal conductivity has been visualized by analytical model of moving point heat source. Rate of cooling has been estimated by using 2-dimensional mathematical expression of cooling rate and it has shown good agreement with experimental temperature cycle. Thermophysical properties have been varied randomly within 0 -10s time span.

Keywords: Thermal history, Gas tungsten arc welding, Butt joint, High carbon steel.

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Authors: Sing-Wu Liou, Yin-Fu Huang

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For identifying the discriminative sequence features between exons and introns, a new paradigm, rescaled-range frameshift analysis (RRFA), was proposed. By RRFA, two new sequence features, the frameshift sensitivity (FS) and the accumulative penta-mer complexity (APC), were discovered which were further integrated into a new feature of larger scale, the persistency in anti-mutation (PAM). The feature-validation experiments were performed on six model organisms to test the power of discrimination. All the experimental results highly support that FS, APC and PAM were all distinguishing features between exons and introns. These identified new sequence features provide new insights into the sequence composition of genes and they have great potentials of forming a new basis for recognizing the exonintron boundaries in gene sequences.

Keywords: Exon-Intron Discrimination, Rescaled-Range Frameshift Analysis, Frameshift Sensitivity, Accumulative Sequence Complexity

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Authors: Shilpy Sharma

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As the web continues to grow exponentially, the idea of crawling the entire web on a regular basis becomes less and less feasible, so the need to include information on specific domain, domain-specific search engines was proposed. As more information becomes available on the World Wide Web, it becomes more difficult to provide effective search tools for information access. Today, people access web information through two main kinds of search interfaces: Browsers (clicking and following hyperlinks) and Query Engines (queries in the form of a set of keywords showing the topic of interest) [2]. Better support is needed for expressing one's information need and returning high quality search results by web search tools. There appears to be a need for systems that do reasoning under uncertainty and are flexible enough to recover from the contradictions, inconsistencies, and irregularities that such reasoning involves. In a multi-view problem, the features of the domain can be partitioned into disjoint subsets (views) that are sufficient to learn the target concept. Semi-supervised, multi-view algorithms, which reduce the amount of labeled data required for learning, rely on the assumptions that the views are compatible and uncorrelated. This paper describes the use of semi-structured machine learning approach with Active learning for the “Domain Specific Search Engines". A domain-specific search engine is “An information access system that allows access to all the information on the web that is relevant to a particular domain. The proposed work shows that with the help of this approach relevant data can be extracted with the minimum queries fired by the user. It requires small number of labeled data and pool of unlabelled data on which the learning algorithm is applied to extract the required data.

Keywords: Search engines; machine learning, Informationretrieval, Active logic.

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Authors: Sh. A. Yousif, M. Bhave

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There is strong evidence that water channel proteins 'aquaporins (AQPs)' are central components in plant-water relations as well as a number of other physiological parameters. We had previously reported the isolation of 24 plasma membrane intrinsic protein (PIP) type AQPs. However, the gene numbers in rice and the polyploid nature of bread wheat indicated a high probability of further genes in the latter. The present work focused on identification of further AQP isoforms in bread wheat. With the use of altered primer design, we identified five genes homologous, designated PIP1;5b, PIP2;9b, TaPIP2;2, TaPIP2;2a, TaPIP2;2b. Sequence alignments indicate PIP1;5b, PIP2;9b are likely to be homeologues of two previously reported genes while the other three are new genes and could be homeologs of each other. The results indicate further AQP diversity in wheat and the sequence data will enable physical mapping of these genes to identify their genomes as well as genetic to determine their association with any quantitative trait loci (QTLs) associated with plant-water relation such as salinity or drought tolerance.

Keywords: Aquaporins, homeologues, PIP, wheat

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Authors: Öznur Özge Özcan, Canan Sercan, Hamza Kulaksız, Mesut Karahan, Korkut Ulucan

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Genetic structure is very important to understand the brain dopamine system which is related to athletic performance. Hopefully, there will be enough studies about athletics performance in the terms of addiction-related genetic markers in the future. In the present study, we intended to investigate the Receptor-2 Gene (DRD2) rs1800497, which is related to brain dopaminergic system. 10 sprinter and 10 endurance athletes were enrolled in the study. Real-Time Polymerase Chain Reaction method was used for genotyping. According to results, A1A1, A1A2 and A2A2 genotypes in athletes were 0 (%0), 3 (%15) and 17 (%85). A1A1 genotype was not found and A2 allele was counted as the dominating allele in our cohort. These findings show that dopaminergic mechanism effects on sport genetic may be explained by the polygenic and multifactorial view.

Keywords: Addiction, athletic performance, genotype, polymorphism, sport genetics.

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Authors: Mina Alibeigi, Sattar Hashemi, Ali Hamzeh

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Since dealing with high dimensional data is computationally complex and sometimes even intractable, recently several feature reductions methods have been developed to reduce the dimensionality of the data in order to simplify the calculation analysis in various applications such as text categorization, signal processing, image retrieval, gene expressions and etc. Among feature reduction techniques, feature selection is one the most popular methods due to the preservation of the original features. In this paper, we propose a new unsupervised feature selection method which will remove redundant features from the original feature space by the use of probability density functions of various features. To show the effectiveness of the proposed method, popular feature selection methods have been implemented and compared. Experimental results on the several datasets derived from UCI repository database, illustrate the effectiveness of our proposed methods in comparison with the other compared methods in terms of both classification accuracy and the number of selected features.

Keywords: Feature, Feature Selection, Filter, Probability Density Function

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Authors: Frank Emmert Streib, Matthias Dehmer, Gökhan H. Bakır, Max Mühlhauser

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In this paper we investigate the influence of external noise on the inference of network structures. The purpose of our simulations is to gain insights in the experimental design of microarray experiments to infer, e.g., transcription regulatory networks from microarray experiments. Here external noise means, that the dynamics of the system under investigation, e.g., temporal changes of mRNA concentration, is affected by measurement errors. Additionally to external noise another problem occurs in the context of microarray experiments. Practically, it is not possible to monitor the mRNA concentration over an arbitrary long time period as demanded by the statistical methods used to learn the underlying network structure. For this reason, we use only short time series to make our simulations more biologically plausible.

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

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Authors: Chinwendu R. Nnabalu, Gioia Falcone, Imma Bortone

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Petroleum refining is a chemical process in which the raw material (crude oil) is converted to finished commercial products for end users. The fluid catalytic cracking (FCC) unit is a key asset in refineries, requiring optimised processes in the context of engineering design. Following the first stage of separation of crude oil in a distillation tower, an additional 40 per cent quantity is attainable in the gasoline pool with further conversion of the downgraded product of crude oil (residue from the distillation tower) using a catalyst in the FCC process. Effective removal of sulphur oxides, nitrogen oxides, carbon and heavy metals from FCC gasoline requires greater separation efficiency and involves an enormous environmental significance. The FCC unit is primarily a reactor and regeneration system which employs cyclone systems for separation.  Catalyst losses in FCC cyclones lead to high particulate matter emission on the regenerator side and fines carryover into the product on the reactor side. This paper aims at demonstrating the importance of FCC unit design criteria in terms of technical performance and compliance with environmental legislation. A systematic review of state-of-the-art FCC technology was carried out, identifying its key technical challenges and sources of emissions.  Case studies of petroleum refineries in Nigeria were assessed against selected global case studies. The review highlights the need for further modelling investigations to help improve FCC design to more effectively meet product specification requirements while complying with stricter environmental legislation.

Keywords: Design, emissions, fluid catalytic cracking, petroleum refineries.

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Authors: JiEun Jeong, Dong Hyun Kim, Bharat Bhusan Patnaik, Se Won Kang, HeeJu Hwang, Yong Hun Jo, Dae-Hyun Seog, YeonSooHan, Yong Seok Lee

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An expressed sequence tag (EST) analysis provideus portions of expressed genes. We have constructed cDNA library and determined randomly sequences from cDNA library clones of T. molitor injected with acholeplasma lysate. We identified the homologous to a galectin gene. As the result of cloning and characterization of novel, we found that the protein has an open reading frame (ORF) of 495 bp, with 164 amino acid residues and molecular weight of 18.5 kDa. To characterize the role of novel Tm-galectin in immune system, we quantified the mRNA level of galectin at different times after treatment with immune elicitors. The galectin mRNA was up-regulated about 7-folds within 18 hrs. This suggests that Tm-galectin is a novel member of animal lectins, and has a role in the process of pathogen recognition. Our study would be helpful for the study on immune defense system and signaling cascade.

Keywords: EST, Innate immunity, Tenebrio molitor, Galectin.

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Authors: Anjali Haloi, Debabrata Das

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Silver nanoparticles inhibit a wide variety of microorganisms. The mechanism of inhibition is not entirely known although it is recognized to be concentration dependent and associated with the disruption of membrane permeability. Data on differential gene expression as a response to nanoparticles could provide insights into the mechanism of this inhibitory effect. Silver nanoparticles were synthesized in yeast growth media using a modification of the Creighton method and characterized with UV-Vis spectrophotometry, transmission electron microscopy (TEM), and X-ray diffraction (XRD). In yeasts grown in the presence of silver nanoparticles, we observed that at concentrations below the minimum inhibitory concentration (MIC) of 48.51 µg/ml, the total RNA content was steady while the cellular protein content declined rapidly. The analysis of the expression levels of KRR1 and PWP2, two important genes involved in rRNA maturation in yeasts, showed up to 258 and 42-fold decreases, respectively, compared to that of control samples. Whether silver nanoparticles have an adverse effect on ribosome assembly and function could be an area of further investigation.

Keywords: Ag NP, yeast, qRT-PCR, KRR1, PWP2.

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Authors: Hongjoong Sin, Jangsoo Lee, Sungju Lee, Seunghwan Yoo, Sanghyuck Lee, Jaesik Lee, Yongjun Lee, Sungchun Kim

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Wireless sensor networks are consisted of hundreds or thousands of small sensors that have limited resources. Energy-efficient techniques are the main issue of wireless sensor networks. This paper proposes an energy efficient agent-based framework in wireless sensor networks. We adopt biologically inspired approaches for wireless sensor networks. Agent operates automatically with their behavior policies as a gene. Agent aggregates other agents to reduce communication and gives high priority to nodes that have enough energy to communicate. Agent behavior policies are optimized by genetic operation at the base station. Simulation results show that our proposed framework increases the lifetime of each node. Each agent selects a next-hop node with neighbor information and behavior policies. Our proposed framework provides self-healing, self-configuration, self-optimization properties to sensor nodes.

Keywords: Agent, Energy Efficiency, Genetic algorithm, Wireless Sensor Networks.

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Authors: D. Estrella, A. Silva, R. Zapata, H. Rubio

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A total of 100 primary caregivers (mothers, fathers, grandparents) with at least one child or grandchild with a diagnosis of congenital bilateral profound deafness were assessed in order to evaluate the functionality of families with a deaf member, who was evaluated by specialists in audiology, molecular biology, genetics and psychology. After confirmation of the clinical diagnosis, DNA from the patients and parents were analyzed in search of the 35delG deletion of the GJB2 gene to determine who possessed the mutation. All primary caregivers were provided psychological support, regardless of whether or not they had the mutation, and prior and subsequent, the family APGAR test was applied. All parents, grandparents were informed of the results of the genetic analysis during the psychological intervention. The family APGAR, after psychological and genetic counseling, showed that 14% perceived their families as functional, 62% moderately functional and 24% dysfunctional. This shows the importance of psychological support in family functionality that has a direct impact on the quality of life of these families.

Keywords: Deafness, psychological support, family, adaptation to disability.

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Authors: Yuhong Lu

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Graves’ Disease (GD), an autoimmune health condition caused by the over reactiveness of the thyroid, affects about 1 in 200 people worldwide. GD is not caused by one specific single nucleotide polymorphism (SNP) or gene mutation, but rather determined by multiple factors, each differing from each other. Malfunction of the genes in Human Leukocyte Antigen (HLA) family tend to play a major role in autoimmune diseases, but other genes, such as LOC101929163, have functions that still remain ambiguous. Currently, little studies were done to study GD, resulting in inconclusive results. This study serves not only to introduce background knowledge about GD, but also to organize and pinpoint the major SNPs and genes that are potentially related to the occurrence of GD in humans. Collected from multiple sources from genome-wide association studies (GWAS) Central, the potential SNPs related to the causes of GD are included in this study. This study has located the genes that are related to those SNPs and closely examines a selected sample. Using the data from this study, scientists will then be able to focus on the most expressed genes in GD patients and develop a treatment for GD.

Keywords: CTLA4, Graves’ Disease, HLA, single nucleotide polymorphism, SNP.

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Authors: S. Fallah, M. Seifi, M. Firoozrai, T. Godarzi, M. Jafarzadeh, L. H. Ghohari

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The ε4 allele of the ε2, ε3 and ε4 protein isoform polymorphism in the gene encoding apolipoprotein E (Apo E) has previously been associated with increased cardiac artery disease (CAD); therefore to investigate the significance of this polymorphism in pathogenesis of CAD in Iranian patients with stenosis and control subjects. To investigate the association between  Apo E polymorphism and coronary artery disease we performed a comparative case control study of the frequency of Apo E  polymorphism in One hundred CAD patients with stenosis who underwent coronary angiography (>50% stenosis) and 100 control subjects (<10% stenosis). The Apo E alleles and genotypes were determined by polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP). We observed an association between the Apo E polymorphism and CAD in this study. These data suggest that the Apo ε4 and ε2 alleles increase the risk for CAD in Iranian population (χ2 =4.26, p= 0.05, OR=2 and χ2 =0.38, p=0.53, OR=1.2). These results suggest that ε4 and ε2 alleles are risk factors for stenosis.

Keywords: Arterial blood vessels, atherosclerosis, cholesterol.

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Authors: Li-Yeh Chuang, Yu-Jen Hou, Jr., Cheng-Hong Yang

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Single nucleotide polymorphisms (SNPs) hold much promise as a basis for disease-gene association. However, research is limited by the cost of genotyping the tremendous number of SNPs. Therefore, it is important to identify a small subset of informative SNPs, the so-called tag SNPs. This subset consists of selected SNPs of the genotypes, and accurately represents the rest of the SNPs. Furthermore, an effective evaluation method is needed to evaluate prediction accuracy of a set of tag SNPs. In this paper, a genetic algorithm (GA) is applied to tag SNP problems, and the K-nearest neighbor (K-NN) serves as a prediction method of tag SNP selection. The experimental data used was taken from the HapMap project; it consists of genotype data rather than haplotype data. The proposed method consistently identified tag SNPs with considerably better prediction accuracy than methods from the literature. At the same time, the number of tag SNPs identified was smaller than the number of tag SNPs in the other methods. The run time of the proposed method was much shorter than the run time of the SVM/STSA method when the same accuracy was reached.

Keywords: Genetic Algorithm (GA), Genotype, Single nucleotide polymorphism (SNP), tag SNPs.

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Authors: Kritsada Khongnomnan, Wittaya Poomipak, Yong Poovorawan, Sunchai Payungporn

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In this study, three subtypes of influenza A viruses (pH1N1, H5N1 and H3N2) which naturally infected human were analyzed by bioinformatic approaches to find candidate human cellular miRNAs targeting viral genomes. There were 76 miRNAs targeting influenza A viruses. Among these candidates, 70 miRNAs were subtypes specifically targeting each subtype of influenza A virus including 21 miRNAs targeted subtype H1N1, 27 miRNAs targeted subtype H5N1 and 22 miRNAs targeted subtype H3N2. The remaining 6 miRNAs target on multiple subtypes of influenza A viruses. Uniquely, hsa-miR-3145 is the only one candidate miRNA targeting PB1 gene of all three subtypes. Obviously, most of the candidate miRNAs are targeting on polymerase complex genes (PB2, PB1 and PA) of influenza A viruses. This study predicted potential human miRNAs targeting on different subtypes of influenza A viruses which might be useful for inhibition of viral replication and for better understanding of the interaction between virus and host cell.

Keywords: Human miRNAs, Influenza A viruses, H1N1, H5N1, H3N2

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Authors: Zeinep A. Berkimbayeva, Almagul T. Mansharipova, Elmira M. Khussainova, Leyla B. Djansugurova

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It is believed that DNA damaging toxic metabolites contributes to the development of different pathological conditions. To prevent harmful influence of toxic agents, cells developed number of protecting mechanisms, such as enzymatic reaction of detoxification of reactive metabolites and repair of DNA damage. The aim of the study was to examine the association between polymorphism of GSTT1/GSTM1 and XRCC1/3 genes and coronary artery disease (CAD) incidence. To examine a polymorphism of these genes in CAD susceptibility in patients and controls, PCR based genotyping assay was performed. For GST genes, frequency of GSTM1 null genotype among CAD affected group was significantly increased than in control group (P<0.001). Frequencies of the GSTT1 null and positive alleles are almost equal in both groups (P>0.1). We found that neither XRCC1 Arg399Gln nor XRCC3 Thr241Met were associated with CAD risk. Obtained data suggests that GSTM1 null genotype carriers are more susceptible to CAD development.

Keywords: Cardiovascular disease, DNA reparation, gene polymorphism, risk factors, xenobiotic detoxification.

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Authors: N. B. Dhayanithi, T. T. Ajith Kumar, T. Balasubramanian

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Present study summarizes the control of Vibrio alginolyticus infection in hatchery reared Clownfish, Amphiprion sebae with the extract of the mangrove plant, Avicennia marina. Fishes with visible symptoms of hemorrhagic spots were chosen and the genomic DNA of the causative bacterium was isolated and sequenced based on 16S rDNA gene. The in vitro assay revealed that a fraction of A. marina leaf extract elucidated with ethyl acetate: methanol (6:4) showed a high activity (28 mm) at 125 μg/ml concentrations. About 4 % of the fraction fed along with live V. alginolyticus was significantly decreased the cumulative mortality (P<0.05) in the experimental groups than the control group. The responsible fraction was investigated by gas chromatography - mass spectroscopy and found the presence of active compounds. This is the first research in India to control vibriosis infection in marine ornamental fish with mangrove leaf extract.

Keywords: Amphiprion seabe, Avicennia marina, Gas Chromatography - Mass Spectroscopy, Vibrio alginolyticus

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: H. Sakamoto, Y. Nakagawara, S. Oguri

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Drought stress is a critical environmental factor that adversely affects crop productivity and quality. Because of their immobile nature, plants have evolved mechanisms to sense and respond to drought stress. We identified a novel locus of Arabidopsis, designated DRA1 (drought responsive ankyrin1), whose disruption leads to increased drought-stress tolerance. DRA1 encodes a transmembrane protein with an ankyrin-repeat motif that has been implicated in diverse cellular processes such as signal transduction. RT-PCR analysis revealed that there were at least two splicing variants of DRA1 transcripts in wild-type plants. In response to drought stress, the levels of DRA1 transcripts retaining second and third introns were increased, whereas these introns were removed under unstressed conditions. These results suggest that DRA1 protein may negatively regulate plant drought tolerance and that the expression of DRA1is regulated in response to drought stress by alternative splicing.

Keywords: Alternative splicing, ankyrin repeat, Arabidopsis, drought tolerance.

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Authors: Oktavian Muhammad Rizki, Appiah Rita, Lastres Oscar, Miller True, Chapman Alec, Tsoukalas Lefteri H.

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The Purdue University Research Reactor-1 (PUR-1) is a 10 kWth pool-type research reactor located at Purdue University’s West Lafayette campus. The reactor was recently upgraded to use entirely digital instrumentation and control systems. However, currently, there is no automated control system to regulate the power in the reactor. We propose a fuzzy logic controller as a form of digital twin to complement the existing digital instrumentation system to monitor and stabilize power control using existing experimental data. This work assesses the feasibility of a power controller based on a Fuzzy Rule-Based System (FRBS) by modelling and simulation with a MATLAB algorithm. The controller uses power error and reactor period as inputs and generates reactivity insertion as output. The reactivity insertion is then converted to control rod height using a logistic function based on information from the recorded experimental reactor control rod data. To test the capability of the proposed fuzzy controller, a point-kinetic reactor model is utilized based on the actual PUR-1 operation conditions and a Monte Carlo N-Particle simulation result of the core to numerically compute the neutronics parameters of reactor behavior. The Point Kinetic Equation (PKE) was employed to model dynamic characteristics of the research reactor since it explains the interactions between the spatial and time varying input and output variables efficiently. The controller is demonstrated computationally using various cases: startup, power maneuver, and shutdown. From the test results, it can be proved that the implemented fuzzy controller can satisfactorily regulate the reactor power to follow demand power without compromising nuclear safety measures.

Keywords: Fuzzy logic controller, power controller, reactivity, research reactor.

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Authors: JiEun Jeong, Se-Won Kang, Hee-Ju Hwang, Sung-Hwa Chae, Sang-Haeng Choi, Hong-SeogPark, YeonSoo Han, Bok-Reul Lee, Dae-Hyun Seog, Yong Seok Lee

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Tofurther advance research on immune-related genes from T. molitor, we constructed acDNA library and analyzed expressed sequence taq (EST) sequences from 1,056 clones. After removing vector sequence and quality checkingthrough thePhred program (trim_alt 0.05 (P-score>20), 1039 sequences were generated. The average length of insert was 792 bp. In addition, we identified 162 clusters, 167 contigs and 391 contigs after clustering and assembling process using a TGICL package. EST sequences were searchedagainst NCBI nr database by local BLAST (blastx, EKeywords: EST, Innate immunity, Tenebriomolitor

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Authors: P. O. Angienda, B. O. Aketch, E. N. Waindi

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Juvenile Nile tilapia subjected to heat treatment at temperatures ranging from 260C to 370C showed positive correlation (P<0.01) between treatment temperatures and resultant sex ratios, while, survival rate of the fry showed a negative correlation against temperature (P<0.01). The optimal temperature for both sex shift towards males and survival rates was 36±0.5°C, producing male percentage of 86.31 and a fry survival of 65.25. To determine the genetic basis of temperature sex-determination in Nile tilapia, we employed three microsatellite markers (Abur36, Abur100 and UNH846). Abur36 predicted the sex of 95% of the heat induced individuals, suggesting that the locus influence sex ratio and its interaction with temperature result in male biased sex ratio. This locus could turn out to be the major sex determining gene operating in Nile tilapia. These markers could be used in marker-assisted selection to select genotypes that give a higher percentage of males for commercial production.

Keywords: Heat treatment, Microsatellite, Nile tilapia, sex-determination.

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Authors: Assyl Bari, Olga Berillo, Saltanat Orazova, Anatoliy Ivashchenko

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Among all microRNAs (miRNAs) in 12 plant species investigated in this study, only miR398 targeted the copper chaperone for superoxide dismutase (CCS). The nucleotide sequences of miRNA binding sites were located in the mRNA protein-coding sequence (CDS) and were highly homologous. These binding sites in CCS mRNA encoded a conservative GDLGTL hexapeptide. The binding sites for miR398 in the CDS of superoxide dismutase 1 mRNA encoded GDLGN pentapeptide. The conservative miR398 binding site located in the CDS of superoxide dismutase 2 mRNA encoded the GDLGNI hexapeptide. The miR398 binding site in the CDS of superoxide dismutase 3 mRNA encoded the GDLGNI or GDLGNV hexapeptide. Gene expression of the entire superoxide dismutase family in the studied plant species was regulated only by miR398. All members of the miR398 family, i.e. miR398a,b,c were connected to one site for each CuZnSOD and chaperone mRNA.

Keywords: MicroRNA, mRNA, plant, superoxide dismutase.

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Authors: Ali Anaissi, Paul J. Kennedy, Madhu Goyal

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Analysis and visualization of microarraydata is veryassistantfor biologists and clinicians in the field of diagnosis and treatment of patients. It allows Clinicians to better understand the structure of microarray and facilitates understanding gene expression in cells. However, microarray dataset is a complex data set and has thousands of features and a very small number of observations. This very high dimensional data set often contains some noise, non-useful information and a small number of relevant features for disease or genotype. This paper proposes a non-linear dimensionality reduction algorithm Local Principal Component (LPC) which aims to maps high dimensional data to a lower dimensional space. The reduced data represents the most important variables underlying the original data. Experimental results and comparisons are presented to show the quality of the proposed algorithm. Moreover, experiments also show how this algorithm reduces high dimensional data whilst preserving the neighbourhoods of the points in the low dimensional space as in the high dimensional space.

Keywords: Linear Dimension Reduction, Non-Linear Dimension Reduction, Principal Component Analysis, Biologists.

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Authors: Henrik L. Funke, Lars Ulke-Winter, Sandra Gelbrich, Lothar Kroll

Abstract:

This work reports about an approach for an automatic adaptation of concrete formulations based on genetic algorithms (GA) to optimize a wide range of different fit-functions. In order to achieve the goal, a method was developed which provides a numerical description of a fibre reinforced concrete (FRC) mixture regarding the production technology and the property spectrum of the concrete. In a first step, the FRC mixture with seven fixed components was characterized by varying amounts of the components. For that purpose, ten concrete mixtures were prepared and tested. The testing procedure comprised flow spread, compressive and bending tensile strength. The analysis and approximation of the determined data was carried out by GAs. The aim was to obtain a closed mathematical expression which best describes the given seven-point cloud of FRC by applying a Gene Expression Programming with Free Coefficients (GEP-FC) strategy. The seven-parametric FRC-mixtures model which is generated according to this method correlated well with the measured data. The developed procedure can be used for concrete mixtures finding closed mathematical expressions, which are based on the measured data.

Keywords: Concrete design, fibre reinforced concrete, genetic algorithms, GEP-FC.

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

Abstract:

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

Keywords: MRSA, mecA genes, ICU, colonization.

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