Search results for: gene pair ranking.

Authors: Ali Raad Hassan

Abstract:

Contact stress analysis between two spur gear teeth was considered in different contact positions, representing a pair of mating gears during rotation. A programme has been developed to plot a pair of teeth in contact. This programme was run for each 3° of pinion rotation from the first location of contact to the last location of contact to produce 10 cases. Each case was represented a sequence position of contact between these two teeth. The programme gives graphic results for the profiles of these teeth in each position and location of contact during rotation. Finite element models were made for these cases and stress analysis was done. The results were presented and finite element analysis results were compared with theoretical calculations, wherever available.

Keywords: Contact stress, Spur gear, Contact ratio, Finite elements

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Authors: Mohammad Javad Kargar, Fatemeh Azimzadeh

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The vast amount of information on the World Wide Web is created and published by many different types of providers. Unlike books and journals, most of this information is not subject to editing or peer review by experts. This lack of quality control and the explosion of web sites make the task of finding quality information on the web especially critical. Meanwhile new facilities for producing web pages such as Blogs make this issue more significant because Blogs have simple content management tools enabling nonexperts to build easily updatable web diaries or online journals. On the other hand despite a decade of active research in information quality (IQ) there is no framework for measuring information quality on the Blogs yet. This paper presents a novel experimental framework for ranking quality of information on the Weblog. The results of data analysis revealed seven IQ dimensions for the Weblog. For each dimension, variables and related coefficients were calculated so that presented framework is able to assess IQ of Weblogs automatically.

Keywords: Information Quality, Weblog, Web Ranking, Web- Quality.

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Authors: Aji P. Wibawa, Andrew Nafalski, Neil Murray, Wayan F. Mahmudy

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Parallel text alignment is proposed as a way of aligning bahasa Indonesia to words in Javanese. Since the one-to-one word translator does not have the facility to translate pragmatic aspects of Javanese, the parallel text alignment model described uses a phrase pair combination. The algorithm aligns the parallel text automatically from the beginning to the end of each sentence. Even though the results of the phrase pair combination outperform the previous algorithm, it is still inefficient. Recording all possible combinations consume more space in the database and time consuming. The original algorithm is modified by applying the edit distance coefficient to improve the data-storage efficiency. As a result, the data-storage consumption is 90% reduced as well as its learning period (42s).

Keywords: Parallel text alignment, phrase pair combination, edit distance coefficient, Javanese-Indonesian language.

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Authors: Min Yao, Kota Aoki, Hiroshi Nagahashi

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In this paper, a novel system recognition of human faces without using face different color photographs is proposed. It mainly in face detection, normalization and recognition. Foot method of combination of Haar-like face determined segmentation and region-based histogram stretchi (RHST) is proposed to achieve more accurate perf using Haar. Apart from an effective angle norm side-face (pose) normalization, which is almost a might be important and beneficial for the prepr introduced. Then histogram-based and photom normalization methods are investigated and ada retinex (ASR) is selected for its satisfactory illumin Finally, weighted multi-block local binary pattern with 3 distance measures is applied for pair-mat Experimental results show its advantageous perfo with PCA and multi-block LBP, based on a principle.

Keywords: Face detection, pair-matching rec normalization, skin color segmentation.

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Authors: I. Nassiri, B. Goliaei, M. Tavassoli

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The ability to distinguish missense nucleotide substitutions that contribute to harmful effect from those that do not is a difficult problem usually accomplished through functional in vivo analyses. In this study, instead current biochemical methods, the effects of missense mutations upon protein structure and function were assayed by means of computational methods and information from the databases. For this order, the effects of new missense mutations in exon 5 of PTEN gene upon protein structure and function were examined. The gene coding for PTEN was identified and localized on chromosome region 10q23.3 as the tumor suppressor gene. The utilization of these methods were shown that c.319G>A and c.341T>G missense mutations that were recognized in patients with breast cancer and Cowden disease, could be pathogenic. This method could be use for analysis of missense mutation in others genes.

Keywords: Bioinformatics, missense mutations, PTEN tumorsuppressor gene.

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Authors: T. Chandrasekhar, K. Thangavel, E. N. Sathishkumar

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Microarrays are made it possible to simultaneously monitor the expression profiles of thousands of genes under various experimental conditions. It is used to identify the co-expressed genes in specific cells or tissues that are actively used to make proteins. This method is used to analysis the gene expression, an important task in bioinformatics research. Cluster analysis of gene expression data has proved to be a useful tool for identifying co-expressed genes, biologically relevant groupings of genes and samples. In this work K-Means algorithms has been applied for clustering of Gene Expression Data. Further, rough set based Quick reduct algorithm has been applied for each cluster in order to select the most similar genes having high correlation. Then the ACV measure is used to evaluate the refined clusters and classification is used to evaluate the proposed method. They could identify compact clusters with feature selection method used to genes are selected.

Keywords: Clustering, Feature selection, Gene expression data, Quick reduct.

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Authors: Dalibor Fiala, Karel Jezek, Francois Rousselot

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In this paper, we present a methodology for finding authoritative researchers by analyzing academic Web sites. We show a case study in which we concentrate on a set of Czech computer science departments- Web sites. We analyze the relations between them via hyperlinks and find the most important ones using several common ranking algorithms. We then examine the contents of the research papers present on these sites and determine the most authoritative Czech authors.

Keywords: Authorities, citation analysis, prestige, ranking algorithms, Web mining.

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Authors: R.Guzman-Martinez, Oscar Garcia-Olalla, R.Alaiz-Rodriguez

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Feature selection plays an important role in applications with high dimensional data. The assessment of the stability of feature selection/ranking algorithms becomes an important issue when the dataset is small and the aim is to gain insight into the underlying process by analyzing the most relevant features. In this work, we propose a graphical approach that enables to analyze the similarity between feature ranking techniques as well as their individual stability. Moreover, it works with whatever stability metric (Canberra distance, Spearman's rank correlation coefficient, Kuncheva's stability index,...). We illustrate this visualization technique evaluating the stability of several feature selection techniques on a spectral binary dataset. Experimental results with a neural-based classifier show that stability and ranking quality may not be linked together and both issues have to be studied jointly in order to offer answers to the domain experts.

Keywords: Feature Selection Stability, Spectral data, Data visualization

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Authors: M. Anandhavalli Gauthaman

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

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

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Authors: Zhou Yingkun, Xu Guorui, Wei Siming, Huang Yongzhang

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With the increasing of the penetration of renewable energy in power system, the whole inertia of the power system is declining, which will endanger the frequency stability of the power system. In order to enhance the inertia, virtual synchronous generator (VSG) has been proposed. In addition, the motor-generator pair (MGP) system is proposed to enhance grid inertia. Both of them need additional equipment to provide instantaneous energy, so the economic problem should be considered. In this paper, the basic working principle of MGP system and VSG are introduced firstly. Then, the technical characteristics and economic investment of MGP/VSG are compared by calculation and simulation. The results show that the MGP system can provide same inertia with less cost than VSG.

Keywords: High renewable energy penetration, inertia of power system, virtual synchronous generator, motor-generator pair system, techno-economic analysis.

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Authors: Seo Young Kim, Toshimitsu Hamasaki

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Microarrays have become the effective, broadly used tools in biological and medical research to address a wide range of problems, including classification of disease subtypes and tumors. Many statistical methods are available for analyzing and systematizing these complex data into meaningful information, and one of the main goals in analyzing gene expression data is the detection of samples or genes with similar expression patterns. In this paper, we express and compare the performance of several clustering methods based on data preprocessing including strategies of normalization or noise clearness. We also evaluate each of these clustering methods with validation measures for both simulated data and real gene expression data. Consequently, clustering methods which are common used in microarray data analysis are affected by normalization and degree of noise and clearness for datasets.

Keywords: Gene expression, clustering, data preprocessing.

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Authors: M. Pandi, K. Premalatha

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A DNA microarray technology is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. Elucidating the patterns hidden in gene expression data offers a tremendous opportunity for an enhanced understanding of functional genomics. However, the large number of genes and the complexity of biological networks greatly increase the challenges of comprehending and interpreting the resulting mass of data, which often consists of millions of measurements. It is handled by clustering which reveals the natural structures and identifying the interesting patterns in the underlying data. In this paper, gene based clustering in gene expression data is proposed using Cuckoo Search with Differential Evolution (CS-DE). The experiment results are analyzed with gene expression benchmark datasets. The results show that CS-DE outperforms CS in benchmark datasets. To find the validation of the clustering results, this work is tested with one internal and one external cluster validation indexes.

Keywords: DNA, Microarray, genomics, Cuckoo Search, Differential Evolution, Gene expression data, Clustering.

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Authors: Li Xinyao, Hong Jianzhong, Wu Wenkai

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In order to make environmental test centrifuge balance automatically and accurately, reduce unbalance centrifugal force, balance adjusting system of centrifuge is designed. The new balance adjusting system comprises motor-reducer, timing belt, screw pair, slider-guideway and four rocker force sensors. According to information obtained by the four rocker force sensors, unbalanced value at both ends of the big arm is computed and heavy block is moved to achieve balance adjusting. In this paper, motor power and torque to move the heavy block is calculated. In full load running progress of centrifuge, the stress-strain of screw pair composed by adjusting nut and big arm are analyzed. A successful application of the balance adjusting system is also put forwarded. The results show that the balance adjusting system can satisfy balance require of environmental test centrifuge.

Keywords: balance adjusting system, centrifuge, screw pair, timing belt

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Authors: I. Boroňová, J. Bernasovská, J. Kmec, E. Petrejčíková

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Dilated cardiomyopathy (DCM) is a severe cardiovascular disorder characterized by progressive systolic dysfunction due to cardiac chamber dilatation and inefficient myocardial contractility often leading to chronic heart failure. Recently, a genome-wide association studies (GWASs) on DCM indicate that the ZBTB17 gene rs10927875 single nucleotide polymorphism is associated with DCM. The aim of the study was to identify the distribution of ZBTB17 gene rs10927875 polymorphism in 50 Slovak patients with DCM and 80 healthy control subjects using the Custom Taqman®SNP Genotyping assays. Risk factors detected at baseline in each group included age, sex, body mass index, smoking status, diabetes and blood pressure. The mean age of patients with DCM was 52.9±6.3 years; the mean age of individuals in control group was 50.3±8.9 years. The distribution of investigated genotypes of rs10927875 polymorphism within ZBTB17 gene in the cohort of Slovak patients with DCM was as follows: CC (38.8%), CT (55.1%), TT (6.1%), in controls: CC (43.8%), CT (51.2%), TT (5.0%). The risk allele T was more common among the patients with dilated cardiomyopathy than in normal controls (33.7% versus 30.6%). The differences in genotype or allele frequencies of ZBTB17 gene rs10927875 polymorphism were not statistically significant (p=0.6908; p=0.6098). The results of this study suggest that ZBTB17 gene rs10927875 polymorphism may be a risk factor for susceptibility to DCM in Slovak patients with DCM. Studies of numerous files and additional functional investigations are needed to fully understand the roles of genetic associations.

Keywords: Dilated cardiomyopathy, SNP polymorphism, ZBTB17 gene.

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Authors: N. Hussain, G. Jaffery, A.N. Sabri, S. Hasnain

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The main aim is to perform mutational analysis of CTLA4 gene Exon 1 in SLE patients. A total of 61 SLE patients fulfilling “American College of Rheumatology (ACR) criteria" and 61 controls were enrolled in this study. The region of CTLA4 gene exon 1 was amplified by using Step-down PCR technique. Extracted DNA of band 354 bp was sequenced to analyze mutations in the exon-1 of CTLA-4 gene. Further, protein sequences were identified from nucleotide sequences of CTLA4 Exon 1 by using Expasy software and through Blast P software it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. No variations were found after patients sequences were compared with that of the control sequence. Furthermore it was found that CTLA4 protein sequences of Pakistani SLE patients were similar to that of Chinese SLE population. Thus CTLA4 gene may not be responsible for an autoimmune disease SLE.

Keywords: American College of Rheumatology criteria, autoimmune disease, Cytotoxic T Lymphocyte Antigen-4, Polymerase Chain Reaction, Systemic Lupus Erythematosus

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Authors: M. Maimunah, G. A. Froemming, H. Nawawi, M. I. Nafeeza, O. Effat, M. Y. Rosmadi, M. S. Mohamed Saifulaman

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Atherosclerosis was identified as a chronic inflammatory process resulting from interactions between plasma lipoproteins, cellular components (monocyte, macrophages, T lymphocytes, endothelial cells and smooth muscle cells) and the extracellular matrix of the arterial wall. Several types of genes were known to express during formation of atherosclerosis. This study is carried out to identify unknown differentially expressed gene (DEG) in atherogenesis. Rabbit’s aorta tissues were stained by H&E for histomorphology. GeneFishing™ PCR analysis was performed from total RNA extracted from the aorta tissues. The DNA fragment from DEG was cloned, sequenced and validated by Real-time PCR. Histomorphology showed intimal thickening in the aorta. DEG detected from ACP-41 was identified as cathepsin B gene and showed upregulation at week-8 and week-12 of atherogenesis. Therefore, ACP-based GeneFishing™ PCR facilitated identification of cathepsin B gene which was differentially expressed during development of atherosclerosis.

Keywords: Atherosclerosis, GeneFishing™ PCR, cathepsin B gene.

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Authors: S. Bag, S. Ramaiah, P. Anitha, K. M. Kumar, P. Lavanya, V. Sivasakhthi, A. Anbarasu

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Gene networks present a graphical view at the level of gene activities and genetic functions and help us to understand complex interactions in a meaningful manner. In the present study, we have analyzed the gene interaction of PPAR-γ (peroxisome proliferator-activated receptor gamma) by search tool for retrieval of interacting genes. We find PPAR-γ is highly networked by genetic interactions with 10 genes: RXRA (retinoid X receptor, alpha), PPARGC1A (peroxisome proliferator-activated receptor gamma, coactivator 1 alpha), NCOA1 (nuclear receptor coactivator 1), NR0B2 (nuclear receptor subfamily 0, group B, member 2), HDAC3 (histone deacetylase 3), MED1 (mediator complex subunit 1), INS (insulin), NCOR2 (nuclear receptor co-repressor 2), PAX8 (paired box 8), ADIPOQ (adiponectin) and it augurs well for the fact that obesity and several other metabolic disorders are inter related.

Keywords: Gene networks, NCOA1, PPARγ, PPARGC1A, RXRA.

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Authors: E. N. Sathishkumar, K. Thangavel, T. Chandrasekhar

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Feature selection is a process to select features which are more informative. It is one of the important steps in knowledge discovery. The problem is that all genes are not important in gene expression data. Some of the genes may be redundant, and others may be irrelevant and noisy. Here a novel approach is proposed Hybrid K-Mean-Quick Reduct (KMQR) algorithm for gene selection from gene expression data. In this study, the entire dataset is divided into clusters by applying K-Means algorithm. Each cluster contains similar genes. The high class discriminated genes has been selected based on their degree of dependence by applying Quick Reduct algorithm to all the clusters. Average Correlation Value (ACV) is calculated for the high class discriminated genes. The clusters which have the ACV value as 1 is determined as significant clusters, whose classification accuracy will be equal or high when comparing to the accuracy of the entire dataset. The proposed algorithm is evaluated using WEKA classifiers and compared. The proposed work shows that the high classification accuracy.

Keywords: Clustering, Gene Selection, K-Mean-Quick Reduct, Rough Sets.

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Authors: Tetsuki Taniguchi, Yoshio Karasawa

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This paper describes a node pair selection scheme in relay-aided multiple source multiple destination communication system based on stable marriage problem. A general case is assumed in which all of source, relay and destination nodes are equipped with multiantenna and carry out multistream transmission. Based on several metrics introduced from inter-node channel condition, the preference order is determined about all source-relay and relay-destination relations, and then the node pairs are determined using Gale-Shapley algorithm. The computer simulations show that the effectiveness of node pair selection is larger in multihop communication. Some additional aspects which are different from relay-less case are also investigated.

Keywords: Relay, multiple input multiple output (MIMO), multiuser, amplify and forward, stable marriage problem, Gale-Shapley algorithm.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

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Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: S. Makal, L. Ozyilmaz, S. Palavaroglu

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Gene, principal unit of inheritance, is an ordered sequence of nucleotides. The genes of eukaryotic organisms include alternating segments of exons and introns. The region of Deoxyribonucleic acid (DNA) within a gene containing instructions for coding a protein is called exon. On the other hand, non-coding regions called introns are another part of DNA that regulates gene expression by removing from the messenger Ribonucleic acid (RNA) in a splicing process. This paper proposes to determine splice junctions that are exon-intron boundaries by analyzing DNA sequences. A splice junction can be either exon-intron (EI) or intron exon (IE). Because of the popularity and compatibility of the artificial neural network (ANN) in genetic fields; various ANN models are applied in this research. Multi-layer Perceptron (MLP), Radial Basis Function (RBF) and Generalized Regression Neural Networks (GRNN) are used to analyze and detect the splice junctions of gene sequences. 10-fold cross validation is used to demonstrate the accuracy of networks. The real performances of these networks are found by applying Receiver Operating Characteristic (ROC) analysis.

Keywords: Gene, neural networks, ROC analysis, splice junctions.

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Authors: Rameswar Debnath, Haruhisa Takahashi

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An evolutionary method whose selection and recombination operations are based on generalization error-bounds of support vector machine (SVM) can select a subset of potentially informative genes for SVM classifier very efficiently [7]. In this paper, we will use the derivative of error-bound (first-order criteria) to select and recombine gene features in the evolutionary process, and compare the performance of the derivative of error-bound with the error-bound itself (zero-order) in the evolutionary process. We also investigate several error-bounds and their derivatives to compare the performance, and find the best criteria for gene selection and classification. We use 7 cancer-related human gene expression datasets to evaluate the performance of the zero-order and first-order criteria of error-bounds. Though both criteria have the same strategy in theoretically, experimental results demonstrate the best criterion for microarray gene expression data.

Keywords: support vector machine, generalization error-bound, feature selection, evolutionary algorithm, microarray data

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Authors: Yasmin Mohd Yacob, Harsa A. Mat Sakim, Nor Ashidi Mat Isa

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Feature selection study is gaining importance due to its contribution to save classification cost in terms of time and computation load. In search of essential features, one of the methods to search the features is via the decision tree. Decision tree act as an intermediate feature space inducer in order to choose essential features. In decision tree-based feature selection, some studies used decision tree as a feature ranker with a direct threshold measure, while others remain the decision tree but utilized pruning condition that act as a threshold mechanism to choose features. This paper proposed threshold measure using Manhattan Hierarchical Cluster distance to be utilized in feature ranking in order to choose relevant features as part of the feature selection process. The result is promising, and this method can be improved in the future by including test cases of a higher number of attributes.

Keywords: Feature ranking, decision tree, hierarchical cluster, Manhattan distance.

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Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias, Hany T. Alashwal, Rohayanti Hassan, FarhanMohamed

Abstract:

The most important property of the Gene Ontology is the terms. These control vocabularies are defined to provide consistent descriptions of gene products that are shareable and computationally accessible by humans, software agent, or other machine-readable meta-data. Each term is associated with information such as definition, synonyms, database references, amino acid sequences, and relationships to other terms. This information has made the Gene Ontology broadly applied in microarray and proteomic analysis. However, the process of searching the terms is still carried out using traditional approach which is based on keyword matching. The weaknesses of this approach are: ignoring semantic relationships between terms, and highly depending on a specialist to find similar terms. Therefore, this study combines semantic similarity measure and genetic algorithm to perform a better retrieval process for searching semantically similar terms. The semantic similarity measure is used to compute similitude strength between two terms. Then, the genetic algorithm is employed to perform batch retrievals and to handle the situation of the large search space of the Gene Ontology graph. The computational results are presented to show the effectiveness of the proposed algorithm.

Keywords: Gene Ontology, Semantic similarity measure, Genetic algorithm, Ontology search

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Authors: Hubert Klar

Abstract:

High double excitation of two-electron atoms has been investigated using hyperpherical coordinates within a modified adiabatic expansion technique. This modification creates a novel fictitious force leading to a spontaneous exchange symmetry breaking at high double excitation. The Pauli principle must therefore be regarded as approximation valid only at low excitation energy. Threshold electron scattering from high Rydberg states shows an unexpected time reversal symmetry breaking. At threshold for double escape we discover a broad (few eV) Cooper pair.

Keywords: Correlation, resonances, threshold ionization, Cooper pair.

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Authors: Alemayehu Geremew Negash

Abstract:

We prove the weak convergence of Mann iteration for a hybrid pair of maps to a common fixed point of a selfmap f and a multivalued f nonexpansive mapping T in Banach space E.  

Keywords: Common fixed point, Mann iteration, Multivalued mapping, weak convergence.

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Authors: Jana Kisková, Dana Gabriková

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Monoamine oxidase A gene (MAOA) is suggested to be a candidate gene implicated in many neuropsychiatric disorders, including autism spectrum disorder (ASD). This meta-analytic review evaluates the relationship between ASD and MAOA markers such as 30 bp variable number tandem repeats in the promoter region (uVNTR) and single nucleotide polymorphisms (SNPs) by using findings from recently published studies. It seems that in Caucasian males, the risk of developing ASD increase with the presence of 4- repeat allele in the promoter region of MAOA gene whereas no differences were found between autistic patients and controls in Egyptian, West Bengal and Korean population. Some studies point to the importance of specific haplotype groups of SNPs and interaction of MAOA with others genes (e. g. FOXP2 or SRY). The results of existing studies are insufficient and further research is needed.

Keywords: Autism spectrum disorder, MAOA, uVNTR, single nucleotide polymorphism.

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Authors: M. Habchi, S.M. Mesli, M. Kotbi

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The Reverse Monte Carlo (RMC) simulation is applied in the study of an aqueous electrolyte LiCl6H2O. On the basis of the available experimental neutron scattering data, RMC computes pair radial distribution functions in order to explore the structural features of the system. The obtained results include some unrealistic features. To overcome this problem, we use the Hybrid Reverse Monte Carlo (HRMC), incorporating an energy constraint in addition to the commonly used constraints derived from experimental data. Our results show a good agreement between experimental and computed partial distribution functions (PDFs) as well as a significant improvement in pair partial distribution curves. This kind of study can be considered as a useful test for a defined interaction model for conventional simulation techniques.

Keywords: RMC simulation, HRMC simulation, energy constraint, screened potential, glassy state, liquid state, partial distribution function, pair partial distribution function.

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Authors: Yasser M. Saad, Heba El-Sebaie Abd El-Sadek

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Some Metapenaeus monoceros cox1 gene fragments were isolated, purified, sequenced, and comparatively analyzed with some other Crustacean Cox1 gene sequences (obtained from National Center for Biotechnology Information). This work was designed for testing the efficiency of this system in reconstruction of phylogenetic relations among some Crustacean species belonging to four genera (Metapenaeus, Artemia, Daphnia and Calanus). The single nucleotide polymorphism and haplotype diversity were calculated for all estimated mt-DNA fragments. The genetic distance values were 0.292, 0.015, 0.151, and 0.09 within Metapenaeus species, Calanus species, Artemia species, and Daphnia species, respectively. The reconstructed phylogenetic tree is clustered into some unique clades. Cytochrome oxidase subunit 1 gene (cox1) was a powerful system in reconstruction of phylogenetic relations among evaluated crustacean species.

Keywords: Crustacean, Genetics, cox1, phylogeny.

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Authors: W. Loongyai, N. Saengsawang, W. Danvilai, C. Kridtayopas, P. Sopannarath, C. Bunchasak

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Betong chicken is a slow growing and a lean strain of chicken, while the rapid growth of broiler is accompanied by increased fat. We investigated the growth performance, fat accumulations, lipid serum biochemical levels and lipoprotein lipase (LPL) gene expression of female Betong (KU line) at the age of 4 and 6 weeks. A total of 80 female Betong chickens (KU line) and 80 female broiler chickens were reared under open system (each group had 4 replicates of 20 chicks per pen). The results showed that feed intake and average daily gain (ADG) of broiler chicken were significantly higher than Betong (KU line) (P < 0.01), while feed conversion ratio (FCR) of Betong (KU line) at week 6 were significantly lower than broiler chicken (P < 0.01) at 6 weeks. At 4 and 6 weeks, two birds per replicate were randomly selected and slaughtered. Carcass weight did not significantly differ between treatments; the percentage of abdominal fat and subcutaneous fat yield was higher in the broiler (P < 0.01) at 4 and 6 week. Total cholesterol and LDL level of broiler were higher than Betong (KU line) at 4 and 6 weeks (P < 0.05). Abdominal fat samples were collected for total RNA extraction. The cDNA was amplified using primers specific for LPL gene expression and analysed using real-time PCR. The results showed that the expression of LPL gene was not different when compared between Betong (KU line) and broiler chickens at the age of 4 and 6 weeks (P > 0.05). Our results indicated that broiler chickens had high growth rate and fat accumulation when compared with Betong (KU line) chickens, whereas LPL gene expression did not differ between breeds.

Keywords: Lipoprotein lipase gene, Betong (KU line), broiler, abdominal fat, gene expression.

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