Search results for: Gene expression data

Authors: M. Kaomek, J. R. Ketudat-Cairns

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The cDNA encoding the 326 amino acids of a Class I basic chitinase gene from Leucaena leucocephala de Wit (KB3, Genbank accession: AAM49597) was cloned under the control of CaMV35S promoter in pCAMBIA 1300 and transferred to Koshihikari. Calli of Koshihikari rice was transformed with agrobacterium with this construct expressing the chitinase and β- glucouronidase (GUS). The frequencies of calli 90 % has been obtained from rice seedlings cultured on NB medium. The high regeneration frequencies, 74% was obtained from calli cultured on regeneration medium containing 4 mg/l BAP, and 7 g/l phytagel at 25°C. Various factors were studied in order to establish a procedure for the transformation of Koshihikari Agrobacterium tumefaciens. Supplementation of 50 mM acetosyringone to the medium during coculivation was important to enhance the frequency to transient transformation. The 4 week-old scutellum-derived calli were excellent starting materials. Selection medium based on NB medium supplement with 40 mg/l hygromycin and 400 mg/l cefotaxime were an optimized medium for selection of transformed rice calli. The percentage of transformation 70 was obtained. Recombinant calli and regenerated rice plants were checked the expression of chitinase and gus by PCR, northern blot gel, southern blot gel, and gus assay. Chitinase and gus were expressed in all parts of recombinant rice. The rice line expressing the KB3 chiitnase was more resistant to the blast fungus Fusarium monoliforme than control line.

Keywords: chitinase, Leucaena leucocephala de Wit, Koshihikari, transgenic rice.

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Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

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Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

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Authors: Hong Ding, Fatiha Benslimane, Isra Marei, Chris R. Triggle

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Hyperglycaemia is a key factor that contributes to the development of diabetes-related microvascular disease and a major risk factor for endothelial dysfunction. In the current study, we have explored glucose-induced abnormal intracellular calcium (Ca2+ i) homeostasis in mouse microvessel endothelial cells (MMECs) in high glucose (HG) (40mmol/L) versus control (low glucose, LG) (11 mmol/L). We demonstrated that the exposure of MMECs to HG for 3 days did not change basal Ca2+ i, however, there was a significant increase of acetylcholine-induced Ca2+ entry. Western blots illustrated that exposure to HG also increased STIM1 (Stromal Interaction Molecule 1), but not Orai1 (the pore forming subunit), protein expression levels. Although the link between HG-induced changes in STIM1 expression, enhanced Ca2+ entry and endothelial dysfunction requires further study, the current data are suggestive that targeting these pathways may reduce the impact of HG on endothelial function.

Keywords: store-operated calcium entry, hyperglycaemia, STIM1, endothelial dysfunction

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Authors: Mohamed Hafez, Georg Hausner

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

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

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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

Keywords: BES1/BZR1, Brassinosteroids, Phylogenetic analysis, Transcription factor.

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

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Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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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: Taeung Yoon, Dahae Chong, Sangho Ahn, Seokho Yoon

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In a chirp spread spectrum (CSS) system, the overlap technique is used for increasing bit rate. More overlaps can offer higher data throughput; however, they may cause more intersymbol interference (ISI) at the same time, resulting in serious bit error rate (BER) performance degradation. In this paper, we perform the BER analysis and derive a closed form BER expression for the overlap-based CSS system. The derived BER expression includes the number of overlaps as a parameter, and thus, would be very useful in determining the number of overlaps for a specified BER. The numerical results demonstrate that the BER derived in a closed form closely agrees with the simulated BER.

Keywords: CSS, DM, chirp, overlap.

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

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

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

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Authors: Dong Hoon Lim

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A series of microarray experiments produces observations of differential expression for thousands of genes across multiple conditions. Principal component analysis(PCA) has been widely used in multivariate data analysis to reduce the dimensionality of the data in order to simplify subsequent analysis and allow for summarization of the data in a parsimonious manner. PCA, which can be implemented via a singular value decomposition(SVD), is useful for analysis of microarray data. For application of PCA using SVD we use the DNA microarray data for the small round blue cell tumors(SRBCT) of childhood by Khan et al.(2001). To decide the number of components which account for sufficient amount of information we draw scree plot. Biplot, a graphic display associated with PCA, reveals important features that exhibit relationship between variables and also the relationship of variables with observations.

Keywords: Principal component analysis, singular value decomposition, microarray data, SRBCT

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Authors: Simon Brown, Raewyn Tuffery

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Candida albicans ATCC 10231 had low endogenous activity of the alternative oxidase compared with that of C. albicans ATCC 10261. In C. albicans ATCC 10231 the endogenous activity declined as the cultures aged. Alternative oxidase activity could be induced in C. albicans ATCC 10231 by treatment with cyanide, but the induction of this activity required the presence of oxygen which could be replaced, at least in part, with high concentrations of potassium ferricyanide. We infer from this that the expression of the gene encoding the alternative oxidase is under the control of a redoxsensitive transcription factor.

Keywords: alternative oxidase, Candida albicans, enzymeinduction, oxygen, redox potential.

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Authors: Vesna Kirandziska, Nevena Ackovska, Ana Madevska Bogdanova

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The problem of emotion recognition is a challenging problem. It is still an open problem from the aspect of both intelligent systems and psychology. In this paper, both voice features and facial features are used for building an emotion recognition system. A Support Vector Machine classifiers are built by using raw data from video recordings. In this paper, the results obtained for the emotion recognition are given, and a discussion about the validity and the expressiveness of different emotions is presented. A comparison between the classifiers build from facial data only, voice data only and from the combination of both data is made here. The need for a better combination of the information from facial expression and voice data is argued.

Keywords: Emotion recognition, facial recognition, signal processing, machine learning.

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Authors: V. Gomathi, Dr. K. Ramar, A. Santhiyaku Jeevakumar

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Facial expression analysis plays a significant role for human computer interaction. Automatic analysis of human facial expression is still a challenging problem with many applications. In this paper, we propose neuro-fuzzy based automatic facial expression recognition system to recognize the human facial expressions like happy, fear, sad, angry, disgust and surprise. Initially facial image is segmented into three regions from which the uniform Local Binary Pattern (LBP) texture features distributions are extracted and represented as a histogram descriptor. The facial expressions are recognized using Multiple Adaptive Neuro Fuzzy Inference System (MANFIS). The proposed system designed and tested with JAFFE face database. The proposed model reports 94.29% of classification accuracy.

Keywords: Adaptive neuro-fuzzy inference system, Facialexpression, Local binary pattern, Uniform Histogram

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

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

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

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Authors: Nadezhda M. Usmanova, Nikolai V. Tomilin

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Mammalian genomes contain large number of retroelements (SINEs, LINEs and LTRs) which could affect expression of protein coding genes through associated transcription factor binding sites (TFBS). Activity of the retroelement-associated TFBS in many genes is confirmed experimentally but their global functional impact remains unclear. Human SINEs (Alu repeats) and mouse SINEs (B1 and B2 repeats) are known to be clustered in GCrich gene rich genome segments consistent with the view that they can contribute to regulation of gene expression. We have shown earlier that Alu are involved in formation of cis-regulatory modules (clusters of TFBS) in human promoters, and other authors reported that Alu located near promoter CpG islands have an increased frequency of CpG dinucleotides suggesting that these Alu are undermethylated. Human Alu and mouse B1/B2 elements have an internal bipartite promoter for RNA polymerase III containing conserved sequence motif called B-box which can bind basal transcription complex TFIIIC. It has been recently shown that TFIIIC binding to B-box leads to formation of a boundary which limits spread of repressive chromatin modifications in S. pombe. SINEassociated B-boxes may have similar function but conservation of TFIIIC binding sites in SINEs located near mammalian promoters has not been studied earlier. Here we analysed abundance and distribution of retroelements (SINEs, LINEs and LTRs) in annotated sequences of the Database of mammalian transcription start sites (DBTSS). Fractions of SINEs in human and mouse promoters are slightly lower than in all genome but >40% of human and mouse promoters contain Alu or B1/B2 elements within -1000 to +200 bp interval relative to transcription start site (TSS). Most of these SINEs is associated with distal segments of promoters (-1000 to -200 bp relative to TSS) indicating that their insertion at distances >200 bp upstream of TSS is tolerated during evolution. Distribution of SINEs in promoters correlates negatively with the distribution of CpG sequences. Using analysis of abundance of 12-mer motifs from the B1 and Alu consensus sequences in genome and DBTSS it has been confirmed that some subsegments of Alu and B1 elements are poorly conserved which depends in part on the presence of CpG dinucleotides. One of these CpG-containing subsegments in B1 elements overlaps with SINE-associated B-box and it shows better conservation in DBTSS compared to genomic sequences. It has been also studied conservation in DBTSS and genome of the B-box containing segments of old (AluJ, AluS) and young (AluY) Alu repeats and found that CpG sequence of the B-box of old Alu is better conserved in DBTSS than in genome. This indicates that Bbox- associated CpGs in promoters are better protected from methylation and mutation than B-box-associated CpGs in genomic SINEs. These results are consistent with the view that potential TFIIIC binding motifs in SINEs associated with human and mouse promoters may be functionally important. These motifs may protect promoters from repressive histone modifications which spread from adjacent sequences. This can potentially explain well known clustering of SINEs in GC-rich gene rich genome compartments and existence of unmethylated CpG islands.

Keywords: Retroelement, promoter, CpG island, DNAmethylation.

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

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

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

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Authors: Chengming Li, Yong Yin, Peipei Guo, Xiaoli Liu

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Without taking account of the attribute richness of POI (point of interest) data and spatial distribution limited by roads, a POI generalization method considering both attribute information and spatial distribution has been proposed against the existing point generalization algorithm merely focusing on overall information of point groups. Hierarchical characteristic of urban POI information expression has been firstly analyzed to point out the measurement feature of the corresponding hierarchy. On this basis, an urban POI generalizing strategy has been put forward: POIs urban road network have been divided into three distribution pattern; corresponding generalization methods have been proposed according to the characteristic of POI data in different distribution patterns. Experimental results showed that the method taking into account both attribute information and spatial distribution characteristics of POI can better implement urban POI generalization in the mapping presentation.

Keywords: POI, Road network, spatial information expression, selection method, distribution pattern.

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Authors: Arash Kosari, Ali Araghi

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A mathematical model for an optical-fiber communication channel is developed which results in an expression that calculates the throughput and loss of the corresponding link. The data are assumed to be transmitted by using of separate photons with different polarizations. The derived model also shows the dependency of data throughput with length of the channel and depolarization factor. It is observed that absorption of photons affects the throughput in a more intensive way in comparison with that of depolarization. Apart from that, the probability of depolarization and the absorption of radiated photons are obtained.

Keywords: Absorption, data throughput, depolarization, optical fiber.

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Authors: Rungsinee Phongpradist, Sawitree Chiampanichayakul, Singkome Tima, Teruna J. Siahaan, Cory J. Berkland, Songyot Anuchapreeda, Chadarat Ampasavate

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The expression of LFA-1 diverges from the physiological condition, thus active targeting carrier can provide the benefits from difference into LFA-1 expression in various conditions. Here, the selectivity of cIBR-conjugated nanoparticles (cIBR-NPs), in terms of uptake, was investigated using PBMCs, Mixed PBMCMolt- 3 cells and Molt-3 cells. The expressions of LFA-1 on Molt-3 cells, from flow cytometry and Western blot, possessed the highest level whereas PBMCs showed the lowest level. The kinetic uptake profiles of cIBR-NPs were obtained by flow cytometry, which the degree of cellular uptake presented a similar trend with the level of LFA-1 indicating the influence of LFA-1 expression on the cellular uptake of cIBR-NPs. The conformation of LFA-1 had a slight effect on the cellular uptake of cIBR-NPs. Overall we demonstrated that cIBR-NPs enhanced cellular uptake and improved the selectivity of drug carriers to LFA-1 on the leukemia cells, which related with the order of LFA-1 expression.

Keywords: cIBR, LFA-1, Molt-3, PBMCs

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Authors: Zhe JIN, Motomichi TOYAMA

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PPX(Pretty Printer for XML) is a query language that offers a concise description method of formatting the XML data into HTML. In this paper, we propose a simple specification of formatting method that is a combination description of automatic layout operators and variables in the layout expression of the GENERATE clause of PPX. This method can automatically format irregular XML data included in a part of XML with layout decision rule that is referred to DTD. In the experiment, a quick comparison shows that PPX requires far less description compared to XSLT or XQuery programs doing same tasks.

Keywords: PPX, Irregular XML data, Layout decision rule, HTML.

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Authors: Uun Yanuhar

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The purpose of research was to know the role of immunogenic protein of 49 kDa from V.alginolyticus which capable to initiate molecule expression of MHC Class II in receptor of Cromileptes altivelis. The method used was in vivo experimental research through testing of immunogenic protein 49 kDa from V.alginolyticus at Cromileptes altivelis (size of 250 - 300 grams) using 3 times booster by injecting an immunogenic protein in a intramuscular manner. Response of expressed MHC molecule was shown using immunocytochemistry method and SEM. Results indicated that adhesin V.alginolyticus 49 kDa which have immunogenic character could trigger expression of MHC class II on receptor of grouper and has been proven by staining using immunocytochemistry and SEM with labeling using antibody anti MHC (anti mouse). This visible expression based on binding between epitopes antigen and antibody anti MHC in the receptor. Using immunocytochemistry, intracellular response of MHC to in vivo induction of immunogenic adhesin from V.alginolyticus was shown.

Keywords: C.altivelis, immunogenic, MHC, V.alginolyticus.

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Authors: Rein Kuusik, Grete Lind

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Generator of hypotheses is a new method for data mining. It makes possible to classify the source data automatically and produces a particular enumeration of patterns. Pattern is an expression (in a certain language) describing facts in a subset of facts. The goal is to describe the source data via patterns and/or IF...THEN rules. Used evaluation criteria are deterministic (not probabilistic). The search results are trees - form that is easy to comprehend and interpret. Generator of hypotheses uses very effective algorithm based on the theory of monotone systems (MS) named MONSA (MONotone System Algorithm).

Keywords: data mining, monotone systems, pattern, rule.

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

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

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

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Authors: Yazhi Huang, Jing Yang, Dingge Ying, Yan Zhang, Vorasuk Shotelersuk, Nattiya Hirankarn, Pak Chung Sham, Yu Lung Lau, Wanling Yang

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Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.

Keywords: Human leukocyte antigens, next generation sequencing, whole exome sequencing, HLA typing.

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Authors: Ali Al-Ataby , Fawzi Al-Naima

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Symbolic Circuit Analysis (SCA) is a technique used to generate the symbolic expression of a network. It has become a well-established technique in circuit analysis and design. The symbolic expression of networks offers excellent way to perform frequency response analysis, sensitivity computation, stability measurements, performance optimization, and fault diagnosis. Many approaches have been proposed in the area of SCA offering different features and capabilities. Numerical Interpolation methods are very common in this context, especially by using the Fast Fourier Transform (FFT). The aim of this paper is to present a method for SCA that depends on the use of Wavelet Transform (WT) as a mathematical tool to generate the symbolic expression for large circuits with minimizing the analysis time by reducing the number of computations.

Keywords: Numerical Interpolation, Sparse Matrices, SymbolicAnalysis, Wavelet Transform.

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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: Ming-Lun Chiang, Hsi-Chia Chen, Chieh Wu, Yu-Ting Tseng, Ming-Ju Chen

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In this study, three strains of Vibrio parahaemolyticus (690, BCRC 13023 and BCRC 13025) were subjected to acid adaptation at pH 5.5 for 90 min. The survival of acid-adapted and non-adapted V. parahaemolyticus strains under simulated gastric condition and their protein expression profiles were investigated. Results showed that acid adaptation increased the survival of the test V. parahaemolyticus strains after exposure to simulated gastric juice (pH 3). Additionally, acid adaptation also affected the protein expression in these V. parahaemolyticus strains. Nine proteins, identified as atpA, atpB, DnaK, GroEL, OmpU, enolase, fructose-bisphosphate aldolase, phosphoglycerate kinase and triosephosphate isomerase, were induced by acid adaptation in two or three of the test strains. These acid-adaptive proteins may play important regulatory roles in the acid tolerance response (ATR) of V. parahaemolyticus.

Keywords: Acid adaptation, protein expression, simulated gastric juice, Vibrio parahaemolyticus

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Authors: H. Merhni, A. Sbiti, I. Ratbi, A. Sefiani

Abstract:

The proximal spinal muscular atrophy (SMA) is a group of neuromuscular disorders characterized by progressive muscle weakness due to the degeneration and loss of anterior motor neurons of the spinal cord. Depending on the age of onset of symptoms and their evolution, four types of SMA, varying in severity, result in a mutations of the SMN gene (survival of Motor neuron). We have analyzed the DNA of 295 patients referred to our genetic counseling; since January 1996 until October 2014; for suspected SMA. The homozygous deletion of exon 7 of the SMN gene was found in 133 patients; of which, 40.6% were born to consanguineous parents. In countries like Morocco, where the frequency of heterozygotes for SMA is high, genetic testing should be offered as first-line and, after careful clinical assessment, especially in newborns and infants with congenital hypotonia unexplained and prognosis compromise. The molecular diagnosis of SMA allows a quick and certainly diagnosis, provide adequate genetic counseling for families at risk and suggest, for couples who want prenatal diagnosis. The analysis of the SMN gene is a perfect example of genetic testing with an excellent cost/benefit ratio that can be of great interest in public health, especially in low-income countries. We emphasize in this work for the benefit of the generalization of molecular diagnosis of SMA by the technique of PCR-enzymatic digestion in other centers in Morocco.

Keywords: Exon7, PCR-digestion, SMA, SMN gene.

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Authors: Raviporn Madarasmi, Anjalee Vacharaksa, Pravej Serichetaphongse

Abstract:

The host response in peri-implant tissue may differ from that in periodontal tissue in a healthy individual. The purpose of this study is to investigate the expression of inflammatory cytokines in peri-implant crevicular fluid (PICF) from single implant with different abutment types in comparison to healthy periodontal tissue. 19 participants with healthy implants and teeth were recruited according to inclusion and exclusion criteria. PICF and gingival crevicular fluid (GCF) was collected using sterile paper points. The expression level of inflammatory cytokines including IL-1α, IL-1β, TNF-α, IFN-γ, IL-6, and IL-8 was assessed using enzyme-linked immunosorbent assay (ELISA). Paired t test was used to compare the expression levels of inflammatory cytokines around natural teeth and peri-implant in PICF and GCF of the same individual. The Independent t-test was used to compare the expression levels of inflammatory cytokines in PICF from titanium and UCLA abutment. Expression of IL-6, TNF-α, and IFN-γ in PICF was not statistically different from GCF among titanium and UCLA abutment group. However, the level of IL-1α in the PICF from the implants with UCLA abutment was significantly higher than GCF (P=0.030). In addition, the level of IL-1β in PICF from the implants with titanium abutment was significantly higher than GCF (P=0.032). When different abutment types was compared, IL-8 expression in PICF from implants with UCLA abutment was significantly higher than titanium abutment (P=0.003).

Keywords: Abutment, dental implant, gingival crevicular fluid and peri-implant crevicular fluid.

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Authors: S. Kherchaoui, A. Houacine

Abstract:

This paper presents a facial expression recognition system. It performs identification and classification of the seven basic expressions; happy, surprise, fear, disgust, sadness, anger, and neutral states. It consists of three main parts. The first one is the detection of a face and the corresponding facial features to extract the most expressive portion of the face, followed by a normalization of the region of interest. Then calculus of curvelet coefficients is performed with dimensionality reduction through principal component analysis. The resulting coefficients are combined with two ratios; mouth ratio and face edge ratio to constitute the whole feature vector. The third step is the classification of the emotional state using the SVM method in the feature space.

Keywords: Facial expression identification, curvelet coefficients, support vector machine (SVM).

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