Search results for: Protein Sequence Analysis

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

Abstract:

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: Michele Sinico

Abstract:

The psychological present has an actual extension. When a sequence of instantaneous stimuli falls in this short interval of time, observers perceive a compresence of events in succession and the temporal order depends on the qualitative relationships between the perceptual properties of the events. Two experiments were carried out to study the influence of perceptual grouping, with and without temporal displacement, on the duration of auditory sequences. The psychophysical method of adjustment was adopted. The first experiment investigated the effect of temporal displacement of a white noise on sequence duration. The second experiment investigated the effect of temporal displacement, along the pitch dimension, on temporal shortening of sequence. The results suggest that the temporal order of sounds, in the case of temporal displacement, is organized along the pitch dimension.

Keywords: Time perception, perceptual present, temporal displacement, gestalt laws of perceptual organization

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Authors: Vipin Saxena, Deepa Raj

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Unified Modeling language (UML) is one of the important modeling languages used for the visual representation of the research problem. In the present paper, UML model is designed for the Instruction pipeline which is used for the evaluation of the instructions of software programs. The class and sequence diagrams are designed & performance is evaluated for instructions of a sample program through a case study.

Keywords: UML, Instruction Pipeline, Class Diagram &Sequence Diagram.

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Authors: Radhika Jain, Sangeeta Goomer

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In the present study an attempt has been made to re-engineer traditional wadi into wholesome ready-to-use cereal-pulse-based chunks rich in protein quality and fibre content. Chunks were made using extrusion-dehydration combination. Two formulations i.e., whole green gram dhal with instant oats and washed green gram dhal with whole oats were formulated. These chunks are versatile in nature as they can be easily incorporated in day-to-day home-made preparations such as pulao, potato curry and kadhi. Cereal-pulse ratio was calculated using NDpCal%. Limiting amino acids such as lysine, tryptophan, methionine, cysteine and threonine were calculated for maximum amino acid profile in cereal-pulse combination. Time-temperature combination for extrusion at 130^oC and dehydration at 65^oC for 7 hours and 15 minutes were standardized to obtain maximum protein and fibre content. Proximate analysis such as moisture, fat and ash content were analyzed. Protein content of formulation was 62.10% and 68.50% respectively. Fibre content of formulations was 2.99% and 2.45%, respectively. Using a 5-point hedonic scale, consumer preference trials of 102 consumers were conducted and analyzed. Evaluation of chunks prepared in potato curry, kadi and pulao showed preferences for colour 82%, 87%, 86%, texture and consistency 80%, 81%, 88%, flavour and aroma 74%, 82%, 86%, after taste 70%, 75%, 86% and overall acceptability 77%, 75%, 88% respectively. High temperature inactivates antinutritional compounds such as trypsin inhibitors, lectins, saponins etc. Hence, availability of protein content was increased. Developed products were palatable and easy to prepare.

Keywords: Extrusion, NDpCal%, protein quality, wadi.

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Authors: Tzyy Rong Jinn, Nguyen Tiep Khac, Tzong Yuan Wu

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Highly pathogenic avian influenza (HPAI) H5N1 viruses have created demand for a cost-effective vaccine to prevent a pandemic of the disease. Here, we report that Trichoplusia ni (T. ni) larvae can act as a cost-effective bioreactor to produce recombinant HA5 (rH5HA) proteins as an potential effective vaccine for chickens. To facilitate the recombinant virus identification, virus titer determination and access the infected larvae, we employed the internal ribosome entry site (IRES) derived from Perina nuda virus (PnV, belongs to insect picorna like Iflavirus genus) to construct a bi-cistronic baculovirus expression vector that can express the rH5HA protein and enhanced green fluorescent protein (EGFP) simultaneously. Western blot analysis revealed that the 70 kDa rH5HA protein and partially cleaved products (40 kDa H5HA1) were generated in T. ni larvae infected with recombinant baculovirus carrying the H5HA gene. These data suggest that the baculovirus-larvae recombinant protein expression system could be a cost-effective platform for H5N1 vaccine production.

Keywords: Avian Influenza, baculovirus, hemagglutinin, Trichoplusia ni larvae

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Authors: Lisa M. Weltzer-Ward, Abbie Brown

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The sequence Analyze, Design, Develop, Implement, and Evaluate (ADDIE) provides a powerful methodology for designing computer-based educational materials. Helping students to understand this design process sequence may be achieved by providing them with direct, guided experience. This article examines such help and guidance and the overall learning process from a student-s personal experience.

Keywords: ADDIE, education, instructional design, web design.

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Authors: Rizkita R. Esyanti, Iriawati, Olga Mardisadora

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Vetiver oil is secondary metabolite that accumulates in Vetiveria zizanioides roots.  The aim of this study was to obtain best type of root culture which produce high amount of vetiver oil, and was similar to metabolites produce from its mother plant.  Protein analysis was also conducted to detect protein, related to putative enzymes, which have a role in terpenoids synthesis in the root culture. The results showed that root culture derived from crown explant produced the best root growth.   The root culture produced primary and lateral roots, ca. 40 branches.  The vetiver oil produced from root culture was analyzed by using GC-MS., and the highest content of terpenoids from roots of crown explant attained 19.024%.  The result of SDS PAGE showed proteins which were ±61 kD and ± 68 kD, each might be related to putative monoterpene synthase and sesquiterpenes complex, respectively. 

Keywords: Protein, Root culture, Terpenoids, Vetiver oil.

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Authors: Alexander Kaplunovsky, Vladimir Khailenko, Alexander Bolshoy, Shara Atambayeva, AnatoliyIvashchenko

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Eukaryotic protein-coding genes are interrupted by spliceosomal introns, which are removed from the RNA transcripts before translation into a protein. The exon-intron structures of different eukaryotic species are quite different from each other, and the evolution of such structures raises many questions. We try to address some of these questions using statistical analysis of whole genomes. We go through all the protein-coding genes in a genome and study correlations between the net length of all the exons in a gene, the number of the exons, and the average length of an exon. We also take average values of these features for each chromosome and study correlations between those averages on the chromosomal level. Our data show universal features of exon-intron structures common to animals, plants, and protists (specifically, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Cryptococcus neoformans, Homo sapiens, Mus musculus, Oryza sativa, and Plasmodium falciparum). We have verified linear correlation between the number of exons in a gene and the length of a protein coded by the gene, while the protein length increases in proportion to the number of exons. On the other hand, the average length of an exon always decreases with the number of exons. Finally, chromosome clustering based on average chromosome properties and parameters of linear regression between the number of exons in a gene and the net length of those exons demonstrates that these average chromosome properties are genome-specific features.

Keywords: Comparative genomics, exon-intron structure, eukaryotic clustering, linear regression.

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Authors: Elaheh Jooybar, Mohammad J. Abdekhodaie, Marcel Karperien, Pieter J. Dijkstra

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In this study, hyaluronic acid (HA) microgels were developed for the goal of protein delivery. First, a hyaluronic acid-tyramine conjugate (HA-TA) was synthesized with a degree of substitution of 13 TA moieties per 100 disaccharide units. Then, HA-TA microdroplets were produced using a water in oil emulsion method and crosslinked in the presence of horseradish peroxidase (HRP) and hydrogen peroxide (H₂O₂). Loading capacity and the release kinetics of lysozyme and BSA, as model proteins, were investigated. It was shown that lysozyme, a cationic protein, can be incorporated efficiently in the HA microgels, while the loading efficiency for BSA, as a negatively charged protein, is low. The release profile of lysozyme showed a sustained release over a period of one month. The results demonstrated that the HA-TA microgels are a good carrier for spatial delivery of cationic proteins for biomedical applications.

Keywords: Microgel, inverse emulsion, protein delivery, hyaluronic acid, crosslinking.

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Authors: Mirzaee Mahmoodabadi Reza, Afghah Massih, Saeedi Somaye

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Pabdeh shaly formation (Paleocene-Oligomiocene) has been expanded in Fars, Khozestan and Lorestan. The lower lithostratigraphic limit of this formation in Shiraz area is distinguished from Gurpi formation by purple shale. Its upper limit is gradational and conformable with Asmari formation. In order to study sequence stratigraphy and microfacies of Pabdeh formation in Shiraz area, one stratigraphic section have been chosen (Zanjiran section). Petrographic studies resulted in the identification of 9 pelagic and calciturbidite microfacies. The calciturbidite microfacies have been formed when the sea level was high, the rate of carbonate deposition was high and it slumped into the deep marine. Sequence stratigraphy studies show that Pabdeh formation in the studied zone consists of two depositional sequences (DS) that the lower contact is erosional (purple shale - type one, SBI or type two, SB2) and the upper contact is correlative conformity (type two, SB2).

Keywords: Pabdeh formation, Shiraz, Microfacies, Purple Shale, Zanjiran Section, Sequence Stratigraphy

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Authors: Sang-Wan Kim, Hoon Lee, Kyung-Ho Choi, Soon-Young Park

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A talking head system (THS) is presented to animate the face of a speaking 3D avatar in such a way that it realistically pronounces the given Korean text. The proposed system consists of SAPI compliant text-to-speech (TTS) engine and MPEG-4 compliant face animation generator. The input to the THS is a unicode text that is to be spoken with synchronized lip shape. The TTS engine generates a phoneme sequence with their duration and audio data. The TTS applies the coarticulation rules to the phoneme sequence and sends a mouth animation sequence to the face modeler. The proposed THS can make more natural lip sync and facial expression by using the face animation generator than those using the conventional visemes only. The experimental results show that our system has great potential for the implementation of talking head for Korean text.

Keywords: Talking head, Lip sync, TTS, MPEG4.

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Authors: Marios Poulos, Eirini Maliagani, Minas Paschopoulos, George Bokos

Abstract:

The purpose of my research proposal is to demonstrate that there is a relationship between EEG and endometrial cancer. The above relationship is based on an Aristotelian Syllogism; since it is known that the 14-3-3 protein is related to the electrical activity of the brain via control of the flow of Na+ and K+ ions and since it is also known that many types of cancer are associated with 14-3-3 protein, it is possible that there is a relationship between EEG and cancer. This research will be carried out by well-defined diagnostic indicators, obtained via the EEG, using signal processing procedures and pattern recognition tools such as neural networks in order to recognize the endometrial cancer type. The current research shall compare the findings from EEG and hysteroscopy performed on women of a wide age range. Moreover, this practice could be expanded to other types of cancer. The implementation of this methodology will be completed with the creation of an ontology. This ontology shall define the concepts existing in this research-s domain and the relationships between them. It will represent the types of relationships between hysteroscopy and EEG findings.

Keywords: Bioinformatics, Protein 14-3-3, EEG, Endometrial cancer, Ontology.

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Authors: J.-H. Moon, D.-O Kim, R.-H. Park

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This paper presents a video matting method, which extracts the foreground and alpha matte from a video sequence. The objective of video matting is finding the foreground and compositing it with the background that is different from the one in the original image. By finding the motion vectors (MVs) using a sliced block matching algorithm (SBMA), we can extract moving regions from the video sequence under the assumption that the foreground is moving and the background is stationary. In practice, foreground areas are not moving through all frames in an image sequence, thus we accumulate moving regions through the image sequence. The boundaries of moving regions are found by Canny edge detector and the foreground region is separated in each frame of the sequence. Remaining regions are defined as background regions. Extracted backgrounds in each frame are combined and reframed as an integrated single background. Based on the estimated background, we compute the frame difference (FD) of each frame. Regions with the FD larger than the threshold are defined as foreground regions, boundaries of foreground regions are defined as unknown regions and the rest of regions are defined as backgrounds. Segmentation information that classifies an image into foreground, background, and unknown regions is called a trimap. Matting process can extract an alpha matte in the unknown region using pixel information in foreground and background regions, and estimate the values of foreground and background pixels in unknown regions. The proposed video matting approach is adaptive and convenient to extract a foreground automatically and to composite a foreground with a background that is different from the original background.

Keywords: Background estimation, Object segmentation, Blockmatching algorithm, Video matting.

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

Abstract:

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

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

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Authors: N.Subramanian, C.Murugesan

Abstract:

This paper is devoted to the study of the general properties of Orlicz space of entire sequence of fuzzy numbers by using infinite matrices.

Keywords: Fuzzy numbers, infinite matrix, Orlicz space, entiresequence.

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Authors: Jihyung Kim, Taejin Kim, Sungho Park, Jun-Dong Cho

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In this paper, we address the problem of reducing the switching activity (SA) in on-chip buses through the use of a bus binding technique in high-level synthesis. While many binding techniques to reduce the SA exist, we present yet another technique for further reducing the switching activity. Our proposed method combines bus binding and data sequence reordering to explore a wider solution space. The problem is formulated as a multiple traveling salesman problem and solved using simulated annealing technique. The experimental results revealed that a binding solution obtained with the proposed method reduces 5.6-27.2% (18.0% on average) and 2.6-12.7% (6.8% on average) of the switching activity when compared with conventional binding-only and hybrid binding-encoding methods, respectively.

Keywords: low power, bus binding, switching activity, multiple traveling salesman problem, data sequence reordering

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Authors: Patrick Nwabueze Okechukwu, Ima Nirwana Soelaiman, Gabriele Anisah Ruth Froemming, Mohd Yusri Idorus, Norazlina Mohamed

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Supplementation of palm vitamin E has been reported to prevent loss of bone density in ovariectomised female rats. The mechanism by which palm vitamin E exerts these effects is still unknown. We hypothesized that palm vitamin E may act by preventing the protein expression changes. Two dimensional poly acyrilamide gel electrophoresis (2-D PAGE) and PD Quest software genomic solutions Investigator (proteomics) was used to analyze the differential protein expression profile in femoral and humeri bones harvested from three groups of rats; sham-operated rats (SO), ovariectomised rats (Ovx) and ovariectomised rats supplemented for 2 months with palm vitamin E. The results showed that there were over 300 valued spot on each of the groups PVE and OVX as compared to about 200 in SO. Comparison between the differential protein expression between OVX and PVE groups showed that ten spots were down –regulated in OVX but up-regulated in PVE. The ten differential spots were separately named P1-P10. The identification and understanding of the pathway of the differential protein expression among the groups is ongoing and may account for the molecular mechanism through which palm vitamin E exert its anti-osteoporotic effect.

Keywords: Palm vitamin E, ovariectomised, osteoporosis protein expression, 2-d-page.

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Authors: Vita Strazdina, Aleksandrs Jemeljanovs, Vita Sterna

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A game animals – elk (Alces alces), deer (Cervus elaphus), roe deer (Capreolus capreolus) or wild boar (Sus scrofa scrofa) - every autumn and winter period provide an excellent investment, diversification of many consumer meals. In last years consumption and assortiment of game meat products significantly increase. Investigations about biochemical composition of game meat are not very much. The meat of wild animals is more favourable for human health because it has lower saturated fatty acids content, but higher content of protein. Therefore the aim of investigations was to compare biochemical composition of ungulates obtained in Latvia.Investigations were carried out in wild animals different regions of Latvia. In the studied samples protein, intramuscular fat, fatty acids and cholesterol were determined. The biochemical analysis of 54 samples were done. Results of analysis showed that protein content 22.36 – 22.92% of all types of meat samples is not different statistically, significantly lower fat content 1.33 ± 0.88% had elk meat samples and 1.59 ± 0.59% roe deer samples. Content of cholesterol was various 64.41 – 95.07% in the ruminant meat samples of different species. From the dietetic point of view the best composition of fatty acids has meat samples of roe deer.

Keywords: dietic product, game meat, intramuscular fat

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Authors: Norlin Pauzi, Ahmad R.M. Yahya, Zairossani Nor, Amirul A. Abdullah

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Strain M was isolated from the latex of Hevea brasiliensis that grow in the rubber farm area of Malaysia Rubber Board. Strain M was tentatively identified as Bacillus sp. Strain M demonstrated high protease production at pH 9, and this was suitable to be applied in rubber processing that was in alkaline conditions. The right and suitable proportion to be used in applying supernatant into the latex was two parts of latex and one part of enzyme. In this proportion, the latex was stable throughout the 72 hours of treatment. The potential of strain M to degrade protein in the natural rubber latex was proven with the reduction of 79.3% nitrogen in 24 hours treatment. Centrifugation process of the latex before undergoing the treatment had increased the protein degradation in latex. Although the centrifugation process did not achieve zero nitrogen content, it had improved the performance of protein denaturing in the natural rubber.

Keywords: Hevea brasiliensis, Bacillus sp., protease, latex.

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Authors: Melvin A. Ballera

Abstract:

Prior literature in the field of adaptive and personalized learning sequence in e-learning have proposed and implemented various mechanisms to improve the learning process such as individualization and personalization, but complex to implement due to expensive algorithmic programming and need of extensive and prior data. The main objective of personalizing learning sequence is to maximize learning by dynamically selecting the closest teaching operation in order to achieve the learning competency of learner. In this paper, a revolutionary technique has been proposed and tested to perform individualization and personalization using modified reversed roulette wheel selection algorithm that runs at O(n). The technique is simpler to implement and is algorithmically less expensive compared to other revolutionary algorithms since it collects the dynamic real time performance matrix such as examinations, reviews, and study to form the RWSA single numerical fitness value. Results show that the implemented system is capable of recommending new learning sequences that lessens time of study based on student's prior knowledge and real performance matrix.

Keywords: E-learning, fitness value, personalized learning sequence, reversed roulette wheel selection algorithms.

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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: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

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The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: Nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation.

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Authors: Anna Trusek-Holownia, Andrzej Noworyta

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Using an enzyme of known specificity the hydrolysis of protein was carried out in a controlled manner. The aim was to obtain oligopeptides being the so-called active peptides or their direct precursors. An original way of expression of the protein hydrolysis kinetics was introduced. Peptide bonds contained in the protein were recognized as a diverse-quality substrate for hydrolysis by the applied protease. This assumption was positively verified taking as an example the hydrolysis of albumin by thermolysin. Peptide linkages for this system should be divided into at least four groups. One of them is a group of bonds non-hydrolyzable by this enzyme. These that are broken are hydrolyzed at a rate that differs even by tens of thousands of times. Designated kinetic constants were k'_F = 10991.4 L/g^.h, k'_M = 14.83L/g^.h, k'_S about 10^-1 L/g^.h for fast, medium and slow bonds, respectively. Moreover, a procedure for unfolding of the protein, conducive to the improved susceptibility to enzymatic hydrolysis (approximately three-fold increase in the rate) was proposed.

Keywords: Peptide bond hydrolysis, kinetics, enzyme specificity, biologically active peptides.

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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: Xiaoli Shen, Yuehui Chen

Abstract:

Interactions among proteins are the basis of various life events. So, it is important to recognize and research protein interaction sites. A control set that contains 149 protein molecules were used here. Then 10 features were extracted and 4 sample sets that contained 9 sliding windows were made according to features. These 4 sample sets were calculated by Radial Basis Functional neutral networks which were optimized by Particle Swarm Optimization respectively. Then 4 groups of results were obtained. Finally, these 4 groups of results were integrated by decision fusion (DF) and Genetic Algorithm based Selected Ensemble (GASEN). A better accuracy was got by DF and GASEN. So, the integrated methods were proved to be effective.

Keywords: protein interaction sites, features, sliding windows, radial basis functional neutral networks, genetic algorithm basedselected ensemble.

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

Abstract:

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: K. Kemih, M. Benslama

Abstract:

This paper investigates the problem of spreading sequence and receiver code synchronization techniques for satellite based CDMA communications systems. The performance of CDMA system depends on the autocorrelation and cross-correlation properties of the used spreading sequences. In this paper we propose the uses of chaotic Lu system to generate binary sequences for spreading codes in a direct sequence spread CDMA system. To minimize multiple access interference (MAI) we propose the use of genetic algorithm for optimum selection of chaotic spreading sequences. To solve the problem of transmitter-receiver synchronization, we use the passivity controls. The concept of semipassivity is defined to find simple conditions which ensure boundedness of the solutions of coupled Lu systems. Numerical results are presented to show the effectiveness of the proposed approach.

Keywords: About Chaotic Lu system, synchronization, Spreading sequence, Genetic Algorithm. Passive System

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Authors: Miloje S. Radenkovic, Tamal Bose

Abstract:

This paper presents the convergence analysis of a prediction based blind equalizer for IIR channels. Predictor parameters are estimated by using the recursive least squares algorithm. It is shown that the prediction error converges almost surely (a.s.) toward a scalar multiple of the unknown input symbol sequence. It is also proved that the convergence rate of the parameter estimation error is of the same order as that in the iterated logarithm law.

Keywords: Adaptive blind equalizer, Recursive leastsquares, Adaptive Filtering, Convergence analysis.

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Authors: Ç. Gökçek-Saraç, Ş. Özen, N. Derin

Abstract:

The N-methyl-D-aspartate (NMDA)-dependent pathway is the major intracellular signaling pathway implemented in both short- and long-term memory formation in the hippocampus which is the most studied brain structure because of its well documented role in learning and memory. However, little is known about the effects of RF-EMR exposure on NMDA receptor signaling pathway including activation of protein kinases, notably Ca²⁺/calmodulin-dependent protein kinase II alpha (CaMKIIα). The aim of the present study was to investigate the effects of acute and chronic 900 MHz RF-EMR exposure on both passive avoidance behaviour and hippocampal levels of CaMKIIα and its phosphorylated form (pCaMKIIα). Rats were divided into the following groups: Sham rats, and rats exposed to 900 MHz RF-EMR for 2 h/day for 1 week (acute group) or 10 weeks (chronic group), respectively. Passive avoidance task was used as a behavioural method. The hippocampal levels of selected kinases were measured using Western Blotting technique. The results of passive avoidance task showed that both acute and chronic exposure to 900 MHz RF-EMR can impair passive avoidance behaviour with minor effects on chronic group of rats. The analysis of western blot data of selected protein kinases demonstrated that hippocampal levels of CaMKIIα and pCaMKIIα were significantly higher in chronic group of rats as compared to acute groups. Taken together, these findings demonstrated that different duration times (1 week vs 10 weeks) of 900 MHz RF-EMR exposure have different effects on both passive avoidance behaviour of rats and hippocampal levels of selected protein kinases.

Keywords: Hippocampus, protein kinase, rat, RF-EMR.

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

Abstract:

Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase–pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed-specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: Kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization.

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