Search results for: Protein Sequences

Authors: Olufunke O. Ezekiel, Ogugua C. Aworh

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Solid state fermentation of cassava peel with emphasis on protein enrichment using Trichoderma viride was evaluated. The effect of five variables: moisture content, pH, particle size (p), nitrogen source and incubation temperature; on the true protein and total sugars of cassava peel was investigated. The optimum fermentation period was established to be 8 days. Total sugars were 5-fold higher at pH 6 relative to pH 4 and 7-fold higher when cassava peels were fermented at 30oC relative to 25oC as well as using ammonium sulfate as the nitrogen source relative to urea or a combination of both. Total sugars ranged between 123.21mg/g at 50% initial moisture content to 374mg/g at 60% and from 190.59mg/g with particle size range of 2.00>p>1.41mm to 310.10mg/g with 4.00>p>3.35mm.True protein ranged from 229.70 mg/g at pH 4 to 284.05 mg/g at pH 6; from 200.87 mg/g with urea as nitrogen source and to 254.50mg/g with ammonium sulfate; from 213.82mg/g at 50% initial moisture content to 254.50mg/g at 60% moisture content, from 205.75mg/g in cassava peel with 5.6>p> 4.75mm to 268.30 in cassava peel with particle size 4.00>p>3.35mm, from 207.57mg/g at 25oC to 254.50mg/g at 30oC Cassava peel with particle size 4.00>p>3.35 mm and initial moisture content of 60% at pH 6.0, 30oC incubation temperature with ammonium sulfate (10g N / kg substrate) was most suitable for protein enrichment with Trichoderma viride. Crude protein increased from 4.21 % in unfermented cassava peel samples to 10.43 % in fermented samples.

Keywords: Cassava peel, Solid state fermentation, Trichoderma viride, Total sugars, True protein.

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

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

Keywords: mobile genetic elements, virulence, bacterial genomes

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

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

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

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Authors: R. Blicha

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High Peak to Average Power Ratio (PAPR) of the transmitted signal is a serious problem in multicarrier systems (MC), such as Orthogonal Frequency Division Multiplexing (OFDM), or in Multi-Carrier Code Division Multiple Access (MC-CDMA) systems, due to large number of subcarriers. This effect is possible reduce with some PAPR reduction techniques. Spreading sequences at the presence of Saleh and Rapp models of high power amplifier (HPA) have big influence on the behavior of system. In this paper we investigate the bit-error-rate (BER) performance of MC-CDMA systems. Basically we can see from simulations that the MC-CDMA system with Iterative algorithm can be providing significantly better results than the MC-CDMA system. The results of our analyses are verified via simulation.

Keywords: MC-CDMA, Iterative algorithm, PAPR, BER, Saleh, Rapp, Spreading Sequences.

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Authors: B. Tah, P. Pal, M. Mahato, R. Sarkar, G. B. Talapatra

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Herein, we report the different types of surface morphology due to the interaction between the pure protein Insulin (INS) and catanionic surfactant mixture of Sodium Dodecyl Sulfate (SDS) and Cetyl Trimethyl Ammonium Bromide (CTAB) at air/water interface obtained by the Langmuir-Blodgett (LB) technique. We characterized the aggregations by Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and Fourier transform infrared spectroscopy (FTIR) in LB films. We found that the INS adsorption increased in presence of catanionic surfactant at air/water interface. The presence of small amount of surfactant induces two-stage growth kinetics due to the pure protein absorption and protein-catanionic surface micelle interaction. The protein remains in native state in presence of small amount of surfactant mixture. Smaller amount of surfactant mixture with INS is producing surface micelle type structure. This may be considered for drug delivery system. On the other hand, INS becomes unfolded and fibrillated in presence of higher amount of surfactant mixture. In both the cases, the protein was successfully immobilized on a glass substrate by the LB technique. These results may find applications in the fundamental science of the physical chemistry of surfactant systems, as well as in the preparation of drug-delivery system.

Keywords: Air/water interface, Catanionic micelle, Insulin, Langmuir-Blodgett film

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Authors: Yuan-Jye Tseng, Fang-Yu Yu, Feng-Yi Huang

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A green design for assembly model is presented to integrate design evaluation and assembly and disassembly sequence planning by evaluating the three activities in one integrated model. For an assembled product, an assembly sequence planning model is required for assembling the product at the start of the product life cycle. A disassembly sequence planning model is needed for disassembling the product at the end. In a green product life cycle, it is important to plan how a product can be disassembled, reused, or recycled, before the product is actually assembled and produced. Given a product requirement, there may be several design alternative cases to design the same product. In the different design cases, the assembly and disassembly sequences for producing the product can be different. In this research, a new model is presented to concurrently evaluate the design and plan the assembly and disassembly sequences. First, the components are represented by using graph based models. Next, a particle swarm optimization (PSO) method with a new encoding scheme is developed. In the new PSO encoding scheme, a particle is represented by a position matrix defining an assembly sequence and a disassembly sequence. The assembly and disassembly sequences can be simultaneously planned with an objective of minimizing the total of assembly costs and disassembly costs. The test results show that the presented method is feasible and efficient for solving the integrated design evaluation and assembly and disassembly sequence planning problem. An example product is implemented and illustrated in this paper.

Keywords: green design, assembly and disassembly sequence planning, green design for assembly, particle swarm optimization.

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Authors: Seung Pil Pack

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Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.

Keywords: Deaminated lesion, DNA-protein interaction, DNA-recognizing enzymes

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Authors: Jyh-Da Wei, Hsin-Chen Tsai

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This work presents a novel means of extracting fixedlength parameters from voice signals, such that words can be recognized in linear time. The power and the zero crossing rate are first calculated segment by segment from a voice signal; by doing so, two feature sequences are generated. We then construct an FIR system across these two sequences. The parameters of this FIR system, used as the input of a multilayer proceptron recognizer, can be derived by recursive LSE (least-square estimation), implying that the complexity of overall process is linear to the signal size. In the second part of this work, we introduce a weighting factor λ to emphasize recent input; therefore, we can further recognize continuous speech signals. Experiments employ the voice signals of numbers, from zero to nine, spoken in Mandarin Chinese. The proposed method is verified to recognize voice signals efficiently and accurately.

Keywords: Speech Recognition, FIR system, Recursive LSE, Multilayer Perceptron

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Authors: S. Petrovska, D. Jonkus, D. Smiltiņa

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κ-casein is one of milk proteins which are very important for milk processing. Genotypes of κ-casein affect milk yield, fat, and protein content. The main factors which affect local Latvian dairy breed milk yield and composition are analyzed in research. Data were collected from 88 Latvian brown and 82 Latvian blue cows in 2015. AA genotype was 0.557 in Latvian brown and 0.232 in Latvian blue breed. BB genotype was 0.034 in Latvian brown and 0.207 in Latvian blue breed. Highest milk yield was observed in Latvian brown (5131.2 ± 172.01 kg), significantly high fat content and fat yield also was in Latvian brown (p < 0.05). Significant differences between κ-casein genotypes were not found in Latvian brown, but highest milk yield (5057 ± 130.23 kg), protein content (3.42 ± 0.03%), and protein yield (171.9 ± 4.34 kg) were with AB genotype. Significantly high fat content was observed in Latvian blue breed with BB genotype (4.29 ± 0.17%) compared with AA genotypes (3.42 ± 0.19). Similar tendency was found in protein content – 3.27 ± 0.16% with BB genotype and 2.59 ± 0.16% with AA genotype (p < 0.05). Milk yield increases by increasing parity. We did not obtain major tendency of changes of milk fat and protein content according parity.

Keywords: κ-casein, polymorphism, dairy cows, milk productivity.

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Authors: Erik Lilienblum, Robert Niese, Bernd Michaelis

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This paper proposes a novel stereo vision technique for top view book scanners which provide us with dense 3d point clouds of page surfaces. This is a precondition to dewarp bound volumes independent of 2d information on the page. Our method is based on algorithms, which normally require the projection of pattern sequences with structured light. We use image sequences of the moving stripe lighting of the top view scanner instead of an additional light projection. Thus the stereo vision setup is simplified without losing measurement accuracy. Furthermore we improve a surface model dewarping method through introducing a difference vector based on real measurements. Although our proposed method is hardly expensive neither in calculation time nor in hardware requirements we present good dewarping results even for difficult examples.

Keywords: stereo vision, 3d surface reconstruction, dewarpingdocuments, book scanner

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Authors: Hadi Seyedarabi, Ali Aghagolzadeh, Sohrab Khanmohammadi

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Face and facial expressions play essential roles in interpersonal communication. Most of the current works on the facial expression recognition attempt to recognize a small set of the prototypic expressions such as happy, surprise, anger, sad, disgust and fear. However the most of the human emotions are communicated by changes in one or two of discrete features. In this paper, we develop a facial expressions synthesis system, based on the facial characteristic points (FCP's) tracking in the frontal image sequences. Selected FCP's are automatically tracked using a crosscorrelation based optical flow. The proposed synthesis system uses a simple deformable facial features model with a few set of control points that can be tracked in original facial image sequences.

Keywords: Deformable face model, facial animation, facialcharacteristic points, optical flow.

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Authors: Jorge Maestre Vidal, Ana Lucila Sandoval Orozco, Luis Javier García Villalba

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With the increase in popularity of mobile devices, new and varied forms of malware have emerged. Consequently, the organizations for cyberdefense have echoed the need to deploy more effective defensive schemes adapted to the challenges posed by these recent monitoring environments. In order to contribute to their development, this paper presents a malware detection strategy for mobile devices based on sequence alignment algorithms. Unlike the previous proposals, only the system calls performed during the startup of applications are studied. In this way, it is possible to efficiently study in depth, the sequences of system calls executed by the applications just downloaded from app stores, and initialize them in a secure and isolated environment. As demonstrated in the performed experimentation, most of the analyzed malicious activities were successfully identified in their boot processes.

Keywords: Android, information security, intrusion detection systems, malware, mobile devices.

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Authors: Homa Torabizadeh

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This study proposes a basic molecular formula for all proteins. A total of 10,739 proteins belonging to 9 different protein groups classified on the basis of their functions were selected randomly. They included enzymes, storage proteins, hormones, signalling proteins, structural proteins, transport proteins, immunoglobulins or antibodies, motor proteins and receptor proteins. After obtaining the protein molecular formula using the ProtParam tool, the H/C, N/C, O/C, and S/C ratios were determined for each randomly selected sample. In this case, H, N, O, and S coefficients were specified per carbon atom. Surprisingly, the results demonstrated that H, N, O, and S coefficients for all 10,739 proteins are similar and highly correlated. This study demonstrates that despite differences in the structure and function, all known proteins have a similar basic molecular formula CnH1.58 ± 0.015nN0.28 ± 0.005nO0.30 ± 0.007nS0.01 ± 0.002n. The total correlation between all coefficients was found to be 0.9999.

Keywords: Protein molecular formula, Basic unit formula, Protparam tool.

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Authors: A.R. Pazoki, A. H. Shirani Rad, D. Habibi, F. Paknejad, S. Kobraee, N. Hadayat

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In the other to Study of drought stress and Selenium spraying effect on superoxide dismotase (SOD) activity of rapeseed (Brassica napus L.) cultivars in Shahr-e-Rey region, an experiment carried out in Split factorial design in the basis of randomized complete blocks with 4 replications in 2006. Irrigation in two levels: Normal irrigation and irrigation with drought stress when the soil electrical conductivity reached to 60 as main factor and rapeseed cultivars in 3 levels Zarfam, Okapi, Opera and selenium spraying at the beginning of flowering stage in 3 levels: 0, 16 and 21 g/ha as sub factor. The results showed that the simple and interaction effect of irrigation, selenium and cultivars on SOD activity had significant difference. In this case Zarfam cultivar with 2010 u.mg-1 protein and Opera with 1454 u.mg-1 protein produced maximum and minimum amounts of SOD activitiy. Interaction effect of irrigation and variety showed that, normal irrigation in Opera with 1115 u.mg-1 protein and drought stress in Zarfam with 2784 u.mg-1 protein conducted to and minimum and maximum amounts of SOD activity. Interaction effect of irrigation, cultivar and selenium on SOD indicated that drought stress condition and 21 gr/ha selenium spraying in Zarfam variety with 3146 u.mg-1 protein gained to highest activities of SOD.

Keywords: Drought stress, Rapeseed, Selenium, Superoxide dismutase.

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Authors: N. Umasuthan, S. D. N. K. Bathige, W. S. Thulasitha, I. Whang, J. Lee

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The MyD88 is an evolutionarily conserved host-expressed adaptor protein that is essential for proper TLR/ IL1R immune-response signaling. A previously identified complete cDNA (1626 bp) of OfMyD88 comprised an ORF of 867 bp encoding a protein of 288 amino acids (32.9 kDa). The gDNA (3761 bp) of OfMyD88 revealed a quinquepartite genome organization composed of 5 exons (with the sizes of 310, 132, 178, 92 and 155 bp) separated by 4 introns. All the introns displayed splice signals consistent with the consensus GT/AG rule. A bipartite domain structure with two domains namely death domain (24-103) coded by 1^st exon, and TIR domain (151-288) coded by last 3 exons were identified through in silico analysis. Moreover, homology modeling of these two domains revealed a similar quaternary folding nature between human and rock bream homologs. A comprehensive comparison of vertebrate MyD88 genes showed that they possess a 5-exonic structure.In this structure, the last three exons were strongly conserved, and this suggests that a rigid structure has been maintained during vertebrate evolution.A cluster of TATA box-like sequences were found 0.25 kb upstream of cDNA starting position. In addition, putative 5'-flanking region of OfMyD88 was predicted to have TFBS implicated with TLR signaling, including copies of NFkB1, APRF/ STAT3, Sp1, IRF1 and 2 and Stat1/2. Using qPCR technique, a ubiquitous mRNA expression was detected in liver and blood. Furthermore, a significantly up-regulated transcriptional expression of OfMyD88 was detected in head kidney (12-24 h; >2-fold), spleen (6 h; 1.5-fold), liver (3 h; 1.9-fold) and intestine (24 h; ~2-fold) post-Fla challenge. These data suggest a crucial role for MyD88 in antibacterial immunity of teleosts.

Keywords: MyD88, Innate immunity, Flagellin, Genomic analysis.

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Authors: Mohammad N. Alanazi, David A. Gustafson

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In this article, we introduce a new approach for analyzing UML designs to detect the inconsistencies between multiple state diagrams and sequence diagrams. The Super State Analysis (SSA) identifies the inconsistencies in super states, single step transitions, and sequences. Because SSA considers multiple UML state diagrams, it discovers inconsistencies that cannot be discovered when considering only a single UML state diagram. We have introduced a transition set that captures relationship information that is not specifiable in UML diagrams. The SSA model uses the transition set to link transitions of multiple state diagrams together. The analysis generates three different sets automatically. These sets are compared to the provided sets to detect the inconsistencies. SSA identifies five types of inconsistencies: impossible super states, unreachable super states, illegal transitions, missing transitions, and illegal sequences.

Keywords: Modeling Languages, Object-Oriented Analysis, Sequence Diagrams, Software Models, State Diagrams, UML.

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Authors: Feng-Yi Huang, Yuan-Jye Tseng

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In the traditional concept of product life cycle management, the activities of design, manufacturing, and assembly are performed in a sequential way. The drawback is that the considerations in design may contradict the considerations in manufacturing and assembly. The different designs of components can lead to different assembly sequences. Therefore, in some cases, a good design may result in a high cost in the downstream assembly activities. In this research, an integrated design evaluation and assembly sequence planning model is presented. Given a product requirement, there may be several design alternative cases to design the components for the same product. If a different design case is selected, the assembly sequence for constructing the product can be different. In this paper, first, the designed components are represented by using graph based models. The graph based models are transformed to assembly precedence constraints and assembly costs. A particle swarm optimization (PSO) approach is presented by encoding a particle using a position matrix defined by the design cases and the assembly sequences. The PSO algorithm simultaneously performs design evaluation and assembly sequence planning with an objective of minimizing the total assembly costs. As a result, the design cases and the assembly sequences can both be optimized. The main contribution lies in the new concept of integrated design evaluation and assembly sequence planning model and the new PSO solution method. The test results show that the presented method is feasible and efficient for solving the integrated design evaluation and assembly planning problem. In this paper, an example product is tested and illustrated.

Keywords: assembly sequence planning, design evaluation, design for assembly, particle swarm optimization

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Authors: Natarajan Vijayarangan, Prasanna S. Bidare

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Cryptography, Image watermarking and E-banking are filled with apparent oxymora and paradoxes. Random sequences are used as keys to encrypt information to be used as watermark during embedding the watermark and also to extract the watermark during detection. Also, the keys are very much utilized for 24x7x365 banking operations. Therefore a deterministic random sequence is very much useful for online applications. In order to obtain the same random sequence, we need to supply the same seed to the generator. Many researchers have used Deterministic Random Number Generators (DRNGs) for cryptographic applications and Pseudo Noise Random sequences (PNs) for watermarking. Even though, there are some weaknesses in PN due to attacks, the research community used it mostly in digital watermarking. On the other hand, DRNGs have not been widely used in online watermarking due to its computational complexity and non-robustness. Therefore, we have invented a new design of generating DRNG using Pi-series to make it useful for online Cryptographic, Digital watermarking and Banking applications.

Keywords: E-tokens, LFSR, non-linear, Pi series, pseudo random number.

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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: Nirmal Kumar, Rita N. Kumar, Anubhuti Bora, Manmeet Kaur Amb

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The whole-cell protein-profiling technique was evaluated for studying differences in banding pattern of three different species of Cyanobacteria i.e. Anabaena fertilissima, Aulosira fertilissima and Westiellopsis prolifica under the influence of four different pesticides-2,4-D (Ethyl Ester of 2,4-Dichloro Phenoxy Acetic Acid), Pencycuron (N-[(4-chlorophenyl)methyl]-Ncyclopentyl- N'–phenylurea), Endosulfan (6,7,8,9,10,10hexachloro- 1,5,5a,6,9,9a-hexahydro-6,9-methano-2,4,3-benzodioxathiepine-3- oxide) and Tebuconazole (1-(4-Chlorophenyl)-4,4-dimethyl-3-(1,2,4- triazol-1-ylmethyl)pentan-3-ol). Whole-cell extracts were obtained by sonication treatment (Sonifier cell disruptor -Branson Digital Sonifier S-450D, USA) and were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). SDS-PAGE analyses of the total protein profile of Anabaena fertilissima, Aulosira fertilissima and Westiellopsis prolifica showed a linear decrease in the protein content with increasing pesticide stress when administered to different concentrations of 2, 4-D, Pencycuron, Endosulfan and Tebuconazole. The results indicate that different stressors exert specific effects on cyanobacterial protein synthesis.

Keywords: Cyanobacteria, pesticide, SDS-PAGE

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

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

Keywords: MicroRNA, mRNA, plant, superoxide dismutase.

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Authors: 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: Kholoud A. Al-Shammery , Badr El-Sabah A. Fetoh, Ahmed M. Alshammari

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Protein and Esterase electrophoresis were used to genetically identify two Saudi tick species. Engorged females of the camel tick Hyalomma dromedarii (Koch) (Acari: Ixodidae) and the cattle tick Boophilus annulatus (Say) (Acari: Ixodidae) ticks collected from infested camels and cattle in the animals resting house at Hail region in KSA were used. The results showed that there are a variation in both of protein and esterase activity levels and a high polymorphism within and between the genera and species of Hyalomma and Boophilus . In conclusion, the protein and esterase electrophoretic analysis used in the present study could successfully distinguish among tick species, commonly found in Saudi Arabia.

Keywords: Molecular biology, The camel tick Hyalomma dromedarii, The cattle tick Boophilus annulatus , Ticks.

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Authors: Rosalyn R. Porle, Ali Chekima, Farrah Wong, G. Sainarayanan

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Arms detection is one of the fundamental problems in human motion analysis application. The arms are considered as the most challenging body part to be detected since its pose and speed varies in image sequences. Moreover, the arms are usually occluded with other body parts such as the head and torso. In this paper, histogram-based skin colour segmentation is proposed to detect the arms in image sequences. Six different colour spaces namely RGB, rgb, HSI, TSL, SCT and CIELAB are evaluated to determine the best colour space for this segmentation procedure. The evaluation is divided into three categories, which are single colour component, colour without luminance and colour with luminance. The performance is measured using True Positive (TP) and True Negative (TN) on 250 images with manual ground truth. The best colour is selected based on the highest TN value followed by the highest TP value.

Keywords: image colour analysis, image motion analysis, skin, wavelet transform.

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Authors: Mourad Moussa, Ali Douik, Hassani Messaoud

Abstract:

In this paper, we present a comparative study between two computer vision systems for objects recognition and tracking, these algorithms describe two different approach based on regions constituted by a set of pixels which parameterized objects in shot sequences. For the image segmentation and objects detection, the FCM technique is used, the overlapping between cluster's distribution is minimized by the use of suitable color space (other that the RGB one). The first technique takes into account a priori probabilities governing the computation of various clusters to track objects. A Parzen kernel method is described and allows identifying the players in each frame, we also show the importance of standard deviation value research of the Gaussian probability density function. Region matching is carried out by an algorithm that operates on the Mahalanobis distance between region descriptors in two subsequent frames and uses singular value decomposition to compute a set of correspondences satisfying both the principle of proximity and the principle of exclusion.

Keywords: Image segmentation, objects tracking, Parzen window, singular value decomposition, target recognition.

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

Abstract:

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: Bahareh Hajirostamloo

Abstract:

Cow milk, is a product of the mammary gland and soymilk is a beverage made from soybeans; it is the liquid that remains after soybeans are soaked. In this research effort, we compared nutritional parameters of this two kind milk such as total fat, fiber, protein, minerals (Ca, Fe and P), fatty acids, carbohydrate, lactose, water, total solids, ash, pH, acidity and calories content in one cup (245 g). Results showed soymilk contains 4.67 grams of fat, 0.52 of fatty acids, 3.18 of fiber, 6.73 of protein, 4.43 of carbohydrate, 0.00 of lactose, 228.51 of water, 10.40 of total solids and 0.66 of ash, also 9.80 milligrams of Ca, 1.42 of Fe, and 120.05 of P, 79 Kcal of calories, pH=6.74 and acidity was 0.24%. Cow milk contains 8.15 grams of fat, 5.07 of fatty acids, 0.00 of fiber, 8.02 of protein, 11.37 of carbohydrate, ´Çá4.27 of lactose, 214.69 of water, 12.90 of total solids, 1.75 of ash, 290.36 milligrams of Ca, 0.12 of Fe, and 226.92 of P, 150 Kcal of calories, pH=6.90 and acidity was 0.21% . Soy milk is one of plant-based complete proteins and cow milk is a rich source of nutrients as well. Cow milk is containing near twice as much fat as and ten times more fatty acids do soymilk. Cow milk contains greater amounts of mineral (except Fe) it contain more than three hundred times the amount of Ca and nearly twice the amount of P as does soymilk but soymilk contains more Fe (ten time more) than does cow milk. Cow milk and soy milk contain nearly identical amounts of protein and water and fiber is a big plus, dairy has none. Although what we choose to drink is really a mater of personal preference and our health objectives but looking at the comparison, soy looks like healthier choices.

Keywords: Soymilk, cow milk, nutritional, comparison.

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Authors: Mahmoud Elmezain, Ayoub Al-Hamadi, Robert Niese, Bernd Michaelis

Abstract:

Real-time hand tracking is a challenging task in many computer vision applications such as gesture recognition. This paper proposes a robust method for hand tracking in a complex environment using Mean-shift analysis and Kalman filter in conjunction with 3D depth map. The depth information solve the overlapping problem between hands and face, which is obtained by passive stereo measuring based on cross correlation and the known calibration data of the cameras. Mean-shift analysis uses the gradient of Bhattacharyya coefficient as a similarity function to derive the candidate of the hand that is most similar to a given hand target model. And then, Kalman filter is used to estimate the position of the hand target. The results of hand tracking, tested on various video sequences, are robust to changes in shape as well as partial occlusion.

Keywords: Computer Vision and Image Analysis, Object Tracking, Gesture Recognition.

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Authors: Michal Mardiak, Jaroslav Polec

Abstract:

In this paper we proposed comparison of four content based objective metrics with results of subjective tests from 80 video sequences. We also include two objective metrics VQM and SSIM to our comparison to serve as “reference” objective metrics because their pros and cons have already been published. Each of the video sequence was preprocessed by the region recognition algorithm and then the particular objective video quality metric were calculated i.e. mutual information, angular distance, moment of angle and normalized cross-correlation measure. The Pearson coefficient was calculated to express metrics relationship to accuracy of the model and the Spearman rank order correlation coefficient to represent the metrics relationship to monotonicity. The results show that model with the mutual information as objective metric provides best result and it is suitable for evaluating quality of video sequences.

Keywords: Objective quality metrics, mutual information, region recognition, content based metrics

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