Search results for: fusion protein.

Authors: Nichole Haag, Kimberly Velk, Tyler McCune, Chun Wu

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Methicillin/multiple-resistant Staphylococcus aureus (MRSA) are infectious bacteria that are resistant to common antibiotics. A previous in silico study in our group has identified a hypothetical protein SAV1226 as one of the potential drug targets. In this study, we reported the bioinformatics characterization, as well as cloning, expression, purification and kinetic assays of hypothetical protein SAV1226 from methicillin/vancomycin-resistant Staphylococcus aureus Mu50 strain. MALDI-TOF/MS analysis revealed a low degree of structural similarity with known proteins. Kinetic assays demonstrated that hypothetical protein SAV1226 is neither a domain of an ATP dependent dihydroxyacetone kinase nor of a phosphotransferase system (PTS) dihydroxyacetone kinase, suggesting that the function of hypothetical protein SAV1226 might be misannotated on public databases such as UniProt and InterProScan 5.

Keywords: Dihydroxyacetone kinase, essential genes, Methicillin-resistant Staphylococcus aureus, drug target.

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Authors: Vernie C. Convicto, Henry P. Aringa, Wilson I. Barredo

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This study presents a conformational model of the helical structures of globular protein particularly ferritin in the framework of white noise path integral formulation by using Associated Legendre functions, Bessel and convolution of Bessel and trigonometric functions as modulating functions. The model incorporates chirality features of proteins and their helix-turn-helix sequence structural motif.

Keywords: Globular protein, modulating function, white noise, winding probability.

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Authors: Leong Lee, Cyriac Kandoth, Jennifer L. Leopold, Ronald L. Frank

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Protein 3D structure prediction has always been an important research area in bioinformatics. In particular, the prediction of secondary structure has been a well-studied research topic. Despite the recent breakthrough of combining multiple sequence alignment information and artificial intelligence algorithms to predict protein secondary structure, the Q3 accuracy of various computational prediction algorithms rarely has exceeded 75%. In a previous paper [1], this research team presented a rule-based method called RT-RICO (Relaxed Threshold Rule Induction from Coverings) to predict protein secondary structure. The average Q3 accuracy on the sample datasets using RT-RICO was 80.3%, an improvement over comparable computational methods. Although this demonstrated that RT-RICO might be a promising approach for predicting secondary structure, the algorithm-s computational complexity and program running time limited its use. Herein a parallelized implementation of a slightly modified RT-RICO approach is presented. This new version of the algorithm facilitated the testing of a much larger dataset of 396 protein domains [2]. Parallelized RTRICO achieved a Q3 score of 74.6%, which is higher than the consensus prediction accuracy of 72.9% that was achieved for the same test dataset by a combination of four secondary structure prediction methods [2].

Keywords: data mining, protein secondary structure prediction, parallelization.

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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: Zarmina Gillani, Nuzhat Huma, Aysha Sameen, Mulazim Hussain Bukhari

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Whey is an excellent food ingredient owing to its high nutritive value and its functional properties. However, composition of whey varies depending on composition of milk, processing conditions, processing method, and its whey protein content. The aim of this study was to prepare a whey powder from raw whey and to determine the influence of different processing temperatures (160 and 180 °C) on the physicochemical, functional properties during storage of 180 days and on whey protein denaturation. Results have shown that temperature significantly (P < 0.05) affects the pH, acidity, non-protein nitrogen (NPN), protein total soluble solids, fat and lactose contents. Significantly (p < 0.05) higher foaming capacity (FC), foam stability (FS), whey protein nitrogen index (WPNI), and a lower turbidity and solubility index (SI) were observed in whey powder processed at 160 °C compared to whey powder processed at 180 °C. During storage of 180 days, slow but progressive changes were noticed on the physicochemical and functional properties of whey powder. Reverse phase-HPLC analysis revealed a significant (P < 0.05) effect of temperature on whey protein contents. Denaturation of β-Lactoglobulin is followed by α-lacalbumin, casein glycomacropeptide (CMP/GMP), and bovine serum albumin (BSA).

Keywords: Whey powder, temperature, denaturation, reverse phase – HPLC.

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

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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: S. Ashrafpour, T. Tohidi Moghadam, B. Ranjbar

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Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 μM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme- AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.

Keywords: Nanocarrier, Nanoparticles, Surface Plasmon Resonance, Quenching Fluorescence.

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Authors: Wadii Boulila, Imed Riadh Farah, Karim Saheb Ettabaa, Basel Solaiman, Henda Ben Ghezala

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This paper investigates the problem of tracking spa¬tiotemporal changes of a satellite image through the use of Knowledge Discovery in Database (KDD). The purpose of this study is to help a given user effectively discover interesting knowledge and then build prediction and decision models. Unfortunately, the KDD process for spatiotemporal data is always marked by several types of imperfections. In our paper, we take these imperfections into consideration in order to provide more accurate decisions. To achieve this objective, different KDD methods are used to discover knowledge in satellite image databases. Each method presents a different point of view of spatiotemporal evolution of a query model (which represents an extracted object from a satellite image). In order to combine these methods, we use the evidence fusion theory which considerably improves the spatiotemporal knowledge discovery process and increases our belief in the spatiotemporal model change. Experimental results of satellite images representing the region of Auckland in New Zealand depict the improvement in the overall change detection as compared to using classical methods.

Keywords: Knowledge discovery in satellite databases, knowledge fusion, data imperfection, data mining, spatiotemporal change detection.

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Authors: Mbaitiga Zacharie

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The objective of the presented work is to implement the Kalman Filter into an application that reduces the influence of the environmental changes over the robot expected to navigate over a terrain of varying friction properties. The Discrete Kalman Filter is used to estimate the robot position, project the estimated current state ahead at time through time update and adjust the projected estimated state by an actual measurement at that time via the measurement update using the data coming from the infrared sensors, ultrasonic sensors and the visual sensor respectively. The navigation test has been performed in a real world environment and has been found to be robust.

Keywords: Kalman filter, sensors fusion, robot navigation.

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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: 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: Sudipta Majumdar, Jayant Bharadwaj

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This paper presents feature level image fusion using Haar lifting wavelet transform. Feature fused is edge and boundary information, which is obtained using wavelet transform modulus maxima criteria. Simulation results show the superiority of the result as entropy, gradient, standard deviation are increased for fused image as compared to input images. The proposed methods have the advantages of simplicity of implementation, fast algorithm, perfect reconstruction, and reduced computational complexity. (Computational cost of Haar wavelet is very small as compared to other lifting wavelets.)

Keywords: Lifting wavelet transform, wavelet transform modulus maxima.

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Authors: Vita Strazdina, Aleksandrs Jemeljanovs, Vita Sterna

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Not all proteins have the same nutritional value, since protein quality strongly depends on its amino acid composition and digestibility. The meat of game animals could be a high protein source because of its well-balanced essential amino acids composition. Investigations about biochemical composition of game meat such as wild boar (Sus scrofa scrofa), roe deer (Capreolus capreolus) and beaver (Castor fiber) are not very much. Therefore, the aim of the investigation was evaluate protein composition of game meat hunted in Latvia. The biochemical analysis, evaluation of connective tissue and essential amino acids in meat samples were done, the amino acids score were calculate. Results of analysis showed that protein content 20.88-22.05% of all types of meat samples is not different statistically. The content of connective tissue from 1.3% in roe deer till 1.5% in beaver meat allowed classified game animal as high quality meat. The sum of essential amino acids in game meat samples were determined 7.05–8.26g100g-1. Roe deer meat has highest protein content and lowest content of connective tissues among game meat hunted in Latvia. Concluded that amino acid score for limiting amino acids phenylalanine and tyrosine is high and shows high biological value of game meat.

Keywords: Dietic product, game meat, amino acids, scores.

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Authors: S. K. Tiwari, Dinesh Kumar Shukla, R. Chandra

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Friction stir welding is a solid state joining process. High strength aluminum alloys are widely used in aircraft and marine industries. Generally, the mechanical properties of fusion welded aluminum joints are poor. As friction stir welding occurs in solid state, no solidification structures are created thereby eliminating the brittle and eutectic phases common in fusion welding of high strength aluminum alloys. In this review the process parameters, microstructural evolution, and effect of friction stir welding on the properties of weld specific to aluminum alloys have been discussed.

Keywords: Aluminum alloys, Friction stir welding (FSW), Microstructure, Properties.

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Authors: H. Ali, K. Hameed, N. Khan

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In DMVC, we have more than one options of sources available for construction of side information. The newer techniques make use of both the techniques simultaneously by constructing a bitmask that determines the source of every block or pixel of the side information. A lot of computation is done to determine each bit in the bitmask. In this paper, we have tried to define areas that can only be well predicted by temporal interpolation and not by multiview interpolation or synthesis. We predict that all such areas that are not covered by two cameras cannot be appropriately predicted by multiview synthesis and if we can identify such areas in the first place, we don-t need to go through the script of computations for all the pixels that lie in those areas. Moreover, this paper also defines a technique based on KLT to mark the above mentioned areas before any other processing is done on the side view.

Keywords: Side Information, Distributed Multiview Video Coding, Fusion, Early Decision.

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

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

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

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Authors: Piercarlo Dondi, Luca Lombardi, Marco Porta

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In the last years numerous applications of Human- Computer Interaction have exploited the capabilities of Time-of- Flight cameras for achieving more and more comfortable and precise interactions. In particular, gesture recognition is one of the most active fields. This work presents a new method for interacting with a virtual object in a 3D space. Our approach is based on the fusion of depth data, supplied by a ToF camera, with color information, supplied by a HD webcam. The hand detection procedure does not require any learning phase and is able to concurrently manage gestures of two hands. The system is robust to the presence in the scene of other objects or people, thanks to the use of the Kalman filter for maintaining the tracking of the hands.

Keywords: Gesture recognition, human-computer interaction, Time-of-Flight camera.

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Authors: Hyun-Koo Kim, Sangmoon Lee, Ho-Youl Jung, Ju H. Park

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We present a system that finds road boundaries and constructs the virtual lane based on fusion data from a laser and a monocular sensor, and detects forward vehicle position even in no lane markers or bad environmental conditions. When the road environment is dark or a lot of vehicles are parked on the both sides of the road, it is difficult to detect lane and road boundary. For this reason we use fusion of laser and vision sensor to extract road boundary to acquire three dimensional data. We use parabolic road model to calculate road boundaries which is based on vehicle and sensors state parameters and construct virtual lane. And then we distinguish vehicle position in each lane.

Keywords: Vehicle Detection, Adaboost, Haar-like Feature, Road Boundary Detection

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Authors: G. Lavanya Devi, Allam Appa Rao, A. Damodaram, GR Sridhar, G. Jaya Suma

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Cluster analysis divides data into groups that are meaningful, useful, or both. Analysis of biological data is creating a new generation of epidemiologic, prognostic, diagnostic and treatment modalities. Clustering of protein sequences is one of the current research topics in the field of computer science. Linear relation is valuable in rule discovery for a given data, such as if value X goes up 1, value Y will go down 3", etc. The classical linear regression models the linear relation of two sequences perfectly. However, if we need to cluster a large repository of protein sequences into groups where sequences have strong linear relationship with each other, it is prohibitively expensive to compare sequences one by one. In this paper, we propose a new technique named General Regression Model Technique Clustering Algorithm (GRMTCA) to benignly handle the problem of linear sequences clustering. GRMT gives a measure, GR*, to tell the degree of linearity of multiple sequences without having to compare each pair of them.

Keywords: Clustering, General Regression Model, Protein Sequences, Similarity Measure.

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Authors: Fiona Browne, Huiru Zheng, Haiying Wang, Francisco Azuaje

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Recent years have seen a growing trend towards the integration of multiple information sources to support large-scale prediction of protein-protein interaction (PPI) networks in model organisms. Despite advances in computational approaches, the combination of multiple “omic" datasets representing the same type of data, e.g. different gene expression datasets, has not been rigorously studied. Furthermore, there is a need to further investigate the inference capability of powerful approaches, such as fullyconnected Bayesian networks, in the context of the prediction of PPI networks. This paper addresses these limitations by proposing a Bayesian approach to integrate multiple datasets, some of which encode the same type of “omic" data to support the identification of PPI networks. The case study reported involved the combination of three gene expression datasets relevant to human heart failure (HF). In comparison with two traditional methods, Naive Bayesian and maximum likelihood ratio approaches, the proposed technique can accurately identify known PPI and can be applied to infer potentially novel interactions.

Keywords: Bayesian network, Classification, Data integration, Protein interaction networks.

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Authors: Gry M, Bergström J, Lengquist J, Lindberg J, Drobin K, Schwenk J, Nilsson P, Schuppe-Koistinen I.

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Sensitive and predictive DILI (Drug Induced Liver Injury) biomarkers are needed in drug R&D to improve early detection of hepatotoxicity. The discovery of DILI biomarkers that demonstrate the predictive power to identify individuals at risk to DILI would represent a major advance in the development of personalized healthcare approaches. In this healthy volunteer acetaminophen study (4g/day for 7 days, with 3 monitored nontreatment days before and 4 after), 450 serum samples from 32 subjects were analyzed using protein profiling by antibody suspension bead arrays. Multiparallel protein profiles were generated using a DILI target protein array with 300 antibodies, where the antibodies were selected based on previous literature findings of putative DILI biomarkers and a screening process using pre dose samples from the same cohort. Of the 32 subjects, 16 were found to develop an elevated ALT value (2Xbaseline, responders). Using the plasma profiling approach together with multivariate statistical analysis some novel findings linked to lipid metabolism were found and more important, endogenous protein profiles in baseline samples (prior to treatment) with predictive power for ALT elevations were identified.

Keywords: DILI, Plasma profiling, PLSDA, Randomforest.

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Authors: J. Davoodi, F. Katouzi

Abstract:

The aim of this research was to calculate the thermal properties of Au3Ni Nanowire. The molecular dynamics (MD) simulation technique was used to obtain the effect of radius size on the energy, the melting temperature and the latent heat of fusion at the isobaric-isothermal (NPT) ensemble. The Quantum Sutton-Chen (Q-SC) many body interatomic potentials energy have been used for Gold (Au) and Nickel (Ni) elements and a mixing rule has been devised to obtain the parameters of these potentials for nanowire stats. Our MD simulation results show the melting temperature and latent heat of fusion increase upon increasing diameter of nanowire. Moreover, the cohesive energy decreased with increasing diameter of nanowire.

Keywords: Au3Ni Nanowire, Thermal properties, Molecular dynamics simulation

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Authors: Irene Luque Ruiz, Manuel Urbano Cuadrado, Miguel Ángel Gómez-Nieto

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New graph similarity methods have been proposed in this work with the aim to refining the chemical information extracted from molecules matching. For this purpose, data fusion of the isomorphic and nonisomorphic subgraphs into a new similarity measure, the Approximate Similarity, was carried out by several approaches. The application of the proposed method to the development of quantitative structure-activity relationships (QSAR) has provided reliable tools for predicting several pharmacological parameters: binding of steroids to the globulin-corticosteroid receptor, the activity of benzodiazepine receptor compounds, and the blood brain barrier permeability. Acceptable results were obtained for the models presented here.

Keywords: Graph similarity, Nonisomorphic dissimilarity, Approximate similarity, Drug activity prediction.

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Authors: B. Bina, M.H. Mehdinejad, Gunnel Dalhammer, Guna RajaraoM. Nikaeen, H. Movahedian Attar

Abstract:

Coagulation of water involves the use of coagulating agents to bring the suspended matter in the raw water together for settling and the filtration stage. Present study is aimed to examine the effects of aluminum sulfate as coagulant in conjunction with Moringa Oleifera Coagulant Protein as coagulant aid on turbidity, hardness, and bacteria in turbid water. A conventional jar test apparatus was employed for the tests. The best removal was observed at a pH of 7 to 7.5 for all turbidities. Turbidity removal efficiency was resulted between % 80 to % 99 by Moringa Oleifera Coagulant Protein as coagulant aid. Dosage of coagulant and coagulant aid decreased with increasing turbidity. In addition, Moringa Oleifera Coagulant Protein significantly has reduced the required dosage of primary coagulant. Residual Al+3 in treated water were less than 0.2 mg/l and meets the environmental protection agency guidelines. The results showed that turbidity reduction of % 85.9- % 98 paralleled by a primary Escherichia coli reduction of 1-3 log units (99.2 – 99.97%) was obtained within the first 1 to 2 h of treatment. In conclusions, Moringa Oleifera Coagulant Protein as coagulant aid can be used for drinking water treatment without the risk of organic or nutrient release. We demonstrated that optimal design method is an efficient approach for optimization of coagulation-flocculation process and appropriate for raw water treatment.

Keywords: MOCP, Coagulant aid, turbidity removal, E.coliremoval, water, treatment

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Authors: Shahram Naghizadeh Raeisi, Ali Alghooneh

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Using membrane technology and modification of milk protein structural properties, a lactose free yogurt was developed. The functional, textural and structural properties of the sample were evaluated and compared with the commercial ones. Results showed that the modification of protein in high fat set yogurt resulted in 11.55%, 18%, 20.21% and 7.08% higher hardness, consistency, water holding capacity, and shininess values compared with the control one. Furthermore, these indices of modified low fat set yogurt were 21.40%, 25.41%, 28.15% & 10.58% higher than the control one, which could be related to the gel network microstructural properties in yogurt formulated with modified protein. In this way, in comparison with the control one, the index of linkage strength (A), the number of linkages (z), and time scale of linkages (λrel) of the high fat modified yogurt were 22.10%, 50.68%, 21.82% higher than the control one; whereas, the average linear distance between two adjacent crosslinks (ξ), was 16.77% lower than the control one. For low fat modified yogurt, A, z, λrel, and ξ indices were 34.30%, 61.70% and 42.60% higher and 19.20% lower than the control one, respectively. The shelf life of modified yogurt was extended to 10 weeks in the refrigerator, while, the control set yogurt had a 3 weeks shelf life. The acidity of high fat and low fat modified yogurts increased from 76 to 84 and 72 to 80 Dornic degrees during 10 weeks of storage, respectively, whereas for control high fat and low fat yogurts they increased from 82 to 122 and 77 to 112 Dornic degrees, respectively. This behavior could be due to the elimination of microorganism’s source of energy in modified yogurt. Furthermore, the calories of high fat and low fat lactose free yogurts were 25% and 40% lower than their control samples, respectively. Generally, results showed that the lactose free yogurt with modified protein, despite of 1% lower protein content than the control one, showed better functional properties, nutritional properties, network parameters, and shelf stability, which could be promising in the set yogurt industry.

Keywords: Lactose free, low calorie, network properties, protein modification.

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Authors: H. Sakamoto, S. Kurosawa, M. Suzuki, S. Oguri

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In Arabidopsis, several genes encoding proteins with ankyrin repeats and transmembrane domains (AtANKTM) have been identified as mediators of biotic and abiotic stress responses. It has been known that the expression of an AtANKTM gene, At2g24600, is induced in response to abiotic stress and that there are four splicing variants derived from this locus. In this study, by RT-PCR and sequencing analysis, an unknown splicing variant of the At2g24600 transcript was identified. Based on differences in the predicted amino acid sequences, the five splicing variants are divided into three groups. The three predicted proteins are highly homologous, yet have different numbers of ankyrinrepeats and transmembrane domains. It is generally considered that ankyrin repeats mediate protein-protein interaction and that the number oftransmembrane domains affects membrane topology of proteins. The protein variants derived from the At2g24600 locus may have different molecular functions each other.

Keywords: Alternative splicing, ankyrin repeats, transmembrane domains, Arabidopsis.

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Authors: Tom Snir, Eitan Rubin

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Mendelian Disease Genes represent a collection of single points of failure for the various systems they constitute. Such genes have been shown, on average, to encode longer proteins than 'non-disease' proteins. Existing models suggest that this results from the increased likeli-hood of longer genes undergoing mutations. Here, we show that in saturated mutagenesis experiments performed on model organisms, where the likelihood of each gene mutating is one, a similar relationship between length and the probability of a gene being lethal was observed. We thus suggest an extended model demonstrating that the likelihood of a mutated gene to produce a severe phenotype is length-dependent. Using the occurrence of conserved domains, we bring evidence that this dependency results from a correlation between protein length and the number of functions it performs. We propose that protein length thus serves as a proxy for protein cardinality in different networks required for the organism's survival and well-being. We use this example to argue that the collection of Mendelian Disease Genes can, and should, be used to study the rules governing systems vulnerability in living organisms.

Keywords: Systems Biology, Protein Length

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Authors: David L. Olson, Stephen B. H. Bruder, Adam S. Watkins, Cleon E. Davis

Abstract:

In global navigation satellite system (GNSS) denied settings, such as indoor environments, autonomous mobile robots are often limited to dead-reckoning navigation techniques to determine their position, velocity, and attitude (PVA). Localization is typically accomplished by employing an inertial measurement unit (IMU), which, while precise in nature, accumulates errors rapidly and severely degrades the localization solution. Standard sensor fusion methods, such as Kalman filtering, aim to fuse precise IMU measurements with accurate aiding sensors to establish a precise and accurate solution. In indoor environments, where GNSS and no other a priori information is known about the environment, effective sensor fusion is difficult to achieve, as accurate aiding sensor choices are sparse. However, an opportunity arises by employing a depth camera in the indoor environment. A depth camera can capture point clouds of the surrounding floors and walls. Extracting attitude from these surfaces can serve as an accurate aiding source, which directly combats errors that arise due to gyroscope imperfections. This configuration for sensor fusion leads to a dramatic reduction of PVA error compared to traditional aiding sensor configurations. This paper provides the theoretical basis for the depth camera aiding sensor method, initial expectations of performance benefit via simulation, and hardware implementation thus verifying its veracity. Hardware implementation is performed on the Quanser Qbot 2™ mobile robot, with a Vector-Nav VN-200™ IMU and Kinect™ camera from Microsoft.

Keywords: Autonomous mobile robotics, dead reckoning, depth camera, inertial navigation, Kalman filtering, localization, sensor fusion.

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Authors: B. Coşgun, Ö. Öztürk

Abstract:

Canola is a specific edible type of rapeseed, developed in the 1970s, which contains about 40 percent oil. This research was carried out to determine the yield and some quality characteristics of some winter canola cultivars during the 2010-2011 vegetation period in Central Anatolia of Turkey. In this research; Oase, Dante, Californium, Excalibur, Elvis, ES Hydromel, Licord, Orkan, Vectra, Nelson, Champlain and NK Petrol winter canola varieties were used as material. The field experiment was set up in a “Randomized Complete Block Design” with three replications on 21 September 2010. In this research; seed yield, oil content, protein content, oil yield and protein yield were examined. As a result of this research; seed yield, oil content, oil yield and protein yield (except protein content) were significant differences between the cultivars. The highest seed yield (6348 kg ha-1) was obtained from the NK Petrol, while the lowest seed yield (3949 kg ha-1) was determined from the Champlain cultivar was obtained. The highest oil content (46.73%) was observed from Oase and the lowest value was obtained from Vectra (41.87%) cultivar. The highest oil yield (2950 kg ha-1) was determined from NK Petrol while the least value (1681 kg ha-1) was determined from Champlain cultivar. The highest protein yield (1539.3 kg ha-1) was obtained from NK Petrol and the lowest protein yield (976.5 kg ha-1) was obtained from Champlain cultivar. The main purpose of the cultivation of oil crops, to increase the yield of oil per unit area. According the result of this research, NK Petrol cultivar which ranks first with regard to both seed yield and oil yield between cultivars as the most suitable winter canola cultivar of local conditions.

Keywords: Cultivar, Oil yield, Rapeseed, Seed Yield.

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