Search results for: Breeding biology

Authors: Yayun Hsu, Henry Horng-Shing Lu

Abstract:

This paper proposes a data-driven, biology-inspired neural segmentation method of 3D drosophila Brainbow images. We use Bayesian Sequential Partitioning algorithm for probabilistic modeling, which can be used to detect somas and to eliminate crosstalk effects. This work attempts to develop an automatic methodology for neuron image segmentation, which nowadays still lacks a complete solution due to the complexity of the image. The proposed method does not need any predetermined, risk-prone thresholds, since biological information is inherently included inside the image processing procedure. Therefore, it is less sensitive to variations in neuron morphology; meanwhile, its flexibility would be beneficial for tracing the intertwining structure of neurons.

Keywords: Brainbow, 3D imaging, image segmentation, neuron morphology, biological data mining, non-parametric learning.

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Authors: Ritu Shitak

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Humans are social mammals, of the primate order. Our biology, our behaviour and our pathologies are unique to us. In our desire to understand, reduce solitary confinement one source of information is the many reports of social isolation of other social mammals, especially primates. A behavioural study was conducted in the department of pharmacology at Indira Gandhi Medical College, Shimla in Himachalpradesh province in India using white albino mice. Different behavioural parameters were observed by using open field, tail suspension, tests for aggressive behaviour and social interactions and the effect of isolation was studied. The results were evaluated and the standard statistics were applied. The said study was done to establish facts that isolation itself impairs social behaviour and can lead to alcohol dependence as well as related drug dependence.

Keywords: Albino Mice, Drug Dependence, Social isolation.

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Authors: Ayman El Sabagh, Celaleddin Barutçular, Hirofumi Saneoka

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Drought is one of the most serious problems posing a grave threat to cereals production including maize. Maize improvement in drought-stress tolerance poses a great challenge as the global need for food and bio-energy increases. Thus, the current study was planned to explore the variations and determine the performance of target traits of maize hybrids at grain growth stage under drought conditions during 2014 under Adana, Mediterranean climate conditions, Turkey. Maize hybrids (Sancia, Indaco, 71May69, Aaccel, Calgary, 70May82, 72May80) were evaluated under (irrigated and water stress). Results revealed that, grain yield and yield traits had a negative effects because of water stress conditions compared with the normal irrigation. As well as, based on the result under normal irrigation, the maximum biological yield and harvest index were recorded. According to the differences among hybrids were found that, significant differences were observed among hybrids with respect to yield and yield traits under current research. Based on the results, grain weight had more effect on grain yield than grain number during grain filling growth stage under water stress conditions. In this concern, according to low drought susceptibility index (less grain yield losses), the hybrid (Indaco) was more stable in grain number and grain weight. Consequently, it may be concluded that this hybrid would be recommended for use in the future breeding programs for production of drought tolerant hybrids.

Keywords: Drought susceptibility index, grain filling, grain yield, maize, water stress.

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Authors: M. F. Miah, K. M. A. Zinnah, M. J. Raihan, H. Ali, M. N. Naser

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As genetic diversity is most important for existing, breeding and production of any fish; this study was undertaken for investigating genetic diversity of freshwater mud eel, Monopterus cuchia at population level where three ecological populations such as flooded area of Sylhet (P1), open water of Moulvibazar (P2) and open water of Sunamganj (P3) districts of Bangladesh were considered. Four arbitrary RAPD primers (OPB-12, C0-4, B-03 and OPB-08) were screened and RAPD banding patterns were analyzed among the populations considering 15 individuals of each population. In total 174, 138 and 149 bands were detected in the populations of P1, P2 and P3 respectively; however, each primer revealed less number of bands in each population. 100% polymorphic loci were recorded in P2 and P3 whereas only one monomorphic locus was observed in P1, recorded 97.5% polymorphism. Different genetic parameters such as inter-individual pairwise similarity, genetic distance, Nei genetic similarity, linkage distances, cluster analysis and allelic information, etc. were considered for measuring genetic diversity. The average inter-individual pairwise similarity was recorded 2.98, 1.47 and 1.35 in P1, P2 and P3 respectively. Considering genetic distance analysis, the highest distance 1 was recorded in P2 and P3 and the lowest genetic distance 0.444 was found in P2. The average Nei genetic similarity was observed 0.19, 0.16 and 0.13 in P1, P2 and P3, respectively; however, the average linkage distance was recorded 24.92, 17.14 and 15.28 in P1, P3 and P2 respectively. Based on linkage distance, genetic clusters were generated in three populations where 6 clades and 7 clusters were found in P1, 3 clades and 5 clusters were observed in P2 and 4 clades and 7 clusters were detected in P3. In addition, allelic information was observed where the frequency of p and q alleles were observed 0.093 and 0.907 in P1, 0.076 and 0.924 in P2, 0.074 and 0.926 in P3 respectively. The average gene diversity was observed highest in P2 (0.132) followed by P3 (0.131) and P1 (0.121) respectively.

Keywords: Genetic diversity, Monopterus cuchia, population, RAPD, Bangladesh.

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Authors: Jerome G. Chandraseelan, Samuel M. D. Oliveira, Antti Häkkinen, Sofia Startceva, Andre S. Ribeiro

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We used live E. coli containing synthetic genetic oscillators to study how the degree of synchrony between the genetic circuits of sister cells changes with temperature. We found that both the mean and the variability of the degree of synchrony between the fluorescence signals from sister cells are affected by temperature. Also, while most pairs of sister cells were found to be highly synchronous in each condition, the number of asynchronous pairs increased with increasing temperature, which was found to be due to disruptions in the oscillations. Finally we provide evidence that these disruptions tend to affect multiple generations as opposed to individual cells. These findings provide insight in how to design more robust synthetic circuits and in how cell division can affect their dynamics.

Keywords: Repressilator, robustness, synchrony, synthetic biology.

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Authors: R. Nandikeswari, M. Sambasivam, V. Anandan

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In the present study fecundity of Terapon jarbua was estimated for 41 matured females from the Bay of Bengal, Pondicherry. The fecundity (F) was found to range from 13,475 to 115,920 in fishes between 173-278mm Total length (TL) and 65- 298 gm weight respectively. The co-efficient of correlation for F/TL (log F = - 4.821 + 4.146 log TL), F/SL (log F = -3.936 + 3.867 log SL), F/WF (log F = 1.229 + 0.730 log TW) and F/GW (log F = 0.724 + 1.113 log GW) were obtained as 0.474, 0.537, 0.641 and 0.908 respectively. The regression line for the TL, SL, WF and GW of the fishes were found to be linear when they were plotted against their fecundity on logarithmic scales. Highly significant (P<0.01) relationship was obtained for all the variables. Hence Total Length, Standard Length, Weight of Fish and Gonad Weight were found to be the best indicators of the fecundity of Terapon jarbua. Gonadosomatic indices of Terapon jarbua showed that the spawning took place in February to July. The overall sex ratio of male to female is 1.28:1 with chi-square value 5.719, significant at 5% level.

Keywords: Fecundity, Gonadosomatic index, Reproductive biology, spawning, Terapon jarbua.

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Authors: Mehmet Ali Avcı, Abdullah Özköse, Ahmet Tamkoç

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Perennial ryegrass (Lolium perenne L.) plants are cultivated for lawn constitution and as forage plants. Considerable number of perennial ryegrass genotypes are present in the flora of our country and they present substantial was performed based on a Project supported bu TUBITAK (Project numver : 106O159) and perannial ryegrass genotypes from 8 provinces were collected during 2006. Seeds of perennial ryegrass were collected from 48 different locations. Populations of turfgrass seeds in flowerpots to be 20 and 1 cm deep greenhouse were sown in three replications at 07.07.2007.Then the growth of turfgrass seedlings in the greenhouse in pots showed sufficiently separated from the plants were planted in each population. Plants planted in the garden of the observation scale of 1-9 was evaluated by the quality, 1 = the weakest / worst, 6 = acceptable and 9 = superior or considered as an ideal. Essentially only recognized in assessing the quality of the color of grass, but the color, density, uniformity, texture (texture), illness or environmental stresses are evaluated as a combination reaction. Turfgrass quality 15.11.2007, 19.03.2008, 27.05.2008, 27.11.2008, 07.03.2009 and 02.06.2009 have been 6 times to be in order. Observations made regarding the quality of grass; 3 years according to seasonal environments turf quality genotypes belonging to 14 different populations were found to be 7.5 and above are reserved for future use in breeding works.The number of genotypes belonging to 41 populations in terms of turfgrass quality was determined as 7.9 of 3 year average seasonal. Argıthan between Doğanhisar (Konya) is located 38.09 latitude and 31.40 longitude, altitude 1158 m in the set that population numbered 41.

Keywords: Genotype, Perennial ryegrass, Turfgrass quality

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Authors: N. Tuncbag, T. Haliloglu, O. Keskin

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Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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Authors: Chih Chin Yang, Lan Hui Huang, Bo Shum Chen, Jia Liang Ke, Chung Lun Tsai

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The control of oxygen flow rate during growth of titanium dioxide by mass flow controller in DC plasma sputtering growth system is studied. The impedance of TiO2 films for inductance effect is influenced by annealing time and oxygen flow rate. As annealing time is increased, the inductance of TiO2 film is the more. The growth condition of optimum and maximum inductance for TiO2 film to serve as sensing device are oxygen flow rate of 15 sccm and large annealing time. The large inductance of TiO2 film will be adopted to fabricate the biosensor to obtain the high sensitivity of sensing in biology.

Keywords: Annealed, Inductance, Silicon substarte, Titanium dioxide

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Authors: H. Bouhamed, A. Rebai, T. Lecroq, M. Jaoua

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The objective of our work is to develop a new approach for discovering knowledge from a large mass of data, the result of applying this approach will be an expert system that will serve as diagnostic tools of a phenomenon related to a huge information system. We first recall the general problem of learning Bayesian network structure from data and suggest a solution for optimizing the complexity by using organizational and optimization methods of data. Afterward we proposed a new heuristic of learning a Multi-Entities Bayesian Networks structures. We have applied our approach to biological facts concerning hereditary complex illnesses where the literatures in biology identify the responsible variables for those diseases. Finally we conclude on the limits arched by this work.

Keywords: Data-organization, data-optimization, automatic knowledge discovery, Multi-Entities Bayesian networks, score merging.

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Authors: Akbar Cahyadhi Pratama Putra, Tantri Utami Widhaningtyas, M. Randy Aswin

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Indonesia, as an archipelagic nation, has a very long coastline with significant potential for marine resources, including mangrove ecosystems. The Lapindo mudflow disaster in Sidoarjo, East Java, resulted in mudflow being discharged into the sea through the Brantas and Porong rivers. The mud material transported by the river flow is feared to be dangerous because it contains harmful substances such as heavy metals. This study aims to map the mangrove ecosystem in terms of its density and assess the impact of the Lapindo mud disaster on the mangrove ecosystem, along with efforts to sustain its continuity. The mapping of the coastal mangrove conditions in Sidoarjo was carried out using remote sensing products, specifically Landsat 7 ETM+ images, taken during dry months in 2002, 2006, 2009, and 2014. The density of mangroves was determined using NDVI, which utilizes band 3 (the red channel) and band 4 (the near IR channel). Image processing to generate NDVI was performed using ENVI 5.1 software. The NDVI results were used to assess mangrove density on a scale from 0 to 1. The growth of mangrove ecosystems, both in terms of area and density, showed a significant increase from year to year. The development of mangrove ecosystems was influenced by the deposition of Lapindo mud in the estuaries of the Porong and Brantas rivers, where the silt provided a suitable medium for the growth of the mangrove ecosystem, leading to an increase in its density. The rise in density was supported by public awareness to mitigate heavy metal contamination, allowing for mangrove breeding near the affected areas.

Keywords: Archipelagic nation, Mangrove, Lapindo mudflow disaster, NDVI.

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Authors: P. Massanyi, L. Kichi, T. Slanina, E. Kolesar, J. Danko, N. Lukac, E. Tvrda, R. Stawarz, A. Kolesarova

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Target of this study was the analysis of the impact of crude glycerol on canine spermatozoa motility, morphology, viability, and membrane integrity. Experiments were realized in vitro. In the study, semen from 5 large dog breeds was used. They were typical representatives of large breeds, coming from healthy rearing, regularly vaccinated and integrated to the further breeding. Semen collections were realized at the owners of animals and in the veterinary clinic. Subsequently the experiments were realized at the Department of Animal Physiology of the SUA in Nitra. The spermatozoa motility was evaluated using CASA analyzer (SpermVisionTM, Minitub, Germany) at the temperature 5 and 37°C for 5 hours. In the study, 13 motility parameters were evaluated. Generally, crude glycerol has generally negative effect on spermatozoa motility. Morphological analysis was realized using Hancock staining and the preparations were evaluated at magnification 1000x using classification tables of morphologically changed spermatozoa. Data clearly detected the highest number of morphologically changed spermatozoa in the experimental groups (know twisted tails, tail torso and tail coiling). For acrosome alterations swelled acrosomes, removed acrosomes and acrosomes with undulated membrane were detected. In this study also the effect of crude glycerol on spermatozoa membrane integrity were analyzed. The highest crude glycerol concentration significantly affects spermatozoa integrity. Results of this study show that crude glycerol has effect of spermatozoa motility, viability, and membrane integrity. Detected changes are related to crude glycerol concentration, temperature, as well as time of incubation.

Keywords: Dog, semen, spermatozoa, acrosome, glycerol, CASA, viability.

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Authors: Fabrizio Logiurato

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Light Polarization has many technological applications, and its discovery was crucial to reveal the transverse nature of the electromagnetic waves. However, despite its fundamental and practical importance, in high school, this property of light is often neglected. This is a pity not only for its conceptual relevance, but also because polarization gives the possibility to perform many brilliant experiments with low cost materials. Moreover, the treatment of this matter lends very well to an interdisciplinary approach between art, biology and technology, which usually makes things more interesting to students. For these reasons, we have developed, and in this work, we introduce a laboratory on light polarization for high school and undergraduate students. They can see beautiful pictures when birefringent materials are set between two crossed polarizing filters. Pupils are very fascinated and drawn into by what they observe. The colourful images remind them of those ones of abstract painting or alien landscapes. With this multidisciplinary teaching method, students are more engaged and participative, and also, the learning process of the respective physics concepts is more effective.

Keywords: Light polarization, optical activity, multidisciplinary education, science and art.

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Authors: M. Eickermann, M. K. Class, J. Junk

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Winter oilseed rape, Brassica napus L., is characterized by a high number of herbicide applications. Therefore, its cultivation can lead to massive contamination of ground water and soil by herbicide and their metabolites. A multi-side long-term field experiment (EFFO, Efficient crop rotation) was set-up in Luxembourg to quantify these effects. Based on soil sampling and laboratory analysis, preliminary results showed reduced dehydrogenase activities of several soil organisms due to herbicide treatments. This effect is highly depending on the soil type. Relation between the dehydrogenase activity and the amount of microbial carbon showed higher variability on the test side with loamy Brown Earth, based on Bunter than on those with sandy-loamy Brown Earth, based on calciferous Sandstone.

Keywords: Cropping system, dehydrogenase activity, herbicides, mechanical weed control, oilseed rape.

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Authors: Achraf El Allali, John R. Rose

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A number of competing methodologies have been developed to identify genes and classify DNA sequences into coding and non-coding sequences. This classification process is fundamental in gene finding and gene annotation tools and is one of the most challenging tasks in bioinformatics and computational biology. An information theory measure based on mutual information has shown good accuracy in classifying DNA sequences into coding and noncoding. In this paper we describe a species independent iterative approach that distinguishes coding from non-coding sequences using the mutual information measure (MIM). A set of sixty prokaryotes is used to extract universal training data. To facilitate comparisons with the published results of other researchers, a test set of 51 bacterial and archaeal genomes was used to evaluate MIM. These results demonstrate that MIM produces superior results while remaining species independent.

Keywords: Coding Non-coding Classification, Entropy, GeneRecognition, Mutual Information.

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Authors: Chandrika M.J., Lariyah M.S., Alicia Y.C. Tang

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Ontology is widely being used as a tool for organizing information, creating the relation between the subjects within the defined knowledge domain area. Various fields such as Civil, Biology, and Management have successful integrated ontology in decision support systems for managing domain knowledge and to assist their decision makers. Gross pollutant traps (GPT) are devices used in trapping and preventing large items or hazardous particles in polluting and entering our waterways. However choosing and determining GPT is a challenge in Malaysia as there are inadequate GPT data repositories being captured and shared. Hence ontology is needed to capture, organize and represent this knowledge into meaningful information which can be contributed to the efficiency of GPT selection in Malaysia urbanization. A GPT Ontology framework is therefore built as the first step to capture GPT knowledge which will then be integrated into the decision support system. This paper will provide several examples of the GPT ontology, and explain how it is constructed by using the Protégé tool.

Keywords: Gross pollutant Trap, Ontology, Protégé.

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Authors: Musammat F. Nahar, Anna Roujeinikova

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Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

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Authors: Valbona Sota, Efigjeni Kongjika

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Wild almond is a woody species, which is difficult to propagate either generatively by seed or by vegetative methods (grafting or cuttings) and also considered as Endangered (EN) in Albania based on IUCN criteria. As a wild relative of cultivated fruit trees, this species represents a source of genetic variability and can be very important in breeding programs and cultivation. For this reason, it would be of interest to use an effective method of in vitro mid-term conservation, which involves strategies to slow plant growth through physicochemical alterations of in vitro growth conditions. Multiplication of wild almond was carried out using zygotic embryos, as primary explants, with the purpose to develop a successful propagation protocol. Results showed that zygotic embryos can proliferate through direct or indirect organogenesis. During subculture, stage was obtained a great number of new plantlets identical to mother plants derived from the zygotic embryos. All in vitro plantlets obtained from subcultures underwent in vitro conservation by minimal growth in low temperature (4ºC) and darkness. The efficiency of this technique was evaluated for 3, 6, and 10 months of conservation period. Maintenance in these conditions reduced micro cuttings growth. Survival and regeneration rates for each period were evaluated and resulted that the maximal time of conservation without subculture on 4ºC was 10 months, but survival and regeneration rates were significantly reduced, specifically 15.6% and 7.6%. An optimal period of conservation in these conditions can be considered the 5-6 months storage, which can lead to 60-50% of survival and regeneration rates. This protocol may be beneficial for mass propagation, mid-term conservation, and for genetic manipulation of wild almond.

Keywords: Micropropagation, minimal growth, storage, wild almond.

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Authors: Usha Chouhan, K. R. Pardasani

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Phylogenies ; The evolutionary histories of groups of species are one of the most widely used tools throughout the life sciences, as well as objects of research with in systematic, evolutionary biology. In every phylogenetic analysis reconstruction produces trees. These trees represent the evolutionary histories of many groups of organisms, bacteria due to horizontal gene transfer and plants due to process of hybridization. The process of gene transfer in bacteria and hybridization in plants lead to reticulate networks, therefore, the methods of constructing trees fail in constructing reticulate networks. In this paper a model has been employed to reconstruct phylogenetic network in honey bee. This network represents reticulate evolution in honey bee. The maximum parsimony approach has been used to obtain this reticulate network.

Keywords: Hybridization, HGT, Reticulate networks, Recombination, Species, Parsimony.

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Authors: Essam Al Daoud

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Genome rearrangement is an important area in computational biology and bioinformatics. The basic problem in genome rearrangements is to compute the edit distance, i.e., the minimum number of operations needed to transform one genome into another. Unfortunately, unsigned genome rearrangement problem is NP-hard. In this study an improved ant colony optimization algorithm to approximate the edit distance is proposed. The main idea is to convert the unsigned permutation to signed permutation and evaluate the ants by using Kaplan algorithm. Two new operations are added to the standard ant colony algorithm: Replacing the worst ants by re-sampling the ants from a new probability distribution and applying the crossover operations on the best ants. The proposed algorithm is tested and compared with the improved breakpoint reversal sort algorithm by using three datasets. The results indicate that the proposed algorithm achieves better accuracy ratio than the previous methods.

Keywords: Ant colony algorithm, Edit distance, Genome breakpoint, Genome rearrangement, Reversal sort.

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Authors: Mohammad Reza Pirestani, Mehdi Shafaghati, Amir Ahmad Dehghani

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From the beginning of creation, human being has ever fought against the ecosystem by changes has made in environment. The most environmental changes on the nature have been done after starting the concentrated life in the same region. Dams are one of the most important buildings in water resources and transferring. These buildings have been made from old times without access to hydrological, hydraulically, hydro mechanical information. Dams have positive and negative effects on environment. Constructing a dam relatively causes equal ecological consequences. According to different criteria, environmental effects of dams can lead short term and long term damages. These effects may influence on the situation and treatment of meteorology, biology, culture, ancient works, etc and severely causes to change and complicate it. So considering importance of positive effects of dam construction, it is necessary to minimize negative environmental effects of dams to achieve a stable development. In this article the considered effects and their solutions in influencing on assessment of destructive environmental effects of dams construction have been surveyed and presented.

Keywords: Dam, Environment, Water Resources, Assessment

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Authors: A. Özköse, A. Tamkoç

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The present study involved analysis of certain characteristics of the perennial ryegrass (Lolium perenne L.) genotypes collected from the natural flora of Ankara, and explores a correlation among them. In order to evaluate the plants for breeding purpose as per Turkey's environmental conditions, the perennial ryegrass plants were collected from natural pasture of Ankara in 2004 and were utilized for the study. Seeds of the collected plants were sown in pots and seedlings were prepared in a greenhouse. In 2005, the seedlings were transplanted at 50 × 50 cm2 intervals in Randomized Complete Blocks Design in an experimental field. In 2007 and 2008, data were recorded from the observations and measurements of 568 perennial ryegrasses. The plant characteristics, which were investigated, included re-growth time in spring, color, density, growth habit, tendency to form inflorescence, time of inflorescence, plant height, length of upper internode, spike length, leaf length, leaf width, leaf area, leaf shape, number of spikelets per spike, seed yield per spike and 1000 grain weight and the correlation analyses were made using this data. Correlation coefficients were estimated between all paired combinations of the studied traits. The yield components exhibited varying trends of association among themselves. Seed yield per spike showed significant and positive association with the number of spikelets per spike, 1000 grain weight, plant height, length of upper internode, spike length, leaf length, leaf width, leaf area and color, but significant and negative association with the growth habit and re-growth time in spring.

Keywords: Correlation, morphological traits, Lolium perenne.

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Authors: Zuwairie Ibrahim, Yusei Tsuboi, Osamu Ono, Marzuki Khalid

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Deoxyribonucleic Acid or DNA computing has emerged as an interdisciplinary field that draws together chemistry, molecular biology, computer science and mathematics. Thus, in this paper, the possibility of DNA-based computing to solve an absolute 1-center problem by molecular manipulations is presented. This is truly the first attempt to solve such a problem by DNA-based computing approach. Since, part of the procedures involve with shortest path computation, research works on DNA computing for shortest path Traveling Salesman Problem, in short, TSP are reviewed. These approaches are studied and only the appropriate one is adapted in designing the computation procedures. This DNA-based computation is designed in such a way that every path is encoded by oligonucleotides and the path-s length is directly proportional to the length of oligonucleotides. Using these properties, gel electrophoresis is performed in order to separate the respective DNA molecules according to their length. One expectation arise from this paper is that it is possible to verify the instance absolute 1-center problem using DNA computing by laboratory experiments.

Keywords: DNA computing, operation research, 1-center problem.

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Authors: T. Niknam, M. Nayeripour, B.Bahmani Firouzi

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Clustering techniques have received attention in many areas including engineering, medicine, biology and data mining. The purpose of clustering is to group together data points, which are close to one another. The K-means algorithm is one of the most widely used techniques for clustering. However, K-means has two shortcomings: dependency on the initial state and convergence to local optima and global solutions of large problems cannot found with reasonable amount of computation effort. In order to overcome local optima problem lots of studies done in clustering. This paper is presented an efficient hybrid evolutionary optimization algorithm based on combining Particle Swarm Optimization (PSO) and Ant Colony Optimization (ACO), called PSO-ACO, for optimally clustering N object into K clusters. The new PSO-ACO algorithm is tested on several data sets, and its performance is compared with those of ACO, PSO and K-means clustering. The simulation results show that the proposed evolutionary optimization algorithm is robust and suitable for handing data clustering.

Keywords: Ant Colony Optimization (ACO), Data clustering, Hybrid evolutionary optimization algorithm, K-means clustering, Particle Swarm Optimization (PSO).

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Authors: D. Estrella, A. Silva, R. Zapata, H. Rubio

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A total of 100 primary caregivers (mothers, fathers, grandparents) with at least one child or grandchild with a diagnosis of congenital bilateral profound deafness were assessed in order to evaluate the functionality of families with a deaf member, who was evaluated by specialists in audiology, molecular biology, genetics and psychology. After confirmation of the clinical diagnosis, DNA from the patients and parents were analyzed in search of the 35delG deletion of the GJB2 gene to determine who possessed the mutation. All primary caregivers were provided psychological support, regardless of whether or not they had the mutation, and prior and subsequent, the family APGAR test was applied. All parents, grandparents were informed of the results of the genetic analysis during the psychological intervention. The family APGAR, after psychological and genetic counseling, showed that 14% perceived their families as functional, 62% moderately functional and 24% dysfunctional. This shows the importance of psychological support in family functionality that has a direct impact on the quality of life of these families.

Keywords: Deafness, psychological support, family, adaptation to disability.

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Authors: Li Ni, Pen ManMan, Li KenLi

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Clustering is an intensive research for some years because of its multifaceted applications, such as biology, information retrieval, medicine, business and so on. The expectation maximization (EM) is a kind of algorithm framework in clustering methods, one of the ten algorithms of machine learning. Traditionally, optimization of objective function has been the standard approach in EM. Hence, research has investigated the utility of evolutionary computing and related techniques in the regard. Chemical Reaction Optimization (CRO) is a recently established method. So the property embedded in CRO is used to solve optimization problems. This paper presents an algorithm framework (EM-CRO) with modified CRO operators based on EM cluster problems. The hybrid algorithm is mainly to solve the problem of initial value sensitivity of the objective function optimization clustering algorithm. Our experiments mainly take the EM classic algorithm:k-means and fuzzy k-means as an example, through the CRO algorithm to optimize its initial value, get K-means-CRO and FKM-CRO algorithm. The experimental results of them show that there is improved efficiency for solving objective function optimization clustering problems.

Keywords: Chemical reaction optimization, expectation maximization, initial, objective function clustering.

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Authors: Joel Arrais, João E. Pereira, João Fernandes, José Luís Oliveira

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The scientific achievements coming from molecular biology depend greatly on the capability of computational applications to analyze the laboratorial results. A comprehensive analysis of an experiment requires typically the simultaneous study of the obtained dataset with data that is available in several distinct public databases. Nevertheless, developing a centralized access to these distributed databases rises up a set of challenges such as: what is the best integration strategy, how to solve nomenclature clashes, how to solve database overlapping data and how to deal with huge datasets. In this paper we present GeNS, a system that uses a simple and yet innovative approach to address several biological data integration issues. Compared with existing systems, the main advantages of GeNS are related to its maintenance simplicity and to its coverage and scalability, in terms of number of supported databases and data types. To support our claims we present the current use of GeNS in two concrete applications. GeNS currently contains more than 140 million of biological relations and it can be publicly downloaded or remotely access through SOAP web services.

Keywords: Data integration, biological databases

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Authors: Rio G. L. D'Souza, K. Chandra Sekaran, A. Kandasamy

Abstract:

The goal of Gene Expression Analysis is to understand the processes that underlie the regulatory networks and pathways controlling inter-cellular and intra-cellular activities. In recent times microarray datasets are extensively used for this purpose. The scope of such analysis has broadened in recent times towards reconstruction of gene networks and other holistic approaches of Systems Biology. Evolutionary methods are proving to be successful in such problems and a number of such methods have been proposed. However all these methods are based on processing of genotypic information. Towards this end, there is a need to develop evolutionary methods that address phenotypic interactions together with genotypic interactions. We present a novel evolutionary approach, called Phenomic algorithm, wherein the focus is on phenotypic interaction. We use the expression profiles of genes to model the interactions between them at the phenotypic level. We apply this algorithm to the yeast sporulation dataset and show that the algorithm can identify gene networks with relative ease.

Keywords: Evolutionary computing, gene expression analysis, gene networks, microarray data analysis, phenomic algorithms.

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Authors: Tom Snir, Eitan Rubin

Abstract:

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: Nurcan Tuncbag, Turkan Haliloglu, Ozlem Keskin

Abstract:

Understanding the cell's large-scale organization is an interesting task in computational biology. Thus, protein-protein interactions can reveal important organization and function of the cell. Here, we investigated the correspondence between protein interactions and function for the yeast. We obtained the correlations among the set of proteins. Then these correlations are clustered using both the hierarchical and biclustering methods. The detailed analyses of proteins in each cluster were carried out by making use of their functional annotations. As a result, we found that some functional classes appear together in almost all biclusters. On the other hand, in hierarchical clustering, the dominancy of one functional class is observed. In the light of the clustering data, we have verified some interactions which were not identified as core interactions in DIP and also, we have characterized some functionally unknown proteins according to the interaction data and functional correlation. In brief, from interaction data to function, some correlated results are noticed about the relationship between interaction and function which might give clues about the organization of the proteins, also to predict new interactions and to characterize functions of unknown proteins.

Keywords: Pair-wise protein interactions, DIP database, functional correlations, biclustering.

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