Scholarly

Fractal Analysis of 16S rRNA Gene Sequences in Archaea Thermophiles

Year: 2008 Volume: 2 Issue: 8 167 - 171 Pages

Abstract: A nucleotide sequence can be expressed as a numerical sequence when each nucleotide is assigned its proton number. A resulting gene numerical sequence can be investigated for its fractal dimension in terms of evolution and chemical properties for comparative studies. We have investigated such nucleotide fluctuation in the 16S rRNA gene of archaea thermophiles. The studied archaea thermophiles were archaeoglobus fulgidus, methanothermobacter thermautotrophicus, methanocaldococcus jannaschii, pyrococcus horikoshii, and thermoplasma acidophilum. The studied five archaea-euryarchaeota thermophiles have fractal dimension values ranging from 1.93 to 1.97. Computer simulation shows that random sequences would have an average of about 2 with a standard deviation about 0.015. The fractal dimension was found to correlate (negative correlation) with the thermophile-s optimal growth temperature with R2 value of 0.90 (N =5). The inclusion of two aracheae-crenarchaeota thermophiles reduces the R2 value to 0.66 (N = 7). Further inclusion of two bacterial thermophiles reduces the R2 value to 0.50 (N =9). The fractal dimension is correlated (positive) to the sequence GC content with an R2 value of 0.89 for the five archaea-euryarchaeota thermophiles (and 0.74 for the entire set of N = 9), although computer simulation shows little correlation. The highest correlation (positive) was found to be between the fractal dimension and di-nucleotide Shannon entropy. However Shannon entropy and sequence GC content were observed to correlate with optimal growth temperature having an R2 of 0.8 (negative), and 0.88 (positive), respectively, for the entire set of 9 thermophiles; thus the correlation lacks species specificity. Together with another correlation study of bacterial radiation dosage with RecA repair gene sequence fractal dimension, it is postulated that fractal dimension analysis is a sensitive tool for studying the relationship between genotype and phenotype among closely related sequences.

Evaluation of Algorithms for Sequential Decision in Biosonar Target Classification

Year: 2007 Volume: 1 Issue: 1 128 - 131 Pages

Abstract: A sequential decision problem, based on the task ofidentifying the species of trees given acoustic echo data collectedfrom them, is considered with well-known stochastic classifiers,including single and mixture Gaussian models. Echoes are processedwith a preprocessing stage based on a model of mammalian cochlearfiltering, using a new discrete low-pass filter characteristic. Stoppingtime performance of the sequential decision process is evaluated andcompared. It is observed that the new low pass filter processingresults in faster sequential decisions.

Entropy Generation for Natural Convection in a Darcy – Brinkman Porous Cavity

Year: 2013 Volume: 7 Issue: 4 605 - 609 Pages

Abstract: The paper provides a numerical investigation of the entropy generation analysis due to natural convection in an inclined square porous cavity. The coupled equations of mass, momentum, energy and species conservation are solved using the Control Volume Finite-Element Method. Effect of medium permeability and inclination angle on entropy generation is analysed. It was found that according to the Darcy number and the porous thermal Raleigh number values, the entropy generation could be mainly due to heat transfer or to fluid friction irreversibility and that entropy generation reaches extremum values for specific inclination angles.

An Information Theoretic Approach to Rescoring Peptides Produced by De Novo Peptide Sequencing

Year: 2010 Volume: 4 Issue: 10 728 - 733 Pages

Abstract: Tandem mass spectrometry (MS/MS) is the engine driving high-throughput protein identification. Protein mixtures possibly representing thousands of proteins from multiple species are treated with proteolytic enzymes, cutting the proteins into smaller peptides that are then analyzed generating MS/MS spectra. The task of determining the identity of the peptide from its spectrum is currently the weak point in the process. Current approaches to de novo sequencing are able to compute candidate peptides efficiently. The problem lies in the limitations of current scoring functions. In this paper we introduce the concept of proteome signature. By examining proteins and compiling proteome signatures (amino acid usage) it is possible to characterize likely combinations of amino acids and better distinguish between candidate peptides. Our results strongly support the hypothesis that a scoring function that considers amino acid usage patterns is better able to distinguish between candidate peptides. This in turn leads to higher accuracy in peptide prediction.

Comparison of Eurocodes EN310 and EN789 in Determining the Bending Strength and Modulus of Elasticity of Red Seraya Plywood Panel

Year: 2012 Volume: 6 Issue: 2 156 - 160 Pages

Abstract: The characteristic bending strength (MOR) and mean modulus of elasticity (MOE) of tropical hardwood red seraya (Shorea spp.) plywood were determined using European Standard EN310 and EN789. The thickness of the test specimen was 4.0mm, 7.0mm, 9.0mm, 12.0mm and 15.0mm. The experiment found that the MOR of red seraya plywood in EN310 is about 12% to 20% and 7% to 24% higher than EN789 whereas MOE were about 28% to 41% and 30% to 36% lower than those obtained from EN 789 for test specimens parallel and perpendicular to the grain direction. The linear regression shows that MOR and MOE for EN789 is about 0.8 times less and 1.5 times more than EN310. The experiment also found that the MOR and MOE of EN310 and EN789 also depend on the wood species that used in the experiment.

Pollution Induced Structural and Physico-Chemical Changes in Algal Community: A Case Study of River Pandu of North India

Year: 2010 Volume: 4 Issue: 11 570 - 574 Pages

Authors:
Seemaa Diwedi

Abstract: The study area receives a wide variety of wastes generated by municipalities and the industries like paints and pigments, metal processing industries, thermal power plants electroprocessing industries etc. The Physico-chemical and structural investigation of water from river Pandu indicated high level of chlorides and calcium which made the water unsuitable for human use. Algae like Cyclotella fumida, Asterionella Formosa, Cladophora glomerata, Pediastrum simplex, Scenedesmus bijuga, Cladophora glomerata were the dominant pollution tolerant species recorded under these conditions. The sensitive and less abundant species of algae included Spirogyra sps., Merismopedia sps. The predominance colonies of Zygnema sps, Phormidium sps, Mycrocystis aeruginosa, Merismopedia minima, Pandorina morum, seems to correlate with high organic contents of Pandu river water. This study assumes significance as some algae can be used as bioindicators of water pollution and algal floral of a municipal drain carrying waste effluents from industrial area Kanpur and discharge them into the river Pandu flowing onto southern outskirts of Kanpur city.

Codon-optimized Carbonic Anhydrase from Dunaliella species: Expression and Characterization

Year: 2012 Volume: 6 Issue: 8 598 - 602 Pages

Authors:
Seung Pil Pack

Abstract: Carbonic anhydrases (CAs) has been focused as biological catalysis for CO2 sequestration process because it can catalyze the conversion of CO2 to bicarbonate. Here, codon-optimized sequence of α type-CA cloned from Duneliala species. (DsCAopt) was constructed, expressed, and characterized. The expression level in E. coli BL21(DE3) was better for codon-optimized DsCAopt than intact sequence of DsCAopt. DsCAopt enzyme shows high-stability at pH 7.6/10.0. In final, we demonstrated that in the Ca2+ solution, DsCAopt enzyme can catalyze well the conversion of CO2 to CaCO3, as the calcite form.

Comparative Analysis of Diversity and Similarity Indices with Special Relevance to Vegetations around Sewage Drains

Year: 2012 Volume: 6 Issue: 9 609 - 611 Pages

Authors:
Ekta Singh

Abstract: Indices summarizing community structure are used to evaluate fundamental community ecology, species interaction, biogeographical factors, and environmental stress. Some of these indices are insensitive to gross community changes induced by contaminants of pollution. Diversity indices and similarity indices are reviewed considering their ecological application, both theoretical and practical. For some useful indices, empirical equations are given to calculate the expected maximum value of the indices to which the observed values can be related at any combination of sample sizes at the experimental sites. This paper examines the effects of sample size and diversity on the expected values of diversity indices and similarity indices, using various formulae. It has been shown that all indices are strongly affected by sample size and diversity. In some indices, this influence is greater than the others and an attempt has been made to deal with these influences.

Assessing Habitat-Suitability Models with a Virtual Species at Khao Nan National Park, Thailand

Year: 2007 Volume: 1 Issue: 1 1 - 6 Pages

Abstract: This study examined a habitat-suitability assessment method namely the Ecological Niche Factor Analysis (ENFA). A virtual species was created and then dispatched in a geographic information system model of a real landscape in three historic scenarios: (1) spreading, (2) equilibrium, and (3) overabundance. In each scenario, the virtual species was sampled and these simulated data sets were used as inputs for the ENFA to reconstruct the habitat suitability model. The 'equilibrium' scenario gives the highest quantity and quality among three scenarios. ENFA was sensitive to the distribution scenarios but not sensitive to sample sizes. The use of a virtual species proved to be a very efficient method, allowing one to fully control the quality of the input data as well as to accurately evaluate the predictive power of the analyses.

Productivity and Energy Management in Desert Urban

Year: 2010 Volume: 4 Issue: 9 279 - 282 Pages

Abstract: Growing world population has fundamental impacts and often catastrophic on natural habitat. The immethodical consumption of energy, destruction of the forests and extinction of plant and animal species are the consequence of this experience. Urban sustainability and sustainable urban development, that is so spoken these days, should be considered as a strategy, goal and policy, beyond just considering environmental issues and protection. The desert-s climate has made a bunch of problems for its residents. Very hot and dry climate in summers of the Iranian desert areas, when there was no access to modern energy source and mechanical cooling systems in the past, made Iranian architects to design a natural ventilation system in their buildings. The structure, like a tower going upward the roof, besides its ornamental application and giving a beautiful view to the building, was used as a spontaneous ventilation system. In this paper, it has been tried to name the problems of the area and it-s inconvenience, then some answers has pointed out in order to solve the problems and as an alternative solution BADGIR (wind-catcher) has been introduced as a solution knowing that it has been playing a major role in dealing with the problems.

Comparison of Vermicompost and Vermiwash Bio-Fertilizers from Vermicomposting Waste Corn Pulp

Year: 2013 Volume: 7 Issue: 6 401 - 404 Pages

Abstract: Vermicomposting is the conversion of organic waste into bio-fertilizers through the action of earthworm. This technology is widely used for organic solid waste management. Waste corn pulp blended with cow dung manure was vermicomposted over 30 days using Eisenia fetida earthworms species. pH, temperature, moisture content, and electrical conductivity were daily monitored. The feedstock, vermicompost and vermiwash were analyzed for nutrient composition. The average temperature and moisture content in the vermi-reactor was 22.5°C and 42.5% respectively. The vermicompost and vermiwash had an almost neutral pH whilst the electrical conductivity was 21% higher in the vermicompost. The nitrogen and potassium content was 57% and 79.6% richer in the vermicompost respectively compared to the vermiwash. However, the vermiwash was 84% richer in phosphorous as compared to vermicompost. Furthermore, the vermiwash was 89.1% and 97.6% richer in Ca and Mg respectively and was 97.8% richer in Na salts compared to the vermicompost. The vermiwash also indicated a significantly higher amount of micronutrients. Both bio-fertilizers were rich in nutrients specification for fertilizers.

Architectural Stratification and Woody Species Diversity of a Subtropical Forest Grown in a Limestone Habitat in Okinawa Island, Japan

Year: 2008 Volume: 2 Issue: 11 307 - 312 Pages

Abstract: The forest stand consisted of four layers. The species composition between the third and the bottom layers was almost similar, whereas it was almost exclusive between the top and the lower three layers. The values of Shannon-s index H' and Pielou-s index J ' tended to increase from the bottom layer upward, except for H' -value of the top layer. The values of H' and J ' were 4.21 bit and 0.73, respectively, for the total stand. High woody species diversity of the forest depended on large trees in the upper layers, which trend was different from a subtropical evergreen broadleaf forest grown in silicate habitat in the northern part of Okinawa Island. The spatial distribution of trees was overlapped between the third and the bottom layers, whereas it was independent or slightly exclusive between the top and the lower three layers. Mean tree weight of each layer decreased from the top toward the bottom layer, whereas the corresponding tree density increased from the top downward. This relationship was analogous to the process of self-thinning plant populations.

Photocatalytic and Sonophotocatalytic Degradation of Reactive Red 120 using Dye Sensitized TiO2 under Visible Light

Year: 2011 Volume: 5 Issue: 1 60 - 65 Pages

Abstract: The accelerated sonophotocatalytic degradation of Reactive Red (RR) 120 dye under visible light using dye sensitized TiO2 activated by ultrasound has been carried out. The effect of sonolysis, photocatalysis and sonophotocatalysis under visible light has been examined to study the influence on the degradation rates by varying the initial substrate concentration, pH and catalyst loading to ascertain the synergistic effect on the degradation techniques. Ultrasonic activation contributes degradation through cavitation leading to the splitting of H2O2 produced by both photocatalysis and sonolysis. This results in the formation of oxidative species, such as singlet oxygen (1O2) and superoxide (O2 -●) radicals in the presence of oxygen. The increase in the amount of reactive radical species which induce faster oxidation of the substrate and degradation of intermediates and also the deaggregation of the photocatalyst are responsible for the synergy observed under sonication. A comparative study of photocatalysis and sonophotocatalysis using TiO2, Hombikat UV 100 and ZnO was also carried out.

Partial Oxidation of Methane in the Pulsed Compression Reactor: Experiments and Simulation

Year: 2010 Volume: 4 Issue: 7 442 - 446 Pages

Abstract: The Pulsed Compression Reactor promises to be a compact, economical and energy efficient alternative to conventional chemical reactors. In this article, the production of synthesis gas using the Pulsed Compression Reactor is investigated. This is done experimentally as well as with simulations. The experiments are done by means of a single shot reactor, which replicates a representative, single reciprocation of the Pulsed Compression Reactor with great control over the reactant composition, reactor temperature and pressure and temperature history. Simulations are done with a relatively simple method, which uses different models for the chemistry and thermodynamic properties of the species in the reactor. Simulation results show very good agreement with the experimental data, and give great insight into the reaction processes that occur within the cycle.

Analysis for a Food Chain Model with Crowley–Martin Functional Response and Time Delay

Year: 2010 Volume: 4 Issue: 1 75 - 78 Pages

Abstract: This paper is concerned with a nonautonomous three species food chain model with Crowley–Martin type functional response and time delay. Using the Mawhin-s continuation theorem in theory of degree, sufficient conditions for existence of periodic solutions are obtained.

On Reversal and Transposition Medians

Year: 2009 Volume: 3 Issue: 6 1555 - 1563 Pages

Authors:
Martin Bader

Abstract: During the last years, the genomes of more and more species have been sequenced, providing data for phylogenetic recon- struction based on genome rearrangement measures. A main task in all phylogenetic reconstruction algorithms is to solve the median of three problem. Although this problem is NP-hard even for the sim- plest distance measures, there are exact algorithms for the breakpoint median and the reversal median that are fast enough for practical use. In this paper, this approach is extended to the transposition median as well as to the weighted reversal and transposition median. Although there is no exact polynomial algorithm known even for the pairwise distances, we will show that it is in most cases possible to solve these problems exactly within reasonable time by using a branch and bound algorithm.

Adhesion Properties of Bifidobacterium Pseudocatenulatum G4 and Bifidobacterium Longum BB536 on HT-29 Human Epithelium Cell Line at Different Times and pH

Year: 2009 Volume: 3 Issue: 1 59 - 63 Pages

Abstract: Adhesion to the human intestinal cell is considered as one of the main selection criteria of lactic acid bacteria for probiotic use. The adhesion ability of two Bifidobacteriums strains Bifidobacterium longum BB536 and Bifidobacterium psudocatenulatum G4 was done using HT-29 human epithelium cell line as in vitro study. Four different level of pH were used 5.6, 5.7, 6.6, and 6.8 with four different times 15, 30, 60, and 120 min. Adhesion was quantified by counting the adhering bacteria after Gram staining. The adhesion of B. longum BB536 was higher than B. psudocatenulatum G4. Both species showed significant different in the adhesion properties at the factors tested. The highest adhesion for both Bifidobacterium was observed at 120 min and the low adhesion was in 15 min. The findings of this study will contribute to the introduction of new effective probiotic strain for future utilization.

Investigation Corn and Soybean Intercropping Advantages in Competition with Redroot Pigweed and Jimsonweed

Year: 2011 Volume: 5 Issue: 9 540 - 542 Pages

Abstract: The spatial variation in plant species associated with intercropping is intended to reduce resource competition between species and increase yield potential. A field experiment was carried out on corn (Zea mays L.) and soybean (Glycine max L.) intercropping in a replacement series experiment with weed contamination consist of: weed free, infestation of redroot pigweed, infestation of jimsonweed and simultaneous infestation of redroot pigweed and jimsonweed in Karaj, Iran during 2007 growing season. The experimental design was a randomized complete block in factorial experiment with replicated thrice. Significant (P≤0.05) differences were observed in yield in intercropping. Corn yield was higher in intercropping, but soybean yield was significantly reduced by corn when intercropped. However, total productivity and land use efficiency were high under the intercropping system even in contamination of either species of weeds. Aggressivity of corn relative to soybean revealed the greater competitive ability of corn than soybean. Land equivalent ratio (LER) more than 1 in all treatments attributed to intercropping advantages and was highest in 50: 50 (corn/soybean) in weed free. These findings suggest that intercropping corn and soybean increase total productivity per unit area and improve land use efficiency. Considering the experimental findings, corn-soybean intercropping (50:50) may be recommended for yield advantage, more efficient utilization of resources, and weed suppression as a biological control.

Evaluation of Guaiacol and Syringol Emission upon Wood Pyrolysis for some Fast Growing Species

Year: 2011 Volume: 5 Issue: 8 704 - 708 Pages

Authors:
Sherif S. Z. Hindi

Abstract: Wood pyrolysis for Casuarina glauca, Casuarina cunninghamiana, Eucalyptus camaldulensis, Eucalyptus microtheca was made at 450°C with 2.5°C/min. in a flowing N2-atmosphere. The Eucalyptus genus wood gave higher values of specific gravity, ash , total extractives, lignin, N2-liquid trap distillate (NLTD) and water trap distillate (WSP) than those for Casuarina genus. The GHC of NLTD was higher for Casuarina genus than that for Eucalyptus genus with the highest value for Casuarina cunninghamiana. Guiacol, 4-ethyl-2-methoxyphenol and syringol were observed in the NLTD of all the four wood species reflecting their parent hardwood lignin origin. Eucalyptus camaldulensis wood had the highest lignin content (28.89%) and was pyrolyzed to the highest values of phenolics (73.01%), guaiacol (11.2%) and syringol (32.28%) contents in methylene chloride fraction (MCF) of NLTD. Accordingly, recoveries of syringol and guaiacol may become economically attractive from Eucalyptus camaldulensis.

Relative Contribution of Livestock Species to Meat Supply in Bauchi Metropolis, Bauchi, Nigeria

Year: 2013 Volume: 7 Issue: 2 103 - 106 Pages

Abstract: Primary and secondary data from the Bauchi abattoir were utilized to determine the relative contributions of different livestock species to meat supply in Bauchi Metropolis. Daily livestock slaughter figures for five months (June – October 2011) indicated that more goats (64.0) were slaughtered than either sheep (47.3) or cattle (41.30) each day (P

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