Iranian Journal of Chemistry and Chemical Engineering
Volume:29 Issue: 4, Jul-Aug 2010

Structural repetitive subsequences are most important portion of biological sequences, which play crucial roles on corresponding sequence’s fold and functionality. Biggest class of the repetitive subsequences is “Transposable Elements” which has its own sub-classes upon contexts’ structures. Many researches have been performed to criticality determine the structure and function of repetitive subsequences. The sequencing noises and the sequences’ substitutions probability are obstacles of these researches. Some statistical and approximation algorithms have introduced to tackle these obstacles. By introducing conspicuous statistical machine learning methods upon Support Vector Machines, machine learning approaches act as potent methods to solve the pattern-finding problem. Support vector machines methods are time efficient approaches, which based on their parameters can be precise and accurate. In this Review, mathematical definition of structural repetitive subsequences are introduced, thereafter proposed algorithm to tackle simple pattern finding problem, which can be applicable on structural patterns are reviewed. Theoretical aspects of Support Vector Machines on computational biology platform are considered. Finally, novel evolutionary Fuzzy SVM will be introduced, which is applicable on wide range of bioinformatics problems especially the problem of structural repetitive subsequences.

The DNA microarray is an important technique that allows researchers to analyze many gene expression data in parallel. Although the data can be more significant if they come out of separate experiments, one of the most challenging phases in the microarray context is the integration of separate expression level datasets that have gathered through different techniques. In this paper, we present a general novel method for the integration of any collected data whose distributions have been linearly transformed. The new method is based on the information theory concepts. More than that, this article presents a new approach for checking of the linearity between two distributions as a validation technique. The validation technique assists in taking the feature reduction process in effect prior to the integration phase. The time complexity of the proposed algorithm is low and the new presented methods show good functionality. The experimental results are presented at the end of the paper.

A binding study of nickel ions by a new recombinant human Growth Hormone (hGH), produced as an injected drug, has been done at 27˚C in NaCl solution (50 mM) using an isothermal titration calorimetry. There is a set of three identical and non-interacting binding sites for nickel ions. The intrinsic dissociation equilibrium constant and the molar enthalpy of binding are 40 μM and -16.5 kJ/mol, respectively. Thermodynamic parameters of nickel ion binding are comparedto the other metal ions. The molar entropy of binding is 29.3 J K-1 mol-1 for Ni2+, less than Cu2+ and more than other metal ions, means that the disorder of the protein structure due to the binding of nickel ions is more than to the other ion metals, except Cu2+. It is expected that nickel ions can prevent from the aggregation of the protein.

The performance of a forced-liquid Vertical Tubular Loop Bioreactor (VTLB), a forced-liquid Horizontal Tubular Loop Bioreactor (HTLB) and a gas-induced External Airlift Loop Bioreactor (EALB) were compared for production of biomass from natural gas. Hydrodynamic characteristics and mass transfer coefficients were determined as functions of design parameters, physical properties of gases as well as operational parameters. Moreover, energy consumption for different gas and liquid flow rates was studied. In the EALB, kinematic viscosity (υg) showed its significant role on mixing time, gas hold-up and kLa and the diffusion coefficient of gas in water (Dg) had a remarkable effect on kLa. It was observed from experimental results that the performance of the VTLB was the best for biomass production. Furthermore, the volumetric mass transfer coefficients for air and methane were determined at different geometrical and operational factors. New correlations for mixing time, gas hold-up and kLa were obtained and expressed separately. Also, the different ratios of methane and air were measured and compared for optimum growth in the VTLB, HTLB and EALB.

In this work, new biodegradable ABCBA type pentablock copolymers with different mole ratio of L-lactide and PPDO-b-PEG-b-PPDO triblock copolymer were synthesized and characterized. In the first step, PPDO-b-PEG-b-PPDO triblock copolymer was synthesized via a ring-opening polymerization of P-Di Oxanone (PDO) monomer with Poly (Ethylene Glycol) (PEG) using stannous octoate (Sn(Oct)2) as the catalyst. In the second step, L-lactide monomers (60 or 80 mole ratio) as the end blocks were added to the resulting prepolymer in presence of stannous octoate (Sn(Oct)2) catalyst. In the first step, Poly (Ethylene Glycol) (PEG) and, in the second step, triblock copolymer acts as the macro-initiator. The obtained pentablock copolymers were identified by 1H and 13CNMR spectroscopy. Intrinsic viscosity of the resulting copolymers was measured via dilute solution viscometry in chloroform as the solvent. The thermal properties (such as melting points, melting enthalpy and crystallinity) and thermal degradation behavior were studied by Differential Scanning Calorimetry (DSC) and Thermal Gravimetric Analysis (TGA). From the obtained results, it was seen that the poly (L-lactide) end blocks show similar crystallization behavior like poly (L-lactide) homopolymer and also melting temperature of pentablock copolymers rise with an increase in L-lactide content.

A new efficient method for the synthesis of carboacyclic nucleosides as biologically interesting compounds via aza-conjugate addition of pyrimidine nucleobases to ,β-unsaturated esters in the presence of catalytic amount of LiOH.H2O (1.2-4.8 mol%) under microwave irradiation is described. This method affords the title compounds in good to excellent yields and in short reaction times.

Sulfur emission from coal combustion presents many environmental problems. The techniques used to reduce the amount of sulfur in coal before combustion, include physical, chemical and biological processes. Biological processes based on degradation of sulfur compounds by microorganisms offer many advantages over the conventional physical and chemical processes. The processes are performed under mild conditions with no harmful reaction products and the value of coal is not affected. In this article the progress achieved to date in biodesulfurization of Tabas coal in pilot plant is reviewed. Effect of particle size and pulp density at constant temperature on coal biodesulfurization investigated in this research. The best results obtained was 45% of pyritic sulfur and 20% of total sulfur in reduction at pulp density of 10% and 0-0.5 mm particle size within 14 days.

The sorption behavior of loofa-immobilized Phanerochaete chrysosporium mycelia in two forms, Live (L) and Heat-Inactivated (HIA), was studied for the removal of Hg2+ ions from aqueous solution. Using the Langmuir isotherm, the two key parameters for the sorption performance, qm and the coefficient b, were obtained; the qm values for Hg2+ ions were 72.46 mg/g and 92.59 mg/g and the b coefficients were 0.073 L/mg and 0.114 L/mg for the L and HIA biosorbents, respectively. Using the Freundlich isotherm, the values of kF were determined as 13.28 and 21.30, and the values of the coefficient n were 3.22 and 3.51 for the L and HIA biosorbents, respectively. Although the biosorption data were well fitted by both the Langmuir and Freundlich models, the Langmuir isotherm gave a better fit, with a higher correlation coefficient than the Freundlich model. Moreover, the essential characteristic of the Langmuir isotherm model, described as the separation factor, was indicative of the favorable adsorption of Hg2+ onto both of the test biosorbents (0

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MFI zeolite membranes were prepared on porous α-alumina substrates, using secondary growth of nano-seeded layers. The resulting membranes were characterized by means of Scanning Electron Microscopy (SEM), X-Ray Diffractometry (XRD), and pervaporation performance tests for separation of Benzene, Toluene and Xylene (BTX) mixture from contaminated water. The morphology, thickness, homogeneity, crystal preferential orientation and permeation properties of these membranes have been studied in relation to the seed layers. Successful separation of BTX mixture from water was performed by using the manufactured MFI zeolite membrane. The influence of temperature, feed concentration on the membrane separation efficiency systematically investigated. The total permeation fluxes were found to increase with increase in temperature and feed concentration. The separation factors increased with increasing feed concentration and decreased with increasing in temperature.

MFI-type zeolite membranes (ZSM-5) were prepared on α-alumina tubular supports and tested for separation of H2/CO mixtures. The effect of pressure and temperature on H2 and CO flows and selectivity was investigated. The best results in this work were obtained with a ZSM-5 membrane prepared over a porous α-alumina tube seeded with zeolite nanocrystals synthesized with microwave technique. In this case the H2 permeance was obtained 2.8 × 10-6 mol/ (m2.s.Pa) with a H2/CO ideal selectivity of 4.9 at 373 K. The permeation results of four gas (H2, CO, N2, CH4) on the synthesized membrane were also investigated.

The microfiltration 0.2 µm Cellulose Acetate (CA) membrane was modified by embedding antibacterial silver nano-particles in the membrane pores. This novel technique was developed to enhance the capability of the microfiltration membrane for removing microorganism including bacteria. The prepared membrane was characterized using Scanning Electron Microscopy (SEM), Energy-Dispersive X-ray Spectroscopy (EDS), water contact angle measurement and Differential Scanning Calorimetry (DSC). Membrane performance was elucidated by flux and rejection measurements using water samples from the pond of a public recreational park in Tehran. For rejection capability of the membrane, the availability of filament and c-shaped species of the phyla Actinobacteria and Spirochetas in the permeate side of the membrane was estimated. Contrary to virgin membrane, the modified membrane was able to remove 100% of Actinobacteria and Spirochetas species from the infected water. Moreover, the wettability of the modified membrane was remarkably changed leading to higher water flux. A potential application of the modified Ag-CA membrane is “sterile filtration” of temperature sensitive fluids.

A hydrophilic macromolecular network is prepared by performing graft copolymerization of poly (sodium acrylate) chains onto salep and silica gel. The reaction parameters affecting the water absorbency of the superabsorbent composite were optimized using Taguchi method. FT-IR spectroscopy and Thermo Gravimetric Analysis (TGA) were used for confirming the structure of the final product and morphology of the synthesized superabsorbent composite was examined by SEM. The swelling behavior of optimum superabsorbent composite was measured in various swelling media. In addition, swelling kinetics and on-off switching behavior were investigated. In order to evaluate the controlled release potential of the matrix, it was loaded with KNO3 and NH4NO3 as a model agrochemical and the release kinetics was studied.

Adsorption of Bovine Serum Albumin (BSA) onto calcium Hydroxyl Apatite (HA), Ca10PO4(OH)2, has been studied by Ultra Violet (UV) spectroscopy. The adsorption isotherms of BSA onto the HA surface at 291.7 K and 303.2 K were satisfactorily presented by Langmuir equation and the evaluated parameters are reported. The specific surface area of HA has been measured by the BET method. The obtained value for the used HA sample was 63 m2/g. The effect of pH on BSA adsorption onto the HA in presence of salts KCl and NaF and phosphate ion has been investigated. In the fixed concentration of BSA (1 mg/mL) it is shown that the pH decreasing causes to increase of the adsorption of BSA onto HA. Considering the role of effective factors in BSA adsorption onto HA such as the size and charge of the BSA and the surface energy of HA showed that the electrostatic repulsion forces between HA and BSA cause a decrease in BSA adsorption onto HA. Also the obtained results indicated that the surface energy of HA predominates the effect of size and charge of BSA.

Thermal cracking of a heavy liquid hydrocarbon was performed in a laboratory scale tubular reactor. Central Composite Design (CCD), was used as an experimental design method. The design variables were Coil Outlet Temperature (COT), feed flow and rate steam ratio. Maximum yield of ethylene was 30.37 wt% at COT, residence time and steam ratio of 869oC, 0.208 s and 1.22 g/g, respectively. Maximum yield of propylene was 15.37 wt% at COT, residence time and steam ratio of 825oC, 0.147 s and 0.95 g/g, respectively. A mechanistic model based on free radical chain reactions was developed using experimental results. Developed reaction network contains 148 reactions for 43 species. Finally, the experimental data were compared with model results. Scatter diagrams showed good agreement between model and experimental data.

In this paper, control of a non-isothermal continuous stirred tank reactor in which two parallel autocatalytic reactions take place has been addressed. The reactor shows chaotic behavior for a certain set of reactor parameters. In order to control the product concentration, an optimal state feedback controller has been designed. Since concentrations of reactor species are not measured, an observer has been designed for implementation of the proposed control scheme. The local asymptotic stability of the closed-loop system including observer dynamics has been shown via the Lyapunov stability theorem. Effectiveness of the proposed controller in load rejection and set point tracking has been illustrated through simulation.

This paper reports a CFD modeling study to investigate the hydrogen-air mixture combustion in a micro scale chamber. Nine species with nineteen reversible reactions were considered in the premixed combustion model. The effect of operational and geometrical conditions including; combustor size, wall conductivity, reactant flow rates and hydrogen feed splitting on combustion stability and outlet gas temperature were investigated. The results show that the wall thermal conductivity has a significant effect on the combustion especially at smaller chamber size with high ratio of chamber surface area to its volume. In addition, the results reveal that high heat loss from chamber wall, small chamber and high input rate may cause flame quenching. Moreover, the modeling results indicate that a stable combustion in a micro combustor can be achieved at an optimum operational condition.

CoFe2O4 Magnetic Nano Particles (MNPs) were synthesized by an efficient method in aqueous medium with the particle sizes of about 20-50 nm. Then, a hybrid nanocomposite of polyaniline (PANI)-CoFe2O4 MNPs has been electrodeposited directly on a stainless steel wire by the potentiostatic method. Microscopic images of electrodeposited PANI and PANI-CoFe2O4 nanocomposite coatings were obtained by scanning electron microscope. The scanning electron microscopic images of polyaniline and its nanocomposite pointed out the influence of CoFe2O4 nanoparticles in the electrodeposition of polyaniline. Dispersion of CoFe2O4 nanoparticles in electrolyte solution during the electrodeposition, creates a nanocomposite with a more surface area than pure polyaniline.

Solid Lipid Nanoparticles (SLNs) have emerged as an alternative colloidal carriers for sustained release of lipophilic drugs with poor absorption and water solubility. This manuscript describes the effect of process variables on the production of Solid Lipid Nanoparticles (SLNs) from beeswax and carnauba wax and ketoprofen release from these carriers. It was found that by increasing drug content from 0.5 to 1.5% w/v the average particle size of SLNs increased from 82 to 116 nm and drug loading increased from 10.7 to 26.6% while entrapment efficiency remained almost constant (≈ 97%). Unexpectedly, the average size of SLNs increased from 82 to 150 nm by increasing homogenization time from 5 to 15 min. Increasing homogenization intensity from 11000 to 24000 rpm resulted in the particle size decrease from 108 to 82 nm. The rate of drug release from nanparticles loaded with 0.5% w/v ketoprofen increased with increasing the ionic concentration of phosphate buffer solution from 0.05 to 0.1 M.

Chromanone derivatives demonstrate remarkable cytotoxity against a varieties of cancer cell lines. Novel 9-[hydroxy(substitutedphenyl)methyl]-2,2-dimethyl-2,3,8,9- tetrahydro-4H,10H-pyrano[2,3-f]chromene-4,10-diones as Glyasperin analogues were synthesized in four steps from known 4-chromone 1. The key step was the preparation of chromane dione 5a by regioselective intramolecular cyclization reaction in 85% yield. Condensation of 5a with substituted aromatic aldehydes afforded corresponding alpha hydroxybenzyl analogues 6a-6e. The cytotoxic study of the synthesized compounds against breast cancer human cell line (T47D) showed moderate cytotoxic activities (IC50=16-40 μM) compared to the positive control drug vincristin (IC50=2.5 μM).

The concept of Resonance Assisted Hydrogen Bond (RAHB), which usually occurs in  diketons, has a remarkable role in chemistry. These molecules, which contain heteroatom particularly O and N, are species with biological interest in protein folding and DNA pairing. Therefore, the amplification of hydrogen bonds strength by substituents may be important in life sciences. In the current research, we have shown that the nature of hydrogen bond in the enol form of heteroatom RAHB systems has partial covalent and electrostatic character. Nonetheless, the strength of hydrogen bonds increases by means of three different groups of substituents, which cannot be attributed to the contributions of resonance structures. Parameters such as bond ellipticity, delocalization indices and bond equalizations cannot help to prove the effect of conjugation on the strength of hydrogen bond in RAHB systems. It is shown by NBO that the primary and secondary hyperconjugative charge transfer caused by substituents help to amplify this type of hydrogen bond. We showed that the existence of -conjugation is necessary only for transformation of electron from substituents to the hydrogen bond as an acceptor of electrons. The strength of RAHB has a rather good correlation with the distance between of two non-connected heteroatoms O and N according to reference [62].