World Academy of Science, Engineering and Technology

Authors: Masaki Yamaguchi, Akira Ito, Noriaki Okamoto, Yoshinori Kawabe, Masamichi Kamihira

Abstract:

Heat-inducible gene expression vectors are useful for hyperthermia-induced cancer gene therapy, because the combination of hyperthermia and gene therapy can considerably improve the therapeutic effects. In the present study, we developed an enhanced heat-inducible transgene expression system in which a heat-shock protein (HSP) promoter and tetracycline-responsive transactivator were combined. When the transactivator plasmid containing the tetracycline-responsive transactivator gene was co-transfected with the reporter gene expression plasmid, a high level of heat-induced gene expression was observed compared with that using the HSP promoter without the transactivator. In vitro evaluation of the therapeutic effect using HeLa cells showed that heat-induced therapeutic gene expression caused cell death in a high percentage of these cells, indicating that this strategy is promising for cancer gene therapy.

Keywords: Inducible gene expression, Gene therapy, Hyperthermia, Heat shock protein, Tetracycline transactivator.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2135

Authors: MD Zaheer Ansari, A.K. Nirala

Abstract:

In this study spatial-temporal speckle correlation techniques have been applied for the quality evaluation of three different Indian fruits namely apple, pear and tomato for the first time. The method is based on the analysis of variations of laser light scattered from biological samples. The results showed that crosscorrelation coefficients of biospeckle patterns change subject to their freshness and the storage conditions. The biospeckle activity was determined by means of the cross-correlation functions of the intensity fluctuations. Significant changes in biospeckle activity were observed during their shelf lives. From the study, it is found that the biospeckle activity decreases with the shelf-life storage time. Further it has been shown that biospeckle activity changes according to their respiration rates.

Keywords: Biospeckle, cross-correlation, respiration, shelf-life.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2491

Authors: Rizna Triana Dewi, Sanro Tachibana, Ahmad Darmawan

Abstract:

The bioassay-guided isolation and purification of an ethyl acetate extract of Aspergillus terreus MC751 led to the characterization of butyrolactone I as an antidiabetic and antioxidant. The antidiabetic activity of butyrolactone I was evaluated by α- glucosidase and α-amylase inhibition assays. Butyrolactone I demonstrated significant concentration-dependent, mixed-type inhibitory activity against yeast α-glucosidase with an IC50 of 54μM. However, the compound exhibited less activity against rat intestinal α-glucosidase and α-amylase. This is the first report on α-glucosidase inhibitory activity of butyrolactone I. The antioxidative activity of butyrolactone I was evaluated based on scavenging effects on 1,1- diphenyl-2-picrylhydrazyl (DPPH) (IC50 =51 μM) and hydrogen peroxide (IC50= 141 μM) radicals as well as a reducing power assay. The results suggest that butyrolactone I is a promising antidiabetic as well as antioxidant and should be considered for clinical trials.

Keywords: Aspergillus terreus MC751, antidiabetic, antioxidant, Butyrolactone I.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2820

Authors: J.E. Park, G.R. Kim, D.J. Yoon, C.H. Sin, I.S. Park, T.S. Bea, M.H. Lee

Abstract:

Carbon nanotubes (CNTs) are attractive because of their excellent chemical durability mechanical strength and electrical properties. Therefore there is interest in CNTs for not only electrical and mechanical application, but also biological and medical application. In this study, the dispersion power of surfactant-treated multiwalled carbon nanotubes (MWCNTs) and their effect on the antibacterial activity were examined. Surfactant was used sodium dodecyl-benzenesulfonate (SDBS). UV-vis absorbance and transmission electron microscopy(TEM) were used to characterize the dispersion of MWCNTs in the aqueous phase, showing that the surfactant molecules had been adsorbed onto the MWCNTs surface. The surfactant-treated MWCNTs exhibited antimicrobial activities to streptococcus mutans. The optical density growth curves and viable cell number determined by the plating method suggested that the antimicrobial activity of surfactant-treated MWCNTs was both concentration and treatment time-dependent.

Keywords: MWCNT, SDBS, surfactant, antibacterial.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3038

Authors: A. H. El-Far, R. R. Gindi, H. A. Abd El-Maksoud, Mohamed Ragaa Ragab Hassanien

Abstract:

Gastric ulceration is a discontinuity in gastric mucosa, usually occurs due to imbalance between the gastric mucosal protective factors, that is called gastric mucosal barrier, and the aggressive factors, to which the mucosa is exposed. This study was carried out on sixty male Sprague-Dowely rats (12- 16 weeks old) allocated into two groups. The first control group and the second Gastric lesion group which induced by oral administration of a single daily dose of aspirin at a dose of 300 mg/kg body weight for 7 consecutive-days (6% aspirin solution will be prepared and each rat will be given 5 ml of that solution/kg body weight). Blood is collected 1, 2 and 3 weeks after induction of gastric ulceration. Significant increase in serum copper, nitric oxide, and prostaglandin E2 all over the period of experiment. Significant decrease in erythrocyte superoxide dismutase (t-SOD) activities, serum (calcium, phosphorus, glucose and insulin) levels. Non-significant changes in serum sodium and potassium levels are obtained.

Keywords: Aspirin, Gastric Ulcer, Prostaglandin E2, Superoxide dismutase

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1613

Authors: Niraj A. Ghanwate, P V Thakare, P R Bhise, Ashish Dhanke, Shubhangi Apotikar

Abstract:

Urinary Tract Infections (UTI) account for an estimated 25-40% nosocomial infection, out of which 90% are associated with urinary catheter, called Catheter associated urinary tract infection (CAUTI). The microbial populations within CAUTI frequently develop as biofilms. In the present study, microbial contamination of indwelling urinary catheters was investigated. Biofilm forming ability of the isolates was determined by tissue culture plate method. Prevention of biofilm formation in the urinary catheter by Pseudomonas aeruginosa was also determined by coating the catheter with some enzymes, gentamycin and EDTA. It was found that 64% of the urinary catheters get contaminated during the course of catheterization. Of the total 6 isolates, biofilm formation was seen in 100% Pseudomonas aeruginosa and E. coli, 90% in Enterococci, 80% in Klebsiella and 66% in S. aureus. It was noted that the biofilm production by Pseudomonas was prolonged by 7 days in amylase, 8 days in protease, 6 days in lysozyme, 7days in gentamycin and 5 days in EDTA treated catheter.

Keywords: CAUTI, biofilm, enzymes, EDTA, Pseudomonas.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2786

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

Abstract:

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

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

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2488

Authors: Pattrarat Teamkao, Paitip Thiravetyan

Abstract:

The aim of this work was to investigate the potential of soil microorganisms and the burhead plant, as well as the combination of soil microorganisms and plants to remediate monoethylene glycol (MEG), diethylene glycol (DEG), and triethylene glycol (TEG) in synthetic wastewater. The result showed that a system containing both burhead plant and soil microorganisms had the highest efficiency in EGs removal. Around 100% of MEG and DEG and 85% of TEG were removed within 15 days of the experiments. However, the burhead plant had higher removal efficiency than soil microorganisms for MEG and DEG but the same for TEG in the study systems. The removal rate of EGs in the study system related to the molecular weight of the compounds and MEG, the smallest glycol, was removed faster than DEG and TEG by both the burhead plant and soil microorganisms in the study system.

Keywords: Ethylene glycol, burhead plant, soil microorganisms, phytoremediation

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3715

Authors: Santosh Kumar, Anand Prakash, Kanak Sinha, Anita K Verma

Abstract:

Vernonia divergens Benth., commonly known as “Insulin Plant” (Fam: Asteraceae) is a potent sugar killer. Locally the leaves of the plant, boiled in water are successfully administered to a large number of diabetic patients. The present study evaluates the putative anti-diabetic ingredients, isolated from the in vivo and in vitro grown plantlets of V. divergens for their antimicrobial and anticancer activities. Sterilized explants of nodal segments were cultured on MS (Musashige and Skoog, 1962) medium in presence of different combinations of hormones. Multiple shoots along with bunch of roots were regenerated at 1mg l-1 BAP and 0.5 mg l-1 NAA. Micro-plantlets were separated and sub-cultured on the double strength (2X) of the above combination of hormones leading to increased length of roots and shoots. These plantlets were successfully transferred to soil and survived well in nature. The ethanol extract of plantlets from both in vivo & in vitro sources were prepared in soxhlet extractor and then concentrated to dryness under reduced pressure in rotary evaporator. Thus obtainedconcentrated extracts showed significant inhibitory activity against gram negative bacteria like Escherichia coli and Pseudomonas aeruginosa but no inhibition was found against gram positive bacteria. Further, these ethanol extracts were screened for in vitro percentage cytotoxicity at different time periods (24 h, 48 h and 72 h) of different dilutions. The in vivo plant extract inhibited the growth of EAC mouse cell lines in the range of 65, 66, 78, and 88% at 100, 50, 25 & 12.5μg mL-1 but at 72 h of treatment. In case of the extract of in vitro origin, the inhibition was found against EAC cell lines even at 48h. During spectrophotometric scanning, the extracts exhibited different maxima (ʎ) - four peaks in in vitro extracts as against single in in vivo preparation suggesting the possible change in the nature of ingredients during micropropagation through tissue culture techniques.

Keywords: Anti-cancer, Anti-microbial, EAC mouse cell, Tissue culture, Vernonia divergens.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2367

Authors: Zaini Mohd-Zain, Mohd-Saufee A.F. Mohd-Ismail, Norlida Buniyamin

Abstract:

Staphylococcus aureus, one of the microflora in a human external auditory canal (EAC) is frequently exposed to highfrequency electromagnetic field (HF-EMF) generated by mobile phones. It is normally non-pathogenic but in certain circumstances, it can cause infections. This study investigates the changes in the physiology of S. aureus when exposed to HF-EMF of a mobile phone. Exponentially grown S. aureus were exposed to two conditions of EMF irradiation (standby-mode and on-call mode) at four durations; 15, 30, 45 and 60 min. Changes in the viability and biofilm production of the S. aureus were compared between the two conditions of exposure. EMF from the standby-mode has enhanced the growth of S. aureus but during on-call, the growth was suppressed. No significant difference in the amount of biofilm produced in both modes of exposure was observed. Thus, HF-EMF of mobile phone affects the viability of S. aureus but not its ability to produce biofilm.

Keywords: Electromagnetic field, mobile phone, biofilm, Staphylococcus aureus

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2014

Authors: Arshad Javaid, Syeda F. Naqvi

Abstract:

Macrophomina phaseolina is a devastating soil-borne fungal plant pathogen that causes charcoal rot disease in many economically important crops worldwide. So far, no registered fungicide is available against this plant pathogen. This study was planned to examine the antifungal activity of an allelopathic grass Cenchrus pennisetiformis (Hochst. & Steud.) Wipff. for the management of M. phaseolina isolated from cowpea [Vigna unguiculata (L.) Walp.] plants suffering from charcoal rot disease. Different parts of the plants viz. inflorescence, shoot and root were extracted in methanol. Laboratory bioassays were carried out using different concentrations (0, 0.5, 1.0, …, 3.0 g mL-1) of methanolic extracts of the test allelopathic grass species to assess the antifungal activity against the pathogen. In general, extracts of all parts of the grass exhibited antifungal activity. All the concentrations of methanolic extracts of shoot and root significantly reduced fungal biomass by 20–73% and 40–80%, respectively. Methanolic shoot extract was fractionated using n-hexane, chloroform, ethyl acetate and n-butanol. Different concentrations of these fractions (3.125, 6.25, …, 200 mg mL-1) were analyzed for their antifungal activity. All the concentrations of n-hexane fraction significantly reduced fungal biomass by 15–96% over corresponding control treatments. Higher concentrations (12.5–200 mg mL-1) of chloroform, ethyl acetate and n-butanol also reduced the fungal biomass significantly by 29–100%, 46–100% and 24–100%, respectively.

Keywords: Antifungal activity, Cenchrus pennisetiformis, Macrophomina phaseolina, natural fungicides

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1817

Authors: Novi Khila Firani, Elisa Nesdyaningtyas

Abstract:

Kwashiorkor is one of nutritional problem in Indonesia, which lead to decrease immune system. This condition causes susceptibility to infectious disease, especially tuberculosis. Development of new tuberculosis vaccine will be an important strategy to eliminate tuberculosis in kwashiorkor. Previous research showed that 38-kDa Mycobacterium tuberculosis protein is one of the potent immunogen. However, the role of oral immunization with 38- kDa Mycobacterium tuberculosis protein to the number of lymphocytes in the rat model of kwashiorkor is still unknown. We used kwashiorkor rat model groups with 4% and 2% low protein diet. Oral immunization with 38-kDa Mycobacterium tuberculosis protein given with 2 booster every week. The lymphocytes number were measured by flowcytometry. There was no significant difference between the number of lymphocytes in the normal rat group and the kwashiorkor rat groups. It may reveal the role of 38-kDa Mycobacterium tuberculosis protein as a potent immunogen that can increase the lymphocytes number from kwashiorkor rat model same as normal rat.

Keywords: kwashiorkor rat, lymphocytes, 38-kDa Mycobacterium tuberculosis protein

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2508

Authors: J. Ruenin, S. Sukprasong, R. Phatthanakun, N. Chomnawang, P. Kuntanawat

Abstract:

In this paper, a simple microfluidic device for monitoring algal cell behavior is proposed. An array of algal microwells is fabricated by PDMS soft-lithography using X-ray LIGA mold, placed on a glass substrate. Two layers of replicated PDMS and substrate are attached by oxygen plasma bonding, creating a microchannel for the microfluidic system. Algal cell are loaded into the microfluidic device, which provides positive charge on the bottom surface of wells. Algal cells, which are negative charged, can be attracted to the bottom of the wells via electrostatic interaction. By varying the concentration of algal cells in the loading suspension, it is possible to obtain wells with a single cell. Liquid medium for cells monitoring are flown continuously over the wells, providing nutrient and waste exchange between the well and the main flow. This device could lead to the uncovering of the quantitative biology of the algae, which is a key to effective and extensive algal utilizations in the field of biotechnology, food industry and bioenergy research and developments.

Keywords: Algal cells, microfluidic device, X-ray LIGA, X-ray lithography, metallic mold, synchrotron light, PDMS

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2428

Authors: N. Chanchay, S. Sirisansaneeyakul, C. Chaiyasut, N. Poosaran

Abstract:

This study aims to screen out and to optimize the major nutrients for maximum carotenoid production and antioxidation characteristics by Rhodotorula rubra. It was found that supplementary of 10 g/l glucose as carbon source, 1 g/l ammonium sulfate as nitrogen source and 1 g/l yeast extract as growth factor in the medium provided the better yield of carotenoid content of 30.39 μg/g cell dry weight the amount of antioxidation of Rhodotorula rubra by DPPH, ABTS and MDA method were 1.463%, 34.21% and 34.09 μmol/l, respectively.

Keywords: Carotenoid, Rhodotorula rubra, Antioxidation, DPPH, ABTS

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2941

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.

Keywords: Carbonic anhydrase, Codon-optimization, Duneliala species, CO2 sequestration

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1646

Authors: Dayana Amira R., Roshanida A.R., Rosli M.I.

Abstract:

Empty Fruit Bunches (EFB) and Palm Oil Mill Effluent (POME) are two main wastes from oil palm industries which contain rich lignocellulose. Degradation of EFB and POME by microorganisms will produce hydrolytic enzyme which will degrade cellulose and hemicellulose during composting process. However, normal composting takes about four to six months to reach maturity. Hence, application of fungi into compost can shorten the period of composting. This study identifies the effect of xylanase and cellulase produced by Aspergillus niger and Trichoderma virens on composting process using EFB and POME. The degradation of EFB and POME indicates the lignocellulolytic capacity of Aspergillus niger and Trichoderma virens with more than 7% decrease in hemicellulose and more than 25% decrease in cellulose for both inoculated compost. Inoculation of Aspergillus niger and Trichoderma virens also increased the enzyme activities during the composting period compared to the control compost by 21% for both xylanase and cellulase. Rapid rise in the activities of cellulase and xylanase was observed by Aspergillus niger with the highest activities of 14.41 FPU/mg and 3.89 IU/mg, respectively. Increased activities of cellulase and xylanase also occurred in inoculation of Trichoderma virens with the highest activities obtained at 13.21 FPU/mg and 4.43 IU/mg, respectively. Therefore, it is evident that the inoculation of fungi can increase the enzyme activities hence effectively degrading the EFB and POME.

Keywords: EFB, cellulase, POME, xylanase

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3079

Authors: Sayed Reza Hashemi, Amir Heidarinasab

Abstract:

Spent Sulfidic Caustic was biologically treated and regenerated for reusing by Thiobacillus denitrificans bacteria, sulfide content oxidized and RSNa reduced dramatically.PH in this test was 11.8 and no neutralization has been done on spent caustic, so spent caustic as the most difficult of industrial wastes to dispose could be regenerate and reuse instead of disposing to sea or deep wells

Keywords: Spent Caustic, Thiobacillus denitrificans, Bioregeneration

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2834

Authors: A. Ashjaran, M. E. Yazdanshenas, A. Rashidi, R. Khajavi, A. Rezaee

Abstract:

fibers of pure cellulose can be made from some bacteria such as acetobacter xylinum. Bacterial cellulose fibers are very pure, tens of nm across and about 0.5 micron long. The fibers are very stiff and, although nobody seems to have measured the strength of individual fibers. Their stiffness up to 70 GPa. Fundamental strengths should be at least greater than those of the best commercial polymers, but best bulk strength seems to about the same as that of steel. They can potentially be produced in industrial quantities at greatly lowered cost and water content, and with triple the yield, by a new process. This article presents a critical review of the available information on the bacterial cellulose as a biological nonwoven fabric with special emphasis on its fermentative production and applications. Characteristics of bacterial cellulose biofabric with respect to its structure and physicochemical properties are discussed. Current and potential applications of bacterial cellulose in textile, nonwoven cloth, paper, films synthetic fiber coating, food, pharmaceutical and other industries are also presented.

Keywords: Microbial cellulose, Biofabric, Microorganisms Acetobacter xylinum, Polysaccharide

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1696

Authors: Sunil Dehipawala, Todd Holden, E. Cheung, Robert Regan, P. Schneider, G. Tremberger Jr, D. Lieberman, T. Cheung

Abstract:

The zinc and iron environments in different growth stages have been studied with EXAFS and XANES with Brookhaven Synchrotron Light Source. Tissue samples included meat, organ, vegetable, leaf, and yeast. The project studied the EXAFS and XANES of tissue samples using Zn and Fe K-edges. Duck embryo samples show that brain and intestine would contain shorter EXFAS determined Zn-N/O bond; as with the cases of fresh yeast versus reconstituted live yeast and green leaf versus yellow leaf. The XANES Fourier transform characteristic-length would be useful as a functionality index for selected types of tissue samples in various physical states. The extension to the development of functional synchrotron imaging for tissue engineering application based on spectroscopic technique is discussed.

Keywords: EXAFS, Fourier Transform, metalloproteins, XANES

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1581

Authors: E. Binaeian, A.M. Rashidi, H. Attar

Abstract:

A comparative evaluation of acute toxicity of synthesized nano silvers using two different procedures (biological and chemical reduction methods) and silver ions on bacteria Vibrio fischeri was investigated. The bacterial light inhibition test as a toxicological endpoint was used by applying of a homemade luminometer. To compare the toxicity effects as a quantitative parameter, a nominal effective concentrations (EC) of chemicals and a susceptibility constant (Z-value) of bacteria, after 5 min and 30 min exposure times, were calculated. After 5 and 30 min contact times, the EC50 values of two silver nanoparticles and the EC20 values were about similar. It demonstrates that toxicity of silvers was independent of their procedure. The EC values of nanoparticles were larger than those of the silver ions. The susceptibilities(Z- Values) of V.fischeri (L/mg) to the silver ions were greater than those of the nano silvers. According to the EC and Z values, the toxicity of silvers decreased in the following order: Silver ions >> silver nanoparticles from chemical reduction method ~ silver nanoparticles from biological method.

Keywords: Bioluminescence, Luminometer, silver nano particles, Toxicity, Vibrio fischeri

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3079

Authors: Chien-Ju Li, Chun-Hui Yu, Chi-Chuan Hwang, Tsunglin Liu , Darby Tien-Hao Chang

Abstract:

De novo genome assembly is always fragmented. Assembly fragmentation is more serious using the popular next generation sequencing (NGS) data because NGS sequences are shorter than the traditional Sanger sequences. As the data throughput of NGS is high, the fragmentations in assemblies are usually not the result of missing data. On the contrary, the assembled sequences, called contigs, are often connected to more than one other contigs in a complicated manner, leading to the fragmentations. False connections in such complicated connections between contigs, named a contig graph, are inevitable because of repeats and sequencing/assembly errors. Simplifying a contig graph by removing false connections directly improves genome assembly. In this work, we have developed a tool, SIMGraph, to resolve ambiguous connections between contigs using NGS data. Applying SIMGraph to the assembly of a fungus and a fish genome, we resolved 27.6% and 60.3% ambiguous contig connections, respectively. These results can reduce the experimental efforts in resolving contig connections.

Keywords: Contig graph, NGS, de novo assembly, scaffold.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1734

Authors: Yi-Ping Fang, Yi-Ting Wong

Abstract:

Transcription factor p53 has a powerful tumor suppressing function that is associated with many cancers. However, p53 of the molecular weight was higher make the limitation across to skin or cell membrane. Thymidine dinucleotide (pTT), an oligonucleotide, can activate the p53 transcription factor. pTT is a hydrophilic and negative charge oligonucleotide, which delivery in to cell membrane need an appropriate carrier. The aim of this study was to improve the bioavailability of the nucleotide fragment, thymidine dinucleotide (pTT), using elasic liposome carriers to deliver the drug into the skin. The study demonstrate that dioleoylphosphocholine (DOPC) incorporated with sodium cholate at molar ratio 1:1 can archived the particle size about 220 nm. This elastic liposome could penetration through skin from stratum corneum to whole epidermis by confocal laser scanning microscopy (CLSM). Moreover, we observed the the slight increase in generation of p53 by western blot.

Keywords: Elastic liposome, Tymidine dinucleotide, p53, Topical delivery

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1838

Authors: Yoshihiro Ochiai

Abstract:

Globin superfamily proteins including myoglobin and hemoglobin, have welcome new members recently, namely, cytoglobin, neuroglobin and globin X, though their physiological functions are still to be addressed. Fish are the excellent models for the study of these globins, but their characteristics have not yet been discussed to date. In the present study, attempts have been made to characterize their structural uniqueness by making use of proteomics approach. This is the first comparative study on the characterization of globin superfamily proteins from fish.

Keywords: Globin, Superfamily, Protein, Fish, Structure

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1275

Authors: Dhananjay C. Joshi, Jung-Hsin Lin

Abstract:

Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.

Keywords: protein-protein docking, protein-protein interaction, molecular mechanics energetics, Poisson-Boltzmann calculations

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1805

Authors: J. Tengrang, T. Rungrotmongkol, S. Hannongbua

Abstract:

Every 2-3 years the influenza B virus serves epidemics. Neuraminidase (NA) is an important target for influenza drug design. Although, oseltamivir, an oral neuraminidase drug, has been shown good inhibitory efficiency against wild-type of influenza B virus, the lower susceptibility to the R152K mutation has been reported. Better understanding of oseltamivir efficiency and resistance toward the influenza B NA wild-type and R152K mutant, respectively, could be useful for rational drug design. Here, two complex systems of wild-type and R152K NAs with oseltamivir bound were studied using molecular dynamics (MD) simulations. Based on 5-ns MD simulation, the loss of notable hydrogen bond and decrease in per-residue decomposition energy from the mutated residue K152 contributed to drug compared to those of R152 in wildtype were found to be a primary source of high-level of oseltamivir resistance due to the R152K mutation.

Keywords: Influenza B neuraminidase, Molecular dynamics simulation, Oseltamivir resistance, R152K mutant

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1910

Authors: Yi-Ping Fang, Hsien-Ting Cheng

Abstract:

Topical photodynamic therapy (PDT) with 5-aminolevulinic acid (ALA) is an alternative therapy for treating superficial cancer, especially for skin or oral cancer. ALA, a precursor of the photosensitizer protoporphyrin IX (PpIX), is present as zwitterions and hydrophilic property which make the low permeability through the cell membrane. Collagen is a traditional carrier; its molecular composed various amino acids which bear positive charge and negative charge. In order to utilize the ion-pairs with ALA and collagen, the study employed various pH values adjusting the net charge. The aim of this study was to compare a series collagen form, including solution, gel and sponge to investigate the topical delivery behavior of ALA. The in vivo confocal laser scanning microscopy (CLSM) study demonstrated that PpIX generation ability was different pattern after apply for 6 h. Gel type could generate high PpIX, and archived more deep of skin depth.

Keywords: 5-Aminolevulinic acid (ALA), Collagen, Ion-pairs, Penetration behavior

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1738

Authors: B. Chouhan, A. Denesyuk, J. Heino, M. S. Johnson, K. Denessiouk

Abstract:

Integrins are a large family of multidomain α/β cell signaling receptors. Some integrins contain an additional inserted I domain, whose earliest expression appears to be with the chordates, since they are observed in the urochordates Ciona intestinalis (vase tunicate) and Halocynthia roretzi (sea pineapple), but not in integrins of earlier diverging species. The domain-s presence is viewed as a hallmark of integrins of higher metazoans, however in vertebrates, there are clearly three structurally-different classes: integrins without I domains, and two groups of integrins with I domains but separable by the presence or absence of an additional αC helix. For example, the αI domains in collagen-binding integrins from Osteichthyes (bony fish) and all higher vertebrates contain the specific αC helix, whereas the αI domains in non-collagen binding integrins from vertebrates and the αI domains from earlier diverging urochordate integrins, i.e. tunicates, do not. Unfortunately, within the early chordates, there is an evolutionary gap due to extinctions between the tunicates and cartilaginous fish. This, coupled with a knowledge gap due to the lack of complete genomic data from surviving species, means that the origin of collagen-binding αC-containing αI domains remains unknown. Here, we analyzed two available genomes from Callorhinchus milii (ghost shark/elephant shark; Chondrichthyes – cartilaginous fish) and Petromyzon marinus (sea lamprey; Agnathostomata), and several available Expression Sequence Tags from two Chondrichthyes species: Raja erinacea (little skate) and Squalus acanthias (dogfish shark); and Eptatretus burgeri (inshore hagfish; Agnathostomata), which evolutionary reside between the urochordates and osteichthyes. In P. marinus, we observed several fragments coding for the αC-containing αI domain, allowing us to shed more light on the evolution of the collagen-binding integrins.

Keywords: Integrin αI domain, integrin evolution, collagen binding, structure, αC helix

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 3672

Authors: Asma Meziti, Hicham Meziti, Kaouthar Boudiaf, Benboubetra Mustapha, Hemama Bouriche.

Abstract:

Nigella sativa L. is an aromatic plant belonging to the family Ranunculaceae. It has been used traditionally, especially in the middle East and India, for the treatment of asthma, cough, bronchitis, headache, rheumatism, fever, influenza and eczema. Several biological activities have been reported in Nigella sativa seeds, including antioxidant. In this context we tried to estimate the antioxidant activity of various extracts prepared from Nigella sativa seeds, methanolic extract (ME), chloroformic extract (CE), hexanic extract (HE : fixed oil), ethyl acetate extract (EAE) water extract (WE). The Folin-Ciocalteu assay showed that CE and EAE contained high level of phenolic compounds 81.31 and 72.43μg GAE/mg of extract respectively. Similarly, the CE and EAE exhibited the highest DPPH radical scavenging activity, with IC50 values of 106.56μg/ml and 121.62μg/ml respectively. In addition, CE and HE showed the most scavenging activity against superoxide radical generated in the PMS-NADH-NBT system with respective IC50 values of 361.86 μg/ml and 371.80 μg/ml, which is comparable to the activity of the standard antioxidant BHT (344.59 μg/ml). Ferrous ion chelating capacity assay showed that WE, EAE and ME are the most active with 40.57, 39.70 and 22.02 mg EDTA-E/g of extract. The inhibition of linoleic acid/ß-carotene coupled oxidation was estimated by ßcarotene bleaching assay, this showed a highest relative antioxidant activity with CE and EAE (69.82% of inhibition). The antioxidant activities of the methanolic extract and the fixed oil are confirmed by an in vivo assay in mice, the daily oral administration of methanolic extract (500 and 800 mg/kg/day) and fixed oil (2 and 4 ml/kg/day) during 21 days, resulted in a significant enhancement of the blood total antioxidant capacity (measured by KRL test) and the plasmatic antioxidant capacity towards DPPH radical.

Keywords: Antioxidant Capacity, Chelating, Phenolic Compounds, Nigella Sativa, Scavenger

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 4290

Authors: Ratanaporn Leesing, Rattanaporn Baojungharn, Thidarat Papone

Abstract:

Compared to oil production from microorganisms, little work has been performed for mixed culture of microalgae and yeast. In this article it is aimed to show high oil accumulation potential of mixed culture of microalgae Chlorella sp. KKU-S2 and oleaginous yeast Torulaspora maleeae Y30 using sugarcane molasses as substrate. The monoculture of T. maleeae Y30 grew faster than that of microalgae Chlorella sp. KKU-S2. In monoculture of yeast, a biomass of 6.4g/L with specific growth rate (m) of 0.265 (1/d) and lipid yield of 0.466g/L were obtained, while 2.53g/L of biomass with m of 0.133 (1/d) and lipid yield of 0.132g/L were obtained for monoculture of Chlorella sp. KKU-S2. The biomass concentration in the mixed culture of T. maleeae Y30 with Chlorella sp. KKU-S2 increased faster and was higher compared with that in the monoculture and mixed culture of microalgae. In mixed culture of microalgae Chlorella sp. KKU-S2 and C. vulgaris TISTR8580, a biomass of 3.47g/L and lipid yield of 0.123 g/L were obtained. In mixed culture of T. maleeae Y30 with Chlorella sp. KKU-S2, a maximum biomass of 7.33 g/L and lipid yield of 0.808g/L were obtained. Maximum cell yield coefficient (YX/S, 0.229g/L), specific yield of lipid (YP/X, 0.11g lipid/g cells) and volumetric lipid production rate (QP, 0.115 g/L/d) were obtained in mixed culture of yeast and microalgae. Clearly, T. maleeae Y30 and Chlorella sp. KKU-S2 use sugarcane molasses as organic nutrients efficiently in mixed culture under mixotrophic growth. The biomass productivity and lipid yield are notably enhanced in comparison with monoculture.

Keywords: Microbial oil, Chlorella sp. KKU-S2, Chlorella vulgaris, Torulaspora maleeae Y30, mixed culture, biodiesel.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2856

Authors: Noor Muzamil Mohamad, Abdul Manaf Ali, Hamzah Mohd Salleh

Abstract:

Phytases (myo-inositol hexakisphosphate phosphohydrolases; EC 3.1.3.8) catalyze the hydrolysis of phytic acid (myoinositol hexakisphosphate) to the mono-, di-, tri-, tetra-, and pentaphosphates of myo-inositol and inorganic phosphate. Therrmophilic bacteria isolated from water sampled from hot spring. About 120 isolates of bacteria were successfully isolated form hot spring water sample and tested for extracellular phytase producing. After 5 passages of the screening on the PSM media, 4 isolates were found stable in producing phytase enzyme. The 16s RDNA sequencing for identification of bacteria using molecular technique revealed that all isolates those positive in phytase producing are belong to Geobacillus spp. And Anoxybacillus spp. Anoxybacillus rupiensis UniSZA-7 were identified for their carbon source utilization using Phenotype Microarray Plate of Biolog and found they utilize several kind of carbon source provided.

Keywords: Phytase, Phytic Acid, Thermophilic Bacteria, PSM Media and Phytase Assay

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2165