Search results for: nucleic acid binding

Authors: Yusra Tariq

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The Grass 37 gene is presently known in tomatoes, which are the source of healthy substances such as ascorbic acid, polyphenols, carotenoids and nutrients. It has a significant impact on the growth and development of humans. The GRASS 37 gene is a plant Transcription factor group assuming significant parts in various reactions of different Abiotic stresses such as (drought, salinity, thermal stresses, temperature, and bright waves) which could highly affect the growth. Tomatoes are very sensitive to temperature, and their growth or production occurs optimally in a temperature range from 21 C to 29.5 C during the daytime and from 18.5 C to 21 C during the night. This protein acts as a positive regulator of salt stress response and abscisic acid signaling. This study summarizes the structure characterized by molecular formula and protein-binding domains by different bioinformatics tools such as Expasy translate tool, Expasy Portparam, Swiss Prot and Inter Pro Scan, Clustal W tool regulatory procedure of GRASS gene components, also their reactions to both biotic and Abiotic stresses.

Keywords: GRAS37, gene, bioinformatics, tool

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Authors: Nusrat Masood, Vijaya Dubey, Suaib Luqman

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Caspase 3, a member of cysteine-aspartic acid protease family, is an imperative indicator for cell death particularly when substantiating apoptosis. Thus, caspase 3 is an interesting target for the discovery and development of anticancer agent. We adopted a four level assessment of both terpenoids and flavonoids and thus experimentally performed the enzymatic assay in cell free system as well as in cancer cell line which was validated through real time expression and molecular interaction studies. A significant difference was observed with both the class of natural products indicating terpenoids as better activators of caspase 3 compared to flavonoids both in the cell free system as well as in cell lines. The expression analysis, activation constant and binding energy also correlate well with the enzyme activity. Overall, terpenoids had an unswerving effect on caspase 3 in all the tested system while flavonoids indirectly affect enzyme activity.

Keywords: Caspase 3, terpenoids, flavonoids, activation constant, binding energy

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Authors: Mala Nath, Nagamani Kompelli, Partha Roy, Snehasish Das

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Two new metal-based anticancer chemotherapeutic agents, [(Ph2Sn)2(HGuO)2(phen)Cl2] 1 and [(Ph3Sn)(HGuO)(phen)]- Cl.CH3OH.H2O 2, were designed, prepared and characterized by analytical and spectral (IR, ESI-Mass, 1H, 13C and 119Sn NMR) techniques. The proposed geometry of Sn(IV) in 1 and 2 is distorted octahedral and distorted trigonal-bipyramidal, respectively. Both 1 and 2 exhibit potential cytotoxicity in vitro against MCF-7, HepG-2 and DU-145 cell lines. The intrinsic binding constant (Kb) values of 1 (2.33 × 105 M-1) and 2 (2.46 × 105 M-1) evaluated from UV-Visible absorption studies suggest non-classical electrostatic mode of interaction via phosphate backbone of DNA double helix. The Stern-Volmer quenching constant (Ksv) of 1 (9.74 × 105 M-1) and 2 (2.9 × 106 M-1) determined by fluorescence studies suggests the groove binding and intercalation mode for 1 and 2, respectively. Effective cleavage of pBR322 DNA is induced by 1. Their interaction with DNA of cancer cells may account for potency.

Keywords: anticancer agents, DNA binding studies, NMR spectroscopy, organotin

Procedia PDF Downloads 258

Authors: Junie B. Billones, Maria Constancia O. Carrillo, Voltaire G. Organo, Stephani Joy Y. Macalino, Inno A. Emnacen, Jamie Bernadette A. Sy

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The drug discovery and development process is generally known to be a very lengthy and labor-intensive process. Therefore, in order to be able to deliver prompt and effective responses to cure certain diseases, there is an urgent need to reduce the time and resources needed to design, develop, and optimize potential drugs. Computer-aided drug design (CADD) is able to alleviate this issue by applying computational power in order to streamline the whole drug discovery process, starting from target identification to lead optimization. This drug design approach can be predominantly applied to diseases that cause major public health concerns, such as tuberculosis. Hitherto, there has been no concrete cure for this disease, especially with the continuing emergence of drug resistant strains. In this study, CADD is employed for tuberculosis by first identifying a key enzyme in the mycobacterium’s metabolic pathway that would make a good drug target. One such potential target is the lipoate protein ligase B enzyme (LipB), which is a key enzyme in the M. tuberculosis metabolic pathway involved in the biosynthesis of the lipoic acid cofactor. Its expression is considerably up-regulated in patients with multi-drug resistant tuberculosis (MDR-TB) and it has no known back-up mechanism that can take over its function when inhibited, making it an extremely attractive target. Using cutting-edge computational methods, compounds from AnalytiCon Discovery Natural Derivatives database were screened and docked against the LipB enzyme in order to rank them based on their binding affinities. Compounds which have better binding affinities than LipB’s known inhibitor, decanoic acid, were subjected to in silico toxicity evaluation using the ADMET and TOPKAT protocols. Out of the 31,692 compounds in the database, 112 of these showed better binding energies than decanoic acid. Furthermore, 12 out of the 112 compounds showed highly promising ADMET and TOPKAT properties. Future studies involving in vitro or in vivo bioassays may be done to further confirm the therapeutic efficacy of these 12 compounds, which eventually may then lead to a novel class of anti-tuberculosis drugs.

Keywords: pharmacophore, molecular docking, lipoate protein ligase B (LipB), ADMET, TOPKAT

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Authors: M. A. Lahmer, K. Guergouri

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The ferromagnetic properties of carbon-doped ZnO (ZnO:CO) and hydrogenated carbon-doped ZnO (ZnO:CO+H) are investigated using the density functional tight binding (DFTB) method. Our results reveal that CO-doped ZnO is a ferromagnetic material with a magnetic moment of 1.3 μB per carbon atom. The presence of hydrogen in the material in the form of CO-H complex decreases the total magnetism of the material without suppressing ferromagnetism. However, the system in this case becomes quickly antiferromagnetic when the C-C separation distance was increased.

Keywords: ZnO, carbon, hydrogen, ferromagnetism, density functional tight binding

Procedia PDF Downloads 287

Authors: Chengliang Xie, Jinhyun Ryu, Hyun Joon Kim, Gyeong Jae Cho, Wan Sung Choi, Sang Soo Kang, Kye Man Cho, Dong Hoon Lee

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Obesity has become a global health problem and a source of major metabolic diseases like type-2 diabetes, hypertension, heart disease, nonalcoholic fatty liver and cancer. Synthetic anti-obesity drugs are effective but very costly and with undesirable side effects, so natural products such as soybean are needed as an alternative for obesity treatment. Lactobacillus Plantarum P1201is a probiotic bacterial strain reported to produce conjugated linoleic acid (CLA) and increase the ratio of aglycone-isoflavone of soybean, both of which have anti-obesity effect. In this study, the anti-obesity effect of the fermented soybean extract with P1201 (FSE) will be evaluated compared with that of the soybean extract (SE) by 3T3-L1 cells as an in vitro model of adipogenesis. 3T3-L1 cells were treated with SE and FSE during the nine days of the differentiation, lipid accumulation was evaluated by oil-red staining and triglyceride content and the mRNA expression level of adipogenic or lipogenic genes were analyzed by RT-PCR and qPCR. The results showed that formation of lipid droplets in differentiated 3T3-L1 cells was inhibited and triglyceride content was reduced by 23.1% after treated with 1000 μg/mL of FSE compared with control. For SE-treated groups, no delipidating effect was observed. The effect of FSE on adipogenesis inhibition can be attributed to the down-regulation of mRNA expressionof CCAAT/enhancer binding protein (C/EBP-α), lipoprotein lipase (LPL), adiponectin, adipocyte fatty acid-binding protein (aP2), fatty acid synthesis (FAS) and CoA carboxylase (ACC). Our results demonstrated that the anti-obesity effect of soybean can be improved by fermentation with P1201, and P1201can be used as a potential probiotic bacterial strain to produce natural anti-obesity food.

Keywords: fermentation, Lactobacillus plantarum P1201, obesity, soybean

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Authors: A. Nusrath Unissa, Sameer Hassan, Luke Elizabeth Hanna

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Altered drug binding may be an important factor in isoniazid (INH) resistance, rather than major changes in the enzyme’s activity as a catalase or peroxidase (KatG). The identification of structural or functional defects in the mutant KatGs responsible for INH resistance remains as an area to be explored. In this connection, the differences in the binding affinity between wild-type (WT) and mutants of KatG were investigated, through the generation of three mutants of KatG, Ser315Thr [S315T], Ser315Asn [S315N], Ser315Arg [S315R] and a WT [S315]) with the help of software-MODELLER. The mutants were docked with INH using the software-GOLD. The affinity is lower for WT than mutant, suggesting the tight binding of INH with the mutant protein compared to WT type. These models provide the in silico evidence for the binding interaction of KatG with INH and implicate the basis for rationalization of INH resistance in naturally occurring KatG mutant strains of Mycobacterium tuberculosis.

Keywords: Mycobacterium tuberculosis, KatG, INH resistance, mutants, modelling, docking

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Authors: Sameer N. Goyal, Chandragauda R. Patil

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Oleanolic acid (3/3-hydroxy-olea-12-en-28-oic acid) and its isomer, Ursolic acid (38-hydroxy-urs-12-en-28-oic acid) are triterpenoids compounds which exist widely in plant kingdom in the free acid form or as glycosidic triterpenoids saponins. The aim of the study is to evaluate intravenously administered oleanolic acid and ursolic acid in doxorubicin induced cardiotoxicity. Cardiotoxicity was induced in albino wistar rat with single intravenous injection of doxorubicin at dose of 67.75mg/kg i.v for 48 hrs at 12 hrs interval following doxorubicin administration in the same model cardioprotective effect of amifostine (90 mg/kg i.v, single dose prior 30 min before doxorubicin administration) was evaluated as standard treatment. Induction of cardiotoxicity was confirmed by rise in cardiac markers in serum such as CK–MB, LDH and also by electrocardiographically. The doxorubicin treated group significantly increased in QT interval, serum CK-MB, serum LDH, SGOT, SGPT and antioxidant parameter. Both the treatment group showed significant protective effect on Hemodynamic, electrocardiographic, biochemical, and antioxidant parameters. The oleanolic acid showed slight protective effect in histological lesions in doxorubicin induced cardiotoxicity. Hence, the results indicate that Oleanolic acid has more cardioprotective potential than ursolic acid against doxorubicin induced cardiotoxicity in rats.

Keywords: cardioprotection, doxorubicin, oleanolic acid, ursolic acid

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Authors: Mingchuan Zhou, Haitao Zhang, Hongfang Ma, Weiyong Ying

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Alumina supported platinum and tin catalysts with different loadings of Pt and Sn were prepared and characterized by low temperature N₂ adsorption/desorption, H₂-temperature programed reduction and CO pulse chemisorption. Pt and Sn below 1% loading were suitable for acetic acid hydrogenation. The best performance over 0.75Pt1Sn/Al₂O₃ can reach 87.55% conversion of acetic acid and 47.39% selectivity of ethanol. The operating conditions of acetic acid hydrogenation over 1Pt1Sn/Al₂O₃ were investigated. High reaction temperature can enhance the conversion of acetic acid, but it decreased total selectivity of ethanol and acetyl acetate. High pressure and low weight hourly space velocity were beneficial to both conversion of acetic acid and selectivity to ethanol.

Keywords: acetic acid, hydrogenation, operating condition, PtSn

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Authors: Dong Tran, Thanh Dac Van, Ly Le

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Hemagglutinin (HA) and Neuraminidase (NA) play an important role in host immune evasion across influenza virus evolution process. The correlation between HA and NA evolution in respect to epitopic evolution and drug interaction has yet to be investigated. In this study, combining of sequence to structure evolution and statistical analysis on epitopic/binding site specificity, we identified potential therapeutic features of HA and NA that show specific antibody binding site of HA and specific binding distribution within NA active site of current inhibitors. Our approach introduces the use of sequence variation and molecular interaction to provide an effective strategy in establishing experimental based distributed representations of protein-protein/ligand complexes. The most important advantage of our method is that it does not require complete dataset of complexes but rather directly inferring feature interaction from sequence variation and molecular interaction. Using correlated sequence analysis, we additionally identified co-evolved mutations associated with maintaining HA/NA structural and functional variability toward immunity and therapeutic treatment. Our investigation on the HA binding specificity revealed unique conserved stalk domain interacts with unique loop domain of universal antibodies (CR9114, CT149, CR8043, CR8020, F16v3, CR6261, F10). On the other hand, NA inhibitors (Oseltamivir, Zaninamivir, Laninamivir) showed specific conserved residue contribution and similar to that of NA substrate (sialic acid) which can be exploited for drug design. Our study provides an important insight into rational design and identification of novel therapeutics targeting universally recognized feature of influenza HA/NA.

Keywords: influenza virus, hemagglutinin (HA), neuraminidase (NA), sequence evolution

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Authors: Sibel Silici

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Palynological spectrum, proximate and fatty acids composition of eight beebread samples obtained from different geographical origins were determined. Beebread moisture contents varied between 11.4-15.9 %, ash 1.9-2.54 %, fat 5.9-11.5 %, and protein between 14.8-24.3 %. To our knowledge, this is the first study investigating fatty acids (FAs) composition of the selected monofloral beebreads. A total of thirty-seven FAs were identified. Of these (9Z, 12Z, 15Z)-octadeca-9, 12, 15-trienoic acid, (9Z, 12Z)-octadeca-9, 12-dienoic acid, hexadecanoic acid, (Z)-octadec-9-enoic acid, (Z)-icos-11-enoic acid and octadecanoic acid were the most abundant in all the samples. Cotton beebread contained the highest level of ω-3 FAs, 41.3 %. Unsaturated/saturated FAs ratios ranged between 1.38 and 2.39 indicating that beebread is a good source of unsaturated FAs. The pollen, proximate and FAs composition of beebread samples of different botanical and geographical origins varied significantly.

Keywords: bee bread, fatty acid composition, proximate composition, pollen analysis

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Authors: Rotchanaphan Hengaroonprasan, Malinee Sriariyanun, Prapakorn Tantayotai, Supacharee Roddecha, Kraipat Cheenkachorn

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Lignocellolusic material is a substance that is resistant to be degraded by microorganisms or hydrolysis enzymes. To be used as materials for biofuel production, it needs pretreatment process to improve efficiency of hydrolysis. In this work, chemical pretreatments on rice straw using three diluted organic acids, including acetic acid, citric acid, oxalic acid, were optimized. Using Response Surface Methodology (RSM), the effect of three pretreatment parameters, acid concentration, treatment time, and reaction temperature, on pretreatment efficiency were statistically evaluated. The results indicated that dilute oxalic acid pretreatment led to the highest enhancement of enzymatic saccharification by commercial cellulase and yielded sugar up to 10.67 mg/ml when using 5.04% oxalic acid at 137.11 oC for 30.01 min. Compared to other acid pretreatment by acetic acid, citric acid, and hydrochloric acid, the maximum sugar yields are 7.07, 6.30, and 8.53 mg/ml, respectively. Here, it was demonstrated that organic acids can be used for pretreatment of lignocellulosic materials to enhance of hydrolysis process, which could be integrated to other applications for various biorefinery processes.

Keywords: lignocellolusic biomass, pretreatment, organic acid response surface methodology, biorefinery

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Authors: A. A Warra, S. Fatima

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The experimental investigation revealed that the hexane extract of onion seed oil has acid value, iodine value, peroxide value, saponification value, relative density and refractive index of 0.03±0.01 mgKOH/g, 129.80±0.21 gI2/100g, 3.00± 0.00 meq H2O2 203.00±0.71 mgKOH/g, 0.82±0.01and 1.44±0.00 respectively. The percentage yield was 50.28±0.01%. The colour of the oil was light green. We restricted our GC-MS spectra interpretation to compounds identification, particularly fatty acids and they are identified as palmitic acid, linolelaidic acid, oleic acid, stearic acid, behenic acid, linolenic acid and eicosatetraenoic acid. The pH , foam ability (cm³), total fatty matter, total alkali and percentage chloride of the onion oil soap were 11.03± 0.02, 75.13±0.15 (cm³), 36.66 ± 0.02 %, 0.92 ± 0.02% and 0.53 ± 0.15 % respectively. The texture was soft and the colour was lighter green. The results indicated that the hexane extract of the onion seed oil has potential for cosmetic industries.

Keywords: onion seeds, soxhlet extraction, physicochemical, GC-MS, cold saponification

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Authors: Asmaa M. Fahim

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In this investigation, the (E)-2-cyano-3-(dimethylamino)-N-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)acrylam-ide (4) which used TAM as a template which interacts with Methacrylic Acid (MAA) monomer, in the presence of CH₃CN as progen. The TAM-MMA complex interactions are dependent on stable hydrogen bonding interaction between the carboxylic acid group of TAM(Template) and the hydroxyl group of MMA(methyl methacrylate) with minimal interference of porogen CH₃CN. The physical computational studies were used to optimize their structures and frequency calculations. The binding energies between TAM with different monomers showed the most stable molar ratio of 1:4, which was confirmed through experimental analysis. The optimized polymers were investigated in industrial applications.

Keywords: molecular imprinted polymer, computational studies, SEM, spectral analysis, industrial applications

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Authors: Chinmayee Choudhury

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Human Melanocortin 4 Receptor (HMC4R) is one of the most potential drug targets for the treatment of obesity which controls the appetite. A deletion of the residues 88-92 in HMC4R is sometimes the cause of severe obesity in the humans. In this study, two homology models are constructed for the normal as well as mutated HMC4Rs and some phytochemicals present in Green Tea, Honey and Cinnamon have been docked to them to study their differential binding to the normal and mutated HMC4R as compared to the natural agonist α- MSH. Two homology models have been constructed for the normal as well as mutated HMC4Rs using the Modeller9v7. Some of the phytochemicals present in Green Tea, Honey, and Cinnamon, which have appetite suppressant activities are constructed, minimized and docked to these normal and mutated HMC4R models using ArgusLab 4.0.1. The mode of binding of the phytochemicals with the Normal and Mutated HMC4Rs have been compared. Further, the mode of binding of these phytochemicals with that of the natural agonist α- Melanocyte Stimulating Hormone(α-MSH) to both normal and mutated HMC4Rs have also been studied. It is observed that the phytochemicals Kaempherol, Epigallocatechin-3-gallate (EGCG) present in Green Tea and Honey, Isorhamnetin, Chlorogenic acid, Chrysin, Galangin, Pinocambrin present in Honey, Cinnamaldehyde, Cinnamyl acetate and Cinnamyl alcohol present in Cinnamon have capacity to form more stable complexes with the Mutated HMC4R as compared to α- MSH. So they may be potential agonists of HMC4R to suppress the appetite.

Keywords: HMC4R, α-MSH, docking, photochemical, appetite suppressant, homology modelling

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Authors: Chand Pasha

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A Simple, accurate and precise spectrophotometric method for the quantitative analysis of determination of 5-aminosalicylic acid is described. This method is based on the reaction of 5-aminosalicylic acid with nitrite in acid medium to form diazonium ion, which is coupled with acetylacetone in basic medium to form azo dyes, which shows absorption maxima at 470 nm. The method obeys Beer’s law in the concentration range of 0.5-11.2 gml-1 of 5-aminosalicylic acid with acetylacetone. The molar absorptivity and Sandell’s sensitivity of 5-aminosalicylic acid -acetylacetone azo dye is 2.672 ×104 lmol-1cm-1, 5.731 × 10-3 gcm-2 respectively. The dye formed is stable for 10 hrs. The optimum reaction conditions and other analytical parameters are evaluated. Interference due to foreign organic compounds have been investigated. The method has been successfully applied to the determination of 5-aminosalicylic acid in pharmaceutical samples.

Keywords: spectrophotometry, diazotization, mesalazine, nitrite, acetylacetone

Procedia PDF Downloads 190

Authors: N. Wijayati, Kusoro Siadi, Hanny Wijaya, Maggy Thenawijjaja Suhartono

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This work describes the lipase-mediated synthesis of α-pinene oxide at ambient temperature. The immobilized lipase from Pseudomonas aeruginosa is used to generate peroxyoctanoic acid directly from octanoic acid and hydrogen peroxide. The peroxy acid formed is then applied for in situ oxidation of α-pinene. High conversion of α-pinene to α-pinene oxide (approximately 78%) was achieved when using 0,1 g enzim lipase, 6 mmol H2O2, dan 5 mmol octanoic acid. Various parameters affecting the conversion of α-pinene to α pinene oxide were studied.

Keywords: α-Pinene; P. aeruginosa; Octanoic acid

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Authors: P. Hari Prasad Reddy, C. H. Rama Vara Prasad, G. Kalyan Kumar

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This paper presents the morphological and mineralogical changes occurring in the soil due to immediate and prolonged interaction with different concentrations of phosphoric acid and sulphuric acid. In order to assess the effect of acid contamination, a series of sediment volume, scanning electron microscopy and X-ray diffraction analysis tests were carried out on soil samples were exposed to different concentrations (1N, 4N and 8N) of phosphoric and sulphuric acid. Experimental results show that both acids showed severe morphological and mineralogical changes with synthesis of neogenic formations mainly at higher concentrations (4N and 8N) and at prolonged duration of interaction (28 and 80 days).

Keywords: phosphoric acid, scanning electron microscopy, sulphuric acid, x-ray diffraction analysis

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Authors: Bakhtishod Matmuratov, Sakhiba Madraximova, Rakhmat Esanov, Alimjan Matchanov

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Studies have been performed to obtain complexes of glycyrrhizic acid and kinetins in a 2:1 ratio. The complex of glycyrrhizic acid and kinetins in a 2:1 ratio was considered evidence of the formation of a molecular complex by determining the molecular masses using chromato-mass spectroscopy and analyzing the IR spectra.

Keywords: monoammonium salt of glycyrrhizic acid, glycyrrhizic acid, supramolecular complex, isomolar series, IR spectroscopy

Procedia PDF Downloads 178

Authors: Edmaritz Hernandez-Pagan, Kanjana Laosuntisuk, Alex Harris, Allison Haynes, David Buitrago, Michael Kudenov, Colleen Doherty

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Rare Earth Elements (REEs) are critical metals for modern electronics, green technologies, and defense systems. However, due to their dispersed nature in the Earth’s crust, frequent co-occurrence with radioactive materials, and similar chemical properties, acquiring and purifying REEs is costly and environmentally damaging, restricting access to these metals. Plants could serve as resources for bioengineering REE mining systems. Although there is limited information on how REEs affect plants at a cellular and molecular level, plants with high REE tolerance and hyperaccumulation have been identified. This dissertation aims to develop a plant-based system for harvesting REEs from industrial waste material with a focus on Acid Mine Drainage (AMD), a toxic coal mining product. The objectives are 1) to develop a non-destructive, in vivo detection method for REE detection in Phytolacca plants (REE hyperaccumulator) plants utilizing fluorescence spectroscopy and with a primary focus on dysprosium, 2) to characterize the uptake of REE and Heavy Metals in Phytolacca americana and Phytolacca acinosa (REE hyperaccumulator) in AMD for potential implementation in the plant-based system, 3) to implement the REE detection method to identify REE-binding proteins and peptides for potential enhancement of uptake and selectivity for targeted REEs in the plants implemented in the plant-based system. The candidates are known REE-binding peptides or proteins, orthologs of known metal-binding proteins from REE hyperaccumulator plants, and novel proteins and peptides identified by comparative plant transcriptomics. Lanmodulin, a high-affinity REE-binding protein from methylotrophic bacteria, is used as a benchmark for the REE-protein binding fluorescence assays and expression in A. thaliana to test for changes in REE plant tolerance and uptake.

Keywords: phytomining, agromining, rare earth elements, pokeweed, phytolacca

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Authors: R. Chanajaree, D. Luanwiset, K. Pongpratea

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Dye removal is an environmental concern because the textile industries have been increasing by world population and industrialization. Adsorption is the technique to find adsorbents to remove dyes from wastewater. This method is low-cost and effective for dye removal. This work tries to develop effective adsorbents using the computational approach because it will be able to predict the possibility of the adsorbents for specific dyes in terms of binding free energies. The computational approach is faster and cheaper than the experimental approach in case of finding the best adsorbents. All starting structures of dyes and adsorbents are optimized by quantum calculation. The complexes between dyes and adsorbents are generated by the docking method. The obtained binding free energies from docking are compared to binding free energies from the experimental data. The calculated energies can be ranked as same as the experimental results. In addition, this work also shows the possible orientation of the complexes. This work used two experimental groups of the complexes of the dyes and adsorbents. In the first group, there are chitosan (adsorbent) and two dyes (reactive red (RR) and direct sun yellow (DY)). In the second group, there are poly(1,2-epoxy-3-phenoxy) propane (PEPP), which is the adsorbent, and 2 dyes of bromocresol green (BCG) and alizarin yellow (AY).

Keywords: dyes removal, binding free energies, quantum calculation, docking

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Authors: Fatih Özogul, Sezen Özçeli̇k, Yesim Özogul

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Lactic, acetic, succinic, propionic, formic and butyric acid production by lactic acid bacteria (LAB) were monitored in M17 broth (the control) and some fish (squid, shrimp, octopus, and eel) infusion broth by using HPLC method. There were significant differences in terms of lactic, acetic, succinic, propionic, formic and butyric acid production (p < 0.005) among bacterial strains. Acetic acid production was the lowest by LAB while succinic acid followed by propionic acid was synthesized at the highest levels. Lactic acid production ranged from 0 to 938 mg/L by all LAB strains in different infusion broth. The highest acetic acid production was found by Lb. acidophilus and Lb. delbrueckii subsp. lactic in octopus and shrimp infusion broth, with values of 872 and 674 mg/L, respectively while formic acid formation ranged from 1747 mg/L by Lb. acidophilus in octopus infusion broth to 69 mg/L by Lb. delbrueckii subsp. lactis in shrimp infusion broth. Propionic acid and butyric acid productions by St. thermophilus were 9852 and 3999 mg/L in shrimp infusion broth while Leu. mes. subsp. cremoris synthesized 312 and 9 mg/L of those organic acid in European squid infusion broth, respectively. Apparently, LAB strains had a great capability to generate succinic acid followed by propionic and butyric acid. In addition, other organic acid production differed significantly depending on bacterial strains and growth medium.

Keywords: Lactic acid bacteria , organic acid, HPLC analysis, growth medium

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Authors: Rawa Delshada, Sanaa G. Hamab, Rastee D. Koyeec

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Eighty patients with suspected ischemic heart disease were enrolled in the present study. They were classified into two groups: patients with positive exercise stress test results (n=40) and control group with negative exercise stress test results (n=40). Serum concentration of troponin I, Heart-type Fatty Acid Binding Protein (H-FABP) and Ischemia Modified Albumin (IMA) were measured one hour after performing stress test. Enzyme Linked Immunosorbent Assay was used to measure both troponin I, H-FABP levels, while IMA levels were measured by albumin cobalt binding test. There was no statistically significant difference in the mean concentration of troponin I between two groups (0.75±0.55ng/ml) for patients with positive test result vs. (0.71±0.55ng/ml) for negative test result group with P>0.05. Contrary to our expectation, mean IMA level was slightly higher among control group (70.88±39.76U/ml) compared to (62.7±51.9U/ml) in positive test result group, but still with no statistically significant difference (P>0.05). Median H-FABP level was also higher among negative exercise stress testing group compared the positive one (2ng/ml vs. 1.9ng/ml respectively), but failed to reach statistically significant difference (P>0.05). When quartiles model used to explore the possible association between each study biomarkers with the others; serum H-FABP level was lowest (1.7ng/ml) in highest quartile of IMA and lowest H-FABP (1.8ng/ml) in highest quartile of troponin I but with no statistically significant association (P>0.05). Myocardial ischemia, more likely occurred after exercise stress test, is not capable of causing troponin I release. Furthermore, an increase in H-FABP and IMA levels after stress test are not reflecting myocardial ischemia. Moreover, the combination of troponin I, H-FABP and IMA after measuring their post exercise levels does not improve the diagnostic utility of exercise stress test enormously.

Keywords: cardiac biomarkers, ischemic heart disease, troponin I, ischemia modified albumin, heart-type fatty acid binding protein, exercise stress testing

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Authors: Asif Mahmood, Shama Shama, Hao Ni, Hao Wang, Yu Ling, Hui Xu, Shixing Yang, Qais Ahmad Naseer, Wen Zhang

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Cardiovirus is a genus of viruses belonging to the family Picornaviridae. Here, we used viral metagenomic techniques to detect the viral nucleic acid in the fecal samples from wild rats in Zhenjiang city in China. Fecal samples were collected from 20 wild rats and pooled into four sample pools and then subjected to libraries construction which were then sequenced on Illumina MiSeq platform. The sequenced reads were analyzed using viral metagenomic analysis pipeline. A novel cardiovirus from feces of a wild rat was identified, named amzj-2018, of which the complete genome was acquired. Phylogenetic analysis based on the complete amino acid sequence of polyprotein revealed that amzj-2018 formed a separate branch located between clusters of Saffold virus and Rat Theilovirus 1 (RTV-1). Phylogenetic analysis based on different regions of the polyproteins, including P1, P2, P3, and P2+P3, respectively, showed discordant trees, where the tree based on P3 region indicated that amzj-2018 clustered separately between Theiler's murine encephalomyelitis virus and RTV-1. The complete genome of a cardiovirus was determined from the feces of wild rats which belonged to a novel type of cardiovirus based on phylogenetic analysis. Whether it is associated with disease needs further investigation.

Keywords: cardiovirus, viral metagenomics, genomic organization, phylogenetic analysis

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Authors: Taimur Khan, Zakirullah, Muhammad Shahab

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The SARS-CoV-2 variant BA.2.86 (Omicron) has emerged with unique mutations that may increase its transmission and infectivity. This study investigates how these mutations alter the Omicron receptor-binding domain's interaction network and dynamic properties (RBD) compared to the wild-type virus, focusing on its binding affinity to the human ACE2 (hACE2) receptor. Protein-protein docking and all-atom molecular dynamics simulations were used to analyze structural and dynamic differences. Despite the structural similarity to the wild-type virus, the Omicron variant exhibits a distinct interaction network involving new residues that enhance its binding capacity. The dynamic analysis reveals increased flexibility in the RBD, particularly in loop regions crucial for hACE2 interaction. Mutations significantly alter the secondary structure, leading to greater flexibility and conformational adaptability compared to the wild type. Binding free energy calculations confirm that the Omicron RBD has a higher binding affinity (-70.47 kcal/mol) to hACE2 than the wild-type RBD (-61.38 kcal/mol). These results suggest that the altered interaction network and enhanced dynamics of the Omicron variant contribute to its increased infectivity, providing insights for the development of targeted therapeutics and vaccines.

Keywords: SARS-CoV-2, molecular dynamic simulation, receptor binding domain, vaccine

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Authors: Ghazi Faisal Najmuldeen, Rosli Mohd Yunus, Nurfarahin Bt Harun, Mardhiana Binti Ismail

Abstract:

The microwave extraction has attracted great interest among the researchers. The main virtue of the microwave technique is cost-effective, time saving and simple handling procedure. Castor beans was chosen because of its high content in fatty acid, especially ricinoleic acid. The purpose of this research is to extract the castor oil by using the microwave assisted extraction (MAE) using ethanol as solvent and to investigate the influence of extraction time on castor oil yield and to characterize the main composition of the produced castor oil by using the GC-MS. It was found that there is a direct dependence between the oil yield and the time of extraction as it increases from 45% to 58% as the time increase from 10 min to 60 min. The major components of castor oil detected by GC-MS were ricinoleic acid, linoleic acid and oleic acid.

Keywords: microwave assisted extraction (MAE), castor oil, ricinoleic acid, linoleic acid

Procedia PDF Downloads 508

Authors: Hafiz Md. Hasan Babu, Khandaker Mohammad Mohi Uddin, Nitish Biswas, Sarreha Tasmin Rikta, Nuzmul Hossain Nahid

Abstract:

Nanomedicine and bioengineering use biological systems that can perform computing operations. In a biocomputational circuit, different types of biomolecules and DNA (Deoxyribose Nucleic Acid) are used as active components. DNA computing has the capability of performing parallel processing and a large storage capacity that makes it diverse from other computing systems. In most processors, the multiplier is treated as a core hardware block, and multiplication is one of the time-consuming and lengthy tasks. In this paper, cost-effective DNA multipliers are designed using algorithms of molecular DNA operations with respect to conventional ones. The speed and storage capacity of a DNA multiplier are also much higher than a traditional silicon-based multiplier.

Keywords: biological systems, DNA multiplier, large storage, parallel processing

Procedia PDF Downloads 218

Authors: Pui Shan Wong, Kosuke Tashiro, Satoru Kuhara, Sachiyo Aburatani

Abstract:

Functional genomics and gene regulation inference has readily expanded our knowledge and understanding of gene interactions with regards to expression regulation. With the advancement of transcriptome sequencing in time-series comes the ability to study the sequential changes of the transcriptome. This method presented here works to augment existing regulation networks accumulated in literature with transcriptome data gathered from time-series experiments to construct a sequential representation of transcription factor activity. This method is applied on a time-series RNA-Seq data set from Escherichia coli as it transitions from growth to stationary phase over five hours. Investigations are conducted on the various metabolic activities in gene regulation processes by taking advantage of the correlation between regulatory gene pairs to examine their activity on a dynamic network. Especially, the changes in metabolic activity during phase transition are analyzed with focus on the pagP gene as well as other associated transcription factors. The visualization of the sequential transcriptional activity is used to describe the change in metabolic pathway activity originating from the pagP transcription factor, phoP. The results show a shift from amino acid and nucleic acid metabolism, to energy metabolism during the transition to stationary phase in E. coli.

Keywords: Escherichia coli, gene regulation, network, time-series

Procedia PDF Downloads 373

Authors: Y. Ruchi, A. Prerna, S. Deepshikha

Abstract:

Amyotrophic lateral sclerosis (ALS), also known as “Lou Gehrig’s disease”. It is a neurodegenerative disease associated with degeneration of motor neurons in the cerebral cortex, brain stem, and spinal cord characterized by distal muscle weakness, atrophy, normal sensation, pyramidal signs and progressive muscular paralysis reflecting. ALS2 is a juvenile autosomal recessive disorder, slowly progressive, that maps to chromosome 2q33 and is associated with mutations in the alsin gene, a putative GTPase regulator. In this paper we have done homology modeling of alsin2 protein using multiple templates (3KCI_A, 4LIM_A, 402W_A, 4D9S_A, and 4DNV_A) designed using the Prime program in Schrödinger software. Further modeled structure is used to identify effective binding sites on the basis of structural and physical properties using sitemap program in Schrödinger software, structural and function analysis is done by using Prosite and ExPASy server that gives insight into conserved domains and motifs that can be used for protein classification. This paper summarizes the structural, functional and binding site property of alsin2 protein. These binding sites can be potential drug target sites and can be used for docking studies.

Keywords: ALS, binding site, homology modeling, neuronal degeneration

Procedia PDF Downloads 390

Authors: Sumeyra Sevim, Gulsum Gizem Topal, Mercan Merve Tengilimoglu-Metin, Banu Sancak, Mevlude Kizil

Abstract:

Aflatoxin M1 (AFM1) represents mutagenic, carcinogenic, hepatotoxic and immunosuppressive properties, and shows adverse effect on human health. Recently the use of probiotics are focused on AFM1 detoxification because of the fact that probiotic strains have a binding ability to AFM1. Moreover, inulin is a prebiotic to improve the ability of probiotic bacteria. Therefore, the aim of the study is to investigate the effect of inulin on AFM1 binding ability of some probiotic bacteria. Yoghurt samples were manufactured by using skim milk powder artificially contaminated with AFM1 at concentration 100 pg/ml. Different samples were prepared for the study as: first sample consists of yoghurt starter bacteria (L. bulgaricus and S. thermophilus), the second sample consists of starter and L. plantarum, starter and B. bifidum ATCC were added to the third sample, starter and B. animalis ATCC 27672 were added to the forth sample, and the fifth sample is a binary culture consisted of starter and B. bifidum and B. animalis. Moreover, the same work groups were prepared with inulin (4%). The samples were incubated at 42°C for 4 hours, then stored for three different time interval (1,5 and 10 days). The toxin was measured by the ELISA. When inulin was added to work groups, there was significant change on AFM1 binding ability at least one sample in all groups except the one with L. plantarum (p<0.05). The highest levels of AFM1 binding ability (68.7%) in samples with inulin were found in the group which B. bifidum was added, whereas the lowest levels of AFM1 binding ability (44.4%) in samples with inulin was found in the fifth sample. The most impressive effect of inulin was found on B.bifidum. In this study, it was obtained that there was a significant effect of storage on AFM1 binding ability in the all groups with inulin except the one with L. plantarum (p<0.05). Consequently, results show that AFM1 detoxification by probiotics have a potential application to reduce toxin concentrations in yoghurt. Besides, inulin has different effects on AFM1 binding ability of each probiotic bacteria strain.

Keywords: aflatoxin M1, inulin, probiotics, storage

Procedia PDF Downloads 317