Search results for: DNA binding profile

Authors: Agnieszka Krzemińska, Katarzyna Świderek, Vicente Molinier, Piotr Paneth

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In order to understand in details the interactions between ligands and the enzyme isotope effects were studied between clinically used drugs that bind in the active site of Human Immunodeficiency Virus Reverse Transcriptase, HIV-1 RT, as well as triazole-based inhibitor that binds in the allosteric pocket of this enzyme. The magnitudes and origins of the resulting binding isotope effects were analyzed. Subsequently, binding isotope effect of the same triazole-based inhibitor bound in the active site were analyzed and compared. Together, these results show differences in binding origins in two sites of the enzyme and allow to analyze binding mode and place of newly synthesized inhibitors. Typical protocol is described below on the example of triazole ligand in the allosteric pocket. Triazole was docked into allosteric cavity of HIV-1 RT with Glide using extra-precision mode as implemented in Schroedinger software. The structure of HIV-1 RT was obtained from Protein Data Bank as structure of PDB ID 2RKI. The pKa for titratable amino acids was calculated using PROPKA software, and in order to neutralize the system 15 Cl- were added using tLEaP package implemented in AMBERTools ver.1.5. Also N-terminals and C-terminals were build using tLEaP. The system was placed in 144x160x144Å3 orthorhombic box of water molecules using NAMD program. Missing parameters for triazole were obtained at the AM1 level using Antechamber software implemented in AMBERTools. The energy minimizations were carried out by means of a conjugate gradient algorithm using NAMD. Then system was heated from 0 to 300 K with temperature increment 0.001 K. Subsequently 2 ns Langevin−Verlet (NVT) MM MD simulation with AMBER force field implemented in NAMD was carried out. Periodic Boundary Conditions and cut-offs for the nonbonding interactions, range radius from 14.5 to 16 Å, are used. After 2 ns relaxation 200 ps of QM/MM MD at 300 K were simulated. The triazole was treated quantum mechanically at the AM1 level, protein was described using AMBER and water molecules were described using TIP3P, as implemented in fDynamo library. Molecules 20 Å apart from the triazole were kept frozen, with cut-offs established on range radius from 14.5 to 16 Å. In order to describe interactions between triazole and RT free energy of binding using Free Energy Perturbation method was done. The change in frequencies from ligand in solution to ligand bounded in enzyme was used to calculate binding isotope effects.

Keywords: binding isotope effects, molecular dynamics, HIV, reverse transcriptase

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Authors: Bright Chukwunwike Uzuegbunam, Wojciech Paslawski, Hans Agren, Christer Halldin, Wolfgang Weber, Markus Luster, Thomas Arzberger, Behrooz Hooshyar Yousefi

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There is a need to develop a PET tracer that will enable to diagnosis and track the progression of Alpha-synucleinopathies (Parkinson’s disease [PD], dementia with Lewy bodies [DLB], multiple system atrophy [MSA]) in living subjects over time. Alpha-synuclein aggregates (a-syn), which are present in all the stages of disease progression, for instance, in PD, are a suitable target for in vivo PET imaging. For this reason, we have developed some promising a-syn tracers based on a disarylbisthiazole (DABTA) scaffold. The precursors are synthesized via a modified Hantzsch thiazole synthesis. The precursors were then radiolabeled via one- or two-step radiofluorination methods. The ligands were initially screened using a combination of molecular dynamics and quantum/molecular mechanics approaches in order to calculate the binding affinity to a-syn (in silico binding experiments). Experimental in vitro binding assays were also performed. The ligands were further screened in other experiments such as log D, in vitro plasma protein binding & plasma stability, biodistribution & brain metabolite analyses in healthy mice. Radiochemical yields were up to 30% - 72% in some cases. Molecular docking revealed possible binding sites in a-syn and also the free energy of binding to those sites (-28.9 - -66.9 kcal/mol), which correlated to the high binding affinity of the DABTAs to a-syn (Ki as low as 0.5 nM) and selectivity (> 100-fold) over Aβ and tau, which usually co-exist with a-synin some pathologies. The log D values range from 2.88 - 2.34, which correlated with free-protein fraction of 0.28% - 0.5%. Biodistribution experiments revealed that the tracers are taken up (5.6 %ID/g - 7.3 %ID/g) in the brain at 5 min (post-injection) p.i., and cleared out (values as low as 0.39 %ID/g were obtained at 120 min p.i. Analyses of the mice brain 20 min p.i. Revealed almost no radiometabolites in the brain in most cases. It can be concluded that in silico study presents a new venue for the rational development of radioligands with suitable features. The results obtained so far are promising and encourage us to further validate the DABTAs in autoradiography, immunohistochemistry, and in vivo imaging in non-human primates and humans.

Keywords: alpha-synuclein aggregates, alpha-synucleinopathies, PET imaging, tracer development

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Authors: Usha Kiran, M. Z. Abdin

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Osmotin is an abundant cationic multifunctional protein discovered in cells of tobacco (Nicotiana tabacum L. var Wisconsin 38) adapted to an environment of low osmotic potential. It provides plants protection from pathogens, hence placed in the PRP family of proteins. The osmotin induced proline accumulation has been reported in plants including transgenic tomato and strawberry conferring tolerance against both biotic and abiotic stresses. The exact mechanism of induction of proline by osmotin is however, not known till date. These observations have led us to hypothesize that osmotin induced proline accumulation could be due to its involvement as transcription factor and/or cell signal pathway modulator in proline biosynthesis. The present investigation was therefore, undertaken to analyze the osmotin protein as transcription factor /cell signalling modulator using bioinformatics tools. The results of available online DNA binding motif search programs revealed that osmotin does not contain DNA-binding motifs. The alignment results of osmotin protein with the protein sequence from DATF showed the homology in the range of 0-20%, suggesting that it might not contain a DNA binding motif. Further to find unique DNA-binding domain, the superimposition of osmotin 3D structure on modeled Arabidopsis transcription factors using Chimera also suggested absence of the same. We, however, found evidence implicating osmotin in cell signaling. With these results, we concluded that osmotin is not a transcription factor but regulating proline biosynthesis and accumulation through cell signaling during abiotic stresses.

Keywords: osmotin, cell signaling modulator, bioinformatic tools, protein

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Authors: Monika Kallubai, Shreya Dubey, Rajagopal Subramanyam

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Our study is all about the biological interactions of synthesized 5β-dihydrocortisol (Dhc) and 5β-dihydrocortisol acetate (DhcA) molecules with carrier protein Human Serum Albumin (HSA). The cytotoxic study was performed on breast cancer cell line (MCF-7) normal human embryonic kidney cell line (HEK293), the IC50 values for MCF-7 cells were 28 and 25 µM, respectively, whereas no toxicity in terms of cell viability was observed with HEK293 cell line. The further experiment proved that Dhc and DhcA induced 35.6% and 37.7% early apoptotic cells and 2.5%, 2.9% late apoptotic cells respectively. Morphological observation of cell death through TUNEL assay revealed that Dhc and DhcA induced apoptosis in MCF-7 cells. The complexes of HSA–Dhc and HSA–DhcA were observed as static quenching, and the binding constants (K) was 4.7±0.03×104 M-1 and 3.9±0.05×104 M-1, and their binding free energies were found to be -6.4 and -6.16 kcal/mol, respectively. The displacement studies confirmed that lidocaine 1.4±0.05×104 M-1 replaced Dhc, and phenylbutazone 1.5±0.05×104 M-1 replaced by DhcA, which explains domain I and domain II are the binding sites for Dhc and DhcA. Further, CD results revealed that the secondary structure of HSA was altered in the presence of Dhc and DhcA. Furthermore, the atomic force microscopy and transmission electron microscopy showed that the dimensions like height and molecular sizes of the HSA–Dhc and HSA–DhcA complex were larger compared to HSA alone. Detailed analysis through molecular dynamics simulations also supported the greater stability of HSA–Dhc and HSA–DhcA complexes, and root-mean-square-fluctuation interpreted the binding site of Dhc as domain IB and domain IIA for DhcA. This information is valuable for the further development of steroid derivatives with improved pharmacological significance as novel anti-cancer drugs.

Keywords: apoptosis, dihydrocortisol, fluorescence quenching, protein conformations

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Authors: Veruska C. Dutra, Mary L. G. S. Senna, Felipe S. Spindler

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The State Park Jalapao - PEJ proved to be one of the protected areas that has attracted tourists from all over the world with its unique scenic landscapes. Although the region already has a considerable tourist flow, to our knowledge there is a lack of continuity of studies in the region capable of drawing a plan of activities, such as the profile of the tourist and analysis of their experiences in the region, carried out from 2006-2007. Therefore, this study was proposed to know the profile and experiences of tourists visiting the park today, making a connection with the earlier study, in order to generate subsidies to trace improvement actions. We conducted interviews with tourists in the main tourism season 2015. The results show that after eight years of carrying out the first study, there were no changes, highlighting the lack of a tourism plan for the park.

Keywords: Jalapao, profile tourist, level, satisfaction

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Authors: Hao Wang, Shengchun Wang, Weidong Wang

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On the influence of train vibration and environmental noise on the measurement of track wear, we proposed a method for automatic extraction of circular arc on the inner or outer side of the rail waist and achieved the high-precision registration of rail profile. Firstly, a polynomial fitting method based on truncated residual histogram was proposed to find the optimal fitting curve of the profile and reduce the influence of noise on profile curve fitting. Then, based on the curvature distribution characteristics of the fitting curve, the interval search algorithm based on dynamic window’s maximum curvature entropy was proposed to realize the automatic segmentation of small circular arc. At last, we fit two circle centers as matching reference points based on small circular arcs on both sides and realized the alignment from the measured profile to the standard designed profile. The static experimental results show that the mean and standard deviation of the method are controlled within 0.01mm with small measurement errors and high repeatability. The dynamic test also verified the repeatability of the method in the train-running environment, and the dynamic measurement deviation of rail wear is within 0.2mm with high repeatability.

Keywords: curvature entropy, profile registration, rail wear, structured light, train-running

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Authors: A. I. O. Zaid

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Deep drawing is considered to be the most widely used sheet metal forming processes among the particularly in automobile and aircraft industries. It is widely used for manufacturing a large number of the body and spare parts. In its simplest form it may be defined as a secondary forming process by which a sheet metal is formed into a cylinder or alike by subjecting the sheet to compressive force through a punch with a flat end of the same geometry as the required shape of the cylinder end while it is held by a blank holder which hinders its movement but does not stop it. The punch and die profile radii play In this paper, the effects of punch and die profile radii on the autographic record, the minimum thickness strain location where the cracks normally start and cause the fracture, the maximum deep drawing force and the total consumed work in the drawing flat ended cylindrical brass cups are investigated. Five punches and five dies each having different profile radii were manufactured for this investigation. Furthermore, their effect on the quality of the drawn cups is also presented and discussed. It was found that the die profile radius has more effect on the maximum drawing force and the total consumed work than the punch profile radius.

Keywords: punch and die profile radii, deep drawing process, maximum drawing force, total consumed work, quality of produced parts, flat ended cylindrical brass cups

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Authors: D. Bhowmik, Y. Tian, Q. Yin, F. Zhu

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Cyclic GMP-AMP synthase (cGAS), recognises cytoplasmic double-stranded DNA (dsDNA), indicative of bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. Viruses also have developed numerous strategies to antagonize the cGAS-STING pathway. Kaposi's sarcoma-associated herpesvirus (KSHV) is a human DNA tumor virus that is the causative agent of Kaposi’s sarcoma and several other malignancies. To persist in the host, consequently causing diseases, KSHV must overcome the host innate immune responses, including the cGAS-STING DNA sensing pathway. We already found that ORF52 or KicGAS (KSHV inhibitor of cGAS), an abundant and basic gamma herpesvirus-conserved tegument protein, directly inhibits cGAS enzymatic activity. To better understand the mechanism, we have performed the biochemical and structural characterization of full-length KicGAS and various mutants in regarding binding to DNA. We observed that KicGAS is capable of self-association and identified the critical residues involved in the oligomerization process. We also characterized the DNA-binding of KicGAS and found that KicGAS cooperatively oligomerizes along the length of the double stranded DNA, the highly conserved basic residues at the c-terminal disordered region are crucial for DNA recognition. Deficiency in oligomerization also affects DNA binding. Thus DNA binding by KicGAS sequesters DNA and prevents it from being detected by cGAS, consequently inhibiting cGAS activation. KicGAS homologues also inhibit cGAS efficiently, suggesting inhibition of cGAS is evolutionarily conserved mechanism among gamma herpesvirus. These results highlight the important viral strategy to evade this innate immune sensor.

Keywords: Kaposi's sarcoma-associated herpesvirus, KSHV, cGAS, DNA binding, inhibition

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Authors: Bin Liu

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As one of the most important tasks in protein sequence analysis, protein remote homology detection has been studied for decades. Currently, the profile-based methods show state-of-the-art performance. Position-Specific Frequency Matrix (PSFM) is widely used profile. However, there exists noise information in the profiles introduced by the amino acids with low frequencies. In this study, we propose a method to remove the noise information in the PSFM by removing the amino acids with low frequencies called Top frequency profile (TFP). Three new matrix transformation methods, including Autocross covariance (ACC) transformation, Tri-gram, and K-separated bigram (KSB), are performed on these profiles to convert them into fixed length feature vectors. Combined with Support Vector Machines (SVMs), the predictors are constructed. Evaluated on two benchmark datasets, and experimental results show that these proposed methods outperform other state-of-the-art predictors.

Keywords: protein remote homology detection, protein fold recognition, top frequency profile, support vector machines

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Authors: Krishnamoorthy Shanmugaraj, Malaichamy Ilanchelian

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Ascorbic acid is an essential component in the diet of humans, and also is a typical long used pharmaceutical agent. In the present contribution, we have carried out a detailed study on the binding interaction of ascorbic acid (AA) with bovine hemoglobin (BHb) using steady state emission, time resolved fluorescence, UV-Vis absorption, circular dichroism (CD), Fourier transform infra-red (FT-IR) and three dimensional emission (3D) spectral studies. The results from the emission spectral studies unveiled that the quenching of BHb emission by AA is attributed to the formation of a complex in the ground state (static in nature) after correcting for inner filter effect. The binding parameters calculated from corrected emission quenching data revealed that BHb exhibited a significant binding affinity towards AA. Moreover, AA induced tertiary and secondary conformational changes of BHb were monitored by UV-Vis absorption, CD, FT-IR and 3D emission spectral studies. The results presented here will help to further understand the credible mechanism of BHb-AA system which is expected to provide insights into conformational and microenvironmental changes of BHb.

Keywords: ascorbic acid, bovine hemoglobin, circular dichroism, three dimensional emission spectral studies

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Authors: Fouzia Perveen, Rumana Qureshi

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The presently studied twelve anticancer drugs are the cytotoxic agents which inhibit the replication of DNA and activity of enzymes involved in DNA replication namely topoisomerase-II, polymerase and helicase and have shown remarkable anticancer activity in clinical trials. In this study, we performed molecular docking studies of twelve antitumor drugs against DNA and DNA enzymes in the presence and absence of ascorbic acid (AA) and developed the quantitative structure-activity relationship (QSAR) model for anticancer activity screening. A number of electronic and steric descriptors were calculated using MOE software package. QSAR was established showing a correlation of binding strength with various physicochemical descriptors. Out of these twelve, eight cytotoxic drugs were tested on Non-Small Cell Lung Cancer cell lines (H-157 and H-1299) in the absence and presence of ascorbic acid and experimental IC50 values were calculated. From the docking studies, binding constants were calculated indicating the strength of drug-DNA and drug-enzyme complex formation and it was correlated to the IC50 values (both experimental and theoretical). These results can offer useful references for directing the molecular design of DNA enzyme inhibitor with improved anticancer activity.

Keywords: ascorbic acid, binding constant, cytotoxic agents, cell culture, DNA, DNA enzymes, molecular docking

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Authors: Mahesh Gupta

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The main goal in the design of a die for extrusion of a complex profile is to obtain a uniform velocity at the die exit. If the velocity at the exit of an extrusion die is not uniform, the shape of the extrudate profile can change significantly after the polymer exits the die. To rectify the extrudate distortion caused by non-uniform exit velocity, calibrators and sizers are often installed along the extrudate cooling system. Furthermore, the profile shape in calibrators and sizers is sometimes gradually changed to intentionally deform the extrudate to the required final product shape. This is exploited to simplify extrusion die design, because a relatively simple profile at the die exit can be modified to obtain a more complex profile by deforming it in calibrators or sizers. The gradual change in the shape of calibrator or sizer profiles can also be used to extrude slightly different profiles from the same die. In the present work, a combined flow, thermal and structural analysis is used to accurately predict distortion of extrudate profile after the polymer leaves a die. Simulations of the flow and extrudate deformation in two different bilayer coextrusion dies with gradually changing profile shape in successive calibrators and sizers will be presented. The effect of non-uniform exit velocity, cooling shrinkage and shape of sizer profiles on extrudate deformation is included in the simulation. The predicted extrudate shape and layer structure is found to match accurately with those in a coextruded product.

Keywords: coextrusion, extrusion die design, finite element method, polymers

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Authors: Khandoker Akib Mohammad

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While analyzing time-to-event data, it is possible that a certain fraction of subjects will never experience the event of interest, and they are said to be cured. When this feature of survival models is taken into account, the models are commonly referred to as cure models. In the presence of covariates, the conditional survival function of the population can be modelled by using the cure model, which depends on the probability of being uncured (incidence) and the conditional survival function of the uncured subjects (latency), and a combination of logistic regression and Cox proportional hazards (PH) regression is used to model the incidence and latency respectively. In this paper, we have shown the asymptotic normality of the profile likelihood estimator via asymptotic expansion of the profile likelihood and obtain the explicit form of the variance estimator with an implicit function in the profile likelihood. We have also shown the efficient score function based on projection theory and the profile likelihood score function are equal. Our contribution in this paper is that we have expressed the efficient information matrix as the variance of the profile likelihood score function. A simulation study suggests that the estimated standard errors from bootstrap samples (SMCURE package) and the profile likelihood score function (our approach) are providing similar and comparable results. The numerical result of our proposed method is also shown by using the melanoma data from SMCURE R-package, and we compare the results with the output obtained from the SMCURE package.

Keywords: Cox PH model, cure model, efficient score function, EM algorithm, implicit function, profile likelihood

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Authors: Milica Karadzic, Lidija Jevric, Sanja Podunavac-Kuzmanovic, Strahinja Kovacevic, Sinisa Markov, Aleksandar Okljesa, Andrea Nikolic, Marija Sakac, Katarina Penov Gasi

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This study considered the microbiological activity determination and molecular docking study for selected steroid derivatives of biomedical importance. Minimal inhibitory concentration (MIC) was determined for steroid derivatives against Staphylococcus aureus using macrodilution method. Some of the investigated steroid derivatives express bacteriostatic effect against Staphylococcus aureus. Molecular docking approaches are the most widely used techniques for predicting the binding mode of a ligand. Molecular docking study was done for steroid derivatives for androgen receptor negative prostate cancer cell line (PC-3) toward Human Cytochrome P450 CYP17A1. The molecules that had the smallest experimental IC50 values confirmed their ability to dock into active place using suitable molecular docking procedure. The binding disposition of those molecules was thoroughly investigated. Microbiological analysis and molecular docking study were conducted with aim to additionally characterize selected steroid derivatives for future investigation regarding their biological activity and to estimate the binding-affinities of investigated derivatives. This article is based upon work from COST Action (TD1305), supported by COST (European Cooperation and Science and Technology).

Keywords: binding affinity, minimal inhibitory concentration, molecular docking, pc-3 cell line, staphylococcus aureus, steroids

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Authors: Ruqaiya Khalil, Saman Usmani, Zaheer Ul-Haq

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The accurate characterization of ligand binding affinity is indispensable for designing molecules with optimized binding affinity. Computational tools help in many directions to predict quantitative correlations between protein-ligand structure and their binding affinities. Molecular dynamics (MD) simulation is a modern state-of-the-art technique to evaluate the underlying basis of ligand-protein interactions by characterizing dynamic and energetic properties during the event. Autoimmune diseases arise from an abnormal immune response of the body against own tissues. The current regimen for the described condition is limited to immune-modulators having compromised pharmacodynamics and pharmacokinetics profiles. One of the key player mediating immunity and tolerance, thus invoking autoimmunity is Interleukin-2; a cytokine influencing the growth of T cells. Molecular dynamics simulation techniques are applied to seek insight into the inhibitory mechanisms of newly synthesized compounds that manifested immunosuppressant potentials during in silico pipeline. In addition to estimation of free energies associated with ligand binding, MD simulation yielded us a great deal of information about ligand-macromolecule interactions to evaluate the pattern of interactions and the molecular basis of inhibition. The present study is a continuum of our efforts to identify interleukin-2 inhibitors of both natural and synthetic origin. Herein, we report molecular dynamics simulation studies of Interluekin-2 complexed with different antagonists previously reported by our group. The study of protein-ligand dynamics enabled us to gain a better understanding of the contribution of different active site residues in ligand binding. The results of the study will be used as the guide to rationalize the fragment based synthesis of drug-like interleukin-2 inhibitors as immune-modulators.

Keywords: immuno-modulators, MD simulation, protein-ligand interaction, structure-based drug design

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Authors: S. M. Dash, K. B. Lua, T. T. Lim

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This paper presents results of numerical and experimental studies on a two-dimensional (2D) flapping elliptic airfoil in a forward flight condition at Reynolds number of 5000. The study is motivated from an earlier investigation which shows that the deterioration in thrust performance of a sinusoidal heaving and pitching 2D (NACA0012) airfoil at high flapping frequency can be recovered by changing the effective angle of attack profile to square wave, sawtooth, or cosine wave shape. To better understand why such modifications lead to superior thrust performance, we take a closer look at the transient aerodynamic force behavior of an airfoil when the effective angle of attack profile changes gradually from a generic smooth trapezoidal profile to a sinusoid shape by modifying the base length of the trapezoid. The choice of using a smooth trapezoidal profile is to avoid the infinite acceleration condition encountered in the square wave profile. Our results show that the enhancement in the time-averaged thrust performance at high flapping frequency can be attributed to the delay and reduction in the drag producing valley region in the transient thrust force coefficient when the effective angle of attack profile changes from sinusoidal to trapezoidal.

Keywords: two-dimensional flapping airfoil, thrust performance, effective angle of attack, CFD, experiments

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Authors: Mohsen Salesi, Seyyed Zoheir Rabei

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Exercise has been considered a cornerstone of diabetes prevention and treatment for decades, but the benefits of resistance training are less clear. The purpose of this study was to determine the impact of resistance training on blood profile and inflammatory marker (CRP) of type 2 diabetes mellitus people. Thirty diabetic male were recruited (age: 50.34±10.28 years) and randomly assigned to 8 weeks resistance exercise training (n=15) and control groups (n=15). Before and after training blood pressure, weight, lipid profile (TC, TG, LDL-c, and HDL-c) and hs-CRP were measured. The resistance exercise training group took part in supervised 50–80 minutes resistance training sessions, three days a week on non-consecutive days for 8 weeks. Each exercise session included approximately 10 min of warm-up and cool-down periods. Results showed that TG significantly decreased (pre 210.19±9.31 vs. 101.12±7.25, p=0.03) and HDL-c significantly increased (pre 42.37±3.15 vs. 47.50±2.19, p=0.01) after exercise training. However, there was no difference between groups in TC, LDL-c, BMI and weight. In addition, a decrease in fasting blood glucose levels showed significant difference between groups (pre 144.65±5.73 vs. 124.21±6.48 p=0.04). Regular resistance exercise training can improve the lipid profile and reducing the cardiovascular risk factors in T2DM patients.

Keywords: lipid profile, resistance exercise, type 2 diabetes mellitus, men

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Authors: Shahnaz Ashrafpour, Tahereh Tohidi Moghadam, Bijan Ranjbar

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Identifying the nature of protein-nanoparticle interactions and favored binding sites is an important issue in functional characterization of biomolecules and their physiological responses. Herein, interaction of silver nanoparticles with lysozyme as a model protein has been monitored via fluorescence spectroscopy. Formation of complex between the biomolecule and silver nanoparticles (AgNPs) induced a steady state reduction in the fluorescence intensity of protein at different concentrations of nanoparticles. Tryptophan fluorescence quenching spectra suggested that silver nanoparticles act as a foreign quencher, approaching the protein via this residue. Analysis of the Stern-Volmer plot showed quenching constant of 3.73 µM−1. Moreover, a single binding site in lysozyme is suggested to play role during interaction with AgNPs, having low affinity of binding compared to gold nanoparticles. Unfolding studies of lysozyme showed that complex of lysozyme-AgNPs has not undergone structural perturbations compared to the bare protein. Results of this effort will pave the way for utilization of sensitive spectroscopic techniques for rational design of nanobiomaterials in biomedical applications.

Keywords: nanocarrier, nanoparticles, surface plasmon resonance, quenching fluorescence

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Authors: Matza Gusto Andika, Malinda Sabrina, Syarie Fatunnisa

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Aerodynamic and aeroelastics studies on the hanger bridge profile are important to analyze the aerodynamic phenomenon and Aeroelastics stability of hanger. Wind tunnel tests were conducted on a model of H-beam profile from hanger bridge. The purpose of this study is to investigate steady aerodynamic characteristics such as lift coefficient (Cl), drag coefficient (Cd), and moment coefficient (Cm) under the different angle of attack for preliminary prediction of aeroelastics stability problems. After investigation the steady aerodynamics characteristics from the model, dynamic testing is also conducted in wind tunnel to know the aeroelastics phenomenon which occurs at the H-beam hanger bridge profile. The studies show that the torsional vortex induced vibration occur when the wind speed is 7.32 m/s until 9.19 m/s with maximum amplitude occur when the wind speed is 8.41 m/s. The result of wind tunnel testing is matching to hanger vibration where occur in the field, so wind tunnel studies has successful to model the problem. In order that the H-beam profile is not good enough for the hanger bridge and need to be modified to minimize the Aeroelastics problem. The modification can be done with structure dynamics modification or aerodynamics modification.

Keywords: aerodynamics, aeroelastic, hanger bridge, h-beam profile, vortex induced vibration, wind tunnel

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Authors: Joanna Dzieńdziora

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Lobbying is an instrument of influence in various decision-making processes. It is also the underestimated issue as a research problem. The lack of research on the modern lobbyist competencies is the most crucial element. The paper presents attempts of finding answers to the following questions: Who should run the lobbying activity? What competencies should a lobbyist possess in order to implement lobbying activities effectively? Searching for answers for the mentioned above questions requires positioning the opportunity to change the image of lobbying in the area of competencies of entities that provide lobbying activities. The aim of the paper is presenting the lobbyist competencies profile in the framework of his professional role. The essence of lobbying activity and its significance in the modern economy as well as areas, the scope of lobbying activities, diagnosis of a modern lobbyist’s competences, lobbyist’s competencies profile that is focused on the professionalization of the lobbying activity, will have been presented in this paper. Indicated research tasks let emerge lobbyist’s competencies in the way that allows identifying and elaborating the lobbyist competencies profile. The profile lets improve lobbying activities. Its elaboration is based on the author’s research results analysis. Taking into consideration the shortages within the theory and research on the lobbying activity, the implementation of this research enables to fill the cognitive gap existing in the theory of management sciences.

Keywords: competencies, competencies profile, lobbying, lobbyist

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Authors: Praveen Kumar, Satish Kumar, Jashanpreet Singh

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Transportation of unrefined crude oil from the production unit to a refinery or large storage area by a pipeline is difficult due to the different properties of crude in various areas. Thus, the design of a crude oil pipeline is a very complex and time consuming process, when considering all the various parameters. There were three very important parameters that play a significant role in the transportation and processing pipeline design; these are: viscosity profile, temperature profile and the velocity profile of waxy crude oil through the crude oil pipeline. Knowledge of the Rheological computational technique is required for better understanding the flow behavior and predicting the flow profile in a crude oil pipeline. From these profile parameters, the material and the emulsion that is best suited for crude oil transportation can be predicted. Rheological computational fluid dynamic technique is a fast method used for designing flow profile in a crude oil pipeline with the help of computational fluid dynamics and rheological modeling. With this technique, the effect of fluid properties including shear rate range with temperature variation, degree of viscosity, elastic modulus and viscous modulus was evaluated under different conditions in a transport pipeline. In this paper, two crude oil samples was used, as well as a prepared emulsion with natural and synthetic additives, at different concentrations ranging from 1,000 ppm to 3,000 ppm. The rheological properties was then evaluated at a temperature range of 25 to 60 °C and which additive was best suited for transportation of crude oil is determined. Commercial computational fluid dynamics (CFD) has been used to generate the flow, velocity and viscosity profile of the emulsions for flow behavior analysis in crude oil transportation pipeline. This rheological CFD design can be further applied in developing designs of pipeline in the future.

Keywords: surfactant, natural, crude oil, rheology, CFD, viscosity

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Authors: Laila H. Abdel-Rahman, Mohamed Shaker S. Adam, Ahmed M. Abu-Dief, Hanan El-Sayed Ahmed

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In this investigation, Cu(II), Pd(II) and Ag(I) complexes with the tetra-dentate DSPH Schiff base ligand were synthesized. The DSPH Schiff base and its complexes were characterized by using different physicochemical and spectral analysis. The results revealed that the metal ions coordinated with DSPH ligand through azomethine nitrogen and phenolic oxygen. Cu(II), Pd(II) and Ag(I) complexes are present in a 1:1 molar ratio. Pd(II) and Ag(I) complexes have square planar geometries while, Cu(II) has a distorted octahedral (Oh) geometry. All investigated complexes are nonelectrolytes. The investigated compounds were tested against different strains of bacteria and fungi. Both prepared compounds showed good results of inhibition against the selected pathogenic microorganism. Moreover, the interaction of investigated complexes with CT-DNA was studied via various techniques and the binding modes are mainly intercalative and grooving modes. Operating Environment MOE package was used to do docking studies for the investigated complexes to explore the potential binding mode and energy. Furthermore, the growth inhibitory effect of the investigated compounds was examined on some cancer cells lines.

Keywords: tetradentate, antimicrobial, CT-DNA interaction, docking, anticancer

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Authors: Ali M. Elgerbi, Obied A. Alwan, Al-Taher O. Alzwei, Abdurrahim A. Elouzi

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The binding of AFM1 to bacteria in phosphate buffer solution depended on many factors such as: availability of energy, incubation period, species and strain of bacteria. Increase in concentration of sugar showed higher removal of AFM1 and faster than in phosphate buffer alone. With 1.0% glucose lactic acid bacteria and bifidobacteria showed toxin removal ranging from 7.7 to 39.7% whereas with 10.0% glucose the percentage removal was 21.8 to 45.4% at 96 hours of incubation.

Keywords: aflatoxin M1, lactic acid bacteria, bifidobacteria , binding, phosphate buffer

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Authors: Ahmed K. Youssef, Shawkat M. B. Aly

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The interaction between ciprofloxacin and bovine serum albumin (BSA) was investigated by UV-Visible absorption and fluorescence spectroscopy. The influence of Cu²⁺ Ca²⁺, Co²⁺, and Fe³⁺ on the Cip-BSA interaction was investigated. The quenching of the BSA fluorescence emission in presence of ciprofloxacin as well as the influence of metal ions on the interaction was analyzed using the Stern-Volmer equation. The Stern-Volmer quenching constant, Kₛᵥ was calculated in presence and absence of the metal ions at the physiological pH of 7.4 using phosphate buffer. The experimental results showed that interaction mainly static in nature and quenching rate constant is decreased in presence of the studied metal ions with exception of Cu²⁺ ions. The decrease observed in the Kₛᵥ values in presence of Co²⁺, Ca²⁺, and Fe³⁺ can be understood on basis of competition between these metal and Cip when both of them existed in the BSA solution. Cu²⁺ induces interaction between Cip and BSA at faster quenching rates as inferred from the observed increase in the Kₛᵥ value. This allowed us to propose that copper (II) ions are directly involved in the process of Cip binding to BSA. The binding constant for Cip on BSA was determined and the metal ions effect on it was examined as well and their values were in line with the Kₛᵥ values.

Keywords: bovine serum albumin, ciprofloxacin, fluorescence, metal ions effect

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Authors: Benarous Khedidja, Yousfi Mohamed

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Infections caused by Candida species manifest in a number of diseases, including candidemia, vulvovaginal candidiasis, endocarditis, and peritonitis. These Candida species have been reported to have lipolytic activity by secretion of lipolytic enzymes such as esterases, lipases and phospholipases. These Extracellular hydrolytic enzymes seem to play an important role in Candida overgrowth. Candidiasis is commonly treated with antimycotics such as clotrimazole and nystatin, which bind to a major component of the fungal cell membrane (ergosterol). This binding forms pores in the membrane that lead to death of the fungus. Due to their secondary effects, scientists have thought of another treatment basing on lipase inhibition but we haven’t found any lipase inhibitors used as candidiasis treatment. In this work, we are interested to lipases inhibitors such as alkaloids as another candidiasis treatment. In the first part, we have proceeded to optimize the alkaloid structures and protein 3D structure using Hyperchem software. Secondly, we have docked inhibitors using Genetic algorithm with GOLD software. The results have shown ten possibilities of binding inhibitor to Candida rugosa lipase (CRL) but only one possibility has been accepted depending on the weakest binding energy.

Keywords: marrubiin, candida rugosa lipase, docking, gold

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Authors: Osama K. Abou-Zied, Saba A. Sulaiman

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We studied the spectroscopy of 25-nm diameter gold nanoparticles (AuNPs), coated with human serum albumin (HSA) as a model drug carrier. The morphology and coating of the AuNPs were examined using transmission electron microscopy and dynamic light scattering. Resonance energy transfer from the sole tryptophan of HSA (Trp214) to the AuNPs was observed in which the fluorescence quenching of Trp214 is dominated by a static mechanism. Using fluorescein (FL) to probe the warfarin drug-binding site in HSA revealed the unchanged nature of the binding cavity on the surface of the AuNPs, indicating the stability of the protein structure on the metal surface. The transient absorption results of the surface plasmonic resonance (SPR) band of the AuNPs show three ultrafast dynamics that are involved in the relaxation process after excitation at 460 nm. The three decay components were assigned to the electron-electron (~ 400 fs), electron-phonon (~ 2.0 ps) and phonon-phonon (200–250 ps) interactions. These dynamics were not changed upon coating the AuNPs with HSA which indicates the chemical and physical stability of the AuNPs upon bioconjugation. Binding of FL in HSA did not have any measurable effect on the bleach recovery dynamics of the SPR band, although both FL and AuNPs were excited at 460 nm. The current study is important for a better understanding of the physical and dynamical properties of protein-coated metal nanoparticles which are expected to help in optimizing their properties for critical applications in nanomedicine.

Keywords: gold nanoparticles, human serum albumin, fluorescein, femtosecond transient absorption

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Authors: Ratchaneewan Maneemaroj, Paveena Noisuwan, Chonlada Lakhonphon

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The smoking is one of the major risk factors in Non-Communicable Disease. Free radicals from cigarette smoke can cause oxidative stress. The oxidative insults can lead to red blood cell (RBC) senescence and are involved in the clearance of red blood cells. The objective of the present study is to assess the association between smoke, oxidative stress evaluated with serum Malondialdehyde (MDA) level and phosphatidylserine (PS) externalization (biomarker of RBC senescence) evaluated with annexin V binding. A total of sixty-four male volunteers aged 25-60 years old were recruited in this study. MDA was measured by colorimetric method. Annexin V binding was detected by flow cytometry. Our results show that there was a significant increase in MDA levels in cigarette smokers as compared to non-smokers (p < 0.001). However, there was no significant different between annexin V binding (% gate) in cigarette smokers and non-smokers (p = 0.978). These results provide evidence of free radical from smoking is associated with oxidative damage to erythrocytes. However, our results suggest that PS externalization is unlikely to have a role in RBC senescence pathway of stressed erythrocytes from cigarette smoke. The other biomarker of RBC senescence should be determined on cigarette smoker erythrocytes.

Keywords: malondialdehyde, phosphatidylserine, RBC senescence, annexin V

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Authors: Bercem Kiran-Yildirim, Volker Gaukel

Abstract:

Ice recrystallization (IR) which occurs especially during frozen storage is an undesired process due to the possible influence on the quality of products. As a result of recrystallization, the total volume of ice remains constant, but the size, number, and shape of ice crystals change. For instance, as indicated in the literature, the size of ice crystals in ice cream increases due to recrystallization. This results in texture deterioration. Therefore, the inhibition of ice recrystallization is of great importance, not only for food industry but also for several other areas where sensitive products are stored frozen, like pharmaceutical products or organs and blood in medicine. Ice-binding proteins (IBPs) have the unique ability to inhibit ice growth and in consequence inhibit recrystallization. This effect is based on their ice binding affinity. In the presence of IBP in a solution, ice crystal growth is inhibited during temperature decrease until a certain temperature is reached. The melting during temperature increase is not influenced. The gap between melting and freezing points is known as thermal hysteresis (TH). In literature, the TH activity is usually investigated under laboratory conditions in IBP buffer solutions. In product applications (e.g., food) there are many other solutes present which may influence the TH activity. In this study, a subset of IBPs, so-called antifreeze proteins (AFPs), is used for the investigation of the influence of sucrose solution concentration on the TH activity. For the investigation, a polarization microscope (Nikon Eclipse LV100ND) equipped with a digital camera (Nikon DS-Ri1) and a cold stage (Linkam LTS420) was used. In a first step, the equipment was established and validated concerning the accuracy of TH measurements based on literature data.

Keywords: ice binding proteins, ice crystals, sucrose solution, thermal hysteresis

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Authors: Phillip Kearney, Constantina Lekakou, Stephen Belcher, Alessandro Sordon

Abstract:

The focus in the automotive industry is to reduce human operator and machine interaction, so manufacturing becomes more automated and safer. The aim is to lower part cost and construction time as well as defects in the parts, sometimes occurring due to the physical limitations of human operators. A move to automate the layup of reinforcement material in composites manufacturing has resulted in the use of tapes that are placed in position by a robotic deposition head, also described as Automated Fibre Placement (AFP). The process of AFP is limited with respect to the finite amount of material that can be loaded into the machine at any one time. Joining two batches of tape material together involves a splice to secure the ends of the finishing tape to the starting edge of the new tape. The splicing method of choice for the majority of prepreg applications is a hand stich method, and as the name suggests requires human input to achieve. This investigation explores three methods for automated splicing, namely, adhesive, binding and stitching. The adhesive technique uses an additional adhesive placed on the tape ends to be joined. Binding uses the binding agent that is already impregnated onto the tape through the application of heat. The stitching method is used as a baseline to compare the new splicing methods to the traditional technique currently in use. As the methods will be used within a High Speed Automated Fibre Placement (HSAFP) process, this meant the parameters of the splices have to meet certain specifications: (a) the splice must be able to endure a load of 50 N in tension applied at a rate of 1 mm/s; (b) the splice must be created in less than 6 seconds, dictated by the capacity of the tape accumulator within the system. The samples for experimentation were manufactured with controlled overlaps, alignment and splicing parameters, these were then tested in tension using a tensile testing machine. Initial analysis explored the use of the impregnated binding agent present on the tape, as in the binding splicing technique. It analysed the effect of temperature and overlap on the strength of the splice. It was found that the optimum splicing temperature was at the higher end of the activation range of the binding agent, 100 °C. The optimum overlap was found to be 25 mm; it was found that there was no improvement in bond strength from 25 mm to 30 mm overlap. The final analysis compared the different splicing methods to the baseline of a stitched bond. It was found that the addition of an adhesive was the best splicing method, achieving a maximum load of over 500 N compared to the 26 N load achieved by a stitching splice and 94 N by the binding method.

Keywords: analysis, automated fibre placement, high speed, splicing

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Authors: Masoud Soltanialvar, Ali Bagherpour

Abstract:

Documented cases of human infection with H9N2 avian influenza viruses, first detected in 1999 in Hong Kong and China, indicate that these viruses can be directly transmitted from birds to humans. In this study, we characterized the mutation in the Hemagglutinin (HA) genes and proteins that correlates with a shift in affinity of the Hemagglutinin (HA) protein from the “avian” type sialic receptors to the “human” type in 10 Iranian isolates. We delineated the genomes and receptor binding profile of HA gene of some field isolates and established their phylogenetic relationship to the other Asian H9N2 sub lineages. A total of 1200 tissue samples collected from 40 farms located in various states of Iran during 2008 – 2010 as part of a program to monitor Avian Influenza Viruses (AIV) infection. To determine the genetic relationship of Iranian viruses, the Hemagglutinin (HA) genes from ten isolates were amplified and sequenced (by RT-PCR method). Nucleotide sequences (orf) of the (HA) genes were used for phylogenetic tree construction. Deduced amino acid sequences showed the presence of L226 (234 in H9 numbering) in all ten Iranian isolates which indicates a preference to binding of α (2–6) sialic acid receptors, so these Iranian H9N2 viruses have the potential to infect human beings. These isolates showed high degree of homology with 2 human H9N2 isolates A/HK/1073/99, A/HK/1074/99. Phylogenetic analysis of showed that all the HA genes of the Iranian H9N2 viruses fall into a single group within a G1-like sublineage which had contributed as donor of six internal genes to H5N1 highly pathogenic avian influenza. The results of this study indicated that all Iranian viruses have the potential to emerge as highly pathogenic influenza virus, and considering the homology of these isolates with human H9N2 strains, it seems that the potential of these avian influenza isolates to infect human should not be overlooked.

Keywords: influenza virus, hemagglutinin, neuraminidase, Iran

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