Search results for: molecular motor

Authors: T. D. Tran, H. Schlegel, R. Neugebauer

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Ball screws are an important component in machine tools. In mechatronic systems and machine tools, a ball screw has to work usually at a high speed. Otherwise the axial compliance of the ball screw, in combination with the inertia of the slide, the motor, the coupling and the screw, will cause an oscillation resonance, which limits the systems bandwidth and consequently influences performance of the motion controller. In this paper, the modal analysis method by measuring and analysing the vibrating parameters of the ball screw system to determine the dynamic characteristic of existing structures is used. On the one hand, the results of this study were obtained by the theoretical analysis and the modal testing of a ball screw system test station with the help of an impact hammer, respectively using excitation by motor. The experimental study showed oscillating forms of the ball screw for each frequency and obtained eigenfrequencies of the ball screw system. On the other hand, in this research a simulation with the help of the numerical modal analysis in order to analyse the oscillation and to find the eigenfrequencies of the ball screw system is used. Furthermore, the model order reduction by modal reduction and also according to Guyan is carried out. On the basis of these results a secure and also rapid commissioning of the control loops with regard to operating in their optimal function is targeted.

Keywords: modal analysis, ball screw, controller system, machine tools

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Authors: Hind O. Osman, Tilal Elsaman, Bashir A. Yousef, Esraa Elhadi, Aimun A. E. Ahmed, Eyman Mohamed Eltayib, Malik Suliman Mohamed, Magdi Awadalla Mohamed

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Epilepsy is the most common neurological condition and cause of substantial morbidity and mortality. In the present study, the molecular hybridization tool was adopted to obtain six Schiff bases of isatin and adamantane-1-carbohydrazide (18–23). Then, their anticonvulsant activity was evaluated using a pentylenetetrazole- (PTZ-) induced seizure model using phenobarbitone as a positive control. Our findings showed that compounds 18–23 provided significant protection against PTZ-induced seizure, and maximum activities were associated with compound 23. Moreover, all investigated compounds increased the latency of induced convulsion and reduced the duration of epilepsy, with compound 23 being the best. Interestingly, most of the synthesized molecules showed a reduction in neurological symptoms and severity of the seizure. Molecular docking studies suggest GABA-A receptor as a potential target, and in silico ADME screening revealed that the pharmaceutical properties of compound 23 are within the specified limit. Thus, compound 23 was identified as a promising candidate that warrants further drug discovery processes.

Keywords: isatin and adamantane, anticonvulsant activity, PTZ-induced seizure, molecular docking

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Authors: Cheng-Chi Yu, Yu-Shiue Wang, Kei-Lin Kuo

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Active Independent Front Steering system is a steering system which can according to vehicle driving situation adjusts the relation of steering angle between inner wheel and outer wheel. In low-speed cornering, AIFS sets the steering angles of inner and outer wheel into Ackerman steering geometry to make vehicle has less cornering radius. Besides, AIFS changes the steering geometry to parallel or even anti-Ackerman steering geometry to keep vehicle stability in high-speed cornering. Therefore, based on the analysis of the vehicle steering behavior from different steering geometries, this study develops a new screw type of active independent front steering system to make vehicles best cornering performance at any speeds. The screw type of active independent front steering system keeps the pinion and separates the rack into main rack and second rack. Two racks connect by a screw. Extra screw rotated motion powered by assistant motor through coupler makes second rack move relative to main rack, which can adjust both steering ratio and steering geometry. First of all, this study distinguishes the steering geometry by using Ackerman percentage and utilizes the software of ADAMS/Car to construct diverse steering geometry models. The different steering geometries are compared at low-speed and high-speed cornering, and then control strategies of the active independent front steering systems could be formulated. Secondly, this study applies closed loop equation to analyze tire steering angles and carries out optimization calculations to make the steering geometry from traditional rack and pinion steering system near to Ackerman steering geometry. Steering characteristics of the optimum steering mechanism and motion characteristics of vehicle installed the steering mechanism are verified by ADAMS/Car models of front suspension and full vehicle respectively. By adding dual auxiliary rack and dual motor to the optimum steering mechanism, the active independent front steering system could be developed to achieve the functions of variable steering ratio and variable steering geometry. At last, this study uses ADAMS/Car and Matlab/Simulink to co-simulate the cornering motion of vehicles confirms the vehicle installed the Active Independent Front Steering (AIFS) system has better handling performance than that with Active Independent Steering (AFS) system or with Electric Power Steering (EPS) system. At low-speed cornering, the vehicles with AIFS system and with AFS system have better maneuverability, less cornering radius, than the traditional vehicle with EPS system because that AIFS and AFS systems both provide function of variable steering ratio. However, there is a slight penalty in the motor(s) power consumption. In addition, because of the capability of variable steering geometry, the vehicle with AIFS system has better high-speed cornering stability, trajectory keeping, and even less motor(s) power consumption than that with EPS system and also with AFS system.

Keywords: active front steering system, active independent front steering system, steering geometry, steering ratio

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Authors: Dong Xie, Jun Zhao, Yiming Weng

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One of the challenges in dental cement biomaterials is how to make a restorative with mechanical strengths and wear resistance that are comparable to contemporary dental resin composites. Currently none of the dental cement restoratives has been used in high stress-bearing sites due to their low mechanical strengths and poor wear-resistance. The objective of this study was to synthesize and characterize the poly(alkenoic acid)s with different molecular structures, use these polymers to formulate a dental cement restorative, and study the effect of molecular structures on reaction kinetics, viscosity, and mechanical strengths of the formed polymers and cement restoratives. In this study, poly(alkenoic acid)s with different molecular structures were synthesized. The purified polymers were formulated with commercial Fuji II LC glass fillers to form the experimental cement restoratives. The reaction kinetics was studied via 1HNMR spectroscopy. The formed restoratives were evaluated using compressive strength, diametral tensile strength, flexural strength, hardness and wear-resistance tests. Specimens were conditioned in distilled water at 37 oC for 24 h prior to testing. Fuji II LC restorative was used as control. The results show that the higher the arm number and initiator concentration, the faster the reaction was. It was also found that the higher the arm number and branching that the polymer had, the lower the viscosity of the polymer in water and the lower the mechanical strengths of the formed restorative. The experimental restoratives were 31-53% in compressive strength, 37-55% in compressive modulus, 80-126% in diametral tensile strength, 76-94% in flexural strength, 4-21% in fracture toughness and 53-96% in hardness higher than Fuji II LC. For wear test, the experimental restoratives were only 5.4-13% of abrasive and 6.4-12% of attritional wear depths of Fuji II LC in each wear cycle. The aging study also showed that all the experimental restoratives increased their strength continuously during 30 days, unlike Fuji II LC. It is concluded that polymer molecular structures have significant and positive impact on mechanical properties of dental cement restoratives.

Keywords: dental materials, polymers, strength, biomaterials

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Authors: Saule Mussabekova

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Forensic investigation of human teeth plays an important role in detection of crime, particularly in cases of personal identification of dead bodies changed by putrefactive processes or skeletonized bodies as well as when finding bodies of unknown persons. 152 teeth have been investigated; 85 of them belonged to men and 67 belonged to women taken from alive people of different age. Teeth have been investigated after extraction. Two types of teeth have been investigated: teeth without integrity violation of dental crown and teeth with different degrees of its violation. Additionally, 517 teeth have been investigated that were collected from dead bodies, 252 of which belonged to women and 265 belonged to men, whatever the cause of death with death limitation from 1 month to 20 years. Isohemagglutinating serums and Coliclons of different series have been used for the research of tooth-group specificity by serological methods according to the AB0 system. Standard protocols of different techniques have been used for DNA purification from teeth (by reagent Chelex 100 produced by Bio-Rad using reagent kit 'DNA IQTM System' produced by Promega company (USA) and using columns 'QIAamp DNA Investigator Kit' produced by Qiagen company). Results of comparative forensic investigation of human teeth using serological and molecular genetic methods have shown that use of serological methods for forensic identification is sensible only in cases of preselection prior to the next molecular genetic investigation as well as in cases of impossibility of corresponding genetic investigation for different objective reasons. A number of advantages of methods of molecular genetics in the dental investigation have been marked, particularly in putrefactive changes, in personal identification. Key moments of modern condition of personal identification have been reflected according to dental state. Prospective directions of advance preparation of material have been emphasized for identification of teeth in forensic practice.

Keywords: dental state, forensic identification, molecular genetic analysis, teeth

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Authors: Patsy Tan, Dana Baltutis

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This presentation demonstrates the effectiveness of music therapy in co-treatment with speech pathology and occupational therapy as an innovative way when working with children and adolescents with complex individual differences to facilitate communication, emotional, motor and social skills development. Each child with special needs and their carer has an individual profile which encompasses their visual-spatial, auditory, language, learning, mental health, family dynamic, sensory-motor, motor planning and sequencing profiles. The most common issues among children with special needs, especially those diagnosed with Autism Spectrum Disorder, are in the areas of regulation, communication, and social-emotional development. The ability of children living with challenges to communicate and use language and understand verbal and non-verbal information, as well as move their bodies to explore and interact with their environments in social situations, depends on the children being regulated both internally and externally and trusting their communication partners and understanding what is happening in the moment. For carers, it is about understanding the tempo, rhythm, pacing, and timing of their own individual profile, as well as the profile of the child they are interacting with, and how these can sync together. In this study, music therapy is used in co-treatment sessions with a speech pathologist and/or an occupational therapist using the DIRFloortime approach to facilitate the regulation, attention, engagement, reciprocity and social-emotional capacities of children presenting with complex individual differences. Documented changes in 10 domains of children’s development over a 12-month period using the Individual Music Therapy Assessment Profile (IMTAP) were observed. Children were assessed biannually, and results show significant improvements in the social-emotional, musicality and receptive language domains indicating that co-treatment with a music therapist using the DIRFloortime framework is highly effective. This presentation will highlight strategies that facilitate regulation, social-emotional and communication development for children and adolescents with complex individual profiles.

Keywords: communication, shared attention, regulation, social emotional

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Authors: C. Labate, M. P. De Santo, G. Lombardo, R. Barberi, M. Lombardo, N. M. Ziebarth

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In the past decades, the importance of corneal biomechanics in the normal and pathological functions of the eye has gained its credibility. In fact, the mechanical properties of biological tissues are essential to their physiological function. We are convinced that an improved understanding of the nanomechanics of corneal tissue is important to understand the basic molecular interactions between collagen fibrils. Ultimately, this information will help in the development of new techniques to cure ocular diseases and in the development of biomimetic materials. Therefore, nanotechnology techniques are powerful tools and, in particular, Atomic Force Microscopy has demonstrated its ability to reliably characterize the biomechanics of biological tissues either at the micro- or nano-level. In the last years, we have investigated the mechanical anisotropy of the human corneal stroma at both the tissue and molecular levels. In particular, we have focused on corneal cross-linking, an established procedure aimed at slowing down or halting the progression of the disease known as keratoconus. We have obtained the first evidence that riboflavin/UV-A corneal cross-linking induces both an increase of the elastic response and a decrease of the viscous response of the most anterior stroma at the scale of stromal molecular interactions.

Keywords: atomic force spectroscopy, corneal stroma, cross-linking, viscoelasticity

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Authors: Çağrı Bekir Baysal, Göktuğ Burak Çalık

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Armored vehicles may have different traction layouts as a result of terrain capabilities and mobility needs. Two main categories of layouts can be separated as wheeled and tracked. Tracked vehicles have superior off-road capabilities but what they gain on terrain performance they lose on mobility front. Wheeled vehicles on the other hand do not have as good terrain capabilities as tracked vehicles but they have superior mobility capabilities such as top speed, range and agility with respect to tracked vehicles. Conventional armored vehicles employ a diesel ICE as main power source. In these vehicles ICE is mechanically connected to the powertrain. This determines the ICE rpm as a result of speed and torque requested by the driver. ICE efficiency changes drastically with torque and speed required and conventional vehicles suffer in terms of fuel consumption because of this. Hybrid electric vehicles employ at least one electric motor in order to improve fuel efficiency. There are different types of hybrid vehicles but main types are Series Hybrid, Parallel Hybrid and Series-Parallel Hybrid. These vehicles introduce an electric motor for traction and also can have a generator electric motor for range extending purposes. Having an electric motor as the traction power source brings the flexibility of either using the ICE as an alternative traction source while it is in efficient range or completely separating the ICE from traction and using it solely considering efficiency. Hybrid configurations have additional advantages for armored vehicles in addition to fuel efficiency. Heat signature, silent operation and prolonged stationary missions can be possible with the help of the high-power battery pack that will be present in the vehicle for hybrid drivetrain. Because of the reasons explained, hybrid armored vehicles are becoming a target area for military and also for vehicle suppliers. In order to have a better idea and starting point when starting a hybrid armored vehicle design, hybrid drivetrain configuration has to be selected after performing a trade-off study. This study has to include vehicle mobility simulations, integration level, vehicle level and performance level criteria. In this study different hybrid traction configurations possible for an 8x8 vehicle is compared using above mentioned criteria set. In order to compare hybrid traction configurations ease of application, cost, weight advantage, reliability, maintainability, redundancy and performance criteria have been used. Performance criteria points have been defined with the help of vehicle simulations and tests. Results of these simulations and tests also help determining required tractive power for an armored vehicle including conditions like trench and obstacle crossing, gradient climb. With the method explained in this study, each configuration is assigned a point for each criterion. This way, correct configuration can be selected objectively for every application. Also, key aspects of armored vehicles, mine protection and ballistic protection will be considered for hybrid configurations. Results are expected to vary for different types of vehicles but it is observed that having longitudinal differential locking capability improves mobility and having high motor count increases complexity in general.

Keywords: armored vehicles, electric drivetrain, electric mobility, hybrid vehicles

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Authors: K. R. Guna, Aldin Justin Sundararaj, B. C. Pillai, A. N. Subash

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A systematic study has been made for ignition delay times measurement behind a reflected shock wave for the low molecular weight hydrocarbon fuel in argon simulated gas mixtures. The low molecular hydrocarbon fuel–oxygen was diluted with argon for desired concentration is taken for the study. The suitability of the shock tube for measuring the ignition delay time is demonstrated by measuring the ignition delay for the liquefied petroleum gas for equivalence ratios (ф=0.5 & 1) in the temperature range 1150-1650 K. The pressure range was fixed from 5-15 bar. The ignition delay was measured by recording the ignition-induced pressure jump and emission from CH radical simultaneously. From conducting experiments, it was found that the ignition delay time for liquefied petroleum gas reduces with increase in temperature. The shock tube was calibrated for ethane-oxygen gas mixture and the results obtained from this study is compared with the earlier reported values and found to be comparably well suited for the measurement of ignition delay times. The above work was carried out using the shock tube facility at propulsion and high enthalpy laboratory, Karunya University.

Keywords: ignition delay, LPG, reflected shock, shock wave

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Authors: Imran Muhammad

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The main cause of infectious disease in the modern world is Mycobacterium Tuberculosis (MT). To combat tuberculosis, new and efficient drugs are an urgent need in the modern world. Schif bases are potent for their biological pharmacophore activity. Thus we selected different Vanillin-based Schiff bases for their binding activity against target enzymes of Mycobacterium tuberculosis that is (DprE1 (decaprenyl phosphoryl-β-D-ribose 2′-epimerase), and DNA gyrase subunit-A), using molecular docking. We evaluate the inhibition potential, interaction, and binding mode of these compounds with the target enzymes.

Keywords: schiff bases, tuberculosis, DNA gyrase, DprE1, docking

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Authors: Samy Madbouly

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The relaxation behavior of biorenewable castor oil-based polyurethane-lignin thin films synthesized in homogenous waterborne dispersions was investigated as a function of concentration at different temperatures and frequencies using broadband dielectric relaxation spectroscopy (BDRS). The molecular dynamics of the glass relaxation process and the local relaxation process of the PU-LS thin films were studied over a wide range of temperatures (-70 to 30 ℃) and frequencies (5 × 10−2 to 0.5 × 107 Hz) for different lignin concentration. Four relaxation processes have been observed namely; ?-, β-, γ-relaxations and ionic conductivity for pure castor oil-based PU and castor oil-lignin-based PU thin films at different temperatures and frequencies ranges. The Vogel-Fulcher-Tammann equation was found to be well described the temperature dependence of the characteristic relaxation times of the ?-relaxation process. However, on the other hand, the molecular dynamics of both β- and γ-relaxation processes were given by the Arrhenius equation. The incorporation of lignin into the castor oil-based PU significantly increased the glass transition temperature and primitivity of the thin films. In addition, the broadness, intensity, and molecular dynamics of the only observed ?-relaxation process were found to be strongly dependent on lignin concentration.

Keywords: castor oil, lignin, polyurethane, dielectric, dispersions

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Authors: Mera-Martínez Daniela

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Dendropsophus minutus, is a species distributed in South America including the slopes of the Andes, the Amazon basin, forests of southeastern Brazil and in Guyana where tropical forests are characteristic. The relationship of amphibians found in this locality is evidenced by molecular markers, with the objective of analyzing if the geographic distance is influencing the structure of the populations of D. minutus in Guyana; we analyzed 65 sequences from the 3 localities of Guyana where haplotype networks, Mantel Test and phylogeny were realized to know the influence. It was evidenced that there is a haplotypic difference in the locality of Guyana compared to Suriname and French Guyana, but this does not have a correlation with the geographic distance, but this one can be influenced by the conditions of the places.

Keywords: phylogeography, Dendropsophus, geographic distance, molecular markers

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Authors: Van Tran Thi Thuy, Dukjoon Kim

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A series of pH- and thermosensitive poly(N-isopropyl acrylamide-co-acrylic acid) were synthesized by radical polymerization and grafted on poly succinimide backbones. The poly succinimide derivatives synthesized were coated on iron oxide magnetic nanoparticles for potential applications in drug delivery systems with theranostic and molecular imaging. The structure of polymer shell was confirmed by FT-IR, H-NMR spectroscopies. Its thermal behavior was tested by UV-Vis spectroscopy. The particle size and its distribution are measured by dynamic light scattering (DLS) and transmission electron microscope (TEM). The mean diameter of the core-shell structure is from 20 to 80 nm.

Keywords: magnetic, nano, PNIPAM, polysuccinimide

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Authors: Paramita Banerjee, K. R. S. Chandrakumar, G. P. Das

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Bulk MgH2 has drawn much attention for the purpose of hydrogen storage because of its high hydrogen storage capacity (~7.7 wt %) as well as low cost and abundant availability. However, its practical usage has been hindered because of its high hydrogen desorption enthalpy (~0.8 eV/H2 molecule), which results in an undesirable desorption temperature of 3000C at 1 bar H2 pressure. To surmount the limitations of bulk MgH2 for the purpose of hydrogen storage, a detailed first-principles density functional theory (DFT) based study on the structure and stability of neutral (Mgm) and positively charged (Mgm+) Mg nanoclusters of different sizes (m = 2, 4, 8 and 12), as well as their interaction with molecular hydrogen (H2), is reported here. It has been found that due to the absence of d-electrons within the Mg atoms, hydrogen remained in molecular form even after its interaction with neutral and charged Mg nanoclusters. Interestingly, the H2 molecules do not enter into the interstitial positions of the nanoclusters. Rather, they remain on the surface by ornamenting these nanoclusters and forming new structures with a gravimetric density higher than 15 wt %. Our observation is that the inclusion of Grimme’s DFT-D3 dispersion correction in this weakly interacting system has a significant effect on binding of the H2 molecules with these nanoclusters. The dispersion corrected interaction energy (IE) values (0.1-0.14 eV/H2 molecule) fall in the right energy window, that is ideal for hydrogen storage. These IE values are further verified by using high-level coupled-cluster calculations with non-iterative triples corrections i.e. CCSD(T), (which has been considered to be a highly accurate quantum chemical method) and thereby confirming the accuracy of our ‘dispersion correction’ incorporated DFT calculations. The significance of the polarization and dispersion energy in binding of the H2 molecules are confirmed by performing energy decomposition analysis (EDA). A total of 16, 24, 32 and 36 H2 molecules can be attached to the neutral and charged nanoclusters of size m = 2, 4, 8 and 12 respectively. Ab-initio molecular dynamics (AIMD) simulation shows that the outermost H2 molecules are desorbed at a rather low temperature viz. 150 K (-1230C) which is expected. However, complete dehydrogenation of these nanoclusters occur at around 1000C. Most importantly, the host nanoclusters remain stable up to ~500 K (2270C). All these results on the adsorption and desorption of molecular hydrogen with neutral and charged Mg nanocluster systems indicate towards the possibility of reducing the dehydrogenation temperature of bulk MgH2 by designing new Mg-based nano materials which will be able to adsorb molecular hydrogen via this weak Mg-H2 interaction, rather than the strong Mg-H bonding. Notwithstanding the fact that in practical applications, these interactions will be further complicated by the effect of substrates as well as interactions with other clusters, the present study has implications on our fundamental understanding to this problem.

Keywords: density functional theory, DFT, hydrogen storage, molecular dynamics, molecular hydrogen adsorption, nanoclusters, physisorption

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Authors: Andreina Giustiniani, Massimiliano Oliveri

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Rhythmic activity in different frequencies could subserve distinct functional roles during visual perception and visual mental imagery. In particular, alpha band activity is thought to play a role in active inhibition of both task-irrelevant regions and processing of non-relevant information. In the present blind placebo-controlled study we applied alpha transcranial alternating current stimulation (tACS) in the occipital cortex both during a basic visual perception and a visual working memory task. To understand if the role of alpha is more related to a general inhibition of distractors or to an inhibition of task-irrelevant regions, we added a non visual distraction to both the tasks.Sixteen adult volunteers performed both a simple perception and a working memory task during 10 Hz tACS. The electrodes were placed over the left and right occipital cortex, the current intensity was 1 mA peak-to-baseline. Sham stimulation was chosen as control condition and in order to elicit the skin sensation similar to the real stimulation, electrical stimulation was applied for short periods (30 s) at the beginning of the session and then turned off. The tasks were split in two sets, in one set distracters were included and in the other set, there were no distracters. Motor interference was added by changing the answer key after subjects completed the first set of trials.The results show that alpha tACS improves working memory only when no motor distracters are added, suggesting a role of alpha tACS in inhibiting non-relevant regions rather than in a general inhibition of distractors. Additionally, we found that alpha tACS does not affect accuracy and hit rates during the visual perception task. These results suggest that alpha activity in the occipital cortex plays a different role in perception and working memory and it could optimize performance in tasks in which attention is internally directed, as in this working memory paradigm, but only when there is not motor distraction. Moreover, alpha tACS improves working memory performance by means of inhibition of task-irrelevant regions while it does not affect perception.

Keywords: alpha activity, interference, perception, working memory

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Authors: K. Ali, M. F. Qamar, M. A. Zaman, M. Younus, I. Khan, S. Ehtisham-ul-Haque, R. Tamkeen, M. I. Rashid, Q. Ali

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This study centers on molecular identification of Haemonchus contortus and isolation of Benz-imidazoles (BZ) resistant strains. Different abattoirs’ of two geographic regions of Punjab (Pakistan) were frequently visited for the collection of worms. Out of 1500 (n=1500) samples that were morphologically confirmed as H. contortus, 30 worms were subjected to molecular procedures for isolation of resistant strains. Resistant worms (n=8) were further subjected to DNA gene sequencing. Bio edit sequence alignment editor software was used to detect the possible mutation, deletion, replacement of nucleotides. Genetic diversity was noticed and genetic variation existing in β-tubulin isotype 1 of the H. contortus population of small ruminants of different regions considered in this study. H. contortus showed three different type of genetic sequences. 75%, 37.5%, 25% and 12.5% of the studied samples showed 100% query cover and identity with isolates and clones of China, UK, Australia and other countries, respectively. Interestingly the neighbor countries such as India and Iran haven’t many similarities with the Pakistani isolates. Thus, it suggests that population density of same genetic makeup H. contortus is scattered worldwide rather than clustering in a single region.

Keywords: Haemonchus contortus, Benzimidazole resistant, β-tubulin-1 gene, abattoirs

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Authors: Sergio Alejandro Cuevas, Catherine Etchebest, Fernando Luis Barroso Da Silva

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The flavivirus genus has several organisms responsible for generating various diseases in humans. Special in Brazil, Zika (ZIKV), Dengue (DENV) and Yellow Fever (YFV) viruses have raised great health concerns due to the high number of cases affecting the area during the last years. Diagnostic is still a difficult issue since the clinical symptoms are highly similar. The understanding of their common structural/dynamical and biomolecular interactions features and differences might suggest alternative strategies towards differential serological diagnostics and therapeutic intervention. Due to their immunogenicity, the primary focus of this study was on the ZIKV, DENV and YFV non-structural proteins 1 (NS1) protein. By means of computational studies, we calculated the main physical chemical properties of this protein from different strains that are directly responsible for the biomolecular interactions and, therefore, can be related to the differential infectivity of the strains. We also mapped the electrostatic differences at both the sequence and structural levels for the strains from Uganda to Brazil that could suggest possible molecular mechanisms for the increase of the virulence of ZIKV. It is interesting to note that despite the small changes in the protein sequence due to the high sequence identity among the studied strains, the electrostatic properties are strongly impacted by the pH which also impact on their biomolecular interactions with partners and, consequently, the molecular viral biology. African and Asian strains are distinguishable. Exploring the interfaces used by NS1 to self-associate in different oligomeric states, and to interact with membranes and the antibody, we could map the strategy used by the ZIKV during its evolutionary process. This indicates possible molecular mechanisms that can explain the different immunological response. By the comparison with the known antibody structure available for the West Nile virus, we demonstrated that the antibody would have difficulties to neutralize the NS1 from the Brazilian strain. The present study also opens up perspectives to computationally design high specificity antibodies.

Keywords: zika, biomolecular interactions, electrostatic interactions, molecular mechanisms

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Authors: Radoslav Stojchevski, Leonid Poretsky, Dimiter Avtanski

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Proinflammatory cytokines play an important role in cancer initiation and progression by mediating the intracellular communication between the cancer cells and tumor microenvironment. Increased tumor growth causing reduced oxygen concentration and oxygen pressure commonly result in hypoxia. Mechanistically, hypoxia is characterized by stabilization and nuclear translocation of hypoxia-inducible factor 1 alpha (HIF-1α) followed by propagation of molecular pathway cascade involving multiple downstream targets. Cobalt(II) chloride (CoCl₂) is commonly used to mimic hypoxia in experimental conditions since it directly induces the expression of HIF-1α. The aim of the present study was to investigate the in vitro effects and the molecular mechanisms by which hypoxia regulates the cytokine secretory profile of breast cancer cells. As a model for this study, we used several breast cancer cell lines bearing various molecular characteristics and metastatic potential (MDA-MB-231 (clauding low, ER-/PR-/HER²⁻), MCF-7 (luminal A, ER⁺/PR⁺/HER²⁻), and BT-474 (liminal B, ER⁺/PR⁺/HER²⁺)). We demonstrated that breast cancer cells secrete numerous cytokines and cytokine ligands, including interleukins, chemokines, and growth factors. Treatment with CoCl₂significantly modulated the breast cancer cells' cytokine expression in a concentration- and time-dependent manner. These effects were mediated via activation of several signaling pathways (JNK/SAPK1, NF-κB, STAT5A/B, and Erk/MAPK1/2). Taken together, the present data define some of the molecular mechanisms by which hypoxia affects the breast cancer cells' cytokine secretory profile, thus contributing to the development of novel therapies for metastatic breast cancer.

Keywords: breast cancer, cytokines, cobalt(II) chloride (CoCl₂), hypoxia

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Authors: Azza T. Tahera, Eman M. Ahmeda, Nadia A. Khalila, Yassin M. Nissanb

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New 3-(pyridin-4-yl)-[1,2,4] triazolo [4,3-b] pyridazine derivatives 2a-i, 4a,b and 6a,b were designed, synthesized and evaluated as cytotoxic agents. All compounds were investigated for their in vitro cytotoxicity at a single dose 10-5M concentration towards 60 cancer cell lines according to USA NCI protocol. The preliminary screening results showed that the majority of tested compounds exhibited remarkable activity against SR (leukemia) cell panel. Molecular docking for all synthesized compounds was performed on the active site of c-Met kinase. The most active compounds, 2f and 4a were further evaluated at a seven dose level screening and their IC50 as a c-Met kinase inhibitors were determined in vitro.

Keywords: triazolopyridazines, pyridazines, cytotoxic activity, cell panel

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Authors: Salma A. El-Marasy, Rehab F. Abdel-Rahman, Reham M. Abd-Elsalam

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The burden of stroke is intensely increasing worldwide. Brain injury following transient or permanent focal cerebral ischemia develops ischemic stroke as a consequence of a complex series of pathophysiological events. The aim of this study is to evaluate the possible neuroprotective effect of a dipeptidyl peptidase-4 inhibitor, vildagliptin, independent on its insulinotropic properties in non-diabetic rats subjected to cerebral ischemia. Anaesthetized Wistar rats were subjected to either left middle cerebral artery occlusion (MCAO) or sham operation followed by reperfusion after 30 min of MCAO. The other three groups were orally administered vildagliptin at 3 dose levels (2.5, 5, 10 mg/kg) for 3 successive weeks before subjected to left focal cerebral ischemia/reperfusion and till the end of the study. Neurological deficit scores and motor activity were assessed 24h following reperfusion. 48h following reperfusion, rats were euthanized and their left brain hemispheres were harvested and used in the biochemical, histopathological, and immunohistochemical investigations. Vildagliptin pretreatment improved neurological score deficit, locomotor activity and motor coordination in MCAO rats. Moreover, vildagliptin reduced malondialdehyde (MDA), elevated reduced glutathione (GSH), phosphotylinosital 3 kinase (PI3K), phosphorylated of protein kinase B (p-AKT), and mechanistic target of rapamycin (mTOR) brain contents in addition to reducing protein expression of caspase-3. Also, vildagliptin showed a dose-dependent attenuation in neuronal cell loss and histopathological alterations in MCAO rats. This study proves that vildagliptin exerted the neuroprotective effect in a dose-dependent manner as shown in amelioration of neuronal cell loss and histopathological damage in MCAO rats, which may be mediated by attenuating neuronal and motor deficits, it’s anti-oxidant property, activation of PI3K/AKT/mTOR pathway and its anti-apoptotic effect.

Keywords: caspase-3, cerebral ischemia, dipeptidyl peptidase-4 inhibitor, oxidative stress, PI3K/AKT/mTOR pathway, rats, vildagliptin

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Authors: Pyar S. Jassal, Sonal Gupta, Neema Chand, Rajni Johar

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In present study, Low molecular weight chitosan naoparticles (LMWCNP) were synthesized by using low molecular weight chitosan (LMWC) and sodium tripolyphosphate for the adsorption of anthraquinone dyes from waste water. The ionic-gel technique was used for this purpose. Size of nanoparticles was determined by “Scherrer equation”. The absorbance was carried out with UV-visible spectrophotometer for Acid Green 25 (AG25) and Reactive Blue 4 (RB4) dyes solutions at λmax 644 and λmax 598 nm respectively. The removal of dyes was dependent on the pH and the optimum adsorption was between pH 2 to 9. The extraction of dyes was linearly dependent on temperature. The equilibrium parameters, RL was calculated by using the Langmuir isotherm and shows that adsorption of dyes is favorable on the LMWCNP. The XRD images of LMWC show a crystalline nature whereas LMWCNP is amorphous one. The thermo gravimetric analysis (TGA) shows that LMWCNP thermally more stable than LMWC. As the contact time increases, percentage removal of Acid Green 25 and Reactive Blue 4 dyes also increases. TEM images reveal the size of the LMWCNP were in the range of 45-50 nm. The capacity of AG25 dye on LMWC was 5.23 mg/g, it compared with LMWCNP capacity which was 6.83 mg/g respectively. The capacity of RB4 dye on LMWC was 2.30 mg/g and 2.34 mg/g was on LMWCNP.

Keywords: low molecular weight chitosan nanoparticles, anthraquinone dye, removal efficiency, adsorption isotherm

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Authors: Sudhir Kumar Sharma, Ramesh Jagannathan

Abstract:

The interaction of organic and inorganic matrices of biological origin resulting in self-assembled structures with unique properties is well established. The development of such self-assembled nanostructures by synthetic and bio-inspired techniques is an established field of active research. Among bio-materials, nacre, a laminar stack of calcium carbonate nanosheets, which are interleaved with organic material, has long been focused research due to its unique mechanical properties. In this paper, we present the development of nacre-like lamellar structures made up of calcium carbonate via a wet chemical route. We used the binding affinity of carboxylate anions and calcium cations using poly (acrylic) acid (PAA) to lead CaCO₃ crystallization. In these experiments, we selected calcium acetate as the precursor molecule along with PAA (Mw ~ 8000 Da). We found that Ca⁺²/COO⁻ ratio provided a tunable control for the morphology and growth of CaCO₃ nanostructures. Drop casting one such formulation on a silicon substrate followed by calcination resulted in co-planner, molecular sheets of CaCO₃, separated by a spacer layer of carbon. The scope of our process could be expanded to produce unit cell thick molecular sheets of other important inorganic materials.

Keywords: self-assembled structures, bio-inspired materials, calcium carbonate, wet chemical route

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Authors: Alireza Jalalvand, Maryam Saleh, Somayeh Behjat Khatouni, Zahra Bahri Najafi, Foroozan Fatahinia, Narges Ismailzadeh, Behrokh Farahmand

Abstract:

Object: In the last two decades, the recent outbreak of Coronavirus (SARS-CoV-2) imposed a global pandemic in the world. Despite the increasing prevalence of the disease, there are no effective drugs to treat it. A suitable and rapid way to afford an effective drug and treat the global pandemic is a computational drug study. This study used molecular docking methods to examine the potential inhibition of over 50 antiviral drugs against three fundamental proteins of SARS-CoV-2. METHODS: Through a literature review, three important proteins (a key protease, RNA-dependent RNA polymerase (RdRp), and spike) were selected as drug targets. Three-dimensional (3D) structures of protease, spike, and RdRP proteins were obtained from the Protein Data Bank. Protein had minimal energy. Over 50 antiviral drugs were considered candidates for protein inhibition and their 3D structures were obtained from drug banks. The Autodock 4.2 software was used to define the molecular docking settings and run the algorithm. RESULTS: Five drugs, including indinavir, lopinavir, saquinavir, nelfinavir, and remdesivir, exhibited the highest inhibitory potency against all three proteins based on the binding energies and drug binding positions deduced from docking and hydrogen-bonding analysis. Conclusions: According to the results, among the drugs mentioned, saquinavir and lopinavir showed the highest inhibitory potency against all three proteins compared to other drugs. It may enter laboratory phase studies as a dual-drug treatment to inhibit SARS-CoV-2.

Keywords: covid-19, drug repositioning, molecular docking, lopinavir, saquinavir

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Authors: Sarah Sayed El- Tawab, Emmanuel Kamal Azix Saba

Abstract:

Objectives: Somatosensory blink reflex (SBR) is an eye blink response obtained from electrical stimulation of peripheral nerves or skin area of the body. It has been studied in various neurological diseases as well as among healthy subjects in different population. We designed this study to detect SBR positivity in patients with facial palsy and patients with post facial syndrome, to relate the facial palsy severity and the presence of SBR, and to associate between trigeminal BR changes and SBR positivity in peripheral facial palsy patients. Methods: 50 patients with peripheral facial palsy and post-facial syndrome 31 age and gender matched healthy volunteers were enrolled to this study. Facial motor conduction studies, trigeminal BR, and SBR were studied in all. Results: SBR was elicited in 67.7% of normal subjects, in 68% of PFS group, and in 32% of PFP group. On the non-paralytic side SBR was found in 28% by paralyzed side stimulation and in 24% by healthy side stimulation among PFP patients. For PFS group SBR was found on the non- paralytic side in 48%. Bilateral SBR elicitability was higher than its unilateral elicitability. Conclusion: Increased brainstem interneurons excitability is not essential to generate SBR. The hypothetical sensory-motor gating mechanism is responsible for SBR generation.

Keywords: somatosensory evoked blink reflex, post facial syndrome, blink reflex, enchanced gain

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Authors: Chro Kawyan

Abstract:

Endothelin-1 (ET-1), the principal individual from the newfound mammalian endothelin group of organically dynamic peptides, was initially distinguished as a 21 buildup powerful vasoconstrictor peptide in vascular endothelial cells. However, it has since been demonstrated to have a wide range of pharmacological activities in tissues both inside and outside the cardiovascular system. Additionally, peptides that have a striking resemblance to ET-1 have been identified as the primary toxic component of snake venom. In addition, late examinations have proposed that warm blooded creatures, including people, produce three unmistakable individuals from this peptide family, ET-1, ET-2 and ET-J, which might have various profiles of organic action and may follow up on particular subtypes of endothelin receptor. Masashi Yanagisawa and Tomoh Masaki survey the ongoing status of the organic chemistry and sub-atomic science of endothelin.

Keywords: thelin, microbiology, molecular biology, cell

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Authors: G. V. Novikov, V. S. Sivozhelezov, S. S. Kolesnikov, K. V. Shaitan

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The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behaviour.

Keywords: seven-transmembrane receptors, constitutive activity, activation, x-ray crystallography, principal component analysis, molecular dynamics simulation

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Authors: Babak Safaei, A. M. Fattahi

Abstract:

In the present study we have investigated axial buckling characteristics of nanocomposite beams reinforced by single-walled carbon nanotubes (SWCNTs). Various types of beam theories including Euler-Bernoulli beam theory, Timoshenko beam theory and Reddy beam theory were used to analyze the buckling behavior of carbon nanotube-reinforced composite beams. Generalized differential quadrature (GDQ) method was utilized to discretize the governing differential equations along with four commonly used boundary conditions. The material properties of the nanocomposite beams were obtained using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long-(10,10) SWCNT composites which were embedded by amorphous polyethylene matrix. Then the results obtained directly from MD simulations were matched with those calculated by the mixture rule to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results were presented to indicate the influences of nanotube volume fractions and end supports on the critical axial buckling loads of nanocomposite beams relevant to long- and short-nanotube composites.

Keywords: nanocomposites, molecular dynamics simulation, axial buckling, generalized differential quadrature (GDQ)

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Authors: Paromik Bhattacharyya, Vijay Kumar, Johannes Van Staden

Abstract:

Micropropagation is an important tool for the conservation of threatened and commercially important plant species of which orchids deserve special attention. Ansellia africana is one such medicinally important orchid species having much commercial significance. Thus, development of regeneration protocols for producing clonally stable regenerates using axillary buds is of much importance. However, for large-scale micropropagation to become not only successful but also acceptable by end-users, somaclonal variations occurring in the plantlets need to be eliminated. In the light of the various factors (genotype, ploidy level, in vitro culture age, explant and culture type, etc.) that may account for the somaclonal variations of divergent genetic changes at the cellular and molecular levels, genetic analysis of micropropagated plants using a multidisciplinary approach is of utmost importance. In the present study, the clonal integrity of the long term micropropagated A. africana plants were assessed using advanced molecular marker system i.e. Start Codon Targeted Polymorphism (SCoT). Our studies recorded a clonally stable regeneration protocol for A. africana with a very high degree of clonal fidelity amongst the regenerates. The results obtained from these molecular analyses could help in modifying the regeneration protocols for obtaining clonally stable true to type plantlets for sustainable commercial use.

Keywords: medicinal orchid micropropagation, start codon targeted polymorphism (SCoT), RAP), traditional African pharmacopoeia, genetic fidelity

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Authors: Mariam Mojally, Randa Abdou, Wisal Bokhari, Sultan Sab, Mohammed Dawoud, Amjad Albohy

Abstract:

Secondary metabolites produced by endophytes are an excellent source of biologically active compounds. In our current study, we evaluated terezine E and 14-hydroxyterezine D for binding to the active site of histone deacetylase (PDB ID: 4CBT) and matrix metalloproteinase 9 (PDB ID: 4H3X) by molecular docking using AutoDock Vina software after having tested their cytotoxic activities on three cell lines (human ductal breast epithelial tumor cells (T47D)-HCC1937), human hepatocarcinoma cell line (HepG2)-HB8065), and human colorectal carcinoma cells (HCT-116)-TCP1006, purchased from ATCC, USA)). Additionally, their antimicrobial activities were investigated, and their minimum inhibitory concentration (MIC) values were determined against P. notatum and S. aureus by the broth microdilution method. Higher cytotoxicity was observed for terezine E against all tested cell lines compared to 14-hydroxyterezine D. Molecular docking results supported the high cytotoxicity of terezine E and showed higher binding affinity with 4CBT with an energy score of 9 kcal/mol. Terezine E showed higher antibacterial and antifungal activities than 14-hydroxyrerezine D: MIC values were 15.45 and 21.73 mg/mL against S. aureus and 8.61 and 11.54 mg/mL against P. notatum, respectively

Keywords: Terezine E, 14-Hydroxyterezine D, cytotoxicity, antimicrobial activity, molecular docking

Procedia PDF Downloads 47

Authors: Sukriti Sabharwal, Sonali Bhattar, Shikhar Saxena

Abstract:

Introduction: COVID-19 molecular diagnostic laboratory is the cornerstone of the COVID-19 disease diagnosis as the patient’s treatment and management protocol depend on the molecular results. For this purpose, it is extremely important that the laboratory conducting these results adheres to the quality management processes to increase the accuracy and validity of the reports generated. We started our own molecular diagnostic setup at the onset of the pandemic. Therefore, we conducted this study to generate our quality management data to help us in improving on our weak points. Materials and Methods: A total of 14561 samples were evaluated by the retrospective observational method. The quality variables analysed were classified into pre-analytical, analytical, and post-analytical variables, and the results were presented in percentages. Results: Among the pre-analytical variables, sample leaking was the most common cause of the rejection of samples (134/14561, 0.92%), followed by non-generation of SRF ID (76/14561, 0.52%) and non-compliance to triple packaging (44/14561, 0.3%). The other pre-analytical aspects assessed were incomplete patient identification (17/14561, 0.11%), insufficient quantity of samples (12/14561, 0.08%), missing forms/samples (7/14561, 0.04%), samples in the wrong vials/empty VTM tubes (5/14561, 0.03%) and LIMS entry not done (2/14561, 0.01%). We are unable to obtain internal quality control in 0.37% of samples (55/14561). We also experienced two incidences of cross-contamination among the samples resulting in false-positive results. Among the post-analytical factors, a total of 0.07% of samples (11/14561) could not be dispatched within the stipulated time frame. Conclusion: Adherence to quality control processes is foremost for the smooth running of any diagnostic laboratory, especially the ones involved in critical reporting. Not only do the indicators help in keeping in check the laboratory parameters but they also allow comparison with other laboratories.

Keywords: laboratory quality management, COVID-19, molecular diagnostics, healthcare

Procedia PDF Downloads 144