Search results for: molecular interactions

Authors: Elahe Moradi, Hoseinali A. Khonakdar

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The escalating interest in renewable polymers is undeniable, albeit accompanied by inherent challenges. In our study, we endeavored to make a significant contribution to environmental conservation by introducing an eco-friendly structure, developed through an innovative approach. Specifically, we enhanced the compatibility between two immiscible polymers, namely poly (lactic acid) (PLA) and poly (butylene adipate-co-terephthalate) (PBAT). Our strategy involved the use of polyhedral oligomeric silsesquioxanes (POSS) nanoparticles, equipped with an epoxy functional group (Epoxy-POSS), to accomplish this objective with solution casting method. The incorporation of 1% nanoparticles into the PLA blend resulted in a decrease in its cold crystallization temperature. Furthermore, these nanoparticles possess the requisite capability to enhance molecular mobility, facilitated by the induction of a lubrication effect. The emergence of a PLA-CO-POSS-CO-PBAT structure at the interface between PLA and PBAT led to a significant amplification of the interactions at the interface of the matrix and the dispersed phase.

Keywords: compatibilization, thermal behavior, structure-properties, nanocomposite, PLA, PBAT

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Authors: Owonikoko Abayomi Dele

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Epilepsy is an unresolved disease that needs urgent attention. It is a brain disorder that affects over sixty-five (65) million people around the globe. Despite the availability of commercial anti-epileptic drugs, the war against this unmet condition is yet to be resolved. Most epilepsy patients are resistant to available anti-epileptic medications thus the need for affordable novel therapy against epilepsy is a necessity. Numerous phytochemicals have been reported for their potency, efficacy and safety as therapeutic agents against many diseases. This study investigated 99 isolated phytochemicals from Chasmanthera dependens and Carissa edulis against carbonic anhydrase (ii) drug target. The absorption, distribution, metabolism, excretion and toxicity (ADMET) of the isolated compounds were examined using admet SAR-2 web server while Swiss ADME was used to analyze the oral bioavailability, drug-likeness and lead-likeness properties of the selected leads. PASS web server was used to predict the biological activities of selected leads while other important physicochemical properties and interactions of the selected leads with the active site of the target after successful molecular docking simulation with the pyrx virtual screening tool were also examined. The results of these study identified seven lead compounds; C49- alpha-carissanol (-7.6 kcal/mol), C13- Catechin (-7.4 kcal/mol), C45- Salicin (-7.4 kcal/mol), C6- Bisnorargemonine (-7.3 kcal/mol), C36- Pallidine (-7.1 kcal/mol), S4- Lacosamide (-7.1 kcal/mol), and S7- Acetazolamide (-6.4 kcal/mol) for CA II (3HS4 receptor). These leads compounds are probable inhibitors of this drug target due to the observed good binding affinities and favourable interactions with the active site of the drug target, excellent ADMET profiles, PASS Properties, drug-likeness, lead-likeness and oral bioavailability properties. The identified leads have better binding energies as compared to the binding energies of the two standards. Thus, seven identified lead compounds can be developed further towards the development of new anti-epileptic medications.

Keywords: drug-likeness, phytochemicals, carbonic anhydrases, metalloeazymes, active site, ADMET

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Authors: A. G. Barua, Uttam Rajkhowa, Pranjal Moni Nath, Nur Abdul Kadir

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Mycobacterium tuberculosis (MTB) is one of the most closely-related intracellular bacterial pathogens, grouped as the M. tuberculosis complex (MTC). MTB, the primary agent of human tuberculosis (TB), can develop clinical TB in animals as 75 percent of canine mycobacterial infection is caused by close contact with an infected human being. In the present study, molecular detection of TB in dogs in three North-eastern states of India, Assam Mizoram, and Nagaland was carried out. So far, there has been a lack of systematic study in these regions, hampered by slow diagnostic methods and poor infrastructure. In an attempt to rectify this situation, molecular epidemiology was carried out for nine months to detect canine TB in a sample of 340 dogs. Isolation of DNA was done with swabs (throat/nasal), nodules of lungs and fluids from 100 suspected dogs and the molecular study were carried out with the help of conventional and real-time PCR. Post-mortem study was also carried out. Our results showed that the prevalence of clinical TB in dogs from a high-risk setting was 1 percent. However, the prevalence of immunological sensitization to M. tuberculosis antigen in dogs living in contact with sputum smeared positive TB cases was almost 50 percent. The latter setting had the maximum impact in terms of TB transmission. During the study period, a survey with a standard questionnaire was carried out in the TB hospitals to study reverse zoonosis. It was observed that an infected human being was one of the major risk factors for dogs to contract the infection. This observation was drawn by examining the probable airborne transmission from humans to their pets or strays. The present study helped to discover the nuances of TB transmission more clearly and systematically as compared to other sporadic tests to detect MTB in canine.

Keywords: Assam and Nagaland, canine TB, India, molecular detection, tuberculosis

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Authors: Fawaz A. Binsarra, Halim Boussabaine

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The notion of complexity science has been attracting the interest of researchers and professionals due to the need of enhancing the efficiency of understanding complex systems dynamic and structure of interactions. In addition, complexity analysis has been used as an approach to investigate complex systems that contains a large number of components interacts with each other to accomplish specific outcomes and emerges specific behavior. The design process is considered as a complex action that involves large number interacted components, which are ranked as design tasks, design team, and the components of the design process. Those three main aspects of the building design process consist of several components that interact with each other as a dynamic system with complex information flow. In this paper, the goal is to uncover the complex structure of information interactions in building design process. The Investigating of Royal Institute of British Architects Plan Of Work 2013 information interactions as a case study to uncover the structure and building design process complexity using network analysis software to model the information interaction will significantly enhance the efficiency of the building design process outcomes.

Keywords: complexity, process, building desgin, Riba, design complexity, network, network analysis

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Authors: Sihana Ahmeti Lika, Merita Dauti, Ledjan Malaj

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The objective of this study is to analyze the prophylactic usage of low molecular weight heparine (LMWH) along pregnancy and the correlation between their usage and month/week of pregnancy, in the Department of Gynecology and Obstetrics, at Clinical Hospital in Tetovo. A retrospective study was undertaken during 01 January–31 December 2012. Over of one year, the total number of patients was 4636. Among the 1447 (32.21%) pregnant women, 298 (20.59%) of them were prescribed LMWH. The majority of patients given LMWH, 119 (39.93%) were diagnosed hypercoagulable. The age group with the highest attendance was 25-35, 141 patients (47.32%). For 195 (65.44%) patients, this was their first pregnancy. Earliest stage of using LMWH was the second month of pregnancy 4 (1.34%) cases. The most common patients, were 70 women along the seventh month (23.49%), followed by 68 in the ninth month of pregnancy (22.81%). Women in the 28th gestational week, were found to be the most affected, a total of 55 (78.57%) were in that week. Clexane 2000 and Fraxiparine 0.3 were the most common for which low molecular weight heparine was prescribed. The number of patients which received Clexane 2000 was 84 (28.19%), followed by those with Fraxiparine 0.3 81 (27.18%). The administration of LMWH is associated with long hospitalization (median 14,6 days).

Keywords: hypercoagulable state, low moleculare weight heparine, month of pregnancy, pregnant women

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Authors: Walid Mousa, Mohamed Nayel, Ahmed Zaghawa, Akram Salama, Ahmed El-Sify, Hesham Rashad, Dina El-Shafey

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Mycoplasmosis in small ruminants constitutes a serious contagious problem in smallholders causing severe economic losses worldwide. This study was conducted to determine the clinical, Minimum Inhibitory Concentration (MIC) and molecular characterization of Mycoplasma species associated in sheep breeding herds in Menoufiya governorate, Egypt. Out of the examination of 400 sheep, 104 (26%) showed respiratory manifestations, nasal discharges, cough and conjunctivitis with systemic body reaction. Meanwhile, out of these examined sheep, only 56 (14%) were positive for mycoplasma isolation onto PPLO(Pleuropneumonia-like organisms) specific medium. The MIC for evaluating the efficacy of sensitivity of Mycoplasma isolates against different antibiotics groups revealed that both the Linospectin and Tylosin with 2ug, 0.25ug/ml concentration were the most effective antibiotics for Mycoplasma isolates. The application of PCR was the rapid, specific and sensitive molecular approach for detection of M. ovipneumoniae, and M. arginine at 390 and 326 bp, respectively, in all tested isolates. In conclusion, the diagnosis of Mycoplsamosis in sheep is important to achieve effective control measures and minimizing the disease dissemination among sheep herds.

Keywords: MIC, mycoplasmosis, PCR, sheep

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Authors: Hosam Abdelhady

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Filming the behaviors of individual DNA molecules in their environment when they interact with individual medicinal nano-polymers in a molecular scale has opened the door to understand the effect of the molecular shape, size, and incubation time with nanocarriers on optimizing the design of robust genetic Nano molecules able to resist the enzymatic degradation, enter the cell, reach to the nucleus and kill individual cancer cells in their environment. To this end, we will show how we applied the 4D AFM as a guide to finetune the design of genetic nanoparticles and to film the effects of these nanoparticles on the nanomechanical and morphological profiles of individual cancer cells.

Keywords: AFM, dendrimers, nanoparticles, DNA, gene therapy, imaging

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Authors: Oscar Corredor, Alexander Guzman, Adan Leon

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Density is a bulk physical property that indicates the quality of a petroleum fraction. It is also a useful property to estimate various physicochemical properties of fraction and petroleum fluids; however, the determination of density of extra heavy residual (EHR) fractions by standard methodologies, (ASTM D70) shows limitations for samples with higher densities than 1.0879 g/cm3. For this reason, a dilution methodology was developed in order to determinate density for those particular fractions, 87 (EHR) fractions were obtained as products of the fractionation of Colombian typical Vacuum Distillation Residual Fractions using molecular distillation (MD) and extraction with Solvent N-hexane in Supercritical Conditions (SFEF) pilot plants. The proposed methodology showed reliable results that can be demonstrated with the standard deviation of repeatability and reproducibility values of 0.0031 and 0.0061 g/ml respectively. In the same way, it was possible to determine densities in fractions EHR up to 1.1647g/cm3 and °API values obtained were ten times less than the water reference value.

Keywords: API, density, vacuum residual, molecular distillation, supercritical fluid extraction

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Authors: Chakrapani Pullagummi, Arun Jyothi Bheemagani, B. Chandra Sekhar Singh, Prem Kumar, A. Roja Rani

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Diabetes mellitus describes a metabolic disorder of multiple aetiology characterized by chronic hyperglycaemia with disturbances of carbohydrate, fat and protein metabolism resulting from defects in insulin secretion and its action. The objective of present study was alloxan induced diabetes in S.D (Sprague Dawley) rats, treated with leaf extract of Andrographis paniculata and bark extract of Erythrina indica. Plant extract treated rats were analyzed biochemically and molecularly. on normal and diabetic rats. The changes in MDA (lipid peroxidation) and glucose (by GOD method) levels in blood of both normal and diabetic rat were analyzed. Diabetes induced rats were treated with methanolic extracts of Andrographis paniculata leaf and Erythrina indica bark which are of medicinal importance. Later after inducing diabetes the rats were treated with medicinal plant extracts, Andrographis paniculata leaf and Erythrina indica bark which are well known for their anti diabetic and antioxidative property in order to control the glucose and MDA levels. The blood plasma of diabetic and normal rats was analyzed for the levels of MDA (lipid peroxidation) and glucose levels. Results of this study suggested that the Andrographis paniculata leaf and Erythrina indica can be used as a potential natural antidiabetic agent for treating and postponing the appearance of complications that arise due to Diabetes. Molecular study deals with the analysis of binding mechanism of 2 selected natural compounds from Andrographis and Erythrina extracts against the novel target for type T2D namely PPAR-γ compared with Rosiglitazone (standard compound). The results revealed that most of the selected herbal lead compounds were effective targets against the receptors. These compounds showed favorable interactions with the amino acid residues thereby substantiating their proven efficacy as anti-diabetic compounds.

Keywords: andrographis paniculata, erythrina indica, alloxan, lipid peroxidation, blood glucose level, PPAR-γ

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Authors: Joshua Paul Steimel, Michael Pappas, Ethan Hall

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Particle-particle interactions are critical in determining the state of an active matter system. Unique and ubiquitous non-equilibrium behavior like swarming, vortexing, spiraling, and much more is governed by interactions between active units or particles. In hybrid active-passive matter systems, the attraction between spinning active units in a 2D monolayer of passive particles is controlled by the mechanical behavior of the passive monolayer. We demonstrate here that the range and dynamics of this attraction can be controlled by changing the composition of the passive monolayer by adding dopant passive particles. These dopant passive particles effectively pin the movement of dislocation motion in the passive media and reduce the probability of defect motion required to erode the bridge of passive particles between active spinners, thus reducing the range of attraction. Additionally, by adding an out of plane component to the magnetic moment and creating a top-like motion a short range repulsion emerges between the top-like particle. At inter-top distances less than four particle diameters apart, the tops repel but beyond that, distance attract up to 13 particle diameters apart. The tops were also able to locally and transiently anneal the passive monolayer. Thus we demonstrate that by tuning several parameters of the hybrid active matter system, one can observe very different emergent behavior.

Keywords: active matter, colloids, ferromagnetic, annealing

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Authors: Shagufta Tabassum

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The study of dielectric properties in a binary mixture of liquids is very useful to understand the liquid structure, molecular interaction, dynamics, and kinematics of the mixture. Time-domain reflectometry (TDR) is a powerful tool for studying the cooperation and molecular dynamics of the H-bonded system. In this paper, we discuss the basic calibration and normalization procedure for time-domain reflectometry measurements. Our approach is to explain the different types of error occur during TDR measurements and how these errors can be eliminated or minimized.

Keywords: time domain reflectometry measurement techinque, cable and connector loss, oscilloscope loss, and normalization technique

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Authors: Mustafa Malki, Ewan R. Pearson

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Tools utilized by health care practitioners to flag potential adverse drug reactions secondary to drug-drug interactions ignore individual genetic variation, which has the potential to markedly alter the severity of these interactions. To our best knowledge, there have been limited published studies on the impact of genetic variation on drug-drug interactions. Therefore, our aim in this project is the discovery of previously unrecognized, clinically important drug-drug-gene interactions (DDGIs) within the list of most commonly used drug combinations in the UK. The UKBB database was utilized to identify the top most frequently prescribed drug combinations in the UK with at least one route of interaction (over than 200 combinations were identified). We have recognised 37 common and unique interacting genes considering all of our drug combinations. Out of around 600 potential genetic variants found in these 37 genes, 100 variants have met the selection criteria (common variant with minor allele frequency ≥ 5%, independence, and has passed HWE test). The association between these variants and the use of each of our top drug combinations has been tested with a case-control analysis under the log-additive model. As the data is cross-sectional, drug intolerance has been identified from the genotype distribution as presented by the lower percentage of patients carrying the risky allele and on the drug combination compared to those free of these risk factors and vice versa with drug tolerance. In GoDARTs database, the same list of common drug combinations identified by the UKBB was utilized here with the same list of candidate genetic variants but with the addition of 14 new SNPs so that we have a total of 114 variants which have met the selection criteria in GoDARTs. From the list of the top 200 drug combinations, we have selected 28 combinations where the two drugs in each combination are known to be used chronically. For each of our 28 combinations, three drug response phenotypes have been identified (drug stop/switch, dose decrease, or dose increase of any of the two drugs during their interaction). The association between each of the three phenotypes belonging to each of our 28 drug combinations has been tested against our 114 candidate genetic variants. The results show replication of four findings between both databases : (1) Omeprazole +Amitriptyline +rs2246709 (A > G) variant in CYP3A4 gene (p-values and ORs with the UKBB and GoDARTs respectively = 0.048,0.037,0.92,and 0.52 (dose increase phenotype)) (2) Simvastatin + Ranitidine + rs9332197 (T > C) variant in CYP2C9 gene (0.024,0.032,0.81, and 5.75 (drug stop/switch phenotype)) (3) Atorvastatin + Doxazosin + rs9282564 (T > C) variant in ABCB1 gene (0.0015,0.0095,1.58,and 3.14 (drug stop/switch phenotype)) (4) Simvastatin + Nifedipine + rs2257401 (C > G) variant in CYP3A7 gene (0.025,0.019,0.77,and 0.30 (drug stop/switch phenotype)). In addition, some other non-replicated, but interesting, significant findings were detected. Our work also provides a great source of information for researchers interested in DD, DG, or DDG interactions studies as it has highlighted the top common drug combinations in the UK with recognizing 114 significant genetic variants related to drugs' pharmacokinetic.

Keywords: adverse drug reactions, common drug combinations, drug-drug-gene interactions, pharmacogenomics

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Authors: Nisha Prakash, Kritika Anand, Arun Barvat, Prabir Pal, Sonachand Adhikari, Suraj P. Khanna

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Group-III nitride semiconductors (GaN, AlN, InN and their ternary and quaternary compounds) have attracted a great deal of attention for the development of high-performance Ultraviolet (UV) photodetectors. Any midgap defect states in the epitaxial grown film have a direct influence on the photodetectors responsivity. The proportion of the midgap defect states can be controlled by the growth parameters. To study this we have grown high quality epitaxial GaN films on MOCVD- grown GaN template using plasma-assisted molecular beam epitaxy (PAMBE) with different growth parameters. Optical and electrical properties of the films were characterized by room temperature photoluminescence and photoconductivity measurements, respectively. The observed persistent photoconductivity behaviour is proportional to the yellow luminescence (YL) and the absolute responsivity has been found to decrease with decreasing YL. The results will be discussed in more detail later.

Keywords: gallium nitride, plasma-assisted molecular beam epitaxy, photoluminescence, photoconductivity, persistent photoconductivity, yellow luminescence

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Authors: Lablali Mohammed, Mes-Adi Hassan, Mazroui M’Hammed

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To tackle the complexity of grasping atomic-scale structures and unraveling the factors affecting the development of thin films. In our work, we perform the deposition of Nb atoms on Cu substrates using the molecular dynamics simulation combined with the embedded atom method to describe the interaction between different atoms. We investigated the impact of varying deposition rates and thermal annealing processes on the microstructural, morphological, and mechanical characteristics of the deposited Nb film. Our findings reveal that Nb atom growth on the Cu substrate occurs in island mode, accompanied by the presence of nucleation phenomena during growth. On the other hand, mixing behavior was observed at the interface between the film and the substrate, where Nb penetration is initially limited to the first Cu layer, whereas Cu atoms diffuse until reaching the third layer in the Nb film. Furthermore, Nb exhibits a BCC structure, with a significant concentration observed at a rate of 5 atoms/ps, and annealing further amplifies these percentages. Deposition at different rates leads to distinct levels of compressive normal and biaxial stress.

Keywords: molecular dynamics, Nb thin film, structure and morphology, atomic penetration

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Authors: Suman Bala, Sunil Kamboj, Vipin Saini

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Quantitative Structure Activity Relationship (QSAR) analysis has been developed to relate antifungal activity of novel substituted 1,3,4-oxadiazole against Candida albicans and Aspergillus niger using computer assisted multiple regression analysis. The study has shown the better relationship between antifungal activities with respect to various descriptors established by multiple regression analysis. The analysis has shown statistically significant correlation with R² values 0.932 and 0.782 against Candida albicans and Aspergillus niger respectively. These derivatives were further subjected to molecular docking studies to investigate the interactions between the target compounds and amino acid residues present in the active site of glucosamine-6-phosphate synthase. All the synthesized compounds have better docking score as compared to standard fluconazole. Our results could be used for the further design as well as development of optimal and potential antifungal agents.

Keywords: 1, 3, 4-oxadiazole, QSAR, multiple linear regression, docking, glucosamine-6-phosphate synthase

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Authors: Nandhana Vivek, Bhaskar Gogoi, Ayyavu Mahesh

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Breast cancer metastasis plays a key role in cancer progression and fatality. The present study examines the potential causes of metastasis in breast cancer by investigating the novel interactions between genes and their pathways. The gene expression profile of GSE99394, GSE1246464, and GSE103865 was downloaded from the GEO data repository to analyze the differentially expressed genes (DEGs). Protein-protein interactions, target factor interactions, pathways and gene relationships, and functional enrichment networks were investigated. The proliferation pathway was shown to be highly expressed in breast cancer progression and metastasis in all three datasets. Gene Ontology analysis revealed 11 DEGs as gene targets to control breast cancer metastasis: LYN, DLGAP5, CXCR4, CDC6, NANOG, IFI30, TXP2, AGTR1, MKI67, and FTH1. Upon studying the function, genomic and proteomic data, and pathway involvement of the target genes, DLGAP5 proved to be a promising candidate due to it being highly differentially expressed in all datasets. The study takes a unique perspective on the avenues through which DLGAP5 promotes metastasis. The current investigation helps pave the way in understanding the role DLGAP5 plays in metastasis, which leads to an increased incidence of death among breast cancer patients.

Keywords: genomics, metastasis, microarray, cancer

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Authors: Diego Liberati

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Standard molecular modeling is traditionally done through Schroedinger equations via the help of powerful tools helping to manage them atom by atom, often needing High Performance Computing. Here, a full portfolio of new tools, conjugating statistical inference in the so called eXplainable Artificial Intelligence framework (in the form of Machine Learning of understandable rules) to the more traditional modeling and simulation control theory of mixed dynamic logic hybrid processes, is offered as quite a general purpose even if making an example to a popular chemical physics set of problems.

Keywords: understandable rules ML, k-means, PCA, PieceWise Affine Auto Regression with eXogenous input

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Authors: Shayli Varasteh Moradi, Wayne A. Johnston, Dejan Gagoski, Kirill Alexandrov

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The demand for a rapid and more efficient technique to identify protein-protein interaction particularly in the areas of therapeutics and diagnostics development is growing. The method described here is a rapid in vitro protein-protein interaction analysis approach based on AlphaLISA technology combined with Leishmania tarentolae cell-free protein production (LTE) system. Cell-free protein synthesis allows the rapid production of recombinant proteins in a multiplexed format. Among available in vitro expression systems, LTE offers several advantages over other eukaryotic cell-free systems. It is based on a fast growing fermentable organism that is inexpensive in cultivation and lysate production. High integrity of proteins produced in this system and the ability to co-express multiple proteins makes it a desirable method for screening protein interactions. Following the translation of protein pairs in LTE system, the physical interaction between proteins of interests is analysed by AlphaLISA assay. The assay is performed using unpurified in vitro translation reaction and therefore can be readily multiplexed. This approach can be used in various research applications such as epitope mapping, antigen-antibody analysis and protein interaction network mapping. The intra-viral protein interaction network of Zika virus was studied using the developed technique. The viral proteins were co-expressed pair-wise in LTE and all possible interactions among viral proteins were tested using AlphaLISA. The assay resulted to the identification of 54 intra-viral protein-protein interactions from which 19 binary interactions were found to be novel. The presented technique provides a powerful tool for rapid analysis of protein-protein interaction with high sensitivity and throughput.

Keywords: AlphaLISA technology, cell-free protein expression, epitope mapping, Leishmania tarentolae, protein-protein interaction

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Authors: E. G. Zaki, M. A. Migahed, A. M. Al-Sabagh, E. A. Khamis

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Inhibition effect of four novel nonionic surfactants based on sulphonamide, of linear alkyl benzene sulphonic acid (LABS), was reacted with 1 mole triethylenetetramine, tetraethylenepentamine then Ethoxylation of amide X 65 type carbon steel in oil wells formation water under H2S environment was investigated by electrochemical measurements. Scanning electron microscopy (SEM) and energy dispersion X-ray (EDX) were used to characterize the steel surface. The results showed that these surfactants act as a corrosion inhibitor in and their inhibition efficiencies depend on the ethylene oxide content in the system. The obtained results showed that the percentage inhibition efficiency (η%) was increased by increasing the inhibitor concentration until the critical micelle concentration (CMC) reached The quantum chemistry calculations were carried out to study the molecular geometry and electronic structure of obtained derivatives. The energy gap between the highest occupied molecular orbital and lowest unoccupied molecular orbital has been calculated using the theoretical computations to reflect the chemical reactivity and kinetic stability of compounds.

Keywords: corrosion, surfactants, steel surface, quantum

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Authors: Sajewicz-Krukowska Joanna, Domańska-Blicharz Katarzyna, Tarasiuk Karolina, Marzec-Kotarska Barbara

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Astroviral infections pose a significant problem in the poultry industry, leading to multiple adverse effects such as decreased egg production, breeding disorders, poor weight gain, and even increased mortality. Commonly observed chicken astrovirus (CAstV) was recently reported to be responsible for "white chicks syndrome" associated with increased embryo/chick mortality. The CAstV-mediated pathogenesis in chicken occurs due to complex interactions between the infectious pathogen and the immune system. Many aspects of CAstV-chicken interactions remain unclear, and there is no information available regarding gene expression changes in the chicken's spleen in response to CAstV infection. We aimed to investigate the molecular background triggered by CAstV infection. Ten 21-day-old SPF White Leghorn chickens were divided into two groups of 5 birds each. One group was inoculated with CAstV, and the other was used as the negative control. On 4th dpi, spleen samples were collected and immediately frozen at -70°C for RNA isolation. We analysed transcriptional profiles of the chickens' spleens at the 4th day following infection using RNA-seq to establish differentially expressed genes (DEGs). The RNA-seq findings were verified by quantitative real-time PCR (qRT-PCR). A total of 31959 transcripts were identified in response to CAstV infection. Eventually 45 DEGs (p-value<0.05; Log2Foldchange>1)were recognized in the spleen after CAstV infection (26 upregulated DEGs and 19 downregulated DEGs). qRT-PCR performed on 4 genes (IFIT5, OASL, RASD1, DDX60) confirmed RNAseq results. Top differentially expressed genes belonged to novel putative IFN-induced CAstV restriction factors. Most of the DEGs were associated with RIG-I–like signalling pathway or, more generally, with an innate antiviral response(upregulated: BLEC3, CMPK2, IFIT5, OASL, DDX60, IFI6, and downregulated: SPIK5, SELENOP, HSPA2, TMEM158, RASD1, YWHAB). The study provided a global analysis of host transcriptional changes that occur during CAstV infection in vivo and proved the cell cycle in the spleen and immune signalling in chickens were predominantly affected upon CAstV infection.

Keywords: chicken astrovirus, CastV, RNA-seq, transcriptome, spleen

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Authors: Wenjin Zhu, Ian E. Jacobs, Henning Sirringhaus

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We have demonstrated a model system for the controlled incorporation of tie-chains into semicrystalline conjugated polymers using blends of different molecular weights that leads to a significant increase in electrical conductivity. Through careful assessment of the microstructural evolution upon tie chain incorporation we have demonstrated that no major changes in phase morphology or structural order in the crystalline domains occur and that the observed enhancement in electrical conductivity can only be explained consistently by tie chains facilitating the transport across grain boundaries between the crystalline domains. Here we studied the thermoelectric properties of aligned, ion exchange-doped ribbon phase PBTTT with blends of different molecular weight components. We demonstrate that in blended films higher electrical conductivities (up to 4810.1 S/cm), Seebeck coefficients and thermoelectric power factors of up to 172.6 μW m-1 K-2 can be achieved than in films with single component molecular weights. We investigate the underpinning thermoelectric transport physics, including structural and spectroscopic characterization, to better understand how controlled tie chain incorporation can be used to enhance the thermoelectric performance of aligned conjugated polymers.

Keywords: organic electronics, thermoelectrics, conjugated polymers, tie chain

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Authors: Zeev Wiesman, Paula Berman, Nitzan Meiri, Charles Linder

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Supramolecular chemistry refers to the domain of chemistry beyond that of molecules and focuses on the chemical systems made up of a discrete number of assembled molecular sub units or components. Biodiesel components self arrangements is closely related/affect their physical properties in combustion systems and emission. Due to technological difficulties, knowledge regarding the molecular packing of FAMEs (biodiesel) in the liquid phase is limited. Spectral tools such as X-ray and NMR are known to provide evidences related to molecular structure organization. Recently, it was reported by our research group that using 1H Time Domain NMR methodology based on relaxation time and self diffusion coefficients, FAMEs clusters with different motilities can be accurately studied in the liquid phase. Head to head dimarization with quasi-smectic clusters organization, based on molecular motion analysis, was clearly demonstrated. These findings about the assembly/packing of the FAME components are directly associated with fluidity/viscosity of the biodiesel. Furthermore, these findings may provide information of micro/nano-particles that are formed in the delivery and injection system of various combustion systems (affected by thermodynamic conditions). Various relevant parameters to combustion such as: distillation/Liquid Gas phase transition, cetane number/ignition delay, shoot, oxidation/NOX emission maybe predicted. These data may open the window for further optimization of FAME/diesel mixture in terms of combustion and emission.

Keywords: supermolecular chemistry, FAMEs, liquid phase, fluidity, LF-NMR

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Authors: Maryam Torabi, Habibi, Abdolahi, Mohammadi, Hassanzadeh, Darban Maghami, Baghi

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Sheeppox Virus (SPPV) and goatpox virus (GTPV) are considerable diseases of sheep, and goats, caused by viruses of the Capripoxvirus (CaPV) genus. They are responsible for economic losses. Animal mortality, morbidity, cost of vaccinations, and restrictions in animal products’ trade are the reasons of economic losses. Control and eradication of CaPV depend on early detection of outbreaks so that molecular detection and genetic analysis could be effective to this aim. This study was undertaken to molecularly characterize SPPV and GTPV strains that have been circulating in Iran. 120 skin papules and nodule biopsies were collected from different regions of Iran and were examined for SPPV, GTPV viruses using TaqMan Real -Time PCR. Some of these amplified genes were sequenced, and phylogenetic trees were constructed. Out of the 120 samples analysed, 98 were positive for CaPV by Real- Time PCR (81.6%), and most of them wereSPPV. then 10 positive samples were sequenced and characterized by amplifying the ORF 103CaPV gene. sequencing and phylogenetic analysis for these positive samples revealed a high percentage of identity with SPPV isolated from different countries in Middle East. In conclusions, molecular characterization revealed nearly complete identity with all recent SPPVs strains in local countries that requires further studies to monitor the virus evolution and transmission pathways to better understand the virus pathobiology that will help for SPPV control.

Keywords: molecular epidemiology, Real-Time PCR, phylogenetic analysis, capripoxviruses

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Authors: Eman M. Sarhan, Doaa A. Ghareeb, Gabriella Ortore, Amr A. Amara, Mohamed M. El-Sayed

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Drug salting and nanoparticle-based drug delivery formulations are considered to be an effective means for rendering the hydrophobic drugs’ nano-scale dispersion in aqueous media, and thus circumventing the pitfalls of their poor solubility as well as enhancing their membrane permeability. The current study aims to increase the bioavailability of quaternary ammonium berberine through acid salting and biodegradable bovine serum albumin (BSA)-based nanoparticulate drug formulation. Berberine hydroxide (BBR-OH) that was chemically synthesized by alkalization of the commercially available berberine hydrochloride (BBR-HCl) was then acidified to get Di-berberine sulfate (BBR)₂SO₄. The purified crystals were spectrally characterized. The desolvation technique was optimized for the preparation of size-controlled BSA-BBR-HCl, BSA-BBR-OH, and BSA-(BBR)₂SO₄ nanoparticles. Particle size, zeta potential, drug release, encapsulation efficiency, Fourier transform infrared spectroscopy (FTIR), tandem MS-MS spectroscopy, energy-dispersive X-ray spectroscopy (EDX), scanning and transmitting electron microscopic examination (SEM, TEM), in vitro bioactivity, and in silico drug-polymer interaction were determined. BSA (PDB ID; 4OR0) protonation state at different pH values was predicted using Amber12 molecular dynamic simulation. Then blind docking was performed using Lamarkian genetic algorithm (LGA) through AutoDock4.2 software. Results proved the purity and the size-controlled synthesis of berberine-BSA-nanoparticles. The possible binding poses, hydrophobic and hydrophilic interactions of berberine on BSA at different pH values were predicted. Antioxidant, anti-hemolytic, and cell differentiated ability of tested drugs and their nano-formulations were evaluated. Thus, drug salting and the potentially effective albumin berberine nanoparticle formulations can be successfully developed using a well-optimized desolvation technique and exhibiting better in vitro cellular bioavailability.

Keywords: berberine, BSA, BBR-OH, BBR-HCl, BSA-BBR-HCl, BSA-BBR-OH, (BBR)₂SO₄, BSA-(BBR)₂SO₄, FTIR, AutoDock4.2 Software, Lamarkian genetic algorithm, SEM, TEM, EDX

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Authors: Amy Williamson, Kerry Armstrong, Jason Edwards, Patricia Obst

Abstract:

Australian national policy endorses a responsive approach to work health and safety (WHS) regulation, combining positive motivators (education and guidance), with compliance monitoring and enforcement to encourage and secure compliance with legislation. Despite theoretical support for responsive regulation, there is limited evidence regarding how to achieve best results in practice. Using positive psychology as a novel paradigm, this study aims to investigate how non-punitive regulatory interactions can be improved to further encourage regulatory compliance in the construction industry. As part of a larger project, semi-structured interviews were conducted with 35 inspectorate staff and 11 managers in the Australian (Queensland) construction industry. Using an inductive, grounded approach, an in-depth qualitative investigation was conducted to identify the positive psychological principles which underpin effective use of the non-punitive aspects of responsive regulation. Results highlighted the importance of effective engagement between inspectors and industry managers. This involved the need to interact cooperatively and encourage compliance with WHS legislation. Several strategies were identified that assisted regulatory interactions and the ability of inspectors to engage. The importance of communication and interpersonal skills was reported to be critical to any interaction, regardless of the nature of the visit and regulatory tools used. In particular, the use of clear and open communication fostered trust and rapport which facilitated more positive interactions. The importance of respect and empathy was also highlighted. The need for provision of guidance and direction on how to achieve compliance was also reported. This related to ensuring companies understand their WHS obligations, providing specific advice regarding how to rectify a breach and meet compliance requirements, and ensuring sufficient follow up to confirm that compliance is successfully achieved. In the absence of imminent risk, allowing companies the opportunity to comply before further action is taken was also highlighted. Increased proactive engagement with industry to educate and promote the vision of safety at work was also reported. Finally, provision of praise and positive feedback was reported to assist interactions and encourage the continuation of good practices. Evidence from positive psychology and organisational psychology was obtained to support the use of each strategy in practice. In particular, the area of positive leadership provided a useful framework to consider the factors and conditions that drive positive interactions within the context of work health and safety and the specific relationship between inspectors and industry managers. This study provides fresh insight into key psychological principles which support non-punitive regulatory interactions in the area of workplace health and safety. The findings of this research contribute to a better understanding of how inspectors can enhance the efficacy of their regulatory interactions to improve compliance with legislation. Encouraging and assisting compliance through effective non-punitive activity offers a sustainable pathway for promoting safety and preventing fatalities and injuries in the construction industry.

Keywords: engagement, non-punitive approaches to compliance, positive interactions in the workplace, work health and safety compliance

Procedia PDF Downloads 149

Authors: S. Ghalem, M. Mesmoudi, I. Daoudand, H. Allali

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The nitrogen-containing bisphosphonates (N-BPs) are well established as the treatments of choice for disorders of excessive bone resorption, myeloma and bone metastases, and osteoporosis. They inhibit farnesyl pyrophosphate synthase (FFPS), a key enzyme in the mevalonate pathway, resulting in inhibition of the prenylation of small GTP-binding proteins in osteoclasts and disruption of their cytoskeleton, adhesion/spreading, and invasion of cancer cells. A very few examples for synthesis of α-amino bisphosphonates based on several amino acids are known from the literature. In the present work, esters of aminoacid react with ketophsophonate (or their analog acid or acyl) to afford the desired products, α-iminophosphonates. The reaction of imine with dimethyl phosphate in the presence of catalytic amount of I2 give ester of α-aminobisphosphonate as sole product in good yield. Finally, we used computational docking methods to predict how several α-aminobisphosphonates bind to FPPS and how R and X influence. Pamidronate, β-aminobisphosphonate already marketed, was used as reference. These results are of interest since they represent a new and simple way to sythesize α-aminobisphosphonates with a free COOH group increased by R2 functionalisable and opening up the possibility of using the molecular docking to facilitate the design of other, novel FFPS inhibitors.

Keywords: drug research, cancer, α-amino bisphosphonates, molecular docking

Procedia PDF Downloads 270

Authors: Hao-Wen Chang, Santhanamoorthi Nachimuthu, Jyh-Chiang Jiang

Abstract:

All-solid-state lithium batteries (ASSLBs) are increasingly recognized as a safer and more reliable alternative to conventional lithium-ion batteries due to their non-flammable nature and enhanced safety performance. ASSLBs utilize a range of solid-state electrolytes, including solid polymer electrolytes (SPEs), inorganic solid electrolytes (ISEs), and composite polymer electrolytes (CPEs). SPEs are particularly valued for their flexibility, ease of processing, and excellent interfacial compatibility with electrodes, though their ionic conductivity remains a significant limitation. ISEs, on the other hand, provide high ionic conductivity, broad electrochemical windows, and strong mechanical properties but often face poor interfacial contact with electrodes, impeding performance. CPEs, which merge the strengths of SPEs and ISEs, represent a compelling solution for next-generation ASSLBs by addressing both electrochemical and mechanical challenges. Despite their potential, the mechanisms governing lithium-ion transport within these systems remain insufficiently understood. In this study, we designed CPEs based on argyrodite-type Li₆PS₅Cl (LPSC) combined with two distinct polymer matrices: poly(ethylene oxide) (PEO) with 24.5 wt% lithium bis(trifluoromethane)sulfonimide (LiTFSI) and polycaprolactone (PCL) with 25.7 wt% LiTFSI. Through density functional theory (DFT) calculations, we investigated the interfacial chemistry of these materials, revealing critical insights into their stability and interactions. Additionally, ab initio molecular dynamics (AIMD) simulations of lithium electrodes interfaced with LPSC layers containing polymers and LiTFSI demonstrated that the polymer matrix significantly mitigates LPSC decomposition, compared to systems with only a lithium electrode and LPSC layers. These findings underscore the pivotal role of CPEs in improving the performance and longevity of ASSLBs, offering a promising path forward for next-generation energy storage technologies.

Keywords: all-solid-state lithium-ion batteries, composite solid electrolytes, DFT calculations, Li-ion transport

Procedia PDF Downloads 19

Authors: Ankur Chaudhuri, Sibani Sen Chakraborty

Abstract:

In human, glutaminyl cyclase activity is highly abundant in neuronal and secretory tissues and is preferentially restricted to hypothalamus and pituitary. The N-terminal modification of β-amyloids (Aβs) peptides by the generation of a pyro-glutamyl (pGlu) modified Aβs (pE-Aβs) is an important process in the initiation of the formation of neurotoxic plaques in Alzheimer’s disease (AD). This process is catalyzed by glutaminyl cyclase (QC). The expression of QC is characteristically up-regulated in the early stage of AD, and the hallmark of the inhibition of QC is the prevention of the formation of pE-Aβs and plaques. A computer-aided drug design (CADD) process was employed to give an idea for the designing of potentially active compounds to understand the inhibitory potency against human glutaminyl cyclase (QC). This work elaborates the ligand-based and structure-based pharmacophore exploration of glutaminyl cyclase (QC) by using the known inhibitors. Three dimensional (3D) quantitative structure-activity relationship (QSAR) methods were applied to 154 compounds with known IC50 values. All the inhibitors were divided into two sets, training-set, and test-sets. Generally, training-set was used to build the quantitative pharmacophore model based on the principle of structural diversity, whereas the test-set was employed to evaluate the predictive ability of the pharmacophore hypotheses. A chemical feature-based pharmacophore model was generated from the known 92 training-set compounds by HypoGen module implemented in Discovery Studio 2017 R2 software package. The best hypothesis was selected (Hypo1) based upon the highest correlation coefficient (0.8906), lowest total cost (463.72), and the lowest root mean square deviation (2.24Å) values. The highest correlation coefficient value indicates greater predictive activity of the hypothesis, whereas the lower root mean square deviation signifies a small deviation of experimental activity from the predicted one. The best pharmacophore model (Hypo1) of the candidate inhibitors predicted comprised four features: two hydrogen bond acceptor, one hydrogen bond donor, and one hydrophobic feature. The Hypo1 was validated by several parameters such as test set activity prediction, cost analysis, Fischer's randomization test, leave-one-out method, and heat map of ligand profiler. The predicted features were then used for virtual screening of potential compounds from NCI, ASINEX, Maybridge and Chembridge databases. More than seven million compounds were used for this purpose. The hit compounds were filtered by drug-likeness and pharmacokinetics properties. The selective hits were docked to the high-resolution three-dimensional structure of the target protein glutaminyl cyclase (PDB ID: 2AFU/2AFW) to filter these hits further. To validate the molecular docking results, the most active compound from the dataset was selected as a reference molecule. From the density functional theory (DFT) study, ten molecules were selected based on their highest HOMO (highest occupied molecular orbitals) energy and the lowest bandgap values. Molecular dynamics simulations with explicit solvation systems of the final ten hit compounds revealed that a large number of non-covalent interactions were formed with the binding site of the human glutaminyl cyclase. It was suggested that the hit compounds reported in this study could help in future designing of potent inhibitors as leads against human glutaminyl cyclase.

Keywords: glutaminyl cyclase, hit lead, pharmacophore model, simulation

Procedia PDF Downloads 130

Authors: Mohammad Reza Ghaani, Niall English

Abstract:

Hydrogen is looked upon as the next-generation clean-energy carrier; the search for an efficient material and method for storing hydrogen has been, and is, pursued relentlessly. Clathrate hydrates are inclusion compounds wherein guest gas molecules like hydrogen are trapped in a host water-lattice framework. These types of materials can be categorised as potentially attractive hosting environments for physical hydrogen storage (i.e., no chemical reaction upon storage). Non-equilibrium molecular dynamics (NEMD) simulations have been performed to investigate thermal-driven break-up of propane-hydrate interfaces with liquid water at 270-300 K, with the propane hydrate containing either one or no hydrogen molecule in each of its small cavities. In addition, two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water: a 001-direct surface cleavage and one with completed cages. The geometric hydrate-ice-liquid distinction criteria of Báez and Clancy were employed to distinguish between the hydrate, ice lattices, and liquid-phase. Consequently, the melting temperatures of interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. The different hydrate-edge terminations for the hydrate-water interface led to statistically-significant differences in the observed melting point and dissociation profile: it was found that the clathrate with the planar interface melts at around 280 K, whilst the melting temperature of the cage-completed interface was determined to be circa 270 K.

Keywords: hydrogen storage, clathrate hydrate, molecular dynamics, thermal dissociation

Procedia PDF Downloads 272

Authors: Paul Awolade, Parvesh Singh

Abstract:

The global threat of pathogenic resistance to available therapeutic agents has become a menace to clinical practice, public health and man’s existence inconsequential. This has therefore led to an exigency in the development of new molecular scaffolds with profound activity profiles. In this vein, a versatile synthetic tool for accessing new molecules by incorporating two or more pharmacophores into a single entity with the unique ability to be recognized by multiple receptors hence leading to an improved bioactivity, known as molecular hybridization, has been explored with tremendous success. Accordingly, aware of the similarity in pharmacological activity spectrum of quinoline and 1,2,3-triazole pharmacophores such as; anti-Alzheimer, anticancer, anti-HIV, antimalarial and antimicrobial to mention but a few, the present study sets out to synthesize hybrids of quinoline and 1,2,3-triazole. The hybrids were accessed via click chemistry using copper catalysed azide-alkyne 1,3-dipolar cycloaddition reaction. All synthesized compounds were evaluated for their pharmaco-potential in an antimicrobial assay out of which the 3-OH derivative emerged as the most active with MIC value of 4 μg/mL against Cryptococcus neoformans; a value superior to standard Fluconazole and comparable to Amphotericin B. Structures of synthesized hybrids were elucidated using appropriate spectroscopic techniques (1H, 13C and 2D NMR, FT-IR and HRMS).

Keywords: bioisostere, click chemistry, molecular hybridization, quinoline, 1, 2, 3-triazole

Procedia PDF Downloads 128