Search results for: molecular mechanisms

Authors: Monisha Isaac

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Use of molecular markers for selecting plants with desired traits has been started long back. Due to their heritable characteristics, they are useful for identification and characterization of specific genotypes. The study involves various types of molecular markers used to select multiple desired characters in plants, their properties, and advantages to improve crop productivity in adverse climatological conditions for the purpose of providing food security to fast-growing global population. The study shows that genetic similarities obtained from molecular markers provide more accurate information and the genetic diversity can be better estimated from the genetic relationship obtained from the dendrogram. The information obtained from markers assisted characterization is more suitable for the crops of economic importance like sugarcane.

Keywords: molecular markers, crop productivity, genetic diversity, genotype

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Authors: Ferid Hammami

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The molecular geometries of the possible conformations of pyruvic acid-water complexes (PA-(H₂O)ₙ = 1- 4) have been fully optimized at DFT/B3LYP/6-311G ++ (d, p) levels of calculation. Among several optimized molecular clusters, the most stable molecular arrangements obtained when one, two, three, and four water molecules are hydrogen-bonded to a central pyruvic acid molecule are presented in this paper. Apposite topological and geometrical parameters are considered as primary indicators of H-bond strength. Atoms in molecules (AIM) analysis shows that pyruvic acid can form a ring structure with water, and the molecular structures are stabilized by both strong O-H...O and C-H...O hydrogen bonds. In large clusters, classical O-H...O hydrogen bonds still exist between water molecules, and a cage-like structure is built around some parts of the central molecule of pyruvic acid. The electrostatic potential energy map (MEP) and the HOMO-LUMO molecular orbital (highest occupied molecular orbital-lowest unoccupied molecular orbital) analysis has been performed for all considered complexes.

Keywords: pyruvic acid, PA-water complex, hydrogen bonding, DFT, AIM, MEP, HOMO-LUMO

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

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

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

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Authors: Mei Hong, Wei Liu, Xuemin Dai, Yanxiong Pan, Xiangling Ji

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Polyamic acid (PAA) is the precursor of polyimide (PI) prepared by a two-step method, its molecular weight and molecular weight distribution not only play an important role during the preparation and processing, but also influence the final performance of PI. However, precise characterization on molecular weight of PAA is still a challenge because of the existence of very complicated interactions in the solution system, including the electrostatic interaction, hydrogen bond interaction, dipole-dipole interaction, etc. Thus, it is necessary to establisha suitable strategy which can completely suppress these complex effects and get reasonable data on molecular weight. Herein, the gel permeation chromatography (GPC) coupled with differential refractive index (RI) and multi-angle laser light scattering (MALLS) detectors were applied to measure the molecular weight of (6FDA-DMB) PAA using different mobile phases, LiBr/DMF, LiBr/H3PO4/THF/DMF, LiBr/HAc/THF/DMF, and LiBr/HAc/DMF, respectively. It was found that combination of LiBr with HAc can shield the above-mentioned complex interactions and is more conducive to the separation of PAA than only addition of LiBr in DMF. LiBr/HAc/DMF was employed for the first time as a mild mobile phase to effectively separate PAA and determine its molecular weight. After a series of conditional experiments, 0.02M LiBr/0.2M HAc/DMF was fixed as an optimized mobile phase to measure the relative and absolute molecular weights of (6FDA-DMB) PAA prepared, and the obtained Mw from GPC-MALLS and GPC-RI were 35,300 g/mol and 125,000 g/mol, respectively. Particularly, such a mobile phase is also applicable to other PAA samples with different structures, and the final results on molecular weight are also reproducible.

Keywords: Polyamic acids, Polyelectrolyte effects, Gel permeation chromatography, Mobile phase, Molecular weight

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Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

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In the present study, the molecular modeling of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives whit significant anticancer activity was carried out. Modelling of studied compounds was performed by CS ChemBioDraw Ultra v12.0 program for drawing 2D molecular structures and CS ChemBio3D Ultra v12.0 for 3D molecular modelling. The obtained 3D structures were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. Full geometry optimization was done by the Austin Model 1 (AM1) until the root mean square (RMS) gradient reached a value smaller than 0.0001 kcal/Åmol using Molecular Orbital Package (MOPAC) program. The obtained physicochemical, lipophilicity and topological descriptors were used for analysis of molecular similarities and dissimilarities applying suitable chemometric methods (principal component analysis and cluster analysis). These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1306.

Keywords: androstane derivatives, anticancer activity, chemometrics, molecular descriptors

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Authors: Binder Hans

Abstract:

Cancer is no longer seen as solely a genetic disease where genetic defects such as mutations and copy number variations affect gene regulation and eventually lead to aberrant cell functioning which can be monitored by transcriptome analysis. It has become obvious that epigenetic alterations represent a further important layer of (de-)regulation of gene activity. For example, aberrant DNA methylation is a hallmark of many cancer types, and methylation patterns were successfully used to subtype cancer heterogeneity. Hence, unraveling the interplay between different omics levels such as genome, transcriptome and epigenome is inevitable for a mechanistic understanding of molecular deregulation causing complex diseases such as cancer. This objective requires powerful downstream integrative bioinformatics methods as an essential prerequisite to discover the whole genome mutational, transcriptome and epigenome landscapes of cancer specimen and to discover cancer genesis, progression and heterogeneity. Basic challenges and tasks arise ‘beyond sequencing’ because of the big size of the data, their complexity, the need to search for hidden structures in the data, for knowledge mining to discover biological function and also systems biology conceptual models to deduce developmental interrelations between different cancer states. These tasks are tightly related to cancer biology as an (epi-)genetic disease giving rise to aberrant genomic regulation under micro-environmental control and clonal evolution which leads to heterogeneous cellular states. Machine learning algorithms such as self organizing maps (SOM) represent one interesting option to tackle these bioinformatics tasks. The SOMmethod enables recognizing complex patterns in large-scale data generated by highthroughput omics technologies. It portrays molecular phenotypes by generating individualized, easy to interpret images of the data landscape in combination with comprehensive analysis options. Our image-based, reductionist machine learning methods provide one interesting perspective how to deal with massive data in the discovery of complex diseases, gliomas, melanomas and colon cancer on molecular level. As an important new challenge, we address the combined portrayal of different omics data such as genome-wide genomic, transcriptomic and methylomic ones. The integrative-omics portrayal approach is based on the joint training of the data and it provides separate personalized data portraits for each patient and data type which can be analyzed by visual inspection as one option. The new method enables an integrative genome-wide view on the omics data types and the underlying regulatory modes. It is applied to high and low-grade gliomas and to melanomas where it disentangles transversal and longitudinal molecular heterogeneity in terms of distinct molecular subtypes and progression paths with prognostic impact.

Keywords: integrative bioinformatics, machine learning, molecular mechanisms of cancer, gliomas and melanomas

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Authors: K. Veluraja

Abstract:

Glycan of glycolipids and glycoproteins is playing a significant role in living systems particularly in molecular recognition processes. Molecular recognition processes are attributed to their occurrence on the surface of the cell, sequential arrangement and type of sugar molecules present in the oligosaccharide structure and glyosidic linkage diversity (glycoinformatics) and conformational diversity (glycoconformatics). Molecular Dynamics Simulation study is a theoretical-cum-computational tool successfully utilized to establish glycoconformatics of glycan. The study on various oligosaccharides of glycan clearly indicates that oligosaccharides do exist in multiple conformational states and these conformational states arise due to the flexibility associated with a glycosidic torsional angle (φ,ψ) . As an example: a single disaccharide structure NeuNacα(2-3) Gal exists in three different conformational states due to the differences in the preferential value of glycosidic torsional angles (φ,ψ). Hence establishing three dimensional structural and conformational models for glycan (cartesian coordinates of every individual atoms of an oligosaccharide structure in a preferred conformation) is quite crucial to understand various molecular recognition processes such as glycan-toxin interaction and glycan-virus interaction. The gycoconformatics models obtained for various glycan through Molecular Dynamics Simulation stored in our 3DSDSCAR (3DSDSCAR.ORG) a public domain database and its utility value in understanding the molecular recognition processes and in drug design venture will be discussed.

Keywords: glycan, glycoconformatics, molecular dynamics simulation, oligosaccharide

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Authors: Amir Bahrami

Abstract:

In the fields of chemical graph theory, molecular topology, and mathematical chemistry, a topological index or a descriptor index also known as a connectivity index is a type of a molecular descriptor that is calculated based on the molecular graph of a chemical compound. Topological indices are numerical parameters of a graph which characterize its topology and are usually graph invariant. Topological indices are used for example in the development of quantitative structure-activity relationships (QSARs) in which the biological activity or other properties of molecules are correlated with their chemical structure. In this paper some descriptor index (descriptor index) of single-walled carbon nanotubes, is determined.

Keywords: chemical graph theory, molecular topology, molecular descriptor, single-walled carbon nanotubes

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Authors: Ahmadreza Jabalameli, Mohammad Ebrahimpour Borujeni

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According to psychodynamic theories, the major personality structure of individuals is formed in the first years of life. Trauma is an inseparable and undeniable part of everyone's life and they inevitably struggle with many traumas that can have a very significant impact on their lives. The present study deals with the relationship between childhood trauma on the formation of defense mechanisms and the role of object relations. The present descriptive study is a correlation with structural equation modeling (SEM). Sample selection is available and consists of 200 knowledgeable traders in Jabalameli Information Technology Company. The results indicate that the experience of childhood trauma with a demographic moderating effect, through the mediating role of object relations can lead to vulnerability to ego reality functionality and immature and psychically disturbed defense mechanisms. In this regard, there is a significant negative relationship between childhood trauma and object relations with mature defense mechanisms.

Keywords: childhood trauma, defense mechanisms, object relations, trade

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Authors: Ameur Soukaina, Zeroual Abdellah, Mazoir Noureddine

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Molecular Electron Density Theory (MEDT) elucidates the regioselectivity of the [4+2] cycloaddition reaction between 3-aroylpyrrolo[1,2-α]quinoxaline-1,2,4(5H)-trione and butyl vinyl ether Regioselectivity and stereoselectivity. The regioselectivity mechanisms of these reactions were investigated by evaluating potential energy surfaces calculated for cycloaddition processes and DFT density-based reactivity indices. These methods have been successfully applied to predict preferred regioisomers for different method alternatives. Reactions were monitored by performing transition state optimizations, calculations of intrinsic reaction coordinates, and activation energies. The observed regioselectivity was rationalized using DFT-based reactivity descriptors such as the Parr function. Solvent effects were also investigated in 1,4-dioxane solvent using a field model for self-consistent reactions. The results were compared with experimental data to find good agreement.

Keywords: cycloaddition, DFT, ELF, MEDT, parr, stereoselectivité

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Authors: Modi Alsubaie, Willem Kuyken, Rebecca Abbott, Barnaby Dunn, Chris Dickens, Tina Keil, William Henley

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Background: Recently, there has been an increased interest in studying the effects of mindfulness-based interventions for people with psychological and physical problems. However, the mechanisms of action in these interventions that lead to beneficial physical and psychological outcomes have yet to be clearly identified. Purpose: The aim of this paper is to review, systematically, the evidence to date on the mechanisms of action in mindfulness interventions in populations with physical and/or psychological conditions. Method: Searches of seven databases (PsycINFO, Medline (Ovid), Cochrane Central Register of Controlled Trials, EMBASE, CINAHL, AMED, ClinicalTrials.gov) were undertaken in June 2014 and July 2015. We evaluated to what extent the studies we identified met the criteria suggested by Kazdin for establishing mechanisms of action within a psychological treatment (2007, 2009). Results: We identified four trials examining mechanisms of mindfulness interventions in those with comorbid psychological and physical health problems and 14 in those with psychological conditions. These studies examined a diverse range of potential mechanisms, including mindfulness and rumination. Of these candidate mechanisms, the most consistent finding was that greater self-reported change in mindfulness mediated superior clinical outcomes. However, very few studies fully met the Kazdin criteria for examining treatment mechanisms. Conclusion: There was evidence that global changes in mindfulness are linked to better outcomes. This evidence pertained more to interventions targeting psychological rather than physical health conditions. While there is promising evidence that MBCT/MBSR intervention effects are mediated by hypothesised mechanisms, there is a lack of methodological rigour in the field of testing mechanisms of action for both MBCT and MBSR, which precludes definitive conclusions.

Keywords: MBCT, MBSR, mechanisms, physical conditions, psychological conditions, systematic review

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Authors: Davoud Beheshtizadeh, Davood Jafari

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Concrete, with its special properties and advantages, has caused it to be widely and increasingly used in construction industry, especially in infrastructures of the country. On the other hand, some defects of concrete and, most importantly, micro-cracks in the concrete after setting have caused the cost of repair and maintenance of infrastructure; therefore, self-healing concretes have been of attention in other countries in the recent years. These concretes have been repaired with general mechanisms such as physical, chemical, biological and combined mechanisms, each of which has different subsets and methods of execution and operation. Also, some of these types of mechanisms are of high importance, which has led to a special production method, and as this subject is new in Iran, this knowledge is almost unknown or at least some part of it has not been considered at all. The present article completely introduces various self-healing mechanisms as a review and tries to present the disadvantages and advantages of each method along with its scope of application.

Keywords: micro-cracks, self-healing concrete, microcapsules, concrete, cement, self-sensitive

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Authors: Wenjun Zhang, Yunqing Du, Steven W. Cranford, Ming L. Wang

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The beginning of 21st century has witnessed new advancements in the design and use of new materials for biosensing applications, from nano to macro, protein to tissue. Traditional analytical methods lack a complete toolset to describe the complexities introduced by living systems, pathological relations, discrete hierarchical materials, cross-phase interactions, and structure-property dependencies. Materiomics – via systematic molecular dynamics (MD) simulation – can provide structure-process-property relations by using a materials science approach linking mechanisms across scales and enables oriented biosensor design. With this approach, DNA biosensors can be utilized to detect disease biomarkers present in individuals’ breath such as acetone for diabetes. Our wireless sensor array based on single-stranded DNA (ssDNA)-decorated single-walled carbon nanotubes (SWNT) has successfully detected trace amount of various chemicals in vapor differentiated by pattern recognition. Here, we present how MD simulation can revolutionize the way of design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. It demonstrates great potential to be utilized to build a library of DNDA sequences for reliable detection of several biomarkers of one specific disease, and as well provides a new methodology of creating, designing, and applying of biosensors.

Keywords: biosensor, DNA, biomarker, molecular dynamics simulation

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Authors: Sunatda Arayachukiat, Shogo Nobukawa, Masayuki Yamaguchi

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A new self-healing material was developed utilizing molecular entanglements for poly(vinyl butyral) (PVB) containing plasticizers. It was found that PVB shows autonomic self-healing behavior even below the glass transition temperature Tg because of marked molecular motion at surface. Moreover, the plasticizer addition enhances the chain mobility, leading to good healing behavior.

Keywords: Poly(vinyl butyral) (PVB), rheological properties, self-healing behaviour, molecular diffusion

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Authors: Mohammadjavad Sotoudeheian

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Heart failure (HF) prevalence, as a global cardiovascular problem, is increasing gradually. A variety of molecular mechanisms contribute to HF. Proteins involved in cardiac contractility regulation, such as ion channels and calcium handling proteins, are altered. Additionally, epigenetic modifications and gene expression can lead to altered cardiac function. Moreover, inflammation and oxidative stress contribute to HF. The progression of HF can be attributed to mitochondrial dysfunction that impairs energy production and increases apoptosis. Molecular mechanisms such as these contribute to the development of cardiomyocyte defects and HF and can be therapeutically targeted. The heart's contractile function is controlled by cardiomyocytes. Calpain, and its related molecules, including Bax, VEGF, and AMPK, are among the proteins involved in regulating cardiomyocyte function. Apoptosis is facilitated by Bax. Cardiomyocyte apoptosis is regulated by this protein. Furthermore, cardiomyocyte survival, contractility, wound healing, and proliferation are all regulated by VEGF, which is produced by cardiomyocytes during inflammation and cytokine stress. Cardiomyocyte proliferation and survival are also influenced by AMPK, an enzyme that plays an active role in energy metabolism. They all play key roles in apoptosis, angiogenesis, hypertrophy, and metabolism during myocardial inflammation. The role of calpains has been linked to several molecular pathways. The calpain pathway plays an important role in signal transduction and apoptosis, as well as autophagy, endocytosis, and exocytosis. Cell death and survival are regulated by these calcium-dependent cysteine proteases that cleave proteins. As a result, protein fragments can be used for various cellular functions. By cleaving adhesion and motility proteins, calcium proteins also contribute to cell migration. HF may be brought about by calpain-mediated pathways. Many physiological processes are mediated by the calpain molecular pathways. Signal transduction, cell death, and cell migration are all regulated by these molecular pathways. Calpain is activated by calcium binding to calmodulin. In the presence of calcium, calmodulin activates calpain. Calpains are stimulated by calcium, which increases matrix metalloproteinases (MMPs). In order to develop novel treatments for these diseases, we must understand how this pathway works. A variety of myocardial remodeling processes involve calpains, including remodeling of the extracellular matrix and hypertrophy of cardiomyocytes. Calpains also play a role in maintaining cardiac homeostasis through apoptosis and autophagy. The development of HF may be in part due to calpain-mediated pathways promoting cardiomyocyte death. Numerous studies have suggested the importance of the Ca2+ -dependent protease calpain in cardiac physiology and pathology. Therefore, it is important to consider this pathway to develop and test therapeutic options in humans that targets calpain in HF. Apoptosis, autophagy, endocytosis, exocytosis, signal transduction, and disease progression all involve calpain molecular pathways. Therefore, it is conceivable that calpain inhibitors might have therapeutic potential as they have been investigated in preclinical models of several conditions in which the enzyme has been implicated that might be treated with them. Ca 2+ - dependent proteases and calpains contribute to adverse ventricular remodeling and HF in multiple experimental models. In this manuscript, we will discuss the calpain molecular pathway's important roles in HF development.

Keywords: calpain, heart failure, autophagy, apoptosis, cardiomyocyte

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Authors: Rajandeep Kaur, Rajeev Gupta

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Background: Chronic myeloid leukemia (CML) is the most common leukaemia in India. The annual incidence of chronic myeloid leukemia in India was originally reported to be 0.8 to 2.2 per 1,00,000 population. CML is a clonal disorder that is usually easily diagnosed because the leukemic cells of more than 95% of patients have a distinctive cytogenetic abnormality, the Philadelphia chromosome (Ph1). The approval of tyrosine kinase inhibitors (TKIs), which target BCR-ABL1 kinase activity, has significantly reduced the mortality rate associated with chronic myeloid leukemia (CML) and revolutionized treatment. Material and Methods: 80 diagnosed cases of CML were taken. Investigations were done. Bone marrow and molecular studies were also done and with EUTOS, patients were stratified into low and high-risk groups and then treatment with Imatinib was given to all patients and the molecular response was evaluated at 6 months and 12 months follow up with BCR-ABL by RT-PCR quantitative assay. Results: In the study population, out of 80 patients in the study population, 40 were females and 40 were males, with M: F is 1:1. Out of total 80 patients’ maximum patients (54) were in 31-60 years age group. Our study showed a most common symptom of presentation is abdominal discomfort followed by fever. Out of the total 80 patients, 25 (31.3%) patients had high EUTOS scores and 55 (68.8%) patients had low EUTOS scores. On 6 months follow up 36.3% of patients had Complete Molecular Response, 16.3% of patients had Major Molecular Response and 47.5% of patients had No Molecular Response but on 12 months follow up 71.3% of patients had Complete Molecular Response, 16.25% of patients had Major Molecular Response and 12.5% patients had No Molecular Response. Conclusion: In this study, we found a significant correlation between EUTOS score and Molecular response at 6 months and 12 months follow up after Imatinib therapy.

Keywords: chronic myeloid leukemia, European treatment and outcome study score, hematological response, molecular response, tyrosine kinase inhibitor

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Authors: Chaoran Liu

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Bioactive polysaccharides and polysaccharide-protein complex derived from mushrooms and fungi have a wide range of immunomodulatory activity with low side-effects and have therefore the potential to be developed as an adjuvant in cancer therapies. Mushrooms sclerotium is rich in polysaccharides and the polysaccharides isolated from the sclerotium of Polyporus rhinocerus have shown potent in vivo and in vitro immunomodulatory effects. Macrophages are considered to be an important component of the innate immune response against bacterial infection and cancer. To better understanding the immunomodulatory effects and its underlying mechanisms of sclerotial water-soluble polysaccharides extracted from P. rhinocerus on macrophages, the objectives of this study are to purify the water-soluble novel sclerotial polysaccharides and to characterize the structure and properties as well as to study the detailed molecular mechanisms of the in vitro immunomodulating effects in murine macrophages. The hot water-soluble fraction PRW from the sclerotium of P. rhinocerus was obtained using solvent extraction. PRW was further fractionated by membrane ultrafiltration to a give a fraction (PRW1) with molecular mass less than 50 kDa. PRW1 was characterized to be a polysaccharide-protein complex composed of 45.7% polysaccharide and 44.2% protein. The chemical structure of the carbohydrate moiety of PRW1 was elucidated by GC and FTIR to be mainly beta-D-glucan with trace amount of galactose and mannose. The immunomodulatory effects of PRW1 on murine RAW 264.7 macrophages were demonstrated in terms of the increase in nitric oxide production and cytokine production. Mechanistically, PRW1 initiates ERK phosphorylation to activate macrophages within 15 min and significantly improves the expression level of inducible NOS (iNOS) from 6 h after treatment. In summary, this study indicates that PRW1 is a potent immunomodulatory agent for macrophages and suggests that mushroom sclerotia from Polyporus rhinocerus requires for further investigation in cancer research.

Keywords: Polyporus rhinocerus, mushroom sclerotia, Polysaccharide-Protein Complex, macrophage activation

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Authors: D. Liu, D. M. Donskoy

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The vibroacoustic modulation method is based on the modulation effect of high-frequency ultrasonic wave (carrier) by low-frequency vibration in the presence of various defects, primarily contact-type such as cracks, delamination, etc. The presence and severity of the defect are measured by the ratio of the spectral sidebands and the carrier in the spectrum of the modulated signal. This approach, however, does not differentiate between amplitude and frequency modulations, AM and FM, respectfully. It was experimentally shown that both modulations could be present in the spectrum, yet each modulation may be associated with different physical mechanisms. AM mechanisms are quite well understood and widely covered in the literature. This paper is a first attempt to explain the generation mechanisms of FM and its correlation with the flaw properties. Here we proposed two possible mechanisms leading to FM modulation based on nonlinear local defect resonance and dynamic acousto-elastic models.

Keywords: non-destructive testing, nonlinear acoustics, structural health monitoring, acousto-elasticity, local defect resonance

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Authors: Sanja O. Podunavac-Kuzmanović, Lidija R. Jevrić, Strahinja Z. Kovačević

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Benzimidazoles are a group of compounds with significant antibacterial, antifungal and anticancer activity. The studied compounds consist of the main benzimidazole structure with different combinations of substituens. This study is based on the two-dimensional and three-dimensional molecular modeling and calculation of molecular descriptors (physicochemical and lipophilicity descriptors) of structurally diverse benzimidazoles. Molecular modeling was carried out by using ChemBio3D Ultra version 14.0 software. The obtained 3D models were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. The obtained set of molecular descriptors was used in principal component analysis (PCA) of possible similarities and dissimilarities among the studied derivatives. After the molecular modeling, the quantitative structure-property relationship (QSPR) analysis was applied in order to get the mathematical models which can be used in prediction of pKb values of structurally similar benzimidazoles. The obtained models are based on statistically valid multiple linear regression (MLR) equations. The calculated cross-validation parameters indicate the high prediction ability of the established QSPR models. This study is financially supported by COST action CM1306 and the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina.

Keywords: benzimidazoles, chemometrics, molecular modeling, molecular descriptors, QSPR

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Authors: Mohamed Abdel-Hamid, Olfat Gamil Shaker, Doha El-Sayed Ellakwa, Eman Fathy Abdel-Maksoud

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Introduction: Despite advances in the knowledge of the molecular virology of hepatitis C virus (HCV), the mechanisms of hepatocellular injury in HCV infection are not completely understood. Hepatitis C viral infection (HCV) influences the susceptibility to apoptosis. This could lead to insufficient antiviral immune response and persistent viral infection. Aim of this study: was to examine whether BCL-2 gene polymorphism at codon 43 (+127G/A or Ala43Thr) has an impact on development of hepatocellular carcinoma caused by chronic hepatitis C Egyptian patients. Subjects and Methods: The study included three groups; group 1: composing of 30 patients with hepatocellular carcinoma (HCC), group 2 composing of 30 patients with HCV, group 3 composing of 30 healthy subjects matching the same age and socioeconomic status were taken as a control group. Gene polymorphism of BCL2 (Ala43Thr) were evaluated by PCR-RFLP technique and measured for all patients and controls. Results: The summed 43Thr genotype was more frequent and statistically significant in HCC patients as compared to control group. This genotype of BCL2 gene may inhibit the programmed cell death which leads to disturbance in tissue and cells homeostasis and reduction in immune regulation. This result leads to viral replication and HCV persistence. Moreover, virus produces variety of mechanisms to block genes participated in apoptosis. This mechanism proves that HCV patients who have 43Thr genotype are more susceptible to HCC. Conclusion: The data suggest for the first time that the BCL2 polymorphism is associated with the susceptibility to HCC in Egyptian populations and might be used as molecular markers for evaluating HCC risk. This study clearly demonstrated that Chronic HCV exhibit a deregulation of apoptosis with the disease progression. This provides an insight into the pathogenesis of chronic HCV infection, and may contribute to the therapy.

Keywords: BCL2 gene, Hepatitis C Virus, Hepatocellular carcinoma, sensitivity, specificity, apoptosis

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Authors: Jannes Quer, Amir Niknejad, Marcus Weber

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Computational Drug Design is often based on Molecular Dynamics simulations of molecular systems. Molecular Dynamics can be used to simulate, e.g., the binding and unbinding event of a small drug-like molecule with regard to the active site of an enzyme or a receptor. However, the time-scale of the overall binding event is many orders of magnitude longer than the time-scale of simulation. Thus, there is a need to speed-up molecular simulations. In order to speed up simulations, the molecular dynamics trajectories have to be ”steared” out of local minimizers of the potential energy surface – the so-called metastabilities – of the molecular system. Increasing the kinetic energy (temperature) is one possibility to accelerate simulated processes. However, with temperature the entropy of the molecular system increases, too. But this kind ”stearing” is not directed enough to stear the molecule out of the minimum toward the saddle point. In this article, we give a new mathematical idea, how a potential energy surface can be changed in such a way, that entropy is kept under control while the trajectories are still steared out of the metastabilities. In order to compute the unsteared transition behaviour based on a steared simulation, we propose to use extrapolation methods. In the end we mathematically show, that our method accelerates the simulations along the direction, in which the curvature of the potential energy surface changes the most, i.e., from local minimizers towards saddle points.

Keywords: extrapolation, Eyring-Kramers, metastability, multilevel sampling

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Authors: Ramin Khamedi, Isa Ahmadi

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In this study acoustic emission (AE) signals obtained during deformation and fracture of two types of ferrite-martensite dual phase steels (DPS) specimens have been analyzed in frequency domain. For this reason two low carbon steels with various amounts of carbon were chosen, and intercritically heat treated. In the introduced method, identifying the mechanisms of failure in the various phases of DPS is done. For this aim, AE monitoring has been used during tensile test of several DPS with various volume fraction of the martensite (VM) and attempted to relate the AE signals and failure mechanisms in these steels. Different signals, which referred to 2-3 micro-mechanisms of failure due to amount of carbon and also VM have been seen. By Fast Fourier Transformation (FFT) of signals in distinct locations, an excellent relationship between peak frequencies in these areas and micro-mechanisms of failure were seen. The results were verified by microscopic observations (SEM).

Keywords: acoustic emission, dual phase steels, deformation, failure, fracture

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Authors: A. Azari, S. S. K. Seyyedi

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One of the unaddressed and open challenges in the nano-networking is the characteristics of noise. The previous analysis, however, has concentrated on end-to-end communication model with no separate modelings for propagation channel and noise. By considering a separate signal propagation and noise model, the design and implementation of an optimum receiver will be much easier. In this paper, we justify consideration of a separate additive Gaussian noise model of a nano-communication system based on the molecular communication channel for which are applicable for MSK and MOSK modulation schemes. The presented noise analysis is based on the Brownian motion process, and advection molecular statistics, where the received random signal has a probability density function whose mean is equal to the mean number of the received molecules. Finally, the justification of received signal magnitude being uncorrelated with additive non-stationary white noise is provided.

Keywords: molecular, noise, diffusion, channel

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Authors: Vun Yee Thien, Kenneth Francis Rodrigues, Clemente Michael Vui Ling Wong, Wilson Thau Lym Yong

Abstract:

Transcriptomes associated with the process of photosynthesis have offered insights into the mechanism of gene regulation in terrestrial plants; however, limited information is available as far as macroalgae are concerned. This investigation aims to decipher the underlying mechanisms associated with photosynthesis in the red alga, Kappaphycus alvarezii, by performing a differential expression analysis on a de novo assembled transcriptomes. Comparative analysis of gene expression was designed to examine the alteration of light qualities and its effect on physiological mechanisms in the red alga. High-throughput paired-end RNA-sequencing was applied to profile the transcriptome of K. alvarezii irradiated with different wavelengths of light (blue 492-455 nm, green 577-492 nm and red 780-622 nm) as compared to the full light spectrum, resulted in more than 60 million reads individually and assembled using Trinity and SOAPdenovo-Trans. The transcripts were annotated in the NCBI non-redundant (nr) protein, SwissProt, KEGG and COG databases with a cutoff E-value of 1e-5 and nearly 30% of transcripts were assigned to functional annotation by Blast searches. Differential expression analysis was performed using edgeR. The DEGs were designated to six categories: BL (blue light) regulated, GL (green light) regulated, RL (red light) regulated, BL or GL regulated, BL or RL regulated, GL or RL regulated, and either BL, GL or RL regulated. These DEGs were mapped to terms in KEGG database and compared with the whole transcriptome background to search for genes that regulated by light quality. The outcomes of this study will enhance our understanding of molecular mechanisms underlying light-induced responses in red algae.

Keywords: de novo transcriptome sequencing, differential gene expression, Kappaphycus alvareziired, red alga

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Authors: Maja Pandža, Sanjin Lovrić, Iva Čolak, Josipa Mandarić, Miro Klarić

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This study explores the role of symptoms related to mood disorders salience on different types of defense mechanisms (mature, neurotic, immature) predominance. Total of 177 both clinical and non-clinical participants in Mostar, Bosnia & Herzegovina, completed a battery of questionnaires associated with defense mechanisms and self-reported depression and anxiety symptoms. The sample was additionally divided into four groups, given the level of symptoms experienced: 1. minimal, 2. mild, 3. moderate, 4. severe depression/anxiety. Participants with minimal anxiety and depression symptoms use mature defense mechanisms more often than other three groups. Immature mechanisms are most commonly used by the group with severe depression/anxiety levels in comparison with other groups. These differences are discussed on the dynamic level of analysis to have a better understanding of the relationship between defense mechanisms' maturity and degree of mood disorders' symptom severity. Also, results given could serve as an implication for the psychotherapeutic treatment plans.

Keywords: anxiety/depression symptoms, clinical/non-clinical sample, defense mechanism maturity, dynamic approach

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Authors: Horaya Mostafa Ahmed

Abstract:

All cultures are inherently predisposed to change and, at the same time, to resisting change. There are dynamic processes operating that encourage the acceptance of new ideas and things, while there are others that encourage changeless stability. Despite the dramatic changes that have taken place in all human cultures, there are cultures still steadfast and resist change. These cultures resist through some culture mechanisms like, cultural boundaries, ethnocentrism, religion, and cultural relativity. So this paper is an attempt to discover these mechanisms of cultural change resistance and to ask is cultural change always required.

Keywords: cultural change, cultural boundaries, cultural relativity, ethnocentrism, religion, resistance

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Authors: Paweł Stączek, Tomasz Plech, Aleksandra Strzelczyk, Katarzyna Dzitko, Monika Wujec, Edyta Kuśmierz, Piotr Paneth, Agata Paneth

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In this contribution, we will describe the inhibitory potency of nine thiosemicarbazide derivatives against bacterial type IIA topoisomerases, their antibacterial profile, and molecular modeling evaluation. We have found that one of the tested compounds, 4-benzoyl-1-(2-methyl-furan-3-ylcarbonyl) thiosemicarbazide, remarkably inhibits the activity of S. aureus DNA gyrase with the IC50 below 5 μM. Besides, this compound displays antibacterial activity on Staphylococcus spp. and E. faecalis at non-cytotoxic concentrations in mammalian cells, with minimal inhibitory concentrations (MICs) values at 25 μg/mL. Based on the enzymatic and molecular modeling studies we propose two factors, i.e. geometry of molecule and hydrophobic/hydrophilic balance as important molecular properties for developing thiosemicarbazide derivatives as potent Staphylococcus aureus DNA gyrase inhibitors.

Keywords: bioactivity, drug design, topoisomerase, molecular modeling

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Authors: K. S. Poutanen, P. Dussort, A. Erkner, S. Fiszman, K. Karnik, M. Kristensen, C. F. M. Marsaux, S. Miquel-Kergoat, S. Pentikäinen, P. Putz, R. E. Steinert, J. Slavin, D. J. Mela

Abstract:

Dietary fiber (DF) intake has been associated with lower body weight or less weight gain. These effects are generally attributed to putative effects of DF on appetite. Many intervention studies have tested the effect of DFs on appetite-related measures, with inconsistent results. However, DF includes a wide category of different compounds with diverse chemical and physical characteristics, and correspondingly diverse effects in human digestion. Thus, inconsistent results between DF consumption and appetite are not surprising. The specific contribution of different compounds with varying physico-chemical properties to appetite control and the mediating mechanisms are not well characterized. This systematic review aimed to assess the influence of specific DF characteristics, including viscosity, gel forming capacity, fermentability, and molecular weight, on appetite-related outcomes in healthy humans. Medline and FSTA databases were searched for controlled human intervention trials, testing the effects of well-characterized DFs on subjective satiety/appetite or energy intake outcomes. Studies were included only if they reported: 1) fiber name and origin, and 2) data on viscosity, gelling properties, fermentability, or molecular weight of the DF materials tested. The search generated 3001 unique records, 322 of which were selected for further consideration from title and abstract screening. Of these, 149 were excluded due to insufficient fiber characterization and 124 for other reasons (not original article, not randomized controlled trial, or no appetite related outcome), leaving 49 papers meeting all the inclusion criteria, most of which reported results from acute testing (<1 day). The eligible 49 papers described 90 comparisons of DFs in foods, beverages or supplements. DF-containing material of interest was efficacious for at least one appetite-related outcome in 51/90 comparisons. Gel-forming DF sources were most consistently efficacious but there were no clear associations between viscosity, MW or fermentability and appetite-related outcomes. A considerable number of papers had to be excluded from the review due to shortcomings in fiber characterization. To build understanding about the impact of DF on satiety/appetite specifically there should be clear hypotheses about the mechanisms behind the proposed beneficial effect of DF material on appetite, and sufficient data about the DF properties relevant for the hypothesized mechanisms to justify clinical testing. The hypothesized mechanisms should also guide the decision about relevant duration of exposure in studies, i.e. are the effects expected to occur during acute time frame (related to stomach emptying, digestion rate, etc.) or develop from sustained exposure (gut fermentation mediated mechanisms). More consistent measurement methods and reporting of fiber specifications and characterization are needed to establish reliable structure-function relationships for DF and health outcomes.

Keywords: appetite, dietary fiber, physico-chemical properties, satiety

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Authors: Sruthi Ramagiri, Rajeev T.

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Free radical damage has been entailed as the major culprit in the ischemic stroke contributing for oxidative damage. Recent investigations on Hydroxy Safflower Yellow A (HSYA) suggested its role in cerebral ischemia and various neurodegenerative disorders with unidentified molecular mechanisms. The current study was designed to investigate putative therapeutic role and possible molecular mechanisms of HSYA administration during the onset of reperfusion in cerebral ischemia-reperfusion (I/R) injury in cerebral stroke. Cerebral stroke was achieved by focal ischemic model. HSYA (10 mg/kg) was injected intravenously via the tail vein 5 minutes before reperfusion. Losses of sensorimotor abilities were evaluated by neurological scoring, spontaneous locomotor activity, and rotarod performance. Extent of oxidative stress was evaluated by biochemical parameters i.e., malondialdehyde (MDA), Glutathione (GSH), Super Oxide Dismutase (SOD) and catalase levels. The infarct volume of brain was assessed by 2,3,5-triphenyl tetrazolium chloride (TTC) staining technique. Increased cerebral injury (I/R) was evidenced by motor impairment, increased infarct volume and elevation of MDA levels along with significant reduction in antioxidant i.e.,MDA levels along with significant reduction in antioxidant i.e., GSH, SOD and catalase levels when compared to sham control. However, post conditioning with HSYA (10 mg/kg, i.v.) at the onset of reperfusion has significantly ameliorated sensorimotor abilities, attenuated MDA levels and reduced the infarct volume as compared with vehicle treated I/R injury group. Moreover, HSYA treatments improved antioxidant enzyme levels as compared with vehicle treated I/R-injury group. In conclusion, it may be suggested that HSYA post conditioning could be novel therapeutic approach against I/R injury in cerebral stroke possibly through its anti-oxidant mechanism.

Keywords: HSYA, Ischemia reperfusion injury, oxidative stress, stroke

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Authors: Hai Hoang, Thanh Xuan Nguyen Thi, Guillaume Galliero

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Coarse-Grained (CG) molecular simulations have shown to be an efficient way to estimate thermophysical (static and dynamic) properties of fluids. Several strategies have been developed and reported in the literature for defining CG molecular models. Among them, those based on a top-down strategy (i.e. CG molecular models related to macroscopic observables), despite being heuristic, have increasingly gained attention. This is probably due to its simplicity in implementation and its ability to provide reasonable results for not only simple but also complex systems. Regarding simple Force-Fields associated with these CG molecular models, it has been found that the four parameters Mie chain model is one of the best compromises to describe thermophysical static properties (e.g. phase diagram, saturation pressure). However, parameterization procedures of these Mie-chain GC molecular models given in literature are generally insufficient to simultaneously provide static and dynamic (e.g. viscosity) properties. To deal with such situations, we have extended the corresponding states by using a quantity associated with the liquid viscosity. Results obtained from molecular simulations have shown that our approach is able to yield good estimates for both static and dynamic thermophysical properties for various real non-associating fluids. In addition, we will show that on simple (e.g. phase diagram, saturation pressure) and complex (e.g. thermodynamic response functions, thermodynamic energy potentials) static properties, results of our scheme generally provides improved results compared to existing approaches.

Keywords: coarse-grained model, mie potential, molecular simulations, thermophysical properties, phase equilibria

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