Search results for: fusion proteins

Authors: Alexander A. Tokmakov

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Cell-free protein synthesis is widely used to synthesize recombinant proteins. It allows genome-scale expression of various polypeptides under strictly controlled uniform conditions. However, only a minor fraction of all proteins can be successfully expressed in the systems of protein synthesis that are currently used. The factors determining expression success are poorly understood. At present, the vast volume of data is accumulated in cell-free expression databases. It makes possible comprehensive bioinformatics analysis and identification of multiple features associated with successful cell-free expression. Here, we describe an approach aimed at identification of multiple physicochemical and structural properties of amino acid sequences associated with protein solubility and aggregation and highlight major correlations obtained using this approach. The developed method includes: categorical assessment of the protein expression data, calculation and prediction of multiple properties of expressed amino acid sequences, correlation of the individual properties with the expression scores, and evaluation of statistical significance of the observed correlations. Using this approach, we revealed a number of statistically significant correlations between calculated and predicted features of protein sequences and their amenability to cell-free expression. It was found that some of the features, such as protein pI, hydrophobicity, presence of signal sequences, etc., are mostly related to protein solubility, whereas the others, such as protein length, number of disulfide bonds, content of secondary structure, etc., affect mainly the expression propensity. We also demonstrated that amenability of polypeptide sequences to cell-free expression correlates with the presence of multiple sites of post-translational modifications. The correlations revealed in this study provide a plethora of important insights into protein folding and rationalization of protein production. The developed bioinformatics approach can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

Keywords: bioinformatics analysis, cell-free protein synthesis, expression success, optimization, recombinant proteins

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Authors: Huawei Bai, Jianguo Yao, Fellow, IEEE

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Atrial fibrillation (AF) is the most common form of heart arrhythmia and is closely associated with mortality and morbidity in heart failure, stroke, and coronary artery disease. The development of single spot optical sensors enables widespread photoplethysmography (PPG) screening, especially for AF, since it represents a more convenient and noninvasive approach. To our knowledge, most existing studies based on public and unbalanced datasets can barely handle the multiple noises sources in the real world and, also, lack interpretability. In this paper, we construct a large- scale PPG dataset using measurements collected from PPG wrist- watch devices worn by volunteers and propose an attention-based two-stream heterogeneous neural network (TSHNN). The first stream is a hybrid neural network consisting of a three-layer one-dimensional convolutional neural network (1D-CNN) and two-layer attention- based bidirectional long short-term memory (Bi-LSTM) network to learn representations from temporally sampled signals. The second stream extracts latent representations from the PPG time-frequency spectrogram using a five-layer CNN. The outputs from both streams are fed into a fusion layer for the outcome. Visualization of the attention weights learned demonstrates the effectiveness of the attention mechanism against noise. The experimental results show that the TSHNN outperforms all the competitive baseline approaches and with 98.09% accuracy, achieves state-of-the-art performance.

Keywords: PPG wearables, atrial fibrillation, feature fusion, attention mechanism, hyber network

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Authors: Saliha Gachi, Mouloud Aissani, Fouad Boubenider

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Friction Stir Welding (FSW) is a solid-state welding technique that can join material without melting the plates to be welded. In this work, we are interested to demonstrate the potentiality of FSW for joining the heat-treatable aluminum alloy 2024-T3 which is reputed as difficult to be welded by fusion techniques. Thereafter, the FSW joint is compared with another one obtained from a conventional fusion process Tungsten Inert Gas (TIG). FSW welds are made up using an FSW tool mounted on a milling machine. Single pass welding was applied to fabricated TIG joint. The comparison between the two processes has been made on the temperature evolution, mechanical and microstructure behavior. The microstructural examination revealed that FSW weld is composed of four zones: Base metal (BM), Heat affected zone (HAZ), Thermo-mechanical affected zone (THAZ) and the nugget zone (NZ). The NZ exhibits a recrystallized equiaxed refined grains that induce better mechanical properties and good ductility compared to TIG joint where the grains have a larger size in the welded region compared with the BM due to the elevated heat input. The microhardness results show that, in FSW weld, the THAZ contains the lowest microhardness values and increase in the NZ; however, in TIG process, the lowest values are localized on the NZ.

Keywords: friction stir welding, tungsten inert gaz, aluminum, microstructure

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Authors: Manuel A. Alonso-Tarajano, Roberto Mosca, Patrick Aloy

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Protein kinases participate in a myriad of cellular processes of major biomedical interest. The in vivo substrate specificity of these enzymes is a process determined by several factors, and despite several years of research on the topic, is still far from being totally understood. In the present work, we have quantified the contributions to the kinase substrate specificity of i) the phosphorylation sites and their surrounding residues in the sequence and of ii) the association of kinases to adaptor or scaffold proteins. We have used position-specific scoring matrices (PSSMs), to represent the stretches of sequences phosphorylated by 93 families of kinases. We have found negative correlations between the number of sequences from which a PSSM is generated and the statistical significance and the performance of that PSSM. Using a subset of 22 statistically significant PSSMs, we have identified specificity determinant residues (SDRs) for 86% of the corresponding kinase families. Our results suggest that different SDRs can function as positive or negative elements of substrate recognition by the different families of kinases. Additionally, we have found that human proteins with known function as adaptors or scaffolds (kAS) tend to interact with a significantly large fraction of the substrates of the kinases to which they associate. Based on this characteristic we have identified a set of 279 potential adaptors/scaffolds (pAS) for human kinases, which is enriched in Pfam domains and functional terms tightly related to the proposed function. Moreover, our results show that for 74.6% of the kinase– pAS association found, the pAS colocalize with the substrates of the kinases they are associated to. Finally, we have found evidence suggesting that the association of kinases to adaptors and scaffolds, may contribute significantly to diminish the in vivo substrate crossed- specificity of protein kinases. In general, our results indicate the relevance of several SDRs for both the positive and negative selection of phosphorylation sites by kinase families and also suggest that the association of kinases to pAS proteins may be an important factor for the localization of the enzymes with their set of substrates.

Keywords: kinase, phosphorylation, substrate specificity, adaptors, scaffolds, cellular colocalization

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Authors: Razieh Karimi Aghcheh, Christian Kubicek, Joseph Strauss, Gerhard Braus

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Filamentous fungi are of considerable economic and social significance for human health, nutrition and in white biotechnology. These organisms are dominant producers of a range of primary metabolites such as citric acid, microbial lipids (biodiesel) and higher unsaturated fatty acids (HUFAs). In particular, they produce also important but structurally complex secondary metabolites with enormous therapeutic applications in pharmaceutical industry, for example: cephalosporin, penicillin, taxol, zeranol and ergot alkaloids. Several fungal secondary metabolites, which are significantly relevant to human health do not only include antibiotics, but also e.g. lovastatin, a well-known antihypercholesterolemic agent produced by Aspergillus. terreus, or aflatoxin, a carcinogen produced by A. flavus. In addition to their roles for human health and agriculture, some fungi are industrially and commercially important: Species of the ascomycete genus Hypocrea spp. (teleomorph of Trichoderma) have been demonstrated as efficient producer of highly active cellulolytic enzymes. This trait makes them effective in disrupting and depolymerization of lignocellulosic materials and thus applicable tools in number of biotechnological areas as diverse as clothes-washing detergent, animal feed, and pulp and fuel productions. Fungal LaeA/LAE1 (Loss of aflR Expression A) homologs their gene products act at the interphase between secondary metabolisms, cellulase production and development. Lack of the corresponding genes results in significant physiological changes including loss of secondary metabolite and lignocellulose degrading enzymes production. At the molecular level, the encoded proteins are presumably methyltransferases or demethylases which act directly or indirectly at heterochromatin and interact with velvet domain proteins. Velvet proteins bind to DNA and affect expression of secondary metabolites (SMs) genes and cellulases. The dynamic interplay between LaeA/LAE1, velvet proteins and additional interaction partners is the key for an understanding of the coordination of metabolic and morphological functions of fungi and is required for a biotechnological control of the formation of desired bioactive products. Aspergilli and Trichoderma represent different biotechnologically significant species with significant differences in the LaeA/LAE1-Velvet protein machinery and their target proteins. We, therefore, performed a comparative study of the interaction partners of this machinery and the dynamics of the various protein-protein interactions using our robust proteomic and mass spectrometry techniques. This enhances our knowledge about the fungal coordination of secondary metabolism, cellulase production and development and thereby will certainly improve recombinant fungal strain construction for the production of industrial secondary metabolite or lignocellulose hydrolytic enzymes.

Keywords: cellulases, LaeA/1, proteomics, secondary metabolites

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Authors: Zuzana Tatarkova, Ivana Pilchova, Michal Cibulka, Martin Kolisek, Peter Racay, Peter Kaplan

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Introduction: Normal functioning of mitochondria is crucial for cardiac performance. Mitochondria undergo mitophagy and biogenesis, and mitochondrial proteins are subject to extensive post-translational modifications. The state of mitochondrial homeostasis reflects overall cellular fitness and longevity. Perturbed mitochondria produce less ATP, release greater amounts of reactive molecules, and are more prone to apoptosis. Therefore mitochondrial turnover is an integral aspect of quality control in which dysfunctional mitochondria are selectively eliminated through mitophagy. Currently, the progressive deterioration of physiological functions is seen as accumulation of modified/damaged proteins with limiting regenerative ability and disturbance of such affected protein-protein communication throughout aging in myocardial cells. Methodologies: For our study was used immunohistochemistry, biochemical methods: spectrophotometry, western blotting, immunodetection as well as more sophisticated 2D electrophoresis and mass spectrometry for evaluation protein-protein interactions and specific post-translational modification. Results and Discussion: Mitochondrial stress response to reactive species was evaluated as electron transport chain (ETC) complexes, redox-active molecules, and their possible communication. Protein-protein interactions revealed a strong linkage between age and ETC protein subunits. Redox state was strongly affected in senescent mitochondria with shift in favor of more pro-oxidizing condition within cardiomyocytes. Acute myocardial ischemia and ischemia-reperfusion (IR) injury affected ETC complexes I, II and IV with no change in complex III. Ischemia induced decrease in total antioxidant capacity, MnSOD, GSH and catalase activity with recovery in some extent during reperfusion. While MnSOD protein content was higher in IR group, activity returned to 95% of control. Nitric oxide is one of the biological molecules that can out compete MnSOD for superoxide and produce peroxynitrite. This process is faster than dismutation and led to the 10-fold higher production of nitrotyrosine after IR injury in adult with higher protection in senescent ones. 2D protein profiling revealed 140 mitochondrial proteins, 12 of them with significant changes after IR injury and 36 individual nitrotyrosine-modified proteins further identified by mass spectrometry. Linking these two groups, 5 proteins were altered after IR as well as nitrated, but only one showed massive nitration per lowering content of protein after IR injury in adult. Conclusions: Senescent cells have greater proportion of protein content, which might be modulated by several post-translational modifications. If these protein modifications are connected to functional consequences and protein-protein interactions are revealed, link may lead to the solution. Assume all together, dysfunctional proteostasis can play a causative role and restoration of protein homeostasis machinery is protective against aging and possibly age-related disorders. This work was supported by the project VEGA 1/0018/18 and by project 'Competence Center for Research and Development in the field of Diagnostics and Therapy of Oncological diseases', ITMS: 26220220153, co-financed from EU sources.

Keywords: aging heart, mitochondria, proteomics, redox state

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Authors: S. D. Zalepugin, A. E. Murzich, D. G. Satskevich, A. B. Palivanov

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Introduction. The incidence of spinal injuries in patients under 18 years of age has increased significantly in recent years, which represents a significant economic, social and medical problem. The most common method of surgical stabilization of spinal fractures in pediatric patients is transpedicular posterior spinal fusion, which is widely used by spinal neurosurgeons in adult patients. Purpose of the study: This study evaluates the results of treatment of thoracolumbar spine lesions in children using the transpedicular screw fixation method. Materials and methods. From 2019 to 2024, 35 children with injuries to the thoracic and lumbar spine underwent surgical treatment using the transpedicular screw fixation method. Among the injured, girls prevailed (21 cases, 60%). The age of the victims ranged from 9 to 17 years. The main causes of damage were: catatrauma (19 cases), road accident (5 cases), sports injury (6 cases), and other reasons - 5 cases. In 5 cases, suicidal attempts occurred. Co-injury was observed in most cases (20 patients, or 57%), which is natural for high-energy injury. Vertebral-spinal injury with neurological disorders was observed in 13 patients, the disorders ranged from mild inferior (4 children) to moderate/severe paraparesis (5 patients) and inferior paraplegia (4 children). 6 children had pelvic organ dysfunction in the form of urinary and fecal retention or incontinence. All thirty-five patients, within a period of 1 to 57 days after the injury, underwent several surgical interventions from the posterior surgical access using a screw fixation method (posterior decompression + spinal fusion). In 12 cases, it was necessary to perform the second stage of surgical treatment - anterior decompression of the spinal cord or its roots. Verticalization of patients was carried out within 1 to 5 days after surgery. Results. In all patients, the nearest, up to 1 year, results were evaluated. In children operated in 2019-2021, the results were studied in terms of 3 to 5 years. The procedures used, clinical results and the quality of the fixative installation were assessed. All patients managed to achieve positive results. The use of internal fixation made it possible to carry out early verticalization of children, eliminate pain syndrome and achieve a regression of neurological disorders in most patients (especially in cases when the operation was performed early after injury - from 1 to 3 days). Within the first month, the ability to self-care was fully restored. Bone fusion was observed within 6-12 months after surgery. There were no complications after surgery. The analysis of postoperative radiographs, CT and MRI images revealed the correct standing of the screws in all cases. Conclusion. The posterior spinal fusion using the new method of screw fixation in pediatric patients allows to achieve durable stabilization of damage, begins early rehabilitation of patients and reduces the duration of hospital treatment by 2-3 times. Thus, we recommend the use of a transpedicular fixator in children as a reliable, technically feasible method for restoring spinal stability with a low risk of intra- and postoperative complications.

Keywords: pediatric patients, spinal injuries, transpedicular stabilization, operative treatment

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Authors: Yi Sun, George Ed Rainger, Steve P. Watson

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Background: Beyond the classical roles in haemostasis and thrombosis, platelets are important in the initiation and development of various thrombo-inflammatory diseases. In atherosclerosis and deep vein thrombosis, for example, platelets bridge monocytes with endothelium and form heterotypic aggregates with monocytes in the circulation. This can alter monocyte phenotype by inducing their activation, stimulating adhesion and migration. These interactions involve cell surface receptor-ligand pairs on both cells. This list is likely incomplete as new interactions of importance to platelet biology are continuing to be discovered as illustrated by our discovery of PEAR-1 binding to FcεR1α. Results: We have developed a highly sensitive avidity-based assay to identify novel extracellular interactions among 126 recombinantly-expressed platelet cell surface and secreted proteins involved in platelet aggregation. In this study, we will use this method to identify novel platelet-monocyte interactions. We aim to identify ligands for orphan receptors and novel partners of well-known proteins. Identified interactions will be studied in preliminary functional assays to demonstrate relevance to the inflammatory processes supporting atherogenesis. Conclusions: Platelet-monocyte interactions are essential for the development of thromboinflammatory disease. Up until relatively recently, technologies only allow us to limit our studies on each individual protein interaction at a single time. These studies propose for the first time to study the cell surface platelet-monocyte interactions in a systematic large-scale approach using a reliable screening method we have developed. If successful, this will likely to identify previously unknown ligands for important receptors that will be investigated in details and also provide a list of novel interactions for the field. This should stimulate studies on developing alternative therapeutic strategies to treat vascular inflammatory disorders such as atherosclerosis, DVT and sepsis and other clinically important inflammatory conditions.

Keywords: membrane proteins, large-scale screening, platelets, recombinant expression

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Authors: Gustavo Menezes De Souza Melo, Arnaud Heitz, Johannes Henrich Schleifenbaum

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Additive manufacturing is a growing market that is taking over in many industries as it offers numerous advantages like new design possibilities, weight-saving solutions, ease of manufacture, and simplification of assemblies. These are all unquestionable technical or financial assets. As to the environmental aspect, additive manufacturing is often discussed whether it is the best solution to decarbonize our industries or if conventional manufacturing remains cleaner. This work presents a life cycle assessment (LCA) comparison based on the technological case of a motorbike swing-arm. We compare the original equipment manufacturer part made with conventional manufacturing (CM) methods to an additive manufacturing (AM) version printed using the laser powder bed fusion process. The AM version has been modified and optimized to achieve better dynamic performance without any regard to weight saving. Lightweight not being a priority in the creation of the 3D printed part brings us a unique perspective in this study. To achieve the LCA, we are using the open-source life cycle, and sustainability software OpenLCA combined with the ReCiPe 2016 at midpoint and endpoint level method. This allows the calculation and the presentation of the results through indicators such as global warming, water use, resource scarcity, etc. The results are then showing the relative impact of the AM version compared to the CM one and give us a key to understand and answer questions about the environmental sustainability of additive manufacturing.

Keywords: additive manufacturing, environmental impact, life cycle assessment, laser powder bed fusion

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Authors: Qin Yang, Fan Zhang, Juan Du, Chongkui Sun, Krishna Kota, Yun-Ling Zheng

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Telomeres are specialized structures at chromosome ends consisting of tandem repetitive DNA sequences [(TTAGGG)n in humans] and associated proteins, which are necessary for telomere function. Telomere lengths are tightly regulated within a narrow range in normal human somatic cells, the basis of cellular senescence and aging. Previous studies have extensively focused on how short telomeres are extended and have demonstrated that telomerase plays a central role in telomere maintenance through elongating the short telomeres. However, the molecular mechanisms of regulating excessively long telomeres are unknown. Here, we found that telomerase enzymatic component hTERT plays a dual role in the regulation of telomeres length. We analyzed single telomere alterations at each chromosomal end led to the discoveries that hTERT shortens excessively long telomeres and elongates short telomeres simultaneously, thus maintaining the optimal telomere length at each chromosomal end for an efficient protection. The hTERT-mediated telomere shortening removes large segments of telomere DNA rapidly without inducing telomere dysfunction foci or affecting cell proliferation, thus it is mechanistically distinct from rapid telomere deletion. We found that expression of hTERT generates telomeric circular DNA, suggesting that telomere homologous recombination may be involved in this telomere shortening process. Moreover, the hTERT-mediated telomere shortening is required its enzymatic activity, but telomerase RNA component hTR is not involved in it. Furthermore, shelterin protein TPP1 interacts with hTERT and recruits it on telomeres to mediate telomere shortening. In addition, telomere-associated proteins, DKC1 and TCAB1 also play roles in this process. This novel hTERT-mediated telomere shortening mechanism not only exists in cancer cells, but also in primary human cells. Thus, the hTERT-mediated telomere shortening is expected to shift the paradigm on current molecular models of telomere length maintenance, with wide-reaching consequences in cancer and aging fields.

Keywords: aging, hTERT, telomerase, telomeres, human cells

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Authors: Azza A. Ali, Mona G. Khalil, Hemat A. Elariny, Shereen S. El Shaer

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Background: Aluminium (Al) is very abundant metal in the earth’s crust. It is a constituent of cooking utensils, medicines, cosmetics, some foods and food additives. Salts of Al are widely used in the treatment of drinking water for purification purposes. Excessive and prolonged exposure to Al causes oxidative stress and impairment of many physiological functions. Its accumulation in liver and kidney causes hepatotoxicity and nephrotoxicity. Social isolation (SI) or Protein malnutrition (PM) also increases oxidative stress and may enhance the toxicity of Al as well as the degeneration in liver and kidney. Epigallocatechin-3-gallate (EGCG) is the most abundant catechin in green tea and has strong antioxidant as well as anti-inflammatory activities and can protect against oxidative stress-induced degenerations. Objective: To study the influence of stress or PM on Al-induced nephrotoxicity and hepatotoxicity in rats, as well as on the potential role of EGCG in providing protection. Methods: Rats received daily AlCl3 (70 mg/kg, IP) for three weeks (Al-toxicity groups) except one normal control group received saline. Al-toxicity groups were divided into four treated and four untreated groups; treated rats received EGCG (10 mg/kg, IP) together with AlCl3. One group of both treated and untreated rats served as control for each of them, and the others were subjected to either stress (mild using isolation or high using electric shock) or to PM (10% casein diet). Specimens of liver and kidney were used for assessment of levels of inflammatory mediators as TNF-α, IL6β, nuclear factor kappa B (NF-κB), oxidative stress (MDA, SOD, TAC, NO), Caspase-3 and for DNA fragmentation as well as for histopathological examinations. Biochemical changes were also measured in the serum as total lipids, cholesterol, triglycerides, glucose, proteins, bilirubin, creatinine and urea as well as the level of Alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and lactate deshydrogenase (LDH). Results: Nephrotoxicity and hepatotoxicity induced by Al were enhanced in rats exposed to stress and to PM. The influence of stress was more pronounced than PM. Al-toxicity was indicated by the increase in liver and kidney MDA, NO, TNF-α, IL-6β, NF-κB, caspase-3, DNA fragmentation and in ALT, AST, ALP, LDH and total lipids, cholesterol, triglycerides, glucose, proteins, bilirubin, creatinine and urea levels, together with the decrease in total proteins, SOD, TAC. EGCG provided protection against hazards of Al as indicated by the decrease in MDA, NO, TNF-α, IL-6β, NF-κB, caspase-3 and DNA fragmentation as well as in levels of ALT, AST, ALP, LDH and total lipids, cholesterol, triglycerides, glucose, proteins, bilirubin, creatinine and urea in liver and kidney, together with the increase in total proteins, SOD, TAC and confirmed by histopathological examinations. It provided more pronounced protection in high stressful conditions than in mild one than in PM. Conclusion: Stress have a bad impact on Al-induced nephrotoxicity and hepatotoxicity more than PM. Thus it can clarify and maximize the role of EGCG in providing protection. Consequently, administration of EGCG is advised with excessive Al-exposure to avoid nephrotoxicity and hepatotoxicity especially in populations more subjected to stress or PM.

Keywords: aluminum, stress, protein malnutrition, nephrotoxicity, hepatotoxicity, epigallocatechin-3-gallate, rats

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Authors: Hajar Zarei, AliAkbar Zarenejadatashgah, Vuk Uskoković, Hiroshi Watabe

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The reactive oxygen species (ROS) generated by radiation in nuclear diagnostic imaging and radiotherapy could damage the structure of the proteins in noncancerous cells surrounding the tumor. The critical factor in many age-related diseases, such as Alzheimer, Parkinson, or Huntington diseases, is the oxidation of proteins by the ROS as molecular triggers of the given pathologies. Our studies by spectroscopic experiments showed doses close to therapeutic ones (1 to 5 Gy) could lead to changes of secondary and tertiary structures in BSA protein macromolecule as a protein model as well as the aggregation of polypeptide chain but without the fragmentation. For this reason, we investigated the radioprotective effects of natural (vitamin C and E) and synthetic materials (CNPs and FIOMPs) on the structural changes in BSA protein induced by gamma irradiation at a therapeutic dose (3Gy). In the presence of both vitamins and synthetic materials, the spectroscopic studies revealed that irradiated BSA was protected from the structural changes caused by ROS, according to in vitro research. The radioprotective property of CNPs and FIOMPs arises from enzyme mimetic activities (catalase, superoxide dismutase, and peroxidase) and their antioxidant capability against hydroxyl radicals. In the case of FIOMPs, a porous structure also leads to increased ROS recombination with each other in the same radiolytic track and subsequently decreased encounters with BSA. The hydrophilicity of vitamin C resulted in the major scavenging of ROS in the solvent, whereas hydrophobic vitamin E localized on the nonpolar patches of the BSA surface, where it did not only neutralize them thanks to the moderate BSA binding constant but also formed a barrier for diffusing ROS. To the best of our knowledge, there has been a persistent lack of studies investigating the radioactive effect of mentioned materials on proteins. Therefore, the results of our studies can open a new widow for application of these common dietary ingredients and new synthetic NPs in improving the safety of radiotherapy.

Keywords: reactive oxygen species, spectroscopy, bovine serum albumin, gamma radiation, radioprotection

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Authors: Shalini Rankawat, Mansi Rankawat, Rahul Dubey, Mazad Zaveri

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Physiological signals such as electrocardiogram (ECG) and arterial blood pressure (ABP) in the intensive care unit (ICU) are often seriously corrupted by noise, artifacts, and missing data, which lead to errors in the estimation of heart rate (HR) and incidences of false alarm from ICU monitors. Clinical support in ICU requires most reliable heart rate estimation. Cardiac activity, because of its relatively high electrical energy, may introduce artifacts in Electroencephalogram (EEG), Electrooculogram (EOG), and Electromyogram (EMG) recordings. This paper presents a robust heart rate estimation method by detection of R-peaks of ECG artifacts in EEG, EMG & EOG signals, using energy-based function and a novel Signal Quality Index (SQI) assessment technique. SQIs of physiological signals (EEG, EMG, & EOG) were obtained by correlation of nonlinear energy operator (teager energy) of these signals with either ECG or ABP signal. HR is estimated from ECG, ABP, EEG, EMG, and EOG signals from separate Kalman filter based upon individual SQIs. Data fusion of each HR estimate was then performed by weighing each estimate by the Kalman filters’ SQI modified innovations. The fused signal HR estimate is more accurate and robust than any of the individual HR estimate. This method was evaluated on MIMIC II data base of PhysioNet from bedside monitors of ICU patients. The method provides an accurate HR estimate even in the presence of noise and artifacts.

Keywords: ECG, ABP, EEG, EMG, EOG, ECG artifacts, Teager-Kaiser energy, heart rate, signal quality index, Kalman filter, data fusion

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Authors: Indu Gaur, Neha Bhadauria, Shilpi Shilpi, Susmita Goswami, Prem D. Sharma, Prabir K. Paul

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The concept of organic agriculture has been accepted as novelty in Indian society, but there is no data available on the human pathogens colonizing plant parts due to such practices. Also, the pattern and mechanism of their colonization need to be understood in order to devise possible strategies for their prevention. In the present study, human pathogenic bacteria were isolated from organically grown tomato plants and five of them were identified as Klebsiella pneumoniae, Enterobacter ludwigii, Serratia fonticola, Stenotrophomonas maltophilia and Chryseobacterium jejuense. Tomato plants were grown in controlled aseptic conditions with 25±1˚C, 70% humidity and 12 hour L/D photoperiod. Six weeks old plants were divided into 6 groups of 25 plants each and treated as follows: Group 1: K. pneumonia, Group 2: E. ludwigii, Group 3: S. fonticola, Group 4: S. maltophilia, Group 5: C. jejuense, Group 6: Sterile distilled water (control). The inoculums for all treatments were prepared by overnight growth with uniform concentration of 108 cells/ml. Leaf samples from above groups were collected at 0.5, 2, 4, 6 and 24 hours post inoculation for the colony forming unit counts (CFU/cm2 of leaf area) of individual pathogens using leaf impression method. These CFU counts were used for the in vivo colonization assay and adherence assay of individual pathogens. Also, resistance of these pathogens to at least 12 antibiotics was studied. Based on these findings S. fonticola was found to be most prominently colonizing the phylloplane of tomato and was further studied. Tomato plants grown in controlled aseptic conditions same as mentioned above were divided into 2 groups of 25 plants each and treated as follows: Group 1: S. fonticola, Group 2: Sterile distilled water (control). Leaf samples from above groups were collected at 0, 24, 48, 72 and 96 hours post inoculation and homogenized in suitable buffers for surface and cell wall protein isolation. Protein samples thus obtained were subjected to isocratic SDS-gel electrophoresis and analyzed. It was observed that presence of S. fonticola could induce the expression of at least 3 additional cell wall proteins at different time intervals. Surface proteins also showed variation in the expression pattern at different sampling intervals. Further identification of these proteins by MALDI-MS and bioinformatics tools revealed the gene(s) involved in the interaction of S. fonticola with tomato phylloplane.

Keywords: cell wall proteins, human pathogenic bacteria, phylloplane, solanum lycopersicum

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Authors: B. Elshafei, X. Mao

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The demand for renewable energy is significantly increasing, major investments are being supplied to the wind power generation industry as a leading source of clean energy. The wind energy sector is entirely dependable and driven by the prediction of wind speed, which by the nature of wind is very stochastic and widely random. This s0tudy employs deep multi-fidelity Gaussian process regression, used to predict wind speeds for medium term time horizons. Data of the RUNE experiment in the west coast of Denmark were provided by the Technical University of Denmark, which represent the wind speed across the study area from the period between December 2015 and March 2016. The study aims to investigate the effect of pre-processing the data by denoising the signal using empirical wavelet transform (EWT) and engaging the vector components of wind speed to increase the number of input data layers for data fusion using deep multi-fidelity Gaussian process regression (GPR). The outcomes were compared using root mean square error (RMSE) and the results demonstrated a significant increase in the accuracy of predictions which demonstrated that using vector components of the wind speed as additional predictors exhibits more accurate predictions than strategies that ignore them, reflecting the importance of the inclusion of all sub data and pre-processing signals for wind speed forecasting models.

Keywords: data fusion, Gaussian process regression, signal denoise, temporal extrapolation

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Authors: Prativa Das, Lay Poh Tan

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Three-dimensional microenvironment is a need to study the event cascades of liver fibrosis in vitro. Electrospun nanofibers modified with essential extracellular matrix proteins can closely mimic the random fibrous structure of native liver extracellular matrix (ECM). In this study, we fabricate a series of 3D electrospun scaffolds by wet electrospinning process modified with different ratios of collagen-I to fibronectin to achieve optimized distribution of these two ECM proteins on the fiber surface. A ratio of 3:1 of collagen-I to fibronectin was found to be optimum for surface modification of electrospun poly(lactic-co-glycolic acid) (PLGA) fibers by chemisorption process. In 3:1 collagen-I to fibronectin modified scaffolds the total protein content increased by ~2 fold compared to collagen-I modified and ~1.5 fold compared to 1:1/9:1 collagen-I to fibronectin modified scaffolds. We have cultured LX-2 cells on this scaffold over 14 days and found that LX-2 cells acquired more quiescent phenotype throughout the culture period and shown significantly lower expression of alpha smooth muscle actin and collagen-I. Thus, this system can be used as a model to study liver fibrosis by using different fibrogenic mediators in vitro.

Keywords: electrospinning, collagen-I and fibronectin, surface modification of fiber, LX-2 cells, liver fibrosis

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Authors: Muhammad Zubair, Aman Ullah, Jianping Wu

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During the last decades, petroleum derived synthetic polymers like polyethylene terephthalate, polyvinylchloride, polyethylene, polypropylene and polystyrene has extensively been used in the field of food packaging and mostly are non-degradable. Biopolymers are a good fit for single-use or short-lived products such as food packaging. Spent hens, a poultry by-product which is of little economic value and their disposal are environmentally harmful. Through current study, we have explored the possibility to transform proteins from spent fowl into green food packaging material. Proteins from spent fowl were extracted within 1 hour using pH shift method with recovery of about 74%. Different plasticizers were tried like glycerol, sorbitol, glutaraldehyde, 1,2 ethylene glycol and 1,2 butanediol. Glycerol was the best plasticizer among all these plasticizers. A naturally occurring and non-toxic cross-linking agent, chitosan, was used to form the chitosan/glycerol/protein blend by casting and compression molding techniques. The mechanical properties were characterized using tensile strength analyzer. The nano-reinforcements with homogeneous dispersion of nanoparticles lead to improved physical properties suggesting that these materials have great potential for food packaging applications.

Keywords: differential scanning calorimetry, dynamic mechanical analysis, scanning electron microscopy, spent hen

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Authors: Lukas Stiburek, Jana Cesnekova, Josef Houstek, Jiri Zeman

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Cellular function depends on mitochondrial function and integrity that is therefore maintained by several classes of proteins possessing chaperone and/or proteolytic activities. In this work, we focused on characterization of LACE1 (lactation elevated 1) function in mitochondrial protein homeostasis maintenance. LACE1 is the human homologue of yeast mitochondrial Afg1 ATPase, a member of SEC18-NSF, PAS1, CDC48-VCP, TBP family. Yeast Afg1 was shown to be involved in mitochondrial complex IV biogenesis, and based on its similarity with CDC48 (p97/VCP) it was suggested to facilitate extraction of polytopic membrane proteins. Here we show that LACE1, which is a mitochondrial integral membrane protein, exists as part of three complexes of approx. 140, 400 and 500 kDa and is essential for maintenance of fused mitochondrial reticulum and lamellar cristae morphology. Using affinity purification of LACE1-FLAG expressed in LACE1 knockdown background we show that the protein physically interacts with mitochondrial inner membrane protease YME1L. We further show that human LACE1 exhibits significant pro-apoptotic activity and that the protein is required for normal function of the mitochondrial respiratory chain. Thus, our work establishes LACE1 as a novel factor with the crucial role in mitochondrial homeostasis maintenance.

Keywords: LACE1, mitochondria, apoptosis, protease

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Authors: Michal Kielbik, Izabela Szulc-Kielbik, Anna Brzostek, Jaroslaw Dziadek, Magdalena Klink

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The goal of many research groups in the world is to find new components that are important for survival of mycobacteria in the host cells. Mycobacterium tuberculosis (Mtb) possesses a number of enzymes degrading cholesterol that are considered to be an important factor for its survival and persistence in host macrophages. One of them - cholesterol oxidase (ChoD), although not being essential for cholesterol degradation, is discussed as a virulence compound, however its involvement in macrophages’ response to Mtb is still not sufficiently determined. The recognition of tubercle bacilli antigens by pathogen recognition receptors is crucial for the initiation of the host innate immune response. An important receptor that has been implicated in the recognition and/or uptake of Mtb is Toll-like receptor type 2 (TLR2). Engagement of TLR2 results in the activation and phosphorylation of intracellular signaling proteins including IRAK-1 and -4, TRAF-6, which in turn leads to the activation of target kinases and transcription factors responsible for bactericidal and pro-inflammatory response of macrophages. The aim of these studies was a detailed clarification of the role of Mtb cholesterol oxidase as a virulence factor affecting the TLR2 signaling pathway in human macrophages. As human macrophages the THP-1 differentiated cells were applied. The virulent wild-type Mtb strain (H37Rv), its mutant lacking a functional copy of gene encoding cholesterol oxidase (∆choD), as well as complimented strain (∆choD–choD) were used. We tested the impact of Mtb strains on the expression of TLR2-depended signaling proteins (mRNA level, cytosolic level and phosphorylation status). The cytokine and bactericidal response of THP-1 derived macrophages infected with Mtb strains in relation to TLR2 signaling pathway dependence was also determined. We found that during the 24-hours of infection process the wild-type and complemented Mtb significantly reduced the cytosolic level and phosphorylation status of IRAK-4 and TRAF-6 proteins in macrophages, that was not observed in the case of ΔchoD mutant. Decreasement of TLR2-dependent signaling proteins, induced by wild-type Mtb, was not dependent on the activity of proteasome. Blocking of TLR2 expression, before infection, effectively prevented the induced by wild-type strain reduction of cytosolic level and phosphorylation of IRAK-4. None of the strains affected the surface expression of TLR2. The mRNA level of IRAK-4 and TRAF-6 genes were significantly increased in macrophages 24 hours post-infection with either of tested strains. However, the impact of wild-type Mtb strain on both examined genes was significantly stronger than its ΔchoD mutant. We also found that wild-type strain stimulated macrophages to release high amount of immunosuppressive IL-10, accompanied by low amount of pro-inflammatory IL-8 and bactericidal nitric oxide in comparison to mutant lacking cholesterol oxidase. The influence of wild-type Mtb on this type of macrophages' response strongly dependent on fully active IRAK-1 and IRAK-4 signaling proteins. In conclusion, Mtb using cholesterol oxidase causes the over-activation of TLR2 signaling proteins leading to the reduction of their cytosolic level and activity resulting in the modulation of macrophages response to allow its intracellular survival. Supported by grant: 2014/15/B/NZ6/01565, National Science Center, Poland

Keywords: Mycobacterium tuberculosis, cholesterol oxidase, macrophages, TLR2-dependent signaling pathway

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Authors: Preecha Yupapin And Somnath

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From the emptiness, the vibration induces the fractal, and the strings are formed. From which the first elementary particle groups, known as quarks, were established. The neutrino and electron are created by them. More elementary particles and life are formed by organic and inorganic substances. The universe is constructed, from which the multi-universe has formed in the same way. universe assumes that the intense energy has escaped from the singularity cone from the multi-universes. Initially, the single mass energy is confined, from which it is disturbed by the space-time distortion. It splits into the entangled pair, where the circular motion is established. It will consider one side of the entangled pair, where the fusion energy of the strong coupling force has formed. The growth of the fusion energy has the quantum physic phenomena, where the moving of the particle along the circumference with a speed faster than light. It introduces the wave-particle duality aspect, which will be saturated at the stopping point. It will be re-run again and again without limitation, which can say that the universe has been created and expanded. The Bose-Einstein condensate (BEC) is released through the singularity by the wormhole, which will be condensed to become a mass associated with the Sun's size. It will circulate(orbit) along the Sun. the consideration of the uncertainty principle is applied, from which the breath control is followed by the uncertainty condition ∆p∆x=∆E∆t~ℏ. The flowing in-out air into a body via a nose has applied momentum and energy control respecting the movement and time, in which the target is that the distortion of space-time will have vanished. Finally, the body is clean which can go to the next procedure, where the mind can escape from the body by the speed of light. However, the borderline between contemplation to being an Arahant is a vacuum, which will be explained.

Keywords: space-time, relativity, enlightenment, emptiness

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Authors: Ritu Chaturvedi, Manoj Paul

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A pot experiment was conducted to investigate the effect of Arbuscular mycorrhizal fungus (AMF) on metal(loid) uptake and accumulation efficiency of Pisum sativum along with physiological and biochemical response. Plants were grown in soil spiked with 50 and 100 mg kg-1 Pb, 25 and 50 mg kg-1 Cd, 50 and 100 mg kg-1 As and a combination of all three metal(loid)s. A parallel set was maintained and inoculated with arbuscular mycorrhizal fungus for comparison. After 60 days, plants were harvested and analysed for metal(loid) content. A steady increase in metal(loid) accumulation was observed on increment of metal(loid) dose and also on AMF inoculation. Plant height, biomass, chlorophyll, carotenoid and carbohydrate content reduced upon metal(loid) exposure. Increase in enzymatic (CAT, SOD and APX) and nonenzymatic (Proline) defence proteins was observed on metal(loid) exposure. AMF inoculation leads to an increase in plant height, biomass, chlorophyll, carotenoids, carbohydrate and enzymatic defence proteins (p≤0.001) under study; whereas proline content was reduced. Considering the accumulation efficiency and adaptive response of plants and alleviation of stress by AMF, this symbiosis can be applied for on-site remediation of Pb and Cd contaminated soil.

Keywords: heavy metal, mycorrhiza, pea, phyroremediation

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Authors: Irena Kostovska, Katerina Tosheska Trajkovska, Svetlana Cekovska, Julijana Brezovska Kavrakova, Hristina Ampova, Sonja Topuzovska, Ognen Kostovski, Goce Spasovski, Danica Labudovic

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Background: Proteinuria is an important feature of secondary nephropathies. The quantitative and qualitative analysis of proteinuria plays an important role in determining the types of proteinuria (glomerular, tubular and mixed), in the diagnosis and prognosis of secondary nephropathies. The damage of the glomerular basement membrane is responsible for a proteinuria characterized by the presence of large amounts of protein with high molecular weights such as albumin (69 kilo Daltons-kD), transferrin (78 kD) and immunoglobulin G (150 kD). An insufficiency of proximal tubular function is the cause of a proteinuria characterized by the presence of proteins with low molecular weight (LMW), such as retinol binding protein (21 kD) and α1-microglobulin (31 kD). In some renal diseases, a mixed glomerular and tubular proteinuria is frequently seen. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) is the most widely used method of analyzing urine proteins for clinical purposes. The main aim of the study is to determine the type of proteinuria in the most common secondary nephropathies such as diabetic, hypertensive nephropathy and preeclampsia. Material and methods: In this study were included 90 subjects: subjects with diabetic nephropathy (n=30), subjects with hypertensive nephropahty (n=30) and pregnant women with preeclampsia (n=30). We divided all subjects according to UM/CR into three subgroups: macroalbuminuric (UM/CR >300 mg/g), microalbuminuric (UM/CR 30-300 mg/g) and normolabuminuric (UM/CR<30 mg/g). In all subjects, we measured microalbumin and creatinine in urine with standard biochemical methods. Separation of urinary proteins was performed by SDS-PAGE, in several stages: linear gel preparation (4-22%), treatment of urinary samples before their application on the gel, electrophoresis, gel fixation, coloring with Coomassie blue, and identification of the separated protein fractions based on standards with exactly known molecular weight. Results: According to urinary microalbumin/creatinin ratio in group of subject with diabetic nephropathy, nine patients were macroalbuminuric, while 21 subject were microalbuminuric. In group of subjects with hypertensive nephropathy, we found macroalbuminuria (n=4), microalbuminuria (n=20) and normoalbuminuria (n=6). All pregnant women with preeclampsia were macroalbuminuric. Electrophoretic separation of urinary proteins showed that in macroalbuminric patients with diabetic nephropathy 56% have mixed proteinuria, 22% have glomerular proteinuria and 22% have tubular proteinuria. In subgroup of subjects with diabetic nephropathy and microalbuminuria, 52% have glomerular proteinuria, 8% have tubular proteinuria, and 40% of subjects have normal electrophoretic findings. All patients with maroalbuminuria and hypertensive nephropathy have mixed proteinuria. In subgroup of patients with microalbuminuria and hypertensive nephropathy, we found: 32% with mixed proteinuria, 27% with normal findings, 23% with tubular, and 18% with glomerular proteinuria. In all normoalbuminruic patiens with hypertensive nephropathy, we detected normal electrophoretic findings. In group of subjects pregnant women with preeclampsia, we found: 81% with mixed proteinuria, 13% with glomerular, and 8% with tubular proteinuria. Conclusion: By SDS PAGE method, we detected that in patients with secondary nephropathies the most common type of proteinuria is mixed proteinuria, indicating both loss of glomerular permeability and tubular function. We can conclude that SDS PAGE is high sensitive method for detection of renal impairment in patients with secondary nephropathies.

Keywords: diabetic nephropathy, preeclampsia, hypertensive nephropathy, SDS PAGE

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Authors: Nilesh Bandekar, Sumita Dasgupta, Luis Alberto Allcahuaman Huaya, Souvik Manna

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Cryptobiosis is a dormant state where all measurable metabolic activities are at a halt, allowing an organism to survive in extreme conditions like low temperature (cryobiosis), extreme drought (anhydrobiosis), etc. This phenomenon is observed especially in tardigrades that can retain this state for decades depending on the abiotic environmental conditions. On returning to favorable conditions, tardigrades re-attain a metabolically active state. In this study, cyanobacteria as a model organism are being chosen to induce cryptobiosis for its effective preservation over a long period of time. Preserving cyanobacteria using this strategy will have multiple space applications because of its ability to produce oxygen. In addition, research has shown the survivability of this organism in space for a certain period of time. Few species of cyanobacterial residents of the soil such as Microcoleus, are able to survive in extreme drought as well. This work specifically focuses on Synechococcus elongatus, an endolith cyanobacteria with multiple benefits. It has the capability to produce 25% oxygen in water bodies. It utilizes carbon dioxide to produce oxygen via photosynthesis and also uses carbon dioxide as an energy source to form glucose via the Calvin cycle. There is a fair possibility of initiating cryptobiosis in such an organism by inducing certain proteins extracted from tardigrades such as Heat Shock Proteins (Hsp27 and Hsp30c) and/or hydrophilic Late Embryogenesis Abundant proteins (LEA). Existing methods like cryopreservation are difficult to execute in space keeping in mind their cost and heavy instrumentation. Also, extensive freezing may cause cellular damage. Therefore, cryptobiosis-induced cyanobacteria for its transportation from Earth to Mars as a part of future terraforming missions on Mars will save resources and increase the effectiveness of preservation. Finally, Cyanobacteria species like Synechococcus elongatus can also produce oxygen and glucose on Mars in favorable conditions and holds the key to terraforming Mars.

Keywords: cryptobiosis, cyanobacteria, glucose, mars, Synechococcus elongatus, tardigrades

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Authors: Soma Banerjee, Aamen Talukdar, Argha Mandal, Dipankar Chaudhuri

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Japanese Encephalitis is a major infectious disease with nearly half the world’s population living in areas where it is prevalent. Currently, treatment for it involves only supportive care and symptom management through vaccination. Due to the lack of antiviral drugs against Japanese Encephalitis Virus (JEV), the quest for such agents remains a priority. For these reasons, simulation studies of drug targets against JEV are important. Towards this purpose, docking experiments of the kinase inhibitors were done against the chosen target NS3 helicase as it is a nucleoside binding protein. Previous efforts regarding computational drug design against JEV revealed some lead molecules by virtual screening using public domain software. To be more specific and accurate regarding finding leads, in this study a proprietary software Schrödinger-GLIDE has been used. Druggability of the pockets in the NS3 helicase crystal structure was first calculated by SITEMAP. Then the sites were screened according to compatibility with ATP. The site which is most compatible with ATP was selected as target. Virtual screening was performed by acquiring ligands from databases: KinaseSARfari, KinaseKnowledgebase and Published inhibitor Set using GLIDE. The 25 ligands with best docking scores from each database were re-docked in XP mode. Protein structure alignment of NS3 was performed using VAST against MMDB, and similar human proteins were docked to all the best scoring ligands. The low scoring ligands were chosen for further studies and the high scoring ligands were screened. Seventy-three ligands were listed as the best scoring ones after performing HTVS. Protein structure alignment of NS3 revealed 3 human proteins with RMSD values lesser than 2Å. Docking results with these three proteins revealed the inhibitors that can interfere and inhibit human proteins. Those inhibitors were screened. Among the ones left, those with docking scores worse than a threshold value were also removed to get the final hits. Analysis of the docked complexes through 2D interaction diagrams revealed the amino acid residues that are essential for ligand binding within the active site. Interaction analysis will help to find a strongly interacting scaffold among the hits. This experiment yielded 21 hits with the best docking scores which could be investigated further for their drug like properties. Aside from getting suitable leads, specific NS3 helicase-inhibitor interactions were identified. Selection of Target modification strategies complementing docking methodologies which can result in choosing better lead compounds are in progress. Those enhanced leads can lead to better in vitro testing.

Keywords: antivirals, docking, glide, high-throughput virtual screening, Japanese encephalitis, ns3 helicase

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Authors: Sri Rahayu, M. Dwi Susan, Aris Soewondo, W. M. Agung Pramana

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Semen is an organic fluid (seminal plasma) that contain spermatozoa. Proteins are one of the major seminal plasma components that modulate sperm functionality, influence sperm capacitation and maintaining the stability of the membrane. Semen freezing is a procedure to preserve sperm cells. The process causes decrease in sperm viability due to temperature shock and oxidation stress. Oxidation stress is a disturbance on phosphorylation that increases ROS concentration, and it produces lipid peroxide in spermatozoa membrane resulted in high MDA (malondialdehyde) concentration. The objective of this study was to examine the effect of freezing on protein and MDA profile of bovine sperm cell and seminal plasma after freezing. Protein and MDA of sperm cell and seminal plasma were isolated from 10 sample. Protein profiles was analyzed by SDS PAGE with separating gel 12,5 %. The concentration of MDA was measured by spectrophotometer. The results of the research indicated that freezing of semen cause lost of the seminal plasma proteins with molecular with 20, 10, and 9 kDa. In addition, the result research showed that protein of the sperm (26, 10, 9, 7, and 6 kDa) had been lost. There were difference MDA concentration of seminal plasma and sperm cell were increase after freezing. MDA concentration of seminal plasma before and after freezing were 2.2 and 2.4 nmol, respectively. MDA concentration of sperm cell before and after freezing were 1,5 and 1.8 nmol, respectively. In conclusion, there were differences protein profiles of spermatozoa before and after semen freezing and freezing cause increasing of the MDA concentration.

Keywords: MDA, semen freezing, SDS PAGE, protein profile

Procedia PDF Downloads 275

Authors: Jinge Liu, Shuyuan Min, Bingchuan Liu, Bangzhao Yin, Bo Peng, Peng Wen, Yun Tian

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WE43 magnesium alloy can be additively manufactured via laser powder bed fusion (LPBF) for biodegradable applications, but the as-built WE43 exhibits an excessively rapid corrosion rate. High-temperature oxidation (HTO) was performed on the as-built WE43 to improve its biodegradation behavior. A sandwich structure including an oxide layer at the surface, a transition layer in the middle, and the matrix was generated influenced by the oxidation reaction and diffusion of RE atoms when heated at 525 ℃for 8 hours. The oxide layer consisted of Y₂O₃ and Nd₂O₃ oxides with a thickness of 2-3 μm. The transition layer is composed of α-Mg and Y₂O₃ with a thickness of 60-70 μm, while Mg24RE5 could be observed except α-Mg and Y₂O₃. The oxide layer and transition layer appeared to have an effective passivation effect. The as-built WE43 lost 40% weight after the in vitro immersion test for three days and finally broke into debris after seven days of immersion. The high-temperature oxidation samples kept the structural integrity and lost only 6.88 % weight after 28-day immersion. The corrosion rate of HTO samples was significantly controlled, which improved the biocompatibility of the as-built WE43 at the same time. The samples after HTO had better osteogenic capability according to ALP activity. Moreover, as built WE43 performed unqualified in cell adhesion and hemolytic test due to its excessively rapid corrosion rate. While as for HTO samples, cells adhered well, and the hemolysis ratio was only 1.59%.

Keywords: laser powder bed fusion, biodegradable metal, high temperature oxidation, biodegradation behavior, WE43

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Authors: Aakansha Gupta, Neha Vadnere, Tapasvi Soni, M. Anbarsi

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Protein secondary structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine and biotechnology. Some aspects of protein functions and genome analysis can be predicted by secondary structure prediction. This is used to help annotate sequences, classify proteins, identify domains, and recognize functional motifs. In this paper, we represent protein secondary structure as a mathematical model. To extract and predict the protein secondary structure from the primary structure, we require a set of parameters. Any constants appearing in the model are specified by these parameters, which also provide a mechanism for efficient and accurate use of data. To estimate these model parameters there are many algorithms out of which the most popular one is the EM algorithm or called the Expectation Maximization Algorithm. These model parameters are estimated with the use of protein datasets like RS126 by using the Bayesian Probabilistic method (data set being categorical). This paper can then be extended into comparing the efficiency of EM algorithm to the other algorithms for estimating the model parameters, which will in turn lead to an efficient component for the Protein Secondary Structure Prediction. Further this paper provides a scope to use these parameters for predicting secondary structure of proteins using machine learning techniques like neural networks and fuzzy logic. The ultimate objective will be to obtain greater accuracy better than the previously achieved.

Keywords: model parameters, expectation maximization algorithm, protein secondary structure prediction, bioinformatics

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Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time-based DNA codes, writing DNA code from scratch

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Authors: Chargui Abderrahman, Nehdi Afef , BelaïD Amine , Djerbi Nadir, Tauc Michel, Hofman Paul, Mograbi Baharia, El May MichèLe

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K63-linked ubiquitination — i.e. conjugation of a chain of ubiquitins (Ub) linked through lys63 — has emerged as a key mechanism regulating signalling transduction pathways. Although critical, very little information is currently available about how subversion of K63 ubiquitination might contribute to cancers and inflammatory diseases. The present study provides the first evidence that Cadmium (Cd), a widespread environmental carcinogen and toxicant, is a powerful activator of K63 ubiquitination. Indeed, Cd induces accumulation of K63 polyUb proteins. Importantly, Cd-induced ubiquitination does not stem on oxidative damage or proteasome impairment. Rather, we demonstrate that Cd not only activates K63 ubiquitination but also amplifies their accumulation by overloading the capacity of autophagy pathway. At molecular level, Cd-induced ubiquitination is correlated with stabilization of HIF-1 and the activation of NF-B, two transcription factors. Strikingly, prolonged cell exposure to high Cd concentrations induces an exaggerated K63 ubiquitination that fosters aggresome formation, thus precluding these proteins from interacting with their downstream nuclear targets. We therefore propose that the aberrant activation of K63 ubiquitination by the carcinogen Cadmium could promote cell proliferation and inflammation at low levels while high levels committed cell to death.

Keywords: cadmium, environmental exposure, Lysine-63-ubiquitination, kidney, apoptosis, proliferation, autophagy

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Authors: Iftikhar Tayubi, Tabrej Khan, Rayan Alsulmi, Abdulrahman Labban

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Spider produces a special kind of substance. This special kind of substance is called a toxin. The toxin is composed of many types of protein, which differs from species to species. Spider toxin consists of several proteins and non-proteins that include various categories of toxins like myotoxin, neurotoxin, cardiotoxin, dendrotoxin, haemorrhagins, and fibrinolytic enzyme. Protein Sequence information with references of toxins was derived from literature and public databases. From the previous findings, the Spider toxin would be the best choice to treat different types of tumors and cancer. There are many therapeutic regimes, which causes more side effects than treatment hence a different approach must be adopted for the treatment of cancer. The combinations of drugs are being encouraged, and dramatic outcomes are reported. Spider toxin is one of the natural cytotoxic compounds. Hence, it is being used to treat different types of tumors; especially its positive effect on breast cancer is being reported during the last few decades. The efficacy of this database is that it can provide a user-friendly interface for users to retrieve the information about Spiders, toxin and toxin protein of different Spiders species. SPIDTOXD provides a single source information about spider toxins, which will be useful for pharmacologists, neuroscientists, toxicologists, medicinal chemists. The well-ordered and accessible web interface allows users to explore the detail information of Spider and toxin proteins. It includes common name, scientific name, entry id, entry name, protein name and length of the protein sequence. The utility of this database is that it can provide a user-friendly interface for users to retrieve the information about Spider, toxin and toxin protein of different Spider species. The database interfaces will satisfy the demands of the scientific community by providing in-depth knowledge about Spider and its toxin. We have adopted the methodology by using A MySQL and PHP and for designing, we used the Smart Draw. The users can thus navigate from one section to another, depending on the field of interest of the user. This database contains a wealth of information on species, toxins, and clinical data, etc. This database will be useful for the scientific community, basic researchers and those interested in potential pharmaceutical Industry.

Keywords: siptoxd, php, mysql, toxin

Procedia PDF Downloads 182