Search results for: protein adsorption

Authors: Gyaltsen Dakpa, K. J. Senthil Kumar, Nai-Wen Tsao, Sheng-Yang Wang

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Context: Coronavirus disease 2019 (COVID-19) is a severe respiratory illness caused by the SARS-CoV-2 virus. One of the hallmarks of COVID-19 is a change in metabolism, which can lead to increased severity and mortality. The mechanism of SARS-CoV-2-mediated perturbations of metabolic pathways has yet to be fully understood. Research Aim: This study aimed to investigate the metabolic alteration caused by SARS-CoV-2 spike protein in Phorbol 12-myristate 13-acetate (PMA)-induced human monocytes (THP-1) and to examine the regulatory effect of natural compounds like Antcins A on SARS-CoV-2 spike protein-induced metabolic alteration. Methodology: The study used a combination of proton nuclear magnetic resonance (1H-NMR) and MetaboAnalyst 5.0 software. THP-1 cells were treated with SARS-CoV-2 spike protein or control, and the metabolomic profiles of the cells were compared. Antcin A was also added to the cells to assess its regulatory effect on SARS-CoV-2 spike protein-induced metabolic alteration. Findings: The study results showed that treatment with SARS-CoV-2 spike protein significantly altered the metabolomic profiles of THP-1 cells. Eight metabolites, including glycerol-phosphocholine, glycine, canadine, sarcosine, phosphoenolpyruvic acid, glutamine, glutamate, and N, N-dimethylglycine, were significantly different between control and spike-protein treatment groups. Antcin A significantly reversed the changes in these metabolites. In addition, treatment with antacid A significantly inhibited SARS-CoV-2 spike protein-mediated up-regulation of TLR-4 and ACE2 receptors. Theoretical Importance The findings of this study suggest that SARS-CoV-2 spike protein can cause significant metabolic alterations in THP-1 cells. Antcin A, a natural compound, has the potential to reverse these metabolic alterations and may be a potential candidate for developing preventive or therapeutic agents for COVID-19. Data Collection: The data for this study was collected from THP-1 cells that were treated with SARS-CoV-2 spike protein or a control. The metabolomic profiles of the cells were then compared using 1H-NMR and MetaboAnalyst 5.0 software. Analysis Procedures: The metabolomic profiles of the THP-1 cells were analyzed using 1H-NMR and MetaboAnalyst 5.0 software. The software was used to identify and quantify the cells' metabolites and compare the control and spike-protein treatment groups. Questions Addressed: The question addressed by this study was whether SARS-CoV-2 spike protein could cause metabolic alterations in THP-1 cells and whether Antcin A can reverse these alterations. Conclusion: The findings of this study suggest that SARS-CoV-2 spike protein can cause significant metabolic alterations in THP-1 cells. Antcin A, a natural compound, has the potential to reverse these metabolic alterations and may be a potential candidate for developing preventive or therapeutic agents for COVID-19.

Keywords: SARS-CoV-2-spike, ¹H-NMR, metabolomics, antcin-A, taiwanofungus camphoratus

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Authors: Kieren Luellman, Makenzi Rockwell, Eduardo Callegari, Nichole Haag, Chun Wu

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Multiple sclerosis (MS) is an autoimmune disorder that damages the myelin sheath of neurons in the central nervous system. The presence of Acinetobacter bacteria and anti-Acinetobacter antibodies in MS patients has led to the hypothesis that the bacteria may contribute to MS pathogenesis. In this study, the protein sequences of Acinetobacter baumannii were compared to five peptides from three mammalian myelin proteins, i.e., Proteolipid Protein (PLP): PLP 139-151, PLP 178-191, Myelin Basic Protein (MBP): MBP 84-104 and Myelin Oligodendrocyte Glycoprotein (MOG): MOG 35-55 and MOG 92-106 respectively, known to induce experimental autoimmune encephalomyelitis (EAE), a condition similar to MS. We found 11 hits (i.e., with five or more amino acid sequence similarity) in Acinetobacter baumannii, which are identical or similar to PLP139-151, 32 hits to PLP178-191, 35 to MBP 84-104, 41 hits to MOG 35-55 and 26 hits to MOG92-106. In addition, Western blotting was used to assess possible interaction between the bacterial proteins and human anti-MBP, anti-MOG, and anti-PLP antibodies produced in rabbits, corresponding to MBP 84-104, MOG 35-55, and PLP 139-151, respectively. We found that both human Polyclonal anti-MOG antibody and anti-PLP antibody recognized a protein or more proteins of the same molecular mass of around 25 kDa. in Acinetobacter baumannii. The results suggested that this/these protein(s) might potentially serve as antigen(s) to induce anti-MOG antibody and anti-PLP antibody production in mammalian B cells. The proteomic study identified 433 hits, among which the sequence of Acinetobacter baumannii protein 491 subunit A matches a previously published enzyme Acinetobacter 3-Oxoadipate CoA-Transferase, in which a fragment of its peptide was observed to recognize MS patient serum via ELISA method. Our findings might pave the road to understanding one of the pathogenesis mechanisms of MS.

Keywords: multiple sclerosis, pathogenesis, Acinetobacter baumannii, antibody recognition

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Authors: Harika Atmaca, Emir Bozkurt, Latife Merve Oktay, Selim Uzunoglu, Ruchan Uslu, Burçak Karaca

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Microarrays have been developed for highly parallel enzyme-linked immunosorbent assay (ELISA) applications. The most common protein arrays are produced by using multiple monoclonal antibodies, since they are robust molecules which can be easily handled and immobilized by standard procedures without loss of activity. Protein expression profiling with protein array technology allows simultaneous analysis of the protein expression pattern of a large number of proteins. Trabectedin, a tetrahydroisoquinoline alkaloid derived from a Caribbean tunicate, Ecteinascidia turbinata, has been shown to have antitumor effects. Here, we used a novel proteomic approach to explore the mechanism of action of trabectedin in prostate cancer cell line PC-3 by apoptosis antibody microarray. XTT cell proliferation kit and Cell Death Detection Elisa Plus Kit (Roche) was used for measuring cytotoxicity and apoptosis. Human Apoptosis Protein Array (R&D Systems) which consists of 35 apoptosis related proteins was used to assess the omic protein expression pattern. Trabectedin induced cytotoxicity and apoptosis in prostate cancer cells in a time and concentration-dependent manner. The expression levels of the death receptor pathway molecules, TRAIL-R1/DR4, TRAIL R2/DR5, TNF R1/TNFRSF1A, FADD were significantly increased by 4.0-, 21.0-, 4.20- and 11.5-fold by trabectedin treatment in PC-3 cells. Moreover, mitochondrial pathway related pro-apoptotic proteins Bax, Bad, Cytochrome c, and Cleaved Caspase-3 expressions were induced by 2.68-, 2.07-, 2.8-, and 4.5-fold and the expression levels of anti-apoptotic proteins Bcl-2 and Bcl-XL were reduced by 3.5- and 5.2-fold in PC-3 cells. Proteomic (antibody microarray) analysis suggests that the mechanism of action of trabectedin may be exerted via the induction of both intrinsic and extrinsic apoptotic pathways. The antibody microarray platform can be utilised to explore the molecular mechanism of action of novel anticancer agents.

Keywords: trabectedin, prostate cancer, omic protein expression profile, apoptosis

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Authors: S. Mowafi, A. Abou El-Kheir, M. Abou Taleb, H. El-Sayed

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Two proteinic biopolymers; namely keratin and sericin, were extracted from their respective natural resources by simple appropriate methods. The said proteins were dissolved in the appropriate solvents followed by regeneration in a form of film polyvinyl alcohol. Protein-starch-potassium iodide (PSPI) composite was prepared by anchoring starch and potassium iodide mixture onto the film surface using appropriate polymeric material. The possibility of using PSPI composite for determination of the concentration of chlorine ions in domestic as well as industrial water was examined. The concentration of chlorine in water was determined spectrophotometrically by measuring the intensity of blue colour of formed between starch and the released iodine obtained by interaction of potassium iodide chlorine in the tested water sample.

Keywords: chlorine, protein, potassium iodide, water

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Authors: Kingsley Izuagbe Ikeke, Abayomi O. Adetuyi

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The study investigated the removal efficiency of crystal violet from aqueous solution using chitosan-charcoal composite as adsorbent. Deproteination was carried out by placing 200g of powdered snail shell in 4% w/v NaOH for 2hours. The sample was then placed in 1% HCl for 24 hours to remove CaCO3. Deacetylation was done by boiling in 50% NaOH for 2hours. 10% Oxalic acid was used to dissolve the chitosan before mixing with charcoal at 55°C to form the composite. The composite was characterized by Fourier Transform Infra-Red and Scanning Electron Microscopy measurements. The efficiency of adsorption was evaluated by varying pH of the solution, contact time, initial concentration and adsorbent dose. Maximum removal of crystal violet by composite and activated charcoal was attained at pH10 while maximum removal of crystal violet by chitosan was achieved at pH 8. The results showed that adsorption of both dyes followed the pseudo-second-order rate equation and fit the Langmuir and Freundlich isotherms. The data showed that composite was best suited for crystal violet removal and also did relatively well in the removal of alizarin red. Thermodynamic parameters such as enthalpy change (ΔHº), free energy change (ΔGº) and entropy change (ΔSº) indicate that adsorption process of Crystal Violet was endothermic, spontaneous and feasible respectively.

Keywords: crystal violet, chitosan−charcoal composite, extraction process, sorption

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Authors: M. Kouyate, M. Sangare, S. Samake, S. Keita, H. G. Kim, D. H. Geschwind

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Background & Objectives: Human genetic studies can be expensive, even unaffordable, in developing countries, partly due to the sequencing costs. Our aim is to pilot the use of bioinformatics tools to guide scientifically valid, locally relevant, and economically sound autism genetic research in Mali. Methods: The following databases, NCBI, HGMD, and LSDB, were used to identify hot point mutations. Phenotype, transmission pattern, theoretical protein expression in the brain, the impact of the mutation on the 3D structure of the protein) were used to prioritize selected autism genes. We used the protein database, Modeller, and clustal W. Results: We found Mef2c (Gly27Ala/Leu38Gln), Pten (Thr131IIle), Prodh (Leu289Met), Nme1 (Ser120Gly), and Dhcr7 (Pro227Thr/Glu224Lys). These mutations were associated with endonucleases BseRI, NspI, PfrJS2IV, BspGI, BsaBI, and SpoDI, respectively. Gly27Ala/Leu38Gln mutations impacted the 3D structure of the Mef2c protein. Mef2c protein sequences across species showed a high percentage of similarity with a highly conserved MADS domain. Discussion: Mef2c, Pten, Prodh, Nme1, and Dhcr 7 gene mutation frequencies in the Malian population will be very informative. PCR coupled with restriction enzyme digestion can be used to screen the targeted gene mutations. Sanger sequencing will be used for confirmation only. This will cut down considerably the sequencing cost for gene-to-gene mutation screening. The knowledge of the 3D structure and potential impact of the mutations on Mef2c protein informed the protein family and altered function (ex. Leu38Gln). Conclusion & Future Work: Bio-informatics will positively impact autism research in Mali. Our approach can be applied to another neuropsychiatric disorder.

Keywords: bioinformatics, endonucleases, autism, Sanger sequencing, point mutations

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Authors: Pooja Kumari, Anandkumar Tengli

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Aurora kinase enzyme, a protein on overexpression, leads to metastasis and is extremely important for women’s health in terms of prevention or treatment. While creating a targeted technique, the aim of the work is to design purine molecules that inhibit in aurora kinase enzyme and helps to suppress breast cancer. Purine molecules attached to an amino acid in DNA block protein synthesis or halt the replication and metastasis caused by the aurora kinase enzyme. Various protein related to the overexpression of aurora protein was docked with purine molecule using Biovia Drug Discovery, the perpetual software. Various parameters like X-ray crystallographic structure, presence of ligand, Ramachandran plot, resolution, etc., were taken into consideration for selecting the target protein. A higher negative binding scored molecule has been taken for simulation studies. According to the available research and computational analyses, purine compounds may be powerful enough to demonstrate a greater affinity for the aurora target. Despite being clinically effective now, purines were originally meant to fight breast cancer by inhibiting the aurora kinase enzyme. In in-silico studies, it is observed that purine compounds have a moderate to high potency compared to other molecules, and our research into the literature revealed that purine molecules have a lower risk of side effects. The research involves the design, synthesis, and identification of active purine molecules against breast cancer. Purines are structurally similar to the normal metabolites of adenine and guanine; hence interfere/compete with protein synthesis and suppress the abnormal proliferation of cells/tissues. As a result, purine target metastasis cells and stop the growth of kinase; purine derivatives bind with DNA and aurora protein which may stop the growth of protein or inhibits replication and stop metastasis of overexpressed aurora kinase enzyme.

Keywords: aurora kinases, in silico studies, medicinal chemistry, combination therapies, chronic cancer, clinical translation

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Authors: Zi-Han Li, Lu Fang, Liang Wu, Dong-Yuan Chang, Manyuan Dong, Liang Ji, Qi Zhang, Ming-Hui Zhao, Sydney C.W. Tang, Lemin Zheng, Min Chen

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Uncoupling of mitochondrial respiration by chemical uncouplers has proven effective in ameliorating obesity, insulin resistance, and hyperglycemia, which were risk factors for diabetic nephropathy (DN). Recently, it was found that annexin A1(ANXA1) could improve mitochondrial function to mitigate DN progression. However, the underlying mechanism is not fully clear yet. Here, it was identified that uncoupling protein 1 (UCP1), an inner membrane protein of mitochondria, as a key to mitochondrial homeostasis improved by ANXA1. Specifically, ANXA1 attenuated mitochondrial dysfunction via appropriately upregulating UCP1 by stabilizing its transcription factor GATA binding protein 3 (GATA3) through combining with thioredoxin. Moreover, specific overexpression of UCP1 in renal cortex rescued renal injuries in diabetic Anxa1-KO mice. UCP1 deletion aggravated renal injuries in HFD/STZ-induced diabetic mice. Mechanistically, UCP1 reduced mitochondrial fission through the aristaless-related homeobox (ARX)/cardiolipin synthase 1 (CRLS1) pathway. Therapeutically, CL316243, a UCP1 agonist, could attenuate established DN in db/db mice. This work established a novel principle to harness the power of uncouplers for the treatment of DN.

Keywords: diabetic nephropathy, uncoupling protein 1, mitochondrial homeostasis, cardiolipin metabolism

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Authors: Hany M. Abd El-Lateef

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Two novel Schiff bases, 5-bromo-2-[(E)-(pyridin-3-ylimino) methyl] phenol (HBSAP) and 5-bromo-2-[(E)-(quinolin-8-ylimino) methyl] phenol (HBSAQ) have been synthesized. They have been characterized by elemental analysis and spectroscopic techniques (UV–Vis, IR and NMR). Moreover, the molecular structure of HBSAP and HBSAQ compounds are determined by single crystal X-ray diffraction technique. The inhibition activity of HBSAP and HBSAQ for carbon steel in 3.5 %NaCl+0.1 M HCl for both short and long immersion time, at different temperatures (20-50 ºC), was investigated using electrochemistry and surface characterization. The potentiodynamic polarization shows that the inhibitors molecule is more adsorbed on the cathodic sites. Its efficiency increases with increasing inhibitor concentrations (92.8 % at the optimal concentration of 10-3 M for HBSAQ). Adsorption of the inhibitors on the carbon steel surface was found to obey Langmuir’s adsorption isotherm with physical/chemical nature of the adsorption, as it is shown also by scanning electron microscopy. Further, the electronic structural calculations using quantum chemical methods were found to be in a good agreement with the results of the experimental studies.

Keywords: carbon steel, Schiff bases, corrosion inhibition, SEM, electrochemical techniques

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Authors: Farideh Halakou, Emel Sen, Attila Gursoy, Ozlem Keskin

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Protein–Protein Interactions (PPIs) mediate major biological processes in living cells. The study of PPIs as networks and analyze the network properties contribute to the identification of genes and proteins associated with diseases. In this study, we have created the sub-networks of brain and lung metastasis from primary tumor in breast cancer. To do so, we used seed genes known to cause metastasis, and produced their interactions through a network-topology based prioritization method named GUILDify. In order to have the experimental support for the sub-networks, we further curated them using STRING database. We proceeded by modeling structures for the interactions lacking complex forms in Protein Data Bank (PDB). The functional enrichment analysis shows that KEGG pathways associated with the immune system and infectious diseases, particularly the chemokine signaling pathway, are important for lung metastasis. On the other hand, pathways related to genetic information processing are more involved in brain metastasis. The structural analyses of the sub-networks vividly demonstrated their difference in terms of using specific interfaces in lung and brain metastasis. Furthermore, the topological analysis identified genes such as RPL5, MMP2, CCR5 and DPP4, which are already known to be associated with lung or brain metastasis. Additionally, we found 6 and 9 putative genes that are specific for lung and brain metastasis, respectively. Our analysis suggests that variations in genes and pathways contributing to these different breast metastasis types may arise due to change in tissue microenvironment. To show the benefits of using structural PPI networks instead of traditional node and edge presentation, we inspect two case studies showing the mutual exclusiveness of interactions and effects of mutations on protein conformation which lead to different signaling.

Keywords: breast cancer, metastasis, PPI networks, protein conformational changes

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Authors: Vusumzi E. Pakade, Themba D. Ntuli, Augustine E. Ofomaja

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Macadamia nutshell biosorbents treated in three different methods (raw Macadamia nutshell powder (RMN), acid-treated Macadamia nutshell (ATMN) and base-treated Macadamia nutshell (BTMN)) were investigated for the adsorption of Cr(VI) from aqueous solutions. Fourier transform infrared spectroscopy (FT-IR) spectra of free and Cr(VI)-loaded sorbents as well as thermogravimetric analysis (TGA) revealed that the acid and base treatments modified the surface properties of the sorbents. The optimum conditions for the adsorption of Cr(VI) by sorbents were pH 2, contact time 10 h, adsorbent dosage 0.2 g L-1, and concentration 100 mg L-1. The different treatment methods altered the surface characteristics of the sorbents and produced different maximum binding capacities of 42.5, 40.6 and 37.5 mg g-1 for RMN, ATMN and BTMN, respectively. The data was fitted into the Langmuir, Freundlich, Redlich-Peterson and Sips isotherms. No single model could clearly explain the data perhaps due to the complexity of process taking place. The kinetic modeling results showed that the process of Cr(VI) biosorption with Macadamia sorbents was better described by a process of chemical sorption in pseudo-second order. These results showed that the three treatment methods yielded different surface properties which then influenced adsorption of Cr(VI) differently.

Keywords: biosorption, chromium(VI), isotherms, Macadamia, reduction, treatment

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Authors: Ishrat Jahan Saifi, Sheelu Shafiq Siddiqi, M. R. Ajmal

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Glycation of protein is very important as well as a harmful process, which may lead to develop DM in human body. Human Serum Albumin (HSA) is the most abundant protein in blood and it is highly prone to glycation by the reducing sugars. 2-¬deoxy d-¬Ribose (dRib) is a highly reactive reducing sugar which is produced in cells as a product of the enzyme thymidine phosphorylase. It is generated during the degradation of DNA in human body. It may cause glycation in HSA rapidly and is involved in the development of DM. In present study, we did in¬vitro glycation of HSA with different concentrations of 2-¬deoxy d-¬ribose and found that dRib glycated HSA rapidly within 4h incubation at 37◦C. UV¬ Spectroscopy, Fluorescence spectroscopy, Fourier transform infrared spectroscopy (FTIR) and Circular Dichroism (CD) technique have been done to determine the structural changes in HSA upon glycation. Results of this study suggested that dRib is the potential glycating agent and it causes alteration in protein structure and biophysical properties which may lead to development and progression of Diabetes mellitus.

Keywords: 2-deoxy D-ribose, human serum albumin, glycation, diabetes mellitus

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Authors: Jafar Ahmadi, Zhohreh Asiaban, Sedigheh Fabriki Ourang

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Brassinosteroids (BRs) regulate cell elongation, vascular differentiation, senescence and stress responses. BRs signal through the BES1/BZR1 family of transcription factors, which regulate hundreds of target genes involved in this pathway. In this research a comprehensive genome-wide analysis was carried out in BES1/BZR1 gene family in Arabidopsis thaliana, Cucumis sativus, Vitis vinifera, Glycin max, and Brachypodium distachyon. Specifications of the desired sequences, dot plot and hydropathy plot were analyzed in the protein and genome sequences of five plant species. The maximum amino acid length was attributed to protein sequence Brdic3g with 374aa and the minimum amino acid length was attributed to protein sequence Gm7g with 163aa. The maximum Instability index was attributed to protein sequence AT1G19350 equal with 79.99 and the minimum Instability index was attributed to protein sequence Gm5g equal with 33.22. Aliphatic index of these protein sequences ranged from 47.82 to 78.79 in Arabidopsis thaliana, 49.91 to 57.50 in Vitis vinifera, 55.09 to 82.43 in Glycin max, 54.09 to 54.28 in Brachypodium distachyon 55.36 to 56.83 in Cucumis sativus. Overall, data obtained from our investigation contributes a better understanding of the complexity of the BES1/BZR1 gene family and provides the first step towards directing future experimental designs to perform systematic analysis of the functions of the BES1/BZR1 gene family.

Keywords: BES1/BZR1, brassinosteroids, phylogenetic analysis, transcription factor

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Authors: Usha Loganathan, Haresh Pandya

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Analysis and correlation of soil properties represent an important outset for precision agriculture and is currently promoted and implemented in the developed world. Establishing relationships among indices of soil salinity has always been a challenging task in salt affected soils necessitating unique approaches for their reclamation and management to sustain long term productivity of Soil. Soil salinity indices like Electrical Conductivity (EC) and Sodium Adsorption Ratio (SAR) are normally used to characterize soils as either sodic or saline sodic. Currently, Determination of Soil sodium adsorption ratio is a more accepted and reliable measure of soil salinity. However, it involves arduous and protracted laboratory investigations which demand evolving new and economical methods to determine SAR based on simple soil salinity index. A linear regression model to predict soil SAR from soil electrical conductivity has been developed and presented in this paper as per which, soil SAR could very well be worked out as a pedotransfer function of soil EC. The present study was carried out in Orathupalayam (11.09-11.11 N latitude and 74.54-77.59 E longitude) in the vicinity of Orathupalayam Reservoir of Noyyal River Basin, India, over a period of 3 consecutive years from September 2013 through February 2016 in different locations chosen randomly through different seasons. The research findings are discussed in the light of micro level farming practices in India and recommend determination of SAR as a low cost technology aiding in the effective management of salt affected agricultural land.

Keywords: electrical conductivity, orathupalayam, pedotranfer function, sodium adsorption ratio

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Authors: Javier Perez-Vaquero, Katryn Junker, Volker Lammers, Petra Foerst

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There is increasing importance to accelerate the transition to sustainable food systems by including environmentally friendly technologies. Our work focuses on protein enrichment and fractionation of agricultural side streams by dry triboelectrostatic separation technology. Materials are fed in particulate form into a system dispersed in a highly turbulent gas stream, whereby the high collision rate of particles against surfaces and other particles greatly enhances the electrostatic charge build-up over the particle surface. A subsequent step takes the charged particles to a delimited zone in the system where there is a highly uniform, intense electric field applied. Because the charge polarity acquired by a particle is influenced by its chemical composition, morphology, and structure, the protein-rich and fiber-rich particles of the starting material get opposite charge polarities, thus following different paths as they move through the region where the electric field is present. The output is two material fractions, which differ in their respective protein content. One is a fiber-rich, low-protein fraction, while the other is a high-protein, low-fiber composition. Prior to testing, materials undergo a milling process, and some samples are stored under controlled humidity conditions. In this way, the influence of both particle size and humidity content was established. We used two oilseed meals: lupine and rapeseed. In addition to a lab-scale separator to perform the experiments, the triboelectric separation process could be successfully scaled up to a mid-scale belt separator, increasing the mass feed from g/sec to kg/hour. The triboelectrostatic separation technology opens a huge potential for the exploitation of so far underutilized alternative protein sources. Agricultural side-streams from cereal and oil production, which are generated in high volumes by the industries, can further be valorized by this process.

Keywords: bench-scale processing, dry separation, protein-enrichment, triboelectrostatic separation

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Authors: John N. Idenyi, Hadimundeen Abdallah, Abigeal D. Adeyemi, Jonathan C. Eya

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Gut microbiomes play a significant role in the growth, metabolism, and health of fish. However, we know very little about the interactive effects of variations in dietary composition and temperature on rainbow trout gut microbiota. Exactly 288 rainbow trout weighing 45.6g ± 0.05 (average ± SD) were fed four isocaloric, isolipidic, and isonitrogenous diets comprising 40% crude protein and 20% crude lipid and formulated as 100 % animal-based protein (AP) and a blend of 50 fish oil (FO)/50 camelina oil (CO), 100 % AP and100 % CO, 100 % plant-based protein (PP) and a blend of 50FO/50CO or 100 % PP and 100 % CO in 14 or 18°C for 150 days. Gut content was analyzed using 16S rRNA gene and shotgun sequencing. The most abundant phyla identified regardless of diet were Tenericutes, Firmicutes, Proteobacteria, Spirochaetes, Bacteroidetes, and Actinobacteria, while Aeromonadaceae and Enterobacteriaceae were dominant families in 18°C. Moreover, gut microbes were dominated by genes relating to an amino acid, carbohydrate, fat, and energy metabolisms and influenced by temperature. The shared functional profiles for all the diets suggest that plant protein sources in combination with CO could be as good as the fish meal with 50/50 FO & CO in rainbow trout farming.

Keywords: aquafeed, aquaculture, microbiome, rainbow trout

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Authors: Raimoana Frogier, Luc Girard, Pierre Bauduin, Diane Rebiscoul, Olivier Diat

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Nano-ions (NIs) are ionic species or clusters of nanometric size. Their low charge density and the delocalization of their charges give special properties to some of NIs belonging to chemical classes of polyoxometalates (POMs) or boron clusters. They have the particularity of interacting non-covalently with neutral hydrated surface or interfaces such as assemblies of surface-active molecules (micelles, vesicles, lyotropic liquid crystals), foam bubbles or emulsion droplets. This makes possible to classify those NIs in the Hofmeister series as superchaotropic ions. The mechanism of adsorption is complex, linked to the simultaneous dehydration of the ion and the molecule or supramolecular assembly with which it can interact, all with an enthalpic gain on the free energy of the system. This interaction process is reversible and is sufficiently pronounced to induce changes in molecular and supramolecular shape or conformation, phase transitions in the liquid phase, all at sub-millimolar ionic concentrations. This new property of some NIs opens up new possibilities for applications in fields as varied as biochemistry for solubilization, recovery of metals of interest by foams in the form of NIs... In order to better understand the physico-chemical mechanisms at the origin of this interaction, we use silicon wafers functionalized by non-ionic oligomers (polyethylene glycol chains or PEG) to study in situ by X-ray reflectivity this interaction of NIs with the grafted chains. This study carried out at ESRF (European Synchrotron Radiation Facility) and has shown that the adsorption of the NIs, such as POMs, has a very fast kinetics. Moreover the distribution of the NIs in the grafted PEG chain layer was quantify. These results are very encouraging and confirm what has been observed on soft interfaces such as micelles or foams. The possibility to play on the density, length and chemical nature of the grafted chains makes this system an ideal tool to provide kinetic and thermodynamic information to decipher the complex mechanisms at the origin of this adsorption.

Keywords: adsorption, nano-ions, solid-liquid interface, superchaotropicity

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Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi

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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.

Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations

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Authors: S. Petrovska, D. Jonkus, D. Smiltiņa

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κ-casein is one of milk proteins which are very important for milk processing. Genotypes of κ-casein affect milk yield, fat, and protein content. The main factors which affect local Latvian dairy breed milk yield and composition are analyzed in research. Data were collected from 88 Latvian brown and 82 Latvian blue cows in 2015. AA genotype was 0.557 in Latvian brown and 0.232 in Latvian blue breed. BB genotype was 0.034 in Latvian brown and 0.207 in Latvian blue breed. Highest milk yield was observed in Latvian brown (5131.2 ± 172.01 kg), significantly high fat content and fat yield also was in Latvian brown (p < 0.05). Significant differences between κ-casein genotypes were not found in Latvian brown, but highest milk yield (5057 ± 130.23 kg), protein content (3.42 ± 0.03%), and protein yield (171.9 ± 4.34 kg) were with AB genotype. Significantly high fat content was observed in Latvian blue breed with BB genotype (4.29 ± 0.17%) compared with AA genotypes (3.42 ± 0.19). Similar tendency was found in protein content – 3.27 ± 0.16% with BB genotype and 2.59 ± 0.16% with AA genotype (p < 0.05). Milk yield increases by increasing parity. We did not obtain major tendency of changes of milk fat and protein content according parity.

Keywords: dairy cows, κ-casein, milk productivity, polymorphism

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Authors: Patarasuda Chaisupa, R. Clay Wright

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The selection of appropriate biomolecular targets is a crucial aspect of biopharmaceutical development. The Auxin-Inducible Degron Degradation (AID) technology has demonstrated remarkable potential in efficiently and rapidly degrading target proteins, thereby enabling the identification and acquisition of drug targets. The AID system also offers a viable method to deplete specific proteins, particularly in cases where the degradation pathway has not been exploited or when the adaptation of proteins, including the cell environment, occurs to compensate for the mutation or gene knockout. In this study, we have engineered an improved AID system tailored to deplete proteins of interest. This AID construct combines the auxin-responsive E3 ubiquitin ligase binding domain, AFB2, and the substrate degron, IAA17, fused to the target genes. Essential genes of fungi with the lowest percent amino acid similarity to human and plant orthologs, according to the Basic Local Alignment Search Tool (BLAST), were cloned into the AID construct in S. cerevisiae (AID-tagged strains) using a modular yeast cloning toolkit for multipart assembly and direct genetic modification. Each E3 ubiquitin ligase and IAA17 degron was fused to a fluorescence protein, allowing for real-time monitoring of protein levels in response to different auxin doses via cytometry. Our AID system exhibited high sensitivity, with an EC50 value of 0.040 µM (SE = 0.016) for AFB2, enabling the specific promotion of IAA17::target protein degradation. Furthermore, we demonstrate how this improved AID system enhances quantitative functional studies of various proteins in fungi. The advancements made in auxin-inducible protein degradation in this study offer a powerful approach to investigating critical target protein viability in fungi, screening protein targets for drugs, and regulating intracellular protein abundance, thus revolutionizing the study of protein function underlying a diverse range of biological processes.

Keywords: synthetic biology, bioengineering, molecular biology, biotechnology

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Authors: Dalia. G. Aseel

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Begomoviruses are economically important plant viruses that infect dicotyledonous plants and exclusively transmitted by the whitefly Bemisia tabaci. Here, replicative form was isolated from Okra, Cotton, Tomato plants and whitefly infected with Begomoviruses. Using coat protein specific primers (AV1), the viral infection was verified with amplicon at 450 bp. The sequence of OLCuV-AV1 gene was recorded and received an accession number (FJ441605) from Genebank. The phylogenetic tree of OLCuV was closely related to Okra leaf curl virus previously isolated from Cameroon and USA with nucleotide sequence identity of 92%. The protein purification was carried out using His-Tag methodology by using Affinity Chromatography. The purified protein was separated on SDS-PAGE analysis and an enriched expected size of band at 30 kDa was observed. Furthermore, RAPD and SDS-PAGE were used to detect genetic variability between different hosts of okra leaf curl virus (OLCuV), cotton leaf curl virus (CLCuV), tomato yellow leaf curl virus (TYLCuV) and the whitefly vector. Finally, the present study would help to understand the relationship between the whitefly and different economical crops in Egypt.

Keywords: okra leaf curl virus, AV1 gene, sequencing, phylogenetic, cloning, purified protein, genetic diversity and viral proteins

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Authors: Po-Jung Huang, Chi-Ching Lee, Bertrand Chin-Ming Tan, Yuan-Ming Yeh, Julie Lichieh Chu, Tin-Wen Chen, Cheng-Yang Lee, Ruei-Chi Gan, Hsuan Liu, Petrus Tang

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Whole-exome sequencing focuses on the protein coding regions of disease/cancer associated genes based on a priori knowledge is the most cost-effective method to study the association between genetic alterations and disease. Recent advances in high throughput sequencing technologies and proteomic techniques has provided an opportunity to integrate genomics and proteomics, allowing readily detectable mutated peptides corresponding to mutated genes. Since sequence database search is the most widely used method for protein identification using Mass spectrometry (MS)-based proteomics technology, a mutant proteome database is required to better approximate the real protein pool to improve disease-associated mutated protein identification. Large-scale whole exome/genome sequencing studies were launched by National Cancer Institute (NCI), Broad Institute, and The Cancer Genome Atlas (TCGA), which provide not only a comprehensive report on the analysis of coding variants in diverse samples cell lines but a invaluable resource for extensive research community. No existing database is available for the collection of mutant protein sequences related to the identified variants in these studies. CMPD is designed to address this issue, serving as a bridge between genomic data and proteomic studies and focusing on protein sequence-altering variations originated from both germline and cancer-associated somatic variations.

Keywords: TCGA, cancer, mutant, proteome

Procedia PDF Downloads 593

Authors: Ling-Ling E, Lin Feng, Hong-Chen Liu, Dong-Sheng Wang, Zhanping Shi, Juncheng Wang, Wei Luo, Yan Lv

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The objective of this study was to compare the effects of the two calcium phosphate composite scaffolds on the attachment, proliferation and osteogenic differentiation of rabbit dental pulp stem cells (DPSCs). One nano-hydroxyapatite/collagen/poly (L-lactide) (nHAC/PLA), imitating the composition and the micro-structure characteristics of the natural bone, was made by Beijing Allgens Medical Science & Technology Co., Ltd. (China). The other beta-tricalcium phosphate (β-TCP), being fully interoperability globular pore structure, was provided by Shanghai Bio-lu Biomaterials Co, Ltd. (China). We compared the absorption water rate and the protein adsorption rate of two scaffolds and the characterization of DPSCs cultured on the culture plate and both scaffolds under osteogenic differentiation media (ODM) treatment. The constructs were then implanted subcutaneously into the back of severe combined immunodeficient (SCID) mice for 8 and 12 weeks to compare their bone formation capacity. The results showed that the ODM-treated DPSCs expressed osteocalcin (OCN), bone sialoprotein (BSP), type I collagen (COLI) and osteopontin (OPN) by immunofluorescence staining. Positive alkaline phosphatase (ALP) staining, calcium deposition and calcium nodules were also observed on the ODM-treated DPSCs. The nHAC/PLA had significantly higher absorption water rate and protein adsorption rate than ß-TCP. The initial attachment of DPSCs seeded onto nHAC/PLA was significantly higher than that onto ß-TCP; and the proliferation rate of the cells was significantly higher than that of ß-TCP on 1, 3 and 7 days of cell culture. DPSCs+ß-TCP had significantly higher ALP activity, calcium/phosphorus content and mineral formation than DPSCs+nHAC/PLA. When implanted into the back of SCID mice, nHAC/PLA alone had no new bone formation, newly formed mature bone and osteoid were only observed in β-TCP alone, DPSCs+nHAC/PLA and DPSCs+β-TCP, and this three groups displayed increased bone formation over the 12-week period. The percentage of total bone formation area had no difference between DPSCs+β-TCP and DPSCs+nHAC/PLA at each time point，but the percentage of mature bone formation area of DPSCs+β-TCP was significantly higher than that of DPSCs+nHAC/PLA. Our results demonstrated that the DPSCs on nHAC/PLA had a better proliferation and that the DPSCs on β-TCP had a more mineralization in vitro, much more newly formed mature bones in vivo were presented in DPSCs+β-TCP group. These findings have provided a further knowledge that scaffold architecture has a different influence on the attachment, proliferation and differentiation of cells. This study may provide insight into the clinical periodontal bone tissue repair with DPSCs+β-TCP construct.

Keywords: dental pulp stem cells, nano-hydroxyapatite/collagen/poly(L-lactide), beta-tricalcium phosphate, periodontal tissue engineering, bone regeneration

Procedia PDF Downloads 335

Authors: R. C. Ferreira, H. H. C. De Lima, A. A. Cândido, O. M. Couto Junior, P. A. Arroyo, K. Q De Carvalho, G. F. Gauze, M. A. S. D. Barros

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Removal of the widespread used drug paracetamol from water was investigated using activated carbon originated from dende coconut mesocarp and babassu coconut mesocarp. Kinetic and equilibrium data were obtained at different values of pH. Babassu activated carbon showed higher efficiency due to its acidity and higher microporosity. Pseudo-second order model was better adjusted to the kinetic results. Equilibrium data may be represented by Langmuir equation. Lower solution pH provided better removal efficiency as the carbonil groups may be attracted by the positively charged carbon surface.

Keywords: adsorption, activated carbon, babassu, dende

Procedia PDF Downloads 373

Authors: Sang Kompiang Wirawan, Pandu Prabowo Jati, I Wayan Warmada

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Klaten Indonesian natural zeolite can be used as powder or pellet adsorbent. Pellet adsorbent has been made from activated natural zeolite powder by a conventional pressing method. Starch and formaldehyde were added as binder to strengthen the construction of zeolite pellet. To increase the absorptivity and its capacity, natural zeolite was activated first chemically and thermally. This research examined adsorption process of water from Isopropyl Alcohol (IPA)-water system using zeolite adsorbent pellet from natural zeolite powder which has been activated with H2SO4 0.1 M and 0.3 M. Adsorbent was pelleted by pressing apparatus at certain pressure to make specification in 1.96 cm diameter, 0.68 cm thickness which the natural zeolite powder (-80 mesh). The system of isopropyl-alcohol water contained 80% isopropyl-alcohol. Adsorption process was held in close-loop continuous apparatus which the zeolite pellet was put inside a column and the solution of IPA-water was circulated at certain flow. Concentration changing was examined thoroughly at a certain time. This adsorption process included mass transfer from bulk liquid into film layer and from film layer into the solid particle. Analysis of rate constant was using first order isotherm model that simulated with MATLAB. Besides using first order isotherm, intra-particle diffusion model was proposed by using pore diffusion model. The study shows that adsorbent activated by H2SO4 0.1 M has good absorptivity with mass transfer constant at 0.1286 min-1.

Keywords: intra-particle diffusion, fractional attainment, first order isotherm, zeolite

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Authors: Sreetama Ghosh, Sundara Ramaprabhu

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Carbon dioxide gas has been a major cause for the worldwide increase in green house effect, which leads to climate change and global warming. So CO₂ capture & sequestration has become an effective way to reduce the concentration of CO₂ in the environment. One such way to capture CO₂ in porous materials is by adsorption process. A potential material in this aspect is porous hexagonal boron nitride or 'white graphene' which is a well-known two-dimensional layered material with very high thermal stability. It had been investigated that the sample with hierarchical pore structure and high specific surface area shows excellent performance in capturing carbon dioxide gas and thereby mitigating the problem of environmental pollution to the certain extent. Besides, the presence of sulfur as well as nitrogen in the sample synergistically helps in the increase in adsorption capacity. In this work, a cost effective single step synthesis of highly porous boron nitride nanosheets doped with sulfur had been demonstrated. Besides, the CO₂ adsorption-desorption studies were carried on using a pressure reduction technique. The studies show that the nanosheets exhibit excellent cyclic stability in storage performance. Thermodynamic studies suggest that the adsorption takes place mainly through physisorption. The studies show that the nanosheets exhibit excellent cyclic stability in storage performance. Further, the surface modification of the highly porous nano sheets carried out by incorporating ionic liquids had further enhanced the capturing capability of CO₂ gas in the nanocomposite, revealing that this particular material has the potential to be an excellent adsorbent of carbon dioxide gas.

Keywords: CO₂ capture, hexagonal boron nitride nanosheets, porous network, sulfur doping

Procedia PDF Downloads 243

Authors: T. Topór, A. Derkowski, P. Ziemiański

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Formation of organic matter (OM)-hosted nanopores upon thermal maturation are one of the key factor controlling methane storage potential in unconventional shale-gas reservoirs. In this study, the subcritical CO₂ and N₂ gas adsorption measurements combined with scanning electron microscopy and supercritical methane adsorption have been used to characterize pore system and methane storage potential in black shales from the Baltic Basin (Poland). The samples were collected from a virtually equivalent Llandovery strata across the basin and represent a complete digenetic sequence, from thermally immature to overmature. The results demonstrate that the thermal maturation is a dominant mechanism controlling the formation of OM micro- and mesopores in the Baltic Basin shales. The formation of micro- and mesopores occurs in the oil window (vitrinite reflectance; leavedVR; ~0.5-0.9%) as a result of oil expulsion from kerogenleft OM highly porous. The generated hydrocarbons then turn into solid bitumen causing pore blocking and substantial decrease in micro- and mesopore volume in late-mature shales (VR ~0.9-1.2%). Both micro- and mesopores are regenerated in a middle of the catagenesis range (VR 1.4-1.9%) due to secondary cracking of OM and gas formation. The micropore volume in investigated shales is almost exclusively controlled by the OM content. The contribution of clay minerals to micropore volume is insignificant and masked by a strong contribution from OM. Methane adsorption capacity in the Baltic Basin shales is predominantly controlled by microporous OM with pores < 1.5 nm. The mesopore volume (2-50 nm) and mesopore surface area have no effect on methane sorption behavior. The adsorbed methane density equivalent, calculated as absolute methane adsorption divided by micropore volume, reviled a decrease of the methane loading potential in micropores with increasing maturity. The highest methane loading potential in micropores is observed for OM before metagenesis (VR < 2%), where the adsorbed methane density equivalent is greater than the density of liquid methane. This implies that, in addition to physical adsorption, absorption of methane in OM may occur before metagenesis. After OM content reduction using NaOCl solution methane adoption capacity substantially decreases, suggesting significantly greater adsorption potential for OM microstructure than for the clay minerals matrix.

Keywords: maturation, methane sorption, organic matter, porosity, shales

Procedia PDF Downloads 237

Authors: Usha Kiran, M. Z. Abdin

Abstract:

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

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

Procedia PDF Downloads 273

Authors: Janneth Gonzalez, Marco Avila, George Barreto

Abstract:

GRP78 participates in multiple functions in the cell during normal and pathological conditions, controlling calcium homeostasis, protein folding and unfolded protein response. GRP78 is located in the endoplasmic reticulum, but it can change its location under stress, hypoxic and apoptotic conditions. NF-κB represents the keystone of the inflammatory process and regulates the transcription of several genes related with apoptosis, differentiation, and cell growth. The possible relationship between GRP78-NF-κB could support and explain several mechanisms that may regulate a variety of cell functions, especially following brain injuries. Although several reports show interactions between NF-κB and heat shock proteins family members, there is a lack of information on how GRP78 may be interacting with NF-κB, and possibly regulating its downstream activation. Therefore, we assessed the computational predictions of the GRP78 (Chain A) and NF-κB complex (IkB alpha and p65) protein-protein interactions. The interaction interface of the docking model showed that the amino acids ASN 47, GLU 215, GLY 403 of GRP78 and THR 54, ASN 182 and HIS 184 of NF-κB are key residues involved in the docking. The electrostatic field between GRP78-NF-κB interfaces and molecular dynamic simulations support the possible interaction between the proteins. In conclusion, this work shed some light in the possible GRP78-NF-κB complex indicating key residues in this crosstalk, which may be used as an input for better drug design strategy targeting NF-κB downstream signaling as a new therapeutic approach following brain injuries.

Keywords: computational biology, protein interactions, Grp78, bioinformatics, molecular dynamics

Procedia PDF Downloads 343

Authors: A. D. Susanti, W. B. Sediawan, S. K. Wirawan, Budhijanto, Ritmaleni

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Rice bran oil contains significant amounts of oryzanol, a natural antioxidant that considered has higher antioxidant activity than vitamin E (tocopherol). Oryzanol reviewed has several health properties and interested in pharmacy, nutrition, and cosmetics. For practical usage, isolation and purification would be necessary due to the low concentration of oryzanol in crude rice bran oil (0.9-2.9%). Batch chromatography has proved as a promising process for the oryzanol recovery, but productivity was still low and scale-up processes of industrial interest have not yet been described. In order to improve productivity of batch chromatography, a continuous chromatography design namely Simulated Moving Bed (SMB) concept have been proposed. The SMB concept has interested for continuous commercial scale separation of binary system (oryzanol and rice bran oil), and rice bran oil still obtained as side product. Design of SMB chromatography for oryzanol separation requires quantification of its equilibrium. In this study, equilibrium of oryzanol separation conducted in batch adsorption using silica as the adsorbent and n-hexane/acetone (9:1) as the eluent. Three isotherm models, namely the Henry, Langmuir, and Freundlich equations, have been applied and modified for the experimental data to establish appropriate correlation for each sample. It turned out that the model quantitatively describe the equilibrium experimental data and will directed for design of SMB chromatography.

Keywords: adsorption, equilibrium, oryzanol, rice bran oil, simulated moving bed

Procedia PDF Downloads 284