Search results for: biomass protein

Authors: Rosaria Tizzani, Tomas Morosinotto, Fabrizio Bezzo, Eleonora Sforza

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Red microalga Porphyridium marinum CCAP 13807/10 has the potential to produce a broad range of commercially valuable chemicals such as PhycoErytrin (PE) and sulphated ExoPolySaccharides (EPS). Multiple abiotic factors influence the growth of Porphyridium sp., e.g. the wavelength of the light source and different cultivation strategies (one or two steps, batch, semi-, and continuous regime). The microalga of interest is cultivated in a two-step system. First, the culture grows photoautotrophically in a controlled bioreactor with pH-dependent CO2 injection, temperature monitoring, light intensity, and LED wavelength remote control in a semicontinuous mode. In the second step, the harvested biomass is subjected to mixotrophic conditions to enhance further growth. Preliminary tests have been performed to define the suitable media, salinity, pH, and organic carbon substrate to obtain the highest biomass productivity. Dynamic light and operational conditions (e.g. HRT) are evaluated to achieve high biomass production, high PE accumulation in the biomass, and high EPS release in the medium. Porphyridium marinum is able to chromatically adapt the photosynthetic apparatus to efficiently exploit the full light spectra composition. The effect of specific narrow LED wavelengths (white W, red R, green G, blue B) and a combination of LEDs (WR, WB, WG, BR, BG, RG) are identified to understand the phenomenon of chromatic adaptation under photoautotrophic conditions. The effect of light intensity, residence time, and light quality are investigated to define optimal operational strategies for full scale commercial applications. Production of biomass, phycobiliproteins, PE, EPS, EPS sulfate content, EPS composition, Chlorophyll-a, and pigment content are monitored to determine the effect of LED wavelength on the cultivation Porphyridium marinum in order to optimize the production of these multiple, highly valuable bioproducts of commercial interest.

Keywords: red microalgae, LED, exopolysaccharide, phycoerythrin

Procedia PDF Downloads 108

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

Procedia PDF Downloads 442

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

Procedia PDF Downloads 377

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

Procedia PDF Downloads 86

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

Procedia PDF Downloads 83

Authors: Rajesh Chandra, Uttam K. Ghosh

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This study demonstrates microalgal bio-diesel generation from a cheap, abundant, non-edible fruit pulp of Cassia fistula L. The Cassia fistula L. fruit pulp aqueous extract (CFAE) was utilized as a growth medium for cultivation of microalga Chlorella minutissima (C. minutissima). This microalga accumulated a high amount of lipids when cultivated with CFAE as a source of nutrition in comparison to BG-11 medium. Different concentrations (10, 20, 30, 40 and 50%) of CFAE diluted with distilled water were used to cultivate microalga. Effects of light intensity and photoperiod were also observed on biomass and lipid yield of microalga. Light intensity of 8000 lux with a photoperiod of 18 h resulted in maximum biomass and lipid yield of 1.28 ± 0.03 and 0.3968 ± 0.05 g/L, respectively when cultivated with 40% CFAE. Fatty acid methyl ester (FAME) profile of bio-diesel obtained shown the presence of myristic acid (C14:0), palmitic acid (C16:0), palmitoleic acid (C16:1), stearic acid (C18:0), linoleic acid (C18:2), linolenic acid (C18:3), arachidic acid (C20:0), and gondoic acid (C20:1), as major fatty acids. These facts reflect that the fruit pulp of Cassia fistula L. can be used for cultivation of C. minutissima.

Keywords: biomass, bio-diesel, Cassia fistula L., C. minutissima, GC-MS, lipid

Procedia PDF Downloads 156

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

Procedia PDF Downloads 244

Authors: Ali Rabah

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This research received no grant or financial support from any public, commercial, or none governmental agency. The author conducted this work as part of his normal research activities as a professor of Chemical Engineering at the University of Khartoum, Sudan. Abstract While fossil oil reserves have been receding, the demand for diesel and gasoline has been growing. In recent years, syngas of biomass origin has been emerging as a viable feedstock for Fischer-Tropsch (FT) synthesis, a process for manufacturing synthetic gasoline and diesel. This paper reports the optimization of syngas quality to match FT synthesis requirements. The optimization model maximizes the thermal efficiency under the constraint of H2/CO≥2.0 and operating conditions of equivalent ratio (0 ≤ ER ≤ 1.0), steam to biomass ratio (0 ≤ SB ≤ 5), and gasification temperature (500 °C ≤ Tg ≤ 1300 °C). The optimization model is executed using the optimization section of the Model Analysis Tools of the Aspen Plus simulator. The model is tested using eleven (11) types of MSW. The optimum operating conditions under which the objective function and the constraint are satisfied are ER=0, SB=0.66-1.22, and Tg=679 - 763°C. Under the optimum operating conditions, the syngas quality is H2=52.38 - 58.67-mole percent, LHV=12.55 - 17.15 MJ/kg, N2=0.38 - 2.33-mole percent, and H2/CO≥2.15. The generalized optimization model reported could be extended to any other type of biomass and coal. Keywords: MSW, Syngas, Optimization, Fischer-Tropsch.

Keywords: syngas, MSW, optimization, Fisher-Tropsh

Procedia PDF Downloads 80

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

Procedia PDF Downloads 339

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

Procedia PDF Downloads 190

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

Procedia PDF Downloads 91

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

Procedia PDF Downloads 175

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

Procedia PDF Downloads 270

Authors: H. M. Takematsu, B. R. De Camargo, E. F. Noronha

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The use of hydrolyzing enzymes for degradation of lignocellulosic biomass is of great concern for the production of second generation ethanol. Although many hollocelulases have already been described in the literature, much more has to be discovered. Therefore, the aim of this study to evaluate hollocelulase production of P. polonicum grown in liquid media containing sugarcane bagasse as the carbon source. From a collection of twenty fungi isolated from Cerrado biome soil, P. polonicum was molecular identified by sequencing of ITS4, βtubulin and Calmodulin genes, and has been chosen to be further investigated regarding its potential production of hydrolyzing enzymes. Spore suspension (1x10-6 ml-1) solution was inoculated in sterilized minimal liquid medium containing 0,5%(w/v) of non-pretreated sugarcane bagasse as the carbon source, and incubated in shaker incubator at 28°C and 120 rpm. The supernatant obtained, was subjected to enzymatic assays to analyze xylanase, mannanase, pectinase and endoglucanase activities. Xylanase activity showed better results (67,36 UI/mg). Xylanases bands were indicated by zymogram and SDS-PAGE, and one of them was partially purified and characterized. It showed maximum activity at 50 °C, was thermostable for 72h at 40°C, and pH5.0 was the optimum observed. This study presents P. polonicum as an interesting source of hollocelulases, especially xylanase, for lignocellulose bio-conversion processes with commercial use.

Keywords: sugarcane bagasse, Cerrado biome , hollocelulase, lignocellulosic biomass

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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

Procedia PDF Downloads 148

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: Widya Anggraini Pamungkas, Rosana Budi Setyawati, Awaludin Fitroh Rifai, Candra Pangesti Setiawan, Anatta Wahyu Budiiman, Inayati, Joko Waluyo, Sunu Herwi Pranolo

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The increase in LPG consumption in Indonesia is not balanced with the amount of supply. The high demand for LPG due to the success of the government's kerosene-to-LPG conversion program and the Covid-19 pandemic in 2020 led to an increase in LPG consumption in the household sector and caused Indonesia's trade balance to experience a deficit. The high consumption of LPG encourages the need for alternative fuels as a substitute or which aims to substitute LPG; one of the materials that can be used is Dimethyl Ether (DME). Dimethyl ether (DME) is an organic compound with the chemical formula CH 3. OCH 3 has a high cetane number and has characteristics similar to LPG. DME can be produced from various sources, such as coal, biomass and natural gas. Based on the economic analysis conducted at 10% IRR, coal has the largest NPV of Rp. 20,034,837,497,241 with a payback period of 3.86 years, then biomass with an NPV of Rp. 10,401,526,072,850 and a payback period of 5.16. the latter is natural gas with an NPV of IDR 7,401,272,559,191 and a payback period of 6.17 years. Of the three sources of raw materials used, if the sensitivity is calculated using the selling price of DME equal to the selling price of LPG, it will get an NPV value that is greater than the NPV value when using the current DME price. The advantages of coal as a raw material for DME are not only because it is profitable, namely: low price and abundant resources, but has high greenhouse gas emissions.

Keywords: LPG, DME, coal, biomass, natural gas

Procedia PDF Downloads 123

Authors: Ebrahim Izadi-Darbandi

Abstract:

In order to investigation the effects of sowing methods, nitrogen and phosphorus application methods in wheat weeds management, an experiment was performed as split plot, based on randomized completely block design with three replications at Research Farm, Faculty of Agriculture, Ferdowsi University of Mashhad, in 2010. Treatments included, wheat sowing methods (single-row with 30 cm distance and twine row on 50 cm width ridges) as main plots and nitrogen and phosphorus application methods (Broadcast and Band) as sub plots. In this experiment, phosphorus and nitrogen sources for fertilization were super phosphate triple (150 kg ha-1) applied before wheat sowing and incorporated with soil and urea (200 kg ha-1) respectively, applied in 2 phases (pre-plant 50%) and near wheat shooting (50%). Results showed that the effect of fertilizers application methods and wheat sowing methods were significant (p≤0.01) on wheat yield increasing and reducing weed-wheat competition. Wheat twine row sowing method, reduced weeds biomass for 25% compared wheat single-row sowing method and increased wheat seed yield and biomass for 60% and 30% respectively. Phosphorus and nitrogen band application reduced weeds biomass for 46% and 53% respectively and increased wheat seed yield for 22% and 33% compared to their broadcast application. The effects of wheat sowing method plus phosphorus and nitrogen application methods interactions, showed that the fertilizers band application and wheat twine-row sowing method were the best methods in wheat yield improvement and reducing wheat-weeds interaction. These results shows that modifying of fertilization methods and wheat sowing method can have important role in fertilizers use efficiency and improving of weeds managements.

Keywords: competition, wheat yield, fertilizer management, biomass

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Authors: Rasmila Kawan, Sanjay Juvekar, Sandeep Salvi, Gufran Beig, Rainer Sauerborn

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Background: Indoor air pollution especially from the use of biomass fuels, remains a potentially large global health threat. The inefficient use of such fuels in poorly ventilated conditions results in high levels of indoor air pollution, most seriously affecting women and young children. Objectives: The main aim of this study was to measure and compare the lung function of the women exposed in the biomass fuels and LPG fuels and relate it to the indoor emission measured using a structured questionnaire, spirometer and filter based low volume samplers respectively. Methodology: This cross-sectional comparative study was conducted among the women (aged > 18 years) living in rural villages of Pune district who were not diagnosed of chronic pulmonary diseases or any other respiratory diseases and using biomass fuels or LPG for cooking for a minimum period of 5 years or more. Data collection was done from April to June 2017 in dry season. Spirometer was performed using the portable, battery-operated ultrasound Easy One spirometer (Spiro bank II, NDD Medical Technologies, Zurich, Switzerland) to determine the lung function over Forced expiratory volume. The primary outcome variable was forced expiratory volume in 1 second (FEV1). Secondary outcome was chronic obstruction pulmonary disease (post bronchodilator FEV1/ Forced Vital Capacity (FVC) < 70%) as defined by the Global Initiative for Obstructive Lung Disease. Potential confounders such as age, height, weight, smoking history, occupation, educational status were considered. Results: Preliminary results showed that the lung function of the women using Biomass fuels (FEV1/FVC = 85% ± 5.13) had comparatively reduced lung function than the LPG users (FEV1/FVC = 86.40% ± 5.32). The mean PM 2.5 mass concentration in the biomass user’s kitchen was 274.34 ± 314.90 and 85.04 ± 97.82 in the LPG user’s kitchen. Black carbon amount was found higher in the biomass users (black carbon = 46.71 ± 46.59 µg/m³) than LPG users (black carbon=11.08 ± 22.97 µg/m³). Most of the houses used separate kitchen. Almost all the houses that used the clean fuel like LPG had minimum amount of the particulate matter 2.5 which might be due to the background pollution and cross ventilation from the houses using biomass fuels. Conclusions: Therefore, there is an urgent need to adopt various strategies to improve indoor air quality. There is a lacking of current state of climate active pollutants emission from different stove designs and identify major deficiencies that need to be tackled. Moreover, the advancement in research tools, measuring technique in particular, is critical for researchers in developing countries to improve their capability to study the emissions for addressing the growing climate change and public health concerns.

Keywords: black carbon, biomass fuels, indoor air pollution, lung function, particulate matter

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Authors: Usha Kiran, M. Z. Abdin

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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

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Authors: Valentine C. Eze, Adam P. Harvey

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Contamination of groundwater and soil by heavy metals and metalloids through anthropogenic activities and natural occurrence poses serious environmental challenges globally. A possible solution to this problem is through phytoremediation of the contaminants using hyper-accumulating plants. Conventional phytoremediation treats the contaminated hyper-accumulator biomass as a waste stream which adds no value to the heavy metal(loid)s decontamination process. This study investigates strategies for remediation of soil contaminated with arsenic and the extractive chemical routes for recovery of arsenic and phosphorus from the hyper-accumulator biomass. Pteris cretica ferns species were investigated for their uptake of arsenic from soil containing 200 ± 3ppm of arsenic. The Pteris cretica ferns were shown to be capable of hyper-accumulation of arsenic, with maximum accumulations of about 4427 ± 79mg to 4875 ± 96mg of As per kg of the dry ferns. The arsenic in the Pteris cretica fronds was extracted into various solvents, with extraction efficiencies of 94.3 ± 2.1% for ethanol-water (1:1 v/v), 81.5 ± 3.2% for 1:1(v/v) methanol-water, and 70.8 ± 2.9% for water alone. The recovery efficiency of arsenic from the molybdic acid complex process 90.8 ± 5.3%. Phosphorus was also recovered from the molybdic acid complex process at 95.1 ± 4.6% efficiency. Quantitative precipitation of Mg₃(AsO₄)₂ and Mg₃(PO₄)₂ occurred in the treatment of the aqueous solutions of arsenic and phosphorus after stripping at pH of 8 – 10. The amounts of Mg₃(AsO₄)₂ and Mg₃(PO₄)₂ obtained were 96 ± 7.2% for arsenic and 94 ± 3.4% for phosphorus. The arsenic nanoparticles produced from the Mg₃(AsO₄)₂ recovered from the biomass have the average particles diameter of 45.5 ± 11.3nm. A two-stage reduction process – a first step pre-reduction of As(V) to As(III) with L-cysteine, followed by NaBH₄ reduction of the As(III) to As(0), was required to produced arsenic nanoparticles from the Mg₃(AsO₄)₂. The arsenic nanoparticles obtained are potentially valuable for medical applications, while the Mg₃(AsO₄)₂ could be used as an insecticide. The phosphorus contents of the Pteris cretica biomass was recovered as phosphomolybdic acid complex and converted to Mg₃(PO₄)₂, which could be useful in productions of fertilizer. Recovery of these valuable products from phytoremediation biomass would incentivize and drive commercial industries’ participation in remediation of contaminated lands.

Keywords: phytoremediation, Pteris cretica, hyper-accumulator, solvent extraction, molybdic acid process, arsenic nanoparticles

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Authors: Janneth Gonzalez, Marco Avila, George Barreto

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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

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Authors: T. Sarat Chandra, M. Maneesh Kumar, S. N. Mudliar, V. S. Chauhan, S. Mukherji, R. Sarada

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The life cycle assessment (LCA) of biodiesel production from freshwater microalgae Scenedesmus dimorphus cultivated in open raceway pond is performed. Various scenarios for biodiesel production were simulated using primary and secondary data. The parameters varied in the modelled scenarios were related to biomass productivity, mode of culture mixing and type of energy source. The process steps included algae cultivation in open raceway ponds, harvesting by chemical flocculation, dewatering by mechanical drying option (MDO) followed by extraction, reaction and purification. Anaerobic digestion of defatted algal biomass (DAB) for biogas generation is considered as a co-product allocation and the energy derived from DAB was thereby used in the upstream of the process. The scenarios were analysed for energy demand, emissions and environmental impacts within the boundary conditions grounded on "cradle to gate" inventory. Across all the Scenarios, cultivation via raceway pond was observed to be energy intensive process. The mode of culture mixing and biomass productivity determined the energy requirements of the cultivation step. Emissions to Freshwater were found to be maximum contributing to 93-97% of total emissions in all the scenarios. Global warming potential (GWP) was the found to be major environmental impact accounting to about 99% of total environmental impacts in all the modelled scenarios. It was noticed that overall emissions and impacts were directly related to energy demand and an inverse relationship was observed with biomass productivity. The geographic location of an energy source affected the environmental impact of a given process. The integration of defatted algal remnants derived electricity with the cultivation system resulted in a 2% reduction in overall energy demand. Direct biogas generation from microalgae post harvesting is also analysed. Energy surplus was observed after using part of the energy in upstream for biomass production. Results suggest biogas production from microalgae post harvesting as an environmentally viable and sustainable option compared to biodiesel production.

Keywords: biomass productivity, energy demand, energy source, Lifecycle Assessment (LCA), microalgae, open raceway pond

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Authors: Fellah Sihem

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The optimal use of soil moisture by culture, is related to the leaf area index, which stood in the cycle and its modulation according to the prevailing stress intensity. For a given stock of water in the soil, cultivar adapted and saving water is one that is no luxury consumption during the preanthesis. It modulates the leaf area index to regulate sweating in the degree of its water supply. In plants water saving, avoidance of dehydration is related to the reduction of water loss by cuticular and stomatal pathways. Muchow and Sinclair reported that the test of relative water content (TRE) is considered the best indicator of leaf water status. The search for indicators of the ability of the plant to make good use of the water, under water stress is a prerequisite for progress in improving performance under water stress. This experiment aims to characterize a set of durum wheat varieties, tested jars and vegetation under different levels of water stress to the surface of the leaf, relative water content, cell integrity, the accumulated biomass and efficiency of water use. The experiment was conducted during the 2005/2006 academic year, at the Agricultural Research Station of the Field Crop Institute of Setif, under semi-controlled conditions. Five genotypes of durum wheat (Triticum durum Desf) were evaluated for their ability to tolerate moderate and severe water stress. The results showed that geno types respond differently to water stress. Dry matter accumulation and growth rate varied among geno types and were significantly reduced. At severe water stress biomass accumulated by Boussalam was the least affected.

Keywords: water stress, triticum durum, biomass, cell membrane integrity, relative water content

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Authors: Sarah Alamolhoda, Kevin J. Smith, Xiaotao Bi, Naoko Ellis

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For millennials, biomass has been the most important source of fuel used to produce energy. Energy derived from biomass is renewable by re-growth of biomass. Various technologies are used to convert biomass to potential renewable products including combustion, gasification, pyrolysis and fermentation. Gasification is the incomplete combustion of biomass in a controlled environment that results in valuable products such as syngas, biooil and biochar. Syngas is a combustible gas consisting of hydrogen (H₂), carbon monoxide (CO), carbon dioxide (CO₂), and traces of methane (CH₄) and nitrogen (N₂). Cleaned syngas can be used as a turbine fuel to generate electricity, raw material for hydrogen and synthetic natural gas production, or as the anode gas of solid oxide fuel cells. In this work, syngas as a product of woody biomass gasification in British Columbia, Canada, was introduced to two consecutive fixed bed reactors to perform a catalytic water gas shift reaction followed by a catalytic methanation reaction. The water gas shift reaction is a well-established industrial process and used to increase the hydrogen content of the syngas before the methanation process. Catalysts were used in the process since both reactions are reversible exothermic, and thermodynamically preferred at lower temperatures while kinetically favored at elevated temperatures. The water gas shift reactor and the methanation reactor were packed with Cu-based catalyst and Ni-based catalyst, respectively. Simulated syngas with different percentages of CO, H₂, CH₄, and CO₂ were fed to the reactors to investigate the effect of operating conditions in the unit. The water gas shift reaction experiments were done in the temperature of 150 ˚C to 200 ˚C, and the pressure of 550 kPa to 830 kPa. Similarly, methanation experiments were run in the temperature of 300 ˚C to 400 ˚C, and the pressure of 2340 kPa to 3450 kPa. The Methanation reaction reached 98% of CO conversion at 340 ˚C and 3450 kPa, in which more than half of CO was converted to CH₄. Increasing the reaction temperature caused reduction in the CO conversion and increase in the CH₄ selectivity. The process was designed to be renewable and release low greenhouse gas emissions. Syngas is a clean burning fuel, however by going through water gas shift reaction, toxic CO was removed, and hydrogen as a green fuel was produced. Moreover, in the methanation process, the syngas energy was transformed to a fuel with higher energy density (per volume) leading to reduction in the amount of required fuel that flows through the equipment and improvement in the process efficiency. Natural gas is about 3.5 times more efficient (energy/ volume) than hydrogen and easier to store and transport. When modification of existing infrastructure is not practical, the partial conversion of renewable hydrogen to natural gas (with up to 15% hydrogen content), the efficiency would be preserved while greenhouse gas emission footprint is eliminated.

Keywords: renewable natural gas, methane, hydrogen, gasification, syngas, catalysis, fuel

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Authors: A. Rajabpour, A. Hadizadeh Kheirkhah

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Heat transfer is of great importance to biological systems in order to function properly. In the present study, specific heat capacity as one of the most important heat transfer properties is calculated for a soluble in water Lysozyme protein. Using equilibrium molecular dynamics (MD) simulation, specific heat capacities of pure water, dry lysozyme, and lysozyme-water solution are calculated at 300K for different weight fractions. It is found that MD results are in good agreement with ideal binary mixing rule at small weight fractions. Results of all simulations have been validated with experimental data.

Keywords: specific heat capacity, molecular dynamics simulation, lysozyme protein, equilibrium

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Authors: Abdorrasoul Malekpour, Mohammad Ghorbani Mojtaba Mortazavi, Mohammadreza Fattahi, Mohammad Hassan Meshkibaf, Ali Fakhrzad, Saeid Salehi, Saeideh Zahedi, Amir Ahmadimoghaddam, Parviz Farzadnia Dr., Mohammadreza Hajyani Asl Bs

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Hepatitis B as an infectious disease has eight main genotypes (A–H). The aim of this study is to Bioinformatically identify Rare Codon Clusters (RCC) in proteins structure of HBV. For detection of protein family accession numbers (Pfam) of HBV proteins; used of uni-prot database and Pfam search tool were used. Obtained Pfam IDs were analyzed in Sherlocc program and RCCs in HBV proteins were detected. In further, the structures of TrEMBL entries proteins studied in PDB database and 3D structures of the HBV proteins and locations of RCCs were visualized and studied using Swiss PDB Viewer software. Pfam search tool have found nine significant hits and 0 insignificant hits in 3 frames. Results of Pfams studied in the Sherlocc program show this program not identified RCCs in the external core antigen (PF08290) and truncated HBeAg protein (PF08290). By contrast the RCCs become identified in Hepatitis core antigen (PF00906) Large envelope protein S (PF00695), X protein (PF00739), DNA polymerase (viral) N-terminal domain (PF00242) and Protein P (Pf00336). In HBV genome, seven RCC identified that found in hepatitis core antigen, large envelope protein S and DNA polymerase proteins and proteins structures of TrEMBL entries sequences that reported in Sherlocc program outputs are not complete. Based on situation of RCC in structure of HBV proteins, it suggested those RCCs are important in HBV life cycle. We hoped that this study provide a new and deep perspective in protein research and drug design for treatment of HBV.

Keywords: rare codon clusters, hepatitis B virus, bioinformatic study, infectious disease

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