Abstract A new and simple micelles-rich restricted access supramolecular solvent-based liquid phase microextraction method (RASUPRASs-LPME) based on the ion-pair complex formation of phosphate (PO43-) ions with ammonium heptamolybdate and malachite green in acidic medium was developed. The phosphate ion concentration after microextraction of the ion-pair complex to the hexagonal aggregates of decanoic acid (DA) was measured with micro-volume UV-Vis spectrophotometer at 625 nm. All analytical parameters which are effective on the method such as acid type and concentration, supramolecular solvent volume, amount of the components forming the complex, sample volume, were optimized. The preconcentration factor (PF), limit of detection (LOD) and limit of quantification (LOQ) for the developed method was found to be 15, 9.6 and 32.1, respectively. The RA-SUPRAs-LPME method was finally applied for the analysis of the phosphate content of different types of water samples.
基于磷酸(PO43-)离子与七钼酸铵和孔雀石绿在酸性介质中形成离子对络合物，建立了一种新的、简单的、富胶束的限制性进入超分子溶剂型液相微萃取方法(RASUPRASs-LPME)。用微体积紫外-可见分光光度计在625 nm处测定了离子对配合物微萃取到癸酸(DA)六方聚集体后的磷酸离子浓度。对酸的种类和浓度、超分子溶剂的体积、络合物组分的量、样品体积等对该方法有影响的分析参数进行了优化。该方法的预富集因子(PF)、检出限(LOD)和定量限(LOQ)分别为15、9.6和32.1。最后应用ra - supra - lpme法对不同类型水样的磷酸盐含量进行分析。
{"title":"Micelle-based restricted access ion-pair microextraction of phosphate at trace levels in water samples for separation, preconcentration and determination","authors":"M. Soylak, Haldun Hilmi Gorucu, E. Yılmaz","doi":"10.2478/ebtj-2020-0010","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0010","url":null,"abstract":"Abstract A new and simple micelles-rich restricted access supramolecular solvent-based liquid phase microextraction method (RASUPRASs-LPME) based on the ion-pair complex formation of phosphate (PO43-) ions with ammonium heptamolybdate and malachite green in acidic medium was developed. The phosphate ion concentration after microextraction of the ion-pair complex to the hexagonal aggregates of decanoic acid (DA) was measured with micro-volume UV-Vis spectrophotometer at 625 nm. All analytical parameters which are effective on the method such as acid type and concentration, supramolecular solvent volume, amount of the components forming the complex, sample volume, were optimized. The preconcentration factor (PF), limit of detection (LOD) and limit of quantification (LOQ) for the developed method was found to be 15, 9.6 and 32.1, respectively. The RA-SUPRAs-LPME method was finally applied for the analysis of the phosphate content of different types of water samples.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"89 - 96"},"PeriodicalIF":1.7,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46786033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. H. Abdelmoneim, Alaa I. Mohammed, Esraa O. Gadim, M. A. Mohammed, Sara H. Hamza, Sara A. Mirghani, T. A. Mahmoud, Mohamed A. Hassan
Abstract Hyperparathyroidism-Jaw Tumor (HPT-JT) is an autosomal dominant disorder with variable expression, with an estimated prevalence of 6.7 per 1,000 population. Genetic testing for predisposing CDC73 (HRPT2) mutations has been an important clinical advance, aimed at early detection and/or treatment to prevent advanced disease. The aim of this study is to assess the most deleterious SNPs mutations on CDC73 gene and to predict their influence on the functional and structural levels using different bioinformatics tools. Method: Computational analysis using twelve different in-silico tools including SIFT, PROVEAN, PolyPhen-2, SNAP2, PhD-SNP, SNPs&GO, P-Mut, I-Mutant ,Project Hope, Chimera, COSMIC and dbSNP Short Genetic Variations were used to identify the impact of mutations in CDC73 gene that might be causing jaw tumor. Results: From (733) SNPs identified in the CDC73 gene we found that only Eleven SNPs (G49C, L63P, L64P, D90H, R222G, W231R, P360S, R441C, R441H, R504S and R504H) has deleterious effect on the function and structure of protein and expected to cause the syndrome. Conclusion: Eleven substantial genetic/molecular aberrations in CDC73 gene identified that could serve as diagnostic markers for hyperparathyroidism-jaw tumor (HPT-JT).
甲状旁腺功能亢进颌骨肿瘤(HPT-JT)是一种常染色体显性遗传病，具有可变的表达，估计患病率为每1000人中6.7人。CDC73 (HRPT2)易感基因检测是一项重要的临床进展，旨在早期发现和/或治疗以预防晚期疾病。本研究的目的是利用不同的生物信息学工具评估CDC73基因上最有害的SNPs突变，并预测其对功能和结构水平的影响。方法:采用SIFT、PROVEAN、polyphen2、SNAP2、PhD-SNP、SNPs&GO、P-Mut、I-Mutant、Project Hope、Chimera、COSMIC和dbSNP Short Genetic Variations等12种不同的计算机工具进行计算分析，确定CDC73基因突变对颌骨肿瘤的影响。结果:从CDC73基因中鉴定的733个snp中，我们发现只有11个snp (G49C、L63P、L64P、D90H、R222G、W231R、P360S、R441C、R441H、R504S和R504H)对蛋白质的功能和结构有有害影响，可能导致该综合征。结论:鉴定出11个CDC73基因显著的遗传/分子畸变，可作为HPT-JT的诊断标记。
{"title":"In silico analysis of CDC73 gene revealing 11 novel SNPs with possible association to Hyperparathyroidism-Jaw Tumor syndrome","authors":"A. H. Abdelmoneim, Alaa I. Mohammed, Esraa O. Gadim, M. A. Mohammed, Sara H. Hamza, Sara A. Mirghani, T. A. Mahmoud, Mohamed A. Hassan","doi":"10.2478/ebtj-2020-0008","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0008","url":null,"abstract":"Abstract Hyperparathyroidism-Jaw Tumor (HPT-JT) is an autosomal dominant disorder with variable expression, with an estimated prevalence of 6.7 per 1,000 population. Genetic testing for predisposing CDC73 (HRPT2) mutations has been an important clinical advance, aimed at early detection and/or treatment to prevent advanced disease. The aim of this study is to assess the most deleterious SNPs mutations on CDC73 gene and to predict their influence on the functional and structural levels using different bioinformatics tools. Method: Computational analysis using twelve different in-silico tools including SIFT, PROVEAN, PolyPhen-2, SNAP2, PhD-SNP, SNPs&GO, P-Mut, I-Mutant ,Project Hope, Chimera, COSMIC and dbSNP Short Genetic Variations were used to identify the impact of mutations in CDC73 gene that might be causing jaw tumor. Results: From (733) SNPs identified in the CDC73 gene we found that only Eleven SNPs (G49C, L63P, L64P, D90H, R222G, W231R, P360S, R441C, R441H, R504S and R504H) has deleterious effect on the function and structure of protein and expected to cause the syndrome. Conclusion: Eleven substantial genetic/molecular aberrations in CDC73 gene identified that could serve as diagnostic markers for hyperparathyroidism-jaw tumor (HPT-JT).","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"67 - 81"},"PeriodicalIF":1.7,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48149661","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract The objective of this work is numerical simulation of the membrane by direct analysis at micro, meso and macro level. This approach includes first a defining and modeling of a basic structural unit, after that simulation of a fragment as a representative element of the membrane structure. Then the results obtained to transfer for the entire membrane module and finally modeling of the membrane as porous media with calculated permeability. The numerical simulation was done with Ansys CFX, using the Darcy’s equation for flow through porous media with configuration of the membrane and second order backward Euler transient scheme for solving the Navier-Stokes equations. The permeability of the membrane is determined at a micro and macro level by computer simulation for different fluids, which allows to evaluating the influence of the viscosity on the flow passing through the membrane. This micro-macro approach is quite efficient and cost-effective because it saves time and requires less computer capacity and allows direct analysis of the complex structure of the membrane modules.
{"title":"Micro-macro transition for numerical simulation of submerged membrane bioreactor","authors":"Moutafchìeva Dessislava, Iliev Veselin","doi":"10.2478/ebtj-2020-0009","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0009","url":null,"abstract":"Abstract The objective of this work is numerical simulation of the membrane by direct analysis at micro, meso and macro level. This approach includes first a defining and modeling of a basic structural unit, after that simulation of a fragment as a representative element of the membrane structure. Then the results obtained to transfer for the entire membrane module and finally modeling of the membrane as porous media with calculated permeability. The numerical simulation was done with Ansys CFX, using the Darcy’s equation for flow through porous media with configuration of the membrane and second order backward Euler transient scheme for solving the Navier-Stokes equations. The permeability of the membrane is determined at a micro and macro level by computer simulation for different fluids, which allows to evaluating the influence of the viscosity on the flow passing through the membrane. This micro-macro approach is quite efficient and cost-effective because it saves time and requires less computer capacity and allows direct analysis of the complex structure of the membrane modules.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"82 - 88"},"PeriodicalIF":1.7,"publicationDate":"2020-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44802896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract In forests, edaphic microbial communities are involved in litter decomposition and soil forming processes, with major contribution to humification, especially bacteria and fungi being responsible for the main ecosystem services fulfilled by the soil. Research has been carried out aiming to characterize the structure and diversity of microbial communities in the Rendzic Leptosols (WRB) under natural deciduous forest from Visterna, Babadag Plateau and to assess their contribution to ecosystem services provided by soil. The paper presents the results of quantitative estimations and taxonomic composition of soil and litter communities of heterotrophic bacteria and fungi, identification of cellulolytic species, as well as the microbial biomass and global physiological activities expressed as soil respiration potential. More than a half of bacterial species were common in litter and soil (SI=57.14%) and were represented by dominant species of fluorescent or non-fluorescent pseudomonads and Bacillus subtilis but no similarity was found between the two fungal communities. Fungal populations included cosmopolitan species, such as antagonists and strong cellulolytic representatives of genera Penicillium, Trichoderma, Mortierella, Chaetomium, Epicoccum, Aspergillus. Microbial density and microbial biomass presented the highest values in the litter (684 mg C x kg-1 d.s.) and in surface horizon Am1 of soil profile than in the bottom layers. The highest diversity was found in Am1 horizon (0-5 cm) H’=1.983 bits and ε=0.869 for cellulolytic community. Soil respiration reflected the intense physiological activity of microbiome, with high values associated to numerous effectives of bacteria and fungi especially in surface horizon. Microorganisms identified contribute to formation of soil by recycling of nutrients, cellulose decomposition, the synthesis of stable organic matter (humic acids), aggregation of soil particles, biological control of pathogens by antagonistic activity. They improve plant uptake of water and nutrients by forming symbioses (ectomycorrhizae), thus modelling the structure of vegetation.
在森林中，土壤微生物群落参与凋落物分解和土壤形成过程，对腐殖化起主要作用，特别是细菌和真菌承担了土壤的主要生态系统服务功能。本文研究了巴巴达格高原Visterna天然落叶林下Rendzic Leptosols (WRB)微生物群落的结构和多样性，并评价了它们对土壤生态系统服务的贡献。本文介绍了异养细菌和真菌的土壤和凋落物群落的定量估计和分类组成，纤维素水解物种的鉴定，以及微生物生物量和以土壤呼吸势表示的全球生理活动的结果。在凋落物和土壤中常见的细菌种类超过一半(SI=57.14%)，以荧光或非荧光假单胞菌和枯草芽孢杆菌为优势种，但两者之间没有相似性。真菌种群包括世界性的物种，如拮抗菌和强纤维素分解代表的青霉属、木霉属、摩氏菌属、毛菌属、表表皮菌属、曲霉属。微生物密度和微生物生物量在凋落物层(684 mg C x kg-1 d.s.)和土壤剖面的表层Am1均高于底层。群落多样性以Am1层位(0 ~ 5 cm)最高，H′=1.983 bit， ε=0.869。土壤呼吸反映了微生物组强烈的生理活性，其值与细菌和真菌的多种有效作用有关，特别是在表层。已确定的微生物通过营养物质的再循环、纤维素的分解、稳定有机物(腐植酸)的合成、土壤颗粒的聚集、通过拮抗活性对病原体的生物控制来促进土壤的形成。它们通过形成共生(外生菌根)来改善植物对水和养分的吸收，从而模拟植被的结构。
{"title":"Assessing the role of soil microbial communities of natural forest ecosystem","authors":"G. Matei, S. Matei, V. Mocanu","doi":"10.2478/ebtj-2020-0001","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0001","url":null,"abstract":"Abstract In forests, edaphic microbial communities are involved in litter decomposition and soil forming processes, with major contribution to humification, especially bacteria and fungi being responsible for the main ecosystem services fulfilled by the soil. Research has been carried out aiming to characterize the structure and diversity of microbial communities in the Rendzic Leptosols (WRB) under natural deciduous forest from Visterna, Babadag Plateau and to assess their contribution to ecosystem services provided by soil. The paper presents the results of quantitative estimations and taxonomic composition of soil and litter communities of heterotrophic bacteria and fungi, identification of cellulolytic species, as well as the microbial biomass and global physiological activities expressed as soil respiration potential. More than a half of bacterial species were common in litter and soil (SI=57.14%) and were represented by dominant species of fluorescent or non-fluorescent pseudomonads and Bacillus subtilis but no similarity was found between the two fungal communities. Fungal populations included cosmopolitan species, such as antagonists and strong cellulolytic representatives of genera Penicillium, Trichoderma, Mortierella, Chaetomium, Epicoccum, Aspergillus. Microbial density and microbial biomass presented the highest values in the litter (684 mg C x kg-1 d.s.) and in surface horizon Am1 of soil profile than in the bottom layers. The highest diversity was found in Am1 horizon (0-5 cm) H’=1.983 bits and ε=0.869 for cellulolytic community. Soil respiration reflected the intense physiological activity of microbiome, with high values associated to numerous effectives of bacteria and fungi especially in surface horizon. Microorganisms identified contribute to formation of soil by recycling of nutrients, cellulose decomposition, the synthesis of stable organic matter (humic acids), aggregation of soil particles, biological control of pathogens by antagonistic activity. They improve plant uptake of water and nutrients by forming symbioses (ectomycorrhizae), thus modelling the structure of vegetation.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"01 - 07"},"PeriodicalIF":1.7,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43590232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract Stressful saline concentrations in soils affect photosynthesis by damaging pigments, photosystems, components of electron transport system, and enzymes involved in the process. Plants respond through very complex stress adaptation mechanisms including proteome modulation, alterations in pigment content, cell osmotic adjustment and control of ion and water homeostasis mechanisms, which stabilize cytosolic glutathione redox potential, etc. The level of plant sensitivity depends on salt toxicity levels, growth stage, physiological and genetic factors. With aim the investigation of the salinity tolerant cultivars, and for the elucidation of mechanisms underlying this complex biological process, here we analyze the impact of four NaCl concentrations (0-50-100-200mM) in growth parameters (root, shoot and leaves length), pigment content (chla, chlb, carotenoids), and GSH content, during seedling of five bread wheat (Triticum aestivum L.) cultivars in modified Hoagland solutions. Based on biometric parameters, pigment synthesis and GSH content cultivar Nogal is salt-sensitive (growth and pigments reduced); cultivar Viktoria is medium-tolerant (growth partially impaired, pigments constant), cultivar Toborzo and cultivar Suba are medium-tolerant (growth partially impaired, pigments increased), cultivar Dajti salt-tolerant (growth partially impaired/ leaves developed, pigments increased). Quantity of GSH in response to different levels of salinity is cultivar specific, and time of exposure to salinity is in negative correlation to GSH content for all investigated cultivars.
{"title":"Compared salt tolerance of five local wheat (Triticum aestivum L.) cultivars of Albania based on morphology, pigment synthesis and glutathione content","authors":"A. Bacu, V. Ibro, Magdalena Nushi","doi":"10.2478/ebtj-2020-0006","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0006","url":null,"abstract":"Abstract Stressful saline concentrations in soils affect photosynthesis by damaging pigments, photosystems, components of electron transport system, and enzymes involved in the process. Plants respond through very complex stress adaptation mechanisms including proteome modulation, alterations in pigment content, cell osmotic adjustment and control of ion and water homeostasis mechanisms, which stabilize cytosolic glutathione redox potential, etc. The level of plant sensitivity depends on salt toxicity levels, growth stage, physiological and genetic factors. With aim the investigation of the salinity tolerant cultivars, and for the elucidation of mechanisms underlying this complex biological process, here we analyze the impact of four NaCl concentrations (0-50-100-200mM) in growth parameters (root, shoot and leaves length), pigment content (chla, chlb, carotenoids), and GSH content, during seedling of five bread wheat (Triticum aestivum L.) cultivars in modified Hoagland solutions. Based on biometric parameters, pigment synthesis and GSH content cultivar Nogal is salt-sensitive (growth and pigments reduced); cultivar Viktoria is medium-tolerant (growth partially impaired, pigments constant), cultivar Toborzo and cultivar Suba are medium-tolerant (growth partially impaired, pigments increased), cultivar Dajti salt-tolerant (growth partially impaired/ leaves developed, pigments increased). Quantity of GSH in response to different levels of salinity is cultivar specific, and time of exposure to salinity is in negative correlation to GSH content for all investigated cultivars.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"42 - 52"},"PeriodicalIF":1.7,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48288823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
M. B. Acar, Ebru Ibis, A. Şimşek, C. Vural, C. Tez, S. Özcan
Abstract Yarrow essential oil is used in complementary and alternative therapy for several diseases. Biological effects of essential oils span various cells and microorganisms. The aim of this study was to investigate the effects of different concentrations of the essential oil obtained from the yarrow plant (Achillea millefolium) on HeLa (CCL-2) cells. The components of the essential oil were studied by means of GC-MS analysis. Out of 10 determined compounds in the essential oil; 1,8-Cineole, Camphor, Beta-eudesmol and Camphene were found to be higher than others; and their biological effects were depicted with Ingeniuty Pathway Analysis (IPA) analysis. Moreover, cell cycle and proliferation tests were conducted on HeLa cells where yarrow plant’s essential oil was used. When extracted yarrow oil applied on HeLA Cells, apoptotic effects had been determined, furthermore proliferation of these cells decreased. In addition, activation of cell cycle control points was observed . Essential oil components could arrest the development of HeLa cells due to induction of cellular damage control mechanisms. In conclusion, we propose that the essential oil had a more repressive effect on HeLa cells, decreases their proliferation and prevented the increase in the number of cells.
{"title":"Evaluation of Achillea millefolium essential oil compounds and biological effects on cervix cancer HeLa cell line","authors":"M. B. Acar, Ebru Ibis, A. Şimşek, C. Vural, C. Tez, S. Özcan","doi":"10.2478/ebtj-2020-0003","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0003","url":null,"abstract":"Abstract Yarrow essential oil is used in complementary and alternative therapy for several diseases. Biological effects of essential oils span various cells and microorganisms. The aim of this study was to investigate the effects of different concentrations of the essential oil obtained from the yarrow plant (Achillea millefolium) on HeLa (CCL-2) cells. The components of the essential oil were studied by means of GC-MS analysis. Out of 10 determined compounds in the essential oil; 1,8-Cineole, Camphor, Beta-eudesmol and Camphene were found to be higher than others; and their biological effects were depicted with Ingeniuty Pathway Analysis (IPA) analysis. Moreover, cell cycle and proliferation tests were conducted on HeLa cells where yarrow plant’s essential oil was used. When extracted yarrow oil applied on HeLA Cells, apoptotic effects had been determined, furthermore proliferation of these cells decreased. In addition, activation of cell cycle control points was observed . Essential oil components could arrest the development of HeLa cells due to induction of cellular damage control mechanisms. In conclusion, we propose that the essential oil had a more repressive effect on HeLa cells, decreases their proliferation and prevented the increase in the number of cells.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"17 - 24"},"PeriodicalIF":1.7,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42273900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract The potential use of asparaginases has gained tremendous significance in the treatment of acute lymphoblastic leukemia (ALL). Earlier studies suggest L-asparaginases (L-ASP) extracted from Escherichia coli and Erwinia aroideae regulates L-asparagine (L-Asn) from the circulating blood. Prolonged exposure to these enzymes may lead to hypersensitivity reactions. So, it is important to find novel asparaginases with anti-cancer properties. The three-dimensional structure of L-ASP I from Vibrio campbellii was determined by homology modeling using EasyModeller v.4.0. The structure was validated with quality indexing tools and was deposited in Protein Model DataBase. Molecular docking was performed between L-ASP I and ligand substrate L-Asn to study enzyme-substrate interactions. Qualitative and quantitative analysis of L-ASP I enzyme was found to be reliable and stable with a significant protein quality factor (LG score: 7.129). The enzyme is a dimer, belongs to α/β class of proteins. The active sites comprises of N-glycosylation site and a catalytic triad (T14-S117-D92). The binding energy of the docked complex was calculated to be -7.45 kcal/mol. The amino acid T14 identified as a primary nucleophile essential for catalytic reaction. The enzyme L-ASP I of V. campbellii provides a detailed view of structure and functional aspects with ligand substrate L-Asn. This in silico investigation has explicitly demonstrated for the first time that cytosolic L-ASP Type I of V. campbellii to have a catalytic triad which was attributed only to periplasmic L-ASP Type II. Thus, L-ASP I can serve as anti-leukemic agent in the treatment, management and control of ALL.
{"title":"Molecular docking study of L-Asparaginase I from Vibrio campbellii in the treatment of acute lymphoblastic leukemia (ALL)","authors":"A. K. Mohideen","doi":"10.2478/ebtj-2020-0002","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0002","url":null,"abstract":"Abstract The potential use of asparaginases has gained tremendous significance in the treatment of acute lymphoblastic leukemia (ALL). Earlier studies suggest L-asparaginases (L-ASP) extracted from Escherichia coli and Erwinia aroideae regulates L-asparagine (L-Asn) from the circulating blood. Prolonged exposure to these enzymes may lead to hypersensitivity reactions. So, it is important to find novel asparaginases with anti-cancer properties. The three-dimensional structure of L-ASP I from Vibrio campbellii was determined by homology modeling using EasyModeller v.4.0. The structure was validated with quality indexing tools and was deposited in Protein Model DataBase. Molecular docking was performed between L-ASP I and ligand substrate L-Asn to study enzyme-substrate interactions. Qualitative and quantitative analysis of L-ASP I enzyme was found to be reliable and stable with a significant protein quality factor (LG score: 7.129). The enzyme is a dimer, belongs to α/β class of proteins. The active sites comprises of N-glycosylation site and a catalytic triad (T14-S117-D92). The binding energy of the docked complex was calculated to be -7.45 kcal/mol. The amino acid T14 identified as a primary nucleophile essential for catalytic reaction. The enzyme L-ASP I of V. campbellii provides a detailed view of structure and functional aspects with ligand substrate L-Asn. This in silico investigation has explicitly demonstrated for the first time that cytosolic L-ASP Type I of V. campbellii to have a catalytic triad which was attributed only to periplasmic L-ASP Type II. Thus, L-ASP I can serve as anti-leukemic agent in the treatment, management and control of ALL.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"16 - 8"},"PeriodicalIF":1.7,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41513596","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract C-terminal amidation is a common feature of wild type membrane disrupting antimicrobial peptides (AMPs). Empirical evidence suggests that this modification increases antimicrobial efficacy. However, the actual role of C-terminal amidation in the molecular mechanism of action of AMPs is not fully understood. Amidation alters two key properties simultaneously: the net charge and helicity of the peptide, both of which are implicated in the mechanism of action. However, the differences between the physicochemical properties of the carboxyl and amide moieties have been disregarded in former studies. In this study we assessed whether the difference in activity is only caused by changes in the helicity and overall charge of a peptide, i.e. whether the chemistry of the terminus is otherwise irrelevant. To do so, the membrane disrupting activity of a modified aurein 1.2 peptide was studied in which a secondary amide was formed with a terminal methyl group, instead of the primary amide as in the wild type peptide. Results of quartz crystal microbalance, dye leakage and circular dichroism experiments show that the activity of the modified peptide is substantially reduced compared to the wild type peptide, in particular that the modified peptide exhibited a much-reduced ability to bind to the membrane. Thus, the primary amide at the C-terminus is required to bind to the membrane, and a secondary amide cannot serve the same purpose. We hypothesize that this difference is related to the hydration state of the terminus. The lack of membrane binding ability of the modified peptide identifies the primary amide moiety at the C terminus as a specific membrane binding motif.
{"title":"The role of C-terminal amidation in the mechanism of action of the antimicrobial peptide aurein 1.2","authors":"M. Shahmiri, A. Mechler","doi":"10.2478/ebtj-2020-0004","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0004","url":null,"abstract":"Abstract C-terminal amidation is a common feature of wild type membrane disrupting antimicrobial peptides (AMPs). Empirical evidence suggests that this modification increases antimicrobial efficacy. However, the actual role of C-terminal amidation in the molecular mechanism of action of AMPs is not fully understood. Amidation alters two key properties simultaneously: the net charge and helicity of the peptide, both of which are implicated in the mechanism of action. However, the differences between the physicochemical properties of the carboxyl and amide moieties have been disregarded in former studies. In this study we assessed whether the difference in activity is only caused by changes in the helicity and overall charge of a peptide, i.e. whether the chemistry of the terminus is otherwise irrelevant. To do so, the membrane disrupting activity of a modified aurein 1.2 peptide was studied in which a secondary amide was formed with a terminal methyl group, instead of the primary amide as in the wild type peptide. Results of quartz crystal microbalance, dye leakage and circular dichroism experiments show that the activity of the modified peptide is substantially reduced compared to the wild type peptide, in particular that the modified peptide exhibited a much-reduced ability to bind to the membrane. Thus, the primary amide at the C-terminus is required to bind to the membrane, and a secondary amide cannot serve the same purpose. We hypothesize that this difference is related to the hydration state of the terminus. The lack of membrane binding ability of the modified peptide identifies the primary amide moiety at the C terminus as a specific membrane binding motif.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"25 - 31"},"PeriodicalIF":1.7,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.2478/ebtj-2020-0004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49584318","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract This study aimed to investigate the effects of possible zinc (Zn) and molybdenum (Mo) contaminations on the critically endangered European Bluestar (Amsonia orientalis). The effects of Zn and Mo were tested in a dose-dependent manner on in vitro cultures. Zn at 0.1 mM in the medium inhibited root development whereas Mo showed the same effect only at ≥2.5 mM concentration. Gradual inhibition of shoot development was observed after treatment with both metals. Protein contents were also negatively affected by increasing metal concentrations, while proline levels increased gradually. Successive increases in metal concentrations resulted in higher hydrogen peroxide (H2O2) and malondialdehyde (MDA) concentrations. The activity of the antioxidant enzymes, peroxidase (POD) and catalase (CAT), were found to be enhanced in response to increasing metal concentrations. Superoxide dismutase (SOD) activity decreased after Zn treatment but increased after Mo treatment. A marked increase in POD and CAT in response to metal stress suggests that these enzymes might have a significant cooperative role in regulating H2O2 production, although CAT, in response to drought and salt stress, has been reported to only play a supplementary role in A. orientalis. These results indicated that A. orientalis is susceptible to long-term Zn stress but can tolerate up to 2.5 mM Mo in the long-term. Deficiency of Mo is more common than high toxic concentrations in the environment. Therefore Zn contamination should be considered as one of the major threats for A. orientalis in its native habitat.
{"title":"Effects of zinc and molybdenum on European Bluestar (Amsonia orientalis): An in vitro study","authors":"Arda Acemi, Y. Duman, Y. Y. Karakus, Fazıl Özen","doi":"10.2478/ebtj-2020-0005","DOIUrl":"https://doi.org/10.2478/ebtj-2020-0005","url":null,"abstract":"Abstract This study aimed to investigate the effects of possible zinc (Zn) and molybdenum (Mo) contaminations on the critically endangered European Bluestar (Amsonia orientalis). The effects of Zn and Mo were tested in a dose-dependent manner on in vitro cultures. Zn at 0.1 mM in the medium inhibited root development whereas Mo showed the same effect only at ≥2.5 mM concentration. Gradual inhibition of shoot development was observed after treatment with both metals. Protein contents were also negatively affected by increasing metal concentrations, while proline levels increased gradually. Successive increases in metal concentrations resulted in higher hydrogen peroxide (H2O2) and malondialdehyde (MDA) concentrations. The activity of the antioxidant enzymes, peroxidase (POD) and catalase (CAT), were found to be enhanced in response to increasing metal concentrations. Superoxide dismutase (SOD) activity decreased after Zn treatment but increased after Mo treatment. A marked increase in POD and CAT in response to metal stress suggests that these enzymes might have a significant cooperative role in regulating H2O2 production, although CAT, in response to drought and salt stress, has been reported to only play a supplementary role in A. orientalis. These results indicated that A. orientalis is susceptible to long-term Zn stress but can tolerate up to 2.5 mM Mo in the long-term. Deficiency of Mo is more common than high toxic concentrations in the environment. Therefore Zn contamination should be considered as one of the major threats for A. orientalis in its native habitat.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"4 1","pages":"32 - 41"},"PeriodicalIF":1.7,"publicationDate":"2020-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41630898","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Abstract The soil degraded and changed by the anthropic activity must be monitored and the awareness of the intrinsic processes will allow a pertinent analysis of the effects of the application of the new technologies on the management and the sustainability of the soil. Two natural and anthropic Phaeozems were analyzed from the point of view of chemical, microbiological characteristics, quality and composition of organic compounds. Total values of microbial biomass and bacterial and fungal counts were generally twice higher in Calcaric Phaeozems than in Verti-Stagnic Phaeozems. The content of humic precursors in Calcaric Phaeozems was quantitatively higher than that determined in Verti-stagnic Phaeozems, with a total content of phenols of 14.6mgGAExg−1d.m., polysaccharides and proteins of 97mgxg−1, respectivelly 16.6mgxl−1. The ascending chromatograms showed specific distribution and higher density of the organic compounds in the CAFT sub-fraction of the Verti-stagnic Phaeozems. Pfeiffer specific chromatograms revealed an enzyme activity much higher than average at the Verti-stagnic Phaeozems, with a well-characterized functional diversity. The nutritional reserve appeared increased but poorly diversified in the Calcaric Phaeozems. Humification processes are intense, colloidal substances are present, the mineral component is very well integrated in the organic material at the Verti-stagnic Phaeozems and complex protein content is well revealed especially in the Calcaric Phaeozems. Capillary dynamolysis reflected a characteristic pattern of Phaeozems soils, with particularities for each soil type, represented by colors, contours and particular forms of the specific structures developed. Both soils presented good conditions for sustaining vegetation either natural or cultivated but results indicated that anthropic intervention determined a more dynamic mineralization of organic matter. Further monitoring of soil organic matter dynamics is needed and adjusting management practices for conservation of biodiversity and global ecosystem protection against the effect of anthropic intervention.
{"title":"Differences in organic matter quality, chemical and microbiological characteristics of two Phaeozems under natural and anthropic influence","authors":"M. Sorin, G. Matei, Dumitrașcu Monica, V. Mocanu","doi":"10.2478/ebtj-2019-0022","DOIUrl":"https://doi.org/10.2478/ebtj-2019-0022","url":null,"abstract":"Abstract The soil degraded and changed by the anthropic activity must be monitored and the awareness of the intrinsic processes will allow a pertinent analysis of the effects of the application of the new technologies on the management and the sustainability of the soil. Two natural and anthropic Phaeozems were analyzed from the point of view of chemical, microbiological characteristics, quality and composition of organic compounds. Total values of microbial biomass and bacterial and fungal counts were generally twice higher in Calcaric Phaeozems than in Verti-Stagnic Phaeozems. The content of humic precursors in Calcaric Phaeozems was quantitatively higher than that determined in Verti-stagnic Phaeozems, with a total content of phenols of 14.6mgGAExg−1d.m., polysaccharides and proteins of 97mgxg−1, respectivelly 16.6mgxl−1. The ascending chromatograms showed specific distribution and higher density of the organic compounds in the CAFT sub-fraction of the Verti-stagnic Phaeozems. Pfeiffer specific chromatograms revealed an enzyme activity much higher than average at the Verti-stagnic Phaeozems, with a well-characterized functional diversity. The nutritional reserve appeared increased but poorly diversified in the Calcaric Phaeozems. Humification processes are intense, colloidal substances are present, the mineral component is very well integrated in the organic material at the Verti-stagnic Phaeozems and complex protein content is well revealed especially in the Calcaric Phaeozems. Capillary dynamolysis reflected a characteristic pattern of Phaeozems soils, with particularities for each soil type, represented by colors, contours and particular forms of the specific structures developed. Both soils presented good conditions for sustaining vegetation either natural or cultivated but results indicated that anthropic intervention determined a more dynamic mineralization of organic matter. Further monitoring of soil organic matter dynamics is needed and adjusting management practices for conservation of biodiversity and global ecosystem protection against the effect of anthropic intervention.","PeriodicalId":22379,"journal":{"name":"The EuroBiotech Journal","volume":"3 1","pages":"182 - 189"},"PeriodicalIF":1.7,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42726807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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