Tabatabaei, M.,
Aghbashlo, M.,
Valijanian, E.,
Kazemi shariat panahi, H.,
Nizami, A.,
Ghanavati, H.,
Sulaiman, A.,
Mirmohamadsadeghi, S.,
Karimi, K. Publication Date: 2020
Renewable Energy (0960-1481)146pp. 1204-1220
This study reviews the innovations and optimizations in biogas production from the biological perspective reported by recently published patents and research works. The proposed biological strategies can be categorized into three different groups, i.e., upstream, mainstream, and downstream approaches. In the first part of this review, upstream strategies, including pretreatments by fungal, microbial consortium, and enzymatic as well as some other biological methods including microaeration, composting, ensiling, and genetic and metabolic engineering are discussed in detail. The impacts of upstream strategies on biogas production as well as their potentials in further improving the biogas industry are comprehensively scrutinized. Despite their promising impacts on biogas production, such biological innovations are time-consuming and require extra equipment and facilities that should be addressed in future studies. Overall, most information on biogas production has been generated through lab-scale investigations and not by commercial plants, undermining the commercial value of these data for the right decision-making. Pilot data would be necessary for techno-economic analyses with acceptable accuracies. Therefore, the future efforts should be directed toward providing the missing data for re-engineering designs, calculations, and life cycle assessment (LCA) of the newly designed biogas plants. © 2019 Elsevier Ltd
Tabatabaei, M.,
Aghbashlo, M.,
Valijanian, E.,
Kazemi shariat panahi, H.,
Nizami, A.,
Ghanavati, H.,
Sulaiman, A.,
Mirmohamadsadeghi, S.,
Karimi, K. Publication Date: 2020
Renewable Energy (0960-1481)146pp. 1392-1407
This review is aimed at detailing and discussing biological innovations and optimizations including upstream, mainstream, and downstream approaches in biogas production elaborated in the recently published patents and research papers. In the first part of this review, upstream strategies including pretreatments by fungal, microbial consortium, and enzymatic as well as some other biological methods including microaeration, composting, ensiling, and genetic and metabolic engineering were comprehensively presented and duly discussed. Despite the fact that these approaches hold great promise for improving the quantity and quality of the evolved biogas, the need for more processing time and extra equipment are the main drawbacks of such strategies. In the second part of this review, mainstream and downstream strategies are reviewed, and their merits and limitations are outlined. Bioaugmentation, anaerobic co-digestion, and integrated biogas production are evaluated as mainstream strategies. Finally, downstream biological approaches used for removal of CO2, H2S, and other impurities are reviewed and discussed. Among the mainstream biological techniques, bioaugmentation is highly advised to accelerate start-up periods at commercial scale while anaerobic co-digestion is recommended to not only enhance biogas yield throughout the operation but also to take advantage of different waste streams. Such mainstream strategies could contribute to improving the economic facets of biogas plants. Despite their currently underdeveloped status, downstream techniques for biological removal of biogas impurities are expected to replace their physiochemical counterparts at industrial scale in future owing to increasingly stringent environmental regulations. © 2019 Elsevier Ltd
Publication Date: 2021
Journal of Microbiology, Biotechnology and Food Sciences (13385178)11(3)pp. 1-5
COVID-19 has shown higher virulence compared to the previous coronavirus epidemics and has shown that it causes damages to the nervous system. In the present study, PrionW web server was used to predict the prion-like domains (PrLDs) in 15 structural and non-structural proteins of SARS-CoV, MERS-CoV and SARS-CoV-2. Among all of these proteins, the results demonstrated one PrLD with the sequence 951EDDYQGKPLEFGATSAALQPEEEQEEDWLDDDSQQTVGQQDGSEDNQTTTIQTIVEVQPQL1012, having an amyloid-core of 988GQQDGSEDNQTTTIQTIVEVQ1009 in the non-structural protein of SARS-CoV-2 with pWALTZ_Score of 59.9936. The sequence of SARS-CoV-2 polyprotein was further investigated by FoldIndex© tool, and a negative fold index was demonstrated at the site of predicted prion-like domain. Multiple sequence alignment of this region with non-structural proteins of SARS-CoV and MERS-CoV, showed that there is no sequence similarity between this predicted region and the corresponding regions of two other viruses. Considering the high similarity between polyproteins of SARS-CoV-2 and SARS-CoV, and their ability to affect the nervous system, it could be suggested that a potential PrLD might be added to SARS-CoV polyprotein. © 2021. All Rights Reserved.
Publication Date: 2021
Phytochemistry (00319422)187
Avicennia marina is a widely distributed mangrove species with high tolerance to salt, oxidative stress and heavy metals. In the preset work, we found that superoxide dismutase (SOD) activity increases in Avicennia marina leaves in response to salt and hydrogen peroxide. Monitoring the SOD using Western blot analysis revealed that the accumulation of SOD increased in response to hydrogen peroxide but not in response to salinity stress. Here we also isolated and cloned a gene encoding AmSOD1 which was classified into the group of plant CuZnSODs based on amino acid sequence analysis. AmSOD1 was heterologously expressed in the soluble fraction of E. coli strain Rosetta (DE3). The cells expressing His-AmSOD1 were more tolerant in response to hydrogen peroxide treatment but not salt stress, suggesting the involvement of AmSOD1 in hydrogen peroxide tolerance. The enzyme His-AmSOD1 exhibited a molecular mass of 38 kDa, but it could be monomer in reducing conditions indicating a double-strand protein with intra-molecular disulfide bridge. There are two copper and two zinc moles per mole of dimer form of His-AmSOD1 suggesting the binding of one copper and one zinc ions to each monomer. The Pure His-AmSOD1 was highly active in vitro and its activity was considerably enhanced when the growth medium of the cells producing AmSOD1 was supplemented with Cu2+. The high stability of the recombinant AmSOD1 after incubation in a broad range pH and high temperature is a distinctive feature for AmSOD1, which may open new insights for application of AmSOD1 as a protein drug in different medical purposes. © 2021 Elsevier Ltd
Publication Date: 2024
PLoS ONE (19326203)19(7)
Bovine viral diarrhea virus (BVDV) is the cause of bovine viral diarrhea disease, one of the most economically important livestock diseases worldwide. The majority of BVD disease control programs rely on the detection and then elimination of persistent infection (PI) cattle, as the continuing source of disease. The main purpose of this study was to design and develop an accurate G-quadruplex-based aptasensor for rapid and simple detection of BVDV-1. In this work, we utilized in silico techniques to design a G-quadruplex aptamer specific for the detection of BVDV-1. Also, the rationally designed aptamer was validated experimentally and was used for developing a colorimetric biosensor based on an aptamer-gold nanoparticle system. Firstly, a pool of G-quadruplex forming ssDNA sequences was constructed. Then, based on the stability score in secondary and tertiary structures and molecular docking score, an aptamer (Apt31) was selected. In the experimental part, gold nanoparticles (AuNPs) with an average particle size of 31.7 nm were synthesized and electrostatically linked with the Apt31. The colorimetric test showed that salt-induced color change of AuNPs from red to purple-blue occurs only in the presence of BVDV-Apt31 complex, after 20 min. These results approved the specificity of Apt31 for BVDV. Furthermore, our biosensor could detect the virus at as low as 0.27 copies/ml, which is an acceptable value in comparison to the qPCR method. The specificity of the aptasensor was confirmed through cross-reactivity testing, while its selectivity was confirmed through plasma testing. The sample analysis showed 90% precision and 94% accuracy. It was concluded that the biosensor was adequately sensitive and specific for the detection of BVDV in plasma samples and could be used as a simple and rapid method on the farm. © 2024 Rabiei et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Nguyen, T.,
Vinayaka, A.C.,
Huynh, V.N.,
Linh, Q.T.,
Andreasen, S.Z.,
Glaby, M.,
Bang, D.D.,
Møller, J.K.,
Wolff, A. Publication Date: 2023
Proceedings of the IEEE International Conference on Micro Electro Mechanical Systems (MEMS) (10846999)2023pp. 437-439
In the ongoing COVID-19 pandemic, sensitive and rapid on-site detection of the SARS-CoV-2 coronavirus has been one of crucial objectives. A point-of-care (PoC) device called PATHPOD for quick, on-site detection of SARS-CoV-2 employing a real-time reverse-transcription loop-mediated isothermal amplification (RT-rLAMP) reaction on a polymer cartridge. The PATHPOD consists of a standalone device (weighing under 1.2 kg) and a cartridge, and can identify 10 distinct samples and 2 controls in less than 50 minutes. The PATHPOD PoC system is fabricated and clinically validated for the first time in this work © 2023 IEEE.
Publication Date: 2020
Phytochemistry (00319422)176
Metallothioneins (MTs) are low molecular weight, cysteine-rich, metal-binding proteins that are important for essential metal homeostasis, protection against oxidative stress, and buffering against toxic heavy metals. In this work the gene encoding an MT type 2 from Avicennia marina (Forssk.) Vierh. (AmMT2) was cloned into pET41a and transformed into the Escherichia coli strain Rosetta (DE3). Following the induction with isopropyl β-D-1-thiogalactopyranoside, AmMT2 was expressed as glutathione-S-transferase (GST)-tagged fusion protein. The accumulation of Zn2+, Cu2+, Fe2+, Ni2+ and Cd2+ for strain R-AmMT2 was 4, 8, 5.4, 2 and 1.6 fold of control strain suggesting the role of AmMT2 in accumulation of metals. Particularly the strain R-AmMT2 was able to accumulate 30.7 mg per g dry weight. The cells expressing AmMT2 was more tolerant to hydrogen peroxide and had higher catalase (CAT) activity. To understand the mechanistic action of AmMT2 hydrogen peroxide tolerance, the activity of CAT in the E. coli protein extract was assayed after addition of pure Fe2+/GST-AmMT complex and Apo/GST-AmMT2 in vitro. Whereas, the activity of CAT did not change by the addition of Apo/GST-AmMT2, the activity of CAT significantly increased after addition of Fe2+/GST-AmMT2. These results show that AmMT2 activates CAT through Fe2+ transfer which subsequently causes the oxidative stress tolerance. © 2020 Elsevier Ltd
Ramezanpour, A.,
Karami, K.,
Kharaziha, M.,
Zakariazadeh, M.,
Lipkowski, J.,
Shahpiri, A.,
Azizi, N.,
Namazian, M. Publication Date: 2021
Polyhedron (02775387)206
Throughout this study, a new palladium (II) complex, trans-[Pd(Naph)2Cl2], with naphazoline hydrochloride (Naphcon) as an imidazole derivative, 2-(naphthalen-1-ylmethyl)-4,5-dihydro-1H-imidazole;hydrochloride, was synthesized and characterized by elemental analysis, spectroscopic methods (UV–Vis, IR, and 1H NMR) and single crystal X-ray structure analysis. The cytotoxicity of Naphcon and the PdII complex were investigated in vitro against human breast (MCF-7) and cervical epithelial carcinoma (HeLa) cancer cells. The results revealed the higher anticancer activity of complex rather that of Naphcon against MCF-7 cell line. The findings of in vitro studies including fluorescence and UV–Vis spectroscopy, circular dichroism (CD), thermal denaturation and viscosity measurement indicated the interaction of the PdII complex with calf-thymus DNA (CT-DNA) via a combination of covalent and non-covalent interactions, whereas the free Naphcon interacted with CT-DNA mainly through the groove binding mode. Moreover, the ability of Naphcon and the PdII complex to cleave pUC57 plasmid DNA was investigated. In addition, the interaction of both Naphcon and its PdII complex was explored with bovine serum albumin (BSA) by means of absorption and fluorescence spectroscopy. The binding constant (Kb) could be calculated for compounds through these spectroscopic methods. Based on the competitive binding studies using Eosin, Ibuprofen and Digoxin as site markers, the binding site of the PdII complex and Naphcon was found to be located on site-III and I of BSA, respectively. Furthermore, protease activity of compounds was examined under physiological conditions. Finally, to validate all data obtained from biophysical studies, the molecular docking simulation was employed as a computational method. © 2021
Publication Date: 2009
EXCLI Journal (16112156)8pp. 190-194
Glutathione S-transferase is a family of multifunctional detoxification enzymes which are mainly cytosolic that detoxify natural and exogenous toxic compounds by conjugation with glutathione. Glutathione, an endogenous tripeptide, is important as either a reducing agent or a nucleophilic scavenger. This molecule alleviates the chemical toxicity in plants by reaction of glutathione S-transferase, and its conjugates can be transported to vacuole or apoplast. The plant soluble glutathione S-transferases grouped today into seven distinct Phi, Tau, Zeta, Theta, lambda, dehydroascorbate reductase, and tetrachlorohydroquinone dehalogenase classes. In this study, bioinformatics analysis of glutathione S-transferase gene in barley was carried out using Tau-class of barley glutathione S-transferase sequences in NCBI GenBank and isolated sequence. DNA extraction, primer design, PCR, electrophoresis, column purifica-tion, DNA sequencing and analysis by some software led to identify new sequences of Tau-class of glutathione S-transferase from barley, which is similar to Tau GST of the diploid wheat. Comparison of the deduced amino acid sequences of the three barley GST genes showed that they have 99% identity with each other but only 45% identity with the new GST. This sequence was submitted to NCBI GenBank with FI131240 accession number.
Publication Date: 2026
Talanta (00399140)297
Equine herpesvirus type 1 (EHV-1) is a globally prevalent equine pathogen responsible for severe respiratory, neurological, and reproductive disorders. Accurate and ultrasensitive detection of EHV-1 is critical for timely disease management. In this study, we report the development of the first G-quadruplex-forming aptamer specifically designed for EHV-1 detection. The aptamer was generated using an in silico approach, and its G-quadruplex conformation was confirmed using circular dichroism (CD) spectroscopy and crystal violet fluorescence assays. Binding affinity and specificity were assessed using a comprehensive panel of analytical techniques, including colorimetric assays, enzyme-linked apta-sorbent assay (ELASA), surface plasmon resonance (SPR), CD spectroscopy, and fluorescence analysis. The aptamer exhibited a high binding affinity in the picomolar range, as determined by SPR. In both colorimetric and ELASA platforms, it enabled the detection of as few as 10 viral particles per milliliter, compared to the 1000 viral particles per milliliter required by conventional PCR. ELASA results demonstrated excellent diagnostic performance, yielding an area under the curve of 0.96. Importantly, this aptamer-based method eliminates the need for DNA extraction, primers, or gel electrophoresis. These findings underscore the aptamer's strong potential as a cost-effective, rapid, and user-friendly point-of-care diagnostic tool for EHV-1, especially in low-resource or field settings. © 2025 Elsevier B.V.
Kirkensgaard, K.G.,
Hägglund, P.,
Shahpiri, A.,
Finnie, C.,
Henriksen, A.,
Svensson, B. Publication Date: 2014
Proteins: Structure, Function and Bioinformatics (10970134)82(4)pp. 607-619
The ubiquitous disulfide reductase thioredoxin (Trx) regulates several important biological processes such as seed germination in plants. Oxidized cytosolic Trx is regenerated by nicotinamide adenine dinucleotide phosphate (NADPH)-dependent thioredoxin reductase (NTR) in a multistep transfer of reducing equivalents from NADPH to Trx via a tightly NTR-bound flavin. Here, interactions between NTR and Trx are predicted by molecular modelling of the barley NTR:Trx complex (HvNTR2:HvTrxh2) and probed by site directed mutagenesis. Enzyme kinetics analysis reveals mutants in a loop of the flavin adenine dinucleotide (FAD)-binding domain of HvNTR2 to strongly affect the interaction with Trx. In particular, Trp42 and Met43 play key roles for recognition of the endogenous HvTrxh2. Trx from Arabidopsis thaliana is also efficiently recycled by HvNTR2 but turnover in this case appears to be less dependent on these two residues, suggesting a distinct mode for NTR:Trx recognition. Comparison between the HvNTR2:HvTrxh2 model and the crystal structure of the Escherichia coli NTR:Trx complex reveals major differences in interactions involving the FAD- and NADPH-binding domains as supported by our experiments. Overall, the findings suggest that NTR:Trx interactions in different biological systems are fine-tuned by multiple intermolecular contacts. © 2013 Wiley Periodicals, Inc.
Alinaghi, M.,
Karami, K.,
Shahpiri, A.,
Nasab, A.K.,
Momtazi-borojeni, A.,
Abdollahi, E.,
Lipkowski, J. Publication Date: 2020
Journal of Molecular Structure (00222860)1219
A novel Pd(II) complex, [Pd(C6H5N2O)2], containing pyridine-2-carbaldehyde oxime ligand has been synthesized and characterized using elemental analysis, Fourier-transform infrared, nuclear magnetic resonance and mass spectroscopy. The single crystal structure of this Pd(II) complex has been determined by X-ray crystallography. Based on the DNA binding studies including ultraviolet visible spectrophotometry, fluorescence emission titration and viscosity measurement, the interaction of Pd(II) complex with calf thymus DNA occurs by groove binding. In the absence of an external reductant, the Pd(II) complex cleaves the supercoiled double-stranded DNA under physiological conditions. Moreover, in the presence of Pd(II) complex, the Bovine Serum Albumin microenvironment and secondary structure change. On the basis of the competitive experiments using site markers, the complex is mainly located in site I of the protein. The binding of the Pd(II) complex to DNA was modeled using molecular docking. The antitumor impacts of the ligand and the Pd(II) complex were evaluated in vitro against the mouse colon carcinoma (C26) and melanoma (B16–F0) tumor cell lines. The antitumor activity has been significantly improved by the complexation process. IC50 values smaller than those of cisplatin have been shown by the Pd(II) complex and oxime ligand against cancer cell lines. In addition, Pd(II) complex has been tested against NIH normal fibroblast cells. Consequently, Pd(II) complex may be considered a selective compound against cancer cells, according to the SI definition. © 2020
Publication Date: 2016
New Journal of Chemistry (11440546)40(11)pp. 9081-9097
A new Pd(ii) complex, [Pd(4-OHPh-tpy)Cl]Cl, with a ligand that is a terpyridine derivative, (4′-(4-hydroxyphenyl)-2,2′,6′,2′′-terpyridine (4-OHPh-tpy)), was prepared and fully characterized. The single crystal structures of 4-OHPh-tpy and its Pd(ii) complex were determined by X-ray crystallography. The in vitro studies (UV-Vis spectroscopy, circular dichroism (CD), rheometry, and gel electrophoresis) show that the Pd(ii) complex interacts with calf-thymus DNA (CT-DNA) via a combination of covalent, intercalation, and hydrogen bonding interactions, whereas the free 4-OHPh-tpy ligand interacts with DNA mainly through intercalation. The Pd(ii) complex cleaves the supercoiled double-stranded DNA under physiological conditions without the need to add an external reductant. The microenvironment and the secondary structure of BSA were also changed in the presence of both the free ligand and the Pd(ii) complex. The Pd(ii) complex was remarkable in exhibiting cleavage of the BSA at micromolar concentrations and short incubation times at physiological pH and temperature. The anti-cancer effects of the free ligand and the Pd(ii) complex were tested in vitro against five human tumor cell lines, including the human breast cancer cell line (MCF-7), lung adenocarcinoma cells (A-549), an erythroleukemic cell line (K562), a colorectal adenocarcinoma cell line (HT-29), and hepatocellular carcinoma (Hep-G2) cells. The Pd(ii) complex showed the IC50 values less than those of cisplatin against the MCF-7, A-549, K562, and HT-29 cancer cell lines. Finally, the binding of the Pd(ii) complex and 4-OHPh-tpy to BSA and DNA was modeled by molecular docking and molecular dynamic simulation methods. © 2016 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.
Publication Date: 2016
Applied Energy (0306-2619)168pp. 216-225
Development of efficient and cost-effective pretreatment prior to hydrolysis is essential for the economical production of biobutanol from lignocelluloses. In this study, acetone pretreatment with a number of advantages over the other pretreatments was used to improve enzymatic hydrolysis and fermentation with Clostridium acetobutylicum for acetone-butanol-ethanol (ABE) production from sweet sorghum bagasse (SSB). Using the pretreatment at 180 °C for 60 min, the yield of enzymatic hydrolysis of SSB was improved to 94.2%, leading to a hydrolysate with 36.3 g/L total sugar, which was subsequently fermented to 11.4 g/L ABE. This process resulted in the production of 78 g butanol, 35 g acetone, 12 g ethanol, 28 g acetic acid, and 6 g butyric acid from each kg of SSB. Through the pretreatment, 143 g lignin per kg of SSB was dissolved into the solvent, with the potential to be recovered as unaltered pure lignin. Furthermore, the co-production of acetone by the ABE fermentation alleviated the concern about unavoidable solvent loss in the pretreatment, i.e., 24 g acetone/kg SSB, using an integrated process for biobutanol production from SSB. The energy equivalent obtained in the form of butanol and ethanol (72 g gasoline equivalent/kg SSB) was higher than that obtainable via ethanolic fermentation (less than 70 g/kg SSB). © 2016 Elsevier Ltd.
Publication Date: 2016
Journal of Mazandaran University of Medical Sciences (17359260)26(135)pp. 32-42
Background and purpose: Avicennia marina (family Acanthaceae) has been used as traditional medicine in Iran to treat some diseases such as ulcers, rheumatism and burns. The present study investigated the in silico and in vitro mutagenicity of the fruit, leaf, seed and stem extracts of Avicennia marina and their effects on human peripheral blood mononuclear cells (PBMC) proliferation. Materials and methods: In this experimental study, air dried and powdered plant materials were extracted by methanol using maceration. The extracts were evaporated to dryness by rotary evaporator at 40°C and were diluted using different PBS concentrations (50, 100, 500, 1000, and 1500 μg/ml). The effect of the methanol extract of this plant on lymphocyte proliferation was measured using MTT assay. The mutagenicity of these extracts was also investigated using Ames test. In silico analysis of 15 dominant compounds of the plant was performed by Toxtree 2.6.6 software. Results: The methanol extracts of the leaf and root had the highest and lowest inducing effect on lymphocyte proliferation, respectively. Leaf and stem extracts of Avicennia marina did not show any mutagenicity on this strain. In silico analysis demonstrated that among 15 compounds, four triterpenoids (Taraxerol, Betulin, Lupeol, and Gossypol) had weak mutagenicity. Conclusion: Avicennia marina showed positive effects on proliferation of lymphocytes and their mutagenicity, therefore, it could be considered as a good candidate in treatment of immunodeficiency diseases. © 2016, Mazandaran University of Medical Sciences. All rights reserved.
Sheikhi, F.,
Babaei, M.,
Rostami, K.,
Azin, M.,
Asadollahi, M.A.,
Ghiaci, P.,
Ebrahimi, M.,
Feizi, A.,
Borodina, I. Publication Date: 2025
FEMS Yeast Research (15671364)25
Saccharomyces cerevisiae is a widely used yeast for industrial production of ethanol. However, elevated ethanol, temperature, and osmotic stress adversely affect fermentation efficiency. In this study, adaptive laboratory evolution for S. cerevisiae CEN.PK 113–7D on higher concentrations of ethanol was performed. After 144 days, the maximum specific growth rate (µmax) increased from 0.0240 to 0.1150 h−1 for the strain evolved on 9% v/v ethanol, and from 0.0002 to 0.0530 h−1 for the strain evolved on 11% v/v ethanol, and the specific glucose uptake rate increased by 30%. The strain evolved on 11% ethanol produced 94.5 g/L ethanol in a fermentation as compared to 78.5 g/L production by a non-evolved strain. By whole-genome sequencing of the evolved clones, we identified multiple coding mutations in genes involved in processes such as stress response, cell growth regulation, pentose phosphate pathway, lipid synthesis, and redox balance. The selected mutations in RKI1, CYC2, ANR2, RGA2, RGA1, LPX1, and LRE1 genes were validated by introducing them in the nonevolved yeast, showing 1.7–5-fold growth improvement at 9% ethanol (P < 0.05). Notably, RGA2, RGA1 and LPX 1 carried an identical missense mutation across three independent clones. The RKI1I208V mutant showed the highest ethanol tolerance, while CYC2N342A achieved the highest ethanol production. © The Author(s) 2025. Published by Oxford University Press on behalf of FEMS.
Noorisafa, F.,
Razmjou, A.,
Taheri kafrani, A.,
Ejeian, F.,
Asadnia, M.,
Ghavamabadi, H.A. Publication Date: 2026
Desalination and Water Treatment (19443994)325
Artificial intelligence (AI) enhances biosensor design by efficiently processing and modeling environmental data. This study employs machine learning algorithms to optimize biosensor parameters for the detection of trace-level heavy metals in aquatic environments, utilizing enzymes, DNAzymes, and aptamers as recognition elements. Machine learning models, including decision trees, random forests, gradient boosting, ensemble neural networks, and GLMM,were trained on extensive laboratory datasets. Among these, the random forest model exhibited the highest predictive accuracy, achieving 71 % for the limit of detection (LOD), 75 % for the minimum concentration of linearity, and 62 % for the maximum concentration of linearity. The AI-driven approach not only enhances biosensor sensitivity but also reduces experimental time and costs, enabling more efficient environmental monitoring. Moreover, this strategy is adaptable for detecting a wide range of pollutants, including chemical fertilizers, emerging contaminants, and micropollutants in aquatic and soil systems. These findings represent a significant step toward next-generation biosensing technologies with potential applications in sustainable environmental monitoring. Copyright © 2026. Published by Elsevier Inc.
Publication Date: 2018
International Journal of Biological Macromolecules (01418130)112pp. 876-881
Nowadays health benefits of bioactive food constituents, known as probiotic microorganisms, are a growing awareness. Cow's milk is a nutritious food containing probiotic bacteria. However, milk allergenicity is one of the most common food allergies. The milk protein, beta-lactoglobulin (BLG), is in about 80% of all main cases of milk allergies for children and infants. With the aim of screening proteolytic strains of lactic acid bacteria to evaluate their potential for the reduction of allergenicity of the major bovine milk proteins, we isolated new proteolytic strains of cocci lactic acid bacteria from traditional Iranian daily products. The proteases produced by these strains had strong proteolytic activity against BLG. Proteolysis of BLG, observed after sodium dodecyl sulfate PAGE, was confirmed by the analysis of the peptide profiles by reversed-phase HPLC. The two isolates were submitted to 16S rDNA sequencing and identified as Lactcoccus lactic subsp. cremoris and Lactcocrus lactic subsp. hordniea. The competitive ELISA experiments confirmed that these isolates, with high proteolytic activity, reduce significantly the allergenicity of BLG. Accordingly, these isolates can reduce the immunoreactivity of bovine milk proteins, which can be helpful for the production of low-allergic dairy products. (C) 2018 Elsevier B.V. All rights reserved.
Publication Date: 2018
International Journal of Biological Macromolecules (01418130)
Nowadays health benefits of bioactive food constituents, known as probiotic microorganisms, are a growing awareness. Cow's milk is a nutritious food containing probiotic bacteria. However, milk allergenicity is one of the most common food allergies. The milk protein, β-lactoglobulin (BLG), is in about 80% of all main cases of milk allergies for children and infants. With the aim of screening proteolytic strains of lactic acid bacteria to evaluate their potential for the reduction of allergenicity of the major bovine milk proteins, we isolated new proteolytic strains of cocci lactic acid bacteria from traditional Iranian dairy products. The proteases produced by these strains had strong proteolytic activity against BLG. Proteolysis of BLG, observed after sodium dodecyl sulfate-PAGE, was confirmed by the analysis of the peptide profiles by reversed-phase HPLC. The two isolates were submitted to 16S rDNA sequencing and identified as Lactcoccus lactis subsp. cremoris and Lactcoccus lactis subsp. hordniea. The competitive ELISA experiments confirmed that these isolates, with high proteolytic activity, reduce significantly the allergenicity of BLG. Accordingly, these isolates can reduce the immunoreactivity of bovine milk proteins, which can be helpful for the production of low-allergic dairy products. © 2018 Elsevier B.V.
Madadi, M.,
Bakr, M.M.,
Abdulkhani, A.,
Zahoor, ,
Asadollahi, M.A.,
Sun, C.,
Sun, F.,
Abomohra, A.E. Publication Date: 2022
Energy Conversion and Management (0196-8904)251
Pretreatment is the key factor for producing fermentable sugars and biofuels from lignocellulosic biomass. However, during pretreatment lignin repolymerization occurs which reduces the efficiency of carbohydrates hydrolysis. In the present study, three additives (2-naphthol-7-sulfonate, 2-naphthol, and mannitol) were evaluated for boosting the effectiveness of combined pretreatment (liquid hot water + green liquor) of pine-wood biomass. The results revealed that supplied additives into combined pretreatment changed the physicochemical structure of lignin, therefore, alleviating the inhibitory effect of lignin repolymerization and notably raised sugars yield (glucose, xylose) ranging from 85% to 93%. XPS and FTIR analyses confirmed that −OH groups of additives led to lower formation of phenolic hydroxyl (PhOH) and higher hydrophilic groups of lignin, accounting for reduced non-specific binding of lignin into cellulase enzymes. Furthermore, additives increased surface lignin coverage, biomass porosity, and fiber swelling by 1.96–2.59, 1.66–1.86, and 1.13–1.29 folds respectively, comparing to corresponding sample without additives caused more liquified and extractable lignin, which notably reduced the surface lignin barrier. Hence, both factors including non-specific binding effect and surface lignin barrier, contributed to reducing lignin repolymerization, thereby increased cellulose accessibility for high production of fermentable sugars and bioethanol in softwood biomass. © 2021 Elsevier Ltd
Publication Date: 2020
Journal of Chemical Technology and Biotechnology (02682575)95(8)pp. 2243-2250
BACKGROUND: Widespread application of enzymes for research and industrial purposes is dependent on enhancing the catalytic capacity. One promising approach to this end is the immobilization of enzymes on novel nanomaterials. In this study, a novel nanocarrier was developed for the immobilization of enzyme on polycaprolactone (PCL)-functionalized magnetic nanoparticles. RESULT: Structural and physicochemical characterization of the PCL-modified magnetic nanocarrier was achieved via Fourier-transform infrared (FTIR) spectra, scanning electron microscopy (SEM), transmission electron microscopy (TEM), thermogravimetric analysis (TGA) and vibration sample magnetometry (VSM). In order to determine the optimal conditions for immobilization, different parameters such as pH, temperature, reaction time and enzyme concentration were evaluated. Based on the results, the optimal biocatalytic activity of immobilized α-amylase was obtained at 65 °C and pH 6.5. Under appropriate conditions, the immobilized α-amylase showed improved storage stability in comparison with free one. Additionally, the reusability of the immobilized system demonstrated >50% enzyme activity, at optimal pH and temperature, after five reaction cycles. CONCLUSION: This finding could be useful in the application of immobilized enzymes for analytical purposes, industrial exploitations, biotechnology, biomedical engineering and other bio-applications. © 2020 Society of Chemical Industry. © 2020 Society of Chemical Industry
Publication Date: 2012
Applied Clay Science (01691317)59pp. 8-12
A new type of modified clay was produced from a Ca-bentonite treated with hydrochloric acid as a surface modifier agent and then with hexadecyltrimethylammonium bromide (HDTMA) as a surfactant to produce an organophilic adsorbent. The specific surface area of the modified clays was 40% higher than the specific surface area of bentonite treated only with HDTMA. A series of kinetic and equilibrium tests was carried out to study the effectiveness of the modification method to improve the bentonite ability to remove phenol from aqueous solutions. The adsorption capacity of modified bentonite was 10 times greater than the natural bentonite. Phenol adsorption was fast and reached equilibrium in 30. min. Adsorption was physical and exothermic and was described with Henry and Freundlich isotherms. © 2012 Elsevier B.V.
Publication Date: 2016
Medicinal Chemistry (15734064)12(8)pp. 795-800
Background: Fungi are an emerging threat in medicine and agriculture and current therapeutics have proved to be insufficient and toxic. This has led to an increased interest in peptide-based therapeutics, especially antifungal peptides (AFPs), being safer and more effective drug candidates against fungal threats. However, screening for peptides with antifungal activity is costly and timeconsuming. However, by using computational techniques, we can overcome these restricting factors. The aim of the present study is to compare different machine learning algorithms in combination with Chou's pseudo amino acid composition in classifying and predicting AFPs to represent a precise model for AFP prediction. Methods: Five different machine learning algorithms frequently used for classification of biological data were used and their performance was evaluated and compared based on their accuracy, sensitivity, specificity and Matthew's correlation coefficient. The two algorithms with the best performance were then further verified with an independent test dataset. Results: SVM and Bagged-C4.5 classifiers had the highest performance results among the five algorithms. Further validations showed that the model generated using SVM can be employed for precise classification and prediction of antifungal peptides. All the performance values of this model were above 80%, making the classifier highly accurate and trustable. Conclusion: Using computational approaches, especially data mining techniques, we can develop a precise prediction model for antifungal peptides. The model developed in this study using SVM can be considered a powerful tool for the prediction of antifungal peptides, which can be the first step in synthesis and discovery of novel fungi targeting agents. © 2016 Bentham Science Publishers.
Publication Date: 2021
Process Safety and Environmental Protection (17443598)152pp. 513-526
Orange wastes, including peel and pulp, were used as a biorefinery feedstock to produce pectin, ethanol, and biogas. The orange wastes were subjected to dilute acid treatment with sulfuric acid (1% w/v) at 94, 100, 140, and 180 °C for 60, 30, and 0 min. The sulfuric acid treatment was performed for pectin extraction, sugars hydrolysis, and lignocellulose pretreatment. The pectin was extracted from the hydrolysate, the liquor was used to produce ethanol, and the pretreated solid was anaerobically digested to produce biogas. The highest pectin extraction yield was 24.7 % (w/w) from orange peel and 23.7 % (w/w) from pulp, which was obtained from the supernatants of treatment at 94 °C for 60 min. Fourier transfer infrared spectrometer results confirmed the similar characteristics of the extracted pectin to a commercial product. The galacturonic acid content (an indicator of pectin purity) of pectin extracted from orange peel was 70.2 % and from orange pulp was 69.9 %, at the optimum conditions. The pectin obtained from the acid treatment at 94 °C for 60 min had a degree of esterification higher than 69 %, whereas it was less than 45 % for that obtained after treatment at 140 °C for 30 min. The maximum ethanol yields of 81.5 % (from peel) and 82.9 % (from pulp) were achieved from the hydrolysate of the acid treatment at 140 °C for 30 min. The highest methane yields were 176.8 mL/g volatile solids (from the untreated peel) and 191.8 mL/g volatile solids (from the untreated pulp). Overall, the maximum total product value was 2,472.9 USD/t orange wastes, which was achieved from dilute acid treatment at 94 °C for 60 min. At the optimal conditions for high production of pectin, without any enzyme consumption, 244 kg of pectin, 26.5 L of ethanol, and 36 m3 of methane were produced from 1 t of orange wastes. © 2021 Institution of Chemical Engineers
Publication Date: 2016
International Journal of Environmental Science and Technology (17351472)13(3)pp. 763-772
Effluent sludge from an anaerobic digester was used as a source of nitrogen, phosphate, sulfur, and other nutrients in the culture medium of ethanol production by the yeast Saccharomyces cerevisiae. Several pretreatments (mechanical, chemical, thermal, and thermo-chemical) were performed on the anaerobic digested sludge (ADS) to make the nutrients accessible to the yeast cells. Preliminary experiments revealed that S. cerevisiae is not able to assimilate the carbon content of the ADS. However, when glucose was added to the medium, ethanol production was observed. The yield of ethanol using untreated ADS was only 10 % of the theoretical yield, but alkaline pretreatment improved it up to 43 %. By separating the hydrolysate of alkaline-treated ADS from the suspended solids, the ethanol yield from the supernatant was further improved up to 65 % of theoretical yield. Alkaline-treated ADS exhibited competitive performance with the mixture of yeast extract and mineral salts in ethanol fermentation. © 2015, Islamic Azad University (IAU).
Publication Date: 2020
Journal of Biotechnology (01681656)308pp. 56-62
Alkaline phosphatase (ALP) and acid phosphatase (ACP) are two important phosphatase enzymes that play fundamental roles in Gram-negative bacteria. Additionally, they are useful for various biotechnological and industrial applications. In the present study, different aspects of bacterial ALPs and ACPs such as pseudo amino acid composition (PseAAC), amino acid composition, dipeptide composition, physicochemical properties, secondary structures and structural motifs were studied. The binding affinity of the phosphomonoesters to ALP and ACP enzymes was predicted by docking, and the activity of ALPs and ACPs were measured using colorimetric assay. ROC curve statistical analysis the machine learning algorithms were applied for classification of these two phosphatase protein groups. The results indicated that the physicochemical properties of ALPs and ACPs were not significantly different, although the aliphatic index and Extinction coefficient of motifs of these two enzymes were significantly different. Classification based on the concept of PseAAC and dipeptide composition also indicated high accuracy. The result of docking demonstrated that the binding free energy of ALPs was less than ACPs and the experimental results demonstrated that the activity of ACPs was more than ALPs. In conclusion, there is a relationship between efficiency and PseAAC and dipeptide compositions of these two enzymes. © 2019 Elsevier B.V.
