Publication Date: 2021
Taxonomy and Biosystematics (23222190)13(46)pp. 27-56
The study of flora characteristics and their relationship with ecological factors in habitats has a particular importance in protected areas. This study aimed to examine the chorological and endemism of the Central Alborz protected area flora. The study area included the slopes of Welwesht, Dahla, and Azadkouh heights in the protected area of Central Alborz, Mazandaran province, Iran. The total number of collected and identified taxa was 331, which belonged to 197 genera and 46 families. During the floristic studies of the region, Nepeta azadkouhensis Saberamoli from Lamiaceae family was identified and introduced as a new species. About 49.25% of taxa were hemicryptophytes, 57.40% of all species belonged to Irano-Turanian chorotype. Forty-six taxa, equal to 13.9% of all taxa, were endemic to Iran. Moreover, 37 species, equal to 82.22% of endemic species, belonged to the vegetation zone of Irano-Turanian. The habitat of mountain steppes, which included mainly grasses and cushion-shaped plants with 24.47% of the total taxa, had the highest species richness. The results of the species richness study in the altitude classes of the endemic taxa showed that more than 70% of the taxa were located in medium to semi-high habitats. The study of the presence of endemic species in vegetation elements confirms the dominance of the Irano-Turanian vegetation zone in the region, reflecting the significant presence and influence of European-Siberian elements. © 2021, University of Isfahan.
Publication Date: 2014
Current Computer-Aided Drug Design (18756697)10(4)pp. 349-353
Acquired immunodeficiency syndrome (AIDS) is one of the most devastating diseases of current century which is caused by the human immunodeficiency virus (HIV). Although great efforts have been done to fight the virus, the need of new therapeutics candidates of any kind still remains. This process needs huge time and experimental endeavor. However, Computer-aided techniques and can speed up the procedure. Currently, cheminformatics tools have proven to be extremely valuable in pharmaceutical research. In the past few decades, a huge number of different molecular descriptors were designed to describe chemical molecules in a quantitative way to make it easy to use them for computational studies. Herein, we present a computational study of anti-HIV small molecules test by the National Cancer Institute (NCI) to introduce the most efficient molecular descriptors for anti-HIV activity. In this regard a dataset of 199 highly active anti-HIV and 174 inactive compounds were defined by 905 molecular descriptors. Data were classified using Random Forest algorithm and the most important molecular descriptors were introduced as the parameters responsible for representing anti-HIV activity. Applying the mentioned computational and cheminformatics methods, it is possible to predict the anti-HIV activity of any given small molecule with high accuracy. © 2014 Bentham Science Publishers.
Publication Date: 2020
International Archives of Allergy and Immunology (14230097)181(11)pp. 813-821
Background: A large number of allergens are derived from plant and animal proteins. A major challenge for researchers is to study the possible allergenic properties of proteins. The aim of this study was in silico analysis and comparison of several physiochemical and structural features of plant- and animal-derived allergen proteins, as well as classifying these proteins based on Chou's pseudo-amino acid composition (PseAAC) concept combined with bioinformatics algorithms. Methods: The physiochemical properties and secondary structure of plant and animal allergens were studied. The classification of the sequences was done using the PseAAC concept incorporated with the deep learning algorithm. Conserved motifs of plant and animal proteins were discovered using the MEME tool. B-cell and T-cell epitopes of the proteins were predicted in conserved motifs. Allergenicity and amino acid composition of epitopes were also analyzed via bioinformatics servers. Results: In comparison of physiochemical features of animal and plant allergens, extinction coefficient was different significantly. Secondary structure prediction showed more random coiled structure in plant allergen proteins compared with animal proteins. Classification of proteins based on PseAAC achieved 88.24% accuracy. The amino acid composition study of predicted B- and T-cell epitopes revealed more aliphatic index in plant-derived epitopes. Conclusions: The results indicated that bioinformatics-based studies could be useful in comparing plant and animal allergens. © 2020 S. Karger AG, Basel. All rights reserved.
Publication Date: 2015
International Journal of Peptide Research and Therapeutics (15733149)21(1)pp. 57-62
Human immunodeficiency virus-1 (HIV-1) is the etiological agent for the global concerning disease "AIDS". The virus infects 35 million people globally and after 30 years, the disease remains a challenge. Despite great efforts in finding efficient treatment strategies, the pandemic of AIDS is continuing and the rate of new infections has not been diminished. Therefore, the need for finding novel treatment strategies is still of great importance. Peptide-based therapeutics has shown promise in the treatment of many challenging diseases such as various types of cancers and also HIV. Since time and money are the two restricting factors in any experimental researches, computer-aided techniques can dramatically reduce time and costs. In the present study, we developed a method based on pseudo amino acid composition of amino acid sequences to classify the anti-HIV-1 peptides using different machine learning algorithms. The performance of each algorithm was investigated and after comparing the performance parameters, the most accurate algorithm was proposed for predicting anti-HIV-1 activity of any given peptide. Having the accuracies of 96.15 and 83.71 % respectively, multilayer perceptron (MLP) and logistic model tree algorithms were primarily shown to be the most accurate ones in classifying anti-HIV-1 peptides. Final results demonstrate that model generated by MLP can be a valuable tool for the classification and prediction of anti- HIV-1 peptides in order to have a preliminary prediction which can be further coupled with experimental assays while reducing time and costs. © Springer Science+Business Media 2014.
The etiology of Multiple Sclerosis (MS) as a multifactorial neurodegenerative disease is still mostly unknown. Various “omic” approaches, including genome-wide association studies, transcriptome analysis, exome sequencing, and epigenome studies are considered to be helpful for better understanding of MS progression and pathophysiology as well as more accurate determination of different MS subtypes. In recent years, the importance of epigenetics in MS pathogenesis, as well as other autoimmune diseases, has been surprisingly well received. Epigenetic therapy, which includes drugs that have the ability to influence the reversible and dynamic epigenetic characteristics, is also identified as a promising therapeutic tool in MS. This chapter will provide a summary of recent studies considering potential roles of epigenetic alterations as biomarkers in MS. © 2018 Elsevier Inc. All rights reserved.
Publication Date: 2024
Perspectives in Plant Ecology, Evolution and Systematics (16180437)63
West Asia, with its high mountain ranges and glacial refugia, stands out as a biodiversity hotspot for various plant taxa, including the taxonomically complex Rubus subgen. Rubus. Despite this significance, our understanding of the evolutionary processes shaping this group in the region has been limited. We employed an integrative approach combining flow cytometry, Sanger sequencing of two plastid regions, microsatellite genotyping, and double digest restriction-site associated DNA sequencing to characterize evolutionary and diversity patterns in West Asian brambles. We identified four diploid and two sexual tetraploid species, with the remaining diversity comprising apomictic tetra- and triploids, mostly belonging to R. ser. Discolores, and sexual pentaploid hybrids/hybridogens derived from R. caesius. Rubus dolichocarpus, newly reported here as diploid, emerged as a significant ancestor for many polyploids. Most apomictic genotypes are locally distributed and only three genotypes exhibit extremely large ranges from Armenia to Kyrgyzstan and from Georgia to Iran. These genotypes are probably of an ancient (Pleistocene) European origin and likely laid the foundations for the evolution of apomicts in West Asia, whose diversification was subsequently boosted by the genetic contribution of sexual taxa. DNA markers confirmed the West Asian origin of Rubus armeniacus, a globally significant invasive species, yet rare in its native range. We report on the first indigenous occurrence of this species based on microsatellite genotyping. Our findings contribute to filling existing gaps in understanding the evolution and diversity of Rubus subgen. Rubus in West Asia. © 2024 Elsevier GmbH
Publication Date: 2020
PLoS ONE (19326203)15(11 November)
Parkinson’s disease (PD) is diagnosed when motor symptoms emerges, which almost 70% of dopamine neurons are lost. Therefore, early diagnosis of PD is crucial to prevent the progress of disease. Blood-based biomarkers, which are minimally invasive, potentially used for diagnosis of PD, including miRNAs. The aim of this study was to assess whether SRRM2 and miR-27a/b-3p could act as early diagnostic biomarkers for PD. Total RNAs from PBMCs of 30 PD’s patients and 14 healthy age and gender matched subjects was extracted. The expression levels of respective genes were assessed. Data were presented applying a two-tailed unpaired t-test and one-way ANOVA. We observed significant downregulation of SRRM2 (p = 0.0002) and miR-27a-3p (p = 0.0001), and up-regulation of miR-27b-3p (p = 0.02) in PBMCs of Parkinson’s patients. Down-regulation of miR-27a-3p is associated with increasing disease severity, whereas the up-regulation of miR-27b-3p was observed mostly at HY-1 and disease duration between 3–5 years. There was a negative correlation between SRRM2 and miR-27b-3p expressions, and miR-27a-3p positively was correlated with miR-27b-3p. Based on functional enrichment analysis, SRRM2 and miR-27a/b-3p acted on common functional pathways. miR-27a/b-3p could potentially predict the progression and severity of PD. Although both miRs had no similarity on expression, a positive correlation between both miRs was identified, supporting their potential role as biomarkers in clinical PD stages. Of note that SRRM2 and miR-27a-3p were able to distinguish PD patients from healthy individuals. Functional analysis of the similarity between genes associated with SRRM2 and miR-27a/b-3p indicates common functional pathways and their dysfunction correlates with molecular etiopathology mechanisms of PD onset. © 2020 Fazeli 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.
Publication Date: 2025
Scientific Reports (20452322)15(1)
Papillary thyroid carcinoma (PTC) is a malignancy with an ambiguous etiology. The competitive endogenous RNA (ceRNA) hypothesis provides a framework for clarifying the molecular mechanisms that drive carcinogenesis. In this study, we constructed a novel ceRNA network to identify reliable diagnostic and prognostic indicators applicable across all stages of PTC. Transcriptome analysis was performed to identify stage-specific hub genes using the MCC, IVI, and MCODE algorithms. A novel five-layer ceRNA network and its associated regulatory network (DE-TF) were constructed. Receiver operating characteristic curves were used to evaluate the diagnostic performance of elements within both networks. A risk assessment model was developed by identifying key genes from the ceRNA and DE-TF components through univariable Cox regression and LASSO regression analyses. RNA-seq findings were validated by RT-qPCR. The correlations between gene expression levels and blood calcium levels were examined. The ceRNA and DE-TF networks contained 33 and 21 components, respectively. Logistic regression analysis identified PKMYT1, E2F1, NFATC1, STAT6, E2F3, LINC02910, GAS5, and TK1 as reliable diagnostic markers for PTC, achieving an AUC of 96.9%. Among these, PKMYT1 and GAS5 were stage-specific markers, showing significant upregulation in highly aggressive PTC tumors compared to less aggressive ones. Both genes demonstrated strong diagnostic value in differentiating high- from low-aggressive tumors, with AUCs of 0.81 and 0.87, respectively. circMET, which was overexpressed in both low- and high-aggressive tumors, showed diagnostic potential in distinguishing low-aggressive tumors from normal adjacent tissues (AUC = 0.81). GAS5 expression demonstrated an association with blood calcium levels. The SERN prognostic model, including STAT6, E2F1, RMI2, and NR4A1, illustrates the importance of these four genes as reliable prognostic markers for overall survival in PTC. Three components of the ceRNA network—PKMYT1, GAS5, and circMET—were significantly associated with PTC aggressiveness. PKMYT1 and GAS5 demonstrated strong diagnostic value in distinguishing high-aggressive from low-aggressive tumors, while circMET showed notable diagnostic efficacy in differentiating low-aggressive PTC tumors from adjacent normal tissues. Furthermore, GAS5 expression levels were correlated with blood calcium levels. © The Author(s) 2025.
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
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: 2019
European Journal of Medical Genetics (18780849)62(9)
Phenylketonuria (PKU) is a metabolic disorder caused by mutations in the phenylalanine hydroxylase (PAH) gene. After thalassemia, PKU is considered as the most common autosomal recessive diseases in the Iranian population. Therefore, an efficient diagnostic strategy is required to identify disease-causing mutations in this population. Following our first report in 2003, here we presented a comprehensive study on the mutation spectrum of the PAH gene in the Iranian population. This study was performed on 280 unrelated chromosomes from 140 Iranian patients with classic PKU. All 13 exons as well as exon-intron boundaries of the PAH gene were analyzed by direct DNA sequencing. Thirty four different mutations were identified by a mutation detection rate of 100%. IVS10-11G > A, p.P281L, R261Q, p.F39del and IVS11+1G > C were the most prevalent mutations with frequencies of 26.07%, 19.3%, 12.86%, 6.07 and 3.93%, respectively. All other mutations represented a relative frequency less than 3.5%. The data from this study provided a comprehensive spectrum of the PAH gene mutations which can facilitate carrier detection and prenatal diagnosis of PKU disease in the Iranian population. © 2018
Publication Date: 2014
Computational Biology and Chemistry (14769271)51pp. 57-62
Aspirin (ASA) is a commonly used nonsteroidal anti-inflammatory drug (NSAID), which exerts its therapeutic effects through inhibition of cyclooxygenase (COX) isoform 2 (COX-2), while the inhibition of COX-1 by ASA leads to apparent side effects. In the present study, the relationship between COX-1 non-synonymous single nucleotide polymorphisms (nsSNPs) and aspirin related side effects was investigated. The functional impacts of 37 nsSNPs on aspirin inhibition potency of COX-1 with COX-1/aspirin molecular docking were computationally analyzed, and each SNP was scored based on DOCK Amber score. The data predicted that 22 nsSNPs could reduce COX-1 inhibition, while 15 nsSNPs showed increasing inhibition level in comparison to the regular COX-1 protein. In order to perform a comparing state, the Amber scores for two Arg119 mutants (R119A and R119Q) were also calculated. Moreover, among nsSNP variants, rs117122585 represented the closest Amber score to R119A mutant. A separate docking computation validated the score and represented a new binding position for ASA that acetyl group was located within the distance of 3.86 Å from Ser529 OH group. This could predict an associated loss of activity of ASA through this nsSNP variant. Our data represent a computational sub-population pattern for aspirin COX-1 related side effects, and provide basis for further research on COX-1/ASA interaction. © 2014 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: 2023
International Journal Of Preventive Medicine (20087802)14(1)pp. 22-22
Publication Date: 2020
Taxonomy and Biosystematics (23222190)12(42)pp. 51-68
The Afus region with 1146 hectares area is located at 10 Km to Buin Miandasht region (Isfahan province) between the northern latitudes of 33° 05΄ and 33° 58΄ and the eastern longitudes 50° 02΄ and 50° 09΄. The purpose of the present study was to investigate the flora of the region. So, the plant species were collected from different places using the survey sampling method during spring, summer, and autumn 2017-2018 and were identified using valid resources. In this study, a complete list of the flora, life forms, chorotypes of plant elements, and endemic plants was prepared. The identified vascular plants in the region were mostly flowering with 184 species belonging to 37 families and 132 genera. Asteraceae (24 genera, 32 species), Apiaceae (12 genera, 12 species), Poaceae (11 genera, 13 species), and lamiaceae (9 genera, 13 species) were the most important families in this region, respectively. The largest genera were Astragalus (12 species), Euphorbia (5 species), Silene and Stachys (4 species), Cousinia, Fritillaria and Scorzonera (3 species) and Centaurea (2 species), respectively. The largest geographic floral element of the region was related to Irano-Turanian region with 136 species (73/9%). Hemicryptophytes (107 species, 58/15%), geophytes (25 species, 13/59 %), theophytes (24 species, 13/04%), chamaephytes (17 species, 9/24%), phanerophytes (7 species, 3/80%), and cryptophytes (4 species, 2/17%) made up the most important life forms, respectively. © 2020, University of Isfahan.
Publication Date: 2022
Frontiers in Veterinary Science (22971769)9
Johne's disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) is a major concern in dairy industry. Since, the pathogenesis of the disease is not clearly known, it is necessary to develop an approach to discover molecular mechanisms behind this disease with high confidence. Biological studies often suffer from issues with reproducibility. Lack of a method to find stable modules in co-expression networks from different datasets related to Johne's disease motivated us to present a computational pipeline to identify non-preserved consensus modules. Two RNA-Seq datasets related to MAP infection were analyzed, and consensus modules were detected and were subjected to the preservation analysis. The non-preserved consensus modules in both datasets were determined as they are modules whose connectivity and density are affected by the disease. Long non-coding RNAs (lncRNAs) and TF genes in the non-preserved consensus modules were identified to construct integrated networks of lncRNA-mRNA-TF. These networks were confirmed by protein-protein interactions (PPIs) networks. Also, the overlapped hub genes between two datasets were considered hub genes of the consensus modules. Out of 66 consensus modules, 21 modules were non-preserved consensus modules, which were common in both datasets and 619 hub genes were members of these modules. Moreover, 34 lncRNA and 152 TF genes were identified in 12 and 19 non-preserved consensus modules, respectively. The predicted PPIs in 17 non-preserved consensus modules were significant, and 283 hub genes were commonly identified in both co-expression and PPIs networks. Functional enrichment analysis revealed that eight out of 21 modules were significantly enriched for biological processes associated with Johne's disease including “inflammatory response,” “interleukin-1-mediated signaling pathway”, “type I interferon signaling pathway,” “cytokine-mediated signaling pathway,” “regulation of interferon-beta production,” and “response to interferon-gamma.” Moreover, some genes (hub mRNA, TF, and lncRNA) were introduced as potential candidates for Johne's disease pathogenesis such as TLR2, NFKB1, IRF1, ATF3, TREM1, CDH26, HMGB1, STAT1, ISG15, CASP3. This study expanded our knowledge of molecular mechanisms involved in Johne's disease, and the presented pipeline enabled us to achieve more valid results. Copyright © 2022 Heidari, Pakdel, Bakhtiarizadeh and Dehghanian.
Publication Date: 2025
Cellular and Molecular Neurobiology (02724340)45(1)
This study aimed to integrate genome-wide association studies (GWAS) with pharmacogenomics data to develop personalized pain and inflammatory therapeutics. Despite recent developments in the clinical utilities of pharmacogenomics, it needs more investigations for uncovering the complicated mechanisms of drugs from a genetic standpoint. The research addresses the increasing misuse of opioids during recovery, emphasizing personalized interventions for opioid use disorder (OUD). Key pain-related pathways were analyzed to uncover their interactions. Five GWAS traits, including pain, inflammatory biomarkers, immune system abnormalities, and opioid-related traits, were examined. Candidate genes extracted from GWAS datasets were refined through in silico analyses, including protein–protein interactions (PPIs), TF-miRNA coregulatory interactions, enrichment analysis (EA), and clustering enrichment analysis (CEA). A network of 50 highly connected genes was identified, with APOE emerging as a top candidate due to its role in cholesterol metabolism and opioid-induced lipid effects. Pharmacogenomics analysis highlighted significant gene annotations, including OPRM1, DRD2, APOE, GRIN2B, and GPR98, linking them to opioid dependence, neurological disorders, and lipid traits. Protein interaction analyses further validated these connections, with implications for epigenetic repair. Our findings reveal a strong association between APOE, opioid use, and Alzheimer’s disease, suggesting potential for novel recovery strategies. Combining HDL-boosting drugs with pro-dopaminergic regulators like KB220 may help prevent relapse. This study underscores the importance of integrating genetic and pharmacogenomic data to advance personalized therapies. © The Author(s) 2025.
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.
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: 2019
Analytical Methods (17599679)11(33)pp. 4233-4241
A novel receptor tyrosine-protein kinase erbB-2 (HER2)-binding affiprobe-named ZHER2:342-RLuc-was designed, produced and assessed in terms of function to detect HER2 positive cells and for preliminary clinical diagnosis. The ZHER2:342 affibody with affinity for HER2 was fused to Renilla luciferase, and the purified affiprobe was used for detection of HER2 positive cells as well as evaluation of surgical specimens from breast cancer patients. The results showed that the affiprobe can specifically bind to HER2 positive cells, and therefore, it may be used for molecular detection. © 2019 The Royal Society of Chemistry.
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
Publication Date: 2016
Journal of the Iranian Chemical Society (1735207X)13(12)pp. 2143-2153
In this report, the main contributions of FMN were employed in the reductive cleavage reaction of AzrC protein (as a member of azoreductase family). Molecular dynamics simulations of three models in the presence and absence of FMN and ligand were performed to gather information about the dynamic nature of active site residues of AzrC. Combination of pairwise decomposition and alanine scanning calculations provides critical information about the FMN binding sites. The MD results analyzed by alanine scanning method revealed the high negative scores for N 10 (A) A, N 12 (A) A, S 17 (A) A and Y 151 (A) A mutations, which were in agreement with pairwise decomposition analyses. Hydrogen bond analyses indicated that these residues play critical roles in establishing appropriate hydrogen bonds between AzrC and FMN. Negative energy results for nonpolar residues such as W 103 (A), M 102 (A) and F 105 (A) and binding free energy analyses of three complexes indicate that the VDW interactions could be regarded as some favorable contribution in FMN and AzrC protein and confirmed the critical role of FMN in ligand binding (35.84 %), in addition to its catalytic function. This information could be used for future experimental investigations. © 2016, Iranian Chemical Society.
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: 2017
Analytical Biochemistry (00032697)537pp. 99-105
Lateral flow assays (LFAs) have promising potentials for point-of-care applications. Recently, many LFAs have been reported that are based on hybridization of oligonucleotide strands. Mostly, biotinylated capture DNAs are immobilized on the surface of a nitrocellulose membrane via streptavidin interactions. During the assay, stable colorful complexes get formed that are visible by naked eyes. Here, we present an inexpensive and unique design of LFA that applies unmodified oligonucleotides at capture lines. The presented LFA do not utilize streptavidin or any other affinity protein. We employ structural switch of molecular beacons (MB) in combination with base stacking hybridization (BSH) phenomenon. The unique design of the reported LFA provided high selectivity for target oligonucleotides. We validated potential applications of the system for detection of DNA mimics of two microRNAs in multiplex assays. © 2017 Elsevier Inc.
Publication Date: 2017
Scientific Reports (20452322)7(1)
Decades of research on the highly modified wings of Drosophila melanogaster has suggested that insect wings are divided into two Anterior-Posterior (A-P) compartments separated by an axis of symmetry. This axis of symmetry is created by a developmental organizer that establishes symmetrical patterns of gene expression that in turn pattern the A-P axis of the wing. Butterflies possess more typical insect wings and butterfly wing colour patterns provide many landmarks for studies of wing structure and development. Using eyespot colour pattern variation in Vanessa butterflies, here we show an additional A-P axis of symmetry running between wing sectors 3 and 4. Boundaries of Drosophila mitotic clones suggest the existence of a previously undetected Far-Posterior (F-P) compartment boundary that coincides with this additional A-P axis. A similar compartment boundary is evident in butterfly mosaic gynandromorphs. We suggest that this additional compartment boundary and its associated developmental organizer create an axis of wing colour pattern symmetry and a gene expression-based combinatorial code, permitting each insect wing compartment to acquire a unique identity and allowing for the individuation of butterfly eyespots. © 2017 The Author(s).
