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: 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: 2023
International Journal Of Preventive Medicine (20087802)14(1)pp. 22-22
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.
Sharafshah, A.,
Bashi naeini, M.M.,
Blum, K.,
Lewandrowski, K.,
Gold, M.S.,
Keshavarz, P.,
Thanos, P.K. 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.
Nazari, M.,
Emamzadeh, R.,
Minai-tehrani, A.,
Nasir shirazi, M.,
Naimi, A. 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: 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: 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: 2020
Microbial Drug Resistance (10766294)26(7)pp. 831-841
The globally increasing incidence of antibiotic resistance in pathogenic microorganisms such as Shigella, a cause of human acute gastrointestinal infections, calls for developing effective alternatives. In this study, the antibiotic resistance pattern, extended-spectrum β-lactamase (ESBL)-production, and molecular characteristics of 70 multidrug-resistant isolates belong to the two most frequent species of Shigella genus, that is, Shigella sonnei (44 isolates) and Shigella flexneri (26 isolates) were investigated. These isolates were used to evaluate both specificity and activity of Shigella-specific bacteriophages, vB_SflS-ISF001, vB_SsoS-ISF002, and a cocktail of both. Twelve out of the 21 tested resistance genes were detected in the isolates. About 59% of S. sonnei and 46% of S. flexneri isolates were identified as ESBL producers. The bacteriophages showed a high efficiency of plating (EOP ≥0.5) in about 75% of the isolates. Moreover, the growth of >85% of the isolates was inhibited by the phage cocktail of vB_SflS-ISF001 and vB_SsoS-ISF002. The phage cocktail was effective against a wide range of ESBL-positive and -negative isolates of S. sonnei and S. flexneri. Therefore, this phage cocktail has the potential to inhibit or significantly decrease the spread of drug-resistant Shigella in humans, food chains, and water/wastewater sanitation systems. © Copyright 2020, Mary Ann Liebert, Inc., publishers 2020.
Publication Date: 2019
Geomicrobiology Journal (01490451)36(2)pp. 123-129
Coal is one of the most important sources of fossil energy on earth. However, direct combustion of coal with a high sulfur content can cause various environmental problems. Other constituents of coal that can cause environmental problems include iron oxide (hematite), iron hydroxide, and silica. In this study, growing and resting cells of Rhodococcus erythropolis strains PD1, R1, and FMF, and R. qingshengii were used in heterotrophic removal of sulfur and bioleaching of iron and silica from coal. All of the mentioned strains have an ability of dibenzothiophene (DBT) desulfurization via 4-S pathway. 2-hydroxybiphenyl, sulfate, and ferric ions (Fe 3+ ) were assayed by Gibb’s test, barium chloride (BaCl 2 ), and thiocyanate ions (SCN − ), respectively. FTIR and XRF analyzer were used for detection of the coal bioleaching process by the selected strain of R. erythropolis (PD1). Results indicated that all strains have the ability to grow on coal as the sulfur source. Among them, strain PD1 produced the highest optical density and continued to grow even after 150-h incubation. In both growing- and resting-cells experiments, strain PD1 desulfurized coal most readily compared to other strains. Results of XRF showed that growing cells of strain PD1 had high desulfurizing ability of coal (46%) compared to resting cells in the absence of any carbon sources (24%). Growing cells of strain PD1 also leached 46% of the iron and 14% of the silicate after 7 days of incubation. Resting cells of PD1 leached 32% of the iron as determined by XRF analysis. Also, growing cells of PD1 removed most SiO 2 from coal as detected and confirmed by FTIR and XRF. To the best of our knowledge, this is the first report on bioleaching of iron and silica from coal by R. erythropolis strain PD1, making it a suitable candidate for coal bioremediation. © 2018, © 2018 Informa UK Limited, trading as Taylor & Francis Group.
Publication Date: 2015
Computational Biology and Chemistry (14769271)58pp. 9-18
Development of a protein-based drug delivery system has major impact on the efficacy and bioavailability of unstable and water insoluble drugs. In the present study, the binding modes of a nonspecific lipid transfer protein (nsLTP2) from Oryza sativa with various nucleosides and analogous molecules were identified. The 3-D structure of the protein was designed and validated using modeler 9.13, Molegro virtual docker and procheck tool, respectively. The binding affinity and strength of interactions, key contributing residues and specificity toward the substrates were accomplished by computational docking and model prediction. The protein presented high affinity to acyclovir and vidarabine as purine-analogous drugs. Binding affinity is influenced by the core template and functional groups of the ligands which are structurally different cause the variation of interaction energies with nsLTP2. Nonetheless, all the evaluated analogous drugs occupy the proximity space at the nsLTP active site with high similarity in their binding modes. Our findings hold great promise for the future applications of nsLTPs in various aspects of pharmaceutical science and molecular biology. © 2015 Published by Elsevier Ltd.
Dehbashi, M.,
Hojati najafabadi, Z.,
Bashi naeini, M.M.,
Ganjalikhany, M.R.,
Cho, W.C.,
Shimosaka, A.,
Navabi, P.,
Ganjalikhani-hakemi, M. Publication Date: 2021
Frontiers in Oncology (2234943X)11
For many years, high-affinity subunit of IL-2 receptor (CD25) has been considered as a promising therapeutic target for different pathologic conditions like allograft rejection, autoimmunity, and cancers. Although CD25 is transiently expressed by newly-activated T cells, it is the hallmark of regulatory T (Treg) cells which are the most important immunosuppressive elements in tumor microenvironment. Thus, Tregs can be considered as a potential target for chimeric antigen receptor (CAR)-based therapeutic approaches. On the other hand, due to some profound adverse effects pertaining to the use of CAR T cells, CAR NK cells have caught researchers’ attention as a safer choice. Based on these, the aim of this study was to design and develop a CAR NK cell against CD25 as the most prominent biomarker of Tregs with the prospect of overcoming immune escape mechanism in solid and liquid cancers. In the current study, an anti-CD25 CAR was designed and evaluated by comprehensive in silico analyses. Then, using lentiviral transduction system, NK-92 cell line was engineered to express this anti-CD25 CAR construct. In vitro functional analyses of anti-CD25 CAR for its reactivity against CD25 antigen as well as for cytotoxicity and cytokine production assays against CD25 bearing Jurkat cell line were done. In silico analyses demonstrated that the anti-CD25 CAR transcript and scFv protein structures were stable and had proper interaction with the target. Also, in vitro analyses showed that the anti-CD25 CAR-engineered NK-92 cells were able to specifically detect and lyse target cells with an appropriate cytokine production and cytotoxic activity. To conclude, the results showed that this novel CAR NK cell is functional and warrant further investigations. © Copyright © 2021 Dehbashi, Hojati, Motovali-bashi, Ganjalikhany, Cho, Shimosaka, Navabi and Ganjalikhani-Hakemi.
Publication Date: 2018
Metabolic Brain Disease (15737365)33(4)pp. 1165-1173
In this study, we introduce a novel compound-primed multiplex ARMS PCR (CPMAP) for simultaneous detection of common PAH gene mutations. This approach was used successfully for simultaneous identification of six most common PAH gene mutations in 137 phenylketonuria patients in the Iranian population. A total of six normal and six mutant allele-specific primers and 4 common primers containing a tag sequence of 12 base pair at the 5ˊ-end were designed and used in two separate optimized multiplex ARMS reactions followed by hot-start PCR. The products were separated and visualized on 3% agarose gel. The CPMAP genotyping data were completely in accordance with the direct sequencing results. The CPMAP suggests a reliable, economical and rapid method for simultaneous detection of PAH point mutations using conventional PCR, which could be applied for diagnosis of other gene mutations. © 2018, Springer Science+Business Media, LLC, part of Springer Nature.
Publication Date: 2022
Cells (20734409)11(24)
To improve the efficacy of trastuzumab, it is essential to understand its mechanism of action. One of the significant issues that makes it difficult to determine the precise mechanism of trastuzumab action is the formation of various HER receptor dimers in HER2-positive breast cancer cells. So far, studies have focused on the role of HER2–HER3 heterodimers, and little is known regarding EGFR–HER2 heterodimers. Here, we study the role of trastuzumab on the cell signaling and cell proliferation mediated by EGFR–HER2 heterodimers in BT474 and SRBR3 cells. EGF stimulates the formation of both EGFR homodimer and EGFR–HER2 heterodimer. Trastuzumab only binds to HER2, not EGFR. Therefore, any effects of trastuzumab on EGF-induced activation of EGFR, HER2, and downstream signaling proteins, as well as cell proliferation, are through its effects on EGFR–HER2 heterodimers. We show that trastuzumab inhibits EGF-induced cell proliferation and cell cycle progression in BT474 and SKBR3 cells. Interestingly trastuzumab strongly inhibits EGF-induced Akt phosphorylation and slightly inhibits EGF-induced Erk activation, in both BT474 and SKBR3 cells. These data suggest the presence of a novel mechanism that allows trastuzumab to inhibit EGR-induced Akt activation and cell proliferation, without blocking EGF-induced EGFR–HER2 heterodimerization and activation. We show that trastuzumab inhibits EGF-induced lipid raft localization of the EGFR–HER2 heterodimer. Disruption of the lipid raft with MβCD blocks HER2-mediated AKT activation in a similar way to trastuzumab. MβCD and trastuzumab synergically inhibit AKT activation. We conclude that trastuzumab inhibits EGF-induced lipid raft localization of EGFR–HER2 heterodimer, which leads to the inhibition of Akt phosphorylation and cell proliferation, without blocking the formation and phosphorylation of the EGFR–HER2 heterodimer. © 2022 by the authors.
Publication Date: 2015
World Journal of Microbiology and Biotechnology (09593993)31(5)pp. 813-821
Sulfur dioxide which is released from petroleum oil combustion causes pollution over the atmosphere and the soil. Biodesulfurization can be used as a complementary method of hydrodesulfurization, the common method of petroleum desulfurization in refineries. Many studies have been carried out to develop biological desulfurization of dibenzothiophene (DBT) with bacterial biocatalysts. However, fungi are capable to metabolize a wide range of aromatic hydrocarbons through cytochrome P450 and their extracellular enzymes. The aim of the present work was isolation and identification of fungi biocatalysts capable for DBT utilization as sulfur source and production of novel metabolites. DBT consumption and the related produced metabolites were analyzed by HPLC and GC–MS respectively. One of the isolated fungi that could utilize DBT as sole sulfur source was identified by both traditional and molecular experiments and registered in NCBI as Exophiala spinifera FM strain (accession no. KC952672). This strain could desulfurize 99 % of DBT (0.3 mM) as sulfur source by co-metabolism reaction with other carbon sources through the same pathway as 4S and produced 2-hydroxy biphenyl (2-HBP) during 7 days of incubation at 30 °C and 180 rpm shaking. However, the isolate was able to transform 2-HBP to 1,3-benzenediol, 5-hexyl. While biphenyl compounds are toxic to leaving cells, biotransformation of them can reduce their toxicity and the fungi will be more tolerant to the final product. These data are the first report about the desulfurization of DBT comparable to 4S-pathway and production of innovative metabolite by E. spinifera FM strain. © 2015, Springer Science+Business Media Dordrecht.
Publication Date: 2003
Biomass and Bioenergy (09619534)25(4)pp. 423-426
A Gram-negative bacterium was isolated from corn root. This isolate is ellipsoidal to rod-shaped and slightly curved. The size of bacterium is 0.6 × (1 - 4) nm and occurring singly, in pairs or in chains. The isolated strain reduces nitrate, oxidizes ethanol to acetic acid, and hydrolyses starch and cellulose. The maximum amylase and Cellulase activities are 20 and 5.5 u ml-1, respectively. In addition, the isolate fixes nitrogen and has a good growth on the media without any nitrogen sources. A nitrogen fixation negative strain (Nif-) was obtained from the isolate by UV mutation. This mutant strain Nif- dose not grow on the media without nitrogen sources, but it has cellulase activities. © 2003 Elsevier Ltd. All rights reserved.
Publication Date: 2015
Gene (03781119)569(2)pp. 233-238
Azo dyes are broadly used in different industries through their chemical stability and ease of synthesis. These dyes are usually identified as critical environmental pollutants and many attentions were performed to degradation of azo dyes using biological systems. In this study, the interactions of an azoreductase from mesophilic gram-positive Bacillus sp. B29, AzrC, with four common azo dyes (orange I, orange II, orange G and acid red 88) were investigated. Fifteen points, double, triple and quadruple mutant forms of AzrC were made using Molegro Virtual Docker 6.0 in order to improve the binding affinity of azo dyes to AzrC. The impact of 15 different mutations on azo dye affinity potency of AzrC was computationally analyzed using AzrC-azo dye molecular docking, and each interaction was scored based on AutoDock 4.2 free binding energy. Our results have indicated that Asn 104 (A), Asn 187 (B), and Tyr 151 (A) make stable hydrogen bond between AzrC and azo dyes. The hydrophobic amino acids like Phe105 (A), Phe 125 (B), and Phe 172 (B) in wild type form make hydrophobic interactions. In addition, the presence of more hydrophobic residues F60 (B), I119 (B), I121 (B) and F132 (B) in mutant forms made more powerful hydrophobic pocket in the active site. In conclusion, recombinant AzrC with quadruple mutations was suggested in order to increase the biodegradation capacity of AzrC through improving its affinity to four studied azo dyes. This study would be promising for future experimental analyses in order to produce recombinant form of AzrC. © 2015 Elsevier B.V..
Publication Date: 2022
European Journal of Clinical Investigation (00142972)52(11)
Background: Diagnosis is one of the main strategies to deal with infectious and deadly diseases such as coronavirus disease 2019 (COVID-19). The global pandemic of COVID-19 has led to an immediate need to expand rapid diagnostic techniques. New isothermal-based methods are being developed for COVID-19 detection aiming to resolve the limitations related to the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) method through immediate samples processing and minimizing false-negative or ambiguous results. Advances in nucleic acid amplification techniques (NAATs) can provide affordable and easy-to-use diagnostic platforms with high sensitivity and specificity in order to be available to the public as approved commercial kits. Aims: The development of point-of-care (POC) testing can assist in rapid clinical decision-making and mitigate burdens on health care facilities. Finally, we discussed the different diagnostic methods based on NAATs for COVID-19 in detail. Comparative parameters are addressed for all assays and Emergency Use Authorizations (EUA)-approved commercial tests are cited. Conclusions: Isothermal-coupled methods and LAMP-based molecular methods have been suggested as suitable portable tests with high diagnostic speed for use in POC testing. © 2022 Stichting European Society for Clinical Investigation Journal Foundation. Published by John Wiley & Sons Ltd.
Mahdavi, S.B.,
Javadirad, S.M.,
Rafieian, M.,
Poursafa, P.,
Zavareh, V.A.,
Daniali, S.S.,
Heidari-beni, M.,
Goodarzi-khoigani, M.,
Vahdatpour, B.,
Mirhendi, H. Publication Date: 2025
Bioimpacts (22285652)15
Introduction: It is believed that DNA methylation can modify disease susceptibility in response to environmental factors as early as the perinatal period. In this study, we aimed to present a streamlined DNA methylation analysis procedure for osteoporosis-related gene promoters in the umbilical cord blood. Methods: The Prospective Epidemiological Research Studies in Iran (PERSIAN) birth cohort was established in 2016. In this study, a total of 300 umbilical cord blood samples were collected at the time of delivery. For all samples, DNA was extracted and converted using sodium bisulfite. Multiple primer sets were designed for Wnt1, Wnt10b, β-catenin, OPG, and RANKL gene promoters in the online MethPrimer platform. Next, bisulfite sequencing PCR (BSP), as the gold standard method for exploring methylated and unmethylated cytosines, was performed in a gradient-controlled setting. The PCR products were then purified and directly sequenced. Subsequently, the chromatograms were interpreted. Results: For Wnt10b, β-catenin, and OPG genes, the converted DNA could be successfully amplified. The frequency of acceptable chromatograms for analysis was 195 for Wnt10b (195/300, 0.65%), 198 for β-catenin (198/300, 0.66%), and 50 for OPG (50/50, 100%). Conclusion: BSP can be efficiently used to investigate the methylation of target gene promoters in umbilical cord blood DNA. © 2025 The Author(s).
Hojati najafabadi, Z.,
Hojati najafabadi, Z.,
Nabavizadeh, N.,
Bressin, A.,
Shboul, M.,
Moreno traspas, R.,
Chia, P.H.,
Bonnard, C.,
Szenker-ravi, E.,
Sarıbaş, B.,
Beillard, E.,
Altunoglu, U. Publication Date: 2023
EMBO Molecular Medicine (1757-4676)15(2)
Exome sequencing has introduced a paradigm shift for the identification of germline variations responsible for Mendelian diseases. However, non-coding regions, which make up 98% of the genome, cannot be captured. The lack of functional annotation for intronic and intergenic variants makes RNA-seq a powerful companion diagnostic. Here, we illustrate this point by identifying six patients with a recessive Osteogenesis Imperfecta (OI) and neonatal progeria syndrome. By integrating homozygosity mapping and RNA-seq, we delineated a deep intronic TAPT1 mutation (c.1237-52 G>A) that segregated with the disease. Using SI-NET-seq, we document that TAPT1's nascent transcription was not affected in patients' fibroblasts, indicating instead that this variant leads to an alteration of pre-mRNA processing. Predicted to serve as an alternative splicing branchpoint, this mutation enhances TAPT1 exon 12 skipping, creating a protein-null allele. Additionally, our study reveals dysregulation of pathways involved in collagen and extracellular matrix biology in disease-relevant cells. Overall, our work highlights the power of transcriptomic approaches in deciphering the repercussions of non-coding variants, as well as in illuminating the molecular mechanisms of human diseases. © 2023 The Authors. Published under the terms of the CC BY 4.0 license.
Publication Date: 2006
Journal of Applied Genetics (12341983)47(1)pp. 79-83
Phenylketonuria is an inherited metabolic disease, which is characterized by increased level of serum phenylalanine (Phe). The quantitative measurement of Phe in the serum is necessary to confirm the disease, and to distinguish phenylketonuria from other forms of hyperphenylalaninemia. In this study, we report a rapid and inexpensive micro-assay for simultaneous detection and quantitative measurement of serum Phe in dry blood-spots. Analysis of the standard curve showed a broad linear Phe range of 120-1800 μmol L -1. Application of this method in conjunction with the standard Guthrie bacterial inhibition assay and high-pressure liquid chromatography in analyzing 34 samples from phenylketonuria patients and control samples produced comparable results, with the regression equation of Y= 0.994 + 0.996. The advantage of this method over the Guthrie bacterial inhibition assay is its ability to measure the serum Phe quantitatively without false positive results. The method was successfully applied to dried blood-spots as well as serum and whole blood samples. The cost per sample is about 20-50 US cents, which is much less than those of high-pressure liquid chromatography and enzymatic commercial kits. The method can be automated, which is suitable for neonatal and mass phenylketonuria screening, especially in developing countries, where funding is a limiting factor.
Publication Date: 2021
Journal of Virological Methods (01660934)293
The bacteriophage (phage) DNA extraction methods for genomics analysis is a critical and time-consuming process. Hence, a rapid and cost-effective method for DNA extraction of phages is favorable for phage biologists. In the present study, a cost-effective, simple and rapid procedure for phage genome extraction in less than 10 min is introduced. Highly concentrated phage lysates were prepared using acetone precipitation followed by extraction using various methods such as commercial kits, TES lysis buffer, potassium iodide, and sodium iodide. The quality of the extracted DNA was analyzed by agarose gel electrophoresis and UV absorbance of DNA at 260 and 280 nm. Finally, the extracted DNA was subjected to restriction digestion and next-generation sequencing to approve the efficiency of the method. Based on the time, cost, and quality of obtained DNA, the acetone precipitation of phages and extraction by potassium iodide or sodium iodide method was determined to be the best method for phage DNA extraction tested in this study. Moreover, the extracted genomic DNA using this method is suitable for phage genomic analysis such as restriction enzyme studies, preparation of DNA library, and also next-generation sequencing. © 2021 Elsevier B.V.
Nazari, M.,
Emamzadeh, R.,
Jahanpanah, M.,
Yazdani, E.,
Radmanesh, R. Publication Date: 2022
International Journal of Biological Macromolecules (01418130)219pp. 1122-1134
High expression of receptor tyrosine-protein kinase erbB-3 (HER3) has been found in several malignancies such as breast cancer. In this study, we designed, produced and evaluated a new affitoxin consisting of a truncated form of diphtheria toxin and a HER3-binding affibody domains. The new affitoxin was expressed in Escherichia coli and purified by affinity chromatography. We evaluated the suitability of affitoxin to kill HER3 positive breast cancer cells with MTT and apoptosis assays. The protein synthesis inhibition was also evaluated. The IC50 value in HER3 negative cells is about 10 times more than HER3 positive cells in new design of affitoxin. The specificity of affitoxin for binding to HER3 positive cells was also investigated with binding assay with flow cytometry. The results show that, the new affitoxin is an anti-cancer molecule with specific binding to HER3 positive cells and may open a new window for the treatment of HER3-positive cancers. © 2022
Publication Date: 2018
Iranian Journal of Science and Technology, Transaction A: Science (10286276)42(4)pp. 1771-1778
Neutral proteases have a large variety of industrial applications. Therefore, the optimization of their production for the large-scale commercial purpose is critical. The present study was aimed to the optimization of nutritional and physical conditions affecting neutral protease production of Aeromonas hydrophila MSB16, not previously reported for this genus. Four key determinants (pH, temperature, glucose and peptone concentration), were selected based on the results of the one-factor-at-a-time (OFAT) method and then optimized by the response surface methodology (RSM). Maximum enzyme production (229.72 U/ml) which was 2.3 folds higher than that of the OFAT method (99.25 U/ml) and 3.15 times higher than unoptimized conditions (72.86 U/ml) was observed at 30 °C, pH 7, 4.5% w/v glucose and 4.5%w/v peptone by using a rotatable central composite design (RCCD). The results showed that the OFAT and RSM strategies were a useful screening and optimization methods for enhancing the protease production of the strain MSB16, respectively. © 2017, Shiraz University.
Moafi, A.,
Rahgozar, S.,
Ghias, M.,
Ahar, E.V.,
Borumand, A.,
Sabbaghi, A.,
Sameti, A.,
Hashemi, S.M. Publication Date: 2011
International Journal Of Preventive Medicine (20088213)2(4)pp. 280-285
Objectives: Obesity and increased blood pressure are identified as risk factors for cardiac and pulmonary disorders. On the other hand, iron deficiency (another preventable disease) is common in adolescence and considered as associated with health impairment. The present study evaluates body mass index (BMI) and its association with blood pressure and hematological indices in freshman students entering the University of Isfahan in 2009. Methods: All the 1675 students who entered the University of Isfahan in September 2009 were examined. Height, weight, BMI, blood pressure, hemoglobin (Hb) and red blood cell (RBC) indices of these students were measured. The prevalence of high blood pressure, its association with BMI and the relation between BMI and anemia, iron deficiency and educational achievement were assessed. Results: All participants, including 514 males and 1161 females, went under clinical observations. The average age was 20.7 ± 3.8. year Among the students, 18.2% of males and 20% of females were underweight. High systolic blood pressure was more common in the students with BMI > 25 kg/m2 (p < 0.001). Anemia was seen in 8.7% of females. In males, however, a relation between anemia frequency and BMI < 18.5 kg/m2 was more distinct (p = 0.002). There was no association between anemia and students' average test scores. Conclusions: High incidence of abnormal BMI in the study population, and its association with systolic blood pressure indicate the importance of nutritional guidelines and counseling programs for freshman students. On the other hand, high incidence of anemia in this population ascertains the necessity of anemia screening programs before academic studies.
Publication Date: 2017
Cancer Chemotherapy and Pharmacology (14320843)80(1)pp. 109-117
Objectives: ATP-binding cassette subfamily C member 4 (ABCC4) encoding MRP4 protein is involved in pediatric acute lymphoblastic leukemia (ALL) drug resistance. The nonsynonymous single nucleotide polymorphism (SNP) rs2274407 (G912T; K304N) is located in the 3′ splice acceptor site of exon 8 of ABCC4 pre-mRNA. The aim of this study was to investigate the prognostic value of rs2274407 in childhood ALL and its possible functional effect on MRP4. Methods: ABCC4 G912T SNP was genotyped in 145 Iranian Philadelphia-negative (Ph−) children with ALL using modified tetra-primer ARMS PCR and evaluated for possible association with 3-year disease-free survival (3DFS). In addition, functional impact of rs2274407 on the MRP4 activity and possible post-transcriptional modifications were bioinformatically and experimentally studied. Results: ABCC4 912T allele carriers (G/T and T/T genotypes) are associated with worse 3DFS in Pre-B cell ALL [P = 0.00019, OR (95% CI) = 13.17 (2.55–68.11)]. In addition, computational studies showed that K304N alteration has no impact on the MRP4 activity. However, it may disrupt the normal splicing process of ABCC4 pre-mRNA. Conclusions: To date, this is the first study that shows the potential functional impact of rs2274407 SNP on the aberrant splicing of ABCC4 mRNA. We also demonstrated a robust association between G912T and pediatric ALL negative outcome, which may be explained by the novel computational studies performed in this study. © 2017, Springer-Verlag Berlin Heidelberg.
