Publication Date: 2017
International Journal of Systematic and Evolutionary Microbiology (14665026)67(9)pp. 3339-3344
A novel halophilic archaeon, designated strain WIIAL99T, was isolated from Lake Meyghan, a hypersaline lake in Iran. Cells of strain WIIAL99T were non-motile, catalase-positive and oxidase-negative. Strain WIIAL99T required at least 2.5 M NaCl and 0.05 M MgCl2 for growth. Optimal growth was achieved at 3.5 M NaCl and 0.1 M MgCl2. The optimum pH and temperature for growth were pH 7.0 and 37–40 °C; it was able to grow at pH 6.0–8.5 and 20–55 °C. Cells lysed in distilled water and the minimal NaCl concentration to prevent cell lysis was 8% (w/v). The major polar lipids of strain WIIAL99T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, disulfated diglycosyl diether and one unidentified glycolipid. The DNA G+C content of strain WIIAL99T was 66.7 mol%. The closest relative was Natronoarchaeum rubrum JCM 17119T with 98.2% similarity in the orthologous 16S rRNA gene sequence. Analysis of 16S rRNA and rpoB′ gene sequences indicated that strain WIIAL99T is a member of the genus Natronoarchaeum in the family Halobacteriaceae and forms a distinct cluster. It was concluded that strain WIIAL99T (=IBRC-M 11062T=LMG 29814T) represents a novel species of the genus Natronoarchaeum, for which the name Natronoarchaeum persicum sp. nov. is proposed. © 2017 IUMS.
Publication Date: 2022
ACS Biomaterials Science and Engineering (23739878)8(11)pp. 4648-4672
Common models used in breast cancer studies, including two-dimensional (2D) cultures and animal models, do not precisely model all aspects of breast tumors. These models do not well simulate the cell-cell and cell-stromal interactions required for normal tumor growth in the body and lake tumor like microenvironment. Three-dimensional (3D) cell culture models are novel approaches to studying breast cancer. They do not have the restrictions of these conventional models and are able to recapitulate the structural architecture, complexity, and specific function of breast tumors and provide similar in vivo responses to therapeutic regimens. These models can be a link between former traditional 2D culture and in vivo models and are necessary for further studies in cancer. This review attempts to summarize the most common 3D in vitro models used in breast cancer studies, including scaffold-free (spheroid and organoid), scaffold-based, and chip-based models, particularly focused on the basic and translational application of these 3D models in drug screening and the tumor microenvironment in breast cancer. © 2022 American Chemical Society. All rights reserved.
Publication Date: 2023
Scientific Reports (20452322)13(1)
MiR-34b-5p has been reported as a non-invasive diagnostic biomarker for infertility. However, no gene targets regulating the mechanism of cation of this miRNA are known. In this study, using gene set enrichment analysis the Inositol 1,4,5-Trisphosphate Receptor Type 1 (ITPR1) gene was identified as the sole target for hsa-miR-34b-5p, and found significantly overexpressed in non-obstructive azoospermia (NOA) patients. This finding was confirmed by qRT-PCR on fresh testicular tissues from NOA patients. Then, pathway enrichment analysis as well as the diagnostic value analysis of hsa-miR-34b-5p/ITPR1 indicated ITPR1 as a hub gene in the calcium (Ca2+)-apoptosis pathway, and a valuable predictive biomarker for NOA. Moreover, gene expression and histological assays showed the association of the effects of ITPR1’s increased expression on spermatogenesis failure through induction of apoptosis in NOA patients. These data suggested that the hsa-miR-34b-5p/ITPR1 axis could serve as a potential regulatory predictive biomarker for human spermatogenesis through the Ca2+-apoptosis pathway cross-talk. © 2023, The Author(s).
Publication Date: 2023
PLoS ONE (19326203)18(8 August)
Autosomal recessive non-syndromic hearing loss (ARNSHL) is a public health concern in the Iranian population, with an incidence of 1 in 166 live births. In the present study, the whole exome sequencing (WES) method was applied to identify the mutation spectrum of NSHL patients negative for GJB2 gene mutations. First, using ARMS PCR followed by Sanger sequencing of the GJB2 gene, 63.15% of mutations in patients with NSHL were identified. Among the identified mutations in GJB2:p.Val43Met and p.Gly21Arg were novel. The remaining patients were subjected to WES, which identified novel mutations including MYO15A:p.Gly39LeufsTer188, ADGRV1:p.Ser5918ValfsTer23, MYO7A: c.5856+2T>c (splicing mutation), FGF3:p.Ser156Cys. The present study emphasized the application of WES as an effective method for molecular diagnosis of NSHL patients negative for GJB2 gene mutations in the Iranian population. © 2023 Broojeni 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: 2017
Genes and Genomics (19769571)39(4)pp. 433-443
Leber’s congenital amaurosis (LCA) is considered as one of the main causes of congenital blindness. In view of the genetically heterogeneous nature of the disease, indirect diagnosis using linkage analysis has proven to be useful in molecular diagnosis procedure. Mutations in AIPL1 gene are one of the leading causes of LCA. In the present study, the application of three single nucleotide polymorphic (SNP) markers related to the gene, including rs7212734, rs11658369 and rs8066853 was evaluated for the first time in the Iranian population. The markers were genotyped using tetra-primer ARMS PCR in 154 unrelated healthy individuals. Haplotype frequency and other characteristics of the markers were examined by using the GENEPOP, PowerMarker and Cubic Exact Solution software. The data indicated the presence of six different haplotypes in the Iranian population. Among them, three haplotypes showed high informativeness with frequencies ≥0.05. Three unrelated Iranian LCA families were analyzed. The p.W278* mutation in exon 6 of AIPL1 was found in all the families using APEX microarray chips. SNP analysis for the families showed the conservation of T−A−A haplotype linked to p.W278* mutation. All families bearing the mutation were from the Isfahan province and a founder effect was suggested in this population. Prenatal diagnosis using the markers led to the successful prediction of the fetus genotypes in all the at risk pregnancies and showed that rs7212734, rs11658369 and rs8066853 can be considered as the three informative markers for linkage analysis in carrier detection and molecular diagnosis of LCA in the Iranian population. © 2017, The Genetics Society of Korea and Springer-Science and Media.
Publication Date: 2015
Gene (18790038)570(2)pp. 180-184
Fragile X syndrome, which is caused by mutation in the FMR1 gene region, is one of the most prevalent forms of mental retardation. Direct diagnosis of the disease is based on PCR and southern blot analysis, but because of technical problems, use of polymorphic DNA markers can be helpful for carrier detection and prenatal diagnosis in families with an affected individual. The polymorphic markers usually show a population-based haplotype frequency and heterozygosity. In the present study, genotyping and analysis of haplotype frequency of three microsatellite markers including DXS998, DXS548 and FRAXAC1 at the FMR1 gene region were carried out in 140 unrelated healthy women and 26 families from the Iranian population. The data indicated the presence of a novel allele for DXS998 in the Iranian population. Estimation of haplotype frequency using Arlequin program showed 50 different DXS998-DXS548-FRAXAC1 haplotypes for the input data of 5, 7 and 4 alleles, respectively. Among these haplotypes five of them showed relatively high frequencies (≥ 0.05). Analysis of linkage disequilibrium (LD) for the unrelated individuals using the PowerMarker computer program, showed that this haplotype combination can be an informative haplotype for linkage analysis in carrier detection and possible molecular diagnosis of fragile X in the Iranian population. © 2015 Elsevier B.V.
Publication Date: 2009
Iranian Journal Of Public Health (22516085)38(4)pp. 136-139
Background: The haplotype phasing is more useful than genotyping markers independently at carrier detection and prenatal diagnosis of diseases. The PAH gene region contains several markers used in detection of PKU disease. In the present study, the efficiency of BglII-EcoRI-VNTR haplotype phasing in Iranian family trios was investigated. Then, this information was compared with those obtained for unrelated individuals. Methods: Blood samples were collected from 20 healthy family trios and 60 unrelated individuals. The genomic DNA was extracted by use of salting-out procedure. The two markers BglII and EcoRI were genotyped by use of PCR-RFLP. The genotype of VNTR marker was identified by use of PCR and electrophoresis. The genotyping data obtained from family trios was used to infer haplotype phase. We also compared this data with results obtained from a widely used method for haplotype frequency inference from unrelated individuals, the PHASE program. Results: The haplotype phase of all members was only ascertained at eight family trios. The comparison of this data with the results obtained by use of PHASE program showed that eight haplotypes [211, 221, 215, 216, 214, 121, 225 and 111] were informative haplotypes in Iranian population. Conclusion: Since diversity of BglII-EcoRI-VNTR haplotypes was high in Iranian population, haplotype phasing at family trios was difficult. The results of this study showed that the genotyping data obtained from family trios could not provide enough information for BglII-EcoRI-VNTR haplotype phasing at Iranian PKU families and the genotyping of other family members was necessary at most cases.
Publication Date: 1996
Journal of Clinical Endocrinology and Metabolism (0021972X)81(12)pp. 4439-4445
Autoantibodies directed against steroid hormone-producing cells (SCA) detectable by immunofluorescence are typically found in a small proportion of patients with premature ovarian failure (POF) as well as in other endocrine autoimmune diseases. The SCA pattern stains cells in the outer zones of the adrenal cortex, ovary, and testis. To identify the molecular target of SCA, an adrenal complementary DNA expression library was screened using SCA- positive serum, and the steroid enzyme 3β-hydroxysteroid dehydrogenase (3βHSD) was identified. Only 1 of 48 (2%) patients with idiopathic POF, not preselected for the presence of other autoimmune diseases, had SCA by immunofluorescence, whereas 10 of 48 (21%) had anti-3βHSD autoantibodies detectable by immunoblot using recombinant human enzyme compared with 6 of 115 (5%) control subjects (P = 0.002). Absorption of SCA-positive serum with recombinant human 3βHSD abolished the immunofluorescence pattern. We also examined the prevalence of anti-3βHSD autoantibodies in other endocrine autoimmune diseases. Two of 112 (2%) diabetic patients, but none of the thyroid or Addisonian patients, had SCA by immunofluorescence. Twenty-six (23%) diabetic subjects (P < 0.001 vs. controls), 3 of 18 thyroid patients (P > 0.05 vs. controls), and none of 4 Addisonian patients had anti-3βHSD autoantibodies. 3βHSD is the first steroid cell autoantigen defined at the molecular level to be associated with idiopathic POF occurring in the absence of other polyglandular diseases. Autoantibodies to 3βHSD in patients with other organ-specific autoimmune diseases indicate that the enzyme behaves as a typical target of polyendocrine autoimmunity. Anti-3βHSD autoantibodies in patients with POF may provide a marker of those subjects whose ovarian failure is autoimmune in origin and, as recent studies suggest, may be salvageable with glucocorticoid treatment.
Publication Date: 2023
Biologia (13369563)78(10)pp. 2717-2721
This correction stands to correct the original article, which due to a processing error was published without its figures. The publisher regrets the error and provided herein are the missing figures. Effect of melatonin and NaCl on fresh weight (A), dry weight (B) and root length (C) of alfalfa root. Values are means (± SD) of fifteen replicates. Different letters indicate significant differences (P < 0.05) based on Duncan’s multiple range test. Melatonin concentrations of 0, 0.1, 10, and 15 µM are used. Data was collected after ten days of treatment with salt and melatonin The performance of alfalfa seedlings with different concentrations of melatonin (0, 0.1, 10 and 15 µM) and salt stress (150 and 200 mM) treatment after ten days Effect of melatonin and NaCl on soluble carbohydrate (A), proline (B) and glycine betaine (C) of alfalfa root. Data are means of five replicates ± SD. Different letters indicate significant differences (P < 0.05) based on Duncan’s multiple range test. Melatonin concentrations of 0, 0.1, 10, and 15 µM are used. Data was collected after ten days of treatment with salt and melatonin Histochemical staining assay of ROS accumulations using DAB (A) and NBT (B) for investigated the effect of 0, 0.1, 10 and 15 µM melatonin and 0, 150 and 200 mM NaCl on H2O2 and O2− content in alfalfa root after ten days of treatment with salt and melatonin. Scale bar = 0.5 mm Effect of melatonin and NaCl on K+ (A), Na+ (B) and K+/Na+ content (C) of alfalfa root. Data are means of five replicates ± SD. Different letters indicate significant differences (P < 0.05) based on Duncan’s multiple range test. Melatonin concentrations of 0, 0.1, 10, and 15 µM are used. Data was collected after ten days of treatment with salt and melatonin Effect of melatonin and NaCl treatment on leaf melatonin content (A), leaf IAA content (B), root melatonin content (C), root IAA content (D), leaf IAA/melatonin ratio (E) and root IAA/melatonin ratio (F) of alfalfa. Data are means of five replications ± SD. Different letters indicate significant differences (P < 0.05) based on Duncan’s multiple range test. Melatonin concentrations of 0, 0.1, 10, and 15 µM are used. Data was collected after ten days of treatment with salt and melatonin Result of biplot principal components 1 and 2 analyses obtained from phytohormones and physiological parameters in alfalfa root subjected to melatonin and salinity (A), and the main objectives (B). © 2023, The Author(s), under exclusive licence to Plant Science and Biodiversity Centre, Slovak Academy of Sciences (SAS), Institute of Zoology, Slovak Academy of Sciences (SAS), Institute of Molecular Biology, Slovak Academy of Sciences (SAS).
Publication Date: 2016
Andrology (20472927)4(3)pp. 492-499
Summary: To evaluate the predictive value of histone demethylase KDM3A to protamine 1 (PRM1) mRNA expression ratio as a reliable marker of sperm retrieval in men with obstructive and non-obstructive azoospermia (NOA). Fifty eight azoospermic men, including 44 with NOA and 14 with obstructive azoospermia (OA). Testis tissue samples were collected from azoospermic men who have been referred for testicular sperm extraction (TESE) and micro-TESE. Relative expression ratio of KDM3A to PRM1 was analyzed after selection of approved reference genes. Histological classification of testis biopsies was performed. Sperm retrieval following TESE and micro-TESE was evaluated. A sperm retrieval prediction sensitivity of 95% was established when the Cq of PRM1 became smaller than the Cq of both KDM3A and GAPDH genes. However, azoospermic men with down-regulated KDM3A and decreased expression of PRM1 mRNA showed very low success for sperm retrieval (<25%), even after micro-TESE surgery. The KDM3A to PRM1 mRNA expression ratio can be used as a reliable marker of successful testicular sperm extraction in men with obstructive and non-obstructive azoospermia with 95% sensitivity. © 2016 American Society of Andrology and European Academy of Andrology.
Dry/solid-state fermentative ethanol production refers to ethanol production by solid-state fermentation (SSF), performed almost in the absence of free water, unlike submerged fermentation (SmF). This article discusses advantages and disadvantages of SSF process for bioethanol production. Furthermore, various factors that influence the SSF ethanol production, including type of microorganism, moisture content, microorganism concentration, particle size, temperature, mixing, and pH as well as their effects on the process were presented and discussed. Moreover, different bioreactor designs which can be used for ethanol production using SSF process are included. © 2020 Elsevier Inc. All rights reserved
Publication Date: 2010
Progress in Neuro-Psychopharmacology and Biological Psychiatry (18784216)34(3)pp. 510-515
Objective: Identification of key molecular changes occurring during epileptogenesis provides better understanding of epilepsy and helps to develop strategies to modify those changes and thus, block the epileptogenic process. Gap junctional communication is thought to be involved in epileptogenesis. This communication can be affected by changes in expression of gap junctional protein subunits called connexins (Cxs). One of the main brain regions involved in epileptogenesis is the hippocampus in which there is a network of gap junctional communication between different cell types. Method: Cx36 and Cx43 expressions at both mRNA and protein level were measured in rat hippocampus during epileptogenesis in the kindling model of epilepsy. Results: Cx36 expression at both mRNA and protein level was upregulated during acquisition of focal seizures but returned to basal level after acquisition of secondarily-generalized seizures. No change in Cx43 gene and protein expression was found during kindling epileptogenesis. Conclusion: These results further point out the significance of Cx36 as a target to modify epileptogenic process and to develop antiepileptogenic treatments. © 2010 Elsevier Inc.
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: 2021
Journal Of Cellular And Molecular Medicine (15821838)25(13)pp. 6148-6160
Combination therapies, using medicinal herbs, are broadly recommended to attenuate the chemotherapy adverse effects. Based on our previous findings considering the anti-leukaemic effects of ginger extract on acute lymphoblastic leukaemia (ALL) cells, the present study was aimed to investigate the anti-cancer role of this pharmaceutical plant on ALL mice models. Moreover, we worked towards identifying the most anti-leukaemic derivative of ginger and the mechanism through which it may exert its cytotoxic impact. In vivo experiments were performed using five groups of six C57BL/6 nude mice, and the anti-leukaemic activity of ginger extract alone or in combination with methotrexate (MTX) was examined. Results showed increased survival rate and reduced damages in mice brain and liver tissues. Subsequently, MTT assay demonstrated synergistic growth inhibitory effect of 6-shogaol (6Sh) and MTX on ALL cell lines and patients primary cells. Eventually, the molecular anti-neoplastic mechanism of 6Sh was evaluated using Bioinformatics. Flow cytometry illustrated 6Sh-mediated apoptosis in Nalm-6 cells confirmed by Western blotting and RT-PCR assays. Further analyses exhibited the generation of reactive oxygen species (ROS) through 6Sh. The current study revealed the in vivo novel anti-leukaemic role of ginger extract, promoted by MTX. Moreover, 6-shogaol was introduced as the major player of ginger cytotoxicity through inducing p53 activity and ROS generation. © 2021 The Authors. Journal of Cellular and Molecular Medicine published by Foundation for Cellular and Molecular Medicine and John Wiley & Sons Ltd.
Publication Date: 2020
Japanese Journal of Clinical Oncology (03682811)50(6)pp. 671-678
Objective: Multidrug resistance and consequent relapse are two major obstacles for treating children with acute lymphoblastic leukemia, the most frequent childhood malignancy. MicroRNAs have potential regulatory roles in response to chemotherapy. The goal of this study was to determine the microRNA that may have effects on the expression level of brain and acute lymphoblastic leukemia (BAALC) and to investigate the in vitro and ex vivo association between their expression levels. Methods: In silico tools were utilized to determine a putative miRNA targeting BALLC. Quantitative real-time polymerase chain reaction was used to investigate expression levels of BAALC and its predicted microRNA, miR-326, in bone marrow samples of 30 children with acute lymphoblastic leukemia and 13 controls, in addition to the resistant and parental CCRF-CEM cell lines. To assess the status of response to therapy, minimal residual disease was measured using single-strand conformation polymorphism. Results: MiR-326 was selected due to the strong possibility of its interaction with BAALC according to the obtained in silico results. Statistical analysis showed a significant downregulation of miR-326 and overexpression of BALLC in drug-resistant acute lymphoblastic leukemia cell line and patients compared with the parental cell line and drug-sensitive patients, respectively (P = 0.015, 0.005, 0.0484 and 0.0005, respectively). The expression profiles of miR-326 and BAALC were inversely correlated (P = 0.028). Conclusions: The results introduced the inversely combined expression levels of miR-326 and BAALC as a novel, independent prognostic biomarker for pediatric acute lymphoblastic leukemia (P = 0.007). Moreover, bioinformatics data showed a possible regulatory role for miR-326 on BAALC mRNA, which may possibly contribute to the development of drug resistance in patients with childhood acute lymphoblastic leukemia. © 2020 The Author(s).
Publication Date: 2019
Methods in Molecular Biology (19406029)1967pp. 285-293
Angiotensinogen mediates an important role in the pathophysiology of preeclampsia, a disorder of pregnancy characterized by hypertension and proteinuria usually after 20 weeks of gestation. Angiotensinogen is found in two distinct posttranslational forms in the plasma, an oxidized and a reduced (free thiol) form. Higher levels of the oxidized form are associated with an increased risk of preeclampsia. We have developed novel ELISA assays to quantitate the levels of total and free thiol angiotensinogen allowing for calculation of the amount of oxidized angiotensinogen species. We describe the methodology for performing these assays. © Springer Science+Business Media, LLC, part of Springer Nature 2019.
Publication Date: 2016
Tumor Biology (14230380)37(6)pp. 7861-7872
Acute lymphoblastic leukemia (ALL) is the major neoplasia type among children. Despite the tremendous success of current treatment strategies, drug resistance still remains a major cause of chemotherapy failure and relapse in pediatric patients. Overwhelming evidence illustrates that microRNAs (miRNAs) act as post-transcriptional regulators of drug-resistance-related genes. The current study was aimed at how dysregulated miRNA-mRNA-signaling pathway interaction networks mediate resistance to four commonly used chemotherapy agents in pediatric ALL, including asparaginase, daunorubicin, prednisolone, and vincristine. Using public expression microarray datasets, a holistic in silico approach was utilized to investigate candidate drug resistance miRNA-mRNA-signaling pathway interaction networks in pediatric ALL. Our systems biology approach nominated significant drug resistance and cross-resistance miRNAs, mRNAs, and cell signaling pathways based on anti-correlative relationship between miRNA and mRNA expression pattern. To sum up, our systemic analysis disclosed either a new potential role of miRNAs, or a possible mechanism of cellular drug resistance, in chemotherapy resistance of pediatric ALL. The current study may shed light on predicting drug response and overcoming drug resistance in childhood ALL for subsequent generations of chemotherapies. © 2015, International Society of Oncology and BioMarkers (ISOBM).
Publication Date: 2013
Journal of Spinal Cord Medicine (20457723)36(1)pp. 66-71
Background: Study of molecular responses to central nervous system injury would be helpful for controlling the harmful pathways post-injury and triggering the useful pathways required for the treatment of injury. Objective: To investigate the expression level of liver X receptor α (LXRα) which has anti-inflammatory effects and pro-apoptotic Bcl-2-associated X protein (Bax) upon spinal cord injury (SCI). Design: To induce SCI, transection was carried out at T9 level of male Wister rats. Approximately 8 mm of rostral, caudal, and epicenter tissues of injured sites in treated rats were chosen for quantitative real-time polymerase chain reaction at the 6, 24, and 72 hours, and 7 and 10 days post-surgery. Results: Our results showed a complicated temporal and spatial pattern of alteration in LXRα and Bax mRNA expression levels after SCI. LXRα expression level followed a homologues pattern (additive and subtractive wave) with a difference in time at three areas of studied. Rostral, caudal, and epicenter expression patterns of Bax were dissimilar in these areas. Gradual increase in the expression of Bax without any decrease at the rostral area was observed, presumably indicating the active transcription process of this gene, regardless of its protein situation. Conclusion: A time lapse significant change in Bax expression level was observed only in the epicenter of injury, emphasizing that apoptotic responses are limited to this area. Furthermore, an increase in LXRα transcription level was observed first in rostral area and then extended to epicentral and caudal areas, implying that inflammation responses extended from rostral to caudal areas. © The Academy of Spinal Cord Injury Professionals, Inc. 2013.
Publication Date: 2019
International Journal Of Aquatic Biology (23225270)7(3)pp. 166-174
The gastrointestinal tract of fishes is a complex ecosystem occupied by a large number of microorganisms, some of them could have potentially-valuable features. This research was conducted to study Bacillus species in the intestine of farmed rainbow trout to examine their probiotic properties, and to provide a new source of probiotics. A total of 23 farmed rainbow trout were sampled and their intestine samples were cultured. Following the morphological assay and biochemical analysis, isolated Bacilli were amplified by polymerase chain reaction and universal primers 27f and 1492r. Bacillus subtilis and B. amyloliquefaciens were isolated from 5 and 3 samples, respectively. Bacillus tequilensis, B. cereus and B. licheniformis were isolated from 1 sample. Probiotic properties of B. subtilis strain MSM 24, B. amyloliquefaciens strain TMM 25 and B. licheniformis strain MR 78 were confirmed. Since probiotic bacteria cause no foodborne diseases, their existence in farmed trout intestines, and their penetration into the fish tissues do not pose any risk to consumers’ health. © 2019 Iranian Society of Ichthyology.
Publication Date: 2025
Biocatalysis and Biotransformation (10292446)43(1)pp. 61-70
Renilla luciferase, a luminescent enzyme, is utilized in gene expression analysis and biosensor technology, and extensive research has been conducted on its structure and function. Glycine is an osmolyte that plays a key role in protein stabilization against denaturation. However, its impact on enzyme properties is unpredictable. This study aimed to investigate the effect of glycine on the kinetics and stability of Renilla luciferase. The data revealed that glycine at a concentration range of 0.1 to 0.6 M improved enzyme kinetics and thermal stability. The highest catalytic efficiency was observed at a concentration of 0.5 M. Molecular dynamics simulations demonstrated that in the presence of 0.5 M glycine, substrate access to the enzyme’s active site was enhanced while the root-mean-square fluctuation (RMSF) of the protein backbone was reduced. Additionally, the analysis of protein-water hydrogen bonding interactions showed an increase in the hydrogen bonding between water molecules and Renilla luciferase. The present study may be used for the formulation of Renilla luciferase for commercial purposes. © 2024 University of Isfahan. Published by Informa UK Limited, trading as Taylor & Francis Group.
Publication Date: 2017
Molecular BioSystems (1742206X)13(3)pp. 470-475
The human immunodeficiency virus (HIV) destroys CD4+ lymphocytes and monitoring these cells is one of the best techniques for studying HIV infection. In the present study a novel bioluminescent probe, super RLuc8-sFv, is developed in order to detect human CD4+ cells by fusion of an anti-human CD4 sFv to the C-terminus of super RLuc8. The results indicate that the probe can bind to CD4+ cells via its sFv domain; also it emits visible light through its signalling domain. Super RLuc8-sFv provides a new gateway for detection of human CD4+ cells using luminometric-based assays and may reduce the difficulties involved in, and the cost of, HIV-related diagnostic tests. © The Royal Society of Chemistry.
Publication Date: 2025
Iranian Journal Of Medical Sciences (17353688)50(2)pp. 98-111
Background: Next-Generation Sequencing (NGS) methods specifically Whole-Exome Sequencing (WES) have demonstrated promising findings with a high accuracy of 91%-99% in Pharmacogenomics (PGx). A PGx-based panel can be utilized to minimize adverse drug reactions (ADRs) and maximize the treatment efficacy. Remarkably, Cancer Pain Management (CPM) is a cutting-edge concept in modern medicine. Thus, this study aimed to investigate the WES results by a PGx-based panel containing genes involved in Pain, Anti-inflammatory, and Immunomodulating agents (PAIma) signaling pathways. Methods: A total of 200 unrelated Iranians (100 western and 100 northern) were included. 100 WES results were analyzed through the PAIma panel. After DNA extraction, 100 samples were genotyped by Multiplex-Amplification-Refractory Mutation System (ARMS) PCR. A primary in silico investigation performed on 128 candidate genes through Protein-Protein Interactions (PPIs) and Gene-miRNA Interactions (GMIs) via the STRING database, and miRTargetLink2, respectively. Additionally, Enrichment Analysis (EA) was applied to find the unknown interplays among these three major pathways by Enrichr. Results: 55,590 annotations through 21 curated pathways were filtered, 900 variants were found, and 128 genes were refined. Finally, 54 candidate variants (48 non-synonymous single nucleotide variants (nsSNVs), 2 stop-gained, 1 frameshift, and 3 splicing) remained. Conclusion: Conclusively, six potentially actionable variants including rs1695 (GSTP1), rs628031 (SLC22A1), rs17863778 (UGT1A7), rs16947 (CYP2D6), rs2257401 (CYP3A7), and rs2515641 (CYP2E1) had the most deviations among Iranians, compared with the reference genome, which should be genotyped for drug prescribing. Remarkably, PPIs, GMIs, and EA revealed potential risks of carcinogenesis and cancer phenotypes resulting from PAIma pathways genes. © Iranian Journal of Medical Sciences.
Publication Date: 2018
Molecular Biology Reports (03014851)45(4)pp. 413-417
Infertility occurs in 10–15% of couples worldwide and close to half of it is caused by male factors. One of the genes that can affect male infertility is CGA. Polymorphisms in CGA gene may affect gene expression, therefore affecting male infertility by disrupting the regulation of this gene. One of the polymorphisms is the substitution of T with A in the miR-1302 binding site in the 3′ untranslated region of the CGA gene. In this study, we explored this polymorphism in Isfahan population. In this case-control study, by the use of Tetra primer-ARMS–PCR technique, rs6631 has been investigated in 224 infertile men and 196 controls. Infertile men were recruited from Isfahan Fertility and Infertility Center. Analysis of genotype and allele frequencies indicated that the differences between case and control populations were significant for rs6631 because P = 0.00 which is above the threshold. We found a significant relationship between this polymorphism and male infertility. This study which performed for the first time in Iran suggests that polymorphism in CGA gene can affect male infertility. Also, this polymorphism has high heterozygosity, so it can be used for further studies in different populations. © 2018, Springer Science+Business Media B.V., part of Springer Nature.
Publication Date: 2015
Tumor Biology (14230380)36(6)pp. 4757-4762
HO-1 gene encodes heme oxygenase-1 enzyme that catalyzes the oxidation of heme to carbon monoxide (CO). It has also been suggested that cells could be protected by the enzyme against stress. A (GT)n dinucleotide repeat at HO-1 promoter is a polymorphic region and modulates gene transcription and associated with some of diseases. In this study, length of polymorphism GT tandem repeat has been determined and classified into two alleles short (≤28) and long (≥29). In present study, association between GT-repeat polymorphism at heme oxygenase-1 gene promoter and increased risk of gastric cancer and metastasis was investigated. Blood samples from 100 control individuals and 60 gastric cancer cases had taken. Genotypic frequencies of (GT)n repeat for samples were determined using PCR technique and polyacrylamide PAGE electrophoresis. At final, higher frequency alleles were sequenced. Our results show that S-allele is significantly higher in cases in comparison with control groups (p = 0/000, odds ratio (OR) = 4/154). It has been shown that individuals with S/S and S/L genotypes are at high risk of having gastric cancer (p = 0/000, OR = 3/789). Statistic data show association between SS genotype and risk of gastric cancer metastasis (p = 0.017, OR = 3.889). But, there is no significant association between clinicopathological characteristics of the patients and risk of gastric cancer metastasis (p > 0.05). Significant association was found between short allele (SS + SL genotypes) and risk of gastric cancer, and also strong association was found between SS genotype and risk of gastric cancer metastasis. © 2015, International Society of Oncology and BioMarkers (ISOBM).
Publication Date: 2013
Gastroenterology And Hepatology From Bed To Bench (20084234)6(1)pp. 18-24
Aim: In our study, we analyzed the allelic frequency of XPD Lys751Gln polymorphism of the XPD gene and the correlation between its variant alleles with colorectal cancer in patients and control groups. Background: Human cells are routinely exposed to mutagenic and carcinogenic aromatic amines via smoking, pollution areas and other sources. These chemicals can form DNA adducts in vivo and thus lead to DNA damage. Amongst the known genetic polymorphisms of the DNA-repair genes the xeroderma pigmentosum group D (XPD, also known as ERCC2) has been the most extensively studied most commonly. Patients and methods: This study has examined the relationship between the XPD Lys 751 Gln polymorphism and colorectal cancer in 88 patients and their 88 age and sex-matched controls. Genomic DNA from peripheral whole blood was extracted using Miller method to determine the genotype of subjects with RFLP-PCR analysis. Results: This study shows cancer patients have more of the heterozygous genotype (XPD Lys 751 Gln) compared to control group. However the results are not statistically significant. Furthermore, colorectal cancer was less common in individuals with recessive homozygous genotype (P< 0.0001). Conclusion: This study suggests that individuals with heterozygous polymorphism (Lys/Gln) may have an increased susceptibility to colorectal cancer compared to other polymorphisms (Lys/Lys and Gln/Gln). © 2013 RIGLD.
Publication Date: 2007
Journal of Biological Sciences (discontinued) (18125719)7(7)pp. 1092-1101
Homologous recombination repair starts with Double-strand Breaks (DSBs) followed by crossing-over and recombination. The expected frequency of meiotic chromosomal exchange in the region of chromosome XII encoding ribosomal DNA in Saccharomyces cerevisiae is 3.5 to 5 events per cell per meiosis. However interchromosomal meiotic recombination in the rDNA gene is very rare, suggesting repression of DSB and crossing-over. On the other band, mitotic events such as intrachromosomal recombination producing 3 μm rDNA circles (which accumulate with cellular age) and unequal sister chromatid exchanges appear to be quite common. This study looked at the rDNA breakage in the strain ORD 1181, a rad50S mutant with SK1 background, which does a relatively fast and near synchronous meiosis. The fine analysis of the rDNA array was performed using restriction endonuclease enzymes that do not cleave within the rDNA array. The results suggest that there are at least two hot regions for chromosome breakage within the rDNA array. According to our previous studies we suggest that the DSB hot regions are in one homologue. However, there is possibility that other homologue is involving in DSB too. © 2007 Asian Network for Scientific Information.
