https://cell.ijbio.ir/ Journal of Cellular and Molecular Research (Iranian Journal of Biology) en daily 1 Sat, 21 Mar 2026 00:00:00 +0330 Sat, 21 Mar 2026 00:00:00 +0330 https://cell.ijbio.ir/article_2521.html With the passage of time, unique old architectures and historical buildings are exposed to physicochemical and biological deteriorations and the dimensions of these damages differ depending on the geographical location, the amount of environmental pollution, the composition of raw materials and its constituent elements. Various agents such as fungi, bacteria, archaea, algae and lichens are involved in biodeterioration. Considering the importance of biological studies in cultural heritage, as well as the construction of Sivand dam and ecosystem changes in the region, deteriogenic bacteria of the stone monument of Cyrus the Great tomb were investigated. It seems that the limestone stones of Cyrus the Great tomb in Pasargadae region of Fars province have provided suitable substrates for the establishment and growth of bacteria. For this purpose, samples were first taken from different parts of the tomb of Cyrus the Great by a non-destructive method using swabs and sterile needles, and were cultured into specific bacterial medium. After purifying the colonies, bacterial isolates were identified at the genus level by morphological, microscopic, biochemical and enzymatic methods. In order to more accurately identify bacterial isolates, molecular methods of 16S rRNA gene sequencing were used. The culture results revealed the presence of different species of bacteria. Most of the identified genera were gram-positive bacteria,. In order to preserve such valuable works, in the next step, we assay ways of removing and controlling these harmful organisms and their effects, in laboratory conditions. Finally, these methods on stone models and in site will be investigated. https://cell.ijbio.ir/article_2401.html Introduction: Breast cancer is the second cause of death from cancer, after lung cancer in women. Most breast cancers originate from the milk ducts. Due to the importance of cancer, the cytotoxic effects of mefenamic acid and phenylalanine on the growth of MCF-7 cells were investigated.Methods: In this experimental study, MCF-7 cells were first cultured. Then different concentrations of mefenamic acid and phenylalanine were treated for 24, 48 and 72 hours. The cytotoxicity of this drug was measured by MTT colorimetric method. DNA electrophoresis of treated cells and Hoechst staining were also used to investigate the occurrence of apoptosis.Findings: MTT test showed that mefenamic acid and phenylalanine amino acid decreased the growth of MCF-7 cells and the greatest effect was in 72 hours after treatment. Also, based on the data of compusyn software, the two compounds of mefenamic acid and phenylalanine in all concentrations in the combined drug synergistically decreased the growth of cells. The results of DNA electrophoresis and Hoechst33342 staining indicated the occurrence of apoptosis in the treated cells.Conclusion: The effects of the combined drug were greater than the effect of each combination alone, so the combined drug can be used as an effective option for the treatment of metastatic ductal carcinoma. https://cell.ijbio.ir/article_2402.html 4-hydroxyphenylpyruvate dioxygenase is an iron-dependent homotetrameric enzyme. In this study, we extracted the gene encoding this enzyme from Paenarthrobacter nitroguajacolicus strain Znu06. The recombinant enzyme was cloned into the pET28a vector. Then expressed in E. coli BL21(DE3) using IPTG inducer and purified using a Ni-NTA Agarose column. SDS-PAGE was employed to evaluate the expression level and the Bradford assay was used to determine the concentration. The activity of the enzyme was assessed at different temperatures and substrate concentrations, followed by performance evaluation using HPLC and examining reaction products. The structure of the enzyme and interactions were studied using bioinformatics tools and servers. The PCR results confirmed a genomic fragment with a length of 1020 bp which encoded an enzyme with 339 amino acid residues with a molecular weight of 34 KD. The sequence was deposited in NCBI with the code MN197545.1. The activity of the enzyme was confirmed through biochemical analysis using spectrophotometry and fluorometry. Sequence alignment using ESPript3 confirmed highly conserved residues, including His 152, His‌ 216, Glu 267, Tyr 257, His 199, and His 248 in the enzyme's active sites. The enzyme seems to promote the reaction towards aryl oxide production due to the absence of hydrogen bond formation in the active site, leading to the lack of homogentisic acid production. https://cell.ijbio.ir/article_2422.html Magnetic iron oxide nanoparticles are promising nanocarriers for novel drug delivery systems due to their low toxicity, biocompatibility, high loading capacity, and controlled drug delivery to cancer cells. This study investigates the effect of magnetic iron oxide nanoparticles coated with polyethylene glycol (PEG) on MCF-7 and T47D (breast adenocarcinoma) cancer cells compared to paclitaxel using the MTT method. In this study, Fe3O4 magnetic nanoparticles were synthesized using the Polyol method, and paclitaxel was loaded onto PEGylated magnetic nanoparticles. FT-IR analysis was used to confirm PEG binding to the nanoparticles and the loading of the drug onto the nanoshell. The average size and crystalline structure of the nanoparticles were characterized using TEM and X-ray diffraction (XRD). Subsequently, the cytotoxic effects were evaluated on MCF-7 and T47D cancer cells using the MTT assay. The FT-IR results indicated the presence of O-H and C-H bands at 3392 cm-1 and 2927 cm-1, correlating with PEG binding to the nanoparticles. The XRD pattern revealed the cubic spinel structure of the magnetite nanoparticles, with a mean size of 12 nm. IC50 values for treatment with PEGylated nanoparticles were 24 and 16 µg for MCF-7 cell lines, and 31 and 21 µg for T47D cell lines at 24 and 48 hours, respectively (p<0.05). This study demonstrates that PEGylation of magnetic nanoparticles can enhance the efficacy of paclitaxel on MCF-7 and T47D cancer cells. Additionally, T47D cells exhibited relatively higher resistance compared to MCF-7 cells. https://cell.ijbio.ir/article_2443.html The incidence of breast cancer among women worldwide is on the rise. In recent decades, advancements in microarray technology have made it possible to collect and analyze extensive relevant data, allowing for a more precise identification of genes involved in the development and progression of cancers. In this study, we extracted and merged three datasets (GSE109169, GSE80754, and GSE72644) containing breast cancer tumor samples and adjacent healthy tissues from the NCBI database. Utilizing appropriate software, we identified key genes with altered expression and evaluated their co-expression. We also determined the gene ontology (GO) for these key genes and examined the associated microRNAs and transcription factors. Our findings revealed that the genes PPARG, LEP, ADIPOQ, LPL, LIPE, FABP4, PLIN1, and CIDEC exhibited significantly decreased expression. Conversely, ten genes—AURKA, DLGAP5, NCAPG, CCNB1, KIF23, KIF11, BUB1B, RRM2, UBE2C, and NUSAP1—showed increased expression. Additionally, two microRNAs, has-miR-6782-5p and has-miR-6836-5p, had the strongest associations with the down-regulated genes, while has-miR-7110-5p and has-miR-7106-5p were most closely linked to the up-regulated genes. Furthermore, PPARG was identified as the most important transcription factor regulating the key down-regulated genes, whereas E2F4, FOXM1, E2F1, and MYC were significant in controlling the up-regulated genes. The results of this study can inform the design of beneficial therapeutic methods to help prevent breast cancer. https://cell.ijbio.ir/article_2461.html Decreased synthesis or increased hydrolysis of acetylcholine in the cholinergic system is one of the causes of Alzheimer's disease. Acetylcholinesterase enzyme inhibition is a therapeutic strategy. A number of natural plant compounds with biological properties such as neuroprotective, antioxidant, antianxiety and antimicrobial effects have been investigated in recent years, which alpha-pinene and quercetin, respectively, from the subgroup of monoterpenoids and flavonols, are among them. Ellman's method was used for determination of inhibition percentage, IC50 value and kinetic type of acetylcholinesterase inhibition. The antioxidant activity of alpha-pinene and quercetin was evaluated s and the results were reported based on the EC50 index. Finally, molecular docking studies were performed to evaluate the above results. Examining the percentage of enzyme inhibition for galantamine, alpha-pinene and quercetin showed IC50 values of 0.001, 0.25 and 15.75 mM respectively. Kinetics of enzyme inhibition by these compounds showed a mixed inhibition pattern (uncompetitive-noncompetitive) for both alpha-pinene and quercetin. Using ascorbate as positive control (EC50= 22.6 µM, antioxidant capacity of alpha-pinene and quercetin were (EC50=1.22 mM) and (EC50=29.5 µM), respectively. Finally, molecular docking studies showed the binding energy for the best state of alpha-pinene and quercetin to be -5.6 and -0.9 kcal/mol, respectively. The results obtained from this study show that both alpha-pinene and quercetin have inhibitory properties of acetylcholinesterase enzyme, but the antioxidant power of quercetin is higher than alpha-pinene. The results of the molecular docking studies were consistent with the experimental results. https://cell.ijbio.ir/article_2474.html Alzheimer’s disease (AD), which is the most common form of dementia, is a complex disorder influenced by genetic and environmental factors. This disease is classified into two main types: early-onset and late-onset. In this study, single nucleotide polymorphisms (SNPs) of the PSEN2 gene were extracted from the dbSNP database in NCBI using bioinformatics methods. The effects of these mutations were evaluated individually using the SIFT, PolyPhen, PANTHER, PROVEAN, and I-MUTANT databases. Among the 646 identified mutations, 161 were predicted to be harmful, and 34 were comprehensively examined as high-risk SNPs. The analysis results indicated that four mutations, A415T, N141Y, Y231C, and A407D, had the most detrimental effects on the structure and stability of the PSEN2 protein. Structural modeling showed that these mutations disrupt protein stability and the function of the γ-secretase complex by altering the size, charge, and hydrophobicity of amino acids, potentially leading to increased accumulation of amyloid beta (Aβ) peptides and the progression of Alzheimer’s disease. The findings of this study suggest that these mutations could serve as potential genetic markers for early diagnosis of the disease and therapeutic targets, highlighting their clinical importance in improving genetic screening and the design of novel drugs. Overall, these results could facilitate future experimental research and the development of personalized medical solutions. https://cell.ijbio.ir/article_2480.html This study provides a detailed examination of the female reproductive organ development in pear (Pyrus communis L.). Samples were collected, fixed in FAA solution, embedded in paraffin, and sectioned using a microtome. Results revealed that pear inflorescence is a corymb, the gynoecium is syncarpous, and the style is solid.The ovules are anatropous, bitegmic, and crassinucellate, with the embryo sac of the Polygonum type. During early development, the archesporial cell differentiates into a megaspore mother cell, and the megaspore tetrad forms in a linear arrangement. Only the chalazal megaspore becomes functional and proceeds through megagametogenesis to form a mature embryo sac consisting of seven cells and eight nuclei. Additionally, the presence of a hypostase at the chalazal pole and a funicular obturator in the ovules was observed, both playing a crucial role in embryo sac nourishment and pollen tube growth. Embryogenesis in pear follows the Asterad type, characterized by an initial T-shaped division of the zygote, followed by the development of a dicotyledonous embryo. By understanding the developmental timing and structure of the ovule and embryo sac, our study provides useful insights for optimizing pollination timing and improving reproductive success, which can ultimately enhance fruit set and guide breeding programs. https://cell.ijbio.ir/article_2491.html The aim of this study is to investigate the role of the HMG protein family in the structure and function of chromatin. HMG proteins are a group of small, non-histone proteins with high mobility that have the ability to bind to DNA. Through this mechanism, they participate in various cellular processes such as gene expression regulation, cell proliferation, and DNA repair. These proteins are classified into three superfamilies: HMGA, HMGN, and HMGB, each of which is divided into different subgroups with unique structures and functions within the cell. The roles of these proteins in cancer occurrence, apoptosis, signaling pathways, blood sugar regulation, and immunity have also been demonstrated. This review study was conducted by collecting and analyzing reputable domestic and international articles. The findings of this study indicate that HMG proteins can enhance chromatin stability and flexibility by altering chromatin dynamics, or conversely, facilitate the binding of transcription factors by loosening the structure. Initially, the structure and function of each group within the HMG protein family are examined separately, followed by their impact on chromatin structure and function. Post-translational modifications in HMG proteins can affect chromatin's binding affinity to other proteins, which is examined in this research. https://cell.ijbio.ir/article_2506.html The production of recombinant proteins is a vital advanced technology in biotechnology that plays a crucial role in life sciences and medicine. Growth factors, such as the basic fibroblast growth factor (bFGF), are of paramount importance in the development of innovative therapies and the enhancement of patients' quality of life due to their key roles in wound healing and cell proliferation. This study aims to produce human recombinant fibroblast growth factor (hbFGF) in the Bacillus subtilis strain, providing an efficient and cost-effective method for producing this vital protein. Bacillus as a host is capable of the secretion of recombinant proteins, enhancing the efficiency and quality of the product while reducing production costs. In this research, the hbFGF gene was initially cloned into the PHT-43 vector, which was then transformed into E. coli Following this, a secondary transformation was performed into Bacillus subtilis. Subsequently, the processes of expression, extraction, and purification of the protein were carried out. Finally, its biological activity was evaluated using assays on the NIH/3T3 cell line. The results demonstrated the successful expression and secretion of hbFGF protein in the Bacillus subtilis strain; however, the quantity of purified protein was not optimal compared to the nickel-column bound protein. Analyses indicated that various proteases in Bacillus subtilis contributed to the cleavage of part of the protein before the His-tag sequence, leading to a decrease in the purity of the final product. To address this issue, it is recommended to utilize engineered strains with greater efficiency that contain protease inhibitors, preventing the cleavage of the produced protein. https://cell.ijbio.ir/article_2507.html Diabetic retinopathy (DR) is one of the leading causes of vision impairment and blindness in middle-aged individuals with diabetes. Hypertension is considered among the most significant risk factors for its development. In diabetic retinopathy, retinal capillaries undergo gradual changes, leading to impaired blood supply in certain areas. Consequently, vascular permeability increases, and in response to ischemia, abnormal new blood vessels proliferate in the retina. The AGT (angiotensinogen) gene is a component of the renin-angiotensin system (RAS), which produces angiotensin II. Elevated levels of angiotensin II in the eye may be associated with inflammation and the pathology of diabetic retinopathy. Diseases linked to the AGT gene include renal tubular dysgenesis, diabetic retinopathy, and hypertension. The aim of this study was to investigate the association between the rs4762 polymorphism of the AGT gene and diabetic retinopathy in an Iranian population. The study was conducted on 150 individuals from Kashan, including 50 healthy controls, 50 diabetic patients without retinopathy, 50 diabetic patients with retinopathy. Blood samples were collected, and DNA was extracted using the salting-out method. The rs4762 polymorphism was analyzed using high-resolution melting (HRM) after appropriate primer design. The findings revealed no significant difference in allele or genotype frequencies of this polymorphism between disease statuses (p > 0.05), and their distribution was nearly uniform across the groups. https://cell.ijbio.ir/article_2508.html Paclitaxel (PTX) is a widely used drug for treating cancers such as breast, ovarian, and lung cancer. However, its therapeutic use is limited due to its high toxicity to healthy tissues and the occurrence of side effects. In this study, with the aim of reducing these side effects, a zeolite-copper oxide/graphene oxide nanocomposite was designed and evaluated as an intelligent carrier for PTX drug delivery. Microscopic and spectroscopic analyses, including Field Emission Scanning Electron Microscopy (FESEM), Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), X-ray Diffraction (XRD), and Fourier Transform Infrared Spectroscopy (FTIR), confirmed the successful synthesis and drug loading. The nanocomposite structure consisted of spherical copper oxide particles (average size 79 nm), graphene oxide sheets, and the high porosity of zeolite. Drug release studies showed that this nanocomposite provides controlled release at physiological (pH=7.4) and faster release under acidic conditions similar to the tumor microenvironment (pH=5.5), which depends on the porous structure and chemical interactions. The drug-free nanocarriers showed low cellular toxicity at high concentrations on the SUM-159 cell line (IC50 > 100 µg/mL), but after PTX loading, a significant decrease in IC50 was observed, indicating increased anticancer effectiveness. Additionally, the three-component nanocomposite had the greatest impact on reducing cell viability by effectively inducing apoptosis. These findings indicate the high potential of the zeolite-copper oxide/graphene oxide nanocomposite for targeted delivery of PTX and minimizing its side effects. https://cell.ijbio.ir/article_2509.html Saccharomyces cerevisiae, a key organism in industrial fermentation, is vulnerable to microbial contaminants causing stuck fermentation. During anaerobic fermentation optimization with baker’s yeast, recurrent fermentation arrest prompted microscopic analysis, revealing a novel coccoid, cocci-like, highly shaking intracellular parasiteparasite within S. cerevisiae and Kluyveromyces marxianus. The parasite exhibited intra- and extracellular localization, with intrinsic autofluorescence) enabling visualization via fluorescence microscopy without staining. Contaminated yeast samples were filtered (0.45 µm) and treated with lyticase to isolate the parasite. While filtration yielded extracellular parasites with diminished motility, lyticase-liberated intracellular forms lost motility rapidly, confirming host dependence. The parasite failed to grow axenically on YPD, NA, or blood agar. Phenotypic characterization identified it as Gram-positive, catalase-negative, and non-hemolytic, with transient susceptibility to streptomycin but no complete eradication. Parasite proliferation correlated with yeast growth phases, peaking during stationary phase and coinciding with fermentation failure. Notably, motility ceased upon yeast removal, implicating metabolic reliance on host-derived factors, while new yeast buds remained parasite-free, suggesting targeted invasion of mature cells. This symbiotic, bacteria-like organism’s autofluorescence provided a unique diagnostic marker, distinguishing it from prior fungal-bacterial associations. Its obligate pseudo-parasitic behavior and disruption of fermentation efficiency underscore its potential role in industrial fermentation challenges. These findings highlight the need for revised contamination control strategies and further research into its biology, transmission mechanisms, and host interactions to mitigate fermentation inefficiencies. The discovery emphasizes the underexplored complexity of microbial contaminants in industrial yeast systems and opens avenues for developing targeted interventions to safeguard fermentation productivity. https://cell.ijbio.ir/article_2522.html In this study, we optimized alpha-amylase production by the thermophilic bacterium Bacillus licheniformis PTCC1721 using a batch fermentation system designed to enhance yield while minimizing production expenses. Precultures were grown in nutrient-rich media formulated from corn and soybean components, and fermentation was conducted in a 2-L fermenter under rigorously monitored operating conditions. To identify the key factors influencing enzyme production, the effects of starch concentration, pH, temperature, interactions between temperature and pH, interactions between temperature and starch, agitation speed and aeration rate were systematically examined using a Taguchi L8 design followed by Analysis Of Variance (ANOVA). Optimization revealed that a temperature of 45°C, pH 8, an agitation speed of 300 rpm, a starch concentration of 20g/L, and an aeration rate of 1vvm over 30 hours resulted in maximal enzyme production. Under these optimal conditions, alpha-amylase activity increased from 60 U/l to 428 U/l, representing a 1/7 fold improvement compared to preoptimization levels, while the specific activity reached 440 U/mg. The combined use of a low-cost corn–soy-based culture medium and optimized process parameters establishes an efficient and economically viable approach for alpha-amylase production. These findings provide a strong foundation for further development and industrial scale-up of the production process. https://cell.ijbio.ir/article_2523.html Accurate simulation of the complexities of diseases such as cancer, neurological disorders, cardiovascular and pulmonary diseases remains highly challenging when using animal models and two-dimensional cell culture systems due to their inherent limitations in reproducing dynamic microenvironments and multicellular interactions. Microfluidic systems, particularly organ-on-a-chip (OoC) technology, provide advanced solutions for disease modeling and tissue engineering. By precisely reconstructing physiological microenvironments, establishing controlled chemical gradients, applying mechanical forces, and generating dynamic three-dimensional architectures, these platforms enable effective simulation of complex cell–cell and cell–extracellular matrix interactions. Key advantages of these systems include reduced sample consumption, increased throughput, lower experimental costs, and enhanced predictive power of preclinical models. In addition, improved experimental reproducibility and the capability for multi-organ integration represent important features of these technologies. These platforms have opened new horizons in studying disease mechanisms, drug screening, and the advancement of personalized medicine. This review focuses on three main areas: disease modeling, tissue engineering, and their applications in cancer, neurological, cardiovascular, pulmonary, hepatic, bone, intestinal, brain, and kidney diseases.