Ferdowsi University of Mashhad

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JCMR METRICS

For more info about other statistics click on: JCMR

  Publication Start Year 2009
  MSRT Grade (1400/ 2021)  A
  Number of Volumes 17
  Number of Issues 34
  Number of Articles 244
  Number of Submissions 449
  Number of Contributors 702
  Article View 1,346,943
  Acceptance Rate 55
  Time to Accept (Days) 56

 

 

 

WELCOME MESSAGE ...

Dear Colleagues,

As the editor in chief and on behalf of our editorial board, it is a real pleasure to invite you to submit your research manuscripts across all areas of biology to the “Journal of Cell and Molecular Research (JCMR)”. JCMR is a biannual open-access online scientific journal published in 2009 for the first time.

For any information on how to prepare your manuscript for submission, please check the guidelines on jcmr.um.ac.ir. If you have any further questions, feel free to contact us through jcmr@um.ac.ir or our journal’s managing editor, Ms. Kazemi (Tel: +98 915 699 6326, E-mail: jcmr@um.ac.ir).

Ahmadreza Bahrami

Editor-in-Chief

Teucrium persicum Methanolic Extract Alters Cellular Homeostasis and Regulates the Expression of MMP-2, MMP-9, TP53, and β-catenin Genes in PC-3 Cells

Pages 72-80

https://doi.org/10.22067/jcmr.2025.95810.1121

Atiye Baghernezhad, Majid Tafrihi, Abasalt Hosseinzadeh Colagar

Abstract Reactive oxygen species (ROS) are highly reactive molecules that play a key role in cellular physiology.in Teucrium persicum, an Iranian endemic plant native to the southern regions of Iran, particularly the Fars province. It has long been used in traditional medicine for the treatment of headaches, abdominal pain, diabetes, inflammation, and hyperlipidemia. Our previous findings demonstrated that treatment of PC-3 prostate cancer cells with T. persicum extract induces significant cytotoxicity and programmed cell death. In the present study, we aimed to further explore the effects of the methanolic extract of T. persicum on lactate dehydrogenase (LDH) activity, intracellular ROS species levels, mitochondrial membrane potential, and the expression of Matrix metalloproteinase-2 (MMP-2), Matrix metalloproteinase-9 (MMP-9), Tumor protein 53 (TP53), and β-catenin (CTNNB1) genes in PC-3 cells. For this purpose, PC-3 cells were treated with both sublethal concentrations and concentrations above the IC₅₀ value of the extract. The results revealed that T. persicum treatment caused marked mitochondrial membrane damage and increased LDH release. These effects were associated with decreased intracellular ROS levels and loss of mitochondrial membrane potential, which correlated with reduced cellular uptake of rhodamine 123 in a dose-dependent manner. Furthermore, gene expression analyses showed that exposure of PC-3 cells to the extract at the IC₅₀ concentration led to significant downregulation of MMP-2, MMP-9, and CTNNB1 genes, accompanied by upregulation of TP53. Collectively, these findings suggest that the methanolic extract of T. persicum can inhibit the proliferation and survival of PC-3 prostate cancer cells through multiple molecular pathways. Further comprehensive studies are warranted to elucidate the precise mechanisms underlying these anticancer effects.

Genotyping of Two Major Genes in Livestock by High Resolution Melt

Pages 81-89

https://doi.org/10.22067/jcmr.2025.90137.1124

Tahereh Hosseinzadeh, Fatemeh Bahri Binabaj, Ali Javadmanesh

Abstract Identification of genes affecting production is one of the important priorities in animal breeding strategies. The introgression of genes with a larger effect on quantitative traits into livestock can improve protein and economic resources. The present study aimed to evaluate high-resolution melting (HRM) analysis for genotyping bone morphogenetic protein receptor type 1B (Fecundity Booroola gene or FecB) in sheep and myostatin (MSTN) in cattle. This study was conducted on blood samples from 19 cattle and 170 sheep including: 19 control samples with approved FecB genotypes and 151 samples with unknown genotypes. After DNA extraction from blood and semen samples, a 176-bp fragment of the MSTN gene in cattle and a 140-bp fragment of the FecB gene in sheep were amplified. HRM was optimized and conducted in all samples then, the PCR-RFLP and sequencing methods were done to prove the HRM genotyping results. The results obtained using the HRM method matched those from sequencing and PCR-RFLP, confirming the effectiveness of HRM for genotyping and enabling rapid and accurate identification of individuals with FecB and MSTN mutations. Melting temperature range for MSTN genotypes was between 80.90 and 81.60 ºC and for FecB genotypes was between 79.6 and 80.50 ºC. Utilizing the HRM method for genotyping will provide researchers and commercial animal producers’ access to a low cost, and easier method to genotype for any SNP detection. In this study, we successfully established a genotyping method for two loci in cattle and sheep economically important genes by high-resolution melting method. This method could be used in a large sample size with a high level of confidence.
 

A Modified Protocol for Isolation and Mitogenic Stimulation of Rat Peripheral Blood Mononuclear Cells

Pages 90-96

https://doi.org/10.22067/jcmr.2025.96193.1123

Saeedeh Pourhamedi, Maryam M. Matin, Azadeh Haghighitalab, Ahmad Reza Bahrami

Abstract Peripheral blood mononuclear cells (PBMCs) are key components of the immune system and serve as a practical in vitro model in many research programs. Despite the widespread applications, popular standard methods for isolating and stimulating PBMCs in rats (rPBMCs) have remained limited. In this study, rPBMCs were isolated from rat peripheral blood using a modified Ficoll density gradient protocol, followed by a short-term adherence step to remove monocytes. A complete blood count (CBC) analysis and Giemsa staining confirmed that the isolated population consisted of approximately 98% lymphocytes, indicating high purity of the isolated cells. The cells were subsequently exposed to different concentrations of mitogens, concanavalin A (ConA; 1.25–10 µg/mL) and phytohemagglutinin (PHA; 1–2%) for 3 and 5 days. Cell proliferation and viability were assessed by MTT assay, and TNF-α secretion was quantified by ELISA. ConA treatment resulted in a concentration-dependent increase in rPBMCs proliferation, with the highest viability rate observed at 1.25–5 µg/mL on day 3. At a concentration of 5 μg/mL, ConA significantly enhanced rPBMCs viability. This elevated level remained constant between days 3 and 5, indicating a sustained cellular response. By comparison, the stimulatory effect of PHA proved either weaker or delayed, as it reached its peak only on day 5. Furthermore, TNF-α analysis revealed that ConA markedly enhanced cytokine secretion, whereas PHA triggered only a modest increase. These findings demonstrate that ConA is a more potent mitogen than PHA in rat PBMCs, promoting both proliferation and cytokine release in a dose-dependent manner. The optimized protocols for isolation and stimulation of rPBMCs presented here, providing a reliable framework for future in vitro studies on immune function and immunomodulation in rat models.

Histological Study of Human Mesenchymal Stem Cells Behavior Cultured on Decellularized Human Gingival Matrix in the Presence of Hyaluronic Acid

Pages 97-108

https://doi.org/10.22067/jcmr.2025.92644.1108

Maryam Alavi, Homa Mollaei, Nasser Mahdavi-Shahri, Masoud Fereidoni, Roya Lari, Maryam M. Matin

Abstract Collagen bioscaffolds show promising results in oral mucosa engineering due to the high biocompatibility and biodegradability of collagen. Because of the high collagen content of gingiva, it can be used to prepare a natural collagen scaffold. Hyaluronic acid (HA) is one of the major components of extracellular matrix that regulates cellular behavior. In the present study, the effects of HA on the behavior of adipose-derived mesenchymal stem cells (Ad-MSCs) cultured on a decellularized gingival matrix were investigated by histological methods. Human gingival tissue (5×5×5 mm) was decellularized using physical methods as well as treatment with sodium dodecyl sulfate and Triton X-100, followed by washing and sterilization procedures. Scaffolds were divided into two groups including soaked scaffolds in HA (0.3% solution) and scaffolds without HA, which served as controls. In the next step, 3×105 Ad-MSCs were seeded on each scaffold in both groups, and histological studies were performed after 1, 2, 3 and 4 weeks of culture. Histological studies revealed effective cell removal and also preservation of collagen fibers in the decellularized gingival connective tissue. In vitro analysis of cellular behaviors showed adhesion and also migration of human Ad-MSCs towards connective tissue matrix, as well as formation of epithelial-like structures. Overall, statistical analyses indicated significant differences in cell density (P<0.01), migration (P<0.001) and nuclear size (P<0.01) at week one in HA-treated scaffolds versus the control group. The results of the present study demonstrated that the extracellular matrix of decellularized human gingival stroma can induce cellular behaviors such as adhesion, proliferation and migration of human Ad-MSCs.

Investigating the Relationship between the rs1800872 Polymorphism of the Interleukin 10 Gene Promoter Region and Breast Cancer in Kerman Province

Articles in Press, Accepted Manuscript, Available Online from 08 November 2025

https://doi.org/10.22067/jcmr.2025.92932.1112

Roya Rostaminiya, Masoumeh Hajirezaei

Abstract Interleukin 10 (IL-10) is a crucial anti-inflammatory cytokine that plays a significant role in immune regulation and is overexpressed in various cancers, including breast cancer. IL-10 is known to modulate immune responses by suppressing the production of inflammatory cytokines, thereby influencing tumor progression and immune evasion. The expression of IL-10 is primarily regulated by single-nucleotide polymorphisms in its promoter region, which can influence its transcriptional activity and, consequently, cancer susceptibility. One such polymorphism, rs1800872, has been extensively investigated for its potential association with breast cancer risk and disease progression in different populations. The objective of this study was to explore the relationship between the rs1800872 polymorphism of the IL-10 gene and breast cancer in women from Kerman province, Iran. In this case-control study, the sample size was calculated using the two-proportion formula and G*Power software, with 80% power and a 5% significance level. Due to limited sample availability, 120 healthy controls and 170 breast cancer patients were included, which was considered sufficient for statistical analysis. Genomic DNA was extracted from these samples, and genotyping for the rs1800872 polymorphism was performed using the Allele-Specific Polymerase Chain Reaction (AS-PCR) method. Statistical analysis using SPSS version 26 and the Chi-square test showed a significant difference in genotype and allele distribution between breast cancer patients and healthy controls (P = 0.001). The AA genotype was more frequent in patients (24.1% vs. 12.5%), with an odds ratio (OR) of 2.66 (95% CI: 1.35–5.22). The A allele was also more common in patients (40.3% vs. 26.25%) with an OR of 1.90 (95% CI: 1.33–2.72), indicating a strong association of the A allele with increased breast cancer risk in the studied population.

Comparison of effector expression profiles in wheat plants infected with three Puccinia graminis f. sp. tritici races: PTRTF, TKTTF and Ug99

Articles in Press, Accepted Manuscript, Available Online from 25 September 2025

https://doi.org/10.22067/jcmr.2025.94520.1117

Sakine Sokhtanlo, Nasrin Moshtaghi, Abdolreza Bagheri

Abstract Wheat stem rust, a devastating fungal disease, threatens global food security through new highly virulent races like Ug99 and TKTTF that overcome plant resistance. Understanding the molecular mechanisms of infection and immune evasion is essential for developing sustainable control strategies. This study elucidates the wheat-Pgt stem rust interaction by identifying pathogen effectors and analyzing genomic variations among three virulent isolates (TKTTF, Ug99, PTRTF). At 96 hours post-inoculation, total RNA was extracted in triplicate from infected leaves of susceptible wheat (cv. Morocco) inoculated with three distinct P. graminis isolates for RNA-seq analysis. Integrated RNA-seq transcriptomics and bioinformatic analyses were employed to characterize effector gene expression profiles and functional attributes. Differential expression analysis revealed a significant upregulation of virulence-associated and metabolic genes in the TKTTF and Ug99 isolates compared to the PTRTF reference isolate. Using Effector P (v5.0) prediction software, we identified 196 high-confidence effector candidates (prediction score >0.5), including both core effectors conserved across isolates and strain-specific variants. Comparative analysis revealed distinct effector repertoires: the Ug99 isolate showed significant enrichment for secreted proteins containing N-terminal signal peptides (SPs), whereas TKTTF predominantly encoded membrane-anchored effectors. Domain analysis identified conserved virulence-associated motifs, including RNA Recognition Motif (RRM) and CDC_Septin domains, implicating their functional importance in pathogen adaptation and host manipulation. Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) showed significant representation (FDR <0.05) across three fundamental categories as biological processes, cellular components and molecular functions, reflecting isolate-specific pathogenic strategies. This study establishes that genomic variation among Puccinia graminis f. sp. tritici (Pgt) isolates drives the evolution of divergent effector profiles and virulence strategies. These findings provide a molecular framework for developing next-generation control measures, including precision engineering of disease resistance in wheat, by identifying effector proteins as critical targets for breeding programs.

Bovine tendon–derived acellular matrix retains native extracellular architecture and supports osteogenic and adipogenic differentiation of human mesenchymal stem cells

Articles in Press, Accepted Manuscript, Available Online from 13 April 2026

https://doi.org/10.22067/jcmr.2026.92836.1111

Mahboubeh Elahifar, Minoo Hosseinimehr, Halimeh Hassanzadeh, Nasser Mahdavi-Shahri, Maryam M. Matin

Abstract The recent advances in stem cell biology and tissue engineering are becoming progressively oriented towards designing natural cellular microenvironments as scaffolds to improve cell growth, differentiation and functional assembly. Scaffolds are one of the most important components of tissue engineering. Decellularized tissues and organs, either alone or combined with other compositions have been successfully used as scaffolds in regenerative medicine. The purpose of this study was fabricating a biological scaffold by decellularization of the bovine tendon as a biomatrix. Biomatrix is one of the scaffolds made of natural extracellular matrix (ECM) components that are derived from decellularized tissues. The effects of biomatrix on the growth and differentiation of human adipose derived mesenchymal stem cells (hAd-MSCs) were then evaluated in vitro. The bovine tendon was decellularized by physical, enzymatic, and chemical treatments. Histological staining demonstrated that these treatments successfully removed the cells and cell debris from tendon while the conservation of collagen, proteoglycans, glycosaminoglycans, and glycoproteins indicated good preservation of the ECM. Furthermore, cell survival, growth and differentiation were assessed on the tendon biomatrix. The results indicated that the biomatrix could support the survival and division of hAd-MSCs. Comparison of culture on biomatrix and plastic surfaces indicated the significant inductive effects of biomatrix on proliferation, osteogenic and adipogenic differentiation potential of the cells. In conclusion, this tendon biomatrix may have useful applications in tissue engineering and regenerative medicine, although further in vivo studies are required to prove this.
Keywords: adipose derived mesenchymal stem cells, biomatrix, scaffolds, tendon, osteogenic differentiation, adipogenic differentiation

A simple method for effective polyethylene glycol-based exosome isolation

Articles in Press, Accepted Manuscript, Available Online from 28 April 2026

https://doi.org/10.22067/jcmr.2026.98095.1132

Razieh Ghazi birjandi, Hesam Dehghani

Abstract Exosomes are extracellular nanovesicles secreted by almost all cells and are present in all body fluids. These natural carriers, which transport biological molecules, consist of proteins, nucleic acids, and lipids. Exosomes' composition reflects the nature and physiological state of their producer cells and plays a widespread role from intercellular communication in normal physiological conditions to contributing to disease progression. There has been increased interest in exosomes as a novel class of biomarkers for diagnosing various diseases or as delivery vehicles. Therefore, the development of an effective exosome isolation method is essential. Some isolation techniques, such as differential ultracentrifugation, ultrafiltration, and size-exclusion chromatography, face challenges in exosome isolation, such as disruption of exosome membrane integrity and loss of exosome functionality, high operational cost, or time-consuming procedure. In this study, we present a polyethylene glycol (PEG)-based method that offers a simple, cost-effective, and efficient way to isolate exosomes from cell culture supernatants. This method aims to overcome limitations associated with conventional isolation techniques, such as high cost and technical complexity. Here, we aimed to optimize a PEG-based method to improve exosome recovery while preserving vesicle integrity. To achieve this, CD9-stably expressing cells were constructed to enhance exosome production. By evaluating the size and morphology of the isolated exosomes using dynamic light scattering (DLS) and transmission electron microscopy, we demonstrated that washing PEG-enriched exosomes with phosphate-buffered saline followed by centrifugation effectively removed excess PEG, yielding exosomes with a Z-average diameter of 170 nm and a polydispersity index of 0.2, indicating natural and uniform particle size.

Ciprofloxacin Modulates Hub Genes and MicroRNAs in Non-small Cell Lung Cancer A549 Cells

Articles in Press, Accepted Manuscript, Available Online from 05 May 2026

https://doi.org/10.22067/jcmr.2026.96265.1125

Naemeh Jafarpour, Amirhossein Ahmadi, Seyed Javad Hosseini, Ahmad Ghasemi

Abstract Ciprofloxacin antibiotics show anti-cancer effects against various cancer cells, partly by inhibiting topoisomerase II. However, ciprofloxacin can also potentiate the RNAi pathway and increase miRNA processing, which leads to the modulation of biological systems, including hub genes. Until now, the effects of ciprofloxacin at the RNAi-enhancing concentration (40 μg/mL) on non-small cell lung cancer (NSCLC) and its hub genes have not been investigated. This study aims to explore this effect. A549 cells, used as a model for NSCLC, were treated with 40 μg/mL ciprofloxacin, and the cytotoxicity, colony formation, migration, cell cycle, and apoptosis were evaluated. Hub genes of NSCLC and their miRNAs were identified using Gene Expression Omnibus database and bioinformatics analysis. The expression of two high-score hub genes and the miRNAs that target these hub genes was measured by qPCR. This study showed that ciprofloxacin resulted in a statistically significant reduction in cell viability of approximately 47% after 96 hours, a decrease in survival fraction by about 60%, and inhibition of cell migration by about 63% at 24 h. Additionally, ciprofloxacin induced G2/M phase cell cycle arrest and early apoptosis by approximately 10% and 30%, respectively, after 96 h. The expression of CCNB1 and CCNA2, the two high-scoring hub genes, significantly decreased, and the expression of miR-132-3p and miR-193-3p miRNAs, which could target CCNB1 and CCNA2, significantly increased (p< 0.05). These findings suggest that ciprofloxacin possesses anti-proliferative and anti-metastatic properties in NSCLC, potentially mediated through a dual mechanism involving Topoisomerase II inhibition and the modulation of the miRNA-CCNA2/CCNB1 axis.

Impact of Light Quality on Growth and Pigments Content of Calothrix and Microchaete

Articles in Press, Accepted Manuscript, Available Online from 01 June 2026

https://doi.org/10.22067/jcmr.2026.98386.1133

Maryam Ameri

Abstract Light quality is a critical environmental factor regulating photosynthetic pigment synthesis and biomass accumulation in cyanobacteria. Understanding how different light wavelengths influence pigment production and growth is essential for optimizing cyanobacterial cultivation for biotechnological applications. This study investigated the effects of red, white, and green light on biomass production, lipophilic pigments (chlorophylls and carotenoids), and phycobiliproteins including phycocyanin (PC), allophycocyanin (APC), and phycoerythrin (PE) in two cyanobacterial strains, Calothrix and Microchaete. Cyanobacteria were subjected to a constant light intensity of 500 lux with a 16/8 h photoperiod, continuous aeration, and a temperature of 25°C throughout the two-week experimental period. In Microchaete, red light maximized biomass, chlorophyll, carotenoid, PC, and APC production, while white light enhanced PE levels. The total phycobiliprotein pool peaked under white and red light, indicating that these two wavelengths are most effective for overall PBP accumulation in this strain. In contrast, Calothrix exhibited distinctly different responses. Green light stimulated chlorophyll and carotenoid accumulation up to 3 fold, white light enhanced biomass and total PBPs, and red light selectively increased PC production. Notably, green light boosted chlorophyll production by 2.5 fold and carotenoid production by 3 fold in Calothrix, demonstrating a unique green-light-driven enhancement of lipophilic pigments. Phycobiliprotein levels in Calothrix reached up to 15- fold higher than Microchaete under green light, highlighting a striking species-specific difference in PBP accumulation. These findings demonstrate species-specific chromatic acclimation strategies and highlight the potential of light engineering for targeted overproduction of high-value pigments in cyanobacteria, providing a basis for light-driven bioprocess optimization.

Unraveling the Role of Musashi Signaling Pathway in Medulloblastoma: Insights from Differential Expression and Co-expression Network Analysis

Articles in Press, Accepted Manuscript, Available Online from 01 June 2026

https://doi.org/10.22067/jcmr.2026.97475.1127

Sina Nasr Esfahani, Bahareh Mazrouei, Fariba Dehghanian, Mohammad Kazemi

Abstract Background Medulloblastoma (MB) is the most common malignant pediatric brain tumor, characterized by molecular heterogeneity and aggressiveness. The Musashi-1 (MSI1) pathway has recently garnered significant interest as a central mediator of medulloblastoma tumorigenesis and tumor growth. The RNA-binding protein (MSI1) has been identified as a key regulator of MB tumorigenesis, promoting cancer stem cell phenotypes and treatment resistance. MSI1 research in medulloblastoma also includes its potential as a prognostic and diagnostic biomarker. Methods In the current study, the role of MSI1 in medulloblastoma was highlighted using differential expression and weighted gene co-expressio network analysis. In this study, the role of MSI1 in Medulloblastoma was explored through bioinformatics analysis of RNA-Seq data of 93 MB samples (GEO datasets: GSE143940, GSE158413, GSE189919) and 266 normal cerebellum samples (GTEx). DESeq2 package was used for differential expression analysis, and WGCNA was employed for the discovery of MSI1-associated co-expression networks. Results A total of 11,055 significantly differentially expressed genes were identified in Medulloblastoma, comprising 5,925 upregulated and 5,130 downregulated genes. WGCNA positioned MSI1 in the Medulloblastoma-specific, non-preserved darkgrey module with hub genes ANO2 (Log2FC: 4.80, p = 0) and CACNA1F (Log2FC: 2.18, p = 9.59E-65), implicating them in MSI1-driven oncogenic mechanisms. MSI2, on the other hand, was positioned in a preserved module, suggesting a more general function. Conclusion These findings highlight MSI1's specificity to Medulloblastoma and its potential as a biomarker and therapeutic target. Upregulation of ANO2 and CACNA1F, as well as MSI1's role in tumor aggressiveness, underscores the need for additional functional exploration to validate their therapeutic relevance. This research helps develop customized treatments to improve outcomes in MB patients.

Comprehensive Analysis of SnRK Gene Family in Cicer arietinum L.

Articles in Press, Accepted Manuscript, Available Online from 14 June 2026

https://doi.org/10.22067/jcmr.2026.97904.1129

Fahimeh Moloudi, Nasrin Moshtaghi, Alireza Seifi

Abstract Sucrose non-fermentation-related protein kinase gene family, known as SnRK, encodes serine/threonine protein kinases. They play crucial and diverse roles in plant responses to biotic and abiotic stresses such as drought, salinity and pathogen attacks. These kinases are involved in various signaling pathways that help plants adapt to adverse environmental conditions. The SnRK family is categorized into three main subfamilies: SnRK1, SnRK2 and SnRK3. Among these, SnRK1 is highly conserved and extensively studied across various plant species. In contrast, SnRK2 and SnRK3 are only plant-specific. In this study, we performed a comprehensive genome-wide analysis of the SnRK gene family in chickpea (Cicer arietinum). Previously, 11 CaSnRK genes had been reported. Our investigation led to the successful identification of new 14 CaSnRK genes, which were annotated based on sequence homology with Arabidopsis SnRK genes. Phylogenetic analysis grouped these genes into three distinct clades corresponding to the three subfamilies, with CaSnRK2 and CaSnRK3 further subdivided into two subgroups each. Gene structure analysis revealed significant variation in intron numbers, particularly within the CaSnRK3 subfamily. Motif composition was found to be specific and highly conserved within each subfamily. Chromosomal localization showed that these genes are distributed across seven of the eight chickpea chromosomes. Overall, our study presents a detailed genomic overview of the SnRK family in chickpea, contributing significantly to a better understanding of their evolutionary relationships and potential functional roles in stress tolerance. We identified a total of 25 CaSnRK genes and classified them into three distinct subgroups based on phylogenetic and structural analyses .

A Bioactive Hydrogel Based on Crocin and Chitosan: Physicochemical Properties, Antibacterial Activity, and Skin Tissue Repair Potential

Articles in Press, Accepted Manuscript, Available Online from 14 June 2026

https://doi.org/10.22067/jcmr.2026.94850.1119

Alishir haidari, Niloofar Khandan-Nasab, Yaser Yousefpoor, Farimah Beheshti, Seyed Mohsen Saleh, saeedeh Askarian

Abstract Hydrogels are ideal wound dressings because they maintain a moist environment and promote healing. In this study, chitosan, a biocompatible and antimicrobial polymer, was combined with crocin, a potent antioxidant derived from saffron, to enhance tissue repair through free radical scavenging.
Three hydrogel formulations were prepared: pure chitosan (CS), and chitosan loaded with 10% w/w (CS CR10) or 30% w/w (CS CR30) crocin. Physicochemical characterization by FE SEM, FT IR, porosity, swelling ratio, and water vapour transmission rate (WVTR) revealed uniform microporous networks with decreasing pore size (125 µm for CS, 113 µm for CS CR10, 87 µm for CS CR30) as crocin concentration increased. The highest porosity was observed in CS CR30 (70%), compared to approximately 60% for CS and CS CR10. All hydrogels exhibited high swelling capacity (equilibrium swelling ratios: CS 1850%, CS CR10 2100%, CS CR30 2280%) and appropriate WVTR values (2100–2450 g/m²/day), which are essential for maintaining a moist wound environment.
Biological evaluations included cytotoxicity (MTT assay on L929 fibroblasts) and wound healing capacity (scratch assay). Glutaraldehyde cross linking reduced cell viability due to residual toxicity (e.g., 45% viable cells for CS, 52% for CS CR10, 61% for CS CR30), whereas NaOH cross linked hydrogels showed good biocompatibility (>85% viability). Crocin containing hydrogels significantly enhanced wound closure: after 24 h, CS CR10 achieved 72% wound closure, and CS CR30 achieved 89% closure, compared to 55% for untreated controls. Antibacterial assays against Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli showed no inhibition zones (negligible activity), indicating the need for additional antimicrobial agents for infected wounds.
In conclusion, the chitosan crocin hydrogel offers promising physicochemical stability and pro healing biological effects, particularly in promoting cell proliferation and wound closure. Therefore, it represents a promising candidate for future skin tissue engineering and wound dressing applications

Discovery of long non-coding RNAs in response to cold stress resistance in chickpea

Articles in Press, Accepted Manuscript, Available Online from 22 August 2026

https://doi.org/10.22067/jcmr.2026.97970.1131

Motahareh Khodadadi Zarrini, Nasrin Moshtaghi, Ali Javadmanesh

Abstract Chickpea (Cicer arietinum L.), a highly nutritious and economically important legume crop, is widely cultivated in over 50 countries around the world and currently ranks as the third most produced legume globally, following common bean and soybean. Cold stress, as a major abiotic stress factor, severely limits plant growth, development, survival, and overall productivity, particularly during early growth stages. This study aimed to identify and characterize genes and long non-coding RNAs (lncRNAs) associated with cold tolerance in two contrasting chickpea cultivars, namely ILC533 (cold-sensitive) and Saral (cold-tolerant), through comprehensive transcriptomic data analysis. Using RNA-seq data, comprising approximately 200 million high-quality reads obtained from leaf samples, a total of 14,956 lncRNAs were identified, including 14,078 novel and 878 previously known lncRNAs. Expression analysis further revealed that, in the Saral cultivar, 427 lncRNAs were significantly up-regulated and 556 were down-regulated, whereas in ILC533, 494 lncRNAs were up-regulated and 454 were down-regulated under cold stress conditions. The majority of the differentially expressed lncRNAs were found to be located on chromosomes 4 and 6, and their predicted target genes, including Dehydration-responsive element-binding protein 1A, Abscisic acid and environmental stress-inducible protein-like, Glycine-rich cell wall structural protein, Calcium-dependent protein kinase 1-like, and Late embryogenesis abundant protein 7, were shown to play important and functional roles in cold tolerance. Gene Ontology analysis further indicated that these genes are actively involved in various biological processes, cellular components, and molecular functions. Additionally, most lncRNAs were predicted to be primarily localized in the cytoplasm, thereby influencing and regulating cytoplasmic functions. Overall, this study confirms the critical regulatory role of lncRNAs in the cold stress response of chickpea and provides valuable insights for future breeding of cold-tolerant varieties.

In silico Study to Identification of Potential SARS-CoV-2 Main Protease Inhibitors: Virtual Drug Screening and Molecular Docking with AutoDock Vina and Molegro Virtual Docker

Volume 13, Issue 2, April 2022, Pages 108-112

https://doi.org/10.22067/jcmr.2021.71517.1013

Mohammad Amin Manavi

Abstract Coronavirus disease 2019 (COVID-19) has emerged in Wuhan, China, and because of fast transmission, it has led to its extensive prevalence in almost all countries, which has made it a global crisis. Drug repurposing is considered a fast way to discover new applications of the current drugs. This study aims to recognize a possible small molecule as a primary protease inhibitor versus the main protease protein of SARS-CoV-2 by computational programs. Virtual screening procedures like using Molegro Virtual Docker, AutoDock Tool, and AutoDock Vina, were done for more than 1600 FDA-approved medicines downloaded from the ZINC database, were employed to characterize new implied molecule inhibitors for the recently published crystal structure of the main protease protein of SARS-CoV-2. Virtual screening results indicated, many drugs including ARBs, cephalosporins, some kinase inhibitors, HMG CoA reductase, and leukotriene receptor antagonist, may inhibit the main protease of SARS-COV-2. Velpatasvir, Molnupiravir, and Ivermectin were selected by virtual screening methods for further studies to find an efficient ligand for the treatment of COVID-19. Due to some other beneficial features, including anti-infectious, anti-inflammatory properties, and ADME profile, they could be a promising drug nominee for repurposing to the treatment of COVID-19. Velpatasvir was selected by some virtual screening methods for further studies to find a suitable ligand for the treatment of COVID-19. Furthermore, more studies need to approve this data and finally clinical trial needs to be done to examine the efficacy of Velpatasvir for the treatment of covid-19 as an anti-viral agent.

A Multi-Faceted Approach for Prediction of Genome Safe Harbor Loci in the Chicken Genome

Volume 13, Issue 1, September 2021, Pages 1-9

https://doi.org/10.22067/jcmr.2021.71604.1015

Nima Dehdilani, Mohsen Fathi Najafi, Hesam Dehghani

Abstract To achieve a reliable and persistent expression, the transgene should be precisely integrated into the genome safe harbor (GSH) loci. Little attention has been paid to find the safe harbor loci of the chicken (Gallus gallus domesticus) genome. Identification and characterization of GSH loci that allow the persistent and reliable expression of knock-in genes could be a major area of interest within the field of transgenic technology and is central to the development of transgenic livestock. Randomly integrated transgenes might encounter position effects and epigenetic silenc­ing, so unstable phenotypes, as well as unreliable and unpredictable expression of the knock-in transgene could occur. In contrast to random gene insertion, site-specific gene targeting provides a superior strategy that exploits homologous recombination to insert a transgene of interest into a pre-determined locus. In this study, based on bioinformatics, gene expression atlas, and Hi-C analyses, the GSH region was predicted in the chicken genome between DRG1 and EIF4ENIF1  genes. To do so, we introduce a fast and easy-to-use pipeline that allows the prediction of orthologue GSH loci in all organisms, especially chickens. In addition, the procedure to design targeting vectors for targeting these predicted GSH regions is described in detail. 

Molecular Simulation of Animal Milk Lactoferrins as Antiviral Agents against Rotavirus: Binding Mechanisms and Therapeutic Implications

Volume 16, Issue 2, April 2025, Pages 67-78

https://doi.org/10.22067/jcmr.2025.85043.1080

Ali Javadmanesh, Atefe Paknafs, Marjan Azghandi

Abstract Rotavirus infections impose a significant global health burden, particularly affecting infants and young children and causing severe gastroenteritis. To combat this viral pathogen, there is a growing interest in exploring the therapeutic potential of lactoferrins derived from different farm animal milk as antiviral agents. This study employed molecular simulation techniques to investigate the intricate binding mechanisms between different animal milk lactoferrins and rotavirus, providing insights into their molecular interactions. These animals included cow, sheep, camel, goat, horse, buffalo, in addition to humans. Molecular dynamics simulation techniques were employed using Gromacs software to simulate the interaction between animal milk lactoferrins and rotavirus. Precise computational models and simulations were conducted to investigate the binding mechanisms and identify critical amino acid residues involved. Our findings indicate that cow lactoferrin exhibits superior interaction with rotavirus compared to other lactoferrin sources. We identified specific binding sites and crucial amino acid residues responsible for these interactions. These results provide insights into the molecular determinants governing the strong binding affinity and specificity of lactoferrins towards rotavirus. This study provided valuable insights for the design of targeted antiviral strategies against rotavirus infections. Animal milk lactoferrins, particularly cow lactoferrin, demonstrated a promising potential as an antiviral agent against retroviruses. These findings enhanced our understanding of the molecular mechanisms underlying lactoferrin-mediated antiviral activity, paving the way for future experimental and clinical investigations in this field and supporting the development of efficient antiviral therapeutics against rotavirus.

Network Analysis of Differential Gene Expression to Identify Hub Genes in Ovarian Cancer

Volume 12, Issue 1, September 2020, Pages 1-9

https://doi.org/10.22067/jcmr.v12i1.85654

Akram Siavoshi, Mahdieh Taghizadeh, Elahe Dookhe, Mehran Piran, Mahsa Saliani, Shahla Mohammad Ganji

Abstract      Epithelial ovarian cancer (EOC), as a challenging disease among women with poor prognosis and unclear molecular pathogenesis, each year is responsible for 140000 deaths globally. Recent progress in the field revealed the importance of proteins as key players of different biological events. Considering the complicated protein interactions, taking a deeper look at protein-protein interactions (PPIs) could be considered as a superior strategy to unravel complex mechanisms encountered with regulatory cell signaling pathways of ovarian cancer. Hence, PPI network analysis was performed on differentially expressed genes (DEGs) of ovarian cancer to discover hub genes which have the potential to be introduced as biomarkers with clinical utility. A PPI network with 600 DEGs was constructed. Network topology analysis determined UBC, FN1, SPP1, ACTB, GAPDH, JUN, and RPL13A, with the highest Degree (K) and betweenness centrality (BC), as shortcuts of the network. KEGG pathway analysis showed that these genes are commonly enriched in ribosome and ECM-receptor interaction pathways. These pivotal hub genes, mainly UBC, FN1, RPL13A, SPP1, and JUN have been reported previously as potential prognostic biomarkers of different types of cancer. However, further experimental molecular studies and computational processes are required to confirm the function and association of the identified hub genes with epithelial ovarian cancer prognosis.

Identification of PI3K Isoforms in Human Prostate Cancer Cell Lines (PC3, DU145) and Human Bladder Carcinoma Cell line (5637)

Volume 7, Issue 1, July 2015, Pages 3-10

https://doi.org/10.22067/jcmr.v7i1.40028

Hajar Aryan, Zahra-Soheila Soheili

Abstract There exists an association between PI3K pathway licentious activity and the considerable feature of high metastatic potential of the genitourinary cancer cells. Although DU 145 and 5637 have functional phosphatase and tensin homolog (PTEN) tumor suppressor gene, which antagonizes PI3K function, PC-3 is null for PTEN gene. In pursuit to explain why PTEN bearing cell lines display high metastatic behavior, we searched for any discrepancy in PI3K isoforms expression pattern between these cell lines. Gathering gene bank data files, specific primers were designed, for all the genes of 12 studied isoforms from 3 different classes of PI3K. Total RNA was extracted and examined by Real- Time PCR to compare the cells for the type and amount of the isoforms which expressed. Cα and R2 isoforms are indicative of an equal expression for PC3 and DU145, R3 transcripts revealed 80% decrease in DU145 and Cβ, R1 and C2α demonstrated an increased expression in DU145. When a comparison is made between 5637 and PC3, it can be seen that although a little decrease in the level of R3 transcripts was demonstrated, the amount of Cα, Cβ, R2, R1 and C2α increased. In conclusion in this study it is proposed that R1, R2, Cα, Cβ , C2α and R1, Cβ , C2α are candidate genes for silencing via RNAi in 5637 and DU145, respectively, to evaluate their roles in metastatic behavior of the both studied PTEN bearing cell lines.

Immunosuppressive Effects of Human Chorionic Gonadotropin (hCG) on Mesenchymal Stromal Cells

Volume 11, Issue 2, March 2020, Pages 90-98

https://doi.org/10.22067/jcmr.v11i2.85667

Sepideh sadat Hosseini, Shadi Mehrzad, Halimeh Hassanzadeh, Hamid Reza Bidkhori, Mahdi Mirahmadi, Madjid Momeni-Moghaddam, Fatemeh Sadeghifar, Moein Farshchian

Abstract      Mesenchymal stem/stromal cells (MSCs) as one of the most important types of adult stem cells secrete a variety of immunomodulatory cytokines. However, their immunomodulatory features strongly depend on the molecular cross-talk between cells and the surrounding microenvironment. Hence, some strategies were proposed to empower their beneficial effects during cell-therapeutic procedures to avoid confusing results. Licensing the cells with chemical compounds could be considered as one of the most applicable methods for induction of anti-inflammatory status in the cells. Human chorionic gonadotropin (hCG) is a pregnancy related hormone which has been shown to be essential for the establishment of a successful pregnancy. HCG supports the implantation of fetus in the maternal endometrium, due to its immunomodulatory effects. Moreover, the regulatory role of hCG has been previously mentioned in case of some autoimmune-based diseases. In the present study, the capacity of this hormone for induction of different immune-encountered genes expression was examined in primary cultures of human adipose tissue derived mesenchymal stem cells (Ad-MSCs). In this regard, Ad-MSCs were exposed to 10 IU of hCG for 72 hours. Molecular studies via quantitative Real-time PCR (qRT-PCR) experiments were performed to detect gene expression modifications based on the application of SYBR Green as the fluorescent dye and in comparison to the RPLP0 as the housekeeping gene. Results confirmed that hCG significantly upregulated TSG-6, TGF-β1, IL-1β and IL-6 expression levels comparing with the control group, while it downregulates COX-2 expression, and had no statistically significant effects on IL-10 andTDO2. In conclusion, priming Ad-MSCs with hCG may enhance the proliferation and immunoregulatory potential of these cells, although it needs further investigations to reveal involved molecular pathways.

The Effects of the DNAi Molecule on Growth and Muscle Weights in Male Wistar Rats

Volume 16, Issue 2, April 2025, Pages 113-120

https://doi.org/10.22067/jcmr.2025.90056.1100

Ali Javadmanesh, Amir Rashid Lamir, Mitra Riasi, Mehrdad Movahed Nasab, Nazila Dardmeh, Helia Khayyami, Kasra Khayami, Elnaz Karbaschian

Abstract The growth and development of skeletal muscle tissue is largely regulated by myostatin during tissue development in embryos. This tissue may overgrow if myostatin expression is deficient. Gene expression may be regulated in a particular way by oligonucleotide antisense molecules. It has been demonstrated that a new DNA-based oligonucleotide can downregulate myostatin expression in a rat model. The purpose of this work was to evaluate the impact of a DNAi-based myostatin inhibitor on the visceral fat and leg muscle weights of Wistar rats undergoing strength training. Three groups of male rats, with an average weight of 203g ± 10.5, were chosen at four weeks of age. These cohorts comprised: 1) DNAi group had resistance training in addition to receiving 10 mg/kg of rat body weight of DNAi. 2) Resistance exercise and saline injection group. Group for injection of saline. Then, weight measurements for the carcass, heart, liver, left kidney, right kidney, spleen, visceral fat, twin muscles, soleus muscle, and left leg were made for each group. Histological assessment of the soleus muscle section was performed. One-way ANOVA was then used to examine the results, and means were compared using Tukey’s test. As the data show, the proposed molecule did not significantly contribute to an increase in body weight, in contrast to previous assumptions. Nonetheless, the twin muscles' relative and absolute weights increased significantly with visceral fat decreased with DNAi injection (P<0.05). Although weekly body weight increase and the final weights were not affected by DNAi injection, this could be explained by the loss of fat tissue during the experiment. This molecule is promising in increasing muscle tissue growth; however, further prolonged experiments and evaluating myostatin gene expression are recommended in future experiments.
 

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