Pub Date : 2025-12-01Epub Date: 2025-11-10DOI: 10.1016/j.jgeb.2025.100593
Aichun Long , Cheng Huang , Tianyun Li , Yuwei Shi , Cuiwei Zhang
Renal clear cell carcinoma (KIRC), the most common subtype of renal cell carcinoma, is characterized by high metastatic potential and heterogeneity.The expression pattern of the ARHGAP26 gene in KIRC, its link to patient prognosis, and its role in the TME immunoregulatory network are not well understood, with significant research gaps. We will analyze ARHGAP26 expression using TCGA and GSCALite databases and assess its association with the tumor microenvironment using the ESTIMATE algorithm. Additionally, we will use the GEO database to examine ARHGAP26 expression across different cell subsets in KIRC and evaluate its correlation with immune cell infiltration using TIMER 2.0. Immunohistochemistry (IHC) will be used to confirm differences in ARHGAP26 expression between renal clear cell carcinoma (KIRC) and adjacent normal tissues. ARHGAP26 expression is higher in KIRC, with a significant difference from normal tissues (p < 0.001). In KIRC patients, high ARHGAP26 expression is linked to longer overall, progression-free, and disease-specific survival, suggesting a tumor suppressor role, though it does not affect the disease-free interval. High ARHGAP26 expression may remodel the tumor stroma and alter the tumor microenvironment by changing the tumor-to-non-tumor cell ratio.
{"title":"Evaluation of ARHGAP26 expression, prognostic significance, and immune infiltration in clear cell renal cell carcinoma","authors":"Aichun Long , Cheng Huang , Tianyun Li , Yuwei Shi , Cuiwei Zhang","doi":"10.1016/j.jgeb.2025.100593","DOIUrl":"10.1016/j.jgeb.2025.100593","url":null,"abstract":"<div><div>Renal clear cell carcinoma (KIRC), the most common subtype of renal cell carcinoma, is characterized by high metastatic potential and heterogeneity.The expression pattern of the <em>ARHGAP26</em> gene in KIRC, its link to patient prognosis, and its role in the TME immunoregulatory network are not well understood, with significant research gaps. We will analyze <em>ARHGAP26</em> expression using TCGA and GSCALite databases and assess its association with the tumor microenvironment using the ESTIMATE algorithm. Additionally, we will use the GEO database to examine <em>ARHGAP26</em> expression across different cell subsets in KIRC and evaluate its correlation with immune cell infiltration using TIMER 2.0. Immunohistochemistry (IHC) will be used to confirm differences in <em>ARHGAP26</em> expression between renal clear cell carcinoma (KIRC) and adjacent normal tissues. <em>ARHGAP26</em> expression is higher in KIRC, with a significant difference from normal tissues (<em>p</em> < 0.001). In KIRC patients, high <em>ARHGAP26</em> expression is linked to longer overall, progression-free, and disease-specific survival, suggesting a tumor suppressor role, though it does not affect the disease-free interval. High <em>ARHGAP26</em> expression may remodel the tumor stroma and alter the tumor microenvironment by changing the tumor-to-non-tumor cell ratio.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100593"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145528327","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Banana (Musa spp.) is a globally important fruit crop, with most cultivated varieties originating from hybridizations between M. acuminata (A genome) and M. balbisiana (B genome). Triploid ABB hybrids, carrying two B-genome and one A-genome sets, are valued for their stress tolerance and adaptability. In Thailand, ‘Kluai Namwa’ (Pisang Awak) is the most widely cultivated ABB cultivar, but it shows considerable phenotypic variation across subvarieties. Because morphological classification is often unreliable, molecular tools are needed to assess genetic identity and diversity. A total of 28 Thai banana genotypes, representing the AA, BB, and ABB genome groups, were analyzed using RAPD and SRAP markers. RAPD produced 109 bands with 93.6 % polymorphism, while SRAP generated 278 bands with 92.5 % polymorphism, indicating substantial genetic variation. The mean polymorphic information content was 0.22 for RAPD and 0.24 for SRAP, confirming the discriminatory power of both marker systems. UPGMA clustering separated the genotypes into two major clusters corresponding to A- and B-genome contributions, a structure further supported by PCoA. Distinctive bands, such as RAPD primer S7 (2.50 kb) and SRAP combination Me6/Em8 (0.80 kb), specifically identified ‘Kluai Hak Muk’ cooking bananas, demonstrating the potential of these markers for cultivar authentication. The genetic stability of 16 ‘Kluai Namwa Mali-Ong’ plantlets from different locations was also evaluated. Results revealed high clonal uniformity (mean similarity = 0.858) with only minor variation, likely reflecting localized cultivation practices. Overall, RAPD and SRAP markers proved effective for genome identification, diversity assessment, and clonal stability monitoring in Thai bananas. These tools will support banana breeding, germplasm conservation, and reliable authentication of high-value cultivars.
{"title":"Genetic differentiation of Pisang Awak subvarieties and genetic variation among ‘Mali-Ong’ plantlets in Thailand using RAPD and SRAP markers","authors":"Thanita Boonsrangsom , Kawee Sujipuli , Duangporn Premjet","doi":"10.1016/j.jgeb.2025.100577","DOIUrl":"10.1016/j.jgeb.2025.100577","url":null,"abstract":"<div><div>Banana (<em>Musa</em> spp.) is a globally important fruit crop, with most cultivated varieties originating from hybridizations between <em>M. acuminata</em> (A genome) and <em>M. balbisiana</em> (B genome). Triploid ABB hybrids, carrying two B-genome and one A-genome sets, are valued for their stress tolerance and adaptability. In Thailand, ‘Kluai Namwa’ (Pisang Awak) is the most widely cultivated ABB cultivar, but it shows considerable phenotypic variation across subvarieties. Because morphological classification is often unreliable, molecular tools are needed to assess genetic identity and diversity. A total of 28 Thai banana genotypes, representing the AA, BB, and ABB genome groups, were analyzed using RAPD and SRAP markers. RAPD produced 109 bands with 93.6 % polymorphism, while SRAP generated 278 bands with 92.5 % polymorphism, indicating substantial genetic variation. The mean polymorphic information content was 0.22 for RAPD and 0.24 for SRAP, confirming the discriminatory power of both marker systems. UPGMA clustering separated the genotypes into two major clusters corresponding to A- and B-genome contributions, a structure further supported by PCoA. Distinctive bands, such as RAPD primer S7 (2.50 kb) and SRAP combination Me6/Em8 (0.80 kb), specifically identified ‘Kluai Hak Muk’ cooking bananas, demonstrating the potential of these markers for cultivar authentication. The genetic stability of 16 ‘Kluai Namwa Mali-Ong’ plantlets from different locations was also evaluated. Results revealed high clonal uniformity (mean similarity = 0.858) with only minor variation, likely reflecting localized cultivation practices. Overall, RAPD and SRAP markers proved effective for genome identification, diversity assessment, and clonal stability monitoring in Thai bananas. These tools will support banana breeding, germplasm conservation, and reliable authentication of high-value cultivars.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100577"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145227471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-10-29DOI: 10.1016/j.jgeb.2025.100604
Ahmed Allahem , Reem Alajmi , Mais Alzarzor Alajami , Sumaiah Al-Ghamdi , Muhammad Amjad Bashir , Jehan Zeb , Khaloud Mohammed Alarjani , Nawal M Al-Malahi , Rewaida Abdel-Gaber
Culex pipiens complex members have been known as important vectors of medical and veterinary arthropod-borne diseases for many pathogens (viral, bacterial, parasitic). Therefore, this study aimed to investigate natural bacterial flora within the Culex pipiens pipiens (Linnaeus,1758) collected from Aleppo City, Syria. Specimens of Cx. p. pipiens were identified based on a pictorial key. The presence of bacterial species was investigated using the PCR technique and special culture media. Results indicated the presence of mine bacterial species, including Wolbachia pipiens, Moraxella catarrhalis, Klebsiella pneumoniae, Staphylococcus aureus, Escherichia coli, Proteus mirabilis, Corynebacterium kutsceri, Clostridium tetani, and Acinetobacter baumannii. Wolbachia controls the sexual behavior of mosquitoes and therefore can be used in biocontrol.
{"title":"Molecular Detection of natural bacterial flora within Culex pipiens pipiens (Diptera: Culicidae) in Aleppo, Syria","authors":"Ahmed Allahem , Reem Alajmi , Mais Alzarzor Alajami , Sumaiah Al-Ghamdi , Muhammad Amjad Bashir , Jehan Zeb , Khaloud Mohammed Alarjani , Nawal M Al-Malahi , Rewaida Abdel-Gaber","doi":"10.1016/j.jgeb.2025.100604","DOIUrl":"10.1016/j.jgeb.2025.100604","url":null,"abstract":"<div><div><em>Culex pipiens</em> complex members have been known as important vectors of medical and veterinary arthropod-borne diseases for many pathogens (viral, bacterial, parasitic). Therefore, this study aimed to investigate natural bacterial flora within the <em>Culex pipiens pipiens</em> (Linnaeus,1758) collected from Aleppo City, Syria. Specimens of <em>Cx. p. pipiens</em> were identified based on a pictorial key. The presence of bacterial species was investigated using the PCR technique and special culture media. Results indicated the presence of mine bacterial species, including <em>Wolbachia pipiens</em>, <em>Moraxella catarrhalis, Klebsiella pneumoniae, Staphylococcus aureus, Escherichia coli, Proteus mirabilis, Corynebacterium kutsceri, Clostridium tetani,</em> and <em>Acinetobacter baumannii</em>. <em>Wolbachia</em> controls the sexual behavior of mosquitoes and therefore can be used in biocontrol.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100604"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145424509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rheumatoid Arthritis (RA) is a chronic autoimmune disease. Right now, different genes play a crucial role in disease development. The objective was to assess the correlation between STAT4 gene polymorphism (SNPs: rs11889341, rs10181656 and rs7574865) and susceptibility to RA progression in Iraqi population.
Methods
Three Hundred Twenty-five RA patients and Three Hundred Twenty-five matched controls were enrolled in this study. The genotyping for SNPs was performed using (Tetra-ARMS) technique. The clinical parameters were obtained through laboratory investigations and clinical examination.
Results
Our results showed obvious statistical significance between cases and control genotypes regarding to SNPs (rs11889341: CC and TT, rs10181656: GG and rs7574865: TT). Additionally, analysis displayed a discrepancy in genotypes frequency of SNPs (rs11889341: CC among family history and Anti-CCP, but TT genotype with RF), (rs7574865: TT within RF and Anti-CCP, GG genotype in relation to family history.
Conclusion
Our study concluded that STAT4 gene polymorphism (SNPs: rs11889341, rs10181656 and rs7574865) were associated with RA development in Iraqi population. Furthermore, the SNPs (rs11889341 and rs7574865) were related to family history, RF and Anti-CCP, while SNP (rs10181656) didn’t display any relation among studied population.
{"title":"STAT4 gene polymorphism promotes progression of rheumatoid arthritis","authors":"Dawood Ali Salim Dawood , Anwar Madlool Al-janabi , Rana Talib Al-Muswie , Lee Suan Chua , U.A. Al‑Sari , Samer Alwazni","doi":"10.1016/j.jgeb.2025.100589","DOIUrl":"10.1016/j.jgeb.2025.100589","url":null,"abstract":"<div><h3>Background</h3><div>Rheumatoid Arthritis (RA) is a chronic autoimmune disease. Right now, different genes play a crucial role in disease development. The objective was to assess the correlation between STAT4 gene polymorphism (SNPs: rs11889341, rs10181656 and rs7574865) and susceptibility to RA progression in Iraqi population.</div></div><div><h3>Methods</h3><div>Three Hundred Twenty-five RA patients and Three Hundred Twenty-five matched controls were enrolled in this study. The genotyping for SNPs was performed using (Tetra-ARMS) technique. The clinical parameters were obtained through laboratory investigations and clinical examination.</div></div><div><h3>Results</h3><div>Our results showed obvious statistical significance between cases and control genotypes regarding to SNPs (rs11889341: CC and TT, rs10181656: GG and rs7574865: TT). Additionally, analysis displayed a discrepancy in genotypes frequency of SNPs (rs11889341: CC among family history and Anti-CCP, but TT genotype with RF), (rs7574865: TT within RF and Anti-CCP, GG genotype in relation to family history.</div></div><div><h3>Conclusion</h3><div>Our study concluded that STAT4 gene polymorphism (SNPs: rs11889341, rs10181656 and rs7574865) were associated with RA development in Iraqi population. Furthermore, the SNPs (rs11889341 and rs7574865) were related to family history, RF and Anti-CCP, while SNP (rs10181656) didn’t display any relation among studied population.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100589"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-10-17DOI: 10.1016/j.jgeb.2025.100603
Sinethemba H. Yakobi, Uchechukwu U. Nwodo
Pseudomonas aeruginosa employs quorum sensing (QS) to regulate virulence and antibiotic resistance, making QS inhibition a promising anti-infective strategy. Here, we computationally evaluated three phytochemicals—baicalin, berberine, and cinnamaldehyde—as QS inhibitors targeting LasR, RhlR, and PqsR regulators. Molecular docking revealed berberine as the most potent PqsR binder (GScore: −6.801 kcal/mol), competitively displacing the native ligand HHQ, while baicalin showed broad-spectrum inhibition of PqsR/RhlR. Cinnamaldehyde exhibited moderate LasR antagonism. Molecular dynamics (100 ns) confirmed complex stability (RMSD < 2.5 Å) and identified key interactions: berberine formed a salt bridge with PqsR Asp264, while baicalin induced allosteric helix destabilization. Pharmacokinetic profiling showed that berberine is rapidly cleared (134.7 mL/min/kg) and poses a risk of drug–drug interactions due to CYP3A4 and CYP2D6 inhibition. This makes formulation strategies or analogue design more suitable than relying on metabolic inhibition. In contrast, baicalin has very poor absorption (bioavailability score: 0.11), indicating that nanoformulation is required to improve its uptake. Cinnamaldehyde demonstrated favourable drug-likeness but required structural optimization to mitigate aldehyde reactivity. This study provides in-silico mechanistic support for phytochemical-mediated QS inhibition in P. aeruginosa, with berberine emerging as a lead candidate for further development. Our integrative approach map water displacement hotspots in PqsR (GIST) and detect a baicalin-linked distal helix perturbation (DSSP) consistent with allostery, and bridges computational prediction and therapeutic design, offering new strategies to combat antimicrobial resistance through virulence attenuation.
{"title":"Structure-based screening and molecular dynamics of phytophytochemicals against pseudomonas aeruginosa quorum sensing systems","authors":"Sinethemba H. Yakobi, Uchechukwu U. Nwodo","doi":"10.1016/j.jgeb.2025.100603","DOIUrl":"10.1016/j.jgeb.2025.100603","url":null,"abstract":"<div><div><em>Pseudomonas aeruginosa</em> employs quorum sensing (QS) to regulate virulence and antibiotic resistance, making QS inhibition a promising anti-infective strategy. Here, we computationally evaluated three phytochemicals—baicalin, berberine, and cinnamaldehyde—as QS inhibitors targeting LasR, RhlR, and PqsR regulators. Molecular docking revealed berberine as the most potent PqsR binder (GScore: −6.801 kcal/mol), competitively displacing the native ligand HHQ, while baicalin showed broad-spectrum inhibition of PqsR/RhlR. Cinnamaldehyde exhibited moderate LasR antagonism. Molecular dynamics (100 ns) confirmed complex stability (RMSD < 2.5 Å) and identified key interactions: berberine formed a salt bridge with PqsR Asp264, while baicalin induced allosteric helix destabilization. Pharmacokinetic profiling showed that berberine is rapidly cleared (134.7 mL/min/kg) and poses a risk of drug–drug interactions due to CYP3A4 and CYP2D6 inhibition. This makes formulation strategies or analogue design more suitable than relying on metabolic inhibition. In contrast, baicalin has very poor absorption (bioavailability score: 0.11), indicating that nanoformulation is required to improve its uptake. Cinnamaldehyde demonstrated favourable drug-likeness but required structural optimization to mitigate aldehyde reactivity. This study provides <em>in-silico</em> mechanistic support for phytochemical-mediated QS inhibition in <em>P. aeruginosa</em>, with berberine emerging as a lead candidate for further development. Our integrative approach map water displacement hotspots in PqsR (GIST) and detect a baicalin-linked distal helix perturbation (DSSP) consistent with allostery, and bridges computational prediction and therapeutic design, offering new strategies to combat antimicrobial resistance through virulence attenuation.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100603"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145332243","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-11-12DOI: 10.1016/j.jgeb.2025.100601
Xuehan Wang , Lin Guo , Yiren Feng, Gang Jin
Objective
To investigate the effective ingredients, crucial molecular targets, and the underlying molecular mechanisms associated with Herba Epimedii (HE) that exhibits anti-cancer effects for treating thyroid cancer (TC) using the network pharmacology approach.
Methods
The Traditional Chinese Medicine Systems Pharmacology (TCMSP) public database was analysed to identify the major bioactive ingredients and target proteins associated with HE. The Human Gene (Gene Cards) database, National Center for Biotechnology Information (NCBI) gene database, and Online Mendelian Inheritance in Man (OMIM) databases were analyzed to search for the disease targets of TC. Based on the overlapped results between HE putative targets and TC targets, the “compound-disease-target” network and a protein–protein interaction (PPI) network were constructed using Cytoscape 3.8.0. The R package was used to perform the Gene Ontology (GO) and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses. Finally, the “compound-disease-pathway-target” network was drawn by integrating all the information.
Results
The results indicated that there were 23 effective bioactive ingredients associated with HE, covering 203 targets, 145 of which were related to TC. Through PPI network topological analysis, 53 targets (including AKT1, JUN, MAPK1, RELA, and IL6) were identified as the major targets of HE. Results recorded from GO functional analyses revealed that significant biological processes were enriched. Results from KEGG analyses revealed that the pathways, such as the TNF, IL-17, and PI3K-Akt signaling pathways, played vital roles in the HE intervention for TC.
Conclusion
We revealed the potential mechanisms through which HE exerts anti-cancer effects in the case of TC. A holistic perspective on multiple ingredients, targets, and pathways has been presented, and the results can potentially help in developing new treatment methods for TC.
{"title":"Investigating the potential anti-cancer mechanism for thyroid cancer: Role of Herba Epimedii via network pharmacology approach","authors":"Xuehan Wang , Lin Guo , Yiren Feng, Gang Jin","doi":"10.1016/j.jgeb.2025.100601","DOIUrl":"10.1016/j.jgeb.2025.100601","url":null,"abstract":"<div><h3>Objective</h3><div>To investigate the effective ingredients, crucial molecular targets, and the underlying molecular mechanisms associated with Herba Epimedii (HE) that exhibits anti-cancer effects for treating thyroid cancer (TC) using the network pharmacology approach.</div></div><div><h3>Methods</h3><div>The Traditional Chinese Medicine Systems Pharmacology (TCMSP) public database was analysed to identify the major bioactive ingredients and target proteins associated with HE. The Human Gene (Gene Cards) database, National Center for Biotechnology Information (NCBI) gene database, and Online Mendelian Inheritance in Man (OMIM) databases were analyzed to search for the disease targets of TC. Based on the overlapped results between HE putative targets and TC targets, the “compound-disease-target” network and a protein–protein interaction (PPI) network were constructed using Cytoscape 3.8.0. The R package was used to perform the Gene Ontology (GO) and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses. Finally, the “compound-disease-pathway-target” network was drawn by integrating all the information.</div></div><div><h3>Results</h3><div>The results indicated that there were 23 effective bioactive ingredients associated with HE, covering 203 targets, 145 of which were related to TC. Through PPI network topological analysis, 53 targets (including AKT1, JUN, MAPK1, RELA, and IL6) were identified as the major targets of HE. Results recorded from GO functional analyses revealed that significant biological processes were enriched. Results from KEGG analyses revealed that the pathways, such as the TNF, IL-17, and PI3K-Akt signaling pathways, played vital roles in the HE intervention for TC.</div></div><div><h3>Conclusion</h3><div>We revealed the potential mechanisms through which HE exerts anti-cancer effects in the case of TC. A holistic perspective on multiple ingredients, targets, and pathways has been presented, and the results can potentially help in developing new treatment methods for TC.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100601"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145528328","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Free radicals contribute to various diseases, while antioxidants, like phenolic compounds and flavonoids, counteract their effects. This study examines the antioxidant, anti-inflammatory, and cytotoxic properties of Xylocarpus granatum bark extracts, emphasizing ethyl acetate fraction (EAF) and the isolated compound from EAF.
The antioxidant constituents like total phenolic and flavonoid contents were quantified and antioxidant activity was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assays. The cytotoxic potential of the extracts and the isolated compound was evaluated against brine shrimp and the MCF-7 breast cancer cell line using the MTT assay. Anti-inflammatory effects were evaluated using heat-induced hemolysis and RBC membrane stabilization assays to assess membrane-stabilizing and anti-inflammatory activity. Molecular docking studies were performed using PyRx and discovery studio.
EAF demonstrated the highest total phenolic content (124.56 ± 1.35 mg GAE/g) and total flavonoid content (24.69 ± 0.48 mg QE/g), with superior performance in DPPH assays with IC50 values of 3.84 µg/ml and that of pure compound, (+) catechin was 3.89 µg/ml. Anti-inflammatory effects revealed strong activity, with EAF and pure compound showing inhibition rates comparable to standard drugs like diclofenac-Na. Cytotoxicity, assessed through brine shrimp lethality and MCF-7 breast cancer cell line assays, highlighted EAF’s potent activity (LC50: 24.15 µg/ml) antiproliferative efficacy in a dose-dependent manner. Molecular docking studies confirmed (+) catechin’s dual role as a COX-2/Caspase 9 inhibitor, elucidating its potential mechanisms of action.
These findings underscore the therapeutic potential of Xylocarpus granatum extracts, particularly EAF and the isolated compound, in managing oxidative stress, inflammation, and cancer progression.
{"title":"Therapeutic potential of Xylocarpus granatum bark extracts: antioxidant, anti-inflammatory, cytotoxic and molecular insights","authors":"Nur-Nahar, Md. Ekramul Islam, Mst. Jannatul Mewa, Mst. Shahnaj Parvin","doi":"10.1016/j.jgeb.2025.100611","DOIUrl":"10.1016/j.jgeb.2025.100611","url":null,"abstract":"<div><div>Free radicals contribute to various diseases, while antioxidants, like phenolic compounds and flavonoids, counteract their effects. This study examines the antioxidant, anti-inflammatory, and cytotoxic properties of <em>Xylocarpus granatum</em> bark extracts, emphasizing ethyl acetate fraction (EAF) and the isolated compound from EAF.</div><div>The antioxidant constituents like total phenolic and flavonoid contents were quantified and antioxidant activity was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assays. The cytotoxic potential of the extracts and the isolated compound was evaluated against brine shrimp and the MCF-7 breast cancer cell line using the MTT assay. Anti-inflammatory effects were evaluated using heat-induced hemolysis and RBC membrane stabilization assays to assess membrane-stabilizing and anti-inflammatory activity. Molecular docking studies were performed using PyRx and discovery studio.</div><div>EAF demonstrated the highest total phenolic content (124.56 ± 1.35 mg GAE/g) and total flavonoid content (24.69 ± 0.48 mg QE/g), with superior performance in DPPH assays with IC<sub>50</sub> values of 3.84 µg/ml and that of pure compound, (+) catechin was 3.89 µg/ml. Anti-inflammatory effects revealed strong activity, with EAF and pure compound showing inhibition rates comparable to standard drugs like diclofenac-Na. Cytotoxicity, assessed through brine shrimp lethality and MCF-7 breast cancer cell line assays, highlighted EAF’s potent activity (LC<sub>50</sub>: 24.15 µg/ml) antiproliferative efficacy in a dose-dependent manner. Molecular docking studies confirmed (+) catechin’s dual role as a COX-2/Caspase 9 inhibitor, elucidating its potential mechanisms of action.</div><div>These findings underscore the therapeutic potential of <em>Xylocarpus granatum</em> extracts, particularly EAF and the isolated compound, in managing oxidative stress, inflammation, and cancer progression.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100611"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145473964","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-11-22DOI: 10.1016/j.jgeb.2025.100617
Fatma El Zahraa A. Elkady , Walaa A. Moselhy , Fatma I. Abo El-Ela , Abeer M. Abd El-Hameed , Mohamed I. Zanaty
The prevalence of hepatotoxicity has sharply increased worldwide in recent decades. Our study aimed to enhance quercetin’s effectiveness against paracetamol (PCM)-induced hepatotoxicity using a quercetin liposome nano formulation. The quercetin liposome (QL) nano formula was fabricated by applying the thin-film hydration method. It was examined via dynamic light scattering, confirmed with a transmission electron microscope (TEM), and followed by assessments of drug-loading capacity, encapsulation efficiency (EE%), and Fourier transform infrared (FTIR) spectroscopy. The release features and cell cytotoxicity were also assessed. The in vivo parameters were completed. We effectively synthesized and characterized the quercetin liposome nanoformula with a 501.9 nm particle size and a –22.8 mV zeta potential. TEM imaging showed that quercetin liposomes were spherical. The EE% for the optimized formulation was 77.1 %. FTIR test confirmed the quercetin liposome spectra. Sustained release behavior of about 67.45 % of quercetin was released from liposomes by 24 h. The IC50 value was reduced from 71.32 µg/ml to 51.28 µg/ml for quercetin and quercetin-loaded liposomes. For the in vivo study, quercetin liposome improved all the altered biochemical markers, alleviating the levels of Malondialdehyde (MDA), Nitric oxide (NO), Superoxide dismutase (SOD), and Glutathione peroxidase (GPx), and upregulating Nuclear factor erythroid 2-related factor 2 (Nrf2) with a downregulation of Kelch-like ECH-associated protein 1 (Keap1), Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), and p38 Mitogen-activated protein kinase (P38 MAPK) gene expression that paralleled the histopathological amelioration. Our results suggested that the quercetin liposome nano formulation had potent hepatoprotective activity through ameliorating biochemical indicators, oxidative stress markers, upregulation of anti-apoptotic genes, and improvement in the histopathological index.
{"title":"Quercetin-liposomes effectively regulated the Nrf2/Keap1 and NF-κB/P38 MAPK signaling pathways and protected the liver against paracetamol-induced damage","authors":"Fatma El Zahraa A. Elkady , Walaa A. Moselhy , Fatma I. Abo El-Ela , Abeer M. Abd El-Hameed , Mohamed I. Zanaty","doi":"10.1016/j.jgeb.2025.100617","DOIUrl":"10.1016/j.jgeb.2025.100617","url":null,"abstract":"<div><div>The prevalence of hepatotoxicity has sharply increased worldwide in recent decades. Our study aimed to enhance quercetin’s effectiveness against paracetamol (PCM)-induced hepatotoxicity using a quercetin liposome nano formulation. The quercetin liposome (QL) nano formula was fabricated by applying the thin-film hydration method. It was examined via dynamic light scattering, confirmed with a transmission electron microscope (TEM), and followed by assessments of drug-loading capacity, encapsulation efficiency (EE%), and Fourier transform infrared (FTIR) spectroscopy. The release features and cell cytotoxicity were also assessed. The in vivo parameters were completed. We effectively synthesized and characterized the quercetin liposome nanoformula with a 501.9 nm particle size and a –22.8 mV zeta potential. TEM imaging showed that quercetin liposomes were spherical. The EE% for the optimized formulation was 77.1 %. FTIR test confirmed the quercetin liposome spectra. Sustained release behavior of about 67.45 % of quercetin was released from liposomes by 24 h. The IC50 value was reduced from 71.32 µg/ml to 51.28 µg/ml for quercetin and quercetin-loaded liposomes. For the in vivo study, quercetin liposome improved all the altered biochemical markers, alleviating the levels of Malondialdehyde (MDA), Nitric oxide (NO), Superoxide dismutase (SOD), and Glutathione peroxidase (GPx), and upregulating Nuclear factor erythroid 2-related factor 2 (<em>Nrf2</em>) with a downregulation of Kelch-like ECH-associated protein 1 (<em>Keap1</em>), Nuclear factor kappa-light-chain-enhancer of activated B cells (<em>NF-κB</em>), and p38 Mitogen-activated protein kinase (<em>P38 MAPK</em>) gene expression that paralleled the histopathological amelioration. Our results suggested that the quercetin liposome nano formulation had potent hepatoprotective activity through ameliorating biochemical indicators, oxidative stress markers, upregulation of anti-apoptotic genes, and improvement in the histopathological index.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100617"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145623558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The NR5A1 gene, encoding Steroidogenic Factor 1 (SF-1), plays a critical role in sex differentiation and spermatogenesis. However, data on NR5A1 variants in sub-Saharan African populations remain limited. This exploratory pilot study aimed to identify and characterize NR5A1 variants in infertile Senegalese men and to assess genotype–phenotype correlations. We conducted a cross-sectional study in 23 infertile Senegalese men, and exons 2 –7 of NR5A1 were sequenced using the Sanger method. Detected variants were analyzed with in silico prediction tools and filtered for rarity (minor allele frequency < 1 %) using the gnomAD database. Genotype–phenotype associations were analyzed using Fisher’s exact test.
Eighty-three percent of patients harbored at least one NR5A1 variant. A novel heterozygous missense variant, c.584C > T (p.Ser195Phe), located in the hinge region of SF-1, was identified in three unrelated individuals presenting with micropenis, testicular hypotrophy, and azoospermia. Several previously described variants were also detected. Genotype–phenotype correlation analysis revealed significant associations between NR5A1 variants and spermatogenic failure, the most common clinical feature (60.8 %). These findings demonstrate substantial genetic variability in NR5A1 among Senegalese men with infertility, and identify a novel missense variant. Our study highlights the relevance of NR5A1 in male infertility screening and emphasizes the importance of incorporating African populations into reproductive genetics research.
编码甾体生成因子1 （SF-1）的NR5A1基因在性别分化和精子发生中起着关键作用。然而，撒哈拉以南非洲人群中NR5A1变异的数据仍然有限。这项探索性初步研究旨在鉴定和表征塞内加尔不育男性的NR5A1变异，并评估基因型-表型相关性。我们对23名塞内加尔不育男性进行了横断面研究，并使用Sanger方法对NR5A1外显子2 -7进行了测序。检测到的变异使用计算机预测工具进行分析，并使用gnomAD数据库过滤罕见度（小等位基因频率<； 1%）。采用Fisher精确检验分析基因型-表型相关性。83%的患者至少携带一种NR5A1变异基因。一种新的杂合错义变异，c.584C > T (p.Ser195Phe)，位于SF-1的铰链区域，在三个无亲缘关系的个体中被发现，表现为小阴茎、睾丸萎缩和无精子症。还检测到几个先前描述的变体。基因型-表型相关分析显示，NR5A1变异与最常见的临床特征生精失败（60.8%）之间存在显著关联。这些发现证明了塞内加尔男性不育症患者NR5A1基因的大量遗传变异，并确定了一种新的错义变异。我们的研究强调了NR5A1在男性不育筛查中的相关性，并强调了将非洲人群纳入生殖遗传学研究的重要性。
{"title":"NR5A1 gene variants in infertile Senegalese men: Discovery of a novel missense variant and genotype-phenotype correlation","authors":"Adji Dieynaba Diallo , Arame Ndiaye , Ndiaga Diop , Fatou Diop Gueye , Mame Venus Gueye , Yacouba Dia , Amath Thiam , Abdoulaye Séga Diallo , Rokhaya Ndiaye , Oumar Faye , Mama Sy","doi":"10.1016/j.jgeb.2025.100578","DOIUrl":"10.1016/j.jgeb.2025.100578","url":null,"abstract":"<div><div>The <em>NR5A1</em> gene, encoding Steroidogenic Factor 1 (SF-1), plays a critical role in sex differentiation and spermatogenesis. However, data on <em>NR5A1</em> variants in sub-Saharan African populations remain limited. This exploratory pilot study aimed to identify and characterize <em>NR5A1</em> variants in infertile Senegalese men and to assess genotype–phenotype correlations. We conducted a cross-sectional study in 23 infertile Senegalese men, and exons 2 –7 of <em>NR5A1</em> were sequenced using the Sanger method. Detected variants were analyzed with in silico prediction tools and filtered for rarity (minor allele frequency < 1 %) using the gnomAD database. Genotype–phenotype associations were analyzed using Fisher’s exact test.</div><div>Eighty-three percent of patients harbored at least one <em>NR5A1</em> variant. A novel heterozygous missense variant, c.584C > T (p.Ser195Phe), located in the hinge region of SF-1, was identified in three unrelated individuals presenting with micropenis, testicular hypotrophy, and azoospermia. Several previously described variants were also detected. Genotype–phenotype correlation analysis revealed significant associations between <em>NR5A1</em> variants and spermatogenic failure, the most common clinical feature (60.8 %). These findings demonstrate substantial genetic variability in <em>NR5A1</em> among Senegalese men with infertility, and identify a novel missense variant. Our study highlights the relevance of <em>NR5A1</em> in male infertility screening and emphasizes the importance of incorporating African populations into reproductive genetics research.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100578"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145227469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-12-01Epub Date: 2025-08-26DOI: 10.1016/j.jgeb.2025.100554
Mostafa Mohamed Khodry , Sawsan M.A. Abuhamdah , Mohammed H. Hassan , Abd El-Naser Abd El-Gaber Ali , Asmaa Ahmed Sayed Khames , Mohammad A.M. Ahmed
This study represents the investigation of the potential link between single nucleotide polymorphisms (SNPs) in the growth arrest-specific 6 (GAS6) gene and preeclampsia (PE) in Egyptian women. Few existing research have explored this association in other populations, prompting this investigation into the relationship between variants of GAS6 SNPs and both the probability and severity of PE. 200 pregnant Egyptian women participated in the study; 100 were normotensive, 50 had mild PE, and 50 had severe PE. RFLP-PCR was used to genotype GAS6 SNPs [NM_000820.4:c.834+7G>A (rs8191974) and NM_000820.4:c.1332C>T (rs1803628)] in patients and controls (mean ages 30.33 ± 7.17 and 27.43 ± 5.14 years, respectively). Key findings included a significantly higher frequency of AA genotype (29 % vs. 7 %; P < 0.001) and A allele (56 % vs. 30 %; P < 0.001, OR = 0.337, 95 % CI = 0.223–0.508) of NM_000820.4:c.834+7G>A in PE patients compared to controls. In contrast, the CC genotype (27 % vs. 4 %; P < 0.001) and wild C allele (59.5 % vs. 49.5 %; P = 0.045, OR = 1.499, 95 % CI = 1.009–2.226) of NM_000820.4:c.1332C>T were also significantly more frequent in PE patients. Within PE cases, severe cases showed a higher frequency of the CC genotype of NM_000820.3:c.1332C > T (38 % vs. 16 % in mild cases; P = 0.009) and C allele (68 % vs. 51 %; P = 0.014, OR = 2.042, 95 % CI = 1.149–3.627). These results indicate an association between PE risk and the A allele and AA genotype of NM_000820.4:c.834+7G>A variants. Within this cohort of Egyptian women, PE development and severity were significantly linked to the presence of the CC genotype and C allele of the NM_000820.4:c.1332C>T variants.
这项研究调查了埃及女性生长抑制特异性6 （GAS6）基因的单核苷酸多态性（snp）与先兆子痫（PE）之间的潜在联系。现有的研究很少在其他人群中探索这种关联，这促使我们研究GAS6 snp变异与PE的概率和严重程度之间的关系。200名埃及孕妇参与了这项研究；100例血压正常，50例轻度PE， 50例重度PE。采用RFLP-PCR对患者和对照组（平均年龄分别为30.33±7.17岁和27.43±5.14岁）的GAS6 snp [NM_000820.4:c.834+7G>A （rs8191974）和NM_000820.4:c.1332C>T (rs1803628)]进行基因分型。主要发现包括与对照组相比，PE患者中AA基因型（29% vs. 7%; P < 0.001）和a等位基因（56% vs. 30%; P < 0.001, OR = 0.337, 95% CI = 0.223-0.508） NM_000820.4:c.834+7G>； a的频率显著高于对照组。相比之下，NM_000820.4: C . 1332cgt；T的CC基因型（27% vs. 4%; P < 0.001）和野生C等位基因（59.5% vs. 49.5%; P = 0.045, OR = 1.499, 95% CI = 1.009-2.226）在PE患者中也明显更常见。在PE病例中，严重病例中CC基因型NM_000820.3:c的频率更高。1332 C在T(38%比16%在温和的情况下;P = 0.009)和C等位基因(68%比51%,P = 0.014 = 2.042, 95% CI = 1.149 - -3.627)。这些结果表明，NM_000820.4:c.834+7G>；A变异的A等位基因和AA基因型与PE风险存在相关性。在这组埃及女性中，PE的发展和严重程度与NM_000820.4: C . 1332c>；T变异的CC基因型和C等位基因的存在显著相关。
{"title":"Profile of GAS6 gene single nucleotide polymorphisms [GAS6 c.834+7G>A (rs8191974), and GAS6 c.1332C>T (rs1803628)] among a cohort of Egyptian women with preeclampsia: Relation to disease risk and severity","authors":"Mostafa Mohamed Khodry , Sawsan M.A. Abuhamdah , Mohammed H. Hassan , Abd El-Naser Abd El-Gaber Ali , Asmaa Ahmed Sayed Khames , Mohammad A.M. Ahmed","doi":"10.1016/j.jgeb.2025.100554","DOIUrl":"10.1016/j.jgeb.2025.100554","url":null,"abstract":"<div><div>This study represents the investigation of the potential link between single nucleotide polymorphisms (SNPs) in the growth arrest-specific 6 (GAS6) gene and preeclampsia (PE) in Egyptian women. Few existing research have explored this association in other populations, prompting this investigation into the relationship between variants of GAS6 SNPs and both the probability and severity of PE. 200 pregnant Egyptian women participated in the study; 100 were normotensive, 50 had mild PE, and 50 had severe PE. RFLP-PCR was used to genotype GAS6 SNPs [NM_000820.4:c.834+7G>A (rs8191974) and NM_000820.4:c.1332C>T (rs1803628)] in patients and controls (mean ages 30.33 ± 7.17 and 27.43 ± 5.14 years, respectively). Key findings included a significantly higher frequency of AA genotype (29 % vs. 7 %; P < 0.001) and A allele (56 % vs. 30 %; P < 0.001, OR = 0.337, 95 % CI = 0.223–0.508) of NM_000820.4:c.834+7G>A in PE patients compared to controls. In contrast, the CC genotype (27 % vs. 4 %; P < 0.001) and wild C allele (59.5 % vs. 49.5 %; P = 0.045, OR = 1.499, 95 % CI = 1.009–2.226) of NM_000820.4:c.1332C>T were also significantly more frequent in PE patients. Within PE cases, severe cases showed a higher frequency of the CC genotype of NM_000820.3:c.1332C > T (38 % vs. 16 % in mild cases; P = 0.009) and C allele (68 % vs. 51 %; P = 0.014, OR = 2.042, 95 % CI = 1.149–3.627). These results indicate an association between PE risk and the A allele and AA genotype of NM_000820.4:c.834+7G>A variants. Within this cohort of Egyptian women, PE development and severity were significantly linked to the presence of the CC genotype and C allele of the NM_000820.4:c.1332C>T variants.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 4","pages":"Article 100554"},"PeriodicalIF":2.8,"publicationDate":"2025-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144896454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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